Prevalence and characterization of multidrug-resistant (type ACSSuT) Salmonella enterica serovar Typhimurium strains in isolates from four gosling farms and a hatchery farm

Salmonella enterica serovar Typhimurium strains of phage types DT104 and U302 are often resistant to ampicillin, chloramphenicol, streptomycin, sulfonamides, and tetracycline (the ACSSuT resistance type) and are major zoonotic pathogens. Increased consumption of goose meat may enhance the risk of transferring S. enterica serovar Typhimurium and other enteric pathogens from geese to human due to the consumption of meats from infected geese or improper preparation of meats. Therefore, we characterized S. enterica serovar Typhimurium strains isolated from four goose farms (farms A, B, C, and D) and one hatchery farm (farm E) to determine the epidemic and genetic differences among them. Antibiotic susceptibility tests and multiplex PCR confirmed that 77.6% (52/67) of strains were ACSSuT strains isolated from farms A, C, and E. Antibiotic-susceptible strains were isolated mostly from farm B, and no strain was observed in farm D. All ACSSuT strains harbored a 94.7-kb virulence plasmid and contained one 1.1-kb conserved segment identical to that of Salmonella genomic island 1. Four genotypes were determined among these S. enterica serovar Typhimurium isolates by pulsed-field gel electrophoresis analysis of XbaI-digested DNA fragments. Most isolates (85.29%; 29/34) of major genotype Ib were ACSSuT strains isolated mainly from goslings of farm C and egg membranes of farm E, a hatchery farm, suggesting that S. enterica serovar Typhimurium strains in isolates from goslings might originate from its hatchery, from the egg membranes to the gosling fluff after hatching. Multiple phage types, types 8, 12, U283, DT104, and U302, were identified. In conclusion, geese were a reservoir of diverse multidrug-resistant (type ACSSuT) S. enterica serovar Typhimurium strains, and each farm was colonized with genetically closely related S. enterica serovar Typhimurium strains.     

Comparison of Typing Methods with a New Procedure Based on Sequence Characterization for Salmonella Serovar Prediction

As the development of molecular serotyping approaches is critical for Salmonella spp., which include >2,600 serovars, we performed an initial evaluation of the ability to identify Salmonella serovars using (i) different molecular subtyping methods and (ii) a newly implemented combined PCR- and sequencing-based approach that directly targets O- and H-antigen-encoding genes. Initial testing was performed using 46 isolates that represent the top 40 Salmonella serovars isolated from human and nonhuman sources, as reported by the U.S. Centers for Disease Control and Prevention and the World Health Organization. Multilocus sequence typing (MLST) was able to accurately predict the serovars for 42/46 isolates and showed the best ability to predict serovars among the subtyping methods tested. Pulsed-field gel electrophoresis (PFGE), ribotyping, and repetitive extragenic palindromic sequence-based PCR (rep-PCR) were able to accurately predict the serovars for 35/46, 34/46, and 30/46 isolates, respectively. Among the methods, S. enterica subsp. enterica serovars 4,5,12:i:−, Typhimurium, and Typhimurium var. 5− were frequently not classified correctly, which is consistent with their close phylogenetic relationship. To develop a PCR- and sequence-based serotyping approach, we integrated available data sources to implement a combination PCR-based O-antigen screening and sequencing of internal fliC and fljB fragments. This approach correctly identified the serovars for 42/46 isolates in the initial set representing the most common Salmonella serovars, as well as for 54/63 isolates representing less common Salmonella serovars. Our study not only indicates that different molecular approaches show the potential to allow for rapid serovar classification of Salmonella isolates, but it also provides data that can help with the selection of molecular serotyping methods to be used by different laboratories.     

Genetic Analysis of Non-Hydrogen Sulfide-Producing Salmonella enterica Serovar Typhimurium and S. enterica Serovar Infantis Isolates in Japan

Whole-genome sequencing of non-H₂S-producing Salmonella enterica serovar Typhimurium and S. enterica serovar Infantis isolates from poultry meat revealed a nonsense mutation in the phsA thiosulfate reductase gene and carriage of a CMY-2 β-lactamase. The lack of production of H₂S might lead to the incorrect identification of S. enterica isolates carrying antimicrobial resistance genes.     

Molecular Characterization of Extended-Spectrum Cephalosporinase-Producing Salmonella enterica Serovar Choleraesuis Isolates from Patients in Thailand and Denmark

