{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,24]],"date-time":"2026-09-24T09:13:34Z","timestamp":1790241214005,"version":"4.1.0"},"reference-count":100,"publisher":"MDPI AG","issue":"12","license":[{"start":{"date-parts":[[2019,11,21]],"date-time":"2019-11-21T00:00:00Z","timestamp":1574294400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001866","name":"Fonds National de la Recherche Luxembourg","doi-asserted-by":"publisher","award":["11823097"],"award-info":[{"award-number":["11823097"]}],"id":[{"id":"10.13039\/501100001866","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Microorganisms"],"abstract":"<jats:p>Matrix-assisted laser desorption\/ionization time of flight mass spectrometry (MALDI-TOF MS) is today the reference method for direct identification of microorganisms in diagnostic laboratories, as it is notably time- and cost-efficient. In the context of increasing cases of enteric diseases with emerging multi-drug resistance patterns, there is an urgent need to adopt an efficient workflow to characterize antimicrobial resistance (AMR). Current approaches, such as antibiograms, are time-consuming and directly impact the \u201cpatient-physician\u201d workflow. Through this mini-review, we summarize how the detection of specific patterns by MALDI-TOF MS, as well as bioinformatics, become more and more essential in research, and how these approaches will help diagnostics in the future. Along the same lines, the idea to export more precise biomarker identification steps by MALDI-TOF(\/TOF) MS data towards AMR identification pipelines is discussed. The study also critically points out that there is currently still a lack of research data and knowledge on different foodborne pathogens as well as several antibiotics families such as macrolides and quinolones, and many questions are still remaining. Finally, the innovative combination of whole-genome sequencing and MALDI-TOF MS could be soon the future for diagnosis of antimicrobial resistance in foodborne pathogens.<\/jats:p>","DOI":"10.3390\/microorganisms7120593","type":"journal-article","created":{"date-parts":[[2019,11,22]],"date-time":"2019-11-22T02:49:27Z","timestamp":1574390967000},"page":"593","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":36,"title":["MALDI-TOF Mass Spectrometry and Specific Biomarkers: Potential New Key for Swift Identification of Antimicrobial Resistance in Foodborne Pathogens"],"prefix":"10.3390","volume":"7","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-2052-8975","authenticated-orcid":false,"given":"Maureen","family":"Feucherolles","sequence":"first","affiliation":[{"name":"Luxembourg Institute of Science and Technology (LIST), Environmental Research and Innovation (ERIN) Department, 41 rue du Brill, 4422 Belvaux, Luxembourg"},{"name":"Facult\u00e9 des Sciences, de la Technologie et de la Communication (FSTC), Doctoral School in Science and Engineering (DSSE), University of Luxembourg, 2 avenue de l\u2019Universit\u00e9, 4365 Esch-sur-Alzette, Luxembourg"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4780-6100","authenticated-orcid":false,"given":"Henry-Michel","family":"Cauchie","sequence":"additional","affiliation":[{"name":"Luxembourg Institute of Science and Technology (LIST), Environmental Research and Innovation (ERIN) Department, 41 rue du Brill, 4422 Belvaux, Luxembourg"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Christian","family":"Penny","sequence":"additional","affiliation":[{"name":"Luxembourg Institute of Science and Technology (LIST), Environmental Research and Innovation (ERIN) Department, 41 rue du Brill, 4422 Belvaux, Luxembourg"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2019,11,21]]},"reference":[{"key":"ref_1","unstructured":"Centers for Disease Control and Prevention (2019, October 09). Antibiotic Use in the United States, 2017: Progress and Opportunities, Available online: https:\/\/www.cdc.gov\/antibiotic-use\/stewardship-report\/index.html."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"431","DOI":"10.1016\/S0924-8579(01)00297-7","article-title":"Use of antimicrobial agents in veterinary medicine and food animal production","volume":"17","author":"Schwarz","year":"2001","journal-title":"Int. J. Antimicrob. Agents"},{"key":"ref_3","first-page":"277","article-title":"The Antibiotic Resistance: Part 1: Causes and Threats","volume":"40","author":"Ventola","year":"2015","journal-title":"P T a Peer Rev. J. Formul. Manag."