Correlation between geographic distance and genetic similarity in an international collection of bovine faecal Escherichia coli O157:H7 isolates

Phylogeographic Analysis Reveals Multiple International transmission Events Have Driven the Global Emergence of Escherichia coli O157:H7

BACKGROUND

Shiga toxin-producing Escherchia coli (STEC) O157:H7 is a zoonotic pathogen that causes numerous food and waterborne disease outbreaks. It is globally distributed, but its origin and the temporal sequence of its geographical spread are unknown.

METHODS

We analyzed whole-genome sequencing data of 757 isolates from 4 continents, and performed a pan-genome analysis to identify the core genome and, from this, extracted single-nucleotide polymorphisms. A timed phylogeographic analysis was performed on a subset of the isolates to investigate its worldwide spread.

RESULTS

The common ancestor of this set of isolates occurred around 1890 (1845-1925) and originated from the Netherlands. Phylogeographic analysis identified 34 major transmission events. The earliest were predominantly intercontinental, moving from Europe to Australia around 1937 (1909-1958), to the United States in 1941 (1921-1962), to Canada in 1960 (1943-1979), and from Australia to New Zealand in 1966 (1943-1982). This pre-dates the first reported human case of E. coli O157:H7, which was in 1975 from the United States.

CONCLUSIONS

Inter- and intra-continental transmission events have resulted in the current international distribution of E. coli O157:H7, and it is likely that these events were facilitated by animal movements (eg, Holstein Friesian cattle). These findings will inform policy on action that is crucial to reduce the further spread of E. coli O157:H7 and other (emerging) STEC strains globally.

Application of kernel smoothing to estimate the spatio-temporal variation in risk of STEC O157 in England

Identifying geographical areas with significantly higher or lower rates of infectious diseases can provide important aetiological clues to inform the development of public health policy and interventions designed to reduce morbidity. We applied kernel smoothing to estimate the spatial and spatio-temporal variation in risk of STEC O157 infection in England between 2009 and 2015, and to explore differences between the residential locations of cases reporting travel and those not reporting travel. We provide evidence that the distribution of STEC O157 infection in England is non-uniform with respect to the distribution of the at-risk population; that the spatial distribution of the three main genetic lineages infecting humans (I, II and I/II) differs significantly and that the spatio-temporal risk is highly dynamic. Our results also indicate that cases of STEC O157 reporting travel within or outside the UK are more likely to live in the south/south-east of the country, meaning that their residential location may not reflect the location of exposure that led to their infection. We suggest that the observed variation in risk reflects exposure to sources of STEC O157 that are geographically prescribed. These differences may be related to a combination of changes in the strains circulating in the ruminant reservoir, animal movements (livestock, birds or wildlife) or the behavior of individuals prior to infection. Further work to identify the importance of behaviours and exposures reported by cases relative to residential location is needed.

Comparative genomics reveals structural and functional features specific to the genome of a foodborne Escherichia coli O157:H7

Background

Escherichia coli O157:H7 (O157) has been linked to numerous foodborne disease outbreaks. The ability to rapidly sequence and analyze genomes is important for understanding epidemiology, virulence, survival, and evolution of outbreak strains. In the current study, we performed comparative genomics to determine structural and functional features of the genome of a foodborne O157 isolate NADC 6564 and infer its evolutionary relationship to other O157 strains.

Results

The chromosome of NADC 6564 contained 5466 kb compared to reference strains Sakai (5498 kb) and EDL933 (5547 kb) and shared 41 of its 43 Linear Conserved Blocks (LCB) with the reference strains. However, 18 of 41 LCB had inverse orientation in NADC 6564 compared to the reference strains. NADC 6564 shared 18 of 19 bacteriophages with reference strains except that the chromosomal positioning of some of the phages differed among these strains. The additional phage (P19) of NADC 6564 was located on a 39-kb insertion element (IE) encoding several hypothetical proteins, an integrase, transposases, transcriptional regulators, an adhesin, and a phosphoethanolamine transferase (PEA). The complete homologs of the 39-kb IE were found in E. coli PCN061 of porcine origin. The IE-encoded PEA showed low homology (32–33%) to four other PEA in NADC 6564 and PEA linked to mobilizable colistin resistance in E. coli but was highly homologous (95%) to a PEA of uropathogenic, avian pathogenic, and enteroaggregative E. coli. NADC 6564 showed slightly higher minimum inhibitory concentration of colistin compared to the reference strains. The 39-kb IE also contained dndBCDE and dptFGH operons encoding DNA S-modification and a restriction pathway, linked to oxidative stress tolerance and self-defense against foreign DNA, respectively. Evolutionary tree analysis grouped NADC 6564 with lineage I O157 strains.

