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Mikucki A, Kahler CM. Microevolution and Its Impact on Hypervirulence, Antimicrobial Resistance, and Vaccine Escape in Neisseria meningitidis. Microorganisms 2023; 11:3005. [PMID: 38138149 PMCID: PMC10745880 DOI: 10.3390/microorganisms11123005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 12/07/2023] [Accepted: 12/14/2023] [Indexed: 12/24/2023] Open
Abstract
Neisseria meningitidis is commensal of the human pharynx and occasionally invades the host, causing the life-threatening illness invasive meningococcal disease. The meningococcus is a highly diverse and adaptable organism thanks to natural competence, a propensity for recombination, and a highly repetitive genome. These mechanisms together result in a high level of antigenic variation to invade diverse human hosts and evade their innate and adaptive immune responses. This review explores the ways in which this diversity contributes to the evolutionary history and population structure of the meningococcus, with a particular focus on microevolution. It examines studies on meningococcal microevolution in the context of within-host evolution and persistent carriage; microevolution in the context of meningococcal outbreaks and epidemics; and the potential of microevolution to contribute to antimicrobial resistance and vaccine escape. A persistent theme is the idea that the process of microevolution contributes to the development of new hyperinvasive meningococcal variants. As such, microevolution in this species has significant potential to drive future public health threats in the form of hypervirulent, antibiotic-resistant, vaccine-escape variants. The implications of this on current vaccination strategies are explored.
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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 6009, Australia;
- Wesfarmers Centre of Vaccines and Infectious Diseases, Telethon Kids Institute, University of Western Australia, Perth, WA 6009, Australia
| | - Charlene M. Kahler
- Marshall Centre for Infectious Diseases Research and Training, School of Biomedical Sciences, University of Western Australia, Perth, WA 6009, Australia;
- Wesfarmers Centre of Vaccines and Infectious Diseases, Telethon Kids Institute, University of Western Australia, Perth, WA 6009, Australia
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2
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Morreale DP, St Geme III JW, Planet PJ. Phylogenomic analysis of the understudied Neisseriaceae species reveals a poly- and paraphyletic Kingella genus. Microbiol Spectr 2023; 11:e0312323. [PMID: 37882538 PMCID: PMC10715097 DOI: 10.1128/spectrum.03123-23] [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: 08/17/2023] [Accepted: 09/15/2023] [Indexed: 10/27/2023] Open
Abstract
IMPORTANCE Understanding the evolutionary relationships between the species in the Neisseriaceae family has been a persistent challenge in bacterial systematics due to high recombination rates in these species. Previous studies of this family have focused on Neisseria meningitidis and N. gonorrhoeae. However, previously understudied Neisseriaceae species are gaining new attention, with Kingella kingae now recognized as a common human pathogen and with Alysiella and Simonsiella being unique in the bacterial world as multicellular organisms. A better understanding of the genomic evolution of the Neisseriaceae can lead to the identification of specific genes and traits that underlie the remarkable diversity of this family.
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Affiliation(s)
- Daniel P. Morreale
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Division of Infectious Diseases, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Joseph W. St Geme III
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Division of Infectious Diseases, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Paul J. Planet
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Division of Infectious Diseases, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Comparative Genomics, American Museum of Natural History, New York, New York, USA
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3
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Silva RA, Ferro CG, Lehner MDS, Paula TJ, Mizubuti ESG. The Population of Sclerotinia sclerotiorum in Brazil Is Structured by Mycelial Compatibility Groups. PLANT DISEASE 2021; 105:3376-3384. [PMID: 33934631 DOI: 10.1094/pdis-01-21-0110-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The genetic structure of the population of Sclerotinia sclerotiorum was analyzed using 238 individuals collected from different hosts. Individuals were characterized for microsatellite genotypes and mycelial compatibility groups (MCGs). A total of 22 MCGs and 64 multilocus lineages (MLLs) were identified. There was a close relationship between the MCGs and MLLs, but there was no association between MLLs and hosts or regions. At least 39 MCGs are present in Brazil, and 68.5% of the isolates were assigned to either MCG 1 or MCG 2. Eight new MCGs were found. Seven genetic groups were identified and associated with MCGs. Most genetic variation (70.0%) was because of differences among MCGs. High values of estimates of linkage disequilibrium among loci were more frequent in the total population (all MCGs). By contrast, there was evidence of random mating in subpopulations defined by MCGs 1 and 2. Additionally, there was evidence of outcrossing in the population of S. sclerotiorum in Brazil. The population was structured by MCGs; lineages originating from asexual reproduction or selfing prevail and are widely distributed in space, are persistent in time, and affect many hosts, but there is evidence of some degree of outcrossing, which may lead to a more genetically variable population in the future.
