Pandemic ST131 Escherichia coli presenting the UPEC/EAEC and ExPEC/EAEC hybrid pathotypes recovered from extraintestinal infections in a clinical setting of the Brazilian Amazon region

Escherichia coli is part of the commensal microbiota of humans and animals gut. However, they may become pathogenic due to the acquisition of virulence factors that provide the ability to cause intestinal or extraintestinal infections, which makes E. coli the main cause of diarrheagenic diseases and urinary tract infections (UTIs) worldwide, respectively. Some strains, known as hybrids, may harbour a mix of virulence determinants of both diarrheagenic (DEC) and extraintestinal E. coli (ExPEC) pathotypes. Reports of hybrid E. coli in Brazil are rare, and the lineages associated with such pathotypes were poorly explored. This study aimed to characterize E. coli strains recovered from extraintestinal infections in a clinical setting of the Brazilian Amazon Region by means of lineage determination, antibiotic resistance profile, and investigation of DEC and ExPEC virulence markers. Fifteen ExPEC strains were recovered from distinct extraintestinal sites from inpatients of the General Hospital of Roraima (GHR), placed in the Brazilian Amazon region. Antibiotic susceptibility test revealed that all strains were multidrug-resistant and most of them, including those recovered from urine, were resistant to fluoroquinolones, the main therapeutic option for treating UTIs, probably due to the presence of Ser83Leu and Asp87Asn substitutions in GyrA. The MLST analysis revealed the polyclonal nature of these ExPEC strains since 11 STs were determined, including local and pandemic lineages, such as ST69 and ST131. Among the 15 isolates, 12 were classified as hybrids, due to the presence of the aggR virulence marker of the Enteroaggregative E. coli (EAEC) pathotype together with at least one ExPEC (iutA, KPSMTII, sfaDE, papC, afaBC, iucD) or Uropathogenic E. coli (UPEC) (vat, fuyA, chuA and yfcV) virulence determinants. These UPEC/EAEC (n=10) and ExPEC/EAEC (n=2) hybrid strains were found among distinct lineages, including new STs, and phylogroups (ST131/B2; ST1196/AxB1; ST9403/A; ST12394/A; NEW1-CC14/B2; NEW2-CC155/B1; NEW3-CC155/B1; NEW4-CC131/B2) and, for the first time, a hybrid phenotype was found in the pandemic ST131 lineage in Brazil. Therefore, this study provides new information on the epidemiological scenario of hybrid E. coli strains, contributing to a better understanding of the occurrence and pathogenic potential of these organisms.