{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,4]],"date-time":"2026-03-04T08:37:41Z","timestamp":1772613461186,"version":"3.50.1"},"reference-count":44,"publisher":"MDPI AG","issue":"3","license":[{"start":{"date-parts":[[2026,3,2]],"date-time":"2026-03-02T00:00:00Z","timestamp":1772409600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100003196","name":"Italian Ministry of Health","doi-asserted-by":"crossref","award":["IZS PLV 07\/23 RC"],"award-info":[{"award-number":["IZS PLV 07\/23 RC"]}],"id":[{"id":"10.13039\/501100003196","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100003196","name":"Italian Ministry of Health","doi-asserted-by":"crossref","award":["J19I23001620001"],"award-info":[{"award-number":["J19I23001620001"]}],"id":[{"id":"10.13039\/501100003196","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Pathogens"],"abstract":"<jats:p>The aim of the present study was to employ a genotypic method (CRISPR PCR) and a phenotypic method (FT-IR combined with Linear Discriminant Analysis, LDA) for the rapid identification and discrimination of major virulent Salmonella serovars. Specifically, a total of 24 Salmonella Enteritidis, 24 Salmonella Typhimurium, 24 S. Typhimurium 4,5,12:i:-, and 14 Salmonella Infantis strains, previously serotyped according to the Kaufmann\u2013White scheme, were analyzed. CRISPR PCR generated serotype-specific amplicons: 850 bp for S. Enteritidis, 700 bp and 2000 bp for S. Typhimurium, 1300 bp and 1500 bp for S. Typhimurium 4,5,12:i:-, and 1000 bp and 1900 bp for S. Infantis. FT-IR spectra of all serotypes were analyzed by LDA, which revealed a clear separation of three serotype-defined groups: S. Enteritidis, S. Infantis, and a group comprising S. Typhimurium and its monophasic variant 4,5,12:i:-. Further discrimination based on CRISPR-defined classes was observed within each serovar: two classes for S. Typhimurium, two for S. Typhimurium 4,5,12:i:-, and three for S. Infantis. Overall, the combined CRISPR PCR and FT-IR-LDA approach provides preliminary evidence supporting the potential application of a combined approach for the epidemiological surveillance of Salmonella.<\/jats:p>","DOI":"10.3390\/pathogens15030267","type":"journal-article","created":{"date-parts":[[2026,3,2]],"date-time":"2026-03-02T16:06:59Z","timestamp":1772467619000},"page":"267","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Characterization of Salmonella spp. Based on CRISPR PCR and FT-IR Approaches: A Pilot Study in Northern Italy"],"prefix":"10.3390","volume":"15","author":[{"given":"Clara","family":"Tramuta","sequence":"first","affiliation":[{"name":"Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d\u2019Aosta, S.C. Sicurezza Alimentare, Via Bologna, 148, 10154 Turin, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2237-5538","authenticated-orcid":false,"given":"Irene","family":"Floris","sequence":"additional","affiliation":[{"name":"Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d\u2019Aosta, S.C. Sicurezza Alimentare, Via Bologna, 148, 10154 Turin, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5871-217X","authenticated-orcid":false,"given":"Monica","family":"Pitti","sequence":"additional","affiliation":[{"name":"Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d\u2019Aosta, S.C. Sicurezza Alimentare, Via Bologna, 148, 10154 Turin, Italy"},{"name":"Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d\u2019Aosta, Centro di Riferimento per la Tipizzazione delle Salmonelle (CeRTiS), Via Bologna, 148, 10154 Turin, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Giulia Federica","family":"Cazzaniga","sequence":"additional","affiliation":[{"name":"Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d\u2019Aosta, S.C. Sicurezza