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

• Published in: Brazilian journal of microbiology Vol. 53; no. 1; pp. 205 - 212
• Main Authors: de Pinho Rodrigues, Káris Maria, de Rezende, Danielle Ferreira, Pinto, Michelle Pessanha, dos Santos Tufic-Garutti, Samantha, Ramalho, João Vitor Almeida, de Araújo Longo, Luís Guilherme, de Carvalho Girão, Valéria Brígido, de Oliveira, Gabriela Caramano, Vilar, Lucas Cecílio, Moreira, Beatriz Meurer
• Format: Journal Article
• Language: English
• Published: Cham Springer International Publishing 01.03.2022; Springer Nature B.V
• Subjects: Ampicillin; Anti-Bacterial Agents - pharmacology; Antibiotics; Antiinfectives and antibacterials; Antimicrobial agents; beta-Lactamases - genetics; Biomedical and Life Sciences; Brazil - epidemiology; Cefazolin; Ciprofloxacin; Clinical Microbiology - Research Paper; Colonization; COVID-19; Cross-Sectional Studies; Diffusion tests; Drug Resistance, Multiple, Bacterial; E coli; Escherichia coli; Escherichia coli Infections - epidemiology; Escherichia coli Infections - microbiology; Fluoroquinolones; Food Microbiology; Genes; Humans; Life Sciences; Medical Microbiology; Microbial Ecology; Microbial Genetics and Genomics; Microbial Sensitivity Tests; Microbiology; Multidrug resistance; Mycology; Pandemics; Penicillin; Public health; Risk analysis; Risk factors; SARS-CoV-2; Sulfamethoxazole; Trimethoprim; Trimethoprim-sulfamethoxazole; Virulence; Brazil; Rio de Janeiro Brazil; ESBL; Antimicrobial resistance; Carriage; Escherichia coli
• ISSN: 1517-8382; 1678-4405; 1678-4405
• DOI: 10.1007/s42770-021-00673-2

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.