1
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Xie Y, Ahmad I, Ikpe TIS, Sofia EF, Seno H. What Influence Could the Acceptance of Visitors Cause on the Epidemic Dynamics of a Reinfectious Disease?: A Mathematical Model. Acta Biotheor 2024; 72:3. [PMID: 38402514 PMCID: PMC10894808 DOI: 10.1007/s10441-024-09478-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2023] [Accepted: 01/30/2024] [Indexed: 02/26/2024]
Abstract
The globalization in business and tourism becomes crucial more and more for the economical sustainability of local communities. In the presence of an epidemic outbreak, there must be such a decision on the policy by the host community as whether to accept visitors or not, the number of acceptable visitors, or the condition for acceptable visitors. Making use of an SIRI type of mathematical model, we consider the influence of visitors on the spread of a reinfectious disease in a community, especially assuming that a certain proportion of accepted visitors are immune. The reinfectivity of disease here means that the immunity gained by either vaccination or recovery is imperfect. With the mathematical results obtained by our analysis on the model for such an epidemic dynamics of resident and visitor populations, we find that the acceptance of visitors could have a significant influence on the disease's endemicity in the community, either suppressive or supportive.
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Affiliation(s)
- Ying Xie
- Department of Mathematical and Information Sciences, Graduate School of Information Sciences, Tohoku University, Aramaki-Aza-Aoba 6-3-09, Aoba-ku, Sendai, 980-8579, Miyagi, Japan
| | - Ishfaq Ahmad
- Department of Mathematical and Information Sciences, Graduate School of Information Sciences, Tohoku University, Aramaki-Aza-Aoba 6-3-09, Aoba-ku, Sendai, 980-8579, Miyagi, Japan
| | - ThankGod I S Ikpe
- Department of Mathematical and Information Sciences, Graduate School of Information Sciences, Tohoku University, Aramaki-Aza-Aoba 6-3-09, Aoba-ku, Sendai, 980-8579, Miyagi, Japan
| | - Elza F Sofia
- Department of Mathematical and Information Sciences, Graduate School of Information Sciences, Tohoku University, Aramaki-Aza-Aoba 6-3-09, Aoba-ku, Sendai, 980-8579, Miyagi, Japan
| | - Hiromi Seno
- Department of Mathematical and Information Sciences, Graduate School of Information Sciences, Tohoku University, Aramaki-Aza-Aoba 6-3-09, Aoba-ku, Sendai, 980-8579, Miyagi, Japan.
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2
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Viney M, Cheynel L. Gut immune responses and evolution of the gut microbiome-a hypothesis. DISCOVERY IMMUNOLOGY 2023; 2:kyad025. [PMID: 38567055 PMCID: PMC10917216 DOI: 10.1093/discim/kyad025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 11/03/2023] [Accepted: 11/22/2023] [Indexed: 04/04/2024]
Abstract
The gut microbiome is an assemblage of microbes that have profound effects on their hosts. The composition of the microbiome is affected by bottom-up, among-taxa interactions and by top-down, host effects, which includes the host immune response. While the high-level composition of the microbiome is generally stable over time, component strains and genotypes will constantly be evolving, with both bottom-up and top-down effects acting as selection pressures, driving microbial evolution. Secretory IgA is a major feature of the gut's adaptive immune response, and a substantial proportion of gut bacteria are coated with IgA, though the effect of this on bacteria is unclear. Here we hypothesize that IgA binding to gut bacteria is a selection pressure that will drive the evolution of IgA-bound bacteria, so that they will have a different evolutionary trajectory than those bacteria not bound by IgA. We know very little about the microbiome of wild animals and even less about their gut immune responses, but it must be a priority to investigate this hypothesis to understand if and how host immune responses contribute to microbiome evolution.
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Affiliation(s)
- Mark Viney
- Department of Evolution, Ecology & Behaviour, University of Liverpool, Liverpool, UK
| | - Louise Cheynel
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, ENTPE, UMR 5023 LEHNA, Villeurbanne, France
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3
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Lin Z, Sun B, Yang X, Jiang Y, Wu S, Lv B, Pan Y, Zhang Q, Wang X, Xiang G, Lou Y, Xiao X. Infectious Disease Diagnosis and Pathogen Identification Platform Based on Multiplex Recombinase Polymerase Amplification-Assisted CRISPR-Cas12a System. ACS Infect Dis 2023; 9:2306-2315. [PMID: 37811564 DOI: 10.1021/acsinfecdis.3c00381] [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: 10/10/2023]
Abstract
Controlling and mitigating infectious diseases caused by multiple pathogens or pathogens with several subtypes require multiplex nucleic acid detection platforms that can detect several target genes rapidly, specifically, sensitively, and simultaneously. Here, we develop a detection platform, termed Multiplex Assay of RPA and Collateral Effect of Cas12a-based System (MARPLES), based on multiplex nucleic acid amplification and Cas12a ssDNase activation to diagnose these diseases and identify their pathogens. We use the clinical specimens of hand, foot, and mouth disease (HFMD) and influenza A to evaluate the feasibility of MARPLES in diagnosing the disease and identifying the pathogen, respectively, and find that MARPLES can accurately diagnose the HFMD associated with enterovirus 71, coxsackievirus A16 (CVA16), CVA6, or CVA10 and identify the exact types of H1N1 and H3N2 in an hour, showing high sensitivity and specificity and 100% predictive agreement with qRT-PCR. Collectively, our findings demonstrate that MARPLES is a promising multiplex nucleic acid detection platform for disease diagnosis and pathogen identification.
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Affiliation(s)
- Ziqin Lin
- Wenzhou Key Laboratory of Sanitary Microbiology, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou 325035, China
| | - Baochang Sun
- Department of Laboratory, Wenzhou Center for Disease Control and Prevention, Wenzhou 325035, China
| | - Xi Yang
- Wenzhou Key Laboratory of Sanitary Microbiology, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou 325035, China
| | - Yayun Jiang
- Department of Clinical Laboratory, People's Hospital of Deyang City, Deyang 618000, China
| | - Sihong Wu
- Wenzhou Key Laboratory of Sanitary Microbiology, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou 325035, China
| | - Binbin Lv
- Department of Laboratory, Wenzhou Center for Disease Control and Prevention, Wenzhou 325035, China
| | - Yajing Pan
- Wenzhou Key Laboratory of Sanitary Microbiology, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou 325035, China
| | - Qingxun Zhang
- Beijing Milu Ecological Research Center, Beijing Academy of Science and Technology, Beijing 100076, China
| | - Xiaoqiong Wang
- Zhuji Institute of Biomedicine, Wenzhou Medical University, Zhuji, Shaoxing 311800, Zhejiang, China
| | - Guangxin Xiang
- Wenzhou Key Laboratory of Sanitary Microbiology, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou 325035, China
| | - Yongliang Lou
- Wenzhou Key Laboratory of Sanitary Microbiology, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou 325035, China
| | - Xingxing Xiao
- Wenzhou Key Laboratory of Sanitary Microbiology, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou 325035, China
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4
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Nie Y, Zhong X, Lin T, Wang W. Pathogen diversity in meta-population networks. CHAOS, SOLITONS, AND FRACTALS 2023; 166:112909. [PMID: 36467017 PMCID: PMC9699689 DOI: 10.1016/j.chaos.2022.112909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 09/15/2022] [Accepted: 11/13/2022] [Indexed: 06/17/2023]
Abstract
The pathogen diversity means that multiple strains coexist, and widely exist in the biology systems. The new mutation of SARS-CoV-2 leading to worldwide pathogen diversity is a typical example. What are the main factors of inducing the pathogen diversity? Previous studies indicated the pathogen mutation is the most important reason for inducing the pathogen diversity. The traffic network and gene network are crucial in shaping the dynamics of pathogen contagion, while their roles for the pathogen diversity still lacking a theoretical study. To this end, we propose a reaction-diffusion process of pathogens with mutations on meta-population networks, which includes population movement and strain mutation. We extend the Microscopic Markov Chain Approach (MMCA) to describe the model. Traffic networks make pathogen diversity more likely to occur in cities with lower infection densities. The likelihood of pathogen diversity is low in cities with short effective distances in the traffic network. Star-type gene network is more likely to lead to pathogen diversity than lattice-type and chain-type gene networks. When pathogen localization is present, infection is localized to strains that are at the endpoints of the gene network. Both the increased probability of movement and mutation promote pathogen diversity. The results also show that the population tends to move to cities with short effective distances, resulting in the infection density is high.
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Affiliation(s)
- Yanyi Nie
- School of Public Health, Chongqing Medical University, Chongqing, 400016, China
- College of Computer Science, Sichuan University, Chengdu 610065, China
| | - Xiaoni Zhong
- School of Public Health, Chongqing Medical University, Chongqing, 400016, China
| | - Tao Lin
- College of Computer Science, Sichuan University, Chengdu 610065, China
| | - Wei Wang
- School of Public Health, Chongqing Medical University, Chongqing, 400016, China
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5
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Bladder Microbiome in the Context of Urological Disorders—Is There a Biomarker Potential for Interstitial Cystitis? Diagnostics (Basel) 2022; 12:diagnostics12020281. [PMID: 35204374 PMCID: PMC8870776 DOI: 10.3390/diagnostics12020281] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 01/14/2022] [Accepted: 01/17/2022] [Indexed: 12/23/2022] Open
Abstract
Since the development of modern cultivation and sequencing techniques, the human microbiome has increasingly become the focus of scientific attention. Even in the bladder, long considered to be a sterile niche, a highly variable and complex microbial colonization has now been demonstrated. Especially in the context of diseases such as interstitial cystitis, whose etiopathogenesis is largely unknown, and whose diagnosis is based on a process of exclusion of confusable diseases, science hopes to gain far-reaching insights for etiology and diagnosis, including the identification of potential biomarkers. While for functional disorders such as urge urinary incontinence and overactive bladder syndrome, initial associations have been demonstrated between reduced microbial diversity and increased symptomatology, as well as shifts in the abundance of specific microorganisms such as Lactobacillus or Proteus, studies in interstitial cystitis show conflicting results and have failed to identify a putative organism or urotype that clearly distinguishes the urinary microbiome of patients with IC/BPS from that of healthy controls. At the present time, therefore, the new insights into the bladder microbiome and its potential influence on urologic disease cannot yet be used in the context of elucidating possible etiopathogenetic causes, as well as in the use of a biomarker for diagnostic or prognostic purposes. Further studies should focus primarily on uniform procedures and detection methods to achieve better comparability of results and increase the likelihood of detecting hidden patterns.