Alimentare, Via Bologna, 148, 10154 Turin, Italy"},{"name":"Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d\u2019Aosta, Centro di Riferimento per la Tipizzazione delle Salmonelle (CeRTiS), Via Bologna, 148, 10154 Turin, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Miriam","family":"Cordovana","sequence":"additional","affiliation":[{"name":"Bruker Daltonics GmbH & Co. KG, 28359 Bremen, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Daniela Manila","family":"Bianchi","sequence":"additional","affiliation":[{"name":"Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d\u2019Aosta, S.C. Sicurezza Alimentare, Via Bologna, 148, 10154 Turin, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2026,3,2]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"e00591-19","DOI":"10.1128\/AEM.00591-19","article-title":"Worldwide Epidemiology of Salmonella Serovars in Animal-Based Foods: A Meta-Analysis","volume":"85","author":"Ferrari","year":"2019","journal-title":"Appl. Environ. Microbiol."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"529","DOI":"10.3934\/microbiol.2017.3.529","article-title":"Foodborne Pathogens","volume":"3","author":"Bintsis","year":"2017","journal-title":"AIMS Microbiol."},{"key":"ref_3","doi-asserted-by":"crossref","unstructured":"Zizza, A., Fallucca, A., Guido, M., Restivo, V., Roveta, M., and Trucchi, C. (2024). Foodborne Infections and Salmonella: Current Primary Prevention Tools and Future Perspectives. Vaccines, 13.","DOI":"10.3390\/vaccines13010029"},{"key":"ref_4","doi-asserted-by":"crossref","unstructured":"European Food Safety Authority (EFSA), and European Centre for Disease Prevention and Control (ECDC) (2025). The European Union One Health 2024 Zoonoses Report. EFSA J., 23, e9759.","DOI":"10.2903\/j.efsa.2025.9759"},{"key":"ref_5","unstructured":"(2026, January 27). National Salmonellosis Control Plan in Poultry 2022\u20132024. Available online: https:\/\/www.izs.it\/IZS\/Benv-News-eng\/National_Salmonellosis_Control_Plan_in_Poultry_2022-2024."},{"key":"ref_6","unstructured":"European Union (2005). Commission Regulation (EC) No 2073\/2005 of 15 November 2005 on Microbiological Criteria for Foodstuffs (Text with EEA Relevance), European Union."},{"key":"ref_7","unstructured":"UNI Ente Italiano di Normazione (Standard No. ISO\/TR 6579-3:2014). Available online: https:\/\/store.uni.com\/iso-tr-6579-3-2014."},{"key":"ref_8","doi-asserted-by":"crossref","unstructured":"Li, J., Wu, S., Zhang, K., Sun, X., Lin, W., Wang, C., and Lin, S. (2024). Clustered Regularly Interspaced Short Palindromic Repeat\/CRISPR-Associated Protein and Its Utility All at Sea: Status, Challenges, and Prospects. Microorganisms, 12.","DOI":"10.3390\/microorganisms12010118"},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"59","DOI":"10.2174\/1874285801812010059","article-title":"Bacterial CRISPR Regions: General Features and Their Potential for Epidemiological Molecular Typing Studies","volume":"12","author":"Karimi","year":"2018","journal-title":"Open Microbiol. J."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"100291","DOI":"10.1016\/j.mtbio.2022.100291","article-title":"Theragnostic Application of Nanoparticle and CRISPR against Food-Borne Multi-Drug Resistant Pathogens","volume":"15","author":"Bhattacharjee","year":"2022","journal-title":"Mater. Today Bio"},{"key":"ref_11","doi-asserted-by":"crossref","unstructured":"Fabre, L., Zhang, J., Guigon, G., Le Hello, S., Guibert, V., Accou-Demartin, M., De Romans, S., Lim, C., Roux, C., and Passet, V. (2012). CRISPR Typing and Subtyping for Improved Laboratory Surveillance of Salmonella Infections. PLoS ONE, 