Rapid Method for Identification of Six Common Species of Mycobacteria Based on Multiplex SNP Analysis

A multiplex method using the SNaPshot technique was developed to screen for six common mycobacterial species: Mycobacteria tuberculosis, M. avium, M. intracellulare, M. chelonae, M. kansasii, and M. gordonae. A total of 468 mycobacterial clinical isolates were subjected to analysis for the presence of the six mycobacterial species by the multiplex SNaPshot method. Of the 468 mycobacterial isolates, 464 (99.15%) could be correctly identified by this assay. The multiplex SNaPshot technique is a promising discriminatory tool for rapid and accurate identification of frequently encountered clinical mycobacterial species.Even though Mycobacterium tuberculosis continues to be a serious health concern worldwide, it has been increasingly recognized that nontuberculous mycobacteria (NTM) are important human pathogens (4, 16, 23). NTM are ubiquitous organisms, with nearly 100 different species found in soil and water that can act as opportunistic pathogens in humans, causing a wide variety of skin and soft tissue infections, lymphadenitis, and lung disease (6, 15). The early differentiation of M. tuberculosis from NTM and the identification of species among NTM are crucial for immediate implementation of the appropriate therapy because susceptible drugs vary widely among different species (9).Conventionally, identification of mycobacteria is carried out by time-consuming biochemical tests that are not always accurate (5, 17, 25). Chromatographic techniques such as high-performance liquid chromatography (HPLC), gas-liquid chromatography (GLC), and thin-layer chromatography (TLC) are labor-intensive, difficult, or expensive (21, 26). DNA sequence analysis of the 16S rRNA gene region is now regarded as the gold standard for the identification of mycobacteria (13, 22, 25, 27). However, equipment and running costs are high. Simple genotypic assays for the identification of mycobacteria, such as Accuprobe (Gen-Probe Inc., San Diego, CA) (1), INNO-LiPA (27), and Genotype Mycobacterium (Hain Diagnostika) (19) are available commercially. Even though these tests are simple, they are often suited for small test volumes and are too expensive for high-throughput laboratories to use in a routine clinical diagnostic setting.In this study, we developed a novel multiplex SNaPshot method using fluorescently labeled terminators and capillary electrophoresis to screen for six common clinically encountered mycobacterial species (M. tuberculosis, M. avium, M. intracellulare, M. chelonae, M. kansasii, and M. gordonae) based on eight single nucleotide polymorphisms (SNPs) located in conserved regions of the 16S rRNA and Hsp65 genes.     

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.     

Rapid identification of mycobacterial whole cells in solid and liquid culture media by matrix-assisted laser desorption ionization-time of flight mass spectrometry

Mycobacterial identification is based on several methods: conventional biochemical tests that require several weeks for accurate identification, and molecular tools that are now routinely used. However, these techniques are expensive and time-consuming. In this study, an alternative method was developed using matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS). This approach allows a characteristic mass spectral fingerprint to be obtained from whole inactivated mycobacterial cells. We engineered a strategy based on specific profiles in order to identify the most clinically relevant species of mycobacteria. To validate the mycobacterial database, a total of 311 strains belonging to 31 distinct species and 4 species complexes grown in Löwenstein-Jensen (LJ) and liquid (mycobacterium growth indicator tube [MGIT]) media were analyzed. No extraction step was required. Correct identifications were obtained for 97% of strains from LJ and 77% from MGIT media. No misidentification was noted. Our results, based on a very simple protocol, suggest that this system may represent a serious alternative for clinical laboratories to identify mycobacterial species.The genus Mycobacterium encompasses over 100 species. The most important mycobacterial diseases are predominantly caused by the Mycobacterium tuberculosis complex. The incidence of other mycobacterial diseases due to nontuberculous mycobacteria (NTM) appears to be increasing in recent years due to the increasing number of immunocompromised individuals (1). Because the treatment of these infections differs depending on the isolated species, the correct and rapid identification of causative organisms is essential.Conventional methods for the identification of mycobacteria were classically based on biochemical tests. They required several weeks for adequate growth, and sometimes accurate identification was not possible. Difficulties, such as the lack of adequate reproducibility, the variability of phenotypes, and the fact that phenotype information is limited to common species, may lead to ambiguous or erroneous results (29). New strategies have been developed in the last decades using molecular biology tools (6, 10, 16, 24). The techniques based on DNA hybridization are sensitive, fast, and simple, but the available commercial assays (AccuProbe; Gen-Probe, San Diego, CA) are able to identify only four species and two complexes of mycobacteria (10). Techniques requiring amplification followed by a hybridization step on a solid support are more complete than probes, but commercially available kits are limited to 5 (GenoType MTBC; Hain Lifescience GmbH, Nehren, Germany), 16 (Inno-LiPa Mycobacteria v2; Innogenetics, Gent, Belgium), or 30 (GenoType Mycobacterium; Hain Lifescience GmbH, Germany) species (19, 22, 30). Systems based on sequencing or enzymatic restriction targeting the hsp65, 16S rRNA, sod, and rpoB genes allow good identification of all mycobacteria at the species level but remain limited to specialized laboratories (14, 17, 23, 31, 36, 37). In addition, they are expensive and time-consuming and require qualified operators (20). Recently, alternatives based on the analysis of mycolic acid by high-performance liquid chromatography (HPLC) (2) or electrospray ionization-tandem mass spectrometry analysis (28) have been proposed. However, these methods are still labor-intensive.Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) allows rapid identification of the most frequently isolated bacteria grown on solid medium by the identification of species-specific profiles obtained from isolated colonies (3-5). This technique is now routinely used in a few laboratories (26, 34). Some authors have used MALDI-TOF MS for rapid identification of Mycobacterium species (12, 18, 21). However, the techniques used require several steps, such as 16S rRNA gene-based techniques (18), cell extractions (12), or a statistical analysis (12, 21). In addition, the number of tested strains in these studies is less than 40, encompassing a maximum of 13 species. It was first reported by Hettick et al. that the analysis of mycobacterial whole cells by MALDI-TOF MS could be used for identification. However, the limited number of strains prevented the engineering of a useful database (11).Recently, we engineered a strategy to identify bacteria using MALDI-TOF MS, based on the choice of a limited number of species-specific profiles (3, 5). The aim of the present work is to extend this strategy to the identification of mycobacterial strains without cell extraction. This method will allow us to have a rapid, accurate, and inexpensive identification tool in routine laboratories. The first step was to build a complete database for mycobacterial species isolated in human pathology. This database was then validated by using clinical strains cultivated in solid and liquid media.     

