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de Block T, De Baetselier I, Van den Bossche D, Abdellati S, Gestels Z, Laumen JGE, Van Dijck C, Vanbaelen T, Claes N, Vandelannoote K, Kenyon C, Harrison O, Santhini Manoharan-Basil S. Genomic oropharyngeal Neisseria surveillance detects MALDI-TOF MS species misidentifications and reveals a novel Neisseria cinerea clade. J Med Microbiol 2024; 73. [PMID: 39212029 DOI: 10.1099/jmm.0.001871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/04/2024] Open
Abstract
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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Affiliation(s)
- Tessa de Block
- Department of Clinical Sciences, Institute of Tropical Medicine, 2000 Antwerp, Belgium
| | - Irith De Baetselier
- Department of Clinical Sciences, Institute of Tropical Medicine, 2000 Antwerp, Belgium
| | | | - Saïd Abdellati
- Department of Clinical Sciences, Institute of Tropical Medicine, 2000 Antwerp, Belgium
| | - Zina Gestels
- Department of Clinical Sciences, Institute of Tropical Medicine, 2000 Antwerp, Belgium
| | | | - Christophe Van Dijck
- Department of Clinical Sciences, Institute of Tropical Medicine, 2000 Antwerp, Belgium
| | - Thibaut Vanbaelen
- Department of Clinical Sciences, Institute of Tropical Medicine, 2000 Antwerp, Belgium
| | - Nathalie Claes
- EMAT, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium
| | - Koen Vandelannoote
- Bacterial Phylogenomics group, Institut Pasteur du Cambodge, Phnom Penh, Cambodia
| | - Chris Kenyon
- Department of Clinical Sciences, Institute of Tropical Medicine, 2000 Antwerp, Belgium
| | - Odile Harrison
- Nuffield Department of Population Health, Infectious Diseases Epidemiology Unit, University of Oxford, Oxford, UK
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Walsh L, Clark SA, Derrick JP, Borrow R. Beyond the usual suspects: Reviewing infections caused by typically-commensal Neisseria species. J Infect 2023; 87:479-489. [PMID: 37797844 DOI: 10.1016/j.jinf.2023.09.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 07/27/2023] [Accepted: 09/22/2023] [Indexed: 10/07/2023]
Abstract
OBJECTIVE Few data outside of individual case reports are available on non-meningococcal, non-gonococcal species of Neisseria as causative agents of invasive disease. This review collates disease, organism and patient information from case reports on the topic. METHODS A literature search was performed examining articles describing diseases caused by non-meningococcal and non-gonococcal Neisseria. FINDINGS Neisseria present as opportunistic pathogens causing a wide variety of diseases including serious presentations, endocarditis being the most common condition described and N. mucosa the most commonly presenting pathogen overall. Disease may occur in otherwise healthy patients, although risk factors for infection include recent surgery, an immunocompromised state, poor oral health, and intravenous drug use. CONCLUSIONS Commensal Neisseria infections are rare but can present serious invasive diseases. Further research is required to determine why some species cause disease more than others or why some are inclined towards particular manifestations.
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Affiliation(s)
- Lloyd Walsh
- Meningococcal Reference Unit, UK Health Security Agency, Manchester M13 9WL, United Kingdom.
