Establishment of a universal size standard strain for use with the PulseNet standardized pulsed-field gel electrophoresis protocols: converting the national databases to the new size standard

Characteristics of a pandemic clone of O3 : K6 and O4 : K68 Vibrio parahaemolyticus isolated in Beira, Mozambique

The genetic characteristics of Vibrio parahaemolyticus strains isolated in 2004 and 2005 in Mozambique were assessed in this study to determine whether the pandemic clone of V. parahaemolyticus O3 : K6 and O4 : K68 serotypes has spread to Mozambique. Fifty-eight V. parahaemolyticus strains isolated from hospitalized diarrhoea patients in Beira, Mozambique, were serotyped for O : K antigens and genotyped for toxR, tdh and trh genes. A group-specific PCR, a PCR that detects the presence of ORF8 of the filamentous phage f237, arbitrarily primed PCR, PFGE and multilocus sequence typing were performed to determine the pandemic status of the strains and their ancestry. All strains of serovars O3 : K6 (n=38) and O4 : K68 (n=4) were identified as a pandemic clonal group by these analyses. These strains are closely related to the pandemic reference strains of O3 : K6 and O4 : K68, which emerged in Asia in 1996 and were later found globally. The pandemic serotypes O3 : K6 and O4 : K68 including reference strains grouped into a single cluster indicating emergence from a common ancestor. The O3 : K58 (n=8), O4 : K13 (n=6), O3 : KUT (n=1) and O8 : K41 (n=1) strains showed unique characteristics different from the pandemic clone.

PCR-based rapid genotyping of Stenotrophomonas maltophilia isolates

Background

All bacterial genomes contain repetitive sequences which are members of specific DNA families. Such repeats may occur as single units, or found clustered in multiple copies in a head-to-tail configuration at specific loci. The number of clustered units per locus is a strain-defining parameter. Assessing the length variability of clusters of repeats is a versatile typing methodology known as multilocus variable number of tandem repeat analysis (MLVA).

Results

Stenotrophomonas maltophilia is an environmental bacterium increasingly involved in nosocomial infections and resistant to most antibiotics. The availability of the whole DNA sequence of the S. maltophilia strain K279a allowed us to set up fast and accurate PCR-based diagnostic protocols based on the measurement of length variations of loci carrying a variable number of short palindromic repeats marking the S. maltophilia genome. On the basis of the amplimers size, it was possible to deduce the number of repeats present at 12 different loci in a collection of S. maltophilia isolates, and therefore label each of them with a digit. PCR-negative regions were labelled 0. Co-amplification of two pairs of loci provided a 4-digit code sufficient for immediate subtyping. By increasing the number of loci analyzed, it should be possible to assign a more specific digit profile to isolates. In general, MLVA data match genotyping data obtained by PFGE (pulsed-field gel electrophoresis). However, some isolates exhibiting the same PCR profiles at all loci display distinct PFGE patterns.

Conclusion

The utilization of the present protocol allows to type several S. maltophilia isolates in hours. The results are immediately interpretable without the need for sophisticated softwares. The data can be easily reproducible, and compared among different laboratories.

Sorbitol-fermenting enterohaemorrhagicEscherichia coliO157:H−causes another outbreak of haemolytic uraemic syndrome in children

An outbreak of haemolytic uraemic syndrome (HUS) among children caused by infection with sorbitol-fermenting enterohaemorrhagicEscherichia coliO157:H−(SF EHEC O157:H−) occurred in Germany in 2002. This pathogen has caused several outbreaks so far, yet its reservoir and routes of transmission remain unknown. SF EHEC O157:H−is easily missed as most laboratory protocols target the more common sorbitol non-fermenting strains. We performed active case-finding, extensive exploratory interviews and a case-control study. Clinical and environmental samples were screened for SF EHEC O157:H−and the isolates were subtyped by pulsed-field gel electrophoresis. We identified 38 case-patients in 11 federal states. Four case-patients died during the acute phase (case-fatality ratio 11%). The case-control study could not identify a single vehicle or source. Further studies are necessary to identify the pathogen's reservoir(s). Stool samples of patients with HUS should be tested with an adequate microbiological set-up to quickly identify SF EHEC O157:H−.

Impact of -2 degrees C superchilling before refrigerated storage (4 and 8 degrees C) on the microbiological and sensory qualities of cold-smoked salmon

Detection and enumeration of Listeria monocytogenes and total spoilage bacteria in 40 batches of cold-smoked salmon (one batch = 42 products from the same day of manufacture) straight from the factory were carried out. If L. monocytogenes was detected in at least one of the nine samples analyzed on receipt at the laboratory, 9 products of the same batch were stored for 10 days at 4 degrees C, which was followed by 18 days at 8 degrees C (control), 12 products were superchilled for 14 days at -2 degrees C, and 12 other products were superchilled for 28 days at -2 degrees C and then stored under the same conditions as the control was stored. L. monocytogenes was detected in 7% of the 40 batches analyzed immediately after receipt at the laboratory. L. monocytogenes prevalence was similar (approximately 25%) throughout the storage at 4 and 8 degrees C, both in control and super-chilled products at -2 degrees C for 14 days. After superchilling for 28 days at -2 degrees C, L. monocytogenes was found in 9% of products, and in 39% at the end of the storage above 0 degree C. Moreover, the L. monocytogenes count was higher after 3 and 4 weeks of storage at 4 and 8 degrees C in products superchilled 28 days at -2 degrees C than in control products or in products superchilled for 14 days. Serotype 1/2a-3a and nine genetic groups were identified and found throughout the storage scenario. At the end of shelf life, sensory characteristics of products superchilled for 28 days at -2 degrees C were slightly modified. A decrease in firmness associated with increased tearing of salmon slices was observed as well as a slight amine odor.

Evidence for growth of enterococci in municipal oxidation ponds, obtained using antibiotic resistance analysis

The Christchurch wastewater treatment plant uses a series of six oxidation ponds to reduce the bacterial load of treated effluent before it is discharged into the local estuary. To ensure that this discharge does not adversely affect water quality in the receiving environment, local regulations specify maximum levels in the discharge for a number of parameters, including enterococci. Between 2001 and 2006, regulations required fewer than 300 enterococci per 100 ml in summer. During this period, the discharge intermittently exceeded this limit, with unexplained levels of enterococci of up to 180,000/100 ml. Characterization of these enterococci by antibiotic resistance analysis showed that enterococci sampled over 4 months had almost identical resistance profiles. In contrast, enterococci from raw sewage and wildfowl from around the oxidation ponds had a diverse range of antibiotic resistance profiles that could be distinguished from each other and also from those of enterococci from the discharge. The hypothesis of a clonal nature of the enterococci in the discharge was supported by molecular genotype analysis, suggesting that these bacteria may have replicated in the pond environment rather than being reflective of breakthrough in the sewage treatment process or the result of recent wildfowl inputs to the ponds. This study highlights the usefulness of antibiotic resistance analysis in identifying this phenomenon and is the first report of apparent replication of a specific type of enterococci in an oxidation pond environment.

