Metagenomics: Aid to combat antimicrobial resistance in diarrhea

Gut Pathogens

Volumn 11, Issue 1, 2019, Pages

  De, Rituparna ^a  

^a NATIONAL INSTITUTE OF CHOLERA AND ENTERIC DISEASES   (India)

Author keywords

Antimicrobial resistance; Antimicrobial resistance genes; Commensal; Diarrhea; Gut; Metagenomics; Microbiome; Pathogen; Probiotics

Indexed keywords

EID: 85073745583     PISSN: None     EISSN: 17574749     Source Type: Journal    
DOI: 10.1186/s13099-019-0331-8     Document Type: Review

References (75)

1. Anderson M, Clift C, Schulze K, Sagan A,Nahrgang S, Ouakrim DA, Mossialos E. Policy Brief 32. Averting the AMR crisis. What are the avenues for policy action for countries in Europe. European Observatory on Health Systems and Policies. 2019. Accessed Sept 2019.
2. Collignon PJ, Conly JM, Andremont A, McEwen SA, Aidara-Kane A, World Health Organization Advisory Group, Bogotá Meeting on Integrated Surveillance of Antimicrobial Resistance (WHO-AGISAR), Agerso Y, Andremont A, Collignon P, Conly J, Dang Ninh T, Donado-Godoy P, et al. World Health Organization ranking of antimicrobials according to their importance in human medicine: A critical step for developing risk management strategies to control antimicrobial resistance from food animal production. Clin Infect Dis. 2016;63(8):1087-93.
3. WHO report on surveillance of antibiotic consumption: 2016-2018 early implementation. Geneva: World Health Organization; 2018. Licence: CC BY-NC-SA 3.0 IGO. https://www.who.int/medicines/areas/rational_use/who-amr-amc-report-20181109.pdf. Accessed Sept 2019.
4. Chokshi A, Sifri Z, Cennimo D, Horng H. Global contributors to antibiotic resistance. J Glob Infect Dis. 2019;11:36-42.
5. Cairns J, Becks L, Jalasvuori M, Hiltunen T. Sublethal streptomycin concentrations and lytic bacteriophage together promote resistance evolution. Philos Trans R Soc B. 2017;372:20160040.
6. Smith SD, Colgan P, Yang F, Rieke EL, Soupir ML, Moorman TB, Allen HK, Howe A. Investigating the dispersal of antibiotic resistance associated genes from manure application to soil and drainage waters in simulated agricultural farmland systems. PLoS ONE. 2019;14(9):e0222470.
7. McEwen SA, Collignon PJ. Antimicrobial resistance: A one health perspective. Microbiol Spectr. 2018. https://doi.org/10.1128/microbiolspec.ARBA-0009-2017.
8. Karp BE, Tate H, Plumblee JR, Dessai U, Whichard JM, Thacker EL, Hale KR, Wilson W, Friedman CR, Griffin PM, McDermott PF. National Antimicrobial Resistance Monitoring System: Two decades of advancing public health through integrated surveillance of antimicrobial resistance. Foodborne Pathog Dis. 2017;14:545-57.
9. Bordier M, Uea-Anuwong T, Binot A, Hendrikx P, Goutard FL. Characteristics of One Health surveillance systems: A systematic literature review. Prev Vet Med. 2018. https://doi.org/10.1016/j.prevetmed.2018.10.005.
10. Hiltunen T, Virta M, Laine AL. Antibiotic resistance in the wild: An eco-evolutionary perspective. Philos Trans R Soc B. 2017;372:20160039.
11. D'Costa VM, King CE, Kalan L, Morar M, Sung WW, Schwarz C, Froese D, Zazula G, Calmels F, Debruyne R, Golding GB, Poinar HN, Wright GD. Antibiotic resistance is ancient. Nature. 2011;477:457-61.
12. Iossa G, White PC. The natural environment: A critical missing link in national action plans on antimicrobial resistance. Bull World Health Organ. 2018;96:858-60.
13. Woolhouse M, Ward M, Van Bunnik B, Farrar J. Antimicrobial resistance in humans, livestock and the wider environment. Philos Trans R Soc Lond B Biol Sci. 2015;370:20140083.
14. Skurnik D, Le Menac'h A, Zurakowski D, Mazel D, Courvalin P, Denamur E, Andremont A, Ruimy R. Integron associated antibiotic resistance and phylogenetic grouping of Escherichia coli isolates from healthy subjects free of recent antibiotic exposure. Antimicrob Agents Chemother. 2005;49(7):3062-5.