| | - Stephen A Clark
- Meningococcal Reference Unit, UK Health Security Agency, Manchester M13 9WL, United Kingdom
| | - Jeremy P Derrick
- School of Biological Sciences, Faculty of Biology, Medicine, and Health, University of Manchester, Manchester M13 9PL, United Kingdom
| | - Ray Borrow
- Meningococcal Reference Unit, UK Health Security Agency, Manchester M13 9WL, United Kingdom
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3
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Asturias EJ, Bai X, Bettinger JA, Borrow R, Castillo DN, Caugant DA, Chacon GC, Dinleyici EC, Echaniz-Aviles G, Garcia L, Glennie L, Harrison LH, Howie RL, Itsko M, Lucidarme J, Marin JEO, Marjuki H, McNamara LA, Mustapha MM, Robinson JL, Romeu B, Sadarangani M, Sáez-Llorens X, Sáfadi MAP, Stephens DS, Stuart JM, Taha MK, Tsang RSW, Vazquez J, De Wals P. Meningococcal disease in North America: Updates from the Global Meningococcal Initiative. J Infect 2022; 85:611-622. [PMID: 36273639 PMCID: PMC11091909 DOI: 10.1016/j.jinf.2022.10.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 10/11/2022] [Accepted: 10/16/2022] [Indexed: 11/06/2022]
Abstract
This review summarizes the recent Global Meningococcal Initiative (GMI) regional meeting, which explored meningococcal disease in North America. Invasive meningococcal disease (IMD) cases are documented through both passive and active surveillance networks. IMD appears to be decreasing in many areas, such as the Dominican Republic (2016: 18 cases; 2021: 2 cases) and Panama (2008: 1 case/100,000; 2021: <0.1 cases/100,000); however, there is notable regional and temporal variation. Outbreaks persist in at-risk subpopulations, such as people experiencing homelessness in the US and migrants in Mexico. The recent emergence of β-lactamase-positive and ciprofloxacin-resistant meningococci in the US is a major concern. While vaccination practices vary across North America, vaccine uptake remains relatively high. Monovalent and multivalent conjugate vaccines (which many countries in North America primarily use) can provide herd protection. However, there is no evidence that group B vaccines reduce meningococcal carriage. The coronavirus pandemic illustrates that following public health crises, enhanced surveillance of disease epidemiology and catch-up vaccine schedules is key. Whole genome sequencing is a key epidemiological tool for identifying IMD strain emergence and the evaluation of vaccine strain coverage. The Global Roadmap on Defeating Meningitis by 2030 remains a focus of the GMI.
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Affiliation(s)
- Edwin J Asturias
- University of Colorado School of Medicine and Colorado School of Public Health, Aurora, CO, USA
| | - Xilian Bai
- Meningococcal Reference Unit, UK Health Security Agency, Manchester, UK
| | - Julie A Bettinger
- Vaccine Evaluation Center, British Colombia Children's Hospital Research Institute, and Department of Pediatrics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Ray Borrow
- Meningococcal Reference Unit, UK Health Security Agency, Manchester, UK.
| | | | | | | | | | - Gabriela Echaniz-Aviles
- Center for Research on Infectious Diseases, Instituto Nacional de Salud Pública, Cuernavaca, Mexico
| | - Luis Garcia
- Center for State Control of Drugs, Medical Devices and Equipment, Cuba
| | | | - Lee H Harrison
- Center for Genomic Epidemiology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Rebecca L Howie
- Meningitis and Vaccine Preventable Diseases Branch, Division of Bacterial Diseases, Centers for Disease Control and Prevention, USA
| | - Mark Itsko
- WDS Inc., Contractor to Meningitis and Vaccine Preventable Diseases Branch, Division of Bacterial Diseases, Centers for Disease Control and Prevention, USA
| | - Jay Lucidarme
- Meningococcal Reference Unit, UK Health Security Agency, Manchester, UK
| | | | - Henju Marjuki
- Meningitis and Vaccine Preventable Diseases Branch, Division of Bacterial Diseases, Centers for Disease Control and Prevention, USA
| | - Lucy A McNamara
- Meningitis and Vaccine Preventable Diseases Branch, Division of Bacterial Diseases, Centers for Disease Control and Prevention, USA
| | | | | | - Belkis Romeu
- Center for State Control of Drugs, Medical Devices and Equipment, Cuba
| | - Manish Sadarangani