Conclusions

These results indicated that differential phage counts and different chromosomal positioning of many bacteriophages and genomic islands might have resulted in recombination events causing altered chromosomal organization in NADC 6564. Evolutionary analysis grouped NADC 6564 with lineage I strains and suggested its earlier divergence from these strains. The ability to perform S-DNA modification might affect tolerance of NADC 6564 to various stressors.

Electronic supplementary material

The online version of this article (10.1186/s12864-019-5568-6) contains supplementary material, which is available to authorized users.

Evidence for an effect of landscape connectivity on Borrelia burgdorferi sensu stricto dispersion in a zone of range expansion

In North America, different strains of the Lyme disease-causing bacterium Borrelia burgdorferi sensu stricto cluster into phylogenetic groups that are associated with different levels of pathogenicity and, for some, specific rodent reservoir hosts. Here we explore whether landscape connectivity, by impacting host dispersal, influences B. burgdorferi s.s. spread patterns. This question is central to modelling spatial patterns of the spread of Lyme disease risk in the zone of northward range-expansion of B. burgdorferi s.s. in southeastern Canada where the study was conducted. We used multi-locus sequence typing (MLST) to characterise B. burgdorferi s.s. in positive ticks collected at 13 sites in southern Quebec, Canada during the early stages of B. burgdorferi s.s. invasion. We used mixed effects logistic regression to investigate whether landscape connectivity (probability of connectivity; PC) affected the probability that samples collected at different sites were of the same strain (MLST sequence type: ST). PC was calculated from a habitat map based on high spatial resolution (15 m) Landsat 8 imagery to identify woodland habitat that are preferred by rodent hosts of B. burgdorferi s.s. There was a significant positive association between the likelihood that two samples were of the same ST and PC, when PC values were grouped into three categories of low, medium and high. When analysing data for individual STs, samples at different sites were significantly more likely to be the same when PC was higher for the rodent-associated ST1. These findings support the hypothesis that dispersion trajectories of B. burgdorferi s.s. in general, and some rodent-associated strains in particular, are at least partly determined by landscape connectivity. This may suggest that dispersion of B. burgdorferi s.s. is more common by terrestrial mammal hosts (which would likely disperse according to landscape connectivity) than by birds, the dispersal of which is likely less constrained by landscape. This study suggests that accounting for landscape connectivity may improve model-based predictions of spatial spread patterns of B. burgdorferi s.s. The findings are consistent with possible past dispersal patterns of B. burgdorferi s.s. as determined by phylogeographic studies.

Whole Genome Sequencing demonstrates that Geographic Variation of Escherichia coli O157 Genotypes Dominates Host Association

Genetic variation in an infectious disease pathogen can be driven by ecological niche dissimilarities arising from different host species and different geographical locations. Whole genome sequencing was used to compare E. coli O157 isolates from host reservoirs (cattle and sheep) from Scotland and to compare genetic variation of isolates (human, animal, environmental/food) obtained from Scotland, New Zealand, Netherlands, Canada and the USA. Nei’s genetic distance calculated from core genome single nucleotide polymorphisms (SNPs) demonstrated that the animal isolates were from the same population. Investigation of the Shiga toxin bacteriophage and their insertion sites (SBI typing) revealed that cattle and sheep isolates had statistically indistinguishable rarefaction profiles, diversity and genotypes. In contrast, isolates from different countries exhibited significant differences in Nei’s genetic distance and SBI typing. Hence, after successful international transmission, which has occurred on multiple occasions, local genetic variation occurs, resulting in a global patchwork of continental and trans-continental phylogeographic clades. These findings are important for three reasons: first, understanding transmission and evolution of infectious diseases associated with multiple host reservoirs and multi-geographic locations; second, highlighting the relevance of the sheep reservoir when considering farm based interventions; and third, improving our understanding of why human disease incidence varies across the world.

