The Use of Machine Learning Methodologies to Analyse Antibiotic and Biocide Susceptibility in Staphylococcus aureus

PLoS ONE

Volumn 8, Issue 2, 2013, Pages

  Coelho, Joana Rosado ^a   Carriço, João André ^a,b   Knight, Daniel ^c,d   Martínez, Jose Luis ^e   Morrissey, Ian ^c,f   Oggioni, Marco Rinaldo ^g   Freitas, Ana Teresa ^a  

^a INESC ID   (Portugal)

^b INSTITUTO DE MEDICINA MOLECULAR   (Portugal)

^c Quotient Bioresearch Ltd   (United Kingdom)

^d UNIVERSITY OF WESTERN AUSTRALIA   (Australia)

^e CENTRO NACIONAL DE BIOTECNOLOGÍA   (Spain)

^f International Health Management Associates Europe Sàrl   (Switzerland)

^g UNIVERSITY OF SIENA   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

BENZALKONIUM CHLORIDE; BIOCIDE; CHLORHEXIDINE; HYPOCHLORITE SODIUM; TRICLOSAN;

ANTIBIOTIC RESISTANCE; ANTIBIOTIC SENSITIVITY; ARTICLE; BACTERIAL STRAIN; BACTERIOSTASIS; BACTERIUM ISOLATE; BIOCIDE SUSCEPTIBILITY; CLUSTER ANALYSIS; CONTROLLED STUDY; DECISION TREE; DRUG SENSITIVITY; HUMAN; IN VITRO STUDY; LEARNING ALGORITHM; MACHINE LEARNING; MINIMUM INHIBITORY CONCENTRATION; MOLECULAR EPIDEMIOLOGY; MULTIDRUG RESISTANCE; NONHUMAN; PHENOTYPE; STAPHYLOCOCCUS AUREUS; VALIDATION STUDY;

ALGORITHMS; ANTI-BACTERIAL AGENTS; ARTIFICIAL INTELLIGENCE; CLUSTER ANALYSIS; DECISION TREES; DISINFECTANTS; DRUG RESISTANCE, BACTERIAL; MICROBIAL SENSITIVITY TESTS; STAPHYLOCOCCUS AUREUS;

EID: 84874218295     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0055582     Document Type: Article

References (60)

