Variation in Susceptibility of Bloodstream Isolates of Candida glabrata to Fluconazole According to Patient Age and Geographic Location in the United States in 2001 to 2007

We examined the susceptibilities to fluconazole of 642 bloodstream infection (BSI) isolates of Candida glabrata and grouped the isolates by patient age and geographic location within the United States. Susceptibility of C. glabrata to fluconazole was lowest in the northeast region (46%) and was highest in the west (76%). The frequencies of isolation and of fluconazole resistance among C. glabrata BSI isolates were higher in the present study (years 2001 to 2007) than in a previous study conducted from 1992 to 2001. Whereas the frequency of C. glabrata increased with patient age, the rate of fluconazole resistance declined. The oldest age group (≥80 years) had the highest proportion of BSI isolates that were C. glabrata (32%) and the lowest rate of fluconazole resistance (5%).Candidemia is without question the most important of the invasive mycoses (6, 33, 35, 61, 65, 68, 78, 86, 88). Treatment of candidemia over the past 20 years has been enhanced considerably by the introduction of fluconazole in 1990 (7, 10, 15, 28, 29, 31, 40, 56-58, 61, 86, 90). Because of its widespread usage, concern about the development of fluconazole resistance among Candida spp. abounds (2, 6, 14, 32, 47, 53, 55, 56, 59, 60, 62, 80, 86). Despite these concerns, fluconazole resistance is relatively uncommon among most species of Candida causing bloodstream infections (BSI) (5, 6, 22, 24, 33, 42, 54, 56, 65, 68, 71, 86). The exception to this statement is Candida glabrata, of which more than 10% of BSI isolates may be highly resistant (MIC ≥ 64 μg/ml) to fluconazole (6, 9, 15, 23, 30, 32, 36, 63-65, 71, 87, 91). Suboptimal fluconazole dosing practices (low dose [<400 mg/day] and poor indications) may lead to an increased frequency of isolation of C. glabrata as an etiological agent of candidemia in hospitalized patients (6, 17, 29, 32, 35, 41, 47, 55, 60, 68, 85) and to increased fluconazole (and other azole) resistance secondary to induction of CDR efflux pumps (2, 11, 13, 16, 43, 47, 50, 55, 69, 77, 83, 84) and may adversely affect the survival of treated patients (7, 10, 29, 40, 59, 90). Among the various Candida species, C. glabrata alone has increased as a cause of BSI in U.S. intensive care units since 1993 (89). Within the United States, the proportion of fungemias due to C. glabrata has been shown to vary from 11% to 37% across the different regions (west, midwest, northeast, and south) of the country (63, 65) and from <10% to >30% within single institutions over the course of several years (9, 48). It has been shown that the prevalence of C. glabrata as a cause of BSI is potentially related to many disparate factors in addition to fluconazole exposure, including geographic characteristics (3, 6, 63-65, 71, 88), patient age (5, 6, 25, 35, 41, 42, 48, 63, 82, 92), and other characteristics of the patient population studied (1, 32, 35, 51). Because C. glabrata is relatively resistant to fluconazole, the frequency with which it causes BSI has important implications for therapy (21, 29, 32, 40, 41, 45, 56, 57, 59, 80, 81, 86, 90).Previously, we examined the susceptibilities to fluconazole of 559 BSI isolates of C. glabrata and grouped the isolates by patient age and geographic location within the United States over the time period from 1992 to 2001 (63). In the present study we build upon this experience and report the fluconazole susceptibilities of 642 BSI isolates of C. glabrata collected from sentinel surveillance sites throughout the United States for the time period from 2001 through 2007 and stratify the results by geographic region and patient age. The activities of voriconazole and the echinocandins against this contemporary collection of C. glabrata isolates are also reported.     

Comparison of Typing Results Obtained for Methicillin-Resistant Staphylococcus aureus Isolates with the DiversiLab System and Pulsed-Field Gel Electrophoresis

We compared the results of typing methicillin-resistant Staphylococcus aureus (MRSA) isolates using the DiversiLab system (DL) to the results obtained using pulsed-field gel electrophoresis (PFGE). One hundred five MRSA isolates of PFGE types USA100 to USA1100 and the Brazilian clone, from the Centers for Disease Control and Prevention (CDC) and Project ICARE strain collections, were typed using DL. In addition, four unique sets of MRSA isolates from purported MRSA outbreaks that had been previously typed by DL, each consisting of six isolates (where five isolates were classified as indistinguishable by DL and one was an unrelated DL type) were typed by PFGE. DL separated the 105 MRSA isolates of known USA types into 11 clusters and six unique banding patterns. DL grouped most of the USA100, USA200, and USA1100 isolates into unique clusters. Multilocus sequence type 8 isolates (i.e., USA300 and USA500) often clustered together at >95% similarity in DL dendrograms. Nevertheless, USA300 and USA500 DL patterns could be distinguished using the pattern overlay function of the DL software. Among the hospital outbreak clusters, PFGE and DL identified the same “unrelated” organism in three of four sets. However, PFGE showed more pattern diversity than did DL, suggesting that two of the sets were less likely to represent true outbreaks. In summary, DL is useful for screening MRSA isolates to rule out potential outbreaks of MRSA in hospitals, but PFGE provides better discrimination of potential outbreak strains and is more useful for confirming strain relatedness and specific USA types.Although pulsed-field gel electrophoresis (PFGE) is often considered the gold standard for typing methicillin-resistant Staphylococcus aureus (MRSA) isolates for epidemiologic studies (8, 12, 13), PFGE requires several days to complete and the results are often difficult for inexperienced users to interpret. On the other hand, DNA sequence-based methods, such as spa typing, which has also been shown to be useful for epidemiologic studies of MRSA (3), are not practical for many clinical laboratories in the United States, which lack access to DNA sequencing facilities. An alternative strain typing method, which is available commercially, is the DiversiLab typing system (DL) (bioMérieux, Inc., Durham, NC), which uses the presence of DNA repetitive elements present in the organism''s genome to determine the genetic relatedness of bacterial and fungal isolates (4-6, 9, 18). DL has been used successfully in several MRSA typing studies to distinguish sporadic from outbreak-related isolates and is noted to be more rapid to perform and easier to learn than PFGE (14, 15). Agreement between DL clusters of organisms and USA PFGE types, as defined by McDougal et al. (12), was reported for five well-defined U.S. outbreaks, although specific data were not shown (14). However, a recent study of representative MRSA strains from the Harmony collection in Europe concluded that while DL, PFGE, and multilocus sequence typing (MLST) provided concordant classification of strains, PFGE showed a higher level of strain discrimination than either DL or MLST (17). Thus, whether DL can differentiate accurately among USA types remains an open question.The goal of this study was to use DL to characterize a series of MRSA isolates of known PFGE types from U.S. hospitals to determine whether DL could (i) differentiate among PFGE types USA100 through USA1100, (ii) identify DL banding patterns that correlated with specific USA types, and (iii) differentiate contemporary outbreak-related MRSA isolates from sporadic isolates collected from U.S. hospitals.     

Multilocus Microsatellite Markers for Molecular Typing of Candida glabrata: Application to Analysis of Genetic Relationships between Bloodstream and Digestive System Isolates

Candida glabrata has emerged as the second most common etiologic agent, after Candida albicans, of superficial and invasive candidiasis in adults. Strain typing is essential for epidemiological investigation, but easy-to-use and reliable typing methods are still lacking. We report the use of a multilocus microsatellite typing method with a set of eight markers on a panel of 180 strains, including 136 blood isolates from hospitalized patients and 34 digestive tract isolates from nonhospitalized patients. A total of 44 different alleles were observed, generating 87 distinct genotypes. In addition to perfect reproducibility, typing ability, and stability, the method had a discriminatory power calculated at 0.97 when all 8 markers were associated, making it suitable for tracing strains. In addition, it is shown that digestive tract isolates differed from blood culture isolates by exhibiting a higher genotypic diversity associated with different allelic frequencies and preferentially did not group in clonal complexes (CCs). The demonstration of the occurrence of microevolution in digestive strains supports the idea that C. glabrata can be a persistent commensal of the human gut.During the last decade, incidence of invasive candidiasis with non-albicans Candida species has increased (40, 46, 48). Candida glabrata is the most significant species that has emerged and now regularly ranks number two, after C. albicans, as the etiologic agent of superficial and invasive candidiasis occurring in adults (17, 27). Reasons for this change in species distribution remain uncertain but may be partially due to the natural resistance of C. glabrata to azole derivates, widely used since the 1980s (6, 10, 26). This lower susceptibility of C. glabrata to azoles (2, 23, 38) and delayed initiation of therapy due to delayed diagnosis (2, 20, 35) may explain in part why the prognosis for C. glabrata candidemia is worse than that for C. albicans candidemia (7, 18, 41, 51).Currently, despite increasing clinical concern, the epidemiology of C. glabrata remains poorly known compared to that of C. albicans. While C. glabrata is considered a commensal of the human digestive tract, its natural reservoir is still uncertain. Possible transmission between patients has been suggested (43), and clusters of invasive infections have been reported (4, 36). An efficient and easy-to-use molecular typing method which would allow tracing strains would also allow better understanding of the spread of this species, notably in a hospital context. Up to now, the most reliable method for C. glabrata typing was Southern blotting with moderately repeated probes (3, 32). However, this method requires the use of radioactive elements, and the sequences of the probes are not available. Sequence-based methods such as multilocus sequence typing (MLST) and multilocus microsatellite analysis have been recently proposed (15, 19, 21), but in all cases one could hope for better discriminatory power.A microsatellite-based typing method using a new set of eight markers has been set up for population genetic analysis of C. glabrata (14). In this work, we positively evaluate this method, which has a discriminatory power calculated at 0.97, for tracing C. glabrata strains. The results of typing a large panel of both blood culture and digestive tract isolates suggest (i) that C. glabrata can undergo microevolution within the gut, supporting a persistent commensal life cycle of C. glabrata, and (ii) that digestive and bloodstream isolates exhibit genetic diversity preferentially induced by polymorphism in some loci.     