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6
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Eck JL, Barrès B, Soubeyrand S, Sirén J, Numminen E, Laine AL. Strain Diversity and Spatial Distribution Are Linked to Epidemic Dynamics in Host Populations. Am Nat 2022; 199:59-74. [DOI: 10.1086/717179] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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7
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Harrison OB, Maiden MCJ. Recent advances in understanding and combatting Neisseria gonorrhoeae: a genomic perspective. Fac Rev 2021; 10:65. [PMID: 34557869 PMCID: PMC8442004 DOI: 10.12703/r/10-65] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The sexually transmitted infection (STI) gonorrhoea remains a major global public health concern. The World Health Organization (WHO) estimates that 87 million new cases in individuals who were 15 to 49 years of age occurred in 2016. The growing number of gonorrhoea cases is concerning given the rise in gonococci developing antimicrobial resistance (AMR). Therefore, a global action plan is needed to facilitate surveillance. Indeed, the WHO has made surveillance leading to the elimination of STIs (including gonorrhoea) a global health priority. The availability of whole genome sequence data offers new opportunities to combat gonorrhoea. This can be through (i) enhanced surveillance of the global prevalence of AMR, (ii) improved understanding of the population biology of the gonococcus, and (iii) opportunities to mine sequence data in the search for vaccine candidates. Here, we review the current status in Neisseria gonorrhoeae genomics. In particular, we explore how genomics continues to advance our understanding of this complex pathogen.
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Affiliation(s)
- Odile B Harrison
- Department of Zoology, University of Oxford, The Peter Medawar Building, Oxford, UK
| | - Martin CJ Maiden
- Department of Zoology, University of Oxford, The Peter Medawar Building, Oxford, UK
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8
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Gjini E, Madec S. The ratio of single to co-colonization is key to complexity in interacting systems with multiple strains. Ecol Evol 2021; 11:8456-8474. [PMID: 34257910 PMCID: PMC8258234 DOI: 10.1002/ece3.7259] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 12/16/2020] [Accepted: 01/12/2021] [Indexed: 11/06/2022] Open
Abstract
The high number and diversity of microbial strains circulating in host populations have motivated extensive research on the mechanisms that maintain biodiversity. However, much of this work focuses on strain-specific and cross-immunity interactions. Another less explored mode of pairwise interaction is via altered susceptibilities to co-colonization in hosts already colonized by one strain. Diversity in such interaction coefficients enables strains to create dynamically their niches for growth and persistence, and "engineer" their common environment. How such a network of interactions with others mediates collective coexistence remains puzzling analytically and computationally difficult to simulate. Furthermore, the gradients modulating stability-complexity regimes in such multi-player endemic systems remain poorly understood. In a recent study (Madec & Gjini, Bulletin of Mathematical Biology, 82), we obtained an analytic representation for N-type coexistence in an SIS epidemiological model with co-colonization. We mapped multi-strain dynamics to a replicator equation using timescale separation. Here, we examine what drives coexistence regimes in such co-colonization system. We find the ratio of single to co-colonization, µ, critically determines the type of equilibrium and number of coexisting strains, and encodes a trade-off between overall transmission intensity R 0 and mean interaction coefficient in strain space, k. Preserving a given coexistence regime, under fixed trait variation, requires balancing between higher mean competition in favorable environments, and higher cooperation in harsher environments, and is consistent with the stress gradient hypothesis. Multi-strain coexistence tends to steady-state attractors for small µ, whereas as µ increases, dynamics tend to more complex attractors. Following strain frequencies, evolutionary dynamics in the system also display contrasting patterns with µ, interpolating between multi-stable and fluctuating selection for cooperation and mean invasion fitness, in the two extremes. This co-colonization framework could be applied more generally, to study invariant principles in collective coexistence, and to quantify how critical shifts in community dynamics get potentiated by mean-field and environmental gradients.
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Affiliation(s)
- Erida Gjini
- Instituto Gulbenkian de CiênciaOeirasPortugal
- Center for Computational and Stochastic MathematicsInstituto Superior TécnicoUniversity of LisbonLisbonPortugal
| | - Sten Madec
- Institut Denis PoissonUniversity of ToursToursFrance
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9
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Goddard FB, Ban R, Barr DB, Brown J, Cannon J, Colford JM, Eisenberg JNS, Ercumen A, Petach H, Freeman MC, Levy K, Luby SP, Moe C, Pickering AJ, Sarnat JA, Stewart J, Thomas E, Taniuchi M, Clasen T. Measuring Environmental Exposure to Enteric Pathogens in Low-Income Settings: Review and Recommendations of an Interdisciplinary Working Group. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2020; 54:11673-11691. [PMID: 32813503 PMCID: PMC7547864 DOI: 10.1021/acs.est.0c02421] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 08/18/2020] [Accepted: 08/19/2020] [Indexed: 05/06/2023]
Abstract
Infections with enteric pathogens impose a heavy disease burden, especially among young children in low-income countries. Recent findings from randomized controlled trials of water, sanitation, and hygiene interventions have raised questions about current methods for assessing environmental exposure to enteric pathogens. Approaches for estimating sources and doses of exposure suffer from a number of shortcomings, including reliance on imperfect indicators of fecal contamination instead of actual pathogens and estimating exposure indirectly from imprecise measurements of pathogens in the environment and human interaction therewith. These shortcomings limit the potential for effective surveillance of exposures, identification of important sources and modes of transmission, and evaluation of the effectiveness of interventions. In this review, we summarize current and emerging approaches used to characterize enteric pathogen hazards in different environmental media as well as human interaction with those media (external measures of exposure), and review methods that measure human infection with enteric pathogens as a proxy for past exposure (internal measures of exposure). We draw from lessons learned in other areas of environmental health to highlight how external and internal measures of exposure can be used to more comprehensively assess exposure. We conclude by recommending strategies for advancing enteric pathogen exposure assessments.
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Affiliation(s)
- Frederick
G. B. Goddard
- Gangarosa
Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, Georgia 30322, United States
| | - Radu Ban
- Bill and
Melinda Gates Foundation, Seattle, Washington 98109, United States
| | - Dana Boyd Barr
- Gangarosa
Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, Georgia 30322, United States
| | - Joe Brown
- School of
Civil and Environmental Engineering, Georgia
Institute of Technology, Atlanta, Georgia 30332, United States
| | - Jennifer Cannon
- Centers
for Disease Control and Prevention Foundation, Atlanta, Georgia 30308, United States
| | - John M. Colford
- Division
of Epidemiology and Biostatistics, School of Public Health, University of California−Berkeley, Berkeley, California 94720, United States
| | - Joseph N. S. Eisenberg
- Department
of Epidemiology, University of Michigan
School of Public Health, Ann Arbor, Michigan 48109, United States
| | - Ayse Ercumen
- Department
of Forestry and Environmental Resources, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Helen Petach
- U.S. Agency
for International Development, Washington, DC 20004, United States
| | - Matthew C. Freeman
- Gangarosa
Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, Georgia 30322, United States
| | - Karen Levy
- Department
of Environmental and Occupational Health Sciences, University of Washington, Seattle, Washington 98105, United States
| | - Stephen P. Luby
- Division
of Infectious Diseases and Geographic Medicine, Stanford University, California 94305, United States
| | - Christine Moe
- Center
for
Global Safe Water, Sanitation and Hygiene, Rollins School of Public
Health, Emory University, Atlanta, Georgia 30322, United States
| | - Amy J. Pickering
- Department
of Civil and Environmental Engineering, School of Engineering, Tufts University, Medford, Massachusetts 02155, United States
| | - Jeremy A. Sarnat
- Gangarosa
Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, Georgia 30322, United States
| | - Jill Stewart
- Department
of Environmental Sciences and Engineering, Gillings School of Global
Public Health, University of North Carolina, Chapel Hill, North Carolina 27599, United States
| | - Evan Thomas
- Mortenson
Center in Global Engineering, University
of Colorado Boulder, Boulder, Colorado 80303, United States
| | - Mami Taniuchi
- Division
of Infectious Diseases and International Health, Department of Medicine, University of Virginia, Charlottesville, Virginia 22903, United States
| | - Thomas Clasen
- Gangarosa
Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, Georgia 30322, United States
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10
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SERS-based immunocapture and detection of pathogenic bacteria using a boronic acid-functionalized polydopamine-coated Au@Ag nanoprobe. Mikrochim Acta 2020; 187:290. [DOI: 10.1007/s00604-020-04248-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 03/30/2020] [Indexed: 10/24/2022]
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11
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Georgieva M, Buckee CO, Lipsitch M. Models of immune selection for multi-locus antigenic diversity of pathogens. Nat Rev Immunol 2019; 19:55-62. [PMID: 30479379 DOI: 10.1038/s41577-018-0092-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
It is well accepted that pathogens can evade recognition and elimination by the host immune system by varying their antigenic targets. Thus, it has become a truism that host immunity is a major driver and determinant of the antigenic diversity of pathogens. However, it remains puzzling how host immunity selects for antigenic diversity at the level of the pathogen population, given that hosts have acquired immune responses to multiple antigens of most pathogens - sometimes through multiple effectors of both humoral and cellular immunity. In this Opinion article, we address this puzzle and the related question of why pathogens often have diversity at multiple antigenic loci. Here, we describe five hypotheses to explain the polymorphism of multiple antigens in a single pathogen species and highlight research relevant to our current models of thinking about multi-locus antigenic diversity.
