High levels of gut carriage of antimicrobial-resistant Escherichia coli in community settings in Rio de Janeiro, Brazil

Abstract

The prevalence and risk factors for gut carriage of antimicrobial-resistant Escherichia coli among individuals living in the community in Rio de Janeiro, Brazil, are unknown. The aim of this study was to determine the prevalence of colonization with antimicrobial-resistant E. coli, including isolates producing ESBL and harboring plasmid-mediated quinolone resistant (PMQR) genes in this community. We performed a cross-sectional study and analyzed fecal specimens of individuals attending outpatient clinics in the city from January 2015 to July 2019. We investigated susceptibility to antimicrobial agents by disc diffusion tests and used PCR to determine ESBL types, PMQR, and the virulence genes that characterize an isolate as extraintestinal pathogenic E. coli (ExPEC). Among the 623 subjects, 212 (34%) carried an isolate resistant to at least one of the tested antimicrobial agents, with the highest frequencies of resistance to ampicillin (26%), trimethoprim-sulfamethoxazole (19%), cefazolin (14%), and ciprofloxacin (CIP, 9%). In addition, 13% (81) of subjects carried a multidrug-resistant-E. coli (MDR-E), including 47 (8% of all isolates) ESBL-producing E. coli (ESBL-E), mainly of CTX-M-8 (15, 32%) and CTX-M-15 (9, 20%) types. PMQR genes were present in 7% (42) of all isolates, including 60% (32) of the 53 resistant to CIP. Previous use of antimicrobial agents, particularly fluoroquinolones, was a risk factor for colonization with MDR-E (25%, 20/81 vs 13%, 70/542, p = 0.01), ESBL-E (28%, 13/47, vs 13%, 77/576, p = 0.01), and resistance to CIP (26%, 14/53, vs 12%, 70/570, p = 0.01). The most pathogenic phylogroups B2, C, and D were 37% of the MDR-E, 30% of the ESBL-E, 38% of the CIP-resistant, and 31% of PMQR gene carrying E. coli isolates. We show that carriage of MDR-E (mostly ESBL-E) reached high levels in the community in Rio de Janeiro, increased by the selection of antimicrobial agents. Much of the resistant E. coli isolates are potential pathogenic strains. The widespread use of antimicrobial agents during the COVID-19 pandemic in Brazil may have worsened this picture.

Occurrence of extended‐spectrum β‐lactamases‐producing Escherichia coli isolates over gradient pollution in an urban tropical estuary

“…A recent survey assessed the prevalence of community gastrointestinal colonisation by antimicrobial‐resistant E. coli in the city of Rio de Janeiro. Between 2015 and 2019, Rodrigues et al (2022) estimated that 8% of individuals in this metropolis carry ESBL‐producing E. coli , while between 2% and 4% of individuals carry potentially AmpC‐producing E. coli (CFO/AMC resistance) and no individual appeared to carry carbapenemase‐producing E. coli .…”

“…Our finding on the predominance of bla CTX‐M among ESBL‐producing E. coli strains isolated in the GB is consistent with observations from studies carried out in other settings, such as clinical (Carvalho et al, 2021), and community (de Souza et al, 2020) being humans, as well as farmed (Botelho et al, 2015), and wild (de Jesus et al, 2019) animals. Rodrigues et al (2022) observed that the prevalence of bla CTX‐M was 98% in ESBL‐producing E. coli strains isolated from individuals in the community in Rio de Janeiro. Therefore, the occurrence of ESBL genes from ESBL‐producing E. coli strains in GB waters seems to be associated with their occurrence in human settings.…”