Stefano Morabito

Typing of intimin genes in human and animal enterohemorrhagic and enteropathogenic Escherichia coli: characterization of a new intimin variant.

ABSTRACT Enteropathogenic Escherichia coli (EPEC) and enterohemorrhagic E. coli (EHEC) produce the characteristic “attaching and effacing” (A/E) lesion of the brush border. Intimin, an outer membrane protein encoded by eae, is responsible for the tight association of both pathogens with the host cell. Severaleae have been cloned from different EPEC and EHEC strains isolated from humans and animals. These sequences are conserved in the N-terminal region but highly variable in the last C-terminal 280 amino acids (aa), where the cell binding activity is localized. Based on these considerations, we developed a panel of specific primers to investigate the eae heterogeneity of the variable 3′ region by using PCR amplification. We then investigated the distribution of the known intimin types in a large collection of EPEC and EHEC strains isolated from humans and different animal species. The existence of a yet-unknown family of intimin was suspected because several EHEC strains, isolated from human and cattle, did not react with any of the specific primer pairs, although these strains were eaepositive when primers amplifying the conserved 5′ end were used. We then cloned and sequenced the eae present in one of these strains (EHEC of serotype O103:H2) and subsequently designed a PCR primer that recognizes in a specific manner the variable 3′ region of this new intimin type. This intimin, referred to as “ɛ,” was present in human and bovine EHEC strains of serogroups O8, O11, O45, O103, O121, and O165. Intimin ɛ is the largest intimin cloned to date (948 aa) and shares the greatest overall sequence identity with intimin β, although analysis of the last C-terminal 280 aa suggests a greater similarity with intimins α and γ.

Multicenter Evaluation of a Sequence-Based Protocol for Subtyping Shiga Toxins and Standardizing Stx Nomenclature

ABSTRACT When Shiga toxin-producing Escherichia coli (STEC) strains emerged as agents of human disease, two types of toxin were identified: Shiga toxin type 1 (Stx1) (almost identical to Shiga toxin produced by Shigella dysenteriae type 1) and the immunologically distinct type 2 (Stx2). Subsequently, numerous STEC strains have been characterized that express toxins with variations in amino acid sequence, some of which confer unique biological properties. These variants were grouped within the Stx1 or Stx2 type and often assigned names to indicate that they were not identical in sequence or phenotype to the main Stx1 or Stx2 type. A lack of specificity or consistency in toxin nomenclature has led to much confusion in the characterization of STEC strains. Because serious outcomes of infection have been attributed to certain Stx subtypes and less so with others, we sought to better define the toxin subtypes within the main Stx1 and Stx2 types. We compared the levels of relatedness of 285 valid sequence variants of Stx1 and Stx2 and identified common sequences characteristic of each of three Stx/Stx1 and seven Stx2 subtypes. A novel, simple PCR subtyping method was developed, independently tested on a battery of 48 prototypic STEC strains, and improved at six clinical and research centers to test the reproducibility, sensitivity, and specificity of the PCR. Using a consistent schema for nomenclature of the Stx toxins and stx genes by phylogenetic sequence-based relatedness of the holotoxin proteins, we developed a typing approach that should obviate the need to bioassay each newly described toxin and that predicts important biological characteristics.

A new Shiga toxin 2 variant (Stx2f) from Escherichia coli isolated from pigeons

ABSTRACT We have isolated Shiga toxin (Stx)-producing Escherichia coli (STEC) strains from the feces of feral pigeons which contained a new Stx2 variant gene designatedstx2f. This gene is most similar tosltIIva of patient E. coli O128:B12 isolate H.I.8. Stx2f reacted only weakly with commercial immunoassays. The prevalence of STEC organisms carrying the stx2fgene in pigeon droppings was 12.5%. The occurrence of a new Stx2 variant in STEC from pigeons enlarges the pool of Stx2 variants and raises the question whether horizontal gene transfer to E. coli pathogenic to humans may occur.

Genetic Diversity of Intimin Genes of Attaching and Effacing Escherichia coli Strains

ABSTRACT In this study, we determined the sequences of four intimin variant genes detected in attaching and effacing Escherichia coli isolates of human origin. Three of them were novel and were designated eae-η (eta), eae-ι (iota), and eae-κ (kappa). The fourth was identical to the recently described eae-ζ (zeta), isolated from a bovine E. coli O84:NM isolate. We compared these sequences with those of published intimin-α, intimin-β, intimin-γ1, intimin-γ2, intimin-ε, and intimin-θ alleles. Sequence analysis of these 10 intimin alleles confirmed extensive genetic diversity within the intimin gene family in E. coli. The genetic diversity was more prominent in the 3′ region (starting at bp 2112), which encodes the binding domain of intimin. Phylogenetic analyses revealed four groups of closely related intimin genes: α and ζ; β and κ; γ1 and γ2/θ; and ε and η. Calculation of homoplasy ratios of sequences of the 5′ region of eae (positions 1 to 2111) revealed evidence for intragenic recombination. Split decomposition analysis also indicates that recombination events have played a role in the evolutionary history of eae. In conclusion, we recommend an eae nomenclature system based on the Greek alphabet and provide an updated PCR scheme for amplification and typing of E. coli eae.

