A B S T R A C TEscherichia coli producing Shiga toxins (Stx) and the attaching-effacing (AE) lesion (AE-STEC) are responsible for (bloody) diarrhoea in humans and calves while the enteropathogenic E. coli (EPEC) producing the AE lesion only cause non-bloody diarrhoea in all mammals. The purpose of this study was (i) to identify the pathotypes of enterohaemolysin-producing E. coli isolated between 2009 and 2013 on EHLY agar from less than 2 month-old diarrhoeic calves with a triplex PCR targeting the stx1, stx2, eae virulence genes; (ii) to serotype the positive isolates with PCR targeting the genes coding for ten most frequent and pathogenic human and calf STEC O serogroups; and (iii) to compare the MLSTypes and virulotypes of calf and human O5 AE-STEC after Whole Genome Sequencing using two server databases (www.genomicepidemiology.org). Of 233 isolates, 206 were triplex PCR-positive: 119 AE-STEC (58%), 78 EPEC (38%) and 9 STEC (4%); and the stx1+eae+ AE-STEC (49.5%) were the most frequent. Of them, 120 isolates (84% of AE-STEC, 23% of EPEC, 22% of STEC) tested positive with one O serogroup PCR: 57 for O26 (47.5%), 36 for O111 (30%), 10 for O103 (8%) and 8 for O5 (7%) serogroups. The analysis of the draft sequences of 15 O5 AE-STEC could not identify any difference correlated to the host. As a conclusion, (i) the AE-STEC associated with diarrhoea in young calves still belong to the same serogroups as previously (O5, O26, O111) but the O103 serogroup may be emerging, (ii) the O5 AE-STEC from calves and humans are genetically similar.2016 Published by Elsevier B.V.

The rumen harbours countless bacteria, archaea, ciliated protozoa, fungi and viruses: various microorganisms that have established multiplicity of relationships to efficiently digest complex plant fibres and polysaccharides to produce volatile fatty acids (VFAs), microbial proteins and vitamins, essentials for the host’s health, growth and performances. Recent studies using omics-based techniques have revealed that changes in rumen microbiota are associated with changes in ruminants’ production and health parameters such as feed efficiency, methane yield, milk composition and ruminal acidity. However, traditionally, rumen microbes were unveiled using anaerobic culture-based techniques, which are at the origin of most of the basic concepts and understanding of the rumen functioning. Isolating and culturing microbes is frequently more difficult and time-consuming and requires more training than molecular techniques, which explains why culture seems to be abandoned in favour of sequencing. Microbial cultures enable the study of substrate preferences and product output, essential growth requirements, biocide production and susceptibilities; obtaining a pure culture also enables genome sequencing of these strains. We propose here, after a brief report of published rumen isolates, a comprehensive review of current advances in molecular methods to identify novel rumen microbes and discuss how culturing and mathematics could enhance our understanding of rumen microbiology.