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Liu Y, Jiang B, Guo Y, Gao Y, Qian J, Qie C, Shao Z, Li Y, Wu Q. Analysis of prevailing pertussis strains from different regions in China after the application of acellular vaccines. Chin Med J (Engl) 2023:00029330-990000000-00618. [PMID: 37200036 DOI: 10.1097/cm9.0000000000002244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Indexed: 05/19/2023] Open
Affiliation(s)
- Yamin Liu
- Department of Respiratory, Tianjin Medical University General Hospital, Tianjin 300052, China
- Institute of Hepatology, Tianjin Second People's Hospital, Tianjin 300192, China
- Department of Infectious Disease, Clinical School of the Second People's Hospital, Tianjin Medical University, Tianjin 300192, China
| | - Bei Jiang
- Institute of Hepatology, Tianjin Second People's Hospital, Tianjin 300192, China
- Department of Infectious Disease, Clinical School of the Second People's Hospital, Tianjin Medical University, Tianjin 300192, China
| | - Yu Guo
- Department of Clinical Laboratory, Nankai Hospital, Tianjin 300100, China
| | - Yuan Gao
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
- State Key Laboratory for Infectious Disease Prevention and Control, Beijing 102206, China
| | - Jing Qian
- Institute of Hepatology, Tianjin Second People's Hospital, Tianjin 300192, China
- Department of Infectious Disease, Clinical School of the Second People's Hospital, Tianjin Medical University, Tianjin 300192, China
| | - Chunhua Qie
- Institute of Hepatology, Tianjin Second People's Hospital, Tianjin 300192, China
- Department of Infectious Disease, Clinical School of the Second People's Hospital, Tianjin Medical University, Tianjin 300192, China
| | - Zhujun Shao
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
- State Key Laboratory for Infectious Disease Prevention and Control, Beijing 102206, China
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, Zhejiang 310005, China
| | - Ying Li
- Institute of Hepatology, Tianjin Second People's Hospital, Tianjin 300192, China
- Department of Infectious Disease, Clinical School of the Second People's Hospital, Tianjin Medical University, Tianjin 300192, China
| | - Qi Wu
- Department of Respiratory, Tianjin Medical University General Hospital, Tianjin 300052, China
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2
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Bridel S, Bouchez V, Brancotte B, Hauck S, Armatys N, Landier A, Mühle E, Guillot S, Toubiana J, Maiden MCJ, Jolley KA, Brisse S. A comprehensive resource for Bordetella genomic epidemiology and biodiversity studies. Nat Commun 2022; 13:3807. [PMID: 35778384 PMCID: PMC9249784 DOI: 10.1038/s41467-022-31517-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 06/21/2022] [Indexed: 11/09/2022] Open
Abstract
The genus Bordetella includes bacteria that are found in the environment and/or associated with humans and other animals. A few closely related species, including Bordetella pertussis, are human pathogens that cause diseases such as whooping cough. Here, we present a large database of Bordetella isolates and genomes and develop genotyping systems for the genus and for the B. pertussis clade. To generate the database, we merge previously existing databases from Oxford University and Institut Pasteur, import genomes from public repositories, and add 83 newly sequenced B. bronchiseptica genomes. The public database currently includes 2582 Bordetella isolates and their provenance data, and 2085 genomes ( https://bigsdb.pasteur.fr/bordetella/ ). We use core-genome multilocus sequence typing (cgMLST) to develop genotyping systems for the whole genus and for B. pertussis, as well as specific schemes to define antigenic, virulence and macrolide resistance profiles. Phylogenetic analyses allow us to redefine evolutionary relationships among known Bordetella species, and to propose potential new species. Our database provides an expandable resource for genotyping of environmental and clinical Bordetella isolates, thus facilitating evolutionary and epidemiological research on whooping cough and other Bordetella infections.
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Affiliation(s)
- Sébastien Bridel
- Institut Pasteur, Université Paris Cité, Biodiversity and Epidemiology of Bacterial Pathogens, Paris, France
| | - Valérie Bouchez
- Institut Pasteur, Université Paris Cité, Biodiversity and Epidemiology of Bacterial Pathogens, Paris, France.,National Reference Center for Whooping Cough and other Bordetella Infections, Institut Pasteur, Paris, France
| | - Bryan Brancotte
- Institut Pasteur, Université Paris Cité, Bioinformatics and Biostatistics Hub, F-75015, Paris, France
| | - Sofia Hauck
- Department of Zoology, University of Oxford, 11a Mansfield Road, Oxford, OX1 3SZ, UK
| | - Nathalie Armatys
- Institut Pasteur, Université Paris Cité, Biodiversity and Epidemiology of Bacterial Pathogens, Paris, France.,National Reference Center for Whooping Cough and other Bordetella Infections, Institut Pasteur, Paris, France
| | - Annie Landier
- Institut Pasteur, Université Paris Cité, Biodiversity and Epidemiology of Bacterial Pathogens, Paris, France.,National Reference Center for Whooping Cough and other Bordetella Infections, Institut Pasteur, Paris, France
| | - Estelle Mühle
- Collection de l´Institut Pasteur, Institut Pasteur, Université Paris Cité, Paris, France
| | - Sophie Guillot
- Institut Pasteur, Université Paris Cité, Biodiversity and Epidemiology of Bacterial Pathogens, Paris, France.,National Reference Center for Whooping Cough and other Bordetella Infections, Institut Pasteur, Paris, France
| | - Julie Toubiana
- Institut Pasteur, Université Paris Cité, Biodiversity and Epidemiology of Bacterial Pathogens, Paris, France.,National Reference Center for Whooping Cough and other Bordetella Infections, Institut Pasteur, Paris, France.,Department of General Pediatrics and Pediatric Infectious Diseases, Université Paris Cité, Hôpital Necker-Enfants Malades, APHP, Paris, France
| | - Martin C J Maiden
- Department of Zoology, University of Oxford, 11a Mansfield Road, Oxford, OX1 3SZ, UK
| | - Keith A Jolley
- Department of Zoology, University of Oxford, 11a Mansfield Road, Oxford, OX1 3SZ, UK
| | - Sylvain Brisse
- Institut Pasteur, Université Paris Cité, Biodiversity and Epidemiology of Bacterial Pathogens, Paris, France. .,National Reference Center for Whooping Cough and other Bordetella Infections, Institut Pasteur, Paris, France.