The objective of this study was to characterize extended-spectrum cephalosporinase (ESC)-producing isolates of Salmonella enterica serovar Choleraesuis recovered from patients in Thailand and Denmark. Twenty-four blood culture isolates from 22 patients were included in the study, of which 23 isolates were recovered from 21 Thai patients during 2003, 2007, or 2008 and one isolate was recovered from a Danish traveler to Thailand. ESC production was confirmed in 13 out of the 24 isolates by MIC testing. Microarray and plasmid profiling (replicon typing and restriction fragment length polymorphism [RFLP]) were used to characterize the genetic mechanisms of antimicrobial resistance in the 13 ESC-producing isolates. Pulsed-field gel electrophoresis (PFGE) and MIC testing were used to compare the clonality between the 13 ESC-producing isolates and the 11 non-ESC-producing isolates. Based on susceptibility patterns, the ESC-producing isolates were more closely related than non-ESC-producing isolates. Microarray, PCR, plasmid profiling, and replicon typing revealed that the 13 ESC-producing isolates harbored either bla_CMY-2 containing incA/C or bla_CTX-M-14 containing incFIIA, incFrepB, and an unknown replicon located on plasmids ranging in size from 75 to 200 kb. The RFLP and replicon typing clustered the isolates into four distinct groups. PFGE revealed 16 unique patterns and five clusters; each cluster contained two or three of the 24 isolates. The isolate from the Danish patient was indistinguishable from two Thai clinical isolates by PFGE. This study revealed the emergence of the bla_CTX-M-14 gene among several clones of Salmonella serovar Choleraesuis. Numerous plasmids were identified containing up to two different ESC genes and four distinct replicons. A “travel-associated” spread was confirmed. Overall, a high degree of clonal diversity between isolates resistant and susceptible to cephalosporins was observed. The findings represent a serious threat to public health for the Thai people and tourists.Salmonella enterica is a common cause of human gastroenteritis and bacteremia worldwide (18, 31), and a wide variety of animals, particularly food animals, have been identified as reservoirs for non-Typhi Salmonella (11, 22, 23). Although approximately 2,600 serovars of Salmonella enterica have been identified, most human infections are caused by a limited number of serovars, and in general these infections are self-limiting. Some Salmonella serovars, including Salmonella Choleraesuis (swine) and Salmonella Dublin (cattle), which are adapted to a specific animal host, have a propensity to cause extraintestinal infections in humans. Compared to those with other serovars of non-Typhi Salmonella, infections with these serovars are associated with higher rates of bacteremia, meningitis, and mortality (4, 5, 24). For patients with severe salmonellosis, antimicrobial chemotherapy may be life-saving. Due to the increasing prevalence of fluoroquinolone resistance, extended-spectrum cephalosporins are increasingly used for the treatment of Salmonella infections in humans (17, 21, 25) and especially for children, for whom treatment of highly resistant Salmonella infections with fluoroquinolones is not advised, since such treatment has been associated with treatment failures (12, 13, 21). Therefore, these compounds have been designated critically important for human health by the World Health Organization (10).We recently reported that the prevalence of human infections with Salmonella serovar Choleraesuis in Thailand increased from 1.5% (n = 87) in 1994 to 9.2% (n = 190) in 2006 (19). The group of people at highest risk for these infections was those between 6 and 40 years of age in the central region of Thailand (19). A 2007 study of Salmonella serovar Choleraesuis isolates from Thailand observed an increasing resistance to both extended-spectrum cephalosporins (ceftriaxone) and fluoroquinolones. Fifty-four isolates obtained between 2003 and 2005 were tested, of which 30% were found to be resistant to an extended-spectrum cephalosporin (ceftriaxone) (25).To date, only two reports, both from Taiwan, have described mechanisms for extended-spectrum cephalosporin resistance in Salmonella serovar Choleraesuis. The first report was published in 2004 with the discovery of the bla_CMY-2 AmpC β-lactamase gene located on a 140-kb F-like plasmid (6). The following year, the same authors detected bla_CTX-M-3 in a Salmonella serovar Choleraesuis isolate from a patient admitted to a university hospital (30). In 2007, a massive increase of fluoroquinolone- and ceftriaxone-resistant Salmonella serovar Choleraesuis isolates was described in Thailand (25).In Taiwan, the usage of antimicrobials in veterinary medicine and as growth promoters in animal feed may have promoted the emergence of resistance (5). Likewise, in Thailand, the extended-spectrum cephalosporin ceftiofur is used as a growth promoter in swine production (25). However, data on antimicrobial usage in disease prevention and as growth promoters are not accessible in both countries.The objective of the present study was to characterize the mechanisms responsible for the emergence of resistance to extended-spectrum cephalosporins in isolates of Salmonella serovar Choleraesuis recovered from patients in Thailand and Denmark.Additional objectives were to determine the clonality of the isolates resistant and susceptible to cephalosporins (ceftriaxone and cefoxitin) using pulsed-field gel electrophoresis (PFGE) and antimicrobial susceptibility testing and to find biological evidence of transmission through international travel.     

