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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: 2] [Impact Index Per Article: 1.0] [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.
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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
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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: 0.8] [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.
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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
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Li L, Deng J, Ma X, Zhou K, Meng Q, Yuan L, Shi W, Wang Q, Li Y, Yao K. High Prevalence of Macrolide-Resistant Bordetella pertussis and ptxP1 Genotype, Mainland China, 2014-2016. Emerg Infect Dis 2020; 25:2205-2214. [PMID: 31742507 PMCID: PMC6874251 DOI: 10.3201/eid2512.181836] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
According to the government of China, reported cases of pertussis have increased remarkably and are still increasing. To determine the genetic relatedness of Bordetella pertussis strains, we compared multilocus variable-number tandem-repeat analysis (MLVA) results for isolates from China with those from Western countries. Among 335 isolates from China, the most common virulence-associated genotype was ptxA1/ptxC1/ptxP1/prn1/fim2–1/fim3A/tcfA2, which was more frequent among isolates from northern than southern China. Isolates of this genotype were highly resistant to erythromycin. We identified 36 ptxP3 strains mainly harboring ptxA1 and prn2 (35/36); ptxP3 strains were sensitive to erythromycin and were less frequently from northern China. For all isolates, the sulfamethoxazole/trimethoprim MIC was low, indicating that this drug should be recommended for patients infected with erythromycin-resistant B. pertussis. MLVA of 150 clinical isolates identified 13 MLVA types, including 3 predominant types. Our results show that isolates circulating in China differ from those in Western countries.
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Kamachi K, Otsuka N, Fumimoto R, Ozawa K, Yao SM, Chiang CS, Luu LDW, Lan R, Shibayama K, Watanabe M. A novel multilocus variable-number tandem repeat analysis for Bordetella parapertussis. J Med Microbiol 2019; 68:1671-1676. [PMID: 31613204 DOI: 10.1099/jmm.0.001095] [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: 11/18/2022] Open
Abstract
Purpose. Human-adapted Bordetella parapertussis is one of the causative agents of whooping cough; however, there are currently no genotyping systems with high discriminatory power for this bacterial pathogen. We therefore aimed to develop a multilocus variable-number tandem repeat analysis (MLVA) for human-adapted B. parapertussis.Methodology. Four highly polymorphic variable number tandem repeat (VNTR) loci in the B. parapertussis genome were selected and amplified by multiplex PCR. MLVA was performed based on the number of tandem repeats at VNTR loci. The discriminatory power of MLVA was evaluated with three laboratory reference strains and 50 human isolates of B. parapertussis.Results. Multiplex PCR-based MLVA characterized 53 B. parapertussis reference strains and isolates into 25 MLVA types and the Simpson diversity index was 0.91 (95 % confidence interval, 0.86-0.97). The three reference strains exhibited different MLVA types. Thirty-one Japanese isolates, ten French isolates and three Taiwanese isolates belonged to fourteen, nine and three MLVA types, respectively. In contrast, all five Australian isolates belonged to the same type. Two Japanese isolates collected from patients with known epidemiological links had the same type.Conclusion. Our novel MLVA method has high discriminatory power for genotyping human B. parapertussis. Regarding this organism, this genotyping system is a promising tool for epidemiological surveillance and investigating outbreaks.
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Affiliation(s)
- Kazunari Kamachi
- Department of Bacteriology II, National Institute of Infectious Diseases, Tokyo, Japan
| | - Nao Otsuka
- Department of Bacteriology II, National Institute of Infectious Diseases, Tokyo, Japan
| | - Rei Fumimoto
- Department of Pediatrics, St Marianna University School of Medicine, Kawasaki, Japan.,Department of Bacteriology II, National Institute of Infectious Diseases, Tokyo, Japan
| | - Kensuke Ozawa
- R & D Center for Diagnostic Reagents, Denka Seiken, Niigata, Japan
| | - Shu-Man Yao
- Center for Diagnostics and Vaccine Development, Centers for Disease Control, Taipei, Taiwan, ROC
| | - Chuen-Sheue Chiang
- Center for Diagnostics and Vaccine Development, Centers for Disease Control, Taipei, Taiwan, ROC
| | - Laurence Don Wai Luu
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia
| | - Ruiting Lan
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia
| | - Keigo Shibayama
- Department of Bacteriology II, National Institute of Infectious Diseases, Tokyo, Japan
| | - Mineo Watanabe
- Present address: Division of Microbiology and Molecular Cell Biology, Nihon Pharmaceutical University, Saitama, Japan.,Graduate School of Infection Control Sciences, Kitasato University, Tokyo, Japan
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Tian Y, da Silva Antunes R, Sidney J, Lindestam Arlehamn CS, Grifoni A, Dhanda SK, Paul S, Peters B, Weiskopf D, Sette A. A Review on T Cell Epitopes Identified Using Prediction and Cell-Mediated Immune Models for Mycobacterium tuberculosis and Bordetella pertussis. Front Immunol 2018; 9:2778. [PMID: 30555469 PMCID: PMC6281829 DOI: 10.3389/fimmu.2018.02778] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Accepted: 11/12/2018] [Indexed: 01/01/2023] Open
Abstract
In the present review, we summarize work from our as well as other groups related to the characterization of bacterial T cell epitopes, with a specific focus on two important pathogens, namely, Mycobacterium tuberculosis (Mtb), the bacterium that causes tuberculosis (TB), and Bordetella pertussis (BP), the bacterium that causes whooping cough. Both bacteria and their associated diseases are of large societal significance. Although vaccines exist for both pathogens, their efficacy is incomplete. It is widely thought that defects and/or alteration in T cell compartments are associated with limited vaccine effectiveness. As discussed below, a full genome-wide map was performed in the case of Mtb. For BP, our focus has thus far been on the antigens contained in the acellular vaccine; a full genome-wide screen is in the planning stage. Nevertheless, the sum-total of the results in the two different bacterial systems allows us to exemplify approaches and techniques that we believe are generally applicable to the mapping and characterization of human immune responses to bacterial pathogens. Finally, we add, as a disclaimer, that this review by design is focused on the work produced by our laboratory as an illustration of approaches to the study of T cell responses to Mtb and BP, and is not meant to be comprehensive, nor to detract from the excellent work performed by many other groups.
