1
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Parrish KM, Gestal MC. Eosinophils as drivers of bacterial immunomodulation and persistence. Infect Immun 2024; 92:e0017524. [PMID: 39007622 PMCID: PMC11385729 DOI: 10.1128/iai.00175-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/16/2024] Open
Abstract
Traditionally, eosinophils have been linked to parasitic infections and pathological disease states. However, emerging literature has unveiled a more nuanced and intricate role for these cells, demonstrating their key functions in maintaining mucosal homeostasis. Eosinophils exhibit diverse phenotypes and exert multifaceted effects during infections, ranging from promoting pathogen persistence to triggering allergic reactions. Our investigations primarily focus on Bordetella spp., with particular emphasis on Bordetella bronchiseptica, a natural murine pathogen that induces diseases in mice akin to pertussis in humans. Recent findings from our published work have unveiled a striking interaction between B. bronchiseptica and eosinophils, facilitated by the btrS-mediated mechanism. This interaction serves to enhance pathogen persistence while concurrently delaying adaptive immune responses. Notably, this role of eosinophils is only noted in the absence of a functional btrS signaling pathway, indicating that wild-type B. bronchiseptica, and possibly other Bordetella spp., possess such adeptness in manipulating eosinophils that the true function of these cells remains obscured during infection. In this review, we present the mounting evidence pointing toward eosinophils as targets of bacterial exploitation, facilitating pathogen persistence and fostering chronic infections in diverse mucosal sites, including the lungs, gut, and skin. We underscore the pivotal role of the master regulator of Bordetella pathogenesis, the sigma factor BtrS, in orchestrating eosinophil-dependent immunomodulation within the context of pulmonary infection. These putative convergent strategies of targeting eosinophils offer promising avenues for the development of novel therapeutics targeting respiratory and other mucosal pathogens.
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Affiliation(s)
- Katelyn M Parrish
- Department of Microbiology and Immunology, Louisiana State University Health Sciences Center at Shreveport, Shreveport, Louisiana, USA
| | - Monica C Gestal
- Department of Microbiology and Immunology, Louisiana State University Health Sciences Center at Shreveport, Shreveport, Louisiana, USA
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2
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Bitzer GJ, Fitzgerald NA, DeJong MA, Cunningham C, Chapman JA, Boehm DT, Pyles GM, Huckaby AB, Miller SJ, Dublin SR, Warden MD, Barbier M, Damron FH. Immunization with an mRNA DTP vaccine protects against pertussis in rats. Infect Immun 2024; 92:e0052023. [PMID: 39016553 PMCID: PMC11320933 DOI: 10.1128/iai.00520-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Accepted: 06/28/2024] [Indexed: 07/18/2024] Open
Abstract
Bordetella pertussis is a Gram-negative bacterium that is the causative agent of the respiratory disease known as pertussis. Since the switch to the acellular vaccines of DTaP and Tap, pertussis cases in the US have risen and cyclically fallen. We have observed that mRNA pertussis vaccines are immunogenic and protective in mice. Here, we further evaluated the pertussis toxoid mRNA antigen and refined the formulation based on optimal pertussis toxin neutralization in vivo. We next evaluated the mRNA pertussis vaccine in Sprague-Dawley rats using an aerosol B. pertussis challenge model paired with whole-body plethysmography to monitor coughing and respiratory function. Female Sprague-Dawley rats were primed and boosted with either commercially available vaccines (DTaP or wP-DTP), an mRNA-DTP vaccine, or mock-vaccinated. The mRNA-DTP vaccine was immunogenic in rats and induced antigen-specific IgG antibodies comparable to DTaP. Rats were then aerosol challenged with a streptomycin-resistant emerging clinical isolate D420Sm1. Bacterial burden was assessed at days 1 and 9 post-challenge, and the mRNA vaccine reduced burden equal to both DTaP and wP-DTP. Whole-body plethysmography revealed that mRNA-DTP vaccinated rats were well protected against coughing which was comparable to the non-challenged group. These data suggest that an mRNA-DTP vaccine is immunogenic in rats and provides protection against aerosolized B. pertussis challenge in Sprague-Dawley rats.
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Affiliation(s)
- Graham J. Bitzer
- Department of Microbiology, Immunology, and Cell Biology, West Virginia University, Morgantown, West Virginia, USA
- West Virginia University Vaccine Development Center, West Virginia University, Morgantown, West Virginia, USA
| | - Nicholas A. Fitzgerald
- Department of Microbiology, Immunology, and Cell Biology, West Virginia University, Morgantown, West Virginia, USA
- West Virginia University Vaccine Development Center, West Virginia University, Morgantown, West Virginia, USA
| | - Megan A. DeJong
- Department of Microbiology, Immunology, and Cell Biology, West Virginia University, Morgantown, West Virginia, USA
- West Virginia University Vaccine Development Center, West Virginia University, Morgantown, West Virginia, USA
| | - Casey Cunningham
- Department of Microbiology, Immunology, and Cell Biology, West Virginia University, Morgantown, West Virginia, USA
- West Virginia University Vaccine Development Center, West Virginia University, Morgantown, West Virginia, USA
| | - Joshua A. Chapman
- Department of Microbiology, Immunology, and Cell Biology, West Virginia University, Morgantown, West Virginia, USA
- West Virginia University Vaccine Development Center, West Virginia University, Morgantown, West Virginia, USA
| | - Dylan T. Boehm
- Department of Microbiology, Immunology, and Cell Biology, West Virginia University, Morgantown, West Virginia, USA
- West Virginia University Vaccine Development Center, West Virginia University, Morgantown, West Virginia, USA
| | - Gage M. Pyles
- Department of Microbiology, Immunology, and Cell Biology, West Virginia University, Morgantown, West Virginia, USA
- West Virginia University Vaccine Development Center, West Virginia University, Morgantown, West Virginia, USA
| | - Annalisa B. Huckaby
- Department of Microbiology, Immunology, and Cell Biology, West Virginia University, Morgantown, West Virginia, USA
- West Virginia University Vaccine Development Center, West Virginia University, Morgantown, West Virginia, USA
| | - Sarah J. Miller
- Department of Microbiology, Immunology, and Cell Biology, West Virginia University, Morgantown, West Virginia, USA
- West Virginia University Vaccine Development Center, West Virginia University, Morgantown, West Virginia, USA
| | - Spencer R. Dublin
- Department of Microbiology, Immunology, and Cell Biology, West Virginia University, Morgantown, West Virginia, USA
- West Virginia University Vaccine Development Center, West Virginia University, Morgantown, West Virginia, USA
| | - Matthew D. Warden
- Department of Microbiology, Immunology, and Cell Biology, West Virginia University, Morgantown, West Virginia, USA
- West Virginia University Vaccine Development Center, West Virginia University, Morgantown, West Virginia, USA
| | - Mariette Barbier
- Department of Microbiology, Immunology, and Cell Biology, West Virginia University, Morgantown, West Virginia, USA
- West Virginia University Vaccine Development Center, West Virginia University, Morgantown, West Virginia, USA
| | - F. Heath Damron
- Department of Microbiology, Immunology, and Cell Biology, West Virginia University, Morgantown, West Virginia, USA
- West Virginia University Vaccine Development Center, West Virginia University, Morgantown, West Virginia, USA
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3
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Domenech de Cellès M, Rohani P. Pertussis vaccines, epidemiology and evolution. Nat Rev Microbiol 2024:10.1038/s41579-024-01064-8. [PMID: 38907021 DOI: 10.1038/s41579-024-01064-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/16/2024] [Indexed: 06/23/2024]
Abstract
Pertussis, which is caused by Bordetella pertussis, has plagued humans for at least 800 years, is highly infectious and can be fatal in the unvaccinated, especially very young infants. Although the rollout of whole-cell pertussis (wP) vaccines in the 1940s and 1950s was associated with a drastic drop in incidence, concerns regarding the reactogenicity of wP vaccines led to the development of a new generation of safer, acellular (aP) vaccines that have been adopted mainly in high-income countries. Over the past 20 years, some countries that boast high aP coverage have experienced a resurgence in pertussis, which has led to substantial debate over the basic immunology, epidemiology and evolutionary biology of the bacterium. Controversy surrounds the duration of natural immunity and vaccine-derived immunity, the ability of vaccines to prevent transmission and severe disease, and the impact of evolution on evading vaccine immunity. Resolving these issues is made challenging by incomplete detection of pertussis cases, the absence of a serological marker of immunity, modest sequencing of the bacterial genome and heterogeneity in diagnostic methods of surveillance. In this Review, we lay out the complexities of contemporary pertussis and, where possible, propose a parsimonious explanation for apparently incongruous observations.
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Affiliation(s)
| | - Pejman Rohani
- Odum School of Ecology, University of Georgia, Athens, GA, USA.
- Center of Ecology of Infectious Diseases, Athens, GA, USA.
- Department of Infectious Diseases, College for Veterinary Medicine, University of Georgia, Athens, GA, USA.
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4
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Wolf MA, O'Hara JM, Bitzer GJ, Narayanan E, Boehm DT, Bevere JR, DeJong MA, Hall JM, Wong TY, Falcone S, Deal CE, Richards A, Green S, Nguyen B, King E, Ogega C, Russo L, Sen-Kilic E, Plante O, Himansu S, Barbier M, Carfi A, Damron FH. Multivalent mRNA-DTP vaccines are immunogenic and provide protection from Bordetella pertussis challenge in mice. NPJ Vaccines 2024; 9:103. [PMID: 38858423 PMCID: PMC11164898 DOI: 10.1038/s41541-024-00890-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 05/13/2024] [Indexed: 06/12/2024] Open
Abstract
Acellular multivalent vaccines for pertussis (DTaP and Tdap) prevent symptomatic disease and infant mortality, but immunity to Bordetella pertussis infection wanes significantly over time resulting in cyclic epidemics of pertussis. The messenger RNA (mRNA) vaccine platform provides an opportunity to address complex bacterial infections with an adaptable approach providing Th1-biased responses. In this study, immunogenicity and challenge models were used to evaluate the mRNA platform with multivalent vaccine formulations targeting both B. pertussis antigens and diphtheria and tetanus toxoids. Immunization with mRNA formulations were immunogenetic, induced antigen specific antibodies, as well as Th1 T cell responses. Upon challenge with either historical or contemporary B. pertussis strains, 6 and 10 valent mRNA DTP vaccine provided protection equal to that of 1/20th human doses of either DTaP or whole cell pertussis vaccines. mRNA DTP immunized mice were also protected from pertussis toxin challenge as measured by prevention of lymphocytosis and leukocytosis. Collectively these pre-clinical mouse studies illustrate the potential of the mRNA platform for multivalent bacterial pathogen vaccines.
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Affiliation(s)
- M Allison Wolf
- Department of Microbiology, Immunology, and Cell Biology, West Virginia University, Morgantown, WV, USA
- Vaccine Development Center at West Virginia University Health Sciences Center, Morgantown, WV, USA
| | | | - Graham J Bitzer
- Department of Microbiology, Immunology, and Cell Biology, West Virginia University, Morgantown, WV, USA
- Vaccine Development Center at West Virginia University Health Sciences Center, Morgantown, WV, USA
| | | | - Dylan T Boehm
- Department of Microbiology, Immunology, and Cell Biology, West Virginia University, Morgantown, WV, USA
- Vaccine Development Center at West Virginia University Health Sciences Center, Morgantown, WV, USA
| | - Justin R Bevere
- Department of Microbiology, Immunology, and Cell Biology, West Virginia University, Morgantown, WV, USA
- Vaccine Development Center at West Virginia University Health Sciences Center, Morgantown, WV, USA
| | - Megan A DeJong
- Department of Microbiology, Immunology, and Cell Biology, West Virginia University, Morgantown, WV, USA
- Vaccine Development Center at West Virginia University Health Sciences Center, Morgantown, WV, USA
| | - Jesse M Hall
- Department of Microbiology, Immunology, and Cell Biology, West Virginia University, Morgantown, WV, USA
- Vaccine Development Center at West Virginia University Health Sciences Center, Morgantown, WV, USA
| | - Ting Y Wong
- Department of Microbiology, Immunology, and Cell Biology, West Virginia University, Morgantown, WV, USA
- Vaccine Development Center at West Virginia University Health Sciences Center, Morgantown, WV, USA
| | | | | | | | | | | | | | | | | | - Emel Sen-Kilic
- Department of Microbiology, Immunology, and Cell Biology, West Virginia University, Morgantown, WV, USA
- Vaccine Development Center at West Virginia University Health Sciences Center, Morgantown, WV, USA
| | | | | | - Mariette Barbier
- Department of Microbiology, Immunology, and Cell Biology, West Virginia University, Morgantown, WV, USA
- Vaccine Development Center at West Virginia University Health Sciences Center, Morgantown, WV, USA
| | | | - F Heath Damron
- Department of Microbiology, Immunology, and Cell Biology, West Virginia University, Morgantown, WV, USA.
- Vaccine Development Center at West Virginia University Health Sciences Center, Morgantown, WV, USA.
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5
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Peng Y, Williams MM, Xiaoli L, Simon A, Fueston H, Tondella ML, Weigand MR. Strengthening Bordetella pertussis genomic surveillance by direct sequencing of residual positive specimens. J Clin Microbiol 2024; 62:e0165323. [PMID: 38445858 PMCID: PMC11005353 DOI: 10.1128/jcm.01653-23] [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: 12/08/2023] [Accepted: 02/12/2024] [Indexed: 03/07/2024] Open
Abstract
Whole-genome sequencing (WGS) of microbial pathogens recovered from patients with infectious disease facilitates high-resolution strain characterization and molecular epidemiology. However, increasing reliance on culture-independent methods to diagnose infectious diseases has resulted in few isolates available for WGS. Here, we report a novel culture-independent approach to genome characterization of Bordetella pertussis, the causative agent of pertussis and a paradigm for insufficient genomic surveillance due to limited culture of clinical isolates. Sequencing libraries constructed directly from residual pertussis-positive diagnostic nasopharyngeal specimens were hybridized with biotinylated RNA "baits" targeting B. pertussis fragments within complex mixtures that contained high concentrations of host and microbial background DNA. Recovery of B. pertussis genome sequence data was evaluated with mock and pooled negative clinical specimens spiked with reducing concentrations of either purified DNA or inactivated cells. Targeted enrichment increased the yield of B. pertussis sequencing reads up to 90% while simultaneously decreasing host reads to less than 10%. Filtered sequencing reads provided sufficient genome coverage to perform characterization via whole-genome single nucleotide polymorphisms and whole-genome multilocus sequencing typing. Moreover, these data were concordant with sequenced isolates recovered from the same specimens such that phylogenetic reconstructions from either consistently clustered the same putatively linked cases. The optimized protocol is suitable for nasopharyngeal specimens with diagnostic IS481 Ct < 35 and >10 ng DNA. Routine implementation of these methods could strengthen surveillance and study of pertussis resurgence by capturing additional cases with genomic characterization.
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Affiliation(s)
- Yanhui Peng
- Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Margaret M. Williams
- Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | | | - Ashley Simon
- Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Heather Fueston
- Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Maria L. Tondella
- Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Michael R. Weigand
- Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
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6
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Natrajan MS, Hall JM, Weigand MR, Peng Y, Williams MM, Momin M, Damron FH, Dubey P, Tondella ML, Pawloski LC. Genome-based prediction of cross-protective, HLA-DR-presented epitopes as putative vaccine antigens for multiple Bordetella species. Microbiol Spectr 2024; 12:e0352723. [PMID: 38054724 PMCID: PMC10783135 DOI: 10.1128/spectrum.03527-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Accepted: 11/07/2023] [Indexed: 12/07/2023] Open
Abstract
IMPORTANCE Pertussis, caused by Bordetella pertussis, can cause debilitating respiratory symptoms, so whole-cell pertussis vaccines (wPVs) were introduced in the 1940s. However, reactogenicity of wPV necessitated the development of acellular pertussis vaccines (aPVs) that were introduced in the 1990s. Since then, until the COVID-19 pandemic began, reported pertussis incidence was increasing, suggesting that aPVs do not induce long-lasting immunity and may not effectively prevent transmission. Additionally, aPVs do not provide protection against other Bordetella species that are observed during outbreaks. The significance of this work is in determining potential new vaccine antigens for multiple Bordetella species that are predicted to elicit long-term immune responses. Genome-based approaches have aided the development of novel vaccines; here, these methods identified Bordetella vaccine candidates that may be cross-protective and predicted to induce strong memory responses. These targets can lead to an improved vaccine with a strong safety profile while also strengthening the longevity of the immune response.