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Affiliation(s)
- Rhaphael A Silva
- Departamento de Fitopatologia, Universidade Federal de Viçosa, Viçosa, Minas Gerais, 36570-900, Brazil
| | - Camila G Ferro
- Departamento de Fitopatologia, Universidade Federal de Viçosa, Viçosa, Minas Gerais, 36570-900, Brazil
| | - Miller da S Lehner
- Departamento de Fitopatologia, Universidade Federal de Viçosa, Viçosa, Minas Gerais, 36570-900, Brazil
| | - Trazilbo J Paula
- Empresa de Pesquisa Agropecuária de Minas Gerais, Viçosa, Minas Gerais, 36570-000, Brazil
| | - Eduardo S G Mizubuti
- Departamento de Fitopatologia, Universidade Federal de Viçosa, Viçosa, Minas Gerais, 36570-900, Brazil
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4
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Tibayrenc M, Ayala FJ. Models in parasite and pathogen evolution: Genomic analysis reveals predominant clonality and progressive evolution at all evolutionary scales in parasitic protozoa, yeasts and bacteria. ADVANCES IN PARASITOLOGY 2021; 111:75-117. [PMID: 33482977 DOI: 10.1016/bs.apar.2020.12.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The predominant clonal evolution (PCE) model of pathogenic microorganisms postulates that the impact of genetic recombination in those pathogens' natural populations is not enough to erase a persistent phylogenetic signal at all evolutionary scales from microevolution till geological times in the whole ecogeographical range of the species considered. We have tested this model with a set of representative parasitic protozoa, yeasts and bacteria in the light of the most recent genomic data. All surveyed species, including those that were considered as highly recombining, exhibit similar PCE patterns above and under the species level, from macro- to micro-evolutionary scales (Russian doll pattern), suggesting gradual evolution. To our knowledge, it is the first time that such a strong common evolutionary feature among very diverse pathogens has been evidenced. The implications of this model for basic biology and applied research are exposed. These implications include our knowledge on the pathogens' reproductive mode, their population structure, the possibility to type strain and to follow up epidemics (molecular epidemiology) and to revisit pathogens' taxonomy through a flexible use of the phylogenetic species concept (Cracraft, 1983).
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Affiliation(s)
- Michel Tibayrenc
- Maladies Infectieuses et Vecteurs Ecologie, Génétique, Evolution et Contrôle, MIVEGEC (IRD 224-CNRS 5290-UM1-UM2), Institut de recherche pour le développement, Montpellier Cedex 5, France.
