{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,27]],"date-time":"2026-09-27T14:08:37Z","timestamp":1790518117485,"version":"4.1.0"},"reference-count":185,"publisher":"MDPI AG","issue":"11","license":[{"start":{"date-parts":[[2026,6,4]],"date-time":"2026-06-04T00:00:00Z","timestamp":1780531200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Scientific Fund of the Republic of Serbia","award":["7042"],"award-info":[{"award-number":["7042"]}]},{"award":["7042"],"award-info":[{"award-number":["7042"]}],"id":[{"id":"https:\/\/ror.org\/02r531a15","id-type":"ROR","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["IJMS"],"abstract":"<jats:p>Infectious diseases remain a major global health concern, with a growing burden of antimicrobial resistance and consequent higher mortality in the human population. Accurate bacterial identification is fundamental across clinical, veterinary, agricultural, and research settings, supporting effective diagnosis, antimicrobial stewardship, infection control, food safety, and environmental monitoring; however, conventional approaches are limited by time constraints, reduced sensitivity, and challenges in detecting fastidious or uncultivable organisms. This review provides a comprehensive overview of classical and advanced methods, including microscopy, culture, biochemical testing, immunological and serological assays, proteomic and spectroscopy-based techniques, and molecular approaches, such as polymerase chain reaction (PCR), digital PCR, DNA hybridization, 16S rRNA gene sequencing, whole-genome sequencing, and metagenomics. The integration of artificial intelligence has further enhanced analytical performance. Nevertheless, harmonization of bioinformatics frameworks remains essential, as variability in algorithm-defined cut-off values limits standardized implementation of whole-genome sequencing in routine laboratories. Emerging technologies, including CRISPR-based diagnostics and phage- and nanomaterial-based detection systems, offer promising alternatives. Overall, the integration of these approaches is expected to improve the accuracy, speed, and applicability of bacterial identification across diverse settings; however, these advances should be implemented cautiously, with standardization remaining a key priority alongside technological modernization.<\/jats:p>","DOI":"10.3390\/ijms27115092","type":"journal-article","created":{"date-parts":[[2026,6,5]],"date-time":"2026-06-05T01:23:21Z","timestamp":1780622601000},"page":"5092","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":5,"title":["Evolving Approaches to Bacterial Identification: A Review of Classical and Modern Techniques"],"prefix":"10.3390","volume":"27","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-1578-2776","authenticated-orcid":false,"given":"Ina","family":"Gajic","sequence":"first","affiliation":[{"name":"Institute of Microbiology and Immunology, Faculty of Medicine, University of Belgrade, 11000 Belgrade, Serbia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0002-4863-5411","authenticated-orcid":false,"given":"Milos","family":"Jovicevic","sequence":"additional","affiliation":[{"name":"Institute of Microbiology and Immunology, Faculty of Medicine, University of Belgrade, 11000 Belgrade, Serbia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0327-4838","authenticated-orcid":false,"given":"Dusan","family":"Kekic","sequence":"additional","affiliation":[{"name":"Institute of Microbiology and Immunology, Faculty of Medicine, University of Belgrade, 11000 Belgrade, Serbia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3727-6583","authenticated-orcid":false,"given":"Jovana","family":"Kabic","sequence":"additional","affiliation":[{"name":"Institute of Microbiology and Immunology, Faculty of Medicine, University of Belgrade, 11000 Belgrade, Serbia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ivan","family":"Vicic","sequence":"additional","affiliation":[{"name":"Department of Food Hygiene and Technology, Faculty of Veterinary Medicine, University of Belgrade, 11000 Belgrade, Serbia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bojana","family":"Lukovic","sequence":"additional","affiliation":[{"name":"College of Health Sciences, Academy of Applied Studies Belgrade, 11000 Belgrade, Serbia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6338-342X","authenticated-orcid":false,"given":"Ana","family":"Tomic","sequence":"additional","affiliation":[{"name":"Faculty of Technology, University of Novi Sad, 21000 Novi Sad, Serbia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9118-4209","authenticated-orcid":false,"given":"Olja","family":"Sovljanski","sequence":"additional","affiliation":[{"name":"Faculty of Technology, University of Novi Sad, 21000 Novi Sad, Serbia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mila","family":"Skoric","sequence":"additional","affiliation":[{"name":"Institute of Microbiology and Immunology, Faculty of Medicine, University of Belgrade, 11000 Belgrade, Serbia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Iva","family":"Sikanic","sequence":"additional","affiliation":[{"name":"Institute of Microbiology and Immunology, Faculty of Medicine, University of Belgrade, 11000 Belgrade, Serbia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5993-0577","authenticated-orcid":false,"given":"Marko","family":"Jankovic","sequence":"additional","affiliation":[{"name":"Institute of Microbiology and Immunology, Faculty of Medicine, University of Belgrade, 11000 Belgrade, Serbia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6039-5978","authenticated-orcid":false,"given":"Aleksandra","family":"Smitran","sequence":"additional","affiliation":[{"name":"Department of Microbiology and Immunology, Faculty of Medicine, University of Banja Luka, 78000 Banja Luka, Bosnia and Herzegovina"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1564-2391","authenticated-orcid":false,"given":"Ljiljana","family":"Bozic","sequence":"additional","affiliation":[{"name":"Department of Microbiology and Immunology, Faculty of Medicine, University of Banja Luka, 78000 Banja Luka, Bosnia and Herzegovina"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bojan","family":"Golic","sequence":"additional","affiliation":[{"name":"Public Institution Veterinary Institute of the Republic of Srpska \u201cDr. Vaso Butozan\u201d, 78000 Banja Luka, Bosnia and Herzegovina"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3373-345X","authenticated-orcid":false,"given":"Jasmina","family":"Basic","sequence":"additional","affiliation":[{"name":"College of Health Sciences, Academy of Applied Studies Belgrade, 11000 Belgrade, Serbia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6097-3216","authenticated-orcid":false,"given":"Nedjeljko","family":"Karabasil","sequence":"additional","affiliation":[{"name":"Department of Food Hygiene and Technology, Faculty of Veterinary Medicine, University of Belgrade, 11000 Belgrade, Serbia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8765-4044","authenticated-orcid":false,"given":"Natasa","family":"Opavski","sequence":"additional","affiliation":[{"name":"Institute of Microbiology and Immunology, Faculty of Medicine, University of Belgrade, 11000 Belgrade, Serbia"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2026,6,4]]},"reference":[{"key":"ref_1","unstructured":"GBD 2019 Diseases and Injuries Collaborators (2020). Global Burden of 369 Diseases and Injuries in 204 Countries and Territories, 1990\u20132019: A Systematic Analysis for the Global Burden of Disease Study 2019. Lancet, 396, 1204\u20131222."