Microbial Genotyping Systems for Infection Control

  • Matthew O’Sullivan
Chapter

Abstract

Microbial genotyping in hospital infection control is traditionally used to confirm outbreaks that have been identified using spatiotemporal surveillance data. However, for organisms of high endemicity, such as methicillin-resistant Staphylococcus aureus (MRSA), this approach may have limited usefulness due to the inability to even suspect outbreaks without first performing molecular typing. New PCR based typing methods have a much faster turn-around time and higher throughput than traditional methods, and open the door to the possibility of performing universal typing rather than the traditional targeted strategy. However, using a universal strategy requires a more robust approach to result interpretation to avoid falsely calling outbreaks of organisms that have similar molecular profiles by chance. This chapter discusses both the targeted and universal approaches to molecular typing in hospital infection control, and the interpretation of typing results using a probabilistic framework. Lastly, the continuous integration of clinical data from electronic medical records with spatiotemporal and molecular surveillance data to produce a complete microbial genotyping system will be explored.

Keywords

Tuberculosis Electrophoresis Bacillus Diarrhea Pseudomonas 

References

  1. Almuneef MA, Baltimore RS, Farrel PA et al. (2001) Molecular typing demonstrating transmission of gram-negative rods in a neonatal intensive care unit in the absence of a recognized epidemic. Clin Infect Dis 32:220–227CrossRefPubMedGoogle Scholar
  2. Amaral MM, Coelho LR, Flores RP et al. (2005) The predominant variant of the Brazilian epidemic clonal complex of methicillin-resistant Staphylococcus aureus has an enhanced ability to produce biofilm and to adhere to and invade airway epithelial cells. J Infect Dis 192:801–810CrossRefPubMedGoogle Scholar
  3. Andrei A, Zervos MJ (2006) The application of molecular techniques to the study of hospital infection. Arch Pathol Lab Med 130:662–668PubMedGoogle Scholar
  4. Asmundsdottir LR, Erlendsdottir H, Haraldsson G et al. (2008) Molecular epidemiology of candidemia: evidence of clusters of smoldering nosocomial infections. Clin Infect Dis 47:e17–24CrossRefPubMedGoogle Scholar
  5. Australian Institute of Health and Welfare (2007) Australian hospital statistics 2005–06. Health services series no. 30. Cat. no. HSE 50. AIHW, CanberraGoogle Scholar
  6. Best M, Neuhauser D (2004) Ignaz Semmelweis and the birth of infection control. Qual Safety Health Care 13:233–234CrossRefPubMedGoogle Scholar
  7. Burke JP (2003) Infection control – a problem for patient safety. N Engl J Med 348:651–656CrossRefPubMedGoogle Scholar
  8. Carretto E, Barbarini D, Farina C et al. (2008) Use of the DiversiLab semiautomated repetitive-sequence-based polymerase chain reaction for epidemiologic analysis on Acinetobacter baumannii isolates in different Italian hospitals. Diagn Microbiol Infect Dis 60:1–7PubMedGoogle Scholar
  9. Casewell MW, Desai N (1983) Survival of multiply-resistant Klebsiella aerogenes and other Gram-negative bacilli on finger-tips. J Hosp Infect 4:350–360CrossRefPubMedGoogle Scholar
  10. Chaves F, Garcia-Martinez J, de Miguel S et al. (2005) Epidemiology and clonality of methicillin-resistant and methicillin-susceptible Staphylococcus aureus causing bacteremia in a tertiary-care hospital in Spain. Infect Control Hosp Epidemiol 26:150–156CrossRefPubMedGoogle Scholar
  11. Clark CM, Driver CR, Munsiff SS et al. (2006) Universal genotyping in tuberculosis control program, New York City, 2001–2003. Emerg Infect Dis 12:719–724PubMedGoogle Scholar
  12. Curran ET, Benneyan JC, Hood J (2002) Controlling methicillin-resistant Staphylococcus aureus: a feedback approach using annotated statistical process control charts. Infect Control Hosp Epidemiol 23:13–18CrossRefPubMedGoogle Scholar
  13. Dziekan G, Hahn A, Thune K et al. (2000) Methicillin-resistant Staphylococcus aureus in a teaching hospital: investigation of nosocomial transmission using a matched case-control study. J Hosp Infect 46:263–270CrossRefPubMedGoogle Scholar
  14. Easmon CS, Hastings MJ, Clare AJ et al. (1981) Nosocomial transmission of group B streptococci. Br Med J (Clin Res Ed) 283:459–461CrossRefGoogle Scholar
