Lívia Caroline Alexandre de Araújo1; Rafael Artur de Queiroz Cavalcanti de Sá2; Sivoneide Maria da Silva2; Francisco Henrique da Silva2; Cíntia Justino Rabelo3; Mariana Gomes Vidal Sampaio3;

1 Centro de Ciências Agrárias, Universidade Federal da Paraíba – CCA/UFPB
2 Centro de Ciências da Saúde, Universidade Federal de Pernambuco – CCS/UFPE
3 Centro Universitário Católica de Quixáda – UNICATÓLICA

Objectives: The research objective was to present the main techniques for identifying pathogenic microorganisms and the application of new technologies for the clinical diagnosis of infectious diseases.

Methods: It was made a search for free and recent journals available online in the databases of Pubmed (National Library of Medicine and the National Institutes), Lilacs (Latin American and Caribbean Literature in Health Sciences), and Scielo (Scientific Electronic Library Online), based on keywords related to the proposed theme.

Results: From the researched literature, it was possible to verify that conventional techniques, despite their limitations, are still widely used for the identification and microbial characterization. However, in the last decades, molecular methods have been widely inserted in the laboratory routine seeking to increase the capacity to detect infectious agents with high sensitivity, specificity, speed, and low cost. Among the various techniques, amplification of DNA sequences is highlighted by the polymerase chain reaction (PCR), the sequencing of the 16S rRNA gene, and other variations of PCR. In addition to these, new technologies have been developed, such as new generation sequencing (NGS) and Matrix-assisted Laser Desorption/ionization-time-of-flight Mass Spectrometry (MALDI-TOF MS).

Conclusion: The development of new technologies that allow rapid, sensitive, reproducible, and low-cost microbial identification, it is of great relevance for clinical microbiology, and consequently, for public health.

Keywords: Bacteria. Genotyping techniques. Microbiological techniques.

Free Full-text PDF

How to cite this article:
Lívia Caroline Alexandre de Araújo; Rafael Artur de Queiroz Cavalcanti de Sá; Sivoneide Maria da Silva; Francisco Henrique da Silva; Cíntia Justino Rabelo; Mariana Gomes Vidal Sampaio.ADVANCES IN THE IDENTIFICATION TECHNIQUES FOR PATHOGENIC MICROORGANISMS.American Journal of Histology and Cytology, 2021, 4:10. DOI: 10.28933/ajohc-2021-05-2005


