Public health value of next-generation DNA sequencing of enterohemorrhagic Escherichia coli isolates from an outbreak.

In 2009, an outbreak of enterohemorrhagic Escherichia coli (EHEC) on an open farm infected 93 persons, and approximately 22% of these individuals developed hemolytic-uremic syndrome (HUS). Genome sequencing was used to investigate outbreak-derived animal and human EHEC isolates. Phylogeny based on the whole-genome sequence was used to place outbreak isolates in the context of the overall E. coli species and the O157:H7 sequence type 11 (ST11) subgroup. Four informative single nucleotide polymorphisms (SNPs) were identified and used to design an assay to type 122 other outbreak isolates. The SNP phylogeny demonstrated that the outbreak strain was from a lineage distinct from previously reported O157:H7 ST11 EHEC and was not a member of the hypervirulent clade 8. The strain harbored determinants for two Stx2 verotoxins and other putative virulence factors. When linked to the epidemiological information, the sequence data indicate that gross contamination of a single outbreak strain occurred across the farm prior to the first clinical report of HUS. The most likely explanation for these results is that a single successful strain of EHEC spread from a single introduction through the farm by clonal expansion and that contamination of the environment (including the possible colonization of several animals) led ultimately to human cases.

Major uropathogenic Escherichia coli strain isolated in the northwest of England identified by multilocus sequence typing.

A total of 88 uropathogenic Escherichia coli isolates, including 68 isolates from urine and 20 isolates from blood, were characterized by multilocus sequence typing (MLST). MLST has identified an important genetic lineage of E. coli, designated sequence type 131 (ST-131), represented by 52 of these isolates, 51 of which were resistant to extended-spectrum cephalosporins. ST-131 appears to be a drug-resistant uropathogenic strain of E. coli responsible for causing urinary tract infections and bacteremia and is widely disseminated among both community and hospital patients from different geographical areas in the northwest of England. Application of MLST has helped to define the population biology which may underpin the epidemiology of pathogenic E. coli strains. The portability of MLST allows the accurate monitoring of this antibiotic-resistant uropathogenic strain of E. coli and will enhance surveillance for this important group of organisms.

UK epidemic Escherichia coli strains A-E, with CTX-M-15 beta-lactamase, all belong to the international O25:H4-ST131 clone.

OBJECTIVES: Uropathogenic and invasive Escherichia coli O25:H4-ST131 isolates producing CTX-M-15 extended-spectrum beta-lactamase (ESBL) enzymes have recently been shown to be disseminated across the globe. In the UK, many CTX-M-15 ESBL-producing E. coli strains have been previously defined as belonging to the epidemic strains A-E, as determined by PFGE. The present study was carried out to define the relationship between these two groups of pathogenic E. coli. METHODS: Multilocus sequence typing and PFGE were used for molecular characterization of a collection of 61 ESBL-producing E. coli isolates from across the UK. RESULTS: Strains A to E all belonged to the ST131 clone, further underscoring the epidemiological importance of this lineage. CONCLUSIONS: The future spread of the ST131 clone, and its UK variants, should be monitored closely and the pathogenic mechanisms explaining their success should be investigated.

Genotyping of enteroaggregative Escherichia coli and identification of target genes for the detection of both typical and atypical strains.

Enteroaggregative Escherichia coli (EAggEC) is an important cause of diarrhea worldwide, and there is a need for better detection methods in diagnostic laboratories. The aims of this study were i) to characterize strains of EAggEC by assigning each isolate a genotypic profile and (ii) to determine target genes for the detection of both typical and atypical EAggEC. The heterogeneity of the EAggEC group makes selection of a single target gene difficult. The plasmid-encoded genes, aat, aggR, and aap, are all appropriate targets for the detection of typical EAggEC. Of the chromosomally encoded genes, aaiA would be the most suitable target gene to identify typical and atypical EAggEC. The astA gene, encoding the enteroaggregative heat stable toxin, although not specific for EAggEC, may be used effectively in combination with other specific EAggEC genes. A polymerase chain reaction test based on the detection of characteristic EAggEC virulence genes, such as aat, astA, and aaiA, would improve EAggEC diagnosis.