1. Falagas ME, Bliziotis IA (2007) Pandrug-resistant Gram-negative bacteria: the dawn of the post-antibiotic era? International Journal of Antimicrobial Agents 29: 630-636. Available: http://www.ncbi.nlm.nih.gov/pubmed/17306965. Accessed 2012 Sep 6.
2. Jansen WTM, Van Der Bruggen JT, Verhoef J, Fluit AC (2006) Bacterial resistance: a sensitive issue complexity of the challenge and containment strategy in Europe. Drug resistance updates reviews and commentaries in antimicrobial and anticancer chemotherapy 9: 123-133. Available: http://www.ncbi.nlm.nih.gov/pubmed/16807066. Accessed 2012 Sep 6.
3. WHO (2007) The world health report-A safer future: global public health security in the 21st century. Available: http://www.who.int/whr/2007/en/index.html. Accessed 2012 Sep 10.
4. EARSS (2005) Annual Report- European Antimicrobial Resistance Surveillance System. Available: http://www.ecdc.europa.eu/en/activities/surveillance/EARS-Net/Documents/2005_EARSS_Annual_Report.pdf. Accessed 2012 Sep 10.
5. Harbarth S, Samore MH (2005) Antimicrobial resistance determinants and future control. Emerging Infectious Diseases 11: 794-801. Available: http://www.ncbi.nlm.nih.gov/pubmed/15963271. Accessed 2012 Sep 7.
6. Russell AD (2002) Antibiotic and biocide resistance in bacteria: Introduction. Symposium series (Society for Applied Microbiology): 1S-3S. Available: http://www.ncbi.nlm.nih.gov/pubmed/12481823. Accessed 2011 May 30.
7. SCCS (2010) Opinion on Triclosan-Antimicrobial Resistance. European Commission: Scientific Committee on Consumer Safety. Available: http://ec.europa.eu/health/scientific_committees/consumer_safety/docs/sccs_o_023.pdf. Accessed 2012 Sep 7.
8. Maillard J-Y, Denyer SP (2009) Emerging bacterial resistance following biocide exposure: should we be concerned? Chimica oggi 27: 26-28. Accessed 2012 Sept 7.
9. Aiello AE, Larson EL, Levy SB (2007) Consumer antibacterial soaps: effective or just risky? Clinical infectious diseases: an official publication of the Infectious Diseases Society of America 45 Suppl 2: S137-47. Available: http://www.ncbi.nlm.nih.gov/pubmed/17683018. Accessed 2012 Apr 12.
10. Levy SB (2001) Antibacterial household products: cause for concern. Emerging Infectious Diseases 7: 512-515. Available: http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2631814&tool=pmcentrez&rendertype=abstract. Accessed 2012 May 30.
11. Parikh SL, Xiao G, Tonge PJ (2000) Inhibition of InhA, the enoyl reductase from Mycobacterium tuberculosis, by triclosan and isoniazid. Biochemistry 39: 7645-7650. Available: http://pubs.acs.org/doi/abs/10.1021/bi0008940. Accessed 2012 Sep 7.
12. Lucey B, Crowley D, Moloney P, Cryan B, Daly M, et al. (2000) Integronlike structures in Campylobacter spp. of human and animal origin. Emerging Infectious Diseases 6: 50-55. Available: http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2627975&tool=pmcentrez&rendertype=abstract. Accessed 2011 Jun 14.
13. Lyon BR, Skurray R (1987) Antimicrobial resistance of Staphylococcus aureus: genetic basis. Microbiology and Molecular Biology Reviews: MMBR 51: 88-134. Available: http://mmbr.asm.org. Accessed 2012 Sep 7.
14. Paulsen IT, Littlejohn TG, Rådström P, Sundström L, Sköld O, et al. (1993) The 3′ conserved segment of integrons contains a gene associated with multidrug resistance to antiseptics and disinfectants. Antimicrobial Agents and Chemotherapy 37: 761-768. Available: http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=187754&tool=pmcentrez&rendertype=abstract. Accessed 2011 Jun 14.
15. Ciusa ML, Furi L, Knight D, Decorosi F, Fondi M, et al. (2012) A novel resistance mechanism to triclosan that suggests horizontal gene transfer and demonstrates a potential selective pressure for reduced biocide susceptibility in clinical strains of Staphylococcus aureus. International Journal of Antimicrobial Agents 40: 210-220. Available: http://linkinghub.elsevier.com/retrieve/pii/S0924857912002051?showall=true. Accessed 2012 Sep 7.