Evidence for a Second Genomic Island Conferring Multidrug Resistance in a Clonal Group of Strains of Salmonella enterica Serovar Typhimurium and its Monophasic Variant Circulating in Italy,Denmark, and the United Kingdom

During the 2000s, a new clonal group with resistances to ampicillin, streptomycin, sulfonamides, and tetracycline (ASSuT) emerged in Italy among strains of Salmonella enterica serovar Typhimurium and its monophasic variant, Salmonella enterica subspecies enterica serovar 4,[5],12:i:−. The PulseNet Europe database allowed us to identify ASSuT strains of both S. Typhimurium and its monophasic variant, isolated in Denmark and the United Kingdom, with the same or very closely related pulsed-field gel electrophoresis (PFGE) patterns as the Italian strains, suggesting that the ASSuT clonal group is circulating in different European countries. With the aim of analyzing the molecular basis of antibiotic resistance, resistance genes were identified and their localization was investigated in 66 ASSuT strains and, as controls, in 11 strains with different resistance patterns and PFGE profiles, belonging both to S. Typhimurium and to its monophasic variant, isolated from humans in Italy, Denmark, and the United Kingdom. All the ASSuT strains were positive for the following resistance genes: bla_TEM-1, strA-strB, sul2, and tet(B). A localization experiment demonstrated that the ASSuT resistance genes are chromosomally located. This study confirms that a multidrug-resistant clonal group, ASSuT, of S. Typhimurium and its monophasic variant has emerged and is circulating in Italy, Denmark, and the United Kingdom. Moreover, the results of this work demonstrate that the multidrug resistance in this clonal group of Salmonella strains is conferred by a new genomic island.Salmonella enterica serovar Typhimurium is one of the most important food-borne zoonotic pathogens across the world, and the increasing occurrence and spread of multidrug-resistant (MDR) strains is a matter of concern. MDR S. Typhimurium definitive phage type 104 (DT104), resistant to ampicillin, chloramphenicol, streptomycin and spectinomycin, sulfonamides, and tetracyclines (resistance type [R type] ACSSpSuT), is a clear example of a clone that emerged in one country (the United Kingdom in the 1980s) and subsequently became widely distributed in at least four continents (41).Recently strains of S. Typhimurium and its monophasic variant, Salmonella enterica serovar 4,[5],12:i:−, characterized by the four-drug resistance (tetraresistance) pattern ASSuT (with or without additional resistances but lacking resistance to chloramphenicol), has emerged in Italy (5). These strains accounted for more than 30% of isolates from cases of human infection during the last 5 years and were also observed among isolates from different farm animal species (20). Pulsed-field gel electrophoresis (PFGE) analysis showed that these tetraresistant strains belonged to a unique clonal group, different from the DT104 ACSSpSuT clone (13). Using the PulseNet Europe database (27), it has been possible to verify that ASSuT strains of S. Typhimurium and its monophasic variant isolated in Denmark and the United Kingdom exhibited PFGE patterns that were the same as or very closely related to those of the Italian strains, suggesting that an ASSuT clonal group was circulating in different European countries.In Denmark, strains with the ASSuT R type accounted for 4.4% of S. Typhimurium strains from humans over the period from 1997 to 2002 (16); during the period from 2003 to 2008, the frequency of ASSuT strains from humans increased, varying from 10 to 22%. Moreover, a study of strains from pigs highlighted that from 2002 to 2006, the main phage type became DT120, and 50% of strains of this phage type belonged to R type ASSuT. Over the same period, the frequency of isolation of DT104 strains decreased (15).In England and Wales, the ASSuT resistance pattern, with additional resistance to furazolidone (Fu), was first detected in 1964 in S. Typhimurium DT29. Such strains, which possessed resistance determinants on both conjugative and nonconjugative plasmids, caused substantive outbreaks in both cattle and humans until 1971 (41). During the 1980s there was an increase, from 1% in 1981 to 8% in 1990, of strains with the ASSuT R type, mainly belonging to DT193 (39). Since 1996, DT193 has been second only to DT104 in cases of human infection; of these strains, 56% were multiresistant, with strains of R type ASSuT predominating. Previous studies have shown that strains of DT193 of R type ASSuT have often been associated with pigs, and outbreaks associated with pigs have been reported (40). In addition, in 2006, strains of DT120 of R type ASSuT, with a unique PFGE profile (STYMXB.0083, according to PulseNet nomenclature), caused an outbreak in northeast England (3). From January 2004 to December 2006, there were 489 strains of R type ASSuT, with or without additional resistances, from a total of 4,426 isolates from human infections (11%) reported to the Health Protection Agency (HPA Salmonella data set 2009; www.HPA.org.uk).In DT104 strains of R type ACSSuSpT, the resistance genes for ampicillin (antibiogram designation A) (bla_PSE-1), chloramphenicol (antibiogram designation C) (floR), streptomycin-spectinomycin (antibiogram designation SSp) (aadA2), sulfonamides (antibiogram designation Su) (sul1), and tetracyclines (antibiogram designation T) [tet(G)] are chromosomally integrated within the 43-kb Salmonella genomic island 1 (SGI-1) (4). In contrast, the genes responsible for the tetraresistance in the ASSuT clonal group have not been identified so far.The aim of this study was to analyze the molecular basis and location of ASSuT tetraresistance in S. Typhimurium and its monophasic variant strains from cases of human infection in Italy, Denmark, and the United Kingdom over the period from 2003 to 2006.     

