Abstract
The treatment of infectious disease centers around the goals of both curing the patient and preventing or at least restricting the spread of disease. In a perfect world, health care professionals would know that these goals have been achieved when the patient’s health is restored and there are no new occurrences of infected patients. However, the real world of infectious disease is far from perfect. The individual patient may present with evidence of recurring or additional infection by a pathogen (e.g., at a different body site). Different members of a patient population may yield cultures of the same organism. In both instances, the question commonly asked is whether multiple isolates of a given pathogen represent the same strain. In the individual patient, this question commonly relates to issues of therapeutic efficacy while in a patient population the concern is infection control. However, in both settings, the resolution of these questions is aided by specific epidemiological assessment. In the past, a variety of methods based on phenotypic characteristics have been used for this purpose including biotype, serotype, susceptibility to antimicrobial agents, or bacteriophages, etc. [1–4]. However, in the 1970, techniques developed for the recombinant DNA laboratory began to find application in the molecular characterization of clinical isolates. These included comparing protein molecular weight distributions by polyacrylamide gel electrophoresis, relative mobility of specific enzymes by starch-gel electrophoresis (multi-locus enzyme electrophoresis), specific antibody reactions with immobilized cellular proteins (immunoblotting), and cellular plasmid content (i.e., plasmid fingerprinting) [2, 5, 6]. However, by 1980 it was clear that comparisons at the genomic level would provide the most fundamental measure of epidemiological relatedness. Thus, molecular typing was born. While a wide range of etiological agents are of clinical concern, this review focuses on molecular approaches to the epidemiological analysis of bacterial pathogens.
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Tenover FC, Arbeit RD, Goering RV (1997) How to select and interpret molecular strain typing methods for epidemiological studies of bacterial infections: a review for healthcare epidemiologists. Infect Control Hosp Epidemiol 18(6):426–439
Riley LW (2004) Molecular epidemiology of infectious disease: principles and practices. ASM, Washington, DC
Chen Y, Brown E, Knabel SJ (2011) Molecular Epidemiology of Foodborne Pathogens. In: Wiedmann M, Zhang W (eds) Genomics of foodborne bacterial pathogens. Springer, New York, pp 403–453
Van Belkum A, Tassios PT, Dijkshoorn L et al (2007) Guidelines for the validation and application of typing methods for use in bacterial epidemiology. Clin Microbiol Infect 13(Suppl 3):1–46
Goering RV (2000) The molecular epidemiology of nosocomial infection: past, present, and future. Rev Med Microbiol 11:145–152
Goering RV (2000) Molecular strain typing for the clinical laboratory: current application and future direction. Clin Microbiol News 22:169–173
Halpern D, Chiapello H, Schbath S et al (2007) Identification of DNA motifs implicated in maintenance of bacterial core genomes by predictive modeling. PLoS Genet 3(9):1614–1621
Lindsay JA, Moore CE, Day NP et al (2006) Microarrays reveal that each of the ten dominant lineages of Staphylococcus aureus has a unique combination of surface-associated and regulatory genes. J Bacteriol 188(2):669–676
Lindsay JA (2010) Genomic variation and evolution of Staphylococcus aureus. Int J Med Microbiol 300(2–3):98–103
Goering RV (2002) The influence of genomics on the molecular epidemiology of nosocomial pathogens. In: Shaw KJ (ed) Pathogen genomics: impact on human health. Humana, Totowa, pp 113–131
