Genomic analysis of multidrug-resistant Escherichia coli from Urban Environmental water sources in Accra, Ghana, Provides Insights into public health implications

Rebecca Tettey; Beverly Egyir; Prudence Tettey; John Arko-Mensah; Samuel Ofori Addo; Christian Owusu-Nyantakyi; William Boateng; Julius Fobil

doi:10.1371/journal.pone.0301531

Genomic analysis of multidrug-resistant Escherichia coli from Urban Environmental water sources in Accra, Ghana, Provides Insights into public health implications

PLoS One. 2024 May 24;19(5):e0301531. doi: 10.1371/journal.pone.0301531. eCollection 2024.

Authors

Rebecca Tettey¹, Beverly Egyir^{2

3}, Prudence Tettey¹, John Arko-Mensah^{1

2}, Samuel Ofori Addo³, Christian Owusu-Nyantakyi³, William Boateng³, Julius Fobil²

Affiliations

¹ Department of Biological, Environmental, and Occupational Health Science, School of Public Health, College of Health Sciences, University of Ghana, Accra, Ghana.
² West African Center for Global Environmental & Occupational Health, College of Health Sciences, University of Ghana, Accra, Ghana.
³ Department of Bacteriology, Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Accra, Ghana.

Abstract

Wastewater discharge into the environment in resource-poor countries poses a threat to public health. Studies in this area within these countries are limited, and the use of high-throughput whole-genome sequencing technologies is lacking. Therefore, understanding of environmental impacts is inadequate. The present study investigated the antibiotic resistance profiles and diversity of beta-lactamases in Escherichia coli strains isolated from environmental water sources in Accra, Ghana. Microbiological analyses were conducted on wastewater samples from three hospitals, a sewage and wastewater treatment plant, and water samples from two urban surface water bodies. Confirmed isolates (N = 57) were selected for phenotypic antibiotic resistance profiles. Multi-drug-resistant isolates (n = 25) were genome sequenced using Illumina MiSeq sequencing technology and screened for sequence types, antibiotic resistance, virulence and beta-lactamase genes, and mobile genetic elements. Isolates were frequently resistant to ampicillin (63%), meropenem (47%), azithromycin (46%), and sulfamethoxazole-trimethoprim (42%). Twenty different sequence types (STs) were identified, including clinically relevant ones such as ST167 and ST21. Five isolates were assigned to novel STs: ST14531 (n = 2), ST14536, ST14537, and ST14538. The isolates belonged to phylogroups A (52%), B1 (44%), and B2 (4%) and carried β-lactamase (TEM-1B, TEM-1C, CTX-M-15, and blaDHA-1) and carbapenemase (OXA-1, OXA-181) resistance genes. Dominant plasmid replicons included Col440I (10.2%) and IncFIB (AP001918) (6.8%). Polluted urban environments in Accra are reservoirs for antibiotic-resistant bacteria, posing a substantial public health risk. The findings underscore the need for targeted public health interventions to mitigate the spread of antibiotic-resistant bacteria and protect public health.

Copyright: © 2024 Tettey et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

MeSH terms

Anti-Bacterial Agents / pharmacology
Drug Resistance, Multiple, Bacterial* / genetics
Escherichia coli* / drug effects
Escherichia coli* / genetics
Escherichia coli* / isolation & purification
Genome, Bacterial
Genomics
Ghana
Humans
Microbial Sensitivity Tests
Phylogeny
Public Health
Sewage / microbiology
Wastewater* / microbiology
Water Microbiology
Whole Genome Sequencing
beta-Lactamases* / genetics

Substances

beta-Lactamases
Wastewater
Anti-Bacterial Agents
Sewage

Grants and funding

This work was partially supported by the BANGA Africa Project (Funded by the Carnegie Fund) awarded to RT, the CAPREX project (RY89) and the SeqAfrica project awarded to BE. Identification of bacteria and antimicrobial susceptibility testing was supported by CAPREX project (RY89). Whole-genome sequencing of E. coli was funded by the SeqAfrica project. The SeqAfrica project is funded by the Department of Health and Social Care’s Fleming Fund using UK aid. The sources of funding were not involved in the study design, sample collection, data analysis, or interpretation.