| | - Francisco J Ayala
- Catedra Francisco Jose Ayala of Science, Technology, and Religion, University of Comillas, Madrid, Spain; 2 Locke Court, Irvine, CA, United States
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Wanford JJ, Holmes JC, Bayliss CD, Green LR. Meningococcal core and accessory phasomes vary by clonal complex. Microb Genom 2020; 6:e000367. [PMID: 32375989 PMCID: PMC7371114 DOI: 10.1099/mgen.0.000367] [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: 12/11/2019] [Accepted: 03/27/2020] [Indexed: 11/21/2022] Open
Abstract
Neisseria meningitidis is a Gram-negative human commensal pathogen, with extensive phenotypic plasticity afforded by phase-variable (PV) gene expression. Phase variation is a stochastic switch in gene expression from an ON to an OFF state, mediated by localized hypermutation of simple sequence repeats (SSRs). Circulating N. meningitidis clones vary in propensity to cause disease, with some clonal complexes (ccs) classified as hypervirulent and others as carriage-associated. We examined the PV gene repertoires, or phasome, of these lineages in order to determine whether phase variation contributes to disease propensity. We analysed 3328 genomes representative of nine circulating meningococcal ccs with PhasomeIt, a tool that identifies PV genes by the presence of SSRs and homologous gene clusters. The presence, absence and functions of all identified PV gene clusters were confirmed by annotation or blast searches within the Neisseria PubMLST database. While no significant differences were detected in the number of PV genes or the core, conserved phasome content between hypervirulent and carriage lineages, individual ccs exhibited major variations in PV gene numbers. Phylogenetic clusters produced by phasome or core genome analyses were similar, indicating co-evolution of PV genes with the core genome. While conservation of PV clusters is high, with 76 % present in all meningococcal isolates, maintenance of an SSR is variable, ranging from conserved in all isolates to present only in a single cc, indicating differing evolutionary trajectories for each lineage. Diverse functional groups of PV genes were present across the meningococcal lineages; however, the majority directly or indirectly influence bacterial surface antigens and could impact on future vaccine development. Finally, we observe that meningococci have open pan phasomes, indicating ongoing evolution of PV gene content and a significant potential for adaptive changes in this clinically relevant genus.
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Affiliation(s)
- Joseph J. Wanford
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - Jonathan C. Holmes
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | | | - Luke R. Green
- Department of Infection, Immunity and Cardiovascular Disease, University of Sheffield, Sheffield, UK
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6
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Population structure and genetic diversity of Trichomonas vaginalis clinical isolates in Australia and Ghana. INFECTION GENETICS AND EVOLUTION 2020; 82:104318. [PMID: 32278146 DOI: 10.1016/j.meegid.2020.104318] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Revised: 04/05/2020] [Accepted: 04/07/2020] [Indexed: 12/30/2022]
Abstract
Population genetic studies of Trichomonas vaginalis have detected high genetic diversity associated with phenotypic differences in clinical presentations. In this study, microscopy and next generation-multi-locus sequence typing (NG-MLST) were used to identify and genetically characterise T. vaginalis isolates from patients in Australia and Ghana. Seventy-one polymorphic nucleotide sites, 36 different alleles, 48 sequence types, 24 of which were novel, were identified among 178 isolates, revealing a geneticallly diverse T. vaginalis population. Polymorphism was found at most loci, clustering genotypes into eight groups among both Australian and Ghanaian isolates, although there was some variation between countries. The number of alleles for each locus ranged from two to nine. Study results confirmed geographic expansion and diversity of the T. vaginalis population. Two-type populations in almost equal frequencies and a third unassigned group were identified in this study. Linkage disequilibrium was observed, suggesting T. vaginalis population is highly clonal. Multillocus disequilibrium was observed even when analysing clades separately, as well as widespread clonal genotypes, suggesting that there is no evidence of recent recombination. A more comprehensive study to assess the extent of genetic diversity and population structure of T. vaginalis and their potential impact on varied pathology observed among infected individuals is recommended.
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7
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Caugant DA, Brynildsrud OB. Neisseria meningitidis: using genomics to understand diversity, evolution and pathogenesis. Nat Rev Microbiol 2019; 18:84-96. [PMID: 31705134 DOI: 10.1038/s41579-019-0282-6] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/25/2019] [Indexed: 01/30/2023]
Abstract
Meningococcal disease remains an important cause of morbidity and death worldwide despite the development and increasing implementation of effective vaccines. Elimination of the disease is hampered by the enormous diversity and antigenic variability of the causative agent, Neisseria meningitidis, one of the most variable bacteria in nature. These features are attained mainly through high rates of horizontal gene transfer and alteration of protein expression through phase variation. The recent availability of whole-genome sequencing (WGS) of large-scale collections of N. meningitidis isolates from various origins, databases to facilitate storage and sharing of WGS data and the concomitant development of effective bioinformatics tools have led to a much more thorough understanding of the diversity of the species, its evolution and population structure and how virulent traits may emerge. Implementation of WGS is already contributing to enhanced epidemiological surveillance and is essential to ascertain the impact of vaccination strategies. This Review summarizes the recent advances provided by WGS studies in our understanding of the biology of N. meningitidis and the epidemiology of meningococcal disease.
