Next Article in Journal
Generation and Characterization of Native and Sialic Acid-Deficient IgE
Next Article in Special Issue
The Effect of Proline on the Freeze-Drying Survival Rate of Bifidobacterium longum CCFM 1029 and Its Inherent Mechanism
Previous Article in Journal
EGFR T751_I759delinsN Mutation in Exon19 Detected by NGS but Not by Real-Time PCR in a Heavily-Treated Patient with NSCLC
Previous Article in Special Issue
Helminths and Bacterial Microbiota: The Interactions of Two of Humans’ “Old Friends”
 
 
Search for Articles:
Title / Keyword
Author / Affiliation / Email
Journal
Article Type
 
 
Advanced Search
 
Section
Special Issue
Volume
Issue
Number
Page
 
Journals
IJMS
Volume 23
Issue 21
10.3390/ijms232113456
ijms-logo
Submit to this Journal Review for this Journal Propose a Special Issue
► Article Menu

Article Menu

share Share announcement Help format_quote Cite question_answer Discuss in SciProfiles
first_page
settings
Order Article Reprints
Font Type:
Arial Georgia Verdana
Font Size:
Aa Aa Aa
Line Spacing:
Column Width:
Background:
Article

Whole Genome Analyses Accurately Identify Neisseria spp. and Limit Taxonomic Ambiguity

by
May Khoder
1,2,†,
Marwan Osman
3,4,*,†,
Issmat I. Kassem
5,
Rayane Rafei
1,
Ahmad Shahin
1,
Pierre Edouard Fournier
2,
Jean-Marc Rolain
2 and
Monzer Hamze
1
1
Laboratoire Microbiologie, Santé et Environnement (LMSE), Doctoral School of Sciences and Technology, Faculty of Public Health, Lebanese University, Tripoli 1300, Lebanon
2
Institut de Recherche pour le Développement (IRD), Microbes, Evolution, Phylogénie et Infection (MEPHI), Faculté de Médecine et de Pharmacie, Aix Marseille Université, 13005 Marseille, France
3
Cornell Atkinson Center for Sustainability, Cornell University, Ithaca, NY 14853, USA
4
Department of Public and Ecosystem Health, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
5
Center for Food Safety, Department of Food Science and Technology, University of Georgia, Griffin, GA 30223-1797, USA
*
Author to whom correspondence should be addressed.
†
These authors contribute equally to this work.
Int. J. Mol. Sci. 2022, 23(21), 13456; https://doi.org/10.3390/ijms232113456
Submission received: 26 September 2022 / Revised: 26 October 2022 / Accepted: 2 November 2022 / Published: 3 November 2022
(This article belongs to the Collection Feature Papers in Molecular Microbiology)
Browse Figures
Review Reports Versions Notes

Abstract

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 Neisseria clinical isolates from the semen of infertile Lebanese men. To determine the phylogenetic relationships among these strains and other Neisseria spp. and to confirm their identity at the genomic level, we compared the genomes of these four isolates with the complete genome sequences of Neisseria gonorrhoeae and Neisseria meningitidis and the draft genomes of Neisseria flavescens, Neisseria perflava, Neisseria mucosa, and Neisseria macacae 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 Neisseria 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 Neisseria 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.
Keywords: Neisseria spp.; identification; whole genome sequencing; taxonomy Neisseria spp.; identification; whole genome sequencing; taxonomy

Share and Cite

MDPI and ACS Style

Khoder, M.; Osman, M.; Kassem, I.I.; Rafei, R.; Shahin, A.; Fournier, P.E.; Rolain, J.-M.; Hamze, M. Whole Genome Analyses Accurately Identify Neisseria spp. and Limit Taxonomic Ambiguity. Int. J. Mol. Sci. 2022, 23, 13456. https://doi.org/10.3390/ijms232113456

AMA Style

Khoder M, Osman M, Kassem II, Rafei R, Shahin A, Fournier PE, Rolain J-M, Hamze M. Whole Genome Analyses Accurately Identify Neisseria spp. and Limit Taxonomic Ambiguity. International Journal of Molecular Sciences. 2022; 23(21):13456. https://doi.org/10.3390/ijms232113456

Chicago/Turabian Style

Khoder, May, Marwan Osman, Issmat I. Kassem, Rayane Rafei, Ahmad Shahin, Pierre Edouard Fournier, Jean-Marc Rolain, and Monzer Hamze. 2022. "Whole Genome Analyses Accurately Identify Neisseria spp. and Limit Taxonomic Ambiguity" International Journal of Molecular Sciences 23, no. 21: 13456. https://doi.org/10.3390/ijms232113456

APA Style

Khoder, M., Osman, M., Kassem, I. I., Rafei, R., Shahin, A., Fournier, P. E., Rolain, J.-M., & Hamze, M. (2022). Whole Genome Analyses Accurately Identify Neisseria spp. and Limit Taxonomic Ambiguity. International Journal of Molecular Sciences, 23(21), 13456. https://doi.org/10.3390/ijms232113456

Note that from the first issue of 2016, this journal uses article numbers instead of page numbers. See further details here.

Article Metrics

Back to TopTop