Tracking antimicrobial resistance transmission in urban and rural communities in Bangladesh: a One Health study of genomic diversity of ESBL-producing and carbapenem-resistant Escherichia coli

Abstract

Antimicrobial resistance (AMR) poses a significant threat to global health and sustainable development goals, especially in low- and middle-income countries (LMICs). This study aimed to understand the transmission of AMR between poultry, humans, and the environment in Bangladesh using a One Health approach. We analyzed the whole genome sequences (WGS) of 117 extended-spectrum β-lactamase-producing Escherichia coli (ESBL-Ec) isolates, with 46 being carbapenem resistant. These isolates were obtained from human (n = 20) and poultry feces (n = 12), as well as proximal environments (wastewater) (n = 85) of three different study sites, including rural households (n = 48), rural poultry farms (n = 20), and urban wet markets (n = 49). The WGS of ESBL-Ec isolates were compared with 58 clinical isolates from global databases. No significant differences in antibiotic resistance genes (ARGs) were observed in ESBL-Ec isolated from humans with and without exposure to poultry. Environmental isolates showed higher ARG diversity than human and poultry isolates. No clonal transmission between poultry and human isolates was found, but wastewater was a reservoir for ESBL-Ec for both. Except for one human isolate, all ESBL-Ec isolates were distinct from clinical isolates. Most isolates (77.8%) carried at least one plasmid replicon type, with IncFII being the most prevalent. IncFIA was predominant in human isolates, while IncFII, Col(MG828), and p0111 were common in poultry. We observed putative sharing of ARG-carrying plasmids among isolates, mainly from wastewater. However, in most cases, bacterial isolates sharing plasmids were also clonally related, suggesting clonal spread was more probable than just plasmid transfer.

Importance: Our study underscores that wastewater discharged from households and wet markets carries antibiotic-resistant organisms from both human and animal sources. Thus, direct disposal of wastewater into the environment not only threatens human health but also endangers food safety by facilitating the spread of antimicrobial resistance (AMR) to surface water, crops, vegetables, and subsequently to food-producing animals. In regions with intensive poultry production heavily reliant on the prophylactic use of antibiotics, compounded by inadequate waste management systems, such as Bangladesh, the ramifications are particularly pronounced. Wastewater serves as a pivotal juncture for the dissemination of antibiotic-resistant organisms and functions as a pathway through which strains of human and animal origin can infiltrate the environment and potentially colonize new hosts. Further research is needed to thoroughly characterize wastewater isolates/populations and understand their potential impact on interconnected environments, communities, and wildlife.

Keywords: ESBL-producing E. coli; antibiotic resistance genes; clonal spread; wastewater; whole genome sequencing.

Fig 1

Statistical tests showing the difference in diversity of ARGs between isolates from three different sources (human, poultry, and environment) and study sites (urban wet markets, rural households, and rural poultry farms). Violin plots comparing the ARG diversity among isolates from different (A) sources and (B) study sites through Kruskal-Wallis test and Dunn pairwise test. Principal coordinate analysis (PCoA) of Jaccard distances of ARGs between isolates from different (C) sources and (D) study sites.

Fig 2

Maximum-likelihood SNP-based phylogenetic tree of 117 ESBL-E. coli isolates from humans (n = 20), poultry (n = 12), and environmental sources (n = 85) in various poultry-intensive sites in Bangladesh. The tree was constructed by trimmed reads and was assembled using Unicycler v0.50. The contigs were annotated using Bakta v1.7.0. The pangenome was calculated using Roary v3.13.0. The SNPs were extracted from the resulting multi-fasta alignment using SNP-sites v2.5.1. A tree was generated from the extracted SNPs using IQtree v2.2.0.3 with bootstrapping set to 1,000 and a standard model of substitution. The resulting SNP tree was visualized with iTOL v5. Blue and green highlights indicate a clonal relationship between isolates (<22 SNPs). Colored rings represent source (inner ring), study site (second ring from the center), phylogroup (third ring), MLST (fourth ring), and serotype (fifth ring).

Fig 3

Grapetree displaying an MSTree v2 generated using cgMLST V1 + HierCC V1. Node ID indicates study sites, such as wet markets, rural households, and rural poultry farms (LM, HH, PF, respectively), and clinical isolates. Colors indicate Clermont phylotype. Distance refers to the number of differing alleles. Combined nodes are <11 alleles different.

Fig 4

Partial maps of (A) IncH plasmid (256,496 bp, fully circularized) and (B) IncX plasmid (33,597 bp, fully circularized) recovered from isolate TR-110-DRW-K1. Annotations based on PROKKA output. Genes encoding hypothetical proteins are not shown. Additional curation of annotations was performed with CARD protein BLAST (for antibiotic resistance genes) and UniProt BLAST. Only ARGs with identity and coverage ≥90% are shown. Blue annotations denote potential mobile genetic elements, red annotations indicate antibiotic/biocide resistance genes, orange annotations correspond to virulence genes, and purple annotations relate to all other annotations.

Fig 5

Partial maps of (A) IncFII plasmid (104,057 bp, un-circularized), (B) IncFIA plasmid (75,415 bp, un-circularized), and (C) IncY plasmid (95,850 bp, fully circularized) recovered from isolate DL-185-SS2-K1. Circular maps of un-circularized plasmids are shown for visualization purposes. Annotations based on PROKKA output. Genes encoding hypothetical proteins are not shown. Additional curation of annotations was performed with CARD protein BLAST (for antibiotic resistance genes) and UniProt BLAST. Only ARGs with identity and coverage ≥90% are shown. Blue annotations denote potential mobile genetic elements, red annotations indicate antibiotic/biocide resistance genes, orange annotations correspond to virulence genes, and purple annotations relate to all other annotations.