7.","DOI":"10.1371\/annotation\/e79cea9a-6716-4519-9e96-31b17bf6a4fb"},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"e9113","DOI":"10.7717\/peerj.9113","article-title":"CRISPR 2 PCR and High Resolution Melting Profiling for Identification and Characterization of Clinically-Relevant Salmonella enterica subsp. Enterica","volume":"8","author":"Wisittipanit","year":"2020","journal-title":"PeerJ"},{"key":"ref_13","doi-asserted-by":"crossref","unstructured":"Manzulli, V., Cordovana, M., Serrecchia, L., Rondinone, V., Pace, L., Farina, D., Cipolletta, D., Caruso, M., Fraccalvieri, R., and Difato, L.M. (2024). Application of Fourier Transform Infrared Spectroscopy to Discriminate Two Closely Related Bacterial Species: Bacillus Anthracis and Bacillus Cereus Sensu Stricto. Microorganisms, 12.","DOI":"10.3390\/microorganisms12010183"},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"106564","DOI":"10.1016\/j.mimet.2022.106564","article-title":"Machine Learning-Based Typing of Salmonella enterica O-Serogroups by the Fourier-Transform Infrared (FTIR) Spectroscopy-Based IR Biotyper System","volume":"201","author":"Cordovana","year":"2022","journal-title":"J. Microbiol. Methods"},{"key":"ref_15","doi-asserted-by":"crossref","unstructured":"Kassem, A., Abbas, L., Coutinho, O., Opara, S., Najaf, H., Kasperek, D., Pokhrel, K., Li, X., and Tiquia-Arashiro, S. (2023). Applications of Fourier Transform-Infrared Spectroscopy in Microbial Cell Biology and Environmental Microbiology: Advances, Challenges, and Future Perspectives. Front. Microbiol., 14.","DOI":"10.3389\/fmicb.2023.1342406"},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"1239","DOI":"10.2217\/fmb-2020-0276","article-title":"Application of Fourier Transform Infrared Spectroscopy for Real-Time Typing of Acinetobacter Baumannii Outbreak in Intensive Care Unit","volume":"16","author":"Lombardo","year":"2021","journal-title":"Future Microbiol."},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"106603","DOI":"10.1016\/j.mimet.2022.106603","article-title":"Comparison of FT-IR with Whole-Genome Sequencing for Identification of Maternal-To-neonate Transmission of Antibiotic-Resistant Bacteria","volume":"202","author":"Azrad","year":"2022","journal-title":"J. Microbiol. Methods"},{"key":"ref_18","doi-asserted-by":"crossref","unstructured":"Curtoni, A., Pastrone, L., Cordovana, M., Bondi, A., Piccinini, G., Genco, M., Bottino, P., Polizzi, C., Cavallo, L., and Mandras, N. (2024). Fourier Transform Infrared Spectroscopy Application for Candida Auris Outbreak Typing in a Referral Intensive Care Unit: Phylogenetic Analysis and Clustering Cut-Off Definition. Microorganisms, 12.","DOI":"10.20944\/preprints202405.1931.v1"},{"key":"ref_19","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_20","doi-asserted-by":"crossref","first-page":"e04119-23","DOI":"10.1128\/spectrum.04119-23","article-title":"Comparative Analysis of IR-Biotyper, MLST, cgMLST, and WGS for Clustering of Vancomycin-Resistant Enterococcus faecium in a Neonatal Intensive Care Unit","volume":"12","author":"Park","year":"2024","journal-title":"Microbiol. Spectr."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"369","DOI":"10.1016\/j.mimet.2011.01.009","article-title":"Fourier Transform Infrared Spectroscopy as a Tool to Characterize Molecular Composition and Stress Response in Foodborne Pathogenic Bacteria","volume":"84","author":"Mouwen","year":"2011","journal-title":"J. Microbiol. Methods"},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"991","DOI":"10.1021\/jf204081g","article-title":"Classification and Structural Analysis of Live and Dead Salmonella Cells Using Fourier Transform Infrared Spectroscopy and Principal Component Analysis","volume":"60","author":"Sundaram","year":"2012","journal-title":"J. Agric. Food Chem."