Bialkowska-Hobrzanska H, Jaskot D, Hammerberg O (1990) Evaluation of restriction endonuclease fingerprinting of chromosomal DNA and plasmid profile analysis for characterization of multiresistant coagulase-negative staphylococci in bacteremic neonates. J Clin Microbiol 28:269–275
Tenover FC, Akerlund T, Gerding DN et al (2011) Comparison of strain typing results for Clostridium difficile isolates from North America. J Clin Microbiol 49(5):1831–1837
Southern EM (1975) Detection of specific sequences among DNA fragments separated by gel electrophoresis. J Mol Biol 98(3):503–517
Van Belkum A (2003) High-throughput epidemiologic typing in clinical microbiology. Clin Microbiol Infect 9:86–100
Thorne N, Borrell S, Evans J et al (2011) IS6110-based global phylogeny of Mycobacterium tuberculosis. Infect Genet Evol 11(1):132–138
Schwartz DC, Saffran W, Welsh J, Haas R, Goldenberg M, Cantor CR (1983) New techniques for purifying large DNA’s and studying their properties and packaging. Cold Spring Harbor Symp Quant Biol 47:189–195
Schwartz DC, Koval M (1989) Conformational dynamics of individual DNA molecules during gel electrophoresis. Nature 338:520–522
Goering RV, Ribot EM, Gerner-Smidt P (2011) Pulsed-field gel electrophoresis: laboratory and epidemiologic considerations for interpretation of data. In: Persing DH, Tenover FC, Tang YW, Nolte FS, Hayden RT et al (eds) Molecular microbiology, 2nd edn. ASM, Washington, DC, pp 167–177
Goering RV (2010) Pulsed field gel electrophoresis: a review of application and interpretation in the molecular epidemiology of infectious disease. Infect Genet Evol 10(7):866–875
McDougal LK, Steward CD, Killgore GE, Chaitram JM, McAllister SK, Tenover FC (2003) Pulsed-field gel electrophoresis typing of oxacillin-resistant Staphylococcus aureus isolates from the United States: establishing a national database. J Clin Microbiol 41(11):5113–5120
Goering RV, McDougal LK, Fosheim GE, Bonnstetter KK, Wolter DJ, Tenover FC (2007) Epidemiologic distribution of the arginine catabolic mobile element among selected methicillin-resistant and methicillin-susceptible Staphylococcus aureus isolates. J Clin Microbiol 45(6):1981–1984
Schwan WR, Briska A, Stahl B et al (2010) Use of optical mapping to sort uropathogenic Escherichia coli strains into distinct subgroups. Microbiology 156(Pt 7):2124–2135
Petersen RF, Litrup E, Larsson JT et al (2011) Molecular characterization of Salmonella typhimurium highly successful outbreak strains. Foodborne Pathog Dis 8(6):655–661
Goering RV, Stemper ME, Shukla SK, Foley SL (2011) Restriction analysis techniques. In: Foley SL, Chen AY, Simjee S, Zervos MJ (eds) Molecular techniques for the study of hospital acquired infection. Wiley-Blackwell, Hoboken, N.J., pp 135–144
Melles DC, Schouls L, Francois P et al (2009) High-throughput typing of Staphylococcus aureus by amplified fragment length polymorphism (AFLP) or multi-locus variable number of tandem repeat analysis (MLVA) reveals consistent strain relatedness. Eur J Clin Microbiol Infect Dis 28(1):39–45
Versalovic J, Koeuth T, Lupski JR (1991) Distribution of repetitive DNA sequences in Eubacteria and application to fingerprinting of bacterial genomes. Nucleic Acids Res 19:6823–6831
Van Belkum A, Sluijter M, De Groot R, Verbrugh H, Hermans PWM (1996) Novel BOX repeat PCR assay for high-resolution typing of Streptococcus pneumoniae strains. J Clin Microbiol 34:1176–1179
Deplano A, Vaneechoutte M, Verschraegen G, Struelens MJ (1997) Typing of Staphylococcus aureus and Staphylococcus epidermidis strains by PCR analysis of Inter-IS256 spacer length polymorphisms. J Clin Microbiol 35:2580–2587
