1
|
Wan M, Zhang G, Yi H. Unraveling the resurgence of pertussis: Insights into epidemiology and global health strategies. Pulmonology 2024:S2531-0437(24)00055-2. [PMID: 38755090 DOI: 10.1016/j.pulmoe.2024.04.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Revised: 04/23/2024] [Accepted: 04/24/2024] [Indexed: 05/18/2024] Open
Affiliation(s)
- Minzhong Wan
- Shantou University Medical College, Shantou 515041, China
| | - Guobin Zhang
- Department of Emergency, Department of Neurosurgery, The First Affiliated Hospital of Shaoyang University, Shaoyang 105471, Hunan Province, China
| | - Hang Yi
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China.
| |
Collapse
|
2
|
Roohparvar Basmenj E, Izadkhah H, Hosseinpour M, Saburi E, Abhaji Ezabadi M, Alipourfard I. A novel approach to design a multiepitope peptide as a vaccine candidate for Bordetella pertussis. J Biomol Struct Dyn 2023:1-13. [PMID: 37937610 DOI: 10.1080/07391102.2023.2278081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 10/26/2023] [Indexed: 11/09/2023]
Abstract
Bordetella pertussis is a very contagious pathogen in humans, causing pertussis disease. Pertussis is one of the 10 leading causes of death due to infectious diseases, especially among infants and children. Antibiotic-resistant strains have recently emerged in this bacterium, and despite the high vaccination coverage, the prevalence of this disease has been increasing recently in both developed and developing countries. The objective of this study is to introduce a novel in silico vaccine candidate aimed at countering B. pertussis effectively. Differing from other comparable studies, this research employed a computational screening methodology to assess the genome of 'Bordetella pertussis 18323.' The purpose was to identify an innovative antigen for the development of a vaccine against B. pertussis. Notably, our investigation introduces an innovative antigen distinguished by its elevated immunogenicity score. Importantly, this antigen lacks toxicity and allergenicity, making it recognizable to the immune system and thus capable of inducing a robust immune response. In the subsequent phase, our antigen was utilized to identify potential epitopes conducive to the construction of a B. pertussis vaccine. These epitopes, alongside linkers, his-tag and adjuvants, were amalgamated to form the vaccine candidate. Subsequently, a comprehensive evaluation of the vaccine was conducted, encompassing various computational tests such as secondary and tertiary structure analysis, physicochemical examination, and structural analysis involving docking and molecular dynamics simulations. Importantly, our vaccine successfully passed all in silico tests.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
| | - Habib Izadkhah
- Department of Computer Science, Faculty of Mathematics, Statistics, and Computer Science, University of Tabriz, Tabriz, Iran
| | - Maryam Hosseinpour
- Department of Medical Genetics and Molecular Medicine, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Ehsan Saburi
- Department of Medical Genetics and Molecular Medicine, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Marjan Abhaji Ezabadi
- Department of Chemical Engineering, Faculty of Engineering, University of Tehran, Tehran, Iran
| | - Iraj Alipourfard
- Institute of Physical Chemistry, Polish Academy of Sciences, Warsaw, Poland
| |
Collapse
|
3
|
Kamachi K, Koide K, Otsuka N, Goto M, Kenri T. Whole-Genome Analysis of Bordetella pertussis MT27 Isolates from School-Associated Outbreaks: Single-Nucleotide Polymorphism Diversity and Threshold of the Outbreak Strains. Microbiol Spectr 2023; 11:e0406522. [PMID: 37191540 PMCID: PMC10269452 DOI: 10.1128/spectrum.04065-22] [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: 10/10/2022] [Accepted: 04/24/2023] [Indexed: 05/17/2023] Open
Abstract
Bordetella pertussis, the causative agent of whooping cough, can cause pertussis outbreaks in humans, especially in school-aged children. Here, we performed whole-genome sequencing of 51 B. pertussis isolates (epidemic strain MT27) collected from patients infected during 6 school-associated outbreaks lasting less than 4 months. We compared their genetic diversity with that of 28 sporadic isolates (non-outbreak MT27 isolates) based on single-nucleotide polymorphisms (SNPs). Our temporal SNP diversity analysis revealed a mean SNP accumulation rate (time-weighted average) of 0.21 SNPs/genome/year during the outbreaks. The outbreak isolates showed a mean of 0.74 SNP differences (median, 0; range, 0 to 5) between 238 isolate pairs, whereas the sporadic isolates had a mean of 16.12 SNP differences (median, 17; range 0 to 36) between 378 isolate pairs. A low SNP diversity was observed in the outbreak isolates. Receiver operating characteristic analysis demonstrated that the optimal cutoff value to distinguish between the outbreak and sporadic isolates was 3 SNPs (Youden's index of 0.90 with a true-positive rate of 0.97 and a false-positive rate of 0.07). Based on these results, we propose an epidemiological threshold of ≤3 SNPs per genome as a reliable marker of B. pertussis strain identity during pertussis outbreaks that span less than 4 months. IMPORTANCE Bordetella pertussis is a highly infectious bacterium that easily causes pertussis outbreaks in humans, especially in school-aged children. In detection and investigation of outbreaks, excluding non-outbreak isolates is important for understanding the bacterial transmission routes. Currently, whole-genome sequencing is widely used for outbreak investigations, and the genetic relatedness of outbreak isolates is assessed based on differences in the number of single-nucleotide polymorphisms (SNPs) in the genomes of different isolates. The optimal SNP threshold defining strain identity has been proposed for many bacterial pathogens, but not for B. pertussis. In this study, we performed whole-genome sequencing of 51 B. pertussis outbreak isolates and identified a genetic threshold of ≤3 SNPs per genome as a marker defining the strain identity during pertussis outbreaks. This study provides a useful marker for identifying and analyzing pertussis outbreaks and can serve as a basis for future epidemiological studies on pertussis.
Collapse
Affiliation(s)
- Kazunari Kamachi
- Department of Bacteriology II, National Institute of Infectious Diseases, Tokyo, Japan
| | - Kentaro Koide
- Department of Bacteriology II, National Institute of Infectious Diseases, Tokyo, Japan
| | - Nao Otsuka
- Department of Bacteriology II, National Institute of Infectious Diseases, Tokyo, Japan
| | - Masataka Goto
- Department of Bacteriology II, National Institute of Infectious Diseases, Tokyo, Japan
| | - Tsuyoshi Kenri
- Department of Bacteriology II, National Institute of Infectious Diseases, Tokyo, Japan
| |
Collapse
|
4
|
Fu P, Zhou J, Meng J, Liu Z, Nijiati Y, He L, Li C, Chen S, Wang A, Yan G, Lu G, Zhou L, Zhai X, Wang C. Emergence and spread of MT28 ptxP3 allele macrolide-resistant Bordetella pertussis from 2021 to 2022 in China. Int J Infect Dis 2023; 128:205-211. [PMID: 36632892 DOI: 10.1016/j.ijid.2023.01.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 12/05/2022] [Accepted: 01/03/2023] [Indexed: 01/11/2023] Open
Abstract
OBJECTIVES To reveal the clinical and molecular characteristics of Bordetella pertussis (BP) prevalent in Shanghai, China. METHODS A total of 9430 children with suspected pertussis from 2021 to 2022 were included, and nasopharyngeal swab samples were collected for polymerase chain reaction detection, culture, antimicrobial susceptibility testing, and 23S rRNA gene A2047G detection. BP strains were typed using multilocus variable-number tandem-repeat analysis and virulence genotyping. RESULTS Of 9430 cases, 5.1% and 1.6% were confirmed by polymerase chain reaction and culture, respectively. Infants (aged <1 year) accounted for 24.7% and presented much more severe symptoms than noninfants. Pertussis was most frequently detected in infants aged 0-6 months (11.3∼14.0%) and children aged >6-10 years (10.8∼21.7%). Macrolide-resistant BP (MRBP) accounted for 89.3%, and all carried the A2047G mutation. There were six multilocus variable-number tandem-repeat analysis types (MTs), including MT28 (62.0%), MT195 (20%), MT27 (10.0%), MT104 (4.7%), MT55 (2.7%), and MT32 (0.7%). BP strains with pertussis toxin (ptx)P3/(pertactin) prn2/ptxC2/ptxA1/(fimbrial proteins) fim2-1/fim3-1, including MT27, MT28, and MT32, accounted for 72.7%, among which MT27 and MT32 were macrolide-sensitive BP, whereas most (94.6∼100%) of MT28 were MRBP. Strains harboring ptxP1/prn1/ptxC1/ptxA1/fim2-1/fim3-1, including MT55, MT104, and MT195, belonged to macrolide-sensitive BP. CONCLUSION The emergence and spread of MT28 ptxP3-MRBP was first reported in China, highlighting the importance of continuous surveillance of ptxP3-MRBP to prevent its potential circulation.