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Affiliation(s)
- Maria Georgieva
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA. .,Department of Physiology, University of Lausanne, Lausanne, Switzerland.
| | - Caroline O Buckee
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Marc Lipsitch
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA.,Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA
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12
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Martins J, Pinto A, Stollenwerk N. The maximum curvature reinfection threshold. ECOLOGICAL COMPLEXITY 2019. [DOI: 10.1016/j.ecocom.2019.100791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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13
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Skuce R, Breadon E, Allen A, Milne G, McCormick C, Hughes C, Rutherford D, Smith G, Thompson S, Graham J, Harwood R, Byrne A. Longitudinal dynamics of herd-level Mycobacterium bovis MLVA type surveillance in cattle in Northern Ireland 2003-2016. INFECTION GENETICS AND EVOLUTION 2019; 79:104131. [PMID: 31786341 DOI: 10.1016/j.meegid.2019.104131] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Revised: 10/28/2019] [Accepted: 11/27/2019] [Indexed: 02/02/2023]
Abstract
Investigating genetically-structured diversity in pathogen populations over time is important to better understand disease maintenance and spread. Herd-level surveillance of Mycobacterium bovis genotypes (multi-locus VNTR analysis types, MLVA types) from all culture-confirmed bovine tuberculosis (TB) herd cases was undertaken in Northern Ireland (NI), generating an unparalleled, longitudinal, population-level 14-year survey for this pathogen. Across this population, 295 genetically-distinct M. bovis MLVA types were identified in the 19,717 M. bovis isolates surveyed. Of these, the most frequent was MLVA type 002 (23.0%); 151 MLVA types were represented more than once, in groups ranging from 2 to 4438 isolates. Only 23 MLVA types were isolated in all 14 years. Investigating inter-annual frequency of M. bovis MLVA types, examples of statistically-significant expansions (MLVA types 002, 004, 006, 009 and 027), contractions (MLVA types 001, 007 and 011) and maintenance (MLVA types 003 and 005) were disclosed, during a period of fluctuating bovine TB herd-level incidence at the NI scale. The fixed period frequency distribution of MLVA types remained highly right-skewed. Novel VNTR copy number variant MLVA types (N = 242; an average of 17 per annum) were identified throughout the survey. The MLVA type distribution in the landscape was not random; MLVA types showed statistically-significant geographical localization and strong spatial associations with Divisional Veterinary Office (DVO) regions. There was also evidence of differential risk of particular MLVA types across breeds (Holstein/Friesian vs. other), age-class, and sex and some evidence of an association between the number of animals testing positive for bovine TB during the disclosing test and particular MLVA types, although there was substantial variation.
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Affiliation(s)
- R Skuce
- Veterinary Sciences Division, Agri-food and Biosciences Institute (AFBI), Stoney Road, Stormont, Belfast BT4 3SD, UK; School of Biological Sciences, Queen's University Belfast, Belfast BT7 1NN, UK.
| | - E Breadon
- Veterinary Sciences Division, Agri-food and Biosciences Institute (AFBI), Stoney Road, Stormont, Belfast BT4 3SD, UK
| | - A Allen
- Veterinary Sciences Division, Agri-food and Biosciences Institute (AFBI), Stoney Road, Stormont, Belfast BT4 3SD, UK
| | - G Milne
- Veterinary Sciences Division, Agri-food and Biosciences Institute (AFBI), Stoney Road, Stormont, Belfast BT4 3SD, UK
| | - C McCormick
- Veterinary Sciences Division, Agri-food and Biosciences Institute (AFBI), Stoney Road, Stormont, Belfast BT4 3SD, UK; Veterinary Service and Animal Health Group, Department of Agriculture, Environment and Rural Affairs, Dundonald House, Stormont, Belfast BT4 3SB, UK
| | - C Hughes
- Veterinary Sciences Division, Agri-food and Biosciences Institute (AFBI), Stoney Road, Stormont, Belfast BT4 3SD, UK
| | - D Rutherford
- Veterinary Sciences Division, Agri-food and Biosciences Institute (AFBI), Stoney Road, Stormont, Belfast BT4 3SD, UK; Faculty of Electrical Engineering, Czech Technical University, Prague, Czech Republic (⁎)current address
| | - G Smith
- Veterinary Sciences Division, Agri-food and Biosciences Institute (AFBI), Stoney Road, Stormont, Belfast BT4 3SD, UK
| | - S Thompson
- Veterinary Sciences Division, Agri-food and Biosciences Institute (AFBI), Stoney Road, Stormont, Belfast BT4 3SD, UK
| | - J Graham
- Veterinary Sciences Division, Agri-food and Biosciences Institute (AFBI), Stoney Road, Stormont, Belfast BT4 3SD, UK
| | - R Harwood
- Veterinary Service and Animal Health Group, Department of Agriculture, Environment and Rural Affairs, Dundonald House, Stormont, Belfast BT4 3SB, UK
| | - A Byrne
- Veterinary Sciences Division, Agri-food and Biosciences Institute (AFBI), Stoney Road, Stormont, Belfast BT4 3SD, UK; School of Biological Sciences, Queen's University Belfast, Belfast BT7 1NN, UK; One-Health Unit, Surveillance, Animal By-Products and TSEs (SAT), Division Department of Agriculture, Food and Marine (DAFM), Agriculture House, Dublin 2, Ireland
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14
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Kwon H, Liu X, Choi EG, Lee JY, Choi S, Kim J, Wang L, Park S, Kim B, Lee Y, Kim J, Kang NY, Chang Y. Development of a Universal Fluorescent Probe for Gram‐Positive Bacteria. Angew Chem Int Ed Engl 2019; 58:8426-8431. [DOI: 10.1002/anie.201902537] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Indexed: 11/06/2022]
Affiliation(s)
- Haw‐Young Kwon
- Center for Self-assembly and ComplexityInstitute for Basic Science (IBS) Pohang Gyeongbuk 37673 Korea
| | - Xiao Liu
- Center for Self-assembly and ComplexityInstitute for Basic Science (IBS) Pohang Gyeongbuk 37673 Korea
- Pohang University of Science and Technology (POSTECH) Pohang Gyeongbuk 37673 Korea
| | - Eun Gyeong Choi
- Department of ChemistryLife Sciences InstituteNational University of Singapore 3 Science Drive 3 117543 Singapore Singapore
| | - Jung Yeol Lee
- New Drug Discovery CenterDaegu-Gyeongbuk Medivalley Innovation Foundation (DGMIF) 80 Chumbok-ro Dong-Gu Daegu 41061 Korea
| | - So‐Young Choi
- Pohang University of Science and Technology (POSTECH) Pohang Gyeongbuk 37673 Korea
| | - Jun‐Young Kim
- SL VAXiGEN A-B1 Korea Bio Park Seongnam-si 134488 Gyenggi-do Korea
| | - Lu Wang
- Department of Chemical BiologyMax-Planck-Institute for Molecular Physiology Otto-Hahn-Strasse 11 44227 Dortmund Germany
| | - Sung‐Jin Park
- Singapore Bioimaging ConsortiumAgency for Science, Technology and Research 11 Biopolis Way, # 02-02 Helios 138667 Singapore Singapore)
| | - Beomsue Kim
- Singapore Bioimaging ConsortiumAgency for Science, Technology and Research 11 Biopolis Way, # 02-02 Helios 138667 Singapore Singapore)
| | - Yong‐An Lee
- Singapore Bioimaging ConsortiumAgency for Science, Technology and Research 11 Biopolis Way, # 02-02 Helios 138667 Singapore Singapore)
| | - Jong‐Jin Kim
- Center for Self-assembly and ComplexityInstitute for Basic Science (IBS) Pohang Gyeongbuk 37673 Korea
| | - Nam Young Kang
- New Drug Discovery CenterDaegu-Gyeongbuk Medivalley Innovation Foundation (DGMIF) 80 Chumbok-ro Dong-Gu Daegu 41061 Korea
| | - Young‐Tae Chang
- Center for Self-assembly and ComplexityInstitute for Basic Science (IBS) Pohang Gyeongbuk 37673 Korea
- Department of ChemistryLife Sciences InstituteNational University of Singapore 3 Science Drive 3 117543 Singapore Singapore
- Singapore Bioimaging ConsortiumAgency for Science, Technology and Research 11 Biopolis Way, # 02-02 Helios 138667 Singapore Singapore)
- Pohang University of Science and Technology (POSTECH) Pohang Gyeongbuk 37673 Korea
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15
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Kwon H, Liu X, Choi EG, Lee JY, Choi S, Kim J, Wang L, Park S, Kim B, Lee Y, Kim J, Kang NY, Chang Y. Development of a Universal Fluorescent Probe for Gram‐Positive Bacteria. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201902537] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Haw‐Young Kwon
- Center for Self-assembly and ComplexityInstitute for Basic Science (IBS) Pohang Gyeongbuk 37673 Korea
| | - Xiao Liu
- Center for Self-assembly and ComplexityInstitute for Basic Science (IBS) Pohang Gyeongbuk 37673 Korea
- Pohang University of Science and Technology (POSTECH) Pohang Gyeongbuk 37673 Korea
| | - Eun Gyeong Choi
- Department of ChemistryLife Sciences InstituteNational University of Singapore 3 Science Drive 3 117543 Singapore Singapore
| | - Jung Yeol Lee
- New Drug Discovery CenterDaegu-Gyeongbuk Medivalley Innovation Foundation (DGMIF) 80 Chumbok-ro Dong-Gu Daegu 41061 Korea
| | - So‐Young Choi
- Pohang University of Science and Technology (POSTECH) Pohang Gyeongbuk 37673 Korea
| | - Jun‐Young Kim
- SL VAXiGEN A-B1 Korea Bio Park Seongnam-si 134488 Gyenggi-do Korea
| | - Lu Wang
- Department of Chemical BiologyMax-Planck-Institute for Molecular Physiology Otto-Hahn-Strasse 11 44227 Dortmund Germany
| | - Sung‐Jin Park
- Singapore Bioimaging ConsortiumAgency for Science, Technology and Research 11 Biopolis Way, # 02-02 Helios 138667 Singapore Singapore)
| | - Beomsue Kim
- Singapore Bioimaging ConsortiumAgency for Science, Technology and Research 11 Biopolis Way, # 02-02 Helios 138667 Singapore Singapore)
| | - Yong‐An Lee
- Singapore Bioimaging ConsortiumAgency for Science, Technology and Research 11 Biopolis Way, # 02-02 Helios 138667 Singapore Singapore)
| | - Jong‐Jin Kim
- Center for Self-assembly and ComplexityInstitute for Basic Science (IBS) Pohang Gyeongbuk 37673 Korea
| | - Nam Young Kang
- New Drug Discovery CenterDaegu-Gyeongbuk Medivalley Innovation Foundation (DGMIF) 80 Chumbok-ro Dong-Gu Daegu 41061 Korea
| | - Young‐Tae Chang
- Center for Self-assembly and ComplexityInstitute for Basic Science (IBS) Pohang Gyeongbuk 37673 Korea
- Department of ChemistryLife Sciences InstituteNational University of Singapore 3 Science Drive 3 117543 Singapore Singapore
- Singapore Bioimaging ConsortiumAgency for Science, Technology and Research 11 Biopolis Way, # 02-02 Helios 138667 Singapore Singapore)
- Pohang University of Science and Technology (POSTECH) Pohang Gyeongbuk 37673 Korea
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16
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Kosoy M, Kosoy R. Complexity and biosemiotics in evolutionary ecology of zoonotic infectious agents. Evol Appl 2018; 11:394-403. [PMID: 29636794 PMCID: PMC5891042 DOI: 10.1111/eva.12503] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Accepted: 06/01/2017] [Indexed: 02/02/2023] Open
Abstract
More is not automatically better. Generation and accumulation of information reflecting the complexity of zoonotic diseases as ecological systems do not necessarily lead to improved interpretation of the obtained information and understanding of these complex systems. The traditional conceptual framework for analysis of diseases ecology is neither designed for, nor adaptable enough, to absorb the mass of diverse sources of relevant information. The multidirectional and multidimensional approaches to analyses form an inevitable part in defining a role of zoonotic pathogens and animal hosts considering the complexity of their inter-relations. And the more data we have, the more involved the interpretation needs to be. The keyword for defining the roles of microbes as pathogens, animals as hosts, and environmental parameters as infection drivers is "functional importance." Microbes can act as pathogens toward their host only if/when they recognize the animal organism as the target. The same is true when the host recognizes the microbe as a pathogen rather than harmless symbiont based on the context of its occurrence in that host. Here, we propose conceptual tools developed in the realm of the interdisciplinary sciences of complexity and biosemiotics for extending beyond the currently dominant mindset in ecology and evolution of infectious diseases. We also consider four distinct hierarchical levels of perception guiding how investigators can approach zoonotic agents, as a subject of their research, representing differences in emphasizing particular elements and their relations versus more unified systemic approaches.
