Tessa de Block, Irith De Baetselier, Dorien Van den Bossche, Saïd Abdellati, Zina Gestels, Jolein Gyonne Elise Laumen, Christophe Van Dijck, Thibaut Vanbaelen, Nathalie Claes, Koen Vandelannoote, Chris Kenyon, Odile Harrison, Sheeba Santhini Manoharan-Basil
{"title":"基因组口咽奈瑟菌监测发现了 MALDI-TOF MS 物种错误鉴定，并揭示了一个新的阴性奈瑟菌支系。","authors":"Tessa de Block, Irith De Baetselier, Dorien Van den Bossche, Saïd Abdellati, Zina Gestels, Jolein Gyonne Elise Laumen, Christophe Van Dijck, Thibaut Vanbaelen, Nathalie Claes, Koen Vandelannoote, Chris Kenyon, Odile Harrison, Sheeba Santhini Manoharan-Basil","doi":"10.1099/jmm.0.001871","DOIUrl":null,"url":null,"abstract":"<p><p><b>Introduction.</b> Commensal <i>Neisseria</i> spp. are highly prevalent in the oropharynx as part of the healthy microbiome. <i>N. meningitidis</i> can colonise the oropharynx too from where it can cause invasive meningococcal disease. To identify <i>N. meningitidis</i>, clinical microbiology laboratories often rely on Matrix Assisted Laser Desorption/Ionisation Time of Flight Mass Spectrometry (MALDI-TOF MS).<b>Hypothesis/Gap statement.</b> <i>N. meningitidis</i> may be misidentified by MALDI-TOF MS.<b>Aim.</b> To conduct genomic surveillance of oropharyngeal <i>Neisseria</i> spp. in order to: (i) verify MALDI-TOF MS species identification, and (ii) characterize commensal <i>Neisseria</i> spp. genomes.<b>Methodology.</b> We analysed whole genome sequence (WGS) data from 119 <i>Neisseria</i> spp. isolates from a surveillance programme for oropharyngeal <i>Neisseria</i> spp. in Belgium. Different species identification methods were compared: (i) MALDI-TOF MS, (ii) Ribosomal Multilocus Sequence Typing (rMLST) and (iii) <i>rplF</i> gene species identification. WGS data were used to further characterize <i>Neisseria</i> species found with supplementary analyses of <i>Neisseria cinerea</i> genomes.<b>Results.</b> Based on genomic species identification, isolates from the oropharyngeal <i>Neisseria</i> surveilence study were composed of the following species: <i>N. meningitidis</i> (<i>n</i>=23)<i>, N. subflava</i> (<i>n</i>=61), <i>N. mucosa</i> (<i>n</i>=15), <i>N. oralis</i> (<i>n</i>=8), <i>N. cinerea</i> (<i>n</i>=5), <i>N. elongata</i> (<i>n</i>=3), <i>N. lactamica</i> (<i>n</i>=2), <i>N. bacilliformis</i> (<i>n</i>=1) and <i>N. polysaccharea</i> (<i>n</i>=1). Of these 119 isolates, four isolates identified as <i>N. meningitidis</i> (<i>n</i>=3) and <i>N. subflava</i> (<i>n</i>=1) by MALDI-TOF MS<i>,</i> were determined to be <i>N. polysaccharea</i> (<i>n</i>=1)<i>, N. cinerea</i> (<i>n</i>=2) and <i>N. mucosa</i> (<i>n</i>=1) by rMLST. Phylogenetic analyses revealed that <i>N. cinerea</i> isolates from the general population (<i>n</i>=3, cluster one) were distinct from those obtained from men who have sex with men (MSM, <i>n</i>=2, cluster two). The latter contained genomes misidentified as <i>N. meningitidis</i> using MALDI-TOF MS. These two <i>N. cinerea</i> clusters persisted after the inclusion of published <i>N. cinerea</i> WGS (<i>n</i>=42). Both <i>N. cinerea</i> clusters were further defined through pangenome and Average Nucleotide Identity (ANI) analyses.<b>Conclusion.</b> This study provides insights into the importance of genomic genus-wide <i>Neisseria</i> surveillance studies to improve the characterization and identification of the <i>Neisseria</i> genus.</p>","PeriodicalId":94093,"journal":{"name":"Journal of medical microbiology","volume":"73 8","pages":""},"PeriodicalIF":0.0000,"publicationDate":"2024-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":"{\"title\":\"Genomic oropharyngeal <i>Neisseria</i> surveillance detects MALDI-TOF MS species misidentifications and reveals a novel <i>Neisseria cinerea</i> clade.