},{"key":"ref_4","unstructured":"Orru\u00f1o, M., Garaizabal, I., Arana, I., and Barcina, I. (2013). Persistence and dissemination of antimicrobial resistances in aquatic systems. Microbial Pathogens and Strategies for Combating Them: Science, Technology and Education, Formatex Research Center."},{"key":"ref_5","unstructured":"The Organisation for Economic Co-operation Development (2018). Stemming the Superbug Tide, OECD Health Policy Studies."},{"key":"ref_6","unstructured":"World Health Organization (2019, October 09). WHO Estimates of the Global Burden of Foodborne Diseases: Foodborne Disease Burden Epidemiology Reference Group 2007\u20132015. Available online: https:\/\/apps.who.int\/iris\/handle\/10665\/199350."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"327","DOI":"10.4103\/0971-5916.198677","article-title":"A review on detection methods used for foodborne pathogens","volume":"144","author":"Priyanka","year":"2016","journal-title":"Indian J. Med. Res."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"287","DOI":"10.1146\/annurev-food-041715-033251","article-title":"Antimicrobial Resistance, Food Safety, and One Health: The Need for Convergence","volume":"7","author":"Lammie","year":"2016","journal-title":"Annu. Rev. Food Sci. Technol."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"14","DOI":"10.3389\/fvets.2018.00014","article-title":"The one Health Concept: 10 years old and a long road ahead","volume":"5","author":"Mavingui","year":"2018","journal-title":"Front. Vet. Sci."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"377","DOI":"10.1093\/trstmh\/trw048","article-title":"Antibiotic resistance is the quintessential One Health issue","volume":"110","author":"Robinson","year":"2016","journal-title":"Trans. R. Soc. Trop. Med. Hyg."},{"key":"ref_11","doi-asserted-by":"crossref","unstructured":"European Food Safety Authority (EFSA) (2013). The European union summary report on trends and sources of zoonoses, zoonotic agents and food-borne outbreaks in 2011. EFSA J., 11, 3129.","DOI":"10.2903\/j.efsa.2013.3129"},{"key":"ref_12","doi-asserted-by":"crossref","unstructured":"European Food Safety Authority (EFSA) (2017). The European Union summary report on trends and sources of zoonoses, zoonotic agents and food-borne outbreaks in 2016. EFSA J., 15, 5077.","DOI":"10.2903\/j.efsa.2017.5077"},{"key":"ref_13","first-page":"1201","article-title":"Campylobacter jejuni Infections: Update on Emerging Issues and Trends","volume":"32","author":"Allos","year":"2002","journal-title":"Clin. Infect. Dis."},{"key":"ref_14","doi-asserted-by":"crossref","unstructured":"Chlebicz, A., and \u015ali\u017cewska, K. (2018). Campylobacteriosis, Salmonellosis, Yersiniosis, and Listeriosis as Zoonotic Foodborne Diseases: A Review. Int. J. Environ. Res. Public Health, 15.","DOI":"10.3390\/ijerph15050863"},{"key":"ref_15","doi-asserted-by":"crossref","unstructured":"Szczepanska, B., Andrzejewska, M., Spica, D., and Klawe, J.J. (2017). Prevalence and antimicrobial resistance of Campylobacter jejuni and Campylobacter coli isolated from children and environmental sources in urban and suburban areas. BMC Microbiol., 17.","DOI":"10.1186\/s12866-017-0991-9"},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"1906","DOI":"10.3389\/fmicb.2018.01906","article-title":"Human campylobacteriosis in Italy: Emergence of multi-drug resistance to ciprofloxacin, tetracycline, and erythromycin","volume":"9","author":"Dionisi","year":"2018","journal-title":"Front. Microbiol."},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"4091856","DOI":"10.1155\/2017\/4091856","article-title":"Antibiotic resistance of Campylobacter recovered from faeces and carcasses of healthy livestock","volume":"2017","author":"Karikari","year":"2017","journal-title":"Biomed. Res. Int."},{"key":"ref_18","first-page":"37","article-title":"Detection of multi-antibiotic resistant Campylobacter coli and Campylobacter jejuni in beef, mutton, chicken and water buffalo meat in Ahvaz, Iran","volume":"10","author":"Maktabi","year":"2019","journal-title":"Artic. Vet. Res. Forum"},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"817","DOI":"10.1016\/j.ijmm.2014.08.015","article-title":"Relevance of Campylobacter to public health\u2014The need for a One Health approach","volume":"304","author":"Schielke","year":"2014","journal-title":"Int. J. Med. Microbiol."