Identification of Five Serotypes of Enteropathogenic Escherichia coli from Diarrheic Calves and Healthy Cattle in Belgium and Comparative Genomics with Shigatoxigenic E. coli

Simple Summary Enteropathogenic Escherichia coli (EPEC) from cattle receive little attention, although some belong to the most notorious O serotypes of attaching/effacing Shigatoxigenic Escherichia coli (AE-STEC) responsible for the uremic and hemolytic syndrome in humans, such as O26. Nevertheless, the O serotypes and virulotypes of the large majority of bovine EPEC remain unidentified. This study aimed to identify five non-classical O serotypes (O123/186, O156, O177, O182, and O183) by a polymerase chain reaction (PCR) among three collections of bovine EPEC from young diarrheic calves, healthy cattle at slaughterhouses, and healthy calves in dairy farms. The virulotypes and sequence types (STs) obtained after the whole genome sequencing of several O156, O177, and O182 bovine EPEC were closely related or identical to the virulotypes and STs of ten bovine and the human AE-STEC of the same O:H serotype. This study allows us to identify more EPEC O serotypes from cattle and to speculate on their evolution. Abstract Enteropathogenic Escherichia coli (EPEC) produce attaching/effacing (AE) lesions and cause non-bloody diarrhea in mammals. A minority of bovine EPEC belong to one of the ten classical serotypes of human and bovine AE-STEC. The purpose of this study was to identify five non-classical O serotypes (O123/186, O156, O177, O182, and O183) among bovine EPEC and to characterize their virulence repertoires by whole genome sequencing. Around 40% of the 307 EPEC from 307 diarrheic calves, 368 EPEC from 47 healthy cattle, and 131 EPEC from 36 healthy calves in dairy farms were analyzed. Serotype O177 was the most frequent among EPEC from diarrheic and healthy calves, while the O156 was the most frequent in healthy cattle. The genomic analysis identified different H serotypes, MLSTypes, and/or eae gene subtypes among the O156 and O177 EPEC, while the O182 was homogeneous. The virulence gene profiles of bovine EPEC were closely related to each other and to the profiles of ten bovine and human AE-STEC. These results emphasize the need for additional studies to identify more O:H serotypes of bovine EPEC and to elucidate their origin and evolution of EPEC with regard to AE-STEC belonging to the same O:H serotypes.

[1]  S. Yamasaki,et al.  Prevalence, O-genotype and Shiga toxin (Stx) 2 subtype of Stx-producing Escherichia coli strains isolated from Argentinean beef cattle , 2021, The Journal of veterinary medical science.

[2]  B. Devleesschauwer,et al.  Occurrence of ‘gang of five’ Shiga toxin‐producing Escherichia coli serogroups on Belgian dairy cattle farms by overshoe sampling , 2020, Letters in applied microbiology.

[3]  B. Devleesschauwer,et al.  Identification of Shigatoxigenic and Enteropathogenic Escherichia coli Serotypes in Healthy Young Dairy Calves in Belgium by Recto-Anal Mucosal Swabbing , 2020, Veterinary sciences.

[4]  B. Devleesschauwer,et al.  Pathogenic potential of Escherichia coli O157 and O26 isolated from young Belgian dairy calves by recto‐anal mucosal swab culturing , 2020, Journal of applied microbiology.

[5]  K. Nakamura,et al.  Genetic characterization of Shigatoxigenic and enteropathogenic Escherichia coli O80:H2 from diarrhoeic and septicaemic calves and relatedness to human Shigatoxigenic E. coli O80:H2 , 2020, Journal of applied microbiology.

[6]  D. Thiry,et al.  Characteristics of Shiga toxin producing- and enteropathogenic Escherichia coli of the emerging serotype O80:H2 isolated from humans and diarrhoeic calves in Belgium. , 2019, Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases.

[7]  S. Bonacorsi,et al.  Emerging Shiga-toxin-producing Escherichia coli serogroup O80 associated hemolytic and uremic syndrome in France, 2013-2016: Differences with other serogroups , 2018, PloS one.

[8]  D. Piérard,et al.  Twenty-seven years of screening for Shiga toxin-producing Escherichia coli in a university hospital. Brussels, Belgium, 1987-2014 , 2018, PloS one.

[9]  N. Korsak,et al.  Low prevalence of the ‘gang of seven’ and absence of the O80:H2 serotypes among Shigatoxigenic and enteropathogenic Escherichia coli (STEC and EPEC) in intestinal contents of healthy cattle at two slaughterhouses in Belgium in 2014 , 2018, Journal of applied microbiology.

[10]  Baohong Wang,et al.  Prevalence and genetic diversity of human diarrheagenic Escherichia coli isolates by multilocus sequence typing. , 2018, International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases.

