Investigating colistin drug resistance: the role of high-throughput sequencing and bioinformatics

F1000Research

Volumn 8, Issue , 2019, Pages

  Aruhomukama, Dickson ^a   Sserwadda, Ivan ^a   Mboowa, Gerald ^a  

^a MAKERERE UNIVERSITY   (Uganda)

Author keywords

Antibiotic resistance; Bioinformatics; Colistin resistance; Genomics; Gram negative bacteria; Pan drug resistance

Indexed keywords

COLISTIN; ANTIINFECTIVE AGENT;

AFRICA; ANTIBIOTIC RESISTANCE; ANTIBIOTIC THERAPY; BIOINFORMATICS; DRUG TARGETING; ENVIRONMENTAL FACTOR; GENOMICS; GEOGRAPHIC DISTRIBUTION; GRAM NEGATIVE BACTERIUM; HIGH THROUGHPUT SEQUENCING; HUMAN; REVIEW; TREND STUDY; BIOLOGY;

ANTI-BACTERIAL AGENTS; COLISTIN; COMPUTATIONAL BIOLOGY; DRUG RESISTANCE, BACTERIAL; GRAM-NEGATIVE BACTERIA; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING;

EID: 85070572192     PISSN: 20461402     EISSN: 1759796X     Source Type: Journal    
DOI: 10.12688/f1000research.18081.2     Document Type: Review

References (57)

