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Ju Y, Zhang Z, Liu M, Lin S, Sun Q, Song Z, Liang W, Tong X, Jie Z, Lu H, Cai K, Chen P, Jin X, Zhang W, Xu X, Yang H, Wang J, Hou Y, Xiao L, Jia H, Zhang T, Guo R. Integrated large-scale metagenome assembly and multi-kingdom network analyses identify sex differences in the human nasal microbiome. Genome Biol 2024; 25:257. [PMID: 39380016 PMCID: PMC11463039 DOI: 10.1186/s13059-024-03389-2] [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: 08/27/2022] [Accepted: 09/06/2024] [Indexed: 10/10/2024] Open
Abstract
BACKGROUND Respiratory diseases impose an immense health burden worldwide. Epidemiological studies have revealed extensive disparities in the incidence and severity of respiratory tract infections between men and women. It has been hypothesized that there might also be a nasal microbiome axis contributing to the observed sex disparities. RESULTS Here, we study the nasal microbiome of healthy young adults in the largest cohort to date with 1593 individuals, using shotgun metagenomic sequencing. We compile the most comprehensive reference catalog for the nasal bacterial community containing 4197 metagenome-assembled genomes and integrate the mycobiome, to provide a valuable resource and a more holistic perspective for the understudied human nasal microbiome. We systematically evaluate sex differences and reveal extensive sex-specific features in both taxonomic and functional levels in the nasal microbiome. Through network analyses, we capture markedly higher ecological stability and antagonistic potentials in the female nasal microbiome compared to the male's. The analysis of the keystone bacteria reveals that the sex-dependent evolutionary characteristics might have contributed to these differences. CONCLUSIONS In summary, we construct the most comprehensive catalog of metagenome-assembled-genomes for the nasal bacterial community to provide a valuable resource for the understudied human nasal microbiome. On top of that, comparative analysis in relative abundance and microbial co-occurrence networks identify extensive sex differences in the respiratory tract community, which may help to further our understanding of the observed sex disparities in the respiratory diseases.
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Affiliation(s)
- Yanmei Ju
- BGI Research, Shenzhen, 518083, China
- Shenzhen Key Laboratory of Human Commensal Microorganisms and Health Research, BGI Research, Shenzhen, 518083, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhe Zhang
- BGI Research, Shenzhen, 518083, China
- Shenzhen Key Laboratory of Human Commensal Microorganisms and Health Research, BGI Research, Shenzhen, 518083, China
| | - Mingliang Liu
- BGI Research, Shenzhen, 518083, China
- Shenzhen Key Laboratory of Human Commensal Microorganisms and Health Research, BGI Research, Shenzhen, 518083, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Shutian Lin
- BGI Research, Shenzhen, 518083, China
- Shenzhen Key Laboratory of Human Commensal Microorganisms and Health Research, BGI Research, Shenzhen, 518083, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Qiang Sun
- BGI Research, Shenzhen, 518083, China
- Shenzhen Key Laboratory of Human Commensal Microorganisms and Health Research, BGI Research, Shenzhen, 518083, China
- Department of Statistical Sciences, University of Toronto, 700 University Ave, Toronto, ON, M5G 1Z5, Canada
| | | | - Weiting Liang
- BGI Research, Shenzhen, 518083, China
- Shenzhen Key Laboratory of Human Commensal Microorganisms and Health Research, BGI Research, Shenzhen, 518083, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xin Tong
- BGI Research, Shenzhen, 518083, China
- Shenzhen Key Laboratory of Human Commensal Microorganisms and Health Research, BGI Research, Shenzhen, 518083, China
| | - Zhuye Jie
- BGI Research, Shenzhen, 518083, China
- Shenzhen Key Laboratory of Human Commensal Microorganisms and Health Research, BGI Research, Shenzhen, 518083, China
| | - Haorong Lu
- China National Genebank, BGI Research, Shenzhen, 518210, China
| | - Kaiye Cai
- BGI Research, Shenzhen, 518083, China
| | | | - Xin Jin
- BGI Research, Shenzhen, 518083, China
| | | | - Xun Xu
- BGI Research, Shenzhen, 518083, China
| | - Huanming Yang
- BGI Research, Shenzhen, 518083, China
- James D, Watson Institute of Genome Sciences, Hangzhou, 310013, China
| | - Jian Wang
- BGI Research, Shenzhen, 518083, China
| | - Yong Hou
- BGI Research, Shenzhen, 518083, China
| | - Liang Xiao
- BGI Research, Shenzhen, 518083, China
- Shenzhen Engineering Laboratory of Detection and Intervention of Human Intestinal Microbiome, BGI Research, Shenzhen, 518083, China
- Qingdao-Europe Advanced Institute for Life Sciences, BGI Research, Qingdao, 266555, China
| | - Huijue Jia
- School of Life Sciences, Fudan University, Shanghai, 200433, China.
- Greater Bay Area Institute of Precision Medicine, Guangzhou, 511458, China.
| | - Tao Zhang
- Shenzhen Key Laboratory of Human Commensal Microorganisms and Health Research, BGI Research, Shenzhen, 518083, China.
- BGI Research, Wuhan, 430074, China.
| | - Ruijin Guo
- BGI Research, Shenzhen, 518083, China.
- Shenzhen Key Laboratory of Human Commensal Microorganisms and Health Research, BGI Research, Shenzhen, 518083, China.
- BGI Research, Wuhan, 430074, China.
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2
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Rendon MA, So M. Zap the clap with DNA: a novel microbicide for preventing Neisseria gonorrhoeae infection. Antimicrob Agents Chemother 2024; 68:e0079424. [PMID: 39150247 PMCID: PMC11459949 DOI: 10.1128/aac.00794-24] [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: 06/03/2024] [Accepted: 07/16/2024] [Indexed: 08/17/2024] Open
Abstract
Each year, Neisseria gonorrhoeae (Ngo) causes over 1.5 million new infections in the United States, and >87 million worldwide. The absence of a vaccine for preventing gonorrhea, the rapid emergence of multidrug-resistant and extremely drug-resistant Ngo strains, and the limited number of antibiotics available for treating gonorrhea underscore the importance of developing new modalities for addressing Ngo infection. Here, we describe DNA-based microbicides that kill Ngo but not commensals. Previously, we showed that Ngo is killed when it takes up differentially methylated DNA with homology to its genome. We exploited this Achilles heel to develop a new class of microbicides for preventing Ngo infection. These microbicides consist of DNA molecules with specific sequences and a methylation pattern different from Ngo DNA. These DNAs kill low-passage and antibiotic-resistant clinical isolates with high efficiency but leave commensals unharmed. Equally important, the DNAs are equally effective against Ngo whether they are in buffered media or personal lubricants. These findings illustrate the potential of this new class of practical, low-cost, self-administered DNA-based microbicides for preventing Ngo transmission during sexual intercourse.
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Affiliation(s)
- Maria A. Rendon
- Department of Immunobiology, the BIO5 Institute, University of Arizona, Tucson, Arizona, USA
| | - Magdalene So
- Department of Immunobiology, the BIO5 Institute, University of Arizona, Tucson, Arizona, USA
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3
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Smith AC, Shrivastava A, Cartee JC, Bélanger M, Sharpe S, Lewis J, Budionno S, Gomez R, Khubbar MK, Pham CD, Gernert KM, Schmerer MW, Raphael BH, Learner ER, Kersh EN, Joseph SJ. Whole-genome sequencing resolves biochemical misidentification of Neisseria species from urogenital specimens. J Clin Microbiol 2024:e0070424. [PMID: 39360841 DOI: 10.1128/jcm.00704-24] [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: 05/09/2024] [Accepted: 08/16/2024] [Indexed: 10/05/2024] Open
Abstract
Neisseria meningitidis (Nm) and Neisseria gonorrhoeae (Ng) are human pathogens that sometimes occupy the same anatomical niche. Ng, the causative agent of gonorrhea, infects 87 million individuals annually worldwide and is an urgent threat due to increasing drug resistance. Ng is a pathogen of the urogenital tract and may infect the oropharyngeal or rectal site, often asymptomatically. Conversely, Nm is an opportunistic pathogen. While often a commensal in the oropharyngeal tract, it is also the leading cause of bacterial meningitis with 1.2 million cases globally, causing significant morbidity and mortality. Horizontal gene transfer (HGT) is likely to occur between Ng and Nm due to their shared anatomical niches and genetic similarity, which poses challenges for accurate detection and treatment. Routine surveillance through the Gonococcal Isolate Surveillance Project and Strengthening the U.S. Response to Resistant Gonorrhea detected six concerning urogenital Neisseria isolates with contradicting species identification in Milwaukee (MIL). While all six isolates were positive for Ng using nucleic acid amplification testing (NAAT) and matrix-assisted laser desorption/ionization time of flight identified the isolates as Ng, two biochemical tests, Gonochek-II and API NH, classified them as Nm. To address this discrepancy, we performed whole-genome sequencing (WGS) using Illumina MiSeq on all isolates and employed various bioinformatics tools. Species detection analysis using BMScan, which uses WGS data, identified all isolates as Ng. Furthermore, Kraken revealed over 98% of WGS reads mapped to the Ng genome and <1% to Nm. Recombination analysis identified putative HGT in all MIL isolates within the γ-glutamyl transpeptidase (ggt) gene, a key component in the biochemical tests used to differentiate between Nm and Ng. Further analysis identified Nm as the source of HGT event. Specifically, the active Nm ggt gene replaced the Ng pseudogenes, ggt1 and ggt2. Together, this study demonstrates that closely related Neisseria species sharing a niche underwent HGT, which led to the misidentification of species following biochemical testing. Importantly, NAAT accurately detected Ng. The misidentification highlights the importance of using WGS to continually evaluate diagnostic or bacterial identification tests.
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Affiliation(s)
- Amanda C Smith
- STD Laboratory Reference and Research Branch, Division of STD Prevention, NCHHSTP, CDC, Atlanta, Georgia, USA
| | - Apurva Shrivastava
- STD Laboratory Reference and Research Branch, Division of STD Prevention, NCHHSTP, CDC, Atlanta, Georgia, USA
- Oak Ridge Institute for Science and Education, Oak Ridge Associated Universities, Oak Ridge, Tennessee, USA
| | - John C Cartee
- STD Laboratory Reference and Research Branch, Division of STD Prevention, NCHHSTP, CDC, Atlanta, Georgia, USA
| | - Myriam Bélanger
- STD Laboratory Reference and Research Branch, Division of STD Prevention, NCHHSTP, CDC, Atlanta, Georgia, USA
| | - Samera Sharpe
- STD Laboratory Reference and Research Branch, Division of STD Prevention, NCHHSTP, CDC, Atlanta, Georgia, USA
| | - Jorden Lewis
- STD Laboratory Reference and Research Branch, Division of STD Prevention, NCHHSTP, CDC, Atlanta, Georgia, USA
- Oak Ridge Institute for Science and Education, Oak Ridge Associated Universities, Oak Ridge, Tennessee, USA
| | - Suzanna Budionno
- City of Milwaukee Health Department Laboratory, Milwaukee, Wisconsin, USA
| | - Raquel Gomez
- City of Milwaukee Health Department Laboratory, Milwaukee, Wisconsin, USA
| | - Manjeet K Khubbar
- City of Milwaukee Health Department Laboratory, Milwaukee, Wisconsin, USA
| | - Cau D Pham
- STD Laboratory Reference and Research Branch, Division of STD Prevention, NCHHSTP, CDC, Atlanta, Georgia, USA
| | - Kim M Gernert
- STD Laboratory Reference and Research Branch, Division of STD Prevention, NCHHSTP, CDC, Atlanta, Georgia, USA
| | - Matthew W Schmerer
- STD Laboratory Reference and Research Branch, Division of STD Prevention, NCHHSTP, CDC, Atlanta, Georgia, USA
| | - Brian H Raphael
- STD Laboratory Reference and Research Branch, Division of STD Prevention, NCHHSTP, CDC, Atlanta, Georgia, USA
| | - Emily R Learner
- STD Laboratory Reference and Research Branch, Division of STD Prevention, NCHHSTP, CDC, Atlanta, Georgia, USA
| | - Ellen N Kersh
- STD Laboratory Reference and Research Branch, Division of STD Prevention, NCHHSTP, CDC, Atlanta, Georgia, USA
| | - Sandeep J Joseph
- STD Laboratory Reference and Research Branch, Division of STD Prevention, NCHHSTP, CDC, Atlanta, Georgia, USA
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4
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Manoharan S, Farman TA, Piliou S, Mastroeni P. Characterisation and Immunogenicity of Neisseria cinerea outer membrane vesicles displaying NadA, NHBA and fHbp from Neisseria meningitidis serogroup B. Front Immunol 2024; 15:1473064. [PMID: 39380985 PMCID: PMC11458423 DOI: 10.3389/fimmu.2024.1473064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2024] [Accepted: 09/04/2024] [Indexed: 10/10/2024] Open
Abstract
More affordable and effective vaccines against bacterial meningitis caused by Neisseria meningitidis serogroup B are still required for global prevention. We have previously shown that modified outer membrane vesicles (mOMVs) from commensal Neisseria cinerea can be used as a platform to induce immune responses against meningococcal antigens. The aim of the present study was to use a combination of two genetically engineered mOMVs to express multiple antigens from N. meningitidis known to be involved in protective immunity to meningococcal meningitis (different variants of factor H binding protein (fHbp), Neisseria Heparin Binding Antigen (NHBA) and Neisseria Adhesin A (NadA)). Antigen expression in the mOMVs was confirmed by Western blotting; detoxification of the lipooligosaccharide (LOS) was confirmed by measuring human Toll-like receptor 4 (hTLR4) activation using in vitro cell assays. Mice immunised with a combination of two mOMVs expressing fHbp, NHBA and NadA produced antibodies to all the antigens. Furthermore, serum bactericidal activity (SBA) was induced by the immunisation, with mOMVs expressing NadA displaying high SBA titres against a nadA+ MenB strain. The work highlights the potential of mOMVs from N. cinerea to induce functional immune responses against multiple antigens involved in the protective immune response to meningococcal disease.
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MESH Headings
- Antigens, Bacterial/immunology
- Antigens, Bacterial/genetics
- Animals
- Adhesins, Bacterial/immunology
- Adhesins, Bacterial/genetics
- Neisseria meningitidis, Serogroup B/immunology
- Bacterial Proteins/immunology
- Bacterial Proteins/genetics
- Mice
- Meningococcal Vaccines/immunology
- Humans
- Antibodies, Bacterial/immunology
- Antibodies, Bacterial/blood
- Meningitis, Meningococcal/immunology
- Meningitis, Meningococcal/prevention & control
- Meningitis, Meningococcal/microbiology
- Neisseria cinerea/immunology
- Bacterial Outer Membrane/immunology
- Female
- Extracellular Vesicles/immunology
- Bacterial Outer Membrane Proteins/immunology
- Bacterial Outer Membrane Proteins/genetics
- Mice, Inbred BALB C
- Carrier Proteins
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Affiliation(s)
- Shathviga Manoharan
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
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5
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Dillard JP, Chan JM. Genetic Manipulation of Neisseria gonorrhoeae and Commensal Neisseria Species. Curr Protoc 2024; 4:e70000. [PMID: 39228292 DOI: 10.1002/cpz1.70000] [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: 09/05/2024]
Abstract
The sexually transmitted pathogen, Neisseria gonorrhoeae, undergoes natural transformation at high frequency. This property has led to the rapid dissemination of antibiotic resistance markers and the panmictic structure of the gonococcal population. However, high-frequency transformation also makes N. gonorrhoeae one of the easiest bacterial species to manipulate genetically in the laboratory. Techniques have been developed that result in transformation frequencies >50%, allowing the identification of mutants by screening and without selection. Constructs have been created to take advantage of this high-frequency transformation, facilitating genetic mutation, complementation, and heterologous gene expression. Similar methods have been developed for N. meningitidis and nonpathogenic Neisseria including N. mucosa and N. musculi. Techniques are described for genetic manipulation of N. gonorrhoeae and commensal Neisseria species, as well as for growth of these fastidious organisms. © 2024 The Author(s). Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Spot transformation of Neisseria gonorrhoeae on agar plates Basic Protocol 2: Spot transformation of commensal Neisseria on agar plates Basic Protocol 3: Transformation of Neisseria gonorrhoeae in liquid culture Basic Protocol 4: Electroporation of Neisseria gonorrhoeae Basic Protocol 5: Creation of unmarked mutations using a positive and negative selection cassette Basic Protocol 6: In vitro mutagenesis of Neisseria gonorrhoeae chromosomal DNA using EZ-Tn5 Basic Protocol 7: Chemical mutagenesis Basic Protocol 8: Complementation on the Neisseria gonorrhoeae chromosome Alternate Protocol 1: Complementation with replicating plasmids Alternate Protocol 2: Complementation on the Neisseria musculi or Neisseria mucosa chromosome Basic Protocol 9: Preparation of chromosomal DNA from Neisseria gonorrhoeae grown on solid medium Alternate Protocol 3: Preparation of chromosomal DNA from Neisseria gonorrhoeae grown in broth Support Protocol: Preparing PCR templates from Neisseria gonorrhoeae colonies.