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Affiliation(s)
- Yuan Tian
- Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, CA, United States
| | | | - John Sidney
- Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, CA, United States
| | | | - Alba Grifoni
- Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, CA, United States
| | - Sandeep Kumar Dhanda
- Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, CA, United States
| | - Sinu Paul
- Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, CA, United States
| | - Bjoern Peters
- Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, CA, United States.,Department of Medicine, University of California San Diego, La Jolla, CA, United States
| | - Daniela Weiskopf
- Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, CA, United States
| | - Alessandro Sette
- Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, CA, United States.,Department of Medicine, University of California San Diego, La Jolla, CA, United States
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Emerging of ptxP3 lineage in Bordetella pertussis strains circulating in a population in northeastern Mexico. Epidemiol Infect 2018; 146:2096-2101. [PMID: 30136639 DOI: 10.1017/s0950268818002303] [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] [Indexed: 11/06/2022] Open
Abstract
We determined the molecular epidemiology of Bordetella pertussis isolates to evaluate its potential impact on pertussis reemergence in a population of Mexico. Symptomatic and asymptomatic cases were included. Pertussis infection was confirmed by culture and real-time polymerase chain reaction (PCR). Selected B. pertussis isolates were further analysed; i.e. clonality was analysed by pulsed-field gel electrophoresis (PFGE) and ptxP-ptxA, prn, fim2 and fim3 typing was performed by PCR and sequencing. Out of 11 864 analysed samples, 687 (5.8%) were positive for pertussis, with 244 (36%) confirmed by both culture and PCR whereas 115 (17%) were positive only by culture and 328 (48%) were positive only by PCR. One predominant clone (clone A, n = 62/113; 55%) and three major subtypes (A1, A2 and A3) were identified by PFGE. All 113 selected isolates had the allelic combination ptxP3-ptxA1. The predominant clone A and the three major subtypes (A1, A2 and A3) corresponded to the emerging genotypes ptxP3-ptxA1-prn2-fim2-1-fim3-2 and ptxP3-ptxA1-prn2-fim2-1-fim3-1. In conclusion, the presence of an endemic clone and three predominant subtypes belonging to the genotypes ptxP3-ptxA1-prn2-fim2-1-fim3-2 and ptxP3-ptxA1-prn2-fim2-1-fim3-1 were detected. This finding supports the global spread/expansion reported for these outbreaks associated genotypes.
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Luu LDW, Octavia S, Zhong L, Raftery MJ, Sintchenko V, Lan R. Proteomic Adaptation of Australian Epidemic Bordetella pertussis. Proteomics 2018; 18:e1700237. [PMID: 29464899 DOI: 10.1002/pmic.201700237] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Revised: 02/08/2018] [Indexed: 12/20/2022]
Abstract
Bordetella pertussis causes whooping cough. The predominant strains in Australia changed to single nucleotide polymorphism (SNP) cluster I (pertussis toxin promoter allele ptxP3/pertactin gene allele prn2) from cluster II (non-ptxP3/non-prn2). Cluster I was mostly responsible for the 2008-2012 Australian epidemic and was found to have higher fitness compared to cluster II using an in vivo mouse competition assay, regardless of host's immunization status. This study aimed to identify proteomic differences that explain higher fitness in cluster I using isobaric tags for relative and absolute quantification (iTRAQ), and high-resolution multiple reaction monitoring (MRM-hr). A few key differences in the whole cell and secretome were identified between the cluster I and II strains tested. In the whole cell, nine proteins were upregulated (>1.2 fold change, q < 0.05) and three were downregulated (<0.8 fold change, q < 0.05) in cluster I. One downregulated protein was BP1569, a TLR2 agonist for Th1 immunity. In the secretome, 12 proteins were upregulated and 1 was downregulated which was Bsp22, a type III secretion system (T3SS) protein. Furthermore, there was a trend of downregulation in three T3SS effectors and other virulence factors. Three proteins were upregulated in both whole cell and supernatant: BP0200, molybdate ABC transporter (ModB), and tracheal colonization factor A (TcfA). Important expression differences in lipoprotein, T3SS, and transport proteins between the cluster I and II strains were identified. These differences may affect immune evasion, virulence and metabolism, and play a role in increased fitness of cluster I.
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Affiliation(s)
- Laurence Don Wai Luu
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Sophie Octavia
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Ling Zhong
- Mark Wainwright Analytical Centre, University of New South Wales, Sydney, New South Wales, Australia
| | - Mark J Raftery
- Mark Wainwright Analytical Centre, University of New South Wales, Sydney, New South Wales, Australia
| | - Vitali Sintchenko
- Centre for Infectious Diseases and Microbiology-Public Health, Institute of Clinical Pathology and Medical Research-Pathology West, Westmead Hospital, New South Wales, Australia
- Marie Bashir Institute for Infectious Diseases and Biosecurity, Sydney Medical School, University of Sydney, New South Wales, Australia
| | - Ruiting Lan
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
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Petridou E, Jensen CB, Arvanitidis A, Giannaki-Psinaki M, Michos A, Krogfelt KA, Petersen RF. Molecular epidemiology of Bordetella pertussis in Greece, 2010-2015. J Med Microbiol 2018; 67:400-407. [PMID: 29458550 PMCID: PMC5882080 DOI: 10.1099/jmm.0.000688] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Purpose To determine the predominant strains of Bordetella pertussis in Greece during 2010–2015. Methodology Infants and children (n=1150) (15 days to 14 years) of Greek, Roma and immigrant origin with different vaccination statuses were hospitalized in Athens, Greece with suspected pertussis infection. IS481/IS1001 real-time PCR confirmed Bordetella spp./B. pertussis infection in 300 samples. A subset of samples (n=153) were analysed by multi-locus variable number tandem repeat analysis (MLVA) and (n=25) by sequence-based typing of the toxin promotor region (ptxP) on DNA extracted from clinical specimens. Results/Key findings A complete MLVA profile was determined in 66 out of 153 samples; the B. pertussis MLVA type 27 (n=55) was the dominant genotype and all tested samples (n=25) expressed the ptxP3 genotype. The vaccine coverage in the Greek population was 90 %; however, the study population expressed complete coverage in 2 out of 264 infants (0–11 months) and in 20 out of 36 children (1–14 years). Roma and immigrant minorities represent 7 % of the Greek population, but make up 50 % of the study population, indicating a low vaccine coverage among these groups. Conclusions The B. pertussis MT27 and ptxP3 genotype is dominant in Greek, Roma and immigrant infants and children hospitalized in Greece. Thus, the predominant MLVA genotype in Greece is similar to other countries using acellular vaccines.
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Affiliation(s)
- Evangelia Petridou
- Department of Clinical Microbiology, ‘Aghia Sophia’ Children's Hospital, Athens, Greece
| | - Christel Barker Jensen
- Department of Virus and Microbiological Special Diagnostics, Parasites & Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Athanasios Arvanitidis
- Department of Virus and Microbiological Special Diagnostics, Parasites & Fungi, Statens Serum Institut, Copenhagen, Denmark
- Department of Bacteria, Parasites & Fungi, Statens Serum Institut, Copenhagen, Denmark
| | | | - Athanasios Michos
- First Department of Pediatrics, National and Kapodistrian University of Athens, ‘Aghia Sophia’ Children's Hospital, Athens, Greece
| | | | - Randi Føns Petersen
- Department of Virus and Microbiological Special Diagnostics, Parasites & Fungi, Statens Serum Institut, Copenhagen, Denmark
- *Correspondence: Randi Føns Petersen,
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Molecular epidemiology of Bordetella pertussis in Cambodia determined by direct genotyping of clinical specimens. Int J Infect Dis 2017; 62:56-58. [PMID: 28751008 DOI: 10.1016/j.ijid.2017.07.015] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Revised: 06/26/2017] [Accepted: 07/16/2017] [Indexed: 11/23/2022] Open
Abstract
OBJECTIVES This study sought to determine the genotypes of circulating Bordetella pertussis, the causative agent of pertussis, in Cambodia by direct molecular typing of clinical specimens. METHODS DNA extracts from nasopharyngeal swabs obtained from 82 pertussis patients in 2008-2016 were analyzed by multilocus variable-number tandem repeat analysis (MLVA). B. pertussis virulence-associated allelic genes (ptxA, prn, and fim3) and the pertussis toxin promoter ptxP were also investigated by DNA sequence-based typing. RESULTS Forty-four DNA extracts (54%) yielded a complete MLVA profile, and these were sorted into 8 MLVA types (MT18, MT26, MT27, MT29, MT43, MT72, MT95, and MT200). MT27 and MT29, which are common in developed countries, were the predominant strain types (total 73%). The predominant profile of virulence-associated allelic genes was the combination of ptxP3/ptxA1/prn2/fim3A (48%). MT27 strains were detected during the entire study period, whereas MT29 strains were only found in 2014-2016. CONCLUSIONS The B. pertussis population in Cambodia, where a whole-cell pertussis vaccine (WCV) has been continuously used, resembled those observed previously in developed countries where acellular pertussis vaccines are used. Circulating B. pertussis strains in Cambodia were distinct from those in other countries using WCVs.