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Affiliation(s)
- Michael Kosoy
- Division of Vector‐Borne DiseasesCenters for Disease Control and PreventionFort CollinsCOUSA
- Global Health AsiaMahidol UniversityBangkokThailand
| | - Roman Kosoy
- Department of Genetics and Genomic SciencesIcahn School of Medicine at Mount SinaiNew YorkNYUSA
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17
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Råberg L, Hagström Å, Andersson M, Bartkova S, Scherman K, Strandh M, Tschirren B. Evolution of antigenic diversity in the tick-transmitted bacteriumBorrelia afzelii: a role for host specialization? J Evol Biol 2017; 30:1034-1041. [DOI: 10.1111/jeb.13075] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Revised: 03/01/2017] [Accepted: 03/20/2017] [Indexed: 01/22/2023]
Affiliation(s)
- L. Råberg
- Department of Biology; Lund University; Lund Sweden
| | - Å. Hagström
- Department of Biology; Lund University; Lund Sweden
| | - M. Andersson
- Department of Biology; Lund University; Lund Sweden
| | - S. Bartkova
- Department of Biology; Lund University; Lund Sweden
| | - K. Scherman
- Department of Biology; Lund University; Lund Sweden
| | - M. Strandh
- Department of Biology; Lund University; Lund Sweden
| | - B. Tschirren
- Department of Biology; Lund University; Lund Sweden
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18
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Bistability of Evolutionary Stable Vaccination Strategies in the Reinfection SIRI Model. Bull Math Biol 2017; 79:853-883. [DOI: 10.1007/s11538-017-0257-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Accepted: 02/10/2017] [Indexed: 10/20/2022]
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19
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Carev M, Kovačić A, Novak A, Tonkić M, Jerončić A. Campylobacter jejunistrains coresistant to tetracycline and ciprofloxacin in patients with gastroenteritis in Croatia. Infect Dis (Lond) 2016; 49:268-276. [DOI: 10.1080/23744235.2016.1258487] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
Affiliation(s)
- Merica Carev
- Department of Microbiology, Public Health Institute of Split and Dalmatia County, Croatia
- Department of Microbiology, University of Split School of Medicine, Croatia
| | - Ana Kovačić
- Department of Ecology, Public Health Institute of Split and Dalmatia County, Croatia
| | - Anita Novak
- Department of Microbiology, University of Split School of Medicine, Croatia
- Department of Microbiology, University Hospital Centre Split, Croatia
| | - Marija Tonkić
- Department of Microbiology, University of Split School of Medicine, Croatia
- Department of Microbiology, University Hospital Centre Split, Croatia
| | - Ana Jerončić
- Department of Research in Biomedicine and Health, University of Split School of Medicine, Croatia
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20
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Gjini E, Madec S. A slow-fast dynamic decomposition links neutral and non-neutral coexistence in interacting multi-strain pathogens. THEOR ECOL-NETH 2016. [DOI: 10.1007/s12080-016-0320-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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21
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Brehony C, Rodrigues CMC, Borrow R, Smith A, Cunney R, Moxon ER, Maiden MCJ. Distribution of Bexsero® Antigen Sequence Types (BASTs) in invasive meningococcal disease isolates: Implications for immunisation. Vaccine 2016; 34:4690-4697. [PMID: 27521232 PMCID: PMC5012890 DOI: 10.1016/j.vaccine.2016.08.015] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Revised: 08/01/2016] [Accepted: 08/03/2016] [Indexed: 01/19/2023]
Abstract
Serogroup B is the only major disease-associated capsular group of Neisseria meningitidis for which no protein-polysaccharide conjugate vaccine is available. This has led to the development of multi-component protein-based vaccines that target serogroup B invasive meningococcal disease (IMD), including Bexsero®, which was implemented for UK infants in 2015, and Trumenba®. Given the diversity of meningococcal protein antigens, post-implementation surveillance of IMD isolates, including characterisation of vaccine antigens, is essential for assessing the effectiveness of such vaccines. Whole genome sequencing (WGS), as realised in the Meningitis Research Foundation Meningococcus Genome Library (MRF-MGL), provides a rapid, comprehensive, and cost-effective approach to this. To facilitate the surveillance of the antigen targets included in Bexsero® (fHbp, PorA, NHBA and NadA) for protective immunity, a Bexsero® Antigen Sequence Type (BAST) scheme, based on deduced peptide sequence variants, was implemented in the PubMLST.org/neisseria database, which includes the MRF-MGL and other isolate collections. This scheme enabled the characterisation of vaccine antigen variants and here the invasive meningococci isolated in Great Britain and Ireland in the epidemiological years 2010/11 to 2013/14 are analysed. Many unique BASTs (647) were present, but nine of these accounted for 39% (775/1966) of isolates, with some temporal and geographic differences in BAST distribution. BASTs were strongly associated with other characteristics, such as serogroup and clonal complex (cc), and a significant increase in BAST-2 was associated with increased prevalence of serogroup W clonal complex 11 meningococci. Potential coverage was assessed by the examination of the antigen peptide sequences present in the vaccine and epidemiological dataset. There were 22.8-30.8% exact peptide matches to Bexsero® components and predicted coverage of 66.1%, based on genotype-phenotype modelling for 63.7% of serogroup B isolates from 2010/14 in UK and Ireland. While there are many caveats to this estimate, it lies within the range of other published estimates.
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Affiliation(s)
- Carina Brehony
- Department of Zoology, University of Oxford, South Parks Road, Oxford, United Kingdom.
| | | | - Ray Borrow
- Public Health England, Meningococcal Reference Unit, Manchester Royal Infirmary, Manchester, United Kingdom.
| | - Andrew Smith
- Scottish Haemophilus, Legionella, Meningococcus and Pneumococcus Reference Laboratory, Glasgow Royal Infirmary, Glasgow, United Kingdom; College of Medical, Veterinary & Life Sciences, University of Glasgow, Glasgow, United Kingdom.
| | - Robert Cunney
- Irish Meningitis and Meningococcal Reference Laboratory, Temple Street Children's University Hospital, Dublin, Ireland.
| | - E Richard Moxon
- Department of Paediatrics, University of Oxford, John Radcliffe Hospital, Oxford, United Kingdom.
| | - Martin C J Maiden
- Department of Zoology, University of Oxford, South Parks Road, Oxford, United Kingdom.
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22
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Roy SW, Ferreira MU. A new model for the origins of allelic dimorphism in Plasmodium falciparum. Parasitol Int 2014; 64:229-37. [PMID: 25251164 DOI: 10.1016/j.parint.2014.09.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2014] [Revised: 07/11/2014] [Accepted: 09/12/2014] [Indexed: 11/17/2022]
Abstract
In his landmark 1987 study of the merozoite surface protein-1 locus in Plasmodium falciparum, Kazuyuki Tanabe and coauthors introduced the phenomenon of allelic dimorphism, in which antigenic diversity is arranged into two maximally diverged haplotypes. Further work has extended this finding to other loci in P. falciparum. Each of the loci at which allelic dimorphism is observed encodes major surface antigens of blood-stage malaria parasites, and is consequently a major vaccine target, thus understanding the origins and implications of allelic dimorphism is of crucial importance. Here we examine the essential features of allelic dimorphism in dimorphic malarial surface antigens. From sequence analysis, we conclude that the ancestral population may have been recombining/multimorphic rather than dimorphic. We hypothesize a pathway to allelic dimorphism in which an ancestral allele-rich recombining population could have undergone a severe population bottleneck, putatively caused by the lateral transfer of P. falciparum from apes to humans. This bottleneck produced a reduction in allelic diversity, favoring the survival of the most divergent alleles, which in turn led to recombination suppression by strong natural selection against recombinants.
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Affiliation(s)
- Scott W Roy
- Department of Biology, San Francisco State University, 1600 Holloway Avenue, San Francisco, CA 94132, USA.
| | - Marcelo U Ferreira
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, Av. Prof. Lineu Prestes 1374, 05508-900 São Paulo, SP, Brazil.
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Adamiak P, Vanderkooi OG, Kellner JD, Schryvers AB, Bettinger JA, Alcantara J. Effectiveness of the standard and an alternative set of Streptococcus pneumoniae multi locus sequence typing primers. BMC Microbiol 2014; 14:143. [PMID: 24889110 PMCID: PMC4057806 DOI: 10.1186/1471-2180-14-143] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2013] [Accepted: 05/14/2014] [Indexed: 11/23/2022] Open
Abstract
Background Multi-locus sequence typing (MLST) is a portable, broadly applicable method for classifying bacterial isolates at an intra-species level. This methodology provides clinical and scientific investigators with a standardized means of monitoring evolution within bacterial populations. MLST uses the DNA sequences from a set of genes such that each unique combination of sequences defines an isolate’s sequence type. In order to reliably determine the sequence of a typing gene, matching sequence reads for both strands of the gene must be obtained. This study assesses the ability of both the standard, and an alternative set of, Streptococcus pneumoniae MLST primers to completely sequence, in both directions, the required typing alleles. Results The results demonstrated that for five (aroE, recP, spi, xpt, ddl) of the seven S. pneumoniae typing alleles, the standard primers were unable to obtain the complete forward and reverse sequences. This is due to the standard primers annealing too closely to the target regions, and current sequencing technology failing to sequence the bases that are too close to the primer. The alternative primer set described here, which includes a combination of primers proposed by the CDC and several designed as part of this study, addresses this limitation by annealing to highly conserved segments further from the target region. This primer set was subsequently employed to sequence type 105 S. pneumoniae isolates collected by the Canadian Immunization Monitoring Program ACTive (IMPACT) over a period of 18 years. Conclusions The inability of several of the standard S. pneumoniae MLST primers to fully sequence the required region was consistently observed and is the result of a shift in sequencing technology occurring after the original primers were designed. The results presented here introduce clear documentation describing this phenomenon into the literature, and provide additional guidance, through the introduction of a widely validated set of alternative primers, to research groups seeking to undertake S. pneumoniae MLST based studies.
