Characterisation of Commensal <i>Escherichia coli</i> Isolated from Apparently Healthy Cattle and Their Attendants in Tanzania

<div><p>While pathogenic types of <i>Escherichia coli</i> are well characterized, relatively little is known about the commensal <i>E</i>. <i>coli</i> flora. In the current study, antimicrobial resistance in commensal <i>E</i>. <i>coli</i> and distribution of ERIC-PCR genotypes among isolates of such bacteria from cattle and cattle attendants on cattle farms in Tanzania were investigated. Seventeen <i>E</i>. <i>coli</i> genomes representing different ERIC-PCR types of commensal <i>E</i>. <i>coli</i> were sequenced in order to determine their possible importance as a reservoir for both antimicrobial resistance genes and virulence factors. Both human and cattle isolates were highly resistant to tetracycline (40.8% and 33.1%), sulphamethazole-trimethoprim (49.0% and 8.8%) and ampicillin (44.9% and 21.3%). However, higher proportion of resistant <i>E</i>. <i>coli</i> and higher frequency of resistance to more than two antimicrobials was found in isolates from cattle attendants than isolates from cattle. Sixteen out of 66 ERIC-PCR genotypes were shared between the two hosts, and among these ones, seven types contained isolates from cattle and cattle attendants from the same farm, suggesting transfer of strains between hosts. Genome-wide analysis showed that the majority of the sequenced cattle isolates were assigned to phylogroups B1, while human isolates represented phylogroups A, C, D and E. In general, <i>in silico</i> resistome and virulence factor identification did not reveal differences between hosts or phylogroups, except for <i>lpfA</i> and <i>iss</i> found to be cattle and B1 phylogroup specific. The most frequent plasmids replicon genes found in strains from both hosts were of <i>IncF</i> type, which are commonly associated with carriage of antimicrobial and virulence genes. Commensal <i>E</i>. <i>coli</i> from cattle and attendants were found to share same genotypes and to carry antimicrobial resistance and virulence genes associated with both intra and extraintestinal <i>E</i>. <i>coli</i> pathotypes.</p>