Abstract
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.
Abbreviations
- AIEC
- adherent invasive E. coli;
- AMR-SSuT
- antimicrobial multidrug resistance to streptomycin, sulfonamide, and tetracycline;
- APEC
- avian pathogenic E. coli;
- BRIG
- BLAST Ring Image Generator;
- CC
- clonal complex;
- CDS
- coding DNA sequence;
- CU
- chaperone usher pathway fimbriae;
- EAEC
- enteroaggregative E. coli;
- ECOR
- E. coli Reference;
- ECP
- E. coli common pilus;
- EHEC
- enterohaemorrhagic E. coli;
- EPEC
- enteropathogenic E. coli;
- ETEC
- enterotoxigenic E. coli;
- ETT2
- E. coli type III secretion system 2;
- ExPEC
- extraintestinal pathogenic E. coli;
- Fec
- ferric iron(III)-dicitrate uptake system;
- FF
- fitness factor;
- Flag-1
- E. coli peritrichous flagella 1 gene cluster;
- Flag-2
- E. coli lateral flagella 2 gene cluster;
- G4C
- group 4 capsule;
- GI
- genomic island;
- GTR
- generalized time-reversible;
- HGT
- horizontal gene transfer;
- IPEC
- intestinal pathogenic E. coli;
- IS
- insertion sequence;
- LEE
- locus of enterocyte effacement;
- LPS
- lipopolysaccharide;
- MAEC
- mastitis-associated E. coli;
- MGE
- mobile genetic element;
- ML
- maximum likelihood;
- MLST
- multi-locus sequence typing;
- MNEC
- newborn meningitis-associated E. coli;
- MPEC
- mammary pathogenic E. coli;
- MST
- minimum spanning tree;
- OG
- orthologous group;
- OMP
- outer membrane protein;
- ORF
- open reading frame;
- PAI
- pathogenicity island;
- PAMP
- pathogen-associated molecular pattern;
- PE
- paired-end;
- PHAST
- PHAge Search Tool;
- PTS
- phosphotransferase system;
- Rhs
- rearrangement hotspot;
- SLV
- single locus variant;
- SPATE
- serine protease autotransporters of Enterobacteriaceae;
- SRA
- Sequence Read Archive;
- ST
- sequence type;
- T2SS
- type II secretion system;
- T3SS
- type III secretion system;
- T5SS
- type V secretion system;
- T6SS
- type VI secretion system;
- UPEC
- uropathogenic E. coli;
- VFDB
- Virulence Factors Database;
- VF
- virulence factor;
- WGA
- whole genome nucleotide alignment.