- Vaccine Evaluation Center, British Colombia Children's Hospital Research Institute, and Department of Pediatrics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Xavier Sáez-Llorens
- Hospital del Niño - Dr José Renán Esquivel, Distinguished Investigator at Senacyt (SNI) and Cevaxin, Panama City, Panama
| | - Marco A P Sáfadi
- Department of Pediatrics, Santa Casa de São Paulo School of Medical Sciences, São Paulo, Brazil
| | - David S Stephens
- Robert W. Woodruff Health Sciences Center, Emory University, Atlanta, GA, USA
| | | | - Muhamed-Kheir Taha
- Institut Pasteur, National Reference Centre for Meningococci and Haemophilus influenzae, Paris, France
| | - Raymond S W Tsang
- National Microbiology Laboratory Branch, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Julio Vazquez
- National Centre of Microbiology, Institute of Health Carlos III, Madrid, Spain
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Sarkar I, Dey P, Rathore SS, Singh GD, Singh RP. Global genomic and proteomic analysis indicates co-evolution of Neisseria species and with their human host. World J Microbiol Biotechnol 2022; 38:149. [PMID: 35773545 DOI: 10.1007/s11274-022-03338-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 06/11/2022] [Indexed: 11/30/2022]
Abstract
Neisseria, a genus from the beta-proteobacteria class, is of potential clinical importance. This genus contains both pathogenic and commensal strains. Gonorrhea and meningitis are two major diseases caused by pathogens belonging to this genus. With the increased use of antimicrobial agents against these pathogens they have evolved the antimicrobial resistance capacity making these diseases nearly untreatable. The set of anti-bacterial resistance genes (resistome) and genes associated with signal processing (secretomes) are crucial for the host-microbial interaction. With the virtue of whole-genome sequences and computational biology, it is now possible to study the genomic and proteomic riddles of Neisseria along with their comprehensive evolutionary and metabolic profiling. We have studied relative synonymous codon usage, amino acid usage, reverse ecology, comparative genomics, evolutionary analysis and pathogen-host (Neisseria-human) interaction through bioinformatics analysis. Our analysis revealed the co-evolution of Neisseria genomes with the human host. Moreover, the co-occurrence of Neisseria and humans has been supported through reverse ecology analysis. A differential pattern of the evolutionary rate of resistomes and secretomes was evident among the pathogenic and commensal strains. Comparative genomics supported the presence of virulent genes in both pathogenic and commensal strains of the select genus. Our analysis also indicated a transition from commensal to pathogenic Neisseria strains through the long run of evolution.
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Affiliation(s)
- Indrani Sarkar
- Salim Ali Centre for Ornithology and Natural History, Anaikatty, Coimbatore, Tamil Nadu, 641 108, India
| | - Prateek Dey
- Salim Ali Centre for Ornithology and Natural History, Anaikatty, Coimbatore, Tamil Nadu, 641 108, India
| | | | | | - Ram Pratap Singh
- Department of Life Science, Central University of South Bihar, Gaya, Bihar, 824236, India.
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Orazi G, Collins AJ, Whitaker RJ. Prediction of Prophages and Their Host Ranges in Pathogenic and Commensal Neisseria Species. mSystems 2022; 7:e0008322. [PMID: 35418239 PMCID: PMC9238386 DOI: 10.1128/msystems.00083-22] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2022] [Accepted: 03/24/2022] [Indexed: 01/03/2023] Open
Abstract
The genus Neisseria includes two pathogenic species, N. gonorrhoeae and N. meningitidis, and numerous commensal species. Neisseria species frequently exchange DNA with one another, primarily via transformation and homologous recombination and via multiple types of mobile genetic elements (MGEs). Few Neisseria bacteriophages (phages) have been identified, and their impact on bacterial physiology is poorly understood. Furthermore, little is known about the range of species that Neisseria phages can infect. In this study, we used three virus prediction tools to scan 248 genomes of 21 different Neisseria species and identified 1,302 unique predicted prophages. Using comparative genomics, we found that many