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Mosiej E, Krysztopa-Grzybowska K, Polak M, Prygiel M, Lutyńska A. Multi-locus variable-number tandem repeat analysis of Bordetella pertussis isolates circulating in Poland in the period 1959-2013. J Med Microbiol 2017; 66:753-761. [PMID: 28598302 DOI: 10.1099/jmm.0.000408] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
PURPOSE Despite the long history of pertussis vaccination and high vaccination coverage in Poland and many other developed countries, pertussis incidence rates have increased substantially, making whooping cough one of the most prevalent vaccine-preventable diseases. Among the factors potentially involved in pertussis resurgence, the adaptation of the Bordetella pertussis population to country-specific vaccine-induced immunity through selection of non-vaccine-type strains still needs detailed studies. METHODOLOGY Multi-locus variable-number tandem repeat analysis (MLVA), also linked to MLST and PFGE profiling, was applied to trace the genetic changes in the B. pertussis population circulating in Poland in the period 1959-2013 versus country-specific vaccine strains. RESULTS Generally, among 174 B. pertussis isolates, 31 MLVA types were detected, of which 11 were not described previously. The predominant MLVA types of recent isolates in Poland were different from those of the typical isolates circulating in other European countries. The MT27 type, currently predominant in Europe, was rarely seen and detected in only five isolates among all studied. The features of the vaccine strains used for production of the pertussis component of a national whole-cell diphtheria-tetanus-pertussis (DTP) vaccine, as studied by MLVA and MLST tools, were found to not match those observed in the currently circulating B. pertussis isolates in Poland. CONCLUSIONS Differences traced by MLVA in relation to the MLST and PFGE profiling confirmed that the B. pertussis strain types currently observed elsewhere in Europe, even if appearing in Poland, were not able to successfully disseminate within a human population in Poland that has been vaccinated with a whole-cell pertussis vaccine not used in other countries.
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Affiliation(s)
- Ewa Mosiej
- Department of Sera and Vaccines Evaluation, National Institute of Public Health-National Institute of Hygiene, 24 Chocimska Street, 00-791 Warsaw, Poland
| | - Katarzyna Krysztopa-Grzybowska
- Department of Sera and Vaccines Evaluation, National Institute of Public Health-National Institute of Hygiene, 24 Chocimska Street, 00-791 Warsaw, Poland
| | - Maciej Polak
- Department of Sera and Vaccines Evaluation, National Institute of Public Health-National Institute of Hygiene, 24 Chocimska Street, 00-791 Warsaw, Poland
| | - Marta Prygiel
- Department of Sera and Vaccines Evaluation, National Institute of Public Health-National Institute of Hygiene, 24 Chocimska Street, 00-791 Warsaw, Poland
| | - Anna Lutyńska
- Department of Sera and Vaccines Evaluation, National Institute of Public Health-National Institute of Hygiene, 24 Chocimska Street, 00-791 Warsaw, Poland
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Saadatian-Elahi M, Plotkin S, Mills KHG, Halperin SA, McIntyre PB, Picot V, Louis J, Johnson DR. Pertussis: Biology, epidemiology and prevention. Vaccine 2016; 34:5819-5826. [PMID: 27780629 DOI: 10.1016/j.vaccine.2016.10.029] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Revised: 10/06/2016] [Accepted: 10/08/2016] [Indexed: 12/14/2022]
Abstract
Despite long-standing vaccination programs, substantial increases in reported cases of pertussis have been described in several countries during the last 5years. Cases among very young infants who are at greatest risk of pertussis-related hospitalizations and mortality are the most alarming. Multiple hypotheses including but not limited to the availability of more sensitive diagnostic tests, greater awareness, and waning vaccine-induced immunity over time have been posited for the current challenges with pertussis. The conference "Pertussis: biology, epidemiology and prevention" held in Annecy-France (November 11-13, 2015) brought together experts and interested individuals to examine these issues and to formulate recommendations for optimal use of current vaccines, with a particular focus on strategies to minimize severe morbidity and mortality among infants during the first months of life. The expert panel concluded that improving vaccination strategies with current vaccines and development of new highly immunogenic and efficacious pertussis vaccines that have acceptable adverse event profiles are currently the two main areas of investigation for the control of pertussis. Some possible pathways forward to address these main challenges are discussed in this report.
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Affiliation(s)
- Mitra Saadatian-Elahi
- Pôle Santé, Recherche, Risques et Vigilances Groupement Hospitalier Edouard Herriot, Unité d'Hygiène, Epidémiologie et Prévention, 5 Place d'Arsonval, 69437 Lyon cedex 03, France.
| | | | - Kingston H G Mills
- School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin 2, Ireland
| | - Scott A Halperin
- Canadian Centre for Vaccinology, Dalhousie University, The IWK Health Centre and Nova Scotia Health Authority, Halifax, Nova Scotia, Canada
| | - Peter B McIntyre
- National Centre for Immunisation Research and Surveillance, The Children's Hospital at Westmead, Sydney, NSW, Australia
| | | | - Jacques Louis
- Fondation Mérieux, 17 rue Bourgelat, 69002 Lyon, France
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Better colonisation of newly emerged Bordetella pertussis in the co-infection mouse model study. Vaccine 2016; 34:3967-71. [PMID: 27346304 DOI: 10.1016/j.vaccine.2016.06.052] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Revised: 05/22/2016] [Accepted: 06/16/2016] [Indexed: 11/24/2022]
Abstract
Molecular epidemiological data indicates that the resurgence of pertussis (whooping cough) in populations with high vaccine coverage is associated with genomic adaptation of Bordetella pertussis, the causative agent of the disease, to vaccine selection pressure. We have previously shown that in the period after the introduction of acellular pertussis vaccine (ACV), the majority of circulating strains in Australia switched to single nucleotide polymorphism (SNP) cluster I (carrying ptxP3/prn2), replacing SNP cluster II (carrying ptxP1/prn3). In this study, we carried out an in vivo competition assay using a mouse model infected with SNP cluster I and II B. pertussis strains from Australia. We found that the SNP cluster I strain colonised better than the SNP cluster II strain, in both naïve and immunised mice, suggesting that SNP cluster I strains had better fitness regardless of immunisation status of the host, consistent with SNP cluster I strains replacing SNP cluster II. Nevertheless, we found that ACV enhanced clearance of both SNP cluster I and II strains from the mouse respiratory tract.