Increasing Incidence and Comparison of Nalidixic Acid-Resistant Salmonella enterica subsp. enterica Serotype Typhimurium Isolates from Humans and Animals

We determined the resistance to quinolone of 309 Salmonella enterica subsp. enterica serotype Typhimurium strains isolated from humans and animals (cattle, pigs, or poultry) in 1995 or 1996. Nalidixic acid resistance increased from 8.5% in 1995 to 18.6% in 1996. The highest resistance levels correlated with a mutation at Ser-83 (or Asp-82). All strains remained ciprofloxacin susceptible. Human and animal isolates were compared by pulsed-field gel electrophoresis, and the banding patterns of the human isolates most closely matched those of the bovine isolates.     

Refined Live Attenuated Salmonella enterica Serovar Typhimurium and Enteritidis Vaccines Mediate Homologous and Heterologous Serogroup Protection in Mice

Invasive nontyphoidal Salmonella (NTS) infections constitute a major health problem among infants and toddlers in sub-Saharan Africa; these infections also occur in infants and the elderly in developed countries. We genetically engineered a Salmonella enterica serovar Typhimurium strain of multilocus sequence type 313, the predominant genotype circulating in sub-Saharan Africa. We evaluated the capacities of S. Typhimurium and Salmonella enterica serovar Enteritidis ΔguaBA ΔclpX live oral vaccines to protect mice against a highly lethal challenge dose of the homologous serovar and determined protection against other group B and D serovars circulating in sub-Saharan Africa. The vaccines S. Typhimurium CVD 1931 and S. Enteritidis CVD 1944 were immunogenic and protected BALB/c mice against 10,000 50% lethal doses (LD₅₀) of S. Typhimurium or S. Enteritidis, respectively. S. Typhimurium CVD 1931 protected mice against the group B serovar Salmonella enterica serovar Stanleyville (91% vaccine efficacy), and S. Enteritidis CVD 1944 protected mice against the group D serovar Salmonella enterica serovar Dublin (85% vaccine efficacy). High rates of survival were observed when mice were infected 12 weeks postimmunization, indicating that the vaccines elicited long-lived protective immunity. Whereas CVD 1931 did not protect against S. Enteritidis R11, CVD 1944 did mediate protection against S. Typhimurium D65 (81% efficacy). These findings suggest that a bivalent (S. Typhimurium and S. Enteritidis) vaccine would provide broad protection against the majority of invasive NTS infections in sub-Saharan Africa.     

Integrative Analysis of Salmonellosis in Israel Reveals Association of Salmonella enterica Serovar 9,12:l,v:? with Extraintestinal Infections,Dissemination of Endemic S. enterica Serovar Typhimurium DT104 Biotypes,and Severe Underreporting of Outbreaks

Salmonella enterica is the leading etiologic agent of bacterial food-borne outbreaks worldwide. This ubiquitous species contains more than 2,600 serovars that may differ in their host specificity, clinical manifestations, and epidemiology. To characterize salmonellosis epidemiology in Israel and to study the association of nontyphoidal Salmonella (NTS) serovars with invasive infections, 48,345 Salmonella cases reported and serotyped at the National Salmonella Reference Center between 1995 and 2012 were analyzed. A quasi-Poisson regression was used to identify irregular clusters of illness, and pulsed-field gel electrophoresis in conjunction with whole-genome sequencing was applied to molecularly characterize strains of interest. Three hundred twenty-nine human salmonellosis clusters were identified, representing an annual average of 23 (95% confidence interval [CI], 20 to 26) potential outbreaks. We show that the previously unsequenced S. enterica serovar 9,12:l,v:− belongs to the B clade of Salmonella enterica subspecies enterica, and we show its frequent association with extraintestinal infections, compared to other NTS serovars. Furthermore, we identified the dissemination of two prevalent Salmonella enterica serovar Typhimurium DT104 clones in Israel, which are genetically distinct from other global DT104 isolates. Accumulatively, these findings indicate a severe underreporting of Salmonella outbreaks in Israel and provide insights into the epidemiology and genomics of prevalent serovars, responsible for recurring illness.     

Detection of <Emphasis Type="Italic">Salmonella enterica</Emphasis> serovar Typhimurium with pUO-StVR2-like virulence-resistance hybrid plasmids in the United Kingdom

The aim of this study was to investigate the presence in the United Kingdom (UK) of Salmonella enterica serovar Typhimurium isolates carrying pUO-StVR2-like virulence-resistance hybrid plasmids that originated from pSLT. One hundred and fifty ampicillin-resistant isolates of S. Typhimurium, collected in different regions of the UK during 2006, were screened for the presence of bla _OXA-1 carried by an InH-like integron (2000 bp/bla _OXA-1-aadA1) characteristic of pUO-StVR2. Positive isolates were tested for the presence of a large plasmid that hybridised with probes specific for the bla _OXA-1 and spvC genes, used as resistance and virulence markers of the hybrid plasmid, respectively. Eleven out of the 150 isolates fulfilled both criteria and were assigned to the S. Typhimurium pUO-StVR2 group. Nine were resistant to ampicillin, chloramphenicol, streptomycin/spectinomycin, sulfonamides and tetracycline, encoded by bla _OXA-1, catA1, aadA1-like, sul1 and tet(B), respectively, and carried a pUO-StVR2-like plasmid of ca. 130 kb. Two contained hybrid plasmids of smaller size and lacked resistance(s) to chloramphenicol or chloramphenicol and tetracycline. The eleven isolates, which showed five and six closely related XbaI and BlnI profiles, respectively, were resistant to nitrofurantoin. In conclusion, multidrug-resistant S. Typhimurium isolates of the pUO-StVR2 group, which are endemic in Spain, were also detected in the UK, albeit with a low frequency (7.3%).     

