1. Eybpoosh S, Haghdoost AA, Mostafavi E, Bahrampour A, Azadmanesh K, Zolala F. Molecular epidemiology of infectious diseases. Electron Physician. 2017;9(8):5149–5158.
2. Schulte PA, Perera FP. Molecular Epidemiology: Principles and Practice. San Diego: Academic Press; 1993. p. 588.
3. Levin BR, Lipsitch M, Bonhoeffer S. Population biology, evolution, and infectious disease: convergence and synthesis. Science. 1999;283(5403):806–809.
4. Foxman B, Riley L. Molecular epidemiology: focus on infection. Am J Epidemiol. 2001;153(12):1135–1141.
5. Huang L, Gao K, Zhong H, Xie Y, Liang B, Ji W, Liu H. Automated classification of group B Streptococcus into different clonal complexes using MALDI-TOF mass spectrometry. Front Mol
Biosci. 2024;11:1355448.
6. Hoang TTH, Dang DA, Pham TH, Luong MH, Tran ND, Nguyen TH, Nguyen TT, Inoue S, Morikawa S, Okutani A. Epidemiological and comparative genomic analysis of Bacillus anthracis
isolated from northern Vietnam. PLoS One. 2020;15(2):e0228116.
7. Ruettger A, Feige J, Slickers P, Schubert E, Morré SA, Pannekoek Y, Herrmann B, de Vries HJ, Ehricht R, Sachse K. Genotyping of Chlamydia trachomatis strains from culture and clinical
samples using an ompA-based DNA microarray assay. Mol Cell Probes. 2011;25(1):19–27.
8. Shekhawat SS, Gaurav A, Joseph B, Kumar H, Kumar N. Random amplified polymorphic DNA-based molecular heterogeneity analysis of Salmonella enterica isolates from foods of animal
origin. Vet World. 2019;12(1):146–154. doi:10.14202/vetworld.2019.146-154.
9. Sampaio P, Gusmão L, Alves C, Amorim A, et al. Highly polymorphic microsatellite for identification of Candida albicans strains. J Clin Microbiol. 2005;43(1):403–407.
10. El Naggar NM, Shawky RM, Serry FME, Emara M. The increased prevalence of rmpA gene in Klebsiella pneumoniae isolates coharboring blaNDM and blaOXA-48-like genes. Microb Drug
Resist. 2024;30(8):317–324.
11. Ahmed El-Domany R, El-Banna T, Sonbol F, Abu-Sayedahmed SH. Co-existence of NDM-1 and OXA-48 genes in carbapenem-resistant Klebsiella pneumoniae clinical isolates in Kafrelsheikh,
Egypt. Afr Health Sci. 2021;21(2):489–496.
12. Brehony C, Domegan L, Foley M, Fitzpatrick M, Cafferkey JP, O’Connell K, Dinesh B, McNamara E, Duffy F, Fitzpatrick F, Burns K. Molecular epidemiology of an extended multiple-species
OXA-48 CPE outbreak in a hospital ward in Ireland, 2018–2019. Antimicrob Steward Healthc Epidemiol. 2021;1(1):e54.
13. Evans DJ, Anjum MF, McBride S, et al. Plasmid-mediated OXA-48 carbapenemase outbreak in a tertiary-care hospital. J Hosp Infect. 2020;104(2):183–189. doi:10.1016/j.jhin.2019.10.017.
14. Kumar H, Kawai T, Akira S. Pathogen recognition by the innate immune system. Nat Rev Microbiol. 2020;18:95–110.
15. Grundmann H, Hellriegel B. Mathematical modelling: a tool for hospital infection control. Lancet Infect Dis. 2006;6(1):39–45.
16. Safdar N, Marx J, Meyer NA, Maki DG. Patient risk factors for nosocomial infection in the intensive care unit: A systematic review. Crit Care Med. 2002;30(3):586–595.
17. Vasylyeva TI, Friedman SR, Paraskevis D, Magiorkinis G. Integrating molecular epidemiology and social network analysis to study infectious diseases: Towards a socio-molecular era for
public health. Infect Genet Evol. 2016;46:248–255.
18. Maroye P, Doermann HP, Rogues AM, Gachie JP, Mégraud F. Investigation of an outbreak of Ralstonia pickettii in a paediatric hospital by RAPD. J Hosp Infect. 2000;44(4):267–272.