Evidence of cross-contamination by Campylobacter spp. of broiler carcasses using genetic characterization of isolates

Campylobacter is recognized as one of the leading cause of gastroenteritis worldwide, and is frequently isolated from the small intestines and ceca microflora of chickens. Twenty-one out of 81 Campylobacter-positive poultry flocks were selected to evaluate the genetic diversity of Campylobacter isolates and to study the distribution of genotypes among flocks. Campylobacter isolates recovered from chicken carcasses and ceca were analyzed by pulsed-field gel electrophoresis (PFGE). Little diversity was found among Campylobacter strains isolated from a given carcass, with a maximum of 2 different genotypes being present. However, at flock level, as many as 4 different profiles were observed. Typing of strains showed that most strains isolated from ceca were similar to those isolated from corresponding broiler carcasses. A total of 39 different macrorestriction profiles were observed, with evidence of Campylobacter cross-contamination among broiler flocks in Quebec slaughterhouses. Surprisingly, some flocks shared related genotypes both with and without sharing similar rearing practices. Existence of such cross-contamination must be considered to in developing strategies to control Campylobacter in chickens, and to avoid bacteria contamination of noncolonized flocks. Further typing studies of Campylobacter found in hatcheries, farm environment, and crates or trucks in Quebec might be helpful in elucidating the kinetics of broiler chicken Campylobacter contamination.

Molecular typing and antimicrobial resistance of Salmonella enterica subspecies enterica serovar Choleraesuis isolates from diseased pigs in Japan

Salmonella enterica serovar Choleraesuis (S. Choleraesuis) isolates derived from diseased pigs in Japan during 2001 and 2005 were analyzed for biotype, based on H(2)S production and dulcitol fermentation, pulsed-field gel electrophoresis (PFGE) profile, and antimicrobial resistance profile. S. Choleraesuis biotype Choleraesuis (biotype Choleraesuis) was classified into one genotype, while varietas Kunzendorf (var. Kunzendorf) was classified into two genotypes. The isolates of var. Kunzendorf belonging to one genotype were isolated in a limited area of Japan. Variation in the antimicrobial resistance pattern was observed in isolates of both biotypes Choleraesuis and var. Kunzendorf. We have also shown that the PFGE profile was associated with the biotype and isolation region of each isolate.

Source tracking of Escherichia coli O157:H7 and Salmonella contamination in the lairage environment at commercial U.S. beef processing plants and identification of an effective intervention

Transportation from the feedlot and lairage at the processing plant have been identified as potential sources of Escherichia coli O157:H7 and Salmonella hide contamination. The objective of this study was to perform a comprehensive tracking analysis of E. coli O157:H7 and Salmonella associated with beef cattle from the feedlot through processing. Cattle (n = 581) were sampled in a feedlot, then transported in multiple lots to three commercial, fed beef processing plants in the United States, where they were sampled again. Samples were collected from the tractor trailers prior to loading cattle and from the lairage environment spaces prior to entry of the study cattle. Pathogen prevalence on cattle hides increased on every lot of cattle between exiting the feedlot and beginning processing. Prior to loading cattle, E. coli O157:H7 was found in 9 (64%) of 14 tractor trailers. E. coli O157:H7 was detected in over 60% of the samples from each lairage environment area, while Salmonella was detected in over 70% of the samples from each lairage environment area. E. coli O157:H7 and Salmonella isolates (n = 3,645) were analyzed using pulsed-field gel electrophoresis. The results of the pulsed-field gel electrophoresis tracking indicate that the transfer of bacteria onto cattle hides that occurs in the lairage environments of U.S beef processing plants accounts for a larger proportion of the hide and carcass contamination than does the initial bacterial population found on the cattle exiting the feedlot. Finally, the results of this study indicate that hide wash cabinets are effective in removing contamination derived from the lairage environment.

Dominance of blaCTX-M within an Australian extended-spectrum beta-lactamase gene pool

bla(CTX-M) genes, particularly bla(CTX-M-15), are the dominant extended-spectrum beta-lactamase (ESBL) genes among clinical isolates of Escherichia coli and Klebsiella pneumoniae in Sydney, Australia, where we also found one example of bla(CTX-M-62), encoding a novel enzyme conferring ceftazidime resistance. ESBL genes were present in diverse community isolates and in a variety of associated conjugative plasmids.

Antimicrobial susceptibility of well-characterised multiresistant CTX-M-producing Escherichia coli: failure of automated systems to detect resistance to piperacillin/tazobactam

This study was designed to determine the in vitro activities of several antimicrobial agents against well-characterised CTX-M-producing Escherichia coli strains isolated from clinical specimens. Minimum inhibitory concentrations (MICs) were determined for 202 extended-spectrum beta-lactamase (ESBL)-producing E. coli using microbroth dilution and Vitek methods according to Clinical and Laboratory Standards Institute criteria. Molecular characterisation was performed using isoelectric focusing and polymerase chain reaction (PCR) with sequencing, whilst strain relatedness was determined by pulsed-field gel electrophoresis (PFGE) using XbaI. Of the 202 ESBL-producing E. coli, 2 produced VEB-1, 12 produced TEM-52, 32 produced SHV types (including SHV-2 and -12) and 156 produced CTX-M types (including CTX-M-2, -3, -14, -15, -24, -27 and -30). The MIC(50) and MIC(90) (MIC for 50% and 90% of the organisms, respectively) for the antimicrobial agents tested were, respectively: piperacillin/tazobactam (TZP), 32mg/L and >256mg/L; ciprofloxacin, 16mg/L and 32mg/L; gentamicin, 8mg/L and 128mg/L; amikacin, 2mg/L and 16mg/L; ertapenem, 0.03mg/L and 0.12mg/L; imipenem, 0.03mg/L and 0.12mg/L; meropenem, 0.03mg/L and 0.03mg/L; and tigecycline 0.12mg/L and 0.5mg/L. Vitek Legacy and Vitek 2 failed to detect TZP resistance in 91 (90%) and 75 (74%) of 101 TZP-resistant ESBL-producing strains, respectively, especially CTX-M-15-producing isolates that co-produced OXA-1. The carbapenems, amikacin and tigecycline had good in vitro activities against multiresistant CTX-M-producing E. coli. We recommend that laboratories using Vitek should employ alternative susceptibility testing methods for TZP before reporting the activity of this agent against ESBL-producing E. coli.

Salmonella enterica serovar Typhimurium typing by prophage-specific PCR

Recent data from microarray analysis have shown that integrated prophages are the most frequent sources of genomic variation between different strains of Salmonella enterica serovar Typhimurium (S. Typhimurium). This led us to hypothesize that PCR detection of the integrated prophages might be an efficient typing tool that could be used as an alternative to PFGE. In this study, we optimized four triplex PCRs specific for 12 target sequences of mostly prophage origin, and tested them in 102 field strains. The same set of strains was also characterized by PFGE. Among the strains, 22 different multiplex PCR, and 25 different PFGE profiles, were identified. Despite the fact that the PFGE was slightly more discriminatory, multiplex PCR typing, owing to its simplicity and potential of simple data sharing between laboratories, represents an interesting user-friendly alternative to PFGE typing of S. Typhimurium.