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Affiliation(s)
- Muktha S. Natrajan
- Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
- Laboratory Leadership Service, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Jesse M. Hall
- Department of Microbial Infection and Immunity, College of Medicine, The Ohio State University, Columbus, Ohio, USA
| | - Michael R. Weigand
- Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Yanhui Peng
- Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Margaret M. Williams
- Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Mohamed Momin
- Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Frederick Heath Damron
- Department of Microbiology, Immunology, and Cell Biology, West Virginia University, Morgantown, West Virginia, USA
| | - Purnima Dubey
- Department of Microbial Infection and Immunity, College of Medicine, The Ohio State University, Columbus, Ohio, USA
| | - Maria Lucia Tondella
- Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Lucia C. Pawloski
- Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
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7
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Moosa F, du Plessis M, Weigand MR, Peng Y, Mogale D, de Gouveia L, Nunes MC, Madhi SA, Zar HJ, Reubenson G, Ismail A, Tondella ML, Cohen C, Walaza S, von Gottberg A, Wolter N. Genomic characterization of Bordetella pertussis in South Africa, 2015-2019. Microb Genom 2023; 9:001162. [PMID: 38117675 PMCID: PMC10763497 DOI: 10.1099/mgen.0.001162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 12/04/2023] [Indexed: 12/22/2023] Open
Abstract
Pertussis remains a public health concern in South Africa, with an increase in reported cases and outbreaks in recent years. Whole genome sequencing was performed on 32 Bordetella pertussis isolates sourced from three different surveillance programmes in South Africa between 2015 and 2019. Genome sequences were characterized using multilocus sequence typing, vaccine antigen genes (ptxP, ptxA, ptxB, prn and fimH) and overall genome structure. All isolates were sequence type 2 and harboured the pertussis toxin promoter allele ptxP3. The dominant genotype was ptxP3-ptxA1-ptxB2-prn2-fimH2 (31/32, 96.9 %), with no pertactin-deficient or other mutations in vaccine antigen genes identified. Amongst 21 isolates yielding closed genome assemblies, eight distinct genome structures were detected, with 61.9 % (13/21) of the isolates exhibiting three predominant structures. Increases in case numbers are probably not due to evolutionary changes in the genome but possibly due to other factors such as the cyclical nature of B. pertussis disease, waning immunity due to the use of acellular vaccines and/or population immunity gaps.
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Affiliation(s)
- Fahima Moosa
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Mignon du Plessis
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Michael R. Weigand
- Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Yanhui Peng
- Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Dineo Mogale
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
| | - Linda de Gouveia
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
| | - Marta C. Nunes
- Department of Science and Technology/National Research Foundation, Vaccine Preventable Diseases, University of the Witwatersrand, Johannesburg, South Africa
| | - Shabir A. Madhi
- South African Medical Research Council Vaccines and Infectious Diseases Analytics Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Wits Infectious Diseases and Oncology Research Institute, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Heather J. Zar
- Department of Pediatrics and Child Health, Red Cross Children’s Hospital, Cape Town, South Africa; MRC Unit on Child and Adolescent Health, University of Cape Town, Cape Town, South Africa
| | - Gary Reubenson
- Rahima Moosa Mother & Child Hospital, Department of Pediatrics & Child Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Arshad Ismail
- Sequencing Core Facility, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
- Department of Biochemistry and Microbiology, Faculty of Science, Engineering and Agriculture, University of Venda, Thohoyandou 0950, South Africa
- Institute for Water and Wastewater Technology, Durban University of Technology, Durban 4000, South Africa
| | - M. Lucia Tondella
- Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Cheryl Cohen
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
- School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Sibongile Walaza
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
- School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Anne von Gottberg
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Nicole Wolter
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
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8
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Wagner GE, Dabernig-Heinz J, Lipp M, Cabal A, Simantzik J, Kohl M, Scheiber M, Lichtenegger S, Ehricht R, Leitner E, Ruppitsch W, Steinmetz I. Real-Time Nanopore Q20+ Sequencing Enables Extremely Fast and Accurate Core Genome MLST Typing and Democratizes Access to High-Resolution Bacterial Pathogen Surveillance. J Clin Microbiol 2023; 61:e0163122. [PMID: 36988494 PMCID: PMC10117118 DOI: 10.1128/jcm.01631-22] [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: 11/04/2022] [Accepted: 02/17/2023] [Indexed: 03/30/2023] Open
Abstract
Next-generation whole-genome sequencing is essential for high-resolution surveillance of bacterial pathogens, for example, during outbreak investigations or for source tracking and escape variant analysis. However, current global sequencing and bioinformatic bottlenecks and a long time to result with standard technologies demand new approaches. In this study, we investigated whether novel nanopore Q20+ long-read chemistry enables standardized and easily accessible high-resolution typing combined with core genome multilocus sequence typing (cgMLST). We set high requirements for discriminatory power by using the slowly evolving bacterium Bordetella pertussis as a model pathogen. Our results show that the increased raw read accuracy enables the description of epidemiological scenarios and phylogenetic linkages at the level of gold-standard short reads. The same was true for our variant analysis of vaccine antigens, resistance genes, and virulence factors, demonstrating that nanopore sequencing is a legitimate competitor in the area of next-generation sequencing (NGS)-based high-resolution bacterial typing. Furthermore, we evaluated the parameters for the fastest possible analysis of the data. By combining the optimized processing pipeline with real-time basecalling, we established a workflow that allows for highly accurate and extremely fast high-resolution typing of bacterial pathogens while sequencing is still in progress. Along with advantages such as low costs and portability, the approach suggested here might democratize modern bacterial typing, enabling more efficient infection control globally.
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Affiliation(s)
- Gabriel E. Wagner
- Diagnostic and Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Graz, Austria
| | - Johanna Dabernig-Heinz
- Diagnostic and Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Graz, Austria
| | - Michaela Lipp
- Diagnostic and Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Graz, Austria
| | - Adriana Cabal
- Austrian Agency for Health and Food Safety, Vienna, Austria
| | - Jonathan Simantzik
- Medical and Life Sciences Faculty, Furtwangen University, Villingen-Schwenningen, Germany
| | - Matthias Kohl
- Medical and Life Sciences Faculty, Furtwangen University, Villingen-Schwenningen, Germany
| | - Martina Scheiber
- Diagnostic and Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Graz, Austria
| | - Sabine Lichtenegger
- Diagnostic and Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Graz, Austria
| | - Ralf Ehricht
- InfectoGnostics Research Campus, Centre for Applied Research, Jena, Germany
- Leibniz-Institute of Photonic Technology (Leibniz-IPHT), Jena, Germany
- Friedrich Schiller University Jena, Institute of Physical Chemistry, Jena, Germany
| | - Eva Leitner
- Diagnostic and Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Graz, Austria
| | | | - Ivo Steinmetz
- Diagnostic and Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Graz, Austria
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9
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Waters EV, Tucker LA, Ahmed JK, Wain J, Langridge GC. Impact of Salmonella genome rearrangement on gene expression. Evol Lett 2022; 6:426-437. [PMID: 36579163 PMCID: PMC9783417 DOI: 10.1002/evl3.305] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 10/03/2022] [Accepted: 11/07/2022] [Indexed: 11/20/2022] Open
Abstract
In addition to nucleotide variation, many bacteria also undergo changes at a much larger scale via rearrangement of their genome structure (GS) around long repeat sequences. These rearrangements result in genome fragments shifting position and/or orientation in the genome without necessarily affecting the underlying nucleotide sequence. To date, scalable techniques have not been applied to GS identification, so it remains unclear how extensive this variation is and the extent of its impact upon gene expression. However, the emergence of multiplexed, long-read sequencing overcomes the scale problem, as reads of several thousand bases are routinely produced that can span long repeat sequences to identify the flanking chromosomal DNA, allowing GS identification. Genome rearrangements were generated in Salmonella enterica serovar Typhi through long-term culture at ambient temperature. Colonies with rearrangements were identified via long-range PCR and subjected to long-read nanopore sequencing to confirm genome variation. Four rearrangements were investigated for differential gene expression using transcriptomics. All isolates with changes in genome arrangement relative to the parent strain were accompanied by changes in gene expression. Rearrangements with similar fragment movements demonstrated similar changes in gene expression. The most extreme rearrangement caused a large imbalance between the origin and terminus of replication and was associated with differential gene expression as a factor of distance moved toward or away from the origin of replication. Genome structure variation may provide a mechanism through which bacteria can quickly adapt to new environments and warrants routine assessment alongside traditional nucleotide-level measures of variation.
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Affiliation(s)
- Emma V. Waters
- Microbes in the Food ChainQuadram Institute BioscienceNorwichNR4 7UQUnited Kingdom
| | - Liam A. Tucker
- Microbes in the Food ChainQuadram Institute BioscienceNorwichNR4 7UQUnited Kingdom
| | - Jana K. Ahmed
- The Wellcome Trust Sanger InstituteCambridgeCB10 1SAUnited Kingdom
| | - John Wain
- Microbes in the Food ChainQuadram Institute BioscienceNorwichNR4 7UQUnited Kingdom
- Norwich Medical SchoolUniversity of East AngliaNorwichNR4 7TJUnited Kingdom
| | - Gemma C. Langridge
- Microbes in the Food ChainQuadram Institute BioscienceNorwichNR4 7UQUnited Kingdom
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10
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Xu Z, Hu D, Luu LDW, Octavia S, Keil AD, Sintchenko V, Tanaka MM, Mooi FR, Robson J, Lan R. Genomic dissection of the microevolution of Australian epidemic Bordetella pertussis. Emerg Microbes Infect 2022; 11:1460-1473. [PMID: 35543519 PMCID: PMC9176669 DOI: 10.1080/22221751.2022.2077129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Whooping cough (pertussis) is a highly contagious respiratory disease caused by the bacterium Bordetella pertussis. Despite high vaccine coverage, pertussis has re-emerged in many countries including Australia and caused two large epidemics in Australia since 2007. Here, we undertook a genomic and phylogeographic study of 385 Australian B. pertussis isolates collected from 2008 to 2017. The Australian B. pertussis population was found to be composed of mostly ptxP3 strains carrying different fim3 alleles, with ptxP3-fim3A genotype expanding far more than ptxP3-fim3B. Within the former, there were six co-circulating epidemic lineages (EL1 to EL6). The multiple ELs emerged, expanded, and then declined at different time points over the two epidemics. In population genetics terms, both hard and soft selective sweeps through vaccine selection pressures have determined the population dynamics of Australian B. pertussis. Relative risk estimation suggests that once a new B. pertussis lineage emerged, it was more likely to spread locally within the first 1.5 years. However, after 1.5 years, any new lineage was likely to expand to a wider region. Phylogenetic analysis revealed the expansion of ptxP3 strains was also associated with replacement of the type III secretion system allele bscI1 with bscI3. bscI3 is associated with decreased T3SS secretion and may allow B. pertussis to reduce immune recognition. This study advanced our understanding of the epidemic population structure and spatial and temporal dynamics of B. pertussis in a highly immunized population.
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Affiliation(s)
- Zheng Xu
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia
| | - Dalong Hu
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia
| | - Laurence Don Wai Luu
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia
| | - Sophie Octavia
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia
| | - Anthony D Keil
- Department of Microbiology, PathWest Laboratory Medicine WA, Perth Children's Hospital, Perth, Australia
| | - Vitali Sintchenko
- Centre for Infectious Diseases and Microbiology-Public Health, Institute of Clinical Pathology and Medical Research, NSW Health Pathology and Westmead Hospital, Sydney, Australia.,Sydney Institute for Infectious Diseases, The University of Sydney, Sydney, Australia
| | - Mark M Tanaka
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia
| | - Frits R Mooi
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia
| | - Jenny Robson
- Sullivan Nicolaides Pathology, Queensland, Australia
| | - Ruiting Lan
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia
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11
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DeJong MA, Wolf MA, Bitzer GJ, Hall JM, Sen-Kilic E, Blake JM, Petty JE, Wong TY, Barbier M, Campbell JD, Bevere JR, Damron FH. CpG 1018® adjuvant enhances Tdap immune responses against Bordetella pertussis in mice. Vaccine 2022; 40:5229-5240. [PMID: 35927132 DOI: 10.1016/j.vaccine.2022.07.030] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 07/18/2022] [Accepted: 07/21/2022] [Indexed: 11/16/2022]
Abstract
Bordetella pertussis is the causative agent of whooping cough (pertussis), a severe respiratory disease that can be fatal, particularly in infants. Despite high vaccine coverage, pertussis remains a problem because the currently used DTaP and Tdap vaccines do not completely prevent infection or transmission. It is well established that the alum adjuvant is a potential weakness of the acellular vaccines because the immunity provided by it is short-term. We aimed to evaluate the potential of CpG 1018® adjuvant to improve antibody responses and enhance protection against B. pertussis challenge in a murine model. A titrated range of Tdap vaccine doses were evaluated in order to best identify the adjuvant capability of CpG 1018. Antibody responses to pertussis toxin (PT), filamentous hemagglutinin (FHA), or the whole bacterium were increased due to the inclusion of CpG 1018. In B. pertussis intranasal challenge studies, we observed improved protection and bacterial clearance from the lower respiratory tract due to adding CpG 1018 to 1/20th the human dose of Tdap. Further, we determined that Tdap and Tdap + CpG 1018 were both capable of facilitating clearance of strains that do not express pertactin (PRN-), which are rising in prevalence. Functional phenotyping of antibodies revealed that the inclusion of CpG 1018 induced more bacterial opsonization and antibodies of the Th1 phenotype (IgG2a and IgG2b). This study demonstrates the potential of adding CpG 1018 to Tdap to improve immunogenicity and protection against B. pertussis compared to the conventional, alum-only adjuvanted Tdap vaccine.
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Affiliation(s)
- Megan A DeJong
- Department of Microbiology, Immunology, and Cell Biology, West Virginia University, Morgantown, WV, USA; Vaccine Development Center at West Virginia University Health Sciences Center, Morgantown, WV, USA
| | - M Allison Wolf
- Department of Microbiology, Immunology, and Cell Biology, West Virginia University, Morgantown, WV, USA; Vaccine Development Center at West Virginia University Health Sciences Center, Morgantown, WV, USA
| | - Graham J Bitzer
- Department of Microbiology, Immunology, and Cell Biology, West Virginia University, Morgantown, WV, USA; Vaccine Development Center at West Virginia University Health Sciences Center, Morgantown, WV, USA
| | - Jesse M Hall
- Department of Microbiology, Immunology, and Cell Biology, West Virginia University, Morgantown, WV, USA; Vaccine Development Center at West Virginia University Health Sciences Center, Morgantown, WV, USA
| | - Emel Sen-Kilic
- Department of Microbiology, Immunology, and Cell Biology, West Virginia University, Morgantown, WV, USA; Vaccine Development Center at West Virginia University Health Sciences Center, Morgantown, WV, USA
| | - Jeanna M Blake
- Department of Microbiology, Immunology, and Cell Biology, West Virginia University, Morgantown, WV, USA; Vaccine Development Center at West Virginia University Health Sciences Center, Morgantown, WV, USA
| | - Jonathan E Petty
- Department of Microbiology, Immunology, and Cell Biology, West Virginia University, Morgantown, WV, USA; Vaccine Development Center at West Virginia University Health Sciences Center, Morgantown, WV, USA
| | - Ting Y Wong
- Department of Microbiology, Immunology, and Cell Biology, West Virginia University, Morgantown, WV, USA; Vaccine Development Center at West Virginia University Health Sciences Center, Morgantown, WV, USA
| | - Mariette Barbier
- Department of Microbiology, Immunology, and Cell Biology, West Virginia University, Morgantown, WV, USA; Vaccine Development Center at West Virginia University Health Sciences Center, Morgantown, WV, USA
| | | | - Justin R Bevere
- Department of Microbiology, Immunology, and Cell Biology, West Virginia University, Morgantown, WV, USA; Vaccine Development Center at West Virginia University Health Sciences Center, Morgantown, WV, USA
| | - F Heath Damron
- Department of Microbiology, Immunology, and Cell Biology, West Virginia University, Morgantown, WV, USA; Vaccine Development Center at West Virginia University Health Sciences Center, Morgantown, WV, USA.
