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

Autoři: David Berendes aff001;  Jackie Knee aff002;  Trent Sumner aff002;  Drew Capone aff002;  Amanda Lai aff002;  Anna Wood aff003;  Siddhartha Patel aff002;  Rassul Nalá aff004;  Oliver Cumming aff005;  Joe Brown aff002
Působiště autorů: Division of Foodborne, Waterborne, and Environmental Diseases, U.S. Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America aff001;  School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, Georgia, United States of America aff002;  Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, Georgia aff003;  National Institute of Health, Maputo, Mozambique aff004;  Department of Disease Control, London School of Tropical Medicine and Hygiene, London, United Kingdom aff005
Vyšlo v časopise: PLoS ONE 14(11)
Kategorie: Research Article
doi: 10.1371/journal.pone.0225464


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.

Klíčová slova:

Antimicrobial resistance – Bacterial pathogens – Diarrhea – Children – Medical risk factors – Pathogens – Sanitation


1. CDDEP. State of the world’s antibiotics, 2015. 2015.

2. Rogawski ET, Platts-Mills JA, Seidman JC, John S, Mahfuz M, Ulak M, et al. Use of antibiotics in children younger than two years in eight countries: a prospective cohort study. Bull World Health Organ. 2016;95:49–61. doi: 10.2471/BLT.16.176123 28053364

3. Global Antibiotic Resistance Partnership, Mozambican Ministry of Health, Centro de investigacao em saude de manhica. Situation Analysis: Antibiotic Use and Resistance in Mozambique. 2015.

4. Keenan JD, Bailey RL, West SK, Arzika AM, Hart J, Weaver J, et al. Azithromycin to Reduce Childhood Mortality in Sub-Saharan Africa. N Engl J Med. 2018;1583–92.

5. Collignon P, Beggs JJ, Walsh TR, Gandra S, Laxminarayan R. Anthropological and socioeconomic factors contributing to global antimicrobial resistance: a univariate and multivariable analysis. Lancet Planet Heal [Internet]. 2018;2(9):e398–405.

6. Graham DW, Collignon P, Davies J, Larsson DGJ, Snape J. Underappreciated role of regionally poor water quality on globally increasing antibiotic resistance. Environ Sci Technol. 2014;48(20):11746–7. doi: 10.1021/es504206x 25330712

7. Graham DW, Giesen MJ, Bunce JT. Strategic approach for prioritising local and regional sanitation interventions for reducing global antibiotic resistance. Water (Switzerland). 2018;11(1).

8. Talukdar PK, Rahman M, Rahman M, Nabi A, Islam Z, Hoque MM, et al. Antimicrobial Resistance, Virulence Factors and Genetic Diversity of Escherichia coli Isolates from Household Water Supply in Dhaka, Bangladesh. PLoS One. 2013;8(4):1–8.

9. Ashbolt NJ, Amézquita A, Backhaus T, Borriello P, Brandt KK, Collignon P, et al. Human health risk assessment (HHRA) for environmental development and transfer of antibiotic resistance. Environ Health Perspect. 2013;121(9):993–1001. doi: 10.1289/ehp.1206316 23838256

10. Fletcher S. Understanding the contribution of environmental factors in the spread of antimicrobial resistance. Environ Health Prev Med. 2015;20(4):243–52. doi: 10.1007/s12199-015-0468-0 25921603

11. Berendes D, Leon J, Kirby A, Clennon J, Raj S, Yakubu H, et al. Household sanitation is associated with lower risk of bacterial and protozoal enteric infections, but not viral infections and diarrhea, in a cohort study in a low-income urban neighborhood in Vellore, India. Trop Med Int Heal [Internet]. 2017;00(00):1–11.

12. Berendes D, Kirby A, Clennon JA, Raj S, Yakubu H, Leon J, et al. The Influence of Household-and Community-Level Sanitation and Fecal Sludge Management on Urban Fecal Contamination in Households and Drains and Enteric Infection in Children. Am J Trop Med Hyg. 2017;96(6):1404–14. doi: 10.4269/ajtmh.16-0170 28719269

13. Laxminarayan R, Duse A, Wattal C, Zaidi AKM, Wertheim HFL, Sumpradit N, et al. Antibiotic resistance-the need for global solutions. Lancet Infect Dis. 2013;13(12):1057–98. doi: 10.1016/S1473-3099(13)70318-9 24252483

14. Vikesland PJ, Pruden A, Alvarez PJJ, Aga DS, Buergmann H, Li X, et al. Towards a Comprehensive Strategy to Mitigate Dissemination of Environmental Sources of Antibiotic Resistance. Environ Sci Technol [Internet]. 2017;acs.est.7b03623.