1. Ramamurthy T, Ghosh A, Pazhani GP, Shinoda S. Current Perspectives on Viable but Non-Culturable [VBNC] Pathogenic Bacteria. Front. Public Heal. 2014, 2, 103.
2. Bochner BR. Global phenotypic characterization of bacteria. FEMS Microbiol. Rev. 2009, 33, 191–205.
3. Lagier JC, Hugon P, Khelaifia S, Fournies PE, La Scola B, Raoult D. The rebirth of culture in microbiology through the example of culturomics to study human gut microbiota. Clin Microbiol Ver. 2015, 28, 237–264.
4. Cliendo AM, Gilbert DN, Ginocchio CC, Hanson KE, May L, Quinn TC et al [2013] Better tests, better care: improved diagnostics for infectious diseases. Clin Infect Dis. 2013, 57[Suppl 3], S139– S170.
5. Buchan BW, Ledeboer NA. Emerging technologies for the clinical microbiology laboratory. Clin. Microbiol. Rev. 2014, 27, 783–822.
6. Palleroni NJ. Pseudomonas classification – a new case history in the taxonomy of Gram-negative bacteria. Antonie Van Leeuwenhoek International Journal of General and Molecular Microbiology. 1993, 64, 231-251.
7. Callaway A, Kostrzewa M, Willershausen B, Schmidt F, Thiede B, Kupper H, Kneist S. Identification of Lactobacilli from deep carious lesions by means of species-specific PCR and MALDI-TOF mass spectrometry. Clin. Lab. 2013, 59, 1373–1379.
8. Duskova M, Sedo O, Ksicova K, Zdrahal Z, Karpıskova R. Identification of lactobacilli isolated from food by genotypic methods and MALDI-TOF MS. Int. J. Food Microbiol. 2012, 159, 107–114.
9. Pendharkar S, Magopane T, Larsson PG, Bruyn G, Gray GE, et al. Identification and characterisation of vaginal lactobacilli from South African women. BMC Infect. Dis. 2013, 13, 43.
10. Deggim-Messmer V, Bloemberg GV, Ritter C, Voit A, Homke R, Keller PM, et al. Diagnostic Molecular Mycobacteriology in Regions With Low Tuberculosis Endemicity: Combining Real-time PCR Assays for Detection of Multiple Mycobacterial Pathogens With Line Probe Assays for Identification of Resistance Mutations. EBioMedicine. 2016, 9, 228–237.
11. Spanoghe M, Jara MG, Riviere J, Lanterbecq D, Gadenne M, Marique T. Development and application of a quantitative real-time PCR assay for rapid detection of the multifaceted yeast Kazachstania servazzii in food. Food Microbiol. 2017, 62, 133–140.
12. Dark MJ. Whole-genome sequencing in bacteriology: state of the art. Infect. Drug Resist. 2013, 6, 115–123.
13. Quainoo S, Coolen JPM, Van Hijum SAFT, Huynen MA, Melchers WJG, Van Schaik W, et al. Whole-Genome Sequencing of Bacterial Pathogens: The Future of Nosocomial Outbreak Analysis. Clin. Microbiol. Rev. 2017, 30, 1015–1063.
14. De Bruyne K, Slabbinck B, Waegeman W, Vauterin P, De Baets B, Vandamme P. Bacterial species identification from MALDI-TOF mass spectra through data analysis and machine learning. Syst Appl Microbiol. 2011, 34[1], 20-9.
15. Martin MS, Santos IC, Carlton DD Jr, Granados P, Hildenbrand ZL, Schug KA. Characterization of bacterial diversity in contaminated groundwater using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Sci Total Environ. 2018, 1, 622-623,1562-1571.
16. Starostin KV, Demidov EA, Bryanskaya AV, Efimov VM, Rozanov AS, Peltek SE. Identification of Bacillus strains by MALDI TOF MS using geometric approach. Sci Rep. 2015, 23[5], 16989.
17. Lo CI, Fall B, Sambe-Ba B, Diawara S, Gueye MW, Mediannikov O, Sokhna C, et al. MALDI-TOF Mass Spectrometry: A Powerful Tool for Clinical Microbiology at Hôpital Principal de Dakar, Senegal [West Africa]. PLoS One. 2015, 30, 10[12].
18. Sharma M, Gautam V, Mahajan M, Rana S, Majumdar M, Ray, P. Direct identification by matrix-assisted laser desorption ionization-time of flight mass spectrometry [MALDI-TOF MS] from positive blood culture bottles: An opportunity to customize growth conditions for fastidious organisms causing bloodstream infections. Indian J Med Res. 2017, 146[4], 541-544.
19. Bergeron MG, Ouellette M. Preventing antibiotic resistance through rapid genotypic identification of bacteria and of their antibiotic resistance genes in the clinical microbiology laboratory. J Clin Microbiol. 1998, 36, 2169–2172.