Disinfectant and antibiotic susceptibility profiles of Escherichia coli O157:H7 strains from cattle carcasses, feces, and hides and ground beef from the United States

The disinfectant and antibiotic susceptibility profiles of 344 Escherichia coli O157:H7 strains from cattle carcasses, feces, and hides and ground beef from the United States were determined. A low prevalence of antibiotic resistance was observed (14%). The highest prevalences of resistance were to sulfisoxazole (10.5%), tetracycline (9.9%), streptomycin (7%), and chloramphenicol (4.9%). Four strains were resistant to eight antibiotics (two strains from ground beef and one strain each from hide and preevisceration carcass swabs of cull cattle at harvest). Pulsed-field gel electrophoresis analysis of the E. coli O157:H7 strains revealed two major groups (designated 1 and 2) composed of 17 and 20 clusters, respectively. Clusters 1A, 1B, 1C, and 1G.1 were associated with multidrug-resistant strains. There was no observed correlation between disinfectant resistance and antibiotic resistance. Sixty-nine (20%) of the 344 strains were resistant to chlorhexidine or benzalkonium chloride or the MICs of benzyldimethyldodecylammonium chloride were elevated. Inducible resistance was observed at elevated concentrations of antibiotics (1.4%) and disinfectants (6.1%). The highest rate of disinfectant inducible resistance was to OdoBan, quaternary ammonium chlorides, and the surface disinfectants F25, FS512, and MG, which are used in dairies, restaurants, and food processing plants. High MICs (1,024 to 4,096 m g/ml) of acetic, lactic, and citric acids were found. The decreasing order of acid potency based on molar MICs (MICs(molar)) was acetic, citric, and lactic acid. The correlation of the concentration of dissociated organic acids and MICs(molar) strongly suggests that the observed inhibition of E. coli O157:H7 was primarily due to dissociated forms of the acids.

Polymorphic Amplified Typing Sequences and Pulsed-Field Gel Electrophoresis Yield Comparable Results in the Strain Typing of a Diverse Set of Bovine Escherichia coli O157:H7 Isolates

Polymorphic amplified typing sequences (PATS), a PCR-based Escherichia coli O157:H7 (O157) strain typing system, targets insertions-deletions and single nucleotide polymorphisms at XbaI and AvrII restriction enzyme sites, respectively, and the virulence genes (stx1, stx2, eae, hlyA) in the O157 genome. In this study, the ability of PATS to discriminate O157 isolates associated with cattle was evaluated. An in-depth comparison of 25 bovine O157 isolates, from different geographic locations across Northwest United States, showed that about 85% of these isolates shared the same dendogram clade by PATS and pulsed-field gel electrophoresis (PFGE), irrespective of the restriction enzyme sites targeted. The Pearson's correlation coefficient, r, calculated at about 0.4, 0.3, and 0.4 for XbaI-based, AvrII-based and combined-enzymes PATS and PFGE similarities, respectively, indicating that these profiles shared a good but not high correlation, an expected inference given that the two techniques discriminate differently. Isolates that grouped differently were better matched to their locations using PATS. Overall, PATS discriminated the bovine O157 isolates without interpretive biases or sophisticated analytical software, and effectively complemented while not duplicating PFGE. With its quick turnaround time, PATS has excellent potential as a convenient tool for early epidemiological or food safety investigations, enabling rapid notification/implementation of quarantine measures.

Phylogeny of Shiga toxin-producing Escherichia coli O157 isolated from cattle and clinically ill humans