1. Giske CG: Contemporary resistance trends and mechanisms for the old antibiotics colistin, temocillin, fosfomycin, mecillinam and nitrofurantoin. Clin Microbiol Infect. 2015; 21(10): 899–905. PubMed Abstract | Publisher Full Text
2. Sonnevend A, Ghazawi A, Alqahtani M, et al.: Plasmid-mediated colistin resistance in Escherichia coli from the Arabian Peninsula. Int J Infect Dis. 2016; 50: 85–90. PubMed Abstract | Publisher Full Text
3. World Health Organization: Antimicrobial resistance: global report on surveillance. World Health Organization. 2014. Reference Source
4. Xavier BB, Lammens C, Ruhal R, et al.: Identification of a novel plasmid-mediated colistin-resistance gene, mcr-2, in Escherichia coli, Belgium, June 2016. Euro Surveill. 2016; 21(27). PubMed Abstract | Publisher Full Text
5. Lowe M, Ehlers MM, Ismail F, et al.: Acinetobacter baumannii: Epidemiological and Beta-Lactamase Data From Two Tertiary Academic Hospitals in Tshwane, South Africa. Front Microbiol. 2018; 9: 1280. Free Full Text PubMed Abstract |Publisher Full Text |
6. Alonso CA, Zarazaga M, Ben Sallem R, et al.: Antibiotic resistance in Escherichia coli in husbandry animals: the African perspective. Lett Appl Microbiol. 2017; 64(5): 318–334. PubMed Abstract | Publisher Full Text
7. Perreten V, Strauss C, Collaud A, et al.: Colistin Resistance Gene mcr-1 in Avian-Pathogenic Escherichia coli in South Africa. Antimicrob Agents Chemother. 2016; 60(7): 4414–15. Free Full Text PubMed Abstract |Publisher Full Text |
8. Sofiane B, Olaitan AO, Ammari H, et al.: Emergence of Colistin-and Carbapenem-Resistant Acinetobacter baumannii ST2 Clinical Isolate in Algeria: First Case Report. Microb Drug Resist. 2015; 21(3): 279–85. PubMed Abstract | Publisher Full Text
9. Carroll M, Rangaiahagari A, Musabeyezu E, et al.: Five-Year Antimicrobial Susceptibility Trends Among Bacterial Isolates from a Tertiary Health-Care Facility in Kigali, Rwanda. Am J Trop Med Hyg. 2016; 95(6): 1277–1283. Free Full Text PubMed Abstract |Publisher Full Text |
10. Sserwadda I, Lukenge M, Mwambi B, et al.: Microbial contaminants isolated from items and work surfaces in the post-operative ward at Kawolo general hospital, Uganda. BMC Infect Dis. 2018; 18(1): 68. Free Full Text PubMed Abstract |Publisher Full Text |
11. Paterson DL, Harris PN: Colistin resistance: a major breach in our last line of defence. Lancet Infect Dis. 2016; 16(2): 132–133. PubMed Abstract | Publisher Full Text
12. Poirel L, Jayol A, Nordmann P: Polymyxins: Antibacterial Activity, Susceptibility Testing, and Resistance Mechanisms Encoded by Plasmids or Chromosomes. Clin Microbiol Rev. 2017; 30(2): 557–596. Free Full Text PubMed Abstract |Publisher Full Text |
13. Gao R, Hu Y, Li Z, et al.: Dissemination and Mechanism for the MCR-1 Colistin Resistance. PLoS Pathog. 2016; 12(11): e1005957. Free Full Text PubMed Abstract |Publisher Full Text |
14. Moffatt JH, Harper M, Harrison P, et al.: Colistin resistance in Acinetobacter baumannii is mediated by complete loss of lipopolysaccharide production. Antimicrob Agents Chemother. 2010; 54(12): 4971–4977. Free Full Text PubMed Abstract |Publisher Full Text |
15. Adams MD, Nickel GC, Bajaksouzian S, et al.: Resistance to colistin in Acinetobacter baumannii associated with mutations in the PmrAB two-component system. Antimicrob Agents Chemother. 2009; 53(9): 3628–3634. Free Full Text PubMed Abstract |Publisher Full Text |
16. Liu YY, Wang Y, Walsh TR, et al.: Emergence of plasmid-mediated colistin resistance mechanism MCR-1 in animals and human beings in China: a microbiological and molecular biological study. Lancet Infect Dis. 2016; 16(2): 161–168. PubMed Abstract | Publisher Full Text
17. Schwarz S, Johnson AP: Transferable resistance to colistin: a new but old threat. J Antimicrob Chemother. 2016; 71(8): 2066–2070. PubMed Abstract | Publisher Full Text
18. Nathan C, Cars O: Antibiotic resistance--problems, progress, and prospects. N Engl J Med. 2014; 371(19): 1761–1763. PubMed Abstract | Publisher Full Text
19. Ferri M, Ranucci E, Romagnoli P, et al.: Antimicrobial resistance: A global emerging threat to public health systems. Crit Rev Food Sci Nutr. 2017; 57(13): 2857–2876. PubMed Abstract | Publisher Full Text
20. Shallcross LJ, Howard SJ, Fowler T, et al.: Tackling the threat of antimicrobial resistance: from policy to sustainable action. Philos Trans R Soc Lond B Biol Sci. 2015; 370(1670): 20140082. Free Full Text PubMed Abstract |Publisher Full Text |
