Modified pulsed-field gel electrophoresis method for DNA degradation-sensitive Salmonella enterica and Escherichia coli strains

Label-Free Immunoassay for Multiplex Detections of Foodborne Bacteria in Chicken Carcass Rinse with Surface Plasmon Resonance Imaging

The frequent outbreaks of foodborne pathogens have stimulated the demand of biosensors capable of rapid and multiplex detection of contaminated food. In this study, surface plasmon resonance imaging (SPRi) was used in simultaneous label-free detection of multiple foodborne pathogens, mainly Salmonella spp. and Shiga-toxin producing Escherichia coli (STEC), in commercial chicken carcass rinse. The antibodies were immobilized on the same SPRi sensor chip as a label-free immunoassay. Their immobilization concentrations were optimized to be ranging from 0.25 to 1.0 mg/mL, and independent of pH values. This label-free immunoassay achieved 10⁶ colony-forming unit (CFU)/mL limit of detection for Salmonella, which was further improved to 1.0 CFU/mL with overnight bacteria enrichment. The injected samples with different bacteria, Salmonella Enteritidis, STEC, and Listeria monocytogenes, have been identified by the same biochip. Moreover, the SPRi signals revealed complex interference effects among coexisting bacteria species in heterogeneous bacteria solutions. This SPRi-based immunoassay demonstrates the great potential in high-throughput screening of multiple pathogenic bacteria coexisting in chicken carcass rinse. The reliability of antibody immobilization and cross-reactions of different antibodies on the same biochip are the major challenges of practical application of SPRi.

Modified PFGE protocol for improving typeability of DNA degradation susceptible nosocomial Klebsiella pneumoniae

Introduction. PFGE is the 'gold standard' method for bacterial subtyping. However, many strains are non-typable by this approach because of DNA degradation by nucleases action.Aim. To evaluate a modified PFGE protocol for typing nosocomial isolates of Klebsiella pneumoniae.Methods. Twenty- five K. pneumoniae isolates previously exposed to DNA degradation were used to optimize an extraction method for elimination of DNases activity before applying Xba1 enzyme. Introducing of sodium dodecyl sulfate (SDS) in different concentrations to the extraction buffer was evaluated for protecting genomic DNA molecule from degradation by nucleases.Results. Addition of 3 % SDS in combination with 3 % N-lauryl sarcosine to the extraction buffer was found to reduce the previously experienced nuclease activity. Pre-examination of plug quality prior to the digestion phase could efficiently reduce the expense of the wasted enzyme.Conclusion. We have successfully devised a PFGE protocol that enhanced the typeability of nosocomial K. pneumoniae.

Salmonella enterica Serotype Panama: An exceptionally virulent cause of illness in children?

Salmonella enterica serotype Panama accounts for <1% of all reported cases of Salmonellosis. Previous reports suggest that it may be unusually virulent in children. We report the case of a family, five of six of whom developed a diarrheal illness due to this organism following exposure during a trip to Costa Rica. Included among these patients were three children, all of whom developed clinical shock requiring aggressive fluid resuscitation, and all of whom ultimately recovered. DNA fingerprinting, using pulsed-field gel electrophoresis, demonstrated that all three children were infected with an identical strain of Salmonella. Moreover, this strain was unique among strains recovered in Nebraska. Clinicians should be aware of the propensity of Salmonella enterica serotype Panama to cause especially severe disease in children; laboratory personnel should be aware of the unique need for thiourea buffering when attempting to perform pulsed-field gel electrophoresis analysis on such strains.

Effects of intramuscularly administered enrofloxacin on the susceptibility of commensal intestinal Escherichia coli in pigs (sus scrofa domestica)

BACKGROUND

In the European Union, various fluoroquinolones are authorised for the treatment of food producing animals. Each administration poses an increased risk of development and spread of antimicrobial resistance. The aim of this study was to investigate the impact of parenteral administration of enrofloxacin on the prevalence of enrofloxacin and ciprofloxacin susceptibilities in the commensal intestinal E. coli population.

METHODS

E. coli isolates from faeces of twelve healthy pigs were included. Six pigs were administered enrofloxacin on day 1 to 3 and after two weeks for further three days. The other pigs formed the control group. MIC values were determined. Virulence and resistance genes were detected by PCR. Phylogenetic grouping was performed by PCR. Enrofloxacin and ciprofloxacin were analysed in sedimentation samples by HPLC.

RESULTS

Susceptibility shifts in commensal E. coli isolates were determined in both groups. Non-wildtype E. coli could be cultivated from two animals of the experimental group for the first time one week after the first administration and from one animal of the control group on day 28. The environmental load with enrofloxacin in sedimentation samples showed the highest amount between days one and five. The repeated parenteral administration of enrofloxacin to pigs resulted in rapidly increased MIC values (day 28: MIC up to 4 mg/L, day 35: MIC ≥ 32mg/L). E. coli populations of the control group in the same stable without direct contact to the experimental group were affected.

