Document Type : Review Article

Authors

1 Department of microbiology and microbial biotechnology, faculty of life sciences and biotechnology, Shahid Beheshti University, Tehran, Iran.

2 Pediatric Infections Research Center, Research Institute for Children’s Health, Shahid Beheshti University of Medical Sciences, Tehran, Iran.

3 Department of Biotechnology, Faculty of Advanced Sciences and Technologies, University of Isfahan, Isfahan, Iran

10.55705/cmbr.2021.143413.1016

Abstract

The main purpose of microbial typing is to evaluate the relationships between microbial isolates. Microbial typing can use for identifying the source of infection by detecting a clonal link between the strains. Moreover, it can analyze outbreaks, antimicrobial-resistant strains, and evaluate the effectiveness of control measures so, the efficiency of monitoring systems would increase. HAIs can affect hospitalized patients in all age ranges with any clinical situation, and lead to death. Molecular epidemiology is useful to determine genetic relatedness between isolated pathogens from patients, and design proper prevention plans to prevent infection through the hospital and community. Nowadays, typing methods for a wide range of bacterial strains are known as essential epidemiological tools to prevent and control infections in hospitals and communities. Although basic typing methods were more focused on phenotypic techniques like antibiogram and serotyping, new methods are based on molecular techniques including PCR-based methods and sequencing-based methods. Due to the high frequency of methods, choosing the right one for research applications seems difficult and requires basic knowledge about all of them. In this review, we aim to introduce the most useful and practical molecular typing techniques. Also, their utilization, advantages, and disadvantages were compared.

Graphical Abstract

Overview of typing techniques as molecular epidemiology tools for bacterial characterization

Keywords

Main Subjects

Selected author of this article by journal

ِDr. Leila Azimi
Shahid Beheshti University of Medical Sciences

Google Scholar(H Index=18)

Open Access

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  1. Ruppitsch W (2016) Molecular typing of bacteria for epidemiological surveillance and outbreak investigation/Molekulare Typisierung von Bakterien für die epidemiologische Überwachung und Ausbruchsabklärung. Die Bodenkultur: Journal of Land Management, Food and Environment 67(4):199-224. doi: https://doi.org/10.1515/boku-2016-0017
  2. Foxman B, Riley L (2001) Molecular epidemiology: focus on infection. American journal of epidemiology 153(12):1135-1141. doi:https://doi.org/10.1093/aje/153.12.1135
  3. Rodríguez-Morales AJ, Balbin-Ramon GJ, Rabaan AA, Sah R, Dhama K, Paniz-Mondolfi A, Pagliano P, Esposito S (2020) Genomic Epidemiology and its importance in the study of the COVID-19 pandemic. genomics 1:3
  4. Jensen AK, Björkman JT, Ethelberg S, Kiil K, Kemp M, Nielsen EM (2016) Molecular typing and epidemiology of human listeriosis cases, Denmark, 2002–2012. Emerging infectious diseases 22(4):625. doi:https://doi.org/10.3201/eid2204.150998
  5. Xiao L, Ryan UM (2007) Molecular epidemiology. In: Cryptosporidium and cryptosporidiosis. CRC press, pp 119-172
  6. Monegro AF, Muppidi V, Regunath H (2020) Hospital acquired infections. Statpearls [Internet])
  7. Alavi M, Rai M (2021) Antisense RNA, the modified CRISPR-Cas9, and metal/metal oxide nanoparticles to inactivate pathogenic bacteria. Cellular, Molecular and Biomedical Reports:52-59
  8. Azimi L, Alaghehbandan R, Asadian M, Alinejad F, Lari AR (2019) Multi-drug resistant Pseudomonas aeruginosa and Klebsiella pneumoniae circulation in a burn hospital, Tehran, Iran. GMS hygiene and infection control 14. doi: https://doi.org/10.3205/dgkh000317
  9. Soleimani N (2018) A Review of Designing New Vaccines to Prevent Hospital-Acquired Antibiotic-Resistant Infections. International Electronic Journal of Medicine 7(2):21-29. doi:https://doi.org/10.31661/iejm861
  10. Azimi L, Talebi M, Khodaei F, Najafi M, Lari AR (2016) Comparison of multiple-locus variable-number tandem-repeat analysis with pulsed-field gel electrophoresis typing of carbapenemases producing Acinetobacter baumannii isolated from burn patients. Burns 42(2):441-445. doi:https://doi.org/10.1016/j.burns.2015.08.024
  11. Crabb HK, Allen JL, Devlin JM, Firestone SM, Wilks CR, Gilkerson JR (2018) Salmonella spp. transmission in a vertically integrated poultry operation: Clustering and diversity analysis using phenotyping (serotyping, phage typing) and genotyping (MLVA). PLoS One 13(7):e0201031. doi:https://doi.org/10.1371/journal.pone.0201031
  12. Ranjbar R, Karami A, Farshad S, Giammanco GM, Mammina C (2014) Typing methods used in the molecular epidemiology of microbial pathogens: a how-to guide. New Microbiologica 37(1):1-15
  13. Magalhães B, Valot B, Abdelbary MM, Prod'hom G, Greub G, Senn L, Blanc DS (2020) Combining standard molecular typing and whole genome sequencing to investigate Pseudomonas aeruginosa epidemiology in intensive care units. Frontiers in public health 8:3. doi:https://doi.org/10.1186/1471-2180-6-9
  14. Abbas-Al-Khafaji ZK, Aubais-aljelehawy Qh (2021) Evaluation of antibiotic resistance and prevalence of multi-antibiotic resistant genes among Acinetobacter baumannii strains isolated from patients admitted to al-yarmouk hospital. Cellular, Molecular and Biomedical Reports:60-68
  15. Christensen H, Bossé J, Angen Ø, Nørskov-Lauritsen N, Bisgaard M (2020) Immunological and molecular techniques used for determination of serotypes in Pasteurellaceae. Methods in Microbiology 47:117-149. doi:https://doi.org/10.1016/bs.mim.2020.01.002
  16. Armin S, Fallah F, Karimi A, Rashidan M, Shirdust M, Azimi L (2017) Genotyping, antimicrobial resistance and virulence factor gene profiles of vancomycin resistance Enterococcus faecalis isolated from blood culture. Microbial pathogenesis 109:300-304. doi:https://doi.org/10.1016/j.micpath.2017.05.039