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Du Q, Wang X, Liu Y, Luan Y, Zhang J, Li Y, Liu X, Ma C, Li H, Wang Z, He Q. Direct molecular typing of Bordetella pertussis from nasopharyngeal specimens in China in 2012-2013. Eur J Clin Microbiol Infect Dis 2016; 35:1211-4. [PMID: 27146879 DOI: 10.1007/s10096-016-2655-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Accepted: 04/18/2016] [Indexed: 11/25/2022]
Abstract
Data on the molecular epidemiology of Bordetella pertussis are limited in developing countries where whole-cell pertussis vaccines (WCVs) have been used. The aim of this study was to determine the genotypes of circulating B. pertussis in China by direct molecular typing of clinical specimens. DNA extracts of 122 nasopharyngeal swabs (NPs) positive for B. pertussis by polymerase chain reaction (PCR) (targeting IS481 and ptx-Pr) from 2012 to 2013 were used for typing using the multiple-locus variable number tandem repeat analysis (MLVA) and also by PCR-based multilocus sequence typing (MLST) of B. pertussis virulence genes (ptxP, prn, and fim3). One hundred and eight DNA extracts (89 %) generated a complete MLVA type (MT). Among the 18 MTs obtained, MT55 (52 %) and MT104 (13 %) were the most common. MT27, which is linked to the ptxP3 allele and is prevalent in many developed countries using acellular pertussis vaccines (ACVs), was only found in 7 (6 %) DNA extracts. Eighty-seven DNA extracts (71 %) produced a complete multiantigen sequence typing (MAST) type. Of them, 77 (89 %) had the ptxP1/prn1/fim3-1 allele profile. Four DNA extracts (5 %) had the ptxP3/prn2/fim3-2 profile and 3 (4 %) had the ptxP3/prn1/fim3-2 allele profile. These seven DNA extracts also harbored MT27. Our result shows that B. pertussis circulating in China was different from those found in countries where ACVs have been in use, supporting the notion that selection pressure induced by WCVs and ACVs on the bacterial population differs.
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Affiliation(s)
- Q Du
- Xi'an Center for Disease Control and Prevention, Xi'an, China
| | - X Wang
- Xi'an Center for Disease Control and Prevention, Xi'an, China
| | - Y Liu
- Xi'an Center for Disease Control and Prevention, Xi'an, China
| | - Y Luan
- Xi'an Center for Disease Control and Prevention, Xi'an, China
| | - J Zhang
- Xi'an Center for Disease Control and Prevention, Xi'an, China
| | - Y Li
- Department of Infectious Diseases, Xi'an Children Hospital, Xi'an, China
| | - X Liu
- Department of Infectious Diseases, Xi'an Children Hospital, Xi'an, China
| | - C Ma
- Xi'an Center for Disease Control and Prevention, Xi'an, China
| | - H Li
- Xi'an Center for Disease Control and Prevention, Xi'an, China
| | - Z Wang
- Xi'an Center for Disease Control and Prevention, Xi'an, China.
| | - Q He
- Department of Medical Microbiology, Capital Medical University, Beijing, China.
- Department of Medical Microbiology and Immunology, University of Turku, Turku, Finland.
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Safarchi A, Octavia S, Wu SZ, Kaur S, Sintchenko V, Gilbert GL, Wood N, McIntyre P, Marshall H, Keil AD, Lan R. Genomic dissection of Australian Bordetella pertussis isolates from the 2008-2012 epidemic. J Infect 2016; 72:468-77. [PMID: 26826518 DOI: 10.1016/j.jinf.2016.01.005] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Revised: 12/15/2015] [Accepted: 01/14/2016] [Indexed: 11/24/2022]
Abstract
OBJECTIVES Despite high pertussis vaccination coverage, Australia experienced a prolonged epidemic in 2008-2012. The predominant Bordetella pertussis genotype harboured pertussis toxin promoter allele, ptxP3, and pertactin gene allele, prn2. The emergence and expansion of prn non-expressing isolates (Prn negative), were also observed. We aimed to investigate the microevolution and genomic diversity of epidemic B. pertussis isolates. METHODS We sequenced 22 B. pertussis isolates collected in 2008-2012 from two states of Australia which are geographically widely separated. Ten of the 22 were Prn negative isolates with three different modes of silencing of prn (prn::IS481F, prn::IS481R and prn::IS1002). Five pre-epidemic isolates were also sequenced for comparison. RESULTS Five single nucleotide polymorphisms were common in the epidemic isolates and differentiated them from pre-epidemic isolates. The Australian epidemic isolates can be divided into five lineages (EL1-EL5) with EL1 containing only Prn negative isolates. Comparison with global isolates showed that three lineages remained geographically and temporally distinct whereas two lineages mixed with isolates from 2012 UK outbreak. CONCLUSION Our results suggest significant diversification and the microevolution of B. pertussis within the 2008-2012 Australian epidemic.
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Affiliation(s)
- Azadeh Safarchi
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Sophie Octavia
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Sunny Z Wu
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Sandeep Kaur
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Vitali Sintchenko
- Centre for Infectious Diseases and Microbiology - Public Health, Institute of Clinical Pathology and Medical Research, Pathology West, Westmead Hospital, New South Wales, Australia; Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, New South Wales, Australia
| | - Gwendolyn L Gilbert
- Centre for Infectious Diseases and Microbiology - Public Health, Institute of Clinical Pathology and Medical Research, Pathology West, Westmead Hospital, New South Wales, Australia; Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, New South Wales, Australia
| | - Nicholas Wood
- National Centre for Immunisation Research and Surveillance of Vaccine Preventable Diseases (NCIRS), The Children's Hospital at Westmead, Westmead, New South Wales 2145, Australia; Discipline of Paediatrics and Child Health, University of Sydney, The Children's Hospital at Westmead, Westmead, New South Wales 2145, Australia; Department of Microbiology and Infectious Diseases, The Children's Hospital at Westmead, New South Wales, Australia
| | - Peter McIntyre
- National Centre for Immunisation Research and Surveillance of Vaccine Preventable Diseases (NCIRS), The Children's Hospital at Westmead, Westmead, New South Wales 2145, Australia; Discipline of Paediatrics and Child Health, University of Sydney, The Children's Hospital at Westmead, Westmead, New South Wales 2145, Australia; Department of Microbiology and Infectious Diseases, The Children's Hospital at Westmead, New South Wales, Australia
| | - Helen Marshall
- Vaccinology and Immunology Research Trials Unit, Women's and Children's Hospital and School of Medicine and Robinson Research Institute, University of Adelaide, South Australia, Australia
| | - Anthony D Keil
- Department of Microbiology, PathWest Laboratory Medicine WA, Princess Margaret Hospital for Children, Perth, Australia
| | - Ruiting Lan
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia.