16. Ferber D (2000) Superbugs on the Hoof? Science 288: 792-794. Available: http://www.sciencemag.org/content/288/5467/792.short. Accessed 2012 Sep 7.
17. Mølbak K, Baggesen DL, Aarestrup FM, Ebbesen JM, Engberg J, et al. (1999) An Outbreak of Multidrug-resistant Salmonella enterica serotype Typhimurium DT104. The New England Journal of Medicine 341: 1420-1425. Available: http://www.ncbi.nlm.nih.gov/pubmed/10547404. Accessed 2012 Sep 7.
18. Chapman J (1998) Characterizing bacterial resistance to preservatives and disinfectants. International Biodeterioration & Biodegradation 41: 241-245. Available: http://linkinghub.elsevier.com/retrieve/pii/S0964830598000250. Accessed 2011 May 30.
19. McMurry LM, Oethinger M, Levy SB (1998) Overexpression of marA, soxS, or acrAB produces resistance to triclosan in laboratory and clinical strains of Escherichia coli. FEMS Microbiology Letters 166: 305-309. Available: http://www.ncbi.nlm.nih.gov/pubmed/9770288. Accessed 2011 Jun 3.
20. MacGowan AP, Wise R (2001) Establishing MIC breakpoints and the interpretation of in vitro susceptibility tests. The Journal of Antimicrobial Chemotherapy 48 Suppl 1: 17-28. Available: http://www.ncbi.nlm.nih.gov/pubmed/11420334. Accessed 2012 Apr 16.
21. EUCAST (2012) European Committee on Antimicrobial Susceptibility Testing-Clinical Breakpoints. Available: http://www.eucast.org/clinical-breakpoints/. Accessed 2012 Sep 10.
22. Ambrose PG (2006) Monte Carlo Simulation in the Evaluation of Susceptibility Breakpoints: Predicting the Future: Insights from the Society of Infectious Diseases Pharmacists. Pharmacotherapy: The Journal of Human Pharmacology and Drug Therapy 26: 129-134. Available: http://dx.doi.org/10.1592/phco.2006.26.1.129. Accessed 2012 Sep 7.
23. Turnidge J, Kahlmeter G, Kronvall G (2006) Statistical characterisation of bacterial wild-type MIC value distributions and the determination of epidemiological cut-off values. Clinical Microbiology and Infection 12: 418-425. Available: http://www.ncbi.nlm.nih.gov/pubmed/16643517. Accessed 2012 Apr 16.
24. Thabaut A, Durosoir JL, Meyran M (1983) La sensibilite de Staphylococcus aureus aux antibiotiques en milieu hospitalier evolution et etat actuel. Médecine et Maladies Infectieuses 13: 128-132. Available: http://www.sciencedirect.com/science/article/pii/S0399077X83801103. Accessed 2012 Sep 7.
25. Tankovic J, Aubry-Damon H, Leclercq R (1997) Résistance aux antibiotiques autres que les bêta-lactamines chez Staphylococcus aureus. Médecine et Maladies Infectieuses 27, Supple: 207-216. Available: http://www.sciencedirect.com/science/article/pii/S0399077X97800224. Accessed 2012 Sep 7.
26. Hugard L, Ndoye B, Saccharin C (1994) Evolution des résistances aux antibiotiques. Comparaison des principaux germes isolés de pus en 1989 et 1992 à l'Hôpital Principal de Dakar. Médecine d'Afrique Noire 41: 31-36. Available: http://cat.inist.fr/?aModele=afficheN&cpsidt=3969009. Accessed 2012 Sep 7.
27. Espigares E, Bueno A, Espigares M, Gálvez R (2006) Isolation of Salmonella serotypes in wastewater and effluent: Effect of treatment and potential risk. International Journal of Hygiene and Environmental Health 209: 103-107. Available: http://www.ncbi.nlm.nih.gov/pubmed/16373208. Accessed 2012 Sep 6.
28. Rouillon S, Ourdanabia S, Jamart S, Hernandez C, Meunier O, (2006) Étude de l'efficacité d'un produit détergent désinfectant pour sols et surfaces sur les souches bactériennes isolées à partir de l'environnement hospitalier. Pathologie Biologie 54: 325-330 doi:10.1016/j.patbio.2006.01.011Accessed 2012 Feb 29.
29. Rutala WA, Weber DJ (2001) Surface disinfection: should we do it? The Journal of Hospital Infection 48: 64-68. Accessed 7 March 2012.
30. Aase B, Sundheim G, Langsrud S, Rørvik LM (2000) Occurrence of and a possible mechanism for resistance to a quaternary ammonium compound in Listeria monocytogenes. International Journal of Food Microbiology 62: 57-63. Available: http://www.ncbi.nlm.nih.gov/pubmed/11139022. Accessed 2012 March 2.