 

  1. Kaufmann M, Pitcher D, Pitt T (2018) Ribotyping of bacterial genomes. In: Methods in Practical Laboratory Bacteriology. CRC Press, pp 123-138
  2. Van Belkum A, Welker M, Pincus D, Charrier J-P, Girard V (2017) Matrix-assisted laser desorption ionization time-of-flight mass spectrometry in clinical microbiology: what are the current issues? Annals of laboratory medicine 37(6):475-483. doi:https://doi.org/10.3343/alm.2017.37.6.475
  3. Besser J, Carleton HA, Gerner-Smidt P, Lindsey RL, Trees E (2018) Next-generation sequencing technologies and their application to the study and control of bacterial infections. Clinical microbiology and infection 24(4):335-341. doi:https://doi.org/10.1016/j.cmi.2017.10.013
  4. Lagha R, Abdallah FB, ALKhammash AA, Amor N, Hassan MM, Mabrouk I, Alhomrani M, Gaber A (2021) Molecular characterization of multidrug resistant Klebsiella pneumoniae clinical isolates recovered from King Abdulaziz Specialist Hospital at Taif City, Saudi Arabia. Journal of Infection and Public Health 14(1):143-151. doi:https://doi.org/10.1016/j.jiph.2020.12.001
  5. Singh A, Goering RV, Simjee S, Foley SL, Zervos MJ (2006) Application of molecular techniques to the study of hospital infection. Clinical microbiology reviews 19(3):512-530. doi:https://doi.org/10.1128/CMR.00025-05
  6. Shibata N, Doi Y, Yamane K, Yagi T, Kurokawa H, Shibayama K, Kato H, Kai K, Arakawa Y (2003) PCR typing of genetic determinants for metallo-β-lactamases and integrases carried by gram-negative bacteria isolated in Japan, with focus on the class 3 integron. Journal of Clinical Microbiology 41(12):5407-5413. doi:https://doi.org/10.1128/JCM.41.12.5407-5413
  7. Van Belkum A (1994) DNA fingerprinting of medically important microorganisms by use of PCR. Clinical Microbiology Reviews 7(2):174-184. doi:https://doi.org/10.1128/CMR.7.2.174
  8. Van Belkum A, Tassios P, Dijkshoorn L, Haeggman S, Cookson B, Fry N, Fussing V, Green J, Feil E, Gerner‐Smidt P (2007) Guidelines for the validation and application of typing methods for use in bacterial epidemiology. Clinical Microbiology and Infection 13:1-46. doi:https://doi.org/10.1111/j.1469-0691.2007.01786.x
  9. Asadian M, Azimi L, Alinejad F, Ostadi Y, Lari AR (2019) Molecular characterization of Acinetobacter baumannii isolated from ventilator-associated pneumonia and burn wound colonization by random amplified polymorphic DNA polymerase chain reaction and the relationship between antibiotic susceptibility and biofilm production. Advanced biomedical research 8. doi:https://doi.org/10.4103/abr.abr_256_18
  10. Bilung LM, Pui CF, Su’ut L, Apun K (2018) Evaluation of BOX-PCR and ERIC-PCR as molecular typing tools for pathogenic Leptospira. Disease markers 2018. doi:https://doi.org/10.1155/2018/1351634
  11. Le Flèche P, Jacques I, Grayon M, Al Dahouk S, Bouchon P, Denoeud F, Nöckler K, Neubauer H, Guilloteau LA, Vergnaud G (2006) Evaluation and selection of tandem repeat loci for a Brucella MLVA typing assay. BMC microbiology 6(1):1-14. doi:https://doi.org/10.1186/1471-2180-6-9
