Whole-Genome Characterisation of ESBL-Producing E. coli Isolated from Drinking Water and Dog Faeces from Rural Andean Households in Peru

Maria Luisa Medina-Pizzali; Apoorva Venkatesh; Maribel Riveros; Diego Cuicapuza; Gabriela Salmon-Mulanovich; Daniel Mäusezahl; Stella M Hartinger

doi:10.3390/antibiotics11050692

Whole-Genome Characterisation of ESBL-Producing E. coli Isolated from Drinking Water and Dog Faeces from Rural Andean Households in Peru

Antibiotics (Basel). 2022 May 20;11(5):692. doi: 10.3390/antibiotics11050692.

Authors

Maria Luisa Medina-Pizzali¹, Apoorva Venkatesh^{2

3}, Maribel Riveros⁴, Diego Cuicapuza⁵, Gabriela Salmon-Mulanovich^{1

6}, Daniel Mäusezahl^{1

2

3}, Stella M Hartinger^{1

2

3}

Affiliations

¹ Research Unit in Integral Development, Environment and Health, School of Public Health and Administration, Universidad Peruana Cayetano Heredia, Lima 15102, Peru.
² Department of Epidemiology and Public Health, Swiss Tropical and Public Health Institute, 4123 Allschwil, Switzerland.
³ University of Basel, 4001 Basel, Switzerland.
⁴ School of Medicine, Universidad Peruana Cayetano Heredia, Lima 15102, Peru.
⁵ Laboratory of Microbial Genomics, Department of Cellular and Molecular Sciences, School of Science and Philosophy, Universidad Peruana Cayetano Heredia, Lima 15102, Peru.
⁶ Institute for Earth, Nature and Energy, Pontificia Universidad Católica del Perú, Lima 15088, Peru.

Abstract

E. coli that produce extended-spectrum β-lactamases (ESBLs) are major multidrug-resistant bacteria. In Peru, only a few reports have characterised the whole genome of ESBL enterobacteria. We aimed to confirm the identity and antimicrobial resistance (AMR) profile of two ESBL isolates from dog faeces and drinking water of rural Andean households and determine serotype, phylogroup, sequence type (ST)/clonal complex (CC), pathogenicity, virulence genes, ESBL genes, and their plasmids. To confirm the identity and AMR profiles, we used the VITEK^®2 system. Whole-genome sequencing (WGS) and bioinformatics analysis were performed subsequently. Both isolates were identified as E. coli, with serotypes -:H46 and O9:H10, phylogroups E and A, and ST/CC 5259/- and 227/10, respectively. The isolates were ESBL-producing, carbapenem-resistant, and not harbouring carbapenemase-encoding genes. Isolate 1143 ST5259 harboured the astA gene, encoding the EAST₁ heat-stable toxin. Both genomes carried ESBL genes (bla_EC-15, bla_CTX-M-8, and bla_CTX-M-55). Nine plasmids were detected, namely IncR, IncFIC(FII), IncI, IncFIB(AP001918), Col(pHAD28), IncFII, IncFII(pHN7A8), IncI1, and IncFIB(AP001918). Finding these potentially pathogenic bacteria is worrisome given their sources and highlights the importance of One-Health research efforts in remote Andean communities.

Keywords: ESBL-producing E. coli; carbapenem resistance; one health; phylogenomic analysis; whole-genome sequencing.

Abstract

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