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"2221","DOI":"10.1016\/S0140-6736(22)02185-7","article-title":"Global Mortality Associated with 33 Bacterial Pathogens in 2019: A Systematic Analysis for the Global Burden of Disease Study 2019","volume":"400","author":"Ikuta","year":"2022","journal-title":"Lancet"},{"key":"ref_3","unstructured":"GBD 2021 Antimicrobial Resistance Collaborators (2024). Global Burden of Bacterial Antimicrobial Resistance 1990\u20132021: A Systematic Analysis with Forecasts to 2050. Lancet, 404, 1199\u20131226."},{"key":"ref_4","unstructured":"World Health Organization (2019). New Report Calls for Urgent Action to Avert Antimicrobial Resistance Crisis, World Health Organization. Available online: https:\/\/www.who.int\/news\/item\/29-04-2019-new-report-calls-for-urgent-action-to-avert-antimicrobial-resistance-crisis."},{"key":"ref_5","doi-asserted-by":"crossref","unstructured":"Tejan, N., Fatima, N., Yaduvanshi, N., Singh, R., Pathak, A., Hasan, I., Patel, S.S., and Sahu, C. (2025). Evaluation of Direct Microbial Identification by MALDI-TOF MS and Antimicrobial Susceptibility Testing for Early Diagnosis of Blood Stream Infections. BMC Microbiol., 25.","DOI":"10.1186\/s12866-025-04401-w"},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"36","DOI":"10.21037\/pm.2019.07.05","article-title":"Acute pelvic inflammatory disease: A narrative review","volume":"2","author":"Greydanus","year":"2019","journal-title":"Pediatr. Med."},{"key":"ref_7","first-page":"e59383","article-title":"A case report and literature review of intestinal perforation due to tuberculosis","volume":"16","year":"2024","journal-title":"Cureus"},{"key":"ref_8","unstructured":"Tripathi, N., Zubair, M., and Sapra, A. (2026). Gram Staining. StatPearls, StatPearls Publishing."},{"key":"ref_9","unstructured":"The Royal College of Pathologists (2026, March 29). of UK Standards for Microbiology Investigations. Available online: https:\/\/www.rcpath.org\/profession\/publications\/standards-for-microbiology-investigations.html."},{"key":"ref_10","unstructured":"Wilmott, R.W., Deterding, R., Li, A., Ratjen, F., Sly, P., Zar, H.J., and Bush, A. (2019). Microbiological Diagnosis of Respiratory Illness. Kendig\u2019s Disorders of the Respiratory Tract in Children, Elsevier. [9th ed.]."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"1249","DOI":"10.1007\/s10096-019-03536-9","article-title":"Culture of All Sputum Samples Irrespective of Quality Adds Value to the Diagnosis of Pneumococcal Community-Acquired Pneumonia in the Elderly","volume":"38","author":"Saukkoriipi","year":"2019","journal-title":"Eur. J. Clin. Microbiol. Infect. Dis."},{"key":"ref_12","unstructured":"Centers for Disease Control and Prevention (CDC) (2026, March 29). Bacterial Vaginosis-STI Treatment Guidelines, Available online: https:\/\/www.cdc.gov\/std\/treatment-guidelines\/bv.htm."},{"key":"ref_13","unstructured":"Centers for Disease Control and Prevention (2026, May 15). Gonococcal Infections Among Adolescents and Adults\u2014STI Treatment Guidelines, Available online: https:\/\/www.cdc.gov\/std\/treatment-guidelines\/gonorrhea-adults.htm."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"e01914-20","DOI":"10.1128\/JCM.01914-20","article-title":"Gram Staining: A Comparison of Two Automated Systems and Manual Staining","volume":"58","author":"Bjedov","year":"2020","journal-title":"J. Clin. Microbiol."},{"key":"ref_15","first-page":"7","article-title":"Pyocyanine biosynthetic genes in clinical and environmental isolates of Pseudomonas aeruginosa and detection of pyocyanine\u2019s antimicrobial effects with or without colloidal silver nanoparticles","volume":"14","author":"Nowroozi","year":"2012","journal-title":"Cell J."},{"key":"ref_16","unstructured":"Procop, G.W., Church, D.L., Hall, G.S., and Janda, W.M. (2020). Koneman\u2019s Color Atlas and Textbook of Diagnostic Microbiology, Jones & Bartlett Learning."},{"key":"ref_17","unstructured":"Brook, I., and Washington, J.A. (2026, February 02). Bailey & Scott\u2019s Diagnostic Microbiology, Available online: https:\/\/catalog.nlm.nih.gov\/discovery\/fulldisplay\/alma9913004593406676\/01NLM_INST:01NLM_INST."},{"key":"ref_18","unstructured":"Faddin, J.F.M. (2000). Biochemical Tests for Identification of Medical Bacteria, Lippincott Williams & Wilkins."},{"key":"ref_19","unstructured":"Mahon, C.R., Lehman, D.C., and Manuselis, G. (2011). Textbook of Diagnostic Microbiology, Saunders\/Elsevier."},{"key":"ref_20","doi-asserted-by":"crossref","unstructured":"Boya, B.R., Kumar, P., Lee, J.-H., and Lee, J. (2021). Diversity of the Tryptophanase Gene and Its Evolutionary Implications in Living Organisms. Microorganisms, 9.","DOI":"10.3390\/microorganisms9102156"},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"358","DOI":"10.1080\/00313029500169303","article-title":"A Comparative Study of the BBL Crystal Enteric\/Nonfermenter Identification System and the Biomerieux API20E and API20NE Identification Systems after Overnight Incubation","volume":"27","author":"Varettas","year":"1995","journal-title":"Pathology"},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"273","DOI":"10.1080\/02724936.1995.11747783","article-title":"An ELISA Assay for the Rapid Diagnosis of Acute Bacterial Meningitis","volume":"15","author":"Salih","year":"1995","journal-title":"Ann. Trop. Paediatr."},{"key":"ref_23","first-page":"278","article-title":"Design of ELISA-Based Diagnostic System for Detection of Enterohaemorrhagic Escherichia coli","volume":"17","author":"Rezaei","year":"2025","journal-title":"Iran. J. Microbiol."},{"key":"ref_24","doi-asserted-by":"crossref","unstructured":"Cao, Q., Shi, W., Wei, Y., Wang, J., Wang, Z., Chong, Q., Guo, Q., Zhang, K., Gai, W., and Gou, H. (2025). Development of an Internalin-Based Double-Antibody Sandwich Quantitative ELISA for the Detection of Listeria monocytogenes in Slaughterhouse Environments. Front. Vet. Sci., 12.","DOI":"10.3389\/fvets.2025.1517845"},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"982","DOI":"10.1080\/07388551.2022.2095253","article-title":"Advanced Diagnostic Methods for Identification of Bacterial Foodborne Pathogens: Contemporary and Upcoming Challenges","volume":"43","author":"Panwar","year":"2023","journal-title":"Crit. Rev. Biotechnol."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"835","DOI":"10.1089\/vbz.2024.0042","article-title":"Lyme Disease Confirmatory Western Blot Is Redundant for Screen Negative Samples in Low Endemic Areas, British Columbia, Canada","volume":"24","author":"Kon","year":"2024","journal-title":"Vector Borne Zoonotic Dis."},{"key":"ref_27","doi-asserted-by":"crossref","unstructured":"Robinson, J.P., Ostafe, R., Iyengar, S.N., Rajwa, B., and Fischer, R. (2023). Flow Cytometry: The Next Revolution. Cells, 12.","DOI":"10.3390\/cells12141875"},{"key":"ref_28","doi-asserted-by":"crossref","unstructured":"Rubio, E., Zboromyrska, Y., Bosch, J., Fernandez-Pittol, M.J., Fidalgo, B.I., Fasanella, A., Mons, A., Rom\u00e1n, A., Casals-Pascual, C., and Vila, J. (2019). Evaluation of Flow Cytometry for the Detection of Bacteria in Biological Fluids. PLoS ONE, 14.","DOI":"10.1371\/journal.pone.0220307"},{"key":"ref_29","doi-asserted-by":"crossref","unstructured":"P\u00e9rez-Viso, B., Martins-Oliveira, I., Gomes, R., Silva-Dias, A., Peixe, L., Novais, \u00c2., Pina-Vaz, C., and Cant\u00f3n, R. (2024). Performance of Flow Cytometry-Based Rapid Assay in Detection of Carbapenemase-Producing Enterobacterales. Int. J. Mol. Sci., 25.","DOI":"10.3390\/ijms25147888"},{"key":"ref_30","doi-asserted-by":"crossref","unstructured":"Nisar, M.A., Ross, K.E., Brown, M.H., Bentham, R., Best, G., and Whiley, H. (2023). Detection and Quantification of Viable but Non-Culturable Legionella pneumophila from Water Samples Using Flow Cytometry-Cell Sorting and Quantitative PCR. Front. Microbiol., 14.","DOI":"10.3389\/fmicb.2023.1094877"},{"key":"ref_31","doi-asserted-by":"crossref","unstructured":"Freen-van Heeren, J.J. (2021). Flow-FISH as a Tool for Studying Bacteria, Fungi and Viruses. BioTech, 10.","DOI":"10.3390\/biotech10040021"},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"145","DOI":"10.1002\/cyto.a.24920","article-title":"Flow Cytometry in Microbiology: A Review of the Current State in Microbiome Research, Probiotics, and Industrial Manufacturing","volume":"107","author":"Czechowska","year":"2025","journal-title":"Cytom. A"},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"2219","DOI":"10.2147\/IDR.S321168","article-title":"Urinary Antigen Testing for Respiratory Infections: Current Perspectives on Utility and Limitations","volume":"15","author":"Kim","year":"2022","journal-title":"Infect. Drug Resist."