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"169","DOI":"10.2217\/fmb-2018-0329","article-title":"Diagnostic stewardship for sepsis: The need for risk stratification to triage patients for fast microbiology workflows","volume":"14","author":"Mangioni","year":"2019","journal-title":"Future Microbiol."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"1124","DOI":"10.1038\/s41467-019-08853-3","article-title":"Global monitoring of antimicrobial resistance based on metagenomics analyses of urban sewage","volume":"10","author":"Hendriksen","year":"2019","journal-title":"Nat. Commun."},{"key":"ref_22","unstructured":"World Health Organization (2019, October 09). Global Antimicrobial Resistance Surveillance System. Manual for Early Implementation. Available online: https:\/\/www.who.int\/antimicrobial-resistance\/publications\/surveillance-system-manual\/en\/."},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"122","DOI":"10.1016\/j.fm.2018.01.018","article-title":"Use of whole-genome sequencing for Campylobacter surveillance from NARMS retail poultry in the United States in 2015","volume":"73","author":"Whitehouse","year":"2018","journal-title":"Food Microbiol."},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1128\/microbiolspec.ARBA-0011-2017","article-title":"Molecular methods for detection of antimicrobial resistance","volume":"5","author":"Anjum","year":"2017","journal-title":"Microbiol. Spectr."},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"20","DOI":"10.1373\/clinchem.2015.239467","article-title":"Evolution of quantitative MALDI-TOF mass spectrometry for clinical applications","volume":"62","author":"Vestal","year":"2016","journal-title":"Clin. Chem."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"219","DOI":"10.1021\/ac60352a007","article-title":"Identification of bacteria using mass spectrometry","volume":"47","author":"Anhalt","year":"1975","journal-title":"Anal. Chem."},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"53","DOI":"10.1016\/0168-1176(87)87041-6","article-title":"Matrix-assisted ultraviolet laser desorption of non-volatile compounds","volume":"78","author":"Karas","year":"1987","journal-title":"Int. J. Mass Spectrom. Ion Process."},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"151","DOI":"10.1002\/rcm.1290020802","article-title":"Protein and polymer analyses up to m\/z 100 000 by laser ionization time-of-flight mass spectrometry","volume":"2","author":"Tanaka","year":"1988","journal-title":"Rapid Commun. Mass Spectrom."},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"547","DOI":"10.1128\/CMR.00072-12","article-title":"Matrix-Assisted laser desorption ionization-time of flight mass spectrometry: A fundamental shift in the routine practice of clinical microbiology","volume":"26","author":"Clark","year":"2013","journal-title":"Clin. Microbiol. Rev."},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"2577","DOI":"10.2174\/1381612054546932","article-title":"Application of MALDI-TOF mass spectrometry in screening and diagnostic research","volume":"11","author":"Pusch","year":"2005","journal-title":"Curr. Pharm. Des."},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"404","DOI":"10.1016\/j.jfda.2019.01.001","article-title":"Current status of MALDI-TOF mass spectrometry in clinical microbiology","volume":"27","author":"Hou","year":"2019","journal-title":"J. Food Drug Anal."},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"S83","DOI":"10.1016\/j.nmni.2018.08.020","article-title":"MALDI-TOF-MS and point of care are disruptive diagnostic tools in Africa","volume":"26","author":"Chabriere","year":"2018","journal-title":"New Microbes New Infect."},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"104","DOI":"10.1016\/j.clinbiochem.2010.06.017","article-title":"MALDI-TOF mass spectrometry tools for bacterial identification in clinical microbiology laboratory","volume":"44","author":"Carbonnelle","year":"2011","journal-title":"Clin. Biochem."