Hag Mediates Adherence of Moraxella catarrhalis to Ciliated Human Airway Cells

Moraxella catarrhalis is a human pathogen causing otitis media in infants and respiratory infections in adults, particularly patients with chronic obstructive pulmonary disease. The surface protein Hag (also designated MID) has previously been shown to be a key adherence factor for several epithelial cell lines relevant to pathogenesis by M. catarrhalis, including NCIH292 lung cells, middle ear cells, and A549 type II pneumocytes. In this study, we demonstrate that Hag mediates adherence to air-liquid interface cultures of normal human bronchial epithelium (NHBE) exhibiting mucociliary activity. Immunofluorescent staining and laser scanning confocal microscopy experiments demonstrated that the M. catarrhalis wild-type isolates O35E, O12E, TTA37, V1171, and McGHS1 bind principally to ciliated NHBE cells and that their corresponding hag mutant strains no longer associate with cilia. The hag gene product of M. catarrhalis isolate O35E was expressed in the heterologous genetic background of a nonadherent Haemophilus influenzae strain, and quantitative assays revealed that the adherence of these recombinant bacteria to NHBE cultures was increased 27-fold. These experiments conclusively demonstrate that the hag gene product is responsible for the previously unidentified tropism of M. catarrhalis for ciliated NHBE cells.Moraxella catarrhalis is a gram-negative pathogen of the middle ear and lower respiratory tract (29, 40, 51, 52, 69, 78). The organism is responsible for ∼15% of bacterial otitis media cases in children and up to 10% of infectious exacerbations in patients with chronic obstructive pulmonary disease (COPD). The cost of treating these ailments places a large financial burden on the health care system, adding up to well over $10 billion per annum in the United States alone (29, 40, 52, 95, 97). In recent years, M. catarrhalis has also been increasingly associated with infections such as bronchitis, conjunctivitis, sinusitis, bacteremia, pneumonia, meningitis, pericarditis, and endocarditis (3, 12, 13, 17-19, 24, 25, 27, 51, 67, 70, 72, 92, 99, 102-104). Therefore, the organism is emerging as an important health problem.M. catarrhalis infections are a matter of concern due to high carriage rates in children, the lack of a preventative vaccine, and the rapid emergence of antibiotic resistance in clinical isolates. Virtually all M. catarrhalis strains are resistant to β-lactams (34, 47, 48, 50, 53, 65, 81, 84). The genes specifying this resistance appear to be gram positive in origin (14, 15), suggesting that the organism could acquire genes conferring resistance to other antibiotics via horizontal transfer. Carriage rates as high as 81.6% have been reported for children (39, 104). In one study, Faden and colleagues analyzed the nasopharynx of 120 children over a 2-year period and showed that 77.5% of these patients became colonized by M. catarrhalis (35). These investigators also observed a direct relationship between the development of otitis media and the frequency of colonization. This high carriage rate, coupled with the emergence of antibiotic resistance, suggests that M. catarrhalis infections may become more prevalent and difficult to treat. This emphasizes the need to study pathogenesis by this bacterium in order to identify vaccine candidates and new targets for therapeutic approaches.One key aspect of pathogenesis by most infectious agents is adherence to mucosal surfaces, because it leads to colonization of the host (11, 16, 83, 93). Crucial to this process are surface proteins termed adhesins, which mediate the binding of microorganisms to human cells and are potential targets for vaccine development. M. catarrhalis has been shown to express several adhesins, namely UspA1 (20, 21, 59, 60, 77, 98), UspA2H (59, 75), Hag (also designated MID) (22, 23, 37, 42, 66), OMPCD (4, 41), McaP (61, 100), and a type 4 pilus (63, 64), as well as the filamentous hemagglutinin-like proteins MhaB1, MhaB2, MchA1, and MchA2 (7, 79). Each of these adhesins was characterized by demonstrating a decrease in the adherence of mutant strains to a variety of human-derived epithelial cell lines, including A549 type II pneumocytes and Chang conjunctival, NCIH292 lung mucoepidermoid, HEp2 laryngeal, and 16HBE14o-polarized bronchial cells. Although all of these cell types are relevant to the diseases caused by M. catarrhalis, they lack important aspects of the pathogen-targeted mucosa, such as the features of cilia and mucociliary activity. The ciliated cells of the respiratory tract and other mucosal membranes keep secretions moving out of the body so as to assist in preventing colonization by invading microbial pathogens (10, 26, 71, 91). Given this critical role in host defense, it is interesting to note that a few bacterial pathogens target ciliated cells for adherence, including Actinobacillus pleuropneumoniae (32), Pseudomonas aeruginosa (38, 108), Mycoplasma pneumoniae (58), Mycoplasma hyopneumoniae (44, 45), and Bordetella species (5, 62, 85, 101).In the present study, M. catarrhalis is shown to specifically bind to ciliated cells of a normal human bronchial epithelium (NHBE) culture exhibiting mucociliary activity. This tropism was found to be conserved among isolates, and analysis of mutants revealed a direct role for the adhesin Hag in binding to ciliated airway cells.     

A Trilocus Sequence Typing Scheme for Hospital Epidemiology and Subspecies Differentiation of an Important Nosocomial Pathogen,Enterococcus faecalis

In this study, we present a trilocus sequence typing (TLST) scheme based on intragenic regions of two antigenic genes, ace and salA (encoding a collagen/laminin adhesin and a cell wall-associated antigen, respectively), and a gene associated with antibiotic resistance, lsa (encoding a putative ABC transporter), for subspecies differentiation of Enterococcus faecalis. Each of the alleles was analyzed using 50 E. faecalis isolates representing 42 diverse multilocus sequence types (ST^M; based on seven housekeeping genes) and four groups of clonally linked (by pulsed-field gel electrophoresis [PFGE]) isolates. The allelic profiles and/or concatenated sequences of the three genes agreed with multilocus sequence typing (MLST) results for typing of 49 of the 50 isolates; in addition to the one exception, two isolates were found to have identical TLST types but were single-locus variants (differing by a single nucleotide) by MLST and were therefore also classified as clonally related by MLST. TLST was also comparable to PFGE for establishing short-term epidemiological relationships, typing all isolates classified as clonally related by PFGE with the same type. TLST was then applied to representative isolates (of each PFGE subtype and isolation year) of a collection of 48 hospital isolates and demonstrated the same relationships between isolates of an outbreak strain as those found by MLST and PFGE. In conclusion, the TLST scheme described here was shown to be successful for investigating short-term epidemiology in a hospital setting and may provide an alternative to MLST for discriminating isolates.Enterococci are commensal members of the gastrointestinal tract flora of humans and animals. Within the last 2 decades, enterococci have emerged as the second to third most frequent cause of nosocomial infections, including endocarditis and bloodstream, urinary tract, and wound infections, among others (8, 15, 19, 24, 39). These organisms are also known to have the ability to acquire and transfer antibiotic resistance genes and virulence-associated genes (37). Although there are more than 30 species of the genus Enterococcus, two species, Enterococcus faecalis and Enterococcus faecium, account for a vast majority of enterococcal clinical and nosocomial infections (15, 21, 35). In the past, several molecular typing studies have shown that specific lineages of pathogenic bacteria arise periodically, proliferate, and spread in the presence of selective pressures (34). Therefore, accurate typing of enterococcal strains is crucial for the identification of particular clones capable of causing infections and with the ability to spread in the hospital environment.A number of phenotypic and genotypic typing methods have been applied to the subspecies differentiation of enterococcal isolates. Phenotypic methods which have been used in the past include serotyping (17, 22, 26) and multilocus enzyme electrophoresis (50). Genotypic methods include, among others (3, 52, 53), ribotyping (14, 38), repetitive sequence-based PCR (25, 35), multilocus variable-number tandem-repeat analysis (49, 54), pulsed-field gel electrophoresis (PFGE) (10, 12, 49), and multilocus sequence typing (MLST) (10, 26, 31, 41). Among these methods, PFGE, based on chromosomal restriction endonuclease digestion patterns, is widely used for the study of hospital outbreaks and is considered by many to be the “gold standard” molecular typing technique (48). However, this methodology has several limitations due to the facts that it is labor-intensive and the results have poor interlaboratory transportability. This technique is also unsuitable for long-term epidemiology and population studies due to changes in restriction sites, genomic rearrangements, and/or acquisition of DNA by a clonal lineage, which may markedly change the restriction pattern (41). A more appropriate typing technique for long-term epidemiology, which is currently also widely used for subspecies differentiation, is MLST. MLST, based on the allelic variations in sequences of multiple loci, unambiguously types strains (23) and offers an advantage over other techniques used for typing, such as PFGE, since the data are objective and easily stored, compared, and shared via the Internet.Two different MLST schemes have been used successfully for differentiation of E. faecalis strains (31, 41). The first scheme, which assessed three antigenic genes and one housekeeping gene, found that the allelic profile of two antigenic genes (ace and salA) was sufficient to discriminate the 22 E. faecalis isolates included therein (31). The second MLST scheme, based on the allelic profiles of seven housekeeping genes, was used to type 110 isolates and provided insight into the population structure as well as long-term epidemiological relationships of E. faecalis strains (41). However, typing studies on other organisms, such as Salmonella enterica serovar Typhimurium and Staphylococcus aureus, have suggested that MLST based on housekeeping genes may not provide enough discriminatory power to study hospital outbreaks or to accurately determine short-term genetic relationships, which can be crucial for hospital epidemiology and infection control purposes (9, 13, 27).Our hypothesis for this work was that a sequence-based methodology applied to genes encoding antigenic or cell surface proteins (rather than housekeeping genes) may potentially be more useful to establish short-term epidemiologic relationships in E. faecalis, since these genes would be more susceptible to evolutionary selective pressures and potentially could identify and discriminate isolates from hospital outbreaks, similar to PFGE.In the present work, the trilocus sequence types (ST^T; sequence type based on three genes) of 50 isolates were compared to their multilocus sequence types (ST^M; sequence type based on seven housekeeping genes). To determine the applicability of trilocus sequence typing (TLST) for a clinical setting, the scheme was also used to type sets of predetermined (by PFGE) clones and was then applied to a collection of hospital isolates from Bogota, Colombia, recently reported by Arias et al. to belong to an ST-2 clonal lineage (1).(Part of this work was presented at the 47th Interscience Conference on Antimicrobial Agents and Chemotherapy, Chicago, IL, 2007.)     