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Affiliation(s)
| | | | | | | | | | - Joenel Alcantara
- Department of Microbiology, Immunology and Infectious Diseases, 3330 Hospital Dr, NW, Calgary, AB T2N 4 N1, Canada.
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24
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MUGHINI-GRAS L, SMID JH, WAGENAAR JA, DE BOER A, HAVELAAR AH, FRIESEMA IHM, FRENCH NP, GRAZIANI C, BUSANI L, VAN PELT W. Campylobacteriosis in returning travellers and potential secondary transmission of exotic strains. Epidemiol Infect 2014; 142:1277-88. [PMID: 23962634 PMCID: PMC9151200 DOI: 10.1017/s0950268813002069] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2013] [Revised: 07/04/2013] [Accepted: 07/31/2013] [Indexed: 11/07/2022] Open
Abstract
SUMMARY Multilocus sequence types (STs) were determined for 232 and 737 Campylobacter jejuni/coli isolates from Dutch travellers and domestically acquired cases, respectively. Putative risk factors for travel-related campylobacteriosis, and for domestically acquired campylobacteriosis caused by exotic STs (putatively carried by returning travellers), were investigated. Travelling to Asia, Africa, Latin America and the Caribbean, and Southern Europe significantly increased the risk of acquiring campylobacteriosis compared to travelling within Western Europe. Besides eating chicken, using antacids, and having chronic enteropathies, we identified eating vegetable salad outside Europe, drinking bottled water in high-risk destinations, and handling/eating undercooked pork as possible risk factors for travel-related campylobacteriosis. Factors associated with domestically acquired campylobacteriosis caused by exotic STs involved predominantly person-to-person contacts around popular holiday periods. We concluded that putative determinants of travel-related campylobacteriosis differ from those of domestically acquired infections and that returning travellers may carry several exotic strains that might subsequently spread to domestic populations even through limited person-to-person transmission.
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Affiliation(s)
- L. MUGHINI-GRAS
- Department of Veterinary Public Health and Food Safety, Istituto Superiore di Sanità, Rome, Italy
- Centre for Infectious Disease Control, National Institute of Public Health and the Environment (RIVM), Bilthoven, The Netherlands
- Department of Infectious Diseases and Immunology, Utrecht University, Utrecht, The Netherlands
| | - J. H. SMID
- Centre for Infectious Disease Control, National Institute of Public Health and the Environment (RIVM), Bilthoven, The Netherlands
- Institute for Risk Assessment Sciences, Utrecht University, Utrecht, The Netherlands
| | - J. A. WAGENAAR
- Department of Infectious Diseases and Immunology, Utrecht University, Utrecht, The Netherlands
- Central Veterinary Institute of Wageningen UR, Lelystad, The Netherlands
- WHO Collaborating Centre for Reference and Research on Campylobacter/OIE Reference Laboratory for Campylobacteriosis, Utrecht/Lelystad, The Netherlands
| | - A. DE BOER
- Central Veterinary Institute of Wageningen UR, Lelystad, The Netherlands
| | - A. H. HAVELAAR
- Centre for Infectious Disease Control, National Institute of Public Health and the Environment (RIVM), Bilthoven, The Netherlands
- Institute for Risk Assessment Sciences, Utrecht University, Utrecht, The Netherlands
| | - I. H. M. FRIESEMA
- Centre for Infectious Disease Control, National Institute of Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - N. P. FRENCH
- Massey University, Palmerston North, New Zealand
| | - C. GRAZIANI
- Department of Veterinary Public Health and Food Safety, Istituto Superiore di Sanità, Rome, Italy
| | - L. BUSANI
- Department of Veterinary Public Health and Food Safety, Istituto Superiore di Sanità, Rome, Italy
| | - W. VAN PELT
- Centre for Infectious Disease Control, National Institute of Public Health and the Environment (RIVM), Bilthoven, The Netherlands
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25
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Bai X, Borrow R. Genetic shifts ofNeisseria meningitidisserogroup B antigens and the quest for a broadly cross-protective vaccine. Expert Rev Vaccines 2014; 9:1203-17. [DOI: 10.1586/erv.10.116] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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26
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Scientific Opinion on the evaluation of molecular typing methods for major food‐borne microbiological hazards and their use for attribution modelling, outbreak investigation and scanning surveillance: Part 1 (evaluation of methods and applications). EFSA J 2013. [DOI: 10.2903/j.efsa.2013.3502] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
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27
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Stumpf RM, Wilson BA, Rivera A, Yildirim S, Yeoman CJ, Polk JD, White BA, Leigh SR. The primate vaginal microbiome: comparative context and implications for human health and disease. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2013; 152 Suppl 57:119-34. [PMID: 24166771 DOI: 10.1002/ajpa.22395] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2013] [Accepted: 08/31/2013] [Indexed: 12/12/2022]
Abstract
The primate body hosts trillions of microbes. Interactions between primate hosts and these microbes profoundly affect primate physiology, reproduction, health, survival, and ultimately, evolution. It is increasingly clear that primate health cannot be understood fully without knowledge of host-microbial interactions. Our goals here are to review what is known about microbiomes of the female reproductive tract and to explore several factors that influence variation within individuals, as well as within and between primate species. Much of our knowledge of microbial variation derives from studies of humans, and from microbes located in nonreproductive regions (e.g., the gut). We review work suggesting that the vaginal microbiota affects female health, fecundity, and pregnancy outcomes, demonstrating the selective potential for these agents. We explore the factors that correlate with microbial variation within species. Initial colonization by microbes depends on the manner of birth; most microbial variation is structured by estrogen levels that change with age (i.e., at puberty and menopause) and through the menstrual cycle. Microbial communities vary by location within the vagina and can depend on the sampling methods used (e.g., swab, lavage, or pap smear). Interindividual differences also exist, and while this variation is not completely understood, evidence points more to differences in estrogen levels, rather than differences in external physical environment. When comparing across species, reproductive-age humans show distinct microbial communities, generally dominated by Lactobacillus, unlike other primates. We develop evolutionary hypotheses to explain the marked differences in microbial communities. While much remains to be done to test these hypotheses, we argue that the ample variation in primate mating and reproductive behavior offers excellent opportunities to evaluate host-microbe coevolution and adaptation.
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Affiliation(s)
- Rebecca M Stumpf
- Department of Anthropology, University of Illinois, Urbana, IL; Institute for Genomic Biology, University of Illinois, Urbana, IL
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28
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Anttila J, Ruokolainen L, Kaitala V, Laakso J. Loss of competition in the outside host environment generates outbreaks of environmental opportunist pathogens. PLoS One 2013; 8:e71621. [PMID: 24244752 PMCID: PMC3752018 DOI: 10.1371/journal.pone.0071621] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2013] [Accepted: 07/01/2013] [Indexed: 01/12/2023] Open
Abstract
Environmentally transmitted pathogens face ecological interactions (e.g., competition, predation, parasitism) in the outside-host environment and host immune system during infection. Despite the ubiquitousness of environmental opportunist pathogens, traditional epidemiology focuses on obligatory pathogens incapable of environmental growth. Here we ask how competitive interactions in the outside-host environment affect the dynamics of an opportunist pathogen. We present a model coupling the classical SI and Lotka–Volterra competition models. In this model we compare a linear infectivity response and a sigmoidal infectivity response. An important assumption is that pathogen virulence is traded off with competitive ability in the environment. Removing this trade-off easily results in host extinction. The sigmoidal response is associated with catastrophic appearances of disease outbreaks when outside-host species richness, or overall competition pressure, decreases. This indicates that alleviating outside-host competition with antibacterial substances that also target the competitors can have unexpected outcomes by providing benefits for opportunist pathogens. These findings may help in developing alternative ways of controlling environmental opportunist pathogens.
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Affiliation(s)
- Jani Anttila
- Integrative Ecology Unit, Department of Biosciences, University of Helsinki, Helsinki, Finland
- * E-mail:
| | - Lasse Ruokolainen
- Integrative Ecology Unit, Department of Biosciences, University of Helsinki, Helsinki, Finland
| | - Veijo Kaitala
- Integrative Ecology Unit, Department of Biosciences, University of Helsinki, Helsinki, Finland
| | - Jouni Laakso
- Integrative Ecology Unit, Department of Biosciences, University of Helsinki, Helsinki, Finland
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29
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Haynes E, Helgason T, Young JPW, Thwaites R, Budge GE. A typing scheme for the honeybee pathogen Melissococcus plutonius allows detection of disease transmission events and a study of the distribution of variants. ENVIRONMENTAL MICROBIOLOGY REPORTS 2013; 5:525-529. [PMID: 23864566 DOI: 10.1111/1758-2229.12057] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2013] [Accepted: 03/20/2013] [Indexed: 06/02/2023]
Abstract
Melissococcus plutonius is the bacterial pathogen that causes European Foulbrood of honeybees, a globally important honeybee brood disease. We have used next-generation sequencing to identify highly polymorphic regions in an otherwise genetically homogenous organism, and used these loci to create a modified MLST scheme. This synthesis of a proven typing scheme format with next-generation sequencing combines reliability and low costs with insights only available from high-throughput sequencing technologies. Using this scheme we show that the global distribution of M.plutonius variants is not uniform. We use the scheme in epidemiological studies to trace movements of infective material around England, insights that would have been impossible to confirm without the typing scheme. We also demonstrate the persistence of local variants over time.