},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"355","DOI":"10.1016\/j.diagmicrobio.2019.03.004","article-title":"Rapid one-step protein extraction method for the identification of mycobacteria using MALDI-TOF MS","volume":"94","author":"Rotcheewaphan","year":"2019","journal-title":"Diagn. Microbiol. Infect. Dis."},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"183","DOI":"10.1007\/s11046-016-0080-x","article-title":"MALDI-TOF-Based Dermatophyte Identification","volume":"182","author":"Ranque","year":"2017","journal-title":"Mycopathologia"},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"540","DOI":"10.1128\/JCM.01565-07","article-title":"Multiplex detection of human herpesviruses from archival specimens by using matrix-assisted laser desorption ionization-time of flight mass spectrometry","volume":"46","author":"Dillner","year":"2008","journal-title":"J. Clin. Microbiol."},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"39","DOI":"10.1016\/j.cimid.2018.05.002","article-title":"MALDI-TOF MS identification of ticks of domestic and wild animals in Algeria and molecular detection of associated microorganisms","volume":"57","author":"Boucheikhchoukh","year":"2018","journal-title":"Comp. Immunol. Microbiol. Infect. Dis."},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"11","DOI":"10.1186\/s13071-017-2597-3","article-title":"MALDI-TOF MS as a new tool for the identification of Dientamoeba fragilis","volume":"11","author":"Calderaro","year":"2018","journal-title":"Parasites Vectors"},{"key":"ref_39","doi-asserted-by":"crossref","unstructured":"Mayer-Scholl, A., Murugaiyan, J., Neumann, J., Bahn, P., Reckinger, S., and N\u00f6ckler, K. (2016). Rapid identification of the foodborne pathogen Trichinella spp. by matrix-assisted laser desorption\/ionization mass spectrometry. PLoS ONE, 11.","DOI":"10.1371\/journal.pone.0152062"},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"245","DOI":"10.1186\/s13071-019-3493-9","article-title":"MALDI-TOF mass spectrometry as a diagnostic tool in human and veterinary helminthology: A systematic review","volume":"12","author":"Feucherolles","year":"2019","journal-title":"Parasite Vectors"},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"791","DOI":"10.3389\/fmicb.2015.00791","article-title":"MALDI-TOF mass spectrometry: An emerging technology for microbial identification and diagnosis","volume":"6","author":"Singhal","year":"2015","journal-title":"Front. Microbiol."},{"key":"ref_42","first-page":"1800193","article-title":"Review of the impact of MALDI-TOF MS in public health and hospital hygiene, 2018","volume":"24","author":"Cercenado","year":"2019","journal-title":"Eurosurveillance"},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"e00095-17","DOI":"10.1128\/CMR.00095-17","article-title":"The cost-effectiveness of rapid diagnostic testing for the diagnosis of bloodstream infections with or without antimicrobial stewardship","volume":"31","author":"Pliakos","year":"2018","journal-title":"Clin. Microbiol. Rev."},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"2577","DOI":"10.3389\/fmicb.2018.02577","article-title":"MALDI-TOF MS applications to the detection of antifungal resistance: State of the art and future perspectives","volume":"9","author":"Florio","year":"2018","journal-title":"Front. Microbiol."},{"key":"ref_45","doi-asserted-by":"crossref","first-page":"1097","DOI":"10.3389\/fmicb.2018.01097","article-title":"Recent advances and ongoing challenges in the diagnosis of microbial infections by MALDI-TOF mass spectrometry","volume":"9","author":"Florio","year":"2018","journal-title":"Front. Microbiol."},{"key":"ref_46","doi-asserted-by":"crossref","first-page":"240","DOI":"10.21037\/atm.2018.06.28","article-title":"MALDI-TOF mass spectrometry technology for detecting biomarkers of antimicrobial resistance: Current achievements and future perspectives","volume":"6","author":"Vrioni","year":"2018","journal-title":"Ann. Transl. Med."},{"key":"ref_47","first-page":"e00037-18","article-title":"Matrix-assisted laser desorption ionization-time of flight mass spectrometry for the rapid detection of antimicrobial resistance mechanisms and beyond","volume":"32","author":"Bou","year":"2019","journal-title":"Clin. Microbiol. Rev."