Acanthamoeba culbertsoni Elicits Soluble Factors That Exert Anti-Microglial Cell Activity

Acanthamoeba culbertsoni is an opportunistic pathogen that causes granulomatous amoebic encephalitis (GAE), a chronic and often fatal disease of the central nervous system (CNS). A hallmark of GAE is the formation of granulomas around the amoebae. These cellular aggregates consist of microglia, macrophages, lymphocytes, and neutrophils, which produce a myriad of proinflammatory soluble factors. In the present study, it is demonstrated that A. culbertsoni secretes serine peptidases that degrade chemokines and cytokines produced by a mouse microglial cell line (BV-2 cells). Furthermore, soluble factors present in cocultures of A. culbertsoni and BV-2 cells, as well as in cocultures of A. culbertsoni and primary neonatal rat cerebral cortex microglia, induced apoptosis of these macrophage-like cells. Collectively, the results indicate that A. culbertsoni can apply a multiplicity of cell contact-independent modes to target macrophage-like cells that exert antiamoeba activities in the CNS.Acanthamoeba culbertsoni belongs to a group of free-living amoebae, such as Balamuthia mandrillaris, Naegleria fowleri, and Sappinia pedata, that can cause disease in humans (46, 56). Acanthamoeba spp. are found worldwide and have been isolated from a variety of environmental sources, including air, soil, dust, tap water, freshwater, seawater, swimming pools, air conditioning units, and contaminated contact lenses (30). Trophozoites feed on bacteria and algae and represent the infective form (47, 56). However, under unfavorable environmental conditions, such as extreme changes in temperature or pH, trophozoites transform into a double-walled, round cyst (22, 45).Acanthamoeba spp. cause an infection of the eye known as amoebic keratitis (AK), an infection of the skin referred to as cutaneous acanthamoebiasis, and a chronic and slowly progressing disease of the central nervous system (CNS) known as granulomatous amoebic encephalitis (GAE) (22, 23, 30, 56). GAE is most prevalent in humans who are immunocompromised (30, 33, 40) and has been reported to occur among individuals infected with the human immunodeficiency virus (HIV) (28). It has been proposed that Acanthamoeba trophozoites access the CNS by passage through the olfactory neuroepithelium (32) or by hematogenous spread from a primary nonneuronal site of infection (23, 24, 33, 53).In immune-competent individuals, GAE is characterized by the formation of granulomas. These cellular aggregates consist of microglia, macrophages, polymorphonuclear cells, T lymphocytes, and B lymphocytes (24, 30). The concerted action of these immune cells results in sequestration of amoebae and is instrumental in slowing the progression of GAE. This outcome is consistent with the observation that granulomas are rarely observed in immunocompromised individuals (34) and in mice with experimentally induced immune suppression following treatment with the cannabinoid delta-9-tetrahydrocannabinol (Δ⁹-THC) (8).Microglia are a resident population of macrophages in the CNS. These cells, along with CNS-invading peripheral macrophages, appear to play a critical early effector role in the control of Acanthamoeba spread during GAE (4, 5, 29, 31). In vitro, microglia have been shown to produce an array of chemokines and cytokines in response to Acanthamoeba (31, 51). However, these factors appear not to have a deleterious effect on these amoebae (29).Acanthamoeba spp. produce serine peptidases, cysteine peptidases, and metallopeptidases (1, 2, 9, 10, 14, 16, 18, 19, 21, 25, 26, 37, 38, 41, 42, 52). In the present study, it is demonstrated that serine peptidases secreted by A. culbertsoni degrade chemokines and cytokines that are produced by immortalized mouse BV-2 microglia-like cells. In addition, soluble factors present in cocultures of A. culbertsoni and BV-2 cells induced apoptosis of the BV-2 cells. Collectively, these results suggest a mode through which A. culbertsoni can evade immune responsiveness in the CNS.     

Characterization of Epidemiologically Unrelated Acinetobacter baumannii Isolates from Four Continents by Use of Multilocus Sequence Typing,Pulsed-Field Gel Electrophoresis,and Sequence-Based Typing of blaOXA-51-like Genes

This study used a diverse collection of epidemiologically unrelated Acinetobacter baumannii isolates to compare the robustness of a multilocus sequence typing (MLST) scheme, based on conserved regions of seven housekeeping genes, gltA, gdhB, recA, cpn60, rpoD, gyrB, and gpi, with that of sequence-based typing of bla_OXA-51-like genes (SBT-bla_OXA-51-like genes). The data obtained by analysis of MLST and SBT-bla_OXA-51-like genes were compared to the data generated by pulsed-field gel electrophoresis (PFGE). The topologies of the phylogenetic trees generated for the gyrB and gpi genes showed evidence of recombination and were inconsistent with those of the trees generated for the other five genes. MLST identified 24 sequence types (STs), of which 19 were novel, and 5 novel alleles. Clonality was demonstrated by eBURST analysis and standardized index of association values of >1 (P < 0.001). MLST data revealed that all isolates harboring the major bla_OXA-51-like alleles OXA-66, OXA-69, and OXA-71 fell within the three major European clonal lineages. However, the MLST data were not always in concordance with the PFGE data, and some isolates containing the same bla_OXA-51-like allele demonstrated <50% relatedness by PFGE. It was concluded that the gyrB and gpi genes are not good candidates for use in MLST analysis and that a SBT-bla_OXA-51-like gene scheme produced results comparable to those produced by MLST for the identification of the major epidemic lineages, with the advantage of having a significantly reduced sequencing cost and time. It is proposed that studies of A. baumannii epidemiology could involve initial screening of bla_OXA-51-like alleles to identify isolates belonging to major epidemic lineages, followed by MLST analysis to categorize isolates from common lineages, with PFGE being reserved for fine-scale typing.Acinetobacter baumannii is a Gram-negative bacterium that causes serious nosocomial infections, especially in critical care units (13, 14, 42). Several outbreaks have been caused by multidrug-resistant (MDR) strains of A. baumannii (23, 33, 43), and the rate of resistance to carbapenems, which have been the antibiotics of choice to treat infections caused by this pathogen, has increased considerably over the last decade (4, 32, 42, 46). In addition, the prevalence of A. baumannii in hospitals has increased worldwide (3, 25, 28, 29, 47), and, therefore, finding suitable molecular typing methods for A. baumannii is essential for epidemiological investigations and infection control studies. Many genomic typing methods have been used, including ribotyping (36), infrequent-restriction-site analysis (48), repetitive extragenic palindromic sequence-based PCR (rep-PCR) (18), random amplified polymorphic DNA (RAPD) analysis (21), amplified fragment length polymorphism (AFLP) analysis (39), and multilocus PCR and electrospray ionization mass spectrometry (PCR/ESI-MS) (6). Pulsed-field gel electrophoresis (PFGE) is still considered the “gold standard” for the typing of bacterial isolates (36), but it has drawbacks when its comes to interchanging data among laboratories for comparison purposes (35) and may lose its discriminatory power when isolates from geographically diverse areas are analyzed.Multilocus sequence typing (MLST) schemes, which use several housekeeping genes, have already been used to type many pathogenic bacteria (15, 17, 20, 40), including A. baumannii (1, 31, 44), and MLST is emerging as an alternative to PFGE. MLST is used mainly for global epidemiology studies, but it has also been used successfully for short-term investigation of an outbreak of meningococcal disease (11). Although MLST has many advantages over other molecular typing methods, many questions remain to be answered, including whether several loci are required to obtain a robust scheme and whether the criteria for the selection of the housekeeping genes are sufficiently reliable to reveal the population structure of the strains analyzed.bla_OXA-51-like genes are unique to A. baumannii and may be used as markers for identification of this species (16). They have also successfully been used as one of three loci in a PCR-based typing scheme that is able to assign isolates of A. baumannii to sequence groups (SGs) that appear to correlate with the major epidemic lineages within the species (41). This raises the question of whether the bla_OXA-51-like genes themselves could be utilized in a typing scheme. Accordingly, the aim of this work was to investigate the robustness of MLST in categorizing epidemiologically unrelated A. baumannii isolates from four continents and to evaluate the use of variations within the intrinsic bla_OXA-51-like gene as a typing tool comparable to MLST.     

Multiple-Locus Variable-Number Tandem-Repeat Analysis of Salmonella enterica Serovar Typhi

Multilocus variable-number tandem repeats (VNTRs) are widely used as molecular markers to differentiate isolates of homogenous pathogenic clones. We explored the genomes of Salmonella enterica serovar Typhi strains CT18 and Ty2 for potential VNTRs. Among the 43 potential VNTRs screened, 2 were found to be polymorphic. Together with seven polymorphic VNTRs from previous studies, they were used to type 73 global serovar Typhi isolates. A total of 70 multilocus VNTR analysis (MLVA) profiles were found, distinguishing all except three pairs of isolates into individual profiles. The discriminatory power was 0.999. Phylogenetic analysis showed that the MLVA profiles can be divided into seven clusters. However, except for the closely related isolates, the relationships derived were in conflict with those inferred from single nucleotide polymorphism (SNP) typing using 38 SNPs done previously. We concluded that MLVA can resolve the relationships only among closely related isolates. A combination of SNP typing and MLVA typing offers the best approach for local and global epidemiology and the evolutionary analysis of serovar Typhi. We suggest that seven of the nine most polymorphic VNTRs be used as a standardized typing scheme for epidemiological typing.Typhoid fever remains a devastating disease in developing countries and is prevalent in areas with inadequate sanitation and poor hygiene. It is a serious systemic disease, spread via the fecal-oral route. Annually, there are more than 16 million cases of typhoid fever with 600,000 deaths reported worldwide (www.who.int). The etiological agent of typhoid fever is Salmonella enterica serovar Typhi, which is highly homogenous (13, 33). The genetic homogeneity of serovar Typhi has significantly impeded the development of suitable typing methods to differentiate serovar Typhi isolates for both phylogenetic and epidemiological purposes.Single nucleotide polymorphisms (SNPs) have recently been shown to be useful markers for typing serovar Typhi isolates (23, 29). SNP typing can resolve the relationships among global serovar Typhi isolates and be more discriminating than widely accepted population genetic methods, including multilocus enzyme electrophoresis (28) and multilocus sequence typing (13). However, some haplotypes or SNP profiles contained many isolates which could not be further differentiated (23, 29). In the study of Roumagnac et al. (29), 88 SNPs differentiated 481 global serovar Typhi isolates into 85 haplotypes. The majority of the isolates belonged to H58 (35%), H50 (12%), and H52 (11%). In the study by Octavia and Lan (23), 38 SNPs distinguished 73 global serovar Typhi isolates into 23 SNP profiles, and the majority of these isolates had SNP profile 10 (32%) and SNP profile 2 (16%). Clearly, SNP typing still has limited discriminatory power.Variable-number tandem repeats (VNTRs) have the potential to be more discriminating than SNPs and also to be used to establish the evolutionary relationships of the isolates. VNTRs are short sequence repeats, which are unique DNA elements repeated in tandem. The polymorphisms in VNTRs are believed to be a result of slippage strand misalignment (17). Therefore, isolates may contain different copy numbers for a repeat locus, allowing differentiation between isolates. Multilocus VNTR analysis (MLVA) involves determination of the number of repeats at multiple VNTR loci, and the number of loci required varies depending on the diversity of the organism studied. MLVA has been particularly effective in typing homogenous clones including Yersinia pestis (1, 14, 21, 25), Bacillus anthracis (8, 11, 12, 34), and Mycobacterium tuberculosis (7, 16, 32, 35, 36). In S. enterica, a few serovars, including serovars Enteritidis, Typhimurium, and Typhi have been studied by MLVA (3, 4, 18-20, 27).Two MLVA studies of serovar Typhi showed different levels of variation of VNTR loci analyzed (20, 27). Liu et al. (20) found five potential VNTR loci designated TR1 to TR5, with the first three showing variation among 59 serovar Typhi isolates from several Asian countries studied. Ramisse et al. (27) found five new polymorphic VNTRs (SAL02, SAL06, SAL10, SAL15, and SAL20). Together with two markers from previous serovar Typhi and Typhimurium studies, TR1 (20) and STTR5/Sal16 (18), a total of seven VNTRs distinguished 27 serovar Typhi isolates from France into 25 MLVA profiles (27). In these two studies, VNTR PCR products were resolved on standard agarose gels. However, the resolution of agarose gels is known to be low, which makes it especially difficult to resolve short repeat units, such as SAL10 with a 2-bp repeat unit. In this study we used seven published VNTRs, including SAL02, SAL06, SAL10, SAL16, SAL20, TR1, and TR2, and two new VNTRs uncovered in this study as markers to explore their potential in studying the molecular evolution of global serovar Typhi isolates. Our MLVA assay employed universal M13 tail primer tagged with a different fluorescent dye to resolve the tandem repeats by capillary electrophoresis. We combined the more rapidly evolving VNTR markers with the slower evolving SNPs to achieve an optimal resolution for typing global serovar Typhi isolates.     

