Identification of shiga toxin-producing Escherichia coli possessing insertionally inactivated Shiga toxin gene

SMRT sequencing reveals differential patterns of methylation in two O111:H- STEC isolates from a hemolytic uremic syndrome outbreak in Australia

In 1995 a severe haemolytic-uremic syndrome (HUS) outbreak in Adelaide occurred. A recent genomic analysis of Shiga toxigenic Escherichia coli (STEC) O111:H- strains 95JB1 and 95NR1 from this outbreak found that the more virulent isolate, 95NR1, harboured two additional copies of the Shiga toxin 2 (Stx2) genes encoded within prophage regions. The structure of the Stx2-converting prophages could not be fully resolved using short-read sequence data alone and it was not clear if there were other genomic differences between 95JB1 and 95NR1. In this study we have used Pacific Biosciences (PacBio) single molecule real-time (SMRT) sequencing to characterise the genome and methylome of 95JB1 and 95NR1. We completely resolved the structure of all prophages including two, tandemly inserted, Stx2-converting prophages in 95NR1 that were absent from 95JB1. Furthermore we defined all insertion sequences and found an additional IS1203 element in the chromosome of 95JB1. Our analysis of the methylome of 95NR1 and 95JB1 identified hemi-methylation of a novel motif (5′-CTGC^m6AG-3′) in more than 4000 sites in the 95NR1 genome. These sites were entirely unmethylated in the 95JB1 genome, and included at least 177 potential promoter regions that could contribute to regulatory differences between the strains. IS1203 mediated deactivation of a novel type IIG methyltransferase in 95JB1 is the likely cause of the observed differential patterns of methylation between 95NR1 and 95JB1. This study demonstrates the capability of PacBio SMRT sequencing to resolve complex prophage regions and reveal the genetic and epigenetic heterogeneity within a clonal population of bacteria.

Dynamics of insertion sequence element IS629 inactivation of verotoxin 2 genes in Escherichia coli O157:H7

There are several anecdotal reports of insertion sequence (IS) element inactivation of verotoxin genes among enterohaemorrhagic Escherichia coli of the serotype O157:H7, a pathogen causing severe gastrointestinal disease in infected humans. These insertions can be expected to drastically reduce the virulence of the bacteria. IS element inactivation has been shown to be reversible in model systems, suggesting the possibility of spontaneous restoration of virulence. In this study, traditional and high-throughput sequencing was used to characterise three patterns of IS629 inactivation of verotoxin 2 genes in EHEC O157:H7, caused by insertion or insertion followed by partial deletion. At least one of the patterns of inactivation appears to have persisted several years among cattle O157:H7, indicating it has no major effect on fitness in the animal reservoir. Digital PCR was used to directly quantify the reversal rates of the insertional inactivation of a selected isolate under laboratory conditions. Inserts were found to be absent from in the order of 1/105 of individual genomes, with significantly higher loss frequencies observed in cultures under nutrient-poor conditions. We conclude that strains with this type of inactivation found in food or animal samples should be considered a threat to human health, and may pose a challenge for PCR-based detection methods.

stx2vhaIs the Dominant Genotype of Shiga Toxin-ProducingEscherichia coliO157:H7 Isolated from Patients and Domestic Animals in Three Regions of China

Shiga toxin-producing Escherichia coli(STEC) O157: H7 strains were isolated from domestic animals and patients from Xuzhou City, Jiangsu Province, China and the bordering Anhui and Henan Provinces and were examined for the stx genotype. Of 390 strains, 277 were identified as genotype stx2vha ; 41, stx2 ; 51, stx2-stx1 ; 1, stx2-stx2vha-stx1 ; 5, stx2-stx2vha ; and 15 were un-typeable. Of the 277 stx2vha-bearing isolates, 116 were isolated from goats; 42, cattle; 38, hens, and 35 from pigs. The study shows stx2vha is the dominant genotype and goats are an important reservoir.

The non-O157 shiga-toxigenic (verocytotoxigenic) Escherichia coli; under-rated pathogens

Following a brief review of the ecology of Escherichia coli in general, the role of Shiga-Toxigenic (Verocytotoxigenic) E. coli (STEC) as pathogens is addressed. While STEC belonging to the serogroup O157 have been extensively studied and shown to be involved in many cases and outbreaks of human disease, the importance of STEC belonging to other serogroups has not been recognized as much. This review addresses the problems associated with these pathogens, demonstrating that increasing the awareness of them is a major part of the problem. This review then demonstrates how widespread isolations especially from food animals and human disease have been, discussing in particular STEC belonging to serogroups O8, O26, O103, O111, O113 and O128. The animal host-specificity of these STEC is also reviewed. In conclusion some methods of improving isolation of these pathogens is addressed.

Escherichia coli O157:H7 in a cohort of weaned, preconditioned range beef calves

Escherichia coli O157:H7 (EC O157) is an important cause of foodborne disease. Cattle are reservoirs for the bacteria and are implicated in transmission to humans. Prevalence data in prefeedlot calves are limited. With the use of sensitive methods, a cohort of weaned beef calves (n = 408) was sampled before and after preconditioning to estimate fecal point prevalence and describe changes in EC O157 fecal shedding. EC O157 isolates were confirmed and characterized by PCR and pulsed-field gel electrophoresis. Calves from 29 cow-calf farms were commingled at three preconditioning sites and placed on a transition ration containing oxytetracycline (200 g/ton) for 45 days. Initial animal-level fecal point prevalence was 2.5% (95% confidence interval, 1 to 5) with a herd-level prevalence of 17.2% (95% confidence interval, 6 to 36). Point prevalence following the preconditioning feeding period was 0%. An unexpected finding in our study was EC O157 isolates that were Shiga toxin-deficient. Pulsed-field gel electrophoresis subtypes of EC O157 were unique in epidemiologically unlinked herds, except one herd that had two unique subtypes. We expected, but observed, neither increased fecal shedding in the cohort nor horizontal transmission of unique EC O157 subtypes. The absence of fecal shedding following the 45-day feeding period might be attributable to seasonal influences, inhibitory concentrations of oxytetracycline in the transition ration, or transient colonization that ended before sampling. EC O157 is apparently widely dispersed at low prevalence in U.S. prefeedlot, weaned calves.