Cattle are a major reservoir for Shiga toxin-producing Escherichia coli O157 (STEC O157) and harbor multiple genetic subtypes that do not all associate with human disease. STEC O157 evolved from an E. coli O55:H7 progenitor; however, a lack of genome sequence has hindered investigations on the divergence of human- and/or cattle-associated subtypes. Our goals were to 1) identify nucleotide polymorphisms for STEC O157 genetic subtype detection, 2) determine the phylogeny of STEC O157 genetic subtypes using polymorphism-derived genotypes and a phage insertion typing system, and 3) compare polymorphism-derived genotypes identified in this study with pulsed field gel electrophoresis (PFGE), the current gold standard for evaluating STEC O157 diversity. Using 762 nucleotide polymorphisms that were originally identified through whole-genome sequencing of 189 STEC O157 human- and cattle-isolated strains, we genotyped a collection of 426 STEC O157 strains. Concatenated polymorphism alleles defined 175 genotypes that were tagged by a minimal set of 138 polymorphisms. Eight major lineages of STEC O157 were identified, of which cattle are a reservoir for seven. Two lineages regularly harbored by cattle accounted for the majority of human disease in this study, whereas another was rarely represented in humans and may have evolved toward reduced human virulence. Notably, cattle are not a known reservoir for E. coli O55:H7 or STEC O157:H⁻ (the first lineage to diverge within the STEC O157 serogroup), which both cause human disease. This result calls into question how cattle may have originally acquired STEC O157. The polymorphism-derived genotypes identified in this study did not surpass PFGE diversity assessed by BlnI and XbaI digestions in a subset of 93 strains. However, our results show that they are highly effective in assessing the evolutionary relatedness of epidemiologically unrelated STEC O157 genetic subtypes, including those associated with the cattle reservoir and human disease.

Diversity of multidrug-resistant salmonella enterica strains associated with cattle at harvest in the United States

The prevalence and diversity of multidrug-resistant (MDR) Salmonella enterica strains associated with cattle at harvest in the United States were examined. Hides and carcasses of cattle were sampled at processing plants (n = 6) located in four geographically distant regions from July 2005 to April 2006. The mean prevalences of Salmonella on hides, preevisceration carcasses (immediately after hide removal), and postintervention carcasses (in the chiller and after the full complement of interventions) were 89.6%, 50.2%, and 0.8%, respectively. The values for MDR Salmonella enterica strains (defined as those resistant to two or more antimicrobials) as percentages of Salmonella prevalence were 16.7% (95% confidence interval [CI], 8.3 to 25.1%; median percent prevalence, 6.9%), 11.7% (95% CI, 4.4 to 19.0%; median, 4.8%), and 0.33% (95% CI, -0.3 to 0.70%; median, 0%), respectively. In this study, 16,218 Salmonella hide and carcass isolates were screened for antimicrobial resistance. Of these, 978 (6.0%) unique MDR S. enterica isolates were identified and serotyped and their XbaI pulsed-field gel electrophoresis (PFGE) profiles determined. The predominant MDR S. enterica serotypes observed were Newport (53.1%), Typhimurium (16.6%), and Uganda (10.9%). Differences in MDR S. enterica prevalence were detected, and PFGE analysis revealed both epidemic clusters (profiles found in plants in multiple regions/seasons) and endemic clusters (profiles observed in plants in limited regions/seasons) within several of the MDR serotypes examined. Despite these differences, multiple-hurdle processing interventions employed at all plants were found to be quite effective and decreased Salmonella carcass contamination by 98.4% (95% CI, 97.6 to 99.7%).

Escherichia coli O157:H7: animal reservoir and sources of human infection

This review surveys the literature on carriage and transmission of enterohemorrhagic Escherichia coli (EHEC) O157:H7 in the context of virulence factors and sampling/culture technique. EHEC of the O157:H7 serotype are worldwide zoonotic pathogens responsible for the majority of severe cases of human EHEC disease. EHEC O157:H7 strains are carried primarily by healthy cattle and other ruminants, but most of the bovine strains are not transmitted to people, and do not exhibit virulence factors associated with human disease. Prevalence of EHEC O157:H7 is probably underestimated. Carriage of EHEC O157:H7 by individual animals is typically short-lived, but pen and farm prevalence of specific isolates may extend for months or years and some carriers, designated as supershedders, may harbor high intestinal numbers of the pathogen for extended periods. The prevalence of EHEC O157:H7 in cattle peaks in the summer and is higher in postweaned calves and heifers than in younger and older animals. Virulent strains of EHEC O157:H7 are rarely harbored by pigs or chickens, but are found in turkeys. The bacteria rarely occur in wildlife with the exception of deer and are only sporadically carried by domestic animals and synanthropic rodents and birds. EHEC O157:H7 occur in amphibian, fish, and invertebrate carriers, and can colonize plant surfaces and tissues via attachment mechanisms different from those mediating intestinal attachment. Strains of EHEC O157:H7 exhibit high genetic variability but typically a small number of genetic types predominate in groups of cattle and a farm environment. Transmission to people occurs primarily via ingestion of inadequately processed contaminated food or water and less frequently through contact with manure, animals, or infected people.