Lack of Insertional-Deletional Polymorphism in a Collection of Mycobacterium ulcerans Isolates from Ghanaian Buruli Ulcer Patients

Mycobacterium ulcerans causes the devastating infectious skin disease Buruli ulcer and has a monomorphic population structure. The resolution of conventional genetic fingerprinting methods is therefore not sufficient for microepidemiological studies aiming to characterize transmission pathways. In a previous comparative genomic hybridization analysis with a microarray covering part of the M. ulcerans genome, we have found extensive insertional-deletional sequence polymorphisms among M. ulcerans isolates of diverse geographic origins that allowed us to distinguish between strains coming from different continents. Since large numbers of insertion sequences are spread over the genome of African M. ulcerans strains, we reasoned that these may drive large sequence polymorphisms in otherwise clonal local mycobacterial populations. In this study, we used a printed DNA microarray covering the whole genome of the Ghanaian M. ulcerans reference strain Agy99 for comparative genomic hybridization. The assay identified multiple regions of difference when DNA of a Japanese M. ulcerans strain was analyzed. In contrast, not a single insertional-deletional genomic variation was found within a panel of disease isolates coming from an area of Ghana where Buruli ulcer is endemic. These results indicate that, despite the expectations deduced from other mycobacterial pathogens, only analyses of single nucleotide polymorphisms will have the potential to differentiate local populations of M. ulcerans.Buruli ulcer (BU) is a severe skin disease characterized by large ulcerative lesions, often leading to deformity and the crippling of extremities. While this neglected tropical disease occurs in more than 30 countries worldwide, it currently has its major focus in West Africa, where the prevalence is greater than that of leprosy, and incidence rates still may be underestimated (61). The social impact of BU endemicity in rural settings of Africa, where children are most affected, is dramatic. Patients often have only limited access to health care and tend to report to health care facilities at advanced stages of disease (20, 49). BU is often concentrated in areas close to stagnant or slow-moving waters. The mode of transmission is not fully understood (13, 36, 44-46, 59, 60), partly because conventional molecular fingerprinting methods have not sufficiently high resolution for microepidemiological analyses (1-4, 10, 11, 23, 24, 27, 33, 51, 53, 55-57).Mycobacterium tuberculosis and related pathogenic mycobacteria exhibit major large sequence polymorphism (LSP)-based interstrain genomic variations (5, 9, 12, 34, 58). From these genomic insertional-deletional (InDel) markers, evolutionary scenarios were drawn for M. tuberculosis, the M. tuberculosis complex, Mycobacterium bovis, the M. bovis BCG vaccine strains, and mycolactone-producing mycobacteria related to Mycobacterium ulcerans (6-8, 25, 27, 38, 50). In recent years, proposed phylogenies were confirmed and refined by whole-genome sequence analysis identifying single nucleotide polymorphisms (SNPs) (16, 17, 21, 22). Combinations of all identified genomic polymorphisms are currently being used for studying mycobacterial evolution and transmission pathways, helping in the prevention of epidemics (34, 37).Comparative genomic hybridization (CGH) analysis of M. ulcerans clinical isolates of diverse geographic origins also revealed extensive LSPs (47). The identified transposable element-associated InDel recombination events are indicative of progressive genome shrinking in M. ulcerans, which has emerged from the environmental mycobacterium Mycobacterium marinum by acquisition of a large virulence plasmid (52). An in-depth comparison of the recently published M. ulcerans genome of strain Agy99 to the progenitor species strain M. marinum M revealed LSPs, named M. ulcerans regions of difference (MURDs) (54). Analysis of large InDel polymorphisms allowed us to distinguish between two distinct lineages: (i) the “classical” lineage representing the most pathogenic genotypes, consisting of those that come from Africa, Australia, and Southeast Asia; and (ii) an “ancestral” lineage comprising strains from China and Japan, South America, and Mexico (29). A total of 209 copies of the insertion sequence (IS) IS2404 and 83 copies of IS2606 have been found interspersed in the genome of the M. ulcerans reference strain Agy99 from Ghana (54). Due to achievements using LSPs in other mycobacterial pathogens, we reasoned that this high abundance of transposable elements may destabilize the general architecture of the genome of African M. ulcerans strains, resulting in a rapid accumulation of LSPs in otherwise monomorphic populations of the pathogen. To assess this experimentally, we performed CGH analyses using a comprehensive whole-genome microarray. Specifically, we tried to identify LSPs within a panel of M. ulcerans strains isolated from the BU lesions of 37 patients from several districts in Ghana between the years 2002 and 2004.     

Acute Immune Response to Mycobacterium massiliense in C57BL/6 and BALB/c Mice

Mycobacterium massiliense is an environmental opportunistic pathogen that has been associated with soft tissue infection after minor surgery. We studied the acute immune response of C57BL/6 and BALB/c mice infected intravenously with 10⁶ CFU of an M. massiliense strain isolated from a nosocomial infection in Brazil. The results presented here show that M. massiliense is virulent and pathogenic to both C57BL/6 and BALB/c mice, inducing a granulomatous inflammatory reaction that involves the activation of macrophages, dendritic cells, and natural killer cells induced by gamma interferon and interleukin-17 (IL-17) in C57BL/6 mice and by IL-12 in BALB/c mice.Mycobacteria that do not belong to the complex Mycobacterium tuberculosis are known as nontuberculous mycobacteria (NTM) or atypical mycobacteria. NTM are ubiquitous microorganisms found worldwide in soil and water (3, 23, 38). These environmental mycobacteria are considered emerging and environmental opportunistic pathogens (6, 23).Mycobacterium massiliense is an environmental nonphotochromogenic, rapidly growing Mycobacterium strain that has been associated with soft-tissue infection after minor surgery or intramuscular injection (3, 5, 17, 22, 26, 46) and with pulmonary infection due to diseases, such as cystic fibrosis (29, 41). This species differs only slightly from Mycobacterium abscessus, sharing a 99.6% sequence identity of their 16S rRNA genes; genetic differences can be observed by comparative sequence analysis of the rpoB and hsp65 genes (1, 25, 42). Infections with these agents tend to respond poorly to macrolide-based chemotherapy (3), even though the organisms are susceptible to clarithromycin (15, 44, 47).M. massiliense infection mainly affects immunocompetent individuals and occasionally is associated with disseminated disease (8). An outbreak of M. massiliense occurred in Goiania, Brazil, where 30 individuals were infected after undergoing knee joint and laparoscopic surgery (5). Despite the fact that the infected individuals were from different hospitals, a unique M. massiliense strain was identified and characterized by pulsed-field gel electrophoresis.Disease pathogenesis involves host-pathogen interactions that directly affect parasite clearance. Typically, when environmental bacteria are passively introduced into the host, rapid bacterial clearance occurs due to an efficient innate immune response (30). Nonetheless, accidental infections with M. massiliense have been described as having a chronic evolution and, in some cases, the disease is disseminated irrespective of the host''s immune status. Such findings raise the possibility that this species is more virulent and/or pathogenic than other environmental mycobacteria, such as M. chelonae and M. abscessus.Recently, a murine model of M. abscessus infection was described, and isogenic mice were shown to be good models to address the immune response of the host (34, 39). In the present study, we analyzed the immune response of C57BL/6 and BALB/c mice infected with a clinical isolate of M. massiliense obtained from the recent outbreak in Goiania, Brazil. We show here that M. massiliense is virulent and pathogenic to both C57BL/6 and BALB/c mice, inducing a granulomatous inflammatory reaction that involves the activation of macrophages, dendritic cells (DCs), and natural killer (NK) cells induced mainly by gamma interferon (IFN-γ) and interleukin-17 (IL-17) in C57BL/6 mice and by IL-12 in BALB/c mice.     