Evaluation and validation of a PulseNet standardized pulsed-field gel electrophoresis protocol for subtyping Vibrio parahaemolyticus: an international multicenter collaborative study

The pandemic spread of Vibrio parahaemolyticus is an international public health issue. Because of the outbreak potential of the organism, it is critical to establish an internationally recognized molecular subtyping protocol for V. parahaemolyticus that is both rapid and robust as a means to monitor its further spread and to guide control measures in combination with epidemiologic data. Here we describe the results of a multicenter, multicountry validation of a new PulseNet International standardized V. parahaemolyticus pulsed-field gel electrophoresis (PFGE) protocol. The results are from a composite analysis of 36 well-characterized V. parahaemolyticus isolates from six participating laboratories, and the isolates represent predominant serotypes and various genotypes isolated from different geographic regions and time periods. The discriminatory power is very high, as 34 out of 36 sporadic V. parahaemolyticus strains tested fell into 34 distinguishable PFGE groups when the data obtained with two restriction enzymes (SfiI and NotI) were combined. PFGE was further able to cluster members of known pandemic serogroups. The study also identified quality measures which may affect the performance of the protocol. Nonadherence to the recommended procedure may lead to high background in the PFGE gel patterns, partial digestion, and poor fragment resolution. When these quality measures were implemented, the PulseNet V. parahaemolyticus protocol was found to be both robust and reproducible among the collaborating laboratories.

Multidrug-resistant Salmonella typhimurium, Pacific Northwest, United States

We compared human and bovine isolates of Salmonella enterica using antimicrobial-drug resistance profiles and pulsed-field gel electrophoresis. From 2000 through 2006, we observed an increase in a novel multidrug-resistant clone of S. Typhimurium with no recognized phage type. This clone may represent an emerging epidemic strain in the Pacific Northwest.

Note. Genetic Diversity of Food Isolates of Salmonella enterica serovar Typhimurium in India

The study aimed to determine the genetic diversity of Salmonella enterica serovar Typhimurium isolates from sprouts and fish samples from India. Twenty-eight S. Typhimurium isolates were genotyped by pulsed-field gel electrophoresis and tested for antibiotic susceptibility, plasmid profile, and presence of virulence genes ( invA and spvC). Three distinct XbaI-pulsed-field profiles (PFPs) were observed. Out of 22 isolates from sprouts, 20 showed PFP-A and remaining two showed PFP-B. All six fish isolates showed PFP-C. All the strains were sensitive to the examined antibiotics except two strains of PFP-A. Two different plasmid profiles P1 and P2 were observed. P2 was observed only in the antibiotic resistant strains. All strains were positive for the invA, whereas spvC was detected only in sprout isolates. There was no specific pattern in occurrence of the genotypes with respect to seasons. However, PFP-A was dominant and was isolated throughout the year. This is the first report to assess the genotypic diversity of S. Typhimurium obtained in foods from India. As S. Typhimurium is the predominant serotype in India, the data generated in this study would be useful in epidemiological studies during outbreaks of Salmonellosis in India.

Response to emerging infection leading to outbreak of linezolid-resistant enterococci

These bacteria have emerged as a hospital problem that appears to be caused by both linezolid exposure and patient-to-patient transmission.

Linezolid was approved in 2000 for treatment of gram-positive coccal infections. We performed a case-control study during a hospital outbreak of linezolid-resistant enterococci (LRE) infections, comparing cases of LRE infection (cases) with linezolid-sensitive enterococci infections (controls). Nasal and perirectal swab samples were obtained from all patients in a 1-day point-prevalence survey. We examined antimicrobial drug use and calculated the defined daily dose of linezolid per 1,000 patient-days. Fifteen LRE cases were identified (13 Enterococcus faecalis and 2 E. faecium); 7 were vancomycin-resistant. Compared with controls, case-patients had increased in-hospital mortality rates and lengths of stay. Multivariate analysis identified independent predictors of LRE infection: prior cultures positive for methicillin-resistant Staphylococcus aureus (adjusted odds ratio [AOR] 27), hospitalization duration before index culture (AOR 1.1 per day), and duration of preceding linezolid therapy (AOR 1.1 per day). Linezolid exposure and patient-to-patient transmission appear to be responsible for LRE infections, an important emerging hospital problem.

Recurrent multistate outbreak of Salmonella Newport associated with tomatoes from contaminated fields, 2005

Salmonella Newport causes more than an estimated 100,000 infections annually in the United States. In 2002, tomatoes grown and packed on the eastern shore of Virginia contaminated with a pan-susceptible S. Newport strain caused illness in 510 patients in 26 states. In July-November 2005, the same strain caused illness in at least 72 patients in 16 states. We conducted a case-control study during the 2005 outbreak, enrolling 29 cases and 140 matched neighbourhood controls. Infection was associated with eating tomatoes (matched odds ratio 9.7, 95% confidence interval 3.3-34.9). Tomatoes were traced back to the eastern shore of Virginia, where the outbreak strain was isolated from pond water used to irrigate tomato fields. Two multistate outbreaks caused by one rare strain, and identification of that strain in irrigation ponds 2 years apart, suggest persistent contamination of tomato fields. Further efforts are needed to prevent produce contamination on farms and throughout the food supply chain.

PulseNet USA standardized pulsed-field gel electrophoresis protocol for subtyping of Vibrio parahaemolyticus

PulseNet is a national molecular subtyping network for foodborne disease surveillance composed of public health and food regulatory agencies. Participants employ molecular subtyping of foodborne pathogens using a standardized method of pulsed-field gel electrophoresis (PFGE) for conducting laboratory-based surveillance of foodborne pathogens. The PulseNet standardized PFGE protocols are developed through a comprehensive testing process. The reproducibility of the protocol undergoes an internal evaluation at the Centers for Disease Control and Prevention and an external evaluation in multiple PulseNet laboratories. Here we describe the development and evaluation of a rapid PFGE protocol for subtyping Vibrio parahaemolyticus for use in PulseNet activities. The protocol was derived from the existing standardized PulseNet protocols for Escherichia coli O157:H7 and Vibrio cholerae. An external evaluation of this protocol was undertaken in collaboration with three PulseNet USA participating public health laboratories. Comparative analysis of the PFGE fingerprints generated by each of these laboratories demonstrated that the protocol is both reliable and reproducible in the hands of multiple users.

Listeria prevalence and Listeria monocytogenes serovar diversity at cull cow and bull processing plants in the United States

Listeria monocytogenes, the causative agent of epidemic and sporadic listeriosis, is routinely isolated from many sources, including cattle, yet information on the prevalence of Listeria in beef processing plants in the United States is minimal. From July 2005 through April 2006, four commercial cow and bull processing plants were sampled in the United States to determine the prevalence of Listeria and the serovar diversity of L. monocytogenes. Samples were collected during the summer, fall, winter, and spring. Listeria prevalence on hides was consistently higher during cooler weather (28 to 92% of samples) than during warmer weather (6 and 77% of samples). The Listeria prevalence data collected from preevisceration carcass ranged from undetectable in some warm season samples to as high as 71% during cooler weather. Listeria on postintervention carcasses in the chill cooler was normally undetectable, with the exception of summer and spring samples from one plant where > 19% of the carcasses were positive for Listeria. On hides, L. monocytogenes serovar 1/2a was the predominant serovar observed, with serovars 1/2b and 4b present 2.5 times less often and serovar 1/2c not detected on any hides sampled. L. monocytogenes serovars 1/2a, 1/2c, and 4b were found on postintervention carcasses. This prevalence study demonstrates that Listeria species are more prevalent on hides during the winter and spring and that interventions being used in cow and bull processing plants appear to be effective in reducing or eliminating Listeria contamination on carcasses.