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Xu Y, Zhang L, Tan Y, Wang L, Zhang S, Wang J. Genetic diversity and population dynamics of Bordetella pertussis in China between 1950–2007. Vaccine 2015; 33:6327-31. [DOI: 10.1016/j.vaccine.2015.09.040] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2015] [Revised: 08/26/2015] [Accepted: 09/15/2015] [Indexed: 10/23/2022]
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16
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Safarchi A, Octavia S, Luu LDW, Tay CY, Sintchenko V, Wood N, Marshall H, McIntyre P, Lan R. Pertactin negative Bordetella pertussis demonstrates higher fitness under vaccine selection pressure in a mixed infection model. Vaccine 2015; 33:6277-81. [PMID: 26432908 DOI: 10.1016/j.vaccine.2015.09.064] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Revised: 09/04/2015] [Accepted: 09/20/2015] [Indexed: 11/25/2022]
Abstract
Whooping cough or pertussis is a highly infectious respiratory disease in humans caused by Bordetella pertussis. The use of acellular vaccines (ACV) has been associated with the recent resurgence of pertussis in developed countries including Australia despite high vaccination coverage where B. pertussis strains that do not express pertactin (Prn), a key antigenic component of the ACV, have emerged and become prevalent. In this study, we used an in vivo competition assay in mice immunised with ACV and in naïve (control) mice to compare the proportion of colonisation with recent clinical Prn positive and Prn negative B. pertussis strains from Australia. The Prn negative strain colonised the respiratory tract more effectively than the Prn positive strain in immunised mice, out-competing the Prn positive strain by day 3 of infection. However, in control mice, the Prn positive strain out-competed the Prn negative strain. Our findings of greater ability of Prn negative strains to colonise ACV-immunised mice are consistent with reports of selective advantage for these strains in ACV-immunised humans.
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Affiliation(s)
- Azadeh Safarchi
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Sophie Octavia
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Laurence Don Wai Luu
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Chin Yen Tay
- Pathology and Laboratory Medicine, University of Western Australia, Perth, Western Australia, Australia
| | - Vitali Sintchenko
- Centre for Infectious Diseases and Microbiology-Public Health, Institute of Clinical Pathology and Medical Research-Pathology West, Westmead Hospital, New South Wales, Australia; Marie Bashir Institute for Infectious Diseases and Biosecurity, University of Sydney, New South Wales, Australia
| | - Nicholas Wood
- National Centre for Immunisation Research and Surveillance, Children's Hospital at Westmead and University of Sydney, New South Wales, Australia
| | - Helen Marshall
- Vaccinology and Immunology Research Trials Unit, Women's and Children's Hospital and School of Paediatrics and Reproductive Health and Robinson Research Institute, University of Adelaide, South Australia, Australia
| | - Peter McIntyre
- National Centre for Immunisation Research and Surveillance, Children's Hospital at Westmead and University of Sydney, New South Wales, Australia
| | - Ruiting Lan
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia.
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Belcher T, Preston A. Bordetella pertussis evolution in the (functional) genomics era. Pathog Dis 2015; 73:ftv064. [PMID: 26297914 DOI: 10.1093/femspd/ftv064] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/20/2015] [Indexed: 11/12/2022] Open
Abstract
The incidence of whooping cough caused by Bordetella pertussis in many developed countries has risen dramatically in recent years. This has been linked to the use of an acellular pertussis vaccine. In addition, it is thought that B. pertussis is adapting under acellular vaccine mediated immune selection pressure, towards vaccine escape. Genomics-based approaches have revolutionized the ability to resolve the fine structure of the global B. pertussis population and its evolution during the era of vaccination. Here, we discuss the current picture of B. pertussis evolution and diversity in the light of the current resurgence, highlight import questions raised by recent studies in this area and discuss the role that functional genomics can play in addressing current knowledge gaps.
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Affiliation(s)
- Thomas Belcher
- Department of Biology and Biochemistry, University of Bath, Bath BA2 7AY, UK
| | - Andrew Preston
- Department of Biology and Biochemistry, University of Bath, Bath BA2 7AY, UK
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18
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Nataprawira HM, Phangkawira E. A retrospective study of acute pertussis in Hasan Sadikin Hospital–Indonesia. JOURNAL OF ACUTE DISEASE 2015. [DOI: 10.1016/s2221-6189(15)30025-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
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19
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Galit SRL, Otsuka N, Furuse Y, Almonia DJV, Sombrero LT, Capeding RZ, Lupisan SP, Saito M, Oshitani H, Hiramatsu Y, Shibayama K, Kamachi K. Molecular epidemiology of Bordetella pertussis in the Philippines in 2012-2014. Int J Infect Dis 2015; 35:24-6. [PMID: 25861926 DOI: 10.1016/j.ijid.2015.04.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Revised: 03/16/2015] [Accepted: 04/01/2015] [Indexed: 11/30/2022] Open
Abstract
OBJECTIVES The present study was designed to determine the genotypes of circulating Bordetella pertussis in the Philippines by direct molecular typing of clinical specimens. METHODS Nasopharyngeal swabs (NPSs) were collected from 50 children hospitalized with pertussis in three hospitals during 2012-2014. Multilocus variable-number tandem repeat analysis (MLVA) was performed on the DNA extracts from NPSs. B. pertussis virulence-associated allelic genes (ptxA, prn, and fim3) and the pertussis toxin promoter, ptxP, were also investigated by DNA sequence-based typing. RESULTS Twenty-six DNA extracts yielded a complete MLVA profile, which were sorted into 10 MLVA types. MLVA type 34 (MT34), which is rare in Australia, Europe, Japan, and the USA, was the predominant strain (50%). Seven MTs (MT29, MT32, MT33, and MT283-286, total 42%) were single-locus variants of MT34, while two (MT141 and MT287, total 8%) were double-locus variants of MT34. All MTs had the combination of virulence-associated allelic genes, ptxP1-ptxA1-prn1-fim3A. CONCLUSIONS The B. pertussis population in the Philippines comprises genetically related strains. These strains are markedly different from those found in patients from other countries where acellular pertussis vaccines are used. The differences in vaccine types between these other countries and the Philippines, where the whole-cell vaccine is still used, may select for distinct populations of B. pertussis.
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Affiliation(s)
| | - Nao Otsuka
- Department of Bacteriology II, National Institute of Infectious Diseases, 4-7-1 Gakuen, Musashimurayama, Tokyo 208-0011, Japan
| | - Yuki Furuse
- Department of Virology, Tohoku University Graduate School of Medicine, Miyagi, Japan
| | | | - Lydia T Sombrero
- Research Institute for Tropical Medicine (RITM), Metro Manila, Philippines
| | - Rosario Z Capeding
- Research Institute for Tropical Medicine (RITM), Metro Manila, Philippines
| | - Socorro P Lupisan
- Research Institute for Tropical Medicine (RITM), Metro Manila, Philippines
| | - Mariko Saito
- Department of Virology, Tohoku University Graduate School of Medicine, Miyagi, Japan; Tohoku-RITM Collaborating Research Center on Emerging and Reemerging Infectious Diseases, Metro Manila, Philippines
| | - Hitoshi Oshitani
- Department of Virology, Tohoku University Graduate School of Medicine, Miyagi, Japan
| | - Yukihiro Hiramatsu
- Department of Bacteriology II, National Institute of Infectious Diseases, 4-7-1 Gakuen, Musashimurayama, Tokyo 208-0011, Japan
| | - Keigo Shibayama
- Department of Bacteriology II, National Institute of Infectious Diseases, 4-7-1 Gakuen, Musashimurayama, Tokyo 208-0011, Japan
| | - Kazunari Kamachi
- Department of Bacteriology II, National Institute of Infectious Diseases, 4-7-1 Gakuen, Musashimurayama, Tokyo 208-0011, Japan.