CONCLUSION

The parenteral administration of enrofloxacin to piglets considerably reduced the number of the susceptible intestinal E. coli population which was replaced by E. coli strains with increased MIC values against enrofloxacin. Subsequently also pigs of the control were affected suggesting a transferability of strains from the experimental group through the environment to the control group especially as we could isolate the same PFGE strains from both pig groups and the environment.

Emergence of a Multidrug-Resistant Shiga Toxin-Producing Enterotoxigenic Escherichia coli Lineage in Diseased Swine in Japan

EnterotoxigenicEscherichia coli(ETEC) and Shiga toxin-producingE. coli(STEC) are important causes of diarrhea and edema disease in swine. The majority of swine-pathogenicE. colistrains belong to a limited range of O serogroups, including O8, O138, O139, O141, O147, O149, and O157, which are the most frequently reported strains worldwide. However, the circumstances of ETEC and STEC infections in Japan remain unknown; there have been few reports on the prevalence or characterization of swine-pathogenicE. coli In the present study, we determined the O serogroups of 967E. coliisolates collected between 1991 and 2014 from diseased swine in Japan, and we found that O139, O149, O116, and OSB9 (O serogroup ofShigella boydiitype 9) were the predominant serogroups. We further analyzed these four O serogroups using pulsed-field gel electrophoresis (PFGE), multilocus sequence typing, and virulence factor profiling. Most of the O139 and O149 strains formed serogroup-specific PFGE clusters (clusters I and II, respectively), whereas the O116 and OSB9 strains were grouped together in the same cluster (cluster III). All of the cluster III strains belonged to a single sequence type (ST88) and carried genes encoding both enterotoxin and Shiga toxin. This PFGE cluster III/ST88 lineage exhibited a high level of multidrug resistance (to a median of 10 antimicrobials). Notably, these bacteria were resistant to fluoroquinolones. Thus, this lineage should be considered a significant risk to animal production due to the toxigenicity and antimicrobial resistance of these bacteria.

Salmonella infection in grey seals (Halichoerus grypus), a marine mammal sentinel species: pathogenicity and molecular typing of Salmonella strains compared with human and livestock isolates

Microbial pollution of the marine environment through land-sea transfer of human and livestock pathogens is of concern. Salmonella was isolated from rectal swabs of free-ranging and stranded grey seal pups (21.1%; 37/175) and compared with strains from the same serovars isolated from human clinical cases, livestock, wild mammals and birds in Scotland, UK to characterize possible transmission routes using pulsed-field gel electrophoresis and multi-locus variable number of tandem repeat analyses. A higher prevalence of Salmonella was found in pups exposed to seawater, suggesting that this may represent a source of this pathogen. Salmonella Bovismorbificans was the most common isolate (18.3% pups; 32/175) and was indistinguishable from isolates found in Scottish cattle. Salmonella Typhimurium was infrequent (2.3% pups; 4/175), mostly similar to isolates found in garden birds and, in one case, identical to a highly multidrug resistant strain isolated from a human child. Salmonella Haifa was rare (1.1% pups; 2/175), but isolates were indistinguishable from that of a human clinical isolate. These results suggest that S. Bovismorbificans may circulate between grey seal and cattle populations and that both S. Typhimurium and S. Haifa isolates are shared with humans, raising concerns of microbial marine pollution.

First report of a multidrug-resistant Klebsiella pneumoniae of sequence type 11 causing sepsis in a free-ranging beaver (Castor fiber)

Klebsiella pneumoniae of sequence type (ST) 11 is a hyper-epidemic nosocomial clone spreading worldwide among humans and also emerging in pets. In this report, we describe a clinical case of fatal sepsis due to this multidrug-resistant (MDR) pathogen in a Eurasian beaver. The isolate showed resistance to six different classes of antimicrobials including third generation cephalosporins and fluoroquinolones. This is the first report describing the detection of a MDR K. pneumoniae ST11 in a free-ranging animal. Our finding highlights the potential for environmental dissemination of hyper-epidemic clones of K. pneumoniae and possible spread in wildlife and cause epizootics.

Third-generation-cephalosporin-resistant Klebsiella pneumoniae isolates from humans and companion animals in Switzerland: spread of a DHA-producing sequence type 11 clone in a veterinary setting

Characterization of third-generation-cephalosporin-resistant Klebsiella pneumoniae isolates originating mainly from one human hospital (n = 22) and one companion animal hospital (n = 25) in Bern (Switzerland) revealed the absence of epidemiological links between human and animal isolates. Human infections were not associated with the spread of any specific clone, while the majority of animal infections were due to K. pneumoniae sequence type 11 isolates producing plasmidic DHA AmpC. This clonal dissemination within the veterinary hospital emphasizes the need for effective infection control practices.