15. Wright GD. Q&A: Antibiotic resistance: Where does it come from and what can we do about it? BMC Biol. 2010;8:123.
16. Schwarz S, Feßler AT, Loncaric I, Wu C, Kadlec K, Wang Y, Shen J. Antimicrobial resistance among staphylococci of animal origin. Microbiol Spectr. 2018. https://doi.org/10.1128/microbiolspec.ARBA-0010-2017.
17. Brinkac L, Voorhies A, Gomez A, Nelson KE. The threat of antimicrobial resistance on the human microbiome. Microb Ecol. 2017;74:1001-8.
18. Bag S, Ghosh TS, Banerjee S, Mehta O, Verma J, Dayal M, Desigamani A, Kumar P, Saha B, Kedia S, Ahuja V, Ramamurthy T, Das B. Molecular insights into antimicrobial resistance traits of commensal human gut microbiota. Microb Ecol. 2019;77:546-57.
19. Wright GD. The antibiotic resistome: The nexus of chemical and genetic diversity. Nat Rev Microbiol. 2007;5:175-86.
20. Forsberg KJ, Patel S, Gibson MK, Lauber CL, Knight R, Fierer N, Dantas G. Bacterial phylogeny structures soil resistomes across habitats. Nature. 2014;509:612-6.
21. Schloss PD, Handelsman J. Biotechnological prospects from metagenomics. Curr Opin Biotechnol. 2003;14:303-10.
22. Thomas T, Gilbert J, Meyer F. Metagenomics- A guide from sampling to data analysis. Microb Inform Exp. 2012;2:3.
23. An introduction to next-generation sequencing technology. 2017. http://www.illumina.com/technology/next-generation-sequencing.html. Accessed Apr 2019.
24. Bag S, Saha B, Mehta O, Anbumani D, Kumar N, Dayal M, et al. An improved method for high quality metagenomics DNA extraction from human and environmental samples. Sci Rep. 2016;6:26775.
25. Klindworth A, Pruesse E, Schweer T, Peplies J, Quast C, Horn M, Glöckner FO. Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies. Nucleic Acids Res. 2013. https://doi.org/10.1093/nar/gks808.
26. Hugenholtz P, Tyson GW. Metagenomics. Nature. 2008;455:481-3.
27. Chen K, Pachter L. Bioinformatics for whole-genome shotgun sequencing of microbial communities. PLoS Comput Biol. 2005;1:e24.
28. Ranjan R, Rani A, Metwally A, McGee HS, Perkins DL. Analysis of the microbiome: Advantages of whole genome shotgun versus 16S amplicon sequencing. Biochem Biophys Res Commun. 2016;469:967-77.
29. Venter JC, Remington K, Heidelberg JF, Halpern AL, Rusch D, Eisen JA, et al. Environmental genome shotgun sequencing of the Sargasso Sea. Science. 2004;304:66-74.
30. Crofts TS, Gasparrini AJ, Dantas G. Next-generation approaches to understand and combat the antibiotic resistome. Nat Rev Microbiol. 2017;15(7):422-34.
31. Handelsman J, Rondon MR, Brady SF, Clardy J, Goodman RM. Molecular biological access to the chemistry of unknown soil microbes: A new frontier for natural products. Chem Biol. 1998;5:R245-9.
32. Gillespie DE, Brady SF, Bettermann AD, et al. Isolation of antibiotics turbomycin A and B from a metagenomic library of soil microbial DNA. Appl Environ Microbiol. 2002;68(9):4301-6.
33. Rondon MR, August PR, Bettermann AD, Brady SF, Grossman TH, Liles MR, et al. Cloning the soil metagenome: A strategy for accessing the genetic and functional diversity of uncultured microorganisms. Appl Environ Microbiol. 2000;66:2541-7.
34. Van der Helm E, Imamovic L, Hashim EMM, van Schaik W, Koza A, Sommer MOA. Rapid resistome mapping using nanopore sequencing. Nucleic Acids Res. 2017. https://doi.org/10.1093/nar/gkw1328.
35. Razavi M, Marathe NP, Gillings MR, Flach CF, Kristiansson E, Larsson JDG. Discovery of the fourth mobile sulfonamide resistance gene. Microbiome. 2017;5:160.