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3
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Wu S, Hu Q, Yang C, Zhou H, Chen H, Zhang Y, Jiang M, He Y, Shi X. Molecular epidemiology of Bordetella pertussis and analysis of vaccine antigen genes from clinical isolates from Shenzhen, China. Ann Clin Microbiol Antimicrob 2021; 20:53. [PMID: 34407803 PMCID: PMC8371876 DOI: 10.1186/s12941-021-00458-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 07/28/2021] [Indexed: 11/10/2022] Open
Abstract
Background Although pertussis cases globally have been controlled through the Expanded Programme on Immunization (EPI), the incidence of pertussis has increased significantly in recent years, with a “resurgence” of pertussis occurring in developed countries with high immunization coverage. Attracted by its fast-developing economy, the population of Shenzhen has reached 14 million and has become one of the top five largest cities by population size in China. The incidence of pertussis here was about 2.02/100,000, far exceeding that of the whole province and the whole country (both < 1/100,000). There are increasing numbers of reports demonstrating variation in Bordetella pertussis antigens and genes, which may be associated with the increased incidence. Fifty strains of Bordetella pertussis isolated from 387 suspected cases were collected in Shenzhen in 2018 for genotypic and molecular epidemiological analysis. Methods There were 387 suspected cases of pertussis enrolled at surveillance sites in Shenzhen from June to August 2018. Nasopharyngeal swabs from suspected pertussis cases were collected for bacterial culture and the identity of putative Bordetella pertussis isolates was confirmed by real-time PCR. The immunization history of each patient was taken. The acellular pertussis vaccine (APV) antigen genes for pertussis toxin (ptxA, ptxC), pertactin (prn) and fimbriae (fim2 and fim3) together with the pertussis toxin promoter region (ptxP) were analyzed by second-generation sequencing. Genetic and phylogenetic analysis was performed using sequences publicly available from GenBank, National Institutes of Health, Bethesda, MD, USA (https://www.ncbi.nlm.nih.gov/genbank/). The antimicrobial susceptibility was test by Kirby-Bauer disk diffusion. Results Fifty strains of Bordetella pertussis were successfully isolated from nasopharyngeal swabs of 387 suspected cases, with a positivity rate of 16.79%, including 28 males and 22 females, accounting for 56.0% and 44.0% respectively. Thirty-eight of the 50 (76%) patients were found to be positive for B. pertussis by culture. Among the positive cases with a history of vaccination, 30 of 42 (71.4%) cases had an incomplete pertussis vaccination history according to the national recommendation. Three phylogenetic groups (PG1-PG3) were identified each containing a predominant genotype. The two vaccines strains, CS and Tohama I, were distantly related to these three groups. Thirty-one out of fifty (62%) isolates belonged to genotype PG1, with the allelic profile prn2/ptxC2/ptxP3/ptxA1/fim3-1/fim2-1. Eighteen out of fifty (36%) isolates contained the A2047G mutation and were highly resistant to erythromycin, and all belonged to genotype PG3 (prn1/ptxA1/ptxP1/ptxC1/fim3-1/fim2-1), which is closely related to the recent epidemic strains found in northern China. Conclusions The positive rate of cases under one-year-old was significantly higher than that of other age groups and should be monitored. The dominant antigen genotypes of 50 Shenzhen isolates are closely related to the epidemic strains in the United States, Australia and many countries in Europe. Despite high rates of immunization with APV, epidemics of pertussis have recently occurred in these countries. Therefore, genomic analysis of circulating isolates of B. pertussis should be continued, for it will benefit the control of whooping cough and development of improved vaccines and therapeutic strategies.
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Affiliation(s)
- Shuang Wu
- Shenzhen Center for Disease Control and Prevention, 8 Longyuan Road, Nanshan District, Shenzhen, China
| | - Qinghua Hu
- Shenzhen Center for Disease Control and Prevention, 8 Longyuan Road, Nanshan District, Shenzhen, China
| | - Chao Yang
- Shenzhen Center for Disease Control and Prevention, 8 Longyuan Road, Nanshan District, Shenzhen, China
| | - Haijian Zhou
- National Institute for Communicable Disease Control and Prevention (ICDC) of China CDC, Beijing, China
| | - Hongyu Chen
- Shenzhen Children's Hospital, Shenzhen, China
| | - Yanwei Zhang
- Shenzhen Center for Disease Control and Prevention, 8 Longyuan Road, Nanshan District, Shenzhen, China
| | - Min Jiang
- Shenzhen Center for Disease Control and Prevention, 8 Longyuan Road, Nanshan District, Shenzhen, China
| | - Yuxiang He
- Shenzhen Center for Disease Control and Prevention, 8 Longyuan Road, Nanshan District, Shenzhen, China
| | - Xiaolu Shi
- Shenzhen Center for Disease Control and Prevention, 8 Longyuan Road, Nanshan District, Shenzhen, China.
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4
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Safarchi A, Octavia S, Nikbin VS, Lotfi MN, Zahraei SM, Tay CY, Lamichhane B, Shahcheraghi F, Lan R. Genomic epidemiology of Iranian Bordetella pertussis: 50 years after the implementation of whole cell vaccine. Emerg Microbes Infect 2020; 8:1416-1427. [PMID: 31543006 PMCID: PMC6764348 DOI: 10.1080/22221751.2019.1665479] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Pertussis caused by Bordetella pertussis, remains a public health problem worldwide, despite high vaccine coverage in infants and children in many countries. Iran has been using whole cell vaccine for the last 50 years with more than 95% vaccination rate since 1988 and has experienced pertussis resurgence in recent years. Here, we sequenced 55 B. pertussis isolates mostly collected from three provinces with the highest number of pertussis cases in Iran, including Tehran, Mazandaran, and Eastern-Azarbayjan from the period of 2008-2016. Most isolates carried ptxP3/prn2 alleles (42/55, 76%), the same genotype as isolates circulating in acellular vaccine-administrating countries. The second most frequent genotype was ptxP3/prn9 (8/55, 14%). Only three isolates (5%) were ptxP1. Phylogenetic analysis showed that Iranian ptxP3 isolates can be divided into eight clades (Clades 1-8) with no temporal association. Most of the isolates from Tehran grouped together as one distinctive clade (Clade 8) with six unique single nucleotide polymorphisms (SNPs). In addition, the prn9 isolates were grouped together as Clade 5 with 12 clade-supporting SNPs. No pertactin deficient isolates were found among the 55 Iranian isolates. Our findings suggest that there is an ongoing adaptation and evolution of B. pertussis regardless of the types of vaccine used.