Prevalence and characterization of Salmonella shed by captive and free-range California sea lions (Zalophus californianus) from a rehabilitation center and three state reserves along the California coast

Salmonella is a genus of zoonotic bacteria that can infect a variety of animals, and may cause gastrointestinal disease in marine mammals. Many of the same Salmonella serotypes are shed by California sea lions (Zalophus californianus) and humans, which poses transmission questions and public health concerns. In this study, 454 fecal samples from three free-ranging California sea lion populations along the California coast and from animals undergoing rehabilitation at The Marine Mammal Center, Sausalito, California, were screened for the presence of Salmonella. In addition to fecal samples, 39 presumed vomitus samples were collected and processed. Of the 454 samples processed, 312 were from free-ranging sites and 142 were from rehabilitating California sea lions. A total of nine fecal samples were positive for Salmonella, yielding a 2.0% overall prevalence, as well as two presumed vomitus samples (5.1% prevalence). Salmonella shedding prevalence was 1.6% in samples collected from free-ranging animals, and 2.8% in rehabilitating animals. Four serotypes were found among the 11 positive samples, with Salmonella Enteritidis the most prevalent (64%). Antimicrobial resistance testing and pulsed-field gel electrophoresis were performed to further characterize isolates. Experiments were carried out to determine the minimal number of Salmonella required for detection by the methods used. It was determined that at least 10' colony-forming units per gram of feces was required for detection. The prevalence of Salmonella Enteritidis, and diversity of serotypes discovered is considerably different from those reported in previous studies. Overall, this study provides new insights into the epidemiology of Salmonella in California sea lions present in multi-use coastal ecosystems.

Lineage-specific distribution of insertion sequence excision enhancer in enterotoxigenic Escherichia coli isolated from swine

Insertion sequences (ISs) are the simplest transposable elements and are widely distributed in bacteria; however, they also play important roles in genome evolution. We recently identified a protein called IS excision enhancer (IEE) in enterohemorrhagic Escherichia coli (EHEC) O157. IEE promotes the excision of IS elements belonging to the IS3 family, such as IS629, as well as several other families. IEE-mediated IS excision generates various genomic deletions that lead to the diversification of the bacterial genome. IEE has been found in a broad range of bacterial species; however, among sequenced E. coli strains, IEE is primarily found in EHEC isolates. In this study, we investigated non-EHEC pathogenic E. coli strains isolated from domestic animals and found that IEE is distributed in specific lineages of enterotoxigenic E. coli (ETEC) strains of serotypes O139 or O149 isolated from swine. The iee gene is located within integrative elements that are similar to SpLE1 of EHEC O157. All iee-positive ETEC lineages also contained multiple copies of IS629, a preferred substrate of IEE, and their genomic locations varied significantly between strains, as observed in O157. These data suggest that IEE may have been transferred among EHEC and ETEC in swine via SpLE1 or SpLE1-like integrative elements. In addition, IS629 is actively moving in the ETEC O139 and O149 genomes and, as in EHEC O157, is promoting the diversification of these genomes in combination with IEE.

Distribution of serotypes and genotypes of Salmonella enterica species in French pig production

The population of Salmonella found at various stages of pig production in France was characterised to analyse the distribution and spread of Salmonella in the pig production chain. We serotyped and genotyped by PFGE 174 isolates collected from breeding pigs from breeding farms, 163 collected from breeding pigs from production farms, and 325 collected from fattening pigs. Forty-seven serovars and 110 genotypes were identified. The major serovars were S Derby (263 isolates) and S Typhimurium (162 isolates). The percentage of S Derby isolates decreased slightly through the production system (44.3, 41.1 per cent and 36.5 per cent) and 79.1 per cent of the S Derby isolates were distributed in the five genotypes common to all three stages. The percentage of S Typhimurium isolates was high for slaughter pigs (40.8 per cent) and 43 of the 46 S Typhimurium genotypes were only identified at this stage. Distributions of S Derby and S Typhimurium between breeding and fattening pigs were different. S Derby was found throughout the pig production pyramid, suggesting that this serotype may be transmitted by the transfer of animals between herds. The presence of multiple S Typhimurium genotypes in fattening pigs suggests that there were many sources of contamination at this stage, with fattening pigs having higher levels of exposure and/or sensitivity to this serotype.

