Estimating the Population-level Prevalence of Antimicrobial-resistant Enteric Bacteria from Latrine Samples

Overview

Journal Antimicrob Resist Infect Control

Publisher Biomed Central

Specialty Infectious Diseases

Date 2022 Aug 20

PMID 35987780

Authors

Sylvia Omulo

Maina Mugoh

Joshua Obiya

Moshe Alando

Douglas R Call

Affiliations

Soon will be listed here.

Abstract

Background: Logistical and economic barriers hamper community-level surveillance for antimicrobial-resistant bacteria in low-income countries. Latrines are commonly used in these settings and offer a low-cost source of surveillance samples. It is unclear, however, whether antimicrobial resistance prevalence estimates from latrine samples reflect estimates generated from randomly sampled people.

Methods: We compared the prevalence of antimicrobial-resistant enteric bacteria from stool samples of people residing in randomly selected households within Kibera-an informal urban settlement in Kenya-to estimates from latrine samples within the same community. Fecal samples were collected between November 2015 and Jan 2016. Presumptive Escherichia coli isolates were collected from each household stool sample (n = 24) and each latrine sample (n = 48), resulting in 8935 and 8210 isolates, respectively. Isolates were tested for resistance to nine antibiotics using the replica-plating technique. Correlation- and Kolmogorov-Smirnov (K-S) tests were used to compare results.

Results: Overall, the prevalence values obtained from latrine samples closely reflected those from stool samples, particularly for low-prevalence (< 15%) resistance phenotypes. Similarly, the distribution of resistance phenotypes was similar between latrine and household samples (r > 0.6; K-S p-values > 0.05).

Conclusions: Although latrine samples did not perfectly estimate household antimicrobial resistance prevalence, they were highly correlated and thus could be employed as low-cost samples to monitor trends in antimicrobial resistance, detect the emergence of new resistance phenotypes and assess the impact of community interventions.

References

Beukes L, King T, Schmidt S . Assessment of pit latrines in a peri-urban community in KwaZulu-Natal (South Africa) as a source of antibiotic resistant E. coli strains. Int J Hyg Environ Health. 2017; 220(8):1279-1284. DOI: 10.1016/j.ijheh.2017.08.002. View

Caudell M, Mair C, Subbiah M, Matthews L, Quinlan R, Quinlan M . Identification of risk factors associated with carriage of resistant Escherichia coli in three culturally diverse ethnic groups in Tanzania: a biological and socioeconomic analysis. Lancet Planet Health. 2018; 2(11):e489-e497. PMC: 6215761. DOI: 10.1016/S2542-5196(18)30225-0. View

Erb S, DMello-Guyett L, Malebo H, Njee R, Matwewe F, Ensink J . High prevalence of ESBL-Producing in private and shared latrines in an informal urban settlement in Dar es Salaam, Tanzania. Antimicrob Resist Infect Control. 2018; 7:3. PMC: 5756337. DOI: 10.1186/s13756-017-0292-y. View

Lautenbach E, Bilker W, Tolomeo P, Maslow J . Impact of diversity of colonizing strains on strategies for sampling Escherichia coli from fecal specimens. J Clin Microbiol. 2008; 46(9):3094-6. PMC: 2546773. DOI: 10.1128/JCM.00945-08. View

Nadimpalli M, Marks S, Montealegre M, Gilman R, Pajuelo M, Saito M . Urban informal settlements as hotspots of antimicrobial resistance and the need to curb environmental transmission. Nat Microbiol. 2020; 5(6):787-795. DOI: 10.1038/s41564-020-0722-0. View

Livermore D . beta-Lactamases: quantity and resistance. Clin Microbiol Infect. 1997; 3 Suppl 4:S10-S19. View

Hendriksen R, Munk P, Njage P, van Bunnik B, McNally L, Lukjancenko O . Global monitoring of antimicrobial resistance based on metagenomics analyses of urban sewage. Nat Commun. 2019; 10(1):1124. PMC: 6408512. DOI: 10.1038/s41467-019-08853-3. View

Prestinaci F, Pezzotti P, Pantosti A . Antimicrobial resistance: a global multifaceted phenomenon. Pathog Glob Health. 2015; 109(7):309-18. PMC: 4768623. DOI: 10.1179/2047773215Y.0000000030. View

Chopra I, Roberts M . Tetracycline antibiotics: mode of action, applications, molecular biology, and epidemiology of bacterial resistance. Microbiol Mol Biol Rev. 2001; 65(2):232-60 ; second page, table of contents. PMC: 99026. DOI: 10.1128/MMBR.65.2.232-260.2001. View

10.

Krzyzanowski Jr F, Zappelini L, Martone-Rocha S, Dropa M, Matte M, Nacache F . Quantification and characterization of Salmonella spp. isolates in sewage sludge with potential usage in agriculture. BMC Microbiol. 2015; 14:263. PMC: 4207900. DOI: 10.1186/s12866-014-0263-x. View

11.

van Elsas J, Semenov A, Costa R, Trevors J . Survival of Escherichia coli in the environment: fundamental and public health aspects. ISME J. 2010; 5(2):173-83. PMC: 3105702. DOI: 10.1038/ismej.2010.80. View

12.

Petersen T, Rasmussen S, Hasman H, Caroe C, Baelum J, Schultz A . Meta-genomic analysis of toilet waste from long distance flights; a step towards global surveillance of infectious diseases and antimicrobial resistance. Sci Rep. 2015; 5:11444. PMC: 4498435. DOI: 10.1038/srep11444. View

13.

Ramay B, Caudell M, Cordon-Rosales C, Archila L, Palmer G, Jarquin C . Antibiotic use and hygiene interact to influence the distribution of antimicrobial-resistant bacteria in low-income communities in Guatemala. Sci Rep. 2020; 10(1):13767. PMC: 7426860. DOI: 10.1038/s41598-020-70741-4. View

14.

Subbiah M, Caudell M, Mair C, Davis M, Matthews L, Quinlan R . Antimicrobial resistant enteric bacteria are widely distributed amongst people, animals and the environment in Tanzania. Nat Commun. 2020; 11(1):228. PMC: 6957491. DOI: 10.1038/s41467-019-13995-5. View

15.

Omulo S, Lofgren E, Mugoh M, Alando M, Obiya J, Kipyegon K . The impact of fecal sample processing on prevalence estimates for antibiotic-resistant Escherichia coli. J Microbiol Methods. 2017; 136:71-77. DOI: 10.1016/j.mimet.2017.03.006. View

16.

Beukes L, Schmidt S . Antibiotic resistance profiles of coagulase-positive and coagulase-negative staphylococci from pit latrine fecal sludge in a peri-urban South African community. Folia Microbiol (Praha). 2018; 63(5):645-651. DOI: 10.1007/s12223-018-0605-4. View

17.

Omulo S, Lofgren E, Lockwood S, Thumbi S, Bigogo G, Ouma A . Carriage of antimicrobial-resistant bacteria in a high-density informal settlement in Kenya is associated with environmental risk-factors. Antimicrob Resist Infect Control. 2021; 10(1):18. PMC: 7821723. DOI: 10.1186/s13756-021-00886-y. View