21. Holmes AH, Moore LS, Sundsfjord A, et al.: Understanding the mechanisms and drivers of antimicrobial resistance. Lancet. 2016; 387(10014): 176–87. PubMed Abstract | Publisher Full Text
22. Redgrave LS, Sutton SB, Webber MA, et al.: Fluoroquinolone resistance: mechanisms, impact on bacteria, and role in evolutionary success. Trends Microbiol. 2014; 22(8): 438–45. PubMed Abstract | Publisher Full Text
23. Blázquez J, Oliver A, Gómez-Gómez JM: Mutation and evolution of antibiotic resistance: antibiotics as promoters of antibiotic resistance? Curr Drug Targets. 2002; 3(4): 345–9. PubMed Abstract | Publisher Full Text
24. Barlow M: What antimicrobial resistance has taught us about horizontal gene transfer. Methods Mol Biol. 2009; 532: 397–411. PubMed Abstract | Publisher Full Text
25. Davies J, Davies D: Origins and evolution of antibiotic resistance. Microbiol Mol Biol Rev. 2010; 74(3): 417–433. Free Full Text PubMed Abstract |Publisher Full Text |
26. Lynch JP III, Clark NM, Zhanel GG: Evolution of antimicrobial resistance among Enterobacteriaceae (focus on extended spectrum β-lactamases and carbapenemases). Expert Opin Pharmacother. 2013; 14(2): 199–210. PubMed Abstract | Publisher Full Text
27. Martínez JL: Natural antibiotic resistance and contamination by antibiotic resistance determinants: the two ages in the evolution of resistance to antimicrobials. Front Microbiol. 2012; 3: 1. Free Full Text PubMed Abstract |Publisher Full Text |
28. Aruhomukama D: Phenotypic Assays for Detection of Extended Spectrum B-Lactamases and Carbapenemases: A Laboratory Guide for Microbiologists. 2018. Publisher Full Text
29. Shaikh S, Fatima J, Shakil S, et al.: Antibiotic resistance and extended spectrum beta-lactamases: Types, epidemiology and treatment. Saudi J Biol Sci. 2015; 22(1): 90–101. Free Full Text PubMed Abstract |Publisher Full Text |
30. Munoz-Price LS, Poirel L, Bonomo RA, et al.: Clinical epidemiology of the global expansion of Klebsiella pneumoniae carbapenemases. Lancet Infect Dis. 2013; 13(9): 785–796. Free Full Text PubMed Abstract |Publisher Full Text |
31. Pitout JD, Nordmann P, Poirel L: Carbapenemase-Producing Klebsiella pneumoniae, a Key Pathogen Set for Global Nosocomial Dominance. Antimicrob Agents Chemother. 2015; 59(10): 5873–84. Free Full Text PubMed Abstract |Publisher Full Text |
32. Thomson KS: Controversies about extended-spectrum and AmpC beta-lactamases. Emerg Infect Dis. 2001; 7(2): 333–6. PubMed Abstract | Free Full Text
33. Lobkovsky E, Moews PC, Liu H, et al.: Evolution of an enzyme activity: crystallographic structure at 2-A resolution of cephalosporinase from the ampC gene of Enterobacter cloacae P99 and comparison with a class A penicillinase. Proc Natl Acad Sci U S A. 1993; 90(23): 11257–11261. Free Full Text PubMed Abstract |Publisher Full Text |
34. Philippon A, Arlet G, Jacoby GA: Plasmid-determined AmpC-type beta-lactamases. Antimicrob Agents Chemother. 2002; 46(1): 1–11. Free Full Text PubMed Abstract |Publisher Full Text |
35. Mohamudha PR, Harish BN, Parija SC: Molecular description of plasmid-mediated AmpC β-lactamases among nosocomial isolates of Escherichia coli & Klebsiella pneumoniae from six different hospitals in India. Indian J Med Res. 2012; 135(1): 114–9. Free Full Text PubMed Abstract |Publisher Full Text |
36. Ghosh B, Mukherjee M: Emergence of co-production of plasmid-mediated AmpC beta-lactamase and ESBL in cefoxitin-resistant uropathogenic Escherichia coli. Eur J Clin Microbiol Infect Dis. 2016; 35(9): 1449–1454. PubMed Abstract | Publisher Full Text
37. Anusuya Devi D, Ramachander R: Detection of Extended-spectrum Beta-lactamases in AMPC Co-producing Bacteria by Disc Diffusion Method in Clinical Isolates of Enterobacteriacae. Indian J Public Health Res Dev. 2016; 7(2): 236–242. Publisher Full Text
38. Capone A, Giannella M, Fortini D, et al.: High rate of colistin resistance among patients with carbapenem-resistant Klebsiella pneumoniae infection accounts for an excess of mortality. Clin Microbiol Infect. 2013; 19(1): E23–E30. PubMed Abstract | Publisher Full Text
39. Ah YM, Kim AJ, Lee JY: Colistin resistance in Klebsiella pneumoniae. Int J Antimicrob Agents. 2014; 44(1): 8–15. PubMed Abstract | Publisher Full Text