19. Zakerifar M, Goli HR, Kaboosi H, Rahmani Z, Peyravii Ghadikolaii F. Capsular gene distribution and RAPD typing of Streptococcus agalactiae isolated from pregnant women. AMB Express.
2024;14(1):13.
20. Arribas R, Tòrtola S, Welsh J, McClelland M, Peinado MA. Arbitrarily primed PCR and RAPDs. In: Micheli MR, Bova R, editors. Fingerprinting Methods Based on Arbitrarily Primed PCR.
Berlin: Springer; 1997. p. 3–20.
21. Spigaglia P, Mastrantonio P. Evaluation of repetitive element sequence-based PCR as a molecular typing method for Clostridium difficile. J Clin Microbiol. 2003;41(6):2454–2457. doi:10.1128/
JCM.41.6.2454-2457.2003.
22. Versalovic J, Koeuth T, Lupski JR. Distribution of repetitive DNA sequences in eubacteria and application to fingerprinting of bacterial genomes. Nucleic Acids Res. 1991;19(24):6823–6831.
23. Abay S, Kayman T, Otlu B, Hizlisoy H, Aydin F, Ertas N. Genetic diversity and antibiotic resistance profiles of Campylobacter jejuni isolates from poultry and humans in Turkey. Int J Food
Microbiol. 2014;178:29–38.
24. Behringer M, Miller WG, Oyarzabal OA. Typing of Campylobacter jejuni and Campylobacter coli isolated from live broilers and retail broiler meat by flaA-RFLP, MLST, PFGE and
REP-PCR. J Microbiol Methods. 2011;84(2):194–201.
25. Bakhshi B, Afshari N, Fallah F. Enterobacterial repetitive intergenic consensus (ERIC)-PCR analysis as a reliable evidence for suspected Shigella spp. outbreaks. Braz J Microbiol. 2018;49(3):529–
533.
26. Hulton CS, Higgins CF, Sharp PM. ERIC sequences: a novel family of repetitive elements in the genomes of Escherichia coli, Salmonella typhimurium and other enterobacteria. Mol Microbiol.
1991;5(4):825–834.
27. Wilson LA, Sharp PM. Enterobacterial repetitive intergenic consensus (ERIC) sequences in Escherichia coli: Evolution and implications for ERIC-PCR. Mol Biol Evol. 2006;23(6):1156–1168.
28. Mirhendi H, Makimura K, Khoramizadeh M, Yamaguchi H. A one-enzyme PCR-RFLP assay for identification of six medically important Candida species. Nihon Ishinkin Gakkai Zasshi.
2006;47(3):225–229.
29. Pang Y, Lu J, Wang Y, Song Y, Wang S, Zhao Y. Study of the rifampin monoresistance mechanism in Mycobacterium tuberculosis. Antimicrob Agents Chemother. 2013;57(2):893–900.
30. Tenover FC, Arbeit RD, Goering RV, Mickelsen PA, Murray BE, Persing DH, Swaminathan B. Interpreting chromosomal DNA restriction patterns produced by pulsed-field gel electrophore-
sis: criteria for bacterial strain typing. J Clin Microbiol. 1995;33(9):2233–2239.
31. Tenover FC, Arbeit RD, Goering RV. How to select and interpret molecular strain typing methods for epidemiological studies of bacterial infections: A review for healthcare epidemiologists.
Infect Control Hosp Epidemiol. 1997;18:426–439.
32. Goering RV. Pulsed-field gel electrophoresis. In: Persing DH, Tenover FC, Versalovic J, Tang Y-W, Unger ER, Relman DA, White TJ, editors. Molecular Microbiology: Diagnostic Principles and
Practice. Washington (DC): ASM Press; 2004. p. 185–196.
33. van Belkum A, Tassios PT, Dijkshoorn L, Haeggman S, Cookson B, Fry NK, Fussing V, Green J, Feil E, Gerner-Smidt P, Brisse S, Struelens M; European Society of Clinical Microbiology and
Infectious Diseases (ESCMID) Study Group on Epidemiological Markers (ESGEM). Guidelines for the validation and application of typing methods for use in bacterial epidemiology. Clin
Microbiol Infect. 2007;13(Suppl 3):1–46.
34. Basım E, Basım H. Pulsed-field gel electrophoresis (PFGE) tekniği ve moleküler biyolojideki kullanımı. Turk J Biol. 2001;25:405–418.