},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"42","DOI":"10.1016\/j.ijid.2020.10.106","article-title":"Evaluation of a Novel Urinary Antigen Test Kit for Diagnosing Legionella Pneumonia","volume":"103","author":"Ito","year":"2021","journal-title":"Int. J. Infect. Dis."},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"e0011422","DOI":"10.1128\/msphere.00114-22","article-title":"Development and Validation of a Sensitive and Robust Multiplex Antigen Capture Assay to Quantify Streptococcus pneumoniae Serotype-Specific Capsular Polysaccharides in Urine","volume":"7","author":"Rajam","year":"2022","journal-title":"mSphere"},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"2635","DOI":"10.1007\/s10096-025-05226-1","article-title":"Impact of Pneumococcal Urinary Antigen Testing on Clinical Outcomes in Patients Hospitalized with Community-Acquired Pneumonia","volume":"44","author":"Kern","year":"2025","journal-title":"Eur. J. Clin. Microbiol. Infect. Dis."},{"key":"ref_37","doi-asserted-by":"crossref","unstructured":"Kinyua, D.M., Memeu, D.M., Mugo Mwenda, C.N., Ventura, B.D., and Velotta, R. (2025). Advancements and Applications of Lateral Flow Assays (LFAs): A Comprehensive Review. Sensors, 25.","DOI":"10.3390\/s25175414"},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"35","DOI":"10.1007\/s00203-025-04239-w","article-title":"Recent Advances in Rapid Detection of Helicobacter pylori by Lateral Flow Assay","volume":"207","author":"Dong","year":"2025","journal-title":"Arch. Microbiol."},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"264","DOI":"10.1007\/s00604-023-05834-8","article-title":"Rapid and Sensitive Detection of E. coli O157:H7 by Lateral Flow Immunoassay and Silver Enhancement","volume":"190","author":"Bazsefidpar","year":"2023","journal-title":"Mikrochim. Acta"},{"key":"ref_40","doi-asserted-by":"crossref","unstructured":"Calderaro, A., and Chezzi, C. (2024). MALDI-TOF MS: A Reliable Tool in the Real Life of the Clinical Microbiology Laboratory. Microorganisms, 12.","DOI":"10.3390\/microorganisms12020322"},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"e00638-24","DOI":"10.1128\/spectrum.00638-24","article-title":"Investigation of different methods in rapid microbial identification directly from positive blood culture bottles by MALDI-TOF MS","volume":"12","author":"Ergon","year":"2024","journal-title":"Microbiol. Spectr."},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"171","DOI":"10.1016\/j.cmi.2017.05.014","article-title":"The Use of Matrix-Assisted Laser Desorption\/Ionization Time-of-Flight Mass Spectrometry for Rapid Bacterial Identification in Patients with Smear-Positive Bacterial Meningitis","volume":"24","author":"Bishop","year":"2018","journal-title":"Clin. Microbiol. Infect."},{"key":"ref_43","doi-asserted-by":"crossref","unstructured":"Neuenschwander, F.R., Gro\u00df, B., and Schubert, S. (2023). Rapid Antibiotic Susceptibility Testing of Gram-Negative Bacteria Directly from Urine Samples of UTI Patients Using MALDI-TOF MS. Antibiotics, 12.","DOI":"10.3390\/antibiotics12061042"},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"108042","DOI":"10.1016\/j.ijid.2025.108042","article-title":"Potential Application of MALDI-TOF MS to Identify Streptococcus parapneumoniae, an Emerging Pathogen Previously Misidentified as Streptococcus pneumoniae","volume":"160","author":"Zhao","year":"2025","journal-title":"Int. J. Infect. Dis."},{"key":"ref_45","doi-asserted-by":"crossref","unstructured":"Audin, E., Dima, P., Chronakis, I.S., and Mendes, A.C. (2026). Spectroscopic Techniques in Bacterial Analysis: Applications of FTIR and Raman\u2014Review. Foods, 15.","DOI":"10.3390\/foods15040644"},{"key":"ref_46","doi-asserted-by":"crossref","unstructured":"Muchaamba, F., and Stephan, R. (2024). A Comprehensive Methodology for Microbial Strain Typing Using Fourier-Transform Infrared Spectroscopy. Methods Protoc., 7.","DOI":"10.3390\/mps7030048"},{"key":"ref_47","doi-asserted-by":"crossref","first-page":"159","DOI":"10.1016\/j.aca.2006.04.086","article-title":"The Potential of Mid Infrared Spectroscopy (MIRS) for Real Time Bioprocess Monitoring","volume":"571","author":"Roychoudhury","year":"2006","journal-title":"Anal. Chim. Acta"},{"key":"ref_48","doi-asserted-by":"crossref","unstructured":"Gani\u0107, T., Pe\u0107inar, I., Nikoli\u0107, B., Keki\u0107, D., Tomi\u0107, N., Cvetkovi\u0107, S., Vuleti\u0107, S., and Miti\u0107-\u0106ulafi\u0107, D. (2025). Evaluation of Cinnamon Essential Oil and Its Emulsion on Biofilm-Associated Components of Acinetobacter baumannii Clinical Strains. Antibiotics, 14.","DOI":"10.3390\/antibiotics14010106"},{"key":"ref_49","doi-asserted-by":"crossref","first-page":"e70085","DOI":"10.1111\/myc.70085","article-title":"Clade Distinction and Tracking of Clonal Spread by Fourier-Transform Infrared Spectroscopy in Multicenter Candida (Candidozyma) auris Outbreak","volume":"68","author":"Souza","year":"2025","journal-title":"Mycoses"},{"key":"ref_50","doi-asserted-by":"crossref","first-page":"1967","DOI":"10.1007\/s10096-025-05162-0","article-title":"Evaluation of Fourier-Transform Infrared Spectroscopy with IR Biotyper\u00ae System for Streptococcus pneumoniae Serotyping","volume":"44","author":"Romero","year":"2025","journal-title":"Eur. J. Clin. Microbiol. Infect. Dis."},{"key":"ref_51","doi-asserted-by":"crossref","first-page":"121369","DOI":"10.1016\/j.saa.2022.121369","article-title":"Efficient Classification of Escherichia coli and Shigella Using FT-IR Spectroscopy and Multivariate Analysis","volume":"279","author":"Feng","year":"2022","journal-title":"Spectrochim. Acta Part. A Mol. Biomol. Spectrosc."},{"key":"ref_52","doi-asserted-by":"crossref","first-page":"106792","DOI":"10.1016\/j.mimet.2023.106792","article-title":"Application of FT-IR Spectroscopy for Mycobacterium abscessus Complex Subspecies Differentiation","volume":"212","author":"Curtoni","year":"2023","journal-title":"J. Microbiol. Methods"},{"key":"ref_53","doi-asserted-by":"crossref","first-page":"3198","DOI":"10.1039\/D5AN00165J","article-title":"Differentiation and Identification of Commensal and Pathogenic Oral Bacteria at Strain Level Using ATR-FTIR Spectroscopy","volume":"150","author":"Frings","year":"2025","journal-title":"Analyst"},{"key":"ref_54","doi-asserted-by":"crossref","first-page":"48","DOI":"10.1016\/j.jhin.2021.11.017","article-title":"Nosocomial Outbreak of Monoclonal VIM Carbapenemase-Producing Enterobacter cloacae Complex in an Intensive Care Unit during the COVID-19 Pandemic: An Integrated Approach","volume":"120","author":"Lemonnier","year":"2022","journal-title":"J. Hosp. Infect."