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Affiliation(s)
- Joseph P Dillard
- Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, Wisconsin
| | - Jia Mun Chan
- Division of Infection and Immunity, University College London, London
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6
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Zhang X, Huang X, Zheng P, Liu E, Bai S, Chen S, Pang Y, Xiao X, Yang H, Guo J. Changes in oral, skin, and gut microbiota in children with atopic dermatitis: a case-control study. Front Microbiol 2024; 15:1442126. [PMID: 39211320 PMCID: PMC11358084 DOI: 10.3389/fmicb.2024.1442126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2024] [Accepted: 07/31/2024] [Indexed: 09/04/2024] Open
Abstract
Introduction Atopic dermatitis (AD) is a common clinical recurrent atopic disease in dermatology, most seen in children and adolescents. In recent years, AD has been found to be closely associated with microbial communities. Methods To explore the synergistic effects between colonizing bacteria from different sites and AD, we comparatively analyzed the skin, oral, and gut microbiota of children with AD (50 individuals) and healthy children (50 individuals) by 16S rRNA gene sequencing. Twenty samples were also randomly selected from both groups for metabolic and macrogenomic sequencing. Results The results of our sequencing study showed reduced microbiota diversity in the oral, skin, and gut of children with AD (P < 0.05). Metabolomics analysis showed that serotonergic synapse, arachidonic acid metabolism, and steroid biosynthesis were downregulated at all three loci in the oral, skin, and gut of children with AD (P < 0.05). Macrogenomic sequencing analysis showed that KEGG functional pathways of the three site flora were involved in oxidative phosphorylation, ubiquitin-mediated proteolysis, mRNA surveillance pathway, ribosome biogenesis in eukaryotes, proteasome, basal transcription factors, peroxisome, MAPK signaling pathway, mitophagy, fatty acid elongation, and so on (P < 0.05). Discussion The combined microbial, metabolic, and macrogenetic analyses identified key bacteria, metabolites, and pathogenic pathways that may be associated with AD development. We provides a more comprehensive and in-depth understanding of the role of the microbiota at different sites in AD patients, pointing to new directions for future diagnosis, treatment and prognosis.
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Affiliation(s)
- Xueer Zhang
- Department of Dermatology, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Xiaomin Huang
- Department of Dermatology, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Pai Zheng
- Department of Dermatology, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - E. Liu
- Department of Dermatology, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Sixian Bai
- Department of Dermatology, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Shuoyu Chen
- Department of Dermatology, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Yaobin Pang
- Department of Dermatology, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Xinyu Xiao
- Department of Dermatology, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Huifang Yang
- Department of Dermatology, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Jing Guo
- Department of Dermatology, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, China
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7
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Boutroux M, Favre-Rochex S, Gorgette O, Touak G, Mühle E, Bouchier C, Chesneau O, Veyrier FJ, Clermont D, Rahi P. Neisseria leonii sp. nov., isolated from the nose, lung, and liver of rabbits. Int J Syst Evol Microbiol 2024; 74:006460. [PMID: 39023135 PMCID: PMC11316581 DOI: 10.1099/ijsem.0.006460] [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: 03/20/2024] [Accepted: 07/05/2024] [Indexed: 07/20/2024] Open
Abstract
A taxogenomic study of three strains (3986T, 51.81, and JF 2415) isolated from rabbits between 1972 and 2000 led to the description of a new Neisseria species. The highest sequence similarity of the 16S rRNA gene was found to Neisseria animalis NCTC 10212T (96.7 %). The 16S rRNA gene similarity above 99 % and average nucleotide identity (ANI) values above 96 % among the strains, indicated that they belong to the same species. At the same time, the strains shared ANI values below 81 % and dDDH values below 24 % with all described Neisseria species. In the bac120 gene phylogenetic tree, the three strains clustered near Neisseria elongata and Neisseria bacilliformis in the Neisseria clade. However, the Neisseria clade is not monophyletic, and includes the type strains of Morococcus cerebrosus, Bergeriella denitrificans, Kingella potus, Uruburuella suis, and Uruburuella testudinis. Neisseria shayeganii clustered outside the clade with members of the genus Eikenella. Amino acid identity (AAI) values were calculated, and a threshold of 71 % was used to circumscribe the genus Neisseria. According to this proposed AAI threshold, strains 3986T, 51.81, and JF 2415 were placed within the genus Neisseria. The cells of the three strains were Gram-stain-negative diplococcobacilli and non-motile. Optimal growth on trypticase soy agar occurred at 37 °C and pH 8.5 in aerobic conditions. Notably, all strains exhibited indole production in the API-NH test, which is atypical for Neisseria and the family Neisseriaceae. The strains exhibited a common set of 68 peaks in their MALDI-TOF MS profiles, facilitating the swift and accurate identification of this species. Based on genotypic and phenotypic data, it is proposed that strains 3986T, 51.81, and JF 2415 represent a novel species within the genus Neisseria, for which the name Neisseria leonii sp. nov. is proposed (type strain 3986T=R726T=CIP 109994T=LMG 32907T).
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Affiliation(s)
- Martin Boutroux
- Institut Pasteur, Université Paris Cité, Center of Biological Resources of Institut Pasteur (CRBIP), 75015 Paris, France
| | - Sandrine Favre-Rochex
- Institut Pasteur, Université Paris Cité, Collection of Institut Pasteur (CIP), 75015 Paris, France
| | - Olivier Gorgette
- Institut Pasteur, Université Paris Cité, Ultrastructural BioImaging Unit, 75015 Paris, France
| | - Gérald Touak
- Institut Pasteur, Université Paris Cité, Collection of Institut Pasteur (CIP), 75015 Paris, France
| | - Estelle Mühle
- Institut Pasteur, Université Paris Cité, Collection of Institut Pasteur (CIP), 75015 Paris, France
| | - Christiane Bouchier
- Institut Pasteur, Université Paris Cité, Collection of Institut Pasteur (CIP), 75015 Paris, France
| | - Olivier Chesneau
- Institut Pasteur, Université Paris Cité, Collection of Institut Pasteur (CIP), 75015 Paris, France
| | - Frédéric J. Veyrier
- INRS-Centre Armand-Frappier Santé Biotechnologie, Bacterial Symbionts Evolution, Laval, Quebec H7V 1B7, Canada
| | - Dominique Clermont
- Institut Pasteur, Université Paris Cité, Collection of Institut Pasteur (CIP), 75015 Paris, France
| | - Praveen Rahi
- Institut Pasteur, Université Paris Cité, Collection of Institut Pasteur (CIP), 75015 Paris, France
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8
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Harris-Jones TN, Chan JM, Hackett KT, Weyand NJ, Schaub RE, Dillard JP. Peptidoglycan fragment release and NOD activation by commensal Neisseria species from humans and other animals. Infect Immun 2024; 92:e0000424. [PMID: 38563734 PMCID: PMC11075463 DOI: 10.1128/iai.00004-24] [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: 01/04/2024] [Accepted: 03/13/2024] [Indexed: 04/04/2024] Open
Abstract
Neisseria gonorrhoeae, a human restricted pathogen, releases inflammatory peptidoglycan (PG) fragments that contribute to the pathophysiology of pelvic inflammatory disease. The genus Neisseria is also home to multiple species of human- or animal-associated Neisseria that form part of the normal microbiota. Here we characterized PG release from the human-associated nonpathogenic species Neisseria lactamica and Neisseria mucosa and animal-associated Neisseria from macaques and wild mice. An N. mucosa strain and an N. lactamica strain were found to release limited amounts of the proinflammatory monomeric PG fragments. However, a single amino acid difference in the PG fragment permease AmpG resulted in increased PG fragment release in a second N. lactamica strain examined. Neisseria isolated from macaques also showed substantial release of PG monomers. The mouse colonizer Neisseria musculi exhibited PG fragment release similar to that seen in N. gonorrhoeae with PG monomers being the predominant fragments released. All the human-associated species were able to stimulate NOD1 and NOD2 responses. N. musculi was a poor inducer of mouse NOD1, but ldcA mutation increased this response. The ability to genetically manipulate N. musculi and examine effects of different PG fragments or differing amounts of PG fragments during mouse colonization will lead to a better understanding of the roles of PG in Neisseria infections. Overall, we found that only some nonpathogenic Neisseria have diminished release of proinflammatory PG fragments, and there are differences even within a species as to types and amounts of PG fragments released.
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Affiliation(s)
- Tiffany N. Harris-Jones
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Jia Mun Chan
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Kathleen T. Hackett
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Nathan J. Weyand
- Department of Biological Sciences, Ohio University, Athens, Ohio, USA
| | - Ryan E. Schaub
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Joseph P. Dillard
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, Wisconsin, USA
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9
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Geslewitz WE, Cardenas A, Zhou X, Zhang Y, Criss AK, Seifert HS. Development and implementation of a Type I-C CRISPR-based programmable repression system for Neisseria gonorrhoeae. mBio 2024; 15:e0302523. [PMID: 38126782 PMCID: PMC10865793 DOI: 10.1128/mbio.03025-23] [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: 11/10/2023] [Accepted: 11/15/2023] [Indexed: 12/23/2023] Open
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR) are prokaryotic adaptive immune systems regularly utilized as DNA-editing tools. While Neisseria gonorrhoeae does not have an endogenous CRISPR, the commensal species Neisseria lactamica encodes a functional Type I-C CRISPR-Cas system. We have established an isopropyl β-d-1-thiogalactopyranoside added (IPTG)-inducible, CRISPR interference (CRISPRi) platform based on the N. lactamica Type I-C CRISPR missing the Cas3 nuclease to allow locus-specific transcriptional repression. As proof of principle, we targeted a non-phase-variable version of the opaD gene. We show that CRISPRi can downregulate opaD gene and protein expression, resulting in bacterial inability to stimulate neutrophil oxidative responses and to bind to an N-terminal fragment of CEACAM1. Importantly, we used CRISPRi to effectively knockdown all the transcripts of all 11 opa genes using a five-spacer CRISPR array, allowing control of the entire phase-variable opa family in strain FA1090. We also report that repression is reversible following IPTG removal. Finally, we showed that the Type I-C CRISPRi system can conditionally reduce the expression of two essential genes. This CRISPRi system will allow the interrogation of every Gc gene, essential and non-essential, to study physiology and pathogenesis and aid in antimicrobial development.IMPORTANCEClustered regularly interspaced short palindromic repeats (CRISPR)-Cas systems have proven instrumental in genetically manipulating many eukaryotic and prokaryotic organisms. Despite its usefulness, a CRISPR system had yet to be developed for use in Neisseria gonorrhoeae (Gc), a bacterium that is the main etiological agent of gonorrhea infection. Here, we developed a programmable and IPTG-inducible Type I-C CRISPR interference (CRISPRi) system derived from the commensal species Neisseria lactamica as a gene repression system in Gc. As opposed to generating genetic knockouts, the Type I-C CRISPRi system allows us to block transcription of specific genes without generating deletions in the DNA. We explored the properties of this system and found that a minimal spacer array is sufficient for gene repression while also facilitating efficient spacer reprogramming. Importantly, we also show that we can use CRISPRi to knockdown genes that are essential to Gc that cannot normally be knocked out under laboratory settings. Gc encodes ~800 essential genes, many of which have no predicted function. We predict that this Type I-C CRISPRi system can be used to help categorize gene functions and perhaps contribute to the development of novel therapeutics for gonorrhea.
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Affiliation(s)
- Wendy E. Geslewitz
- Department of Microbiology and Immunology, Northwestern University, Chicago, Illinois, USA
| | - Amaris Cardenas
- Department of Microbiology, Immunology, and Cancer Biology, University of Virginia, Charlottesville, Virginia, USA
| | - Xufei Zhou
- Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan, USA
| | - Yan Zhang
- Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan, USA
| | - Alison K. Criss
- Department of Microbiology, Immunology, and Cancer Biology, University of Virginia, Charlottesville, Virginia, USA
| | - H Steven Seifert
- Department of Microbiology and Immunology, Northwestern University, Chicago, Illinois, USA
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10
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Hioki T, Soejima K, Goto Y, Sugiura M, Umemura T, Ishihara Y, Mutoh Y, Sakanashi D, Mikamo H. Co-infection with Neisseria mucosa in a patient with tuberculous otitis media. J Otol 2024; 19:1-4. [PMID: 38313762 PMCID: PMC10837539 DOI: 10.1016/j.joto.2023.10.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 09/27/2023] [Accepted: 10/11/2023] [Indexed: 02/06/2024] Open
Abstract
Tuberculous otitis media (TOM) is a rare manifestation caused by Mycobacterium tuberculosis with low incidence rates among extrapulmonary tuberculosis cases. Diagnosis is often delayed because of the presence of several clinical manifestations and the high prevalence of secondary bacterial infections. Few reports have attributed secondary bacterial infections in patients with TOM to commensal Neisseria. Thus, understanding the pathogenic mechanisms and clinical features of commensal Neisseria is important, considering its recent presentation as an infection-causing pathogen. Neisseria mucosa is a commensal inhabitant in humans and is generally considered non-pathogenic but can cause infection in rare cases. Here, we report an atypical secondary infection caused by Neisseria mucosa in an 81-year-old woman with TOM being treated for pulmonary tuberculosis. Direct purulent otorrhea smear microscopy revealed no acid-fast bacilli using Ziehl-Neelsen staining, whereas the phagocytosis of gram-negative cocci by white blood cells was confirmed using Gram staining. Otorrhea culture revealed the growth of N. mucosa. Subsequently, M. tuberculosis infection in the otorrhea was identified using a culture-based method. Vigilance is critical for the early detection of TOM to prevent further complications. This report raises awareness regarding TOM and provides insight into the pathogenicity of N. mucosa in otitis media.