Cohort Study of Molecular Identification and Typing of Mycobacterium abscessus,Mycobacterium massiliense,and Mycobacterium bolletii

Mycobacterium abscessus is the most common cause of rapidly growing mycobacterial chronic lung disease. Recently, two new M. abscessus-related species, M. massiliense and M. bolletii, have been described. Health care-associated outbreaks have recently been investigated by the use of molecular identification and typing tools; however, very little is known about the natural epidemiology and pathogenicity of M. massiliense or M. bolletii outside of outbreak situations. The differentiation of these two species from M. abscessus is difficult and relies on the sequencing of one or more housekeeping genes. We performed extensive molecular identification and typing of 42 clinical isolates of M. abscessus, M. massiliense, and M. bolletii from patients monitored at the NIH between 1999 and 2007. The corresponding clinical data were also examined. Partial sequencing of rpoB, hsp65, and secA led to the unambiguous identification of 26 M. abscessus isolates, 7 M. massiliense isolates, and 2 M. bolletii isolates. The identification results for seven other isolates were ambiguous and warranted further sequencing and an integrated phylogenetic analysis. Strain relatedness was assessed by repetitive-sequence-based PCR (rep-PCR) and pulsed-field gel electrophoresis (PFGE), which showed the characteristic clonal groups for each species. Five isolates with ambiguous species identities as M. abscessus-M. massiliense by rpoB, hsp65, and secA sequencing clustered as a distinct group by rep-PCR and PFGE together with the M. massiliense type strain. Overall, the clinical manifestations of disease caused by each species were similar. In summary, a multilocus sequencing approach (not just rpoB partial sequencing) is required for division of M. abscessus and closely related species. Molecular typing complements sequence-based identification and provides information on prevalent clones with possible relevant clinical aspects.Rapidly growing mycobacteria (RGM) are ubiquitous organisms increasingly emerging as important human pathogens. Mycobacterium abscessus is commonly associated with wound infections and abscess formation and is the most frequent RGM causing chronic lung disease, often in immunocompromised patients (15, 22, 24). M. abscessus is also notable for its resistance to treatment and the poor clinical outcome of infection with the organism (22, 24). Within the past decade, two new species of mycobacteria closely related to M. abscessus, M. massiliense and M. bolletii, have been described (1, 3). Information on the pathogenic role of M. massiliense and M. bolletii is still scant. Recent reports have described the isolation of M. massiliense from two patients in the United States (29) and one patient in Italy (35) and, lately, the identification of M. massiliense and M. bolletii among South Korean isolates (18). Both M. massiliense and M. bolletii have also been linked to health care-associated outbreaks (8, 19, 37).The species-level identification of RGM can provide the first indication of antibiotic susceptibility and can suggest the appropriate type of patient management. For example, M. abscessus is more resistant to many antibiotics both in vivo and in vitro than M. fortuitum and M. mucogenicum, but it is usually susceptible to amikacin and clarithromycin (6, 15, 24). M. massiliense was originally reported to be distinguishable from M. abscessus and related species by its susceptibility to doxycycline (3); however, resistant isolates have since been described (19, 37), suggesting that antibiotic susceptibility results may not reliably differentiate among these closely related species.Although 16S rRNA gene sequencing has been used for the identification of nontuberculous mycobacteria (NTM), including RGM, it has limited value in distinguishing among some closely related species (9, 14). Therefore, the use of several other gene targets for the identification of mycobacteria has been proposed (2, 5, 11, 23, 25, 31, 32, 39, 41). Discrimination among M. abscessus, M. massiliense, and M. bolletii (which have identical 16S rRNA gene sequences) has proven to be difficult, with sequencing of different gene targets often providing conflicting results. Among these gene targets, partial sequencing of rpoB has increasingly been used (1, 19, 29, 37).Genotypic analysis of NTM has proven useful not only in the investigation of outbreaks and pseudo-outbreaks (38) but also in characterizing the molecular epidemiology of strains, and in assessing clonal distribution and expansion (4, 7, 13, 17). In particular, molecular typing has recently been used for the characterization of health care-related outbreaks of M. massiliense and M. bolletii (19, 37).We sought to perform a thorough molecular investigation, including strain identification and typing, for a series of 42 clinical isolates (CIs) of M. abscessus, M. massiliense, and M. bolleti from patients monitored in our institution between 1999 and 2007. A retrospective patient chart review assessed demographics, underlying conditions, and clinical history.The 42 CIs and 3 type strains were subjected to multilocus sequence analysis, including sequencing of rpoB, hsp65, secA, and the internally transcribed spacer (ITS) region. The relatedness among the isolates was assessed by use of an automated repetitive-sequence-based PCR (rep-PCR) and pulsed-field gel electrophoresis (PFGE). This is the most extensive molecular characterization of non-outbreak-related isolates from patients with M. abscessus, M. massiliense, and M. bolletii infections.     

emm and C-Repeat Region Molecular Typing of Beta-Hemolytic Streptococci in a Tropical Country: Implications for Vaccine Development

We designed a study to investigate the molecular epidemiology of group A streptococcal (GAS) and group C and G streptococcal (GCS and GGS) disease in Fiji, a country which is known to have a high burden of streptococcal disease. Molecular typing of the N-terminal portion (emm typing) of the M protein was performed with 817 isolates (535 GAS and 282 GCS/GGS). We also performed genotyping of the C-repeat region in 769 of these isolates to identify J14 sequence types. The profile of emm types for Fiji was very different from that found for the United States and Europe. There were no dominant emm types and a large number of overlapping types among clinical disease states. Commonly found GAS emm types in industrialized countries, including emm1, emm12, and emm28, were not found among GAS isolates from Fiji. Over 93% of GAS isolates and over 99% of GCS/GGS isolates that underwent J14 sequence typing contained either J14.0 or J14.1. Our data have implications for GAS vaccine development in developing countries and suggest that a vaccine based upon the conserved region of the M protein may be a feasible option for Fiji and potentially for other tropical developing countries.The group A streptococcus (GAS) is an important cause of morbidity and mortality globally, with variation in disease burden between populations (9). A greater burden of GAS disease occurs in developing countries, particularly those located in the tropics, than in industrialized nations (9). The spectrums of GAS disease also differ between developed and developing countries. In many developing countries, GAS impetigo is often endemic, with resultant high rates of acute poststreptococcal glomerulonephritis, acute rheumatic fever, and rheumatic heart disease leading to at least 200,000 deaths annually, and the burden of invasive disease has probably been underestimated (9, 43). In industrialized countries, a massive number of cases of GAS pharyngitis leads to significant economic impact (27) and invasive disease leads to a significant number of deaths (25, 26).The molecular epidemiologies of GAS disease appear to differ between industrialized and developing nations, although there is a paucity of data from developing nations (5, 9). There are a number of different methods used to characterize GAS, with sequence typing of the 5′ N-terminal end of the M protein gene (emm) the most widely used (3, 17, 18). There have been recent large epidemiologic studies that have used emm sequence typing to investigate the molecular epidemiology of GAS pharyngitis and invasive GAS disease in industrialized nations, most notably in the United States, Canada, and Europe (16, 26, 37) (R. R. Tanz, S. T. Shulman, W. Kabat, E. Kabat, E. Cederlund, D. Patel, Z. Li, V. Sakota, J. B. Dale, and B. Beall, presented at the XVIth Lancefield International Symposium on Streptococci and Streptococcal Diseases, Palm Cove, Queensland, Australia, 2005). Far fewer studies have been conducted in developing nations. The limited available data suggest that numerous new emm types and subtypes have been discovered that have not previously been observed in industrialized countries (40, 45), that the diversity of emm types in developing countries is greater than that in industrialized countries (23, 32-34, 40, 45), and that the majority of isolates are of emm types traditionally associated with impetigo, irrespective of the clinical site of recovery of the isolates (5, 6, 23, 33, 40).Molecular epidemiologic data have implications for vaccine design. Although a number of antigens have shown promise as potential vaccine candidates, only one vaccine, a 26-valent M-protein-based vaccine, has reached clinical trials in recent times (15, 24). Serotypes for this vaccine were chosen if they were known to be common causes of invasive GAS disease or uncomplicated pharyngitis in the United States or if they were associated with rheumatic fever in classical studies from the United States in the mid-20th century (14). While this vaccine is likely to be efficacious in the United States, concerns have been raised about the transferability of this vaccine to developing-country settings (8).Alternative approaches to a multivalent vaccine strategy include the development of a conserved-epitope vaccine. A number of conserved epitopes have been identified and are under investigation, including some within the portion of the M protein closest to the cell wall (the C-repeat region) which appear to be relatively conserved (2, 11, 31, 36). An example is the J8 peptide, a B-cell epitope, contained within the larger sequence J14 (named J14.0 in this article for clarity) (28, 29). Following the discovery of J14.0, a number of J14 sequence types have been identified (47). To date, across all C-repeat regions, there have been 55 different J14 sequence types described, which have been named in the order that they have been discovered (J14.0 to J14.54) (47). Typing of the C-repeat region by the J14 sequence type of GAS has been employed previously (47). J14 sequence type is relevant to J8 because antibodies raised against J8 in mice provide cross-protective immunity against GAS isolates containing J14.0 and J14.1 (Michael Batzloff, Queensland Institute of Medical Research, unpublished data). Antibodies raised against the J14.0 peptide in mice have been shown to opsonize GAS strains belonging to a variety of emm subtypes that contain J14 sequences other than the J14.0 sequence type, including J14.2 (47).Group C streptococci (GCS) and group G streptococci (GGS) are emerging infectious agents, particularly as a cause of invasive disease and of epidemic pharyngitis (19, 35, 48). We have observed higher than expected rates of invasive GCS/GGS in Fiji, as well as high pharyngeal carriage among school children (43). There is also some evidence to suggest that these organisms may play a role in the pathogenesis of acute rheumatic fever and poststreptococcal glomerulonephritis (13, 30). There are very few data regarding emm sequence typing of GCS/GGS and no available data regarding sequence typing of the C-repeat region of these organisms (22).We designed a study to investigate the molecular epidemiology of GAS and GCS/GGS disease in a tropical setting known to have a high burden of invasive, pharyngeal, and impetiginous streptococcal disease (42-44). Because of the implications for vaccine development, we included molecular typing of both the 5′ end of the M protein (emm sequence typing) and the C-repeat region of the M protein (J14 sequence typing).     