Epidemiological Analysis of Salmonella enteritidis Isolates from Humans and Broiler Chickens in Thailand by Phage Typing and Pulsed-Field Gel Electrophoresis

To determine the phage types (PT) of Salmonella enteritidis found in Thailand and to clarify the potential for human infection by S. enteritidis in broiler chicken meat, human and poultry isolates taken from Thailand between 1990 and 1997 were phage typed and analyzed by pulsed-field gel electrophoresis (PFGE). Ten different PT were found among the 302 isolates phage typed, with PT 4 being the most frequent in human (73.9%) and poultry (76.2%) isolates, followed by PT 1 (8.0%), 8 (3.6%), and 7a (2.2%) in human isolates and by PT 7a (4.9%), 1 (3.7%), and 12 (2.4%) in poultry isolates. Of the 53 isolates analyzed by PFGE, 45 showed an indistinguishable pattern (pattern A) by BlnI-digested PFGE and the other 8 isolates showed a very similar pattern that differed by only a few bands. These results indicate the spread of a genetically identical clone of S. enteritidis in humans and poultry in Thailand.     

Associations between Heat-Stable (O) and Heat-Labile (HL) Serogroup Antigens of Campylobacter jejuni: Evidence for Interstrain Relationships within Three O/HL Serovars

A comparative examination of the heat-stable (O) and heat-labile (HL) serogrouping results for 9,024 sporadic human isolates of Campylobacter jejuni revealed conserved associations between specific O and HL antigens (O/HL serovars). Forty-nine percent of the isolates which grouped for both O and HL antigens belonged to one of three serovars: O 4 complex/HL 1 (17.9%), O 1/HL 2 (16.8%), or O 50/HL 7 (14.5%). Other common serovars were O 2/HL 4 (8.3%), O 6/HL 6 (8.1%), O 53/HL 11 (4.5%), O 19/HL 17 (3.3%), O 5/HL 9 (3.3%), O 9/HL 9 (3.2%), and O 23/HL 5 (3.1%). These 10 serovars accounted for 83.1% of the serogroupable isolates. A large number of strains (41.3%) could be typed by only one of the two methods or could not be serogrouped (11%). Strains belonging to three serovars, O 2/HL 4, O 50/HL 7, and O 23/HL 5, were further characterized by combining data from expressed features (O/HL serogroups, phage groups, and biotypes) with restriction fragment length polymorphism genotypes. These polyphasic data demonstrated that within each serovar, individual isolates showed substantial conservation of both genomic and phenotypic characteristics. The essentially clonal nature of the three serovars confirmed the potential of combined O and HL serogrouping as a practical and phylogenetically valid method for investigating the epidemiology of sporadic C. jejuni infection.     

Enteric salmonellosis disrupts the microbial ecology of the murine gastrointestinal tract

The commensal microbiota protects the murine host from enteric pathogens. Nevertheless, specific pathogens are able to colonize the intestinal tract and invade, despite the presence of an intact biota. Possibly, effective pathogens disrupt the indigenous microbiota, either directly through pathogen-commensal interaction, indirectly via the host mucosal immune response to the pathogen, or by a combination of these factors. This study investigates the effect of peroral Salmonella enterica serovar Typhimurium infection on the intestinal microbiota. Since the majority of the intestinal microbiota cannot be cultured by conventional techniques, molecular approaches using 16S rRNA sequences were applied. Several major bacterial groups were assayed using quantitative PCR. Administration of either the 50% lethal dose (LD₅₀) or 10× LD₅₀ of Salmonella enterica serovar Typhimurium caused changes in the microbiota throughout the intestinal tract over the time course of infection. A 95% decrease in total bacterial number was noted in the cecum and large intestine with 10× LD₅₀ S. enterica serovar Typhimurium challenge at 7 days postinfection, concurrent with gross evidence of diarrhea. In addition, alterations in microbiota composition preceded the onset of diarrhea, suggesting the involvement of pathogen-commensal interactions and/or host responses unrelated to diarrhea. Microbiota alterations were not permanent and reverted to the microbiota of uninfected mice by 1 month postinfection. Infection with a Salmonella pathogenicity island 1 (SPI1) mutant did not result in microbiota alterations, while SPI2 mutant infections triggered partial changes. Neither mutant was capable of prolonged colonization or induction of mucosal inflammation. These data suggest that several Salmonella virulence factors, particularly those involved in the local mucosal host response, are required for disruption of the intestinal ecosystem.     

