Whole Genome Analyses Accurately Identify <i>Neisseria</i> spp. and Limit Taxonomic Ambiguity
Genome sequencing facilitates the study of bacterial taxonomy and allows the re-evaluation of the taxonomic relationships between species. Here, we aimed to analyze the draft genomes of four commensal <i>Neisseria</i> clinical isolates from the semen of infertile Lebanese men. To determi...
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| Format: | Article |
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MDPI AG
2022-11-01
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| Series: | International Journal of Molecular Sciences |
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| Online Access: | https://www.mdpi.com/1422-0067/23/21/13456 |
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| author | May Khoder Marwan Osman Issmat I. Kassem Rayane Rafei Ahmad Shahin Pierre Edouard Fournier Jean-Marc Rolain Monzer Hamze |
| author_facet | May Khoder Marwan Osman Issmat I. Kassem Rayane Rafei Ahmad Shahin Pierre Edouard Fournier Jean-Marc Rolain Monzer Hamze |
| author_sort | May Khoder |
| collection | DOAJ |
| description | Genome sequencing facilitates the study of bacterial taxonomy and allows the re-evaluation of the taxonomic relationships between species. Here, we aimed to analyze the draft genomes of four commensal <i>Neisseria</i> clinical isolates from the semen of infertile Lebanese men. To determine the phylogenetic relationships among these strains and other <i>Neisseria</i> spp. and to confirm their identity at the genomic level, we compared the genomes of these four isolates with the complete genome sequences of <i>Neisseria gonorrhoeae</i> and <i>Neisseria meningitidis</i> and the draft genomes of <i>Neisseria flavescens</i>, <i>Neisseria perflava</i>, <i>Neisseria mucosa</i>, and <i>Neisseria macacae</i> that are available in the NCBI Genbank database. Our findings revealed that the WGS analysis accurately identified and corroborated the matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) species identities of the <i>Neisseria</i> isolates. The combination of three well-established genome-based taxonomic tools (in silico DNA-DNA Hybridization, Ortho Average Nucleotide identity, and pangenomic studies) proved to be relatively the best identification approach. Notably, we also discovered that some <i>Neisseria</i> strains that are deposited in databases contain many taxonomical errors. The latter is very important and must be addressed to prevent misdiagnosis and missing emerging etiologies. We also highlight the need for robust cut-offs to delineate the species using genomic tools. |
| first_indexed | 2024-03-09T18:59:44Z |
| format | Article |
| id | doaj.art-8dbc2422ef884bfd8021430b65fff7ba |
| institution | Directory Open Access Journal |
| issn | 1661-6596 1422-0067 |
| language | English |
| last_indexed | 2024-03-09T18:59:44Z |
| publishDate | 2022-11-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | International Journal of Molecular Sciences |
| spelling | doaj.art-8dbc2422ef884bfd8021430b65fff7ba2023-11-24T05:08:13ZengMDPI AGInternational Journal of Molecular Sciences1661-65961422-00672022-11-0123211345610.3390/ijms232113456Whole Genome Analyses Accurately Identify <i>Neisseria</i> spp. and Limit Taxonomic AmbiguityMay Khoder0Marwan Osman1Issmat I. Kassem2Rayane Rafei3Ahmad Shahin4Pierre Edouard Fournier5Jean-Marc Rolain6Monzer Hamze7Laboratoire Microbiologie, Santé et Environnement (LMSE), Doctoral School of Sciences and Technology, Faculty of Public Health, Lebanese University, Tripoli 1300, LebanonCornell Atkinson Center for Sustainability, Cornell University, Ithaca, NY 14853, USACenter for Food Safety, Department of Food Science and Technology, University of Georgia, Griffin, GA 30223-1797, USALaboratoire Microbiologie, Santé et Environnement (LMSE), Doctoral School of Sciences and Technology, Faculty of Public Health, Lebanese University, Tripoli 1300, LebanonLaboratoire Microbiologie, Santé et Environnement (LMSE), Doctoral School of Sciences and Technology, Faculty of Public Health, Lebanese University, Tripoli 1300, LebanonInstitut de Recherche pour le Développement (IRD), Microbes, Evolution, Phylogénie et Infection (MEPHI), Faculté de Médecine et de Pharmacie, Aix Marseille Université, 13005 Marseille, FranceInstitut de Recherche pour le Développement (IRD), Microbes, Evolution, Phylogénie et Infection (MEPHI), Faculté de Médecine et de Pharmacie, Aix Marseille Université, 13005 Marseille, FranceLaboratoire Microbiologie, Santé et Environnement (LMSE), Doctoral School of Sciences and Technology, Faculty of Public Health, Lebanese University, Tripoli 1300, LebanonGenome sequencing facilitates the study of bacterial taxonomy and allows the re-evaluation of the taxonomic relationships between species. Here, we aimed to analyze the draft genomes of four commensal <i>Neisseria</i> clinical isolates from the semen of infertile Lebanese men. To determine the phylogenetic relationships among these strains and other <i>Neisseria</i> spp. and to confirm their identity at the genomic level, we compared the genomes of these four isolates with the complete genome sequences of <i>Neisseria gonorrhoeae</i> and <i>Neisseria meningitidis</i> and the draft genomes of <i>Neisseria flavescens</i>, <i>Neisseria perflava</i>, <i>Neisseria mucosa</i>, and <i>Neisseria macacae</i> that are available in the NCBI Genbank database. Our findings revealed that the WGS analysis accurately identified and corroborated the matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) species identities of the <i>Neisseria</i> isolates. The combination of three well-established genome-based taxonomic tools (in silico DNA-DNA Hybridization, Ortho Average Nucleotide identity, and pangenomic studies) proved to be relatively the best identification approach. Notably, we also discovered that some <i>Neisseria</i> strains that are deposited in databases contain many taxonomical errors. The latter is very important and must be addressed to prevent misdiagnosis and missing emerging etiologies. We also highlight the need for robust cut-offs to delineate the species using genomic tools.https://www.mdpi.com/1422-0067/23/21/13456<i>Neisseria</i> spp.identificationwhole genome sequencingtaxonomy |
| spellingShingle | May Khoder Marwan Osman Issmat I. Kassem Rayane Rafei Ahmad Shahin Pierre Edouard Fournier Jean-Marc Rolain Monzer Hamze Whole Genome Analyses Accurately Identify <i>Neisseria</i> spp. and Limit Taxonomic Ambiguity International Journal of Molecular Sciences <i>Neisseria</i> spp. identification whole genome sequencing taxonomy |
| title | Whole Genome Analyses Accurately Identify <i>Neisseria</i> spp. and Limit Taxonomic Ambiguity |
| title_full | Whole Genome Analyses Accurately Identify <i>Neisseria</i> spp. and Limit Taxonomic Ambiguity |
| title_fullStr | Whole Genome Analyses Accurately Identify <i>Neisseria</i> spp. and Limit Taxonomic Ambiguity |
| title_full_unstemmed | Whole Genome Analyses Accurately Identify <i>Neisseria</i> spp. and Limit Taxonomic Ambiguity |
| title_short | Whole Genome Analyses Accurately Identify <i>Neisseria</i> spp. and Limit Taxonomic Ambiguity |
| title_sort | whole genome analyses accurately identify i neisseria i spp and limit taxonomic ambiguity |
| topic | <i>Neisseria</i> spp. identification whole genome sequencing taxonomy |
| url | https://www.mdpi.com/1422-0067/23/21/13456 |
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