\",\"authors\":\"Tessa de Block, Irith De Baetselier, Dorien Van den Bossche, Saïd Abdellati, Zina Gestels, Jolein Gyonne Elise Laumen, Christophe Van Dijck, Thibaut Vanbaelen, Nathalie Claes, Koen Vandelannoote, Chris Kenyon, Odile Harrison, Sheeba Santhini Manoharan-Basil\",\"doi\":\"10.1099/jmm.0.001871\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<p><p><b>Introduction.</b> Commensal <i>Neisseria</i> spp. are highly prevalent in the oropharynx as part of the healthy microbiome. <i>N. meningitidis</i> can colonise the oropharynx too from where it can cause invasive meningococcal disease. To identify <i>N. meningitidis</i>, clinical microbiology laboratories often rely on Matrix Assisted Laser Desorption/Ionisation Time of Flight Mass Spectrometry (MALDI-TOF MS).<b>Hypothesis/Gap statement.</b> <i>N. meningitidis</i> may be misidentified by MALDI-TOF MS.<b>Aim.</b> To conduct genomic surveillance of oropharyngeal <i>Neisseria</i> spp. in order to: (i) verify MALDI-TOF MS species identification, and (ii) characterize commensal <i>Neisseria</i> spp. genomes.<b>Methodology.</b> We analysed whole genome sequence (WGS) data from 119 <i>Neisseria</i> spp. isolates from a surveillance programme for oropharyngeal <i>Neisseria</i> spp. in Belgium. Different species identification methods were compared: (i) MALDI-TOF MS, (ii) Ribosomal Multilocus Sequence Typing (rMLST) and (iii) <i>rplF</i> gene species identification. WGS data were used to further characterize <i>Neisseria</i> species found with supplementary analyses of <i>Neisseria cinerea</i> genomes.<b>Results.</b> Based on genomic species identification, isolates from the oropharyngeal <i>Neisseria</i> surveilence study were composed of the following species: <i>N. meningitidis</i> (<i>n</i>=23)<i>, N. subflava</i> (<i>n</i>=61), <i>N. mucosa</i> (<i>n</i>=15), <i>N. oralis</i> (<i>n</i>=8), <i>N. cinerea</i> (<i>n</i>=5), <i>N. elongata</i> (<i>n</i>=3), <i>N. lactamica</i> (<i>n</i>=2), <i>N. bacilliformis</i> (<i>n</i>=1) and <i>N. polysaccharea</i> (<i>n</i>=1). Of these 119 isolates, four isolates identified as <i>N. meningitidis</i> (<i>n</i>=3) and <i>N. subflava</i> (<i>n</i>=1) by MALDI-TOF MS<i>,</i> were determined to be <i>N. polysaccharea</i> (<i>n</i>=1)<i>, N. cinerea</i> (<i>n</i>=2) and <i>N. mucosa</i> (<i>n</i>=1) by rMLST. Phylogenetic analyses revealed that <i>N. cinerea</i> isolates from the general population (<i>n</i>=3, cluster one) were distinct from those obtained from men who have sex with men (MSM, <i>n</i>=2, cluster two). The latter contained genomes misidentified as <i>N. meningitidis</i> using MALDI-TOF MS. These two <i>N. cinerea</i> clusters persisted after the inclusion of published <i>N. cinerea</i> WGS (<i>n</i>=42). Both <i>N. cinerea</i> clusters were further defined through pangenome and Average Nucleotide Identity (ANI) analyses.<b>Conclusion.</b> This study provides insights into the importance of genomic genus-wide <i>Neisseria</i> surveillance studies to improve the characterization and identification of the <i>Neisseria</i> genus.</p>\",\"PeriodicalId\":94093,\"journal\":{\"name\":\"Journal of medical microbiology\",\"volume\":\"73 8\",\"pages\":\"\"},\"PeriodicalIF\":0.0000,\"publicationDate\":\"2024-08-01\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Journal of medical microbiology\",\"FirstCategoryId\":\"1085\",\"ListUrlMain\":\"https://doi.org/10.1099/jmm.0.001871\",\"RegionNum\":0,\"RegionCategory\":null,\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"\",\"JCRName\":\"\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Journal of medical microbiology","FirstCategoryId":"1085","ListUrlMain":"https://doi.org/10.1099/jmm.0.001871","RegionNum":0,"RegionCategory":null,"ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"","JCRName":"","Score":null,"Total":0}
