{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,28]],"date-time":"2026-10-28T18:51:26Z","timestamp":1793213486853,"version":"4.5.0"},"reference-count":23,"publisher":"American Society for Microbiology","issue":"5","license":[{"start":{"date-parts":[[2024,5,2]],"date-time":"2024-05-02T00:00:00Z","timestamp":1714608000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2024,5,2]],"date-time":"2024-05-02T00:00:00Z","timestamp":1714608000000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/journals.asm.org\/non-commercial-tdm-license"}],"funder":[{"name":"Science Committee of the Ministry of Education and Science of the Republic of Kazakhstan","award":["No.AP09259123"],"award-info":[{"award-number":["No.AP09259123"]}]},{"name":"Science Committee of the Ministry of Education and Science of the Republic of Kazakhstan","award":["No. AP19679717"],"award-info":[{"award-number":["No. AP19679717"]}]},{"DOI":"10.13039\/501100000024","name":"Canadian Institutes of Health Research","doi-asserted-by":"publisher","award":["Postdoctoral fellowship (Competition #202210MFE)"],"award-info":[{"award-number":["Postdoctoral fellowship (Competition #202210MFE)"]}],"id":[{"id":"10.13039\/501100000024","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Faculty Development Competitive Research Grant (COVID) from Nazarbayev University","award":["280720FD1902"],"award-info":[{"award-number":["280720FD1902"]}]}],"content-domain":{"domain":["journals.asm.org"],"crossmark-restriction":true},"short-container-title":["Microbiol Spectr"],"published-print":{"date-parts":[[2024,5,2]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n          <jats:sec>\n            <jats:title\/>\n            <jats:p>Matrix-assisted laser desorption\/ionization time-of-flight mass spectrometry (MALDI-TOF MS) could aid the diagnosis of acute respiratory infections (ARIs) owing to its affordability and high-throughput capacity. MALDI-TOF MS has been proposed for use on commonly available respiratory samples, without specialized sample preparation, making this technology especially attractive for implementation in low-resource regions. Here, we assessed the utility of MALDI-TOF MS in differentiating severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) vs non-COVID acute respiratory infections (NCARIs) in a clinical lab setting in Kazakhstan. Nasopharyngeal swabs were collected from inpatients and outpatients with respiratory symptoms and from asymptomatic controls (ACs) in 2020\u20132022. PCR was used to differentiate SARS-CoV-2+ and NCARI cases. MALDI-TOF MS spectra were obtained for a total of 252 samples (115 SARS-CoV-2+, 98 NCARIs, and 39 ACs) without specialized sample preparation. In our first sub-analysis, we followed a published protocol for peak preprocessing and machine learning (ML), trained on publicly available spectra from South American SARS-CoV-2+ and NCARI samples. In our second sub-analysis, we trained ML models on a peak intensity matrix representative of both South American (SA) and Kazakhstan (Kaz) samples. Applying the established MALDI-TOF MS pipeline \u201cas is\u201d resulted in a high detection rate for SARS-CoV-2+ samples (91.0%), but low accuracy for NCARIs (48.0%) and ACs (67.0%) by the top-performing random forest model. After re-training of the ML algorithms on the SA-Kaz peak intensity matrix, the accuracy of detection by the top-performing support vector machine with radial basis function kernel model was at 88.0%, 95.0%, and 78% for the Kazakhstan SARS-CoV-2+, NCARI, and AC subjects, respectively, with a SARS-CoV-2 vs rest receiver operating characteristic area under the curve of 0.983 [0.958, 0.987]; a high differentiation accuracy was maintained for the South American SARS-CoV-2 and NCARIs. MALDI-TOF MS\/ML is a feasible approach for the differentiation of ARI without specialized sample preparation. The implementation of MALDI-TOF MS\/ML in a real clinical lab setting will necessitate continuous optimization to keep up with the rapidly evolving landscape of ARI.