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Affiliation(s)
- Edward Haynes
- University of York, Wentworth Way, York, YO10 5DD, UK
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30
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Maiden MCJ. The impact of protein-conjugate polysaccharide vaccines: an endgame for meningitis? Philos Trans R Soc Lond B Biol Sci 2013; 368:20120147. [PMID: 23798695 PMCID: PMC3720045 DOI: 10.1098/rstb.2012.0147] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
The development and implementation of conjugate polysaccharide vaccines against invasive bacterial diseases, specifically those caused by the encapsulated bacteria Neisseria meningitidis, Haemophilus influenzae and Streptococcus pneumoniae, has been one of the most effective public health innovations of the last 25 years. These vaccines have resulted in significant reductions in childhood morbidity and mortality worldwide, with their effectiveness due in large part to their ability to induce long-lasting immunity in a range of age groups. At the population level this immunity reduces carriage and interrupts transmission resulting in herd immunity; however, these beneficial effects can be counterbalanced by the selection pressures that immunity against carriage can impose, potentially promoting the emergence and spread of virulent vaccine escape variants. Studies following the implementation of meningococcal serogroup C vaccines improved our understanding of these effects in relation to the biology of accidental pathogens such as the meningococcus. This understanding has enabled the refinement of the implementation of conjugate polysaccharide vaccines against meningitis-associated bacteria, and will be crucial in maintaining and improving vaccine control of these infections. To date there is little evidence for the spread of virulent vaccine escape variants of the meningococcus and H. influenzae, although this has been reported in pneumococci.
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Affiliation(s)
- Martin C J Maiden
- Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK.
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Sethu P, Putty K, Lian Y, Kalia A. Connecting Microbial Population Genetics with Microbial Pathogenesis. Bioinformatics 2013. [DOI: 10.4018/978-1-4666-3604-0.ch039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
A bacterial species typically includes heterogeneous collections of genetically diverse isolates. How genetic diversity within bacterial populations influences the clinical outcome of infection remains mostly indeterminate. In part, this is due to a lack of technologies that can enable contemporaneous systems-level interrogation of host-pathogen interaction using multiple, genetically diverse bacterial strains. This chapter presents a prototype microfluidic cell array (MCA) that allows simultaneous elucidation of molecular events during infection of human cells in a semi-automated fashion. It shows that infection of human cells with up to sixteen genetically diverse bacterial isolates can be studied simultaneously. The versatility of MCAs is enhanced by incorporation of a gradient generator that allows interrogation of host-pathogen interaction under four different concentrations of any given environmental variable at the same time. Availability of high throughput MCAs should foster studies that can determine how differences in bacterial gene pools and concentration-dependent environmental variables affect the outcome of host-pathogen interaction.
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Dingle KE, Didelot X, Ansari MA, Eyre DW, Vaughan A, Griffiths D, Ip CLC, Batty EM, Golubchik T, Bowden R, Jolley KA, Hood DW, Fawley WN, Walker AS, Peto TE, Wilcox MH, Crook DW. Recombinational switching of the Clostridium difficile S-layer and a novel glycosylation gene cluster revealed by large-scale whole-genome sequencing. J Infect Dis 2013; 207:675-86. [PMID: 23204167 PMCID: PMC3549603 DOI: 10.1093/infdis/jis734] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2012] [Accepted: 09/18/2012] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Clostridium difficile is a major cause of nosocomial diarrhea, with 30-day mortality reaching 30%. The cell surface comprises a paracrystalline proteinaceous S-layer encoded by the slpA gene within the cell wall protein (cwp) gene cluster. Our purpose was to understand the diversity and evolution of slpA and nearby genes also encoding immunodominant cell surface antigens. METHODS Whole-genome sequences were determined for 57 C. difficile isolates representative of the population structure and different clinical phenotypes. Phylogenetic analyses were performed on their genomic region (>63 kb) spanning the cwp cluster. RESULTS Genetic diversity across the cwp cluster peaked within slpA, cwp66 (adhesin), and secA2 (secretory translocase). These genes formed a 10-kb cassette, of which 12 divergent variants were found. Homologous recombination involving this cassette caused it to associate randomly with genotype. One cassette contained a novel insertion (length, approximately 24 kb) that resembled S-layer glycosylation gene clusters. CONCLUSIONS Genetic exchange of S-layer cassettes parallels polysaccharide capsular switching in other species. Both cause major antigenic shifts, while the remainder of the genome is unchanged. C. difficile genotype is therefore not predictive of antigenic type. S-layer switching and immune escape could help explain temporal and geographic variation in C. difficile epidemiology and may inform genotyping and vaccination strategies.
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Affiliation(s)
- Kate E Dingle
- Nuffield Department of Clinical Medicine, Oxford Biomedical Research Centre, John Radcliffe Hospital, UK.
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Saleem M, Prince SM, Rigby SEJ, Imran M, Patel H, Chan H, Sanders H, Maiden MCJ, Feavers IM, Derrick JP. Use of a molecular decoy to segregate transport from antigenicity in the FrpB iron transporter from Neisseria meningitidis. PLoS One 2013; 8:e56746. [PMID: 23457610 PMCID: PMC3574120 DOI: 10.1371/journal.pone.0056746] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2012] [Accepted: 01/14/2013] [Indexed: 11/25/2022] Open
Abstract
FrpB is an outer membrane transporter from Neisseria meningitidis, the causative agent of meningococcal meningitis. It is a member of the TonB-dependent transporter (TBDT) family and is responsible for iron uptake into the periplasm. FrpB is subject to a high degree of antigenic variation, principally through a region of hypervariable sequence exposed at the cell surface. From the crystal structures of two FrpB antigenic variants, we identify a bound ferric ion within the structure which induces structural changes on binding which are consistent with it being the transported substrate. Binding experiments, followed by elemental analysis, verified that FrpB binds Fe3+ with high affinity. EPR spectra of the bound Fe3+ ion confirmed that its chemical environment was consistent with that observed in the crystal structure. Fe3+ binding was reduced or abolished on mutation of the Fe3+-chelating residues. FrpB orthologs were identified in other Gram-negative bacteria which showed absolute conservation of the coordinating residues, suggesting the existence of a specific TBDT sub-family dedicated to the transport of Fe3+. The region of antigenic hypervariability lies in a separate, external sub-domain, whose structure is conserved in both the F3-3 and F5-1 variants, despite their sequence divergence. We conclude that the antigenic sub-domain has arisen separately as a result of immune selection pressure to distract the immune response from the primary transport function. This would enable FrpB to function as a transporter independently of antibody binding, by using the antigenic sub-domain as a ‘molecular decoy’ to distract immune surveillance.
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Affiliation(s)
- Muhammad Saleem
- Michael Smith Building, Faculty of Life Sciences, University of Manchester, Oxford Road, Manchester, United Kingdom
| | - Stephen M. Prince
- Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester, United Kingdom
| | - Stephen E. J. Rigby
- Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester, United Kingdom
| | - Muhammad Imran
- Michael Smith Building, Faculty of Life Sciences, University of Manchester, Oxford Road, Manchester, United Kingdom
| | - Hema Patel
- National Institute for Biological Standards and Control, Health Protection Agency, Blanche Lane, South Mimms, Potters Bar, Hertfordshire, United Kingdom
| | - Hannah Chan
- National Institute for Biological Standards and Control, Health Protection Agency, Blanche Lane, South Mimms, Potters Bar, Hertfordshire, United Kingdom
| | - Holly Sanders
- National Institute for Biological Standards and Control, Health Protection Agency, Blanche Lane, South Mimms, Potters Bar, Hertfordshire, United Kingdom
| | - Martin C. J. Maiden
- Department of Zoology, University of Oxford, South Parks Road, Oxford, United Kingdom
| | - Ian M. Feavers
- National Institute for Biological Standards and Control, Health Protection Agency, Blanche Lane, South Mimms, Potters Bar, Hertfordshire, United Kingdom
| | - Jeremy P. Derrick
- Michael Smith Building, Faculty of Life Sciences, University of Manchester, Oxford Road, Manchester, United Kingdom
- * E-mail:
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Natural competence is a major mechanism for horizontal DNA transfer in the oral pathogen Porphyromonas gingivalis. mBio 2012; 3:mBio.00231-11. [PMID: 22294679 PMCID: PMC3268665 DOI: 10.1128/mbio.00231-11] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Porphyromonas gingivalis is a Gram-negative anaerobe that resides exclusively in the human oral cavity. Long-term colonization by P. gingivalis requires the bacteria to evade host immune responses while adapting to the changing host physiology and alterations in the composition of the oral microflora. The genetic diversity of P. gingivalis appears to reflect the variability of its habitat; however, little is known about the molecular mechanisms generating this diversity. Previously, our research group established that chromosomal DNA transfer occurs between P. gingivalis strains. In this study, we examine the role of putative DNA transfer genes in conjugation and transformation and demonstrate that natural competence mediated by comF is the dominant form of chromosomal DNA transfer, with transfer by a conjugation-like mechanism playing a minor role. Our results reveal that natural competence mechanisms are present in multiple strains of P. gingivalis, and DNA uptake is not sensitive to DNA source or modification status. Furthermore, extracellular DNA was observed for the first time in P. gingivalis biofilms and is predicted to be the major DNA source for horizontal transfer and allelic exchange between strains. We propose that exchange of DNA in plaque biofilms by a transformation-like process is of major ecological importance in the survival and persistence of P. gingivalis in the challenging oral environment. P. gingivalis colonizes the oral cavities of humans worldwide. The long-term persistence of these bacteria can lead to the development of chronic periodontitis and host morbidity associated with tooth loss. P. gingivalis is a genetically diverse species, and this variability is believed to contribute to its successful colonization and survival in diverse human hosts, as well as evasion of host immune defenses and immunization strategies. We establish here that natural competence is the major driving force behind P. gingivalis DNA exchange and that conjugative DNA transfer plays a minor role. Furthermore, we reveal for the first time the presence of extracellular DNA in P. gingivalis biofilms, which is most likely the source of DNA exchanged between strains within dental plaque. These studies expand our understanding of the mechanisms used by this important member of the human oral flora to transition its relationship with the host from a commensal to a pathogenic relationship.
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Noda T, Murakami K, Asai T, Etoh Y, Ishihara T, Kuroki T, Horikawa K, Fujimoto S. Multi-locus sequence typing of Salmonella enterica subsp. enterica serovar Enteritidis strains in Japan between 1973 and 2004. Acta Vet Scand 2011; 53:38. [PMID: 21672260 PMCID: PMC3126718 DOI: 10.1186/1751-0147-53-38] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2011] [Accepted: 06/15/2011] [Indexed: 11/10/2022] Open
Abstract
Salmonella enterica subsp. enterica serovar Enteritidis (S. Enteritidis) was responsible for a worldwide pandemic during the 1980s and 1990s; however, changes in the dominant lineage before and after this event remain unknown. This study determined S. Enteritidis lineages before and after this pandemic event in Japan using multilocus sequence typing (MLST). Thirty S. Enteritidis strains were collected in Japan between 1973 and 2004, consisting of 27 human strains from individual episodes, a bovine strain, a liquid egg strain and an eggshell strain. Strains showed nine phage types and 17 pulsed-field profiles with pulsed-field gel electrophoresis. All strains had homologous type 11 sequences without any nucleotide differences in seven housekeeping genes. These MLST results suggest that S. Enteritidis with the diversities revealed by phage typing and pulsed-field profiling has a highly clonal population. Although type 11 S. Enteritidis may exhibit both pleiotropic surface structure and pulsed-field type variation, it is likely to be a stable lineage derived from an ancestor before the 1980s and/or 1990s pandemic in Japan.