},{"key":"ref_48","doi-asserted-by":"crossref","first-page":"48","DOI":"10.1016\/j.ymeth.2016.01.008","article-title":"MBT-ASTRA: A suitable tool for fast antibiotic susceptibility testing?","volume":"104","author":"Sparbier","year":"2016","journal-title":"Methods"},{"key":"ref_49","doi-asserted-by":"crossref","first-page":"767","DOI":"10.1002\/prca.201300042","article-title":"MALDI-TOF MS: An upcoming tool for rapid detection of antibiotic resistance in microorganisms","volume":"7","author":"Kostrzewa","year":"2013","journal-title":"Proteomics-Clin. Appl."},{"key":"ref_50","doi-asserted-by":"crossref","unstructured":"Ballest\u00e9, R.N. (2018). Proteomics: Technology and Applications. The Use of Mass Spectrometry Technology (MALDI-TOF) in Clinical Microbiology, Academic Press.","DOI":"10.1016\/B978-0-12-814451-0.00001-0"},{"key":"ref_51","doi-asserted-by":"crossref","first-page":"295","DOI":"10.1099\/0022-1317-49-3-295","article-title":"Rapid discrimination between methicillin-sensitive and methicillin-resistant Staphylococcus aureus by intact cell mass spectrometry","volume":"49","author":"Claydon","year":"2000","journal-title":"J. Med. Microbiol."},{"key":"ref_52","doi-asserted-by":"crossref","first-page":"5487","DOI":"10.1021\/ac020109k","article-title":"Identification of Staphylococcus aureus and determination of its methicillin resistance by matrix-assisted laser desorption\/ionization time-of-flight mass spectrometry","volume":"74","author":"Du","year":"2002","journal-title":"Anal. Chem."},{"key":"ref_53","doi-asserted-by":"crossref","first-page":"1051","DOI":"10.1128\/AEM.69.2.1051-1058.2003","article-title":"Bacteriocin detection from whole bacteria by matrix-assisted laser desorption ionization-time of flight mass spectrometry","volume":"69","author":"Hindre","year":"2003","journal-title":"Appl. Environ. Microbiol."},{"key":"ref_54","doi-asserted-by":"crossref","first-page":"1633","DOI":"10.1007\/s00216-007-1558-7","article-title":"Discrimination between wild-type and ampicillin-resistant Escherichia coli by matrix-assisted laser desorption\/ionization time-of-flight mass spectrometry","volume":"389","author":"Camara","year":"2007","journal-title":"Anal. Bioanal. Chem."},{"key":"ref_55","doi-asserted-by":"crossref","first-page":"1584","DOI":"10.1099\/jmm.0.031336-0","article-title":"Differentiation of division I (cfiA-negative) and division II (cfiA-positive) Bacteroides fragilis strains by matrix-assisted laser desorption\/ionization time of-flight mass spectrometry","volume":"60","author":"Nagy","year":"2011","journal-title":"J. Med. Microbiol."},{"key":"ref_56","doi-asserted-by":"crossref","first-page":"2179","DOI":"10.1128\/JCM.00503-12","article-title":"Detection of OmpK36 porin loss in Klebsiella spp. by matrix-assisted laser desorption ionization time of flight mass spectrometry","volume":"50","author":"Cai","year":"2012","journal-title":"J. Clin. Microbiol."},{"key":"ref_57","doi-asserted-by":"crossref","first-page":"2918","DOI":"10.1128\/JCM.01000-12","article-title":"Use of matrix-assisted laser desorption ionization-time of flight mass spectrometry to identify vancomycin-resistant enterococci and investigate the epidemiology of an outbreak","volume":"50","author":"Griffin","year":"2012","journal-title":"J. Clin. Microbiol."},{"key":"ref_58","doi-asserted-by":"crossref","first-page":"S57","DOI":"10.1097\/01.PAT.0000426852.32930.4a","article-title":"Rapid identification of VRE with MALDI-TOF MS","volume":"45","author":"Griffin","year":"2013","journal-title":"Pathology"},{"key":"ref_59","doi-asserted-by":"crossref","first-page":"2804","DOI":"10.1128\/JCM.00694-14","article-title":"A rapid matrix-assisted laser desorption ionization-time of flight mass spectrometry-based method for single-plasmid tracking in an outbreak of carbapenem-resistant Enterobacteriaceae","volume":"52","author":"Lau","year":"2014","journal-title":"J. Clin. Microbiol."},{"key":"ref_60","doi-asserted-by":"crossref","first-page":"818","DOI":"10.3389\/fmicb.2016.00818","article-title":"A designed experiments approach to optimizing MALDI-TOF MS spectrum processing parameters enhances detection of antibiotic resistance in Campylobacter jejuni","volume":"7","author":"Penny","year":"2016","journal-title":"Front. Microbiol."