{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,23]],"date-time":"2026-10-23T05:41:23Z","timestamp":1792734083861,"version":"4.5.0"},"reference-count":62,"publisher":"Wiley","issue":"9","license":[{"start":{"date-parts":[[2024,9,10]],"date-time":"2024-09-10T00:00:00Z","timestamp":1725926400000},"content-version":"vor","delay-in-days":9,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0\/"}],"content-domain":{"domain":["enviromicro-journals.onlinelibrary.wiley.com"],"crossmark-restriction":true},"short-container-title":["Microbial Biotechnology"],"published-print":{"date-parts":[[2024,9]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>\n                    <jats:italic>Mycobacterium abscessus<\/jats:italic>\n                    (MABS) displays differential subspecies susceptibility to macrolides. Thus, identifying MABS's subspecies (\n                    <jats:italic>M. abscessus<\/jats:italic>\n                    ,\n                    <jats:italic>M. bolletii<\/jats:italic>\n                    and\n                    <jats:italic>M. massiliense<\/jats:italic>\n                    ) is a clinical necessity for guiding treatment decisions. We aimed to assess the potential of Machine Learning (ML)\u2010based classifiers coupled to Matrix\u2010Assisted Laser Desorption\/Ionization Time\u2010of\u2010Flight (MALDI\u2010TOF) MS to identify MABS subspecies. Two spectral databases were created by using 40 confirmed MABS strains. Spectra were obtained by using MALDI\u2010TOF MS from strains cultivated on solid (Columbia Blood Agar, CBA) or liquid (MGIT\u00ae) media for 1 to 13\u2009days. Each database was divided into a dataset for ML\u2010based pipeline development and a dataset to assess the performance. An in\u2010house programme was developed to identify discriminant peaks specific to each subspecies. The peak\u2010based approach successfully distinguished\n                    <jats:italic>M. massiliense<\/jats:italic>\n                    from the other subspecies for strains grown on CBA. The ML approach achieved 100% accuracy for subspecies identification on CBA, falling to 77.5% on MGIT\u00ae. This study validates the usefulness of ML, in particular the Random Forest algorithm, to discriminate MABS subspecies by MALDI\u2010TOF MS. However, identification in MGIT\u00ae, a medium largely used in mycobacteriology laboratories, is not yet reliable and should be a development priority.\n                  <\/jats:p>","DOI":"10.1111\/1751-7915.14545","type":"journal-article","created":{"date-parts":[[2024,9,11]],"date-time":"2024-09-11T01:38:56Z","timestamp":1726018736000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":9,"title":["Contribution of machine learning for subspecies identification from\n                    <i>Mycobacterium abscessus<\/i>\n                    with MALDI\u2010TOF MS in solid and liquid media"],"prefix":"10.1111","volume":"17","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-5211-5796","authenticated-orcid":false,"given":"Alexandre","family":"Godmer","sequence":"first","affiliation":[{"name":"U1135, Centre d'Immunologie et des Maladies Infectieuses (Cimi\u2010Paris) Sorbonne Universit\u00e9  Paris France"},{"name":"AP\u2010HP, Sorbonne Universit\u00e9 (Assistance Publique H\u00f4pitaux de Paris), D\u00e9partement de Bact\u00e9riologie Groupe Hospitalier Universitaire, Sorbonne Universit\u00e9, H\u00f4pital  Paris France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lise","family":"Bigey","sequence":"additional","affiliation":[{"name":"U1135, Centre d'Immunologie et des Maladies Infectieuses (Cimi\u2010Paris) Sorbonne Universit\u00e9  Paris France"},{"name":"DER (D\u00e9partement d'Enseignement et de Recherche) de Biologie, ENS Paris\u2010Saclay Universit\u00e9 Paris\u2010Saclay  Gif\u2010sur\u2010Yvette France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Quentin","family":"Giai\u2010Gianetto","sequence":"additional","affiliation":[{"name":"Institut Pasteur Universit\u00e9 Paris Cit\u00e9, Bioinformatics and Biostatistics HUB  Paris France"},{"name":"Institut Pasteur Universit\u00e9 Paris Cit\u00e9, Proteomics Platform, Mass Spectrometry for Biology Unit, UAR CNRS 2024  Paris France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gautier","family":"Pierrat","sequence":"additional","affiliation":[{"name":"AP\u2010HP, Sorbonne Universit\u00e9 (Assistance Publique H\u00f4pitaux de Paris), D\u00e9partement de Bact\u00e9riologie Groupe Hospitalier Universitaire, Sorbonne Universit\u00e9, H\u00f4pital  Paris France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3891-0216","authenticated-orcid":false,"given":"Noshine","family":"Mohammad","sequence":"additional","affiliation":[{"name":"Inserm, Institut Pierre\u2010Louis d'Epid\u00e9miologie et de Sant\u00e9 Publique, IPLESP, AP\u2010HP, Groupe Hospitalier Piti\u00e9\u2010Salp\u00eatri\u00e8re, Service de Parasitologie\u2010 Mycologie Sorbonne Universit\u00e9  Paris France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Faiza","family":"Mougari","sequence":"additional","affiliation":[{"name":"Service de Mycobact\u00e9riologie sp\u00e9cialis\u00e9e et de r\u00e9f\u00e9rence, Centre National de R\u00e9f\u00e9rence des Mycobact\u00e9ries (Laboratoire associ\u00e9), APHP GHU Nord Universit\u00e9 Paris Cit\u00e9, INSERM IAME UMR  Paris France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Renaud","family":"Piarroux","sequence":"additional","affiliation":[{"name":"Inserm, Institut Pierre\u2010Louis d'Epid\u00e9miologie et de Sant\u00e9 Publique, IPLESP, AP\u2010HP, Groupe Hospitalier Piti\u00e9\u2010Salp\u00eatri\u00e8re, Service de Parasitologie\u2010 Mycologie Sorbonne Universit\u00e9  Paris France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nicolas","family":"Veziris","sequence":"additional","affiliation":[{"name":"U1135, Centre d'Immunologie et des Maladies Infectieuses (Cimi\u2010Paris) Sorbonne Universit\u00e9  Paris France"},{"name":"AP\u2010HP, Sorbonne Universit\u00e9 (Assistance Publique H\u00f4pitaux de Paris), D\u00e9partement de Bact\u00e9riologie Groupe Hospitalier Universitaire, Sorbonne Universit\u00e9, H\u00f4pital  Paris France"},{"name":"AP\u2010HP, Sorbonne Universit\u00e9 (Assistance Publique H\u00f4pitaux de Paris) Centre National de R\u00e9f\u00e9rence des Mycobact\u00e9ries et de la R\u00e9sistance des Mycobact\u00e9ries aux Antituberculeux  Paris France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alexandra","family":"Aubry","sequence":"additional","affiliation":[{"name":"U1135, Centre d'Immunologie et des Maladies Infectieuses (Cimi\u2010Paris) Sorbonne Universit\u00e9  Paris France"},{"name":"AP\u2010HP, Sorbonne Universit\u00e9 (Assistance Publique H\u00f4pitaux de Paris) Centre National de R\u00e9f\u00e9rence des Mycobact\u00e9ries et de la R\u00e9sistance des Mycobact\u00e9ries aux Antituberculeux  Paris 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