3.3. E. coli PMPU strain carried a wide resistome to antibiotics, heavy metals, and disinfectants
PMPU strain belonged to sequence type ST58 and serotype O102:H30. This strain harbored a resistome against antibiotics, heavy metals, and disinfectants. WGS analysis identified the presence of genes encoding resistance to cephalosporins (bla CTX-M-8 andbla TEM-1B), tetracyclines [tet(A) ], aminoglycosides [aph(3”)Ib and aph(6)-Id ], sulfonamides (sul2 ), and trimethoprim (dfrA8 ). In addition, PMPU strain showed mutations in gyrA (Ser-83-Leu and Asp-87-Asn) and parC (Ser-80-Iso) genes, conferring resistance to quinolones. Moreover, genes conferring resistance to heavy metals (i.e., lead, arsenic, copper, silver, antimony, zinc, tellurium, tungsten, magnesium, cobalt, nickel, manganese, cadmium, mercury, iron, molybdenum, chromium, selenium, and vanadium), and biocides commonly used as disinfectants in domiciliary and hospital settings [i.e., quaternary ammonium compounds (QACs), acridines, chlorhexidine, sodium dodecyl sulphate, ethidium bromide, hydrochloric acid, hydrogen peroxide, and sodium hydroxide] were found (Figure 2). Regarding to plasmidome in PMPU strain, IncI1 and IncQ1 plasmid replicons were detected.
E. coli ST58 is a globally disseminated clone previously reported in humans, food-production animals, wildlife and the environment, supporting a broad adaptation, persistence and a worldwide dissemination of this clone (McKinnon, Roy Chowdhury, & Djordjevic, 2018; Borges, Tarlton, & Riley, 2019; Zurfluh et al., 2019; EnteroBase, 2020; De Carvalho et al., 2020). In Brazil, E. coli ST58 has been isolated from humans, poultry, peri-urban wild animals, and polluted mangrove ecosystem (Sacramento et al., 2018; Borges et al., 2019; De Carvalho et al., 2020). On the other hand, MDR or ESBL-producing E. coliserotype O102:H30 has been recurrently identified in hospitalized human patients, mainly with urinary tract infection (Gonçalves et al., 2009; Cergole-Novella et al., 2010; Cergole-Novella, Pignatari, & Guth, 2015).
We further investigated the genomic relatedness among E. coli PMPU isolate identified in this study and 123 assembled genomes of E. coli belonging to ST58 from different sources of origin and countries, available in EnteroBase database (https://enterobase.warwick.ac.uk/). In the minimum spanning tree of the whole genome analysis based on the wgMLST scheme from EnteroBase, E. coli PMPU isolate showed high genetic relatedness compared to livestock isolates from Japan (ESC_QA8442AA_AS and ESC_QA8026AA_AS) and Belgium (ESC_QA7365AA_AS), an animal companion isolate from Canada (dog; ESC_YA3357AA_AS), and an environment isolate from Japan (ESC_HA7644AA_AS) (Figure 3). These phylogenetically related isolates were collected between 2013 and 2018, supporting rapid adaptation and dissemination of this E . coli clone.