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.     

Cellular Responses to Mycobacterial Antigens Are Present in Bronchoalveolar Lavage Fluid Used in the Diagnosis of Sarcoidosis

Considerable evidence supports the concept that CD4⁺ T cells are important in sarcoidosis pathogenesis, but the antigens responsible for the observed Th1 immunophenotype remain elusive. The epidemiologic association with bioaerosols and the presence of granulomatous inflammation support consideration of mycobacterial antigens. To explore the role of mycobacterial antigens in sarcoidosis immunopathogenesis, we assessed the immune recognition of mycobacterial antigens, the 6-kDa early secreted antigenic protein (ESAT-6) and catalase-peroxidase (KatG), by T cells derived from bronchoalveolar lavage (BAL) fluid obtained during diagnostic bronchoscopy. We report the presence of antigen-specific recognition of ESAT-6 and KatG in T cells from BAL fluid of 32/44 sarcoidosis subjects, compared to 1/27 controls (P < 0.0001). CD4⁺ T cells were primarily responsible for immune recognition (32/44 sarcoidosis subjects), although CD8⁺ T-cell responses were observed (25/41 sarcoidosis subjects). Recognition was significantly absent from BAL fluid cells of patients with other lung diseases, including infectious granulomatous diseases. Blocking of Toll-like receptor 2 reduced the strength of the observed immune response. The presence of immune responses to mycobacterial antigens in cells from BAL fluid used for sarcoidosis diagnosis suggests a strong association between mycobacteria and sarcoidosis pathogenesis. Inhibition of immune recognition with monoclonal antibody against Toll-like receptor 2 suggests that induction of innate immunity by mycobacteria contributes to the polarized Th1 immune response.Sarcoidosis is a multisystem granulomatous disease of unknown etiology, characterized by a Th1 immunophenotype. The epidemiology and immunology of sarcoidosis suggest that an infectious agent could be involved in its pathogenesis. Immunologic studies of sarcoidosis have detected oligoclonal T cells in the sarcoid granuloma, consistent with a major histocompatibility complex-restricted antigen-driven process (33, 42). Analysis of cells from bronchoalveolar lavage (BAL) fluid from patients with acute forms of sarcoidosis has demonstrated overrepresentation of specific T-cell receptor alleles in combination with DRB3*0101 and DRB1*0301 major histocompatibility complex restrictions, strongly implicating an antigen-specific response in sarcoidosis pathogenesis (21).Because sarcoidosis most commonly involves the lungs, eyes, and skin, the search for environmental causes has centered on exposures to airborne antigens (26). Several reports have noted associations with occupations such as agriculture, metalworking, firefighting, and the handling of building supplies (3, 30, 32, 38). The association of sarcoidosis with these occupations raises the possibility that disease may be caused by exposure to microbial bioaerosols, including inorganic particles, insecticides, and aerosols from moldy environments (3, 32, 35, 39). Sarcoidosis also demonstrates a seasonal and geographic variability (12, 29, 34, 50). The transmissibility, clustering of cases, and geographic and seasonal variability suggest that environmental factors are important in the acquisition of sarcoidosis. Moreover, these environmental risk factors correlate well with the typical distribution of environmental mycobacteria.The potential role of mycobacteria in sarcoidosis immunopathogenesis is supported by recent studies reporting detection of mycobacterial proteins and nucleic acids in sarcoidosis granulomas, as well as humoral and peripheral cellular immune responses to mycobacterial antigen in sarcoidosis subjects (4, 9, 13-17, 22, 44). However, in order to understand disease pathogenesis, it is crucial to analyze the immunologic response at the site of active sarcoidosis involvement. Although sarcoidosis is a systemic disease, it most commonly affects the lungs. Taking advantage of the observation that most patients undergo bronchoscopy with BAL as a routine investigation (49), we assessed the specific immune recognition of mycobacterial virulence factors by T cells from BAL fluid derived from sarcoidosis patients from geographically distinct locales.In order to investigate the role of mycobacterial antigen in lung involvement in sarcoidosis, we analyzed specific responses of BAL fluid-derived T cells to the mycobacterial 6-kDa early secreted antigenic protein (ESAT-6) and catalase-peroxidase (KatG). We chose ESAT-6 and KatG peptides due to prior reports of systemic cellular immune responses to these microbial virulence factors in sarcoidosis subjects (9, 13).     