Frye SR, Healy M (2011) Repetitive sequence-based PCR typing of bacteria and fungi. In: Persing DH, Tenover FC, Tang YW, Nolte FS, Hayden RT, Van Belkum A (eds) Molecular microbiology: diagnostic principles and practice. ASM, Washington, DC, pp 199–212
Ross TL, Merz WG, Farkosh M, Carroll KC (2005) Comparison of an automated repetitive sequence-based PCR microbial typing system to pulsed-field gel electrophoresis for analysis of outbreaks of methicillin-resistant Staphylococcus aureus. J Clin Microbiol 43(11):5642–5647
Roussel S, Felix B, Colaneri C et al (2010) Semi-automated repetitive-sequence-based polymerase chain reaction compared to pulsed-field gel electrophoresis for Listeria monocytogenes subtyping. Foodborne Pathog Dis 7(9):1005–1012
Bouchet V, Huot H, Goldstein R (2008) Molecular genetic basis of ribotyping. Clin Microbiol Rev 21(2):262–273
Tenover FC, Novak-Weekley S, Woods CW et al (2010) Impact of strain types on detection of toxigenic Clostridium difficile: comparison of molecular diagnostic and enzyme immunoassay approaches. J Clin Microbiol 48(10):3719–3724
Valiente E, Dawson LF, Cairns MD, Stabler RA, Wren BW (2011) Emergence of new PCR-ribotypes from the hypervirulent Clostridium difficile 027 lineage. J Med Microbiol 61(Pt 1):49–56
Solomon K, Fanning S, McDermott S et al (2011) PCR ribotype prevalence and molecular basis of macrolide-lincosamide-streptogramin B (MLSB) and fluoroquinolone resistance in Irish clinical Clostridium difficile isolates. J Antimicrob Chemother 66(9):1976–1982
Gerding DN (2010) Global epidemiology of Clostridium difficile infection in 2010. Infect Control Hosp Epidemiol 31(Suppl 1):S32–S34
Katayama Y, Ito T, Hiramatsu K (2000) A new class of genetic element, staphylococcus cassette chromosome mec, encodes methicillin resistance in Staphylococcus aureus. Antimicrob Agents Chemother 44:1549–1555
IWG-SCC (2009) Classification of staphylococcal cassette chromosome mec (SCCmec): guidelines for reporting novel SCCmec elements. Antimicrob Agents Chemother 53(12):4961–4967
Kondo Y, Ito T, Ma XX et al (2007) Combination of multiplex PCRs for staphylococcal cassette chromosome mec type assignment: rapid identification system for mec, ccr, and major differences in junkyard regions. Antimicrob Agents Chemother 51(1):264–274
Milheirico C, Oliveira DC, De Lencastre H (2007) Multiplex PCR strategy for subtyping the staphylococcal cassette chromosome mec type IV in methicillin-resistant Staphylococcus aureus: ‘SCCmec IV multiplex’. J Antimicrob Chemother 60(1):42–48
Oliveira DC, De Lencastre H (2002) Multiplex PCR strategy for rapid identification of structural types and variants of the mec element in methicillin-resistant Staphylococcus aureus. Antimicrob Agents Chemother 46(7):2155–2161
Deurenberg RH, Stobberingh EE (2008) The evolution of Staphylococcus aureus. Infect Genet Evol 8:747–763
Van Belkum A, Scherer S, van Alphen L, Verbrugh H (1998) Short-sequence DNA repeats in prokaryotic genomes. Microbiol Mol Biol Rev 62:275–293
Lindstedt BA (2005) Multiple-locus variable number tandem repeats analysis for genetic fingerprinting of pathogenic bacteria. Electrophoresis 26(13):2567–2582
Hammerschmidt S, Muller A, Sillmann H et al (1996) Capsule phase variation in Neisseria meningitidis serogroup B by slipped-strand mispairing in the polysialyltransferase gene (siaD): correlation with bacterial invasion and the outbreak of meningococcal disease. Mol Microbiol 20(6):1211–1220
Pourcel C, Vergnaud G (2011) Strain typing using multiple “variable number of tandem repeat” analysis and genetic element CRISPR. In: Persing DH, Tenover FC, Tang YW, Nolte FS, Hayden RT, Van Belkum A (eds) Molecular microbiology: diagnostic principles and practice, 2nd edn. ASM, Washington, DC, pp 179–197
