Whole genome sequencing of ESBL-producing Escherichia coli isolates recovered from humans, animals and environmental sources in Accra, Ghana: WHO tricycle pilot project

Extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli (ESBL-Ec) significantly impacts patient outcomes, and has gained global attention. This study employed whole-genome sequencing to profile ESBL-Ec isolated from animals, humans and environmental sources in Ghana. E. coli isolated from environmental (rivers, slaughter slabs, wastewater samples), human (blood and faecal samples) and animal (caecal samples) specimens were confirmed using MALDI-TOF MS. ESBL production was detected using the double disk diffusion method. Whole genome sequencing was performed on ESBL-positive isolates. Using bioinformatics tools, sequence data analysis was performed to determine antimicrobial resistance (AMR) and virulence genes, plasmid replicons and genetic relatedness of ESBL-positive isolates. The sequenced ESBL-Ec isolates ( n = 190) originated from the environment (60.5%, 115/190), animals (20.5%, 39/190), and humans (18.9%, 36/190). Several AMR genes [ aph(3’’)-Ib , aph(6)-Id , bla CTX−M−15 , bla TEM−1B , dfrA14 , qnrS1 , sul2 , tet(A) ] were common to all three sources. The most prevalent AMR genes in the environment were bla CTX−M−15 (90.4%, 104/115) and sul2 (68.7%, 79/115), which encode resistance to beta-lactams and sulphonamides respectively. These genes were also predominant in human isolates. Among ESBL-Ec genomes from animals, genes encoding resistance to beta-lactams [ bla CTX−M−15 ; (64.1%, 25/39)] and tetracyclines [ tetA ; (64.1%, 25/39)] were prevalent. Most genomes (86.3%) possessed plasmid replicons, with majority of the replicons being IncFIB(AP001918) (46.8%, 89/190) and IncFIA (32.1%, 61/190). The genomes predominantly harboured virulence genes responsible for adhesion ( csgA , nlpI , yehD , fimH , fdeC ), invasion ( hlyE , aslA ), acid resistance ( gad ), tellurite resistance ( terC ), as well as the hha gene, which regulates the expression of virulence genes. Among all three sources, the predominant sequence types were ST10 (10.5%, 20/190), ST167 (8.9%, 17/190), ST38 (6.8%, 13/190), ST3580 (5.8%, 11/190) and ST46 (5.3%, 10/190). ESBL-Ec isolates mostly belonged to serotype O89:H10 (10.0%, 19/190), O8:H4 (6.32%, 12/190), O89:H9 (5.8%, 11/190) and O153:H9 (5.8%, 11/190). The majority of the genomes were found to belong to phylogroup A (47.9%, 91/190) followed by B1 (30.5%, 58/190) and D (10.5%, 20/190). Clusters of ESBL-Ec at a threshold of ≤ 10 allele pairwise differences were identified across humans, animals, and the environment in Ghana, demonstrating high genetic relatedness and potential shared clonal lineages across sectors. Whole-genome sequencing provided valuable insights into the sequence types, resistance gene profiles, and virulence gene content of ESBL-Ec strains derived from humans, animals, and environmental samples within our setting. The detection of global ESBL-Ec clones across various sources indicates their widespread distribution emphasizing the potential for transmission within the One Health framework. These findings highlight the critical need for continuous surveillance to monitor the rise and spread of AMR bacteria, to guide effective integrated surveillance strategies.