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Peng Y, Williams MM, Xiaoli L, Simon A, Fueston H, Tondella ML, Weigand MR. Strengthening Bordetella pertussis genomic surveillance by direct sequencing of residual positive specimens. J Clin Microbiol 2024; 62:e0165323. [PMID: 38445858 PMCID: PMC11005353 DOI: 10.1128/jcm.01653-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Accepted: 02/12/2024] [Indexed: 03/07/2024] Open
Abstract
Whole-genome sequencing (WGS) of microbial pathogens recovered from patients with infectious disease facilitates high-resolution strain characterization and molecular epidemiology. However, increasing reliance on culture-independent methods to diagnose infectious diseases has resulted in few isolates available for WGS. Here, we report a novel culture-independent approach to genome characterization of Bordetella pertussis, the causative agent of pertussis and a paradigm for insufficient genomic surveillance due to limited culture of clinical isolates. Sequencing libraries constructed directly from residual pertussis-positive diagnostic nasopharyngeal specimens were hybridized with biotinylated RNA "baits" targeting B. pertussis fragments within complex mixtures that contained high concentrations of host and microbial background DNA. Recovery of B. pertussis genome sequence data was evaluated with mock and pooled negative clinical specimens spiked with reducing concentrations of either purified DNA or inactivated cells. Targeted enrichment increased the yield of B. pertussis sequencing reads up to 90% while simultaneously decreasing host reads to less than 10%. Filtered sequencing reads provided sufficient genome coverage to perform characterization via whole-genome single nucleotide polymorphisms and whole-genome multilocus sequencing typing. Moreover, these data were concordant with sequenced isolates recovered from the same specimens such that phylogenetic reconstructions from either consistently clustered the same putatively linked cases. The optimized protocol is suitable for nasopharyngeal specimens with diagnostic IS481 Ct < 35 and >10 ng DNA. Routine implementation of these methods could strengthen surveillance and study of pertussis resurgence by capturing additional cases with genomic characterization.
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Affiliation(s)
- Yanhui Peng
- Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Margaret M. Williams
- Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | | | - Ashley Simon
- Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Heather Fueston
- Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Maria L. Tondella
- Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Michael R. Weigand
- Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
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Moosa F, du Plessis M, Weigand MR, Peng Y, Mogale D, de Gouveia L, Nunes MC, Madhi SA, Zar HJ, Reubenson G, Ismail A, Tondella ML, Cohen C, Walaza S, von Gottberg A, Wolter N. Genomic characterization of Bordetella pertussis in South Africa, 2015-2019. Microb Genom 2023; 9:001162. [PMID: 38117675 PMCID: PMC10763497 DOI: 10.1099/mgen.0.001162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 12/04/2023] [Indexed: 12/22/2023] Open
Abstract
Pertussis remains a public health concern in South Africa, with an increase in reported cases and outbreaks in recent years. Whole genome sequencing was performed on 32 Bordetella pertussis isolates sourced from three different surveillance programmes in South Africa between 2015 and 2019. Genome sequences were characterized using multilocus sequence typing, vaccine antigen genes (ptxP, ptxA, ptxB, prn and fimH) and overall genome structure. All isolates were sequence type 2 and harboured the pertussis toxin promoter allele ptxP3. The dominant genotype was ptxP3-ptxA1-ptxB2-prn2-fimH2 (31/32, 96.9 %), with no pertactin-deficient or other mutations in vaccine antigen genes identified. Amongst 21 isolates yielding closed genome assemblies, eight distinct genome structures were detected, with 61.9 % (13/21) of the isolates exhibiting three predominant structures. Increases in case numbers are probably not due to evolutionary changes in the genome but possibly due to other factors such as the cyclical nature of B. pertussis disease, waning immunity due to the use of acellular vaccines and/or population immunity gaps.
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Affiliation(s)
- Fahima Moosa
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Mignon du Plessis
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Michael R. Weigand
- Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Yanhui Peng
- Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Dineo Mogale
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
| | - Linda de Gouveia
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
| | - Marta C. Nunes
- Department of Science and Technology/National Research Foundation, Vaccine Preventable Diseases, University of the Witwatersrand, Johannesburg, South Africa
| | - Shabir A. Madhi
- South African Medical Research Council Vaccines and Infectious Diseases Analytics Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Wits Infectious Diseases and Oncology Research Institute, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Heather J. Zar
- Department of Pediatrics and Child Health, Red Cross Children’s Hospital, Cape Town, South Africa; MRC Unit on Child and Adolescent Health, University of Cape Town, Cape Town, South Africa
| | - Gary Reubenson
- Rahima Moosa Mother & Child Hospital, Department of Pediatrics & Child Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Arshad Ismail
- Sequencing Core Facility, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
- Department of Biochemistry and Microbiology, Faculty of Science, Engineering and Agriculture, University of Venda, Thohoyandou 0950, South Africa
- Institute for Water and Wastewater Technology, Durban University of Technology, Durban 4000, South Africa
| | - M. Lucia Tondella
- Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Cheryl Cohen
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
- School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Sibongile Walaza
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
- School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Anne von Gottberg
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Nicole Wolter
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
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3
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Ivaska L, Barkoff AM, Mertsola J, He Q. Macrolide Resistance in Bordetella pertussis: Current Situation and Future Challenges. Antibiotics (Basel) 2022; 11:1570. [PMID: 36358225 PMCID: PMC9686491 DOI: 10.3390/antibiotics11111570] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 10/31/2022] [Accepted: 11/05/2022] [Indexed: 01/19/2024] Open
Abstract
Pertussis is a highly contagious respiratory infection caused by Bordetella pertussis bacterium. The mainstay of treatment is macrolide antibiotics that reduce transmissibility, shorten the duration of symptoms and decrease mortality in infants. Recently, the macrolide resistance of B. pertussis has been reported globally but is especially widespread in mainland China. In this review, we aim to summarise the current understanding of the epidemiology, resistance mechanisms and clinical implications of B. pertussis macrolide resistance. Since the first appearance of macrolide-resistant B. pertussis in Arizona, USA, in 1994, only sporadic cases have been reported outside China. In certain parts of China, on the other hand, up to 70-100% of the recent clinical isolates have been found to be macrolide resistant. Reasons for macrolide resistance being centred upon China during the last decade can only be speculated on, but the dominant B. pertussis lineage is different between China and most of the high-income countries. It seems evident that efforts to increase awareness, guide molecular epidemiological surveillance and carry out systematic screening of B. pertussis positive samples for macrolide resistance should be implemented globally. In addition, practices to improve the clinical care of infants with pertussis caused by resistant strains should be studied vigorously.