36. Fouhy F, Ogilvie LA, Jones BV, Ross RP, Ryan AC, Dempsey EM, et al. Identification of aminoglycoside and β-lactam resistance genes from within an infant gut functional metagenomic library. PLoS ONE. 2014;9:e108016.
37. 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:e78822.
38. 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. 2018;9:3891.
39. Ghosh TS, Gupta SS, Nair GB, Mande SS. In silico analysis of antibiotic resistance genes in the gut microflora of individuals from diverse geographies and age-groups. PLoS ONE. 2013;8:e83823.
40. Forslund K, Sunagawa S, Kultima JR, Mende DR, Arumugam M, Typas A, Bork P. Country-specific antibiotic use practices impact the human gut resistome. Genome Res. 2013;23:1163-9.
41. Yatsunenko T, Rey FE, Manary MJ, Trehan I, Dominguez-Bello MG, Contreras M, et al. Human gut microbiome viewed across age and geography. Nature. 2012;486:222-7.
42. Rampelli S, Schnorr SL, Consolandi C, Turroni S, Severgnini M, Peano C, et al. Metagenome sequencing of the Hadza Hunter-Gatherer gut microbiota. Curr Biol. 2015;25:1682-93.
43. Segata N. Gut microbiome: Westernization and the disappearance of intestinal diversity. Curr Biol. 2015;25:R611-3.
44. Das B, Ghosh TS, Kedia S, Rampal R, Saxena S, Bag S, et al. Analysis of the gut microbiome of rural and urban healthy indians living in sea level and high altitude areas. Sci Rep. 2018;8:10104.
45. Xia Y, Zhu Y, Li Q, Lu J. Human gut resistome can be country-specific. PeerJ. 2019;7:e6389.
46. Hendriksen RS, Munk P, Njage P, van Bunnik B, McNally L, Lukjancenko O, Röder T, Nieuwenhuijse D, Pedersen SK, Kjeldgaard J, Kaas RS, Clausen PTLC, et al. Global monitoring of antimicrobial resistance based on metagenomics analyses of urban sewage. Nat Commun. 2019;10(1):1124.
47. Dos Santos DF, Istvan P, Quirini BF, Kruger RH. Functional metagenomics as a tool for identification of new antibiotic resistance genes from natural environments. Microb Ecol. 2017;73(2):479-91.
48. Berglund F, Österlund T, Boulund F, Marathe NP, Larsson DGJ, Kristiansson E. Identification and reconstruction of novel antibiotic resistance genes from metagenomes. Microbiome. 2019;7:52.
49. Pal C, Bengtsson-Palme J, Kristiansson E, Larsson DG. The structure and diversity of human, animal and environmental resistomes. Microbiome. 2016;4:54.
50. Fitzpatrick D, Walsh F. Antibiotic resistance genes across a wide variety of metagenomes. FEMS Microbiol Ecol. 2016;92:2.
51. Forsberg KJ, Reyes A, Wang B, Selleck EM, Sommer MO, Dantas G. The shared antibiotic resistome of soil bacteria and human pathogens. Science. 2012;337:1107-11.
52. Tyagi A, Singh B, Billekallu Thammegowda NK, Singh NK. Shotgun metagenomics offers novel insights into taxonomic compositions, metabolic pathways and antibiotic resistance genes in fish gut microbiome. Arch Microbiol. 2019;201:295-303.
53. Ribeiro da Cunha B, Fonseca LP, Calado CRC. Antibiotic discovery: Where have we come from, where do we go? Antibiotics. 2019;8(2):45.
54. Kim JH, Cheong HK, Jeon BH. Burden of disease attributable to inadequate drinking water, sanitation, and hygiene in Korea. J Korean Med Sci. 2018;33:46.
55. Workie HM, Sharifabdilahi AS, Addis EM. Mothers' knowledge, attitude and practice towards the prevention and home-based management of diarrheal disease among under-five children in Diredawa, Eastern Ethiopia, 2016: A cross-sectional study. BMC Pediatr. 2018;18:358.
56. Molecular methods for antimicrobial resistance (AMR) diagnostics to enhance the Global Antimicrobial Resistance Surveillance System. Geneva: World Health Organization; 2019 (WHO/WSI/AMR/2019.1). https://www.who.int/glass/resources/publications/molecular-methods-for-amr-diagnostics/en/. Accessed Apr 2019.