31. Beier RC, Bischoff KM, Ziprin RL, Poole TL, Nisbet DJ (2005) Chlorhexidine susceptibility, virulence factors, and antibiotic resistance of beta-hemolytic Escherichia coli isolated from neonatal swine with diarrhea. Bulletin of Environmental Contamination and Toxicology 75: 835-844. Available: http://www.ncbi.nlm.nih.gov/pubmed/16400568. Accessed 2012 Mar 7.
32. Soumet C, Ragimbeau C, Maris P (2005) Screening of benzalkonium chloride resistance in Listeria monocytogenes strains isolated during cold smoked fish production. Letters in Applied Microbiology 41: 291-296. Available: http://www.ncbi.nlm.nih.gov/pubmed/16108923. Accessed 2012 Mar 2.
33. Copitch JL, Whitehead RN, Webber MA (2010) Prevalence of decreased susceptibility to triclosan in Salmonella enterica isolates from animals and humans and association with multiple drug resistance. International Journal of Antimicrobial Agents 36: 247-251. Available: http://www.ncbi.nlm.nih.gov/pubmed/20541914. Accessed 2012 Mar 2.
34. Beier RC, Anderson PN, Hume ME, Poole TL, Duke SE, et al. (2011) Prevalence of decreased susceptibility to triclosan in Salmonella enterica isolates from animals and humans and association with multiple drug resistance. Foodborne Pathogens and Disease 8: 593-600. Available: http://www.ncbi.nlm.nih.gov/pubmed/21235389. Accessed 2012 Mar 7.
35. Lambert RJW (2004) Comparative analysis of antibiotic and antimicrobial biocide susceptibility data in clinical isolates of methicillin-sensitive Staphylococcus aureus, methicillin-resistant Staphylococcus aureus and Pseudomonas aeruginosa between 1989 and 2000. Journal of Applied Microbiology 97: 699-711. Available: http://dx.doi.org/10.1111/j.13652672.2004.02345.x. Accessed 2012 Sep 17.
36. Adriaans P, Zantinge D (1997) Data Mining. Addison-Wesley Longman Publishing Co., Inc. p.
37. Mitchell T (1997) Machine Learning. McGraw-Hill Education. p.
38. CLSI (2009) Methods for Dilution Antimicrobial Susceptibility Tests for Bacteria that grow aerobically; Approved Standard- Eighth Edition. CLSI document M07-A8. Available: http://www.clsi.org/source/orders/free/m07-a8.pdf. Accessed 2011 Jun 8.
39. NCCLS (1999) Methods for Determining Bactericidal Activity of Antimicrobial Agents; Approved Guideline. NCCLS document M26-A. Available:http://www.clsi.org/source/orders/free/m26-a.pdf. Accessed 2012 Sep 12.
40. Hochberg Y, Tamhane A (1987) Multiple Comparison Procedures. John Wiley & Sons. p.
41. Abdi H, (2007) The Bonferonni and Šidák Corrections for Multiple Comparisons. In: Salkind NJ, editor. Encyclopedia of Measurement and Statistics. Thousand Oaks, Vol. 1: 103-107.
42. Hesterberg T, Monaghan S, Moore D, Clipson A, Epstein R, (2003) Bootstrap Methods and Permutation Tests. The Practice of Business Statistics. W. H. Freeman, Vol. 47: 1-70.
43. Marchini J, Donnelly P, Cardon LR (2005) Genome-wide strategies for detecting multiple loci that influence complex diseases. Nature Genetics 37: 413-417. Available: http://www.ncbi.nlm.nih.gov/pubmed/15793588. Accessed 2011 May 4.
44. Li M, Wang K, Grant SFA, Hakonarson H, Li C (2009) ATOM: a powerful gene-based association test by combining optimally weighted markers. Bioinformatics 25: 497-503. Available: http://www.ncbi.nlm.nih.gov/pubmed/19074959. Accessed 2011 May 4.
45. Anunciação O, Gomes B, Vinga S, Gaspar J, Oliveira A, et al. (2010) A Data Mining Approach for the Detection of High-Risk Breast Cancer Groups. In: Rocha M, Riverola F, Shatkay H, Corchado J, editors. Advances in Bioinformatics. Springer Berlin Heidelberg, Vol. 74. 43-51. Available: http://www.springerlink.com/content/l55k63p457721384/. Accessed 2012 Sep 12.
46. Weisstein EW (2012) Fisher's Exact Test. From MathWorld-A Wolfram Web Resource. Available: http://mathworld.wolfram.com/FishersExactTest.html. Accessed 2012 Sep 12.
