Gut carriage of antimicrobial resistance genes among young children in urban Maputo, Mozambique: Associations with enteric pathogen carriage and environmental risk factors

• Type of Material: Article
• Authors: David Berendes, Emory University; Jackie Knee, Georgia Institute of Technology; Trent Sumner, Georgia Institute of Technology; Drew Capone, Georgia Institute of Technology; Amanda Lai, Georgia Institute of Technology; Anna Wood, Emory University; Siddhartha Patel, Georgia Institute of Technology; Rassul Nala, National Institutes of Health; Oliver Cumming, London School of Hygiene and Tropical Medicine; Joe Brown, Georgia Institute of Technology
• Language: English
• Date: 2019-11-22
• Publisher: Public Library Science
• Publication Version: Final Published Version
• Copyright Statement: This is an open access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose.
• License: Creative Commons Attribution 4.0 International
• Final Published Version (URL): http://dx.doi.org/10.1371/journal.pone.0225464
• Title of Journal or Parent Work: PLOS One
• Volume: 14
• Issue: 11
• Start Page: e0225464
• End Page: e0225464
• Grant/Funding Information: Funding for this study came from the United States Agency for International Development under Translating Research to Action (Cooperative Agreement # GHS-A-00-09-00015-00, usaid.gov), the Bill and Melinda Gates Foundation (OPP1137224, gatesfoundation.org), and subaward T846289 from the Emory HERCULES center (prime award: NIH/NIEHS/5P50ES026071-02, niehs.nih.gov).; JB and OC obtained all funds.
• Keywords: BACTERIA; RESISTOME; Science & Technology - Other Topics; Multidisciplinary Sciences; ANTIBIOTIC-RESISTANCE; PANEL; FECAL SLUDGE MANAGEMENT; Science & Technology; INFECTION; TETRACYCLINE RESISTANCE; SANITATION; MECHANISMS; ESCHERICHIA-COLI

Abstract

This is an open access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the Creative Commons CC0 public domain dedication. Because poor sanitation is hypothesized as a major direct and indirect pathway of exposure to antimicrobial resistance genes (ARGs), we sought to determine a) the prevalence of and b) environmental risk factors for gut carriage of key ARGs in a pediatric cohort at high risk of enteric infections due to poor water, sanitation, and hygiene (WASH) conditions. We investigated ARGs in stool from young children in crowded, low-income settlements of Maputo, Mozambique, and explored potential associations with concurrent enteric pathogen carriage, diarrhea, and environmental risk factors, including WASH. We collected stool from 120 children <14 months old and tested specimens via quantal, multiplex molecular assays for common bacterial, viral, and protozoan enteric pathogens and 84 ARGs encoding potential resistance to 7 antibiotic classes. We estimated associations between ARG detection (number and diversity detected) and concurrently-measured enteric pathogen carriage, recently-reported diarrhea, and risk factors in the child’s living environment. The most commonly-detected ARGs encoded resistance to macrolides, lincosamides, and streptogramins (100% of children); tetracyclines (98%); β-lactams (94%), aminoglycosides (84%); fluoroquinolones (48%); and vancomycin (38%). Neither concurrent diarrhea nor measured environmental (including WASH) conditions were associated with ARG detection in adjusted models. Enteric pathogen carriage and ARG detection were associated: on average, 18% more ARGs were detected in stool from children carrying bacterial pathogens than those without (adjusted risk ratio (RR): 1.18, 95% confidence interval (CI): 1.02, 1.37), with 16% fewer ARGs detected in children carrying parasitic pathogens (protozoans, adjusted RR: 0.84, 95% CI: 0.71, 0.99). We observed gut ARGs conferring potential resistance to a range of antibiotics in this at-risk cohort that had high rates of enteric infection, even among children <14 months-old. Gut ARGs did not appear closely correlated with WASH, though environmental conditions were generally poor. ARG carriage may be associated with concurrent carriage of bacterial enteric pathogens, suggesting indirect linkages to WASH that merit further investigation.