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Affiliation(s)
- Azadeh Safarchi
- Pertussis Reference Laboratory, Department of Bacteriology, Pasteur Institute of Iran , Tehran , Islamic Republic of Iran.,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
| | - Vajihe Sadat Nikbin
- Pertussis Reference Laboratory, Department of Bacteriology, Pasteur Institute of Iran , Tehran , Islamic Republic of Iran
| | - Masoumeh Nakhost Lotfi
- Pertussis Reference Laboratory, Department of Bacteriology, Pasteur Institute of Iran , Tehran , Islamic Republic of Iran
| | - Seyed Mohsen Zahraei
- Centre for Communicable Disease Control, Ministry of Health and Medical Education , Tehran , Islamic Republic of Iran
| | - Chin Yen Tay
- Pathology and Laboratory Medicine, University of Western Australia , Perth , Australia
| | - Binit Lamichhane
- Pathology and Laboratory Medicine, University of Western Australia , Perth , Australia
| | - Fereshteh Shahcheraghi
- Pertussis Reference Laboratory, Department of Bacteriology, Pasteur Institute of Iran , Tehran , Islamic Republic of Iran
| | - Ruiting Lan
- School of Biotechnology and Biomolecular Sciences, University of New South Wales , Sydney , Australia
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5
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Abstract
Whole-cell and acellular pertussis vaccines are used globally against Bordetella pertussis. Various vaccine reference strains are used globally for the production of such vaccines. Whole-cell and acellular pertussis vaccines are used globally against Bordetella pertussis. Various vaccine reference strains are used globally for the production of such vaccines. We report here a draft genome sequence for Bordetella pertussis strain BP 165, which is used by the Serum Institute of India in the production of acellular pertussis vaccine.
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6
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Shi W, Kou Y, Jiang H, Gao F, Kong W, Su W, Xu F, Jiang C. Novel intranasal pertussis vaccine based on bacterium-like particles as a mucosal adjuvant. Immunol Lett 2018; 198:26-32. [PMID: 29601940 DOI: 10.1016/j.imlet.2018.03.012] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Revised: 03/08/2018] [Accepted: 03/23/2018] [Indexed: 12/31/2022]
Abstract
Pertussis, or whooping cough, has recently reemerged as a major public health threat despite high levels of vaccination. The development of a novel pertussis vaccine, especially an intranasal (i.n.) vaccine is undoubtedly necessary, and mucosal adjuvants have been explored to enhance the immune response. In the present study, bacterium-like particles (BLPs) were adopted as a mucosal adjuvant for an i.n. pertussis vaccine and evaluated on the ability to induce serum and mucosal antibodies as well as potency against i.n. challenge in mice. Groups with or without aluminum adjuvant were also evaluated through both i.n. and intraperitoneal inoculations. Vaccination with BLPs via the i.n. route led to rapid IgG and IgA production and provided strong protection against inflammation induced by infection. The results support an i.n. pertussis vaccine with BLPs adjuvant as a promising candidate to elicit protective immunity against whooping cough.
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Affiliation(s)
- Wei Shi
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun 130012, P.R. China
| | - Yiming Kou
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun 130012, P.R. China
| | - Hao Jiang
- The Third Hospital of Jilin University, Jilin University, Changchun 130012, P.R. China
| | - Feng Gao
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun 130012, P.R. China; Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, School of Life Sciences, Jilin University, Changchun 130012, P.R. China
| | - Wei Kong
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun 130012, P.R. China; Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, School of Life Sciences, Jilin University, Changchun 130012, P.R. China
| | - Weiheng Su
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun 130012, P.R. China; Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, School of Life Sciences, Jilin University, Changchun 130012, P.R. China
| | - Fei Xu
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun 130012, P.R. China; Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, School of Life Sciences, Jilin University, Changchun 130012, P.R. China.
| | - Chunlai Jiang
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun 130012, P.R. China; Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, School of Life Sciences, Jilin University, Changchun 130012, P.R. China.
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7
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Branco Dos Santos F, Olivier BG, Boele J, Smessaert V, De Rop P, Krumpochova P, Klau GW, Giera M, Dehottay P, Teusink B, Goffin P. Probing the Genome-Scale Metabolic Landscape of Bordetella pertussis, the Causative Agent of Whooping Cough. Appl Environ Microbiol 2017; 83:e01528-17. [PMID: 28842544 PMCID: PMC5648915 DOI: 10.1128/aem.01528-17] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Accepted: 08/23/2017] [Indexed: 11/20/2022] Open
Abstract
Whooping cough is a highly contagious respiratory disease caused by Bordetella pertussis Despite widespread vaccination, its incidence has been rising alarmingly, and yet, the physiology of B. pertussis remains poorly understood. We combined genome-scale metabolic reconstruction, a novel optimization algorithm, and experimental data to probe the full metabolic potential of this pathogen, using B. pertussis strain Tohama I as a reference. Experimental validation showed that B. pertussis secretes a significant proportion of nitrogen as arginine and purine nucleosides, which may contribute to modulation of the host response. We also found that B. pertussis can be unexpectedly versatile, being able to metabolize many compounds while displaying minimal nutrient requirements. It can grow without cysteine, using inorganic sulfur sources, such as thiosulfate, and it can grow on organic acids, such as citrate or lactate, as sole carbon sources, providing in vivo demonstration that its tricarboxylic acid (TCA) cycle is functional. Although the metabolic reconstruction of eight additional strains indicates that the structural genes underlying this metabolic flexibility are widespread, experimental validation suggests a role of strain-specific regulatory mechanisms in shaping metabolic capabilities. Among five alternative strains tested, three strains were shown to grow on substrate combinations requiring a functional TCA cycle, but only one strain could use thiosulfate. Finally, the metabolic model was used to rationally design growth media with >2-fold improvements in pertussis toxin production. This study thus provides novel insights into B. pertussis physiology and highlights the potential, but also the limitations, of models based solely on metabolic gene content.IMPORTANCE The metabolic capabilities of Bordetella pertussis, the causative agent of whooping cough, were investigated from a systems-level perspective. We constructed a comprehensive genome-scale metabolic model for B. pertussis and challenged its predictions experimentally. This systems approach shed light on new potential host-microbe interactions and allowed us to rationally design novel growth media with >2-fold improvements in pertussis toxin production. Most importantly, we also uncovered the potential for metabolic flexibility of B. pertussis (significantly larger range of substrates than previously alleged; novel active pathways allowing growth in minimal, nearly mineral nutrient combinations where only the carbon source must be organic), although our results also highlight the importance of strain-specific regulatory determinants in shaping metabolic capabilities. Deciphering the underlying regulatory mechanisms appears to be crucial for a comprehensive understanding of B. pertussis's lifestyle and the epidemiology of whooping cough. The contribution of metabolic models in this context will require the extension of the genome-scale metabolic model to integrate this regulatory dimension.