Diverse genetic markers concordantly identify bovine origin Escherichia coli O157 genotypes underrepresented in human disease

Genetic markers previously reported to occur at significantly different frequencies in isolates of Escherichia coli O157:H7 obtained from cattle and from clinically affected humans concordantly delineate at least five genetic groups. Isolates in three of these groups consistently carry one or more markers rarely found among clinical isolates.

Perceptions, practices, and consequences associated with foodborne pathogens and the feeding of raw meat to dogs

This study explored the impact of feeding raw meat to dogs on the fecal prevalence of several enteric bacterial zoonotic pathogens. Campylobacter jejuni was isolated from 1/42 (2.6%) raw meat-fed dogs. Salmonella enterica was isolated from 2/40 (5%) of the raw meat feeds, 6/42 (14%) raw meat-fed dog feces, none of the dogs that did not receive raw meat (P = 0.001), 4/38 (10.5%) of the vacuum cleaner waste samples from households where raw meat was fed, and 2/44 (4.5%) of vacuum cleaner waste samples from households where raw meat was not fed to dogs (P = 0.41). Responses to a questionnaire probing practices and beliefs regarding raw meat feeding that was administered to dog owners demonstrated that dog owners may either not be aware or refuse to acknowledge the risks associated with raw meat-feeding; thus, they may neglect to conduct adequate intervention strategies to prevent zoonoses among themselves and their families.

Phylogenetic classification of Escherichia coli O157:H7 strains of human and bovine origin using a novel set of nucleotide polymorphisms

Novel SNPs from human and bovine O157:H7 E. coli isolates are mapped, revealing that the majority of human disease is caused by a bovine subset of this strain.

Background

Cattle are a reservoir of Shiga toxin-producing Escherichia coli O157:H7 (STEC O157), and are known to harbor subtypes not typically found in clinically ill humans. Consequently, nucleotide polymorphisms previously discovered via strains originating from human outbreaks may be restricted in their ability to distinguish STEC O157 genetic subtypes present in cattle. The objectives of this study were firstly to identify nucleotide polymorphisms in a diverse sampling of human and bovine STEC O157 strains, secondly to classify strains of either bovine or human origin by polymorphism-derived genotypes, and finally to compare the genotype diversity with pulsed-field gel electrophoresis (PFGE), a method currently used for assessing STEC O157 diversity.

Results

High-throughput 454 sequencing of pooled STEC O157 strain DNAs from human clinical cases (n = 91) and cattle (n = 102) identified 16,218 putative polymorphisms. From those, 178 were selected primarily within genomic regions conserved across E. coli serotypes and genotyped in 261 STEC O157 strains. Forty-two unique genotypes were observed that are tagged by a minimal set of 32 polymorphisms. Phylogenetic trees of the genotypes are divided into clades that represent strains of cattle origin, or cattle and human origin. Although PFGE diversity surpassed genotype diversity overall, ten PFGE patterns each occurred with multiple strains having different genotypes.

Conclusions

Deep sequencing of pooled STEC O157 DNAs proved highly effective in polymorphism discovery. A polymorphism set has been identified that characterizes genetic diversity within STEC O157 strains of bovine origin, and a subset observed in human strains. The set may complement current techniques used to classify strains implicated in disease outbreaks.

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.

Investigation of public health issues by regional field disease investigation units

The conventional means of delivering animal health services to agricultural animal producers (private veterinary practitioners and state animal disease diagnostic laboratories) leave a gap where important regional disease problems are inefficiently addressed. This gap was successfully targeted by Dr. Clive Gay in the development of the Field Disease Investigation Unit (FDIU) for the northwestern region of the United States. The FDIU has also successfully targeted several zoonotic public health concerns and its success demonstrates the existence of a similar gap in the investigation and control of important public health issues including disseminated Salmonella clones and emergence of antimicrobial resistance.