引用次数: 0
摘要
简介。作为健康微生物群的一部分，共生奈瑟氏菌在口咽部非常普遍。脑膜炎奈瑟菌也可在口咽部定植，并在口咽部引起侵袭性脑膜炎球菌疾病。临床微生物实验室通常使用基质辅助激光解吸/电离飞行时间质谱法（MALDI-TOF MS）来鉴定脑膜炎双球菌。脑膜炎双球菌可能会被 MALDI-TOF MS 错误识别。对口咽奈瑟菌属进行基因组监测，以便(i)验证 MALDI-TOF MS 的物种鉴定，(ii)确定共生奈瑟氏菌属基因组的特征。我们分析了来自比利时口咽奈瑟菌属监测计划的 119 株奈瑟菌属分离物的全基因组序列（WGS）数据。比较了不同的物种鉴定方法：(i) MALDI-TOF MS，(ii) 核糖体多焦点序列分型（rMLST）和 (iii) rplF 基因物种鉴定。利用 WGS 数据进一步确定了所发现的奈瑟菌种的特征，并对奈瑟菌基因组进行了补充分析。根据基因组物种鉴定，从口咽奈瑟菌调查研究中分离的奈瑟菌由以下物种组成：脑膜炎奈瑟菌（n=23）、亚弗拉伐奈瑟菌（n=61）、粘膜奈瑟菌（n=15）、口腔奈瑟菌（n=8）、细小奈瑟菌（n=5）、细长奈瑟菌（n=3）、内酰胺奈瑟菌（n=2）、棒状奈瑟菌（n=1）和多形奈瑟菌（n=1）。在这 119 个分离物中，有 4 个分离物通过 MALDI-TOF MS 鉴定为脑膜炎双球菌（n=3）和亚弗拉伐双球菌（n=1），而通过 rMLST 鉴定为多发性脑膜炎双球菌（n=1）、糜烂性脑膜炎双球菌（n=2）和粘液性脑膜炎双球菌（n=1）。系统发育分析表明，来自普通人群的 N. cinerea 分离物（n=3，第一群组）与来自男男性行为者（MSM，n=2，第二群组）的分离物截然不同。后者包含的基因组被 MALDI-TOF MS 误认为是脑膜炎球菌。在纳入已发表的 N. cinerea WGS（n=42）后，这两个 N. cinerea 群体仍然存在。通过pangenome和平均核苷酸同一性（ANI）分析，这两个N. cinerea聚类得到了进一步界定。本研究深入探讨了全基因组奈瑟菌属监测研究对改进奈瑟菌属特征描述和鉴定的重要性。
Genomic oropharyngeal Neisseria surveillance detects MALDI-TOF MS species misidentifications and reveals a novel Neisseria cinerea clade.
Introduction. Commensal Neisseria spp. are highly prevalent in the oropharynx as part of the healthy microbiome. N. meningitidis can colonise the oropharynx too from where it can cause invasive meningococcal disease. To identify N. meningitidis, clinical microbiology laboratories often rely on Matrix Assisted Laser Desorption/Ionisation Time of Flight Mass Spectrometry (MALDI-TOF MS).Hypothesis/Gap statement.N. meningitidis may be misidentified by MALDI-TOF MS.Aim. To conduct genomic surveillance of oropharyngeal Neisseria spp. in order to: (i) verify MALDI-TOF MS species identification, and (ii) characterize commensal Neisseria spp. genomes.Methodology. We analysed whole genome sequence (WGS) data from 119 Neisseria spp. isolates from a surveillance programme for oropharyngeal Neisseria spp. in Belgium. Different species identification methods were compared: (i) MALDI-TOF MS, (ii) Ribosomal Multilocus Sequence Typing (rMLST) and (iii) rplF gene species identification. WGS data were used to further characterize Neisseria species found with supplementary analyses of Neisseria cinerea genomes.Results. Based on genomic species identification, isolates from the oropharyngeal Neisseria surveilence study were composed of the following species: N. meningitidis (n=23), N. subflava (n=61), N. mucosa (n=15), N. oralis (n=8), N. cinerea (n=5), N. elongata (n=3), N. lactamica (n=2), N. bacilliformis (n=1) and N. polysaccharea (n=1). Of these 119 isolates, four isolates identified as N. meningitidis (n=3) and N. subflava (n=1) by MALDI-TOF MS, were determined to be N. polysaccharea (n=1), N. cinerea (n=2) and N. mucosa (n=1) by rMLST. Phylogenetic analyses revealed that N. cinerea isolates from the general population (n=3, cluster one) were distinct from those obtained from men who have sex with men (MSM, n=2, cluster two). The latter contained genomes misidentified as N. meningitidis using MALDI-TOF MS. These two N. cinerea clusters persisted after the inclusion of published N. cinerea WGS (n=42). Both N. cinerea clusters were further defined through pangenome and Average Nucleotide Identity (ANI) analyses.Conclusion. This study provides insights into the importance of genomic genus-wide Neisseria surveillance studies to improve the characterization and identification of the Neisseria genus.
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