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Affiliation(s)
- Lauri Ivaska
- Department of Paediatrics and Adolescent Medicine, Turku University Hospital and University of Turku, 20521 Turku, Finland
- InFLAMES Research Flagship Center, University of Turku, 20520 Turku, Finland
| | - Alex-Mikael Barkoff
- Institute of Biomedicine, Centre for Infections and Immunity, University of Turku, 20520 Turku, Finland
| | - Jussi Mertsola
- Department of Paediatrics and Adolescent Medicine, Turku University Hospital and University of Turku, 20521 Turku, Finland
- Institute of Biomedicine, Centre for Infections and Immunity, University of Turku, 20520 Turku, Finland
| | - Qiushui He
- InFLAMES Research Flagship Center, University of Turku, 20520 Turku, Finland
- Institute of Biomedicine, Centre for Infections and Immunity, University of Turku, 20520 Turku, Finland
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Wu X, Du Q, Li D, Yuan L, Meng Q, Fu Z, Xu H, Yao K, Zhao R. A Cross-Sectional Study Revealing the Emergence of Erythromycin-Resistant Bordetella pertussis Carrying ptxP3 Alleles in China. Front Microbiol 2022; 13:901617. [PMID: 35923401 PMCID: PMC9342848 DOI: 10.3389/fmicb.2022.901617] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 06/15/2022] [Indexed: 11/13/2022] Open
Abstract
Background Previous limited studies have identified that Bordetella pertussis (B. pertussis) isolates circulating in China possess distinct molecular features and high rates of erythromycin-resistance (ER). Their evolution and potential impact on the prevention and control of global pertussis are worthy of attention. Methods The present cross-sectional study involved 311 non-duplicate and unrelated B. pertussis strains isolated from Chinese children from 2017 to 2019. Their antimicrobial susceptibilities were assessed using both E-test strips and Kirby-Bauer (KB) disk diffusion methods. Seven virulence-related genes (ptxA, ptxC, ptxP, prn, fim2, fim3, and tcfA2) and the A2047G mutation in the 23S rRNA gene were detected by PCR. Based on the susceptibilities and genotypes, 50 isolates were selected for multi-locus variable-number tandem-repeat analysis (MLVA) typing and whole-genome sequencing. Results A total of 311 B. pertussis strains were isolated from children with a median age of 4 months (interquartile range: 2–9 months). Strains carrying the ptxP1 allele were more frequent (84.9%, 264/311), were always ER (except for one strain), and were mainly related to ptxA1/ptxC1/prn1 alleles (99.6%, 263/264). The remaining 47 (15.1%) strains carried the ptxP3 allele, mainly harboring the ptxA1/ptxC2/prn2 alleles (93.6%, 44/47), and were sensitive to erythromycin (except for two strains). The two ER-ptxP3 isolates were first identified in China, belonged to MT27 and MT28 according to MLVA, and were classified into sub-lineage IVd by phylogenetic analysis of their genome sequences. This sub-lineage also includes many strains carrying the ptxP3 allele spreading in developed countries. For each tested antimicrobial, the susceptibilities judged by KB disks were consistent with those determined by E-test strips. Conclusion The present results reveal that B. pertussis strains with the ptxP1-ER profile still dominate in China, and a few strains carrying the ptxP3 allele have acquired the A2047G mutation in the 23S rRNA gene and the ER phenotype. The surveillance of the drug susceptibility of B. pertussis is necessary for all countries, and the KB disk method can be adopted as a screening test.
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Affiliation(s)
- Xiaoying Wu
- Department of Infectious Diseases, Children’s Hospital of Chongqing Medical University, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Child Infection and Immunity, Chongqing, China
| | - Qianqian Du
- Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, MOE Key Laboratory of Major Diseases in Children, Beijing Pediatric Research Institute, Beijing Children’s Hospital, Capital Medical University, National Center for Children’s Health, Beijing, China
| | - Dongfang Li
- BGI Pathogenesis Pharmaceutical Technology, BGI-Shenzhen, Shenzhen, China
| | - Lin Yuan
- Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, MOE Key Laboratory of Major Diseases in Children, Beijing Pediatric Research Institute, Beijing Children’s Hospital, Capital Medical University, National Center for Children’s Health, Beijing, China
| | - Qinghong Meng
- Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, MOE Key Laboratory of Major Diseases in Children, Beijing Pediatric Research Institute, Beijing Children’s Hospital, Capital Medical University, National Center for Children’s Health, Beijing, China
| | - Zhou Fu
- Department of Respiratory Diseases, Children’s Hospital of Chongqing Medical University, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Pediatrics, Chongqing, China
| | - Hongmei Xu
- Department of Infectious Diseases, Children’s Hospital of Chongqing Medical University, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Child Infection and Immunity, Chongqing, China
| | - Kaihu Yao
- Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, MOE Key Laboratory of Major Diseases in Children, Beijing Pediatric Research Institute, Beijing Children’s Hospital, Capital Medical University, National Center for Children’s Health, Beijing, China
- *Correspondence: Kaihu Yao,
| | - Ruiqiu Zhao
- Department of Infectious Diseases, Children’s Hospital of Chongqing Medical University, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Child Infection and Immunity, Chongqing, China
- Ruiqiu Zhao,
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Versteegen P, Barkoff AM, Valente Pinto M, van de Kasteele J, Knuutila A, Bibi S, de Rond L, Teräsjärvi J, Sanders K, de Zeeuw-Brouwer ML, Luoto R, ten Hulscher H, Clutterbuck EA, Sanders EAM, Mertsola J, Berbers GAM, He Q, Kelly DF, Buisman AM. Memory B Cell Activation Induced by Pertussis Booster Vaccination in Four Age Groups of Three Countries. Front Immunol 2022; 13:864674. [PMID: 35677044 PMCID: PMC9168128 DOI: 10.3389/fimmu.2022.864674] [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: 01/28/2022] [Accepted: 04/21/2022] [Indexed: 11/13/2022] Open
Abstract
