Population Structure of Escherichia coli Isolated From the Human Bloodstream, Human and Animal Feces, and the Environment in Northern Tanzania.

Abstract

Extraintestinal pathogenic Escherichia coli (ExPEC) are a leading cause of human bloodstream infections (BSIs) in sub-Saharan Africa, yet few studies have characterized African strains implicated in BSI or explored their potential reservoirs. We enrolled febrile patients at 2 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. Of 3046 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. We found a high diversity of STs 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.