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12
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Brandal LT, Vestrheim DF, Bruvik T, Roness RB, Bjørnstad ML, Greve-Isdahl M, Steens A, Brynildsrud OB. Evolution of Bordetella pertussis in the acellular vaccine era in Norway, 1996 to 2019. Eur J Clin Microbiol Infect Dis 2022; 41:913-924. [PMID: 35543837 PMCID: PMC9135841 DOI: 10.1007/s10096-022-04453-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 04/28/2022] [Indexed: 01/16/2023]
Abstract
We described the population structure of Bordetella pertussis (B. pertussis) in Norway from 1996 to 2019 and determined if there were evolutionary shifts and whether these correlated with changes in the childhood immunization program. We selected 180 B. pertussis isolates, 22 from the whole cell vaccine (WCV) era (1996-1997) and 158 from the acellular vaccine (ACV) era (1998-2019). We conducted whole genome sequencing and determined the distribution and frequency of allelic variants and temporal changes of ACV genes. Norwegian B. pertussis isolates were evenly distributed across a phylogenetic tree that included global strains. We identified seven different allelic profiles of ACV genes (A-F), in which profiles A1, A2, and B dominated (89%), all having pertussis toxin (ptxA) allele 1, pertussis toxin promoter (ptxP) allele 3, and pertactin (prn) allele 2 present. Isolates with ptxP1 and prn1 were not detected after 2007, whereas the prn2 allele likely emerged prior to 1972, and ptxP3 before the early 1980s. Allele conversions of ACV genes all occurred prior to the introduction of ACV. Sixteen percent of our isolates showed mutations within the prn gene. ACV and its booster doses (implemented for children in 2007 and adolescents in 2013) might have contributed to evolvement of a more uniform B. pertussis population, with recent circulating strains having ptxA1, ptxP3, and prn2 present, and an increasing number of prn mutations. These strains clearly deviate from ACV strains (ptxA1, ptxP1, prn1), and this could have implications for vaccine efficiency and, therefore, prevention and control of pertussis.
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Affiliation(s)
- Lin T Brandal
- Norwegian Institute of Public Health, Oslo, Norway.
- European Program for Public Health Microbiology Training (EUPHEM), European Centre for Disease Prevention and Control (ECDC), Stockholm, Sweden.
| | | | | | | | | | | | | | - Ola B Brynildsrud
- Norwegian Institute of Public Health, Oslo, Norway
- Norwegian University of Life Sciences, Ås, Norway
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13
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Lefrancq N, Bouchez V, Fernandes N, Barkoff AM, Bosch T, Dalby T, Åkerlund T, Darenberg J, Fabianova K, Vestrheim DF, Fry NK, González-López JJ, Gullsby K, Habington A, He Q, Litt D, Martini H, Piérard D, Stefanelli P, Stegger M, Zavadilova J, Armatys N, Landier A, Guillot S, Hong SL, Lemey P, Parkhill J, Toubiana J, Cauchemez S, Salje H, Brisse S. Global spatial dynamics and vaccine-induced fitness changes of Bordetella pertussis. Sci Transl Med 2022; 14:eabn3253. [PMID: 35476597 DOI: 10.1126/scitranslmed.abn3253] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
As with other pathogens, competitive interactions between Bordetella pertussis strains drive infection risk. Vaccines are thought to perturb strain diversity through shifts in immune pressures; however, this has rarely been measured because of inadequate data and analytical tools. We used 3344 sequences from 23 countries to show that, on average, there are 28.1 transmission chains circulating within a subnational region, with the number of chains strongly associated with host population size. It took 5 to 10 years for B. pertussis to be homogeneously distributed throughout Europe, with the same time frame required for the United States. Increased fitness of pertactin-deficient strains after implementation of acellular vaccines, but reduced fitness otherwise, can explain long-term genotype dynamics. These findings highlight the role of vaccine policy in shifting local diversity of a pathogen that is responsible for 160,000 deaths annually.
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Affiliation(s)
- Noémie Lefrancq
- Insitut Pasteur, Université Paris Cité, Mathematical Modelling of Infectious Diseases Unit, UMR2000, CNRS, 75015 Paris, France.,Department of Genetics, University of Cambridge, Cambridge CB2 3EH, UK
| | - Valérie Bouchez
- Institut Pasteur, Université Paris Cité, Biodiversity and Epidemiology of Bacterial Pathogens, 75724 Paris, France.,National Reference Center for Whooping Cough and Other Bordetella Infections, 75724 Paris, France
| | - Nadia Fernandes
- Institut Pasteur, Université Paris Cité, Biodiversity and Epidemiology of Bacterial Pathogens, 75724 Paris, France
| | - Alex-Mikael Barkoff
- University of Turku UTU, Institute of Biomedicine, Research Center for Infections and Immunity, FI-20520 Turku, Finland
| | - Thijs Bosch
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), 3720 BA Bilthoven, Netherlands
| | - Tine Dalby
- Statens Serum Institut, Bacteria, Parasites and Fungi/Infectious Disease Preparedness, 2300 Copenhagen, Denmark
| | - Thomas Åkerlund
- The Public Health Agency of Sweden, Unit for Laboratory Surveillance of Bacterial Pathogens, SE-171 82 Solna, Sweden
| | - Jessica Darenberg
- The Public Health Agency of Sweden, Unit for Laboratory Surveillance of Bacterial Pathogens, SE-171 82 Solna, Sweden
| | - Katerina Fabianova
- National Institute of Public Health, Department of Infectious Diseases Epidemiology, CZ-10000 Prague, Czech Republic
| | - Didrik F Vestrheim
- Norwegian Institute of Public Health, Department of Infectious Disease Control and Vaccine, N-0213 Oslo, Norway
| | - Norman K Fry
- Respiratory and Vaccine Preventable Bacteria Reference Unit, Public Health England-National Infection Service, London NW9 5EQ, UK.,Immunisation and Countermeasures Division, Public Health England-National Infection Service, London NW9 5EQ, UK
| | - Juan José González-López
- University Hospital Vall d'Hebron, Microbiology Department, 08035 Barcelona, Spain.,Universitat Autònoma de Barcelona, Department of Genetics and Microbiology, 08193 Barcelona, Spain
| | - Karolina Gullsby
- Centre for Research and Development, Uppsala University/Region Gävleborg, 80187 Gävle, Sweden
| | - Adele Habington
- Molecular Microbiology Laboratory, Children's Health Ireland, Crumlin, D12 N512 Dublin, Ireland
| | - Qiushui He
- University of Turku UTU, Institute of Biomedicine, Research Center for Infections and Immunity, FI-20520 Turku, Finland.,InFLAMES Research Flagship Center, University of Turku, FI-20520 Turku, Finland
| | - David Litt
- Respiratory and Vaccine Preventable Bacteria Reference Unit, Public Health England-National Infection Service, London NW9 5EQ, UK
| | - Helena Martini
- Department of Microbiology, National Reference Centre for Bordetella pertussis, Universitair Ziekenhuis Brussel, Vrije Universiteit Brussel (VUB), B-1090 Brussels, Belgium
| | - Denis Piérard
- Department of Microbiology, National Reference Centre for Bordetella pertussis, Universitair Ziekenhuis Brussel, Vrije Universiteit Brussel (VUB), B-1090 Brussels, Belgium
| | - Paola Stefanelli
- Department of Infectious Diseases, Istituto Superiore di Sanità, IT-00161 Rome, Italy
| | - Marc Stegger
- Statens Serum Institut, Bacteria, Parasites and Fungi/Infectious Disease Preparedness, 2300 Copenhagen, Denmark
| | - Jana Zavadilova
- National Institute of Public Health, National Reference Laboratory for Pertussis and Diphtheria, 100 00 Prague, Czech Republic
| | - Nathalie Armatys
- Institut Pasteur, Université Paris Cité, Biodiversity and Epidemiology of Bacterial Pathogens, 75724 Paris, France.,National Reference Center for Whooping Cough and Other Bordetella Infections, 75724 Paris, France
| | - Annie Landier
- Institut Pasteur, Université Paris Cité, Biodiversity and Epidemiology of Bacterial Pathogens, 75724 Paris, France.,National Reference Center for Whooping Cough and Other Bordetella Infections, 75724 Paris, France
| | - Sophie Guillot
- Institut Pasteur, Université Paris Cité, Biodiversity and Epidemiology of Bacterial Pathogens, 75724 Paris, France.,National Reference Center for Whooping Cough and Other Bordetella Infections, 75724 Paris, France
| | - Samuel L Hong
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, 3000 Leuven, Belgium
| | - Philippe Lemey
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, 3000 Leuven, Belgium
| | - Julian Parkhill
- Department of Veterinary Medicine, University of Cambridge, Cambridge CB3 0ES, UK
| | - Julie Toubiana
- Institut Pasteur, Université Paris Cité, Biodiversity and Epidemiology of Bacterial Pathogens, 75724 Paris, France.,National Reference Center for Whooping Cough and Other Bordetella Infections, 75724 Paris, France.,Université Paris Cité, Department of General Paediatrics and Paediatric Infectious Diseases, Necker-Enfants Malades Hospital, APHP, 75015 Paris, France
| | - Simon Cauchemez
- Insitut Pasteur, Université Paris Cité, Mathematical Modelling of Infectious Diseases Unit, UMR2000, CNRS, 75015 Paris, France
| | - Henrik Salje
- Insitut Pasteur, Université Paris Cité, Mathematical Modelling of Infectious Diseases Unit, UMR2000, CNRS, 75015 Paris, France.,Department of Genetics, University of Cambridge, Cambridge CB2 3EH, UK
| | - Sylvain Brisse
- Institut Pasteur, Université Paris Cité, Biodiversity and Epidemiology of Bacterial Pathogens, 75724 Paris, France.,National Reference Center for Whooping Cough and Other Bordetella Infections, 75724 Paris, France
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14
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Mir-Cros A, Moreno-Mingorance A, Martín-Gómez MT, Abad R, Bloise I, Campins M, González-Praetorius A, Gutiérrez MN, Martín-González H, Muñoz-Almagro C, Orellana MÁ, de Pablos M, Roca-Grande J, Rodrigo C, Rodríguez ME, Uriona S, Vidal MJ, Pumarola T, Larrosa MN, González-López JJ. Pertactin-Deficient Bordetella pertussis with Unusual Mechanism of Pertactin Disruption, Spain, 1986-2018. Emerg Infect Dis 2022; 28:967-976. [PMID: 35447067 PMCID: PMC9045434 DOI: 10.3201/eid2805.211958] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Bordetella pertussis not expressing pertactin has increased in countries using acellular pertussis vaccines (ACV). The deficiency is mostly caused by pertactin gene disruption by IS481. To assess the effect of the transition from whole-cell vaccine to ACV on the emergence of B. pertussis not expressing pertactin in Spain, we studied 342 isolates collected during 1986–2018. We identified 93 pertactin-deficient isolates. All were detected after introduction of ACV and represented 38% of isolates collected during the ACV period; 58.1% belonged to a genetic cluster of isolates carrying the unusual prn::del(–292, 1340) mutation. Pertactin inactivation by IS481 insertion was identified in 23.7% of pertactin-deficient isolates, arising independently multiple times and in different phylogenetic branches. Our findings support the emergence and dissemination of a cluster of B. pertussis with an infrequent mechanism of pertactin disruption in Spain, probably resulting from introduction of ACV.
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15
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Adler A, Poirier S, Pagni M, Maillard J, Holliger C. Disentangle genus microdiversity within a complex microbial community by using a multi-distance long-read binning method: example of Candidatus Accumulibacter. Environ Microbiol 2022; 24:2136-2156. [PMID: 35315560 PMCID: PMC9311429 DOI: 10.1111/1462-2920.15947] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Accepted: 02/19/2022] [Indexed: 11/26/2022]
Abstract
Complete genomes can be recovered from metagenomes by assembling and binning DNA sequences into metagenome assembled genomes (MAGs). Yet, the presence of microdiversity can hamper the assembly and binning processes, possibly yielding chimeric, highly fragmented and incomplete genomes. Here, the metagenomes of four samples of aerobic granular sludge bioreactors containing Candidatus (Ca.) Accumulibacter, a phosphate-accumulating organism of interest for wastewater treatment, were sequenced with both PacBio and Illumina. Different strategies of genome assembly and binning were investigated, including published protocols and a binning procedure adapted to the binning of long contigs (MuLoBiSC). Multiple criteria were considered to select the best strategy for Ca. Accumulibacter, whose multiple strains in every sample represent a challenging microdiversity. In this case, the best strategy relies on long-read only assembly and a custom binning procedure including MuLoBiSC in metaWRAP. Several high-quality Ca. Accumulibacter MAGs, including a novel species, were obtained independently from different samples. Comparative genomic analysis showed that MAGs retrieved in different samples harbour genomic rearrangements in addition to accumulation of point mutations. The microdiversity of Ca. Accumulibacter, likely driven by mobile genetic elements, causes major difficulties in recovering MAGs, but it is also a hallmark of the panmictic lifestyle of these bacteria.
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Affiliation(s)
- Aline Adler
- Laboratory for Environmental Biotechnology, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Simon Poirier
- Laboratory for Environmental Biotechnology, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Marco Pagni
- Laboratory for Environmental Biotechnology, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.,Vital-IT Group, SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Julien Maillard
- Laboratory for Environmental Biotechnology, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.,IFP Energie nouvelles, 1 et 4 avenue de Bois-Préau, 92852, Rueil-Malmaison Cedex, France
| | - Christof Holliger
- Laboratory for Environmental Biotechnology, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
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16
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Abrahams JS, Weigand MR, Ring N, MacArthur I, Etty J, Peng S, Williams MM, Bready B, Catalano AP, Davis JR, Kaiser MD, Oliver JS, Sage JM, Bagby S, Tondella ML, Gorringe AR, Preston A. Towards comprehensive understanding of bacterial genetic diversity: large-scale amplifications in Bordetella pertussis and Mycobacterium tuberculosis. Microb Genom 2022; 8:000761. [PMID: 35143385 PMCID: PMC8942028 DOI: 10.1099/mgen.0.000761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 12/11/2021] [Indexed: 11/18/2022] Open
Abstract
Bacterial genetic diversity is often described solely using base-pair changes despite a wide variety of other mutation types likely being major contributors. Tandem duplication/amplifications are thought to be widespread among bacteria but due to their often-intractable size and instability, comprehensive studies of these mutations are rare. We define a methodology to investigate amplifications in bacterial genomes based on read depth of genome sequence data as a proxy for copy number. We demonstrate the approach with Bordetella pertussis, whose insertion sequence element-rich genome provides extensive scope for amplifications to occur. Analysis of data for 2430 B. pertussis isolates identified 272 putative amplifications, of which 94 % were located at 11 hotspot loci. We demonstrate limited phylogenetic connection for the occurrence of amplifications, suggesting unstable and sporadic characteristics. Genome instability was further described in vitro using long-read sequencing via the Nanopore platform, which revealed that clonally derived laboratory cultures produced heterogenous populations rapidly. We extended this research to analyse a population of 1000 isolates of another important pathogen, Mycobacterium tuberculosis. We found 590 amplifications in M. tuberculosis, and like B. pertussis, these occurred primarily at hotspots. Genes amplified in B. pertussis include those involved in motility and respiration, whilst in M. tuberuclosis, functions included intracellular growth and regulation of virulence. Using publicly available short-read data we predicted previously unrecognized, large amplifications in B. pertussis and M. tuberculosis. This reveals the unrecognized and dynamic genetic diversity of B. pertussis and M. tuberculosis, highlighting the need for a more holistic understanding of bacterial genetics.