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Affiliation(s)
- Filipe Branco Dos Santos
- Systems Bioinformatics/AIMMS, Vrije University Amsterdam, Amsterdam, The Netherlands
- Molecular Microbial Physiology, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - Brett G Olivier
- Systems Bioinformatics/AIMMS, Vrije University Amsterdam, Amsterdam, The Netherlands
- Centrum Wiskunde & Informatica (CWI), Amsterdam, The Netherlands
| | - Joost Boele
- Systems Bioinformatics/AIMMS, Vrije University Amsterdam, Amsterdam, The Netherlands
| | | | | | - Petra Krumpochova
- Systems Bioinformatics/AIMMS, Vrije University Amsterdam, Amsterdam, The Netherlands
| | - Gunnar W Klau
- Centrum Wiskunde & Informatica (CWI), Amsterdam, The Netherlands
- Algorithmic Bioinformatics, Heinrich Heine University, Düsseldorf, Germany
| | - Martin Giera
- Systems Bioinformatics/AIMMS, Vrije University Amsterdam, Amsterdam, The Netherlands
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
| | | | - Bas Teusink
- Systems Bioinformatics/AIMMS, Vrije University Amsterdam, Amsterdam, The Netherlands
| | - Philippe Goffin
- GSK Vaccines, Rixensart, Belgium
- Laboratoire de Génétique et Physiologie Bactérienne, IBMM, Faculté des Sciences, Université Libre de Bruxelles (ULB), Gosselies, Belgium
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8
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Oh H, Shin J, Ato M, Ma X, Williams D, Han K, Kim YJ, Kang H, Jung K, Hanada K, Ochiai M, Hung PV, Park S, Ahn C. The First Meeting of the National Control Laboratories for Vaccines and Biologicals in the Western Pacific in 2016. Osong Public Health Res Perspect 2017. [PMCID: PMC5402844 DOI: 10.24171/j.phrp.2017.8.1.13] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Affiliation(s)
- Hokyung Oh
- Blood Products Division, National Institute of Food and Drug Safety Evaluation, Ministry of Food and Drug Safety, Cheongju, Korea
| | - Jinho Shin
- World Health Organization, Regional Office for the Western Pacific, Manila, Philippines
| | - Manabu Ato
- National Institute of Infectious Diseases, Tokyo, Japan
| | - Xiao Ma
- National Institutes for Food and Drug Control, China Food and Drug Administration, Beijing, China
| | - David Williams
- Department of Pharmacology and Therapeutics, University of Melbourne, Parkville, VIC, Australia
| | - Kiwon Han
- Blood Products Division, National Institute of Food and Drug Safety Evaluation, Ministry of Food and Drug Safety, Cheongju, Korea
| | - Yang Jin Kim
- Department of Statistics, Sookmyung Women’s University College of Science, Seoul, Korea
| | - Hyunggoo Kang
- Department of Emergency Medicine, Hanyang University College of Medicine, Seoul, Korea
| | - Kikyung Jung
- Blood Products Division, National Institute of Food and Drug Safety Evaluation, Ministry of Food and Drug Safety, Cheongju, Korea
| | | | - Masaki Ochiai
- National Institute of Infectious Diseases, Tokyo, Japan
| | - Pham Van Hung
- National Institute for Control of Vaccine and Biological, Ministry of Health Vietnam, Hanoi, Vietnam
| | - Sangmi Park
- Blood Products Division, National Institute of Food and Drug Safety Evaluation, Ministry of Food and Drug Safety, Cheongju, Korea
- Department of Manufacturing Pharmacy, Chungbuk National University College of Pharmacy, Cheongju, Korea
| | - Chiyoung Ahn
- Blood Products Division, National Institute of Food and Drug Safety Evaluation, Ministry of Food and Drug Safety, Cheongju, Korea
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9
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Linz B, Ivanov YV, Preston A, Brinkac L, Parkhill J, Kim M, Harris SR, Goodfield LL, Fry NK, Gorringe AR, Nicholson TL, Register KB, Losada L, Harvill ET. Acquisition and loss of virulence-associated factors during genome evolution and speciation in three clades of Bordetella species. BMC Genomics 2016; 17:767. [PMID: 27716057 PMCID: PMC5045587 DOI: 10.1186/s12864-016-3112-5] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2015] [Accepted: 09/23/2016] [Indexed: 11/10/2022] Open
Abstract
Background The genus Bordetella consists of nine species that include important respiratory pathogens such as the ‘classical’ species B. bronchiseptica, B. pertussis and B. parapertussis and six more distantly related and less extensively studied species. Here we analyze sequence diversity and gene content of 128 genome sequences from all nine species with focus on the evolution of virulence-associated factors. Results Both genome-wide sequence-based and gene content-based phylogenetic trees divide the genus into three species clades. The phylogenies are congruent between species suggesting genus-wide co-evolution of sequence diversity and gene content, but less correlated within species, mainly because of strain-specific presence of many different prophages. We compared the genomes with focus on virulence-associated genes and identified multiple clade-specific, species-specific and strain-specific events of gene acquisition and gene loss, including genes encoding O-antigens, protein secretion systems and bacterial toxins. Gene loss was more frequent than gene gain throughout the evolution, and loss of hundreds of genes was associated with the origin of several species, including the recently evolved human-restricted B. pertussis and B. holmesii, B. parapertussis and the avian pathogen B. avium. Conclusions Acquisition and loss of multiple genes drive the evolution and speciation in the genus Bordetella, including large scale gene loss associated with the origin of several species. Recent loss and functional inactivation of genes, including those encoding pertussis vaccine components and bacterial toxins, in individual strains emphasize ongoing evolution. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3112-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Bodo Linz
- Department of Veterinary and Biomedical Sciences, Pennsylvania State University, University Park, PA 16802, USA.