BackgroundImmunogenicity of acellular pertussis (aP) vaccines is conventionally assessed by measuring antibody responses but antibody concentrations wane quickly after vaccination. Memory B cells, however, are critical in sustaining long-term protection and therefore may be an important factor when assessing pertussis immunity after vaccination.AimWe studied pertussis specific memory B cell (re)activation induced by an aP booster vaccination in four different age groups within three countries.Materials and methodsFrom a phase IV longitudinal interventional study, 268 participants across Finland, the Netherlands and the United Kingdom were included and received a 3-component pertussis booster vaccine: children (7-10y, n=53), adolescents (11-15y, n=66), young adults (20-34y, n=74), and older adults (60-70y, n=75). Memory B cells at baseline, day 28, and 1 year post-vaccination were measured by a pertussis toxin (Ptx), filamentous haemagglutinin (FHA), and pertactin (Prn) specific ELISpot assay. Antibody results measured previously were available for comparison. Furthermore, study participants were distributed into groups based on their baseline memory B cell frequencies, vaccine responses were monitored between these groups.ResultsGeometric mean (GM) memory B cell frequencies for pertussis antigens at baseline were low. At 28 days post-vaccination, these frequencies increased within each age group and were still elevated one year post-booster compared to baseline. Highest frequencies at day 28 were found within adolescents (GM: 5, 21, and 13, for Ptx, FHA and Prn, respectively) and lowest within older adults (GM: 2, 9, and 3, respectively). Moderate to strong correlations between memory B cell frequencies at day 28 and antibody concentrations at day 28 and 1 year were observed for Prn. Memory B cell frequencies > 1 per 100,000 PBMCs at baseline were associated with significantly higher memory responses after 28 days and 1 year.ConclusionsAn aP booster vaccine (re)activated memory B cells in all age groups. Still elevated memory B cell frequencies after one year indicates enhanced immunological memory. However, antigen specific memory B cell activation seems weaker in older adults, which might reflect immunosenescence. Furthermore, the presence of circulating memory B cells at baseline positively affects memory B cell responses. This study was registered at www.clinicaltrialsregister.eu: No. 2016-003678-42.
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Affiliation(s)
- Pauline Versteegen
- National Institute for Public Health and the Environment, Centre for Infectious Disease Control, Bilthoven, Netherlands
| | - Alex-Mikael Barkoff
- Institute of Biomedicine, Microbiology, Virology and Immunology, and Turku University Hospital, University of Turku, Turku, Finland
| | - Marta Valente Pinto
- Department of Paediatrics, Oxford Vaccine Group, University of Oxford, Oxford, United Kingdom
| | - Jan van de Kasteele
- National Institute for Public Health and the Environment, Centre for Infectious Disease Control, Bilthoven, Netherlands
| | - Aapo Knuutila
- Institute of Biomedicine, Microbiology, Virology and Immunology, and Turku University Hospital, University of Turku, Turku, Finland
| | - Sagida Bibi
- Department of Paediatrics, Oxford Vaccine Group, University of Oxford, Oxford, United Kingdom
| | - Lia de Rond
- National Institute for Public Health and the Environment, Centre for Infectious Disease Control, Bilthoven, Netherlands
| | - Johanna Teräsjärvi
- Institute of Biomedicine, Microbiology, Virology and Immunology, and Turku University Hospital, University of Turku, Turku, Finland
| | - Katherine Sanders
- Department of Paediatrics, Oxford Vaccine Group, University of Oxford, Oxford, United Kingdom
| | - Mary-lène de Zeeuw-Brouwer
- National Institute for Public Health and the Environment, Centre for Infectious Disease Control, Bilthoven, Netherlands
| | - Raakel Luoto
- Institute of Biomedicine, Microbiology, Virology and Immunology, and Turku University Hospital, University of Turku, Turku, Finland
| | - Hinke ten Hulscher
- National Institute for Public Health and the Environment, Centre for Infectious Disease Control, Bilthoven, Netherlands
| | | | - Elisabeth A. M. Sanders
- National Institute for Public Health and the Environment, Centre for Infectious Disease Control, Bilthoven, Netherlands
- Department of Paediatric Immunology and Infectious Diseases, Wilhelmina Children’s Hospital, Utrecht, Netherlands
| | - Jussi Mertsola
- Institute of Biomedicine, Microbiology, Virology and Immunology, and Turku University Hospital, University of Turku, Turku, Finland
| | - Guy A. M. Berbers
- National Institute for Public Health and the Environment, Centre for Infectious Disease Control, Bilthoven, Netherlands
| | - Qiushui He
- Institute of Biomedicine, Microbiology, Virology and Immunology, and Turku University Hospital, University of Turku, Turku, Finland
| | - Dominic F. Kelly
- Department of Paediatrics, Oxford Vaccine Group, University of Oxford, Oxford, United Kingdom
- Oxford NIHR Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom
| | - Anne-Marie Buisman
- National Institute for Public Health and the Environment, Centre for Infectious Disease Control, Bilthoven, Netherlands
- *Correspondence: Anne-Marie Buisman,
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Ring N, Davies H, Morgan J, Sundaresan M, Tiong A, Preston A, Bagby S. Comparative genomics of Bordetella pertussis isolates from New Zealand, a country with an uncommonly high incidence of whooping cough. Microb Genom 2022; 8:000756. [PMID: 35084300 PMCID: PMC8914352 DOI: 10.1099/mgen.0.000756] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 12/03/2021] [Indexed: 11/18/2022] Open
Abstract
Whooping cough, the respiratory disease caused by Bordetella pertussis, has undergone a wide-spread resurgence over the last several decades. Previously, we developed a pipeline to assemble the repetitive B. pertussis genome into closed sequences using hybrid nanopore and Illumina sequencing. Here, this sequencing pipeline was used to conduct a more high-throughput, longitudinal screen of 66 strains isolated between 1982 and 2018 in New Zealand. New Zealand has a higher incidence of whooping cough than many other countries; usually at least twice as many cases per 100000 people as the USA and UK and often even higher, despite similar rates of vaccine uptake. To the best of our knowledge, these strains are the first New Zealand B. pertussis isolates to be sequenced. The analyses here show that, on the whole, genomic trends in New Zealand B. pertussis isolates, such as changing allelic profile in vaccine-related genes and increasing pertactin deficiency, have paralleled those seen elsewhere in the world. At the same time, phylogenetic comparisons of the New Zealand isolates with global isolates suggest that a number of strains are circulating in New Zealand, which cluster separately from other global strains, but which are closely related to each other. The results of this study add to a growing body of knowledge regarding recent changes to the B. pertussis genome, and are the first genetic investigation into B. pertussis isolates from New Zealand.