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Affiliation(s)
- Jonathan S. Abrahams
- Department of Biology and Biochemistry and Milner Centre for Evolution, University of Bath, Bath, UK
| | - Michael R. Weigand
- Division of Bacterial Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Natalie Ring
- Department of Biology and Biochemistry and Milner Centre for Evolution, University of Bath, Bath, UK
| | - Iain MacArthur
- Department of Biology and Biochemistry and Milner Centre for Evolution, University of Bath, Bath, UK
| | - Joss Etty
- Department of Biology and Biochemistry and Milner Centre for Evolution, University of Bath, Bath, UK
| | - Scott Peng
- Division of Bacterial Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Margaret M. Williams
- Division of Bacterial Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | | | | | | | | | | | | | - Stefan Bagby
- Department of Biology and Biochemistry and Milner Centre for Evolution, University of Bath, Bath, UK
| | - M. Lucia Tondella
- Division of Bacterial Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | | | - Andrew Preston
- Department of Biology and Biochemistry and Milner Centre for Evolution, University of Bath, Bath, UK
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17
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Ring N, Davies H, Morgan J, Sundaresan M, Tiong A, Preston A, Bagby S. Comparative genomics of Bordetella pertussis isolates from New Zealand, a country with an uncommonly high incidence of whooping cough. Microb Genom 2022; 8:000756. [PMID: 35084300 PMCID: PMC8914352 DOI: 10.1099/mgen.0.000756] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 12/03/2021] [Indexed: 11/18/2022] Open
Abstract
Whooping cough, the respiratory disease caused by Bordetella pertussis, has undergone a wide-spread resurgence over the last several decades. Previously, we developed a pipeline to assemble the repetitive B. pertussis genome into closed sequences using hybrid nanopore and Illumina sequencing. Here, this sequencing pipeline was used to conduct a more high-throughput, longitudinal screen of 66 strains isolated between 1982 and 2018 in New Zealand. New Zealand has a higher incidence of whooping cough than many other countries; usually at least twice as many cases per 100000 people as the USA and UK and often even higher, despite similar rates of vaccine uptake. To the best of our knowledge, these strains are the first New Zealand B. pertussis isolates to be sequenced. The analyses here show that, on the whole, genomic trends in New Zealand B. pertussis isolates, such as changing allelic profile in vaccine-related genes and increasing pertactin deficiency, have paralleled those seen elsewhere in the world. At the same time, phylogenetic comparisons of the New Zealand isolates with global isolates suggest that a number of strains are circulating in New Zealand, which cluster separately from other global strains, but which are closely related to each other. The results of this study add to a growing body of knowledge regarding recent changes to the B. pertussis genome, and are the first genetic investigation into B. pertussis isolates from New Zealand.
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Affiliation(s)
- Natalie Ring
- Department of Biology and Biochemistry, University of Bath, UK
- Roslin Institute, University of Edinburgh, UK
| | - Heather Davies
- Institute of Environmental Science and Research, Porirua, New Zealand
| | - Julie Morgan
- Institute of Environmental Science and Research, Porirua, New Zealand
| | | | - Audrey Tiong
- Institute of Environmental Science and Research, Porirua, New Zealand
| | - Andrew Preston
- Department of Biology and Biochemistry, University of Bath, UK
| | - Stefan Bagby
- Department of Biology and Biochemistry, University of Bath, UK
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18
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Hall JM, Kang J, Kenney SM, Wong TY, Bitzer GJ, Kelly CO, Kisamore CA, Boehm DT, DeJong MA, Wolf MA, Sen-Kilic E, Horspool AM, Bevere JR, Barbier M, Damron FH. Reinvestigating the Coughing Rat Model of Pertussis To Understand Bordetella pertussis Pathogenesis. Infect Immun 2021; 89:e0030421. [PMID: 34125597 PMCID: PMC8594615 DOI: 10.1128/iai.00304-21] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 06/05/2021] [Indexed: 12/04/2022] Open
Abstract
Bordetella pertussis is a highly contagious bacterium that is the causative agent of whooping cough (pertussis). Currently, acellular pertussis vaccines (aP, DTaP, and Tdap) are used to prevent pertussis disease. However, it is clear that the aP vaccine efficacy quickly wanes, resulting in the reemergence of pertussis. Furthermore, recent work performed by the CDC suggest that current circulating strains are genetically distinct from strains of the past. The emergence of genetically diverging strains, combined with waning aP vaccine efficacy, calls for reevaluation of current animal models of pertussis. In this study, we used the rat model of pertussis to compare two genetically divergent strains Tohama 1 and D420. We intranasally challenged 7-week-old Sprague-Dawley rats with 108 viable Tohama 1 and D420 and measured the hallmark signs/symptoms of B. pertussis infection such as neutrophilia, pulmonary inflammation, and paroxysmal cough using whole-body plethysmography. Onset of cough occurred between 2 and 4 days after B. pertussis challenge, averaging five coughs per 15 min, with peak coughing occurring at day 8 postinfection, averaging upward of 13 coughs per 15 min. However, we observed an increase of coughs in rats infected with clinical isolate D420 through 12 days postchallenge. The rats exhibited increased bronchial restriction following B. pertussis infection. Histology of the lung and flow cytometry confirm both cellular infiltration and pulmonary inflammation. D420 infection induced higher production of anti-B. pertussis IgM antibodies compared to Tohama 1 infection. The coughing rat model provides a way of characterizing disease manifestation differences between B. pertussis strains.
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Affiliation(s)
- Jesse M. Hall
- Department of Microbiology, Immunology and Cell Biology, School of Medicine, West Virginia University, Morgantown, West Virginia, USA
- Vaccine Development Center, WVU Health Sciences Center, Morgantown, West Virginia, USA
| | - Jason Kang
- Department of Microbiology, Immunology and Cell Biology, School of Medicine, West Virginia University, Morgantown, West Virginia, USA
- Vaccine Development Center, WVU Health Sciences Center, Morgantown, West Virginia, USA
| | - Sophia M. Kenney
- Department of Microbiology, Immunology and Cell Biology, School of Medicine, West Virginia University, Morgantown, West Virginia, USA
- Vaccine Development Center, WVU Health Sciences Center, Morgantown, West Virginia, USA
| | - Ting Y. Wong
- Department of Microbiology, Immunology and Cell Biology, School of Medicine, West Virginia University, Morgantown, West Virginia, USA
- Vaccine Development Center, WVU Health Sciences Center, Morgantown, West Virginia, USA
| | - Graham J. Bitzer
- Department of Microbiology, Immunology and Cell Biology, School of Medicine, West Virginia University, Morgantown, West Virginia, USA
- Vaccine Development Center, WVU Health Sciences Center, Morgantown, West Virginia, USA
| | - Claire O. Kelly
- Department of Microbiology, Immunology and Cell Biology, School of Medicine, West Virginia University, Morgantown, West Virginia, USA
- Vaccine Development Center, WVU Health Sciences Center, Morgantown, West Virginia, USA
| | - Caleb A. Kisamore
- Department of Microbiology, Immunology and Cell Biology, School of Medicine, West Virginia University, Morgantown, West Virginia, USA
- Vaccine Development Center, WVU Health Sciences Center, Morgantown, West Virginia, USA
| | - Dylan T. Boehm
- Department of Microbiology, Immunology and Cell Biology, School of Medicine, West Virginia University, Morgantown, West Virginia, USA
- Vaccine Development Center, WVU Health Sciences Center, Morgantown, West Virginia, USA
| | - Megan A. DeJong
- Department of Microbiology, Immunology and Cell Biology, School of Medicine, West Virginia University, Morgantown, West Virginia, USA
- Vaccine Development Center, WVU Health Sciences Center, Morgantown, West Virginia, USA
| | - M. Allison Wolf
- Department of Microbiology, Immunology and Cell Biology, School of Medicine, West Virginia University, Morgantown, West Virginia, USA
- Vaccine Development Center, WVU Health Sciences Center, Morgantown, West Virginia, USA
| | - Emel Sen-Kilic
- Department of Microbiology, Immunology and Cell Biology, School of Medicine, West Virginia University, Morgantown, West Virginia, USA
- Vaccine Development Center, WVU Health Sciences Center, Morgantown, West Virginia, USA
| | - Alexander M. Horspool
- Department of Microbiology, Immunology and Cell Biology, School of Medicine, West Virginia University, Morgantown, West Virginia, USA
- Vaccine Development Center, WVU Health Sciences Center, Morgantown, West Virginia, USA
| | - Justin R. Bevere
- Department of Microbiology, Immunology and Cell Biology, School of Medicine, West Virginia University, Morgantown, West Virginia, USA
- Vaccine Development Center, WVU Health Sciences Center, Morgantown, West Virginia, USA
| | - Mariette Barbier
- Department of Microbiology, Immunology and Cell Biology, School of Medicine, West Virginia University, Morgantown, West Virginia, USA
- Vaccine Development Center, WVU Health Sciences Center, Morgantown, West Virginia, USA
| | - F. Heath Damron
- Department of Microbiology, Immunology and Cell Biology, School of Medicine, West Virginia University, Morgantown, West Virginia, USA
- Vaccine Development Center, WVU Health Sciences Center, Morgantown, West Virginia, USA
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19
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A Unique Reverse Adaptation Mechanism Assists Bordetella pertussis in Resistance to Both Scarcity and Toxicity of Manganese. mBio 2021; 12:e0190221. [PMID: 34700381 PMCID: PMC8546581 DOI: 10.1128/mbio.01902-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The ability of bacterial pathogens to acquire essential micronutrients is critical for their survival in the host environment. Manganese plays a complex role in the virulence of a variety of pathogens due to its function as an antioxidant and enzymatic cofactor. Therefore, host cells deprive pathogens of manganese to prevent or attenuate infection. Here, we show that evolution of the human-restricted pathogen Bordetella pertussis has selected for an inhibitory duplication within a manganese exporter of the calcium:cation antiporter superfamily. Intriguingly, upon exposure to toxic levels of manganese, the nonfunctional exporter becomes operative in resister cells due to a unique reverse adaptation mechanism. However, compared with wild-type (wt) cells, the resisters carrying a functional copy of the exporter displayed strongly reduced intracellular levels of manganese and impaired growth under oxidative stress. Apparently, inactivation of the manganese exporter and the resulting accumulation of manganese in the cytosol benefited the pathogen by improving its survival under stress conditions. The inhibitory duplication within the exporter gene is highly conserved among B. pertussis strains, absent from all other Bordetella species and from a vast majority of organisms across all kingdoms of life. Therefore, we conclude that inactivation of the exporter gene represents an exceptional example of a flexible genome decay strategy employed by a human pathogen to adapt to its exclusive host.
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20
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Belcher T, Dubois V, Rivera-Millot A, Locht C, Jacob-Dubuisson F. Pathogenicity and virulence of Bordetella pertussis and its adaptation to its strictly human host. Virulence 2021; 12:2608-2632. [PMID: 34590541 PMCID: PMC8489951 DOI: 10.1080/21505594.2021.1980987] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
The highly contagious whooping cough agent Bordetella pertussis has evolved as a human-restricted pathogen from a progenitor which also gave rise to Bordetella parapertussis and Bordetella bronchiseptica. While the latter colonizes a broad range of mammals and is able to survive in the environment, B. pertussis has lost its ability to survive outside its host through massive genome decay. Instead, it has become a highly successful human pathogen by the acquisition of tightly regulated virulence factors and evolutionary adaptation of its metabolism to its particular niche. By the deployment of an arsenal of highly sophisticated virulence factors it overcomes many of the innate immune defenses. It also interferes with vaccine-induced adaptive immunity by various mechanisms. Here, we review data from invitro, human and animal models to illustrate the mechanisms of adaptation to the human respiratory tract and provide evidence of ongoing evolutionary adaptation as a highly successful human pathogen.
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Affiliation(s)
- Thomas Belcher
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR 8204 - CIIL - Center for Infection and Immunity of Lille, Lille, France
| | - Violaine Dubois
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR 8204 - CIIL - Center for Infection and Immunity of Lille, Lille, France
| | - Alex Rivera-Millot
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR 8204 - CIIL - Center for Infection and Immunity of Lille, Lille, France
| | - Camille Locht
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR 8204 - CIIL - Center for Infection and Immunity of Lille, Lille, France
| | - Françoise Jacob-Dubuisson
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR 8204 - CIIL - Center for Infection and Immunity of Lille, Lille, France
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21
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Cabal A, Schmid D, Hell M, Chakeri A, Mustafa-Korninger E, Wojna A, Stöger A, Möst J, Leitner E, Hyden P, Rattei T, Habington A, Wiedermann U, Allerberger F, Ruppitsch W. Isolate-Based Surveillance of Bordetella pertussis, Austria, 2018-2020. Emerg Infect Dis 2021; 27:862-871. [PMID: 33622477 PMCID: PMC7920692 DOI: 10.3201/eid2703.202314] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Pertussis is a vaccine-preventable disease, and its recent resurgence might be attributable to the emergence of strains that differ genetically from the vaccine strain. We describe a novel pertussis isolate-based surveillance system and a core genome multilocus sequence typing scheme to assess Bordetella pertussis genetic variability and investigate the increased incidence of pertussis in Austria. During 2018–2020, we obtained 123 B. pertussis isolates and typed them with the new scheme (2,983 targets and preliminary cluster threshold of <6 alleles). B. pertussis isolates in Austria differed genetically from the vaccine strain, both in their core genomes and in their vaccine antigen genes; 31.7% of the isolates were pertactin-deficient. We detected 8 clusters, 1 of them with pertactin-deficient isolates and possibly part of a local outbreak. National expansion of the isolate-based surveillance system is needed to implement pertussis-control strategies.
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22
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Dienstbier A, Amman F, Petráčková D, Štipl D, Čapek J, Zavadilová J, Fabiánová K, Držmíšek J, Kumar D, Wildung M, Pouchnik D, Večerek B. Comparative Omics Analysis of Historic and Recent Isolates of Bordetella pertussis and Effects of Genome Rearrangements on Evolution. Emerg Infect Dis 2021; 27:57-68. [PMID: 33350934 PMCID: PMC7774529 DOI: 10.3201/eid2701.191541] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Despite high vaccination coverage, pertussis is increasing in many industrialized countries, including the Czech Republic. To better understand Bordetella pertussis resurgence, we analyzed historic strains and recent clinical isolates by using a comparative omics approach. Whole-genome sequencing showed that historic and recent isolates of B. pertussis have substantial variation in genome organization and form separate phylogenetic clusters. Subsequent RNA sequence analysis and liquid chromatography with mass tandem spectrometry analyses showed that these variations translated into discretely separated transcriptomic and proteomic profiles. When compared with historic strains, recent isolates showed increased expression of flagellar genes and genes involved in lipopolysaccharide biosynthesis and decreased expression of polysaccharide capsule genes. Compared with reference strain Tohama I, all strains had increased expression and production of the type III secretion system apparatus. We detected the potential link between observed effects and insertion sequence element–induced changes in gene context only for a few genes.
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23
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Genomic Surveillance and Improved Molecular Typing of Bordetella pertussis Using wgMLST. J Clin Microbiol 2021; 59:JCM.02726-20. [PMID: 33627319 DOI: 10.1128/jcm.02726-20] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Accepted: 02/18/2021] [Indexed: 01/03/2023] Open
Abstract
Multilocus sequence typing (MLST) provides allele-based characterization of bacterial pathogens in a standardized framework. However, classical MLST schemes for Bordetella pertussis, the causative agent of whooping cough, seldom reveal diversity among the small number of gene targets and thereby fail to delineate population structure. To improve the discriminatory power of allele-based molecular typing of B. pertussis, we have developed a whole-genome MLST (wgMLST) scheme from 225 reference-quality genome assemblies. Iterative refinement and allele curation resulted in a scheme of 3,506 coding sequences and covering 81.4% of the B. pertussis genome. This wgMLST scheme was further evaluated with data from a convenience sample of 2,389 B. pertussis isolates sequenced on Illumina instruments, including isolates from known outbreaks and epidemics previously characterized by existing molecular assays, as well as replicates collected from individual patients. wgMLST demonstrated concordance with whole-genome single nucleotide polymorphism (SNP) profiles, accurately resolved outbreak and sporadic cases in a retrospective comparison, and clustered replicate isolates collected from individual patients during diagnostic confirmation. Additionally, a reanalysis of isolates from two statewide epidemics using wgMLST reconstructed the population structures of circulating strains with increased resolution, revealing new clusters of related cases. Comparison with an existing core genome (cgMLST) scheme highlights the stable gene content of this bacterium and forms the initial foundation for necessary standardization. These results demonstrate the utility of wgMLST for improving B. pertussis characterization and genomic surveillance during the current pertussis disease resurgence.