<\/jats:p>\n            <jats:sec>\n              <jats:title>IMPORTANCE<\/jats:title>\n              <jats:p>In this proof-of-concept study, the authors used matrix-assisted laser desorption\/ionization time-of-flight mass spectrometry (MALDI-TOF MS) and machine learning (ML) to identify and distinguish acute respiratory infections (ARI) caused by SARS-CoV-2 versus other pathogens in low-resource clinical settings, without the need for specialized sample preparation. The ML models were trained on a varied collection of MALDI-TOF MS spectra from studies conducted in Kazakhstan and South America. Initially, the MALDI-TOF MS\/ML pipeline, trained exclusively on South American samples, exhibited diminished effectiveness in recognizing non-SARS-CoV-2 infections from Kazakhstan. Incorporation of spectral signatures from Kazakhstan substantially increased the accuracy of detection. These results underscore the potential of employing MALDI-TOF MS\/ML in resource-constrained settings to augment current approaches for detecting and differentiating ARI.<\/jats:p>\n            <\/jats:sec>\n          <\/jats:sec>","DOI":"10.1128\/spectrum.04068-23","type":"journal-article","created":{"date-parts":[[2024,3,18]],"date-time":"2024-03-18T14:51:07Z","timestamp":1710773467000},"update-policy":"https:\/\/doi.org\/10.1128\/asmj-crossmark-policy-page","source":"Crossref","is-referenced-by-count":12,"title":["Application of MALDI-TOF MS and machine learning for the detection of SARS-CoV-2 and non-SARS-CoV-2 respiratory infections"],"prefix":"10.1128","volume":"12","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-7136-7921","authenticated-orcid":false,"given":"Sergey","family":"Yegorov","sequence":"first","affiliation":[{"name":"Department of Biochemistry and Biomedical Sciences, Michael G. DeGroote Institute for Infectious Disease Research, McMaster Immunology Research Centre, McMaster University, Hamilton, Ontario, Canada"},{"name":"School of Sciences and Humanities, Nazarbayev University, Astana, Kazakhstan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7173-3138","authenticated-orcid":false,"given":"Irina","family":"Kadyrova","sequence":"additional","affiliation":[{"name":"Research Centre, Karaganda Medical University, Karaganda, Kazakhstan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ilya","family":"Korshukov","sequence":"additional","affiliation":[{"name":"Research Centre, Karaganda Medical University, Karaganda, Kazakhstan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7136-7921","authenticated-orcid":false,"given":"Aidana","family":"Sultanbekova","sequence":"additional","affiliation":[{"name":"Research Centre, Karaganda Medical University, Karaganda, Kazakhstan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yevgeniya","family":"Kolesnikova","sequence":"additional","affiliation":[{"name":"Research Centre, Karaganda Medical University, Karaganda, Kazakhstan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Valentina","family":"Barkhanskaya","sequence":"additional","affiliation":[{"name":"Research Centre, Karaganda Medical University, Karaganda, Kazakhstan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tatiana","family":"Bashirova","sequence":"additional","affiliation":[{"name":"City Centre for Primary Medical and Sanitary Care, Karaganda, Kazakhstan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yerzhan","family":"Zhunusov","sequence":"additional","affiliation":[{"name":"Infectious Disease Centre of the Karaganda Regional Clinical Hospital, Karaganda, Kazakhstan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yevgeniya","family":"Li","sequence":"additional","affiliation":[{"name":"Infectious Disease Centre of the Karaganda Regional Clinical Hospital, Karaganda, Kazakhstan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Viktoriya","family":"Parakhina","sequence":"additional","affiliation":[{"name":"Infectious Disease Centre of the Karaganda Regional Clinical Hospital, Karaganda, Kazakhstan"},{"name":"Department of Internal Diseases, Karaganda Medical University, Karaganda, Kazakhstan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Svetlana","family":"Kolesnichenko","sequence":"additional","affiliation":[{"name":"Research Centre, Karaganda Medical University, Karaganda, Kazakhstan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yeldar","family":"Baiken","sequence":"additional","affiliation":[{"name":"School of Sciences and Humanities, Nazarbayev University, Astana, Kazakhstan"},{"name":"National Laboratory Astana, Centre for Life Sciences, Nazarbayev University, Astana, Kazakhstan"},{"name":"School of Engineering and Digital Sciences, Nazarbayev University, Astana, Kazakhstan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bakhyt","family":"Matkarimov","sequence":"additional","affiliation":[{"name":"National