| | - Yury V Ivanov
- Department of Veterinary and Biomedical Sciences, Pennsylvania State University, University Park, PA 16802, USA
| | - Andrew Preston
- The Millner Centre for Evolution and Department of Biology and Biochemistry, University of Bath, Bath, UK
| | | | - Julian Parkhill
- Pathogen Genomics, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | - Maria Kim
- J. Craig Venter Institute, Rockville, MD, USA
| | - Simon R Harris
- Pathogen Genomics, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | - Laura L Goodfield
- Department of Veterinary and Biomedical Sciences, Pennsylvania State University, University Park, PA 16802, USA
| | - Norman K Fry
- Public Health England, Respiratory and Vaccine Preventable Bacteria Reference Unit, London, UK
| | | | - Tracy L Nicholson
- USDA, Agricultural Research Service, National Animal Disease Center, Ames, IA, USA
| | - Karen B Register
- USDA, Agricultural Research Service, National Animal Disease Center, Ames, IA, USA
| | | | - Eric T Harvill
- Department of Veterinary and Biomedical Sciences, Pennsylvania State University, University Park, PA 16802, USA. .,Singapore Centre on Environmental Life Sciences Engineering, Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore 637551, Singapore. .,Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA 30602, USA.
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10
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Bowden KE, Weigand MR, Peng Y, Cassiday PK, Sammons S, Knipe K, Rowe LA, Loparev V, Sheth M, Weening K, Tondella ML, Williams MM. Genome Structural Diversity among 31 Bordetella pertussis Isolates from Two Recent U.S. Whooping Cough Statewide Epidemics. mSphere 2016; 1:e00036-16. [PMID: 27303739 PMCID: PMC4888882 DOI: 10.1128/msphere.00036-16] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Accepted: 04/03/2016] [Indexed: 11/20/2022] Open
Abstract
During 2010 and 2012, California and Vermont, respectively, experienced statewide epidemics of pertussis with differences seen in the demographic affected, case clinical presentation, and molecular epidemiology of the circulating strains. To overcome limitations of the current molecular typing methods for pertussis, we utilized whole-genome sequencing to gain a broader understanding of how current circulating strains are causing large epidemics. Through the use of combined next-generation sequencing technologies, this study compared de novo, single-contig genome assemblies from 31 out of 33 Bordetella pertussis isolates collected during two separate pertussis statewide epidemics and 2 resequenced vaccine strains. Final genome architecture assemblies were verified with whole-genome optical mapping. Sixteen distinct genome rearrangement profiles were observed in epidemic isolate genomes, all of which were distinct from the genome structures of the two resequenced vaccine strains. These rearrangements appear to be mediated by repetitive sequence elements, such as high-copy-number mobile genetic elements and rRNA operons. Additionally, novel and previously identified single nucleotide polymorphisms were detected in 10 virulence-related genes in the epidemic isolates. Whole-genome variation analysis identified state-specific variants, and coding regions bearing nonsynonymous mutations were classified into functional annotated orthologous groups. Comprehensive studies on whole genomes are needed to understand the resurgence of pertussis and develop novel tools to better characterize the molecular epidemiology of evolving B. pertussis populations. IMPORTANCE Pertussis, or whooping cough, is the most poorly controlled vaccine-preventable bacterial disease in the United States, which has experienced a resurgence for more than a decade. Once viewed as a monomorphic pathogen, B. pertussis strains circulating during epidemics exhibit diversity visible on a genome structural level, previously undetectable by traditional sequence analysis using short-read technologies. For the first time, we combine short- and long-read sequencing platforms with restriction optical mapping for single-contig, de novo assembly of 31 isolates to investigate two geographically and temporally independent U.S. pertussis epidemics. These complete genomes reshape our understanding of B. pertussis evolution and strengthen molecular epidemiology toward one day understanding the resurgence of pertussis.
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Affiliation(s)
- Katherine E. Bowden
- Division of Bacterial Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Michael R. Weigand
- Division of Bacterial Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Yanhui Peng
- Division of Bacterial Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Pamela K. Cassiday
- Division of Bacterial Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Scott Sammons
- Biotechnology Core Facility Branch, Division of Scientific Resources, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Kristen Knipe
- Biotechnology Core Facility Branch, Division of Scientific Resources, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Lori A. Rowe
- Biotechnology Core Facility Branch, Division of Scientific Resources, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Vladimir Loparev
- Biotechnology Core Facility Branch, Division of Scientific Resources, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Mili Sheth
- Biotechnology Core Facility Branch, Division of Scientific Resources, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Keeley Weening
- Vermont Department of Health Laboratory, Burlington, Vermont, USA
| | - M. Lucia Tondella
- 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
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11
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Safarchi A, Octavia S, Wu SZ, Kaur S, Sintchenko V, Gilbert GL, Wood N, McIntyre P, Marshall H, Keil AD, Lan R. Genomic dissection of Australian Bordetella pertussis isolates from the 2008-2012 epidemic. J Infect 2016; 72:468-77. [PMID: 26826518 DOI: 10.1016/j.jinf.2016.01.005] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Revised: 12/15/2015] [Accepted: 01/14/2016] [Indexed: 11/24/2022]
Abstract
OBJECTIVES Despite high pertussis vaccination coverage, Australia experienced a prolonged epidemic in 2008-2012. The predominant Bordetella pertussis genotype harboured pertussis toxin promoter allele, ptxP3, and pertactin gene allele, prn2. The emergence and expansion of prn non-expressing isolates (Prn negative), were also observed. We aimed to investigate the microevolution and genomic diversity of epidemic B. pertussis isolates. METHODS We sequenced 22 B. pertussis isolates collected in 2008-2012 from two states of Australia which are geographically widely separated. Ten of the 22 were Prn negative isolates with three different modes of silencing of prn (prn::IS481F, prn::IS481R and prn::IS1002). Five pre-epidemic isolates were also sequenced for comparison. RESULTS Five single nucleotide polymorphisms were common in the epidemic isolates and differentiated them from pre-epidemic isolates. The Australian epidemic isolates can be divided into five lineages (EL1-EL5) with EL1 containing only Prn negative isolates. Comparison with global isolates showed that three lineages remained geographically and temporally distinct whereas two lineages mixed with isolates from 2012 UK outbreak. CONCLUSION Our results suggest significant diversification and the microevolution of B. pertussis within the 2008-2012 Australian epidemic.