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Affiliation(s)
- Dominique A Caugant
- Division for Infection Control and Environmental Health, Norwegian Institute of Public Health, Oslo, Norway. .,Department of Community Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway.
| | - Ola B Brynildsrud
- Division for Infection Control and Environmental Health, Norwegian Institute of Public Health, Oslo, Norway.,Department of Food Safety and Infection Biology, Faculty of Veterinary Science, Norwegian University of Life Science, Oslo, Norway
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8
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Lamelas A, Hamid AWM, Dangy JP, Hauser J, Jud M, Röltgen K, Hodgson A, Junghanss T, Harris SR, Parkhill J, Bentley SD, Pluschke G. Loss of Genomic Diversity in a Neisseria meningitidis Clone Through a Colonization Bottleneck. Genome Biol Evol 2018; 10:2102-2109. [PMID: 30060167 PMCID: PMC6110524 DOI: 10.1093/gbe/evy152] [Citation(s) in RCA: 2] [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] [Accepted: 07/26/2018] [Indexed: 01/11/2023] Open
Abstract
Neisseria meningitidis is the leading cause of epidemic meningitis in the "meningitis belt" of Africa, where clonal waves of colonization and disease are observed. Point mutations and horizontal gene exchange lead to constant diversification of meningococcal populations during clonal spread. Maintaining a high genomic diversity may be an evolutionary strategy of meningococci that increases chances of fixing occasionally new highly successful "fit genotypes". We have performed a longitudinal study of meningococcal carriage and disease in northern Ghana by analyzing cerebrospinal fluid samples from all suspected meningitis cases and monitoring carriage of meningococci by twice yearly colonization surveys. In the framework of this study, we observed complete replacement of an A: sequence types (ST)-2859 clone by a W: ST-2881 clone. However, after a gap of 1 year, A: ST-2859 meningococci re-emerged both as colonizer and meningitis causing agent. Our whole genome sequencing analyses compared the A population isolated prior to the W colonization and disease wave with the re-emerging A meningococci. This analysis revealed expansion of one clone differing in only one nonsynonymous SNP from several isolates already present in the original A: ST-2859 population. The colonization bottleneck caused by the competing W meningococci thus resulted in a profound reduction in genomic diversity of the A meningococcal population.
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Affiliation(s)
- Araceli Lamelas
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Switzerland
- Red de Estudios Moleculares Avanzados, Instituto de Ecología A. C., Xalapa, Veracruz, México
| | - Abdul-Wahab M Hamid
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Switzerland
- Navrongo Health Research Centre, Ministry of Health, Navrongo, Ghana
| | - Jean-Pierre Dangy
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Switzerland
| | - Julia Hauser
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Switzerland
| | - Maja Jud
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Switzerland
| | - Katharina Röltgen
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Switzerland
| | - Abraham Hodgson
- Navrongo Health Research Centre, Ministry of Health, Navrongo, Ghana
- Research and Development Division, Ghana Health Service, Accra, Ghana
| | - Thomas Junghanss
- Section of Clinical Tropical Medicine, University Hospital Heidelberg, Germany
| | - Simon R Harris
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Julian Parkhill
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Stephen D Bentley
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Gerd Pluschke
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Switzerland
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9
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Acuña-Amador L, Primot A, Cadieu E, Roulet A, Barloy-Hubler F. Genomic repeats, misassembly and reannotation: a case study with long-read resequencing of Porphyromonas gingivalis reference strains. BMC Genomics 2018; 19:54. [PMID: 29338683 PMCID: PMC5771137 DOI: 10.1186/s12864-017-4429-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Accepted: 12/29/2017] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Without knowledge of their genomic sequences, it is impossible to make functional models of the bacteria that make up human and animal microbiota. Unfortunately, the vast majority of publicly available genomes are only working drafts, an incompleteness that causes numerous problems and constitutes a major obstacle to genotypic and phenotypic interpretation. In this work, we began with an example from the class Bacteroidia in the phylum Bacteroidetes, which is preponderant among human orodigestive microbiota. We successfully identify the genetic loci responsible for assembly