15. Calero-Cáceres W, Melgarejo A, Colomer-Lluch M, Stoll C, Lucena F, Jofre J, et al. Sludge as a potential important source of antibiotic resistance genes in both the bacterial and bacteriophage fractions. Environ Sci Technol. 2014;48(13):7602–11. doi: 10.1021/es501851s 24873655

16. Finley RL, Collignon P, Larsson DGJ, Mcewen SA, Li XZ, Gaze WH, et al. The scourge of antibiotic resistance: The important role of the environment. Clin Infect Dis. 2013;57(5):704–10. doi: 10.1093/cid/cit355 23723195

17. Bouki C, Venieri D, Diamadopoulos E. Detection and fate of antibiotic resistant bacteria in wastewater treatment plants: A review. Ecotoxicol Environ Saf [Internet]. 2013;91:1–9. 23414720

18. Karkman A, Pärnänen K, Larsson DGJ. Fecal pollution explains antibiotic resistance gene abundances in anthropogenically impacted environments. Nat Commun [Internet]. 2018;10(80):341487.

19. Berendes DM, Sumner TA, Brown JM. Safely Managed Sanitation for All Means Fecal Sludge Management for At Least 1.8 Billion People in Low and Middle Income Countries. Environ Sci Technol. 2017;51(5):3074–83. doi: 10.1021/acs.est.6b06019 28128924

20. UNICEF, WHO. Progress on Drinking Water, Sanitation and Hygiene [Internet]. 2017.

21. Baum R, Luh J, Bartram J. Sanitation: A global estimate of sewerage connections without treatment and the resulting impact on MDG progress. Environ Sci Technol. 2013;47(4):1994–2000. doi: 10.1021/es304284f 23323809

22. Berendes DM, Yang PJ, Lai A, Hu D, Brown J. Estimation of global recoverable human and animal faecal biomass. Nat Sustain [Internet]. 2018 Nov 13 [cited 2018 Nov 13];1(11):679–85.

23. McLain JE, Cytryn E, Durso LM, Young S. Culture-based Methods for Detection of Antibiotic Resistance in Agroecosystems: Advantages, Challenges, and Gaps in Knowledge. J Environ Qual [Internet]. 2016;0(0):0.

24. Berendonk TU, Manaia CM, Merlin C, Fatta-Kassinos D, Cytryn E, Walsh F, et al. Tackling antibiotic resistance: the environmental framework. Nat Rev Microbiol [Internet]. 2015;13(5):310–7. 25817583

25. Suzuki S, Horinouchi T, Furusawa C. Prediction of antibiotic resistance by gene expression profiles. Nat Commun [Internet]. 2014;5:5792. 25517437

26. Brown J, Cumming O, Bartram J, Cairncross S, Ensink J, Holcomb D, et al. A controlled, before-and-after trial of an urban sanitation intervention to reduce enteric infections in children: research protocol for the Maputo Sanitation (MapSan) study, Mozambique. BMJ Open [Internet]. 2015;5(6):e008215. doi: 10.1136/bmjopen-2015-008215 26088809

27. Perry MD, Corden SA, Howe RA. Evaluation of the luminex xTAG Gastrointestinal Pathogen Panel and the Savyon Diagnostics Gastrointestinal Infection Panel for the detection of enteric pathogens in clinical samples. J Med Microbiol. 2014;63(2014):1419–26.

28. Navidad JF, Griswold DJ, Gradus MS, Bhattacharyya S. Evaluation of Luminex xTAG Gastrointestinal Pathogen Analyte-Specific Reagents for High-Throughput, Simultaneous Detection of Bacteria, Viruses, and Parasites of Clinical and Public Health Importance. J Clin Microbiol [Internet]. 2013;51(9):3018–24. doi: 10.1128/JCM.00896-13 23850948

29. Patel A, Navidad J, Bhattacharyya S. Site-specific clinical evaluation of the Luminex xTAG gastrointestinal pathogen panel for detection of infectious gastroenteritis in fecal specimens. J Clin Microbiol. 2014;52(8):3068–71. doi: 10.1128/JCM.01393-14 24899032

30. Igbokwe H, Bhattacharyya S, Gradus S, Khubbar M, Griswold D, Navidad J, et al. Preponderance of toxigenic Escherichia coli in stool pathogens correlates with toxin detection in accessible drinking-water sources. Epidemiol Infect [Internet]. 2014;1–11.