57. Centers for Disease Control and Prevention. https://www.cdc.gov/drugresistance/threat-report-2013/pdf/ar-threats-2013-508.pdf. Accessed Apr 2019.
58. Centers for Disease Control and Prevention. https://www.cdc.gov/drugresistance/biggest_threats.html. Accessed Apr 2019.
59. Frost I, Van Boeckel TP, Pires J, Craig J, Laxminarayan R. Global geographic trends in antimicrobial resistance: The role of international travel. J Travel Med. 2019. https://doi.org/10.1093/jtm/taz036.
60. Miao Z, Li S, Wang L, Song W, Zhou Y. Antimicrobial resistance and molecular epidemiology of ESBL-producing Escherichia coli isolated from outpatients in town hospitals of Shandong province, China. Front Microbiol. 2017;8:63. https://doi.org/10.3389/fmicb.2017.00063.
61. Patil S, Chen X, Lian M, Wen F. Phenotypic and genotypic characterization of multi-drug-resistant Escherichia coli isolates harboring blaCTX-M group extended-spectrum β-lactamases recovered from pediatric patients in Shenzen, southern China. Infect Drug Resist. 2019;2019(12):1325-32. https://doi.org/10.2147/IDR.S199861.
62. Bozzi CN, Baffoni L, Gaggià F, Di Gioia D. Therapeutic microbiology: Role of Bifidobacterium breve as food supplement for the prevention/treatment of paediatric diseases. Nutrients. 2018;10:11.
63. Goldenberg JZ, Yap C, Lytvyn L, Lo CK, Beardsley J, Mertz D, et al. Probiotics for the prevention of Clostridium difficile-associated diarrhea in adults and children. Cochrane Database Syst Rev. 2017;12:CD006095.
64. Ouwehand AC, Forssten S, Hibberd AA, Lyra A, Stahl B. Probiotic approach to prevent antibiotic resistance. Ann Med. 2016;48:246-55.
65. Xu H, Zhao F, Hou Q, Huang W, Liu Y, Zhang H, et al. Metagenomic analysis revealed beneficial effects of probiotics in improving the composition and function of the gut microbiota in dogs with diarrhoea. Food Funct. 2019. https://doi.org/10.1039/c9fo00087a.
66. Kumar P, Bag S, Ghosh TS, Dey P, Dayal M, Saha B, et al. Molecular insights into antimicrobial resistance traits of multidrug resistant enteric pathogens isolated from India. Sci Rep. 2017;7:14468.
67. George F, Daniel C, Thomas M, Singer E, Guilbaud A, Tessier FJ, et al. Occurrence and dynamism of lactic acid bacteria in distinct ecological niches: A multifaceted functional health perspective. Front Microbiol. 2018;9:2899.
68. Lakin SM, Dean C, Noyes NR, Dettenwanger A, Ross AS, Doster E, Rovira P, Abdo Z, Jones KL, Ruiz J, Belk KE, Morley PS, et al. MEGARes: An antimicrobial resistance database for high throughput sequencing. Nucleic Acids Res. 2017;45(D1):D574-80. https://doi.org/10.1093/nar/gkw1009.
69. Bag S, Ghosh TS, Das B. Complete genome sequence of Faecalibacterium prausnitzii isolated from the gut of a healthy Indian adult. Genome Announc. 2017;5:46.
70. Negatu DA, Yamada Y, Xi Y, Go ML, Zimmerman M, Ganapathy U, et al. Gut microbiota metabolite indole propionic acid targets tryptophan biosynthesis in Mycobacterium tuberculosis. MBio. 2019;10:2.
71. Bansept F, Marrec L, Bitbol AF, Loverdo C. Antibody-mediated cross linking of gut bacteria hinders the spread of antibiotic resistance. Evolution. 2019. https://doi.org/10.1111/evo.13730.
72. Mikonranta L, Buckling A, Jalasvuori M, Raymond B. Targeting antibiotic resistant bacteria with phage reduces bacterial density in an insect host. Biol Lett. 2019;15:20180895.
73. Hu Y, Hugerth LW, Bengtsson C. Bacteriophages synergize with the gut microbial community to combat Salmonella. mSystems. 2018;3:5.
74. Mamo G. Anaerobes as sources of bioactive compounds and health promoting tools. Adv Biochem Eng Biotechnol. 2016;156:433-64.
75. Guarino A, Giannattasio A. New molecular approaches in the diagnosis of acute diarrhea: Advantages for clinicians and researchers. Curr Opin Gastroenterol. 2011;27:24-9.