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.