31. Deng J, Luo X, Wang R, Jiang L, Ding X, Hao W, et al. A comparison of Luminex xTAG® Gastrointestinal Pathogen Panel (xTAG GPP) and routine tests for the detection of enteropathogens circulating in Southern China. Diagn Microbiol Infect Dis [Internet]. 2015;83(3):325–30. 26318973

32. Duong VT, Phat VV, Tuyen HT, Dung TTN, Trung PD, Van Minh P, et al. Evaluation of luminex xTAG gastrointestinal pathogen panel assay for detection of multiple diarrheal pathogens in fecal samples in Vietnam. J Clin Microbiol. 2016;54(4):1094–100. doi: 10.1128/JCM.03321-15 26865681

33. Eibach D, Krumkamp R, Hahn A, Sarpong N, Adu-Sarkodie Y, Leva A, et al. Application of a multiplex PCR assay for the detection of gastrointestinal pathogens in a rural African setting. BMC Infect Dis [Internet]. 2016;16(1):1–6.

34. Jouhten H, Mattila E, Arkkila P, Satokari R. Reduction of Antibiotic Resistance Genes in Intestinal Microbiota of Patients With Recurrent Clostridium difficile Infection After Fecal Microbiota Transplantation. Clin Infect Dis. 2016;63(5):710–1. doi: 10.1093/cid/ciw390 27317794

35. Hu H, Han X, Shi X, Wang J, Han L, Chen D, et al. Temporal changes of antibiotic-resistance genes and bacterial communities in two contrasting soils. FEMS Microbiol Ecol. 2016;92(2):1–13.

36. Han XM, Hu HW, Shi XZ, Wang JT, Han LL, Chen D, et al. Impacts of reclaimed water irrigation on soil antibiotic resistome in urban parks of Victoria, Australia. Environ Pollut [Internet]. 2016;211:48–57. 26736055

37. Vikram A, Rovira P, Agga GE, Arthur TM, Bosilevac JM, Wheeler TL, et al. Impact of “raised without antibiotics” beef cattle production practices on occurrences of antimicrobial resistance. Appl Environ Microbiol. 2017;83(22):1–15.

38. Agga GE, Arthur TM, Durso LM, Harhay DM, Schmidt JW. Antimicrobial-resistant bacterial populations and antimicrobial resistance genes obtained from environments impacted by livestock and municipal waste. PLoS One [Internet]. 2015;10(7):1–19.

39. Knee J, Sumner T, Adriano Z, Berendes D, de Bruijn E, Schmidt W-P, et al. Risk factors for childhood enteric infection in urban Maputo, Mozambique: A cross-sectional study. PLoS Negl Trop Dis [Internet]. 2018 Nov 12;12(11):e0006956. 30419034

40. Schreiner M. Simple Poverty Scorecard ® Poverty-Assessment Tool Mozambique. 2013.

41. Pielou EC. Shannon’s Formula as a Measure of Specific Diversity: Its Use and Misuse. Am Nat. 1966;100(914):463–5.

42. Simpson EH. Measurement of Diversity. Nature [Internet]. 1949 Apr 30;163:688.

43. Pärnänen K, Karkman A, Hultman J, Lyra C, Bengtsson-Palme J, Larsson DGJ, et al. Maternal gut and breast milk microbiota affect infant gut antibiotic resistome and mobile genetic elements. Nat Commun [Internet]. 2018;9(1):1–11.

44. Fisher JC, Murat Eren A, Green HC, Shanks OC, Morrison HG, Vineis JH, et al. Comparison of sewage and animal fecal microbiomes by using oligotyping reveals potential human fecal indicators in multiple taxonomic groups. Appl Environ Microbiol. 2015;81(20):7023–33. doi: 10.1128/AEM.01524-15 26231648

45. Ma Y, Wilson CA, Novak JT, Riffat R, Aynur S, Murthy S, et al. Effect of various sludge digestion conditions on sulfonamide, macrolide, and tetracycline resistance genes and class i integrons. Environ Sci Technol. 2011;45(18):7855–61. doi: 10.1021/es200827t 21815642

46. Jacoby GA, Munoz-price LS. The New Beta-Lactamases. N Engl J Med. 2005;352(4):380–91. doi: 10.1056/NEJMra041359 15673804

47. R Core Team. R: A language and environment for statistical computing. [Internet]. Vienna, Austria: R Foundation for Statistical Computing; 2015.