},{"key":"ref_55","doi-asserted-by":"crossref","first-page":"411","DOI":"10.1111\/zph.13046","article-title":"Investigation of a Staphylococcus aureus Sequence Type 72 Food Poisoning Outbreak Associated with Food-handler Contamination in Italy","volume":"70","author":"Savini","year":"2023","journal-title":"Zoonoses Public Health"},{"key":"ref_56","doi-asserted-by":"crossref","unstructured":"Kakizaki, N., Asai, K., Kuroda, M., Watanabe, R., Kujiraoka, M., Sekizuka, T., Katagiri, M., Moriyama, H., Watanabe, M., and Saida, Y. (2023). Rapid Identification of Bacteria Using a Multiplex Polymerase Chain Reaction System for Acute Abdominal Infections. Front. Microbiol., 14.","DOI":"10.3389\/fmicb.2023.1220651"},{"key":"ref_57","doi-asserted-by":"crossref","first-page":"116214","DOI":"10.1016\/j.diagmicrobio.2024.116214","article-title":"Rapid Multiplex Real-Time PCR Assay Using a Portable Device for the Detection of Oral Pathogens","volume":"109","author":"Wint","year":"2024","journal-title":"Diagn. Microbiol. Infect. Dis."},{"key":"ref_58","doi-asserted-by":"crossref","unstructured":"Hu, L., Wang, X., and Li, Q. (2025). Methodology and Application of Multiplex PCR-Dipstick DNA Chromatography for the Detection of Eight Respiratory Bacterial Pathogens. Front. Cell. Infect. Microbiol., 15.","DOI":"10.3389\/fcimb.2025.1558612"},{"key":"ref_59","doi-asserted-by":"crossref","unstructured":"Dung, T.T.N., Phat, V.V., Vinh, C., Lan, N.P.H., Phuong, N.L.N., Ngan, L.T.Q., Thwaites, G., Thwaites, L., Rabaa, M., and Nguyen, A.T.K. (2024). Development and Validation of Multiplex Real-Time PCR for Simultaneous Detection of Six Bacterial Pathogens Causing Lower Respiratory Tract Infections and Antimicrobial Resistance Genes. BMC Infect. Dis., 24.","DOI":"10.1186\/s12879-024-09028-2"},{"key":"ref_60","doi-asserted-by":"crossref","unstructured":"K\u00f6me\u00e7, S., Durmu\u015f, M.A., Ceylan, A.N., and Korkusuz, R. (2025). A Novel PCR Panel for Bacterial Detection in Lower Respiratory Tract Infections: A Comparative Study with Culture Results. Pathogens, 14.","DOI":"10.3390\/pathogens14101017"},{"key":"ref_61","doi-asserted-by":"crossref","first-page":"64","DOI":"10.1186\/s12348-024-00446-6","article-title":"Rapid, Multiplex and Automated Detection of Bacteria and Fungi in Endophthalmitis via a Microfluidic Real-Time Pcr System","volume":"14","author":"Wang","year":"2024","journal-title":"J. Ophthal Inflamm. Infect."},{"key":"ref_62","first-page":"77","article-title":"Recent developments in PCR technology","volume":"Volume 5","author":"Singh","year":"2023","journal-title":"Advances in Biological Sciences and Biotechnology"},{"key":"ref_63","doi-asserted-by":"crossref","unstructured":"Sancha Dominguez, L., Cotos Su\u00e1rez, A., S\u00e1nchez Ledesma, M., and Mu\u00f1oz Bellido, J.L. (2024). Present and Future Applications of Digital PCR in Infectious Diseases Diagnosis. Diagnostics, 14.","DOI":"10.20944\/preprints202403.1182.v1"},{"key":"ref_64","doi-asserted-by":"crossref","unstructured":"Mirabile, A., Sangiorgio, G., Bonacci, P.G., Bivona, D., Nicitra, E., Bonomo, C., Bongiorno, D., Stefani, S., and Musso, N. (2024). Advancing Pathogen Identification: The Role of Digital PCR in Enhancing Diagnostic Power in Different Settings. Diagnostics, 14.","DOI":"10.3390\/diagnostics14151598"},{"key":"ref_65","doi-asserted-by":"crossref","unstructured":"Dai, X., Cao, M., and Wang, Z. (2025). Digital Melting Curve Analysis for Multiplex Quantification of Nucleic Acids on Droplet Digital PCR. Biosensors, 15.","DOI":"10.3390\/bios15010036"},{"key":"ref_66","doi-asserted-by":"crossref","unstructured":"Sellar\u00e8s-Crous, A., Mart\u00ednez-Trejo, A., Arnalda-Mu\u00f1oz, N., Gatti, G., Villanueva-L\u00f3pez, M., Vergara-G\u00f3mez, A., Marco-Revert\u00e9, F., Espasa-Soley, M., and Vila-Estap\u00e9, J. (2025). Assessment of a Rapid Diagnostic Test Based on Loop-Mediated Isothermal Amplification (LAMP) to Identify the Most Frequent Pathogens Causing Hospital-Acquired Pneumonia. Front. Cell. Infect. Microbiol., 15.","DOI":"10.3389\/fcimb.2025.1609666"},{"key":"ref_67","first-page":"100120","article-title":"Recent Advances in Loop-Mediated Isothermal Amplification (LAMP) for Rapid and Efficient Detection of Pathogens","volume":"3","author":"Garg","year":"2022","journal-title":"Curr. Res. Microb. Sci."},{"key":"ref_68","doi-asserted-by":"crossref","first-page":"23","DOI":"10.1186\/s42483-023-00179-9","article-title":"Development of a Portable DNA Extraction and Cross-Priming Amplification (CPA) Tool for Rapid in-Situ Visual Diagnosis of Plant Diseases","volume":"5","author":"Li","year":"2023","journal-title":"Phytopathol. Res."},{"key":"ref_69","doi-asserted-by":"crossref","first-page":"246","DOI":"10.1038\/srep00246","article-title":"Cross Priming Amplification: Mechanism and Optimization for Isothermal DNA Amplification","volume":"2","author":"Xu","year":"2012","journal-title":"Sci. Rep."},{"key":"ref_70","doi-asserted-by":"crossref","unstructured":"Li, X., Zhu, S., Zhang, X., Ren, Y., He, J., Zhou, J., Yin, L., Wang, G., Zhong, T., and Wang, L. (2023). Advances in the Application of Recombinase-Aided Amplification Combined with CRISPR-Cas Technology in Quick Detection of Pathogenic Microbes. Front. Bioeng. Biotechnol., 11.","DOI":"10.3389\/fbioe.2023.1215466"},{"key":"ref_71","doi-asserted-by":"crossref","unstructured":"Selvam, K., Ahmad Najib, M., Khalid, M.F., Ozsoz, M., and Aziah, I. (2022). CRISPR-Cas Systems-Based Bacterial Detection: A Scoping Review. Diagnostics, 12.","DOI":"10.3390\/diagnostics12061335"},{"key":"ref_72","doi-asserted-by":"crossref","first-page":"39562","DOI":"10.1021\/acsomega.2c04513","article-title":"CRISPR\/Cas-Based Biosensor as a New Age Detection Method for Pathogenic Bacteria","volume":"7","author":"Chakraborty","year":"2022","journal-title":"ACS Omega"},{"key":"ref_73","doi-asserted-by":"crossref","first-page":"112445","DOI":"10.1016\/j.bios.2020.112445","article-title":"Point-of-Care CRISPR\/Cas Nucleic Acid Detection: Recent Advances, Challenges and Opportunities","volume":"166","author":"Berendsen","year":"2020","journal-title":"Biosens. Bioelectron."},{"key":"ref_74","unstructured":"Islam, M.T., Molla, K., Bhowmik, P., and Xie, K. (2025). Surface-Enhanced Raman Scattering -Based CRISPR-Cas Assay on Microfluidic Paper Analytical Devices for Supersensitive Detection of Pathogenic Bacteria in Foods. CRISPR-Cas Methods: Volume 3, Springer."},{"key":"ref_75","doi-asserted-by":"crossref","first-page":"107036","DOI":"10.1016\/j.microc.2021.107036","article-title":"Pathogen Detection Strategy Based on CRISPR","volume":"174","author":"Tian","year":"2022","journal-title":"Microchem. J."},{"key":"ref_76","doi-asserted-by":"crossref","first-page":"19126","DOI":"10.1073\/pnas.0906412106","article-title":"Shifting the Genomic Gold Standard for the Prokaryotic Species Definition","volume":"106","author":"Richter","year":"2009","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_77","doi-asserted-by":"crossref","first-page":"3474","DOI":"10.1128\/JCM.43.7.3474-3478.2005","article-title":"Interpretive Criteria for Use of AccuProbe for Identification of Mycobacterium avium Complex Directly from 7H9 Broth Cultures","volume":"43","author":"Cloud","year":"2005","journal-title":"J. Clin. Microbiol."},{"key":"ref_78","doi-asserted-by":"crossref","first-page":"3600","DOI":"10.1128\/JCM.00744-09","article-title":"Evaluation of a New Test, Genotype HelicoDR, for Molecular Detection of Antibiotic Resistance in Helicobacter pylori","volume":"47","author":"Cambau","year":"2009","journal-title":"J. Clin. Microbiol."},{"key":"ref_79","doi-asserted-by":"crossref","first-page":"3433","DOI":"10.1128\/JCM.01417-14","article-title":"Evaluation of FilmArray and Verigene Systems for Rapid Identification of Positive Blood Cultures","volume":"52","author":"Bhatti","year":"2014","journal-title":"J. Clin. Microbiol."