Collapse
Affiliation(s)
- Pan Fu
- Department of Clinical Microbiology Laboratory, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China; Nosocomial Infection Control Department, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Jinlan Zhou
- Pediatric intensive care unit, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Jianhua Meng
- Department of Hematology and Oncology, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Zhiwei Liu
- Department of Clinical Laboratory, Taian Maternity and Child Health Hospital, Taian, Shandong Province, China
| | - Yaxier Nijiati
- Orthopedics Department, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Leiyan He
- Department of Clinical Microbiology Laboratory, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Chunling Li
- Department of Clinical Microbiology Laboratory, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Saige Chen
- Department of Clinical Microbiology Laboratory, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Aimin Wang
- Department of Clinical Microbiology Laboratory, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Gangfeng Yan
- Pediatric intensive care unit, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Guoping Lu
- Pediatric intensive care unit, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Lijun Zhou
- Outpatient and Emergency Management Office, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China.
| | - Xiaowen Zhai
- Department of Hematology and Oncology, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China.
| | - Chuanqing Wang
- Department of Clinical Microbiology Laboratory, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China; Nosocomial Infection Control Department, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China.
| |
Collapse
|
5
|
Szwejser-Zawislak E, Wilk MM, Piszczek P, Krawczyk J, Wilczyńska D, Hozbor D. Evaluation of Whole-Cell and Acellular Pertussis Vaccines in the Context of Long-Term Herd Immunity. Vaccines (Basel) 2022; 11:vaccines11010001. [PMID: 36679846 PMCID: PMC9863224 DOI: 10.3390/vaccines11010001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Revised: 12/04/2022] [Accepted: 12/13/2022] [Indexed: 12/24/2022] Open
Abstract
After the pertussis vaccine had been introduced in the 1940s and was shown to be very successful in reducing the morbidity and mortality associated with the disease, the possibility of improving both vaccine composition and vaccination schedules has become the subject of continuous interest. As a result, we are witnessing a considerable heterogeneity in pertussis vaccination policies, which remains beyond universal consensus. Many pertussis-related deaths still occur in low- and middle-income countries; however, these deaths are attributable to gaps in vaccination coverage and limited access to healthcare in these countries, rather than to the poor efficacy of the first generation of pertussis vaccine consisting in inactivated and detoxified whole cell pathogen (wP). In many, particularly high-income countries, a switch was made in the 1990s to the use of acellular pertussis (aP) vaccine, to reduce the rate of post-vaccination adverse events and thereby achieve a higher percentage of children vaccinated. However the epidemiological data collected over the past few decades, even in those high-income countries, show an increase in pertussis prevalence and morbidity rates, triggering a wide-ranging debate on the causes of pertussis resurgence and the effectiveness of current pertussis prevention strategies, as well as on the efficacy of available pertussis vaccines and immunization schedules. The current article presents a systematic review of scientific reports on the evaluation of the use of whole-cell and acellular pertussis vaccines, in the context of long-term immunity and vaccines efficacy.
Collapse
Affiliation(s)
- Ewa Szwejser-Zawislak
- Institute of Biotechnology of Serums and Vaccines Biomed, Al. Sosnowa 8, 30-224 Krakow, Poland
| | - Mieszko M. Wilk
- Department of Immunology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Krakow, Poland
| | - Piotr Piszczek
- Institute of Biotechnology of Serums and Vaccines Biomed, Al. Sosnowa 8, 30-224 Krakow, Poland
| | - Justyna Krawczyk
- Institute of Biotechnology of Serums and Vaccines Biomed, Al. Sosnowa 8, 30-224 Krakow, Poland
| | - Daria Wilczyńska
- Institute of Biotechnology of Serums and Vaccines Biomed, Al. Sosnowa 8, 30-224 Krakow, Poland
| | - Daniela Hozbor
- VacSal Laboratory, Institute of Biotechnology and Molecular Biology, Faculty of Sciences, National University of La Plata (UNLP), National Council for Scientific and Technical Research (CONICET), La Plata 1900, Argentina
- Correspondence:
| |
Collapse
|
6
|
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.
Collapse
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
| |
Collapse
|
7
|
Safarchi A, Saedi S, Tay CY, Lamichhane B, Nakhost Lotfi M, Shahcheraghi F. Genome Characteristic of Bordetella parapertussis Isolated from Iran. Curr Microbiol 2022; 79:314. [PMID: 36088519 PMCID: PMC9464130 DOI: 10.1007/s00284-022-03009-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 08/23/2022] [Indexed: 11/28/2022]
Abstract
AbstractPertussis also known as whooping cough is a respiratory infection in humans particularly with severe symptoms in infants and usually caused by Bordetella pertussis. However, Bordetella parapertussis can also cause a similar clinical syndrome. During 2012 to 2015, from nasal swabs sent from different provinces to the pertussis reference laboratory of Pasture Institute of Iran for pertussis confirmation, seven B. parapertussis isolates were identified by bacterial culture, biochemical tests, and the presence of IS1001 insertion in the genome. The expression of pertactin (Prn) as one the major virulence factor for bacterial adhesion was investigated using western blot. Moreover, the genomic characteristic of one recently collected isolate, IRBP134, from a seven-month infant was investigated using Illumina NextSeq sequencing protocol. The results revealed the genome with G+C content 65% and genome size 4.7 Mbp. A total of 81 single nucleotide polymorphisms and 13 short insertions and deletions were found in the genome compared to the B. parapertussis 12822 as a reference genome showing ongoing evolutionary changes. A phylogeny relationship of IRBP134 was also investigated using global B. parapertussis available genomes.
Collapse
Affiliation(s)
- Azadeh Safarchi
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052 Australia
- Department of Bacteriology, Pasteur Institute of Iran, Tehran, 1316943551 Islamic Republic of Iran
| | - Samaneh Saedi
- Department of Bacteriology, Pasteur Institute of Iran, Tehran, 1316943551 Islamic Republic of Iran
| | - Chin Yen Tay
- The Marshal Centre for Infectious Disease Research and Training, University of Western Australia, Perth, WA 6009 Australia
| | - Binit Lamichhane
- The Marshal Centre for Infectious Disease Research and Training, University of Western Australia, Perth, WA 6009 Australia
| | - Masoumeh Nakhost Lotfi
- Department of Bacteriology, Pasteur Institute of Iran, Tehran, 1316943551 Islamic Republic of Iran
| | - Fereshteh Shahcheraghi
- Department of Bacteriology, Pasteur Institute of Iran, Tehran, 1316943551 Islamic Republic of Iran
| |
Collapse
|
8
|
Characterization of Bordetella pertussis Strains Isolated from India. Pathogens 2022; 11:pathogens11070794. [PMID: 35890038 PMCID: PMC9322502 DOI: 10.3390/pathogens11070794] [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: 05/16/2022] [Revised: 06/11/2022] [Accepted: 06/16/2022] [Indexed: 11/25/2022] Open
Abstract
Despite high level vaccination and the availability of two different types of vaccines, whole cell (wP) and acellular vaccines (aP), the resurgence of pertussis has been reported in many countries. Antigenic variation within circulating and vaccine strains is the most documented reason reported for the resurgence of pertussis. Research on genetic divergence among circulating and vaccine strains has largely been reported in countries using aP vaccines. There are inadequate data available for antigenic variation in B. pertussis from wP-using countries. India has used wP for more than 40 years in their primary immunization program. The present study reports five clinical isolates of B. pertussis from samples of pediatric patients with pertussis symptoms observed in India. Genotypic and phenotypic characterization of clinical isolates were performed by serotyping, genotyping, whole genome analyses and comparative genomics. All clinical isolates showed serotype 1, 2 and 3 based on the presence of fimbriae 2 and 3. Genotyping showed genetic similarities in allele types for five aP genes within vaccine strains and clinical isolates reported from India. The presence of the ptxP3 genotype was observed in two out of five clinical isolates. Whole-genome sequencing was performed for clinical isolates using the hybrid strategy of combining Illumina (short reads) and oxford nanopore (long reads) sequencing strategies. Clinical isolates (n = 5) and vaccine strains (n = 7) genomes of B. pertussis from India were compared with 744 B. pertussis closed genomes available in the public databases. The phylogenomic comparison of B. pertussis genomes reported from India will be advantageous in better understanding pertussis resurgence reported globally with respect to pathogen adaptation.
Collapse
|
9
|
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: 9] [Impact Index Per Article: 4.5] [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.
Collapse
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
| |
Collapse
|
10
|
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.
Collapse
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
| |
Collapse
|
11
|
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: 20] [Impact Index Per Article: 6.7] [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.