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24
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Damron FH, Barbier M, Dubey P, Edwards KM, Gu XX, Klein NP, Lu K, Mills KHG, Pasetti MF, Read RC, Rohani P, Sebo P, Harvill ET. Overcoming Waning Immunity in Pertussis Vaccines: Workshop of the National Institute of Allergy and Infectious Diseases. THE JOURNAL OF IMMUNOLOGY 2021; 205:877-882. [PMID: 32769142 DOI: 10.4049/jimmunol.2000676] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 06/09/2020] [Indexed: 01/21/2023]
Abstract
Despite high vaccine coverage in many parts of the world, pertussis is resurging in a number of areas in which acellular vaccines are the primary vaccine administered to infants and young children. This is attributed in part to the suboptimal and short-lived immunity elicited by acellular pertussis vaccines and to their inability to prevent nasal colonization and transmission of the etiologic agent Bordetella pertussis In response to this escalating public health concern, the National Institute of Allergy and Infectious Diseases held the workshop "Overcoming Waning Immunity in Pertussis Vaccines" in September 2019 to identify issues and possible solutions for the defects in immunity stimulated by acellular pertussis vaccines. Discussions covered aspects of the current problem, gaps in knowledge and possible paths forward. This review summarizes presentations and discussions of some of the key points that were raised by the workshop.
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Affiliation(s)
- F Heath Damron
- Department of Microbiology, Immunology, and Cell Biology and Vaccine Development Center at West Virginia University Health Sciences Center, West Virginia University, Morgantown, WV 26506
| | - Mariette Barbier
- Department of Microbiology, Immunology, and Cell Biology and Vaccine Development Center at West Virginia University Health Sciences Center, West Virginia University, Morgantown, WV 26506
| | - Purnima Dubey
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH 43210
| | - Kathryn M Edwards
- Division of Infectious Diseases, Department of Pediatrics, Vanderbilt University School of Medicine, Nashville, TN 37232
| | - Xin-Xing Gu
- Division of Microbiology and Infectious Diseases, National Institutes of Health, Washington, D.C. 20852
| | - Nicola P Klein
- Kaiser Permanente Vaccine Study Center, Kaiser Permanente Northern California, Oakland, CA 94611
| | - Kristina Lu
- Division of Microbiology and Infectious Diseases, National Institutes of Health, Washington, D.C. 20852
| | - Kingston H G Mills
- School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin D02 PN40, Ireland
| | - Marcela F Pasetti
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD 21201
| | - Robert C Read
- National Institute for Health Research Southampton Biomedical Research Centre, University Hospital Southampton and Faculty of Medicine, University of Southampton, Southampton SO16 6YD, United Kingdom
| | - Pejman Rohani
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA 30602.,Odum School of Ecology, University of Georgia, Athens, GA 30602; and
| | - Peter Sebo
- Institute of Microbiology of the Czech Academy of Sciences, 142 20 Prague 4, Czech Republic
| | - Eric T Harvill
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA 30602;
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25
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Nagy-Staron A, Tomasek K, Caruso Carter C, Sonnleitner E, Kavčič B, Paixão T, Guet CC. Local genetic context shapes the function of a gene regulatory network. eLife 2021; 10:e65993. [PMID: 33683203 PMCID: PMC7968929 DOI: 10.7554/elife.65993] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 02/19/2021] [Indexed: 11/13/2022] Open
Abstract
Gene expression levels are influenced by multiple coexisting molecular mechanisms. Some of these interactions such as those of transcription factors and promoters have been studied extensively. However, predicting phenotypes of gene regulatory networks (GRNs) remains a major challenge. Here, we use a well-defined synthetic GRN to study in Escherichia coli how network phenotypes depend on local genetic context, i.e. the genetic neighborhood of a transcription factor and its relative position. We show that one GRN with fixed topology can display not only quantitatively but also qualitatively different phenotypes, depending solely on the local genetic context of its components. Transcriptional read-through is the main molecular mechanism that places one transcriptional unit (TU) within two separate regulons without the need for complex regulatory sequences. We propose that relative order of individual TUs, with its potential for combinatorial complexity, plays an important role in shaping phenotypes of GRNs.
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Affiliation(s)
- Anna Nagy-Staron
- Institute of Science and Technology AustriaKlosterneuburgAustria
| | - Kathrin Tomasek
- Institute of Science and Technology AustriaKlosterneuburgAustria
| | | | - Elisabeth Sonnleitner
- Department of MicrobiologyImmunobiology and Genetics, Max F. Perutz Laboratories, Center Of Molecular Biology, University of ViennaViennaAustria
| | - Bor Kavčič
- Institute of Science and Technology AustriaKlosterneuburgAustria
| | - Tiago Paixão
- Institute of Science and Technology AustriaKlosterneuburgAustria
| | - Calin C Guet
- Institute of Science and Technology AustriaKlosterneuburgAustria
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26
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Novák J, Jurnečka D, Linhartová I, Holubová J, Staněk O, Štipl D, Dienstbier A, Večerek B, Azevedo N, Provazník J, Beneš V, Šebo P. A Mutation Upstream of the rplN-rpsD Ribosomal Operon Downregulates Bordetella pertussis Virulence Factor Production without Compromising Bacterial Survival within Human Macrophages. mSystems 2020; 5:e00612-20. [PMID: 33293402 PMCID: PMC7742992 DOI: 10.1128/msystems.00612-20] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 11/06/2020] [Indexed: 11/20/2022] Open
Abstract
The BvgS/BvgA two-component system controls expression of ∼550 genes of Bordetella pertussis, of which, ∼245 virulence-related genes are positively regulated by the BvgS-phosphorylated transcriptional regulator protein BvgA (BvgA∼P). We found that a single G-to-T nucleotide transversion in the 5'-untranslated region (5'-UTR) of the rplN gene enhanced transcription of the ribosomal protein operon and of the rpoA gene and provoked global dysregulation of B. pertussis genome expression. This comprised overproduction of the alpha subunit (RpoA) of the DNA-dependent RNA polymerase, downregulated BvgA and BvgS protein production, and impaired production and secretion of virulence factors by the mutant. Nonetheless, the mutant survived like the parental bacteria for >2 weeks inside infected primary human macrophages and persisted within infected mouse lungs for a longer period than wild-type B. pertussis These observations suggest that downregulation of virulence factor production by bacteria internalized into host cells may enable persistence of the whooping cough agent in the airways.IMPORTANCE We show that a spontaneous mutation that upregulates transcription of an operon encoding ribosomal proteins and causes overproduction of the downstream-encoded α subunit (RpoA) of RNA polymerase causes global effects on gene expression levels and proteome composition of Bordetella pertussis Nevertheless, the resulting important downregulation of the BvgAS-controlled expression of virulence factors of the whooping cough agent did not compromise its capacity to persist for prolonged periods inside primary human macrophage cells, and it even enhanced its capacity to persist in infected mouse lungs. These observations suggest that the modulation of BvgAS-controlled expression of virulence factors may occur also during natural infections of human airways by Bordetella pertussis and may possibly account for long-term persistence of the pathogen within infected cells of the airways.
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Affiliation(s)
- Jakub Novák
- Laboratory of Molecular Biology of Bacterial Pathogens, Institute of Microbiology of the Czech Academy of Sciences, Prague, Czech Republic
| | - David Jurnečka
- Laboratory of Molecular Biology of Bacterial Pathogens, Institute of Microbiology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Irena Linhartová
- Laboratory of Molecular Biology of Bacterial Pathogens, Institute of Microbiology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Jana Holubová
- Laboratory of Molecular Biology of Bacterial Pathogens, Institute of Microbiology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Ondřej Staněk
- Laboratory of Molecular Biology of Bacterial Pathogens, Institute of Microbiology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Daniel Štipl
- Laboratory of Post-Transcriptional Control of Gene Expression, Institute of Microbiology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Ana Dienstbier
- Laboratory of Post-Transcriptional Control of Gene Expression, Institute of Microbiology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Branislav Večerek
- Laboratory of Post-Transcriptional Control of Gene Expression, Institute of Microbiology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Nayara Azevedo
- Genomics Core Facility, European Molecular Biology Laboratory, Services and Technology Unit, Heidelberg, Germany
| | - Jan Provazník
- Genomics Core Facility, European Molecular Biology Laboratory, Services and Technology Unit, Heidelberg, Germany
| | - Vladimír Beneš
- Genomics Core Facility, European Molecular Biology Laboratory, Services and Technology Unit, Heidelberg, Germany
| | - Peter Šebo
- Laboratory of Molecular Biology of Bacterial Pathogens, Institute of Microbiology of the Czech Academy of Sciences, Prague, Czech Republic
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27
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Locht C, Carbonetti NH, Cherry JD, Damron FH, Edwards KM, Fernandez R, Harvill ET, Hozbor D, Mills KHG, Rodriguez ME, Mascart F. Highlights of the 12th International Bordetella Symposium. Clin Infect Dis 2020; 71:2521-2526. [PMID: 32463883 PMCID: PMC7713684 DOI: 10.1093/cid/ciaa651] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Accepted: 05/22/2020] [Indexed: 11/13/2022] Open
Abstract
To commemorate the 100th anniversary of the Nobel prize being awarded to Jules Bordet, the discoverer of Bordetella pertussis, the 12th International Bordetella Symposium was held from 9 to 12 April 2019 at the Université Libre de Bruxelles, where Jules Bordet studied and was Professor of Microbiology. The symposium attracted more than 300 Bordetella experts from 34 countries. They discussed the latest epidemiologic data and clinical aspects of pertussis, Bordetella biology and pathogenesis, immunology and vaccine development, and genomics and evolution. Advanced technological and methodological tools provided novel insights into the genomic diversity of Bordetella and a better understanding of pertussis disease and vaccine performance. New molecular approaches revealed previously unrecognized complexity of virulence gene regulation. Innovative insights into the immune responses to infection by Bordetella resulted in the development of new vaccine candidates. Such discoveries will aid in the design of more effective approaches to control pertussis and other Bordetella-related diseases.
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Affiliation(s)
- Camille Locht
- Université Lille, Centre National de la Recherche Scientifique, Inserm, Centre Hospitalier Universitaire Lille, Institut Pasteur de Lille, U1019, Unité Mixte de Recherche 8204, Center for Infection and Immunity of Lille, Lille, France
| | - Nicholas H Carbonetti
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - James D Cherry
- David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California, USA
| | - F Heath Damron
- Department of Microbiology, Immunology and Cell Biology, West Virginia University, Morgantown, West Virginia, USA
- Vaccine Development Center at West Virginia University Health Science Center, West Virginia University, Morgantown, West Virginia, USA
| | - Kathryn M Edwards
- Division of Pediatric Infectious Diseases, Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Rachel Fernandez
- Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia, Canada
| | - Eric T Harvill
- Department of Infectious Diseases, College of Veterinary Sciences, University of Georgia, Athens, Georgia, USA
| | - Daniela Hozbor
- Laboratorio VacSal, Instituto de Biotecnología y Biología Molecular, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Consejo Nacional de Investigaciones Cientificas y Técnicas, La Plata, Argentina
| | - Kingston H G Mills
- School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin, Ireland
| | - Maria Eugenia Rodriguez
- Centro de Investigacion y Desarrollo en Fermentaciones Industriales, Consejo Nacional de Investigaciones Cientificas y Técnicas, La Plata, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Argentina
| | - Françoise Mascart
- Laboratory of Vaccinology and Mucosal Immunity, Université Libre de Bruxelles, Brussels, Belgium
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28
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Blackwood CB, Sen-Kilic E, Boehm DT, Hall JM, Varney ME, Wong TY, Bradford SD, Bevere JR, Witt WT, Damron FH, Barbier M. Innate and Adaptive Immune Responses against Bordetella pertussis and Pseudomonas aeruginosa in a Murine Model of Mucosal Vaccination against Respiratory Infection. Vaccines (Basel) 2020; 8:vaccines8040647. [PMID: 33153066 PMCID: PMC7712645 DOI: 10.3390/vaccines8040647] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 10/23/2020] [Accepted: 10/28/2020] [Indexed: 12/26/2022] Open
Abstract
Whole cell vaccines are frequently the first generation of vaccines tested for pathogens and can inform the design of subsequent acellular or subunit vaccines. For respiratory pathogens, administration of vaccines at the mucosal surface can facilitate the generation of a localized mucosal immune response. Here, we examined the innate and vaccine-induced immune responses to infection by two respiratory pathogens: Bordetella pertussis and Pseudomonas aeruginosa. In a model of intranasal administration of whole cell vaccines (WCVs) with the adjuvant curdlan, we examined local and systemic immune responses following infection. These studies showed that intranasal vaccination with a WCV led to a reduction of the bacterial burden in the airways of animals infected with the respective pathogen. However, there were unique changes in the cytokines produced, cells recruited, and inflammation at the site of infection. Both mucosal vaccinations induced antibodies that bind the target pathogen, but linear regression and principal component analysis revealed that protection from these pathogens is not solely related to antibody titer. Protection from P. aeruginosa correlated to a reduction in lung weight, blood lymphocytes and neutrophils, and the cytokines IL-6, TNF-α, KC/GRO, and IL-10, and promotion of serum IgG antibodies and the cytokine IFN-γ in the lung. Protection from B. pertussis infection correlated strongly with increased anti-B-pertussis serum IgG antibodies. These findings reveal valuable correlates of protection for mucosal vaccination that can be used for further development of both B. pertussis and P. aeruginosa vaccines.
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Barkoff AM, Mertsola J, Pierard D, Dalby T, Hoegh SV, Guillot S, Stefanelli P, van Gent M, Berbers G, Vestrheim D, Greve-Isdahl M, Wehlin L, Ljungman M, Fry NK, Markey K, He Q. Pertactin-deficient Bordetella pertussis isolates: evidence of increased circulation in Europe, 1998 to 2015. ACTA ACUST UNITED AC 2020; 24. [PMID: 30782265 PMCID: PMC6381657 DOI: 10.2807/1560-7917.es.2019.24.7.1700832] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Introduction Pertussis outbreaks have occurred in several industrialised countries using acellular pertussis vaccines (ACVs) since the 1990s. High prevalence of pertactin (PRN)-deficient Bordetella pertussis isolates has been found in these countries. Aims To evaluate in Europe: (i) whether proportions of PRN-deficient strains increased in consecutive collections of B. pertussis clinical isolates; (ii) if the frequency of PRN-deficient strains in countries correlated with the time since ACV introduction; (iii) the presence of pertussis toxin (PT)-, filamentous haemagglutinin (FHA)- or fimbriae (Fim)-deficient isolates. Methods B. pertussis clinical isolates were obtained from different European countries during four periods (EUpert I–IV studies): 1998 to 2001 (n = 102), 2004 to 2005 (n = 154), 2007 to 2009 (n = 140) and 2012 to 2015 (n = 265). The isolates’ selection criteria remained unchanged in all periods. PRN, PT, FHA and Fim2 and Fim3 expression were assessed by ELISA. Results In each period 1.0% (1/102), 1.9% (3/154), 6.4% (9/140) and 24.9% (66/265) of isolates were PRN-deficient. In EUpert IV, PRN-deficient isolates occurred in all countries sampled and in six countries their frequency was higher than in EUpert III (for Sweden and the United Kingdom, p < 0.0001 and p = 0.0155, respectively). Sweden and Italy which used ACVs since the mid 1990s had the highest frequencies (69%; 20/29 and 55%; 11/20, respectively) while Finland, where primary immunisations with ACV containing PRN dated from 2009 had the lowest (3.6%). Throughout the study, no PT- or FHA-deficient isolate and one Fim2/3-deficient was detected. Conclusion Results suggest that the longer the period since the introduction of ACVs containing PRN, the higher the frequency of circulating PRN-deficient isolates.