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Affiliation(s)
- Tatsuya Hioki
- Department of Clinical Laboratory, Tosei General Hospital, 160 Nishioiwake-cho, Seto, Aichi, 489-8642, Japan
| | - Kazuaki Soejima
- Department of Respiratory Medicine and Allergy, Tosei General Hospital, 160 Nishioiwake-cho, Seto, Aichi, 489-8642, Japan
| | - Yuki Goto
- Department of Otolaryngology, Tosei General Hospital, 160 Nishioiwake-cho, Seto, Aichi, 489-8642, Japan
| | - Makoto Sugiura
- Department of Otolaryngology, Tosei General Hospital, 160 Nishioiwake-cho, Seto, Aichi, 489-8642, Japan
| | - Takumi Umemura
- Department of Infection Control Team, Tosei General Hospital, 160 Nishioiwake-cho, Seto, Aichi, 489-8642, Japan
| | - Yoshimi Ishihara
- Department of Clinical Laboratory, Tosei General Hospital, 160 Nishioiwake-cho, Seto, Aichi, 489-8642, Japan
| | - Yoshikazu Mutoh
- Department of Infectious Diseases, Tosei General Hospital, 160 Nishioiwake-cho, Seto, Aichi, 489-8642, Japan
| | - Daisuke Sakanashi
- Department of Infection Prevention and Control, Aichi Medical University Hospital, 1-1 Yazakokarimata, Nagakute, Aichi, 480-1195, Japan
| | - Hiroshige Mikamo
- Department of Infection Prevention and Control, Aichi Medical University Hospital, 1-1 Yazakokarimata, Nagakute, Aichi, 480-1195, Japan
- Department of Clinical Infectious Diseases, Aichi Medical University, 1-1 Yazakokarimata, Nagakute, Aichi, 480-1195, Japan
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11
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Piliou S, Farman TA, Marini A, Manoharan S, Mastroeni P. Commensal Neisseria cinerea outer membrane vesicles as a platform for the delivery of meningococcal and gonococcal antigens to the immune system. Vaccine 2023; 41:7671-7681. [PMID: 38008665 DOI: 10.1016/j.vaccine.2023.11.034] [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: 09/18/2023] [Revised: 11/17/2023] [Accepted: 11/17/2023] [Indexed: 11/28/2023]
Abstract
An affordable, accessible, and broadly protective vaccine is required to tackle the re-occurring bacterial meningococcal epidemics in Sub-Saharan Africa as well as an effective control of multi-drug resistant strains of gonococcus. Outer membrane vesicles (OMVs) secreted from Gram-negative bacteria represent an attractive platform for antigen delivery to the immune system and therefore for development of multi-component vaccines. In this study, we describe the generation of modified OMVs (mOMVs) from commensal biosafety-level 1 (BSL-1) Neisseria cinerea ATCC® 14685TM, which is phylogenetically close to the pathogenic bacteria Neisseria meningitidis and Neisseria gonorrhoeae. mOMVs were prepared from N. cinerea engineered to express heterologous antigens from N. meningitidis (factor H binding protein (fHbp) and Neisseria Heparin Binding Antigen (NHBA-2)) and from N. gonorrhoeae (NHBA-542). Mice immunised with the mOMVs produced antibodies against fHbp and NHBA. The work indicates that mOMV from N. cinerea can be used as a platform to induce immune responses against antigens involved in the protective immune response against meningococcal and gonococcal diseases.
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Affiliation(s)
- Stavroula Piliou
- Department of Veterinary Medicine, University of Cambridge, Cambridge CB3 0ES, UK
| | - Theo A Farman
- Department of Veterinary Medicine, University of Cambridge, Cambridge CB3 0ES, UK
| | - Arianna Marini
- Department of Veterinary Medicine, University of Cambridge, Cambridge CB3 0ES, UK
| | - Shathviga Manoharan
- Department of Veterinary Medicine, University of Cambridge, Cambridge CB3 0ES, UK.
| | - Pietro Mastroeni
- Department of Veterinary Medicine, University of Cambridge, Cambridge CB3 0ES, UK
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12
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Eriksson L, Johannesen TB, Stenmark B, Jacobsson S, Säll O, Hedberg ST, Fredlund H, Stegger M, Mölling P. Genetic variants linked to the phenotypic outcome of invasive disease and carriage of Neisseria meningitidis. Microb Genom 2023; 9:001124. [PMID: 37874326 PMCID: PMC10634450 DOI: 10.1099/mgen.0.001124] [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: 05/16/2023] [Accepted: 10/10/2023] [Indexed: 10/25/2023] Open
Abstract
Neisseria meningitidis can be a human commensal in the upper respiratory tract but is also capable of causing invasive diseases such as meningococcal meningitis and septicaemia. No specific genetic markers have been detected to distinguish carriage from disease isolates. The aim here was to find genetic traits that could be linked to phenotypic outcomes associated with carriage versus invasive N. meningitidis disease through a bacterial genome-wide association study (GWAS). In this study, invasive N. meningitidis isolates collected in Sweden (n=103) and carriage isolates collected at Örebro University, Sweden (n=213) 2018-2019 were analysed. The GWAS analysis, treeWAS, was applied to single-nucleotide polymorphisms (SNPs), genes and k-mers. One gene and one non-synonymous SNP were associated with invasive disease and seven genes and one non-synonymous SNP were associated with carriage isolates. The gene associated with invasive disease encodes a phage transposase (NEIS1048), and the associated invasive SNP glmU S373C encodes the enzyme N-acetylglucosamine 1-phosphate (GlcNAC 1-P) uridyltransferase. Of the genes associated with carriage isolates, a gene variant of porB encoding PorB class 3, the genes pilE/pilS and tspB have known functions. The SNP associated with carriage was fkbp D33N, encoding a FK506-binding protein (FKBP). K-mers from PilS, tbpB and tspB were found to be associated with carriage, while k-mers from mtrD and tbpA were associated with invasiveness. In the genes fkbp, glmU, PilC and pilE, k-mers were found that were associated with both carriage and invasive isolates, indicating that specific variations within these genes could play a role in invasiveness. The data presented here highlight genetic traits that are significantly associated with invasive or carriage N. meningitidis across the species population. These traits could prove essential to our understanding of the pathogenicity of N. meningitidis and could help to identify future vaccine targets.
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Affiliation(s)
- Lorraine Eriksson
- Department of Laboratory Medicine, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - Thor Bech Johannesen
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Bianca Stenmark
- Department of Laboratory Medicine, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - Susanne Jacobsson
- Department of Laboratory Medicine, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - Olof Säll
- Department of Infectious Diseases, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - Sara Thulin Hedberg
- Department of Laboratory Medicine, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - Hans Fredlund
- Department of Laboratory Medicine, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - Marc Stegger
- Department of Laboratory Medicine, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Paula Mölling
- Department of Laboratory Medicine, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
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13
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Yang C, Zhao L, Zhou J, Cheng Y, Yang J, Zhou H, Luo W, Lu S, Jin D, Pu J, Zhang S, Liu L, Xu J. Neisseria lisongii sp. nov. and Neisseria yangbaofengii sp. nov., isolated from the respiratory tracts of marmots. Int J Syst Evol Microbiol 2023; 73. [PMID: 37610801 DOI: 10.1099/ijsem.0.006002] [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: 08/24/2023] Open
Abstract
Four Gram-stain-negative, oxidase-positive, non-motile, cocci-shaped bacteria strains (ZJ106T, ZJ104, ZJ785T and ZJ930) were isolated from marmot respiratory tracts. Phylogenetic analyses based on 16S rRNA genes, 53 ribosomal protein sequences and 441 core genes supported that all four strains belonged to the genus Neisseria with close relatives Neisseria weixii 10022T and Neisseria iguanae ATCC 51483T. Average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values were below the species-level thresholds (95-96 % for ANI, and 70 % for dDDH). The major fatty acids of all four strains were C16 : 1 ω7c /C16 : 1 ω6c, C16 : 0 and C18 : 1 ω9c. Major polar lipids were composed of diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylglycerol. MK-8 was the major menaquinone. Based on Virulence Factor Database analysis, the four strains were found to contain NspA and PorB H-factor binding proteins that promote evasion of host immunity. Strains ZJ106T and ZJ104 contained structures similar to the capsule synthesis manipulator of Neisseria meningitidis. Based on phenotypic and phylogenetic evidence, we propose that strains ZJ106T and ZJ785T represent two novel species of the genus Neisseria, respectively, with the names Neisseria lisongii sp. nov. and Neisseria yangbaofengii sp. nov. The type strains are ZJ106T (=GDMCC 1.3111T=JCM 35323T) and ZJ785T (=GDMCC 1.1998T=KCTC 82336T).
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Affiliation(s)
- Caixin Yang
- Department of Epidemiology, School of Public Health, Shanxi Medical University, Taiyuan, Shanxi 030001, PR China
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Lijun Zhao
- Department of Epidemiology, School of Public Health, Shanxi Medical University, Taiyuan, Shanxi 030001, PR China
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Juan Zhou
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Yanpeng Cheng
- Shenzhen Center for Disease Control and Prevention, Shenzhen 518000, PR China
| | - Jing Yang
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Huimin Zhou
- Department of Epidemiology, School of Public Health, Shanxi Medical University, Taiyuan, Shanxi 030001, PR China
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Wenbo Luo
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Shan Lu
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
- Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing 102206, PR China
| | - Dong Jin
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
- Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing 102206, PR China
| | - Ji Pu
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Sihui Zhang
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing 100191, PR China
| | - Liyun Liu
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Jianguo Xu
- Department of Epidemiology, School of Public Health, Shanxi Medical University, Taiyuan, Shanxi 030001, PR China
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
- Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing 102206, PR China
- Institute of Public Health, Nankai University, Tianjin 300305, PR China
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14
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Calder A, Snyder LAS. Diversity of the type VI secretion systems in the Neisseria spp. Microb Genom 2023; 9. [PMID: 37052605 DOI: 10.1099/mgen.0.000986] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/14/2023] Open
Abstract
Complete Type VI Secretion Systems were identified in the genome sequence data of Neisseria subflava isolates sourced from throat swabs of human volunteers. The previous report was the first to describe two complete Type VI Secretion Systems in these isolates, both of which were distinct in terms of their gene organization and sequence homology. Since publication of the first report, Type VI Secretion System subtypes have been identified in Neisseria spp. The characteristics of each type in N. subflava are further investigated here and in the context of the other Neisseria spp., including identification of the lineages containing the different types and subtypes. Type VI Secretion Systems use VgrG for delivery of toxin effector proteins; several copies of vgrG and associated effector / immunity pairs are present in Neisseria spp. Based on sequence similarity between strains and species, these core Type VI Secretion System genes, vgrG, and effector / immunity genes may diversify via horizontal gene transfer, an instrument for gene acquisition and repair in Neisseria spp.
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Affiliation(s)
- Alan Calder
- School of Life Sciences, Pharmacy, and Chemistry, Kingston University, Penrhyn Road, Kingston upon Thames, KT1 2EE, UK
| | - Lori A S Snyder
- School of Life Sciences, Pharmacy, and Chemistry, Kingston University, Penrhyn Road, Kingston upon Thames, KT1 2EE, UK
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15
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Belachew T, Assefa M, Tefera Z, Fenta A, Biset S. Colonization Rate and Associated Factors of Non-Pathogenic Neisseria Species, and Moraxella catarrhalis Among Healthy School Children in Gondar, Northwest Ethiopia. Infect Drug Resist 2023; 16:369-378. [PMID: 36714354 PMCID: PMC9879043 DOI: 10.2147/idr.s395343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Accepted: 01/11/2023] [Indexed: 01/23/2023] Open
Abstract
Background Although commensal Neisseria species inhabiting mucosal surfaces in the upper respiratory tract (URT) are rarely associated with infections, their presence in the area has been linked to the development of immunity against N. meningitidis and the source of antibiotic resistance determinants in pathogenic species. M. catarrhalis in the oropharynx of children is also a predisposing factor for otitis media. As a result, determining the oropharyngeal carriage rate of these commensal species and associated factors among healthy schoolchildren is substantial. Materials and Methods This community-based cross-sectional study was conducted in Gondar, Northwest Ethiopia, from January to April 2019. A multi-stage and simple random sampling technique were used to select schools and participants, respectively. A total of 524 oropharyngeal swabs were collected using cotton swabs. Modified Thayer-Martin media was used for primary bacterial isolation, and battery of biochemical tests was performed to identify species. For frequencies, descriptive statistics were computed and the logistic regression model was used to see the relationship between dependent and independent variables. Results A total of 524 healthy schoolchildren with a mean age of 12.2 ± 2.74 years participated in this study. The overall oropharyngeal carriage rate was 21.8% (114/524). Of these, N. meningitidis, N. lactamica, N. sicca, and M. catarrhalis were identified in 53 (46.5%), 14 (12.3%), 11 (9.6%), and 36 (31.6%) children, respectively. The culture positivity rate was higher at a younger age, which was 8.1%, 11.3%, and 14.9% in ages between 15-18, 11-14, and 7-10, respectively. The oropharyngeal carriage was significantly associated with the number of students per class (>40). Conclusion There is a higher proportion of carriers of commensal N. lactamica and M. catarrhalis in Gondar town schoolchildren. The oropharyngeal carriage rate was associated with a crowded classroom. The characterization of non-pathogenic Neisseria species and M. catarrhalis in the study area can support the diagnosis of patients suspected of having N. meningitis infections.
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Affiliation(s)
- Teshome Belachew
- Department of Medical Microbiology, School of Biomedical and Laboratory Sciences, College of Medicine and Health Sciences, University of Gondar, Gondar, Ethiopia
| | - Muluneh Assefa
- Department of Medical Microbiology, School of Biomedical and Laboratory Sciences, College of Medicine and Health Sciences, University of Gondar, Gondar, Ethiopia
| | | | | | - Sirak Biset
- Department of Medical Microbiology, School of Biomedical and Laboratory Sciences, College of Medicine and Health Sciences, University of Gondar, Gondar, Ethiopia,Correspondence: Sirak Biset, Tel +251-911-598-568, Email
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16
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Shaskolskiy B, Kravtsov D, Kandinov I, Dementieva E, Gryadunov D. Genomic Diversity and Chromosomal Rearrangements in Neisseria gonorrhoeae and Neisseria meningitidis. Int J Mol Sci 2022; 23:ijms232415644. [PMID: 36555284 PMCID: PMC9778887 DOI: 10.3390/ijms232415644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 11/18/2022] [Accepted: 12/07/2022] [Indexed: 12/14/2022] Open
Abstract
Chromosomal rearrangements in N. gonorrhoeae and N. meningitidis were studied with the determination of mobile elements and their role in rearrangements. The results of whole-genome sequencing and de novo genome assembly for 50 N. gonorrhoeae isolates collected in Russia were compared with 96 genomes of N. gonorrhoeae and 138 genomes of N. meningitidis from the databases. Rearrangement events with the determination of the coordinates of syntenic blocks were analyzed using the SibeliaZ software v.1.2.5, the minimum number of events that allow one genome to pass into another was calculated using the DCJ-indel model using the UniMoG program v.1.0. Population-level analysis revealed a stronger correlation between changes in the gene order and phylogenetic proximity for N. meningitidis in contrast to N. gonorrhoeae. Mobile elements were identified, including Correa elements; Spencer-Smith elements (in N. gonorrhoeae); Neisserial intergenic mosaic elements; IS elements of IS5, IS30, IS110, IS1595 groups; Nf1-Nf3 prophages; NgoФ1-NgoФ9 prophages; and Mu-like prophages Pnm1, Pnm2, MuMenB (in N. meningitidis). More than 44% of the observed rearrangements most likely occurred with the participation of mobile elements, including prophages. No differences were found between the Russian and global N. gonorrhoeae population both in terms of rearrangement events and in the number of transposable elements in genomes.
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17
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Warinner C. An Archaeology of Microbes. JOURNAL OF ANTHROPOLOGICAL RESEARCH 2022. [DOI: 10.1086/721976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Christina Warinner
- Department of Anthropology, Harvard University, Cambridge MA, USA 02138, and Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany 04103
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18
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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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19
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Cho W, York AG, Wang R, Wyche TP, Piizzi G, Flavell RA, Crawford JM. N-Acyl Amides from Neisseria meningitidis and Their Role in Sphingosine Receptor Signaling. Chembiochem 2022; 23:e202200490. [PMID: 36112057 PMCID: PMC9762135 DOI: 10.1002/cbic.202200490] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 09/15/2022] [Indexed: 02/03/2023]
Abstract
Neisseria meningitidis is a Gram-negative opportunistic pathogen that is responsible for causing human diseases with high mortality, such as septicemia and meningitis. The molecular mechanisms N. meningitidis employ to manipulate the immune system, translocate the mucosal and blood-brain barriers, and exert virulence are largely unknown. Human-associated bacteria encode a variety of bioactive small molecules with growing evidence for N-acyl amides as being important signaling molecules. However, only a small fraction of these metabolites has been identified from the human microbiota thus far. Here, we heterologously expressed an N-acyltransferase encoded in the obligate human pathogen N. meningitidis and identified 30 N-acyl amides with representative members serving as agonists of the G-protein coupled receptor (GPCR) S1PR4. During this process, we also characterized two mammalian N-acyl amides derived from the bovine medium. Both groups of metabolites suppress anti-inflammatory interleukin-10 signaling in human macrophage cell types, but they also suppress the pro-inflammatory interleukin-17A+ population in TH 17-differentiated CD4+ T cells.