Collapse
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
| |
Collapse
|
12
|
Saedi S, Safarchi A, Moghadam FT, Heidarzadeh S, Nikbin VS, Shahcheraghi F. Fha Deficient Bordetella pertussis Isolates in Iran with 50 Years Whole Cell Pertussis Vaccination. IRANIAN JOURNAL OF PUBLIC HEALTH 2021; 50:1454-1462. [PMID: 34568185 PMCID: PMC8426785 DOI: 10.18502/ijph.v50i7.6636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/16/2020] [Accepted: 05/19/2020] [Indexed: 11/24/2022]
Abstract
Background: Bordetella pertussis, a highly contagious respiratory. Notably, the resurgence of pertussis has recently been associated with the lacking production of vaccine virulence factors. This study aimed to screen pertactin (Prn) and filamentous hemagglutinin (Fha) production in Iran with 50 years’ whole cell vaccine (WCV) immunization program. Methods: Overall, 130 B. pertussis isolates collected from Pertussis Reference Laboratory of Iran during 2005–2018. Real-time PCR was performed by targeting IS481, ptxP, IS1001 and IS1002 for species confirmation of B. pertussis. Western-blot was used to evaluate the expression of virulence factors (pertactin and filamentous hemagglutinin). Results: All tested B. pertussis isolates expressed Prn and all except two isolates expressed Fha. We have sequenced genomes of these strains and identified differences compared with genome reference B. pertussis Tohama I. Conclusion: Many countries reporting Prn and Fha-deficiency due to acellular vaccine (ACV) pressure. Our results demonstrate in a country with WCV history, Fha-deficient isolates may rise independently. However, Prn-deficient isolates are more under the ACV pressure in B. pertussis isolates. Continues surveillance will provide a better understanding of the effect of WCV on the evolution of the pathogen deficiency.
Collapse
Affiliation(s)
- Samaneh Saedi
- Department of Bacteriology, Pasteur Institute of Iran, Tehran, Iran
| | - Azadeh Safarchi
- Department of Bacteriology, Pasteur Institute of Iran, Tehran, Iran
| | | | - Siamak Heidarzadeh
- Department of Microbiology and Virology, School of Medicine, Zanjan University of Medical Sciences, Zanjan, Iran
| | | | - Fereshteh Shahcheraghi
- Pertussis Reference Laboratory, Department of Bacteriology, Pasteur Institute of Iran, Tehran, Iran
| |
Collapse
|
13
|
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.
Collapse
|
14
|
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.
Collapse
|
15
|
Kamachi K, Yao SM, Chiang CS, Koide K, Otsuka N, Shibayama K. Rapid and simple SNP genotyping for Bordetella pertussis epidemic strain MT27 based on a multiplexed single-base extension assay. Sci Rep 2021; 11:4823. [PMID: 33649512 PMCID: PMC7921669 DOI: 10.1038/s41598-021-84409-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 02/17/2021] [Indexed: 11/25/2022] Open
Abstract
Multilocus variable-number tandem repeat analysis (MLVA) is widely used for genotyping of Bordetella pertussis, the causative bacteria for pertussis. However, MLVA genotyping is losing its discriminate power because prevalence of the epidemic MT27 strain (MLVA-27) is increasing worldwide. To address this, we developed a single nucleotide polymorphism (SNP) genotyping method for MT27 based on multiplexed single-base extension (SBE) assay. A total of 237 MT27 isolates collected in Japan during 1999–2018 were genotyped and classified into ten SNP genotypes (SG1 to SG10) with a Simpson’s diversity index (DI) of 0.79 (95% CI 0.76–0.82). Temporal trends showed a marked increase in the genotypic diversity in the 2010s: Simpson’s DI was zero in 1999–2004, 0.16 in 2005–2009, 0.83 in 2010–2014, and 0.76 in 2015–2018. This indicates that the SNP genotyping is applicable to the recently circulating MT27 strain. Additionally, almost all outbreak-associated MT27 isolates were classified into the same SNP genotypes for each outbreak. Multiplexed SBE assay allows for rapid and simple genotyping, indicating that the SNP genotyping can potentially be a useful tool for subtyping the B. pertussis MT27 strain in routine surveillance and outbreak investigations.
Collapse
Affiliation(s)
- Kazunari Kamachi
- Department of Bacteriology II, National Institute of Infectious Diseases, Tokyo, Japan.
| | - Shu-Man Yao
- Center for Diagnostics and Vaccine Development, Centers for Disease Control, Taipei, Taiwan
| | - Chuen-Sheue Chiang
- Center for Diagnostics and Vaccine Development, Centers for Disease Control, Taipei, Taiwan
| | - Kentaro Koide
- Department of Bacteriology II, National Institute of Infectious Diseases, Tokyo, 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
| |
Collapse
|
16
|
Van Goethem N, Struelens MJ, De Keersmaecker SCJ, Roosens NHC, Robert A, Quoilin S, Van Oyen H, Devleesschauwer B. Perceived utility and feasibility of pathogen genomics for public health practice: a survey among public health professionals working in the field of infectious diseases, Belgium, 2019. BMC Public Health 2020; 20:1318. [PMID: 32867727 PMCID: PMC7456758 DOI: 10.1186/s12889-020-09428-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Accepted: 08/23/2020] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Pathogen genomics is increasingly being translated from the research setting into the activities of public health professionals operating at different levels. This survey aims to appraise the literacy level and gather the opinions of public health experts and allied professionals working in the field of infectious diseases in Belgium concerning the implementation of next-generation sequencing (NGS) in public health practice. METHODS In May 2019, Belgian public health and healthcare professionals were invited to complete an online survey containing eight main topics including background questions, general attitude towards pathogen genomics for public health practice and main concerns, genomic literacy, current and planned NGS activities, place of NGS in diagnostic microbiology pathways, data sharing obstacles, end-user requirements, and key drivers for the implementation of NGS. Descriptive statistics were used to report on the frequency distribution of multiple choice responses whereas thematic analysis was used to analyze free text responses. A multivariable logistic regression model was constructed to identify important predictors for a positive attitude towards the implementation of pathogen genomics in public health practice. RESULTS 146 out of the 753 invited public health professionals completed the survey. 63% of respondents indicated that public health agencies should be using genomics to understand and control infectious diseases. Having a high level of expertise in the field of pathogen genomics was the strongest predictor of a positive attitude (OR = 4.04, 95% CI = 1.11 - 17.23). A significantly higher proportion of data providers indicated to have followed training in the field of pathogen genomics compared to data end-users (p < 0.001). Overall, 79% of participants expressed interest in receiving further training. Main concerns were related to the cost of sequencing technologies, data sharing, data integration, interdisciplinary working, and bioinformatics expertise. CONCLUSIONS Belgian health professionals expressed favorable views about implementation of pathogen genomics in their work activities related to infectious disease surveillance and control. They expressed the need for suitable training initiatives to strengthen their competences in the field. Their perception of the utility and feasibility of pathogen genomics for public health purposes will be a key driver for its further implementation.
Collapse
Affiliation(s)
- N Van Goethem
- Scientific Directorate of Epidemiology and public health, Sciensano, J. Wytsmanstraat 14, 1050, Brussels, Belgium. .,Department of Epidemiology and Biostatistics, Institut de recherche expérimentale et clinique, Faculty of Public Health, Université catholique de Louvain, Clos Chapelle-aux-champs 30, 1200, Woluwe-Saint-Lambert, Belgium.
| | - M J Struelens
- Surveillance Section, European Centre for Disease Prevention and Control, Gustav den III:s Boulevard, 169 73 Solna, Stockholm, Sweden.,Faculté de Médecine, Université libre de Bruxelles, 808 route de Lennik, 1070, Brussels, Belgium
| | - S C J De Keersmaecker
- Transversal activities in Applied Genomics, Sciensano, J. Wytsmanstraat 14, 1050, Brussels, Belgium
| | - N H C Roosens
- Transversal activities in Applied Genomics, Sciensano, J. Wytsmanstraat 14, 1050, Brussels, Belgium
| | - A Robert
- Department of Epidemiology and Biostatistics, Institut de recherche expérimentale et clinique, Faculty of Public Health, Université catholique de Louvain, Clos Chapelle-aux-champs 30, 1200, Woluwe-Saint-Lambert, Belgium
| | - S Quoilin
- Scientific Directorate of Epidemiology and public health, Sciensano, J. Wytsmanstraat 14, 1050, Brussels, Belgium
| | - H Van Oyen
- Scientific Directorate of Epidemiology and public health, Sciensano, J. Wytsmanstraat 14, 1050, Brussels, Belgium.,Department of Public Health and Primary Care, Faculty of Medicine, Ghent University, De Pintelaan 185, 9000, Ghent, Belgium
| | - B Devleesschauwer
- Scientific Directorate of Epidemiology and public health, Sciensano, J. Wytsmanstraat 14, 1050, Brussels, Belgium.,Department of Veterinary Public Health and Food Safety, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, 9820, Merelbeke, Belgium
| |
Collapse
|
17
|
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.