Porcine E. coli: virulence-associated genes, resistance genes and adhesion and probiotic activity tested by a new screening method

We established an automated screening method to characterize adhesion of Escherichia coli to intestinal porcine epithelial cells (IPEC-J2) and their probiotic activity against infection by enteropathogenic E. coli (EPEC). 104 intestinal E. coli isolates from domestic pigs were tested by PCR for the occurrence of virulence-associated genes, genes coding for resistances to antimicrobial agents and metals, and for phylogenetic origin by PCR. Adhesion rates and probiotic activity were examined for correlation with the presence of these genes. Finally, data were compared with those from 93 E. coli isolates from wild boars.

Isolates from domestic pigs carried a broad variety of all tested genes and showed great diversity in gene patterns. Adhesions varied with a maximum of 18.3 or 24.2 mean bacteria adherence per epithelial cell after 2 or 6 hours respectively. Most isolates from domestic pigs and wild boars showed low adherence, with no correlation between adhesion/probiotic activity and E. coli genes or gene clusters. The gene sfa/foc, encoding for a subunit of F1C fimbriae did show a positive correlative association with adherence and probiotic activity; however E. coli isolates from wild boars with the sfa/foc gene showed less adhesion and probiotic activity than E. coli with the sfa/foc gene isolated from domestic pigs after 6 hour incubation.

In conclusion, screening porcine E. coli for virulence associated genes genes, adhesion to intestinal epithelial cells, and probiotic activity revealed a single important adhesion factor, several probiotic candidates, and showed important differences between E. coli of domestic pigs and wild boars.

Analyses of intestinal commensal Escherichia coli strains from wild boars suggest adaptation to conventional pig production conditions

To test the hypothesis that Escherichia coli populations have adapted to conventional pig production practices, we comparatively tested intestinal commensal E. coli from wild boars versus isolates from domestic pigs by analyzing virulence-associated factors, adhesion, and metabolic activities. Virulence-associated genes typical for intestinal pathogenic E. coli (inVAGs) were sporadically detected among E. coli from wild boars except the adhesion-related gene paa and the enterotoxin-encoding gene astA. In contrast, several VAGs typical for extraintestinal pathogenic E. coli (exVAGs) were common in E. coli from wild boars. The exVAG chuA occurred more often in E. coli from wild boars compared to E. coli from domestic pigs. 23.5% of E. coli from wild boars belonged to EcoR group B2 which is higher than observed for E. coli from clinically healthy domestic pigs. Furthermore, E. coli from wild boars were more efficient in fermentation of carbohydrate sources (dulcitol, inositol, d-sucrose, d-tagatose), and adhered better to the intestinal porcine epithelial cell line IPEC-J2. In conclusion, our findings point towards an adaptation of porcine intestinal E. coli to a specific intestinal milieu caused by different animal living conditions.

Phosphorothioate DNA as an antioxidant in bacteria

Diverse bacteria contain DNA with sulfur incorporated stereo-specifically into their DNA backbone at specific sequences (phosphorothioation). We found that in vitro oxidation of phosphorothioate (PT) DNA by hydrogen peroxide (H(2)O(2)) or peracetic acid has two possible outcomes: DNA backbone cleavage or sulfur removal resulting in restoration of normal DNA backbone. The physiological relevance of this redox reaction was investigated by challenging PT DNA hosting Salmonella enterica cells using H(2)O(2). DNA phosphorothioation was found to correlate with increasing resistance to the growth inhibition by H(2)O(2). Resistance to H(2)O(2) was abolished when each of the three dnd genes, required for phosphorothioation, was inactivated. In vivo, PT DNA is more resistant to the double-strand break damage caused by H(2)O(2) than PT-free DNA. Furthermore, sulfur on the modified DNA was consumed and the DNA was converted to PT-free state when the bacteria were incubated with H(2)O(2). These findings are consistent with a hypothesis that phosphorothioation modification endows DNA with reducing chemical property, which protects the hosting bacteria against peroxide, explaining why this modification is maintained by diverse bacteria.

A novel host-specific restriction system associated with DNA backbone S-modification in Salmonella

A novel, site-specific, DNA backbone S-modification (phosphorothioation) has been discovered, but its in vivo function(s) have remained obscure. Here, we report that the enteropathogenic Salmonella enterica serovar Cerro 87, which possesses S-modified DNA, restricts DNA isolated from Escherichia coli, while protecting its own DNA by site-specific phosphorothioation. A cloned 15-kb gene cluster from S. enterica conferred both host-specific restriction and DNA S-modification on E. coli. Mutational analysis of the gene cluster proved unambiguously that the S-modification prevented host-specific restriction specified by the same gene cluster. Restriction activity required three genes in addition to at least four contiguous genes necessary for DNA S-modification. This functional overlap ensures that restriction of heterologous DNA occurs only when the host DNA is protected by phosphorothioation. Meanwhile, this novel type of host-specific restriction and modification system was identified in many diverse bacteria. As in the case of methylation-specific restriction systems, targeted inactivation of this gene cluster should facilitate genetic manipulation of these bacteria, as we demonstrate in Salmonella.