Identification of Salmonella enterica serovar Dublin-specific sequences by subtractive hybridization and analysis of their role in intestinal colonization and systemic translocation in cattle

Salmonella enterica serovar Dublin is a host-restricted serovar associated with typhoidal disease in cattle. In contrast, the fowl-associated serovar S. enterica serovar Gallinarum is avirulent in calves, yet it invades ileal mucosa and induces enteritis at levels comparable to those induced by S. enterica serovar Dublin. Suppression subtractive hybridization was employed to identify S. enterica serovar Dublin strain SD3246 genes absent from S. enterica serovar Gallinarum strain SG9. Forty-one S. enterica serovar Dublin fragments were cloned and sequenced. Among these, 24 mobile-element-associated genes were identified, and 12 clones exhibited similarity with sequences of known or predicted function in other serovars. Three S. enterica serovar Dublin-specific regions were homologous to regions from the genome of Enterobacter sp. strain 638. Sequencing of fragments adjacent to these three sequences revealed the presence of a 21-kb genomic island, designated S. enterica serovar Dublin island 1 (SDI-1). PCR analysis and Southern blotting showed that SDI-1 is highly conserved within S. enterica serovar Dublin isolates but rarely found in other serovars. To probe the role of genes identified by subtractive hybridization in vivo, 24 signature-tagged S. enterica serovar Dublin SD3246 mutants lacking loci not present in Salmonella serovar Gallinarum SG9 were created and screened by oral challenge of cattle. Though attenuation of tagged SG9 and SD3246 Salmonella pathogenicity island-1 (SPI-1) and SPI-2 mutant strains was detected, no obvious defects of these 24 mutants were detected. Subsequently, a ΔSDI-1 mutant was found to exhibit weak but significant attenuation compared with the parent strain in coinfection of calves. SDI-1 mutation did not impair invasion, intramacrophage survival, or virulence in mice, implying that SDI-1 does not influence fitness per se and may act in a host-specific manner.     

Successive emergence of extended-spectrum beta-lactamase-producing and carbapenemase-producing Enterobacter aerogenes isolates in a university hospital

Sixty-two clinical isolates of Enterobacter aerogenes resistant to expanded-spectrum cephalosporins were collected between July 2003 and May 2005. Among these isolates, 23 (37.1%) were imipenem (IPM) susceptible, and 39 (62.9%) were IPM insusceptible, of which 89.7% (35/39) were resistant and 10.3% (4/39) were intermediate. Isolate genotypes were compared by pulsed-field gel electrophoresis. Of 62 isolates, 48 belonged to epidemic pulsotype A (77.4%). This pulsotype included 37.5% and 58.4% of β-lactam phenotypes b and a, respectively. Nine isolates (14.5%) belonged to pulsotype E, which included 22.3% and 77.7% of phenotypes b and a, respectively. The β-lactamases with pIs of 5.4, 6.5, 8.2, and 8.2 corresponded to extended-spectrum β-lactamases (ESBLs) TEM-20, TEM-24, SHV-5, and SHV-12, respectively. Of 39 IPM-insusceptible E. aerogenes isolates, 26 (66.6%) were determined to be metallo-β-lactamase producers, by using a phenotypic method. Of these isolates, 24 harbored a bla_IMP-1 gene encoding a protein with a pI of >9.5, and two carried the bla_VIM-2 gene encoding a protein with a pI of 5.3, corresponding to β-lactamases IMP-1 and VIM-2, respectively. The remaining 13 (33.4%) isolates were negative for the bla_IMP-1 and bla_VIM-2 genes but showed an alteration of their outer membrane proteins (OMPs). Ten of these isolates produced the two possible OMPs (32 and 42 kDa), with IPM MICs between 8 and 32 μg/ml, and three others produced only a 32-kDa OMP with IPM MICs >32 μg/ml. This work demonstrates that, in addition to resistance to expanded-spectrum cephalosporins, IPM resistance can occur in ESBL-producing E. aerogenes isolates by carbapenemase production or by the loss of porin in the outer membrane.     

Nasopharyngeal Haemophilus influenzae carriage in Japanese children attending day-care centers

We conducted a prospective bacteriological survey to investigate antibiotic resistance-related genetic characteristics and the turnover of nasopharyngeal Haemophilus influenzae carriage in healthy children in day-care centers (DCCs). A total of 363 nasopharyngeal mucus samples were collected from children aged 0 to 6 years attending two DCCs in the summer of 2004 (n = 184) and the following winter (n = 179). We obtained 172 H. influenzae isolates and analyzed them by antimicrobial susceptibility testing, PCR for bla_TEM-1 and the penicillin-binding protein (PBP) gene, and pulsed-field gel electrophoresis (PFGE). The overall carriage rate was 47.4% (172/363), and 37.2% of the isolates (64/172) were ampicillin (AMP) resistant. All the resistant isolates had a PBP mutation(s), while only three isolates had TEM-1. The carriage rate was significantly higher in the winter than in the summer (56.4% and 38.6%, respectively), owing to the increase in the numbers of AMP-susceptible H. influenzae isolates in the winter. Children aged ≤3 years showed a higher rate of carriage of H. influenzae isolates with an AMP resistance gene(s) than those aged ≥4 years (21.9% and 12.6%, respectively). Forty-two strains with different PFGE patterns were obtained from among the 172 isolates. Only five strains were observed in both seasons. None of the strains isolated in the summer was isolated from the same carrier in the winter. Twenty-seven strains (64.3%) were isolated from two or more children, and 25 of these were each isolated from children belonging to the same DCC. These results indicate the spread of H. influenzae, particularly those with a PBP mutation(s), and the highly vigorous genetic turnover and substantial horizontal transmission of this pathogen in healthy children attending DCCs in Japan.     