Collapse
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.
| |
Collapse
|
18
|
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.
Collapse
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
| |
Collapse
|
19
|
Status and potential of bacterial genomics for public health practice: a scoping review. Implement Sci 2019; 14:79. [PMID: 31409417 PMCID: PMC6692930 DOI: 10.1186/s13012-019-0930-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Accepted: 07/26/2019] [Indexed: 01/10/2023] Open
Abstract
Background Next-generation sequencing (NGS) is increasingly being translated into routine public health practice, affecting the surveillance and control of many pathogens. The purpose of this scoping review is to identify and characterize the recent literature concerning the application of bacterial pathogen genomics for public health practice and to assess the added value, challenges, and needs related to its implementation from an epidemiologist’s perspective. Methods In this scoping review, a systematic PubMed search with forward and backward snowballing was performed to identify manuscripts in English published between January 2015 and September 2018. Included studies had to describe the application of NGS on bacterial isolates within a public health setting. The studied pathogen, year of publication, country, number of isolates, sampling fraction, setting, public health application, study aim, level of implementation, time orientation of the NGS analyses, and key findings were extracted from each study. Due to a large heterogeneity of settings, applications, pathogens, and study measurements, a descriptive narrative synthesis of the eligible studies was performed. Results Out of the 275 included articles, 164 were outbreak investigations, 70 focused on strategy-oriented surveillance, and 41 on control-oriented surveillance. Main applications included the use of whole-genome sequencing (WGS) data for (1) source tracing, (2) early outbreak detection, (3) unraveling transmission dynamics, (4) monitoring drug resistance, (5) detecting cross-border transmission events, (6) identifying the emergence of strains with enhanced virulence or zoonotic potential, and (7) assessing the impact of prevention and control programs. The superior resolution over conventional typing methods to infer transmission routes was reported as an added value, as well as the ability to simultaneously characterize the resistome and virulome of the studied pathogen. However, the full potential of pathogen genomics can only be reached through its integration with high-quality contextual data. Conclusions For several pathogens, it is time for a shift from proof-of-concept studies to routine use of WGS during outbreak investigations and surveillance activities. However, some implementation challenges from the epidemiologist’s perspective remain, such as data integration, quality of contextual data, sampling strategies, and meaningful interpretations. Interdisciplinary, inter-sectoral, and international collaborations are key for an appropriate genomics-informed surveillance. Electronic supplementary material The online version of this article (10.1186/s13012-019-0930-2) contains supplementary material, which is available to authorized users.
Collapse
|
20
|
Ben Fraj I, Bouchez V, Smaoui H, Kechrid A, Brisse S. Genome characteristics of Bordetella pertussis isolates from Tunisia. J Med Microbiol 2019; 68:1320-1323. [PMID: 31329091 DOI: 10.1099/jmm.0.001042] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The recent increase in pertussis cases observed in some countries may have several causes, including the evolution of Bordetella pertussis populations towards escape of vaccine-induced immunity. Most genomic studies of B. pertussis isolates performed so far are from countries that use acellular vaccines. The objective was to analyse genomic sequences of isolates collected during the 2014 whooping cough epidemic in Tunisia, a country where whole-cell vaccines are used. Ten Tunisian isolates and four vaccine strains were sequenced and compared to 169 isolates from countries where acellular vaccines are used. Phylogenetic analysis showed that Tunisian isolates are diverse, demonstrating a multi-strain 2014 epidemic peak, and are intermixed with those circulating in other world regions, showing inter-country transmission. Consistently, Tunisian isolates have antigen variant composition observed in other world regions. No pertactin-deficient strain was observed. The Tunisian B. pertussis population appears to be largely connected with populations from other countries.
Collapse
Affiliation(s)
- Ikram Ben Fraj
- University of Tunis El Manar, Children's Hospital of Tunis, Laboratory of Microbiology, UR12ES01, Tunis, Tunisia
| | - Valérie Bouchez
- National Reference Center for Whooping Cough and other Bordetella infections, Paris, France.,Institut Pasteur, Biodiversity and Epidemiology of Bacterial Pathogens, Paris, France
| | - Hanen Smaoui
- University of Tunis El Manar, Children's Hospital of Tunis, Laboratory of Microbiology, UR12ES01, Tunis, Tunisia
| | - Amel Kechrid
- University of Tunis El Manar, Children's Hospital of Tunis, Laboratory of Microbiology, UR12ES01, Tunis, Tunisia
| | - Sylvain Brisse
- Institut Pasteur, Biodiversity and Epidemiology of Bacterial Pathogens, Paris, France.,National Reference Center for Whooping Cough and other Bordetella infections, Paris, France
| |
Collapse
|
21
|
Esposito S, Stefanelli P, Fry NK, Fedele G, He Q, Paterson P, Tan T, Knuf M, Rodrigo C, Weil Olivier C, Flanagan KL, Hung I, Lutsar I, Edwards K, O'Ryan M, Principi N. Pertussis Prevention: Reasons for Resurgence, and Differences in the Current Acellular Pertussis Vaccines. Front Immunol 2019; 10:1344. [PMID: 31333640 PMCID: PMC6616129 DOI: 10.3389/fimmu.2019.01344] [Citation(s) in RCA: 96] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2019] [Accepted: 05/28/2019] [Indexed: 12/21/2022] Open
Abstract
Pertussis is an acute respiratory disease caused by Bordetella pertussis. Due to its frequency and severity, prevention of pertussis has been considered an important public health issue for many years. The development of the whole-cell pertussis vaccine (wPV) and its introduction into the pediatric immunization schedule was associated with a marked reduction in pertussis cases in the vaccinated cohort. However, due to the frequency of local and systemic adverse events after immunization with wPV, work on a less reactive vaccine was undertaken based on isolated B. pertussis components that induced protective immune responses with fewer local and systemic reactions. These component vaccines were termed acellular vaccines and contained one or more pertussis antigens, including pertussis toxin (PT), filamentous haemagglutinin (FHA), pertactin (PRN), and fimbrial proteins 2 (FIM2) and 3 (FIM3). Preparations containing up to five components were developed, and several efficacy trials clearly demonstrated that the aPVs were able to confer comparable short-term protection than the most effective wPVs with fewer local and systemic reactions. There has been a resurgence of pertussis observed in recent years. This paper reports the results of a Consensus Conference organized by the World Association for Infectious Disease and Immunological Disorders (WAidid) on June 22, 2018, in Perugia, Italy, with the goal of evaluating the most important reasons for the pertussis resurgence and the role of different aPVs in this resurgence.
Collapse
Affiliation(s)
- Susanna Esposito
- Department of Surgical and Biomedical Sciences, Paediatric Clinic, Università degli Studi di Perugia, Perugia, Italy
| | - Paola Stefanelli
- Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - Norman K. Fry
- Immunisation and Countermeasures Division, Public Health England–National Infection Service, London, United Kingdom
| | - Giorgio Fedele
- Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - Qiushui He
- Institute of Biomedicine, University of Turku, Turku, Finland
- Department of Medical Microbiology, Capital Medical University, Beijing, China
| | - Pauline Paterson
- Department of Infectious Disease Epidemiology, The Vaccine Confidence Project TM, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Tina Tan
- Division of Pediatric Infectious Diseases, Department of Pediatrics, Northwestern University Feinberg School of Medicine, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, IL, United States
| | - Markus Knuf
- Children's Hospital, Helios HSk, Wiesbaden, Germany
- Department of Pediatrics, University Medicine, Mainz, Germany
| | - Carlos Rodrigo
- Department of Pediatrics, Vall d'Hebron University Hospital, Barcelona, Spain
- School of Medicine-Germans Trias i Pujol University Hospita, Universidad Autónoma de Barcelona, Barcelona, Spain
| | | | - Katie L. Flanagan
- School of Medicine, College of Health and Medicine, University of Tasmania, Hobart, TAS, Australia
- School of Health and Biomedical Science, RMIT University, Melbourne, VIC, Australia
- Department of Immunology and Pathology, Monash University, Melbourne, VIC, Australia
| | - Ivan Hung
- Department of Medicine, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Iria Lutsar
- Department of Microbiology, Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
| | - Kathryn Edwards
- Division of Pediatric Infectious Diseases, Department of Pediatrics, Vanderbilt University School of Medicine, Nashville, TN, United States
| | - Miguel O'Ryan
- Microbiology and Mycology Program, Faculty of Medicine, Institute of Immunology and Immunotherapy, University of Chile, Santiago, Chile
| | | | | |
Collapse
|
22
|
Fumimoto R, Otsuka N, Kamiya H, Sunagawa T, Tanaka-Taya K, Kamachi K, Shibayama K. Seroprevalence of IgA and IgM antibodies to Bordetella pertussis in healthy Japanese donors: Assessment for the serological diagnosis of pertussis. PLoS One 2019; 14:e0219255. [PMID: 31260500 PMCID: PMC6602288 DOI: 10.1371/journal.pone.0219255] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2018] [Accepted: 06/19/2019] [Indexed: 12/03/2022] Open
Abstract
Pertussis is a human respiratory infection caused by the gram-negative bacterium, Bordetella pertussis. To evaluate the pertussis burden and vaccine efficacy, diagnosis and epidemiological surveillance should be based on accurate and valid diagnostic methods. Recently, the serodiagnostic tests Novagnost Bordetella pertussis IgA and IgM were approved in Japan for pertussis diagnostics. Although the anti-pertussis toxin (PT) IgG assay has been used for pertussis diagnosis worldwide, little is known about the anti-B. pertussis IgA and IgM assays. In this study, serum samples from 460 healthy donors were examined to determine the seroprevalence of anti-B. pertussis IgA and IgM in a Japanese population, and its correlation with donor age. Our data demonstrated that anti-B. pertussis IgA and IgM are positively and negatively correlated with age (r = 0.27, r = -0.37; P < 0.001, respectively). Age-specific analysis revealed high titers of anti-B. pertussis IgA in adults (46–50 years), while anti-B. pertussis IgM titers were high in schoolchildren (6–10, 11–15 years). When applying the arbitrary cut-off values for these ages, 17.6% and 39.5% of healthy donors were interpreted as pertussis-positive or indeterminate with anti-B. pertussis IgA (46–50 years) and IgM (11–15 years) titers, respectively. Overall, our findings indicated that the Novagnost Bordetella pertussis IgA and IgM testing could be greatly affected by subject age, limiting its value for pertussis diagnosis.