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Affiliation(s)
- Azadeh Safarchi
- 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
| | - Sunny Z Wu
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Sandeep Kaur
- School of Biotechnology and Biomolecular Sciences, 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, The University of Sydney, New South Wales, Australia
| | - Gwendolyn L Gilbert
- 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, The University of Sydney, New South Wales, Australia
| | - Nicholas Wood
- National Centre for Immunisation Research and Surveillance of Vaccine Preventable Diseases (NCIRS), The Children's Hospital at Westmead, Westmead, New South Wales 2145, Australia; Discipline of Paediatrics and Child Health, University of Sydney, The Children's Hospital at Westmead, Westmead, New South Wales 2145, Australia; Department of Microbiology and Infectious Diseases, The Children's Hospital at Westmead, New South Wales, Australia
| | - Peter McIntyre
- National Centre for Immunisation Research and Surveillance of Vaccine Preventable Diseases (NCIRS), The Children's Hospital at Westmead, Westmead, New South Wales 2145, Australia; Discipline of Paediatrics and Child Health, University of Sydney, The Children's Hospital at Westmead, Westmead, New South Wales 2145, Australia; Department of Microbiology and Infectious Diseases, The Children's Hospital at Westmead, New South Wales, Australia
| | - Helen Marshall
- Vaccinology and Immunology Research Trials Unit, Women's and Children's Hospital and School of Medicine and Robinson Research Institute, University of Adelaide, South Australia, Australia
| | - Anthony D Keil
- Department of Microbiology, PathWest Laboratory Medicine WA, Princess Margaret Hospital for Children, Perth, Australia
| | - Ruiting Lan
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia.
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12
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Bart MJ, van der Heide HGJ, Zeddeman A, Heuvelman K, van Gent M, Mooi FR. Complete Genome Sequences of 11 Bordetella pertussis Strains Representing the Pandemic ptxP3 Lineage. GENOME ANNOUNCEMENTS 2015; 3:e01394-15. [PMID: 26607899 PMCID: PMC4661318 DOI: 10.1128/genomea.01394-15] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Accepted: 10/16/2015] [Indexed: 01/31/2023]
Abstract
Pathogen adaptation has contributed to the resurgence of pertussis. To facilitate our understanding of this adaptation we report here 11 completely closed and annotated Bordetella pertussis genomes representing the pandemic ptxP3 lineage. Our analyses included six strains which do not produce the vaccine components pertactin and/or filamentous hemagglutinin.
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Affiliation(s)
- Marieke J Bart
- Department of Pediatrics, Laboratory of Pediatric Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands Centre for Infectious Diseases Control (CIb), National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Han G J van der Heide
- Centre for Infectious Diseases Control (CIb), National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Anne Zeddeman
- Department of Pediatrics, Laboratory of Pediatric Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands Centre for Infectious Diseases Control (CIb), National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Kees Heuvelman
- Centre for Infectious Diseases Control (CIb), National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Marjolein van Gent
- Centre for Infectious Diseases Control (CIb), National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Frits R Mooi
- Department of Pediatrics, Laboratory of Pediatric Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands Centre for Infectious Diseases Control (CIb), National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
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13
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Single Amino Acid Polymorphisms of Pertussis Toxin Subunit S2 (PtxB) Affect Protein Function. PLoS One 2015; 10:e0137379. [PMID: 26375454 PMCID: PMC4573519 DOI: 10.1371/journal.pone.0137379] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2014] [Accepted: 08/17/2015] [Indexed: 11/19/2022] Open
Abstract
Whooping cough due to Bordetella pertussis is increasing in incidence, in part due to accumulation of mutations which increase bacterial fitness in highly vaccinated populations. Polymorphisms in the pertussis toxin, ptxA and ptxB genes, and the pertactin, prn genes of clinical isolates of Bordetella pertussis collected in Cincinnati from 1989 through 2005 were examined. While the ptxA and prn genotypes were variable, all 48 strains had the ptxB2 genotype; ptxB1 encodes glycine at amino acid 18 of the S2 subunit of pertussis toxin, while ptxB2 encodes serine. We investigated antigenic and functional differences of PtxB1 and PtxB2. The S2 protein was not very immunogenic. Only a few vaccinated or individuals infected with B. pertussis developed antibody responses to the S2 subunit, and these sera recognized both polymorphic forms equally well. Amino acid 18 of S2 is in a glycan binding domain, and the PtxB forms displayed differences in receptor recognition and toxicity. PtxB1 bound better to the glycoprotein, fetuin, and Jurkat T cells in vitro, but the two forms were equally effective at promoting CHO cell clustering. To investigate in vivo activity of Ptx, one μg of Ptx was administered to DDY mice and blood was collected on 4 days after injection. PtxB2 was more effective at promoting lymphocytosis in mice.
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14
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Xu Y, Liu B, Gröndahl-Yli-Hannuksila K, Tan Y, Feng L, Kallonen T, Wang L, Peng D, He Q, Wang L, Zhang S. Whole-genome sequencing reveals the effect of vaccination on the evolution of Bordetella pertussis. Sci Rep 2015; 5:12888. [PMID: 26283022 PMCID: PMC4539551 DOI: 10.1038/srep12888] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Accepted: 07/10/2015] [Indexed: 12/11/2022] Open
Abstract
Herd immunity can potentially induce a change of circulating viruses. However, it remains largely unknown that how bacterial pathogens adapt to vaccination. In this study, Bordetella pertussis, the causative agent of whooping cough, was selected as an example to explore possible effect of vaccination on the bacterial pathogen. We sequenced and analysed the complete genomes of 40 B. pertussis strains from Finland and China, as well as 11 previously sequenced strains from the Netherlands, where different vaccination strategies have been used over the past 50 years. The results showed that the molecular clock moved at different rates in these countries and in distinct periods, which suggested that evolution of the B. pertussis population was closely associated with the country vaccination coverage. Comparative whole-genome analyses indicated that evolution in this human-restricted pathogen was mainly characterised by ongoing genetic shift and gene loss. Furthermore, 116 SNPs were specifically detected in currently circulating ptxP3-containing strains. The finding might explain the successful emergence of this lineage and its spread worldwide. Collectively, our results suggest that the immune pressure of vaccination is one major driving force for the evolution of B. pertussis, which facilitates further exploration of the pathogenicity of B. pertussis.