Characterization of a Campylobacter jejuni VirK Protein Homolog as a Novel Virulence Determinant

Campylobacter jejuni is a leading cause of food-borne illness in the United States. Despite significant recent advances, its mechanisms of pathogenesis are poorly understood. A unique feature of this pathogen is that, with some exceptions, it lacks homologs of known virulence factors from other pathogens. Through a genetic screen, we have identified a C. jejuni homolog of the VirK family of virulence factors, which is essential for antimicrobial peptide resistance and mouse virulence.Campylobacter jejuni is a leading cause of infectious diarrhea in industrialized and developing countries (2, 67). Although most often self-limiting, C. jejuni infections can also lead to severe disease and harmful sequelae, such as Guillain-Barré syndrome (4, 55). Despite the significant progress made during the past few years, the mechanisms of C. jejuni pathogenesis remain poorly understood. A number of potential virulence factors have been identified, and in some cases, their role in virulence and/or colonization has been demonstrated in animal models of infection. For example, motility has been shown to be crucial in order for C. jejuni to colonize or cause disease in several animal models of infection (1, 15, 30, 54). A variety of surface structures, such as adhesins (34, 40, 64) and polysaccharides (5, 6), and glycosylation systems (38, 74), which presumably modify some of these surface structures, have also been shown to be important for infection. Additional studies have revealed the importance of specific metabolic pathways in C. jejuni growth both in vitro and within animals (16, 25, 31, 60, 76). The ability of C. jejuni to invade and survive within nonphagocytic cells has also been proposed to be an important virulence determinant (21, 41, 57, 58, 68, 75, 80).The available genome sequences of several C. jejuni strains have provided significant insight into C. jejuni physiology and metabolism (22, 32, 62, 63, 65). Remarkably, however, analysis of these C. jejuni genome sequences has revealed very few homologs of common virulence factors from other pathogens. A notable exception is the toxin CDT (cytolethal distending toxin), which is also encoded by several other important bacterial pathogens (36, 44, 45). In this paper we describe the identification of a transposon insertion mutant in C. jejuni 81-176, which results in increased susceptibility to antimicrobial peptides and a significant defect in the ability of the organism to cause disease in an animal model of infection. The insertion mutant was mapped to the CJJ81176_1087 open reading frame (Cj1069 in the C. jejuni NCT 11168 reference strain), which encodes a protein with very significant amino acid sequence similarity to the VirK (DUF535) family of virulence factors (13, 20, 56).     

Tracking the Emerging Human Pathogen Pseudallescheria boydii by Using Highly Specific Monoclonal Antibodies

Pseudallescheria boydii has long been known to cause white grain mycetoma in immunocompetent humans, but it has recently emerged as an opportunistic pathogen of humans, causing potentially fatal invasive infections in immunocompromised individuals and evacuees of natural disasters, such as tsunamis and hurricanes. The diagnosis of P. boydii is problematic since it exhibits morphological characteristics similar to those of other hyaline fungi that cause infectious diseases, such as Aspergillus fumigatus and Scedosporium prolificans. This paper describes the development of immunoglobulin M (IgM) and IgG1 κ-light chain monoclonal antibodies (MAbs) specific to P. boydii and certain closely related fungi. The MAbs bind to an immunodominant carbohydrate epitope on an extracellular 120-kDa antigen present in the spore and hyphal cell walls of P. boydii and Scedosporium apiospermum. The MAbs do not react with S. prolificans, Scedosporium dehoogii, or a large number of clinically relevant fungi, including A. fumigatus, Candida albicans, Cryptococcus neoformans, Fusarium solani, and Rhizopus oryzae. The MAbs were used in immunofluorescence and double-antibody sandwich enzyme-linked immunosorbent assays (DAS-ELISAs) to accurately differentiate P. boydii from other infectious fungi and to track the pathogen in environmental samples. Specificity of the DAS-ELISA was confirmed by sequencing of the internally transcribed spacer 1 (ITS1)-5.8S-ITS2 rRNA-encoding regions of environmental isolates.Pseudallescheria boydii is an infectious fungal pathogen of humans (7, 16, 40, 58, 59). It is the etiologic agent of white grain mycetoma in immunocompetent humans (7) and has emerged over recent years as the cause of fatal disseminated infections in individuals with neutropenia, AIDS, diabetes, renal failure, bone marrow or solid organ transplants, systemic lupus erythematous, and Crohn''s disease; in those undergoing corticosteroid treatment; and in leukemia and lymphoma patients (1, 2, 3, 18, 27, 31, 32, 34, 36, 37, 38, 47, 49, 52). The fungus is the most prevalent species after Aspergillus fumigatus in the lungs of cystic fibrosis patients (8), where it causes allergic bronchopulmonary disease (5) and chronic lung lesions simulating aspergillosis (24). Near-drowning incidents and recent natural disasters, such as the Indonesian tsunami in 2004, have shown P. boydii and the related species Scedosporium apiospermum and Scedosporium aurantiacum to be the causes of fatal central nervous system infections and pneumonia in immunocompetent victims who have aspirated polluted water (4, 11, 12, 21, 22, 25, 30, 33, 57). Its significance as a potential pathogen of disaster evacuees has led to its recent inclusion in the Centers for Disease Control and Prevention list of infectious etiologies in persons with altered mental statuses, central nervous system syndromes, or respiratory illness.P. boydii is thought to be an underdiagnosed fungus (60), and misidentification is one of the reasons that the mortality rate due to invasive pseudallescheriasis is high. Detection of invasive P. boydii infections, based on cytopathology and histopathology, is problematic since it can occur in tissue and bronchoalveolar and bronchial washing specimens with other hyaline septated fungi, such as Aspergillus and Fusarium spp. (7, 23, 53, 60), which exhibit similar morphological characteristics upon microscopic examination (2, 23, 24, 28, 37, 44, 53, 60). Early diagnosis of infection by P. boydii and differentiation from other agents of hyalohyphomycosis is imperative, since it is refractory to antifungal compounds, such as amphotericin B, that are commonly administered for the control of fungal infections (10, 39, 58).The immunological diagnosis of Pseudallescheria infections has focused on the detection of antigens by counterimmunoelectrophoresis, and by immunohistological techniques using polyclonal fluorescent antibodies, but cross-reactions with antigens from other fungi, such as Aspergillus species, occurs (7, 19, 23). Pinto and coworkers (41, 42) isolated a peptidorhamnomannan from hyphae of P. boydii and proposed the antigen as a diagnostic marker for the pathogen. Cross-reactivity with Sporothrix schenckii and with Aspergillus have, however, been noted (23, 41). Furthermore, it is uncertain whether a similar antigen is present in the related pathogenic species S. prolificans, an important consideration in patient groups susceptible to mixed Scedosporium infections (6, 18).Hybridoma technology allows the production of highly specific MAbs that are able to differentiate between closely related species of fungi (54, 55, 56). The purpose of this paper is to report the development of MAbs specific to P. boydii and certain closely related species and their use to accurately discriminate among P. boydii, A. fumigatus, and other human pathogenic fungi by using immunofluorescence and double-antibody sandwich enzyme-linked immunosorbent assays (DAS-ELISAs).Currently, the natural environmental habitat of P. boydii is unknown, but nutrient-rich, brackish waters, such as estuaries, have been suggested (9, 17). In combination with a semiselective isolation procedure, I show how the DAS-ELISA can be used to rapidly and accurately track the pathogen in naturally infested estuarine muds, and in doing so illustrate the potential of the DAS-ELISA as a diagnostic platform for detection of P. boydii and related species within the Pseudallescheria complex.     