Detection of enteroaggregative Escherichia coli in faecal samples from patients in the community with diarrhoea.

The aim of this study was to assess the usefulness of a multiplex PCR assay targeting the aat, aaiA and astA genes for the detection of typical and atypical enteroaggregative Escherichia coli (EAEC) in bacterial cultures from faecal samples from patients with community-acquired diarrhoea. The isolates harbouring these genes were also tested using the HEp-2 cell-adhesion assay to clarify their EAEC status. aat, aai or astA was found in E. coli faecal isolates from 39 (7.8 %) of 500 patients, and 20 of these strains adhered to HEp-2 cells in a pattern characteristic of EAEC. Eight isolates carrying the aai or astA gene but not the aat gene were shown to be HEp-2 cell test positive, although 12 strains with this genotype were HEp-2 cell test negative. Using the HEp-2 adhesion assay as the gold standard, the addition of primers detecting aaiA and astA to the aat PCR increased the number of EAEC isolates detected, but identified strains of E. coli that were not EAEC. The variety of genotypes exhibiting aggregative adherence highlights the problems associated with developing a molecular diagnostic test for EAEC. This PCR assay detects a variety of strains exhibiting characteristics of the EAEC group, making it a useful tool for identifying both typical and atypical EAEC.

Use of a microarray to assess the distribution of plasmid and chromosomal virulence genes in strains of enteroaggregative Escherichia coli.

A DNA microarray was used to analyze the distribution of plasmid and chromosomal genes among strains of enteroaggregative Escherichia coli (EAEC) isolated from a prospective diarrhoea surveillance study in the United Kingdom. Target genes were extracted from existing databases and from the genome sequence of prototype EAEC strain 042. We found that strains exhibiting the aggregative adherence (AA) phenotype could be broadly divided into two groups depending upon whether they harboured genes from the EAEC virulence plasmid (pAA) and a set of chromosomal genes found in EAEC strain 042. Several chromosomal loci were inherited en bloc, and were more common in strains which we designated Group 1; genes at the pheU locus were particularly conserved. Genes encoded on the pAA plasmid and those under control of the master regulator AggR were also concentrated in the Group 1 EAEC. A gene encoding a type 1 pilin allele was detected more frequently in Group 2 EAEC. Our data suggest that strains previously designated as typical EAEC harbour a large number of conserved plasmid and chromosomal loci, further illuminating a package of virulence genes common to the most important EAEC.

Isolation and characterization of Shiga toxin-producing Escherichia coli O157:H7 from beef, pork and cattle fecal samples in Changchun, China.

Meat samples and fecal specimens from adult cattle were collected in Changchun, China and were examined for presence of Shiga toxin-producing Escherichia coli (STEC) serogroup O157. STEC O157 strains were isolated from 2 (5%) of 40 beef, 1 (3.3%) of 30 pork, and 3 (1.7%) of 176 adult cattle fecal samples. The strains belonged to phage types (PT) 4, 8, or 47. Two beef strains and a strain previously isolated from a patient in Shandong, China, were PT-4 and showed a similar PFGE pattern, suggesting the possibility of food-borne transmission. It is suggested that cattle are a reservoir of STEC O157:H7 and meat products are contaminated by this pathogen in Changchun, China as well as in other countries.

In vitro activity of rifaximin against clinical isolates of Escherichia coli and other enteropathogenic bacteria isolated from travellers returning to the UK.