breaks and misassemblies and demonstrate the importance and usefulness of long-read sequencing and curated reannotation. RESULTS We showed that the fragmentation in Bacteroidia draft genomes assembled from massively parallel sequencing linearly correlates with genomic repeats of the same or greater size than the reads. We also demonstrated that some of these repeats, especially the long ones, correspond to misassembled loci in three reference Porphyromonas gingivalis genomes marked as circularized (thus complete or finished). We prove that even at modest coverage (30X), long-read resequencing together with PCR contiguity verification (rrn operons and an integrative and conjugative element or ICE) can be used to identify and correct the wrongly combined or assembled regions. Finally, although time-consuming and labor-intensive, consistent manual biocuration of three P. gingivalis strains allowed us to compare and correct the existing genomic annotations, resulting in a more accurate interpretation of the genomic differences among these strains. CONCLUSIONS In this study, we demonstrate the usefulness and importance of long-read sequencing in verifying published genomes (even when complete) and generating assemblies for new bacterial strains/species with high genomic plasticity. We also show that when combined with biological validation processes and diligent biocurated annotation, this strategy helps reduce the propagation of errors in shared databases, thus limiting false conclusions based on incomplete or misleading information.
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Affiliation(s)
- Luis Acuña-Amador
- Institut de Génétique et Développement de Rennes, CNRS, UMR6290, Université de Rennes 1, Rennes, France.,Laboratorio de Investigación en Bacteriología Anaerobia, Centro de Investigación en Enfermedades Tropicales, Facultad de Microbiología, Universidad de Costa Rica, San José, Costa Rica
| | - Aline Primot
- Institut de Génétique et Développement de Rennes, CNRS, UMR6290, Université de Rennes 1, Rennes, France
| | - Edouard Cadieu
- Institut de Génétique et Développement de Rennes, CNRS, UMR6290, Université de Rennes 1, Rennes, France
| | - Alain Roulet
- GenoToul Genome & Transcriptome (GeT-PlaGe), INRA, US1426, Castanet-Tolosan, France
| | - Frédérique Barloy-Hubler
- Institut de Génétique et Développement de Rennes, CNRS, UMR6290, Université de Rennes 1, Rennes, France.
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Hauck S, Maiden MCJ. Clonally Evolving Pathogenic Bacteria. MOLECULAR MECHANISMS OF MICROBIAL EVOLUTION 2018. [DOI: 10.1007/978-3-319-69078-0_12] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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11
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Lamelas A, Hauser J, Dangy JP, Hamid AWM, Röltgen K, Abdul Sater MR, Hodgson A, Sie A, Junghanss T, Harris SR, Parkhill J, Bentley SD, Pluschke G. Emergence and genomic diversification of a virulent serogroup W:ST-2881(CC175) Neisseria meningitidis clone in the African meningitis belt. Microb Genom 2017; 3:e000120. [PMID: 29026659 PMCID: PMC5610715 DOI: 10.1099/mgen.0.000120] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Accepted: 05/10/2017] [Indexed: 12/21/2022] Open
Abstract
Countries of the African 'meningitis belt' are susceptible to meningococcal meningitis outbreaks. While in the past major epidemics have been primarily caused by serogroup A meningococci, W strains are currently responsible for most of the cases. After an epidemic in Mecca in 2000, W:ST-11 strains have caused many outbreaks worldwide. An unrelated W:ST-2881 clone was described for the first time in 2002, with the first meningitis cases caused by these bacteria reported in 2003. Here we describe results of a comparative whole-genome analysis of 74 W:ST-2881 strains isolated within the framework of two longitudinal colonization and disease studies conducted in Ghana and Burkina Faso. Genomic data indicate that the W:ST-2881 clone has emerged from Y:ST-175(CC175) bacteria by capsule switching. The circulating W:ST-2881 populations were composed of a variety of closely related but distinct genomic variants with no systematic differences between colonization and disease isolates. Two distinct and geographically clustered phylogenetic clonal variants were identified in Burkina Faso and a third in Ghana. On the basis of the presence or absence of 17 recombination fragments, the Ghanaian variant could be differentiated into five clusters. All 25 Ghanaian disease isolates clustered together with 23 out of 40 Ghanaian isolates associated with carriage within one cluster, indicating that W:ST-2881 clusters differ in virulence. More than half of the genes affected by horizontal gene transfer encoded proteins of the 'cell envelope' and the 'transport/binding protein' categories, which indicates that exchange of non-capsular antigens plays an important role in immune evasion.