Variable number of tandem repeats and pulsed-field gel electrophoresis cluster analysis of enterohemorrhagic Escherichia coli serovar O157 strains

Ninety-five enterohemorrhagic Escherichia coli serovar O157 strains, including 30 strains isolated from 13 intrafamily outbreaks and 14 strains isolated from 3 mass outbreaks, were studied by pulsed-field gel electrophoresis (PFGE) and variable number of tandem repeats (VNTR) typing, and the resulting data were subjected to cluster analysis. Cluster analysis of the VNTR typing data revealed that 57 (60.0%) of 95 strains, including all epidemiologically linked strains, formed clusters with at least 95% similarity. Cluster analysis of the PFGE patterns revealed that 67 (70.5%) of 95 strains, including all but 1 of the epidemiologically linked strains, formed clusters with 90% similarity. The number of epidemiologically unlinked strains forming clusters was significantly less by VNTR cluster analysis than by PFGE cluster analysis. The congruence value between PFGE and VNTR cluster analysis was low and did not show an obvious correlation. With two-step cluster analysis, the number of clustered epidemiologically unlinked strains by PFGE cluster analysis that were divided by subsequent VNTR cluster analysis was significantly higher than the number by VNTR cluster analysis that were divided by subsequent PFGE cluster analysis. These results indicate that VNTR cluster analysis is more efficient than PFGE cluster analysis as an epidemiological tool to trace the transmission of enterohemorrhagic E. coli O157.

Pulsed-Field Gel Electrophoresis Subtyping Database for FoodborneSalmonella entericaSerotype Discrimination

Nontyphoid Salmonella is one of the main causes of bacterial gastroenteritis worldwide and is responsible for 65% of reported outbreaks of foodborne diseases in France. Serotyping is widely used for isolate preliminary identification, but it poorly discriminates strains. Rapid, efficient molecular subtyping tools have therefore been developed for the investigation of outbreaks. We evaluated the performance of the pulsed-field gel electrophoresis (PFGE) method for discrimination of 31 Salmonella serotypes frequently isolated in France. We set up a genomic database of Salmonella strains isolated from food, animals, the environment, and humans to improve the management of contamination and reactions to foodborne disease outbreaks. We studied 1128 isolates by PFGE, according to the standardized PulseNet protocol. We identified 452 PFGE patterns, 67.5% of which corresponded to a single isolate. The ability of this method to distinguish between isolates was estimated by calculating the Simpson index and the 95% confidence interval. Values obtained ranged between 0.33 (0.11-0.54) to 0.99 (0.96-1.00), depending on serotype. Epidemiological information about isolates was used for analyses of intra- and interserotype diversity results and for determining whether PFGE patterns were linked to the source of the isolate. Clustering analysis of the PFGE patterns obtained confirmed that serotype and PFGE genotype were closely linked. Some PFGE patterns were identified as major patterns, each of these patterns being found in at least 10 isolates. The database generated has already proved its effectiveness in epidemiological investigations in livestock production and foodborne outbreaks.

Clonal expansion and microevolution of quinolone-resistant Salmonella enterica serotype typhi in Vietnam from 1996 to 2004

Salmonella enterica serotype Typhi clinical isolates (n = 91) resistant to nalidixic acid (Nal(r)) were collected from sporadic cases and minor outbreaks throughout Vietnam between 1996 and 2004. These isolates were typed and compared by four methods: Vi phage typing, PstI ribotyping, XbaI and SpeI pulsed-field gel electrophoresis (PFGE), and single-nucleotide polymorphism (SNP) analysis. The results indicated that 65% of the isolates were not typeable by Vi phage typing. In contrast, the ribotyping and, with more accuracy, the SNP analysis methods indicated that all Nal(r) isolates belonged to a single clone (ribotype 3a, haplotype H58) that was found previously and that largely consisted of plasmid-encoded multidrug-resistant serotype Typhi isolates. PFGE demonstrated the occurrence of microevolution within this clone. We identified two major combined PFGE profiles: X1-S1 and X3-S6. X3-S6 predominated between 1996 and 2002 but was replaced by X1-S1 after 2002. Nevertheless, PFGE, with a Simpson's index of 0.78, was not considered an optimal discriminatory method for investigating typhoid fever outbreaks in Vietnam. The rate of quinolone resistance increased and the rate of multidrug resistance decreased during the study period. From 2002 to 2004, 80.6% of the isolates from South Vietnam were resistant only to Nal. The mechanism of Nal resistance in most of the isolates (94%) was a mutation in the quinolone resistance-determining chromosomal region of gyrA that led to the amino acid substitution Ser83Phe. No plasmid-located qnrA, qnrB, or qnrS was detected.

Comparison of different electrophoretic parameters of Pulse-Field Gel Electrophoresis for Vibrio cholerae subtyping

Molecular subtyping is used to distinguish pathogenic bacterial strains during epidemiological surveys of infectious diseases and the discovery of novel pathogens. There is a need to standardize protocols involving Pulse-Field Gel Electrophoresis (PFGE), a crucial method in molecular subtyping, to make inter-laboratory results comparable and information exchange possible. The PFGE pattern varies with electrophoretic parameters (EPs), so it is important to select the parameter that can distinguish the patterns better. To optimize EPs of PFGE for Vibrio cholerae, we analyzed 24 isolates of V. cholerae O1 biotype El Tor and 26 isolates of O139 by PFGE with Not|. We used four different EPs and compared the similarity coefficients from the four groups by Friedman test. Based on the principle that the electrophoretic parameter producing smaller similarity in the PFGE patterns has higher level of discriminatory power, the one producing the smallest similarity coefficients is considered to be optimal. This method could be applied to determine the optimal molecular subtyping protocol for other bacteria.

Tandem repeat analysis for surveillance of human Salmonella Typhimurium infections

Multiple-locus variable-number tandem repeats analysis improves surveillance and outbreak investigations.

In Denmark, as part of the national laboratory-based surveillance system of human enteric infections, all Salmonella Typhimurium isolates are currently subtyped by using phage typing, antimicrobial resistance profiles, and pulsed-field gel electrophoresis (PFGE). We evaluated the value of real-time typing that uses multiple-locus-number tandem-repeats analysis (MLVA) of Salmonella enterica serotype Typhimurium (S. Typhimurium) to detect possible outbreaks. Because only a few subtypes identified by PFGE and phage typing account for most infections, we included MLVA typing in the routine surveillance in a 2-year period beginning December 2003. The 1,019 typed isolates were separated into 148 PFGE types and 373 MLVA types. Several possible outbreaks were detected and confirmed. MLVA was particularly valuable for discriminating within the most common phage types. MLVA was superior to PFGE for both surveillance and outbreak investigations of S. Typhimurium.

