{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,24]],"date-time":"2026-07-24T03:03:57Z","timestamp":1784862237749,"version":"3.55.0"},"reference-count":73,"publisher":"Microbiology Society","issue":"8","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,8,30]]},"abstract":"<jats:p>\n                  <jats:bold>Introduction.<\/jats:bold> Commensal <jats:italic>Neisseria<\/jats:italic> spp. are highly prevalent in the oropharynx as part of the healthy microbiome. <jats:italic>N. meningitidis<\/jats:italic> can colonise the oropharynx too from where it can cause invasive meningococcal disease. To identify <jats:italic>N. meningitidis<\/jats:italic>, clinical microbiology laboratories often rely on Matrix Assisted Laser Desorption\/Ionisation Time of Flight Mass Spectrometry (MALDI-TOF MS).<\/jats:p>\n               <jats:p>\n                  <jats:bold>Hypothesis\/Gap statement.<\/jats:bold>\n                  <jats:italic>N. meningitidis<\/jats:italic> may be misidentified by MALDI-TOF MS.<\/jats:p>\n               <jats:p>\n                  <jats:bold>Aim.<\/jats:bold> To conduct genomic surveillance of oropharyngeal <jats:italic>Neisseria<\/jats:italic> spp. in order to: (i) verify MALDI-TOF MS species identification, and (ii) characterize commensal <jats:italic>Neisseria<\/jats:italic> spp. genomes.<\/jats:p>\n               <jats:p>\n                  <jats:bold>Methodology.<\/jats:bold> We analysed whole genome sequence (WGS) data from 119 <jats:italic>Neisseria<\/jats:italic> spp. isolates from a surveillance programme for oropharyngeal <jats:italic>Neisseria<\/jats:italic> spp. in Belgium. Different species identification methods were compared: (i) MALDI-TOF MS, (ii) Ribosomal Multilocus Sequence Typing (rMLST) and (iii) <jats:italic>rplF<\/jats:italic> gene species identification. WGS data were used to further characterize <jats:italic>Neisseria<\/jats:italic> species found with supplementary analyses of <jats:italic>Neisseria cinerea<\/jats:italic> genomes.<\/jats:p>\n               <jats:p>\n                  <jats:bold>Results.<\/jats:bold> Based on genomic species identification, isolates from the oropharyngeal <jats:italic>Neisseria<\/jats:italic> surveilence study were composed of the following species: <jats:italic>N. meningitidis<\/jats:italic> (<jats:italic>n<\/jats:italic>=23)<jats:italic>, N. subflava<\/jats:italic> (<jats:italic>n<\/jats:italic>=61), <jats:italic>N. mucosa<\/jats:italic> (<jats:italic>n<\/jats:italic>=15), <jats:italic>N. oralis<\/jats:italic> (<jats:italic>n<\/jats:italic>=8), <jats:italic>N. cinerea<\/jats:italic> (<jats:italic>n<\/jats:italic>=5), <jats:italic>N. elongata<\/jats:italic> (<jats:italic>n<\/jats:italic>=3), <jats:italic>N. lactamica<\/jats:italic> (<jats:italic>n<\/jats:italic>=2), <jats:italic>N. bacilliformis<\/jats:italic> (<jats:italic>n<\/jats:italic>=1) and <jats:italic>N. polysaccharea<\/jats:italic> (<jats:italic>n<\/jats:italic>=1). Of these 119 isolates, four isolates identified as <jats:italic>N. meningitidis<\/jats:italic> (<jats:italic>n<\/jats:italic>=3) and <jats:italic>N. subflava<\/jats:italic> (<jats:italic>n<\/jats:italic>=1) by MALDI-TOF MS<jats:italic>,<\/jats:italic> were determined to be <jats:italic>N. polysaccharea<\/jats:italic> (<jats:italic>n<\/jats:italic>=1)<jats:italic>, N. cinerea<\/jats:italic> (<jats:italic>n<\/jats:italic>=2) and <jats:italic>N. mucosa<\/jats:italic> (<jats:italic>n<\/jats:italic>=1) by rMLST. Phylogenetic analyses revealed that <jats:italic>N. cinerea<\/jats:italic> isolates from the general population (<jats:italic>n<\/jats:italic>=3, cluster one) were distinct from those obtained from men who have sex with men (MSM, <jats:italic>n<\/jats:italic>=2, cluster two). The latter contained genomes misidentified as <jats:italic>N. meningitidis<\/jats:italic> using MALDI-TOF MS. These two <jats:italic>N. cinerea<\/jats:italic> clusters persisted after the inclusion of published <jats:italic>N. cinerea<\/jats:italic> WGS (<jats:italic>n<\/jats:italic>=42). Both <jats:italic>N. cinerea<\/jats:italic> clusters were further defined through pangenome and Average Nucleotide Identity (ANI) analyses.<\/jats:p>\n               <jats:p>\n                  <jats:bold>Conclusion.<\/jats:bold> This study provides insights into the importance of genomic genus-wide <jats:italic>Neisseria<\/jats:italic> surveillance studies to improve the characterization and identification of the <jats:italic>Neisseria<\/jats:italic> genus.<\/jats:p>","DOI":"10.1099\/jmm.0.001871","type":"journal-article","created":{"date-parts":[[2024,8,30]],"date-time":"2024-08-30T09:18:36Z","timestamp":1725009516000},"source":"Crossref","is-referenced-by-count":4,"title":["Genomic oropharyngeal Neisseria surveillance detects MALDI-TOF MS species misidentifications and reveals a novel Neisseria cinerea clade"],"prefix":"10.1099","volume":"73","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-3294-0147","authenticated-orcid":false,"given":"Tessa","family":"de 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