},{"key":"ref_80","doi-asserted-by":"crossref","first-page":"61","DOI":"10.1016\/j.ymeth.2019.01.005","article-title":"Multiplexed Detection and Identification of Respiratory Pathogens Using the NxTAG\u00ae Respiratory Pathogen Panel","volume":"158","author":"Gonsalves","year":"2019","journal-title":"Methods"},{"key":"ref_81","doi-asserted-by":"crossref","first-page":"2427804","DOI":"10.1080\/22221751.2024.2427804","article-title":"Distribution of Clostridioides difficile Ribotypes and Sequence Types across Humans, Animals and Food in 13 European Countries","volume":"13","author":"Rupnik","year":"2024","journal-title":"Emerg. Microbes Infect."},{"key":"ref_82","doi-asserted-by":"crossref","first-page":"3830","DOI":"10.1038\/s41598-024-51499-5","article-title":"Selection and Validation of Reference Genes Suitable for Gene Expression Analysis by Reverse Transcription Quantitative Real-Time PCR in Acinetobacter baumannii","volume":"14","author":"Baboghlian","year":"2024","journal-title":"Sci. Rep."},{"key":"ref_83","doi-asserted-by":"crossref","unstructured":"Buetas, E., Jord\u00e1n-L\u00f3pez, M., L\u00f3pez-Rold\u00e1n, A., D\u2019Auria, G., Mart\u00ednez-Priego, L., De Marco, G., Carda-Di\u00e9guez, M., and Mira, A. (2024). Full-Length 16S rRNA Gene Sequencing by PacBio Improves Taxonomic Resolution in Human Microbiome Samples. BMC Genom., 25.","DOI":"10.1186\/s12864-024-10213-5"},{"key":"ref_84","doi-asserted-by":"crossref","unstructured":"Gomes, E., Ara\u00fajo, D., Nogueira, T., Oliveira, R., Silva, S., Oliveira, L.V.N., Azevedo, N.F., Almeida, C., and Castro, J. (2025). Advances in Whole Genome Sequencing for Foodborne Pathogens: Implications for Clinical Infectious Disease Surveillance and Public Health. Front. Cell. Infect. Microbiol., 15.","DOI":"10.3389\/fcimb.2025.1593219"},{"key":"ref_85","doi-asserted-by":"crossref","first-page":"538","DOI":"10.1089\/fpd.2020.2908","article-title":"Application of Whole-Genome Sequencing in the National Molecular Tracing Network for Foodborne Disease Surveillance in China","volume":"18","author":"Li","year":"2021","journal-title":"Foodborne Pathog. Dis."},{"key":"ref_86","doi-asserted-by":"crossref","first-page":"74","DOI":"10.1016\/j.cofs.2016.04.004","article-title":"Significance of Whole Genome Sequencing for Surveillance, Source Attribution and Microbial Risk Assessment of Foodborne Pathogens","volume":"8","author":"Franz","year":"2016","journal-title":"Curr. Opin. Food Sci."},{"key":"ref_87","first-page":"5898","article-title":"Whole genome sequencing and metagenomics for outbreak investigation, source attribution and risk assessment of food-borne microorganisms","volume":"17","author":"Koutsoumanis","year":"2019","journal-title":"EFSA J."},{"key":"ref_88","doi-asserted-by":"crossref","first-page":"100003","DOI":"10.1016\/j.jfp.2022.10.002","article-title":"Wholegenome Sequencing as the Gold Standard Approach for Control of Listeria monocytogenes in the Food Chain","volume":"86","author":"Lakicevic","year":"2023","journal-title":"J. Food Prot."},{"key":"ref_89","doi-asserted-by":"crossref","unstructured":"Aldea, A.C., Digu\u021b\u0103, F.C., Presacan, O., Voaide\u0219, C., Toma, R.C., and Matei, F. (2025). Detecting antibiotic resistance: Classical, molecular, advanced bioengineering, and AI-enhanced approaches. Front. Microbiol., 16.","DOI":"10.3389\/fmicb.2025.1673343"},{"key":"ref_90","doi-asserted-by":"crossref","unstructured":"European Food Safety Authority (EFSA) (2024). EFSA Statement on the Requirements for Whole Genome Sequence Analysis of Microorganisms Intentionally Used in the Food Chain. EFSA J., 22, e8912.","DOI":"10.2903\/j.efsa.2024.8912"},{"key":"ref_91","doi-asserted-by":"crossref","first-page":"481","DOI":"10.1038\/455481a","article-title":"Metagenomics","volume":"455","author":"Hugenholtz","year":"2008","journal-title":"Nature"},{"key":"ref_92","first-page":"001203","article-title":"On the Limits of 16S rRNA Gene-Based Metagenome Prediction and Functional Profiling","volume":"10","author":"Matchado","year":"2024","journal-title":"Microb. Genom."},{"key":"ref_93","doi-asserted-by":"crossref","first-page":"100391","DOI":"10.1016\/j.crmeth.2022.100391","article-title":"Comprehensive Evaluation of Shotgun Metagenomics, Amplicon Sequencing, and Harmonization of These Platforms for Epidemiological Studies","volume":"3","author":"Usyk","year":"2023","journal-title":"Cell Rep. Methods"},{"key":"ref_94","doi-asserted-by":"crossref","first-page":"16","DOI":"10.1038\/s44259-024-00033-8","article-title":"Limitations of Current Techniques in Clinical Antimicrobial Resistance Diagnosis: Examples and Future Prospects","volume":"2","author":"Hassall","year":"2024","journal-title":"npj Antimicrob. Resist."},{"key":"ref_95","doi-asserted-by":"crossref","first-page":"448","DOI":"10.4315\/JFP-21-301","article-title":"Metagenomics Approaches for Improving Food Safety: A Review","volume":"85","author":"Billington","year":"2022","journal-title":"J. Food Prot."},{"key":"ref_96","doi-asserted-by":"crossref","first-page":"33","DOI":"10.1186\/s12941-024-00690-7","article-title":"Antimicrobial Resistance Prediction by Clinical Metagenomics in Pediatric Severe Pneumonia Patients","volume":"23","author":"Gan","year":"2024","journal-title":"Ann. Clin. Microbiol. Antimicrob."},{"key":"ref_97","doi-asserted-by":"crossref","unstructured":"Rong, R., Long, Y., Li, Y., Lin, L., Yang, J., Hu, Z., Liu, D., and Chen, P. (2026). Metagenomic and Targeted Next-Generation Sequencing in Infectious Disease Diagnostics: Current Applications, Challenges, and Future Perspectives. Diagnostics, 16.","DOI":"10.3390\/diagnostics16070991"},{"key":"ref_98","doi-asserted-by":"crossref","first-page":"giz043","DOI":"10.1093\/gigascience\/giz043","article-title":"Ultra-Deep, Long-Read Nanopore Sequencing of Mock Microbial Community Standards","volume":"8","author":"Nicholls","year":"2019","journal-title":"Gigascience"},{"key":"ref_99","doi-asserted-by":"crossref","unstructured":"Scarano, C., Veneruso, I., De Simone, R.R., Di Bonito, G., Secondino, A., and D\u2019Argenio, V. (2024). The Third-Generation Sequencing Challenge: Novel Insights for the Omic Sciences. Biomolecules, 14.","DOI":"10.3390\/biom14050568"},{"key":"ref_100","doi-asserted-by":"crossref","first-page":"e0004825","DOI":"10.1128\/jcm.00048-25","article-title":"Evaluation of MicroScan and VITEK 2 Systems for Susceptibility Testing of Enterobacterales with Updated Breakpoints","volume":"63","author":"Richter","year":"2025","journal-title":"J. Clin. Microbiol."},{"key":"ref_101","doi-asserted-by":"crossref","first-page":"e0161722","DOI":"10.1128\/jcm.01617-22","article-title":"Evaluation of Piperacillin-Tazobactam Testing against Enterobacterales by the Phoenix, MicroScan, and Vitek2 Tests Using Updated Clinical and Laboratory Standards Institute Breakpoints","volume":"61","author":"Manuel","year":"2023","journal-title":"J. Clin. Microbiol."},{"key":"ref_102","doi-asserted-by":"crossref","unstructured":"Mencacci, A., De Socio, G.V., Pirelli, E., Bondi, P., and Cenci, E. (2023). Laboratory Automation, Informatics, and Artificial Intelligence: Current and Future Perspectives in Clinical Microbiology. Front. Cell. Infect. Microbiol., 13.","DOI":"10.3389\/fcimb.2023.1188684"},{"key":"ref_103","doi-asserted-by":"crossref","first-page":"589","DOI":"10.1111\/lam.13450","article-title":"Evaluation and Validation of Biolog OmniLog\u00ae System for Antibacterial Activity Assays","volume":"72","author":"Cruz","year":"2021","journal-title":"Lett. Appl. Microbiol."},{"key":"ref_104","doi-asserted-by":"crossref","first-page":"2915018","DOI":"10.1155\/2022\/2915018","article-title":"The Value of GeneXpert MTB\/RIF for Detection in Tuberculosis: A Bibliometrics-Based Analysis and Review","volume":"2022","author":"Li","year":"2022","journal-title":"J. Anal. Methods Chem."},{"key":"ref_105","unstructured":"Cepheid (2026, April 03). Package Inserts. Available online: https:\/\/infomine.cepheideurope.com\/."