40. Olaitan AO, Diene SM, Kempf M, et al.: Worldwide emergence of colistin resistance in Klebsiella pneumoniae from healthy humans and patients in Lao PDR, Thailand, Israel, Nigeria and France owing to inactivation of the PhoP/ PhoQ regulator mgrB: an epidemiological and molecular study. Int J Antimicrob Agents. 2014; 44(6): 500–507. PubMed Abstract | Publisher Full Text
41. Qureshi ZA, Hittle LE, O'Hara JA, et al.: Colistin-resistant Acinetobacter baumannii: beyond carbapenem resistance. Clin Infect Dis. 2015; 60(9): 1295–1303. Free Full Text PubMed Abstract |Publisher Full Text |
42. McGann P, Snesrud E, Maybank R, et al.: Escherichia coli harboring mcr-1 and blaCTX-M on a novel IncF plasmid: first report of mcr-1 in the United States. Antimicrob Agents Chemother. 2016; 60(7): 4420–4421. Free Full Text PubMed Abstract |Publisher Full Text |
43. Falgenhauer L, Waezsada SE, Yao Y, et al.: Colistin resistance gene mcr-1 in extended-spectrum β-lactamase-producing and carbapenemase-producing Gram-negative bacteria in Germany. Lancet Infect Dis. 2016; 16(3): 282–283. PubMed Abstract | Publisher Full Text
44. Malhotra-Kumar S, Xavier BB, Das AJ, et al.: Colistin resistance gene mcr-1 harboured on a multidrug resistant plasmid. Lancet Infect Dis. 2016; 16(3): 283–284. PubMed Abstract | Publisher Full Text
45. Poirel L, Kieffer N, Liassine N, et al.: Plasmid-mediated carbapenem and colistin resistance in a clinical isolate of Escherichia coli. Lancet Infect Dis. 2016; 16(3): 281. PubMed Abstract | Publisher Full Text
46. Du H, Chen L, Tang YW, et al.: Emergence of the mcr-1 colistin resistance gene in carbapenem-resistant Enterobacteriaceae. Lancet Infect Dis. 2016; 16(3): 287–288. PubMed Abstract | Publisher Full Text
47. Monaco M, Giani T, Raffone M, et al.: Colistin resistance superimposed to endemic carbapenem-resistant Klebsiella pneumoniae: a rapidly evolving problem in Italy, November 2013 to April 2014. Euro Surveill. 2014; 19(42): pii: 20939. PubMed Abstract | Publisher Full Text
48. Kwong JC, McCallum N, Sintchenko V, et al.: Whole genome sequencing in clinical and public health microbiology. Pathology. 2015; 47(3): 199–210. Free Full Text PubMed Abstract |Publisher Full Text |
49. Rossen JWA, Friedrich AW, Moran-Gilad J: Practical issues in implementing whole-genome-sequencing in routine diagnostic microbiology. Clin Microbiol Infect. 2018; 24(4): 355–360. PubMed Abstract | Publisher Full Text
50. Nijhuis RH, Oueslati S, Zhou K, et al.: OXY-2-15, a novel variant showing increased ceftazidime hydrolytic activity. J Antimicrob Chemother. 2015; 70(5): 1429–1433. PubMed Abstract | Publisher Full Text
51. Ferdous M, Kooistra-Smid AM, Zhou K, et al.: Virulence, Antimicrobial Resistance Properties and Phylogenetic Background of Non-H7 Enteropathogenic Escherichia coli O157. Front Microbiol. 2016; 7: 1540. Free Full Text PubMed Abstract |Publisher Full Text |
52. Dunne WM Jr, Westblade LF, Ford B: Next-generation and whole-genome sequencing in the diagnostic clinical microbiology laboratory. Eur J Clin Microbiol Infect Dis. 2012; 31(8): 1719–1726. PubMed Abstract | Publisher Full Text
53. Hasman H, Hammerum AM, Hansen F, et al.: Detection of mcr-1 encoding plasmid-mediated colistin-resistant Escherichia coli isolates from human bloodstream infection and imported chicken meat, Denmark 2015. Euro Surveill. (Online Ed) 2015; 20(49): 1–5. PubMed Abstract | Publisher Full Text
54. Donà V, Bernasconi OJ, Pires J, et al.: Heterogeneous Genetic Location of mcr-1 in Colistin-Resistant Escherichia coli Isolates from Humans and Retail Chicken Meat in Switzerland: Emergence of mcr-1-Carrying IncK2 Plasmids. Antimicrob Agents Chemother. 2017; 61(11): pii: e01245-17. Free Full Text PubMed Abstract |Publisher Full Text |
55. Chandra H, Bishnoi P, Yadav A, et al.: Antimicrobial Resistance and the Alternative Resources with Special Emphasis on Plant-Based Antimicrobials-A Review. Plants (Basel). 2017; 6(2): pii: E16. Free Full Text PubMed Abstract |Publisher Full Text |
56. Wright GD: Q&A: Antibiotic resistance: where does it come from and what can we do about it? BMC Biol. 2010; 8(1): 123. Free Full Text PubMed Abstract |Publisher Full Text |
57. Prestinaci F, Pezzotti P, Pantosti A: Antimicrobial resistance: a global multifaceted phenomenon. Pathog Glob Health. 2015; 109(7): 309–318. PubMed Abstract |Publisher Full Text |Free Full Text