Super-shedding and the link between human infection and livestock carriage of Escherichia coli O157

Cattle that excrete more Escherichia coli O157 than others are known as super-shedders. Super-shedding has important consequences for the epidemiology of E. coli O157 in cattle--its main reservoir--and for the risk of human infection, particularly owing to environmental exposure. Ultimately, control measures targeted at super-shedders may prove to be highly effective. We currently have only a limited understanding of both the nature and the determinants of super-shedding. However, super-shedding has been observed to be associated with colonization at the terminal rectum and might also occur more often with certain pathogen phage types. More generally, epidemiological evidence suggests that super-shedding might be important in other bacterial and viral infections.

Enhanced subtyping scheme for Salmonella enteritidis

To improve pulsed-field gel electrophoresis–based strain discrimination of 76 Salmonella Enteritidis strains, we evaluated 6 macro-restriction endonucleases, separately and in various combinations. One 3-enzyme subset, SfiI/PacI/NotI, was highly discriminatory. Five different indices, including the Simpson diversity index, supported this 3-enzyme combination for improved differentiation of S. Enteritidis.

Incidence and tracking of Escherichia coli O157:H7 in a major produce production region in California

Fresh vegetables have become associated with outbreaks caused by Escherichia coli O157:H7 (EcO157). Between 1995-2006, 22 produce outbreaks were documented in the United States, with nearly half traced to lettuce or spinach grown in California. Outbreaks between 2002 and 2006 induced investigations of possible sources of pre-harvest contamination on implicated farms in the Salinas and San Juan valleys of California, and a survey of the Salinas watershed. EcO157 was isolated at least once from 15 of 22 different watershed sites over a 19 month period. The incidence of EcO157 increased significantly when heavy rain caused an increased flow rate in the rivers. Approximately 1000 EcO157 isolates obtained from cultures of>100 individual samples were typed using Multi-Locus Variable-number-tandem-repeat Analysis (MLVA) to assist in identifying potential fate and transport of EcO157 in this region. A subset of these environmental isolates were typed by Pulse Field Gel Electrophoresis (PFGE) in order to make comparisons with human clinical isolates associated with outbreak and sporadic illness. Recurrence of identical and closely related EcO157 strains from specific locations in the Salinas and San Juan valleys suggests that transport of the pathogen is usually restricted. In a preliminary study, EcO157 was detected in water at multiple locations in a low-flow creek only within 135 meters of a point source. However, possible transport up to 32 km was detected during periods of higher water flow associated with flooding. During the 2006 baby spinach outbreak investigation, transport was also detected where water was unlikely to be involved. These results indicate that contamination of the environment is a dynamic process involving multiple sources and methods of transport. Intensive studies of the sources, incidence, fate and transport of EcO157 near produce production are required to determine the mechanisms of pre-harvest contamination and potential risks for human illness.

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.

Selection for functional diversity drives accumulation of point mutations in Dr adhesins of Escherichia coli

Immune escape is considered to be the driving force behind structural variability of major antigens on the surface of bacterial pathogens, such as fimbriae. In the Dr family of Escherichia coli adhesins, structural and adhesive functions are carried out by the same subunit. Dr adhesins have been shown to bind decay-accelerating factor (DAF), collagen IV, and carcinoembryonic antigen-related cell adhesion molecules (CEACAMs). We show that genes encoding Dr adhesins from 100 E. coli strains form eight structural groups with a high level of amino acid sequence diversity between them. However, genes comprising each group differ from each other by only a small number of point mutations. Out of 66 polymorphisms identified within the groups, only three were synonymous mutations, indicating strong positive selection for amino acid replacements. Functional analysis of intragroup variants comprising the Dr haemagglutinin (DraE) group revealed that the point mutations result in distinctly different binding phenotypes, with a tendency of increased affinity to DAF, decreased sensitivity of DAF binding to inhibition by chloramphenicol, and loss of binding capability to collagen, CEACAM3 and CEACAM6. Thus, variability by point mutation of major antigenic proteins on the bacterial surface can be a signature of selection for functional modification.