},{"key":"ref_106","doi-asserted-by":"crossref","unstructured":"Kamel, N.A., Alshahrani, M.Y., Aboshanab, K.M., and El Borhamy, M.I. (2022). Evaluation of the BioFire FilmArray Pneumonia Panel Plus to the Conventional Diagnostic Methods in Determining the Microbiological Etiology of Hospital-Acquired Pneumonia. Biology, 11.","DOI":"10.3390\/biology11030377"},{"key":"ref_107","doi-asserted-by":"crossref","unstructured":"Daniels, R., El Omda, T., and Mokbel, K. (2024). Improving Antimicrobial Stewardship in Acute Sore Throat: Comparison of FeverPAIN and McIsaac Scores with Molecular Point of Care Testing Using Abbott ID NOW. Diagnostics, 14.","DOI":"10.20944\/preprints202410.0487.v1"},{"key":"ref_108","unstructured":"CLSI (2026). Performance Standards for Antimicrobial Susceptibility Testing, Clinical and Laboratory Standards Institute. [36th ed.]. Available online: https:\/\/clsi.org\/shop\/standards\/m100\/."},{"key":"ref_109","unstructured":"World Data Centre for Microorganisms (WDCM) (2026, April 03). WDCM Reference Strain Catalogue. Available online: https:\/\/refs.wdcm.org\/."},{"key":"ref_110","unstructured":"(2026, April 03). American Type Culture Collection (ATCC). ATCC: The Global Bioresource Center. Available online: https:\/\/www.atcc.org\/."},{"key":"ref_111","unstructured":"Murray, P.R., Rosenthal, K.S., and Pfaller, M.A. (2020). Medical Microbiology, Elsevier. [9th ed.]."},{"key":"ref_112","unstructured":"American Type Culture Collection (ATCC) (2026, April 04). Escherichia coli (Migula) Castellani and Chalmers\u201435218\u2122. Available online: https:\/\/www.atcc.org\/products\/35218."},{"key":"ref_113","unstructured":"American Type Culture Collection (ATCC) (2026, April 04). Klebsiella quasipneumoniae Brisse et al.\u2014700603\u2122. Available online: https:\/\/www.atcc.org\/products\/700603."},{"key":"ref_114","unstructured":"CLSI (2024). Methods for Dilution Antimicrobial Susceptibility Tests for Bacteria That Grow Aerobically, Clinical and Laboratory Standards Institute. [12th ed.]. Available online: https:\/\/clsi.org\/shop\/standards\/m07\/."},{"key":"ref_115","unstructured":"American Type Culture Collection (ATCC) (2026, April 04). Enterococcus faecalis (Andrewes and Horder) Schleifer and Kilpper-Balz\u201351299-MINI-PACK. Available online: https:\/\/www.atcc.org\/products\/51299-mini-pack."},{"key":"ref_116","unstructured":"American Type Culture Collection (ATCC) (2026, April 04). Staphylococcus aureus subsp. aureus Rosenbach\u201443300\u2122. Available online: https:\/\/www.atcc.org\/products\/43300."},{"key":"ref_117","unstructured":"American Type Culture Collection (ATCC) (2026, April 04). Haemophilus influenzae (Lehmann and Neumann) Winslow et al.\u201449247\u2122. Available online: https:\/\/www.atcc.org\/products\/49247."},{"key":"ref_118","unstructured":"American Type Culture Collection (ATCC) (2026, April 04). Neisseria gonorrhoeae (Zopf) Trevisan\u201449226\u2122. Available online: https:\/\/www.atcc.org\/products\/49226."},{"key":"ref_119","unstructured":"CLSI (2016). Methods for Antimicrobial Dilution and Disk Susceptibility Testing of Infrequently Isolated or Fastidious Bacteria, Clinical and Laboratory Standards Institute. [3rd ed.]. Available online: https:\/\/clsi.org\/shop\/standards\/m45\/."},{"key":"ref_120","unstructured":"CLSI (2018). Methods for Antimicrobial Susceptibility Testing of Anaerobic Bacteria, Clinical and Laboratory Standards Institute. [9th ed.]. Available online: https:\/\/clsi.org\/shop\/standards\/m11\/."},{"key":"ref_121","unstructured":"(2022). Medical Laboratories\u2014Requirements for Quality and Competence (Standard No. ISO 15189:2022)."},{"key":"ref_122","doi-asserted-by":"crossref","first-page":"2","DOI":"10.1186\/1476-0711-12-2","article-title":"Rapid Identification of Bacteria and Candida Using PNA-FISH from Blood and Peritoneal Fluid Cultures: A Retrospective Clinical Study","volume":"12","author":"Harris","year":"2013","journal-title":"Ann. Clin. Microbiol. Antimicrob."},{"key":"ref_123","doi-asserted-by":"crossref","first-page":"481","DOI":"10.33073\/pjm-2022-050","article-title":"Rapid and Simple Approaches for Diagnosis of Staphylococcus aureus in Bloodstream Infections","volume":"71","author":"Duan","year":"2022","journal-title":"Pol. J. Microbiol."},{"key":"ref_124","doi-asserted-by":"crossref","first-page":"116950","DOI":"10.1016\/j.bios.2024.116950","article-title":"Fast and Accurate Multi-Bacterial Identification Using Cleavable and FRET-Based Peptide Nucleic Acid Probes","volume":"271","author":"Kim","year":"2025","journal-title":"Biosens. Bioelectron."},{"key":"ref_125","doi-asserted-by":"crossref","first-page":"464","DOI":"10.1093\/jbcr\/irz047","article-title":"Clinical Utility of PNA-FISH for Burn Wound Diagnostics: A Noninvasive, Culture-Independent Technique for Rapid Identification of Pathogenic Organisms in Burn Wounds","volume":"40","author":"Weaver","year":"2019","journal-title":"J. Burn. Care Res."},{"key":"ref_126","doi-asserted-by":"crossref","first-page":"110635","DOI":"10.1016\/j.vetimm.2023.110635","article-title":"Rapid Detection of Mycobacterium bovis in Bovine Cytological Smears and Tissue Sections by Peptide Nucleic Acid Fluorescence In-Situ Hybridization","volume":"262","author":"Javed","year":"2023","journal-title":"Vet. Immunol. Immunopathol."},{"key":"ref_127","doi-asserted-by":"crossref","unstructured":"Oliveira, B.B., Fernandes, A.R., and Baptista, P.V. (2024). Assessing the Gene Silencing Potential of AuNP-Based Approaches on Conventional 2D Cell Culture versus 3D Tumor Spheroid. Front. Bioeng. Biotechnol., 12.","DOI":"10.3389\/fbioe.2024.1320729"},{"key":"ref_128","doi-asserted-by":"crossref","first-page":"462","DOI":"10.1128\/CMR.00020-13","article-title":"Clinical Application of Volatile Organic Compound Analysis for Detecting Infectious Diseases","volume":"26","author":"Sethi","year":"2013","journal-title":"Clin. Microbiol. Rev."},{"key":"ref_129","doi-asserted-by":"crossref","first-page":"960","DOI":"10.1016\/j.trac.2011.03.011","article-title":"Analysis of Biogenic Volatile Organic Compounds in Human Health and Disease","volume":"30","author":"Dummer","year":"2011","journal-title":"TrAC Trends Anal. Chem."},{"key":"ref_130","doi-asserted-by":"crossref","unstructured":"Beliz\u00e1rio, J.E., Faintuch, J., and Malpartida, M.G. (2020). Breath Biopsy and Discovery of Exclusive Volatile Organic Compounds for Diagnosis of Infectious Diseases. Front. Cell. Infect. Microbiol., 10.","DOI":"10.3389\/fcimb.2020.564194"},{"key":"ref_131","doi-asserted-by":"crossref","first-page":"9431","DOI":"10.1038\/s41598-018-27504-z","article-title":"Validation of Biofilm Formation on Human Skin Wound Models and Demonstration of Clinically Translatable Bacteria-Specific Volatile Signatures","volume":"8","author":"Ashrafi","year":"2018","journal-title":"Sci. Rep."},{"key":"ref_132","doi-asserted-by":"crossref","first-page":"267","DOI":"10.1007\/s00284-005-0018-x","article-title":"Diagnosis of Bacteria in Vitro by Mass Spectrometric Fingerprinting:A Pilot Study","volume":"51","author":"Lechner","year":"2005","journal-title":"Curr. Microbiol."},{"key":"ref_133","doi-asserted-by":"crossref","first-page":"5930","DOI":"10.1021\/ac050348i","article-title":"Species-Specific Bacteria Identification Using Differential Mobility Spectrometry and Bioinformatics Pattern Recognition","volume":"77","author":"Shnayderman","year":"2005","journal-title":"Anal. Chem."},{"key":"ref_134","doi-asserted-by":"crossref","first-page":"775","DOI":"10.1007\/s10096-009-0700-1","article-title":"Device-Independent, Real-Time Identification of Bacterial Pathogens with a Metal Oxide-Based Olfactory Sensor","volume":"28","author":"Bruins","year":"2009","journal-title":"Eur. J. Clin. Microbiol. Infect. Dis."