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Sadarangani M, Pollard AJ, Gray-Owen SD. Opa proteins and CEACAMs: pathways of immune engagement for pathogenic Neisseria. FEMS Microbiol Rev 2011; 35:498-514. [PMID: 21204865 DOI: 10.1111/j.1574-6976.2010.00260.x] [Citation(s) in RCA: 107] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Neisseria meningitidis and Neisseria gonorrhoeae are globally important pathogens, which in part owe their success to their ability to successfully evade human immune responses over long periods. The phase-variable opacity-associated (Opa) adhesin proteins are a major surface component of these organisms, and are responsible for bacterial adherence and entry into host cells and interactions with the immune system. Most immune interactions are mediated via binding to members of the carcinoembryonic antigen cell adhesion molecule (CEACAM) family. These Opa variants are able to bind to different receptors of the CEACAM family on epithelial cells, neutrophils, and T and B lymphocytes, influencing the innate and adaptive immune responses. Increased epithelial cell adhesion creates the potential for prolonged infection, invasion and dissemination. Furthermore, Opa proteins may inhibit T-lymphocyte activation and proliferation, B-cell antibody production, and innate inflammatory responses by infected epithelia, in addition to conferring increased resistance to antibody-dependent, complement-mediated killing. While vaccines containing Opa proteins could induce adhesion-blocking and bactericidal antibodies, the consequence of CEACAM binding by a candidate Opa-containing vaccine requires further investigation. This review summarizes current knowledge of the immunological consequences of the interaction between meningococcal and gonococcal Opa proteins and human CEACAMs, considering the implications for pathogenesis and vaccine development.
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Affiliation(s)
- Manish Sadarangani
- Oxford Vaccine Group, Department of Paediatrics, Centre for Clinical Vaccinology and Tropical Medicine, University of Oxford, Churchill Hospital, Oxford, UK.
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Hellgren O, Andersson M, Råberg L. The genetic structure of Borrelia afzelii varies with geographic but not ecological sampling scale. J Evol Biol 2010; 24:159-67. [PMID: 20964784 DOI: 10.1111/j.1420-9101.2010.02148.x] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The genetic structure of a pathogen is an important determinant of its potential rate of adaptation and can thereby influence the dynamics of host-parasite interactions. We investigated how the genetic structure of Borrelia afzelii varies with geographic and ecological sampling scale. Genetic structure was measured as the degree of linkage disequilibrium (LD) across three loci. To test for the effects of geographic and ecological scale, we calculated LD across or within populations 4-82 km apart and across or within different mammal host species. There was highly significant LD across populations and host species. However, there was also evidence for genome-wide recombination, and the LD largely resulted from epidemic spread of certain haplotypes, rather than lack of recombination. Interestingly, the degree of LD was higher in each population than in the sample as a whole, i.e. LD increased with decreasing geographic scale. In contrast, there was no effect of ecological sampling scale on LD. Strong LD may impede the rate of adaptive evolution. Our results suggest this effect might be particularly strong at a small geographic scale.
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Affiliation(s)
- O Hellgren
- Department of Animal Ecology, Lund University, Lund, Sweden
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38
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Yero D, Vipond C, Climent Y, Sardiñas G, Feavers IM, Pajón R. Variation in the Neisseria meningitidis FadL-like protein: an evolutionary model for a relatively low-abundance surface antigen. MICROBIOLOGY-SGM 2010; 156:3596-3608. [PMID: 20817647 DOI: 10.1099/mic.0.043182-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The molecular diversity of a novel Neisseria meningitidis antigen, encoded by the ORF NMB0088 of MC58 (FadL-like protein), was assessed in a panel of 64 diverse meningococcal strains. The panel consisted of strains belonging to different serogroups, serotypes, serosubtypes and MLST sequence types, of different clinical sources, years and countries of isolation. Based on the sequence variability of the protein, the FadL-like protein has been divided into four variant groups in this species. Antigen variants were associated with specific serogroups and MLST clonal complexes. Maximum-likelihood analyses were used to determine the relationships among sequences and to compare the selection pressures acting on the encoded protein. Furthermore, a model of population genetics and molecular evolution was used to detect natural selection in DNA sequences using the non-synonymous : synonymous substitution (d(N) : d(S)) ratio. The meningococcal sequences were also compared with those of the related surface protein in non-pathogenic commensal Neisseria species to investigate potential horizontal gene transfer. The N. meningitidis fadL gene was subject to only weak positive selection pressure and was less diverse than meningococcal major outer-membrane proteins. The majority of the variability in fadL was due to recombination among existing alleles from the same or related species that resulted in a discrete mosaic structure in the meningococcal population. In general, the population structuring observed based on the FadL-like membrane protein indicates that it is under intermediate immune selection. However, the emergence of a new subvariant within the hyperinvasive lineages demonstrates the phenotypic adaptability of N. meningitidis, probably in response to selective pressure.
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Affiliation(s)
- Daniel Yero
- Department of Molecular Biology, Division of Biotechnology, Finlay Institute, Havana, Cuba
| | - Caroline Vipond
- Division of Bacteriology, National Institute for Biological Standards and Control, Blanche Lane, South Mimms, Potters Bar, Hertfordshire, UK
| | - Yanet Climent
- Department of Molecular Biology, Division of Biotechnology, Finlay Institute, Havana, Cuba
| | - Gretel Sardiñas
- Division of Vaccines, Center for Genetic Engineering and Biotechnology, Havana, Cuba
| | - Ian M Feavers
- Division of Bacteriology, National Institute for Biological Standards and Control, Blanche Lane, South Mimms, Potters Bar, Hertfordshire, UK
| | - Rolando Pajón
- Center for Immunobiology and Vaccine Development, Children's Hospital Oakland Research Institute, Oakland, CA 94609, USA
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The genetic structure of Neisseria meningitidis populations in Cuba before and after the introduction of a serogroup BC vaccine. INFECTION GENETICS AND EVOLUTION 2010; 10:546-54. [DOI: 10.1016/j.meegid.2010.02.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2009] [Revised: 02/04/2010] [Accepted: 02/05/2010] [Indexed: 11/20/2022]
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Evans NJ, Harrison OB, Clow K, Derrick JP, Feavers IM, Maiden MCJ. Variation and molecular evolution of HmbR, the Neisseria meningitidis haemoglobin receptor. MICROBIOLOGY-SGM 2010; 156:1384-1393. [PMID: 20150237 PMCID: PMC3068627 DOI: 10.1099/mic.0.036475-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Meningococcal disease caused by serogroup B Neisseria meningitidis remains an important health problem in many parts of the world, and there are currently no comprehensive vaccines. Poor immunogenicity, combined with immunological identity to human sialic acids, have hindered the development of a serogroup B conjugate vaccine, resulting in the development of alternative vaccine candidates, including many outer-membrane protein (OMP)-based formulations. However, the design of protein-based meningococcal vaccines is complicated by the high level of genetic and antigenic diversity of the meningococcus. Knowledge of the extent and structuring of this diversity can have implications for the use of particular proteins as potential vaccine candidates. With this in mind, the diversity of the meningococcal OMP HmbR was investigated among N. meningitidis isolates representative of major hyper-invasive lineages. In common with other meningococcal antigens, the genetic diversity of hmbR resulted from a combination of intraspecies horizontal genetic exchange and de novo mutation. Furthermore, genealogical analysis showed an association of hmbR genes with clonal complexes and the occurrence of two hmbR families, A and B. Three variable regions (VR1–VR3), located in loops 2, 3 and 4, were observed with clonal complex structuring of VR types. A minority of codons (3.9 %), located within putative surface-exposed loop regions of a 2D model, were under diversifying selection, indicating regions of the protein likely to be subject to immune attack.
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Affiliation(s)
- Nicholas J. Evans
- Faculty of Life Sciences, University of Manchester, 131 Princess Street, Manchester M1 7DN, UK
- National Institute for Biological Standards and Control, South Mimms, Potters Bar, Hertfordshire EN6 3QG, UK
| | - Odile B. Harrison
- The Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK
| | - Kirsten Clow
- National Institute for Biological Standards and Control, South Mimms, Potters Bar, Hertfordshire EN6 3QG, UK
| | - Jeremy P. Derrick
- Faculty of Life Sciences, University of Manchester, 131 Princess Street, Manchester M1 7DN, UK
| | - Ian M. Feavers
- National Institute for Biological Standards and Control, South Mimms, Potters Bar, Hertfordshire EN6 3QG, UK
| | - Martin C. J. Maiden
- The Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK
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Cody AJ, Colles FM, Sheppard SK, Maiden MC. Where does Campylobacter come from? A molecular odyssey. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2010; 659:47-56. [PMID: 20204754 PMCID: PMC3977344 DOI: 10.1007/978-1-4419-0981-7_4] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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Linking questions to practices in the study of microbial pathogens: Sampling bias and typing methods. INFECTION GENETICS AND EVOLUTION 2009; 9:1418-23. [DOI: 10.1016/j.meegid.2009.08.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2009] [Revised: 08/21/2009] [Accepted: 08/21/2009] [Indexed: 01/10/2023]
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Rodriguez-Valera F, Martin-Cuadrado AB, Rodriguez-Brito B, Pasić L, Thingstad TF, Rohwer F, Mira A. Explaining microbial population genomics through phage predation. Nat Rev Microbiol 2009; 7:828-36. [PMID: 19834481 DOI: 10.1038/nrmicro2235] [Citation(s) in RCA: 439] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The remarkable differences that have been detected by metagenomics in the genomes of strains of the same bacterial species are difficult to reconcile with the widely accepted paradigm that periodic selection within bacterial populations will regularly purge genomic diversity by clonal replacement. We have found that many of the genes that differ between strains affect regions that are potential phage recognition targets. We therefore propose the constant-diversity dynamics model, in which the diversity of prokaryotic populations is preserved by phage predation. We provide supporting evidence for this model from metagenomics, mathematical analysis and computer simulations. Periodic selection and phage predation dynamics are not mutually exclusive; we compare their predictions to shed light on the ecological circumstances under which each type of dynamics could predominate.