Molecular typing of Salmonella enterica serovar Sofia in Australia by pulsed-field gel electrophoresis and repetitive element PCR typing

AIMS

In this study, we used two molecular fingerprinting methods to investigate the genetic and clonal relationship shared by Australian Salmonella Sofia isolates.

METHODS AND RESULTS

A total of 84 Australian Salm. Sofia isolates from various states in Australia were typed using pulsed-field gel electrophoresis (PFGE) (XbaI and SpeI) and repetitive element PCR (REP1R-I primer). The previous problem of DNA degradation of Salm. Sofia strains was solved by modifying the lysis solution used to treat the bacterial plugs, allowing Salm. Sofia to be subtyped using PFGE. Molecular typing of isolates resulted in the generation of eight XbaI, six SpeI and five REP1 pattern profiles. Individual typing methods showed low discrimination index values (<0·5), indicating the poor discriminatory ability of the methods. However, the combination of the typing methods was able to improve the discrimination of isolates, further dividing them into 16 subtypes and raising the index value to 0·721.

CONCLUSIONS

The combination of typing methods was shown to be the best approach to fingerprint Salm. Sofia. The Australian Salm. Sofia isolates only showed limited genetic diversity and probably share a clonal relationship. A majority of the Salm. Sofia isolates were not geographically restricted with the predominant pattern subtype observed amongst the isolates from various states.

SIGNIFICANCE AND IMPACT OF THE STUDY

We have successfully devised a PFGE protocol that counteracts DNase activity of Salm. Sofia, enabling typing of this serovar.

Technical improvement to prevent DNA degradation of Leptospira spp. in pulsed field gel electrophoresis

Leptospirosis is a public health problem. Infection with pathogenic Leptospira occurs by exposure to many environments and is traditionally associated with occupational risk activities. Pulsed-field gel electrophoresis was used to investigate the epidemiological relatedness among Leptospira isolates. However, analysis by PFGE yielded inconclusive data as a result of extensive DNA degradation. This degradation can be significantly reduced by the inclusion of thiourea in the electrophoresis buffer, improving the analysis of DNA banding patterns.

Prevalence and characterization of salmonellae in commercial ground beef in the United States

Commercially produced ground beef samples (n = 4,136) were collected from seven regions of the United States over a 24-month period (July 2005 to June 2007) and analyzed for the presence of Salmonella enterica by using methods that concurrently provided total prevalence and enumerable levels. The overall prevalence of Salmonella strains was 4.2%. Enumeration showed that 94.2% were present at levels below 2 CFU/g. Regional monthly prevalences of Salmonella strains varied from 1.8% to 6.5% but were not statistically different (P > 0.05). All Salmonella isolates were serotyped and their antibiotic susceptibilities determined and analyzed by pulsed-field gel electrophoresis (PFGE). The most common serotypes identified were Salmonella enterica serotypes Montevideo, Anatum, Muenster, and Mbandaka, with these accounting for one-half of the isolates obtained. The prevalence of multidrug-resistant (MDR) Salmonella was determined to be 0.6%. The most common MDR serotypes were Salmonella enterica serotypes Dublin, Reading, and Typhimurium. MDR strains had resistance to between 2 and 10 antibiotics. There were no regional differences in prevalence of MDR Salmonella. PFGE analysis revealed that indistinguishable XbaI and AvrII restriction digest patterns (RDPs) could be observed in isolates of the same serotype found in different regions and months of sampling. The RDPs of 19 Salmonella strains were compared to RDPs in the PulseNet USA database. Thirteen were indistinguishable from existing patterns, and the number of records for each ranged from 1 to 478. These data show that Salmonella prevalence in commercial ground beef is low and suggest that attempts to identify sources contributing to Salmonella in ground beef by serotype, antibiogram, and PFGE cannot be made without additional documented evidence.