},{"key":"ref_61","doi-asserted-by":"crossref","first-page":"257","DOI":"10.1016\/j.diagmicrobio.2016.08.001","article-title":"The presence of a single MALDI-TOF mass spectral peak predicts methicillin resistance in staphylococci","volume":"86","author":"Rhoads","year":"2016","journal-title":"Diagn. Microbiol. Infect. Dis."},{"key":"ref_62","first-page":"3359","article-title":"Rapid detection and discrimination of chromosome- and MCR-plasmid-mediated resistance to polymyxins by MALDI-TOF MS in Escherichia coli: The MALDIxin test","volume":"73","author":"Dortet","year":"2018","journal-title":"J. Antimicrob. Chemother."},{"key":"ref_63","doi-asserted-by":"crossref","first-page":"120","DOI":"10.1016\/j.mimet.2019.02.020","article-title":"Di MALDI-TOF MS based procedure to detect KPC-2 directly from positive blood culture bottles and colonies","volume":"159","author":"Costa","year":"2019","journal-title":"J. Microbiol. Methods"},{"key":"ref_64","doi-asserted-by":"crossref","first-page":"30","DOI":"10.1016\/j.anaerobe.2019.01.011","article-title":"High prevalence of division II (cfiA positive) isolates among blood stream Bacteroides fragilis in Slovenia as determined by MALDI-TOF MS","volume":"58","author":"Jeverica","year":"2019","journal-title":"Anaerobe"},{"key":"ref_65","doi-asserted-by":"crossref","first-page":"2640","DOI":"10.1093\/jac\/dks261","article-title":"Identification of acquired antimicrobial resistance genes","volume":"67","author":"Zankari","year":"2012","journal-title":"J. Antimicrob. Chemother."},{"key":"ref_66","doi-asserted-by":"crossref","first-page":"550707","DOI":"10.1128\/AAC.00483-19","article-title":"Validating the NCBI AMRFinder tool and resistance gene database using antimicrobial resistance genotype-phenotype correlation in a collection of NARMS isolates","volume":"63","author":"Feldgarden","year":"2019","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref_67","doi-asserted-by":"crossref","first-page":"2346","DOI":"10.1093\/bioinformatics\/btw136","article-title":"ARGs-OAP: Online analysis pipeline for antibiotic resistance genes detection from metagenomic data using an integrated structured ARG-database","volume":"32","author":"Yang","year":"2016","journal-title":"Bioinformatics"},{"key":"ref_68","doi-asserted-by":"crossref","unstructured":"Rowe, W., Baker, K.S., Verner-Jeffreys, D., Baker-Austin, C., Ryan, J.J., Maskell, D., and Pearce, G. (2015). Search engine for antimicrobial resistance: A cloud compatible pipeline and web interface for rapidly detecting antimicrobial resistance genes directly from sequence data. PLoS ONE, 10.","DOI":"10.1371\/journal.pone.0133492"},{"key":"ref_69","unstructured":"Argoty, G.A.A., Guron, G.K., Garner, E., Riquelme, M.V., Heath, L., Pruden, A., Vikesland, P., and Zhang, L. (2018). ARG-miner: A web platform for crowdsourcing-based curation of antibiotic resistance genes. BioRxiv, 274282."},{"key":"ref_70","doi-asserted-by":"crossref","first-page":"4173","DOI":"10.1007\/s00436-016-5193-0","article-title":"New detection method in experimental mice for schistosomiasis: ClinProTool and matrix-assisted laser desorption\/ionization time-of-flight mass spectrometry","volume":"115","author":"Huang","year":"2016","journal-title":"Parasitol. Res."},{"key":"ref_71","doi-asserted-by":"crossref","first-page":"98","DOI":"10.1016\/j.mimet.2014.07.016","article-title":"Rapid detection and identification of strains carrying carbapenemases directly from positive blood cultures using MALDI-TOF MS","volume":"105","author":"Riazzo","year":"2014","journal-title":"J. Microbiol. Methods"},{"key":"ref_72","unstructured":"Gharbia, H.N.S.S.E. (2017). Analysis of MALDI-TOF MS Spectra using the BioNumerics Software. MALDI-TOF and Tandem MS for Clinical Microbiology, First Edition, John Wiley & Sons Ltd."},{"key":"ref_73","doi-asserted-by":"crossref","first-page":"54","DOI":"10.1016\/j.mimet.2017.01.009","article-title":"Custom database development and biomarker discovery methods for MALDI-TOF mass spectrometry-based identification of high-consequence bacterial pathogens","volume":"134","author":"Tracz","year":"2017","journal-title":"J. Microbiol. Methods"},{"key":"ref_74","doi-asserted-by":"crossref","unstructured":"Rodrigues, C., Passet, V., Brisse, S., and Brisse, S. (2018). Identification of Klebsiella pneumoniae complex members using MALDI-TOF mass spectrometry. Front. Microbiol.","DOI":"10.1101\/350579"},{"key":"ref_75","doi-asserted-by":"crossref","first-page":"45572","DOI":"10.1038\/srep45572","article-title":"Potential of MALDI-TOF MS as an alternative approach for capsular typing Streptococcus pneumoniae isolates","volume":"7","author":"Pinto","year":"2017","journal-title":"Sci. Rep."