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Affiliation(s)
- Francisco Rodriguez-Valera
- Departmento de Producción Vegetal y Microbiología, Universidad Miguel Hernandez, San Juan de Alicante, Spain
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Population dynamics of genetically diverse Plasmodium falciparum lineages: community-based prospective study in rural Amazonia. Parasitology 2009; 136:1097-105. [PMID: 19631016 DOI: 10.1017/s0031182009990539] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Temporal changes in the prevalence of antigenic variants in Plasmodium falciparum populations have been interpreted as evidence of immune-mediated frequency-dependent selection, but evolutively neutral processes may generate similar patterns of serotype replacement. Over 4 years, we investigated the population dynamics of P. falciparum polymorphisms at the community level by using 11 putatively neutral microsatellite markers. Plasmodium falciparum populations were less diverse than sympatric P. vivax isolates, with less multiple-clone infections, lower number of alleles per locus and lower virtual heterozygosity, but both species showed significant multilocus linkage disequilibrium. Evolutively neutral P. falciparum polymorphisms showed a high turnover rate, with few lineages persisting for several months in the population. Similar results had previously been obtained, in the same community, for sympatric P. vivax isolates. In contrast, the prevalence of the 2 dimorphic types of a major antigen, MSP-2, remained remarkably stable throughout the study period. We suggest that the relatively fast turnover of parasite lineages represents the typical population dynamics of neutral polymorphisms in small populations, with clear implications for the detection of frequency-dependent selection of polymorphisms.
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Genotypic comparison of invasive Neisseria meningitidis serogroup Y isolates from the United States, South Africa, and Israel, isolated from 1999 through 2002. J Clin Microbiol 2009; 47:2787-93. [PMID: 19571028 DOI: 10.1128/jcm.00091-09] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The proportion of meningococcal disease in the United States, South Africa, and Israel caused by Neisseria meningitidis serogroup Y (NmY) was greater than the worldwide average during the period 1999-2002. Genotypic characterization of 300 NmY isolates by multilocus sequence typing, 16S rRNA gene sequencing, and PorA variable region typing was conducted to determine the relationships of the isolates from these three countries. Seventy different genotypes were found. Two groups of ST-23 clonal complex isolates accounted for 88% of the U.S. isolates, 12% of the South African isolates, and 96% of the isolates from Israel. The single common clone (ST-23/16S-19/P1.5-2,10-1) represented 57, 5, and 35% of the NmY isolates from the United States, South Africa, and Israel. The predominant clone in South Africa (ST-175/16S-21/P1.5-1,2-2), and 11 other closely related clones made up 77% of the South African study isolates and were not found among the isolates from the United States or Israel. ST-175 was the predicted founder of the ST-175 clonal complex, and isolates of ST-175 and related sequence types have been described previously in other African countries. Continued active surveillance and genetic characterization of NmY isolates causing disease in the United States, South Africa, and Israel will provide valuable data for local and global epidemiology and allow monitoring for any expansion of existing clonal complexes and detection of the emergence of new virulent clones in the population.
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Evidence for horizontal gene transfer of two antigenically distinct O antigens in Bordetella bronchiseptica. Infect Immun 2009; 77:3249-57. [PMID: 19528223 DOI: 10.1128/iai.01448-08] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Host immunity is a major driving force of antigenic diversity, resulting in pathogens that can evade immunity induced by closely related strains. Here we show that two Bordetella bronchiseptica strains, RB50 and 1289, express two antigenically distinct O-antigen serotypes (O1 and O2, respectively). When 18 additional B. bronchiseptica strains were serotyped, all were found to express either the O1 or O2 serotype. Comparative genomic hybridization and PCR screening showed that the expression of either the O1 or O2 serotype correlated with the strain containing either the classical or alternative O-antigen locus, respectively. Multilocus sequence typing analysis of 49 B. bronchiseptica strains was used to build a phylogenetic tree, which revealed that the two O-antigen loci did not associate with a particular lineage, evidence that these loci are horizontally transferred between B. bronchiseptica strains. From experiments using mice vaccinated with purified lipopolysaccharide from strain RB50 (O1), 1289 (O2), or RB50Deltawbm (O antigen deficient), our data indicate that these O antigens do not confer cross-protection in vivo. The lack of cross-immunity between O-antigen serotypes appears to contribute to inefficient antibody-mediated clearance between strains. Together, these data are consistent with the idea that the O-antigen loci of B. bronchiseptica are horizontally transferred between strains and encode antigenically distinct serotypes, resulting in inefficient cross-immunity.
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Caugant DA, Maiden MCJ. Meningococcal carriage and disease--population biology and evolution. Vaccine 2009; 27 Suppl 2:B64-70. [PMID: 19464092 PMCID: PMC2719693 DOI: 10.1016/j.vaccine.2009.04.061] [Citation(s) in RCA: 264] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Meningococcal disease occurs worldwide with incidence rates varying from 1 to 1000 cases per 100,000. The causative organism, Neisseria meningitidis, is an obligate commensal of humans, which normally colonizes the mucosa of the upper respiratory tract without causing invasive disease, a phenomenon known as carriage. Studies using molecular methods have demonstrated the extensive genetic diversity of meningocococci isolated from carriers, in contrast to a limited number of genetic types, known as the hyperinvasive lineages, associated with invasive disease. Population and evolutionary models that invoke positive selection can be used to resolve the apparent paradox of virulent lineages persisting during the global spread of a non-clonal and normally commensal bacterium. The application of insights gained from studies of meningococcal population biology and evolution is important in understanding the spread of disease, as well as in vaccine development and implementation, especially with regard to the challenge of producing comprehensive vaccines based on sub-capsular antigens and measuring their effectiveness.
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Affiliation(s)
- Dominique A Caugant
- WHO Collaborating Centre for Reference and Research on Meningococci, Norwegian Institute of Public Health, Oslo, Norway.
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Wodarz D, Levy DN. Multiple HIV-1 infection of cells and the evolutionary dynamics of cytotoxic T lymphocyte escape mutants. Evolution 2009; 63:2326-39. [PMID: 19486149 DOI: 10.1111/j.1558-5646.2009.00727.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Cytotoxic T lymphocytes (CTL) are an important branch of the immune system, killing virus-infected cells. Many viruses can mutate so that infected cells are not killed by CTL anymore. This escape can contribute to virus persistence and disease. A prominent example is HIV-1. The evolutionary dynamics of CTL escape mutants in vivo have been studied experimentally and mathematically, assuming that a cell can only be infected with one HIV particle at a time. However, according to data, multiple virus particles frequently infect the same cell, a process called coinfection. Here, we study the evolutionary dynamics of CTL escape mutants in the context of coinfection. A mathematical model suggests that an intermediate strength of the CTL response against the wild-type is most detrimental for an escape mutant, minimizing overall virus load and even leading to its extinction. A weaker or, paradoxically, stronger CTL response against the wild-type both lead to the persistence of the escape mutant and higher virus load. It is hypothesized that an intermediate strength of the CTL response, and thus the suboptimal virus suppression observed in HIV-1 infection, might be adaptive to minimize the impact of existing CTL escape mutants on overall virus load.
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Affiliation(s)
- Dominik Wodarz
- Department of Ecology and Evolutionary Biology and Department of Mathematics, 321 Steinhaus Hall, University of California, Irvine, California 92697, USA.
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Yang L, Zhang X, Peng J, Zhu Y, Dong J, Xu J, Jin Q. Distribution of surface-protein variants of hyperinvasive meningococci in China. J Infect 2009; 58:358-67. [PMID: 19324418 DOI: 10.1016/j.jinf.2009.02.020] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2008] [Revised: 02/24/2009] [Accepted: 02/25/2009] [Indexed: 11/20/2022]
Abstract
OBJECTIVE Information regarding the different types of FetA and PorB meningococci that circulate in various regions of the world is still scarce. The present study investigated the distribution of FetA and PorB variable region (VR) types among meningococci belonging to hyperinvasive lineages circulating in China. METHODS The approach consisted of genotypic analysis of 201 Neisseria meningitidis strains belonging to hyperinvasive lineages isolated in China during the period 1956-2006. RESULTS Sixteen different PorB types were found, 8 of which were newly identified. Of the 24 different FetA VR types, 3 were determined to be novel. Particular combinations of FetA and PorB types associated with distinct clonal complexes were also observed. Most cases of invasive disease were caused by five individual clones: A: P1.7-1,10: F5-5: ST-3 (cc1) with P3.6,11,10,7 (class 3 PorB protein; VR1-6, VR2-11, VR3-10, and VR4-7); A: P1.20,9: F3-1: ST-5 (cc5) with P3.4,11,10,7; A: P1.20,9: F3-1: ST-5 (cc5) with P3.9,11,10,7; A: P1.20,9: F3-1: ST-7 (cc5) with P3.4,11,10,7; and C: P1.7-2,14: F3-3: ST-4821 (cc4821) with P3.9,15,6,7. CONCLUSION A number of antigen-gene variants and combinations exhibited broad temporal and geographic distributions, although several invasive clones were mainly associated with a specified timeframe. The changes that are increasingly emerging in circulating strains and the prevalent clone replacement describe the molecular epidemiology of meningococcal disease in China. Our findings have implications for both public-health monitoring and further study of this organism.
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Affiliation(s)
- Li Yang
- State Key Laboratory for Molecular Virology and Genetic Engineering, Institute of Pathogen Biology, Chinese Academy of Medical Sciences, Beijing, China
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Distribution and genetic variability of three vaccine components in a panel of strains representative of the diversity of serogroup B meningococcus. Vaccine 2009; 27:2794-803. [PMID: 19428890 DOI: 10.1016/j.vaccine.2009.02.098] [Citation(s) in RCA: 108] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2008] [Revised: 02/21/2009] [Accepted: 02/26/2009] [Indexed: 11/20/2022]
Abstract
With the aim of studying the molecular diversity of the antigens of a new recombinant vaccine against meningococcus serogroup B, the three genes coding for the main vaccine components GNA (Genome-derived Neisseria Antigen) 1870 (fHbp, factor H Binding Protein), GNA1994 (NadA, Neisseria adhesin A) and GNA2132 were sequenced in a panel of 85 strains collected worldwide and selected as representative of the serogroup B meningococcal diversity. No correlations were found between vaccine antigen variability and serogroup, geographic area and year of isolation. Although a relevant clustering was found with MLST clonal complexes, each showing an almost specific antigen variant repertoire, the prediction of the antigen assortment was not possible on the basis of MLST alone. Therefore, classification of meningococcus on the basis of MLST only is not sufficient to predict vaccine antigens diversity. Sequencing each gene in the different strains will be important to evaluate antigen conservation and assortment and to allow a future prediction of potential vaccine coverage.
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