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Affiliation(s)
- Alex-Mikael Barkoff
- Institute of Biomedicine, Department of Microbiology, Virology and Immunology, University of Turku, Turku, Finland
| | - Jussi Mertsola
- Department of Pediatrics and Adolescent Medicine, Turku University Hospital, Turku, Finland
| | - Denis Pierard
- Department of Microbiology, Universitair Ziekenhuis Brussel (UZ Brussel), Vrije Universiteit Brussel (VUB), Brussels, Belgium
| | - Tine Dalby
- Statens Serum Institut, Infectious Disease Preparedness - Bacteria, Parasites and Fungi, Copenhagen, Denmark
| | - Silje Vermedal Hoegh
- Department of Clinical Microbiology, Odense, University Hospital, Odense, Denmark
| | - Sophie Guillot
- Institut Pasteur, Centre National de Référence de la Coqueluche et autres Bordetelloses, Paris, France
| | - Paola Stefanelli
- Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - Marjolein van Gent
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Guy Berbers
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Didrik Vestrheim
- Department of Vaccine Preventable Diseases, Norwegian Institute of Public Health, Oslo, Norway
| | - Margrethe Greve-Isdahl
- Department of Vaccine Preventable Diseases, Norwegian Institute of Public Health, Oslo, Norway
| | - Lena Wehlin
- Department of Microbiology, Public Health Agency of Sweden, Solna, Sweden
| | | | - Norman K Fry
- Respiratory and Vaccine Preventable Bacteria Reference Unit, Public Health England - National Infection Service, London, United Kingdom
| | - Kevin Markey
- National Institute for Biological Standards and Control, Potters Bar, United Kingdom
| | - Qiushui He
- Department of Medical Microbiology, Capital Medical University, Beijing, China.,Institute of Biomedicine, Department of Microbiology, Virology and Immunology, University of Turku, Turku, Finland
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Guillot S, Mizrahi A, Armatys N, Chat L, Le Monnier A, Brisse S, Toubiana J. Low Detection Rate of Bordetella pertussis Using the BioFire FilmArray Respiratory Panel 2 plus. Open Forum Infect Dis 2020; 7:ofaa267. [PMID: 32793765 PMCID: PMC7415305 DOI: 10.1093/ofid/ofaa267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Accepted: 06/26/2020] [Indexed: 11/13/2022] Open
Abstract
Syndromic respiratory panels are increasingly used worldwide. Their performance for detection of Bordetella pertussis needs to be evaluated. We found that the FilmArray Respiratory Panel 2plus (RP2+) assay, which uses the pertussis toxin promoter target for B. pertussis, can only detect highly charged samples. Negative RP2+ results should not be interpreted as an absence of B. pertussis in clinical samples.
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Affiliation(s)
- Sophie Guillot
- Biodiversity and Epidemiology of Bacterial Pathogens, Institut Pasteur, Paris, France.,National Reference Center for Whooping Cough and Other Bordetella Infections, Institut Pasteur, Paris, France
| | - Assaf Mizrahi
- Clinical Microbiology Laboratory, Saint Joseph Hospital, Paris, France.,Institut Micalis, UMR1319, Université Paris-Saclay, INRAe, AgroParisTech, Bactéries Pathogènes et Santé, Chatenay-Malabry, France
| | - Nathalie Armatys
- Biodiversity and Epidemiology of Bacterial Pathogens, Institut Pasteur, Paris, France.,National Reference Center for Whooping Cough and Other Bordetella Infections, Institut Pasteur, Paris, France
| | - Laureen Chat
- Clinical Microbiology Laboratory, Saint Joseph Hospital, Paris, France
| | - Alban Le Monnier
- Clinical Microbiology Laboratory, Saint Joseph Hospital, Paris, France.,Institut Micalis, UMR1319, Université Paris-Saclay, INRAe, AgroParisTech, Bactéries Pathogènes et Santé, Chatenay-Malabry, France
| | - Sylvain Brisse
- Biodiversity and Epidemiology of Bacterial Pathogens, Institut Pasteur, Paris, France.,National Reference Center for Whooping Cough and Other Bordetella Infections, Institut Pasteur, Paris, France
| | - Julie Toubiana
- Biodiversity and Epidemiology of Bacterial Pathogens, Institut Pasteur, Paris, France.,National Reference Center for Whooping Cough and Other Bordetella Infections, Institut Pasteur, Paris, France.,General Paediatrics and Paediatric Infectious Diseases Department, Hôpital Necker-Enfants Malades, APHP, Université de Paris, Paris, France
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Alai S, Ghattargi VC, Gautam M, Patel K, Pawar SP, Dhotre DP, Shaligram U, Gairola S. Comparative genomics of whole-cell pertussis vaccine strains from India. BMC Genomics 2020; 21:345. [PMID: 32381023 PMCID: PMC7204287 DOI: 10.1186/s12864-020-6724-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2020] [Accepted: 04/06/2020] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND Despite high vaccination coverage using acellular (ACV) and whole-cell pertussis (WCV) vaccines, the resurgence of pertussis is observed globally. Genetic divergence in circulating strains of Bordetella pertussis has been reported as one of the contributing factors for the resurgence of the disease. Our current knowledge of B. pertussis genetic evolution in circulating strains is mostly based on studies conducted in countries using ACVs targeting only a few antigens used in the production of ACVs. To better understand the adaptation to vaccine-induced selection pressure, it will be essential to study B. pertussis populations in developing countries which are using WCVs. India is a significant user and global supplier of WCVs. We report here comparative genome analyses of vaccine and clinical isolates reported from India. Whole-genome sequences obtained from vaccine strains: WCV (J445, J446, J447 and J448), ACV (BP165) were compared with Tohama-I reference strain and recently reported clinical isolates from India (BPD1, BPD2). Core genome-based phylogenetic analysis was also performed using 166 isolates reported from countries using ACV. RESULTS Whole-genome analysis of vaccine and clinical isolates reported from India revealed high genetic similarity and conserved genome among strains. Phylogenetic analysis showed that clinical and vaccine strains share genetic closeness with reference strain Tohama-I. The allelic profile of vaccine strains (J445:ptxP1/ptxA2/prn1/fim2-1/fim3-1; J446: ptxP2/ptxA4/prn7/fim2-2/fim3-1; J447 and J448: ptxP1/ptxA1/ prn1/fim2-1/fim3-1), which matched entirely with clinical isolates (BPD1:ptxP1/ptxA1/prn1/fim2-1 and BPD2: ptxP1/ptxA1/prn1/fim2-1) reported from India. Multi-locus sequence typing (MLST) demonstrated the presence of dominant sequence types ST2 and primitive ST1 in vaccine strains which will allow better coverage against circulating strains of B. pertussis. CONCLUSIONS The study provides a detailed characterization of vaccine and clinical strains reported from India, which will further facilitate epidemiological studies on genetic shifts in countries which are using WCVs in their immunization programs.
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Affiliation(s)
- Shweta Alai
- Department of Health and Biological Sciences, Symbiosis International University, Pune, Maharashtra, 412115, India
| | - Vikas C Ghattargi
- National Centre for Microbial Resource, National Centre for Cell Science, Pune, Maharashtra, 411021, India
| | - Manish Gautam
- Serum Institute of India Pvt. Ltd, Pune, Maharashtra, 411028, India
| | - Krunal Patel
- Serum Institute of India Pvt. Ltd, Pune, Maharashtra, 411028, India
| | - Shrikant P Pawar
- National Centre for Microbial Resource, National Centre for Cell Science, Pune, Maharashtra, 411021, India
| | - Dhiraj P Dhotre
- National Centre for Microbial Resource, National Centre for Cell Science, Pune, Maharashtra, 411021, India
| | - Umesh Shaligram
- Serum Institute of India Pvt. Ltd, Pune, Maharashtra, 411028, India
| | - Sunil Gairola
- Serum Institute of India Pvt. Ltd, Pune, Maharashtra, 411028, India.
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Saedi S, Safarchi A, Noofeli M, Tadayon K, Tay ACY, Lamichhane B, Rahimi H, Shahcheraghi F. Genome diversity and evolutionary characteristics of clinical isolates of Bordetella pertussis circulating in Iran. IRANIAN JOURNAL OF MICROBIOLOGY 2020; 12:1-10. [PMID: 32322373 PMCID: PMC7163038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
BACKGROUND AND OBJECTIVES The re-emergence of pertussis still is being reported all over the world. Pathogen adaptation and antigenic divergence of circulating isolates from vaccine strains are the main reasons of infection resurgence. Waning immunity is also an important factor contributing to resurgence of pertussis. MATERIALS AND METHODS The genetic diversity and evolutionary characteristics of circulating Iranian isolates of Bordetella pertussis during February 2015 to October 2018 was investigated by pulsed-field gel electrophoresis (PFGE) and subsequently ptxA, ptxP and fim3 alleles were characterized. The next generation genome sequencing was then used to compare the genomics of ptxP1 and ptxP3 of selected isolates from PFGE dendrogram. RESULTS PFGE differentiated 62 clinical isolates and vaccine and reference strains into 19 PFGE profiles, indicating the higher level of heterogeneity in the population during 2015-2018. The predominant B. pertussis genotype harbored pertussis toxin promoter allele, ptxP3 and the expansion of ptxA1 isolates, were also observed in our population. CONCLUSION No changes in allelic profile of predominant clone in recent years was observed but antigenic divergence between recently circulating isolates and the vaccine strain has been progressed and significantly was higher than previous studies. The comparative genomic analysis of the ptxP3 and ptxP1 isolates indicate that changes in ptxP3 genome structure including 32 unique SNPs and three unique indels may have contributed to the expansion of the ptxP3 clone. We compared ptxP3 and ptxP1 isolates in pathogenicity-associated genes and found five of them were specific for the ptxP3 isolates. The polymorphisms in pathogenicity-associated genes suggest structural adaptations for these virulence factors.
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Affiliation(s)
- Samaneh Saedi
- Department of Bacteriology, Pasteur Institute of Iran, Tehran, Iran
| | - Azadeh Safarchi
- Department of Bacteriology, Pasteur Institute of Iran, Tehran, Iran
| | - Mojtaba Noofeli
- Department of Human Bacterial Vaccine, Razi Vaccine & Serum Research Institute, Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran
| | - Keyvan Tadayon
- Department of Aerobic Bacterial Research and Vaccine Production, Razi Vaccine & Serum Research Institute, Karaj, Iran
| | - Alfred Chin Yen Tay
- The Marshall Centre for Infectious Diseases Research and Training, The University of Western Australia, Nedlands, Western Australia, Australia,Shenzhen Dapeng New District Kuichong People Hospital, Shenzhen, Guangdong, China
| | - Binit Lamichhane
- The Marshall Centre for Infectious Diseases Research and Training, The University of Western Australia, Nedlands, Western Australia, Australia
| | - Hamzeh Rahimi
- Department of Molecular Medicine, Pasteur Institute of Iran, Tehran, Iran
| | - Fereshteh Shahcheraghi
- Department of Bacteriology, Pasteur Institute of Iran, Tehran, Iran,Corresponding author: Fereshteh Shahcheraghi, PhD, Department of Bacteriology, Pasteur Institute of Iran, Tehran, Iran. Tel/Fax: +98-21-66405535,
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Weigand MR, Williams MM, Peng Y, Kania D, Pawloski LC, Tondella ML. Genomic Survey of Bordetella pertussis Diversity, United States, 2000-2013. Emerg Infect Dis 2019; 25:780-783. [PMID: 30882317 PMCID: PMC6433035 DOI: 10.3201/eid2504.180812] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
We characterized 170 complete genome assemblies from clinical Bordetella pertussis isolates representing geographic and temporal diversity in the United States. These data capture genotypic shifts, including increased pertactin deficiency, occurring amid the current pertussis disease resurgence and provide a foundation for needed research to direct future public health control strategies.
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34
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Xu Z, Octavia S, Luu LDW, Payne M, Timms V, Tay CY, Keil AD, Sintchenko V, Guiso N, Lan R. Pertactin-Negative and Filamentous Hemagglutinin-Negative Bordetella pertussis, Australia, 2013-2017. Emerg Infect Dis 2019; 25:1196-1199. [PMID: 31107218 PMCID: PMC6537726 DOI: 10.3201/eid2506.180240] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
During the 2008–2012 pertussis epidemic in Australia, pertactin (Prn)–negative Bordetella pertussis emerged. We analyzed 78 isolates from the 2013–2017 epidemic and documented continued expansion of Prn-negative ptxP3 B. pertussis strains. We also detected a filamentous hemagglutinin-negative and Prn-negative B. pertussis isolate.
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35
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Weigand MR, Peng Y, Batra D, Burroughs M, Davis JK, Knipe K, Loparev VN, Johnson T, Juieng P, Rowe LA, Sheth M, Tang K, Unoarumhi Y, Williams MM, Tondella ML. Conserved Patterns of Symmetric Inversion in the Genome Evolution of Bordetella Respiratory Pathogens. mSystems 2019; 4:e00702-19. [PMID: 31744907 PMCID: PMC6867878 DOI: 10.1128/msystems.00702-19] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Accepted: 11/01/2019] [Indexed: 12/11/2022] Open
Abstract
Whooping cough (pertussis), primarily caused by Bordetella pertussis, has resurged in the United States, and circulating strains exhibit considerable chromosome structural fluidity in the form of rearrangement and deletion. The genus Bordetella includes additional pathogenic species infecting various animals, some even causing pertussis-like respiratory disease in humans; however, investigation of their genome evolution has been limited. We studied chromosome structure in complete genome sequences from 167 Bordetella species isolates, as well as 469 B. pertussis isolates, to gain a generalized understanding of rearrangement patterns among these related pathogens. Observed changes in gene order primarily resulted from large inversions and were only detected in species with genomes harboring multicopy insertion sequence (IS) elements, most notably B. holmesii and B. parapertussis While genomes of B. pertussis contain >240 copies of IS481, IS elements appear less numerous in other species and yield less chromosome structural diversity through rearrangement. These data were further used to predict all possible rearrangements between IS element copies present in Bordetella genomes, revealing that only a subset is observed among circulating strains. Therefore, while it appears that rearrangement occurs less frequently in other species than in B. pertussis, these clinically relevant respiratory pathogens likely experience similar mutation of gene order. The resulting chromosome structural fluidity presents both challenges and opportunity for the study of Bordetella respiratory pathogens.IMPORTANCE Bordetella pertussis is the primary agent of whooping cough (pertussis). The Bordetella genus includes additional pathogens of animals and humans, including some that cause pertussis-like respiratory illness. The chromosome of B. pertussis has previously been shown to exhibit considerable structural rearrangement, but insufficient data have prevented comparable investigation in related species. In this study, we analyze chromosome structure variation in several Bordetella species to gain a generalized understanding of rearrangement patterns in this genus. Just as in B. pertussis, we observed inversions in other species that likely result from common mutational processes. We used these data to further predict additional, unobserved inversions, suggesting that specific genome structures may be preferred in each species.