Isolation of Verocytotoxin-producing Escherichia coli O157:H7 from cattle at slaughter in Italy.

Cattle arriving for slaughter at a large abattoir in northern Italy between April 1997 and January 1998 were examined for intestinal carriage of Verocytotoxin-producing Escherichia coli (VTEC) O157 using an immunomagnetic separation technique. Sixty sorbitol non-fermenting VTEC O157 strains were isolated from 59 (13.1%) of the 450 cattle examined. In particular, VTEC O157 was found in 37 (16.6%) of 223 feedlot cattle and in 22 (16.1%) of 137 dairy cull cows, but not in the 90 veal calves sampled. The isolation rate was higher during warm weather (17.5%), falling to an average of 2.9% during the winter months. VT-negative, O157 latex-agglutinating E. coli strains were isolated from 23 (5.1%) of the 450 animals. PCR analysis showed that all 60 VTEC O157 strains carried the VT2 gene and that 25 strains also carried the VT1 gene. In addition, four of the VT-negative, O157 latex-agglutinating E. coli strains carried the VT2 gene. Atypical biochemical features were observed in some VTEC O157: two strains (3.3%) showed beta-glucuronidase activity, and seven (11.7%) produced urease.

Detection of Salmonella spp., Yersinia enterocolitica and verocytotoxin-producing Escherichia coli O157 in pigs at slaughter in Italy.

From December 1999 to December 2000, 150 pigs were randomly selected in two large abattoirs of northern Italy. Caecal material and carcass swabs were collected and examined for Salmonella, Yersinia enterocolitica, and Escherichia coli O157. Tonsils were examined for Salmonella and Y. enterocolitica. Salmonella was isolated from the intestinal content of 55 (36.7%) specimens, from 8 (5.3%) tonsils, and from 9 (6.0%) carcasses. Ten different serotypes were detected; the more common were Salmonella derby (37.8%), Salmonella bredeney (21.6%), and Salmonella typhimurium (14.8%). S. typhimurium isolates that belonged to phage-types DT104 and DT208 were 45% and 27.3%, respectively; 18.2% belonged to U302 and 9.1% were non-typeable. Y. enterocolitica was detected in the intestinal matter of 6 (4.0%) slaughtered pigs and in 22 (14.7%) tonsils; however, this pathogen was not found on carcasses. The majority of Y. enterocolitica isolates (82.1%) belonged to serotype O:3 biotype 4, one (3.6%) belonged to serotype O:9, and 13% did not belong to any known biotype. Verocytotoxin-producing E. coli (VTEC) O157 was isolated from the intestinal content of one (0.7%) slaughtered pig and from one (0.7%) carcass; four (2.7%) faecal samples contained E. coli O157 strains negative for the presence of both eae and VT genes.

Detection and characterization of Shiga toxin-producing Escherichia coli in feral pigeons.

Escherichia coli strains producing a variant of Shiga toxin 2 (Stx2), designated Stx2f, have been recently described in the stools of feral pigeons. During 1997-1998, 649 pigeons were trapped and examined in three different squares of Rome. Stool samples were collected from each bird and enrichment cultures were examined for the presence of Stx by the vero cell assay. Stx-producing E. coli (STEC) were isolated from the positive cultures and characterized by serotyping and PCR analysis of stx and other virulence-related genes. Stx was detected in 10.8% of the stool enrichment cultures. The percentage of positive birds did not differ significantly for the three flocks considered and the season of sample collection. Conversely, STEC carriage was significantly more frequent in young than in adult birds (17.9 versus 8.2%). None of the birds examined showed signs of disease. STEC strains were isolated from 30 of 42 Stx-positive cultures examined. All the strains produced Stx2f, and most of them possessed genes encoding for intimin and the cytolethal distending toxin (CLDT). Six serogroups were identified, but most of the isolates belonged to O45, O18ab, and O75. Molecular typing indicated that most of the isolates within a flock were clonally-related. This work confirms that pigeons represent a natural reservoir of STEC strains characterized by the production of the toxin variant Stx2f, and by the frequent presence of eae and cldt genes. Further work is needed to clarify whether these STEC may represent a cause of avian disease or even a potential health hazard for humans.