Clonal dissemination of Escherichia coli O157:H7 subtypes among dairy farms in northeast Ohio

To ascertain the extent to which indistinguishable strains of Escherichia coli O157:H7 are shared between farms, molecular characterization was performed on E. coli O157:H7 isolates recovered during a longitudinal study of 20 dairy farms in northeast Ohio. Of the 20 dairy farms sampled, 16 were located in a primary area and 4 were located in two other distant geographical areas. A total of 92 E. coli O157:H7 isolates obtained from bovine fecal samples, water trough sediment samples, free-stall bedding, and wild-bird excreta samples were characterized. Fifty genetic subtypes were observed among the isolates using XbaI and BlnI restriction endonucleases. Most restriction endonuclease digestion profiles (REDPs) were spatially and temporally clustered. However, four REDPs from multiple sources were found to be indistinguishable by pulsed-field gel electrophoresis between four pairs of farms. The geographical distance between farms which shared an indistinguishable E. coli O157:H7 REDP ranged from 9 to 50 km, and the on-farm sources sharing indistinguishable REDPs included cattle and wild bird feces and free-stall bedding. Within the study population, E. coli O157:H7 REDP subtypes were disseminated with considerable frequency among farms in close geographic proximity, and nonbovine sources may contribute to the transmission of this organism between farms.

Ecology of Escherichia coli O157:H7 in Commercial Dairies in Southern Alberta

Shedding of Escherichia coli O157:H7 was monitored monthly over a 1-yr period by collecting pooled fecal pats (FECAL) and manila ropes orally accessed for 4 h (ROPE) from multiple pens of cattle in 5 commercial dairies in southern Alberta, Canada. Using immunomagnetic separation, E. coli O157:H7 was isolated from cows on 4 of the dairies and from 13.5% of FECAL and 1.1% of ROPE samples. Pulsed-field gel electrophoresis of XbaI- and SpeI-digested bacterial DNA of the 65 isolates produced 23 unique restriction endonuclease digestion patterns, although 92% of the isolates belonged to 3 restriction endonuclease digestion pattern clusters sharing a minimum 90% homology. Collection of positive isolates was 15 times more likely from June through September. Across dairies, peak somatic cell count occurred in July, August, September, and November. The likelihood of positive isolates was 2.6 times higher in calves and heifers compared with mature cows. This study indicates that ROPE would be of little value for the detection of E. coli O157:H7 in dairy herds unless oral contact with ROPE could be increased in mature animals. Additionally, mitigation strategies for E. coli O157:H7 should be targeted to the months of July, August, and September and toward immature animals for maximum impact. All farms displayed unique combinations of seasonality of shedding and diversity of E. coli O157:H7 subtypes. The fact that seasonal prevalence of E. coli O157:H7 largely coincided with peak somatic cell count within climatically controlled dairy barns suggests that similar environmental factors may be enhancing fecal shedding E. coli O157:H7 and the incidence of mastitis.

Molecular subtyping for Escherichia coli O157: H7 isolated in Taiwan

Enterohaemorrhagic Escherichia coli O157: H7 is an important pathogen these days. Outbreaks of its infection have been reported all over the world, in Australia, Canada, Japan, the United States, south Africa, and various countries in Europe. In the summer of 2001, the first clinical infection by E. coli O157: H7 was identified in Taiwan. In this study, the standard procedures for molecular subtyping were applied to several strains collected in Taiwan as well as from elsewhere. The two molecular subtyping methods we used are pulsed-field gel electrophoresis (PFGE) and amplified fragment length polymorphism (AFLP). The isolates from the U.S.A., Canada, Japan, and Taiwan each showed a unique molecular fingerprinting pattern. The environmental strains isolated in Taiwan showed closer relationships with each other, and their similarity was in the range of 75-85%. The first clinical strain isolated in Taiwan in 2001 was similar to the strains from North America but not closely related to the Taiwanese environmental strains. Our surveys showed that some local E. coli O157: H7 strains did exist in Taiwan, but there had been only one official case report of the infection by local E. coli O157: H7. The eating habits of the people and the geographic distribution of the pathogen are considered crucial risk factors in Taiwan. The establishment of a database of our own and joining the global network database are important tasks if we want to control such agricultural and food-borne pathogens, and reduce the number of victims and amount sufferings, as well as the economic losses due to the infection.