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Affiliation(s)
- Natalie Ring
- Department of Biology and Biochemistry, University of Bath, UK
- Roslin Institute, University of Edinburgh, UK
| | - Heather Davies
- Institute of Environmental Science and Research, Porirua, New Zealand
| | - Julie Morgan
- Institute of Environmental Science and Research, Porirua, New Zealand
| | | | - Audrey Tiong
- Institute of Environmental Science and Research, Porirua, New Zealand
| | - Andrew Preston
- Department of Biology and Biochemistry, University of Bath, UK
| | - Stefan Bagby
- Department of Biology and Biochemistry, University of Bath, UK
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Cabal A, Schmid D, Hell M, Chakeri A, Mustafa-Korninger E, Wojna A, Stöger A, Möst J, Leitner E, Hyden P, Rattei T, Habington A, Wiedermann U, Allerberger F, Ruppitsch W. Isolate-Based Surveillance of Bordetella pertussis, Austria, 2018-2020. Emerg Infect Dis 2021; 27:862-871. [PMID: 33622477 PMCID: PMC7920692 DOI: 10.3201/eid2703.202314] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Pertussis is a vaccine-preventable disease, and its recent resurgence might be attributable to the emergence of strains that differ genetically from the vaccine strain. We describe a novel pertussis isolate-based surveillance system and a core genome multilocus sequence typing scheme to assess Bordetella pertussis genetic variability and investigate the increased incidence of pertussis in Austria. During 2018–2020, we obtained 123 B. pertussis isolates and typed them with the new scheme (2,983 targets and preliminary cluster threshold of <6 alleles). B. pertussis isolates in Austria differed genetically from the vaccine strain, both in their core genomes and in their vaccine antigen genes; 31.7% of the isolates were pertactin-deficient. We detected 8 clusters, 1 of them with pertactin-deficient isolates and possibly part of a local outbreak. National expansion of the isolate-based surveillance system is needed to implement pertussis-control strategies.
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Genomic Surveillance and Improved Molecular Typing of Bordetella pertussis Using wgMLST. J Clin Microbiol 2021; 59:JCM.02726-20. [PMID: 33627319 DOI: 10.1128/jcm.02726-20] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Accepted: 02/18/2021] [Indexed: 01/03/2023] Open
Abstract
Multilocus sequence typing (MLST) provides allele-based characterization of bacterial pathogens in a standardized framework. However, classical MLST schemes for Bordetella pertussis, the causative agent of whooping cough, seldom reveal diversity among the small number of gene targets and thereby fail to delineate population structure. To improve the discriminatory power of allele-based molecular typing of B. pertussis, we have developed a whole-genome MLST (wgMLST) scheme from 225 reference-quality genome assemblies. Iterative refinement and allele curation resulted in a scheme of 3,506 coding sequences and covering 81.4% of the B. pertussis genome. This wgMLST scheme was further evaluated with data from a convenience sample of 2,389 B. pertussis isolates sequenced on Illumina instruments, including isolates from known outbreaks and epidemics previously characterized by existing molecular assays, as well as replicates collected from individual patients. wgMLST demonstrated concordance with whole-genome single nucleotide polymorphism (SNP) profiles, accurately resolved outbreak and sporadic cases in a retrospective comparison, and clustered replicate isolates collected from individual patients during diagnostic confirmation. Additionally, a reanalysis of isolates from two statewide epidemics using wgMLST reconstructed the population structures of circulating strains with increased resolution, revealing new clusters of related cases. Comparison with an existing core genome (cgMLST) scheme highlights the stable gene content of this bacterium and forms the initial foundation for necessary standardization. These results demonstrate the utility of wgMLST for improving B. pertussis characterization and genomic surveillance during the current pertussis disease resurgence.
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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.