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Affiliation(s)
- Araceli Lamelas
- 1Swiss Tropical and Public Health Institute, Socinstrasse 57, 4051 Basel, Switzerland.,2Red de Estudios Moleculares Avanzados, Instituto de Ecologia, Veracruz, Mexico
| | - Julia Hauser
- 1Swiss Tropical and Public Health Institute, Socinstrasse 57, 4051 Basel, Switzerland.,3University of Basel, Basel, Switzerland
| | - Jean-Pierre Dangy
- 1Swiss Tropical and Public Health Institute, Socinstrasse 57, 4051 Basel, Switzerland.,3University of Basel, Basel, Switzerland
| | - Abdul-Wahab M Hamid
- 3University of Basel, Basel, Switzerland.,4Navrongo Health Research Centre, Navrongo, Ghana
| | - Katharina Röltgen
- 1Swiss Tropical and Public Health Institute, Socinstrasse 57, 4051 Basel, Switzerland.,3University of Basel, Basel, Switzerland
| | - Mohamad R Abdul Sater
- 1Swiss Tropical and Public Health Institute, Socinstrasse 57, 4051 Basel, Switzerland.,3University of Basel, Basel, Switzerland
| | | | - Ali Sie
- 5Center de Recherche en Sante de Nouna, Nouna, Burkina Faso
| | - Thomas Junghanss
- 6Section of Clinical Tropical Medicine, University Hospital Heidelberg, Heidelberg, Germany
| | - Simon R Harris
- 7Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Julian Parkhill
- 7Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Stephen D Bentley
- 7Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Gerd Pluschke
- 1Swiss Tropical and Public Health Institute, Socinstrasse 57, 4051 Basel, Switzerland.,3University of Basel, Basel, Switzerland
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12
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Tibayrenc M, Ayala FJ. Is Predominant Clonal Evolution a Common Evolutionary Adaptation to Parasitism in Pathogenic Parasitic Protozoa, Fungi, Bacteria, and Viruses? ADVANCES IN PARASITOLOGY 2016; 97:243-325. [PMID: 28325372 DOI: 10.1016/bs.apar.2016.08.007] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
We propose that predominant clonal evolution (PCE) in microbial pathogens be defined as restrained recombination on an evolutionary scale, with genetic exchange scarce enough to not break the prevalent pattern of clonal population structure. The main features of PCE are (1) strong linkage disequilibrium, (2) the widespread occurrence of stable genetic clusters blurred by occasional bouts of genetic exchange ('near-clades'), (3) the existence of a "clonality threshold", beyond which recombination is efficiently countered by PCE, and near-clades irreversibly diverge. We hypothesize that the PCE features are not mainly due to natural selection but also chiefly originate from in-built genetic properties of pathogens. We show that the PCE model obtains even in microbes that have been considered as 'highly recombining', such as Neisseria meningitidis, and that some clonality features are observed even in Plasmodium, which has been long described as panmictic. Lastly, we provide evidence that PCE features are also observed in viruses, taking into account their extremely fast genetic turnover. The PCE model provides a convenient population genetic framework for any kind of micropathogen. It makes it possible to describe convenient units of analysis (clones and near-clades) for all applied studies. Due to PCE features, these units of analysis are stable in space and time, and clearly delimited. The PCE model opens up the possibility of revisiting the problem of species definition in these organisms. We hypothesize that PCE constitutes a major evolutionary strategy for protozoa, fungi, bacteria, and viruses to adapt to parasitism.
