Prevalence of antimicrobial resistance genes and integrons in commensal Gram-negative bacteria in a college community

Abstract

Although the human intestinal microbiome has been shown to harbor antimicrobial drug-resistance genes (ARG), the prevalence of such genes in a healthy population and their impact on extraintestinal infections that occur in that community are not well established. This study sought to identify ARG prevalence and their mobile elements in the intestines of a healthy community population at a California university, and compared these genes to those found in uropathogenic Escherichia coli isolated from patients with community-acquired urinary tract infection (CA-UTI). We isolated Gram-negative bacteria (GNB) from fecal samples of healthy volunteers and screened them by polymerase chain reaction (PCR) for ARG encoding resistance against ampicillin (AMP), trimethoprim-sulfamethoxazole (TMP-SMX), gentamicin (GENT), and colistin (COL). We found antimicrobial resistant GNB from 85 (83%) of 102 non-redundant rectal swab samples. Sixty-seven (66%) of these samples contained ß-lactamase genes (blaTEM, blaSHV, blaCTX-M, blaOXA,blaOXY), dihydrofolate reductase (DHFR) genes (dhfr-A17, dhfr-A7, dhfr-A5, dhfr-A21, dhfr-A1, dhfr-A15, and dhfr-B3), and aminoglycoside resistance genes (aadA5, aadA1, and aadB). Integron sequences were found in 37 fecal samples. These genes were found in 11 different GNB species isolated from the fecal samples. The same ARG were found in E. coli strains isolated from patients with CA-UTI examined at the college outpatient health clinic. The high prevalence of clinically-common ARG and integrons harbored by GNB in the intestine of a healthy population suggest that human intestines may serve as a major reservoir of these mobile ARG that appear in E. coli strains causing extraintestinal infections in the same community.ImportanceIncreasing frequency of antimicrobial resistance (AMR) in human pathogenic bacteria has compromised our ability to treat infections. Since mobile antibiotic resistance genes (ARG) are readily exchanged between different species of bacteria through horizontal gene transfer, there is interest in investigating sources of these genes. The normal intestinal flora has been shown to contain a wide variety of ARG, which may have been introduced via food-containing AMR bacteria. We sought to assess the prevalence of ARG carriage in the intestines of a healthy population and determine if these ARG are found in E. coli strains that cause community-acquired urinary tract infection (CA-UTI) in the same community. Our findings indicate that the human intestine may serve as an important reservoir as well as a site in which ARG are transferred into E. coli that cause UTI. Further research is needed to reduce ARG carriage and devise new strategies to prevent AMR infections.

Multilocus sequence typing of Escherichia coli isolates from urinary tract infection patients and from fecal samples of healthy subjects in a college community

“…We excluded subjects with any medical history of urinary tract corrective surgery or abnormality, bladder catheterization, or hospitalization in the 6 months before the fecal sample collection. As part of a separate study (Rubin, Mussio, Xu, Suh, & Riley, 2020), participants were given a pre‐addressed kit containing a rectal swab in Cary‐Blair transport media (Becton Dickinson BBLTM), two biosafety bags, detailed collection instructions, and a questionnaire asking about age, gender, recent antibiotic use, history of UTI, and lifestyle characteristics. Participants were instructed to send the rectal swab and the completed questionnaire back to the study laboratory via the United States Postal Service (USPS) immediately after collection.…”

Risk factors for fecal carriage of multidrug-resistantEscherichia coliin a college community: a penalized regression model

“…As far as we know, this is the first study to find association of dietary habits with carriage of multidrug-resistant E. coli in healthy United States adult population. Previously, our fecal sample collection and surveillance conducted at the same college community from June to October 2018 identified the prevalence of drug resistant Gram-negative bacteria among healthy volunteers and ARGs carried by these fecal bacteria [23]. We reported the high prevalence of clinically common ARGs and integrons harbored by these Gram-negative bacteria [23].…”

“…Previously, our fecal sample collection and surveillance conducted at the same college community from June to October 2018 identified the prevalence of drug resistant Gram-negative bacteria among healthy volunteers and ARGs carried by these fecal bacteria [23]. We reported the high prevalence of clinically common ARGs and integrons harbored by these Gram-negative bacteria [23]. In the present study, we aimed to identify risk factors for carriage of commensal drug-resistant E. coli.…”

“…In our previous study, we found 81% of healthy volunteers at a college community to harbor intestinal drug-resistant commensal Gram-negative bacteria [23]. They included 12 species of Gram-negative bacteria that harbored a variety of ARGs and integrons that are frequently found among extraintestinal pathogenic E. coli (ExPEC) [23]. Risk factors for the carriage of these ARGs, however, were not determined.…”

Prevalence of beta-lactam drug-resistance genes in commensal Escherichia coli contaminating ready-to-eat lettuce

“…The analysis of beta-lactamase genes was performed according to previously 100 published reports (16,17). Primers (Table S1) Fisher's exact test with significance set at p ≤0.05.…”