Biochip System for Rapid and Accurate Identification of Mycobacterial Species from Isolates and Sputum

The accurate detection of mycobacterial species from isolates and clinical samples is important for pathogenic diagnosis and treatment and for disease control. There is an urgent need for the development of a rapid, simple, and accurate detection method. We established a biochip assay system, including a biochip, sample preparation apparatus, hybridization instrument, chip washing machine, and laser confocal scanner equipped with interpretation software for automatic diagnosis. The biochip simultaneously identified 17 common mycobacterial species by targeting the differences in the 16S rRNA. The system was assessed with 64 reference strains and 296 Mycobacterium tuberculosis and 243 nontuberculous mycobacterial isolates, as well as 138 other bacteria and 195 sputum samples, and then compared to DNA sequencing. The entire biochip assay took 6 h. The concordance rate between the biochip assay and the DNA sequencing results was 100%. In conclusion, the biochip system provides a simple, rapid, reliable, and highly accurate clinical assay for determination of mycobacterial species in a 6-h procedure, from either culture isolates or sputum samples, allowing earlier pathogen-adapted antimicrobial therapy in patients.Mycobacterium tuberculosis is an important pathogen; it is responsible for 1.3 to 1.7 million mortalities worldwide in 2007 (26). However, the incidence of opportunistic infections by nontuberculous mycobacteria (NTM) has gradually increased, causing a number of different NTM diseases (4, 5, 14). This apparent increase is thought to be the consequence of several factors; the increased use of diagnostic methods that can identify these agents has contributed to this number, while the AIDS epidemic is a principal cause (18). A report on a nationwide random survey in China on the epidemiology of tuberculosis in 2000 revealed that 11.1% of the 441 bacterial strains isolated from patient sputum were NTM (15). The low level of identification of NTM is partially due to the use of conventional methods, which rely on growth characteristics, colony morphology, pigment production, and biochemical tests. Because of the slow growth of mycobacteria, the methods are time-consuming, taking 4 to 8 weeks to complete. Extensive experience in the interpretation of the results of biochemical tests is also required, and the identity of specific species from cultures is often difficult to determine, resulting in possible misidentification. As a result of these numerous limitations, conventional methods are not widely used by the majority of clinical laboratories in China. However, the correct identification of NTM is clinically important because most NTM are naturally resistant to first-line antituberculosis drugs, and different species of NTM are sensitive to different antibiotics drugs. Thus, there is an urgent need for the development of a rapid, simple, and accurate method for mycobacterium species identification (21).Recently, different nucleic acid based molecular assays such as DNA sequencing (1), microarray assay (6, 16, 25), PCR-restriction fragment length polymorphism (RFLP) assays (23), and commercial kits such as Accuprobe (Gen-Probe, San Diego, CA) (2), GenoType (Hain, Germany), (19, 20), and INNO-LiPA (Innogenetics, Belgium) (24), have emerged as rapid tools for species identification. The molecular identification methods are based on the polymorphisms in the 16S rRNA (1) or 16S-23S rRNA spacer regions (24) or 23S rRNA (20) or hsp65 genes (12). The 16S rRNA gene sequences of most mycobacterial species are well known and can be found in online databases. Although the molecular methods mentioned above have greatly improved the diagnosis of NTM, there is still a need for a quick, semiautomated or fully automated, total solution-based system to meet the high-throughput demands of busy clinics, particularly for large centers with numerous patients.We report here a rapid diagnosis solution that includes a biochip, apparatus for sample preparation, chip hybridization, washing and data acquisition, and dedicated software for automated diagnosis. The biochip is designed to detect differences in 16S rRNA sequences for mycobacteria species identification. The entire process is semiautomatic and high throughput. The automated determination of species could also eliminate some elements of operator error.     

Efficient Differentiation of Mycobacterium avium Complex Species and Subspecies by Use of Five-Target Multiplex PCR

Infections caused by the Mycobacterium avium complex (MAC) are on the rise in both human and veterinary medicine. A means of effectively discriminating among closely related yet pathogenetically diverse members of the MAC would enable better diagnosis and treatment as well as further our understanding of the epidemiology of these pathogens. In this study, a five-target multiplex PCR designed to discriminate MAC organisms isolated from liquid culture media was developed. This MAC multiplex was designed to amplify a 16S rRNA gene target common to all Mycobacterium species, a chromosomal target called DT1 that is unique to M. avium subsp. avium serotypes 2 and 3, to M. avium subsp. silvaticum, and to M. intracellulare, and three insertion sequences, IS900, IS901, and IS1311. The pattern of amplification results allowed determination of whether isolates were mycobacteria, whether they were members of the MAC, and whether they belonged to one of three major MAC subspecies, M. avium subsp. paratuberculosis, M. avium subsp. avium, and M. avium subsp. hominissuis. Analytical sensitivity was 10 fg of M. avium subsp. paratuberculosis genomic DNA, 5 to 10 fg of M. avium subsp. avium genomic DNA, and 2 to 5 fg of DNA from other mycobacterial species. Identification accuracy of the MAC multiplex was evaluated by testing 53 bacterial reference strains consisting of 28 different mycobacterial species and 12 nonmycobacterial species. Identification accuracy in a clinical setting was evaluated for 223 clinical MAC isolates independently identified by other methods. Isolate identification agreement between the MAC multiplex and these comparison assays was 100%. The novel MAC multiplex is a rapid, reliable, and simple assay for discrimination of MAC species and subspecies in liquid culture media.Since the early 1980s, there has been an increase in disease caused by organisms broadly categorized as nontuberculous mycobacteria (NTM), a generic term for mycobacteria not in the Mycobacterium tuberculosis complex and other than M. leprae (32). Of these NTM, Mycobacterium avium complex (MAC) species are the most common cause of human and animal disease globally (6, 14, 16, 24). The clinical relevance of the MAC in humans has been amplified in recent decades with the increasing population of immunocompromised individuals resulting from longer life expectancy, immunosuppressive chemotherapy, and the AIDS pandemic (27). The MAC is divided into two main species: M. avium and M. intracellulare. M. avium is further subdivided (per Turenne et al.) into four subspecies: M. avium subsp. avium, M. avium subsp. hominissuis, M. avium subsp. paratuberculosis, and M. avium subsp. silvaticum (39).Members of the family Mycobacteriaceae, comprising the MAC, differ in virulence and ecology. Those designated M. avium subsp. hominissuis are genomically diverse, low-virulence, opportunistic pathogens for both animals and humans. The majority of human M. avium subsp. hominissuis infections occur in HIV-immunocompromised people, immunocompetent persons with underling pulmonary disease, and children with cystic fibrosis (2, 12, 17). Considered ubiquitous in the environment (the most likely source of infection for humans), M. avium subsp. hominissuis has been isolated from water, soil, and dust (9). Domestic water distribution systems have been reported as possible sources of M. avium subsp. hominissuis infections in hospitals, homes, and commercial buildings (26, 27). In animals, M. avium subsp. hominissuis is found as a cause of lymphadenitis of the head and mesenteric lymph nodes of swine recognized at slaughter.Mycobacterium avium subsp. avium has long been recognized as a primary pathogen causing avian tuberculosis in wild and domestic birds (37, 38). Members of this subspecies also sporadically cause disease in other animals (6, 15, 30).For veterinarians, the MAC member of greatest importance is M. avium subsp. paratuberculosis. This MAC member causes a chronic granulomatous enteritis called Johne''s disease or paratuberculosis, most often in ruminants (16, 22, 31). Mycobacterium avium subsp. paratuberculosis is capable of infecting and causing disease a wide array of animal species, including nonhuman primates, without need of immunosuppressive coinfections. The herd-level prevalence of M. avium subsp. paratuberculosis infections in dairy cattle exceeds 50% in most major dairy product-producing countries (29, 31). Two systematic reviews and meta-analyses report a consistent association of M. avium subsp. paratuberculosis with Crohn''s disease, and the zoonotic potential of M. avium subsp. paratuberculosis continues to be a controversial subject discussed in the literature (1, 11). Unlike for most other M. avium subspecies, isolation of M. avium subsp. paratuberculosis requires the addition of the siderophore mycobactin to culture media and prolonged culture incubation for successful isolation from a tissue, soil, or fecal samples (43). After this lengthy incubation period with special media, resultant acid-fast organisms then need to be accurately identified.Unlike the M. avium subspecies, whose type strains were obtained from nonhuman hosts, the type strain of M. intracellulare (ATCC 13950) was isolated from a human, specifically a child who died from disseminated disease. Recently, numerous isolates considered to be M. intracellulare were reclassified as M. chimaera sp. nov. as part of the MAC (35). Few of these isolates were found to be clinically relevant, suggesting that this MAC species has low pathogenicity, and this factor is crucial to therapeutic decision making. Mycobacterium intracellulare appears to have a distinct environmental niche, more prevalent in biofilms and at significantly higher CFU numbers than M. avium (10, 36). It accounts for more documented human infections than M. avium subsp. hominissuis in several countries, including South Korea and Japan (19, 20, 23).Contemporary methods for MAC identification, e.g., high-performance liquid chromatography (HPLC) of cell wall mycolic acids, and genetic probes based on rRNA targets, e.g., AccuProbe, cannot discriminate among M. avium subspecies (2, 9). Given the differences in pathogenicity among M. avium subspecies and the implications regarding the infection source, a practical and accurate method of simply identifying M. avium subspecies is needed (13, 25, 35). In this study, we describe the specificity, discrimination capacity, and sensitivity of a novel five-target PCR, called the MAC multiplex, using a wide array of reference and clinical MAC isolates and numerous nonmycobacterial organisms.     