Salmonella Sofia differs from other poultry-associated Salmonella serovars with respect to cell surface hydrophobicity

Salmonella enterica is one of the most important foodborne pathogens. Salmonella enterica subsp. II 4,12:b:- (Salmonella Sofia) is commonly found in Australian poultry. It has been suggested that physicochemical properties such as surface charge and hydrophobicity may affect bacterial attachment to surfaces and their ability to persist in food systems. A possible link between hydrophobicity cell surface charge and persistence of Salmonella from the poultry system was examined. Hydrophobicity of Salmonella Sofia (n = 14), Salmonella Typhimurium (n = 6), Salmonella Infantis (n = 3), and Salmonella Virchow (n = 2) was assayed using hydrophobic interaction chromatography, bacterial adherence to hydrocarbons (BATH), using xylene or hexadecane, and the contact angle method (CAM). Cellular surface charge (CSC) of the isolates was determined using zeta potential measurements. The majority (12 of 14) of Salmonella Sofia isolates were found to be hydrophobic when assayed using BATH with xylene, except isolates S1635 and S1636, and the other serovars were found to be hydrophilic. Salmonella Sofia isolates were not significantly different (P > 0.05) from isolates of other serovars as measured by hydrophobic interaction, BATH with hexadecane, or the CAM. No significant differences (P > 0.05) in zeta potential measurements were observed between isolates. Principal component analysis using results from all four measures of hydrophobicity allowed clear differentiation between isolates of the serovar Salmonella Sofia (except S1635 and S1636) and those of other Salmonella serovars. Differences in physicochemical properties may be a contributing factor to the Salmonella Sofia serovar's ability to attach to surfaces and persist in a food system.

Antimalarial therapy selection for quinolone resistance among Escherichia coli in the absence of quinolone exposure, in tropical South America

Background

Bacterial resistance to antibiotics is thought to develop only in the presence of antibiotic pressure. Here we show evidence to suggest that fluoroquinolone resistance in Escherichia coli has developed in the absence of fluoroquinolone use.

Methods

Over 4 years, outreach clinic attendees in one moderately remote and five very remote villages in rural Guyana were surveyed for the presence of rectal carriage of ciprofloxacin-resistant Gram-negative bacilli (GNB). Drinking water was tested for the presence of resistant GNB by culture, and the presence of antibacterial agents and chloroquine by HPLC. The development of ciprofloxacin resistance in E. coli was examined after serial exposure to chloroquine. Patient and laboratory isolates of E. coli resistant to ciprofloxacin were assessed by PCR-sequencing for quinolone-resistance-determining-region (QRDR) mutations.

Results

In the very remote villages, 4.8% of patients carried ciprofloxacin-resistant E. coli with QRDR mutations despite no local availability of quinolones. However, there had been extensive local use of chloroquine, with higher prevalence of resistance seen in the villages shortly after a Plasmodium vivax epidemic (p<0.01). Antibacterial agents were not found in the drinking water, but chloroquine was demonstrated to be present. Chloroquine was found to inhibit the growth of E. coli in vitro. Replica plating demonstrated that 2-step QRDR mutations could be induced in E. coli in response to chloroquine.

Conclusions

In these remote communities, the heavy use of chloroquine to treat malaria likely selected for ciprofloxacin resistance in E. coli. This may be an important public health problem in malarious areas.

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.

DNA modification by sulfur: analysis of the sequence recognition specificity surrounding the modification sites

The Dnd (DNA degradation) phenotype, reflecting a novel DNA modification by sulfur in Streptomyces lividans 1326, was strongly aggravated when one (dndB) of the five genes (dndABCDE) controlling it was mutated. Electrophoretic banding patterns of a plasmid (pHZ209), reflecting DNA degradation, displayed a clear change from a preferential modification site in strain 1326 to more random modifications in the mutant. Fourteen randomly modifiable sites on pHZ209 were localized, and each seemed to be able to be modified only once. Residues in a region (5′-c–cGGCCgccg-3′) including a highly conserved 4-bp central core (5′-GGCC-3′) in a well-documented preferential modification site were assessed for their necessity by site-directed mutagenesis. While the central core (GGCC) was found to be stringently required in 1326 and in the mutant, ‘gccg’ flanking its right could either abolish or reduce the modification frequency only in the mutant, and two separate nucleotides to the left had no dramatic effect. The lack of essentiality of DndB for S-modification suggests that it might only be required for enhancing or stabilizing the activity of a protein complex at the required preferential modification site, or resolving secondary structures flanking the modifiable site(s), known to constitute an obstacle for efficient modification.