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Affiliation(s)
- M Tibayrenc
- Institut de Recherche pour le Développement, Montpellier, France
| | - F J Ayala
- University of California at Irvine, United States
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13
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Mustapha MM, Marsh JW, Krauland MG, Fernandez JO, de Lemos APS, Dunning Hotopp JC, Wang X, Mayer LW, Lawrence JG, Hiller NL, Harrison LH. Genomic Investigation Reveals Highly Conserved, Mosaic, Recombination Events Associated with Capsular Switching among Invasive Neisseria meningitidis Serogroup W Sequence Type (ST)-11 Strains. Genome Biol Evol 2016; 8:2065-75. [PMID: 27289093 PMCID: PMC4943193 DOI: 10.1093/gbe/evw122] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Neisseria meningitidis is an important cause of meningococcal disease globally. Sequence type (ST)-11 clonal complex (cc11) is a hypervirulent meningococcal lineage historically associated with serogroup C capsule and is believed to have acquired the W capsule through a C to W capsular switching event. We studied the sequence of capsule gene cluster (cps) and adjoining genomic regions of 524 invasive W cc11 strains isolated globally. We identified recombination breakpoints corresponding to two distinct recombination events within W cc11: A 8.4-kb recombinant region likely acquired from W cc22 including the sialic acid/glycosyl-transferase gene, csw resulted in a C→W change in capsular phenotype and a 13.7-kb recombinant segment likely acquired from Y cc23 lineage includes 4.5 kb of cps genes and 8.2 kb downstream of the cps cluster resulting in allelic changes in capsule translocation genes. A vast majority of W cc11 strains (497/524, 94.8%) retain both recombination events as evidenced by sharing identical or very closely related capsular allelic profiles. These data suggest that the W cc11 capsular switch involved two separate recombination events and that current global W cc11 meningococcal disease is caused by strains bearing this mosaic capsular switch.
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Affiliation(s)
| | - Jane W Marsh
- Infectious Diseases Epidemiology Research Unit, University of Pittsburgh
| | - Mary G Krauland
- Public Health Dynamics Laboratory, Graduate School of Public Health, University of Pittsburgh
| | - Jorge O Fernandez
- Molecular Genetics Laboratory, Public Health Institute of Chile, Santiago, Chile
| | | | - Julie C Dunning Hotopp
- The Institute for Genome Sciences, University of Maryland School of Medicine, University of Maryland, Baltimore
| | - Xin Wang
- Meningitis and Vaccine Preventable Diseases Branch, Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Leonard W Mayer
- Meningitis and Vaccine Preventable Diseases Branch, Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | | | - N Luisa Hiller
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, USA
| | - Lee H Harrison
- Infectious Diseases Epidemiology Research Unit, University of Pittsburgh
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Ramírez JD, Llewellyn MS. Response to Tibayrenc and Ayala: reproductive clonality in protozoan pathogens - truth or artefact? Mol Ecol 2015; 24:5782-4. [DOI: 10.1111/mec.13442] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Revised: 10/22/2015] [Accepted: 10/27/2015] [Indexed: 01/11/2023]
Affiliation(s)
- J. D. Ramírez
- Grupo de Investigaciones Microbiológicas - UR (GIMUR); Facultad de Ciencias Naturales y Matemáticas; Universidad del Rosario; Bogotá Colombia
| | - M. S. Llewellyn
- Institute of Biodiversity; Animal Health and Comparative Medicine; University of Glasgow; Glasgow UK
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