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Affiliation(s)
- Wooyoung Cho
- Department of Chemistry, Yale University, New Haven, CT, USA
- Institute of Biomolecular Design & Discovery, Yale University, West Haven, CT, USA
| | - Autumn G. York
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Rurun Wang
- Exploratory Science Center, Merck & Co., Inc., Cambridge, MA, USA
| | - Thomas P. Wyche
- Exploratory Science Center, Merck & Co., Inc., Cambridge, MA, USA
| | - Grazia Piizzi
- Exploratory Science Center, Merck & Co., Inc., Cambridge, MA, USA
| | - Richard A. Flavell
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
- Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT, USA
| | - Jason M. Crawford
- Department of Chemistry, Yale University, New Haven, CT, USA
- Institute of Biomolecular Design & Discovery, Yale University, West Haven, CT, USA
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT, USA
- correspondence,
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20
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Diop A, Torrance EL, Stott CM, Bobay LM. Gene flow and introgression are pervasive forces shaping the evolution of bacterial species. Genome Biol 2022; 23:239. [PMID: 36357919 PMCID: PMC9650840 DOI: 10.1186/s13059-022-02809-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 10/24/2022] [Indexed: 11/11/2022] Open
Abstract
BACKGROUND Although originally thought to evolve clonally, studies have revealed that most bacteria exchange DNA. However, it remains unclear to what extent gene flow shapes the evolution of bacterial genomes and maintains the cohesion of species. RESULTS Here, we analyze the patterns of gene flow within and between >2600 bacterial species. Our results show that fewer than 10% of bacterial species are truly clonal, indicating that purely asexual species are rare in nature. We further demonstrate that the taxonomic criterion of ~95% genome sequence identity routinely used to define bacterial species does not accurately represent a level of divergence that imposes an effective barrier to gene flow across bacterial species. Interruption of gene flow can occur at various sequence identities across lineages, generally from 90 to 98% genome identity. This likely explains why a ~95% genome sequence identity threshold has empirically been judged as a good approximation to define bacterial species. Our results support a universal mechanism where the availability of identical genomic DNA segments required to initiate homologous recombination is the primary determinant of gene flow and species boundaries in bacteria. We show that these barriers of gene flow remain porous since many distinct species maintain some level of gene flow, similar to introgression in sexual organisms. CONCLUSIONS Overall, bacterial evolution and speciation are likely shaped by similar forces driving the evolution of sexual organisms. Our findings support a model where the interruption of gene flow-although not necessarily the initial cause of speciation-leads to the establishment of permanent and irreversible species borders.
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Affiliation(s)
- Awa Diop
- grid.266860.c0000 0001 0671 255XDepartment of Biology, University of North Carolina Greensboro, Greensboro, North Carolina, 321 McIver Street, PO Box 26170, Greensboro, NC 27402 USA
| | - Ellis L. Torrance
- grid.266860.c0000 0001 0671 255XDepartment of Biology, University of North Carolina Greensboro, Greensboro, North Carolina, 321 McIver Street, PO Box 26170, Greensboro, NC 27402 USA
| | - Caroline M. Stott
- grid.266860.c0000 0001 0671 255XDepartment of Biology, University of North Carolina Greensboro, Greensboro, North Carolina, 321 McIver Street, PO Box 26170, Greensboro, NC 27402 USA
| | - Louis-Marie Bobay
- grid.266860.c0000 0001 0671 255XDepartment of Biology, University of North Carolina Greensboro, Greensboro, North Carolina, 321 McIver Street, PO Box 26170, Greensboro, NC 27402 USA
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21
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Maynard-Smith L, Derrick JP, Borrow R, Lucidarme J, Maiden MCJ, Heyderman RS, Harrison OB. Genome-Wide Association Studies Identify an Association of Transferrin Binding Protein B Variation and Invasive Serogroup Y Meningococcal Disease in Older Adults. J Infect Dis 2022; 226:2204-2214. [PMID: 36322504 PMCID: PMC9748998 DOI: 10.1093/infdis/jiac430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 10/24/2022] [Accepted: 10/31/2022] [Indexed: 11/27/2022] Open
Abstract
BACKGROUND Neisseria meningitidis serogroup Y, especially ST-23 clonal complex (Y:cc23), represents a larger proportion of invasive meningococcal disease (IMD) in older adults compared to younger individuals. This study explored the meningococcal genetic variation underlying this association. METHODS Maximum-likelihood phylogenies and the pangenome were analyzed using whole-genome sequence (WGS) data from 200 Y:cc23 isolates in the Neisseria PubMLST database. Genome-wide association studies (GWAS) were performed on WGS data from 250 Y:cc23 isolates from individuals with IMD aged ≥65 years versus < 65 years. RESULTS Y:cc23 meningococcal variants did not cluster by age group or disease phenotype in phylogenetic analyses. Pangenome comparisons found no differences in presence or absence of genes in IMD isolates from the different age groups. GWAS identified differences in nucleotide polymorphisms within the transferrin-binding protein B (tbpB) gene in isolates from individuals ≥65 years of age. TbpB structure modelling suggests these may impact binding of human transferrin. CONCLUSIONS These data suggest differential iron scavenging capacity amongst Y:cc23 meningococci isolated from older compared to younger patients. Iron acquisition is essential for many bacterial pathogens including the meningococcus. These polymorphisms may facilitate colonization, thereby increasing the risk of disease in vulnerable older people with altered nasopharyngeal microbiomes and nutritional status.
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Affiliation(s)
- Laura Maynard-Smith
- Correspondence: Laura Maynard-Smith, MBBS, Division of Infection and Immunity, University College London, Gower Street, London WC1E 6BT, UK ()
| | - Jeremy P Derrick
- Faculty of Biology, Medicine, and Health, University of Manchester, Manchester, United Kingdom
| | - Ray Borrow
- Meningococcal Reference Unit, UK Health Security Agency, Manchester, United Kingdom
| | - Jay Lucidarme
- Meningococcal Reference Unit, UK Health Security Agency, Manchester, United Kingdom
| | | | - Robert S Heyderman
- Division of Infection and Immunity, University College London, London, United Kingdom
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22
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Stoudenmire JL, Greenawalt AN, Cornelissen CN. Stealthy microbes: How Neisseria gonorrhoeae hijacks bulwarked iron during infection. Front Cell Infect Microbiol 2022; 12:1017348. [PMID: 36189345 PMCID: PMC9519893 DOI: 10.3389/fcimb.2022.1017348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 08/30/2022] [Indexed: 11/13/2022] Open
Abstract
Transition metals are essential for metalloprotein function among all domains of life. Humans utilize nutritional immunity to limit bacterial infections, employing metalloproteins such as hemoglobin, transferrin, and lactoferrin across a variety of physiological niches to sequester iron from invading bacteria. Consequently, some bacteria have evolved mechanisms to pirate the sequestered metals and thrive in these metal-restricted environments. Neisseria gonorrhoeae, the causative agent of the sexually transmitted infection gonorrhea, causes devastating disease worldwide and is an example of a bacterium capable of circumventing human nutritional immunity. Via production of specific outer-membrane metallotransporters, N. gonorrhoeae is capable of extracting iron directly from human innate immunity metalloproteins. This review focuses on the function and expression of each metalloprotein at gonococcal infection sites, as well as what is known about how the gonococcus accesses bound iron.
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Affiliation(s)
| | | | - Cynthia Nau Cornelissen
- Center for Translational Immunology, Institute for Biomedical Sciences, Georgia State University, Atlanta, GA, United States
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23
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de Korne-Elenbaas J, Bruisten SM, van Dam AP, Maiden MCJ, Harrison OB. The Neisseria gonorrhoeae Accessory Genome and Its Association with the Core Genome and Antimicrobial Resistance. Microbiol Spectr 2022; 10:e0265421. [PMID: 35604129 PMCID: PMC9241924 DOI: 10.1128/spectrum.02654-21] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 04/14/2022] [Indexed: 01/22/2023] Open
Abstract
The bacterial accessory genome provides the genetic flexibility needed to facilitate environment and host adaptation. In Neisseria gonorrhoeae, known accessory elements include plasmids which can transfer and mediate antimicrobial resistance (AMR); however, chromosomal accessory genes could also play a role in AMR. Here, the gonococcal accessory genome was characterized using gene-by-gene approaches and its association with the core genome and AMR were assessed. The gonococcal accessory gene pool consisted of 247 genes, which were mainly genes located on large mobile genetic elements, phage associated genes, or genes encoding putative secretion systems. Accessory elements showed similar synteny across genomes, indicating either a predisposition for particular genomic locations or ancestral inheritance that are conserved during strain expansion. Significant associations were found between the prevalence of accessory elements and core genome multi-locus sequence types (cgMLST), consistent with a structured gonococcal population despite frequent horizontal gene transfer (HGT). Increased prevalence of putative DNA exchange regulators was significantly associated with AMR, which included a putative secretion system, methyltransferases and a toxin-antitoxin system. Although frequent HGT results in high genetic diversity in the gonococcus, we found that this is mediated by a small gene pool. In fact, a highly organized genome composition was identified with a strong association between the accessory and core genome. Increased prevalence of DNA exchange regulators in antimicrobial resistant isolates suggests that genetic material exchange plays a role in the development or maintenance of AMR. These findings enhance our understanding of gonococcal genome architecture and have important implications for gonococcal population biology. IMPORTANCE The emergence of antimicrobial resistance (AMR) against third generation cephalosporins in Neisseria gonorrhoeae is a major public health concern, as these are antibiotics of last resort for the effective treatment of gonorrhea. Although the resistance mechanisms against this class of antibiotics have not been entirely resolved, resistance against other classes of antibiotics, such as tetracyclines, is known to be mediated through plasmids, which are known gonococcal extra-chromosomal accessory elements. A complete assessment of the chromosomal accessory genome content and its role in AMR has not yet been undertaken. Here, we comprehensively characterize the gonococcal accessory genome to better understand genome architecture as well as the evolution and mechanisms of AMR in this species.
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Affiliation(s)
- Jolinda de Korne-Elenbaas
- Public Health Laboratory, Department of Infectious Diseases, Public Health Service of Amsterdam, Amsterdam, the Netherlands
- Amsterdam UMC, University of Amsterdam, Department of Medical Microbiology, Amsterdam Institute for Infection and Immunity (AI&II), Academic Medical Center, Amsterdam, the Netherlands
| | - Sylvia M. Bruisten
- Public Health Laboratory, Department of Infectious Diseases, Public Health Service of Amsterdam, Amsterdam, the Netherlands
- Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity (AI&II), Amsterdam, the Netherlands
| | - Alje P. van Dam
- Public Health Laboratory, Department of Infectious Diseases, Public Health Service of Amsterdam, Amsterdam, the Netherlands
- Amsterdam UMC, University of Amsterdam, Department of Medical Microbiology, Amsterdam Institute for Infection and Immunity (AI&II), Academic Medical Center, Amsterdam, the Netherlands
| | - Martin C. J. Maiden
- Department of Zoology, Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| | - Odile B. Harrison
- Department of Zoology, Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
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24
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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: 4.0] [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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25
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Baerentsen R, Tang CM, Exley RM. Et tu, Neisseria? Conflicts of Interest Between Neisseria Species. Front Cell Infect Microbiol 2022; 12:913292. [PMID: 35811666 PMCID: PMC9263626 DOI: 10.3389/fcimb.2022.913292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 05/27/2022] [Indexed: 11/24/2022] Open
Abstract
Neisseria meningitidis and Neisseria gonorrhoeae are two obligate human pathogens that have evolved to be uniquely adapted to their host. The meningococcus is frequently carried asymptomatically in the nasopharynx, while gonococcal infection of the urogenital tract usually elicits a marked local inflammatory response. Other members of the Neisseria genus are abundant in the upper airway where they could engage in co-operative or competitive interactions with both these pathogens. Here, we briefly outline the potential sites of contact between Neisseria spp. in the body, with emphasis on the upper airway, and describe the growing yet circumstantial evidence for antagonism from carriage studies and human volunteer challenge models with Neisseria lactamica. Recent laboratory studies have characterized antagonistic mechanisms that enable competition between Neisseria species. Several of these mechanisms, including Multiple Adhesin family (Mafs), Two Partner Secretion Systems, and Type VI secretion system, involve direct contact between bacteria; the genetic organisation of these systems, and the domain structure of their effector molecules have striking similarities. Additionally, DNA from one species of Neisseria can be toxic to another species, following uptake. More research is needed to define the full repertoire of antagonistic mechanisms in Neisseria spp., their distribution in strains, their range of activity, and contribution to survival in vivo. Understanding the targets of effectors could reveal how antagonistic relationships between close relatives shape subsequent interactions between pathogens and their hosts.
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26
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Rhodes KA, Ma MC, Rendón MA, So M. Neisseria genes required for persistence identified via in vivo screening of a transposon mutant library. PLoS Pathog 2022; 18:e1010497. [PMID: 35580146 PMCID: PMC9140248 DOI: 10.1371/journal.ppat.1010497] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 05/27/2022] [Accepted: 04/04/2022] [Indexed: 11/30/2022] Open
Abstract
The mechanisms used by human adapted commensal Neisseria to shape and maintain a niche in their host are poorly defined. These organisms are common members of the mucosal microbiota and share many putative host interaction factors with Neisseria meningitidis and Neisseria gonorrhoeae. Evaluating the role of these shared factors during host carriage may provide insight into bacterial mechanisms driving both commensalism and asymptomatic infection across the genus. We identified host interaction factors required for niche development and maintenance through in vivo screening of a transposon mutant library of Neisseria musculi, a commensal of wild-caught mice which persistently and asymptomatically colonizes the oral cavity and gut of CAST/EiJ and A/J mice. Approximately 500 candidate genes involved in long-term host interaction were identified. These included homologs of putative N. meningitidis and N. gonorrhoeae virulence factors which have been shown to modulate host interactions in vitro. Importantly, many candidate genes have no assigned function, illustrating how much remains to be learned about Neisseria persistence. Many genes of unknown function are conserved in human adapted Neisseria species; they are likely to provide a gateway for understanding the mechanisms allowing pathogenic and commensal Neisseria to establish and maintain a niche in their natural hosts. Validation of a subset of candidate genes confirmed a role for a polysaccharide capsule in N. musculi persistence but not colonization. Our findings highlight the potential utility of the Neisseria musculi-mouse model as a tool for studying the pathogenic Neisseria; our work represents a first step towards the identification of novel host interaction factors conserved across the genus. The Neisseria genus contains many genetically related commensals of animals and humans, and two human pathogens, Neisseria gonorrhoeae and Neisseria meningitidis. The mechanisms allowing commensal Neisseria to maintain a niche in their host is little understood. To identify genes required for persistence, we screened a library of transposon mutants of Neisseria musculi, a commensal of wild-caught mice, in CAST/EiJ mice, which persistently and asymptomatically colonizes. Approximately 500 candidate host interaction genes were identified. A subset of these are homologs of N. meningitidis and N. gonorrhoeae genes known to modulate pathogen-host interactions in vitro. Many candidate genes have no known function, demonstrating how much remains to be learned about N. musculi niche maintenance. As many genes of unknown function are conserved in human adapted Neisseria, they provide a gateway for understanding Neisseria persistence mechanisms in general.
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Affiliation(s)
- Katherine A. Rhodes
- Immunobiology Department, University of Arizona, Tucson, Arizona, United States of America
- BIO5 Institute, University of Arizona, Tucson, Arizona, United States of America
- * E-mail:
| | - Man Cheong Ma
- Immunobiology Department, University of Arizona, Tucson, Arizona, United States of America
- BIO5 Institute, University of Arizona, Tucson, Arizona, United States of America
| | - María A. Rendón
- Immunobiology Department, University of Arizona, Tucson, Arizona, United States of America
- BIO5 Institute, University of Arizona, Tucson, Arizona, United States of America
| | - Magdalene So
- Immunobiology Department, University of Arizona, Tucson, Arizona, United States of America
- BIO5 Institute, University of Arizona, Tucson, Arizona, United States of America
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27
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Nyongesa S, Chenal M, Bernet È, Coudray F, Veyrier FJ. Sequential markerless genetic manipulations of species from the Neisseria genus. Can J Microbiol 2022; 68:551-560. [PMID: 35512370 DOI: 10.1139/cjm-2022-0024] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The development of simple and highly efficient strategies for genetic modifications are essential for post-genetic studies aimed at characterizing gene functions for various applications. We sought to develop a reliable system for Neisseria species that allows for both unmarked and accumulation of multiple genetic modifications in a single strain. In this work we developed and validated three-gene cassettes named RPLK and RPCC, comprising of an antibiotic resistance marker for positive selection, the phenotypic selection marker lacZ or mCherry, and the counter selection gene rpsL. These cassettes can be transformed with high efficiency across the Neisseria genus while significantly reducing the number of false positives compared to similar approaches. We exemplify the versatility and application of these systems by obtaining unmarked luminescent strains (knock-in) or mutants (knock-out) in different pathogenic and commensal species across the Neisseria genus in addition to the cumulative deletion of six loci in a single strain of Neisseria elongata.