Rifaximin is licensed in the EU and USA for treating travellers' diarrhoea caused by non-invasive bacteria. Selection for resistance mechanisms of public health significance might occur if these are linked to rifamycin resistance. Rifaximin MICs were determined by agar dilution for 90 isolates each of Escherichia coli, Shigella spp., nontyphoidal Salmonella enterica, typhoidal S. enterica and Campylobacter spp., an additional 60 E. coli with CTX-M ESBLs isolated from patients with travellers' diarrhoea, and 30 non-diarrhoeal carbapenemase-producing E. coli. Comparators were rifampicin, ciprofloxacin, azithromycin, trimethoprim/sulfamethoxazole and doxycycline. Isolates with rifaximin MICs>32 mg/L were screened for arr genes, and critical rpoB regions were sequenced. Rifaximin was active at ≤32 mg/L against 436/450 (96.9%) diverse Enterobacteriaceae, whereas 81/90 (90%) Campylobacter spp. were resistant to rifaximin at ≥128 mg/L. Rifaximin MICs were ≥128 mg/L for two Shigella and five MDR E. coli producing NDM (n = 3), OXA-48 (n = 1) or CTX-M-15 (n = 1). Two of the five MDR E. coli had plasmids harbouring arr-2 together with bla(NDM), and two (one each with bla(NDM) and bla(CTX-M-15)) had His526Asn substitutions in RpoB. The rifamycin resistance mechanism remained undefined in one MDR E. coli isolate (with bla(OXA-48)) and the two Shigella isolates. Rifaximin showed good in vitro activity against diverse Enterobacteriaceae but was largely inactive against Campylobacter spp. Rifaximin has potential to co-select MDR E. coli in the gut flora, but much stronger associations were seen between ESBL and/or carbapenemase production and resistance to alternative treatments for travellers' diarrhoea, notably ciprofloxacin and azithromycin.

Assessment of a real-time PCR for the detection and characterization of verocytotoxigenic Escherichia coli.

The European Union Reference Laboratory (EU-RL) has produced guidelines for a real-time PCR for the detection of verocytotoxigenic Escherichia coli (VTEC). In this study, we validated the EU-RL assay on 545 strains of VTEC and evaluated the utility of the assay for the detection of VTEC from stool specimens. The validation study on cultures showed that the EU-RL VTEC PCR was 99.3% sensitive for the detection of vtx genes; only strains harbouring vtx2f genes were not detected. The assay was 100% sensitive and 100% specific for the detection of both the eae and O157 rfbE genes. In a prospective study involving 500 stool samples, the EU-RL VTEC PCR detected vtx genes in 12.4% of specimens, compared to 3.8% specimens found to be culture-positive for E. coli O157 using the Health Protection Agency national standard culture method. This study showed that the EU-RL VTEC assay was reliable and robust, and an effective rapid screening method for the detection of VTEC from stool specimens.

Application of fluorescent amplified fragment length polymorphism for comparison of human and animal isolates of Yersinia enterocolitica.

An amplified fragment length polymorphism (AFLP) method, developed to genotype Yersinia enterocolitica, has been used to investigate 70 representative strains isolated from humans, pigs, sheep, and cattle in the United Kingdom. AFLP primarily distinguished Y. enterocolitica strains according to their biotype, with strains dividing into two distinct clusters: cluster A, comprising largely the putatively pathogenic biotypes (BT2 to -4), and cluster B, comprising the putatively nonpathogenic biotype 1A strains and a single BT1B isolate. Within these two clusters, subclusters formed largely on the basis of serotype. However, AFLP profiles also allowed differentiation of strains within these serotype-related subclusters, indicating the high discriminatory power of the technique for Y. enterocolitica. Investigation of the relationship between strain AFLP profile and host confirmed that pigs are, and provides further proof that sheep may be, potential sources of human infection with putatively pathogenic strains. However, the results suggest that some strains causing human disease do not come from veterinary sources identifiable at this time. The distribution of some BT1A isolates within cluster A raises questions about the relationship between virulence potential and biotype.

Childhood hemolytic uremic syndrome, United Kingdom and Ireland.

We conducted prospective surveillance of childhood hemolytic uremic syndrome (HUS) from 1997 to 2001 to describe disease incidence and clinical, epidemiologic and microbiologic characteristics. We compared our findings, where possible, with those of a previous study conducted from 1985 to 1988. The average annual incidence of HUS for the United Kingdom and Ireland (0.71/100,000) was unchanged from 1985 to 1988. The overall early mortality had halved, but the reduction in mortality was almost entirely accounted for by improved outcome in patients with diarrhea-associated HUS. The principal infective cause of diarrhea-associated HUS was Shiga toxin-producing Escherichia coli O157 (STEC O157), although in the 1997-2001 survey STEC O157 phage type (PT) 21/28 had replaced STEC O157 PT2 as the predominant PT. The risk of developing diarrhea-associated HUS was significantly higher in children infected with STEC O157 PT 2 and PT 21/28 compared with other PTs. Hypertension as a complication of HUS was greatly reduced in patients with diarrhea-associated HUS.