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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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Lin X, Zou J, Yao K, Li L, Zhong L. Analysis of antibiotic sensitivity and resistance genes of Bordetella pertussis in Chinese children. Medicine (Baltimore) 2021; 100:e24090. [PMID: 33466172 PMCID: PMC10545409 DOI: 10.1097/md.0000000000024090] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Revised: 11/18/2020] [Accepted: 11/19/2020] [Indexed: 11/25/2022] Open
Abstract
OBJECTIVE To understood the pathogen detection status and clinical characteristics of suspected pertussis in children and to observe the drug sensitivity and drug resistance genes of Bordetella pertussis (B. pertussis). METHODS Three hundred fifty-one cases were collected and their nasopharyngeal swab samples were analyzed by culture and fluorescent quantitative polymerase chain reaction. The susceptibility to erythromycin, clindamycin, ampicillin, levofloxacin, and sulfamethoxazole-trimethoprim were tested by E-test for the positive strains, and the susceptibility to erythromycin was also tested for the KB disk diffusion method. The 23S rRNA gene of the positive strains was amplified and sequenced, and statistical analysis was performed in conjunction with clinical data. RESULTS The positive rate of bacterial culture was 16.8% (59/351), and the positive rate of PCR was 62.4% (219/351). Two cases were positive about bacterial culture and negative for PCR. There were 221 confirmed cases of pertussis. The E-test results showed that the rate of the sensitivity of the 55 strains of pertussis to erythromycin and clindamycin was 50.9% (28/55), the minimum antibiotic concentration50 (MIC50) and MIC90 values were 0.094/>256 and 0.75/>256 mg/L, respectively, and the MIC50/MIC90 to ampicillin, levofloxacin, and sulfamethoxazole were 0.125/0.19, 0.38/0.5, and 0.125/0.25 mg/L, respectively. The KB disk diffusion method showed 27 of the 55 strains 49.1% (27/55) was resistant to erythromycin; all of the resistant strains had the 23S rRNA gene A2047G mutation, and their MIC of erythromycin was >256 mg/L. CONCLUSION The diagnosis of pertussis by a fluorescent quantitative polymerase chain reaction method is more sensitive than that of bacterial culture. The resistance of B. pertussis to erythromycin was prominent. All of the strains of B. pertussis resistant to erythromycin in our center had the A2047G mutation of the 23S rRNA gene.
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Affiliation(s)
- XiaoJuan Lin
- Department of Pediatrics, Hunan Provincial Key Laboratory of Pediatric Respirology, Hunan Provincial People's Hospital, Changsha
| | - Jun Zou
- Department of Pediatrics, Hunan Provincial Key Laboratory of Pediatric Respirology, Hunan Provincial People's Hospital, Changsha
| | - Kaihu Yao
- Microbiology Laboratory of Beijing Children's Hospital, Capital Medical University, Beijing, China
| | - Lijun Li
- Microbiology Laboratory of Beijing Children's Hospital, Capital Medical University, Beijing, China
| | - Lili Zhong
- Department of Pediatrics, Hunan Provincial Key Laboratory of Pediatric Respirology, Hunan Provincial People's Hospital, Changsha
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11
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Yao K, Deng J, Ma X, Dai W, Chen Q, Zhou K, Ye J, Shi W, Wang H, Li D, Wang H, Wang J, Zhang J, Wu D, Xie G, Shen K, Zheng Y, Yang Y. The epidemic of erythromycin-resistant Bordetella pertussis with limited genome variation associated with pertussis resurgence in China. Expert Rev Vaccines 2020; 19:1093-1099. [PMID: 33034224 DOI: 10.1080/14760584.2020.1831916] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
BACKGROUND The resurgence of Bordetella pertussis infections leading to whooping cough is a concern in many parts of the world. The number of pertussis cases in China has increased significantly since 2013. RESEARCH DESIGN AND METHODS In this study, whole-genome sequencing analysis was performed for 388 B. pertussis strains isolated in China from the 1970s to 2018, combining 594 published strains from around the world. RESULTS This study revealed that lineage V diverged about 50 years ago in China, while lineage IV is dominant in the other countries. It also revealed that the erythromycin-resistant sub-lineages Va, Vb, and Vc with limited genomic variation emerged 11 ~ 12 years ago. These three sub-lineages were identified after the co-purified acellular vaccines (cp-ACVs) completely replaced the previous whole cell vaccines (WCVs) after the national immunization program of 2012. It suggests that the cp-ACVs cannot induce immunity that is potent enough to restrict the spread of the lineage V, antibiotic abuse further favors the spread of this lineage in China. CONCLUSIONS These findings demand a reassessment of the immunization strategy and development of new vaccines in China to stop the resurgence and drug resistance of B. pertussis.
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Affiliation(s)
- Kaihu Yao
- Beijing Pediatric Research Institute of Beijing Children's Hospital Affiliated to Capital Medical University , Beijing, China
| | - Jikui Deng
- Department of Infectious Disease and Department of Pulmonology, Shenzhen Children's Hospital , Shenzhen, China
| | - Xiang Ma
- Pediatric Department, Jinan Children's Hospital , Jinan, China
| | - Wenkui Dai
- WeHealthGene Institute , Shenzhen, China
| | - Qiang Chen
- Department of Pulmonology, Jiangxi Provincial Children's Hospital , Nanchang, China
| | - Kai Zhou
- Department of Infectious Disease, Nanjing Children's Hospital , Nanjing, China
| | - Jinyan Ye
- Clinical Laboratory, Jiaxing University Affiliated Women and Children Hospital , Jiaxing, China
| | - Wei Shi
- Beijing Pediatric Research Institute of Beijing Children's Hospital Affiliated to Capital Medical University , Beijing, China
| | - Heping Wang
- Department of Infectious Disease and Department of Pulmonology, Shenzhen Children's Hospital , Shenzhen, China
| | | | - Hongmei Wang
- Department of Infectious Disease and Department of Pulmonology, Shenzhen Children's Hospital , Shenzhen, China
| | - Jingmin Wang
- Beijing Pediatric Research Institute of Beijing Children's Hospital Affiliated to Capital Medical University , Beijing, China.,Pediatric Department, Peking University First Hospital , Beijing, China
| | - Jiaosheng Zhang
- Department of Infectious Disease and Department of Pulmonology, Shenzhen Children's Hospital , Shenzhen, China
| | - Danxia Wu