Avian-Pathogenic Escherichia coli Strains Are Similar to Neonatal Meningitis E. coli Strains and Are Able To Cause Meningitis in the Rat Model of Human Disease

Escherichia coli strains causing avian colibacillosis and human neonatal meningitis, urinary tract infections, and septicemia are collectively known as extraintestinal pathogenic E. coli (ExPEC). Characterization of ExPEC strains using various typing techniques has shown that they harbor many similarities, despite their isolation from different host species, leading to the hypothesis that ExPEC may have zoonotic potential. The present study examined a subset of ExPEC strains: neonatal meningitis E. coli (NMEC) strains and avian-pathogenic E. coli (APEC) strains belonging to the O18 serogroup. The study found that they were not easily differentiated on the basis of multilocus sequence typing, phylogenetic typing, or carriage of large virulence plasmids. Among the APEC strains examined, one strain was found to be an outlier, based on the results of these typing methods, and demonstrated reduced virulence in murine and avian pathogenicity models. Some of the APEC strains tested in a rat model of human neonatal meningitis were able to cause meningitis, demonstrating APEC''s ability to cause disease in mammals, lending support to the hypothesis that APEC strains have zoonotic potential. In addition, some NMEC strains were able to cause avian colisepticemia, providing further support for this hypothesis. However, not all of the NMEC and APEC strains tested were able to cause disease in avian and murine hosts, despite the apparent similarities in their known virulence attributes. Thus, it appears that a subset of NMEC and APEC strains harbors zoonotic potential, while other strains do not, suggesting that unknown mechanisms underlie host specificity in some ExPEC strains.Escherichia coli strains causing extraintestinal disease are known as extraintestinal pathogenic E. coli (ExPEC) and include the uropathogenic E. coli (UPEC), neonatal meningitis E. coli (NMEC), and avian-pathogenic E. coli (APEC) subpathotypes. Recent studies have shown that members of various ExPEC subpathotypes harbor similar virulence-associated genes, despite their isolation from varied hosts and tissues (3, 8, 10, 20, 25, 27, 30, 32), and genomic sequencing of APEC O1 revealed that only 4.5% of the genome was not found in the other ExPEC strains sequenced (17). More recently, a cluster of isolates from human and avian hosts thought to represent potential zoonotic pathogens has been identified (20).Common among the isolates of this mixed cluster are genes associated with the conserved region of large virulence plasmids, which are a defining trait of the APEC subpathotype (15, 19, 24, 36, 37) and which are essential for APEC virulence (5, 23). Interestingly, a closely related plasmid that was associated with high-level bacteremia in a neonatal rat meningitis model has also been described in an NMEC isolate (30).Other virulence traits are also shared among ExPEC subpathotypes. Indeed, few traits, if any, appear to be exclusive to a particular ExPEC subpathotype, and in fact, some traits that were thought to be exclusive have been shown to contribute to the pathogenesis of more than one condition (8).Such similarities in the virulence traits found among APEC and other ExPEC subpathotypes have led to speculation that APEC has zoonotic potential (20, 25, 27) and may be a food-borne source of ExPEC causing disease in humans (10, 14, 18, 22). Indeed, ExPEC strains have been identified in retail foods and poultry products (7, 11, 12, 18), and at least one study has found avian isolates to be indistinguishable from human isolates (10). However, other studies showed that human ExPEC strains were clearly distinct from avian strains (6) and that the consumption of poultry or contact with poultry did not correlate with the colonization of antimicrobial-resistant E. coli (34).Here, we seek to further test the hypothesis that APEC strains have zoonotic potential. Of particular interest are O18 strains, which are common among human NMEC strains but which are also found among APEC strains (20, 26). In fact, it has been suggested that APEC O18:K1:H7 strains are potential human pathogens (27). Though it has been shown that human ExPEC strains can cause avian colibacillosis similar to that caused by APEC, suggesting that these ExPEC strains are not host specific (26), it has also been reported that E. coli strains from avian septicemia are more virulent to chicks than NMEC strains (33). However, the ability of APEC to cause disease in mammals has not yet been established.The aim of the present study was to explore the zoonotic potential of NMEC and APEC O18 strains by comparing their plasmid contents, genotypes, phylogenetic group assignments, pulsed-field gel electrophoresis (PFGE) patterns, and sequence types (ST), determined by multilocus sequence typing (MLST), and their abilities to cause disease in the rat model of human neonatal meningitis and chicken models of avian colisepticemia.     

Molecular Identification and Susceptibility of Trichosporon Species Isolated from Clinical Specimens in Qatar: Isolation of Trichosporon dohaense Taj-Aldeen,Meis & Boekhout sp. nov.

Trichosporon species have been reported as emerging pathogens and usually occur in severely immunocompromised patients. In the present work, 27 clinical isolates of Trichosporon species were recovered from 27 patients. The patients were not immunocompromised, except for one with acute myeloid leukemia. Sequence analysis revealed the isolation of Trichosporon dohaense Taj-Aldeen, Meis & Boekhout sp. nov., with CBS 10761^T as the holotype strain, belonging to the Ovoides clade. In the D1-D2 large-subunit rRNA gene analysis, T. dohaense is a sister species to T. coremiiforme, and in the internal transcribed spacer analysis, the species is basal to the other species of this clade. Molecular identification of the strains yielded 17 T. asahii, 3 T. inkin, 2 T. japonicum, 2 T. faecale, and 3 T. dohaense isolates. The former four species exhibited low MICs for five antifungal azoles but showed high MICs for amphotericin B. T. dohaense demonstrated the lowest amphotericin B MIC (1 mg/liter). For the majority of T. asahii isolates, amphotericin B MICs were high (MIC at which 90% of isolates were inhibited [MIC₉₀], ≥16 mg/liter), and except for fluconazole (MIC₉₀, 8 mg/liter), the azole MICs were low: MIC₉₀s were 0.5 mg/liter for itraconazole, 0.25 mg/liter for voriconazole, 0.25 mg/liter for posaconazole, and 0.125 mg/liter for isavuconazole. The echinocandins, caspofungin and anidulafungin, demonstrated no activity against Trichosporon species.Trichosporon species are yeast-like fungi, widely distributed in nature and commonly isolated from soil and other environmental sources, which have been involved in a variety of opportunistic infections and have been recognized as emerging fungal pathogens in immunocompromised hosts (19, 79, 80). Disseminated Trichosporon infections are potentially life-threatening and are often fatal in neutropenic patients (7, 22). Although uncommon, pathogenic species of this genus have been reported increasingly, mostly in patients with malignant diseases (3, 6, 9, 10, 11, 20, 32, 44, 47, 48, 63, 77), neonates (18, 56, 84), a bone marrow transplant recipient (22), a solid organ transplant recipient (50), and patients with human immunodeficiency virus (34, 35, 46). Trichosporon has also been reported to cause fungemia (5, 9, 25, 29, 30, 33, 53, 62). Members of the genus Trichosporon have occasionally been implicated as nail pathogens (16, 28, 74) and in subcutaneous infections (66). Trichosporon is considered an opportunistic agent, and therefore, recovery of Trichosporon species capable of growing at 37°C, especially from immunocompromised patients, should be regarded as potentially significant. Several reports have addressed the difficulty of identifying Trichosporon to the species level by physiological and biochemical characteristics (2, 64); therefore, molecular methods based on the sequencing of the internal transcribed spacer (ITS) have been developed (15, 69, 71, 72).In the present paper, we report the isolation of Trichosporon species from clinical specimens over a 4-year period in Qatar, the poor performance of biochemical identification methods, the significance of molecular identification, and the antifungal susceptibility data for the isolates. While investigating the molecular identification of Trichosporon species, we found three strains that do not match any of the published strains in the literature. We describe this organism as Trichosporon dohaense Taj-Aldeen, Meis & Boekhout, sp. nov., the name proposed for this species.     

Physical and Chemical Characterization and Immunologic Properties of Salmonella enterica Serovar Typhi Capsular Polysaccharide-Diphtheria Toxoid Conjugates

Typhoid fever remains a serious public health problem in developing countries, especially among young children. Recent studies showed more than 50% of typhoid cases are in children under 5 years old. Licensed vaccines, such as Salmonella enterica serovar Typhi capsular Vi, did not confer protection against typhoid fever for this age group. Vi conjugate, prepared by binding Vi to Pseudomonas aeruginosa recombinant exoprotein A (rEPA), induces protective levels of antibody at as young as 2 years old. Because of the lack of regulatory precedent for rEPA in licensing vaccines, we employed diphtheria toxoid (DT) as the carrier protein to accommodate accessibility in developing countries. Five lots of Vi-DT conjugates were prepared using adipic acid dihydrazide (ADH) as the linker. All 5 lots showed consistency in their physical and chemical characteristics and final yields. These Vi-DT conjugates elicited levels of IgG anti-Vi in young mice significantly higher than those in mice injected with Vi alone and induced a booster response upon reinjection. This booster effect was absent if the Vi replaced one of the two conjugate injections. Vi-DT was stable under repeated freeze-thaw (20 cycles). We plan to perform clinical evaluation of the safety and immunogenicity of Vi-DT when added to the infant combination vaccines.Typhoid fever, a serious systemic infection caused by Salmonella enterica serovar Typhi, remains a major public health problem in Central Asia, Southeast Asia, Africa, and Latin America (11, 52, 53). It was estimated that more than 21 million cases of typhoid fever and >200,000 deaths occurred in 2000 (10). The treatment of patients and management of asymptomatic carriers are becoming more difficult due to the worldwide emergence of multidrug-resistant (MDR) strains (2, 15, 29, 42, 43). Vaccination is considered the most promising strategy for the control of typhoid fever in developing countries (11, 19, 52, 53).Typhoid fever in children younger than 5 years old has often been unrecognized due to atypical clinical symptoms, difficulties in the number and volume of blood drawings, and use of less than optimal culture media (35, 46). Several studies have shown that the incidence of typhoid fever among children less than 5 years old is similar to that in school age children and young adults (14, 27, 34, 50, 51).The 3 licensed typhoid vaccines have limited efficacy, and none are suitable for young children under 5 years old. The use of heat-inactivated whole-cell vaccine was suspended in many countries because of its reactogenicity. The parenteral Vi polysaccharide and the live attenuated oral Ty21a vaccine were introduced in the late 1980s; both vaccines are well accepted and confer moderate protection (50 to 70%) in older children and adults. However, neither vaccine is licensed for routine immunization of infants (52).The Vi capsular polysaccharide is both an essential virulence factor and a protective antigen for S. Typhi (36, 38, 39). The concentration of serum IgG anti-Vi is correlated with immunity to the pathogen (22, 25, 26, 28, 36, 38, 49). However, Vi is not suitable for routine immunization of infants and young children because of its age-related immunogenicity and T-cell independence. As was shown for other capsular polysaccharides, such as Haemophilus influenzae type b (8, 37); meningococcus groups A, C, and W135; and Streptococcus pneumoniae (12, 20), Vi covalently bound with protein conferred T-cell dependence and increased immunogenicity (48-50). To date, diphtheria toxoid (DT), tetanus toxoid (TT), cholera toxins (CT), the B subunit of the heat-labile toxin (LT-B) of Escherichia coli, recombinant outer membrane protein of Klebsiella pneumoniae (rP40), and iron-regulated outer-membrane proteins (IROMPs) of S. Typhi have served as carriers for Vi polysaccharide in laboratory studies (16, 17, 32, 48-50; personal communications). An improved method was developed (24), utilizing adipic acid dihydrazide (ADH) as the linker and Pseudomonas aeruginosa recombinant exoprotein A (rEPA) as the carrier. Clinical trials of Vi-rEPA conjugates conferred 89% protection in Vietnamese children 2 to 5 years old for 46 months (23, 26, 28). The level of serum IgG anti-Vi induced by Vi-rEPA conjugates was correlated with prevention of typhoid fever in these studies (7, 21-23, 26, 28).One limitation of using rEPA as the carrier protein is the lack of regulatory precedent in licensing vaccines. In this report, five lots of Vi conjugates using DT manufactured by pharmaceutical companies in China and India were prepared (24, 48, 49). Modifications of conjugation procedures were made for the purposes of easy adoption and scale up by manufacturers. The stability of Vi-DT was studied for the feasibility of stockpiling in disaster relief.Another important aspect of conjugate vaccine implementation is the optimum immunization formulation and schedule using alternating injections of polysaccharide and conjugate. Priming or boosting effects of polysaccharide on its conjugate vaccine have been observed in infants injected with pneumococcal and meningococcal vaccines (3, 4, 31, 40). There was no consistent conclusion about various types of polysaccharides studied (6, 9, 31, 40, 41). Here, we compared the immune response of Vi polysaccharide injected before or after the administration of Vi-DT with the responses of those receiving 2 injections of Vi-DT. We also investigated the dosage effect for the purpose of better formulation.     