35. Soll DR. The use of DNA fingerprinting for epidemiological typing and gene mapping in Candida albicans. Clin Microbiol Rev. 2000;13(2):332–70.
36. Guducuoglu H, Gultepe B, Otlu B, Bektas A, Yildirim O, Tuncer O, Berktas M. Candida albicans outbreak associated with total parenteral nutrition in the neonatal unit. Indian J Med Microbiol.
2016;34(2):202–207.
37. Tanrıverdi ES. (2022). Klinik örneklerden elde edilen Candida parapsilosis izolatları arasındaki klonal ilişkilerin araştırılmasında kullanılan yöntemlerin karşılaştırılması. (Tıpta Uzmanlık
Tezi) İnönü Üniversitesi Tıp Fakültesi Tıbbi Mikrobiyoloji Anabilim Dalı, Malatya.
38. Otlu B. Enfeksiyon etkeni ve kolonize Candida albicans suşlarının PFGE ve AP-PCR ile genotiplendirilmesi. Doktora Tezi. Gazi Üniversitesi, 2004.
39. Schouls LM, Spalburg EC, van Luit M, Huijsdens XW, Pluister GN, van Santen-Verheuvel MG, van der Heide HG, Grundmann H, Heck ME, de Neeling AJ. Multiple-locus variable number
tandem repeat analysis of Staphylococcus aureus: comparison with pulsed-field gel electrophoresis and spa-typing. PLoS One. 2009;4(4):e5082.
40. Maleki A, Kaviar VH, Koupaei M, Haddadi MH, Kalani BS, Valadbeigi H, Karamolahi S, Omidi N, Hashemian M, Sadeghifard N, Mohamadi J, Heidary M, Khoshnood S. Molecular typing
and antibiotic resistance patterns among clinical isolates of Acinetobacter baumannii recovered from burn patients in Tehran, Iran. Front Microbiol. 2022;13:994303.
41. Ei PW, Aung WW, Lee JS, Choi GE, Chang CL. Molecular strain typing of Mycobacterium tuberculosis: a review of frequently used methods. J Korean Med Sci. 2016;31(11):1673–1683.
42. Williams O, Abeel T, Casali N, Cohen K, Pym AS, Mungall SB, et al. Fatal nosocomial MDR TB identified through routine genetic analysis and whole-genome sequencing. Emerg Infect Dis.
2015;21(6):1082–1084.
43. Shorten RJ, Gillespie SH, Sule O, Lipman M, McHugh TD. Molecular strain typing of Mycobacterium tuberculosis isolates from a suspected outbreak involving a faulty bronchoscope. J Hosp
Infect. 2005;61(1):86–87.
44. Spruijtenburg B, Meis JF, Verweij PE, de Groot T, Meijer EFJ. Short Tandem Repeat Genotyping of Medically Important Fungi: A Comprehensive Review of a Powerful Tool with Extensive
Future Potential. Mycopathologia. 2024 Aug 3;189(5):72.
45. Diab-Elschahawi M, Forstner C, Hagen F, Meis JF, Lassnigg A. Candida parapsilosis multicenter study: microsatellite genotyping reveals routes of nosocomial infection. J Clin Microbiol.
2012;50(3):1299–1306.
46. Maiden MC, Bygraves JA, Feil E, Morelli G, Russell JE, Urwin R, Zhang Q, Zhou J, Zurth K, Caugant DA, Feavers IM, Achtman M, Spratt BG. Multilocus sequence typing: a portable approach
to the identification of clones within populations of pathogenic microorganisms. Proc Natl Acad Sci U S A. 1998;95(6):3140–3145.
47. Ruppitsch W. Molecular typing of bacteria for epidemiological surveillance and outbreak investigation / Molekulare Typisierung von Bakterien für die epidemiologische Überwachung und
Ausbruchsabklärung. Die Bodenkultur. 2016;67(4):199–224.
48. Leeper MM, Tolar BM, Griswold T, Vidyaprakash E, Hise KB, Williams GM, Im SB, Chen JC, Pouseele H, Carleton HA. Evaluation of whole and core genome multilocus sequence typing
allele schemes for Salmonella enterica outbreak detection in a national surveillance network, PulseNet USA. Front Microbiol. 2023 Sep 21; 14:1254777.