},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"e00159-25","DOI":"10.1128\/spectrum.00159-25","article-title":"Development of a Robust FT-IR Typing System for Salmonella enterica, Enhancing Performance through Hierarchical Classification","volume":"13","author":"Wozniak","year":"2025","journal-title":"Microbiol. Spectr."},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"1739","DOI":"10.1007\/s00216-006-0851-1","article-title":"Fourier Transform Infrared (FT-IR) Spectroscopy in Bacteriology: Towards a Reference Method for Bacteria Discrimination","volume":"387","author":"Preisner","year":"2007","journal-title":"Anal. Bioanal. Chem."},{"key":"ref_25","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_26","doi-asserted-by":"crossref","unstructured":"Cordovana, M., Mauder, N., Kostrzewa, M., Wille, A., Rojak, S., Hagen, R.M., Ambretti, S., Pongolini, S., Soliani, L., and Justesen, U.S. (2021). Classification of Salmonella enterica of the (Para-)Typhoid Fever Group by Fourier-Transform Infrared (FTIR) Spectroscopy. Microorganisms, 9.","DOI":"10.3390\/microorganisms9040853"},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"e27402","DOI":"10.1016\/j.heliyon.2024.e27402","article-title":"Strain Typing and Antimicrobial Susceptibility of Salmonella enterica Albany Isolates from Duck Farms in South Korea","volume":"10","author":"Han","year":"2024","journal-title":"Heliyon"},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"101004","DOI":"10.1016\/j.onehlt.2025.101004","article-title":"Rapid Serotype-Independent Differential Detection of Biofilm-Positive and Biofilm-Negative Salmonella Using Fourier Transform Infrared Biotyping","volume":"20","author":"Shrestha","year":"2025","journal-title":"One Health"},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"465","DOI":"10.1007\/s42770-024-01563-z","article-title":"Comparative Analysis of Biofilm Structures in Salmonella Typhimurium DMC4 Strain and Its Dam and seqA Gene Mutants Using Fourier Transform Infrared Spectroscopy (FT-IR) and Raman Spectroscopy Methods","volume":"56","year":"2025","journal-title":"Braz. J. Microbiol."},{"key":"ref_30","first-page":"M54","article-title":"Detection of Sublethal Thermal Injury in Salmonella enterica Serotype Typhimurium and Listeria monocytogenes Using Fourier Transform Infrared (FT-IR) Spectroscopy (4000 to 600 cm\u22121)","volume":"73","author":"Lin","year":"2008","journal-title":"J. Food Sci."},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"349","DOI":"10.1093\/jac\/dkad387","article-title":"Use of Fourier-Transform Infrared Spectroscopy for Real-Time Outbreak Investigation of OXA-48-Producing Escherichia coli","volume":"79","author":"Kon","year":"2024","journal-title":"J. Antimicrob. Chemother."},{"key":"ref_32","doi-asserted-by":"crossref","unstructured":"Deidda, F., Cordovana, M., Bozzi Cionci, N., Graziano, T., Di Gioia, D., and Pane, M. (2022). In-Process Real-Time Probiotic Phenotypic Strain Identity Tracking: The Use of Fourier Transform Infrared Spectroscopy. Front. Microbiol., 13.","DOI":"10.3389\/fmicb.2022.1052420"},{"key":"ref_33","doi-asserted-by":"crossref","unstructured":"Li, X., Zhu, L., Wang, X., Li, J., and Tang, B. (2022). Evaluation of IR Biotyper for Lactiplantibacillus Plantarum Typing and Its Application Potential in Probiotic Preliminary Screening. Front. Microbiol., 13.","DOI":"10.3389\/fmicb.2022.823120"},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"165","DOI":"10.1007\/s00253-025-13550-x","article-title":"Application of MALDI-TOF MS and FT-IR Spectroscopy in Identification and Antibiotic Resistance Profiling of Lactic Acid Bacteria","volume":"109","author":"Kocsis","year":"2025","journal-title":"Appl. Microbiol. Biotechnol."