Collapse
Affiliation(s)
- Rei Fumimoto
- Department of Bacteriology II, National Institute of Infectious Diseases, Musashimurayama, Tokyo, Japan
- Department of Pediatrics, St Marianna University School of Medicine, Kawasaki, Japan
| | - Nao Otsuka
- Department of Bacteriology II, National Institute of Infectious Diseases, Musashimurayama, Tokyo, Japan
- * E-mail:
| | - Hajime Kamiya
- Infectious Disease Surveillance Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Tomimasa Sunagawa
- Infectious Disease Surveillance Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Keiko Tanaka-Taya
- Infectious Disease Surveillance Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Kazunari Kamachi
- Department of Bacteriology II, National Institute of Infectious Diseases, Musashimurayama, Tokyo, Japan
| | - Keigo Shibayama
- Department of Bacteriology II, National Institute of Infectious Diseases, Musashimurayama, Tokyo, Japan
| |
Collapse
|
23
|
Gonyar LA, Gelbach PE, McDuffie DG, Koeppel AF, Chen Q, Lee G, Temple LM, Stibitz S, Hewlett EL, Papin JA, Damron FH, Eby JC. In Vivo Gene Essentiality and Metabolism in Bordetella pertussis. mSphere 2019; 4:e00694-18. [PMID: 31118307 PMCID: PMC6531889 DOI: 10.1128/msphere.00694-18] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Accepted: 05/10/2019] [Indexed: 12/30/2022] Open
Abstract
Bordetella pertussis is the causative agent of whooping cough, a serious respiratory illness affecting children and adults, associated with prolonged cough and potential mortality. Whooping cough has reemerged in recent years, emphasizing a need for increased knowledge of basic mechanisms of B. pertussis growth and pathogenicity. While previous studies have provided insight into in vitro gene essentiality of this organism, very little is known about in vivo gene essentiality, a critical gap in knowledge, since B. pertussis has no previously identified environmental reservoir and is isolated from human respiratory tract samples. We hypothesize that the metabolic capabilities of B. pertussis are especially tailored to the respiratory tract and that many of the genes involved in B. pertussis metabolism would be required to establish infection in vivo In this study, we generated a diverse library of transposon mutants and then used it to probe gene essentiality in vivo in a murine model of infection. Using the CON-ARTIST pipeline, 117 genes were identified as conditionally essential at 1 day postinfection, and 169 genes were identified as conditionally essential at 3 days postinfection. Most of the identified genes were associated with metabolism, and we utilized two existing genome-scale metabolic network reconstructions to probe the effects of individual essential genes on biomass synthesis. This analysis suggested a critical role for glucose metabolism and lipooligosaccharide biosynthesis in vivo This is the first genome-wide evaluation of in vivo gene essentiality in B. pertussis and provides tools for future exploration.IMPORTANCE Our study describes the first in vivo transposon sequencing (Tn-seq) analysis of B. pertussis and identifies genes predicted to be essential for in vivo growth in a murine model of intranasal infection, generating key resources for future investigations into B. pertussis pathogenesis and vaccine design.
Collapse
Affiliation(s)
- Laura A Gonyar
- Department of Pediatrics, University of Virginia, Charlottesville, Virginia, USA
- Department of Medicine, Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, Virginia, USA
| | - Patrick E Gelbach
- Department of Biomedical Engineering, University of Virginia, Charlottesville, Virginia, USA
| | - Dennis G McDuffie
- Department of Biomedical Engineering, University of Virginia, Charlottesville, Virginia, USA
| | - Alexander F Koeppel
- Department of Medicine, University of Virginia, Charlottesville, Virginia, USA
| | - Qing Chen
- Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland, USA
| | - Gloria Lee
- Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland, USA
| | - Louise M Temple
- Department of Integrated Science and Technology, James Madison University, Harrisonburg, Virginia, USA
| | - Scott Stibitz
- Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland, USA
| | - Erik L Hewlett
- Department of Medicine, Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, Virginia, USA
| | - Jason A Papin
- Department of Medicine, Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, Virginia, USA
- Department of Biomedical Engineering, University of Virginia, Charlottesville, Virginia, USA
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, Virginia, USA
| | - F Heath Damron
- Department of Microbiology, Immunology and Cell Biology, West Virginia University, Morgantown, West Virginia, USA
- Vaccine Development Center, West Virginia University Health Sciences Center, Morgantown, West Virginia, USA
| | - Joshua C Eby
- Department of Medicine, Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, Virginia, USA
| |
Collapse
|
24
|
Lewnard JA, Reingold AL. Emerging Challenges and Opportunities in Infectious Disease Epidemiology. Am J Epidemiol 2019; 188:873-882. [PMID: 30877295 PMCID: PMC7109842 DOI: 10.1093/aje/kwy264] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Revised: 11/28/2018] [Accepted: 11/29/2018] [Indexed: 12/12/2022] Open
Abstract
Much of the intellectual tradition of modern epidemiology stems from efforts to understand and combat chronic diseases persisting through the 20th century epidemiologic transition of countries such as the United States and United Kingdom. After decades of relative obscurity, infectious disease epidemiology has undergone an intellectual rebirth in recent years amid increasing recognition of the threat posed by both new and familiar pathogens. Here, we review the emerging coalescence of infectious disease epidemiology around a core set of study designs and statistical methods bearing little resemblance to the chronic disease epidemiology toolkit. We offer our outlook on challenges and opportunities facing the field, including the integration of novel molecular and digital information sources into disease surveillance, the assimilation of such data into models of pathogen spread, and the increasing contribution of models to public health practice. We next consider emerging paradigms in causal inference for infectious diseases, ranging from approaches to evaluating vaccines and antimicrobial therapies to the task of ascribing clinical syndromes to etiologic microorganisms, an age-old problem transformed by our increasing ability to characterize human-associated microbiota. These areas represent an increasingly important component of epidemiology training programs for future generations of researchers and practitioners.
Collapse
Affiliation(s)
- Joseph A Lewnard
- Division of Epidemiology and Biostatistics, School of Public Health, University of California, Berkeley, Berkeley, California
- Correspondence to Dr. Joseph A. Lewnard, Division of Epidemiology and Biostatistics, School of Public Health, University of California, Berkeley, 2121 Berkeley Way, Berkeley, CA 94720 (e-mail: )
| | - Arthur L Reingold
- Division of Epidemiology and Biostatistics, School of Public Health, University of California, Berkeley, Berkeley, California
| |
Collapse
|
25
|
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.