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Affiliation(s)
- Michael R Weigand
- Division of Bacterial Disease, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Yanhui Peng
- Division of Bacterial Disease, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Dhwani Batra
- Division of Scientific Resources, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Mark Burroughs
- Division of Scientific Resources, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Jamie K Davis
- Division of Scientific Resources, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Kristen Knipe
- Division of Scientific Resources, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Vladimir N Loparev
- Division of Scientific Resources, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Taccara Johnson
- Division of Bacterial Disease, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Phalasy Juieng
- Division of Scientific Resources, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Lori A Rowe
- Division of Scientific Resources, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Mili Sheth
- Division of Scientific Resources, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Kevin Tang
- Division of Scientific Resources, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Yvette Unoarumhi
- Division of Scientific Resources, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Margaret M Williams
- Division of Bacterial Disease, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - M Lucia Tondella
- Division of Bacterial Disease, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
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Xu Z, Wang Z, Luan Y, Li Y, Liu X, Peng X, Octavia S, Payne M, Lan R. Genomic epidemiology of erythromycin-resistant Bordetella pertussis in China. Emerg Microbes Infect 2019; 8:461-470. [PMID: 30898080 PMCID: PMC6455148 DOI: 10.1080/22221751.2019.1587315] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
Macrolides such as erythromycin are the empirical treatment of Bordetella pertussis infections. China has experienced an increase in erythromycin-resistant B. pertussis isolates since they were first reported in 2013. Here, we undertook a genomic study on Chinese B. pertussis isolates from 2012 to 2015 to elucidate the origins and phylogenetic relationships of erythromycin-resistant B. pertussis isolates in China. A total of 167 Chinese B. pertussis isolates were used for antibiotic sensitivity testing and multiple locus variable-number tandem repeat (VNTR) analysis (MLVA). All except four isolates were erythromycin-resistant and of the four erythromycin-sensitive isolates, three were non-ptxP1. MLVA types (MT), MT55, MT104 and MT195 were the predominant types. Fifty of those isolates were used for whole genome sequencing and phylogenetic analysis. Genome sequencing and phylogenetic analysis revealed three independent erythromycin-resistant lineages and all resistant isolates carried a mutation in the 23S rRNA gene. A novel fhaB3 allele was found uniquely in Chinese ptxP1 isolates and these Chinese ptxP1-ptxA1-fhaB3 had a 5-fold higher mutation rate than the global ptxP1-ptxA1 B. pertussis population. Our results suggest that the evolution of Chinese B. pertussis is likely to be driven by selection pressure from both vaccination and antibiotics. The emergence of the new non-vaccine fhaB3 allele in Chinese B. pertussis population may be a result of selection from vaccination, whereas the expansion of ptxP1-fhaB3 lineages was most likely to be the result of selection pressure from antibiotics. Further monitoring of B. pertussis in China is required to better understand the evolution of the pathogen.
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Affiliation(s)
- Zheng Xu
- a School of Biotechnology and Biomolecular Sciences , University of New South Wales , Sydney , Australia
| | - Zengguo Wang
- b Xi'an Center for Disease Prevention and Control , Xi'an , People's Republic of China.,c Department of Infectious Diseases , Xi'an Children's Hospital , Xi'an , People's Republic of China
| | - Yang Luan
- b Xi'an Center for Disease Prevention and Control , Xi'an , People's Republic of China
| | - Yarong Li
- c Department of Infectious Diseases , Xi'an Children's Hospital , Xi'an , People's Republic of China
| | - Xiaoguai Liu
- c Department of Infectious Diseases , Xi'an Children's Hospital , Xi'an , People's Republic of China
| | - Xiaokang Peng
- c Department of Infectious Diseases , Xi'an Children's Hospital , Xi'an , People's Republic of China
| | - Sophie Octavia
- a School of Biotechnology and Biomolecular Sciences , University of New South Wales , Sydney , Australia
| | - Michael Payne
- a School of Biotechnology and Biomolecular Sciences , University of New South Wales , Sydney , Australia
| | - Ruiting Lan
- a School of Biotechnology and Biomolecular Sciences , University of New South Wales , Sydney , Australia
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Bouchez V, Guglielmini J, Dazas M, Landier A, Toubiana J, Guillot S, Criscuolo A, Brisse S. Genomic Sequencing of Bordetella pertussis for Epidemiology and Global Surveillance of Whooping Cough. Emerg Infect Dis 2019; 24:988-994. [PMID: 29774847 PMCID: PMC6004856 DOI: 10.3201/eid2406.171464] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Bordetella pertussis causes whooping cough, a highly contagious respiratory disease that is reemerging in many world regions. The spread of antigen-deficient strains may threaten acellular vaccine efficacy. Dynamics of strain transmission are poorly defined because of shortcomings in current strain genotyping methods. Our objective was to develop a whole-genome genotyping strategy with sufficient resolution for local epidemiologic questions and sufficient reproducibility to enable international comparisons of clinical isolates. We defined a core genome multilocus sequence typing scheme comprising 2,038 loci and demonstrated its congruence with whole-genome single-nucleotide polymorphism variation. Most cases of intrafamilial groups of isolates or of multiple isolates recovered from the same patient were distinguished from temporally and geographically cocirculating isolates. However, epidemiologically unrelated isolates were sometimes nearly undistinguishable. We set up a publicly accessible core genome multilocus sequence typing database to enable global comparisons of B. pertussis isolates, opening the way for internationally coordinated surveillance.
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How Genomics Is Changing What We Know About the Evolution and Genome of Bordetella pertussis. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1183:1-17. [PMID: 31321755 DOI: 10.1007/5584_2019_401] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The evolution of Bordetella pertussis from a common ancestor similar to Bordetella bronchiseptica has occurred through large-scale gene loss, inactivation and rearrangements, largely driven by the spread of insertion sequence element repeats throughout the genome. B. pertussis is widely considered to be monomorphic, and recent evolution of the B. pertussis genome appears to, at least in part, be driven by vaccine-based selection. Given the recent global resurgence of whooping cough despite the wide-spread use of vaccination, a more thorough understanding of B. pertussis genomics could be highly informative. In this chapter we discuss the evolution of B. pertussis, including how vaccination is changing the circulating B. pertussis population at the gene-level, and how new sequencing technologies are revealing previously unknown levels of inter- and intra-strain variation at the genome-level.
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Stefanelli P. Pertussis: Identification, Prevention and Control. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1183:127-136. [PMID: 31321754 DOI: 10.1007/5584_2019_408] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Pertussis is a vaccine-preventable disease. Despite the high vaccination coverage among children, pertussis is considered a re-emerging disease for which identification, prevention and control strategies need to be improved. To control pertussis it is important to maintain a high vaccination coverage to protect the age groups considered at high risk for the disease. Laboratory confirmation of Bordetella pertussis infection together with a differential diagnostic test for other Bordetellae are prerequisite for a correct and timely diagnosis of pertussis. Moreover, investigations of antimicrobial susceptibility and whole genome sequencing may permit to monitor the circulation of antimicrobials resistant and/or vaccine-escape strains. Finally, the preventive framework should no longer consider pertussis exclusively as a childhood infectious disease, since adults may play a role in transmission events.
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Affiliation(s)
- Paola Stefanelli
- Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy.
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Molecular Epidemiology of Bordetella pertussis. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1183:19-33. [PMID: 31342459 DOI: 10.1007/5584_2019_402] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Although vaccination has been effective, Bordetella pertussis is increasingly causing epidemics, especially in industrialized countries using acellular vaccines (aPs). One factor behind the increased circulation is the molecular changes on the pathogen level. After pertussis vaccinations were introduced, changes in the fimbrial (Fim) serotype of the circulating strains was observed. When bacterial typing methods improved, further changes between the vaccine and circulating strains, especially among the common virulence genes including pertussis toxin (PT) and pertactin (PRN) were noticed. Moreover, development of genome based techniques including pulsed-field gel electrophoresis (PFGE), multiple-locus variable number tandem repeat analysis (MLVA) and whole-genome sequencing (WGS) have offered a better resolution to monitor B. pertussis strains. After the introduction of aP vaccines, B. pertussis strains that are deficient to vaccine antigens, especially PRN, have appeared widely. On the other hand, antimicrobial resistance to first line drugs (macrolides) against B. pertussis is still low in many countries and therefore no globally evaluated antimicrobial susceptibility test values have been recommended. In this review, we focus on the molecular changes in the bacteria, which have or may have affected the past and current epidemiology of pertussis.
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Complete Genome Sequences of Bordetella pertussis Clinical Isolate FR5810 and Reference Strain Tohama from Combined Oxford Nanopore and Illumina Sequencing. Microbiol Resour Announc 2018; 7:MRA01207-18. [PMID: 30533789 PMCID: PMC6256476 DOI: 10.1128/mra.01207-18] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Accepted: 10/19/2018] [Indexed: 11/20/2022] Open
Abstract
Here, we describe the complete genome sequences of two Bordetella pertussis strains, FR5810, a clinical isolate recovered from the respiratory tract of an infant, and Tohama, a key reference strain for the species. Sequences were obtained using a hybrid approach combining Oxford Nanopore Technologies MinION and Illumina NextSeq 500 sequence data.
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Ring N, Abrahams JS, Jain M, Olsen H, Preston A, Bagby S. Resolving the complex Bordetella pertussis genome using barcoded nanopore sequencing. Microb Genom 2018; 4:e000234. [PMID: 30461375 PMCID: PMC6321869 DOI: 10.1099/mgen.0.000234] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2018] [Accepted: 10/12/2018] [Indexed: 11/30/2022] Open
Abstract
The genome of Bordetella pertussis is complex, with high G+C content and many repeats, each longer than 1000 bp. Long-read sequencing offers the opportunity to produce single-contig B. pertussis assemblies using sequencing reads which are longer than the repetitive sections, with the potential to reveal genomic features which were previously unobservable in multi-contig assemblies produced by short-read sequencing alone. We used an R9.4 MinION flow cell and barcoding to sequence five B. pertussis strains in a single sequencing run. We then trialled combinations of the many nanopore user community-built long-read analysis tools to establish the current optimal assembly pipeline for B. pertussis genome sequences. This pipeline produced closed genome sequences for four strains, allowing visualization of inter-strain genomic rearrangement. Read mapping to the Tohama I reference genome suggests that the remaining strain contains an ultra-long duplicated region (almost 200 kbp), which was not resolved by our pipeline; further investigation also revealed that a second strain that was seemingly resolved by our pipeline may contain an even longer duplication, albeit in a small subset of cells. We have therefore demonstrated the ability to resolve the structure of several B. pertussis strains per single barcoded nanopore flow cell, but the genomes with highest complexity (e.g. very large duplicated regions) remain only partially resolved using the standard library preparation and will require an alternative library preparation method. For full strain characterization, we recommend hybrid assembly of long and short reads together; for comparison of genome arrangement, assembly using long reads alone is sufficient.
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Affiliation(s)
- Natalie Ring
- Department of Biology and Biochemistry and the Milner Centre for Evolution, University of Bath, Bath, UK
| | - Jonathan S. Abrahams
- Department of Biology and Biochemistry and the Milner Centre for Evolution, University of Bath, Bath, UK
| | - Miten Jain
- UC Santa Cruz Genomics Institute, 1156 High Street, Santa Cruz, CA 95064, USA
| | - Hugh Olsen
- UC Santa Cruz Genomics Institute, 1156 High Street, Santa Cruz, CA 95064, USA
| | - Andrew Preston
- Department of Biology and Biochemistry and the Milner Centre for Evolution, University of Bath, Bath, UK
| | - Stefan Bagby
- Department of Biology and Biochemistry and the Milner Centre for Evolution, University of Bath, Bath, UK
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Boehm DT, Hall JM, Wong TY, DiVenere AM, Sen-Kilic E, Bevere JR, Bradford SD, Blackwood CB, Elkins CM, DeRoos KA, Gray MC, Cooper CG, Varney ME, Maynard JA, Hewlett EL, Barbier M, Damron FH. Evaluation of Adenylate Cyclase Toxoid Antigen in Acellular Pertussis Vaccines by Using a Bordetella pertussis Challenge Model in Mice. Infect Immun 2018; 86:e00857-17. [PMID: 30012638 PMCID: PMC6204743 DOI: 10.1128/iai.00857-17] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Accepted: 07/10/2018] [Indexed: 12/21/2022] Open
Abstract
Bordetella pertussis is the primary causative agent of pertussis (whooping cough), which is a respiratory infection that leads to a violent cough and can be fatal in infants. There is a need to develop more effective vaccines because of the resurgence of cases of pertussis in the United States since the switch from the whole-cell pertussis vaccines (wP) to the acellular pertussis vaccines (aP; diphtheria-tetanus-acellular-pertussis vaccine/tetanus-diphtheria-pertussis vaccine). Adenylate cyclase toxin (ACT) is a major virulence factor of B. pertussis that is (i) required for establishment of infection, (ii) an effective immunogen, and (iii) a protective antigen. The C-terminal repeats-in-toxin domain (RTX) of ACT is sufficient to induce production of toxin-neutralizing antibodies. In this study, we characterized the effectiveness of vaccines containing the RTX antigen against experimental murine infection with B. pertussis RTX was not protective as a single-antigen vaccine against B. pertussis challenge, and adding RTX to 1/5 human dose of aP did not enhance protection. Since the doses of aP used in murine studies are not proportionate to mouse/human body masses, we titrated the aP from 1/20 to 1/160 of the human dose. Mice receiving 1/80 human aP dose had bacterial burden comparable to those of naive controls. Adding RTX antigen to the 1/80 aP base resulted in enhanced bacterial clearance. Inclusion of RTX induced production of antibodies recognizing RTX, enhanced production of anti-pertussis toxin, decreased secretion of proinflammatory cytokines, such as interleukin-6, and decreased recruitment of total macrophages in the lung. This study shows that adding RTX antigen to an appropriate dose of aP can enhance protection against B. pertussis challenge in mice.
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Affiliation(s)
- Dylan T Boehm
- Department of Microbiology, Immunology, and Cell Biology, West Virginia University, Morgantown, West Virginia, USA
- Vaccine Development Center at West Virginia University Health Sciences Center, Morgantown, West Virginia, USA
| | - Jesse M Hall
- Department of Microbiology, Immunology, and Cell Biology, West Virginia University, Morgantown, West Virginia, USA
- Vaccine Development Center at West Virginia University Health Sciences Center, Morgantown, West Virginia, USA
| | - Ting Y Wong
- Department of Microbiology, Immunology, and Cell Biology, West Virginia University, Morgantown, West Virginia, USA
- Vaccine Development Center at West Virginia University Health Sciences Center, Morgantown, West Virginia, USA
| | - Andrea M DiVenere
- Department of Chemical Engineering, University of Texas at Austin, Austin, Texas, USA
| | - Emel Sen-Kilic
- Department of Microbiology, Immunology, and Cell Biology, West Virginia University, Morgantown, West Virginia, USA
- Vaccine Development Center at West Virginia University Health Sciences Center, Morgantown, West Virginia, USA
| | - Justin R Bevere
- Department of Microbiology, Immunology, and Cell Biology, West Virginia University, Morgantown, West Virginia, USA
- Vaccine Development Center at West Virginia University Health Sciences Center, Morgantown, West Virginia, USA
| | - Shelby D Bradford
- Department of Microbiology, Immunology, and Cell Biology, West Virginia University, Morgantown, West Virginia, USA
- Vaccine Development Center at West Virginia University Health Sciences Center, Morgantown, West Virginia, USA
| | - Catherine B Blackwood
- Department of Microbiology, Immunology, and Cell Biology, West Virginia University, Morgantown, West Virginia, USA
- Vaccine Development Center at West Virginia University Health Sciences Center, Morgantown, West Virginia, USA
| | - Cody M Elkins
- Department of Microbiology, Immunology, and Cell Biology, West Virginia University, Morgantown, West Virginia, USA
| | - Katherine A DeRoos
- Department of Microbiology, Immunology, and Cell Biology, West Virginia University, Morgantown, West Virginia, USA
- Vaccine Development Center at West Virginia University Health Sciences Center, Morgantown, West Virginia, USA
| | - Mary C Gray
- Department of Medicine, Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, Virginia, USA
| | - C Garret Cooper
- Vaccine Development Center at West Virginia University Health Sciences Center, Morgantown, West Virginia, USA
- Department of Medicine, Section of Infectious Diseases, West Virginia University, Morgantown, West Virginia, USA
| | - Melinda E Varney
- Department of Microbiology, Immunology, and Cell Biology, West Virginia University, Morgantown, West Virginia, USA
- Vaccine Development Center at West Virginia University Health Sciences Center, Morgantown, West Virginia, USA
| | - Jennifer A Maynard
- Department of Chemical Engineering, University of Texas at Austin, Austin, Texas, USA
| | - Erik L Hewlett
- Department of Medicine, Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, Virginia, USA
| | - Mariette Barbier
- Department of Microbiology, Immunology, and Cell Biology, West Virginia University, Morgantown, West Virginia, USA
- Vaccine Development Center at West Virginia University Health Sciences Center, Morgantown, West Virginia, USA
| | - F Heath Damron
- Department of Microbiology, Immunology, and Cell Biology, West Virginia University, Morgantown, West Virginia, USA
- Vaccine Development Center at West Virginia University Health Sciences Center, Morgantown, West Virginia, USA
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Dienstbier A, Pouchnik D, Wildung M, Amman F, Hofacker IL, Parkhill J, Holubova J, Sebo P, Vecerek B. Comparative genomics of Czech vaccine strains of Bordetella pertussis. Pathog Dis 2018; 76:5089975. [PMID: 30184175 DOI: 10.1093/femspd/fty071] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2018] [Accepted: 08/30/2018] [Indexed: 11/13/2022] Open
Abstract
Bordetella pertussis is a strictly human pathogen causing the respiratory infectious disease called whooping cough or pertussis. B. pertussis adaptation to acellular pertussis vaccine pressure has been repeatedly highlighted, but recent data indicate that adaptation of circulating strains started already in the era of the whole cell pertussis vaccine (wP) use. We sequenced the genomes of five B. pertussis wP vaccine strains isolated in the former Czechoslovakia in the pre-wP (1954-1957) and early wP (1958-1965) eras, when only limited population travel into and out of the country was possible. Four isolates exhibit a similar genome organization and form a distinct phylogenetic cluster with a geographic signature. The fifth strain is rather distinct, both in genome organization and SNP-based phylogeny. Surprisingly, despite isolation of this strain before 1966, its closest sequenced relative appears to be a recent isolate from the US. On the genome content level, the five vaccine strains contained both new and already described regions of difference. One of the new regions contains duplicated genes potentially associated with transport across the membrane. The prevalence of this region in recent isolates indicates that its spread might be associated with selective advantage leading to increased strain fitness.