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Affiliation(s)
- Sammy Nyongesa
- INRS, 14851, Centre Armand-Frappier Santé Biotechnologie, Quebec, Quebec, Canada;
| | - Martin Chenal
- INRS, 14851, Centre Armand-Frappier Santé Biotechnologie, Quebec, Quebec, Canada;
| | - Ève Bernet
- INRS, 14851, Centre Armand-Frappier Santé Biotechnologie, Quebec, Quebec, Canada;
| | - Florian Coudray
- INRS, 14851, Centre Armand-Frappier Santé Biotechnologie, Quebec, Quebec, Canada;
| | - Frédéric J Veyrier
- INRS, 14851, Centre Armand-Frappier Santé Biotechnologie, Quebec, Quebec, Canada;
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28
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Mikucki A, McCluskey NR, Kahler CM. The Host-Pathogen Interactions and Epicellular Lifestyle of Neisseria meningitidis. Front Cell Infect Microbiol 2022; 12:862935. [PMID: 35531336 PMCID: PMC9072670 DOI: 10.3389/fcimb.2022.862935] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 02/28/2022] [Indexed: 01/17/2023] Open
Abstract
Neisseria meningitidis is a gram-negative diplococcus and a transient commensal of the human nasopharynx. It shares and competes for this niche with a number of other Neisseria species including N. lactamica, N. cinerea and N. mucosa. Unlike these other members of the genus, N. meningitidis may become invasive, crossing the epithelium of the nasopharynx and entering the bloodstream, where it rapidly proliferates causing a syndrome known as Invasive Meningococcal Disease (IMD). IMD progresses rapidly to cause septic shock and meningitis and is often fatal despite aggressive antibiotic therapy. While many of the ways in which meningococci survive in the host environment have been well studied, recent insights into the interactions between N. meningitidis and the epithelial, serum, and endothelial environments have expanded our understanding of how IMD develops. This review seeks to incorporate recent work into the established model of pathogenesis. In particular, we focus on the competition that N. meningitidis faces in the nasopharynx from other Neisseria species, and how the genetic diversity of the meningococcus contributes to the wide range of inflammatory and pathogenic potentials observed among different lineages.
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Affiliation(s)
- August Mikucki
- Marshall Centre for Infectious Diseases Research and Training, School of Biomedical Sciences, University of Western Australia, Perth, WA, Australia
| | - Nicolie R. McCluskey
- Marshall Centre for Infectious Diseases Research and Training, School of Biomedical Sciences, University of Western Australia, Perth, WA, Australia
- College of Science, Health, Engineering and Education, Telethon Kids Institute, Murdoch University, Perth, WA, Australia
| | - Charlene M. Kahler
- Marshall Centre for Infectious Diseases Research and Training, School of Biomedical Sciences, University of Western Australia, Perth, WA, Australia
- *Correspondence: Charlene M. Kahler,
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29
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Laumen JGE, Abdellati S, Manoharan-Basil SS, Van Dijck C, Van den Bossche D, De Baetselier I, de Block T, Malhotra-Kumar S, Soentjes P, Pirnay JP, Kenyon C, Merabishvili M. Screening of Anorectal and Oropharyngeal Samples Fails to Detect Bacteriophages Infecting Neisseria gonorrhoeae. Antibiotics (Basel) 2022; 11:268. [PMID: 35203870 PMCID: PMC8868155 DOI: 10.3390/antibiotics11020268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 02/09/2022] [Accepted: 02/14/2022] [Indexed: 01/27/2023] Open
Abstract
There are real concerns that Neisseria gonorrhoeae may become untreatable in the near future due to the rapid emergence of antimicrobial resistance. Alternative therapies are thus urgently required. Bacteriophages active against N. gonorrhoeae could play an important role as an antibiotic-sparing therapy. To the best of our knowledge, no bacteriophages active against N. gonorrhoeae have ever been found. The aim of this study was to screen for bacteriophages able to lyse N. gonorrhoeae in oropharyngeal and anorectal swabs of 74 men who have sex with men attending a sexual health clinic in Antwerp, Belgium. We screened 210 swabs but were unable to identify an anti-gonococcal bacteriophage. This is the first report of a pilot screening that systematically searched for anti-gonococcal phages directly from clinical swabs. Further studies may consider screening for phages at other anatomical sites (e.g., stool samples, urine) or in environmental settings (e.g., toilet sewage water of sex clubs or sexually transmitted infection clinics) where N. gonorrhoeae can be found.
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Affiliation(s)
- Jolein Gyonne Elise Laumen
- Department of Clinical Sciences, Institute of Tropical Medicine, 2000 Antwerp, Belgium; (S.A.); (S.S.M.-B.); (C.V.D.); (D.V.d.B.); (I.D.B.); (T.d.B.); (P.S.); (C.K.)
- Laboratory of Medical Microbiology, Vaccine and Infectious Disease Institute, University of Antwerp, Campus Drie Eiken, 2610 Wilrijk, Belgium;
| | - Saïd Abdellati
- Department of Clinical Sciences, Institute of Tropical Medicine, 2000 Antwerp, Belgium; (S.A.); (S.S.M.-B.); (C.V.D.); (D.V.d.B.); (I.D.B.); (T.d.B.); (P.S.); (C.K.)
| | - Sheeba Santhini Manoharan-Basil
- Department of Clinical Sciences, Institute of Tropical Medicine, 2000 Antwerp, Belgium; (S.A.); (S.S.M.-B.); (C.V.D.); (D.V.d.B.); (I.D.B.); (T.d.B.); (P.S.); (C.K.)
| | - Christophe Van Dijck
- Department of Clinical Sciences, Institute of Tropical Medicine, 2000 Antwerp, Belgium; (S.A.); (S.S.M.-B.); (C.V.D.); (D.V.d.B.); (I.D.B.); (T.d.B.); (P.S.); (C.K.)
- Laboratory of Medical Microbiology, Vaccine and Infectious Disease Institute, University of Antwerp, Campus Drie Eiken, 2610 Wilrijk, Belgium;
| | - Dorien Van den Bossche
- Department of Clinical Sciences, Institute of Tropical Medicine, 2000 Antwerp, Belgium; (S.A.); (S.S.M.-B.); (C.V.D.); (D.V.d.B.); (I.D.B.); (T.d.B.); (P.S.); (C.K.)
| | - Irith De Baetselier
- Department of Clinical Sciences, Institute of Tropical Medicine, 2000 Antwerp, Belgium; (S.A.); (S.S.M.-B.); (C.V.D.); (D.V.d.B.); (I.D.B.); (T.d.B.); (P.S.); (C.K.)
| | - Tessa de Block
- Department of Clinical Sciences, Institute of Tropical Medicine, 2000 Antwerp, Belgium; (S.A.); (S.S.M.-B.); (C.V.D.); (D.V.d.B.); (I.D.B.); (T.d.B.); (P.S.); (C.K.)
| | - Surbhi Malhotra-Kumar
- Laboratory of Medical Microbiology, Vaccine and Infectious Disease Institute, University of Antwerp, Campus Drie Eiken, 2610 Wilrijk, Belgium;
| | - Patrick Soentjes
- Department of Clinical Sciences, Institute of Tropical Medicine, 2000 Antwerp, Belgium; (S.A.); (S.S.M.-B.); (C.V.D.); (D.V.d.B.); (I.D.B.); (T.d.B.); (P.S.); (C.K.)
- Center for Infectious Diseases, Queen Astrid Military Hospital, Neder-over-Heembeek, 1120 Brussels, Belgium
| | - Jean-Paul Pirnay
- Laboratory for Molecular and Cellular Technology (LabMCT), Queen Astrid Military Hospital, Neder-over-Heembeek, 1120 Brussels, Belgium; (J.-P.P.); (M.M.)
| | - Chris Kenyon
- Department of Clinical Sciences, Institute of Tropical Medicine, 2000 Antwerp, Belgium; (S.A.); (S.S.M.-B.); (C.V.D.); (D.V.d.B.); (I.D.B.); (T.d.B.); (P.S.); (C.K.)
- Department of Medicine, University of Cape Town, Cape Town 7701, South Africa
| | - Maia Merabishvili
- Laboratory for Molecular and Cellular Technology (LabMCT), Queen Astrid Military Hospital, Neder-over-Heembeek, 1120 Brussels, Belgium; (J.-P.P.); (M.M.)
- Microbiology and Virology (EIBMV), Eliava Institute of Bacteriophage, Tbilisi 0162, Georgia
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Abstract
Neisseria gonorrhoeae is an obligate human pathogen that is the cause of the sexually transmitted disease gonorrhoea. Recently, there has been a surge in gonorrhoea cases that has been exacerbated by the rapid rise in gonococcal multidrug resistance to all useful antimicrobials resulting in this organism becoming a significant public health burden. Therefore, there is a clear and present need to understand the organism's biology through its physiology and pathogenesis to help develop new intervention strategies. The gonococcus initially colonises and adheres to host mucosal surfaces utilising a type IV pilus that helps with microcolony formation. Other adhesion strategies include the porin, PorB, and the phase variable outer membrane protein Opa. The gonococcus is able to subvert complement mediated killing and opsonisation by sialylation of its lipooligosaccharide and deploys a series of anti-phagocytic mechanisms. N. gonorrhoeae is a fastidious organism that is able to grow on a limited number of primary carbon sources such as glucose and lactate. The utilization of lactate by the gonococcus has been implicated in a number of pathogenicity mechanisms. The bacterium lives mainly in microaerobic environments and can grow both aerobically and anaerobically with the aid of nitrite. The gonococcus does not produce siderophores for scavenging iron but can utilize some produced by other bacteria, and it is able to successful chelate iron from host haem, transferrin and lactoferrin. The gonococcus is an incredibly versatile human pathogen; in the following chapter, we detail the intricate mechanisms used by the bacterium to invade and survive within the host.
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Affiliation(s)
- Luke R Green
- Department of Infection, Immunity & Cardiovascular Disease, University of Sheffield, Sheffield, United Kingdom
| | - Joby Cole
- Department of Infection, Immunity & Cardiovascular Disease, University of Sheffield, Sheffield, United Kingdom
| | - Ernesto Feliz Diaz Parga
- Department of Infection, Immunity & Cardiovascular Disease, University of Sheffield, Sheffield, United Kingdom
| | - Jonathan G Shaw
- Department of Infection, Immunity & Cardiovascular Disease, University of Sheffield, Sheffield, United Kingdom.
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31
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Mullally CA, Mikucki A, Wise MJ, Kahler CM. Modelling evolutionary pathways for commensalism and hypervirulence in Neisseria meningitidis. Microb Genom 2021; 7. [PMID: 34704920 PMCID: PMC8627216 DOI: 10.1099/mgen.0.000662] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Neisseria meningitidis, the meningococcus, resides exclusively in humans and causes invasive meningococcal disease (IMD). The population of N. meningitidis is structured into stable clonal complexes by limited horizontal recombination in this naturally transformable species. N. meningitidis is an opportunistic pathogen, with some clonal complexes, such as cc53, effectively acting as commensal colonizers, while other genetic lineages, such as cc11, are rarely colonizers but are over-represented in IMD and are termed hypervirulent. This study examined theoretical evolutionary pathways for pathogenic and commensal lineages by examining the prevalence of horizontally acquired genomic islands (GIs) and loss-of-function (LOF) mutations. Using a collection of 4850 genomes from the BIGSdb database, we identified 82 GIs in the pan-genome of 11 lineages (10 hypervirulent and one commensal lineage). A new computational tool, Phaser, was used to identify frameshift mutations, which were examined for statistically significant association with genetic lineage. Phaser identified a total of 144 frameshift loci of which 105 were shown to have a statistically significant non-random distribution in phase status. The 82 GIs, but not the LOF loci, were associated with genetic lineage and invasiveness using the disease carriage ratio metric. These observations have been integrated into a new model that infers the early events of the evolution of the human adapted meningococcus. These pathways are enriched for GIs that are involved in modulating attachment to the host, growth rate, iron uptake and toxin expression which are proposed to increase competition within the meningococcal population for the limited environmental niche of the human nasopharynx. We surmise that competition for the host mucosal surface with the nasopharyngeal microbiome has led to the selection of isolates with traits that enable access to cell types (non-phagocytic and phagocytic) in the submucosal tissues leading to an increased risk for IMD.
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Affiliation(s)
- Christopher A. Mullally
- The Marshall Center for Infectious Diseases Research and Training, School of Biomedical Science, University of Western Australia, Perth, Australia
| | - August Mikucki
- The Marshall Center for Infectious Diseases Research and Training, School of Biomedical Science, University of Western Australia, Perth, Australia
| | - Michael J. Wise
- The Marshall Center for Infectious Diseases Research and Training, School of Biomedical Science, University of Western Australia, Perth, Australia
- School of Physics, Mathematics and Computing, University of Western Australia, Perth, Australia
| | - Charlene M. Kahler
- The Marshall Center for Infectious Diseases Research and Training, School of Biomedical Science, University of Western Australia, Perth, Australia
- Telethon Kids Institute, Perth Children’s Hospital, Perth, Australia
- *Correspondence: Charlene M. Kahler,
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32
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Custodio R, Ford RM, Ellison CJ, Liu G, Mickute G, Tang CM, Exley RM. Type VI secretion system killing by commensal Neisseria is influenced by expression of type four pili. eLife 2021; 10:63755. [PMID: 34232858 PMCID: PMC8263058 DOI: 10.7554/elife.63755] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 06/27/2021] [Indexed: 12/14/2022] Open
Abstract
Type VI Secretion Systems (T6SSs) are widespread in bacteria and can dictate the development and organisation of polymicrobial ecosystems by mediating contact dependent killing. In Neisseria species, including Neisseria cinerea a commensal of the human respiratory tract, interbacterial contacts are mediated by Type four pili (Tfp) which promote formation of aggregates and govern the spatial dynamics of growing Neisseria microcolonies. Here, we show that N. cinerea expresses a plasmid-encoded T6SS that is active and can limit growth of related pathogens. We explored the impact of Tfp on N. cinerea T6SS-dependent killing within a colony and show that pilus expression by a prey strain enhances susceptibility to T6SS compared to a non-piliated prey, by preventing segregation from a T6SS-wielding attacker. Our findings have important implications for understanding how spatial constraints during contact-dependent antagonism can shape the evolution of microbial communities.
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Affiliation(s)
- Rafael Custodio
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| | - Rhian M Ford
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| | - Cara J Ellison
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| | - Guangyu Liu
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| | - Gerda Mickute
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| | - Christoph M Tang
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| | - Rachel M Exley
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
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33
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MacAlasdair N, Pesonen M, Brynildsrud O, Eldholm V, Kristiansen PA, Corander J, Caugant DA, Bentley SD. The effect of recombination on the evolution of a population of Neisseria meningitidis. Genome Res 2021; 31:1258-1268. [PMID: 34108268 PMCID: PMC8256868 DOI: 10.1101/gr.264465.120] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 04/22/2021] [Indexed: 12/02/2022]
Abstract
Neisseria meningitidis (the meningococcus) is a major human pathogen with a history of high invasive disease burden, particularly in sub-Saharan Africa. Our current understanding of the evolution of meningococcal genomes is limited by the rarity of large-scale genomic population studies and lack of in-depth investigation of the genomic events associated with routine pathogen transmission. Here, we fill this knowledge gap by a detailed analysis of 2839 meningococcal genomes obtained through a carriage study of over 50,000 samples collected systematically in Burkina Faso, West Africa, before, during, and after the serogroup A vaccine rollout, 2009-2012. Our findings indicate that the meningococcal genome is highly dynamic, with highly recombinant loci and frequent gene sharing across deeply separated lineages in a structured population. Furthermore, our findings illustrate how population structure can correlate with genome flexibility, as some lineages in Burkina Faso are orders of magnitude more recombinant than others. We also examine the effect of selection on the population, in particular how it is correlated with recombination. We find that recombination principally acts to prevent the accumulation of deleterious mutations, although we do also find an example of recombination acting to speed the adaptation of a gene. In general, we show the importance of recombination in the evolution of a geographically expansive population with deep population structure in a short timescale. This has important consequences for our ability to both foresee the outcomes of vaccination programs and, using surveillance data, predict when lineages of the meningococcus are likely to become a public health concern.