Collapse
|
26
|
Yilmaz Ç, Özcengiz E, Özcengiz G. Recombinant outer membrane protein Q and putative lipoprotein from Bordetella pertussis inducing strong humoral response were not protective alone in the murine lung colonization model. Turk J Biol 2019; 42:123-131. [PMID: 30814874 DOI: 10.3906/biy-1709-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
Despite high vaccination coverage after introduction of whole cell (wP) and acellular pertussis (aP) vaccines, pertussis resurgence has been reported in many countries. aP vaccines are commonly preferred due to side effects of wP vaccines and formulated with aluminum hydroxide (Alum), which is not an effective adjuvant to eliminate Bordetella pertussis. Low efficiency of current aP vaccines is thought to be the main reason for the resurgence for which newer generation aP vaccines are needed. In the present study, immunogenicity and protective efficacy of outer membrane protein Q (OmpQ) and a putative lipoprotein (Lpp) from B. pertussis were investigated in mice by using two diefrent adjuvants, monophosphoryl lipid A (MPLA) or Alum. OmpQ and putative Lpp were cloned, expressed, and purified from Escherichia coli. The proteins were formulated to immunize mice. Both recombinant OmpQ and putative Lpp induced a significant increase in immunoglobulin G1 (IgG1) and immunoglobulin G2a (IgG2a) responses compared to the control group. Moreover, MPLA-adjuvanted formulations resulted in higher IgG2a levels than Alum-adjuvanted ones. However, there were no significant differences between test and control groups regarding interferon-gamma (IFN-γ) levels, and the mice lung colonization experiments indicated that neither rOmpQ nor rLpp could confer protection alone against B. pertussis challenge.
Collapse
Affiliation(s)
- Çiğdem Yilmaz
- Department of Biological Sciences, Middle East Technical University , Ankara , Turkey
| | | | - Gülay Özcengiz
- Department of Biological Sciences, Middle East Technical University , Ankara , Turkey
| |
Collapse
|
27
|
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.
Collapse
|
28
|
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.
Collapse
|
29
|
Pertactin-deficient Bordetella pertussis isolates in Poland-a country with whole-cell pertussis primary vaccination. Microbes Infect 2018; 21:170-175. [PMID: 30580013 DOI: 10.1016/j.micinf.2018.12.001] [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: 07/30/2018] [Revised: 12/05/2018] [Accepted: 12/07/2018] [Indexed: 11/24/2022]
Abstract
The introduction of pertussis vaccination in the 1950s resulted in a significant decrease in the incidence of disease. However, since the 1990s many highly vaccinated countries have observed the re-emergence of the disease. One of the causes of this phenomenon might be related to the adaptation of Bordetella pertussis to vaccination. The purpose of the presented study was an investigation of the emergence and spread of vaccine antigen-deficient B. pertussis isolates in Poland and genomic characterization of the currently circulating pathogen population using PFGE, MLVA and MAST. The results revealed that all tested isolates expressed Ptx, FHA and ACT antigens but 15.4% (4/26) of isolates from 2010 to 2016 were Prn-deficient. Moreover, one TcfA-deficient isolate was collected in 2015. The genotyping showed a genetic distinction between the isolates circulating in 2010-2016 and isolates from previous periods. The majority of currently circulating isolates belonged to PFGE group IV (96.2%), type MT27 (73.1%), and carried ptxA1-ptxC2-ptxP3-prn2-tcfA2-fim2-1-fim3-1 alleles (61.5%). The unique genetic structure of the B. pertussis population in Poland has changed since 2010 and became similar to that observed in countries with aP vaccination. This could be a result of increasing use of aP vaccines (60% of primary vaccination in 2013) over wP vaccines, which have been broadly used for primary vaccination in Poland for decades.
Collapse
|
30
|
Luu LDW, Octavia S, Zhong L, Raftery MJ, Sintchenko V, Lan R. Comparison of the Whole Cell Proteome and Secretome of Epidemic Bordetella pertussis Strains From the 2008-2012 Australian Epidemic Under Sulfate-Modulating Conditions. Front Microbiol 2018; 9:2851. [PMID: 30538686 PMCID: PMC6277516 DOI: 10.3389/fmicb.2018.02851] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Accepted: 11/06/2018] [Indexed: 01/19/2023] Open
Abstract
Sulfate is an important modulator for virulence factor expression in Bordetella pertussis, the causative organism for whooping cough. During infection, sulfate is released when respiratory epithelial cells are damaged which can affect gene expression. The current predominant strains in Australia are found in single nucleotide polymorphism (SNP) cluster I (ptxP3/prn2). It has been reported that ptxP3 strains have higher mRNA expression of virulence genes than ptxP1 strains under intermediate sulfate-modulating conditions (5 mM MgSO4). Our previous proteomic study compared L1423 (cluster I, ptxP3) and L1191 (cluster II, ptxP1) in Thalen-IJssel (THIJS) media without sulfate modulation and identified an upregulation of transport proteins and a downregulation of immunogenic proteins. To determine whether proteomic differences exist between cluster I and cluster II strains in intermediate modulating conditions, this study compared the whole cell proteome and secretome between L1423 and L1191 grown in THIJS media with 5 mM MgSO4 using iTRAQ and high-resolution multiple reaction monitoring (MRM-hr). Two proteins (BP0200 and BP1175) in the whole cell were upregulated in L1423 [fold change (FC) >1.2, false discovery rate (FDR) <0.05]. In the secretome, four proteins from the type III secretion system (T3SS) effectors were downregulated (FC < 0.8, FDR < 0.05) while six proteins, including two adhesins, pertactin (Prn) and tracheal colonization factor A (TcfA), were upregulated which were consistent with our previous proteomic study. The upregulation of Prn and TcfA in SNP cluster I may result in improved adhesion while the downregulation of the T3SS and other immunogenic proteins may reduce immune recognition, which may contribute to the increased fitness of cluster I B. pertussis strains.
Collapse
Affiliation(s)
- Laurence Don Wai Luu
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Sophie Octavia
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Ling Zhong
- Bioanalytical Mass Spectrometry Facility, University of New South Wales, Sydney, NSW, Australia
| | - Mark J Raftery
- Bioanalytical Mass Spectrometry Facility, University of New South Wales, Sydney, NSW, Australia
| | - Vitali Sintchenko
- Centre for Infectious Diseases and Microbiology-Public Health, Institute of Clinical Pathology and Medical Research - NSW Health Pathology, Westmead Hospital, Sydney, NSW, Australia.,Marie Bashir Institute for Infectious Diseases and Biosecurity, Sydney Medical School, University of Sydney, Sydney, NSW, Australia
| | - Ruiting Lan
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| |
Collapse
|
31
|
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. [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [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.
Collapse
Affiliation(s)
- Natalie Ring
- 1Department of Biology and Biochemistry and the Milner Centre for Evolution, University of Bath, Bath, UK
| | - Jonathan S Abrahams
- 1Department of Biology and Biochemistry and the Milner Centre for Evolution, University of Bath, Bath, UK
| | - Miten Jain
- 2UC Santa Cruz Genomics Institute, 1156 High Street, Santa Cruz, CA 95064, USA
| | - Hugh Olsen
- 2UC Santa Cruz Genomics Institute, 1156 High Street, Santa Cruz, CA 95064, USA
| | - Andrew Preston
- 1Department of Biology and Biochemistry and the Milner Centre for Evolution, University of Bath, Bath, UK
| | - Stefan Bagby
- 1Department of Biology and Biochemistry and the Milner Centre for Evolution, University of Bath, Bath, UK
| |
Collapse
|
32
|
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.
Collapse
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
| |
Collapse
|
33
|
Brookes C, Freire-Martin I, Cavell B, Alexander F, Taylor S, Persaud R, Fry N, Preston A, Diavatopoulos D, Gorringe A. Bordetella pertussis isolates vary in their interactions with human complement components. Emerg Microbes Infect 2018; 7:81. [PMID: 29739922 PMCID: PMC5940884 DOI: 10.1038/s41426-018-0084-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Revised: 04/04/2018] [Accepted: 04/09/2018] [Indexed: 12/16/2022]
Abstract
Whooping cough is a re-emerging respiratory tract infection. It has become clear that there is a need for better understanding of protective immune responses and variation between Bordetella pertussis strains to aid the development of improved vaccines. In order to survive in the host, B. pertussis has evolved mechanisms to evade complement-mediated killing, including the ability to bind complement-regulatory proteins. Here we evaluate the variation in interactions with the complement system among recently isolated strains. Isolates whose genomes appear highly similar and cluster together on a SNP-based dendrogram were found to vary significantly in resistance to complement-mediated killing and in the deposition of C3b/iC3b, C5b-9 and C1 esterase inhibitor (C1-INH). The key role of Vag8 as a receptor for C1-INH was confirmed and its expression was shown to vary in a panel of isolates. A Vag8 knockout mutant showed increased sensitivity to complement-mediated killing. Antibodies in convalescent sera blocked C1-INH binding to B. pertussis and may play an important role in natural immunity.