[11]  High-Quality Complete Genome Sequences of Three Bovine Shiga Toxin-Producing Escherichia coli O177:H- (fliCH25) Isolates Harboring Virulent stx2 and Multiple Plasmids , 2018, Genome Announcements.

[12]  Danil Kim,et al.  Prevalence, virulence potential, and pulsed-field gel electrophoresis profiling of Shiga toxin-producing Escherichia coli strains from cattle , 2017, Gut Pathogens.

[13]  S. Monecke,et al.  Genetic makeup of Shiga toxin-producing Escherichia coli in relation to clinical symptoms and duration of shedding: a microarray analysis of isolates from Swedish children , 2017, European Journal of Clinical Microbiology & Infectious Diseases.

[14]  T. Hayashi,et al.  Identification of Shiga toxin-producing (STEC) and enteropathogenic (EPEC) Escherichia coli in diarrhoeic calves and comparative genomics of O5 bovine and human STEC. , 2017, Veterinary Microbiology.

[15]  L. Geue,et al.  The Accessory Genome of Shiga Toxin-Producing Escherichia coli Defines a Persistent Colonization Type in Cattle , 2016, Applied and Environmental Microbiology.

[16]  Frank M. Aarestrup,et al.  Rapid and Easy In Silico Serotyping of Escherichia coli Isolates by Use of Whole-Genome Sequencing Data , 2015, Journal of Clinical Microbiology.

[17]  S. Iyoda,et al.  Escherichia coli O-Genotyping PCR: a Comprehensive and Practical Platform for Molecular O Serogrouping , 2015, Journal of Clinical Microbiology.

[18]  Fangfang Xia,et al.  RASTtk: A modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes , 2015, Scientific Reports.

[19]  F. Navarro-Garcia,et al.  Escherichia coli O104:H4 Pathogenesis: an Enteroaggregative E. coli/Shiga Toxin-Producing E. coli Explosive Cocktail of High Virulence. , 2014, Microbiology spectrum.

[20]  Y. Kirino,et al.  Identification of O serotypes, genotypes, and virulotypes of Shiga toxin-producing Escherichia coli isolates, including non-O157 from beef cattle in Japan. , 2014, Journal of food protection.

[21]  Ole Lund,et al.  Real-Time Whole-Genome Sequencing for Routine Typing, Surveillance, and Outbreak Detection of Verotoxigenic Escherichia coli , 2014, Journal of Clinical Microbiology.

[22]  É. Oswald,et al.  Intimin Gene (eae) Subtype-Based Real-Time PCR Strategy for Specific Detection of Shiga Toxin-Producing Escherichia coli Serotypes O157:H7, O26:H11, O103:H2, O111:H8, and O145:H28 in Cattle Feces , 2013, Applied and Environmental Microbiology.

[23]  Koichiro Tamura,et al.  MEGA6: Molecular Evolutionary Genetics Analysis version 6.0. , 2013, Molecular biology and evolution.

[24]  Sergey I. Nikolenko,et al.  SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing , 2012, J. Comput. Biol..

[25]  H. De Greve,et al.  O157:H7 and O104:H4 Vero/Shiga toxin-producing Escherichia coli outbreaks: respective role of cattle and humans , 2012, Veterinary Research.

[26]  Ole Lund,et al.  Multilocus Sequence Typing of Total-Genome-Sequenced Bacteria , 2012, Journal of Clinical Microbiology.

[27]  H. Vu-Khac,et al.  Virulence factors in Escherichia coli isolated from calves with diarrhea in Vietnam , 2011, Journal of veterinary science.

[28]  D. Ussery,et al.  Comparison of 61 Sequenced Escherichia coli Genomes , 2010, Microbial Ecology.

[29]  C. Médigue,et al.  The Plasmid of Escherichia coli Strain S88 (O45:K1:H7) That Causes Neonatal Meningitis Is Closely Related to Avian Pathogenic E. coli Plasmids and Is Associated with High-Level Bacteremia in a Neonatal Rat Meningitis Model , 2009, Infection and Immunity.

[30]  A. Mellmann,et al.  Shiga toxin-negative attaching and effacing Escherichia coli: distinct clinical associations with bacterial phylogeny and virulence traits and inferred in-host pathogen evolution. , 2008, Clinical infectious diseases : an official publication of the Infectious Diseases Society of America.

[31]  M. Gilmour,et al.  Isolation and Genetic Characterization of a Coinfection of Non-O157 Shiga Toxin-Producing Escherichia coli , 2007, Journal of Clinical Microbiology.

[32]  W. Yam,et al.  A Newly Discovered Verotoxin Variant, VT2g, Produced by Bovine Verocytotoxigenic Escherichia coli , 2003, Applied and Environmental Microbiology.