49. European Centre for Disease Prevention and Control (ECDC). (2018). Protocol for cgMLST-based typing of Klebsiella pneumoniae. Stockholm: ECDC. Erişim adresi: https://www.ecdc.europa.
eu/en/publications-data/protocol-cgmlst-based-typing-klebsiella-pneumoniae
50. Grillová L, Picardeau M. Core genome multi-locus sequence typing analyses of Leptospira spp. using the Bacterial Isolate Genome Sequence Database. Methods Mol Biol. 2020;2134:11–21.
51. Ruppitsch W, Pietzka A, Prior K, Bletz S, Fernandez HL, Allerberger F, Harmsen D, Mellmann A. Defining and evaluating a core genome multilocus sequence typing scheme for whole-geno-
me sequence-based typing of Listeria monocytogenes. J Clin Microbiol. 2015;53(9):2869–2876.
52. Uelze L, Grützke J, Borowiak M, Hammerl JA, Juraschek K, Deneke C, Tausch SH, Malorny B. Typing methods based on whole genome sequencing data. One Health Outlook. 2020;2:3.
53. Leeper MM, Tolar BM, Griswold T, Vidyaprakash E, Hise KB, Williams GM, Im SB, Chen JC, Pouseele H, Carleton HA. Evaluation of whole and core genome multilocus sequence typing
allele schemes for Salmonella enterica outbreak detection in a national surveillance network, PulseNet USA. Front Microbiol. 2023;14:1254777.
54. Quainoo S, Coolen JPM, van Hijum SAFT, Huynen MA, Melchers WJG, van Schaik W, Wertheim HFL. Whole-genome sequencing of bacterial pathogens: the future of nosocomial outbreak
analysis. Clin Microbiol Rev. 2017;30(4):1015–1063.
55. Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol.
2012;19(5):455–477.
56. Waldeck F, Seiffert SN, Manser S, Zemp D, Walt A, Berger C, et al. Outbreak investigation including molecular characterization of community associated methicillin-resistant Staphylococcus
aureus in a primary and secondary school in Eastern Switzerland. Sci Rep. 2022;12(1):19826.
57. FDA. GenomeTrakr network. U.S. Food and Drug Administration. [Internet]. Available from: https://www.fda.gov/food/whole-genome-sequencing-wgs-program/genometrakr-network
58. CDC. About PulseNet. Centers for Disease Control and Prevention. [Internet]. Available from: https://www.cdc.gov/pulsenet/hcp/about/index.html
59. ECDC. Whole genome sequencing – new ECDC framework suggests priority diseases and pathogens. European Centre for Disease Prevention and Control. [Internet]. Available from: https://
www.ecdc.europa.eu/en/news-events/whole-genome-sequencing-new-ecdc-framework-suggests-priority-diseases-and
60. Wang R, van Dorp L, Shaw LP, et al. The global distribution and spread of the mobilized colistin resistance gene mcr-1. Nat Commun. 2018;9(1):1179.
61. Jagadeesan B, Baert L, Wiedmann M, et al. The use of next generation sequencing for improving food safety: Translation into practice. Food Microbiol. 2019;79:96-115.
62. Wang HY, Hsieh TT, Chung CR, Chang HC, Horng JT, Lu JJ, et al. Efficiently predicting vancomycin resistance of Enterococcus faecium from MALDI-TOF MS spectra using a deep lear-
ning-based approach. Front Microbiol. 2022;13:821233.
63. García-Salguero M, Rodríguez-Baño J, Gutiérrez-Gutiérrez B, Cortés G, Pascual A, Rodríguez-Rojas L. Comparison of MALDI-TOF MS, rep-PCR and PFGE for typing Acinetobacter bau-
mannii clinical isolates. J Hosp Infect. 2021;113:131–138.
64. Busby B, Gilchrist CA, Lipworth S, Dallman T, Jones S, Snitkin ES, et al. MALDI-TOF mass spectrometry lacks the discriminatory power to reliably assign Acinetobacter baumannii to clonal
lineages defined by whole genome sequencing. J Clin Microbiol. 2023;61(5):e00022-23.
65. Struelens MJ, Black A, Köser CU, Moran-Gilad J, Revez J, Török ME. Real-time genomic surveillance for enhanced control of infectious diseases. Front Sci. 2024;3:1298248.