- Department of Pulmonology, Jiangxi Provincial Children's Hospital , Nanchang, China
| | - Gan Xie
- Beijing Pediatric Research Institute of Beijing Children's Hospital Affiliated to Capital Medical University , Beijing, China.,Department of Infectious Disease and Department of Pulmonology, Shenzhen Children's Hospital , Shenzhen, China
| | - Kunling Shen
- Beijing Pediatric Research Institute of Beijing Children's Hospital Affiliated to Capital Medical University , Beijing, China
| | - Yuejie Zheng
- Department of Infectious Disease and Department of Pulmonology, Shenzhen Children's Hospital , Shenzhen, China
| | - Yonghong Yang
- Beijing Pediatric Research Institute of Beijing Children's Hospital Affiliated to Capital Medical University , Beijing, China.,Department of Infectious Disease and Department of Pulmonology, Shenzhen Children's Hospital , Shenzhen, China.,WeHealthGene Institute , Shenzhen, China
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12
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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: 29] [Impact Index Per Article: 7.3] [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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13
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Saedi S, Safarchi A, Noofeli M, Tadayon K, Tay ACY, Lamichhane B, Rahimi H, Shahcheraghi F. Genome diversity and evolutionary characteristics of clinical isolates of Bordetella pertussis circulating in Iran. IRANIAN JOURNAL OF MICROBIOLOGY 2020; 12:1-10. [PMID: 32322373 PMCID: PMC7163038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
BACKGROUND AND OBJECTIVES The re-emergence of pertussis still is being reported all over the world. Pathogen adaptation and antigenic divergence of circulating isolates from vaccine strains are the main reasons of infection resurgence. Waning immunity is also an important factor contributing to resurgence of pertussis. MATERIALS AND METHODS The genetic diversity and evolutionary characteristics of circulating Iranian isolates of Bordetella pertussis during February 2015 to October 2018 was investigated by pulsed-field gel electrophoresis (PFGE) and subsequently ptxA, ptxP and fim3 alleles were characterized. The next generation genome sequencing was then used to compare the genomics of ptxP1 and ptxP3 of selected isolates from PFGE dendrogram. RESULTS PFGE differentiated 62 clinical isolates and vaccine and reference strains into 19 PFGE profiles, indicating the higher level of heterogeneity in the population during 2015-2018. The predominant B. pertussis genotype harbored pertussis toxin promoter allele, ptxP3 and the expansion of ptxA1 isolates, were also observed in our population. CONCLUSION No changes in allelic profile of predominant clone in recent years was observed but antigenic divergence between recently circulating isolates and the vaccine strain has been progressed and significantly was higher than previous studies. The comparative genomic analysis of the ptxP3 and ptxP1 isolates indicate that changes in ptxP3 genome structure including 32 unique SNPs and three unique indels may have contributed to the expansion of the ptxP3 clone. We compared ptxP3 and ptxP1 isolates in pathogenicity-associated genes and found five of them were specific for the ptxP3 isolates. The polymorphisms in pathogenicity-associated genes suggest structural adaptations for these virulence factors.
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Affiliation(s)
- Samaneh Saedi
- Department of Bacteriology, Pasteur Institute of Iran, Tehran, Iran
| | - Azadeh Safarchi
- Department of Bacteriology, Pasteur Institute of Iran, Tehran, Iran
| | - Mojtaba Noofeli
- Department of Human Bacterial Vaccine, Razi Vaccine & Serum Research Institute, Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran
| | - Keyvan Tadayon
- Department of Aerobic Bacterial Research and Vaccine Production, Razi Vaccine & Serum Research Institute, Karaj, Iran
| | - Alfred Chin Yen Tay
- The Marshall Centre for Infectious Diseases Research and Training, The University of Western Australia, Nedlands, Western Australia, Australia,Shenzhen Dapeng New District Kuichong People Hospital, Shenzhen, Guangdong, China
| | - Binit Lamichhane
- The Marshall Centre for Infectious Diseases Research and Training, The University of Western Australia, Nedlands, Western Australia, Australia
| | - Hamzeh Rahimi
- Department of Molecular Medicine, Pasteur Institute of Iran, Tehran, Iran
| | - Fereshteh Shahcheraghi
- Department of Bacteriology, Pasteur Institute of Iran, Tehran, Iran,Corresponding author: Fereshteh Shahcheraghi, PhD, Department of Bacteriology, Pasteur Institute of Iran, Tehran, Iran. Tel/Fax: +98-21-66405535,
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14
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Mir-Cros A, Moreno-Mingorance A, Martín-Gómez MT, Codina G, Cornejo-Sánchez T, Rajadell M, Van Esso D, Rodrigo C, Campins M, Jané M, Pumarola T, Fàbrega A, González-López JJ. Population dynamics and antigenic drift of Bordetella pertussis following whole cell vaccine replacement, Barcelona, Spain, 1986-2015. Emerg Microbes Infect 2019; 8:1711-1720. [PMID: 31769735 PMCID: PMC6882445 DOI: 10.1080/22221751.2019.1694395] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Among the factors associated with the resurgence of whooping cough, special emphasis has been given to pathogen adaptation after the introduction of the acellular vaccine (ACV). To assess the impact of the vaccine transition strategy from whole-cell vaccine (WCV) to ACV on population dynamics of Bordetella pertussis in Barcelona (Spain), we studied 339 isolates collected from 1986 to 2015 by PFGE and multi-locus variable-number tandem repeat analysis (MLVA). Additionally, allelic variants for the pertussis toxin and its promoter, pertactin, type 3 fimbriae and fimbrial serotyping were assessed to determine its antigenic drift. A shift was observed in the B. pertussis population as well as in its antigenic profile concurrently with the introduction of ACV in Barcelona. Four out of the five most prevalent PFGE profiles were replaced by new profiles following the ACV introduction. MLVA type 27 was the dominant genotype, and its frequency increased from 25% to 79.3% after WCV replacement. Antigen typing demonstrated the emergence of prn2, ptxP3, fim3-2 and a shift from the fimbriae 3 to the fimbriae 2 serotypes after the ACV introduction. Our findings support the presence of population and antigenic dynamic changes in B. pertussis likely driven by the introduction of ACV.