48. Bates D, Maechler M, Bolker B, Walker S. Fitting Linear Mixed-Effects Models Using lme4. J Stat Softw [Internet]. 2014;67(1):1–48.

49. Oksanen J, Blanchet FG, Kindt R, Legendre P, Minchin PR, O’Hara RB, et al. vegan: Community Ecology Package. R package version 2.3–0. 2015. R Found Stat Comput Vienna, Austria. 2015;

50. Gosalbes MJ, Vallès Y, Jiménez-Hernández N, Balle C, Riva P, Miravet-Verde S, et al. High frequencies of antibiotic resistance genes in infants’ meconium and early fecal samples. J Dev Orig Health Dis [Internet]. 2016;7(01):35–44.

51. de Vries LE, Vallès Y, Agersø Y, Vaishampayan PA, García-Montaner A, Kuehl J V., et al. The gut as reservoir of antibiotic resistance: Microbial diversity of tetracycline resistance in mother and infant. PLoS One. 2011;6(6).

52. Karami N, Nowrouzian F, Adlerberth I, Wold AE. Tetracycline Resistance in Escherichia coli and Persistence in the Infantile Colonic Microbiota Tetracycline Resistance in Escherichia coli and Persistence in the Infantile Colonic Microbiota. Antimicrob Agents Chemother. 2006;50(1):156–61. doi: 10.1128/AAC.50.1.156-161.2006 16377681

53. Alicea-Serrano AM, Contreras M, Magris M, Hidalgo G, Dominguez-Bello MG. Tetracycline resistance genes acquired at birth. Arch Microbiol. 2013;195(6):447–51. doi: 10.1007/s00203-012-0864-4 23483141

54. von Wintersdorff CJ, Wolffs PF, Savelkoul PH, Nijsen RR, Lau S, Gerhold K, et al. The gut resistome is highly dynamic during the first months of life. Future Microbiol [Internet]. 2016;11:501–10. 27064174

55. Moore AM, Patel S, Forsberg KJ, Wang B, Bentley G, Razia Y, et al. Pediatric fecal microbiota harbor diverse and novel antibiotic resistance genes. PLoS One. 2013;8(11).

56. Sutcliffe JG. Nucleotide sequence of the ampicillin resistance gene of Escherichia coli plasmid pBR322. Proc Natl Acad Sci [Internet]. 1978;75(8):3737–41. 358200

57. Kao SJ, You I, Clewell DB, Donabedian SM, Zervos MJ, Petrin J, et al. Detection of the high-level aminoglycoside resistance gene aph(2”)-Ib in Enterococcus faecium. Antimicrob Agents Chemother. 2000;44(10):2876–9. doi: 10.1128/aac.44.10.2876-2879.2000 10991878

58. Mandomando I, Jaintilal D, Pons MJ, Valles X, Espasa M, Mensa L, et al. Antimicrobial Susceptibility and Mechanisms of Resistance in Shigella and Salmonella Isolates from Children under Five Years of Age with Diarrhea in Rural Mozambique. Antimicrob Agents Chemother. 2009;53(6):2450–4. 19332670

59. Chirindze LM, Zimba TF, Sekyere JO, Govinden U, Chenia HY, Sundsfjord A, et al. Faecal colonization of E. coli and Klebsiella spp. producing extended-spectrum beta-lactamases and plasmid-mediated AmpC in Mozambican university students. BMC Infect Dis. 2018;18(1):1–8. doi: 10.1186/s12879-017-2892-9

60. Moore AM, Ahmadi S, Patel S, Gibson MK, Wang B, Ndao IM, et al. Gut resistome development in healthy twin pairs in the first year of life. Microbiome [Internet]. 2015;3(1):27.

61. Rolain JM. Food and human gut as reservoirs of transferable antibiotic resistance encoding genes. Front Microbiol. 2013;4(JUN):1–10.