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Affiliation(s)
- Neil MacAlasdair
- Parasites and Microbes, Wellcome Sanger Institute, Cambridge CB10 1SA, United Kingdom
| | - Maiju Pesonen
- Oslo Centre for Biostatistics and Epidemiology (OCBE), Oslo University Hospital Research Support Services, Blindern, 0317 Oslo, Norway
| | - Ola Brynildsrud
- Division for Infection Control and Environmental Health, Norwegian Institute of Public Health, 0213 Oslo, Norway
- Department of Food Safety and Infection Biology, Faculty of Veterinary Science, Norwegian University of Life Science, 0454 Oslo, Norway
| | - Vegard Eldholm
- Division for Infection Control and Environmental Health, Norwegian Institute of Public Health, 0213 Oslo, Norway
| | - Paul A Kristiansen
- Division for Infection Control and Environmental Health, Norwegian Institute of Public Health, 0213 Oslo, Norway
| | - Jukka Corander
- Parasites and Microbes, Wellcome Sanger Institute, Cambridge CB10 1SA, United Kingdom
- University of Oslo, Department of Biostatistics, Blindern, 0317 Oslo, Norway
- Helsinki Institute for Information Technology HIIT, Department of Mathematics and Statistics, University of Helsinki, 00014 Helsinki, Finland
| | - Dominique A Caugant
- Division for Infection Control and Environmental Health, Norwegian Institute of Public Health, 0213 Oslo, Norway
- Department of Community Medicine, Faculty of Medicine, University of Oslo, Blindern, 0316 Oslo, Norway
| | - Stephen D Bentley
- Parasites and Microbes, Wellcome Sanger Institute, Cambridge CB10 1SA, United Kingdom
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Schörner MA, Passarelli‐Araujo H, Scheffer MC, Hartmann Barazzetti F, Motta Martins J, de Melo Machado H, Palmeiro JK, Bazzo ML. Genomic analysis of Neisseria elongata isolate from a patient with infective endocarditis. FEBS Open Bio 2021; 11:1987-1996. [PMID: 34038628 PMCID: PMC8406478 DOI: 10.1002/2211-5463.13201] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 04/28/2021] [Accepted: 05/24/2021] [Indexed: 11/24/2022] Open
Abstract
Neisseria elongata is part of the commensal microbiota of the oropharynx. Although it is not considered pathogenic to humans, N. elongata has been implicated in several cases of infective endocarditis (IE). Here, we report a case of IE caused by N. elongata subsp. nitroreducens (Nel_M001) and compare its genome with 17 N. elongata genomes available in GenBank. We also evaluated resistance and virulence profiles with Comprehensive Antibiotic Resistance and Virulence Finder databases. The results showed a wide diversity among N. elongata isolates. Based on the pangenome cumulative curve, we demonstrate that N. elongata has an open pangenome. We found several different resistance genes, mainly associated with antibiotic efflux pumps. A wide range of virulence genes was observed, predominantly pilus formation genes. Nel_M001 was the only isolate to present two copies of some pilus genes and not present nspA gene. Together, our results provide insights into how this commensal microorganism can cause IE and may assist further biological investigations on nonpathogenic Neisseria spp. Case reporting and pangenome analyses are critical for enhancing our understanding of IE pathogenesis, as well as for alerting physicians and microbiologists to enable rapid identification and treatment to avoid unfavorable outcomes.
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Affiliation(s)
- Marcos André Schörner
- Molecular Biology, Microbiology and Serology LaboratoryFederal University of Santa CatarinaFlorianopolisBrazil
| | - Hemanoel Passarelli‐Araujo
- Department of Biochemistry and ImmunologyBiological Sciences InstituteFederal University of Minas GeraisBelo HorizonteBrazil
| | - Mara Cristina Scheffer
- Polydoro Ernani de São Thiago University HospitalFederal University of Santa CatarinaFlorianopolisBrazil
| | | | - Jessica Motta Martins
- Molecular Biology, Microbiology and Serology LaboratoryFederal University of Santa CatarinaFlorianopolisBrazil
| | - Hanalydia de Melo Machado
- Molecular Biology, Microbiology and Serology LaboratoryFederal University of Santa CatarinaFlorianopolisBrazil
| | | | - Maria Luiza Bazzo
- Molecular Biology, Microbiology and Serology LaboratoryFederal University of Santa CatarinaFlorianopolisBrazil
- Department of Clinical AnalysisFederal University of Santa CatarinaFlorianopolisBrazil
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Singh R, Kusalik A, Dillon JAR. Bioinformatics tools used for whole-genome sequencing analysis of Neisseria gonorrhoeae: a literature review. Brief Funct Genomics 2021; 21:78-89. [PMID: 34170311 DOI: 10.1093/bfgp/elab028] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 05/21/2021] [Accepted: 05/24/2021] [Indexed: 01/02/2023] Open
Abstract
Whole-genome sequencing (WGS) data are well established for the investigation of gonococcal transmission, antimicrobial resistance prediction, population structure determination and population dynamics. A variety of bioinformatics tools, repositories, services and platforms have been applied to manage and analyze Neisseria gonorrhoeae WGS datasets. This review provides an overview of the various bioinformatics approaches and resources used in 105 published studies (as of 30 April 2021). The challenges in the analysis of N. gonorrhoeae WGS datasets, as well as future bioinformatics requirements, are also discussed.
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Affiliation(s)
- Reema Singh
- Department of Biochemistry, Microbiology and Immunology
| | - Anthony Kusalik
- Department of Computer Science at the University of Saskatchewan
| | - Jo-Anne R Dillon
- Department of Biochemistry Microbiology and Immunology, College of Medicine, c/o Vaccine and Infectious Disease Organization, University of Saskatchewan, 120 Veterinary Road, Saskatoon, Saskatchewan S7N5E3, Canada
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Antimicrobial Resistance Profiles of Human Commensal Neisseria Species. Antibiotics (Basel) 2021; 10:antibiotics10050538. [PMID: 34066576 PMCID: PMC8148603 DOI: 10.3390/antibiotics10050538] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 04/23/2021] [Accepted: 04/27/2021] [Indexed: 11/17/2022] Open
Abstract
Pathogenic Neisseria gonorrhoeae causes the sexually transmitted infection gonorrhea. N. gonorrhoeae has evolved high levels of antimicrobial resistance (AR) leading to therapeutic failures even in dual-therapy treatment with azithromycin and ceftriaxone. AR mechanisms can be acquired by genetic transfer from closely related species, such as naturally competent commensal Neisseria species. At present, little is known about the antimicrobial resistance profiles of commensal Neisseria. Here, we characterized the phenotypic resistance profile of four commensal Neisseria species (N. lactamica, N. cinerea, N. mucosa, and N. elongata) against 10 commonly used antibiotics, and compared their profiles to 4 N. gonorrhoeae strains, using disk diffusion and minimal inhibitory concentration assays. Overall, we observed that 3 of the 4 commensals were more resistant to several antibiotics than pathogenic N. gonorrhoeae strains. Next, we compared publicly available protein sequences of known AR genes, including penicillin-binding-protein 2 (PBP2) from commensals and N. gonorrhoeae strains. We found mutations in PBP2 known to confer resistance in N. gonorrhoeae also present in commensal Neisseria sequences. Our results suggest that commensal Neisseria have unexplored antibiotic resistance gene pools that may be exchanged with pathogenic N. gonorrhoeae, possibly impairing drug development and clinical treatment.
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37
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Reyes Díaz LM, Lastre González MDSJB, Cuello M, Sierra-González VG, Ramos Pupo R, Lantero MI, Harandi AM, Black S, Pérez O. VA-MENGOC-BC Vaccination Induces Serum and Mucosal Anti Neisseria gonorrhoeae Immune Responses and Reduces the Incidence of Gonorrhea. Pediatr Infect Dis J 2021; 40:375-381. [PMID: 33591079 DOI: 10.1097/inf.0000000000003047] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
BACKGROUND Overall, there are over 30 different sexually transmitted infections with Neisseria gonorrhoeae being the third most frequent with a reported 78 million cases per year. Gonococcal infection causes genital inflammation, which can be a risk factor for others sexually transmitted infections, particularly human immunodeficiency virus. Gonorrhea is a treatable disease, but recently an increase in antibiotic resistance has been of concern. There are currently no vaccines available. However, parenteral vaccination with anti N. meningitidis serogroup B vaccine has been reported to decrease the incidence of gonococcal burden in New Zealand and in Cuba despite the fact that parenteral vaccination is not deemed to induce mucosal IgA. Here we explore possible mechanisms of protection against gonococcal infection through parenteral meningococcal B vaccination. METHODS Ninety-two serum, saliva and oropharyngeal swabs samples of young adults (healthy and Neisseria carriers) of the internal higher school were obtained. They have been vaccinated with VA-MENGOC-BC (MBV) during their infancy and boosted with a third dose during this study. Serum and saliva samples were analyzed by ELISA and Western blot to measured IgG and IgA antibodies against N. meningitidis and N. gonorrhoeae antigens. N. meningitidis carriers were determined by standard microbiologic test. In addition, we reviewed epidemiologic data for N. meningitidis and N. gonorrhoeae infections in Cuba. RESULTS Epidemiologic data show the influence of MBV over gonorrhea incidence suggesting to be dependent of sexual arrival age of vaccines but not over syphilis. Laboratorial data permit the detection of 70 and 22 noncarriers and carriers of N. meningitidis, respectively. Serum anti-MBV antigens (PL) responses were boosted by a third dose and were independent of carriage stages, but saliva anti-PL IgA responses were only present and were significant induced in carriers subjects. Carriers boosted with a third dose of MBV induced similar antigonococcal and -PL saliva IgA and serum IgG responses; meanwhile, serum antigonococcal IgG was significantly lower. In saliva, at least 2 gonococcal antigens were identified by Western blot. Finally, gonococcal-specific mucosal IgA antibody responses, in addition to the serum IgG antibodies, might contributed to the reduction of the incidence of N. gonorrhoeae. We hypothesize that this might have contributed to the observed reductions of the incidence of N. gonorrhoeae. CONCLUSION These results suggest a mechanism for the influence of a Proteoliposome-based meningococcal BC vaccine on gonococcal incidence.
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Affiliation(s)
- Laura M Reyes Díaz
- From the Instituto de Ciencias Básicas y Preclínicas "Victoria de Girón," Havana, Cuba
| | | | - Maribel Cuello
- Facultad de Ingenierías, Universidad Técnica "Luis Vargas Torres" de Esmeraldas, Esmeralda, Ecuador
| | | | - Raúl Ramos Pupo
- Immunology Department, Instituto de Ciencias Básicas y Preclínicas "Victoria de Girón," Havana, Cuba
- Biomedical Research Institute (BIOMED), Faculty of Medicine and Life Science, Hasselt University, Hasselt, Belgium
| | | | - Ali M Harandi
- Department of Microbiology & Immunology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Vaccine Evaluation Center, British Columbia Children's Hospital Research Institute, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Steven Black
- Cincinnati Children's Hospital, Cincinnati, Ohio
| | - Oliver Pérez
- From the Instituto de Ciencias Básicas y Preclínicas "Victoria de Girón," Havana, Cuba
- Latin American and Caribean Association of Immunology (ALACI), Havana, Cuba
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38
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Hou L, Wang L, Qiu Y, Xiong Y, Xiao H, Yi H, Wen X, Lin Z, Wang Z, Yang X, Jiang Z. Effects of Protein Restriction and Subsequent Realimentation on Body Composition, Gut Microbiota and Metabolite Profiles in Weaned Piglets. Animals (Basel) 2021; 11:ani11030686. [PMID: 33806535 PMCID: PMC8001264 DOI: 10.3390/ani11030686] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2021] [Revised: 02/21/2021] [Accepted: 02/27/2021] [Indexed: 02/07/2023] Open
Abstract
Simple Summary Protein restriction strategies are often used in weaned piglets to reduce the incidence of intestinal disorders that are sensitive to dietary protein supply, but may lead to a decline in production performance. Subsequent protein realimentation can alleviate the detrimental effects of reduced dietary protein on growth. However, the effects of protein realimentation on the body composition, gut microbiota and metabolite profiles of piglets are poorly understood. The present study, combining comparative slaughter methods, microbiome and metabolome analyses, demonstrated that protein restriction and subsequent realimentation lead to compensatory growth and compensatory protein deposition in piglets, and contribute to animal intestinal health by altering the gut microbiota and metabolite profiles. Abstract The objective of this study was to evaluate the effects of protein restriction and subsequent protein realimentation on the body composition, gut microbiota and metabolite profiles of piglets. Fifty weaned piglets were randomly assigned to two treatments: a normal protein (NP) group (20% crude protein (CP)) or a low protein (LP) group (16% CP) with five animals per pen and five pens per group. Treatment diets were fed for 14 d during the protein restriction phase, and then all pigs were fed the same nursery diets with a normal CP level (19% CP) during the protein realimentation phase until they reached an average target body weight (BW) of 25 ± 0.15 kg. At day 14 and the end of the experiment, one piglet close to the average BW of each pen was slaughtered to determine body composition, microbial composition and microbial metabolites. Results showed that there was no difference (p > 0.05) in the experimental days to reach target BW between the LP and NP groups. The average daily gain (ADG) and gain:feed ratio (G:F) during the protein restriction phase as well as BW at day 14, were significantly decreased (p < 0.05) in the LP group compared with the NP group. However, there were no significant differences (p > 0.05) during the protein realimentation phase and the overall experiment. Similarly, piglets in the LP group showed a significantly decreased body protein content (p < 0.05) at day 14, but not (p > 0.05) at the end of the experiment. The relative abundance of Parabacteroides, Butyricicoccus, Olsenella, Succinivibrio and Pseudoramibacter were significantly increased (p < 0.05), while the relative abundance of Alloprevotella and Faecalicoccus were significantly decreased (p < 0.05) in the LP group at day 14. At the end of the experiment, the piglets in the LP group showed a higher (p < 0.05) colonic relative abundances of Parabacteroides, unidentified Christensenellaceae and Caproiciproducens, and a lower (p < 0.05) relative abundance of unidentified Prevotellaceae, Haemophilus, Marvinbryantia, Faecalibaculum, Neisseria and Dubosiella than those in the NP group. Metabolomics analyses indicated that tryptophan metabolism and vitamin metabolism were enriched in the LP group at day 14, and glycerophospholipid metabolism and fatty acid esters of hydroxy fatty acid metabolism were enriched at the end of the experiment. Moreover, Spearman’s correlation analysis demonstrated that the microbial composition was highly correlated with changes in colonic metabolites. Collectively, these results indicated that protein restriction and subsequent realimentation lead to compensatory growth and compensatory protein deposition in piglets and contribute to animal intestinal health by altering the gut microbiota and its metabolites.
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Affiliation(s)
- Lei Hou
- Institute of Animal Nutrition, Northeast Agricultural University, Harbin 150030, China;
| | - Li Wang
- Institute of Animal Science, Guangdong Academy of Agricultural Sciences, State Key Laboratory of Livestock and Poultry Breeding, Ministry of Agriculture Key Laboratory of Animal Nutrition and Feed Science in South China, Guangdong Provincial Key Laboratory of Animal Breeding and Nutrition, Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510640, China; (Y.Q.); (Y.X.); (H.X.); (H.Y.); (X.W.); (Z.L.); (Z.W.); (X.Y.)