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Affiliation(s)
- Ana Dienstbier
- Institute of Microbiology v.v.i., Laboratory of post-transcriptional control of gene expression, 14220 Prague, Czech Republic
| | - Derek Pouchnik
- Laboratory for Biotechnology and Bioanalysis, Center for Reproductive Biology, Washington State University, Pullman, Washington 99164-7520
| | - Mark Wildung
- Laboratory for Biotechnology and Bioanalysis, Center for Reproductive Biology, Washington State University, Pullman, Washington 99164-7520
| | - Fabian Amman
- University of Vienna, Institute for Theoretical Chemistry, Währinger Straße 17, A-1090 Vienna, Austria
| | - Ivo L Hofacker
- University of Vienna, Institute for Theoretical Chemistry, Währinger Straße 17, A-1090 Vienna, Austria.,University of Vienna, Research group BCB, Faculty of Computer Science, Währinger Straße 24, 1090 Vienna, Austria
| | - Julian Parkhill
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SA Cambridge, UK
| | - Jana Holubova
- Institute of Microbiology v.v.i, Laboratory of molecular biology of bacterial pathogens, 14220 Prague, Czech Republic
| | - Peter Sebo
- Institute of Microbiology v.v.i, Laboratory of molecular biology of bacterial pathogens, 14220 Prague, Czech Republic
| | - Branislav Vecerek
- Institute of Microbiology v.v.i., Laboratory of post-transcriptional control of gene expression, 14220 Prague, Czech Republic
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45
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Pertussis Outbreak in a Primary School in China: Infection and Transmission of the Macrolide-resistant Bordetella pertussis. Pediatr Infect Dis J 2018; 37:e145-e148. [PMID: 29088029 DOI: 10.1097/inf.0000000000001814] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
BACKGROUND A pertussis outbreak was studied in a primary school in Xi'an, China, in March 2016. The school consisted of 536 pupils 6-12 years of age who were divided into 12 classes of 6 grades (2 classes for each grade). The identified index case was an 11-year-old girl at class 2 of grade 5. METHODS Interview was conducted and nasopharyngeal swabs were taken from all pupils (N = 94) in the 2 classes of grade 5. Nasopharyngeal swabs were tested by both culture and polymerase chain reaction (PCR). RESULTS Four culture- and 17 PCR-positive cases were identified in 94 pupils. Infection rate was significantly higher in class 2 compared with that in class 1 [37.0% (17/46) vs. 14.6% (7/48), χ(2) = 4.26, P < 0.05]. All Bordetella pertussis isolates were macrolide-resistant, harbored prn1/ptxP1/fim3-1 as previously reported and belonged to multilocus variable tandem repeat analysis type MLVA 195. Of the 17 DNAs positive for diagnostic PCR, 12 were also positive for 23S ribosomal RNA PCR. All the 12 DNAs had the A2047G mutation of 23S rRNA gene of B. pertussis. CONCLUSIONS This study described a pertussis outbreak caused by macrolide-resistant B. pertussis in a primary school and indicated that close contact of index case causes the bacterial transmission.
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Amman F, D'Halluin A, Antoine R, Huot L, Bibova I, Keidel K, Slupek S, Bouquet P, Coutte L, Caboche S, Locht C, Vecerek B, Hot D. Primary transcriptome analysis reveals importance of IS elements for the shaping of the transcriptional landscape of Bordetella pertussis. RNA Biol 2018; 15:967-975. [PMID: 29683387 PMCID: PMC6161684 DOI: 10.1080/15476286.2018.1462655] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Accepted: 04/03/2018] [Indexed: 12/25/2022] Open
Abstract
Bordetella pertussis is the causative agent of whooping cough, a respiratory disease still considered as a major public health threat and for which recent re-emergence has been observed. Constant reshuffling of Bordetella pertussis genome organization was observed during evolution. These rearrangements are essentially mediated by Insertion Sequences (IS), a mobile genetic elements present in more than 230 copies in the genome, which are supposed to be one of the driving forces enabling the pathogen to escape from vaccine-induced immunity. Here we use high-throughput sequencing approaches (RNA-seq and differential RNA-seq), to decipher Bordetella pertussis transcriptome characteristics and to evaluate the impact of IS elements on transcriptome architecture. Transcriptional organization was determined by identification of transcription start sites and revealed also a large variety of non-coding RNAs including sRNAs, leaderless mRNAs or long 3' and 5'UTR including seven riboswitches. Unusual topological organizations, such as overlapping 5'- or 3'-extremities between oppositely orientated mRNA were also unveiled. The pivotal role of IS elements in the transcriptome architecture and their effect on the transcription of neighboring genes was examined. This effect is mediated by the introduction of IS harbored promoters or by emergence of hybrid promoters. This study revealed that in addition to their impact on genome rearrangements, most of the IS also impact on the expression of their flanking genes. Furthermore, the transcripts produced by IS are strain-specific due to the strain to strain variation in IS copy number and genomic context.
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Affiliation(s)
- Fabian Amman
- University of Vienna, Theoretical Biochemistry Group, Institute for Theoretical Chemistry, Vienna, Austria
| | - Alexandre D'Halluin
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR8204 - CIIL - Center for Infection and Immunity of Lille, Lille, France
| | - Rudy Antoine
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR8204 - CIIL - Center for Infection and Immunity of Lille, Lille, France
| | - Ludovic Huot
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR8204 - CIIL - Center for Infection and Immunity of Lille, Lille, France
| | - Ilona Bibova
- Institute of Microbiology of the ASCR; Laboratory of post-transcriptional control of gene expression, Prague, Czech Republic
| | - Kristina Keidel
- Institute of Microbiology of the ASCR; Laboratory of post-transcriptional control of gene expression, Prague, Czech Republic
| | - Stéphanie Slupek
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR8204 - CIIL - Center for Infection and Immunity of Lille, Lille, France
| | - Peggy Bouquet
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR8204 - CIIL - Center for Infection and Immunity of Lille, Lille, France
| | - Loïc Coutte
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR8204 - CIIL - Center for Infection and Immunity of Lille, Lille, France
| | - Ségolène Caboche
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR8204 - CIIL - Center for Infection and Immunity of Lille, Lille, France
| | - Camille Locht
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR8204 - CIIL - Center for Infection and Immunity of Lille, Lille, France
| | - Branislav Vecerek
- Institute of Microbiology of the ASCR; Laboratory of post-transcriptional control of gene expression, Prague, Czech Republic
| | - David Hot
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR8204 - CIIL - Center for Infection and Immunity of Lille, Lille, France
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47
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Zomer A, Otsuka N, Hiramatsu Y, Kamachi K, Nishimura N, Ozaki T, Poolman J, Geurtsen J. Bordetella pertussis population dynamics and phylogeny in Japan after adoption of acellular pertussis vaccines. Microb Genom 2018; 4. [PMID: 29771235 PMCID: PMC5994715 DOI: 10.1099/mgen.0.000180] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Bordetella pertussis, the causative agent of whooping cough, has experienced a resurgence in the past 15 years, despite the existence of both whole-cell and acellular vaccines. Here, we performed whole genome sequencing analysis of 149 clinical strains, provided by the National Institute of Infectious Diseases (NIID), Japan, isolated in 1982–2014, after Japan became the first country to adopt acellular vaccines against B. pertussis. Additionally, we sequenced 39 strains provided by the Konan Kosei Hospital in Aichi prefecture, Japan, isolated in 2008–2013. The genome sequences afforded insight into B. pertussis genome variability and population dynamics in Japan, and revealed that the B. pertussis population in Japan was characterized by two major clades that divided more than 40 years ago. The pertactin gene was disrupted in about 20 % of the 149 NIID isolates, by either a deletion within the signal sequence (ΔSS) or the insertion of IS element IS481 (prn :: IS481). Phylogeny suggests that the parent clones for these isolates originated in Japan. Divergence dating traced the first generation of the pertactin-deficient mutants in Japan to around 1990, and indicated that strains containing the alternative pertactin allele prn2 may have appeared in Japan around 1974. Molecular clock data suggested that observed fluctuations in B. pertussis population size may have coincided with changes in vaccine usage in the country. The continuing failure to eradicate the disease warrants an exploration of novel vaccine compositions.
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Affiliation(s)
- Aldert Zomer
- 1Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Nao Otsuka
- 2Department of Bacteriology II, National Institute of Infectious Diseases, Musashimurayama, Tokyo, Japan
| | - Yukihiro Hiramatsu
- 2Department of Bacteriology II, National Institute of Infectious Diseases, Musashimurayama, Tokyo, Japan.,†Present address: Department of Molecular Bacteriology, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, Japan
| | - Kazunari Kamachi
- 2Department of Bacteriology II, National Institute of Infectious Diseases, Musashimurayama, Tokyo, Japan
| | - Naoko Nishimura
- 3Department of Pediatrics, Konan Kosei Hospital, Takaya-cho, Konan, Aichi, Japan
| | - Takao Ozaki
- 3Department of Pediatrics, Konan Kosei Hospital, Takaya-cho, Konan, Aichi, Japan
| | - Jan Poolman
- 4Janssen Vaccines and Prevention B.V., Leiden, The Netherlands
| | - Jeroen Geurtsen
- 4Janssen Vaccines and Prevention B.V., Leiden, The Netherlands
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Surveillance of Circulating Bordetella pertussis Strains in Europe during 1998 to 2015. J Clin Microbiol 2018; 56:JCM.01998-17. [PMID: 29491017 DOI: 10.1128/jcm.01998-17] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Accepted: 02/23/2018] [Indexed: 12/15/2022] Open
Abstract
One reason for increased pertussis incidence is the adaptation of Bordetella pertussis to vaccine-induced immunity by modulating its genomic structure. This study, EUpert IV, includes 265 isolates collected from nine European countries during 2012 to 2015 (n = 265) and compares the results to previous EUpert I to III studies (1998 to 2009). The analyses included genotyping, serotyping, pulsed-field gel electrophoresis (PFGE), and multilocus variable-number tandem-repeat analysis (MLVA). Genotyping results showed only small variations among the common virulence genes of B. pertussis The frequencies of serotypes Fim2 and Fim3 varied among the four collections. Genomic analyses showed that MLVA type 27 increased to 80% between the periods of 1998 to 2001 and 2012 to 2015. Two PFGE profiles, BpSR3 (29.4%) and BpSR10 (27.2%), constituted more than 50% of the circulating isolates in the present collection. Our study indicates that the European B. pertussis population is changing and became more homogenous after the introduction of acellular pertussis vaccines.
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49
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Luu LDW, Octavia S, Zhong L, Raftery MJ, Sintchenko V, Lan R. Proteomic Adaptation of Australian Epidemic Bordetella pertussis. Proteomics 2018; 18:e1700237. [PMID: 29464899 DOI: 10.1002/pmic.201700237] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Revised: 02/08/2018] [Indexed: 12/20/2022]
Abstract
Bordetella pertussis causes whooping cough. The predominant strains in Australia changed to single nucleotide polymorphism (SNP) cluster I (pertussis toxin promoter allele ptxP3/pertactin gene allele prn2) from cluster II (non-ptxP3/non-prn2). Cluster I was mostly responsible for the 2008-2012 Australian epidemic and was found to have higher fitness compared to cluster II using an in vivo mouse competition assay, regardless of host's immunization status. This study aimed to identify proteomic differences that explain higher fitness in cluster I using isobaric tags for relative and absolute quantification (iTRAQ), and high-resolution multiple reaction monitoring (MRM-hr). A few key differences in the whole cell and secretome were identified between the cluster I and II strains tested. In the whole cell, nine proteins were upregulated (>1.2 fold change, q < 0.05) and three were downregulated (<0.8 fold change, q < 0.05) in cluster I. One downregulated protein was BP1569, a TLR2 agonist for Th1 immunity. In the secretome, 12 proteins were upregulated and 1 was downregulated which was Bsp22, a type III secretion system (T3SS) protein. Furthermore, there was a trend of downregulation in three T3SS effectors and other virulence factors. Three proteins were upregulated in both whole cell and supernatant: BP0200, molybdate ABC transporter (ModB), and tracheal colonization factor A (TcfA). Important expression differences in lipoprotein, T3SS, and transport proteins between the cluster I and II strains were identified. These differences may affect immune evasion, virulence and metabolism, and play a role in increased fitness of cluster I.
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Affiliation(s)
- Laurence Don Wai Luu
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Sophie Octavia
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Ling Zhong
- Mark Wainwright Analytical Centre, University of New South Wales, Sydney, New South Wales, Australia
| | - Mark J Raftery
- Mark Wainwright Analytical Centre, University of New South Wales, Sydney, New South Wales, Australia
| | - Vitali Sintchenko
- Centre for Infectious Diseases and Microbiology-Public Health, Institute of Clinical Pathology and Medical Research-Pathology West, Westmead Hospital, New South Wales, Australia
- Marie Bashir Institute for Infectious Diseases and Biosecurity, Sydney Medical School, University of Sydney, New South Wales, Australia
| | - Ruiting Lan
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
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50
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Screening and Genomic Characterization of Filamentous Hemagglutinin-Deficient Bordetella pertussis. Infect Immun 2018; 86:IAI.00869-17. [PMID: 29358336 DOI: 10.1128/iai.00869-17] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Accepted: 01/18/2018] [Indexed: 11/20/2022] Open
Abstract
Despite high vaccine coverage, pertussis cases in the United States have increased over the last decade. Growing evidence suggests that disease resurgence results, in part, from genetic divergence of circulating strain populations away from vaccine references. The United States employs acellular vaccines exclusively, and current Bordetella pertussis isolates are predominantly deficient in at least one immunogen, pertactin (Prn). First detected in the United States retrospectively in a 1994 isolate, the rapid spread of Prn deficiency is likely vaccine driven, raising concerns about whether other acellular vaccine immunogens experience similar pressures, as further antigenic changes could potentially threaten vaccine efficacy. We developed an electrochemiluminescent antibody capture assay to monitor the production of the acellular vaccine immunogen filamentous hemagglutinin (Fha). Screening 722 U.S. surveillance isolates collected from 2010 to 2016 identified two that were both Prn and Fha deficient. Three additional Fha-deficient laboratory strains were also identified from a historic collection of 65 isolates dating back to 1935. Whole-genome sequencing of deficient isolates revealed putative, underlying genetic changes. Only four isolates harbored mutations to known genes involved in Fha production, highlighting the complexity of its regulation. The chromosomes of two Fha-deficient isolates included unexpected structural variation that did not appear to influence Fha production. Furthermore, insertion sequence disruption of fhaB was also detected in a previously identified pertussis toxin-deficient isolate that still produced normal levels of Fha. These results demonstrate the genetic potential for additional vaccine immunogen deficiency and underscore the importance of continued surveillance of circulating B. pertussis evolution in response to vaccine pressure.
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