},{"key":"ref_76","doi-asserted-by":"crossref","first-page":"105685","DOI":"10.1016\/j.mimet.2019.105685","article-title":"Bacterial identification using a SCIEX 5800 TOF\/TOF MALDI research instrument and an external database","volume":"164","author":"Huber","year":"2019","journal-title":"J. Microbiol. Methods"},{"key":"ref_77","doi-asserted-by":"crossref","unstructured":"Karlsson, R., Gonzales-Siles, L., Boulund, F., Lindgren, \u00c5., Svensson-Stadler, L., Karlsson, A., Kristiansson, E., and Moore, E.R.B. (2017). Proteotyping: Tandem mass spectrometry shotgun proteomic characterization and typing of pathogenic microorganisms. MALDI-TOF and Tandem MS for Clinical Microbiology, John Wiley & Sons Ltd.","DOI":"10.1002\/9781118960226.ch16"},{"key":"ref_78","doi-asserted-by":"crossref","first-page":"2","DOI":"10.1016\/j.syapm.2010.11.013","article-title":"Applications of whole-cell matrix-assisted laser-desorption\/ionization time-of-flight mass spectrometry in systematic microbiology","volume":"34","author":"Welker","year":"2011","journal-title":"Syst. Appl. Microbiol."},{"key":"ref_79","doi-asserted-by":"crossref","unstructured":"Greaves, J., Roboz, J., and Roboz, J. (2013). Mass Spectrometry for the Novice, First Edition, CRC Press.","DOI":"10.1201\/b15436"},{"key":"ref_80","doi-asserted-by":"crossref","first-page":"784","DOI":"10.1016\/S1044-0305(02)00393-8","article-title":"De novo sequencing of peptides using MALDI\/TOF-TOF","volume":"13","author":"Yergey","year":"2002","journal-title":"J. Am. Soc. Mass Spectrom."},{"key":"ref_81","doi-asserted-by":"crossref","first-page":"463","DOI":"10.1517\/phgs.4.4.463.22753","article-title":"Mass spectrometry-based clinical proteomics","volume":"4","author":"Pusch","year":"2003","journal-title":"Pharmacogenomics"},{"key":"ref_82","doi-asserted-by":"crossref","first-page":"4246","DOI":"10.1002\/pmic.200500764","article-title":"Comparative proteomic analysis of Staphylococcus aureus strains with differences in resistance to the cell wall-targeting antibiotic vancomycin","volume":"6","author":"Pieper","year":"2006","journal-title":"Proteomics"},{"key":"ref_83","doi-asserted-by":"crossref","unstructured":"Shah, A.J., Mkrtchyan, H.V., Xu, Z., Serafim, V., and Shah, H.N. (2017). Determination of antimicrobial resistance using tandem mass spectrometry. MALDI-TOF and Tandem MS for Clinical Microbiology, John Wiley & Sons Ltd.","DOI":"10.1002\/9781118960226.ch15"},{"key":"ref_84","doi-asserted-by":"crossref","first-page":"695","DOI":"10.1080\/14789450.2019.1645603","article-title":"An Update on the Routine Application of MALDI-TOF MS in Clinical Microbiology","volume":"8","author":"Welker","year":"2019","journal-title":"Expert Rev Proteomics"},{"key":"ref_85","unstructured":"Bruker (2019, June 22). Bruker Launches MALDI Biotyper Sirius at ASM Microbe Conference. Available online: https:\/\/www.prnewswire.com\/news-releases\/bruker-launches-maldi-biotyper-sirius-at-asm-microbe-conference-300871836.html."},{"key":"ref_86","unstructured":"Bruker (2019, September 10). Innovation with Integrity Changing Microbiology MALDI Biotyper \u00ae Subtyping Module. Available online: https:\/\/www.bruker.com\/fileadmin\/user_upload\/8-PDF-Docs\/Separations_MassSpectrometry\/Literature\/Brochures\/1851663_MBT_Subtyping_brochure_04-2017_ebook.pdf."},{"key":"ref_87","doi-asserted-by":"crossref","unstructured":"Cordovana, M., Pranada, A.B., Ambretti, S., and Kostrzewa, M. (2019). MALDI-TOF bacterial subtyping to detect antibiotic resistance. Clin. Mass Spectrom., in press.","DOI":"10.1016\/j.clinms.2019.06.002"},{"key":"ref_88","doi-asserted-by":"crossref","first-page":"35","DOI":"10.1128\/JCM.01643-15","article-title":"Clinical performance of a matrix-assisted laser desorption ionization time of flight mass spectrometry method for detection of certain bla KPC -containing plasmids","volume":"54","author":"Youn","year":"2016","journal-title":"J. Clin. Microbiol."