Gamma interferon-independent effects of interleukin-12 on immunity to Salmonella enterica serovar Typhimurium

Interleukin-12 (IL-12) and IL-18 are both central to the induction of gamma interferon (IFN-γ), and various roles for IL-12 and IL-18 in control of intracellular microbial infections have been demonstrated. We used IL-12p40^−/− and IL-18^−/− mice to further investigate the role of IL-12 and IL-18 in control of Salmonella enterica serovar Typhimurium. While C57BL/6 and IL-18^−/− mice were able to resolve attenuated S. enterica serovar Typhimurium infections, the IL-12p40^−/− mice succumbed to a high bacterial burden after 60 days. Using ovalbumin (OVA)-specific T-cell receptor transgenic T cells (OT-II cells), we demonstrated that following oral infection with recombinant S. enterica serovar Typhimurium expressing OVA, the OT-II cells proliferated in the mesenteric lymph nodes of C57BL/6 and IL-18^−/− mice but not in IL-12p40^−/− mice. In addition, we demonstrated by flow cytometry that equivalent or increased numbers of T cells produced IFN-γ in IL-12p40^−/− mice compared with the numbers of T cells that produced IFN-γ in C57BL/6 and IL-18^−/− mice. Finally, we demonstrated that removal of macrophages from S. enterica serovar Typhimurium-infected C57BL/6 and IL-12p40^−/− mice did not affect the bacterial load, suggesting that impaired control of S. enterica serovar Typhimurium infection in the absence of IL-12p40 is not due to reduced macrophage bactericidal activities, while IL-18^−/− mice did rely on the presence of macrophages for control of the infection. Our results suggest that IL-12p40, but not IL-18, is critical to resolution of infections with attenuated S. enterica serovar Typhimurium and that especially the effects of IL-12p40 on proliferative responses of CD4⁺ T cells, but not the ability of these cells to produce IFN-γ, are important in the resolution of infection by this intracellular bacterial pathogen.     

Ciprofloxacin-resistant Salmonella enterica serovar typhi from Kuwait with novel mutations in gyrA and parC genes

Blood isolates of Salmonella enterica serovar Typhi from two recently returned Bangladeshi patients in Kuwait were ciprofloxacin resistant, with ciprofloxacin MICs of 12 mg/liter for both isolates. Both isolates had three novel gyrA mutations (55-Leu→Trp, 87-Asp→Ala, and 106-Gln→Arg) and three novel parC mutations (84-Glu→Lys, 106-Trp→Gly, and 128-Tyr→Asp).     