predictions are dissimilar from prophages and other MGEs previously described to infect Neisseria species. We also identified similar predicted prophages in genomes of different Neisseria species. Additionally, we examined CRISPR-Cas targeting of each Neisseria genome and predicted prophage. While CRISPR targeting of chromosomal DNA appears to be common among several Neisseria species, we found that 20% of the prophages we predicted are targeted significantly more than the rest of the bacterial genome in which they were identified (i.e., backbone). Furthermore, many predicted prophages are targeted by CRISPR spacers encoded by other species. We then used these results to infer additional host species of known Neisseria prophages and predictions that are highly targeted relative to the backbone. Together, our results suggest that we have identified novel Neisseria prophages, several of which may infect multiple Neisseria species. These findings have important implications for understanding horizontal gene transfer between members of this genus. IMPORTANCE Drug-resistant Neisseria gonorrhoeae is a major threat to human health. Commensal Neisseria species are thought to serve as reservoirs of antibiotic resistance and virulence genes for the pathogenic species N. gonorrhoeae and N. meningitidis. Therefore, it is important to understand both the diversity of mobile genetic elements (MGEs) that can mediate horizontal gene transfer within this genus and the breadth of species these MGEs can infect. In particular, few bacteriophages (phages) are known to infect Neisseria species. In this study, we identified a large number of candidate phages integrated in the genomes of commensal and pathogenic Neisseria species, many of which appear to be novel phages. Importantly, we discovered extensive interspecies targeting of predicted phages by Neisseria CRISPR-Cas systems, which may reflect their movement between different species. Uncovering the diversity and host range of phages is essential for understanding how they influence the evolution of their microbial hosts.
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Affiliation(s)
- Giulia Orazi
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Alan J. Collins
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Rachel J. Whitaker
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
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Calder A, Menkiti CJ, Çağdaş A, Lisboa Santos J, Streich R, Wong A, Avini AH, Bojang E, Yogamanoharan K, Sivanesan N, Ali B, Ashrafi M, Issa A, Kaur T, Latif A, Mohamed HAS, Maqsood A, Tamang L, Swager E, Stringer AJ, Snyder LAS. Virulence genes and previously unexplored gene clusters in four commensal Neisseria spp. isolated from the human throat expand the neisserial gene repertoire. Microb Genom 2020; 6. [PMID: 32845827 PMCID: PMC7643975 DOI: 10.1099/mgen.0.000423] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Commensal non-pathogenic Neisseria spp. live within the human host alongside the pathogenic Neisseria meningitidis and Neisseria gonorrhoeae and due to natural competence, horizontal gene transfer within the genus is possible and has been observed. Four distinct Neisseria spp. isolates taken from the throats of two human volunteers have been assessed here using a combination of microbiological and bioinformatics techniques. Three of the isolates have been identified as Neisseria subflava biovar perflava and one as Neisseria cinerea. Specific gene clusters have been identified within these commensal isolate genome sequences that are believed to encode a Type VI Secretion System, a newly identified CRISPR system, a Type IV Secretion System unlike that in other Neisseria spp., a hemin transporter, and a haem acquisition and utilization system. This investigation is the first to investigate these systems in either the non-pathogenic or pathogenic Neisseria spp. In addition, the N. subflava biovar perflava possess previously unreported capsule loci and sequences have been identified in all four isolates that are similar to genes seen within the pathogens that are associated with virulence. These data from the four commensal isolates provide further evidence for a Neisseria spp. gene pool and highlight the presence of systems within the commensals with functions still to be explored.