Multiple typing for the epidemiological study of the contamination of broilers with Salmonella from the hatchery to the slaughterhouse

Eighteen Belgian broiler flocks were followed from the hatchery to the slaughterhouse by a multiple typing approach (sero-, geno-, and phage types) for the investigation of the transmission of Salmonella and its subtypes. For 12 of the 18 flocks, there was no correlation between the serotypes found preharvest and those isolated from the feces in the transport crates and on the carcasses in the slaughterhouse. Serotypes found in the crates were usually also found on the carcasses. In 5 of the 10 flocks with Salmonella-positive broilers, complex contamination patterns with the involvement of different serotypes, genotypes, or both were revealed. In two of these flocks (flocks 8 and 9), the Salmonella Enteritidis contamination of the broilers could be traced to the hatchery. In flock 9, evidence was found for the acquisition, during rearing, of a megaplasmid in the Salmonella Enteritidis strain. In the other three positive flocks (flocks 6, 7, and 10), the environment and movable material (e.g., footwear) played a determining role in the infection and shedding pattern of the broilers. For flocks 6 and 7, reared consecutively in the same broiler house, a persistent Salmonella Hadar geno/phage type predominated in the preharvest period, while another Salmonella Hadar geno/phage type was found in the house or the environment but never in the broilers. Only for the above-mentioned five flocks were the same strains that were found preharvest also recovered from the carcasses, although these strains were not predominant on the carcasses, with the exception of one flock (flock 10). In conclusion, it can be said that most of the time, Salmonella strains that contaminate Belgian broiler carcasses do not predominate in the preharvest environment.

Genotypic characterization of Salmonella by multilocus sequence typing, pulsed-field gel electrophoresis and amplified fragment length polymorphism

Molecular typing is an important tool in surveillance and outbreak investigations of human Salmonella infections. In this study, three molecular typing methods were used to investigate the discriminatory ability, reproducibility and the genetic relationship between 110 Salmonella enterica subspecies enterica isolates. A total of 25 serotypes were investigated that had been isolated from humans or veterinary sources in Denmark between 1995 and 2001. All isolates were genotyped by multilocus sequence typing (MLST), pulsed-field gel electrophoresis (PFGE) and amplified fragment length polymorphism (AFLP). When making genetic trees, all three methods resulted in similar clustering that often corresponded with serotype, although some serotypes displayed more diversity than others. Of the three techniques, MLST was the easiest to interpret and compare between laboratories. Unfortunately the seven housekeeping genes used in this MLST scheme lacked diversity and the ability to discriminate between isolates were higher with both PFGE and AFLP. The discriminatory power of AFLP and PFGE were similar but PFGE fingerprints were both easier to reproduce, interpret and less time-consuming to analyze when compared to AFLP. PFGE is the therefore the preferred molecular typing method for surveillance and outbreak investigations, whereas AFLP is most useful for local outbreak investigations.

Application of molecular genetic methods in diagnostics and epidemiology of food-borne bacterial pathogens

Salmonella enterica, Campylobacter and Yersinia species, Shiga toxin-producing Escherichia coli (STEC), Listeria monocytogenes and Clostridium perfringens are the bacterial pathogens constituting the greatest burden of food-borne disease in Finland. Several molecular genetic methods have been applied to diagnose, discriminate and survey these bacteria. PCR, PCR-RFLP and PFGE are the most widely and successfully used. However, these methods are unable to replace conventional and internationally standardised phenotyping. Electronic database libraries of the different genomic profiles will enable continuous surveillance of infections and detection of possible infection clusters at an early stage. Furthermore, whole-genome sequence data have opened up new insights into epidemiological surveillance. Laboratory-based surveillance performed in a timely manner and exploiting adequate methods, and co-operation at local, national and international levels are among the key elements in preventing food-borne diseases. This paper reviews different applications of molecular genetic methods for investigating enteric bacterial pathogens and gives examples of the methods successfully used in diagnostics and epidemiological studies in Finland.

Subtracted restriction fingerprinting--a new typing technique using magnetic capture of tagged restriction fragments

Molecular typing of bacterial pathogens is an important issue in the epidemiological analysis of emerging infections in humans and animals. Numerous methods have been developed for and applied to a wide variety of bacteria of medical, veterinary and zoonotic importance. The present minireview provides a description of a new typing approach designated subtracted restriction fingerprinting (SRF), its use for typing of Salmonella isolates and a comparison with the most widely used typing techniques for these bacteria. SRF is based on double restriction endonuclease digestion of whole cell DNA, followed by a fill-in reaction with specifically tagged nucleotides and subtractive capture of selected restriction fragments. This results in a reduced number of fragments optimal for separation in standard agarose gels.

Detection of a Salmonella enterica serovar California strain spreading in spanish feed mills and genetic characterization with DNA microarrays

We performed an epidemiological study on Salmonella isolated from raw plant-based feed in Spanish mills. Overall, 32 different Salmonella serovars were detected. Despite its rare occurrence in humans and animals, Salmonella enterica serovar California was found to be the predominant serovar in Spanish feed mills. Different typing techniques showed that isolates of this serovar were genetically closely related, and comparative genomic hybridization using microarray technology revealed 23 S. enterica serovar Typhimurium LT2 gene clusters that are absent from serovar California.