},{"key":"ref_89","doi-asserted-by":"crossref","first-page":"59","DOI":"10.1016\/j.anaerobe.2014.10.009","article-title":"Identification of antimicrobial resistance genes in multidrug-resistant clinical Bacteroides fragilis isolates by whole genome shotgun sequencing","volume":"31","author":"Sydenham","year":"2015","journal-title":"Anaerobe"},{"key":"ref_90","doi-asserted-by":"crossref","first-page":"1002.e1","DOI":"10.1016\/j.cmi.2016.08.001","article-title":"Using whole genome sequencing to identify resistance determinants and predict antimicrobial resistance phenotypes for year 2015 invasive pneumococcal disease isolates recovered in the United States","volume":"22","author":"Metcalf","year":"2016","journal-title":"Clin. Microbiol. Infect."},{"key":"ref_91","doi-asserted-by":"crossref","first-page":"2763","DOI":"10.1093\/jac\/dkv186","article-title":"WGS accurately predicts antimicrobial resistance in Escherichia coli","volume":"70","author":"Tyson","year":"2015","journal-title":"J. Antimicrob. Chemother."},{"key":"ref_92","doi-asserted-by":"crossref","first-page":"495","DOI":"10.1007\/s10096-016-2824-4","article-title":"MALDI-TOF MS meets WGS in a VRE outbreak investigation","volume":"36","author":"Schlebusch","year":"2017","journal-title":"Eur. J. Clin. Microbiol. Infect. Dis."},{"key":"ref_93","doi-asserted-by":"crossref","first-page":"320","DOI":"10.3201\/eid2302.161321","article-title":"Determination of Elizabethkingia diversity by MALDI-TOF mass spectrometry and whole-genome sequencing","volume":"23","author":"Eriksen","year":"2017","journal-title":"Emerg. Infect. Dis."},{"key":"ref_94","unstructured":"Batz, M.B., Hoffmann, S.A., and Morris, J.G. (2019, September 10). Ranking the Risks: The 10 Pathogen-Food Combinations with the Greatest Burden on Public Health. Available online: https:\/\/folio.iupui.edu\/bitstream\/handle\/10244\/1022\/72267report.pdf?sequence=1."},{"key":"ref_95","doi-asserted-by":"crossref","unstructured":"Zautner, A.E., Masanta, W.O., Tareen, A.M., Weig, M., Lugert, R., Gro\u00df, U., and Bader, O. (2013). Discrimination of multilocus sequence typing-based Campylobacter jejuni subgroups by MALDI-TOF mass spectrometry. BMC Microbiol., 13.","DOI":"10.1186\/1471-2180-13-247"},{"key":"ref_96","doi-asserted-by":"crossref","first-page":"62","DOI":"10.1556\/1886.2019.00006","article-title":"Differentiation of Campylobacter fetus subspecies by proteotyping","volume":"9","author":"Emele","year":"2019","journal-title":"Eur. J. Microbiol. Immunol."},{"key":"ref_97","doi-asserted-by":"crossref","first-page":"4244","DOI":"10.1038\/s41598-019-40842-w","article-title":"Proteotyping as alternate typing method to differentiate Campylobacter coli clades","volume":"9","author":"Emele","year":"2019","journal-title":"Sci. Rep."},{"key":"ref_98","first-page":"e54165","article-title":"Subtyping of Campylobacter jejuni ssp. doylei isolates using mass spectrometry-based phyloproteomics (MSPP)","volume":"116","author":"Zautner","year":"2016","journal-title":"J. Vis. Exp."},{"key":"ref_99","doi-asserted-by":"crossref","first-page":"193","DOI":"10.12688\/f1000research.12328.1","article-title":"Antibiotic treatment of acute gastroenteritis in children","volume":"7","author":"Guarino","year":"2018","journal-title":"F1000Research"},{"key":"ref_100","unstructured":"World Health Organization (2019, September 05). Critically Important Antimicrobials for Human Medicine 6th Revision 2018. Ranking of Medically Important Antimicrobials for Risk Management of Antimicrobial Resistance Due to Non-Human Use. Available online: https:\/\/www.who.int\/foodsafety\/publications\/antimicrobials-sixth\/en\/."}],"container-title":["Microorganisms"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2076-2607\/7\/12\/593\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,11]],"date-time":"2025-10-11T13:36:21Z","timestamp":1760189781000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2076-2607\/7\/12\/593"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2019,11,21]]},"references-count":100,"journal-issue":{"issue":"12","published-online":{"date-parts":[[2019,12]]}},"alternative-id":["microorganisms7120593"],"URL":"https:\/\/doi.org\/10.3390\/microorganisms7120593","relation":{},"ISSN":["2076-2607"],"issn-type":[{"value":"2076-2607","type":"electronic"}],"subject":[],"published":{"date-parts":[[2019,11,21]]}}}