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.     

Improvement in Mycobacterial Yield and Reduced Time to Detection in Pediatric Samples by Use of a Nutrient Broth Growth Supplement

There is an urgent need to improve the methods used for the bacteriological diagnosis of childhood mycobacterial disease. This study compared the mycobacterial yields and the times to detection (in days) of mycobacteria in pediatric clinical specimens by using Mycobacterial Growth Indicator Tubes (MGITs) and solid Löwenstein-Jensen (LJ) slants with and without a nutrient broth supplement. A total of 801 specimens from 493 patients were processed: 82.8% were gastric aspirate specimens, 15.6% were sputum specimens, and 1.6% were fine-needle-aspiration biopsy specimens. The mycobacterial yield obtained with MGITs (with and without nutrient broth) was 11.0%, and that obtained with LJ slants was 1.6% (P < 0.001). Of the 88 positive cultures, 62 were detected in MGITs and 73 were detected in MGITs supplemented with nutrient broth (P = 0.11). The mean time to detection in MGITs (without nutrient broth) was 18.5 days, whereas it was 12.4 days in MGITs with nutrient broth (P < 0.001). Supplementation of standard MGITs improved the mycobacterial yield and significantly reduced the time to detection of mycobacteria in pediatric samples.The accurate diagnosis of childhood tuberculosis remains a major challenge (6, 24), since the paucibacillary nature of the disease in children and the difficulty of specimen collection hamper bacteriological confirmation of the diagnosis. Clinical diagnosis is complicated by the nonspecific symptoms and signs associated with pediatric tuberculosis, particularly in children with human immunodeficiency virus (HIV) infection (3, 9, 14). The traditional growth media used to cultivate mycobacteria include solid egg-based Löwenstein-Jensen (LJ) slants and Middlebrook (7H9) liquid broth-based media, such as that used in the Bactec Mycobacterial Growth Indicator Tube (MGIT) (21, 23).Growth supplements are widely used to improve the culture yield of fastidious organisms (10, 11). For the improved recovery of Mycobacterium bovis BCG, 7H9 broth (glycerol, bovine albumin fraction, glucose, sodium chloride) has been supplemented with Tween 80 (10% polyoxyethylene sorbitan mono-oleate solution), but the benefits appeared to be limited (7). The Bactec MGIT uses 7H9 broth supplemented with oleic acid, albumin, dextrose, and catalase (OADC) to enhance the growth of mycobacteria (21). The supplementation of 7H9 broth with a nutrient broth (modified Dubos liquid medium) containing beef extract and peptone has been recommended for the enhanced recovery of mycobacteria from inocula containing few organisms (5, 18), but data on its performance in a routine diagnostic laboratory and especially with pediatric specimens are limited. The development of tests that allow the rapid and reliable confirmation of mycobacterial infection in children has been identified as a high research priority (15, 17).This study evaluated whether the addition of a meat extract-based growth supplement (Bacto TB nutrient broth; Difco Laboratories Inc., Detroit, MI) to standard culture medium improves the mycobacterial yield and the time to detection of mycobacteria achieved during routine processing of specimens from children with suspected mycobacterial disease. The composition of the Bacto TB broth is available on request.(This study was performed in partial fulfillment of the master''s degree of W. Brittle.)     