Bannerman TL, Hancock GA, Tenover FC, Miller JM (1995) Pulsed-field gel electrophoresis as a replacement for bacteriophage typing of Staphylococcus aureus. J Clin Microbiol 33:551–555
Swaminathan B, Barrett TJ, Hunter SB, Tauxe RV (2001) PulseNet: the molecular subtyping network for foodborne bacterial disease surveillance, United States. Emerg Infect Dis 7:382–389
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 41:5442–5448
Church DL, Chow BL, Lloyd T, Gregson DB (2011) Comparison of automated repetitive-sequence-based polymerase chain reaction and spa typing versus pulsed-field gel electrophoresis for molecular typing of methicillin-resistant Staphylococcus aureus. Diagn Microbiol Infect Dis 69:30–37
Frenay HME, Bunschoten AE, Schouls LM et al (1996) Molecular typing of methicillin-resistant Staphylococcus aureus on the basis of protein A gene polymorphism. Eur J Clin Microbiol Infect Dis 15:60–64
Shopsin B, Gomez M, Montgomery SO et al (1999) Evaluation of protein A gene polymorphic region DNA sequencing for typing of Staphylococcus aureus strains. J Clin Microbiol 37:3556–3563
Bessen DE (2009) Population biology of the human restricted pathogen, Streptococcus pyogenes. Infect Genet Evol 9:581–593
Steer AC, Law I, Matatolu L, Beall BW, Carapetis JR (2009) Global emm type distribution of group A streptococci: systematic review and implications for vaccine development. Lancet Infect Dis 9:611–616
Wajima T, Murayama SY, Sunaoshi K, Nakayama E, Sunakawa K, Ubukata K (2008) Distribution of emm type and antibiotic susceptibility of group A streptococci causing invasive and noninvasive disease. J Med Microbiol 57:1383–1388
Tanaka D, Gyobu Y, Kodama H et al (2002) emm typing of group A streptococcus clinical isolates: identification of dominant types for throat and skin isolates. Microbiol Immunol 46(7):419–423
Ryffel C, Bucher R, Kayser FH, Berger-Bächi B (1991) The Staphylococcus aureus mec determinant comprises an unusual cluster of direct repeats and codes for a gene product similar to the Escherichia coli sn-glycerophosphoryl diester phosphodiesterase. J Bacteriol 173:7416–7422
Ionescu R, Mediavilla JR, Chen L et al (2010) Molecular characterization and antibiotic susceptibility of Staphylococcus aureus from a multidisciplinary hospital in Romania. Microb Drug Resist 16:263–272
Goering RV, Morrison D, Al-Doori Z, Edwards GF, Gemmell CG (2008) Usefulness of mec-associated direct repeat unit (dru) typing in the epidemiological analysis of highly clonal methicillin-resistant Staphylococcus aureus in Scotland. Clin Microbiol Infect 14:964–969
Fessler A, Scott C, Kadlec K, Ehricht R, Monecke S, Schwarz S (2010) Characterization of methicillin-resistant Staphylococcus aureus ST398 from cases of bovine mastitis. J Antimicrob Chemother 65:619–625
Shore AC, Rossney AS, Kinnevey PM et al (2010) Enhanced discrimination of highly clonal ST22-methicillin-resistant Staphylococcus aureus IV isolates achieved by combining spa, dru, and pulsed-field gel electrophoresis typing data. J Clin Microbiol 48(5):1839–1852
Smyth DS, Wong A, Robinson DA (2011) Cross-species spread of SCCmec IV subtypes in staphylococci. Infect Genet Evol 11:446–453
Smyth DS, McDougal LK, Gran FW et al (2010) Population structure of a hybrid clonal group of methicillin-resistant Staphylococcus aureus, ST239-MRSA-III. PLoS One 5:e8582
Maiden MCJ, Bygraves JA, Feil E et al (1998) Multilocus sequence typing: a portable approach to the identification of clones within populations of pathogenic microorganisms. Proc Natl Acad Sci U S A 95:3140–5145
Feil EJ, Spratt BG (2001) Recombination and the population structures of bacterial pathogens. Annu Rev Microbiol 55:561–590