Collapse
Affiliation(s)
| | | | | | | | | | - Ruby Persaud
- Public Health England, Porton Down, Salisbury, UK
| | - Norman Fry
- Public Health England, 61 Colindale Avenue, London, UK
| | - Andrew Preston
- Department of Biology and Biochemistry, The Milner Centre for Evolution, University of Bath, Bath, UK
| | - Dimitri Diavatopoulos
- Laboratory of Medical immunology, Nijmegen Medical Centre, Radboud University, Nijmegen, The Netherlands
| | | |
Collapse
|
34
|
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.
Collapse
|
35
|
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.
Collapse
|
36
|
Abstract
Whooping cough is a highly contagious, acute respiratory disease, caused by the Gram-negative bacterium Bordetella pertussis (Bp). Despite the introduction and widespread use of vaccines starting in the 1950s pertussis cases continue to be reported, with a significant global impact. The role of specific virulence factors in disease and the immune mechanisms associated with protection following natural infection or vaccination are still not completely understood. The recently-developed baboon model of clinical pertussis provides a valuable tool for the study of pertussis. Baboons infected with B. pertussis exhibit all of the manifestations of human pertussis including paroxysmal coughing, mucus production, leukocytosis and transmission. The establishment of this model provides the opportunity to address unanswered questions about the natural progression of this disease and host responses to infection and vaccination in a very relevant model. In this review, we present an overview of our knowledge of pertussis along with recent advances resulting from use of the baboon model. Remaining questions and future research directions are discussed. We hope that the knowledge gained through use of the baboon model of pertussis and clinical studies will allow the development of more efficacious vaccines, conferring long lasting protection against disease and transmission.
Collapse
Affiliation(s)
- Marta V Pinto
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK.
| | - Tod J Merkel
- Laboratory of Respiratory and Special Pathogens, Center for Biologics Evaluation and Research, Food and Drug Administration, Bethesda, MD, USA.
| |
Collapse
|
37
|
Abstract
Currently used vaccines have had major effects on eliminating common infections, largely by duplicating the immune responses induced by natural infections. Now vaccinology faces more complex problems, such as waning antibody, immunosenescence, evasion of immunity by the pathogen, deviation of immunity by the microbiome, induction of inhibitory responses, and complexity of the antigens required for protection. Fortunately, vaccine development is now incorporating knowledge from immunology, structural biology, systems biology and synthetic chemistry to meet these challenges. In addition, international organisations are developing new funding and licensing pathways for vaccines aimed at pathogens with epidemic potential that emerge from tropical areas.
Collapse
Affiliation(s)
| | - Marta V Pinto
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK.
| | - Manish Sadarangani
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK; Vaccine Evaluation Center, BC Children's Hospital Research Institute, University of British Columbia, Vancouver BC, Canada.
| | - Stanley A Plotkin
- Department of Pediatrics, University of Pennsylvania, Philadelphia, USA.
| |
Collapse
|
38
|
Burdin N, Handy LK, Plotkin SA. What Is Wrong with Pertussis Vaccine Immunity? The Problem of Waning Effectiveness of Pertussis Vaccines. Cold Spring Harb Perspect Biol 2017; 9:a029454. [PMID: 28289064 PMCID: PMC5710106 DOI: 10.1101/cshperspect.a029454] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Pertussis is resurgent in some countries, particularly those in which children receive acellular pertussis (aP) vaccines in early infancy and boosters later in life. Immunologic studies show that, whereas whole-cell pertussis (wP) vaccines orient the immune system toward Th1/Th17 responses, acellular pertussis vaccines orient toward Th1/Th2 responses. Although aP vaccines do provide protection during the first years of life, the change in T-cell priming results in waning effectiveness of aP as early as 2-3 years post-boosters. Although other factors, such as increased virulence of pertussis strains, better diagnosis, and better surveillance may play a role, the increase in pertussis appears to be the result of waning immunity. In addition, studies in baboon models, requiring confirmation in humans, show that aP is less able to prevent nasopharyngeal colonization of Bordetella pertussis than wP or natural infection.
Collapse
Affiliation(s)
- Nicolas Burdin
- EU Research and Non Clinical Safety, R&D, Sanofi Pasteur, Campus Mérieux, 69280 Marcy l'Etoile, France
| | - Lori Kestenbaum Handy
- Assistant Professor of Pediatrics, Sidney Kimmel Medical College at Thomas Jefferson University, Division of Infectious Diseases, Nemours/Alfred I. duPont Hospital for Children, Wilmington, Delaware 19803
| | - Stanley A Plotkin
- Emeritus Professor of Pediatrics, University of Pennsylvania, Vaxconsult, Doylestown, Pennsylvania 18902
| |
Collapse
|
39
|
Abstract
PURPOSE OF REVIEW The purpose of this review is to summarize and discuss recent findings and selected topics of interest in Bordetella pertussis virulence and pathogenesis and treatment of pertussis. It is not intended to cover issues on immune responses to B. pertussis infection or problems with currently used pertussis vaccines. RECENT FINDINGS Studies on the activities of various B. pertussis virulence factors include the immunomodulatory activities of filamentous hemagglutinin, fimbriae, and adenylate cyclase toxin. Recently emerging B. pertussis strains show evidence of genetic selection for vaccine escape mutants, with changes in vaccine antigen-expressing genes, some of which may have increased the virulence of this pathogen. Severe and fatal pertussis in young infants continues to be a problem, with several studies highlighting predictors of fatality, including the extreme leukocytosis associated with this infection. Treatments for pertussis are extremely limited, though early antibiotic intervention may be beneficial. Neutralizing pertussis toxin activity may be an effective strategy, as well as targeting two host proteins, pendrin and sphingosine-1-phosphate receptors, as novel potential therapeutic interventions. SUMMARY Pertussis is reemerging as a major public health problem and continued basic research is revealing information on bacterial virulence and disease pathogenesis, as well as potential novel strategies for vaccination and targets for therapeutic intervention.
Collapse
|
40
|
The History of Bordetella pertussis Genome Evolution Includes Structural Rearrangement. J Bacteriol 2017; 199:JB.00806-16. [PMID: 28167525 DOI: 10.1128/jb.00806-16] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Accepted: 02/03/2017] [Indexed: 01/08/2023] Open
Abstract
Despite high pertussis vaccine coverage, reported cases of whooping cough (pertussis) have increased over the last decade in the United States and other developed countries. Although Bordetella pertussis is well known for its limited gene sequence variation, recent advances in long-read sequencing technology have begun to reveal genomic structural heterogeneity among otherwise indistinguishable isolates, even within geographically or temporally defined epidemics. We have compared rearrangements among complete genome assemblies from 257 B. pertussis isolates to examine the potential evolution of the chromosomal structure in a pathogen with minimal gene nucleotide sequence diversity. Discrete changes in gene order were identified that differentiated genomes from vaccine reference strains and clinical isolates of various genotypes, frequently along phylogenetic boundaries defined by single nucleotide polymorphisms. The observed rearrangements were primarily large inversions centered on the replication origin or terminus and flanked by IS481, a mobile genetic element with >240 copies per genome and previously suspected to mediate rearrangements and deletions by homologous recombination. These data illustrate that structural genome evolution in B. pertussis is not limited to reduction but also includes rearrangement. Therefore, although genomes of clinical isolates are structurally diverse, specific changes in gene order are conserved, perhaps due to positive selection, providing novel information for investigating disease resurgence and molecular epidemiology.IMPORTANCE Whooping cough, primarily caused by Bordetella pertussis, has resurged in the United States even though the coverage with pertussis-containing vaccines remains high. The rise in reported cases has included increased disease rates among all vaccinated age groups, provoking questions about the pathogen's evolution. The chromosome of B. pertussis includes a large number of repetitive mobile genetic elements that obstruct genome analysis. However, these mobile elements facilitate large rearrangements that alter the order and orientation of essential protein-encoding genes, which otherwise exhibit little nucleotide sequence diversity. By comparing the complete genome assemblies from 257 isolates, we show that specific rearrangements have been conserved throughout recent evolutionary history, perhaps by eliciting changes in gene expression, which may also provide useful information for molecular epidemiology.
