The Journal of infectious diseases · 2026
Population Structure of Escherichia coli Isolated From the Human Bloodstream, Human and Animal Feces, and the Environment in Northern Tanzania.
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Madut Deng B, Rubach Matthew P, Scheutz Flemming, Call Douglas R, Gogry Firdoos A, Carugati Manuela, Kalengo Nathaniel, Marandu Annette, Maze Michael J, Morrissey Anne B, Lwezaula Bingileki F, Mmbaga Blandina T, Kilonzo Kajiru G, Maro Venance P, Crump John A
Аннотация
BACKGROUND: 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.
METHODS: 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.
FINDINGS: 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.
CONCLUSIONS: 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.
METHODS: 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.
FINDINGS: 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.
CONCLUSIONS: 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.