62. Montealegre MC, Roy S, Böni F, Hossain MI, Navab-Daneshmand T, Caduff L, et al. Risk factors for detection, survival, and growth of antibiotic-resistant and pathogenic Escherichia coli in household soils in rural Bangladesh. Appl Environ Microbiol [Internet]. 2018;(October):AEM.01978-18.

63. Mandomando I, Macete E, Ruiz J, Sanz S, Abacassamo F, Valles X, et al. Etiology of diarrhea in children younger than 5 years of age admitted in a rural hospital of southern Mozambique. Am J Trop Med Hyg. 2007;76(3):522–7. 17360878

64. Mshana SE, Matee M, Rweyemamu M. Antimicrobial resistance in human and animal pathogens in Zambia, Democratic Republic of Congo, Mozambique and Tanzania : an urgent need of a sustainable surveillance system. Ann Clin Microbiol Antimicrob [Internet]. 2013;12(1):1. Annals of Clinical Microbiology and Antimicrobials

65. Manko A, Motta JP, Cotton JA, Feener T, Oyeyemi A, Vallance BA, et al. Giardia co-infection promotes the secretion of antimicrobial peptides beta-defensin 2 and trefoil factor 3 and attenuates attaching and effacing bacteria-induced intestinal disease. PLoS One. 2017;12(6):1–22.

66. Cotton JA, Motta JP, Schenck LP, Hirota SA, Beck PL, Buret AG. Giardia duodenalis infection reduces granulocyte infiltration in an in vivo model of bacterial toxin-induced colitis and attenuates inflammation in human intestinal tissue. PLoS One. 2014;9(10):1–15.

67. Cotton J, Amat C, Buret A. Disruptions of Host Immunity and Inflammation by Giardia Duodenalis: Potential Consequences for Co-Infections in the Gastro-Intestinal Tract. Pathogens [Internet]. 2015;4(4):764–92. doi: 10.3390/pathogens4040764 26569316

68. Huddleston JR. Horizontal gene transfer in the human gastrointestinal tract: Potential spread of antibiotic resistance genes. Infect Drug Resist. 2014;7:167–76. doi: 10.2147/IDR.S48820 25018641

69. Wright GD. The antibiotic resistome: the nexus of chemical and genetic diversity. NatRevMicrobiol [Internet]. 2007;5(1740–1534 (Electronic)):175–86. c:%5CKARSTEN%5CPDFs%5CAntibiotika-PDFs%5CAnti-2007%5CWright-The antibiotic resistome- the nexus of chemical and genetic diversity.pdf

70. Pal C, Bengtsson-Palme J, Kristiansson E, Larsson DGJ. The structure and diversity of human, animal and environmental resistomes. Microbiome [Internet]. 2016;4(1):54. 27717408

71. Silbergeld EK, Graham J, Price LB. Industrial food animal production, antimicrobial resistance, and human health. Annu Rev Public Health [Internet]. 2008;29(March 2014):151–69.

72. Sarmah AK, Meyer MT, Boxall ABA. A global perspective on the use, sales, exposure pathways, occurrence, fate and effects of veterinary antibiotics (VAs) in the environment. Chemosphere. 2006;65(5):725–59. doi: 10.1016/j.chemosphere.2006.03.026 16677683

73. Karanika S, Karantanos T, Arvanitis M, Grigoras C, Mylonakis E. Fecal Colonization With Extended-spectrum Beta- lactamase–Producing Enterobacteriaceae and Risk Factors Among Healthy Individuals : A Systematic Review and Metaanalysis. Clin Infect Dis. 2016;63(3):310–8. doi: 10.1093/cid/ciw283 27143671

74. Forsberg KJ, Reyes A, Wang B, Selleck EM, Sommer MOA, Dantas G. The shared antibiotic resistome of soil bacteria and human pathogens. Science (80-). 2012;337(6098):1107–11.

75. Gibson MK, Forsberg KJ, Dantas G. Improved annotation of antibiotic resistance determinants reveals microbial resistomes cluster by ecology. ISME J [Internet]. 2014;9(1):1–10.

76. Arango-Argoty GA, Garner E, Pruden A, Heath LS, Vikesland P, Zhang L. DeepARG : A deep learning approach for predicting antibiotic resistance genes from metagenomic data. bioRxiv. 2017;pre-print.

Článek vyšel v časopise


2019 Číslo 11