},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"149","DOI":"10.1016\/j.mimet.2004.06.011","article-title":"FT-IR Spectroscopy for Identification of Closely Related Lactobacilli","volume":"59","author":"Oust","year":"2004","journal-title":"J. Microbiol. Methods"},{"key":"ref_36","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_37","doi-asserted-by":"crossref","unstructured":"Dopu\u0111, M., \u0160uto, S., Toma\u0161kovi\u0107, D., Hlebi\u0107, L., Peinovi\u0107, L., \u0160pi\u010di\u0107, S., Zdelar Tuk, M., Reil, I., Humski, A., and Kompes, G. (2025). AI-Enhanced FT-IR Spectroscopy: Evaluation of a Novel Tool for High-Throughput Serovar Typing of Salmonella enterica subsp. enterica in Croatia. Pathogens, 14.","DOI":"10.3390\/pathogens14090856"},{"key":"ref_38","unstructured":"(2026, January 05). Kauffmann-White and Le Minor. Antigenic formulae of the Salmonella Serovars. Available online: https:\/\/www.pasteur.fr\/sites\/default\/files\/veng_0.pdf."},{"key":"ref_39","unstructured":"Tramuta, C., Frizziero, S., Bianchi, D.M., Pitti, M., Martucci, F., and Decastelli, L. (2022, January 7). Caratterizzazione Genetica di Ceppi di Salmonella spp. Mediante Amplificazione Delle Sequenze Clustered Regulary Interspaced Short Palindromic Repeat (CRISPR). Proceedings of the Atti Convegno Sidilv, Ischia, Italy."},{"key":"ref_40","unstructured":"Pitti, M., Tramuta, C., Cazzaniga, G.F., and Bianchi, D.M. (2025, January 23\u201325). Genetic Characterization of Salmonella spp. Based on CRISPR Sequence. Proceedings of the Atti I3S Congress, Saint-Malo, France."},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"135","DOI":"10.1590\/1806-9061-2016-0371","article-title":"Serotyping and Genotyping of Salmonella Strains Isolated from Broilers, Chicken Carcasses Before and After Chilling, and Frozen Chicken Breasts Produced in the States of Mato Grosso Do Sul and Santa Catarina, Brazil","volume":"19","author":"Machado","year":"2017","journal-title":"Braz. J. Poult. Sci."},{"key":"ref_42","first-page":"97","article-title":"Genotyping of Salmonella spp. on the Basis of CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats)","volume":"16","author":"Jiksing","year":"2020","journal-title":"Malays. J. Microbiol."},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"81","DOI":"10.1016\/j.vetmic.2017.02.010","article-title":"Genetic Analysis of Salmonella enterica Serovar Gallinarum Biovar Pullorum Based on Characterization and Evolution of CRISPR Sequence","volume":"203","author":"Xie","year":"2017","journal-title":"Vet. Microbiol."},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"138","DOI":"10.1111\/lam.13296","article-title":"Conserved CRISPR Arrays in Salmonella enterica Serovar Infantis Can Serve as qPCR Targets to Detect Infantis in Mixed Serovar Populations","volume":"71","author":"Richards","year":"2020","journal-title":"Lett. Appl. Microbiol."}],"container-title":["Pathogens"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2076-0817\/15\/3\/267\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,3,4]],"date-time":"2026-03-04T05:20:20Z","timestamp":1772601620000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2076-0817\/15\/3\/267"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,3,2]]},"references-count":44,"journal-issue":{"issue":"3","published-online":{"date-parts":[[2026,3]]}},"alternative-id":["pathogens15030267"],"URL":"https:\/\/doi.org\/10.3390\/pathogens15030267","relation":{},"ISSN":["2076-0817"],"issn-type":[{"value":"2076-0817","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,3,2]]}}}