Laboratory Astana, Centre for Life Sciences, Nazarbayev University, Astana, Kazakhstan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dmitriy","family":"Vazenmiller","sequence":"additional","affiliation":[{"name":"Research Centre, Karaganda Medical University, Karaganda, Kazakhstan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Matthew S.","family":"Miller","sequence":"additional","affiliation":[{"name":"Department of Biochemistry and Biomedical Sciences, Michael G. DeGroote Institute for Infectious Disease Research, McMaster Immunology Research Centre, McMaster University, Hamilton, Ontario, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gonzalo H.","family":"Hortelano","sequence":"additional","affiliation":[{"name":"School of Sciences and Humanities, Nazarbayev University, Astana, Kazakhstan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anar","family":"Turmukhambetova","sequence":"additional","affiliation":[{"name":"Research Centre, Karaganda Medical University, Karaganda, Kazakhstan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Antonella E.","family":"Chesca","sequence":"additional","affiliation":[{"name":"Faculty of Medicine, Transilvania University, Bra\u0219ov, Romania"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dmitriy","family":"Babenko","sequence":"additional","affiliation":[{"name":"Research Centre, Karaganda Medical University, Karaganda, Kazakhstan"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"235","reference":[{"key":"e_1_3_5_2_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.lanepe.2021.100096"},{"key":"e_1_3_5_3_2","doi-asserted-by":"publisher","DOI":"10.1093\/cid\/ciaa508"},{"key":"e_1_3_5_4_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.metabol.2021.154922"},{"key":"e_1_3_5_5_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41587-020-0644-7"},{"key":"e_1_3_5_6_2","doi-asserted-by":"publisher","DOI":"10.3389\/fmed.2021.661358"},{"key":"e_1_3_5_7_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-021-87463-w"},{"key":"e_1_3_5_8_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0272008"},{"key":"e_1_3_5_9_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-022-17514-3"},{"key":"e_1_3_5_10_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0293074"},{"key":"e_1_3_5_11_2","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/bts447"},{"key":"e_1_3_5_12_2","doi-asserted-by":"publisher","DOI":"10.18637\/jss.v025.i01"},{"key":"e_1_3_5_13_2","unstructured":"Extract and visualize the results of multivariate data analyses. 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The nasopharyngeal virome in adults with acute respiratory infection. bioRxiv. doi:10.1101\/2023.08.21.554191","DOI":"10.1101\/2023.08.21.554191"},{"key":"e_1_3_5_22_2","doi-asserted-by":"publisher","DOI":"10.7717\/peerj.15008"},{"key":"e_1_3_5_23_2","doi-asserted-by":"publisher","DOI":"10.1128\/MRA.00749-23"},{"key":"e_1_3_5_24_2","doi-asserted-by":"publisher","DOI":"10.1128\/spectrum.01492-23"}],"container-title":["Microbiology Spectrum"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/journals.asm.org\/doi\/pdf\/10.1128\/spectrum.04068-23","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/journals.asm.org\/doi\/pdf\/10.1128\/spectrum.04068-23","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,5,2]],"date-time":"2024-05-02T13:05:19Z","timestamp":1714655119000},"score":1,"resource":{"primary":{"URL":"https:\/\/journals.asm.org\/doi\/10.1128\/spectrum.04068-23"}},"subtitle":[],"editor":[{"given":"Heba H.","family":"Mostafa","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2024,5,2]]},"references-count":23,"journal-issue":{"issue":"5","published-print":{"date-parts":[[2024,5,2]]}},"alternative-id":["10.1128\/spectrum.04068-23"],"URL":"https:\/\/doi.org\/10.1128\/spectrum.04068-23","relation":{},"ISSN":["2165-0497"],"issn-type":[{"value":"2165-0497","type":"electronic"}],"subject":[],"published":{"date-parts":[[2024,5,2]]},"assertion":[{"value":"2023-12-01","order":0,"name":"received","label":"Received","group":{"name":"publication_history","label":"Publication History"}},{"value":"2024-02-28","order":1,"name":"accepted","label":"Accepted","group":{"name":"publication_history","label":"Publication History"}},{"value":"2024-03-18","order":2,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}],"article-number":"e04068-23"}}