},{"key":"ref_135","doi-asserted-by":"crossref","first-page":"027102","DOI":"10.1088\/1752-7155\/10\/2\/027102","article-title":"Breath Analysis for Noninvasively Differentiating Acinetobacter baumannii Ventilator-Associated Pneumonia from Its Respiratory Tract Colonization of Ventilated Patients","volume":"10","author":"Gao","year":"2016","journal-title":"J. Breath. Res."},{"key":"ref_136","doi-asserted-by":"crossref","first-page":"228","DOI":"10.1097\/MCP.0b013e328351f98b","article-title":"Developments in Novel Breath Tests for Bacterial and Fungal Pulmonary Infection","volume":"18","author":"Chambers","year":"2012","journal-title":"Curr. Opin. Pulm. Med."},{"key":"ref_137","doi-asserted-by":"crossref","first-page":"145","DOI":"10.1016\/j.tube.2010.01.003","article-title":"Breath Biomarkers of Active Pulmonary Tuberculosis","volume":"90","author":"Phillips","year":"2010","journal-title":"Tuberculosis"},{"key":"ref_138","doi-asserted-by":"crossref","first-page":"314","DOI":"10.1016\/j.tube.2012.04.002","article-title":"Point-of-Care Breath Test for Biomarkers of Active Pulmonary Tuberculosis","volume":"92","author":"Phillips","year":"2012","journal-title":"Tuberculosis"},{"key":"ref_139","doi-asserted-by":"crossref","first-page":"44","DOI":"10.1016\/j.tube.2006.03.004","article-title":"Volatile Biomarkers of Pulmonary Tuberculosis in the Breath","volume":"87","author":"Phillips","year":"2007","journal-title":"Tuberculosis"},{"key":"ref_140","doi-asserted-by":"crossref","first-page":"6245","DOI":"10.1007\/s00253-021-11469-7","article-title":"Identification of Volatile Compounds from Bacteria by Spectrometric Methods in Medicine Diagnostic and Other Areas: Current State and Perspectives","volume":"105","author":"Euler","year":"2021","journal-title":"Appl. Microbiol. Biotechnol."},{"key":"ref_141","doi-asserted-by":"crossref","first-page":"127991","DOI":"10.1016\/j.talanta.2025.127991","article-title":"Volatile Organic Compounds (VOCs) Detection for the Identification of Bacterial Infections in Clinical Wound Samples","volume":"292","author":"Azimzadeh","year":"2025","journal-title":"Talanta"},{"key":"ref_142","doi-asserted-by":"crossref","first-page":"1069","DOI":"10.4155\/bio-2017-0051","article-title":"Mass Spectrometric Techniques for the Analysis of Volatile Organic Compounds Emitted from Bacteria","volume":"9","author":"Ratiu","year":"2017","journal-title":"Bioanalysis"},{"key":"ref_143","doi-asserted-by":"crossref","first-page":"5790","DOI":"10.1039\/D3AN01554H","article-title":"Nanomaterial-Based Biosensors for the Detection of Foodborne Bacteria: A Review","volume":"148","author":"Zheng","year":"2023","journal-title":"Analyst"},{"key":"ref_144","doi-asserted-by":"crossref","first-page":"25128","DOI":"10.1021\/acs.jafc.5c05560","article-title":"Harnessing Nanomaterials for Cutting-Edge Biosensing of Foodborne Bacterial Pathogens","volume":"73","author":"Tay","year":"2025","journal-title":"J. Agric. Food Chem."},{"key":"ref_145","doi-asserted-by":"crossref","unstructured":"Basso, C.R., Filho, M.V.B., Gavioli, V.D., Parra, J.P.R.L.L., Castro, G.R., and Pedrosa, V.A. (2025). Recent Advances in Nanomaterials for Enhanced Colorimetric Detection of Viruses and Bacteria. Chemosensors, 13.","DOI":"10.3390\/chemosensors13030112"},{"key":"ref_146","doi-asserted-by":"crossref","first-page":"e32020","DOI":"10.1016\/j.heliyon.2024.e32020","article-title":"Nanotechnology Improves the Detection of Bacteria: Recent Advances and Future Perspectives","volume":"10","author":"Takallu","year":"2024","journal-title":"Heliyon"},{"key":"ref_147","doi-asserted-by":"crossref","first-page":"120","DOI":"10.1186\/s11671-024-04065-x","article-title":"Nanomaterial-Based Sensors for Microbe Detection: A Review","volume":"19","author":"Khan","year":"2024","journal-title":"Discov. Nano"},{"key":"ref_148","doi-asserted-by":"crossref","first-page":"104214","DOI":"10.1016\/j.tifs.2023.104214","article-title":"Nanomaterials-Based Fluorescent Assays for Pathogenic Bacteria in Food-Related Matrices","volume":"142","author":"Wu","year":"2023","journal-title":"Trends Food Sci. Technol."},{"key":"ref_149","doi-asserted-by":"crossref","first-page":"100394","DOI":"10.1016\/j.snr.2025.100394","article-title":"A Comprehensive Review of Nanozyme Construction Strategies and Their Applications in Environmental Analysis","volume":"10","author":"Elagamy","year":"2025","journal-title":"Sens. Actuators Rep."},{"key":"ref_150","doi-asserted-by":"crossref","first-page":"143","DOI":"10.4161\/bact.1.3.16710","article-title":"Reporter Bacteriophage A511::celB Transduces a Hyperthermostable Glycosidase from Pyrococcus furiosus for Rapid and Simple Detection of Viable Listeria Cells","volume":"1","author":"Hagens","year":"2011","journal-title":"Bacteriophage"},{"key":"ref_151","doi-asserted-by":"crossref","unstructured":"Rees, C., and Botsaris, G. (2012). The Use of Phage for Detection, Antibiotic Sensitivity Testing and Enumeration. Underst. Tuberc.-Glob. Exp. Innov. Approaches Diagn., 293\u2013306.","DOI":"10.5772\/29734"},{"key":"ref_152","first-page":"176","article-title":"The Application of Bacteriophage Diagnostics for Bacterial Pathogens in the Agricultural Supply Chain: From Farm-to-Fork","volume":"1","author":"Jones","year":"2020","journal-title":"Phage"},{"key":"ref_153","doi-asserted-by":"crossref","first-page":"997","DOI":"10.1007\/s11033-025-10967-5","article-title":"Bacteriophages as a Modern Diagnostic Tool: Innovations, Applications and Challenges","volume":"52","author":"Olszewska","year":"2025","journal-title":"Mol. Biol. Rep."},{"key":"ref_154","doi-asserted-by":"crossref","unstructured":"Meile, S., Kilcher, S., Loessner, M.J., and Dunne, M. (2020). Reporter Phage-Based Detection of Bacterial Pathogens: Design Guidelines and Recent Developments. Viruses, 12.","DOI":"10.3390\/v12090944"},{"key":"ref_155","doi-asserted-by":"crossref","unstructured":"Cardona, P.-J. (2012). Understanding Tuberculosis: Global Experiences and Innovative Approaches to the Diagnosis, InTech.","DOI":"10.5772\/1483"},{"key":"ref_156","doi-asserted-by":"crossref","first-page":"223","DOI":"10.1111\/j.1365-2672.2005.02596.x","article-title":"Mycobacteriophage and Their Application to Disease Control","volume":"99","author":"McNerney","year":"2005","journal-title":"J. Appl. Microbiol."},{"key":"ref_157","doi-asserted-by":"crossref","first-page":"683","DOI":"10.1002\/jctb.439","article-title":"Phage as a Diagnostic-the Use of Phage in TB Diagnosis","volume":"76","author":"Mole","year":"2001","journal-title":"J. Chem. Technol. Biotechnol."},{"key":"ref_158","doi-asserted-by":"crossref","first-page":"fuab052","DOI":"10.1093\/femsre\/fuab052","article-title":"Phage Display and Other Peptide Display Technologies","volume":"46","author":"Jaroszewicz","year":"2022","journal-title":"FEMS Microbiol. Rev."},{"key":"ref_159","doi-asserted-by":"crossref","first-page":"e00872","DOI":"10.1016\/j.btre.2024.e00872","article-title":"Bacteriophage-Based Biosensors Technology: Materials, Fabrications, Efficiencies and Shortcomings","volume":"45","author":"Haq","year":"2025","journal-title":"Biotechnol. Rep."},{"key":"ref_160","doi-asserted-by":"crossref","first-page":"1817","DOI":"10.4161\/hv.21703","article-title":"Phage Display--a Powerful Technique for Immunotherapy: 1. Introduction and Potential of Therapeutic Applications","volume":"8","author":"Bazan","year":"2012","journal-title":"Hum. Vaccin. Immunother."},{"key":"ref_161","doi-asserted-by":"crossref","first-page":"44","DOI":"10.1038\/s41591-018-0300-7","article-title":"High-Performance Medicine: The Convergence of Human and Artificial Intelligence","volume":"25","author":"Topol","year":"2019","journal-title":"Nat. Med."