Population structure of Escherichia coli isolated from the human bloodstream, human and animal feces, and the environment in northern Tanzania

Abstract

Background: Extraintestinal pathogenic Escherichia coli (ExPEC) are a leading cause of human bloodstream infections (BSI) in sub-Saharan Africa, yet few studies have characterized African strains implicated in BSI or explored their potential reservoirs.

Methods: We enrolled febrile patients at two hospitals in Moshi, Tanzania, 2007-2019, and performed blood cultures. Whole genome sequencing was conducted on E. coli originating from the bloodstream to characterize sequence types (STs), serotypes, and theoretical coverage of a 9-valent ExPEC polysaccharide conjugate vaccine (ExPEC9V). Separately, we evaluated 601 E. coli whole genome sequences from humans, animals, and environmental sources in nearby communities. We assessed genetic relatedness between bloodstream and community isolates based on single-nucleotide polymorphisms and allele differences.

Findings: Of 3,046 participants receiving blood culture, 48 (0.2%) had BSI yielding 48 E. coli isolates. The median (range) age of participants with E. coli BSI was 40.7 (0.3-89.0) years, and 32 (68.1%) were female. We identified 16 STs including ST131 (n=16, 33.3%), ST73 (n=10, 20.8%), and ST69 (n=6, 12.5%), and 19 O groups including O25 (n=13, 27.1%), O6 (n=10, 20.3%), O17 (n=4, 8.3%), and O18 (n=4, 8.3%). Theoretical coverage for an ExPEC9V was 72.9%. None of the bloodstream and community E. coli pairs were closely related.

Conclusions: We found a high diversity of sequence types among E. coli human bloodstream isolates in Tanzania. Despite this diversity, we observed that an EXPEC9V in development would provide good coverage. Reservoir attribution studies at finer spatial and temporal scales may better identify transmission networks and reservoirs of ExPECs.

Keywords: Escherichia coli; Africa; Tanzania; bacteremia; whole genome sequencing.