Aanensen DM, Spratt BG (2005) The multilocus sequence typing network: mlst.net. Nucleic Acids Res 33(Web Server issue):W728–W733
Yan Y, Cui Y, Han H et al (2011) Extended MLST-based population genetics and phylogeny of Vibrio parahaemolyticus with high levels of recombination. Int J Food Microbiol 145:106–112
Ch’ng SL, Octavia S, Xia Q et al (2011) Population structure and evolution of pathogenicity of Yersinia pseudotuberculosis. Appl Environ Microbiol 77:768–775
Litrup E, Torpdahl M, Malorny B, Huehn S, Christensen H, Nielsen EM (2010) Association between phylogeny, virulence potential and serovars of Salmonella enterica. Infect Genet Evol 10:1132–1139
Miller MB, Tang YW (2009) Basic concepts of microarrays and potential applications in clinical microbiology. Clin Microbiol Rev 22:611–633
Musser JM, Shelburne SA III (2009) A decade of molecular pathogenomic analysis of group A Streptococcus. J Clin Invest 119:2455–2463
Li W, Raoult D, Fournier PE (2009) Bacterial strain typing in the genomic era. FEMS Microbiol Rev 33:892–916
Dunbar SA (2006) Applications of Luminex xMAP technology for rapid, high-throughput multiplexed nucleic acid detection. Clin Chim Acta 363:71–82
Sanger F, Nicklen S, Coulson AR (1977) DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci U S A 74:5463–5467
Mellmann A, Harmsen D, Cummings CA et al (2011) Prospective genomic characterization of the German enterohemorrhagic Escherichia coli O104:H4 outbreak by rapid next generation sequencing technology. PLoS One 6:e22751
Rasko DA, Webster DR, Sahl JW et al (2011) Origins of the E. coli strain causing an outbreak of hemolytic-uremic syndrome in Germany. N Engl J Med 365:709–717
Willemse-Erix DF, Jachtenberg JW, Schut TB et al (2010) Towards Raman-based epidemiological typing of Pseudomonas aeruginosa. J Biophotonics 3:506–511
Wulf MW, Willemse-Erix D, Verduin CM, Puppels G, van Belkum A, Maquelin K (2012) The use of Raman spectroscopy in the epidemiology of methicillin-resistant Staphylococcus aureus of human- and animal-related clonal lineages. Clin Microbiol Infect 18(2):147–152
Moura H, Woolfitt AR, Carvalho MG et al (2008) MALDI-TOF mass spectrometry as a tool for differentiation of invasive and noninvasive Streptococcus pyogenes isolates. FEMS Immunol Med Microbiol 53:333–342
Wolters M, Rohde H, Maier T et al (2011) MALDI-TOF MS fingerprinting allows for discrimination of major methicillin-resistant Staphylococcus aureus lineages. Int J Med Microbiol 301:64–68
Williamson YM, Moura H, Woolfitt AR et al (2008) Differentiation of Streptococcus pneumoniae conjunctivitis outbreak isolates by matrix-assisted laser desorption ionization-time of flight mass spectrometry. Appl Environ Microbiol 74:5891–5897
Dieckmann R, Malorny B (2011) Rapid screening of epidemiologically important Salmonella enterica subsp. enterica serovars by whole-cell matrix-assisted laser desorption ionization-time of flight mass spectrometry. Appl Environ Microbiol 77(12):4136–4146
Goering RV (1998) The molecular epidemiology of nosocomial infection: an overview of principles, application, and interpretation. In: Specter S, Bendinelli M, Friedman H (eds) Rapid detection of infectious agents, 1st edn. Plenum, New York, pp 131–157
Rademaker JL, Savelkoul P (2004) PCR amplification-based microbial typing. In: Persing DH, Tenover FC, Versalovic J, Tang YW, Unger ER, Relman DA et al (eds) Molecular microbiology: diagnostic principles and practice. ASM, Washington, DC, pp 197–221
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Goering, R.V. (2013). Molecular Typing Techniques: State of the Art. In: Tang, YW., Stratton, C. (eds) Advanced Techniques in Diagnostic Microbiology. Springer, Boston, MA. https://doi.org/10.1007/978-1-4614-3970-7_13
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