Comparison of the molecular genotypes of Escherichia coli O157:H7 from the hides of beef cattle in different regions of North America

Cattle hides become contaminated with Escherichia coli O157:H7 via pathogen transmission in the feedlot, during transport, and while in the lairage environment at the processing facility, and the bacteria can be transferred to beef carcasses during processing. Several studies have shown that E. coli O157:H7 strains possessing indistinguishable restriction digest patterns (RDPs) can be isolated from distant locations. Most of these studies, however, examined RDPs from strains isolated within a single region of the United States or Canada. The experiment described in the present study was designed to identify the molecular genotypes of E. coli O157:H7 isolates from beef cattle hides in nine major cattle-producing regions of North America. Prevalence for E. coli O157:H7 in beef cattle hide samples ranged from 9 to 85%. Pulsed-field gel electrophoresis (PFGE) analysis of XbaI-digested genomic DNA from 1,193 E. coli O157:H7 isolates resulted in 277 unique RDPs. Of the 277 unique XbaI RDPs, 54 contained isolates collected from multiple regions. After two subsequent rounds of PFGE analysis (BlnI and SpeI), there were still many isolates (n = 154) that could not be distinguished from others, even though they were collected from different regions separated by large geographical distances. On multiple occasions, strains isolated from cattle hides in Canada had RDPs that were indistinguishable after three enzyme digestions from cattle hide isolates collected in Kansas and Nebraska. This information clearly shows that strains with indistinguishable RDPs originate from multiple sources that can be separated by large distances and that this should be taken into account when the source tracking of isolates is based on PFGE.

Recurrent and sporadic Listeria monocytogenes contamination in alheiras represents considerable diversity, including virulence-attenuated isolates

Microbiological characterization of alheiras, traditional smoked meat sausages produced in northern Portugal, had previously shown that more than 60% of the lots analyzed were contaminated with Listeria monocytogenes at levels higher than 100 CFU/g. In order to better understand L. monocytogenes contamination patterns in alheiras, we characterized 128 L. monocytogenes isolates from alheiras using a variety of subtyping techniques (i.e., molecular serotyping; arsenic, cadmium, and tetracycline resistance typing; and pulsed-field gel electrophoresis [PFGE]). Subtyping of isolates from products collected on two separate dates provided evidence for the persistence of specific L. monocytogenes PFGE types in the production and distribution chains of alheiras from four different processors. A subset of 21 isolates was further characterized using ribotyping and Caco-2 cell invasion assays to evaluate the pathogenic potential of L. monocytogenes present in alheiras. Caco-2 invasion assays revealed seven isolates with invasion efficiencies that were less than 20% of that of the control strain 10403S. All seven isolates had premature stop codons in inlA that represented three distinct mutations, which had previously been observed in isolates from the United States or France. Our findings indicate the need for a comprehensive approach to control L. monocytogenes in alheiras, including strategies to reduce persistence. The presence of considerable diversity in invasion phenotypes among L. monocytogenes strains present in alheiras, including the presence of subtypes likely to be virulence attenuated, may provide an opportunity to initially focus control strategies on the subtypes most likely to cause human disease.

Shiga toxin gene loss and transfer in vitro and in vivo during enterohemorrhagic Escherichia coli O26 infection in humans

Escherichia coli serogroup O26 consists of enterohemorrhagic E. coli (EHEC) and atypical enteropathogenic E. coli (aEPEC). The former produces Shiga toxins (Stx), major determinants of EHEC pathogenicity, encoded by bacteriophages; the latter is Stx negative. We have isolated EHEC O26 from patient stools early in illness and aEPEC O26 from stools later in illness, and vice versa. Intrapatient EHEC and aEPEC isolates had quite similar pulsed-field gel electrophoresis (PFGE) patterns, suggesting that they might have arisen by conversion between the EHEC and aEPEC pathotypes during infection. To test this hypothesis, we asked whether EHEC O26 can lose stx genes and whether aEPEC O26 can be lysogenized with Stx-encoding phages from EHEC O26 in vitro. The stx2 loss associated with the loss of Stx2-encoding phages occurred in 10% to 14% of colonies tested. Conversely, Stx2- and, to a lesser extent, Stx1-encoding bacteriophages from EHEC O26 lysogenized aEPEC O26 isolates, converting them to EHEC strains. In the lysogens and EHEC O26 donors, Stx2-converting bacteriophages integrated in yecE or wrbA. The loss and gain of Stx-converting bacteriophages diversifies PFGE patterns; this parallels findings of similar but not identical PFGE patterns in the intrapatient EHEC and aEPEC O26 isolates. EHEC O26 and aEPEC O26 thus exist as a dynamic system whose members undergo ephemeral interconversions via loss and gain of Stx-encoding phages to yield different pathotypes. The suggested occurrence of this process in the human intestine has diagnostic, clinical, epidemiological, and evolutionary implications.

Distribution of epidemic clonal genetic markers among Listeria monocytogenes 4b isolates

Recent genome sequencing of isolates of Listeria monocytogenes serotype 4b implicated in some major outbreaks of foodborne listeriosis has revealed unique genetic markers in these isolates. The isolates were grouped into two distinct epidemic clones, ECI and ECII. In the present study, selected ECI- and ECII-specific genetic markers were detected in 16 and 15 of 89 L. monocytogenes 4b isolates, respectively. The ECI markers were found in 6 of 34 clinical isolates, 9 of 50 food isolates, and 1 of 5 environmental isolates, and the ECII markers were detected in 7 of 34 clinical isolates, 7 of 50 food isolates, and 1 of 5 environmental isolates. Hence, of the isolates with the epidemic clonal genetic markers, 38% (13 of 34) were of clinical origin, 32% (16 of 50) were of food origin, and 40% (2 of 5) were of environmental origin. The predominance of the epidemic clonal markers among the clinical and environmental isolates supports the hypothesis that these markers are correlated with the pathogenic potential of strains and with their environmental persistence. Several isolates had only one epidemic clonal marker, either the ECI-specific marker 133 or the ECII-specific marker 4bSF18. Pulsed-field gel electrophoresis analysis revealed higher genomic diversity among the strains with ECII-like characteristics than among those strains carrying the ECI-specific genetic markers.

Prevalence, numbers, and subtypes of Campylobacter jejuni and Campylobacter coli in uncooked retail meat samples

A national quantitative survey of Campylobacter jejuni and Campylobacter coli in 1,011 uncooked retail meat samples (beef, unweaned veal, chicken, lamb and mutton, and pork) was undertaken from August 2003 to June 2004 to establish baseline proportionality data. The presence, number, and type of Campylobacter present in each sample was assessed. Prevalences of C. jejuni and C. coli were 89.1% in chicken, 9.1% in pork, 6.9% in lamb and mutton, 3.5% in beef, and 10% in unweaned veal. C. jejuni was identified in the majority of positive samples (246 of 259). In chicken samples positive for C. jejuni, 40.2% had counts of <0.3 most probable number (MPN)/g, 50.5% had 0.3 to 10.0 MPN/g, 8.8% had 10.1 to 50.0 MPN/g, and 0.5% had 110 MPN/g. In other meats (49 samples), Campylobacter counts were < or = 0.3 MPN/g, except for one unweaned veal sample at > 10.9 MPN/g. Penner serotyping and SmaI macrorestriction genotyping using pulsed-field gel electrophoresis with 247 isolates revealed 17 Penner serotypes and 56 electrophoresis profiles. Seven Penner serotypes (HS1 complex, 2, 4 complex, 6, 11, 27, and 42) were represented by 10 or more isolates from chicken. When data from both typing methods were combined, 62 sero-genotypes were generated. In a comparison of these sero-genotypes with historical data for isolates from human cases, 71% of the beef isolates, 50% of the lamb and mutton isolates, 50% of the pork isolates, 41% of the chicken isolates, and 25% of the unweaned veal isolates were common to both sources. These results provide baseline proportionality profiles of Campylobacter in these five meats and will facilitate exposure assessment in combination with other information such as consumption data and subsequent quantitative risk assessment.

