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

Abstract

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.Data SummaryPhylogenetic tree, clinical data, and epidemiological data were visualized using Microreact (https://microreact.org/project/NigeriaEcoliInvasive/d0dc3660) and Phandango (for visualization of pangenome, tree, and metadata). All the sequence data have been deposited in the ENA under the project ID PRJEB29739 (https://www.ebi.ac.uk/ena/browser/view/PRJEB29739). Accessions can be found in Table S6.

Characterization of virulent Escherichia coli in healthy pet dog feces: Implications for public health

“…However, most of the known epidemic E. coli strains such as STs-224, 162, 155, 297, and 2067 occurred rarely. It is thus clear that most isolates recovered in this study did not fall into widely circulated E. coli lineages of ST131, and ST10 complexrelated isolates in Nigeria (Aibinu et al, 2012;Ogbolu et al, 2020;Afolayan et al, 2022). It is well known that ST2541 and others 162,155,297) belong to the global lineage associated with ESBL in E. coli isolated from dogs in Asia, Europe, and America lpfA,sitA,lpfA,lpfA,sitA, traT- 5, terC-23, lpfA, gad-, hra-11, hra-6, F17a(5), f17G-6 Commensal ST13029/B1 terC-5, terC-23, lpfA, gad-, astA-4, tsh-3, ompT-, sitA IncI1-I-α, IncX1.4 bla TEM-84 , tetA Commensal terC-5, terC-23, lpfA, gad-, hra-11, hra-6, F17a(5) Nevertheless, the E. coli phylogroup structure A (n=8,25.0%) and B1 (n=21,67.74%) agree with the previous report of Vega-Manriquez and colleagues who reported a similar pattern of phylogroup A (n=5) and B1 (n=21) in E. coli strains isolated from dogs (Vega-Manriquez et al, 2020).…”