Pulsed-field gel electrophoresis-based subtyping of DNA degradation-sensitive Salmonella enterica subsp. enterica serovar Livingstone and serovar Cerro isolates obtained from a chicken layer farm

Salmonella enterica serovar subsp. enterica Livingstone and serovar Cerro isolates from a commercial egg-producing farm, which had previously been untypeable by pulsed-field gel electrophoresis (PFGE) because of DNA degradation during the PFGE process, successfully gave banding patterns using electrophoresis buffer supplemented with 50 microM thiourea. By PFGE in the presence of thiourea, DNA degradation-sensitive S. enterica serovar Cerro isolates from the commercial egg-producing farm were found to be genetically unrelated to S. enterica serovar Cerro isolates that gave the patterns in the absence of thiourea. Forty-five of 50 (90%) S. enterica serovar Livingstone isolates from the farm showed arbitrarily designated XbaI-digested patterns X1 and X2 that were distinguished by one-band difference and had an identical BlnI-digested pattern. In one of the two layer houses in the farm, the numbers of isolates having the pattern X2 increased from 57% in 1997 to 89% in 1998, whereas virtually all the isolates obtained from the other house in the same period showed the profile X1. This suggests that strains having the pattern X2 might have an advantage to preferentially colonize in the former house.

Improving typeability of multiple bacterial species using pulsed-field gel electrophoresis and thiourea

Although pulsed-field gel electrophoresis is considered the "gold standard" technique for molecular typing, typeability may not be excellent for some bacterial species because of DNA degradation. Previous reports suggest that the addition of thiourea in the gel buffer can improved the typeability for some species. In the present study, 66 Gram-negative strains (seven species) known to be affected by DNA degradation and four control strains were evaluated by PFGE with and without the addition of 50 microg/M of thiourea to the buffer used in the electrophoresis. Macrorestriction patterns were obtained for all K. pneumoniae, S. marcescens, P. aeruginosa, and Salmonella spp., for 95.4% of E. coli, and for 50% of E. cloacae strains from the gels performed in the buffer with throurea. However, typeability was not improved for Acinetobacter spp. The range of non-typeable species for which thiourea can limit the problem of DNA degradation is considerably wider than described in previous publications.

Comparison of phenotypic traits and genetic relatedness of Salmonella enterica subspecies arizonae isolates from a colony of ridgenose rattlesnakes with osteomyelitis

Reptiles are well-known sources of human Salmonella infections; however, little is known about the ability of Salmonella to cause disease in reptiles. Thirty-seven isolates of Salmonella enterica subspecies arizonae (S. arizonae) were obtained from retrospective and prospective studies of a closed colony of ridgenose rattlesnakes (Crotalus willardi) with osteomyelitis. All isolates (N = 7) from bone lesions were of a single serotype, 56:z4,z23, and this serotype was found on only 1 occasion among 8 other serotypes isolated from 21 cloacal and intestinal samples. The remainder (N = 7) of serotype 56:z4,z23 isolates were from other extraintestinal sites, including liver, ovary, blood, and testis. S. arizonae isolates were susceptible to most antimicrobials, and plasmid profiles did not correlate with serotype or antimicrobial resistance. Isolates of the 56:z4,z23 serotype (N = 14) formed a tight cluster with 95% similarity by XbaI macrorestriction analysis. Individual isolates of serotypes, 56:z4,z23, 38:(k)-z35, and 48:i-z invaded HeLa cells but an isolate of serotype 50:r-z did not. The same individual isolates of serotype 56:z4,z23 and 48:i-z also invaded viper heart cells. The Salmonella InvA gene was detected by polymerase chain reaction (PCR) in all S. arizonae serotypes tested, including 5 serotype 56:z4,z23 isolates and individual isolates of serotypes 48:i-z and 50:r-z. A source or possible explanation for increased virulence of S. arizonae serotype 56:z4,z23 in this unique host has not been found.

A fluorescent amplified fragment length polymorphism study of Salmonella enterica serovar Sofia, the major Salmonella serovar isolated from chickens in Australia

Fluorescent amplified fragment length polymorphism (FAFLP) analysis was performed on 68 isolates of Salmonella enterica subsp. salamae serovar Sofia (S. Sofia). Fifty eight isolates were obtained over a period of approximately 15 years from a range of human, chicken industry and environmental sources throughout Australia. A further ten isolates were identified from human and poultry sources in Israel from 1972 to 1987. Analysis of FAFLP profiles for fragments between 50 to 500 base pairs in length indicated distinct clusters of isolates. All but seven isolates clustered into four groups of >90% similarity and all isolates displayed at least 70% similarity with each other. No cluster could be attributed to a particular geographical, temporal or source-of-isolation origin. It is concluded that S. Sofia is genetically variable with certain clones persisting over time but no group appears unique to Australia.