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Affiliation(s)
- Yinghua Xu
- Key Laboratory of the Ministry of Health for Research on Quality and Standardization of Biotech Products, National Institutes of Food and Drug Control, Beijing 100050, P. R. China
| | - Bin Liu
- 1] TEDA School of Biological Sciences and Biotechnology, Nankai University, Tianjin 300457, P.R. China [2] Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, 23 Hongda Street, Tianjin 300457, P. R. China
| | | | - Yajun Tan
- Key Laboratory of the Ministry of Health for Research on Quality and Standardization of Biotech Products, National Institutes of Food and Drug Control, Beijing 100050, P. R. China
| | - Lu Feng
- 1] TEDA School of Biological Sciences and Biotechnology, Nankai University, Tianjin 300457, P.R. China [2] Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, 23 Hongda Street, Tianjin 300457, P. R. China
| | - Teemu Kallonen
- Department of Medical Microbiology and Immunology, Turku University, Turku 20520, Finland
| | - Lichan Wang
- Key Laboratory of the Ministry of Health for Research on Quality and Standardization of Biotech Products, National Institutes of Food and Drug Control, Beijing 100050, P. R. China
| | - Ding Peng
- 1] TEDA School of Biological Sciences and Biotechnology, Nankai University, Tianjin 300457, P.R. China [2] Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, 23 Hongda Street, Tianjin 300457, P. R. China
| | - Qiushui He
- 1] Department of Medical Microbiology and Immunology, Turku University, Turku 20520, Finland [2] Department of Infectious Disease Surveillance and Control, National Institute for Health and Welfare, Turku 20520, Finland [3] Department of Medical Microbiology, Capital Medical University, Beijing 100069, P. R. China
| | - Lei Wang
- 1] TEDA School of Biological Sciences and Biotechnology, Nankai University, Tianjin 300457, P.R. China [2] Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, 23 Hongda Street, Tianjin 300457, P. R. China [3] State Key Laboratory of Medicinal Chemical Biology, Nankai University 300457, Tianjin, P. R. China
| | - Shumin Zhang
- Key Laboratory of the Ministry of Health for Research on Quality and Standardization of Biotech Products, National Institutes of Food and Drug Control, Beijing 100050, P. R. China
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15
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Complete Genome Sequences of Bordetella pertussis Isolates B1917 and B1920, Representing Two Predominant Global Lineages. GENOME ANNOUNCEMENTS 2014; 2:2/6/e01301-14. [PMID: 25540342 PMCID: PMC4276820 DOI: 10.1128/genomea.01301-14] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Bordetella pertussis is the causative agent of pertussis, a disease which has resurged despite vaccination. We report the complete, annotated genomes of isolates B1917 and B1920, representing two lineages predominating globally in the last 50 years. The B1917 lineage has been associated with the resurgence of pertussis in the 1990s.
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16
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Abstract
Bordetella pertussis produces two serologically distinct fimbriae, Fim2 and Fim3. Expression of these antigens is governed by the BvgA/S system and by the length of a poly(C) tract in the promoter of each gene. Fim2 and Fim3 are important antigens for whole cell pertussis vaccines as clinical trials have shown an association of anti-fimbriae antibody-mediated agglutination and protection. The current five component acellular pertussis vaccine contains co-purified Fim2/3 and provided good efficacy in clinical trials with the anti-Fim antibody response correlating with protection when pre and post exposure antibody levels were analysed. The predominant serotype of B. pertussis isolates has changed over time in most countries but it is not understood whether this is vaccine-driven or whether serotype is linked to the prevailing predominant genotype. Recent studies have shown that both Fim2 and Fim3 are expressed during infection and that Fim2 is more immunogenic than Fim3 in the acellular vaccine.
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17
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Miyaji Y, Otsuka N, Toyoizumi-Ajisaka H, Shibayama K, Kamachi K. Genetic analysis of Bordetella pertussis isolates from the 2008-2010 pertussis epidemic in Japan. PLoS One 2013; 8:e77165. [PMID: 24124606 PMCID: PMC3790747 DOI: 10.1371/journal.pone.0077165] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2013] [Accepted: 09/09/2013] [Indexed: 02/04/2023] Open
Abstract
A large pertussis epidemic occurred between 2008 and 2010 in Japan. To investigate epidemic strains, we analyzed 33 Bordetella pertussis isolates from the epidemic period by sequencing virulence-associated genes (fim3, ptxP, ptxA, and prn) and performing multilocus variable-number tandem repeat analysis (MLVA), and compared these results with those of 101 isolates from non-epidemic, earlier and later time periods. DNA sequencing of the fim3 allele revealed that the frequency of fim3B was 4.3%, 12.8%, 30.3%, and 5.1% within isolates in 2002–2004, 2005–2007, 2008–2010, and 2011–2012, respectively. The isolation rate of the fim3B strain therefore temporarily increased during the epidemic period 2008–2010. In contrast, the frequencies of the virulence-associated allelic variants, ptxP3, ptxA1, and prn2, increased with time during overall study period, indicating that these variants were not directly involved in the occurrence of the 2008–2010 epidemic. MLVA genotyping in combination with analysis of allele types showed that the prevalence of an MT27d strain temporarily increased in the epidemic period, and that this strain carried virulence-associated allelic variants (fim3B, ptxP3, ptxA1, and prn2) also identified in recent epidemic strains of Australia, Europe, and the US. Phenotypic analyses revealed that the serotype Fim3 strain was predominant (≥87%) during all the periods studied, and that the frequency of adhesion pertactin (Prn) non-expressing B. pertussis decreased by half in the epidemic period. All MT27d strains expressed Prn and Fim3 proteins, suggesting that B. pertussis MT27d strains expressing Prn and Fim3B have the potential to cause large epidemics worldwide.