Mannheimia haemolytica and Its Leukotoxin Cause Neutrophil Extracellular Trap Formation by Bovine Neutrophils

Mannheimia haemolytica is an important member of the bovine respiratory disease complex, which is characterized by abundant neutrophil infiltration into the alveoli and fibrin deposition. Recently several authors have reported that human neutrophils release neutrophil extracellular traps (NETs), which are protein-studded DNA matrices capable of trapping and killing pathogens. Here, we demonstrate that the leukotoxin (LKT) of M. haemolytica causes NET formation by bovine neutrophils in a CD18-dependent manner. Using an unacylated, noncytotoxic pro-LKT produced by an ΔlktC mutant of M. haemolytica, we show that binding of unacylated pro-LKT stimulates NET formation despite a lack of cytotoxicity. Inhibition of LKT binding to the CD18 chain of lymphocyte function-associated antigen 1 (LFA-1) on bovine neutrophils reduced NET formation in response to LKT or M. haemolytica cells. Further investigation revealed that NETs formed in response to M. haemolytica are capable of trapping and killing a portion of the bacterial cells. NET formation was confirmed by confocal microscopy and by scanning and transmission electron microscopy. Prior exposure of bovine neutrophils to LKT enhanced subsequent trapping and killing of M. haemolytica cells in bovine NETs. Understanding NET formation in response to M. haemolytica and its LKT provides a new perspective on how neutrophils contribute to the pathogenesis of bovine respiratory disease.Mannheimia haemolytica is a member of the bovine respiratory disease complex (BRD), causing a severe fibrinous pleuropneumonia sometimes referred to as shipping fever. The pneumonia is characterized by intense neutrophil infiltration in alveoli, intra-alveolar hemorrhage, fibrin deposition, and consolidation of the lungs (42, 56). The importance of neutrophils in the production of inflammatory mediators, recruitment of other leukocytes, and lung damage (17, 56, 67, 74) was demonstrated in calves that were depleted of neutrophils before challenge with M. haemolytica (10, 56). Neutrophil-depleted calves displayed less lung pathology than did control calves infected with M. haemolytica (10, 56). From these data, it is clear that neutrophils are a key player in the pathology of bovine pleuropneumonia; however, the mechanisms by which they contribute to host defense and tissue destruction are not clearly defined.The most important virulence factor for M. haemolytica is its leukotoxin (LKT), a 104-kDa exotoxin produced during logarithmic-phase growth (18, 32). LKT is a member of the repeats-in-toxin (RTX) toxin family of exoproteins produced by a wide variety of Gram-negative bacteria, including Escherichia coli, Actinobacillus pleuoropneumoniae, and Aggregatibacter actinomycetemcomitans (70). RTX toxins are characterized by a C-terminal glycine-rich nonapeptide repeat region (-G-G-X-G-X-D-X-U-X, where U is a hydrophobic residue) that binds calcium (Ca²⁺). The latter is required for membrane binding and cytotoxicity (30, 70). RTX toxins can insert into the plasma membrane of target cells, causing lysis and necrotic cell death (30, 70). The N-terminal domain contains amphipathic and hydrophobic domains believed to be required for pore stabilization and formation, respectively (70). More recently, it was shown that LKT also causes apoptosis via a caspase 9-dependent pathway and that LKT is internalized and transported via the cytoskeleton to mitochondria (4-6).The leukotoxin operon contains the genes lktC, lktA, lktB, and lktD (36, 37, 58). lktA encodes the inactive pro-LKT protein that is not cytotoxic until acylated (62) by the transacylase encoded by lktC. lktB and lktD encode proteins responsible for leader sequence-independent secretion of LKT from the bacterial cell (36, 37, 58). The acylated LKT then binds the CD18 chain of the β₂-integrin lymphocyte function-associated antigen 1 (LFA-1) (3, 21-26, 33, 40, 41, 44, 55, 63) on ruminant leukocytes. LKT binding to amino acids 5 to 17 of the signal sequence of CD18 is required for cell death and restricts cytotoxicity to ruminant leukocytes, because the signal sequence for CD18 is not present on mature leukocytes from other mammalian species (55). Other investigators have shown that both the pro- form and mature LKT are capable of binding CD18, although the pro-LKT does not cause cytotoxicity (62). No biological role has been assigned to the pro- form of LKT.Recently, several authors have shown that human neutrophils are able to undergo a form of cell death, called NETosis, that is distinct from apoptosis and necrosis (12, 13, 31, 51, 69). NETosis is defined as the release of nuclear DNA from an activated neutrophil into the extracellular environment, with little concomitant release of lactate dehydrogenase (LDH) (12). The extracellular DNA and associated proteins (e.g., histones) released by activated neutrophils have been termed neutrophil extracellular traps (NETs) (12). There are four steps leading to NET formation. These are neutrophil activation, nuclear envelope degradation, mixing of nuclear DNA with cytosolic proteins, and extrusion of the DNA-protein mixture from the cell (31). Treatment of human neutrophils with interleukin-8 (IL-8), phorbol 12-myristate 13-acetate (PMA), or lipopolysaccharide (LPS) causes NET formation (12, 31, 69). NET formation also occurs in response to prokaryotic and eukaryotic pathogens (12, 35, 64). To date, no bacterial exotoxin has been shown to cause NET formation.NETs are composed of extracellular DNA that is studded with antimicrobial proteins. The latter include nuclear histones and primary, secondary, and tertiary granular components such as neutrophil elastase, myeloperoxidase, lactoferrin, and gelatinase (51, 69). When neutrophils become activated and commit to NET formation, they also are capable of trapping and killing pathogens. To date, NETs have been shown to kill a variety of Gram-negative and Gram-positive bacteria, fungi, and protozoans (2, 7-9, 12, 13, 15, 19, 20, 27, 28, 31, 34, 35, 43, 50-53, 59, 64, 67, 70). Here, we examine if M. haemolytica and its LKT cause NET formation by bovine neutrophils and whether NETs are capable of trapping and killing M. haemolytica cells in vitro.     

Extracellular Vesicles from Cryptococcus neoformans Modulate Macrophage Functions

Cryptococcus neoformans and distantly related fungal species release extracellular vesicles that traverse the cell wall and contain a varied assortment of components, some of which have been associated with virulence. Previous studies have suggested that these extracellular vesicles are produced in vitro and during animal infection, but the role of vesicular secretion during the interaction of fungi with host cells remains unknown. In this report, we demonstrate by fluorescence microscopy that mammalian macrophages can incorporate extracellular vesicles produced by C. neoformans. Incubation of cryptococcal vesicles with murine macrophages resulted in increased levels of extracellular tumor necrosis factor alpha (TNF-α), interleukin-10 (IL-10), and transforming growth factor β (TGF-β). Vesicle preparations also resulted in a dose-dependent stimulation of nitric oxide production by phagocytes, suggesting that vesicle components stimulate macrophages to produce antimicrobial compounds. Treated macrophages were more effective at killing C. neoformans yeast. Our results indicate that the extracellular vesicles of C. neoformans can stimulate macrophage function, apparently activating these phagocytic cells to enhance their antimicrobial activity. These results establish that cryptococcal vesicles are biologically active.Cryptococcus neoformans is an encapsulated yeast that causes disease in diverse species, including humans. Infection is most commonly acquired by inhalation of environmental propagules. C. neoformans rarely causes disease in immunocompetent individuals, but patients with immunological disorders can develop disseminated and neural cryptococcosis (63).Extracellular microbial products have been amply demonstrated to modulate the interaction between host cells and pathogens. Many virulence factors and immunogens are released in their soluble forms by fungal cells to the extracellular space (4, 9, 16, 19, 37, 49, 53, 60, 62, 65, 67). C. neoformans, for instance, constitutively secretes large amounts of its capsular polysaccharide glucuronoxylomannan (GXM) (61). Disease progress is associated with detection of GXM, which is a potent modulator of the immune response (reviewed in reference 81). Other secreted virulence-related factors include galactoxylomannan (GalXM) (14), phospholipases (16), and urease (12, 62). In addition to acting as virulence factors, culture supernatant components are immunogenic, conferring protection against C. neoformans infection (51, 53).Phagocytes are particularly important effector cells in the control of systemic mycoses (54). The interaction of C. neoformans with phagocytes, including macrophages, monocytes, dendritic cells, and neutrophils, has been widely studied (23, 32, 43, 46, 50, 59, 68, 77). Cryptococcal GXM is antiphagocytic (34) and a powerful immunomodulator (45, 79). C. neoformans capsule size directly correlates with the efficacy of phagocytosis in vitro (6, 15, 82). Phagocytosis of C. neoformans can result in either fungal killing (24, 30) or survival (2, 3, 39-41, 71, 80). Killing of C. neoformans apparently involves the production of oxidative species (24), while the mechanisms of fungal escape include phagosome extrusion, cell-to-cell spread, and phagosomal permeabilization (2, 3, 40, 41, 71). Capsular polysaccharides and melanin are known to modulate the interaction of C. neoformans with phagocytes in favor of the fungus (27, 39, 47, 48, 71, 72, 74, 76), but the role of other structures in the outcome of yeast phagocytosis is virtually unknown.A number of recent studies have shown that GXM, GalXM, pigments, proteins, and lipids are trafficked in vesicles that traverse the cell wall (7, 14, 20, 56, 57, 62, 64, 65). Extracellular vesicles are also produced by the pathogens Candida albicans, C. parapsilosis, Sporothrix schenckii, and Histoplasma capsulatum, as well as by the model yeast Saccharomyces cerevisiae (1), suggesting that extracellular vesicle secretion is a general property of fungal cells. Secreted vesicles are heterogeneous. For instance, vesicles secreted by C. neoformans were classified into four different groups based on morphology and electron density (64). Additionally, vesicle diameter ranges from 30 to 400 nm, with the majority having dimensions of 100 to 150 nm (20, 64, 65). The combined use of serology, biochemistry, proteomics, and lipidomics led to the identification of 2 polysaccharides, phospholipids, 4 neutral lipids, and 76 proteins as extracellular vesicle components secreted by C. neoformans, which means that at least 81 different molecules are released to the extracellular milieu by vesicular secretion (14, 57, 64). It is likely that this number is an underestimate resulting from the difficulty of proteomic studies in vesicles from highly encapsulated cryptococcal cells, since a higher number of vesicular proteins were characterized in other fungi. For example, in H. capsulatum, proteomics and lipidomics of extracellular vesicles revealed an even more complex composition, including 283 proteins and 17 different phospholipids (1).In this study, we evaluated the influence of extracellular vesicles on the fate of C. neoformans after phagocytosis by mouse macrophages. Our results show that fungal vesicles are biologically active and stimulate macrophages. Moreover, our results demonstrate that vesicles from an acapsular mutant strain were more effective in eliciting macrophage activation and augmenting fungal killing than vesicles from encapsulated strains. Taken together, our findings suggest that fungal secretory vesicles have the potential to influence the interaction of C. neoformans with host cells.     