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20
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Lam C, Octavia S, Ricafort L, Sintchenko V, Gilbert GL, Wood N, McIntyre P, Marshall H, Guiso N, Keil AD, Lawrence A, Robson J, Hogg G, Lan R. Rapid increase in pertactin-deficient Bordetella pertussis isolates, Australia. Emerg Infect Dis 2014; 20:626-33. [PMID: 24655754 PMCID: PMC3966384 DOI: 10.3201/eid2004.131478] [Citation(s) in RCA: 119] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Acellular vaccines against Bordetella pertussis were introduced in Australia in 1997. By 2000, these vaccines had replaced whole-cell vaccines. During 2008–2012, a large outbreak of pertussis occurred. During this period, 30% (96/320) of B. pertussis isolates did not express the vaccine antigen pertactin (prn). Multiple mechanisms of prn inactivation were documented, including IS481 and IS1002 disruptions, a variation within a homopolymeric tract, and deletion of the prn gene. The mechanism of lack of expression of prn in 16 (17%) isolates could not be determined at the sequence level. These findings suggest that B. pertussis not expressing prn arose independently multiple times since 2008, rather than by expansion of a single prn-negative clone. All but 1 isolate had ptxA1, prn2, and ptxP3, the alleles representative of currently circulating strains in Australia. This pattern is consistent with continuing evolution of B. pertussis in response to vaccine selection pressure.
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Soubeyrand B, Greenberg M, Tibayrenc M, Louis J, Dutel C, Simondon F, Saadatian-Elahi M. Vaccination: an evolutionary engine for pathogens? Conference report. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2014; 27:137-141. [PMID: 25050487 DOI: 10.1016/j.meegid.2014.07.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2014] [Accepted: 07/05/2014] [Indexed: 06/03/2023]
Affiliation(s)
- B Soubeyrand
- Medical Affairs, Sanofi Pasteur MSD, 162 Avenue Jean Jaurès CS 50712, 69367 Lyon Cedex 07, France
| | - M Greenberg
- Department of Epidemiology, Sanofi Pasteur, 2 Avenue du Pont Pasteur, 69367 Lyon Cedex 07, France
| | - M Tibayrenc
- Maladies Infectieuses et Vecteurs Ecologie, Génétique, Evolution et Contrôle - MIVEGEC (IRD 224-CNRS 5290-UM1-UM2), Centre IRD, Montpellier Cedex 5, France
| | - J Louis
- Fondation Mérieux, 17 rue Bourgelat, 69002 Lyon, France
| | - C Dutel
- Fondation Mérieux, 17 rue Bourgelat, 69002 Lyon, France
| | - F Simondon
- Department of Epidemiology, Sanofi Pasteur MSD, 162 Avenue Jean Jaurès CS 50712, 69367 Lyon Cedex 07, France
| | - M Saadatian-Elahi
- Groupement Hospitalier Edouard Herriot, Service d'Hygiène, Epidémiologie et Prévention, Bâtiment 1, 5, place d'Arsonval, 69437 Lyon Cedex 03, France.
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22
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Molecular epidemiology of the pertussis epidemic in Washington State in 2012. J Clin Microbiol 2014; 52:3549-57. [PMID: 25031439 DOI: 10.1128/jcm.01189-14] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Although pertussis disease is vaccine preventable, Washington State experienced a substantial rise in pertussis incidence beginning in 2011. By June 2012, the reported cases reached 2,520 (37.5 cases per 100,000 residents), a 1,300% increase compared with the same period in 2011. We assessed the molecular epidemiology of this statewide epidemic using 240 isolates collected from case patients reported from 19 of 39 Washington counties during 2012 to 2013. The typing methods included pulsed-field gel electrophoresis (PFGE), multilocus variable number tandem repeat analysis (MLVA), multilocus sequence typing (MLST), and pertactin gene (prn) mutational analysis. Using the scheme PFGE-MLVA-MLST-prn mutations-Prn deficiency, the 240 isolates comprised 65 distinct typing profiles. Thirty-one PFGE types were found, with the most common types, CDC013 (n = 51), CDC237 (n = 44), and CDC002 (n = 42), accounting for 57% of them. Eleven MLVA types were observed, mainly comprising type 27 (n = 183, 76%). Seven MLST types were identified, with the majority of the isolates typing as prn2-ptxP3-ptxA1-fim3-1 (n = 157, 65%). Four different prn mutations accounted for the 76% of isolates exhibiting pertactin deficiency. PFGE provided the highest discriminatory power (D = 0.87) and was found to be a more powerful typing method than MLVA and MLST combined (D = 0.67). This study provides evidence for the continued predominance of MLVA 27 and prn2-ptxP3-ptxA1 alleles, along with the reemergence of the fim3-1 allele. Our results indicate that the Bordetella pertussis population causing this epidemic was diverse, with a few molecular types predominating. The PFGE, MLVA, and MLST profiles were consistent with the predominate types circulating in the United States and other countries. For prn, several mutations were present in multiple molecular types.
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Substantial gaps in knowledge of Bordetella pertussis antibody and T cell epitopes relevant for natural immunity and vaccine efficacy. Hum Immunol 2014; 75:440-51. [PMID: 24530743 DOI: 10.1016/j.humimm.2014.02.013] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2013] [Revised: 01/03/2014] [Accepted: 02/04/2014] [Indexed: 11/21/2022]
Abstract
The recent increase in whooping cough in vaccinated populations has been attributed to waning immunity associated with the acellular vaccine. The Immune Epitope Database (IEDB) is a repository of immune epitope data from the published literature and includes T cell and antibody epitopes for human pathogens. The IEDB conducted a review of the epitope literature, which revealed 300 Bordetella pertussis-related epitopes from 39 references. Epitope data are currently available for six virulence factors of B. pertussis: pertussis toxin, pertactin, fimbrial 2, fimbrial 3, adenylate cyclase and filamentous hemagglutinin. The majority of epitopes were defined for antibody reactivity; fewer T cell determinants were reported. Analysis of available protective correlates data revealed a number of candidate epitopes; however few are defined in humans and few have been shown to be protective. Moreover, there are a limited number of studies defining epitopes from natural infection versus whole cell or acellular/subunit vaccines. The relationship between epitope location and structural features, as well as antigenic drift (SNP analysis) was also investigated. We conclude that the cumulative data is yet insufficient to address many fundamental questions related to vaccine failure and this underscores the need for further investigation of B. pertussis immunity at the molecular level.