Relationship of pulsed-field profiles with key phage types of Salmonella enterica serotype Enteritidis in Europe: results of an international multi-centre study

Salmonella is one of the most common causes of foodborne infection in Europe with Salmonella enterica serovar Enteritidis (S. Enteritidis) being the most commonly identified serovar. The predominant phage type for S. Enteritidis is phage type (PT) 4, although PT 8 has increased in incidence. Within these phage types, pulsed-field gel electrophoresis (PFGE) provides a method of further subdivision. The international project, Salm-gene, was established in 2001 to develop a database of PFGE profiles within nine European countries and to establish criteria for real-time pattern recognition. It uses DNA fingerprints of salmonellas to investigate outbreaks and to evaluate trends and emerging issues of foodborne infection within Europe. The Salm-gene database contains details of about 11 700 S. Enteritidis isolates, demonstrating more than 65 unique PFGE profiles. The clonal nature of S. Enteritidis is evidenced by the high similarity and distribution of PFGE profiles. Over 56% (6603/11 716) of the submitted isolates of several different phage types were profile SENTXB.0001, although this profile is most closely associated with PT 4. The next most common profiles, SENTXB.0002 and SENTXB.0005, were closely associated with PT 8 and PT 21 respectively. Studies to investigate the relationship of profile types with outbreaks and possible vehicles of infection suggest that the incidence of PFGE profile SENTXB.0002, and thus PT 8, in some countries may be due to importation of foods or food production animals from Eastern Europe, where PT 8 is amongst the most frequently identified phage types. Collation of subtyping data, especially in the commonly recognized phage types, is necessary in order to evaluate trends and emerging issues in salmonella infection.

Prevalence and genetic properties of Salmonella enterica serovar typhimurium definitive phage type 104 isolated from Rattus norvegicus and Rattus rattus house rats in Yokohama City, Japan

Salmonella enterica serovar Typhimurium was isolated from the intestinal contents of Rattus rattus and Rattus norvegicus house rats captured at two buildings, designated buildings J and YS, in Yokohama City, Japan. From October 1997 to September 1998, 52 of 339 (15.3%) house rats were found to carry Salmonella serovar Typhimurium definitive phage type 104 (DT104). In building J, 26 of 161 (16.1%) house rats carried DT104 over the 1-year study period, compared to 26 of 178 (14.6%) rats in building YS. The isolation rates of DT104 from R. rattus and R. norvegicus were similar in the two buildings. Most DT104 strains from building J (24 of 26) showed resistance to ampicillin, chloramphenicol, streptomycin, sulfisoxazole, and tetracycline and contained both the 1.0- and 1.2-kbp integrons, carrying genes pse1, pasppflo-like, aadA2, sulI, and tet(G). All DT104 strains from building YS were resistant to ampicillin and sulfisoxazole, and had the 1.2-kbp integron carrying pse1 and sulI. Cluster analysis of pulsed-field gel electrophoresis patterns of BlnI-digested DT104 DNAs showed that 22 of 26 DT104 strains from building J and 24 of 26 strains from building YS could be grouped into separate clusters each specific for the building origin. These results indicated that DT104 strains were prevalent in house rat colonies in each building and suggest that house rats may play an important role in the epidemiology of DT104.

Molecular epidemiology of CTX-M-producing Escherichia coli in the Calgary Health Region: emergence of CTX-M-15-producing isolates

A study was designed to describe the molecular epidemiology of CTX-M-producing Escherichia coli over a 6-year period (2000 to 2005) in a large well-defined Canadian region with a centralized laboratory system. Molecular characterization was done by isoelectric focusing, PCR, and automated sequencing, while genetic relatedness was determined by pulsed-field gel electrophoresis with XbaI. Of the 552 viable extended-spectrum beta-lactamase-producing E. coli isolates isolated, 354 (64%) were positive for blaCTX-M genes associated with ISEcp1; 211 produced CTX-M-14, 128 produced CTX-M-15, 5 produced CTX-M-2, 4 produced CTX-M-3, 4 produced CTX-M-24, and 2 produced CTX-M-27. CTX-M-positive isolates were significantly more resistant to the fluoroquinolones than CTX-M-negative isolates, while CTX-M-15 producers were more likely to be resistant to gentamicin and tobramycin. There was a predominance of CTX-M-14 during the first 4 years of the study period, with community outbreaks associated with cluster 14A during 2000, 2001, and 2003. A substantial increase in CTX-M-15 producers occurred during the last 18 months and was due to clusters 15A and 15AR (where AR indicates related to A) in the hospital and nursing home sectors. Our results demonstrate that the persistence and dissemination of CTX-M genes among E. coli populations in larger geographic health care regions is dynamic, with the continuous emergence of clonally related CTX-M-15. This study illustrates the importance of molecular surveillance in tracking CTX-M-producing E. coli strains in the community and investigating their influx into hospitals.

Transportation and lairage environment effects on prevalence, numbers, and diversity of Escherichia coli O157:H7 on hides and carcasses of beef cattle at processing

Hide has been established as the main source of carcass contamination during cattle processing; therefore, it is crucial to minimize the amount of Escherichia coli O157:H7 on cattle hides before slaughter. Several potential sources of E. coli O157: H7 are encountered during transportation and in the lairage environment at beef-processing facilities that could increase the prevalence and numbers of E. coli O157:H7 on the hides of cattle. On three separate occasions, samples were obtained from cattle at the feedlot and again after cattle were stunned and exsanguinated at the processing plant (286 total animals). The prevalence of E. coli O157:H7 on hides increased from 50.3 to 94.4% between the time cattle were loaded onto tractor-trailers at the feedlot and the time hides were removed in the processing plant. Before transport, nine animals had E. coli O157:H7 in high numbers (> 0.4 CFU/cm2) on their hides. When sampled at the slaughter facility, the number of animals with high hide numbers had increased to 70. Overall, only 29% of the E. coli O157:H7 isolates collected postharvest (221 of 764) matched pulsed-field gel electrophoresis types collected before transport. The results of this study indicate that transport to and lairage at processing plants can lead to increases in the prevalence and degree of E. coli O157:H7 contamination on hides and the number of E. coli O157:H7 pulsed-field gel electrophoresis types associated with the animals. More study is needed to confirm the mechanism by which additional E. coli O157:H7 strains contaminate cattle hides during transport and lairage and to design interventions to prevent this contamination.