Prevalence of CTX-M β-Lactamases in Philadelphia,Pennsylvania

CTX-M β-lactamases were thought to be rare in the United States, but a recent study in Texas showed that up to 70% of extended-spectrum β-lactamase (ESBL)-containing members of the Enterobacteriaceae family were CTX-M positive (J. S. Lewis, M. Herrera, B. Wickes, J. E. Patterson, and J. H. Jorgensen, Antimicrob. Agents Chemother. 51:4015-4021, 2007). We used PCR to detect CTX-M in all 291 extended-spectrum cephalosporin-resistant gram-negative bacteria isolated in our laboratory during 2007. Thirty (48%) Escherichia coli isolates, 6 (3%) Klebsiella sp. isolates, and 7 (100%) Proteus mirabilis isolates tested were CTX-M positive, with 15% of all Enterobacteriaceae tested being positive. The E. coli CTX-M groups were I (57%), IV (37%), II (3%), and not groupable (3%); three of the group IV isolates were positive for CTX-M-18, and three of the group I isolates were positive for CTX-M-15. One of seven positive P. mirabilis isolates was in group II, with the remainder being positive for a CTX-M-25-like β-lactamase; and 33% of the Klebsiella sp. isolates were in group I or IV, with the remainder not being in groups I to IV. CTX-M-producing bacteria were isolated from urine (n = 13), blood (n = 13), wounds (n = 12), and the respiratory tract (n = 4). All 31 CTX-M-positive isolates tested for the presence of ESBL were confirmed to produce ESBLs by the use of tests recommended by the CLSI. Pulsed-field gel electrophoresis of the CTX-M-positive isolates showed that six P. mirabilis isolates were clonal and that there were seven different E. coli clusters. Five of seven P. mirabilis isolates were from blood cultures. The CLSI tests for the confirmation of ESBL production reliably detect these isolates if both cefotaxime and ceftazidime are tested, but only about half would be classified as a possible CTX-M producers on the basis of the antibiogram alone. A new panprimer set increases the ability to detect CTX-M-producing strains. CTX-M-positive bacteria are common in our geographic region, are often invasive, and, with the exception of P. mirabilis, are multiclonal.CTX-M β-lactamases were thought to be uncommon in North America, although they are common on many other continents (1, 8, 10). CTX-M β-lactamases are extended-spectrum β-lactamases (ESBLs) that mainly inactivate cefotaxime and ceftriaxone and that have less activity against ceftazidime (8). As opposed to the usual epidemiology of other ESBL-positive members of the Enterobacteriaceae family, which are mainly nosocomial, CTX-M β-lactamase producers often appear to be community acquired, albeit in debilitated people with prior antibiotic exposure (8). The recognition of this group of resistant bacteria could have importance for decisions on empirical antibiotic therapy and could influence the accuracy of current procedures for screening for ESBLs. On the basis of the findings of a recent study from Texas showing that 70% of recent ESBL-producing isolates contained CTX-M β-lactamases (7), we tested all extended-spectrum cephalosporin-resistant Enterobacteriaceae isolated in the Clinical Microbiology Laboratory at the Hospital of the University of Pennsylvania (HUP) in 2007, as well as all multidrug-resistant Acinetobacter baumannii isolates recovered during the same time period. We show that CTX-M β-lactamases are common among extended-spectrum cephalosporin-resistant Escherichia coli and Proteus mirabilis isolates recovered from patients in hospitals in Philadelphia, PA.(This study was presented in abstract form at the 48th Interscience Conference on Antimicrobial Agents and Chemotherapy, Washington, DC, 2008.)     

Antimicrobial resistance trends in blood culture positive Salmonella Typhi isolates from Pondicherry,India, 2005–2009

Typhoid fever is caused by Salmonella enterica serovar Typhi, a major public health concern in developing countries. Recently, there has been an upsurge in the occurrence of bacterial isolates that are resistant to ciprofloxacin, and the emergence of broad spectrum β-lactamases in typhoidal salmonellae constitutes a new challenge for the clinician. A total of 337 blood culture isolates of S. Typhi, isolated from Pondicherry, India, between January 2005 and December 2009, were investigated using phenotypic, molecular and serological methods. Of the 337 isolates, 74 (22%) were found to be multidrug resistant (MDR) and 264 (78%) nalidixic acid resistant (NAR). Isolates with reduced susceptibility to ciprofloxacin possessed single mutations in the gyrA gene. A high rate of resistance (8%) was found to ciprofloxacin. All isolates with a ciprofloxacin MIC ≥ 4 mg/L possessed both double mutations in the QRDR of the gyrA gene and a single mutation in the parC gene. Active efflux pump mechanisms were also found to be involved in ciprofloxacin resistance. Finally, a large number of PFGE patterns (non-clonal genotypes) were observed among the S. Typhi isolates. In conclusion, a high rate of ciprofloxacin resistance was observed in comparison to other endemic areas in blood culture isolates of S. Typhi from Pondicherry, India, with steadily increasing NAR but decreasing MDR isolations over the study period. This is most likely to be due to an increased use of ciprofloxacin as a first-line drug of choice over more traditional antimicrobial agents for the treatment of typhoid fever.     

Identification of CTX-M15-, SHV-28-producing Klebsiella pneumoniae ST15 as an epidemic clone in the Copenhagen area using a semi-automated Rep-PCR typing assay

Rapid molecular typing methods can be a valuable aid in the investigation of suspected outbreaks. We used a semi-automated repetitive sequence-based polymerase chain reaction (Rep-PCR) typing assay and pulsed field gel electrophoresis (PFGE) to investigate the relationship between local Klebsiella pneumoniae (K. pneumoniae) producing extended spectrum β-lactamases (ESBLs) and their relation to recognized Danish outbreak strains. PFGE and Rep-PCR produced similar clustering among isolates. Individual isolates from each cluster were further characterized by PCR amplification and sequencing of bla _TEM, bla _SHV, and bla _CTX-M, and multilocus sequence typing (MLST). Thirty-five out of 52 ESBL-producing K. pneumoniae isolates were ST15 and bla _CTX-M15, bla _SHV-28, and bla _TEM-1 positive by PCR. Ten out of 52 were ST16 and tested positive for bla _CTX-M15, bla _SHV-1, and bla _TEM-1. Isolates from previously recognized hospital outbreaks were also ST15 and PCR positive for bla _CTX-M15, bla _SHV-28, and bla _TEM-1, and typed within the main cluster by both Rep-PCR and PFGE. In conclusion, K. pneumoniae ST15 containing bla _CTX-M15 and bla _SHV-28 constitutes an epidemic clone in the Copenhagen area and this clone can be rapidly recognized by semi-automated Rep-PCR.