Rapid Identification of Mycobacterium tuberculosis and Nontuberculous Mycobacteria by Multiplex,Real-Time PCR

The rapid identification of mycobacteria from culture is of primary importance for the administration of empirical antibiotic therapy and for the implementation of public health measures, yet there are few commercially available assays that can easily and accurately identify the mycobacteria in culture in a timely manner. Here we report on the development of a multiplex, real-time PCR assay that can identify 93% of the pathogenic mycobacteria in our laboratory in two parallel reactions. The mycobacteria identified by this assay include the Mycobacterium tuberculosis complex (MTC), the M. avium complex (MAC), the M. chelonae-M. abscessus group (MCAG), the M. fortuitum group (MFG), and M. mucogenicum. The primer targets included the 16S rRNA gene and the internal transcribed spacer. The assay was initially validated with a repository of reference strains and was subsequently tested with 314 clinical cultures identified by the AccuProbe assay or high-performance liquid chromatography. Of the 314 cultures tested, multiplex, real-time PCR produced congruent results for 99.8% of the 1,559 targets evaluated. The sensitivity and the specificity were each 99% or greater for MTC (n = 96), MAC (n = 97), MCAG (n = 68), and M. mucogenicum (n = 9) and 95% and 100%, respectively, for MFG (n = 19). We conclude that this multiplex, real-time PCR assay is a useful diagnostic tool for the rapid and accurate identification of MTC and clinically relevant nontuberculous mycobacteria.Mycobacterium tuberculosis, the causative agent of tuberculosis, is among the leading infectious causes of death in developing nations (23). In resource-rich countries, where tuberculosis is not endemic, nontuberculous mycobacteria (NTM) are responsible for the majority of mycobacterial infections in both immunocompromised and immunocompetent individuals (14). The clinical gravity of mycobacterial infections necessitates rapid isolation by culture and timely identification by the appropriate diagnostic assays. Rapid identification not only serves to focus empirical antibiotic therapy and thus avoid unnecessary drug exposure but also may aid with the appropriate respiratory isolation and prevention of secondary cases (15).Few molecular methods commercially available in the United States easily and rapidly identify mycobacteria in culture. Although the AccuProbe assay by Gen-Probe (San Diego, CA) is sufficient for the identification of isolates of the Mycobacterium tuberculosis complex (MTC) and the M. avium complex (MAC) (37), it lacks probe sets specific for rapidly growing mycobacteria, such as the M. chelonae-M. abscessus group (MCAG) and the M. fortuitum group (MFG), which make up approximately 30% of the pathogenic mycobacteria in the Clinical Microbiology Laboratory of Stanford Hospital (Stanford, CA). MCAG consists of M. chelonae, M. abscessus, and M. immunogenum; MFG consists of M. fortuitum, M. senegalense, M. farcinogenes, M. porcinum, M. septicum, M. peregrinum, and M. alvei (11). For these isolates, other methods, such as biochemical reactions (6, 33), high-performance liquid chromatography (HPLC) (13), and DNA sequencing (17), are required for identification. To address the need for a simple and rapid molecular assay with a broader identification scope, we developed a multiplex, real-time PCR assay that can identify 93% of the pathogenic mycobacterial isolates (both slowly growing and rapidly growing) recovered in the Clinical Microbiology Laboratory of Stanford Hospital. This assay simplifies the identification of MTC and MAC and also accommodates the identification of rapidly growing mycobacteria. Although conventional PCR-based and singleplex, real-time PCR assays for the identification of MTC and NTM have previously been reported (3, 7, 18, 19, 25, 29, 30, 32, 35), multiplex, real-time PCR assays with simple interpretative criteria have not been developed. A multiplex, real-time PCR assay for the identification of 18 mycobacterial species, including MTC and rapidly growing mycobacteria, was recently described (21); however, the complex nature of this assay may preclude its use in the routine laboratory. The only simple application of PCR for the identification of rapidly growing mycobacteria consists of PCR-restriction analysis (8, 36). Multiplex, real-time PCR has several crucial advantages over conventional PCR. Besides the ease of use and rapid availability of results, it also eliminates the need for postamplification handling and thus the potential contamination of the laboratory.Here we describe the development and validation of a multiplex, real-time PCR assay for the simple identification of MTC and clinically relevant NTM.     

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.     

Amino Acid Changes in Elongation Factor Tu of Mycoplasma pneumoniae and Mycoplasma genitalium Influence Fibronectin Binding

Mycoplasma pneumoniae and Mycoplasma genitalium are closely related organisms that cause distinct clinical manifestations and possess different tissue predilections despite their high degree of genome homology. We reported earlier that surface-localized M. pneumoniae elongation factor Tu (EF-Tu_Mp) mediates binding to the extracellular matrix component fibronectin (Fn) through the carboxyl region of EF-Tu. In this study, we demonstrate that surface-associated M. genitalium EF-Tu (EF-Tu_Mg), in spite of sharing 96% identity with EF-Tu_Mp, does not bind Fn. We utilized this finding to identify the essential amino acids of EF-Tu_Mp that mediate Fn interactions by generating modified recombinant EF-Tu proteins with amino acid changes corresponding to those of EF-Tu_Mg. Amino acid changes in serine 343, proline 345, and threonine 357 were sufficient to significantly reduce the Fn binding of EF-Tu_Mp. Synthetic peptides corresponding to this region of EF-Tu_Mp (EF-Tu_Mp 340-358) blocked both recombinant EF-Tu_Mp and radiolabeled M. pneumoniae cell binding to Fn. In contrast, EF-Tu_Mg 340-358 peptides exhibited minimal blocking activity, reinforcing the specificity of EF-Tu-Fn interactions as mediators of microbial colonization and tissue tropism.Many pathogens express surface proteins that facilitate colonization and cellular invasion (12, 39, 44, 49, 55). The human mycoplasmas, Mycoplasma pneumoniae and Mycoplasma genitalium, have genome sizes of 816,394 bp (20) and 580,070 bp (12), respectively, with the latter considered the smallest self-replicating biological cell (14, 38). These bacterial pathogens possess terminal tip-like structures comprised of specific membrane adhesins and adherence-related accessory proteins that mediate surface parasitism of target cells (5) and are essential for virulence (4). While adherence of virulent M. pneumoniae is mediated primarily by tip organelle-associated adhesins (10, 24), the absence of these proteins in hemadsorption-negative mutants (HA⁻ class II mutants) (17) still permits detectable adherence (18), suggesting the involvement of alternative mechanisms by which mycoplasmas bind to host cells.Recently, we showed that M. pneumoniae surface-associated elongation factor Tu (EF-Tu_Mp; MPN665) and the pyruvate dehydrogenase E1 beta subunit (MPN392) interact with fibronectin (Fn) (11). In addition, we demonstrated that HA⁻ class II mutants also bind Fn through EF-Tu (11). Fn is an abundantly available pathogen target (22) that exists in soluble form in blood fluids and plasma and in fibrillar form in the extracellular matrix (56). M. pneumoniae could readily access the extracellular matrix through virulence-related determinants following epithelial cell damage (29) and could directly bind to subepithelial tissue targets through EF-Tu interactions with Fn. Furthermore, these distinct pathogenic pathways may also contribute to the ability of M. pneumoniae to invade and to establish intracellular and perinuclear residence (9, 57).Detailed analyses of EF-Tu_Mp-Fn interactions revealed the critical role of the carboxyl region of EF-Tu (amino acids 192 to 219 and 314 to 394) in Fn recognition (3). Other mycoplasmas with tip organelles, such as Mycoplasma penetrans and Mycoplasma gallisepticum, have been reported to bind Fn through a 65-kDa protein (13) and the PlpA and Hlp3 proteins (34).Following our initial findings of EF-Tu_Mp-Fn interactions, surface-associated EF-Tu proteins from other microorganisms, including Lactobacillus johnsonii, Listeria monocytogenes, and Pseudomonas aeruginosa, were reported to bind mucin (16), fibrinogen (43), plasminogen, and factor H (32). Since EF-Tu is one of the most highly conserved proteins in mycoplasmas, it has been used to create an EF-Tu sequence-based mycoplasma phylogeny tree. This allows the classification of the human pathogens, M. genitalium and M. pneumoniae, along with M. gallisepticum, a poultry pathogen, in the same group (28). M. pneumoniae is an established pathogen of the respiratory tract (54) but has also been isolated from the urogenital tract (15). M. genitalium, an emerging sexually transmitted disease pathogen (27, 51), has also been associated with respiratory (6) and joint (50) pathologies. It has been suggested that the tissue-specific tropisms and pathogenic mechanisms of these two mycoplasmas are determined by genetic distinctions between them (19). Most of the open reading frames proposed for M. genitalium are present in M. pneumoniae. Overall, M. pneumoniae and M. genitalium share 67.4% average identity at the amino acid level, while conserved housekeeping proteins exhibit 70 to 97% identity (19). Among the latter proteins, EF-Tu displays a high sequence identity (96%).In this study, we compared EF-Tu-Fn binding between M. pneumoniae and M. genitalium and discovered biological and biochemical differences that facilitated the identification of key amino acids responsible for these interactions. Such distinctions provide evidence of unique colonization capabilities of these bacteria.     