Genetic profiling of enterohemorrhagic Escherichia coli strains in relation to clonality and clinical signs of infection.

Sixty-seven human strains of enterohemorrhagic Escherichia coli (EHEC) (from patients with more or less severe symptoms) were serogrouped and arranged according to pulsed-field gel electrophoresis (PFGE) patterns. We used PCR to investigate the strains according to known or putative virulence factors, and associations with disease were studied. All EHEC strains with the same PFGE pattern belonged to the same serogroup. On the contrary, two serogroups (O157 and O8) included strains with different PFGE patterns. We found several different combinations of chromosomal and plasmid-borne determinants, encoding the putative virulence factors, among the strains. As judged from clinical symptoms, there was no marked difference in pathogenicity among the strains and their combinations of virulence traits. All strains of O157 had the genes coding for verocytotoxin (VT) 2, intimin (eaeA), E. coli hemolysin (E-hly), and secreted serine protease (espP). Among EHEC non-O157 strains, the genes coding for VT1 and VT2 were equally dispersed. EaeA positivity was just as common among VT1- as VT2-positive strains. Among the plasmid-borne determinants, E-hly and espP were the most common and E-hly might be a pathogenicity marker among EHEC non-O157 strains. The conclusion is that PFGE is a very useful tool in epidemiological studies. The EHEC plasmids are heterogeneous in their gene composition, with the four plasmid-borne determinants found in many combinations. There was no reliable correlation between chromosomal and plasmid-borne virulence factors and human disease.

VTEC O157 subtypes associated with the most severe clinical symptoms in humans constitute a minor part of VTEC O157 isolates from Danish cattle.

The aim of this study was to compare the distribution of VTEC O157 subtypes isolated from human sporadic infections with those in the Danish bovine reservoir, and to correlate the subtypes with the severity of the clinical symptoms in humans. The study included a total of 149 Danish eae-positive VTEC O157 isolates (63 of bovine origin and 86 from human clinical cases) isolated between 1987 and 2001. All were analysed by vtx-PCR-RFLP and phage typing. The vtx-PCR-RFLP showed that isolates carrying the vtx2 gene was more than four times as prevalent among the human clinical isolates (55%) as compared to the bovine isolates (13%). Furthermore, a significant correlation between the presence of the vtx2 gene and development of haemolytic-uraemic syndrome was found. The 149 isolates encompassed 16 different phage types (PTs). The majority (87%) of the human clinical isolates were identified, as PT2, PT4, PT8 or PT14 while only 46% of the bovine isolates belonged to these PTs. PT8 and PT14 were found at similar rates among bovine (36%) and human isolates (40%). However, the predominant PTs in the human isolates, PT2 (19%) and PT4 (28%), were only identified in 2% and 8%, respectively, of the bovine isolates. All but one PT2 and PT4 isolate carried either vtx2 alone or in combination with vtx2c, whereas none of the PT8 and PT14 isolates carried vtx2. The significant overlap between vtx/phage type combinations in bovine and human clinical isolates indicate that cattle are an important reservoir for human VTEC O157 infections in Denmark. However, the vtx2-carrying isolates, causing the most severe clinical symptoms, constitute only a minor fraction of the isolates from the Danish bovine reservoir.

Distribution of the saa gene in strains of Shiga toxin-producing Escherichia coli of human and bovine origins.

Certain strains of Shiga toxin-producing Escherichia coli (STEC) which do not have the locus of enterocyte effacement pathogenicity island carry the STEC autoagglutinating adhesin (saa) gene. The distribution of the saa gene in STEC isolates from patients with hemolytic-uremic syndrome (HUS), patients with less severe diarrheal disease, asymptomatic individuals, and healthy cattle was examined. saa-positive strains were detected more frequently (P < 0.001) in STEC strains from bovines (32 of 56 strains) than in those from humans (8 of 91 strains). No significant association (P = 0.135) was found between the saa gene and STEC isolated from patients with HUS (6 of 46 strains) or diarrhea (2 of 29 strains) and from healthy controls (0 of 16 strains).