TY - JOUR T1 - No evidence for a bovine mastitis <em>Escherichia coli</em> pathotype JF - bioRxiv DO - 10.1101/096479 SP - 096479 AU - Andreas Leimbach AU - Anja Poehlein AU - John Vollmers AU - Dennis Göerlich AU - Rolf Daniel AU - Ulrich Dobrindt Y1 - 2017/01/01 UR - http://biorxiv.org/content/early/2017/04/21/096479.abstract N2 - Background Escherichia coli bovine mastitis is a disease of significant economic importance in the dairy industry. Molecular characterization of mastitis-associated E. coli (MAEC) did not result in the identification of common traits. Nevertheless, a mammary pathogenic E. coli (MPEC) pathotype has been proposed suggesting virulence traits that differentiate MAEC from commensal E. coli. The present study was designed to investigate the MPEC pathotype hypothesis by comparing the genomes of MAEC and commensal bovine E. coli.Results We sequenced the genomes of eight E. coli isolated from bovine mastitis cases and six fecal commensal isolates from udder-healthy cows. We analyzed the phylogenetic history of bovine E. coli genomes by supplementing this strain panel with eleven bovine-associated E. coli from public databases. The majority of the isolates originate from phylogroups A and B1, but neither MAEC nor commensal strains could be unambiguously distinguished by phylogenetic lineage. The gene content of both MAEC and commensal strains is highly diverse and dominated by their phylogenetic background. Although individual strains carry some typical E. coli virulence-associated genes, no traits important for pathogenicity could be specifically attributed to MAEC. Instead, both commensal strains and MAEC have very few gene families enriched in either pathotype. Only the aerobactin siderophore gene cluster was enriched in commensal E. coli within our strain panel.Conclusions This is the first characterization of a phylogenetically diverse strain panel including several MAEC and commensal isolates. With our comparative genomics approach we could not confirm previous studies that argue for a positive selection of specific traits enabling MAEC to elicit bovine mastitis. Instead, MAEC are facultative and opportunistic pathogens recruited from the highly diverse bovine gastrointestinal microbiota. Virulence-associated genes implicated in mastitis are a by-product of commensalism with the primary function to enhance fitness in the bovine gastrointestinal tract. Therefore, we put the definition of the MPEC pathotype into question and suggest to designate corresponding isolates as MAEC.AbbreviationsAIECadherent invasive E. coli;AMR-SSuTantimicrobial multidrug resistance to streptomycin, sulfonamide, and tetracycline;APECavian pathogenic E. coli;BRIGBLAST Ring Image Generator;CCclonal complex;CDScoding DNA sequence;CUchaperone usher pathway fimbriae;EAECenteroaggregative E. coli;ECORE. coli Reference;ECPE. coli common pilus;EHECenterohaemorrhagic E. coli;EPECenteropathogenic E. coli;ETECenterotoxigenic E. coli;ETT2E. coli type III secretion system 2;ExPECextraintestinal pathogenic E. coli;Fecferric iron(III)-dicitrate uptake system;FFfitness factor;Flag-1E. coli peritrichous flagella 1 gene cluster;Flag-2E. coli lateral flagella 2 gene cluster;G4Cgroup 4 capsule;GIgenomic island;GTRgeneralized time-reversible;HGThorizontal gene transfer;IPECintestinal pathogenic E. coli;ISinsertion sequence;LEElocus of enterocyte effacement;LPSlipopolysaccharide;MAECmastitis-associated E. coli;MGEmobile genetic element;MLmaximum likelihood;MLSTmulti-locus sequence typing;MNECnewborn meningitis-associated E. coli;MPECmammary pathogenic E. coli;MSTminimum spanning tree;OGorthologous group;OMPouter membrane protein;ORFopen reading frame;PAIpathogenicity island;PAMPpathogen-associated molecular pattern;PEpaired-end;PHASTPHAge Search Tool;PTSphosphotransferase system;Rhsrearrangement hotspot;SLVsingle locus variant;SPATEserine protease autotransporters of Enterobacteriaceae;SRASequence Read Archive;STsequence type;T2SStype II secretion system;T3SStype III secretion system;T5SStype V secretion system;T6SStype VI secretion system;UPECuropathogenic E. coli;VFDBVirulence Factors Database;VFvirulence factor;WGAwhole genome nucleotide alignment. ER -