  15. Edgeworth JD, Yadegarfar G, Pathak S et al. (2007) An outbreak in an intensive care unit of a strain of methicillin-resistant Staphylococcus aureus sequence type 239 associated with an increased rate of vascular access device-related bacteremia. Clin Infect Dis 44:493–501CrossRefPubMedGoogle Scholar
  16. Fontana C, Favaro M, Pistoia ES et al. (2007) The combined use of VIGI@ct (bioMerieux) and fluorescent amplified length fragment polymorphisms in the investigation of potential outbreaks. J Hosp Infect 66:262–268CrossRefPubMedGoogle Scholar
  17. Fontana C, Favaro M, Minelli S et al. (2008) Acinetobacter baumannii in intensive care unit: a novel system to study clonal relationship among the isolates. BMC Infect Dis 8:79CrossRefPubMedGoogle Scholar
  18. Hacek DM, Suriano T, Noskin GA et al. (1999) Medical and economic benefit of a comprehensive infection control program that includes routine determination of microbial clonality. Am J Clin Pathol 111:647–654PubMedGoogle Scholar
  19. Hacek DM, Cordell RL, Noskin GA et al. (2004) Computer-assisted surveillance for detecting clonal outbreaks of nosocomial infection. J Clin Microbiol 42:1170–1175CrossRefPubMedGoogle Scholar
  20. Harmsen D, Claus H, Witte W et al. (2003) Typing of methicillin-resistant Staphylococcus aureus in a university hospital setting by using novel software for spa repeat determination and database management. J Clin Microbiol 41:5442–5448CrossRefPubMedGoogle Scholar
  21. Hartstein AI, Denny MA, Morthland VH et al. (1995) Control of methicillin-resistant Staphylococcus aureus in a hospital and an intensive care unit. Infect Control Hosp Epidemiol 16:405–411CrossRefPubMedGoogle Scholar
  22. Hartstein AI, LeMonte AM, Iwamoto PK (1997) DNA typing and control of methicillin-resistant Staphylococcus aureus at two affiliated hospitals. Infect Control Hosp Epidemiol 18:42–48CrossRefPubMedGoogle Scholar
  23. Imataki O, Makimoto A, Kato S et al. (2006) Coincidental outbreak of methicillin-resistant Staphylococcus aureus in a hematopoietic stem cell transplantation unit. Am J Hematol 81:664–669CrossRefPubMedGoogle Scholar
  24. Jaeschke R, Guyatt GH, Sackett DL (1994) Users’ guides to the medical literature. III. How to use an article about a diagnostic test. B. What are the results and will they help me in caring for my patients? The Evidence-Based Medicine Working Group. J Am Med Assoc 271:703–707CrossRefGoogle Scholar
  25. Kim HJ, Kim SY, Seo WH et al. (2006) Outbreak of late-onset group B streptococcal infections in healthy newborn infants after discharge from a maternity hospital: a case report. J Korean Med Sci 21:347–350CrossRefPubMedGoogle Scholar
  26. Labbe AC, Poirier L, Maccannell D et al. (2008) Clostridium difficile infections in a Canadian tertiary care hospital before and during a regional epidemic associated with the BI/NAP1/027 strain. Antimicrob Agents Chemother 52:3180–3187CrossRefPubMedGoogle Scholar
  27. Loo VG, Poirier L, Miller MA et al. (2005) A predominantly clonal multi-institutional outbreak of Clostridium difficile-associated diarrhea with high morbidity and mortality. N Engl J Med 353:2442–2449CrossRefPubMedGoogle Scholar
  28. Lopman BA, Gallimore C, Gray JJ et al. (2006) Linking healthcare associated norovirus outbreaks: a molecular epidemiologic method for investigating transmission. BMC Infect Dis 6:108CrossRefPubMedGoogle Scholar
  29. Macfarlane L, Walker J, Borrow R et al. (1999) Improved recognition of MRSA case clusters by the application of molecular subtyping using pulsed-field gel electrophoresis. J Hosp Infect 41:29–37CrossRefPubMedGoogle Scholar
  30. Mascini EM, Troelstra A, Beitsma M et al. (2006) Genotyping and preemptive isolation to control an outbreak of vancomycin-resistant Enterococcus faecium. Clin Infect Dis 42:739–746CrossRefPubMedGoogle Scholar
  31. Mellmann A, Friedrich AW, Rosenkotter N et al. (2006) Automated DNA sequence-based early warning system for the detection of methicillin-resistant Staphylococcus aureus outbreaks. PLoS Med 3:e33CrossRefPubMedGoogle Scholar
  32. Morton AP, Whitby M, McLaws M-L et al. (2001) The application of statistical process control charts to the detection and monitoring of hospital-acquired infections. J Qual Clin Pract 21:112–117CrossRefPubMedGoogle Scholar
