An ST131 clade and a Phylogroup A clade bearing a novel Escherichia coli O-antigen cluster predominate among bloodstream E. coli isolates from southwest Nigeria hospitals
Escherichia coli bloodstream infections are typically attributed to a limited number of lineages that carry virulence factors associated with invasion and, in recent years, are increasingly multiply antimicrobial resistant. In Nigeria, E. coli is a common cause of bloodstream infections but the identity of circulating clones is largely unknown and surveillance of their antimicrobial resistance has been limited. We verified, susceptibility-tested and whole genome-sequenced 68 bloodstream E. coli isolates recovered between 2016 and 2018 at three sentinel sites in southwestern Nigeria. Resistance to antimicrobials commonly used in Nigeria was high, reaching 100 % (n = 67) for trimethoprim, 92.5 % (n = 62) for ampicillin, 79.1 % (n = 53) for ciprofloxacin, and 55.2 % (n = 37) for aminoglycosides. All the isolates were susceptible to carbapenems and colistin. The strain set included isolates from globally disseminated high-risk clones including those belonging to ST12 (n=2), ST131 (n=12), and ST648 (n = 4). Twenty-three (33.82%) of the isolates clustered within two clades. The first of these consisted of ST131 strains, comprised of O16:H5 and O25:H4 sub-lineages. The second was an ST10-ST167 complex clade comprised of strains carrying capsular genes that may have originated in Klebsiella. We additionally determined that four ST90 strains from one sentinel represented a retrospectively detected outbreak. Our data demonstrate that a broad repertoire of invasive E. coli isolates cause bloodstream infections in southwest Nigeria. In addition to pandemic lineages, particularly ST131, these include a previously undescribed lineage. Genomic surveillance is valuable for tracking these and other clones and for outbreak identification.