Pulsed-field gel electrophoresis (PFGE) analysis of temporally matched Listeria monocytogenes isolates from human clinical cases, foods, ruminant farms, and urban and natural environments reveals source-associated as well as widely distributed PFGE types

A total of 495 temporally and geographically matched Listeria monocytogenes isolates from human clinical cases, foods, ruminant farms, and urban and natural environments were used to investigate L. monocytogenes pulsed-field gel electrophoresis (PFGE) type diversity. Two-enzyme (AscI and ApaI) PFGE discriminated 310 PFGE types and exhibited higher overall discriminatory power (Simpson's index of discrimination [D] = 0.995) than either EcoRI ribotyping (D = 0.950) or AscI or ApaI single-enzyme PFGE (D = 0.992 for both). Seven PFGE types showed significant associations with specific sources, including one and four PFGE types, respectively, associated with human clinical cases and foods. Spatial analysis of 13 PFGE types occurring >5 times showed that two PFGE types were specific to a single processing facility each, where they appear to have persisted over time. Nine PFGE types were geographically widespread and occurred among isolates from multiple sources. For example, a PFGE type that matched isolates from listeriosis outbreaks in Los Angeles and Switzerland occurred among isolates from farms (n = 7), human clinical cases (n = 4), environmental sources (n = 3), and foods (n = 1). Our data indicate that (i) PFGE is highly discriminatory for the subtyping of L. monocytogenes, (ii) some L. monocytogenes PFGE types are associated with specific sources, and (iii) some L. monocytogenes PFGE types are widely distributed and appear to be stable and pandemic. Large PFGE type databases representing isolates from different sources are thus needed to appropriately interpret subtype data in epidemiological investigations and to identify common as well as source-specific PFGE types.

Antimicrobial resistance in Salmonella enterica serovar Dublin isolates from beef and dairy sources

Salmonella enterica serovar Dublin (S. Dublin) is a cattle-adapted Salmonella serovar, so if antimicrobial resistance in S. Dublin arises as a result of antimicrobial use this most likely occurs within the cattle reservoir without impact from antimicrobial use in humans. We tested the antimicrobial resistance of bovine-origin S. Dublin isolates from 1986 through 2004 using a standard disk diffusion method. High proportions of isolates throughout the time period were resistant to one or more antimicrobials, and a marked increase in resistance to ceftazidime occurred between 2000 and 2004. Dairy-origin isolates were more likely to be resistant to several antibiotics than were isolates from beef operations where exposure to antimicrobials is likely to be less frequent. Plasmid analysis of a subset of isolates also supported the hypothesis that antimicrobial resistance traits in the cattle-adapted serovar Dublin were acquired within the bovine host environment.

Lysine Decarboxylase-Negative Salmonella enterica Serovar Enteritidis: Antibiotic Susceptibility, Phage and PFGE Typing

One hundred twenty Salmonella Enteritidis isolates collected from 1992 to 2005 in Nagasaki prefecture (65 isolates from 40 outbreak cases, 44 from sporadic diarrhea patients, and 11 from chicken-related products) were investigated by their antibiotic susceptibility profiles, phage typing, and pulsed-field gel electrophoresis (PFGE) typing. Out of them, 18 were identified as lysine decarboxylase (LDC)-negative isolates, and 15 showed resistance toward streptomycin. Based on the PFGE typing, the isolates were classified into five clusters by UPGMA clustering method. Three LDC-negative isolates belonged to cluster A and were of phage type (PT) 4 and isolated between 2000 and 2004. Other 15 LDC-negative isolates belonged to cluster E. They were PT1, reacted but did not conform (RDNC), or untypable and were isolated between 2001 and 2004. LDC-negative isolates of the cluster A differed from LDC-negative isolates of the cluster E in antibiotic susceptibility profiles, phage typing, and PFGE typing. LDC-negative isolates of the cluster E were isolated after 2001 in Nagasaki prefecture.

Guidelines for the validation and application of typing methods for use in bacterial epidemiology

For bacterial typing to be useful, the development, validation and appropriate application of typing methods must follow unified criteria. Over a decade ago, ESGEM, the ESCMID (Europen Society for Clinical Microbiology and Infectious Diseases) Study Group on Epidemiological Markers, produced guidelines for optimal use and quality assessment of the then most frequently used typing procedures. We present here an update of these guidelines, taking into account the spectacular increase in the number and quality of typing methods made available over the past decade. Newer and older, phenotypic and genotypic methods for typing of all clinically relevant bacterial species are described according to their principles, advantages and disadvantages. Criteria for their evaluation and application and the interpretation of their results are proposed. Finally, the issues of reporting, standardisation, quality assessment and international networks are discussed. It must be emphasised that typing results can never stand alone and need to be interpreted in the context of all available epidemiological, clinical and demographical data relating to the infectious disease under investigation. A strategic effort on the part of all workers in the field is thus mandatory to combat emerging infectious diseases, as is financial support from national and international granting bodies and health authorities.

Identification of putative ancestors of the multidrug-resistant Salmonella enterica serovar typhimurium DT104 clone harboring the Salmonella genomic island 1

The origin of multidrug-resistant Salmonella enterica serovar typhimurium (S. typhimurium) harboring the Salmonella Genomic Island 1 (SGI1), which was detected for the first time in the mid-1980s is unknown. In this study, we performed microarray genomotyping of four multidrug-resistant SGI1 positive strains and found that unlike the S. typhimurium LT2 strain, the multidrug-resistant strains lacked genes STM0517-0529 allowing the utilization of allantoin as a sole nitrogen source. We extended this observation by PCR screening of additional 120 S. typhimurium field strains and found that this locus was absent in all SGI1 positive and also in 24% of SGI1 negative strains, which were proposed to be the original recipients of SGI1. To prove this hypothesis, we compared the STM0517-0529 negative strains (with or without the SGI1) by PFGE and PCR prophage typing and found that 8 out of 11 of the SGI1 negative strains and 17 out of 22 SGI1 positive strains were of identical PFGE pattern and PCR prophage pattern, while this specific pattern was never observed among STM0517-0529 positive strains. We therefore propose that a lineage of the S. typhimurium DT104 sensitive strain first lost the ability to metabolize allantoin and then acquired SGI1.

International Life Sciences Institute North America Listeria monocytogenes strain collection: development of standard Listeria monocytogenes strain sets for research and validation studies

Research and development efforts on bacterial foodborne pathogens, including the development of novel detection and subtyping methods, as well as validation studies for intervention strategies can greatly be enhanced through the availability and use of standardized strain collections. These types of strain collections are available for some foodborne pathogens, such as Salmonella and Escherichia coli. We have developed a standard Listeria monocytogenes strain collection that has not been previously available. The strain collection includes (i) a diversity set of 25 isolates chosen to represent a genetically diverse set of L. monocytogenes isolates as well as a single hemolytic Listeria innocua strain and (ii) an outbreak set, which includes 21 human and food isolates from nine major human listeriosis outbreaks that occurred between 1981 and 2002. The diversity set represents all three genetic L. monocytogenes lineages (I, n = 9; II, n = 9; and III, n = 6) as well as nine different serotypes. Molecular subtyping by EcoRI automated ribotyping and pulsed-field gel electrophoresis (PFGE) with AscI and ApaI separated the 25 isolates in the diversity set into 23 ribotypes and 25 PFGE types, confirming that this isolate set represents considerable genetic diversity. Molecular subtyping of isolates in the outbreak set confirmed that human and food isolates were identical by ribotype and PFGE, except for human and food isolates for two outbreaks, which displayed related but distinct PFGE patterns. Subtype and source data for all isolates in this strain collection are available on the Internet and are linked to the PathogenTracker database (www.pathogentracker.com), which allows the addition of new, relevant information on these isolates, including links to publications that have used isolates from this collection. We have thus developed a core L. monocytogenes strain collection, which will provide a resource for L. monocytogenes research and development efforts with centralized Internet-based data curation and integration.