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Miyaji Y, Otsuka N, Toyoizumi-Ajisaka H, Shibayama K, Kamachi K. Genetic analysis of Bordetella pertussis isolates from the 2008-2010 pertussis epidemic in Japan. PLoS One 2013; 8:e77165. [PMID: 24124606 PMCID: PMC3790747 DOI: 10.1371/journal.pone.0077165] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2013] [Accepted: 09/09/2013] [Indexed: 02/04/2023] Open
Abstract
A large pertussis epidemic occurred between 2008 and 2010 in Japan. To investigate epidemic strains, we analyzed 33 Bordetella pertussis isolates from the epidemic period by sequencing virulence-associated genes (fim3, ptxP, ptxA, and prn) and performing multilocus variable-number tandem repeat analysis (MLVA), and compared these results with those of 101 isolates from non-epidemic, earlier and later time periods. DNA sequencing of the fim3 allele revealed that the frequency of fim3B was 4.3%, 12.8%, 30.3%, and 5.1% within isolates in 2002–2004, 2005–2007, 2008–2010, and 2011–2012, respectively. The isolation rate of the fim3B strain therefore temporarily increased during the epidemic period 2008–2010. In contrast, the frequencies of the virulence-associated allelic variants, ptxP3, ptxA1, and prn2, increased with time during overall study period, indicating that these variants were not directly involved in the occurrence of the 2008–2010 epidemic. MLVA genotyping in combination with analysis of allele types showed that the prevalence of an MT27d strain temporarily increased in the epidemic period, and that this strain carried virulence-associated allelic variants (fim3B, ptxP3, ptxA1, and prn2) also identified in recent epidemic strains of Australia, Europe, and the US. Phenotypic analyses revealed that the serotype Fim3 strain was predominant (≥87%) during all the periods studied, and that the frequency of adhesion pertactin (Prn) non-expressing B. pertussis decreased by half in the epidemic period. All MT27d strains expressed Prn and Fim3 proteins, suggesting that B. pertussis MT27d strains expressing Prn and Fim3B have the potential to cause large epidemics worldwide.
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Affiliation(s)
- Yusuke Miyaji
- Department of Bacteriology II, National Institute of Infectious Diseases, Tokyo, Japan
- Department of Pediatrics, St Marianna University School of Medicine, Kawasaki, Japan
| | - Nao Otsuka
- Department of Bacteriology II, National Institute of Infectious Diseases, Tokyo, Japan
| | | | - Keigo Shibayama
- Department of Bacteriology II, National Institute of Infectious Diseases, Tokyo, Japan
| | - Kazunari Kamachi
- Department of Bacteriology II, National Institute of Infectious Diseases, Tokyo, Japan
- * E-mail:
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Poland GA. Pertussis outbreaks and pertussis vaccines: new insights, new concerns, new recommendations? Vaccine 2013; 30:6957-9. [PMID: 23141958 DOI: 10.1016/j.vaccine.2012.09.084] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2012] [Accepted: 09/19/2012] [Indexed: 11/17/2022]
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Petersen RF, Dalby T, Dragsted DM, Mooi F, Lambertsen L. Temporal trends in Bordetella pertussis populations, Denmark, 1949-2010. Emerg Infect Dis 2013; 18:767-74. [PMID: 22515990 PMCID: PMC3358084 DOI: 10.3201/eid1805.110812] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Reduced genetic diversity possibly resulted from introduction of pertussis vaccines We used multilocus variable-number tandem repeat analysis and multiple antigen sequence typing to characterize isolates of Bordetella pertussis strains circulating in Denmark during periods with and without pertussis vaccination coverage. Our results show substantial shifts in the B. pertussis population over time and a reduction in genetic diversity. These changes might have resulted from the introduction of pertussis vaccines in Denmark and other parts of Europe. The predominant strains currently circulating in Denmark resemble those in other European countries.
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27
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Schmidtke AJ, Boney KO, Martin SW, Skoff TH, Tondella ML, Tatti KM. Population diversity among Bordetella pertussis isolates, United States, 1935-2009. Emerg Infect Dis 2013; 18:1248-55. [PMID: 22841154 PMCID: PMC3414039 DOI: 10.3201/eid1808.120082] [Citation(s) in RCA: 90] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Resurgence of pertussis was not directly correlated with changes in vaccine composition or schedule. Since the 1980s, pertussis notifications in the United States have been increasing. To determine the types of Bordetella pertussis responsible for these increases, we divided 661 B. pertussis isolates collected in the United States during 1935–2009 into 8 periods related to the introduction of novel vaccines or changes in vaccination schedule. B. pertussis diversity was highest from 1970–1990 (94%) but declined to ≈70% after 1991 and has remained constant. During 2006–2009, 81.6% of the strains encoded multilocus sequence type prn2-ptxP3-ptxS1A-fim3B, and 64% were multilocus variable number tandem repeat analysis type 27. US trends were consistent with those seen internationally; emergence and predominance of the fim3B allele was the only molecular characteristic associated with the increase in pertussis notifications. Changes in the vaccine composition and schedule were not the direct selection pressures that resulted in the allele changes present in the current B. pertussis population.
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Octavia S, Sintchenko V, Gilbert GL, Lawrence A, Keil AD, Hogg G, Lan R. Newly Emerging Clones of Bordetella pertussis Carrying prn2 and ptxP3 Alleles Implicated in Australian Pertussis Epidemic in 2008–2010. J Infect Dis 2012; 205:1220-4. [DOI: 10.1093/infdis/jis178] [Citation(s) in RCA: 121] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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Prevalence and genetic characterization of pertactin-deficient Bordetella pertussis in Japan. PLoS One 2012; 7:e31985. [PMID: 22348138 PMCID: PMC3279416 DOI: 10.1371/journal.pone.0031985] [Citation(s) in RCA: 110] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2011] [Accepted: 01/19/2012] [Indexed: 01/02/2023] Open
Abstract
The adhesin pertactin (Prn) is one of the major virulence factors of Bordetella pertussis, the etiological agent of whooping cough. However, a significant prevalence of Prn-deficient (Prn−) B. pertussis was observed in Japan. The Prn− isolate was first discovered in 1997, and 33 (27%) Prn− isolates were identified among 121 B. pertussis isolates collected from 1990 to 2009. Sequence analysis revealed that all the Prn− isolates harbor exclusively the vaccine-type prn1 allele and that loss of Prn expression is caused by 2 different mutations: an 84-bp deletion of the prn signal sequence (prn1ΔSS, n = 24) and an IS481 insertion in prn1 (prn1::IS481, n = 9). The frequency of Prn− isolates, notably those harboring prn1ΔSS, significantly increased since the early 2000s, and Prn− isolates were subsequently found nationwide. Multilocus variable-number tandem repeat analysis (MLVA) revealed that 24 (73%) of 33 Prn− isolates belong to MLVA-186, and 6 and 3 Prn− isolates belong to MLVA-194 and MLVA-226, respectively. The 3 MLVA types are phylogenetically closely related, suggesting that the 2 Prn− clinical strains (harboring prn1ΔSS and prn1::IS481) have clonally expanded in Japan. Growth competition assays in vitro also demonstrated that Prn− isolates have a higher growth potential than the Prn+ back-mutants from which they were derived. Our observations suggested that human host factors (genetic factors and immune status) that select for Prn− strains have arisen and that Prn expression is not essential for fitness under these conditions.