- Correspondence: (L.W.); (Z.J.)
| | - Yueqin Qiu
- Institute of Animal Science, Guangdong Academy of Agricultural Sciences, State Key Laboratory of Livestock and Poultry Breeding, Ministry of Agriculture Key Laboratory of Animal Nutrition and Feed Science in South China, Guangdong Provincial Key Laboratory of Animal Breeding and Nutrition, Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510640, China; (Y.Q.); (Y.X.); (H.X.); (H.Y.); (X.W.); (Z.L.); (Z.W.); (X.Y.)
| | - YunXia Xiong
- Institute of Animal Science, Guangdong Academy of Agricultural Sciences, State Key Laboratory of Livestock and Poultry Breeding, Ministry of Agriculture Key Laboratory of Animal Nutrition and Feed Science in South China, Guangdong Provincial Key Laboratory of Animal Breeding and Nutrition, Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510640, China; (Y.Q.); (Y.X.); (H.X.); (H.Y.); (X.W.); (Z.L.); (Z.W.); (X.Y.)
| | - Hao Xiao
- Institute of Animal Science, Guangdong Academy of Agricultural Sciences, State Key Laboratory of Livestock and Poultry Breeding, Ministry of Agriculture Key Laboratory of Animal Nutrition and Feed Science in South China, Guangdong Provincial Key Laboratory of Animal Breeding and Nutrition, Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510640, China; (Y.Q.); (Y.X.); (H.X.); (H.Y.); (X.W.); (Z.L.); (Z.W.); (X.Y.)
| | - Hongbo Yi
- Institute of Animal Science, Guangdong Academy of Agricultural Sciences, State Key Laboratory of Livestock and Poultry Breeding, Ministry of Agriculture Key Laboratory of Animal Nutrition and Feed Science in South China, Guangdong Provincial Key Laboratory of Animal Breeding and Nutrition, Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510640, China; (Y.Q.); (Y.X.); (H.X.); (H.Y.); (X.W.); (Z.L.); (Z.W.); (X.Y.)
| | - Xiaolu Wen
- Institute of Animal Science, Guangdong Academy of Agricultural Sciences, State Key Laboratory of Livestock and Poultry Breeding, Ministry of Agriculture Key Laboratory of Animal Nutrition and Feed Science in South China, Guangdong Provincial Key Laboratory of Animal Breeding and Nutrition, Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510640, China; (Y.Q.); (Y.X.); (H.X.); (H.Y.); (X.W.); (Z.L.); (Z.W.); (X.Y.)
| | - Zeling Lin
- Institute of Animal Science, Guangdong Academy of Agricultural Sciences, State Key Laboratory of Livestock and Poultry Breeding, Ministry of Agriculture Key Laboratory of Animal Nutrition and Feed Science in South China, Guangdong Provincial Key Laboratory of Animal Breeding and Nutrition, Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510640, China; (Y.Q.); (Y.X.); (H.X.); (H.Y.); (X.W.); (Z.L.); (Z.W.); (X.Y.)
| | - Zhikang Wang
- Institute of Animal Science, Guangdong Academy of Agricultural Sciences, State Key Laboratory of Livestock and Poultry Breeding, Ministry of Agriculture Key Laboratory of Animal Nutrition and Feed Science in South China, Guangdong Provincial Key Laboratory of Animal Breeding and Nutrition, Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510640, China; (Y.Q.); (Y.X.); (H.X.); (H.Y.); (X.W.); (Z.L.); (Z.W.); (X.Y.)
| | - Xuefen Yang
- Institute of Animal Science, Guangdong Academy of Agricultural Sciences, State Key Laboratory of Livestock and Poultry Breeding, Ministry of Agriculture Key Laboratory of Animal Nutrition and Feed Science in South China, Guangdong Provincial Key Laboratory of Animal Breeding and Nutrition, Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510640, China; (Y.Q.); (Y.X.); (H.X.); (H.Y.); (X.W.); (Z.L.); (Z.W.); (X.Y.)
| | - Zongyong Jiang
- Institute of Animal Nutrition, Northeast Agricultural University, Harbin 150030, China;
- Institute of Animal Science, Guangdong Academy of Agricultural Sciences, State Key Laboratory of Livestock and Poultry Breeding, Ministry of Agriculture Key Laboratory of Animal Nutrition and Feed Science in South China, Guangdong Provincial Key Laboratory of Animal Breeding and Nutrition, Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510640, China; (Y.Q.); (Y.X.); (H.X.); (H.Y.); (X.W.); (Z.L.); (Z.W.); (X.Y.)
- Correspondence: (L.W.); (Z.J.)
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Sukhum KV, Jean S, Wallace M, Anderson N, Burnham CA, Dantas G. Genomic Characterization of Emerging Bacterial Uropathogen Neisseria meningitidis, Which Was Misidentified as Neisseria gonorrhoeae by Nucleic Acid Amplification Testing. J Clin Microbiol 2021; 59:e01699-20. [PMID: 33177123 PMCID: PMC8111160 DOI: 10.1128/jcm.01699-20] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 11/05/2020] [Indexed: 02/07/2023] Open
Abstract
Neisseria meningitidis and Neisseria gonorrhoeae are pathogenic bacteria that can cause human infections. While N. meningitidis infections are associated with bacterial meningitis and bacteremia, a strain of N. meningitidis, isolated from the urogenital system, has recently been associated with urethritis. As this strain is becoming prominent as an emerging pathogen, it is essential to assess identification tools for N. meningitidis and N. gonorrhoeae urogenital isolates. Consecutive N. meningitidis isolates recovered from urogenital cultures of symptomatic patients with presumptive diagnoses of gonorrhea and a random selection of N. gonorrhoeae isolates recovered from the same population within the same time frame were characterized with routine identification systems, antimicrobial susceptibility testing, and whole-genome sequencing. Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS), multilocus sequence typing, 16S rRNA gene sequence, and average nucleotide identity methods accurately identified 95% (18/19) of N. meningitidis and N. gonorrhoeae isolates. With the Aptima Combo 2 CT/NG test, 30% (3/10) of N. meningitidis isolates were misidentified as N. gonorrhoeae, but no misidentifications were found with the Xpert CT/NG nucleic acid amplification test (NAAT). Phylogenetic core genome and single nucleotide polymorphism (SNP)-based grouping analyses showed that urogenital N. meningitidis isolates were highly related and phylogenetically distinct from N. gonorrhoeae and respiratory N. meningitidis isolates but similar to urogenital N. meningitidis isolates from patients with urethritis in the United States. Urogenital N. meningitidis isolates were predominantly azithromycin resistant, while N. gonorrhoeae isolates were azithromycin susceptible. These data indicate that urogenital isolates of N. meningitidis can cause false-positive detections with N. gonorrhoeae diagnostic assays. Misidentification of urogenital N. meningitidis isolates may confound public health-related activities for gonorrhea, and future studies are needed to understand the impact on clinical outcome of N. meningitidis urogenital infection.
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Affiliation(s)
- Kimberley V Sukhum
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA
- Department of Pathology and Immunology, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA
| | - Sophonie Jean
- Department of Pathology and Immunology, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA
- Department of Pathology & Laboratory Medicine, Nationwide Children's Hospital, Columbus, Ohio, USA
| | - Meghan Wallace
- Department of Pathology and Immunology, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA
| | - Neil Anderson
- Department of Pathology and Immunology, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA
| | - C A Burnham
- Department of Pathology and Immunology, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA
- Department of Medicine, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA
- Department of Pediatrics, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA
- Department of Molecular Microbiology, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA
| | - Gautam Dantas
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA
- Department of Pathology and Immunology, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA
- Department of Molecular Microbiology, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, Missouri, USA
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40
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Kahler CM. Neisseria species and their complicated relationships with human health. MICROBIOLOGY AUSTRALIA 2021. [DOI: 10.1071/ma21024] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Neisseria spp. are a transient low abundance member of the human microbiome. This species contains the very well described pathogens, Neisseria gonorrhoeae and N. meningitidis. Recent advances in molecular typing have revealed that this genus is more diverse than previously thought and that commensal species may have important roles in inhibiting the growth the pathogens. This short review summates these new findings and examines the evidence that the relatively under-reported Neisseria commensal species maybe beneficial to human health.
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41
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Al Suwayyid BA, Rankine-Wilson L, Speers DJ, Wise MJ, Coombs GW, Kahler CM. Meningococcal Disease-Associated Prophage-Like Elements Are Present in Neisseria gonorrhoeae and Some Commensal Neisseria Species. Genome Biol Evol 2020; 12:3938-3950. [PMID: 32031617 PMCID: PMC7058167 DOI: 10.1093/gbe/evaa023] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/04/2020] [Indexed: 12/14/2022] Open
Abstract
Neisseria spp. possess four genogroups of filamentous prophages, termed Nf1 to 4. A filamentous bacteriophage from the Nf1 genogroup termed meningococcal disease-associated phage (MDA φ) is associated with clonal complexes of Neisseria meningitidis that cause invasive meningococcal disease. Recently, we recovered an isolate of Neisseria gonorrhoeae (ExNg63) from a rare case of gonococcal meningitis, and found that it possessed a region with 90% similarity to Nf1 prophages, specifically, the meningococcal MDA φ. This led to the hypothesis that the Nf1 prophage may be more widely distributed amongst the genus Neisseria. An analysis of 92 reference genomes revealed the presence of intact Nf1 prophages in the commensal species, Neisseria lactamica and Neisseria cinerea in addition to the pathogen N. gonorrhoeae. In N. gonorrhoeae, Nf1 prophages had a restricted distribution but were present in all representatives of MLST ST1918. Of the 160 phage integration sites identified, only one common insertion site was found between one isolate of N. gonorrhoeae and N. meningitidis. There was an absence of any obvious conservation of the receptor for prophage entry, PilE, suggesting that the phage may have been obtained by natural transformation. An examination of the restriction modification systems and mutated mismatch repair systems with prophage presence suggested that there was no obvious preference for these hosts. A timed phylogeny inferred that N. meningitidis was the donor of the Nf1 prophages in N. lactamica and N. gonorrhoeae. Further work is required to determine whether Nf1 prophages are active and can act as accessory colonization factors in these species.
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Affiliation(s)
- Barakat A Al Suwayyid
- The Marshall Centre for Infectious Diseases Research and Training, The University of Western Australia, Crawley, Australia.,School of Biomedical Sciences, The University of Western Australia, Crawley, Australia.,Ministry of Education, Riyadh, Saudi Arabia
| | - Leah Rankine-Wilson
- The Marshall Centre for Infectious Diseases Research and Training, The University of Western Australia, Crawley, Australia.,School of Biomedical Sciences, The University of Western Australia, Crawley, Australia
| | - David J Speers
- Department of Microbiology, PathWest Laboratory Medicine WA, Queen Elizabeth II Medical Centre, Nedlands, Australia.,School of Medicine and Pharmacology, University of Western Australia, Crawley, Australia
| | - Michael J Wise
- The Marshall Centre for Infectious Diseases Research and Training, The University of Western Australia, Crawley, Australia.,Computer Science and Software Engineering, The University of Western Australia, Crawley, Australia
| | - Geoffrey W Coombs
- Department of Microbiology, PathWest Laboratory Medicine WA, Fiona Stanley Hospital, Murdoch, Australia.,Antimicrobial Resistance and Infectious Diseases Research Laboratory, School of Veterinary Life Sciences, Murdoch University, Australia
| | - Charlene M Kahler
- The Marshall Centre for Infectious Diseases Research and Training, The University of Western Australia, Crawley, Australia.,School of Biomedical Sciences, The University of Western Australia, Crawley, Australia
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42
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Aho EL, Ogle JM, Finck AM. The Human Microbiome as a Focus of Antibiotic Discovery: Neisseria mucosa Displays Activity Against Neisseria gonorrhoeae. Front Microbiol 2020; 11:577762. [PMID: 33343520 PMCID: PMC7744932 DOI: 10.3389/fmicb.2020.577762] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 11/09/2020] [Indexed: 01/06/2023] Open
Abstract
Neisseria gonorrhoeae infections are a serious global health problem. This organism has developed disturbing levels of antibiotic resistance, resulting in the need for new approaches to prevent and treat gonorrhea. The genus Neisseria also includes several members of the human microbiome that live in close association with an array of microbial partners in a variety of niches. We designed an undergraduate antibiotic discovery project to examine a panel of nonpathogenic Neisseria species for their ability to produce antimicrobial secondary metabolites. Five strains belonging to the N. mucosa species group displayed activity against other Neisseria in delayed antagonism assays; three of these were active against N. gonorrhoeae. The antimicrobial compound secreted by N. mucosa NRL 9300 remained active in the presence of catalase, trypsin, and HEPES buffer, and effectively inhibited a DNA uptake mutant of N. gonorrhoeae. Antimicrobial activity was also retained in an ethyl acetate extract of plate grown N. mucosa NRL 9300. These data suggest N. mucosa produces an antimicrobial secondary metabolite that is distinct from previously described antigonococcal agents. This work also serves as a demonstration project that could easily be adapted to studying other members of the human microbiome in undergraduate settings. We offer the perspective that both introductory and more advanced course-based and apprentice-style antibiotic discovery projects focused on the microbiome have the potential to enrich undergraduate curricula and we describe transferrable techniques and strategies to facilitate project design.
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Affiliation(s)
- Ellen L Aho
- Department of Biology, Concordia College, Moorhead, MN, United States
| | - Jenie M Ogle
- Department of Biology, Concordia College, Moorhead, MN, United States
| | - Anna M Finck
- Department of Biology, Concordia College, Moorhead, MN, United States
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43
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Cheng Z, Do T, Mankia K, Meade J, Hunt L, Clerehugh V, Speirs A, Tugnait A, Emery P, Devine D. Dysbiosis in the oral microbiomes of anti-CCP positive individuals at risk of developing rheumatoid arthritis. Ann Rheum Dis 2020; 80:162-168. [PMID: 33004333 DOI: 10.1136/annrheumdis-2020-216972] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Revised: 08/25/2020] [Accepted: 08/25/2020] [Indexed: 12/21/2022]
Abstract
OBJECTIVES An increased prevalence of periodontitis and perturbation of the oral microbiome has been identified in patients with rheumatoid arthritis (RA). The periodontal pathogen Porphyromonas gingivalis may cause local citrullination of proteins, potentially triggering anti-citrullinated protein antibody production. However, it is not known if oral dysbiosis precedes the onset of clinical arthritis. This study comprehensively characterised the oral microbiome in anti-cyclic citrullinated peptide (anti-CCP) positive at-risk individuals without clinical synovitis (CCP+at risk). METHODS Subgingival plaque was collected from periodontally healthy and diseased sites in 48 CCP+at risk, 26 early RA and 32 asymptomatic healthy control (HC) individuals. DNA libraries were sequenced on the Illumina HiSeq 3000 platform. Taxonomic profile and functional capability of the subgingival microbiome were compared between groups. RESULTS At periodontally healthy sites, CCP+at risk individuals had significantly lower microbial richness compared with HC and early RA groups (p=0.004 and 0.021). Microbial community alterations were found at phylum, genus and species levels. A large proportion of the community differed significantly in membership (523 species; 35.6%) and structure (575 species; 39.1%) comparing CCP+at risk and HC groups. Certain core species, including P. gingivalis, had higher relative abundance in the CCP+at risk group. Seventeen clusters of orthologous gene functional units were significantly over-represented in the CCP+at risk group compared with HC (adjusted p value <0.05). CONCLUSION Anti-CCP positive at-risk individuals have dysbiotic subgingival microbiomes and increased abundance of P. gingivalis compared with controls. This supports the hypothesis that the oral microbiome and specifically P. gingivalis are important in RA initiation.