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Affiliation(s)
- Alba Mir-Cros
- Department of Clinical Microbiology, Hospital Universitari Vall d'Hebron, Barcelona, Spain.,Department of Microbiology and Genetics, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Albert Moreno-Mingorance
- Department of Clinical Microbiology, Hospital Universitari Vall d'Hebron, Barcelona, Spain.,Department of Microbiology and Genetics, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - M Teresa Martín-Gómez
- Department of Clinical Microbiology, Hospital Universitari Vall d'Hebron, Barcelona, Spain
| | - Gema Codina
- Department of Clinical Microbiology, Hospital Universitari Vall d'Hebron, Barcelona, Spain
| | - Thais Cornejo-Sánchez
- Department of Clinical Microbiology, Hospital Universitari Vall d'Hebron, Barcelona, Spain
| | - Mireia Rajadell
- Department of Clinical Microbiology, Hospital Universitari Vall d'Hebron, Barcelona, Spain.,Department of Microbiology and Genetics, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Diego Van Esso
- Primary Care Health Centre Service 'Muntanya', Catalan Institute of Health, Barcelona, Spain
| | - Carlos Rodrigo
- Department of Paediatrics, Hospital Universitari Vall d'Hebron, Barcelona, Spain
| | - Magda Campins
- Department of Preventive Medicine and Epidemiology, Hospital Universitari Vall d'Hebron, Barcelona, Spain
| | - Mireia Jané
- Public Health Agency of Catalonia, Barcelona, Spain
| | - Tomàs Pumarola
- Department of Clinical Microbiology, Hospital Universitari Vall d'Hebron, Barcelona, Spain.,Department of Microbiology and Genetics, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Anna Fàbrega
- Department of Clinical Microbiology, Hospital Universitari Vall d'Hebron, Barcelona, Spain.,Faculty of Health Sciences, University of Vic - Central University of Catalonia (UVic-UCC), Manresa, Spain
| | - Juan José González-López
- Department of Clinical Microbiology, Hospital Universitari Vall d'Hebron, Barcelona, Spain.,Department of Microbiology and Genetics, Universitat Autònoma de Barcelona, Barcelona, Spain
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15
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Knapp JK, Wilson ML, Murray S, Boulton ML. Evaluating the role of cough duration in the pertussis case definition among Michigan cases, 2000-2010. Prev Med Rep 2019; 16:100973. [PMID: 31485391 PMCID: PMC6715955 DOI: 10.1016/j.pmedr.2019.100973] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Revised: 08/09/2019] [Accepted: 08/15/2019] [Indexed: 11/17/2022] Open
Abstract
Impressive reductions in pertussis have been achieved in the U.S. during the 20th century through childhood vaccination. Over the past two decades, increasing pertussis incidence has highlighted the need for accurate and timely reporting of cases to improve prevention and control efforts. We assessed components of the pertussis case definition, comparing use of clinical characteristics and laboratory results and their effects on internal validity, including an examination of the 2014 infant case definition. All reported pertussis cases in Michigan during 2000–2010 with data on cough length (N = 3310) were analyzed using multivariate statistics to internally validate reported cases, and calculate odds of meeting the clinical case definition, including a cough of at least 14 days. Cough duration of reported cases averaged 32 days and was longer with greater time interval between cough onset and initial presentation to a physician. Only about half of reported cases had positive laboratory results. Among cases seeking medical evaluation prior to meeting the cough duration required to fulfill the clinical case definition, the presence of positive lab results doubled the odds that the cough duration was not met compared to cases without a positive lab test. Clinical characteristics of pertussis are frequently ignored in applying the case classification. Relying solely on laboratory confirmation and disregarding clinical characteristics results in undiagnosed pertussis cases among those who are vaccinated, among adults, and among anyone who delays seeking care. This may prevent use of appropriate prevention and prophylaxis in contacts. Increasing incidence of pertussis in the U.S. makes accurate diagnosis and reporting of cases essential to control efforts. Many pertussis cases with positive laboratory tests sought medical evaluation prior to meeting the cough duration criterion. Clinical characteristics of pertussis are frequently ignored by public health and medical professionals in classifying cases. Laboratory confirmation without accompanying clinical characteristics may result in mis-diagnosis of pertussis.
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Affiliation(s)
- Jennifer K. Knapp
- Dept. of Epidemiology, University of Michigan School of Public Health, Ann Arbor, MI 48109, USA
- Corresponding author.
| | - Mark L. Wilson
- Dept. of Epidemiology, University of Michigan School of Public Health, Ann Arbor, MI 48109, USA
| | - Susan Murray
- Dept. of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI 48109, USA
| | - Matthew L. Boulton
- Dept. of Epidemiology, University of Michigan School of Public Health, Ann Arbor, MI 48109, USA
- Dept. of Internal Medicine, Infectious Diseases Division, Michigan Medicine, University of Michigan, Ann Arbor, MI 48109, USA
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16
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Tsang RSW, Shuel M, Cronin K, Deng S, Whyte K, Marchand-Austin A, Ma J, Bolotin S, Crowcroft N, Schwartz K, Van Domselaar G, Graham M, Jamieson FB. The evolving nature of Bordetella pertussis in Ontario, Canada, 2009-2017: strains with shifting genotypes and pertactin deficiency. Can J Microbiol 2019; 65:823-830. [PMID: 31295416 DOI: 10.1139/cjm-2019-0128] [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: 11/22/2022]
Abstract
This study examined the evolving nature of Bordetella pertussis in Ontario, Canada, by characterizing isolates for their genotypes and expression of pertactin (PRN). From 2009 to 2017, 413 B. pertussis were cultured from pertussis cases at the Public Health Ontario Laboratory. Their genotypes were determined by partial gene sequence analysis of their virulence and (or) vaccine antigens: filamentous haemagglutinin, PRN, fimbriae 3, and pertussis toxin, including the promoter region. Expression of PRN was measured by Western immunoblot. Two predominant genotypes, ST-1 and ST-2, were found throughout the study and were responsible for 47.5% and 46.3% of all case isolates, respectively. The prevalence of ST-1 appeared to fluctuate from 80.3% in 2009 to 20.0% in 2014 and 58.5% in 2017, while the prevalence of ST-2 changed from 18.4% in 2009 to 80.0% in 2014 and 26.2% in 2017. A PRN-deficient strain was first noted in 2011 (16.7%), and its prevalence increased to 70.8% in 2016 but decreased to 46.2% in 2017. More ST-2 (46.6%) than ST-1 (16.8%) strains were associated with PRN deficiency. Newer ST-21 and ST-22 found in 2015-2017 were uniformly PRN deficient. The impact of the evolving nature of B. pertussis on disease epidemiology requires further longitudinal studies.