47. Francisco AP, Bugalho M, Ramirez M, Carriço JA (2009) Global optimal eBURST analysis of multilocus typing data using a graphic matroid approach. BMC Bioinformatics 10: 152. Available: http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2705362&tool=pmcentrez&rendertype=abstract. Accessed 2012 Sep 12.
48. Francisco AP, Vaz C, Monteiro PT, Melo-Cristino J, Ramirez M, et al. (2012) PHYLOViZ: Phylogenetic Inference and Data Visualization for Sequence Based Typing Methods. BMC Bioinformatics 13: 87. Available: http://www.biomedcentral.com/1471-2105/13/87. Accessed 2011 May 9.
49. Tarca AL, Carey VJ, Chen X, Romero R, Drǎghici S (2007) Machine Learning and Its Applications to Biology. PLoS Computational Biology 3: e116. Available: http://www.ncbi.nlm.nih.gov/pubmed/17604446. Accessed 2012 Sep 12.
50. Kraskov A, St H, Andrzejak RG, Grassberger P (2008) Hierarchical Clustering Based on Mutual Information. Europhysics Letters 70. Available: http://iopscience.iop.org/0295-5075/70/2/278. Accessed 2012 Mar 12.
51. CLSI (2010) Performance Standards for Antimicrobial Susceptibility Testing?; Twentieth Informational Supplement. CLSI document M100-S20.
52. Magiorakos A-P, Srinivasan A, Carey RB, Carmeli Y, Falagas ME, et al. (2012) Multidrug-resistant, extensively drug-resistant and pandrug-resistant bacteria: an international expert proposal for interim standard definitions for acquired resistance. Clinical Microbiology and Infection 18: 268-281. Available: http://dx.doi.org/10.1111/j.1469-0691.2011.03570.x. Accessed 2012 Sep 17.
53. Russell AD (2004) Whither triclosan? The Journal of Antimicrobial Chemotherapy 53: 693-695. Available: http://www.ncbi.nlm.nih.gov/pubmed/15073159. Accessed 14 August 2010.
54. Bailey AM, Constantinidou C, Ivens A, Garvey MI, Webber M a, et al. (2009) Exposure of Escherichia coli and Salmonella enterica serovar Typhimurium to triclosan induces a species-specific response, including drug detoxification. The Journal of Antimicrobial Chemotherapy 64: 973-985. Available: http://www.ncbi.nlm.nih.gov/pubmed/19759044. Accessed 2012 Mar 5.
55. Birosová L, Mikulásová M (2009) Development of triclosan and antibiotic resistance in Salmonella enterica serovar Typhimurium. Journal of Medical Microbiology 58: 436-441. Available: http://www.ncbi.nlm.nih.gov/pubmed/19273638. Accessed 2012 May 30.
56. Chuanchuen R, Beinlich K, Hoang TT, Becher A, Karkhoff-Schweizer RR, et al. (2001) Cross-resistance between triclosan and antibiotics in Pseudomonas aeruginosa is mediated by multidrug efflux pumps: exposure of a susceptible mutant strain to triclosan selects nfxB mutants overexpressing MexCD-OprJ. Antimicrobial Agents and Chemotherapy 45: 428-432. Available: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11158736. Accessed 2012 Sep 12.
57. Chuanchuen R, Narasaki CT, Schweizer HP (2002) The MexJK efflux pump of Pseudomonas aeruginosa requires OprM for antibiotic efflux but not for efflux of triclosan. Journal of Bacteriology 184: 5036-5044. Available: http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=135324&tool=pmcentrez&rendertype=abstract. Accessed 2012 Sep 12.
58. Hernández A, Ruiz FM, Romero A, Martínez JL (2011) The Binding of Triclosan to SmeT, the Repressor of the Multidrug Efflux Pump SmeDEF, Induces Antibiotic Resistance in Stenotrophomonas maltophilia. PLoS Pathogens 7: 12. Available: http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3128119&tool=pmcentrez&rendertype=abstract. Accessed 2012 Sep 12.
59. Sanchez P, Moreno E, Martinez JL (2005) The biocide triclosan selects Stenotrophomonas maltophilia mutants that overproduce the SmeDEF multidrug efflux pump. Antimicrobial Agents and Chemotherapy 49: 781-782. Available: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC547238/. Accessed 2012 Sep 12.
60. Katzung BG, Masters SB, Trevor AJ (2009) Basic and Clinical Pharmacology. 11th ed. McGraw-Hill Medical (Lange Basic Science). p.