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Affiliation(s)
- Zijian Cheng
- Division of Oral Biology, University of Leeds, School of Dentistry, Leeds, UK.,The Affiliated Stomatology Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.,Key Laboratory of Oral Biomedical Research of Zhejiang Province, Zhejiang University School of Stomatology, Hangzhou, China
| | - Thuy Do
- Division of Oral Biology, University of Leeds, School of Dentistry, Leeds, UK
| | - Kulveer Mankia
- Leeds Institute of Rheumatic and Musculoskeletal Medicine, University of Leeds, School of Medicine, Leeds, UK.,NIHR Leeds Musculoskeletal Biomedical Research Unit, Leeds Teaching Hospitals NHS Trust, Leeds, UK
| | - Josephine Meade
- Division of Oral Biology, University of Leeds, School of Dentistry, Leeds, UK
| | - Laura Hunt
- Leeds Institute of Rheumatic and Musculoskeletal Medicine, University of Leeds, School of Medicine, Leeds, UK.,NIHR Leeds Musculoskeletal Biomedical Research Unit, Leeds Teaching Hospitals NHS Trust, Leeds, UK
| | - Val Clerehugh
- Division of Restorative Dentistry, University of Leeds, School of Dentistry, Leeds, UK
| | - Alastair Speirs
- Leeds Dental Institute, Leeds Teaching Hospitals NHS Trust, Leeds, UK
| | - Aradhna Tugnait
- Division of Restorative Dentistry, University of Leeds, School of Dentistry, Leeds, UK
| | - Paul Emery
- Leeds Institute of Rheumatic and Musculoskeletal Medicine, University of Leeds, School of Medicine, Leeds, UK.,NIHR Leeds Musculoskeletal Biomedical Research Unit, Leeds Teaching Hospitals NHS Trust, Leeds, UK
| | - Deirdre Devine
- Division of Oral Biology, University of Leeds, School of Dentistry, Leeds, UK
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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: 1.8] [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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Thapa E, Knauss HM, Colvin BA, Fischer BA, Weyand NJ. Persistence Dynamics of Antimicrobial-Resistant Neisseria in the Pharynx of Rhesus Macaques. Antimicrob Agents Chemother 2020; 64:e02232-19. [PMID: 32423958 PMCID: PMC7526842 DOI: 10.1128/aac.02232-19] [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: 11/06/2019] [Accepted: 05/13/2020] [Indexed: 11/20/2022] Open
Abstract
Pharyngeal infections by Neisseria gonorrhoeae are often asymptomatic, making them difficult to treat. However, in vivo animal modeling of human pharyngeal infections by pathogenic Neisseria species is challenging due to numerous host tropism barriers. We have relied on rhesus macaques to investigate pharyngeal persistence of naturally occurring Neisseria species in response to antibiotics. These species include Neisseria mucosa, Neisseria oralis, and a species unique to macaques. Four animals previously treated intramuscularly with the fluoroquinolone enrofloxacin for 2 weeks were monitored for persistence of their preexisting Neisseria populations for a period of 10 weeks. Enrofloxacin exposure did not eliminate preexisting flora from two of the four animals. Characterization of a collection of macaque Neisseria isolates supported the hypothesis that pharyngeal persistence was linked to reduced enrofloxacin susceptibility conferred by mutations in either gyrA or parC Interestingly, we observed a change in neisserial population dynamics for several weeks following enrofloxacin exposure. Enrofloxacin appeared to promote competition between strains for dominance in the pharyngeal niche. Specifically, following enrofloxacin treatment, strains bearing single gyrA mutations and low MICs persisted long-term. In contrast, strains with both gyrA and parC mutations and high MICs became culturally undetectable, consistent with the hypothesis that they were less fit. Our study has provided insight into pharyngeal persistence dynamics of Neisseria species bearing fluoroquinolone resistance determinants. The rhesus macaque provides a valuable host animal that may be used in the future to simulate treatment failures associated with the presence of antimicrobial-resistant Neisseria spp. in the human pharynx.
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Affiliation(s)
- Eliza Thapa
- Department of Biological Sciences, Ohio University, Athens, Ohio, USA
| | - Hanna M Knauss
- Department of Biological Sciences, Ohio University, Athens, Ohio, USA
| | - Benjamin A Colvin
- Department of Biological Sciences, Ohio University, Athens, Ohio, USA
| | | | - Nathan J Weyand
- Department of Biological Sciences, Ohio University, Athens, Ohio, USA
- The Infectious and Tropical Disease Institute, Ohio University, Athens, Ohio, USA
- Molecular and Cellular Biology Program, Ohio University, Athens, Ohio, USA
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46
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Dong HV, Pham LQ, Nguyen HT, Nguyen MXB, Nguyen TV, May F, Le GM, Klausner JD. Decreased Cephalosporin Susceptibility of Oropharyngeal Neisseria Species in Antibiotic-using Men Who Have Sex With Men in Hanoi, Vietnam. Clin Infect Dis 2020; 70:1169-1175. [PMID: 31049592 PMCID: PMC7319061 DOI: 10.1093/cid/ciz365] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2019] [Accepted: 04/30/2019] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Neisseria gonorrhoeae (NG) infections are a global health burden. NG resistance to cephalosporins, which is increasingly reported, is an imminent threat to public health. Many hypothesize that commensal Neisseria species are an important reservoir for genetic material conferring antimicrobial resistance in NG; however, clinical data are lacking. METHODS Men who have sex with men (MSM) in Hanoi, Vietnam, completed a questionnaire regarding antibiotic use. We collected pharyngeal specimens, cultured Neisseria species, and measured minimum inhibitory concentrations (MICs) to ciprofloxacin, cefixime, ceftriaxone, and cefpodoxime. Using MIC criteria for antimicrobial susceptibility in NG, we categorized the Neisseria species and compared mean MIC levels between different antibiotic user groups. RESULTS Of 207 participants, 38% used at least 1 antibiotic in the past 6 months; 52% without a prescription. A median of 1 Neisseria species was cultured from each participant (range, 1-4) with 10 different Neisseria species identified overall. The proportion of Neisseria with reduced susceptibility to ciprofloxacin was 93%, cefpodoxime 84%, cefixime 31%, and ceftriaxone 28%. Antibiotic use within the past month was strongly associated with Neisseria species having increased MICs to cefixime, ceftriaxone, and cefpodoxime (mean MIC ratios of 6.27, 4.11, and 7.70, respectively), compared with those who used antibiotics between 1 and 6 months prior (P < .05, all comparisons). CONCLUSIONS MSM in our study often used antibiotics without a prescription. At least 1 commensal Neisseria species colonized all men. Recent use of any antibiotics may select for oropharyngeal Neisseria species with antimicrobial resistance. The normal flora of the oropharynx may be an important source of antimicrobial resistance in Neisseria gonorrhoeae.
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Affiliation(s)
- Huan V Dong
- Charles R. Drew University of Medicine and Sciences
- Department of Medicine, David Geffen School of Medicine
| | - Loc Q Pham
- Fielding School of Public Health, University of California, Los Angeles
- Center for Research and Training on Substance Abuse–HIV, Hanoi Medical University
| | - Hoa T Nguyen
- Department of Microbiology, National Hospital for Tropical Diseases, Hanoi, Vietnam
| | - Minh X B Nguyen
- Center for Research and Training on Substance Abuse–HIV, Hanoi Medical University
- Department of Health Behavior, University of North Carolina at Chapel Hill
| | - Trung V Nguyen
- Department of Microbiology, National Hospital for Tropical Diseases, Hanoi, Vietnam
- Department of Microbiology, Hanoi Medical University, Vietnam
| | - Folasade May
- Department of Medicine, David Geffen School of Medicine
| | - Giang M Le
- Center for Research and Training on Substance Abuse–HIV, Hanoi Medical University
| | - Jeffrey D Klausner
- Department of Medicine, David Geffen School of Medicine
- Fielding School of Public Health, University of California, Los Angeles
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47
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Custodio R, Johnson E, Liu G, Tang CM, Exley RM. Commensal Neisseria cinerea impairs Neisseria meningitidis microcolony development and reduces pathogen colonisation of epithelial cells. PLoS Pathog 2020; 16:e1008372. [PMID: 32208456 PMCID: PMC7092958 DOI: 10.1371/journal.ppat.1008372] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Accepted: 01/31/2020] [Indexed: 12/16/2022] Open
Abstract
It is increasingly being recognised that the interplay between commensal and pathogenic bacteria can dictate the outcome of infection. Consequently, there is a need to understand how commensals interact with their human host and influence pathogen behaviour at epithelial surfaces. Neisseria meningitidis, a leading cause of sepsis and meningitis, exclusively colonises the human nasopharynx and shares this niche with several other Neisseria species, including the commensal Neisseria cinerea. Here, we demonstrate that during adhesion to human epithelial cells N. cinerea co-localises with molecules that are also recruited by the meningococcus, and show that, similar to N. meningitidis, N. cinerea forms dynamic microcolonies on the cell surface in a Type four pilus (Tfp) dependent manner. Finally, we demonstrate that N. cinerea colocalises with N. meningitidis on the epithelial cell surface, limits the size and motility of meningococcal microcolonies, and impairs the effective colonisation of epithelial cells by the pathogen. Our data establish that commensal Neisseria can mimic and affect the behaviour of a pathogen on epithelial cell surfaces.
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Affiliation(s)
- Rafael Custodio
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| | - Errin Johnson
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| | - Guangyu Liu
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| | - Christoph M. Tang
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| | - Rachel M. Exley
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
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Stenmark B, Harrison OB, Eriksson L, Anton BP, Fomenkov A, Roberts RJ, Tooming-Klunderud A, Bratcher HB, Bray JE, Thulin-Hedberg S, Maiden MCJ, Mölling P. Complete genome and methylome analysis of Neisseria meningitidis associated with increased serogroup Y disease. Sci Rep 2020; 10:3644. [PMID: 32108139 PMCID: PMC7046676 DOI: 10.1038/s41598-020-59509-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Accepted: 01/22/2020] [Indexed: 12/22/2022] Open
Abstract
Invasive meningococcal disease (IMD) due to serogroup Y Neisseria meningitidis emerged in Europe during the 2000s. Draft genomes of serogroup Y isolates in Sweden revealed that although the population structure of these isolates was similar to other serogroup Y isolates internationally, a distinct strain (YI) and more specifically a sublineage (1) of this strain was responsible for the increase of serogroup Y IMD in Sweden. We performed single molecule real-time (SMRT) sequencing on eight serogroup Y isolates from different sublineages to unravel the genetic and epigenetic factors delineating them, in order to understand the serogroup Y emergence. Extensive comparisons between the serogroup Y sublineages of all coding sequences, complex genomic regions, intergenic regions, and methylation motifs revealed small point mutations in genes mainly encoding hypothetical and metabolic proteins, and non-synonymous variants in genes involved in adhesion, iron acquisition, and endotoxin production. The methylation motif CACNNNNNTAC was only found in isolates of sublineage 2. Only seven genes were putatively differentially expressed, and another two genes encoding hypothetical proteins were only present in sublineage 2. These data suggest that the serogroup Y IMD increase in Sweden was most probably due to small changes in genes important for colonization and transmission.
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Affiliation(s)
- Bianca Stenmark
- Department of Laboratory Medicine, Faculty of Medicine and Health, Örebro University, Örebro, Sweden.
| | - Odile B Harrison
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Lorraine Eriksson
- Department of Laboratory Medicine, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | | | | | | | - Ave Tooming-Klunderud
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Oslo, Norway
| | - Holly B Bratcher
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - James E Bray
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Sara Thulin-Hedberg
- Department of Laboratory Medicine, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | | | - Paula Mölling
- Department of Laboratory Medicine, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
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Kargar F, Savardashtaki A, Mortazavi M, Mahani MT, Amani AM, Ghasemi Y, Nezafat N. In SilicoStudy of 1, 4 Alpha Glucan Branching Enzyme and Substrate Docking Studies. CURR PROTEOMICS 2020. [DOI: 10.2174/1570164616666190401204009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Background:The 1,4-alpha-glucan branching protein (GlgB) plays an important role in the glycogen biosynthesis and the deficiency in this enzyme has resulted in Glycogen storage disease and accumulation of an amylopectin-like polysaccharide. Consequently, this enzyme was considered a special topic in clinical and biotechnological research. One of the newly introduced GlgB belongs to the Neisseria sp. HMSC071A01 (Ref.Seq. WP_049335546). For in silico analysis, the 3D molecular modeling of this enzyme was conducted in the I-TASSER web server.Methods:For a better evaluation, the important characteristics of this enzyme such as functional properties, metabolic pathway and activity were investigated in the TargetP software. Additionally, the phylogenetic tree and secondary structure of this enzyme were studied by Mafft and Prabi software, respectively. Finally, the binding site properties (the maltoheptaose as substrate) were studied using the AutoDock Vina.Results:By drawing the phylogenetic tree, the closest species were the taxonomic group of Betaproteobacteria. The results showed that the structure of this enzyme had 34.45% of the alpha helix and 45.45% of the random coil. Our analysis predicted that this enzyme has a potential signal peptide in the protein sequence.Conclusion:By these analyses, a new understanding was developed related to the sequence and structure of this enzyme. Our findings can further be used in some fields of clinical and industrial biotechnology.
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Affiliation(s)
- Farzane Kargar
- Department of Biotechnology, Institute of Science and High Technology and Environmental Science, Graduate University of Advanced Technology, Kerman, Iran
| | - Amir Savardashtaki
- Department of Medical Biotechnology, School of Advanced Medical Sciences and Technologies Shiraz University of Medical Sciences Shiraz, Iran
| | - Mojtaba Mortazavi
- Department of Biotechnology, Institute of Science and High Technology and Environmental Science, Graduate University of Advanced Technology, Kerman, Iran
| | - Masoud Torkzadeh Mahani
- Department of Biotechnology, Institute of Science and High Technology and Environmental Science, Graduate University of Advanced Technology, Kerman, Iran
| | - Ali Mohammad Amani
- Department of Medical Nanotechnology, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, 71348- 14336, Iran
| | - Younes Ghasemi
- Department of Medical Biotechnology, School of Advanced Medical Sciences and Technologies Shiraz University of Medical Sciences Shiraz, Iran
| | - Navid Nezafat
- Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
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Genetic determinants of genus-level glycan diversity in a bacterial protein glycosylation system. PLoS Genet 2019; 15:e1008532. [PMID: 31869330 PMCID: PMC6959607 DOI: 10.1371/journal.pgen.1008532] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 01/14/2020] [Accepted: 11/22/2019] [Indexed: 12/27/2022] Open
Abstract
The human pathogens N. gonorrhoeae and N. meningitidis display robust intra- and interstrain glycan diversity associated with their O-linked protein glycosylation (pgl) systems. In an effort to better understand the evolution and function of protein glycosylation operating there, we aimed to determine if other human-restricted, Neisseria species similarly glycosylate proteins and if so, to assess the levels of glycoform diversity. Comparative genomics revealed the conservation of a subset of genes minimally required for O-linked protein glycosylation glycan and established those pgl genes as core genome constituents of the genus. In conjunction with mass spectrometric–based glycan phenotyping, we found that extant glycoform repertoires in N. gonorrhoeae, N. meningitidis and the closely related species N. polysaccharea and N. lactamica reflect the functional replacement of a progenitor glycan biosynthetic pathway. This replacement involved loss of pgl gene components of the primordial pathway coincident with the acquisition of two exogenous glycosyltransferase genes. Critical to this discovery was the identification of a ubiquitous but previously unrecognized glycosyltransferase gene (pglP) that has uniquely undergone parallel but independent pseudogenization in N. gonorrhoeae and N. meningitidis. We suggest that the pseudogenization events are driven by processes of compositional epistasis leading to gene decay. Additionally, we documented instances where inter-species recombination influences pgl gene status and creates discordant genetic interactions due ostensibly to the multi-locus nature of pgl gene networks. In summary, these findings provide a novel perspective on the evolution of protein glycosylation systems and identify phylogenetically informative, genetic differences associated with Neisseria species. Bacteria express a remarkable diversity of sugars and oligosaccharides in conjunction with protein glycosylation systems. Currently however, little is known about the evolutionary processes and selective forces shaping glycan biosynthetic pathways. The closely related bacterial pathogens Neisseria gonorrhoeae and Neisseria meningitidis remain serious sources of human disease and these species express antigenically variable oligosaccharides as components of their broad-spectrum, O‐linked protein glycosylation (pgl) systems. With the exception of isolates of Neisseria elongata subspecies glycolytica, the status of such post-translational modifications in related commensal species colonizing humans remains largely undefined. Here, we exploit new data from further studies of protein glycosylation in Neisseria elongata subspecies glycolytica to address these concerns. Employing comparative genomics and glycan phenotyping, we show that related pgl systems are indeed expressed by all human-restricted Neisseria species but identify unique gene gain and loss events as well as loss-of-function polymorphisms that accommodate a dramatic shift in glycoform structure occurring across the genus. These findings constitute novel perspectives on both the evolution of protein glycosylation systems in general and the macroevolutionary processes occurring in related bacterial species residing within a single host.
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