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.     

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).     

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.     

Rapid Mycobacterial Liquid Culture-Screening Method for Mycobacterium avium Complex Based on Secreted Antigen-Capture Enzyme-Linked Immunosorbent Assay

Sensors in automated liquid culture systems for mycobacteria, such as MGIT, BacT/Alert 3D, and Trek ESP II, flag growth of any type of bacteria; a positive signal does not mean that the target mycobacteria are present. All signal-positive cultures thus require additional and often laborious testing. An immunoassay was developed to screen liquid mycobacterial cultures for evidence of Mycobacterium avium complex (MAC). The method, called the MAC-enzyme-linked immunosorbent assay (ELISA), relies on detection of MAC-specific secreted antigens in liquid culture. Secreted MAC antigens were captured by the MAC-ELISA with polyclonal anti- Mycobacterium avium subsp. paratuberculosis chicken immunoglobulin Y (IgY), detected using rabbit anti-MAC IgG, and then revealed using horseradish peroxidase-conjugated goat anti-rabbit IgG. When the MAC-ELISA was evaluated using pure cultures of known mycobacterial (n = 75) and nonmycobacterial (n = 17) organisms, no false-positive or false-negative MAC-ELISA results were found. By receiver operator characteristic (ROC) analysis of 1,275 previously identified clinical isolates, at the assay optimal cutoff the diagnostic sensitivity and specificity of the MAC-ELISA were 92.6% (95% confidence interval [95% CI], 90.3 to 94.5) and 99.9% (95% CI, 99.2 to 100), respectively, with an area under the ROC curve of 0.992. Prospective evaluation of the MAC-ELISA with an additional 652 clinical samples inoculated into MGIT ParaTB medium and signaling positive per the manufacturer''s instructions found that the MAC-ELISA was effective in determining those cultures that actually contained MAC species and warranting the resources required to identify the organism by PCR. Of these 652 MGIT-positive cultures, the MAC-ELISA correctly identified 96.8% (of 219 MAC-ELISA-positive cultures) as truly containing MAC mycobacteria, based on PCR or high-performance liquid chromatography (HPLC) as reference tests. Only 6 of 433 MGIT signal-positive cultures (1.4%) were MAC-ELISA false negative, and only 7 of 219 MGIT signal-negative cultures (3.2%) were false positive. The MAC-ELISA is a low-cost, rapid, sensitive, and specific test for MAC in liquid cultures. It could be used in conjunction with or independent of automated culture reading instrumentation. For maximal accuracy and subspecies-specific identification, use of a confirmatory multiplex MAC PCR is recommended.Members of the Mycobacterium avium complex (MAC) are a family of intracellular bacterial pathogens causing significant disease in both animals and humans. The complex contains four subspecies of M. avium: M. avium subsp. avium, M. avium subsp. paratuberculosis, M. avium subsp. hominissuis, and M. avium subsp. silvaticum (24, 35). Mycobacterium intracellulare is also a member of the complex (20, 35).The clinical importance of MAC infection has increased in recent decades because of the greater population of immunocompromised individuals with longer life expectancies, immunosuppressive chemotherapy, and the spread of human immunodeficiency virus infection (8, 20, 25, 27). With AIDS patients, the incidence of disseminated mycobacterial infection caused by MAC strains can reach up to 50% (19). Although these mycobacterial infections are not often characterized to subspecies, it appears that M. avium subsp. hominissuis is most often involved with AIDS patients (3, 4, 18, 24, 35). In addition, M. avium subsp. hominissuis causes infection in a subset of patients without an obvious immune defect (13) or underlying pulmonary disease and in children with lymphadenitis or cystic fibrosis (31). In virtually all cases, these organisms are believed to be of environmental origin: surface water, tap water, soil, dust, or food (22, 24, 29, 38). M. avium subsp. avium, ubiquitous in the environment and more virulent than M. avium subsp. hominissuis, is distinguished by the insertion element IS901 (24). While capable of infecting multiple animal species, M. avium subsp. avium is commonly isolated from birds as one of the causes of avian tuberculosis (26, 32). M. avium subsp. silvaticum, also called the “wood pigeon bacillus,” is uncommonly isolated but reported to cause enteritis in ruminants as well as disseminated infection in other hosts (33).M. avium subsp. paratuberculosis infection causes paratuberculosis (Johne''s disease) characterized by chronic granulomatous enteritis in animals, most often ruminants (9, 21). This organism grows very slowly in vitro (slower than most “slow-growing” mycobacteria), is dependent on mycobactin for growth in vitro, and is alone in containing IS900 in its genome (15, 16, 23). M. avium subsp. paratuberculosis has a broad host range and is implicated by some in the pathogenesis of Crohn''s disease in humans (1, 12). The inability of M. avium subsp. paratuberculosis to produce the siderophore mycobactin renders it incapable of replication in the environment, with the possible exception of inside free-living amoeba, and so it is considered an obligate parasite of animals and possibly humans (6). Paratuberculosis has emerged as a common and costly disease for the dairy industry (16). Surveys indicate that at least 68% of U.S. dairy herds are M. avium subsp. paratuberculosis infected (36).Microbiological culture remains a mainstay for diagnosis of mycobacterial infections, since it has greater sensitivity than PCR-based methods and yields the living isolates necessary for antibiotic susceptibility testing and molecular epidemiology. Because culture on conventional solid bacteriological media is laborious and slow, liquid culture-based mycobacterial detection systems, such the Bactec, MGIT, Trek ESP, and BacT/Alert 3D systems, have become commonplace in clinical laboratories, offering the advantages of automation and shorter detection times from clinical samples (5, 7, 17, 37). However, a positive signal during culture with any of these systems is simply a nonspecific indication of any sort of microbial growth (37). Thus, specimen processing and decontamination protocols to selectively kill nonmycobacterial microflora in the clinical or environmental samples are key components for an effective assay (7, 34). Although a number of different protocols have been described (7, 11, 28, 34), a standard protocol specifically designed for optimal recovery of MAC has not yet been established.Numerous PCRs are performed in our laboratory in response to these signal-positive cultures; in the last year, approximately 45% did not contain the pathogen of interest, MAC (unpublished data). This sample management approach is inefficient and labor-intensive.To better focus PCR resources on those cultures most likely to contain MAC, a novel enzyme-linked immunosorbent assay (ELISA) was designed to detect secreted MAC antigens in culture medium fluid. This assay, called the MAC-ELISA, was then evaluated for analytical and diagnostic specificity and sensitivity, first using pure cultures and then cultures derived from clinical samples.     