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Affiliation(s)
- Yusuke Miyaji
- Department of Bacteriology II, National Institute of Infectious Diseases, Tokyo, Japan
- Department of Pediatrics, St Marianna University School of Medicine, Kawasaki, Japan
| | - Nao Otsuka
- Department of Bacteriology II, National Institute of Infectious Diseases, Tokyo, Japan
| | | | - Keigo Shibayama
- Department of Bacteriology II, National Institute of Infectious Diseases, Tokyo, Japan
| | - Kazunari Kamachi
- Department of Bacteriology II, National Institute of Infectious Diseases, Tokyo, Japan
- * E-mail:
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18
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Park J, Zhang Y, Buboltz AM, Zhang X, Schuster SC, Ahuja U, Liu M, Miller JF, Sebaihia M, Bentley SD, Parkhill J, Harvill ET. Comparative genomics of the classical Bordetella subspecies: the evolution and exchange of virulence-associated diversity amongst closely related pathogens. BMC Genomics 2012; 13:545. [PMID: 23051057 PMCID: PMC3533505 DOI: 10.1186/1471-2164-13-545] [Citation(s) in RCA: 85] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2012] [Accepted: 09/21/2012] [Indexed: 12/04/2022] Open
Abstract
Background The classical Bordetella subspecies are phylogenetically closely related, yet differ in some of the most interesting and important characteristics of pathogens, such as host range, virulence and persistence. The compelling picture from previous comparisons of the three sequenced genomes was of genome degradation, with substantial loss of genome content (up to 24%) associated with adaptation to humans. Results For a more comprehensive picture of lineage evolution, we employed comparative genomic and phylogenomic analyses using seven additional diverse, newly sequenced Bordetella isolates. Genome-wide single nucleotide polymorphism (SNP) analysis supports a reevaluation of the phylogenetic relationships between the classical Bordetella subspecies, and suggests a closer link between ovine and human B. parapertussis lineages than has been previously proposed. Comparative analyses of genome content revealed that only 50% of the pan-genome is conserved in all strains, reflecting substantial diversity of genome content in these closely related pathogens that may relate to their different host ranges, virulence and persistence characteristics. Strikingly, these analyses suggest possible horizontal gene transfer (HGT) events in multiple loci encoding virulence factors, including O-antigen and pertussis toxin (Ptx). Segments of the pertussis toxin locus (ptx) and its secretion system locus (ptl) appear to have been acquired by the classical Bordetella subspecies and are divergent in different lineages, suggesting functional divergence in the classical Bordetellae. Conclusions Together, these observations, especially in key virulence factors, reveal that multiple mechanisms, such as point mutations, gain or loss of genes, as well as HGTs, contribute to the substantial phenotypic diversity of these versatile subspecies in various hosts.
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Affiliation(s)
- Jihye Park
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, USA
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19
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van Gent M, Bart MJ, van der Heide HGJ, Heuvelman KJ, Mooi FR. Small mutations in Bordetella pertussis are associated with selective sweeps. PLoS One 2012; 7:e46407. [PMID: 23029513 PMCID: PMC3460923 DOI: 10.1371/journal.pone.0046407] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2012] [Accepted: 08/31/2012] [Indexed: 01/31/2023] Open
Abstract
Bordetella pertussis is the causative agent of pertussis, a highly contagious disease of the human respiratory tract. Despite high vaccination coverage, pertussis has resurged and has become one of the most prevalent vaccine-preventable diseases in developed countries. We have proposed that both waning immunity and pathogen adaptation have contributed to the persistence and resurgence of pertussis. Allelic variation has been found in virulence-associated genes coding for the pertussis toxin A subunit (ptxA), pertactin (prn), serotype 2 fimbriae (fim2), serotype 3 fimbriae (fim3) and the promoter for pertussis toxin (ptxP). In this study, we investigated how more than 60 years of vaccination has affected the Dutch B. pertussis population by combining data from phylogeny, genomics and temporal trends in strain frequencies. Our main focus was on the ptxA, prn, fim3 and ptxP genes. However, we also compared the genomes of 11 Dutch strains belonging to successful lineages. Our results showed that, between 1949 and 2010, the Dutch B. pertussis population has undergone as least four selective sweeps that were associated with small mutations in ptxA, prn, fim3 and ptxP. Phylogenetic analysis revealed a stepwise adaptation in which mutations accumulated clonally. Genomic analysis revealed a number of additional mutations which may have a contributed to the selective sweeps. Five large deletions were identified which were fixed in the pathogen population. However, only one was linked to a selective sweep. No evidence was found for a role of gene acquisition in pathogen adaptation. Our results suggest that the B. pertussis gene repertoire is already well adapted to its current niche and required only fine tuning to persist in the face of vaccination. Further, this work shows that small mutations, even single SNPs, can drive large changes in the populations of bacterial pathogens within a time span of six to 19 years.
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Affiliation(s)
- Marjolein van Gent
- Laboratory for Infectious Diseases and Screening, Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Marieke J. Bart
- Laboratory for Infectious Diseases and Screening, Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Han G. J. van der Heide
- Laboratory for Infectious Diseases and Screening, Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Kees J. Heuvelman
- Laboratory for Infectious Diseases and Screening, Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Frits R. Mooi
- Laboratory for Infectious Diseases and Screening, Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
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20
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Nelson OW, Garrity GM. Genome sequences of Bacteria and Archaea published outside of Standards in Genomic Sciences, June – September 2011. Stand Genomic Sci 2011. [DOI: 10.4056/sigs.2324675] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
- Oranmiyan W. Nelson
- 1Editorial Office, Standards in Genomic Sciences and Department of Microbiology, Michigan State University, East Lansing, MI, USA
| | - George M. Garrity
- 1Editorial Office, Standards in Genomic Sciences and Department of Microbiology, Michigan State University, East Lansing, MI, USA
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21
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Nelson OW, Garrity GM. Genome sequences published outside of Standards in Genomic Sciences, January – June 2011. Stand Genomic Sci 2011. [DOI: 10.4056/sigs.2044675] [Citation(s) in RCA: 122] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
- Oranmiyan W. Nelson
- 1Editorial Office, Standards in Genomic Sciences and Department of Microbiology, Michigan State University, East Lansing, MI, USA
| | - George M. Garrity
- 1Editorial Office, Standards in Genomic Sciences and Department of Microbiology, Michigan State University, East Lansing, MI, USA
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