Introduction:
Escherichia coli is the most abundant facultative anaerobic commensal microorganism of the gut microbiota. E. coli strains can also cause intra- or extra-intestinal infections. Antimicrobial resistance in E. coli is increasing, including drugs commonly used in clinical therapy, such as fluoroquinolones. Mutations in the chromosomal genes gyrA and parC are the main fluoroquinolone resistance mechanisms, but plasmid-mediated fluoroquinolone resistance determinants (DPRF) also play an important role in the resistance to this drug.
Objectives:
determine the prevalence of ciprofloxacin (CIP) resistant or DPRF-harboring E. coli correlating to demographic and clinical variables. Identify the phylogenetic groups and the presence of pathogenic extra-intestinal (ExPEC), in a cross-sectional study analysing faecal samples from individuals in the community of Rio de Janeiro.
Methodology:
Samples were obtained by an anal swab from healthy individuals who attended three Health Unities in Rio de Janeiro from 2015 to 2019. Demographic and clinical data were collected with a structured questionnaire. Fecal samples were seeded on MacConkey agar without/with antimicrobial selective pressure and identified by MALDI-TOF-MS. Antimicrobial susceptibility was performed according to the CLSI recommendations (2020). Identification of phylogenetic groups, DPR and virulence genes were performed by PCR. Mutations in gyrA and parC genes, and confirmation of the aac(6’)-Ib-cr variant were identified by sequencing. Statistical analyzes were performed using the chi-square or Fisher’s exact test (p<0.05).
Results:
A total of 623 E. coli isolates were identified, of which 13% were MDR, 9% CIP resistant and 7% DPRF-harboring. Considering other antimicrobials, the highest resistance rates were observed for ampicillin (26%), sulfamethoxazole-trimethoprim (19%), cefazolin (14%) and cefotaxime (8%). The prevalence of mutations in gyrA and parC was 47% and 40%, respectively. The most frequent phylogroups were A or C (49%), B2 (16%) and B1 (14%). The most frequent virulence genes were fimH (98%), fyuA (69%) and RPai (64%). Among B2, D/E or F phylogrups samples, 59% were classified as ExPEC. The use of antimicrobials was associated with gut colonization by CIP-resistant E. coli (p<0.01).
Conclusions:
The presence of ExPEC, CIP-resistant and DPRF-harboring isolates in the gut microbiota may represent a threat to possible infectious that could be difficult to treat.