  12. Ardakani MA, Ranjbar R (2016) Molecular typing of uropathogenic E. coli strains by the ERIC-PCR method. Electronic physician 8(4):2291. doi:https://doi.org/10.19082/2291
  13. Schmitt S, Stephan R, Huebschke E, Schaefle D, Merz A, Johler S (2020) DNA microarray-based characterization and antimicrobial resistance phenotypes of clinical MRSA strains from animal hosts. Journal of Veterinary Science 21(4). doi:https://doi.org/10.4142/jvs.2020.21.e54
  14. Gaiarsa S, Batisti Biffignandi G, Esposito EP, Castelli M, Jolley KA, Brisse S, Sassera D, Zarrilli R (2019) Comparative analysis of the two Acinetobacter baumannii multilocus sequence typing (MLST) schemes. Frontiers in microbiology 10:930. doi:https://doi.org/10.3389/fmicb.2019.00930
  15. Scholz CF, Jensen A (2017) Development of a Single Locus Sequence Typing (SLST) scheme for typing bacterial species directly from complex communities. In: Bacterial Pathogenesis. Springer, pp 97-107. doi:https://doi.org/10.1007/978-1-4939-6673-8_7
  16. Kwok P-Y (2001) Methods for genotyping single nucleotide polymorphisms. Annual review of genomics and human genetics 2(1):235-258. doi:https://doi.org/10.1146/annurev.genom.2.1.235
  17. Hallin M, Deplano A, Struelens MJ (2012) Molecular typing of bacterial pathogens: a tool for the epidemiological study and control of infectious diseases. In: New frontiers of molecular epidemiology of infectious diseases. Springer, pp 9-25. doi:https://doi.org/10.1007/978-94-007-2114-2_2
  18. Tümmler B (2020) Molecular epidemiology in current times. Environmental Microbiology 22(12):4909-4918. doi:https://doi.org/10.1111/1462-2920.15238
  19. Prado-Vivar MB, Ortiz L, Reyes J, Villacis E, Fornasini M, Baldeon ME, Cardenas PA (2019) Molecular typing of a large nosocomial outbreak of KPC-producing bacteria in the biggest tertiary-care hospital of Quito, Ecuador. Journal of global antimicrobial resistance 19:328-332. doi:https://doi.org/10.1016/j.jgar.2019.05.014
  20. Sharma-Kuinkel BK, Rude TH, Fowler VG (2014) Pulse field gel electrophoresis. In: The Genetic Manipulation of Staphylococci. Springer, pp 117-130
  21. García H, Cervantes-Luna B, González-Cabello H, Miranda-Novales G (2018) Risk factors for nosocomial infections after cardiac surgery in newborns with congenital heart disease. Pediatrics & Neonatology 59(4):404-409. doi:https://doi.org/10.1186/s12879-020-4769-6
  22. Corcione S, Pensa A, Castiglione A, Lupia T, Bortolaso B, Romeo MR, Stella M, Rosa FGD (2021) Epidemiology, prevalence and risk factors for infections in burn patients: Results from a regional burn centre’s analysis. Journal of Chemotherapy 33(1):62-66. doi:https://doi.org/10.1080/1120009X.2020.1780776
  23. Sikora A, Zahra F (2021) Nosocomial infections. StatPearls [Internet])
  24. Baran I, Aksu N (2016) Phenotypic and genotypic characteristics of carbapenem-resistant Enterobacteriaceae in a tertiary-level reference hospital in Turkey. Ann Clin Microbiol Antimicrob 15:20. doi:https://doi.org/10.1186/s12941-016-0136-2