Molecular epidemiology of multidrug-resistant Shigella dysenteriae type 1 causing dysentery outbreaks in Central African Republic, 2003–2004

Shigella dysenteriae type 1 (Sd1) represents a particular threat in developing countries because of the severity of the infection and its epidemic potential. Antimicrobial susceptibility testing and molecular subtyping by pulsed-field gel electrophoresis (PFGE) and plasmid profiling (PP) of Sd1 isolates collected during two dysentery outbreaks (2013 and 445 cases of bloody diarrhoea) in Central African Republic (CAR) during the period 2003-2004 were reported. Eleven Sd1 comparison strains (CS) acquired by travellers or residents of Africa (n=10) or Asia (n=1) between 1993 and 2003 were also analysed. The 19 Sd1 isolates recovered from CAR outbreaks were multidrug resistant, although susceptible to quinolones and fluoroquinolones. Molecular subtyping by PFGE was more discriminatory than PP. The PFGE using XbaI and NotI restriction enzymes indicated that the two outbreaks were due to two different clones and also revealed a genetic diversity among the CS recovered from outbreak or sporadic cases between 1993 and 2003. This study was the result of a fruitful collaboration between field physicians and microbiologists. The data collected will serve as the basis for establishing long-term monitoring of Sd1 in CAR.

Molecular epidemiology of metallo-beta-lactamase-producing Pseudomonas aeruginosa in the Calgary Health Region: emergence of VIM-2-producing isolates

A study was designed to describe the molecular epidemiology of carbapenem-resistant (CR) Pseudomonas aeruginosa in a large well-defined geographical region with a centralized laboratory system serving one pediatric and three large adult hospitals (acute care centers I, II, and III). Molecular characterization was done using PCR with sequencing of the integron-associated gene cassettes. Pulsed-field gel electrophoresis (PFGE) using a modified combined Stenotrophomas maltophilia and Streptococcus pneumoniae protocol with SpeI was performed on CR P. aeruginosa strains isolated in the Calgary Health Region during 2002-2006. The majority (96%) of metallo-beta-lactamase (MBL)-producing isolates produced VIM-2 with gene cassettes aacC1 and aacA4, while 4% produced IMP-7 with gene cassettes aacC4 and aacC1. Eighty-six percent of VIM-2 producers belonged to a cluster (MBLV) that was responsible for nosocomial outbreaks during 2003 (intensive care unit) and 2004 (bone marrow transplant unit) at acute care center I. Environmental isolates from these units also belonged to MBLV. The majority of strains from cluster MBLVR (related to MBLV) were present in acute care center III. Isolates producing IMP-7 belonged to a different cluster (MBLI) and were related to strains described during the 1990 s. PFGE of the MBL-negative CR strains showed that 37% belonged to a closely related cluster, NMBL, whose members were predominantly isolated from acute care center II. Our findings suggest that CR and dissemination of MBL clusters among P. aeruginosa populations in large geographic healthcare regions are dynamic processes that require continuous molecular surveillance.

The key role of pulsed-field gel electrophoresis in investigation of a large multiserotype and multistate food-borne outbreak of Salmonella infections centered in Pennsylvania

Five different serotypes of Salmonella enterica were implicated in a large outbreak linked to fresh Roma tomatoes served at gas station deli counters in Pennsylvania and nearby states during July 2004: S. enterica serotypes Javiana, Anatum, Thompson, Typhimurium, and Muenchen. One of these serotypes, Anatum, was isolated from both tomatoes and patients. Pulsed-field gel electrophoresis (PFGE) played a key role in identifying the outbreak-associated isolates and distinguishing them from unrelated sporadic isolates. It also demonstrated that the genetic fingerprints of serotype Anatum isolates derived from patients were indistinguishable from those derived from tomatoes. Rapid communication of PFGE fingerprints with other public health laboratories through the Centers for Disease Control and Prevention's PulseNet USA national molecular surveillance network for bacterial food-borne pathogens facilitated the tracking of this outbreak in other states. The work described in this report emphasizes the laboratory's role in core public health functions and services, thereby providing a highly visible example of public health in action.

Involvement of closely related strains of a new clonal group of Listeria monocytogenes in the 1998-99 and 2002 multistate outbreaks of foodborne listeriosis in the United States

In 1998-99, a multistate outbreak of listeriosis in the United States was associated with contaminated hot dogs and was caused by a strain of Listeria monocytogenes serotype 4b that had been only rarely encountered before in the national PulseNet database. Upon further characterization, the strains from this outbreak were designated as Epidemic Clone II (ECII). ECII isolates exhibited diversification in a genomic region ("region 18") that was otherwise conserved among L. monocytogenes of serotype 4b. Additional unique genetic markers were identified through genome sequencing of one of the isolates from the 1998-99 outbreak. In 2002, another multistate outbreak of listeriosis also involved bacteria of serotype 4b and was attributed to contaminated turkey deli meats. Molecular subtyping data revealed that the macrorestriction patterns of the isolates from the 1998-99 and 2002 outbreaks were closely related. In addition, the 2002 outbreak isolates harbored chromosomal genetic markers found to be unique to, and typical of, the 1998-99 outbreak isolates, including diversification in genomic region 18. Macroarray- based subtyping using chromosomal sequences confirmed the close genetic relatedness between the isolates from the two outbreaks. Genomic content was highly conserved among isolates from each outbreak, with differences detected only in prophage and internalin-like gene sequences. However, since these differences were observed among isolates from each of the outbreaks, they did not differentiate the 1998-99 isolates as a group from those of the 2002 outbreak. Two of 15 randomly chosen serotype 4b clinical isolates from a non-outbreak period (calendar year 2003) appeared to be closely related to the 1998-99 and 2002 outbreak isolates. These findings suggest that both multistate outbreaks of listeriosis in the United States involved closely related members of a single clonal group (ECII) that had not been identified in outbreaks prior to 1998. Since the outbreaks involved different food vehicles and processing plants, the findings suggest establishment of ECII in a still unidentified reservoir in the United States, from which the organisms were introduced to different processing plants.

The suitable restriction enzymes for pulsed-field gel electrophoresis analysis of Bordetella pertussis

We searched the restriction enzymes with rare cutting sites on the genome of Bordetella pertussis strain Tohama I using the Restriction Digest Tool software provided in the Institute for Genomic Research web site. The usefulness of 5 enzymes for pulsed-field gel electrophoresis (PFGE) analysis was evaluated with 68 B. pertussis isolates. The results indicated that AflII, DraI, SpeI, and XbaI were useful enzymes, and AflII was the best one for PFGE analysis of B. pertussis isolates.