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Lam C, Octavia S, Bahrame Z, Sintchenko V, Gilbert GL, Lan R. Selection and emergence of pertussis toxin promoter ptxP3 allele in the evolution of Bordetella pertussis. INFECTION GENETICS AND EVOLUTION 2012; 12:492-5. [PMID: 22293463 DOI: 10.1016/j.meegid.2012.01.001] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2011] [Revised: 12/20/2011] [Accepted: 01/04/2012] [Indexed: 11/17/2022]
Abstract
Evolutionary studies using single nucleotide polymorphisms (SNPs) have separated Bordetella pertussis isolates into six major clusters, with recent isolates forming cluster I. The expansion of cluster I isolates was characterised by changes in genes encoding antigenic components in acellular vaccines, including pertactin (Prn). Here, we determined the initial emergence of the pertussis toxin promoter allele, ptxP3, from an evolutionary perspective. This allele was previously shown in a study from the Netherlands to be associated with increased pertussis toxin production as a result of a single base mutation in the ptxP. The ptxP region of 313 worldwide isolates was sequenced, including 208 isolates from Australia collected over a 40 year period. Eight alleles were identified, of which only two predominated: ptxP1 and ptxP3. One novel allele was also found. ptxP3 was only found in SNP cluster I of B. pertussis and its emergence is concurrent with the change to the non-vaccine prn2 allele. Our results suggest that the globally distributed cluster I of B. pertussis has the ability to evade vaccine induced selection pressure.
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Affiliation(s)
- Connie Lam
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia
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van Gent M, Bart MJ, van der Heide HGJ, Heuvelman KJ, Kallonen T, He Q, Mertsola J, Advani A, Hallander HO, Janssens K, Hermans PW, Mooi FR. SNP-based typing: a useful tool to study Bordetella pertussis populations. PLoS One 2011; 6:e20340. [PMID: 21647370 PMCID: PMC3103551 DOI: 10.1371/journal.pone.0020340] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2011] [Accepted: 04/29/2011] [Indexed: 11/19/2022] Open
Abstract
To monitor changes in Bordetella pertussis populations, mainly two typing methods are used; Pulsed-Field Gel Electrophoresis (PFGE) and Multiple-Locus Variable-Number Tandem Repeat Analysis (MLVA). In this study, a single nucleotide polymorphism (SNP) typing method, based on 87 SNPs, was developed and compared with PFGE and MLVA. The discriminatory indices of SNP typing, PFGE and MLVA were found to be 0.85, 0.95 and 0.83, respectively. Phylogenetic analysis, using SNP typing as Gold Standard, revealed false homoplasies in the PFGE and MLVA trees. Further, in contrast to the SNP-based tree, the PFGE- and MLVA-based trees did not reveal a positive correlation between root-to-tip distance and the isolation year of strains. Thus PFGE and MLVA do not allow an estimation of the relative age of the selected strains. In conclusion, SNP typing was found to be phylogenetically more informative than PFGE and more discriminative than MLVA. Further, in contrast to PFGE, it is readily standardized allowing interlaboratory comparisons. We applied SNP typing to study strains with a novel allele for the pertussis toxin promoter, ptxP3, which have a worldwide distribution and which have replaced the resident ptxP1 strains in the last 20 years. Previously, we showed that ptxP3 strains showed increased pertussis toxin expression and that their emergence was associated with increased notification in the Netherlands. SNP typing showed that the ptxP3 strains isolated in the Americas, Asia, Australia and Europe formed a monophyletic branch which recently diverged from ptxP1 strains. Two predominant ptxP3 SNP types were identified which spread worldwide. The widespread use of SNP typing will enhance our understanding of the evolution and global epidemiology of B. pertussis.
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Affiliation(s)
- Marjolein van Gent
- Laboratory for Infectious Diseases and Screening, Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Marieke J. Bart
- Laboratory for Infectious Diseases and Screening, Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Han G. J. van der Heide
- Laboratory for Infectious Diseases and Screening, Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Kees J. Heuvelman
- Laboratory for Infectious Diseases and Screening, Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Teemu Kallonen
- Department of Infectious Disease Surveillance and Control, National Institute for Health and Welfare, Turku, Finland
- Turku Graduate School for Biomedical Sciences, University of Turku, Turku, Finland
| | - Qiushui He
- Department of Infectious Disease Surveillance and Control, National Institute for Health and Welfare, Turku, Finland
| | - Jussi Mertsola
- Department of Infectious Disease Surveillance and Control, National Institute for Health and Welfare, Turku, Finland
| | - Abdolreza Advani
- Department of Bacteriology, Swedish Institute for Infectious Disease Control, Solna, Sweden
| | - Hans O. Hallander
- Department of Bacteriology, Swedish Institute for Infectious Disease Control, Solna, Sweden
| | | | - Peter W. Hermans
- Laboratory of Pediatric Infectious Diseases, Radboud University Nijmegen Medical Center, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - Frits R. Mooi
- Laboratory for Infectious Diseases and Screening, Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
- * E-mail:
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Octavia S, Maharjan RP, Sintchenko V, Stevenson G, Reeves PR, Gilbert GL, Lan R. Insight into evolution of Bordetella pertussis from comparative genomic analysis: evidence of vaccine-driven selection. Mol Biol Evol 2010; 28:707-15. [PMID: 20833694 DOI: 10.1093/molbev/msq245] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Despite high vaccine coverage, pertussis incidence has increased substantially in recent years in many countries. A significant factor that may be contributing to this increase is adaptation to the vaccine by Bordetella pertussis, the causative agent of pertussis. In this study, we first assessed the genetic diversity of B. pertussis by microarray-based comparative genome sequencing of 10 isolates representing diverse genotypes and different years of isolation. We discovered 171 single nucleotide polymorphisms (SNPs) in a total of 1.4 Mb genome analyzed. The frequency of base changes was estimated as one per 32 kb per isolate, confirming that B. pertussis is one of the least variable bacterial pathogens. We then analyzed an international collection of 316 B. pertussis isolates using a subset of 65 of the SNPs and identified 42 distinct SNP profiles (SPs). Phylogenetic analysis grouped the SPs into six clusters. The majority of recent isolates belonged to clusters I-IV and were descendants of a single prevaccine lineage. Cluster I appeared to be a major clone with a worldwide distribution. Typing of genes encoding acellular vaccine (ACV) antigens, ptxA, prn, fhaB, fim2, and fim3 revealed the emergence and increasing incidence of non-ACV alleles occurring in clusters I and IV, which may have been driven by ACV immune selection. Our findings suggest that B. pertussis, despite its high population homogeneity, is evolving in response to vaccination pressure with recent expansion of clones carrying variants of genes encoding ACV antigens.
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Affiliation(s)
- Sophie Octavia
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
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