  33. Muldrew KL, Tang YW, Li H et al. (2008) Clonal dissemination of Staphylococcus epidermidis in an oncology ward. J Clin Microbiol 46:3391–3396CrossRefPubMedGoogle Scholar
  34. Otter JA, French GL (2006) Nosocomial transmission of community-associated methicillin-resistant Staphylococcus aureus: an emerging threat. Lancet Infect Dis 6:753–755CrossRefPubMedGoogle Scholar
  35. Papakyriacou H, Vaz D, Simor A et al. (2000) Molecular analysis of the accessory gene regulator (agr) locus and balance of virulence factor expression in epidemic methicillin-resistant Staphylococcus aureus. J Infect Dis 181:990–1000CrossRefPubMedGoogle Scholar
  36. Patel M, Waites KB, Hoesley CJ et al. (2008) Emergence of USA300 MRSA in a tertiary medical centre: implications for epidemiological studies. J Hosp Infect 68:208–213CrossRefPubMedGoogle Scholar
  37. Peleg AY, Franklin C, Bell JM et al. (2005) Dissemination of the metallo-beta-lactamase gene blaIMP-4 among gram-negative pathogens in a clinical setting in Australia. Clin Infect Dis 41:1549–1556CrossRefPubMedGoogle Scholar
  38. Peterson LR, Petzel RA, Clabots CR et al. (1993) Medical technologists using molecular epidemiology as part of the infection control team. Diagn Microbiol Infect Dis 16:303–311CrossRefPubMedGoogle Scholar
  39. Pfaller MA, Herwaldt LA (1997) The clinical microbiology laboratory and infection control: emerging pathogens, antimicrobial resistance, and new technology. Clin Infect Dis 25:858–870CrossRefPubMedGoogle Scholar
  40. Pfaller MA, Wakefield DS, Hollis R et al. (1991) The clinical microbiology laboratory as an aid in infection control. The application of molecular techniques in epidemiologic studies of methicillin-resistant Staphylococcus aureus. Diagn Microbiol Infect Dis 14:209–217CrossRefPubMedGoogle Scholar
  41. Phillips I (1991) Epidemic potential and pathogenicity in outbreaks of infection with EMRSA and EMREC. J Hosp Infect 18(Suppl A):197–201CrossRefPubMedGoogle Scholar
  42. Pimentel JD, Low J, Styles K et al. (2005) Control of an outbreak of multi-drug-resistant Acinetobacter baumannii in an intensive care unit and a surgical ward. J Hosp Infect 59:249–253CrossRefPubMedGoogle Scholar
  43. Prospero E, Barbadoro P, Savini S et al. (2006) Cluster of Pseudomonas aeruginosa catheter-related bloodstream infections traced to contaminated multidose heparinized saline solutions in a medical ward. Int J Hyg Environ Health 209:553–556CrossRefPubMedGoogle Scholar
  44. Ramage L, Green K, Pyskir D et al. (1996) An outbreak of fatal nosocomial infections due to group A streptococcus on a medical ward. Infect Control Hosp Epidemiol 17:429–431CrossRefPubMedGoogle Scholar
  45. Riley LW (2004) Principles and approaches. Molecular epidemiology of infectious diseases: principles and practices. ASM Press, Washington, DCGoogle Scholar
  46. Schmoldt S, Schuhegger R, Wendler T et al. (2008) Molecular evidence of nosocomial Pneumocystis jirovecii transmission among 16 patients after kidney transplantation. J Clin Microbiol 46:966–971CrossRefPubMedGoogle Scholar
  47. Trilla A, Nettleman MD, Hollis RJ et al. (1993) Restriction endonuclease analysis of plasmid DNA from methicillin-resistant Staphylococcus aureus: clinical application over a three-year period. Infect Control Hosp Epidemiol 14:29–35CrossRefPubMedGoogle Scholar
  48. Wagenvoort JHT, Sluijsmans W, Penders RJR (2000) Better environmental survival of outbreak vs. sporadic MRSA isolates. J Hosp Infect 45:231–234CrossRefPubMedGoogle Scholar
  49. Weber S, Pfaller MA, Herwaldt LA (1997) Role of molecular epidemiology in infection control. Infect Dis Clin North Am 11:257–278CrossRefPubMedGoogle Scholar
  50. Wilcox MH, Fitzgerald P, Freeman J et al. (2000) A five year outbreak of methicillin-susceptible Staphylococcus aureus phage type 53,85 in a regional neonatal unit. Epidemiol Infect 124:37–45CrossRefPubMedGoogle Scholar
  51. Wright MO, Perencevich EN, Novak C et al. (2004) Preliminary assessment of an automated surveillance system for infection control. Infect Control Hosp Epidemiol 25:325–332CrossRefPubMedGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC 2010

Authors and Affiliations

  • Matthew O’Sullivan
    • 1
  1. 1.Centre for Infectious Diseases and MicrobiologySydney West Area Health ServiceSydneyAustralia

Personalised recommendations