Evaluation of Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry for Identification of Clinically Important Yeast Species

We evaluated the use of matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) for the rapid identification of yeast species. Using Bruker Daltonics MALDI BioTyper software, we created a spectral database library with m/z ratios of 2,000 to 20,000 Da for 109 type and reference strains of yeast (44 species in 8 genera). The database was tested for accuracy by use of 194 clinical isolates (23 species in 6 genera). A total of 192 (99.0%) of the clinical isolates were identified accurately by MALDI-TOF MS. The MALDI-TOF MS-based method was found to be reproducible and accurate, with low consumable costs and minimal preparation time.Invasive fungal infections due to opportunistic pathogens are a significant cause of morbidity and mortality (2, 5, 8). The current rise in fungal infections correlates with the widespread use of broad-spectrum antibacterial agents, prolonged hospitalization of critically ill patients, and the increased number of immunocompromised patients. Candida species comprise the fourth most common cause of nosocomial bloodstream infections, and Cryptococcus neoformans is the most common cause of fungus-related mortality in HIV-infected patients (15, 19). While Candida albicans is still involved in more than half of all Candida-related bloodstream infections, an increase in recovery of non-C. albicans Candida spp., Rhodotorula spp., Trichosporon spp., and Malassezia spp. has occurred (2, 29). Treatment with amphotericin B may be useful for these organisms and inefficient for those belonging to other genera (5, 8). While many Candida species remain susceptible to fluconazole, it is important to differentiate the more resistant organisms, namely, Candida glabrata, Candida krusei, Rhodotorula spp., and some members of the genus Trichosporon. Additionally, Rhodotorula spp. have an innate resistance to voriconazole, and Trichosporon, Cryptococcus, and Rhodotorula are intrinsically resistant to the echinocandins (1, 15). These organisms present new challenges not only to treatment but also to standard identification methods used in the clinical laboratory (4, 8, 28).Commercially available biochemical test systems identify most of the commonly isolated species of yeast accurately but may result in no identification or misidentification of more-unusual isolates (4, 21, 28). Additionally, samples for these tests must be incubated for 1 to 3 days before results are obtained. To overcome the inaccuracies of biochemical identification methods, nucleic acid-based tests have been developed. These tests amplify and then sequence a target gene, such as the rRNA genes or the internal transcribed spacer (ITS) region (9, 10, 14, 17). While these assays are highly accurate, they require considerable processing time and costly reagents.As an alternative to biochemical and genome-based identification schemes, proteomic profiling by mass spectral analysis was recently evaluated for use in species differentiation of a variety of microorganisms. Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF) is emerging as a rapid and accurate tool for identifying pathogens, including Gram-positive and Gram-negative bacteria, mycobacteria, molds, and yeast species (3, 6, 11-13, 16, 18, 22, 23, 27). The technique can be performed rapidly, with minimal consumable expenses, and produces reproducible, species-specific spectral patterns that are not dependent upon the age of culture, growth conditions, or medium selection (7, 13, 20, 26).In this work, we present the development of a yeast database library consisting of 109 type and reference strains (44 species in 8 genera), and we tested the robustness and accuracy of this library by using 194 well-characterized clinical isolates (23 species in 6 genera).     

Molecular Phylogenetic Diversity of Dermatologic and Other Human Pathogenic Fusarial Isolates from Hospitals in Northern and Central Italy

Fifty-eight fusaria isolated from 50 Italian patients between 2004 and 2007 were subject to multilocus DNA sequence typing to characterize the spectrum of species and circulating sequence types (STs) associated with dermatological infections, especially onychomycoses and paronychia, and other fusarioses in northern and central Italy. Sequence typing revealed that the isolates were nearly evenly divided among the Fusarium solani species complex (FSSC; n = 18), the F. oxysporum species complex (FOSC; n = 20), and the Gibberella (Fusarium) fujikuroi species complex (GFSC; n = 20). The three-locus typing scheme used for members of the FSSC identified 18 novel STs distributed among six phylogenetically distinct species, yielding an index of discrimination of 1.0. Phylogenetic analysis of the FOSC two-locus data set identified nine STs, including four which were novel, and nine isolates of ST 33, the previously described widespread clonal lineage. With the inclusion of eight epidemiologically unrelated ST 33 isolates, the FOSC typing scheme scored a discrimination index of 0.787. The two-locus GFSC typing scheme, which was primarily designed to identify species, received the lowest discrimination index, with a score of 0.492. The GFSC scheme, however, was used to successfully identify 17 isolates as F. verticillioides, 2 as F. sacchari, and 1 as F. guttiforme. This is the first report that F. guttiforme causes a human mycotic infection, which was supported by detailed morphological analysis. In addition, the results of a pathogenicity experiment revealed that the human isolate of F. guttiforme was able to induce fusariosis of pineapple, heretofore its only known host.Fusarium is a large genus of hyaline filamentous molds best known as the most important group of mycotoxigenic plant pathogens (15, 21, 24). Fusaria have also emerged over the past 3 decades as opportunistic pathogens of immunocompetent and immunocompromised hosts (27). Infections in healthy individuals typically remain localized and include keratitis, especially in association with ocular trauma; onychomycosis of the toenails or fingernails; allergic sinusitis; paronychia; and dermatomycoses (11, 13, 18, 28, 34). By way of contrast, fusarioses in artificially immunosuppressed or immunocompromised patients can become life-threatening systemic infections if they become disseminated within the bloodstream, especially if the individual is persistently and severely neutropenic (50). Deeply invasive fusarial infections pose a significant challenge to infectious disease specialists because, with the exception of limited success with liposomal amphotericin B, most species show high levels of resistance to all antifungals currently available (1, 4, 5, 36, 39).Several species-level molecular phylogenetic analyses of medically important fusaria over the past decade have revealed that the most commonly reported species (i.e., Fusarium solani, F. moniliforme, F. oxysporum, F. incarnatum, F. chlamydosporum, and F. dimerum) actually represent species complexes that collectively contain approximately 70 medically relevant species (31, 32, 35, 36, 37, 52). Typing schemes have been developed for these six species complexes and have focused on the identification of species limits on the basis of multilocus genealogical concordance (46), in contrast to schemes for the high-resolution typing of the strains within a species (6, 29). The fusarial studies have revealed that the majority of clinically important fusaria cannot be identified by the use of morphology alone (36, 37), and therefore, accurate reporting of the etiological agent typically requires a DNA sequence-based identification (7). These studies have also revealed the necessity of developing species and sequence type (ST) nomenclatures within the F. solani species complex (FSSC), the F. oxysporum species complex (FOSC), the F. incarnatum/F. equiseti species complex (FIESC), and the F. chlamydosporum species complex (FCSC), in which close to two-thirds of the species (i.e., ∼40) lack Latin binomials. Fortunately, all of the clinically relevant species within the Gibberella (Fusarium) fujikuroi species complex (GFSC; until recently, generally reported as F. moniliforme) and most of those within the F. dimerum species complex (FDSC) have been formally described (31, 42). Sequence-based typing has revealed that members of the FSSC, FOSC, and GFSC are collectively the cause of approximately 80% of all fusarial infections of humans and other animals, with members of the other three complexes accounting for most of the remainder.Due in part to the increased awareness of clinicians, coupled with their possible insurgence, onychomycoses and acute and chronic cutaneous infections caused by Fusarium spp. are increasingly being reported in immunocompetent patients (10, 16, 18, 22, 40, 43). Paronychial and other dermatomycotic fusarial infections, including dermatitis, represent a challenge for the clinician, since an incorrect diagnosis may lead to topical steroidal therapy and local and/or systemic antibiotic therapy, which can delay recovery and increase morbidity (23). Moreover, onychomycotic infections require careful monitoring within the neutropenic patient population because they can progress into life-threatening disseminated infections (50).The present molecular phylogenetic study was conducted to (i) identify the etiological agents of 46 dermatological fusaria and 12 other fusarial pathogens associated with diverse mycotic infections occurring in the Lombardy and Piedmont regions in northern Italy and in the Marche region in central Italy during the period from 2004 through 2007; (ii) assess the prediction, on the basis of the available typing data, that most of the clinically relevant fusaria are nested within the FSSC, FOSC, or GFSC; (iii) determine the index of discrimination of the DNA typing schemes employed (19); and (iv) assess whether the novel human pathogen Fusarium guttiforme, which was recovered from a human paronychial infection, is pathogenic for its only known host, Ananas comosus (L.) Merr. (pineapple).