Identification of Domains of the Hag/MID Surface Protein Recognized by Systemic and Mucosal Antibodies in Adults with Chronic Obstructive Pulmonary Disease following Clearance of Moraxella catarrhalis

Moraxella catarrhalis is a common cause of respiratory tract infection in the setting of chronic obstructive pulmonary disease (COPD). Adults with COPD acquire and clear strains of M. catarrhalis from the respiratory tract continuously and develop strain-specific protection following clearance of a strain. In previous work, we identified Hag/MID (Moraxella immunoglobulin D-binding protein), a large multifunctional surface protein that acts as an adhesin and hemagglutinin, as a target of antibody responses in adults with COPD after clearance of M. catarrhalis. The goal of the present study was to characterize the domains of Hag/MID to which humans make antibodies, including both systemic and mucosal antibody responses. Analysis of recombinant peptide constructs, which spanned the M. catarrhalis strain O35E Hag/MID protein, with well-characterized serum and sputum samples revealed that most adults with COPD made antibodies directed toward a region of the molecule bounded by amino acids 706 to 863. Serum immunoglobulin G (IgG) and IgA purified from sputum both recognized the same domain. Some flanking sequence of this fragment was necessary for the epitope(s) in this region to maintain its conformation to bind human antibodies. These results reveal that humans consistently generate both systemic and mucosal antibody responses to an immunodominant region of the Hag/MID molecule, which was previously shown to overlap with several biologically relevant domains, including epithelial cell adherence, IgD binding, collagen binding, and hemagglutination.Chronic obstructive pulmonary disease (COPD) is a debilitating disorder that is the fourth most common cause of death in the United States (1, 2). The course of the disease is characterized by intermittent exacerbations that result in enormous morbidity, including lost work time, hospital admissions, respiratory failure, and sometimes death (31). Moraxella catarrhalis is the second most common cause of exacerbations of COPD after nontypeable Haemophilus influenzae (30). It is estimated that M. catarrhalis causes 2 to 4 million exacerbations per year in the United States (19).Adults with COPD acquire and clear strains of M. catarrhalis from the respiratory tract continuously. When an individual acquires M. catarrhalis, the organism is cleared efficiently after a short duration (∼30 days) of carriage. Patients then develop strain-specific protection from reacquisition of the same strain (19). This observation that humans develop apparent protective responses to the organism after clearing it from the respiratory tract provides the opportunity to begin to understand protective immune responses to M. catarrhalis.The identification of surface antigens that are targets of human antibody responses in the setting of COPD has been investigated recently by several research groups. A hallmark of antibody responses to respiratory tract bacterial pathogens in COPD is variability among individuals. Several surface antigens are the targets of antibody responses in a small proportion of adults with COPD following infection with M. catarrhalis (OMP E, CopB, lipooligosacccharide, Msp22, Msp75, and Msp78) (17, 18, 28). By contrast, selected surface antigens appear to be more consistent targets of antibody responses in a larger proportion of adults with COPD. These antigens include outer membrane protein CD, UspA1, UspA2, transferrin binding protein B, and Hag/MID (Moraxella immunoglobulin D [IgD]-binding protein) (17, 18, 20, 33). The present study focuses on Hag/MID, which was the target for new systemic and mucosal antibody responses in a large proportion of adults with COPD who acquired and cleared M. catarrhalis in our prospective study (17-19).Approximately 86% of strains of M. catarrhalis contain a hag gene (also called mid) and express its product (4, 7, 16, 24, 25, 34). Hag/MID is a multifunctional protein that acts as an adhesin for human respiratory epithelial cells, a B-cell mitogen, binds IgD, and mediates hemagglutination (3, 4, 6, 9, 12, 22, 24, 26). Hag/MID is an autotransporter protein in the largest known family of virulence factors expressed by gram-negative bacteria (5, 10). The hag gene encodes a protein of ∼2,000 amino acids that exists as a multimer on the bacterial surface. Expression of Hag/MID is subject to translational phase variation via slipped strand mispairing in a homopolymeric guanine track (16).The goal of the present study was to characterize both the systemic and mucosal antibody responses to Hag/MID in adults with COPD who have acquired and cleared M. catarrhalis from the respiratory tract. Emphasis is placed on identifying the key domains in the Hag/MID protein with regard to both systemic and mucosal antibody responses.