A mosaic pathogenicity island made up of the locus of enterocyte effacement and a pathogenicity island of Escherichia coli O157:H7 is frequently present in attaching and effacing E. coli

ABSTRACT Enteropathogenic Escherichiacoli (EPEC) and enterohemorragic E. coli (EHEC) possess a pathogenicity island (PAI), termed the locus of enterocyte effacement (LEE), which confers the capability to cause the characteristic attaching and effacing lesions of the brush border. Due to this common property, these organisms are also termed attaching and effacing E. coli (AEEC). Sequencing of the EHEC O157 genome recently revealed the presence of other putative PAIs in the chromosome of this organism. In this article, we report on the presence of four of those PAIs in a panel of 133 E. coli strains belonging to different pathogroups and serotypes. One of these PAIs, termed O122 in strain EDL 933 and SpLE3 in strain Sakai, was observed in most of the AEEC strains examined but not in the other groups of E. coli. It was also found to contain the virulence-associated gene efa1/lifA. In EHEC O157, PAI O122 is located 0.7 Mb away from the LEE. Conversely, we demonstrated that in many EHEC non-O157 strains and EPEC strains belonging to eight serogroups, PAI O122 and the LEE are physically linked to form a cointegrated structure. This structure can be considered a mosaic PAI that could have been acquired originally by AEEC. In some clones, such as EHEC O157, the LEE-O122 mosaic PAI might have undergone recombinational events, resulting in the insertion of the portion referred to as PAI O122 in a different location.

Enterohemorrhagic Escherichia coli O26:H11/H−: A New Virulent Clone Emerges in Europe

BACKGROUND Enterohemorrhagic Escherichia coli (EHEC) O26 causes diarrhea and hemolytic uremic syndrome (HUS). Strains harboring the stx1a gene prevail, but strains with stx2a as the sole Shiga toxin-encoding gene are now emerging. The traits and virulence of the latter set of strains are unknown. We correlated stx genotypes of 272 EHEC O26 strains isolated in 7 European countries between 1996 and 2012 with disease phenotypes. We determined phylogeny, clonal structure, and plasmid gene profiles of the isolates and portray geographic and temporal distribution of the different subgroups. METHODS The stx genotypes and plasmid genes were identified using polymerase chain reaction, phylogeny was assigned using multilocus sequence typing, and clonal relatedness was established using pulsed-field gel electrophoresis. RESULTS Of the 272 EHEC O26 isolates, 107 (39.3%), 139 (51.1%), and 26 (9.6%) possessed stx1a, stx2a, or both genes, respectively. Strains harboring stx2a only were significantly associated with HUS (odds ratio, 14.2; 95% confidence interval, 7.9-25.6; P < .001) compared to other stx genotypes. The stx2a-harboring strains consist of 2 phylogenetically distinct groups defined by sequence type (ST) 21 and ST29. The ST29 strains are highly conserved and correspond by plasmid genes to the new virulent clone of EHEC O26 that emerged in Germany in the 1990s. This new clone occurred in 6 of the 7 countries and represented approximately 50% of all stx2a-harboring EHEC O26 strains isolated between 1996 and 2012. CONCLUSIONS A new highly virulent clone of EHEC O26 has emerged in Europe. Its reservoirs and sources warrant identification.

Faecal carriage of Verocytotoxin-producing Escherichia coli O157 and carcass contamination in cattle at slaughter in northern Italy

A study on the prevalence of the faecal carriage of Verocytotoxin (VT)-producing Escherichia coli (VTEC) O157 and on the rate of carcass contamination was carried out on feedlot cattle and dairy cows at slaughter in northern Italy. Between April 1998 and January 1999, 12 sampling visits were performed on different days in seven different slaughterhouses. At each visit, 5-12 animals consecutively slaughtered were selected. From each animal, faeces were collected from the rectum immediately after slaughter and surface swabs were taken from the leg region and the diaphragmatic insertion of the carcass. All samples were examined for the presence of VTEC O157 using an immunomagnetic separation technique. A total of 100 animals coming from 60 different farms were examined. In total, VTEC O157 was isolated from the intestinal content of 17, and from the carcasses of 12 of the 100 animals examined. In particular, VTEC O157 was recovered from six (35.3%) out of the 17 carcasses from which the organism had previously been isolated from rectal content and from six (7.3%) of the 82 carcasses of the stool-negative cattle. In seven carcasses, VTEC O157 was isolated from the leg area, in two carcasses from the diaphragmatic area, and in three carcasses from both areas. Major differences in the prevalence of VTEC O157 were observed in the different groups of cattle sampled. In 7 of the 12 sampling visits, all the specimens examined were negative, while 16 of the 17 positive stool samples and 11 of the 12 positive carcass swabs were collected during three of the visits, performed in June in three different abattoirs. In these three visits, the ratios between the percentage of animals carrying VTEC O157 in the stools and the percentage of contaminated carcasses were 0.33, 0.57, and 1.66, respectively; thus, confirming that slaughter practices can largely influence the rate of carcass contamination. Phage typing and PFGE analysis of VTEC O157 isolated from samples collected at the same visit suggested that both auto- and cross-contamination occurred.