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Affiliation(s)
- Alan Calder
- School of Life Sciences, Pharmacy, and Chemistry, Kingston University, Kingston upon Thames, KT1 2EE, UK
| | - Chukwuma Jude Menkiti
- School of Life Sciences, Pharmacy, and Chemistry, Kingston University, Kingston upon Thames, KT1 2EE, UK
| | - Aylin Çağdaş
- School of Life Sciences, Pharmacy, and Chemistry, Kingston University, Kingston upon Thames, KT1 2EE, UK
| | - Jefferson Lisboa Santos
- School of Life Sciences, Pharmacy, and Chemistry, Kingston University, Kingston upon Thames, KT1 2EE, UK
| | - Ricarda Streich
- School of Life Sciences, Pharmacy, and Chemistry, Kingston University, Kingston upon Thames, KT1 2EE, UK
| | - Alice Wong
- School of Life Sciences, Pharmacy, and Chemistry, Kingston University, Kingston upon Thames, KT1 2EE, UK
| | - Amir H Avini
- School of Life Sciences, Pharmacy, and Chemistry, Kingston University, Kingston upon Thames, KT1 2EE, UK
| | - Ebrima Bojang
- School of Life Sciences, Pharmacy, and Chemistry, Kingston University, Kingston upon Thames, KT1 2EE, UK
| | - Karththeepan Yogamanoharan
- School of Life Sciences, Pharmacy, and Chemistry, Kingston University, Kingston upon Thames, KT1 2EE, UK
| | - Nivetha Sivanesan
- School of Life Sciences, Pharmacy, and Chemistry, Kingston University, Kingston upon Thames, KT1 2EE, UK
| | - Besma Ali
- School of Life Sciences, Pharmacy, and Chemistry, Kingston University, Kingston upon Thames, KT1 2EE, UK
| | - Mariam Ashrafi
- School of Life Sciences, Pharmacy, and Chemistry, Kingston University, Kingston upon Thames, KT1 2EE, UK
| | - Abdirizak Issa
- School of Life Sciences, Pharmacy, and Chemistry, Kingston University, Kingston upon Thames, KT1 2EE, UK
| | - Tajinder Kaur
- School of Life Sciences, Pharmacy, and Chemistry, Kingston University, Kingston upon Thames, KT1 2EE, UK
| | - Aisha Latif
- School of Life Sciences, Pharmacy, and Chemistry, Kingston University, Kingston upon Thames, KT1 2EE, UK
| | - Hani A Sheik Mohamed
- School of Life Sciences, Pharmacy, and Chemistry, Kingston University, Kingston upon Thames, KT1 2EE, UK
| | - Atifa Maqsood
- School of Life Sciences, Pharmacy, and Chemistry, Kingston University, Kingston upon Thames, KT1 2EE, UK
| | - Laxmi Tamang
- School of Life Sciences, Pharmacy, and Chemistry, Kingston University, Kingston upon Thames, KT1 2EE, UK
| | - Emily Swager
- School of Life Sciences, Pharmacy, and Chemistry, Kingston University, Kingston upon Thames, KT1 2EE, UK
| | - Alex J Stringer
- School of Life Sciences, Pharmacy, and Chemistry, Kingston University, Kingston upon Thames, KT1 2EE, UK
| | - Lori A S Snyder
- School of Life Sciences, Pharmacy, and Chemistry, Kingston University, Kingston upon Thames, KT1 2EE, UK
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Lung abscess due to Neisseria meningitidis serogroup X-unexpected virulence of a commensal resulting from putative serogroup B capsular switching. Eur J Clin Microbiol Infect Dis 2020; 39:2327-2334. [PMID: 32666483 DOI: 10.1007/s10096-020-03977-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Accepted: 07/02/2020] [Indexed: 12/19/2022]
Abstract
To report the first case of a lung abscess caused by Neisseria meningitidis (Nm) and to genetically characterize the rare underlying capsule switching event. The strain (PT NmX) was subjected to whole genome sequencing, and a comparative gene-by-gene analysis was performed based on 1605 N. meningitidis core loci that constitute the MLST core-genome scheme (cgMLST) V1.0. All ~ 9,600 genomes available on Neisseria PubMLST (until 30th November 2019) from all serogroups were used to better identify the genome make-up of the PT NmX strain. This strain was found to be highly divergent from other NmX reported worldwide and to belong to a new sequence type (ST-14273), with the finetype X: P1.19,15-1:F5-2. Moreover, it revealed a closer genetic proximity to strains from serogroup B than to other serogroups, suggesting a genome backbone associated with serogroup B, while it presents a capsule synthesis region derived from a NmX strain. We describe a new hybrid NmB/X isolate from a noninvasive meningococcal infection, causing lung abscess. Despite capsular switching events involving serogroup X are rare, it may lead to the emergence of pathogenic potential. Studies should continue to better understand the molecular basis underlying Neisseria strains' ability to spread to body compartments other than the tissues for which their tropism is already known.
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