},{"key":"ref_162","doi-asserted-by":"crossref","first-page":"1310","DOI":"10.1016\/j.cmi.2020.03.014","article-title":"Machine Learning for Microbial Identification and Antimicrobial Susceptibility Testing on MALDI-TOF Mass Spectra: A Systematic Review","volume":"26","author":"Weis","year":"2020","journal-title":"Clin. Microbiol. Infect."},{"key":"ref_163","doi-asserted-by":"crossref","first-page":"23","DOI":"10.1186\/s40168-018-0401-z","article-title":"DeepARG: A Deep Learning Approach for Predicting Antibiotic Resistance Genes from Metagenomic Data","volume":"6","author":"Garner","year":"2018","journal-title":"Microbiome"},{"key":"ref_164","doi-asserted-by":"crossref","first-page":"1666","DOI":"10.1093\/bioinformatics\/btx801","article-title":"Machine Learning for Classifying Tuberculosis Drug-Resistance from DNA Sequencing Data","volume":"34","author":"Yang","year":"2018","journal-title":"Bioinformatics"},{"key":"ref_165","doi-asserted-by":"crossref","first-page":"117399","DOI":"10.1016\/j.bios.2025.117399","article-title":"Artificial Intelligence in Bacterial Diagnostics and Antimicrobial Susceptibility Testing: Current Advances and Future Prospects","volume":"280","author":"Lee","year":"2025","journal-title":"Biosens. Bioelectron."},{"key":"ref_166","doi-asserted-by":"crossref","unstructured":"Alsulimani, A., Akhter, N., Jameela, F., Ashgar, R.I., Jawed, A., Hassani, M.A., and Dar, S.A. (2024). The Impact of Artificial Intelligence on Microbial Diagnosis. Microorganisms, 12.","DOI":"10.3390\/microorganisms12061051"},{"key":"ref_167","doi-asserted-by":"crossref","first-page":"116","DOI":"10.1038\/s41586-019-1390-1","article-title":"A Clinically Applicable Approach to Continuous Prediction of Future Acute Kidney Injury","volume":"572","author":"Glorot","year":"2019","journal-title":"Nature"},{"key":"ref_168","doi-asserted-by":"crossref","first-page":"149","DOI":"10.1093\/cid\/cix731","article-title":"Machine Learning for Healthcare: On the Verge of a Major Shift in Healthcare Epidemiology","volume":"66","author":"Wiens","year":"2018","journal-title":"Clin. Infect. Dis."},{"key":"ref_169","doi-asserted-by":"crossref","first-page":"24","DOI":"10.1038\/s41591-018-0316-z","article-title":"A Guide to Deep Learning in Healthcare","volume":"25","author":"Esteva","year":"2019","journal-title":"Nat. Med."},{"key":"ref_170","doi-asserted-by":"crossref","first-page":"i2","DOI":"10.1093\/jac\/dkae275","article-title":"Evolving Strategies in Microbe Identification-a Comprehensive Review of Biochemical, MALDI-TOF MS and Molecular Testing Methods","volume":"79","author":"Arbefeville","year":"2024","journal-title":"J. Antimicrob. Chemother."},{"key":"ref_171","doi-asserted-by":"crossref","unstructured":"Koritnik, T., Cvetkovikj, I., Zendri, F., Blum, S.E., Chaintoutis, S.C., Kopp, P.A., Hare, C., \u0160tritof, Z., Kittl, S., and Gon\u00e7alves, J. (2024). Towards Harmonized Laboratory Methodologies in Veterinary Clinical Bacteriology: Outcomes of a European Survey. Front. Microbiol., 15.","DOI":"10.3389\/fmicb.2024.1443755"},{"key":"ref_172","doi-asserted-by":"crossref","first-page":"47","DOI":"10.1016\/j.clinmicnews.2023.03.001","article-title":"The Molecular Technology Revolution and Bacterial Identification: Unexpected Consequences for Clinical Microbiologists","volume":"45","author":"Janda","year":"2023","journal-title":"Clin. Microbiol. Newsl."},{"key":"ref_173","doi-asserted-by":"crossref","first-page":"109","DOI":"10.1007\/s00203-025-04675-8","article-title":"Food-Borne Bacterial Pathogens: Emerging Approaches in Detection and Prevention","volume":"208","author":"Shafi","year":"2026","journal-title":"Arch. Microbiol."},{"key":"ref_174","doi-asserted-by":"crossref","unstructured":"Suzzi, G., and Corsetti, A. (2020). Food Microbiology: The Past and the New Challenges for the Next 10 Years. Front. Microbiol., 11.","DOI":"10.3389\/fmicb.2020.00237"},{"key":"ref_175","first-page":"475","article-title":"Multiplex PCR for Detection and Identification of Microbial Pathogens","volume":"10","author":"Poritz","year":"2018","journal-title":"Adv. Tech. Diagn. Microbiol."},{"key":"ref_176","doi-asserted-by":"crossref","first-page":"2433","DOI":"10.1111\/1541-4337.13153","article-title":"Molecular Detection and Characterization of Foodborne Bacteria: Recent Progresses and Remaining Challenges","volume":"22","author":"Hadi","year":"2023","journal-title":"Compr. Rev. Food Sci. Food Saf."},{"key":"ref_177","doi-asserted-by":"crossref","unstructured":"Boukharouba, A., Gonz\u00e1lez, A., Garc\u00eda-Ferr\u00fas, M., Ferr\u00fas, M.A., and Botella, S. (2022). Simultaneous Detection of Four Main Foodborne Pathogens in Ready-to-Eat Food by Using a Simple and Rapid Multiplex PCR (mPCR) Assay. Int. J. Environ. Res. Public. Health, 19.","DOI":"10.3390\/ijerph19031031"},{"key":"ref_178","unstructured":"(2020). Microbiology of the Food Chain-Horizontal Method for the Detection, Enumeration and Serotyping of Salmonella-Part 1: Detection of Salmonella spp. (ISO 6579-1:2017 + Amd.1:2020); German Version EN ISO 6579-1:2017 + A1:2020 (Standard No. DIN EN ISO 6579-1:2020). Available online: https:\/\/webstore.ansi.org\/standards\/din\/dineniso65792020."},{"key":"ref_179","unstructured":"Program, H.F. (2026). BAM Chapter 5: Salmonella, FDA."},{"key":"ref_180","doi-asserted-by":"crossref","first-page":"bpae090","DOI":"10.1093\/biomethods\/bpae090","article-title":"Development of a Large-Scale Rapid LAMP Diagnostic Testing Platform for Pandemic Preparedness and Outbreak Response","volume":"9","author":"Jim","year":"2024","journal-title":"Biol. Methods Protoc."},{"key":"ref_181","doi-asserted-by":"crossref","first-page":"16430","DOI":"10.1038\/s41598-021-95799-6","article-title":"A Molecular Test Based on RT-LAMP for Rapid, Sensitive and Inexpensive Colorimetric Detection of SARS-CoV-2 in Clinical Samples","volume":"11","author":"Amaral","year":"2021","journal-title":"Sci. Rep."},{"key":"ref_182","doi-asserted-by":"crossref","first-page":"110395","DOI":"10.1016\/j.compag.2025.110395","article-title":"Artificial Intelligence in Veterinary and Animal Science: Applications, Challenges, and Future Prospects","volume":"235","year":"2025","journal-title":"Comput. Electron. Agric."},{"key":"ref_183","doi-asserted-by":"crossref","unstructured":"European Food Safety Authority, and European Centre for Disease Prevention and Control (2022). The European Union One Health 2021 Zoonoses Report. EFSA J., 20, e07666.","DOI":"10.2903\/j.efsa.2022.7666"},{"key":"ref_184","doi-asserted-by":"crossref","unstructured":"Nam, N.N., Do, H.D.K., Loan Trinh, K.T., and Lee, N.Y. (2023). Metagenomics: An Effective Approach for Exploring Microbial Diversity and Functions. Foods, 12.","DOI":"10.3390\/foods12112140"},{"key":"ref_185","doi-asserted-by":"crossref","unstructured":"Hirani, R., Noruzi, K., Khuram, H., Hussaini, A.S., Aifuwa, E.I., Ely, K.E., Lewis, J.M., Gabr, A.E., Smiley, A., and Tiwari, R.K. (2024). Artificial Intelligence and Healthcare: A Journey through History, Present Innovations, and Future Possibilities. Life, 14.","DOI":"10.3390\/life14050557"}],"container-title":["International Journal of Molecular Sciences"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/1422-0067\/27\/11\/5092\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,6,5]],"date-time":"2026-06-05T01:28:46Z","timestamp":1780622926000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/1422-0067\/27\/11\/5092"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,6,4]]},"references-count":185,"journal-issue":{"issue":"11","published-online":{"date-parts":[[2026,6]]}},"alternative-id":["ijms27115092"],"URL":"https:\/\/doi.org\/10.3390\/ijms27115092","relation":{},"ISSN":["1422-0067"],"issn-type":[{"value":"1422-0067","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,6,4]]}}}