20. Tang YW, Ellis NM, Hopkins MK et al. Comparison of phenotypic and genotypic techniques for identification of unusual aerobic pathogenic gram-negative bacilli. J Clin Microbio. 1998, 36, 3674–3679.
21. Lagier JC, Hugon P, Khelaifia S, Fournier PE, La Scola B, Raoult, D. The Rebirth of Culture in Microbiology through the Example of Culturomics to Study Human Gut Microbiota. Clin. Microbiol. Rev. 2015, 28, 237–264.
22. de Boer E, Beumer RR. Methodology for detection and typing of foodborne microorganisms. International Journal of Food Microbiology. 1999, 50, 119-130.
23. Koneman EW, Allen SD, Janda WM, Schreckenberger PC, Winn Junir, WC. Diagnóstico microbiológico: texto e atlas colorido. 5.ed. Rio deJaneiro: MEDSI, 2001.
24. Hofmann MA, Renzullo S, Mader M, Chaignat V, Worwa G, Thuer B. Genetic characterization of Toggenburg orbivirus, a new bluetongue virus, from goats, Switzerland. Emerg Infect Dis [serial on the Internet]. 2008
25. Sibley CD, Peirano G, Church DL. Molecular methods for pathogen and microbial community detection and characterization: current and potential application in diagnostic microbiology. Infection, genetics and evolution. 2012, 12 [3], 505-21.
26. Srinivasan R, Kraoz U, Volegova M, Mackichan J, Kato-maeda M, Miller S, et al. Use of 16S rRNA Gene for Identification of a Broad Range of Clinically Relevant Bacterial Pathogens. PLoS ONE. 2015, 10[2].
27. Clarridge III JE. Impact of 16S rRNA gene sequence analysis for identification of bacteria on clinical microbiology and infectious diseases. Clinical Microbiology Reviews. 2004, 17 [4], 840-862.
28. Coutinho HLC, Oliver VM, Manfio GP, Rosado AS. Evaluating the microbial diversity of soil samples: metodologial innovation. Anais da Academia Brasileira de Ciências. 1999, 71, 3, 491-503, 1999.
29. Giebel R, Woden C, Rust SM, Kleinheiz GT, Robbins M. Microbial fingerprinting using matrx-assisted laser desorption ionization timeof flight mas spectrometry [MALDI-TOF MS] Aplications and Challenges. Adv Appl Microbiol. 2010, 71, 149-184.
30. Avanzi IR, Gracioso LH, Baltazar MD, Karolski B, Perpetuo EA, do Nascimento CA. Rapid bacteria identification from environmental mining samples using MALDI-TOF MS analysis. Environ Sci Pollut Res Int. 2017, 24[4], 3717-3726.
31. Carbonnelle E, Grohs P, Jacquier H, Day N, Tenza S, Dewailly A, et al.. Robustness of two MALDI-TOF mass spectrometry systems for bacterial identification. J Microbiol Methods. 2012, 89[2].
32. Yu J, Liu J, Li Y, Yu J, Zhu W, Liu Y, Shen L. Rapid detection of carbapenemase activity of Enterobacteriaceae isolated from positive blood cultures by MALDI-TOF MS. Ann Clin Microbiol Antimicrob. 2018, 18,17[1]:22.
33. Zhang T, Ding J, Rao X, Yu J, Chu M, Ren W, et al. Analysis of methicillin-resistant Staphylococcus aureus major clonal lineages by Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry [MALDI-TOF MS]. J Microbiol Methods. 2015, 117,122-7.
34. Nakano S, Matsumura Y, Ito Y, Fujisawa T, Chang B, Suga S, et al. Development and evaluation of MALDI-TOF MS-based serotyping for Streptococcus pneumoniae. Eur J Clin Microbiol Infect Dis. 2015, 34[11], 2191-8.
35. Foster AG. Rapid Identification of microbes in positive blood cultures by use of the vitek MS matrix-assisted laser desorption ionization-time of flight mass spectrometry system. J. Clin. Microbiol. 2013, 51, 3717–3719.
36. Tadros M, Petrich A. Evaluation of MALDI-TOF mass spectrometry and Sepsityper KitTM for the direct identification of organisms from sterile body fluids in a Canadian pediatric hospital. Can. J. Infect. Dis. Med. Microbiol. 2013, 24, 191–194.

Terms of Use/Privacy Policy/ Disclaimer/ Other Policies:
You agree that by using our site, you have read, understood, and agreed to be bound by all of our terms of use/privacy policy/ disclaimer/ other policies (click here for details).

This work and its PDF file(s) are licensed under a Creative Commons Attribution-NonCommercial 4.0 International License.