Fluctuations in the occurrence of Escherichia coli O157:H7 on a Norwegian farm*

AIM

To describe the distribution of Escherichia coli O157:H7 on a sporadically positive dairy farm and on possible contact farms over a one-year period.

METHODS AND RESULTS

Environmental and faecal samples from all animals at the farm, and faecal samples from animals at contact farms were analysed for E. coli O157:H7 by immunomagnetic separation methods or VIDAS. Confirmed isolates were tested for cytotoxicity in the Vero cell assay and typed by PFGE. Escherichia coli O157:H7 (stx2 and eae) of the same PFGE type were isolated from cattle, sheep, hens and environmental samples at variable levels during summer and fall 2002, but were not detected in 2003.

CONCLUSIONS

Escherichia coli O157:H7 had a widespread distribution on the farm investigated, but the original source of contamination could not be identified. The occurrence of this bacterium on the farm did not result in any detectable increase in gastrointestinal disease in the associated population.

SIGNIFICANCE AND IMPACT OF THE STUDY

Despite a low endemic level of E. coli O157:H7 in the Norwegian cattle population, the growth and spread of this potentially important bacterium may occur.

Spatial epidemiology and natural population structure of Campylobacter jejuni colonizing a farmland ecosystem

Recent progress in determining the population structure of Campylobacter jejuni, and discerning associations between genotypes and specific niches, has emphasized the shortfall in our understanding of the ecology and epidemiology of this bacterium. We examined the natural structure of the C. jejuni community associated with cattle farmland in the UK by structured spatiotemporal sampling of habitats, including livestock and wild animal faeces, environmental water and soil, over a 10-week period within a 100 km2 area. A total of 172 isolates were characterized using multilocus sequence typing into 65 sequence types (STs). Isolates from cattle faeces were significantly over-represented in the ST-61 complex, whereas isolates from wildlife faeces and water were more likely to belong to the ST-45 complex and a number of unusual STs, many of which were first encountered during this study. Sampling within a narrow spatiotemporal window permitted the application of novel statistical methods exploring the relationship between the genetic relatedness and spatial separation of isolates. This approach showed that isolates from the same sampling squares and squares separated by <1.0 km were genetically more similar than isolates separated by greater distances. Our study demonstrates the potential of multilocus sequence typing combined with spatial modelling in exploring natural transmission pathways for C. jejuni.

The Shiga toxin-producing Escherichia coli, their ruminant hosts, and potential on-farm interventions: a review

The emergence of Shiga toxin-producing Escherichia coli serotype O157:H7 as a major human pathogen over the last 2 decades has focused attention on this organism’s ruminant hosts. Despite implementation of conventional control methods, people continue to become seriously ill from contaminated meat or other food products, manure-contaminated drinking and recreational water, and direct contact with ruminants. E. coli O157:H7 can cause life-threatening disease, and is a particular threat to children, through acute and chronic kidney damage. Compared with other food-borne bacteria, E. coli O157:H7 has a remarkably low infectious dose and is environmentally robust. Cattle are largely unaffected by this organism and have been identified as the major source of E. coli O157:H7 entering the human food chain. Other Shiga toxin-producing E. coli can be pathogenic to humans and there is increasing evidence that their significance has been underestimated. Governments around the world have acted to tighten food safety regulations, and to investigate animal sources and on-farm control of this and related organisms. Potential intervention strategies on-farm include: feed and water hygiene, altered feeding regimes, specific E. coli vaccines, antibacterials, antibiotics, probiotics, and biological agents or products such as bacteriophages, bacteriocins, or colicins.

Human Escherichia coli O157:H7 genetic marker in isolates of bovine origin

The antiterminator Q gene of bacteriophage 933W (Q₉₃₃) was identified upstream of the stx₂ gene in 90% of human disease–origin Escherichia coli O157:H7 isolates and in 44.5% of bovine isolates. Shiga toxin production was higher in Q₉₃₃-positive isolates than Q₉₃₃-negative isolates. This genetic marker may provide a useful molecular tool for epidemiologic studies.