Collapse
|
41
|
Short-Read Whole-Genome Sequencing for Laboratory-Based Surveillance of Bordetella pertussis. J Clin Microbiol 2017; 55:1446-1453. [PMID: 28228490 DOI: 10.1128/jcm.02436-16] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Accepted: 02/13/2017] [Indexed: 11/20/2022] Open
Abstract
Bordetella pertussis is a Gram-negative bacterium that causes respiratory infections in humans. Ongoing molecular surveillance of B. pertussis acellular vaccine (aP) antigens is critical for understanding the interaction between evolutionary pressures, disease pathogenesis, and vaccine effectiveness. Methods currently used to characterize aP components are relatively labor-intensive and low throughput. To address this challenge, we sought to derive aP antigen genotypes from minimally processed short-read whole-genome sequencing data generated from 40 clinical B. pertussis isolates and analyzed using the SRST2 bioinformatic package. SRST2 was able to identify aP antigen genotypes for all antigens with the exception of pertactin, possibly due to low read coverage in GC-rich low-complexity regions of variation. Two main genotypes were observed in addition to a singular third genotype that contained an 84-bp deletion that was identified by SRST2 despite the issues in allele calling. This method has the potential to generate large pools of B. pertussis molecular data that can be linked to clinical and epidemiological information to facilitate research of vaccine effectiveness and disease severity in the context of emerging vaccine antigen-deficient strains.
Collapse
|
42
|
Complete Genome Sequences of Four Bordetella pertussis Vaccine Reference Strains from Serum Institute of India. GENOME ANNOUNCEMENTS 2016; 4:4/6/e01404-16. [PMID: 28007855 PMCID: PMC5180383 DOI: 10.1128/genomea.01404-16] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Serum Institute of India is among the world’s largest vaccine producers. Here, we report the complete genome sequences for four Bordetella pertussis strains used by Serum Institute of India in the production of whole-cell pertussis vaccines.
Collapse
|
43
|
Lapidot R, Gill CJ. The Pertussis resurgence: putting together the pieces of the puzzle. TROPICAL DISEASES TRAVEL MEDICINE AND VACCINES 2016; 2:26. [PMID: 28883970 PMCID: PMC5530967 DOI: 10.1186/s40794-016-0043-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Accepted: 11/23/2016] [Indexed: 01/13/2023]
Abstract
Pertussis incidence is rising in almost every country where acellular pertussis (aP) vaccines have been introduced, and is occurring across all age groups from infancy to adulthood. The key question is why? While several known factors such as waning of immunity, detection bias due to more sensitive tests and higher awareness of the disease among practitioners, and evolutionary shifts among B. pertussis all likely contribute, collectively, these do not adequately explain the existing epidemiologic data, suggesting that additional factors also contribute. Key amongst these is recent data indicating that the immune responses induced by aP vaccines differ fundamentally from those induced by the whole cell pertussis (wP) vaccines, and do not lead to mucosal immunity. If so, it appears likely that differences in how the two categories of vaccines work, may be pivotal to our overall understanding of the pertussis resurgence.
Collapse
Affiliation(s)
- Rotem Lapidot
- Department of Pediatric Infectious Diseases, Boston Medical Center, Boston, MA USA
| | - Christopher J Gill
- Department of Global Health, Boston University School of Public Health, Boston, MA USA.,Center for Global Health and Development, Boston University School of Public Health, 801 Massachusetts Avenue, Boston, MA 02118 USA
| |
Collapse
|
44
|
Octavia S, Wu SZ, Kaur S, Valinsky L, Marva E, Moran-Gilad J, Lan R. Whole-genome sequencing and comparative genomic analysis of Bordetella pertussis isolates from the 2007-2008 epidemic in Israel. J Infect 2016; 74:204-207. [PMID: 27914992 DOI: 10.1016/j.jinf.2016.11.012] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Accepted: 11/25/2016] [Indexed: 10/20/2022]
Affiliation(s)
- 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
| | - Lea Valinsky
- Public Health Services, Ministry of Health, Jerusalem, Israel
| | - Esther Marva
- Public Health Services, Ministry of Health, Jerusalem, Israel
| | - Jacob Moran-Gilad
- Public Health Services, Ministry of Health, Jerusalem, Israel; Department of Health Systems Management, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel; ESCMID Study Group for Genomic and Molecular Diagnostics (ESGMD), Israel
| | - Ruiting Lan
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia.
| |
Collapse
|
45
|
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.
Collapse
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.
| |
Collapse
|
46
|
Complete Genome Sequences of Bordetella pertussis Vaccine Reference Strains 134 and 10536. GENOME ANNOUNCEMENTS 2016; 4:4/5/e00979-16. [PMID: 27635001 PMCID: PMC5026441 DOI: 10.1128/genomea.00979-16] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Vaccine formulations and vaccination programs against whooping cough (pertussis) vary worldwide. Here, we report the complete genome sequences of two divergent Bordetella pertussis reference strains used in the production of pertussis vaccines.
Collapse
|
47
|
Shuel M, Lefebvre B, Whyte K, Hayden K, De Serres G, Brousseau N, Tsang RS. Antigenic and genetic characterization of Bordetella pertussis recovered from Quebec, Canada, 2002–2014: detection of a genetic shift. Can J Microbiol 2016; 62:437-41. [DOI: 10.1139/cjm-2015-0781] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Despite vaccination, cyclical peaks of Bordetella pertussis incidence rates are still observed in Canada and other developed countries, making pertussis one of the most prevalent vaccine preventable bacterial diseases. In the postacellular vaccine era, evolution of bacterial strains has resulted in strains with altered vaccine antigens. Previous Canadian studies have focused on isolates mainly from the provinces of Ontario and Alberta, with only small numbers of isolates from other provinces. Therefore, in this study, we examined a larger sample (n = 52) of isolates from Quebec, Canada, between 2002 and 2014. Isolates were characterized by serotype, sequence type, and prevalence of pertactin deficiency. The Quebec isolates shared characteristics similar to other Canadian isolates and to isolates circulating globally. Although pertactin-deficient isolates were not present, a significant shift in sequence type was observed in more recent years. This study highlights the importance of continually monitoring disease-causing isolates to track evolutionary trends and gain a better understanding of the molecular epidemiology of pertussis in Canada.
Collapse
Affiliation(s)
- Michelle Shuel
- Public Health Agency of Canada, National Microbiology Laboratory, Winnipeg, Manitoba, Canada
| | - Brigitte Lefebvre
- Laboratoire de santé publique du Québec, Sainte-Anne-de-Bellevue, Quebec, Canada
| | - Kathleen Whyte
- Public Health Agency of Canada, National Microbiology Laboratory, Winnipeg, Manitoba, Canada
| | - Kristy Hayden
- Public Health Agency of Canada, National Microbiology Laboratory, Winnipeg, Manitoba, Canada
| | - Gaston De Serres
- Institut National de Sante Publique du Québec, Quebec, Canada
- Laval University, Quebec, Canada
| | | | - Raymond S.W. Tsang
- Public Health Agency of Canada, National Microbiology Laboratory, Winnipeg, Manitoba, Canada
| |
Collapse
|
48
|
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: 40] [Impact Index Per Article: 5.0] [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.
Collapse
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
| |
Collapse
|
49
|
Sealey KL, Belcher T, Preston A. Bordetella pertussis epidemiology and evolution in the light of pertussis resurgence. INFECTION GENETICS AND EVOLUTION 2016; 40:136-143. [PMID: 26932577 DOI: 10.1016/j.meegid.2016.02.032] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Revised: 02/16/2016] [Accepted: 02/25/2016] [Indexed: 11/28/2022]
Abstract
Whooping cough, or pertussis, is resurgent in many countries world-wide. This is linked to switching from the use of whole cell vaccines to acellular vaccines in developed countries. Current evidence suggests that this has resulted in the earlier waning of vaccine-induced immunity, an increase in asymptomatic infection with concomitant increases in transmission and increased selection pressure for Bordetellapertussis variants that are better able to evade vaccine-mediated immunity than older isolates. This review discusses recent findings in B. pertussis epidemiology and evolution in the light of pertussis resurgence, and highlights the important role for genomics-based studies in monitoring B. pertussis adaptation.
Collapse
Affiliation(s)
- Katie L Sealey
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, UK
| | - Thomas Belcher
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, UK
| | - Andrew Preston
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, UK.
| |
Collapse
|
50
|
Preston A. The role of B. pertussis vaccine antigen gene variants in pertussis resurgence and possible consequences for vaccine development. Hum Vaccin Immunother 2016; 12:1274-6. [PMID: 26889694 DOI: 10.1080/21645515.2015.1137402] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Whooping cough, or pertussis, caused by Bordetella pertussis is considered resurgent in a number of countries world-wide, despite continued high level vaccine coverage. Among a number of causes for this that have been proposed, is the emergence of B. pertussis strains expressing variants of the antigens contained in acellular pertussis vaccines; i.e. the evolution of B. pertussis toward vaccine escape. This commentary highlights the contradictory nature of evidence for this but also discusses the importance of understanding the role of B. pertussis adaptation to vaccine-mediated immune selection pressures for vaccine-mediated pertussis control strategies.
Collapse
Affiliation(s)
- Andrew Preston
- a Milner Center for Evolution and Department of Biology and Biochemistry, University of Bath , Bath , UK
| |
Collapse
|