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Affiliation(s)
- Raymond S W Tsang
- Public Health Agency of Canada, National Microbiology Laboratory, Winnipeg, Manitoba, Canada
| | - Michelle Shuel
- Public Health Agency of Canada, National Microbiology Laboratory, Winnipeg, Manitoba, Canada
| | - Kirby Cronin
- Public Health Agency of Canada, National Microbiology Laboratory, Winnipeg, Manitoba, Canada.,Public Health Ontario Laboratory, Public Health Ontario, Toronto, Ontario, Canada
| | - Saul Deng
- Public Health Agency of Canada, National Microbiology Laboratory, Winnipeg, Manitoba, Canada
| | - Kathleen Whyte
- Public Health Agency of Canada, National Microbiology Laboratory, Winnipeg, Manitoba, Canada
| | - Alex Marchand-Austin
- Public Health Ontario Laboratory, Public Health Ontario, Toronto, Ontario, Canada
| | - Jennifer Ma
- Public Health Ontario Laboratory, Public Health Ontario, Toronto, Ontario, Canada
| | - Shelly Bolotin
- Public Health Ontario Laboratory, Public Health Ontario, Toronto, Ontario, Canada.,University of Toronto, Toronto, Ontario, Canada
| | - Natasha Crowcroft
- Public Health Ontario Laboratory, Public Health Ontario, Toronto, Ontario, Canada.,University of Toronto, Toronto, Ontario, Canada
| | - Kevin Schwartz
- Public Health Ontario Laboratory, Public Health Ontario, Toronto, Ontario, Canada
| | - Gary Van Domselaar
- Public Health Agency of Canada, National Microbiology Laboratory, Winnipeg, Manitoba, Canada
| | - Morag Graham
- Public Health Agency of Canada, National Microbiology Laboratory, Winnipeg, Manitoba, Canada
| | - Frances B Jamieson
- Public Health Ontario Laboratory, Public Health Ontario, Toronto, Ontario, Canada.,University of Toronto, Toronto, Ontario, Canada
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17
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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.
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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
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18
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How Genomics Is Changing What We Know About the Evolution and Genome of Bordetella pertussis. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1183:1-17. [PMID: 31321755 DOI: 10.1007/5584_2019_401] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The evolution of Bordetella pertussis from a common ancestor similar to Bordetella bronchiseptica has occurred through large-scale gene loss, inactivation and rearrangements, largely driven by the spread of insertion sequence element repeats throughout the genome. B. pertussis is widely considered to be monomorphic, and recent evolution of the B. pertussis genome appears to, at least in part, be driven by vaccine-based selection. Given the recent global resurgence of whooping cough despite the wide-spread use of vaccination, a more thorough understanding of B. pertussis genomics could be highly informative. In this chapter we discuss the evolution of B. pertussis, including how vaccination is changing the circulating B. pertussis population at the gene-level, and how new sequencing technologies are revealing previously unknown levels of inter- and intra-strain variation at the genome-level.
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19
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Molecular Epidemiology of Bordetella pertussis. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1183:19-33. [PMID: 31342459 DOI: 10.1007/5584_2019_402] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Although vaccination has been effective, Bordetella pertussis is increasingly causing epidemics, especially in industrialized countries using acellular vaccines (aPs). One factor behind the increased circulation is the molecular changes on the pathogen level. After pertussis vaccinations were introduced, changes in the fimbrial (Fim) serotype of the circulating strains was observed. When bacterial typing methods improved, further changes between the vaccine and circulating strains, especially among the common virulence genes including pertussis toxin (PT) and pertactin (PRN) were noticed. Moreover, development of genome based techniques including pulsed-field gel electrophoresis (PFGE), multiple-locus variable number tandem repeat analysis (MLVA) and whole-genome sequencing (WGS) have offered a better resolution to monitor B. pertussis strains. After the introduction of aP vaccines, B. pertussis strains that are deficient to vaccine antigens, especially PRN, have appeared widely. On the other hand, antimicrobial resistance to first line drugs (macrolides) against B. pertussis is still low in many countries and therefore no globally evaluated antimicrobial susceptibility test values have been recommended. In this review, we focus on the molecular changes in the bacteria, which have or may have affected the past and current epidemiology of pertussis.
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20
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Ben Fraj I, Kechrid A, Guillot S, Bouchez V, Brisse S, Guiso N, Smaoui H. Pertussis epidemiology in Tunisian infants and children and characterization of Bordetella pertussis isolates: results of a 9-year surveillance study, 2007 to 2016. J Med Microbiol 2018; 68:241-247. [PMID: 30526740 DOI: 10.1099/jmm.0.000892] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
PURPOSE Pertussis remains a public health concern in most countries. Our study aimed to prospectively explore the epidemiology of pertussis in the Tunis area of Tunisia between 2007 and 2016, and to characterize the virulence-associated genes of the collected Bordetella pertussis isolates. METHODOLOGY Infants and children hospitalized at the Children's Hospital of Tunis, Tunisia, between 2007 and 2016 for suspicion of pertussis were enrolled in the study. Culture and real-time PCR (qPCR) assays targeting IS481, IS1001, recA, H-IS1001 and ptxP were used to confirm the pertussis diagnosis. Phenotypic and genotypic characterization of recovered isolates was performed.Results/Key findings. A total of 1844 children were included in the study. Overall, 306 children (16.6 %) with Bordetella infection were confirmed by qPCR. Among them, 265 (86.6 %) were confirmed as having B. pertussis (IS481+, ptxP+, H-IS1001-), 18 (5.9 %) as having Bordetella parapertussis (IS481-, IS1001+) and 11 (3.6 %) as having Bordetella spp. (IS481+, ptxP-, H-IS1001-). No Bordetella holmesii (IS481+, IS1001-, H-IS1001+) was identified. The estimated pertussis incidence in the Tunis area was 134/100 000 in children aged less than 5 years. Two epidemic peaks were observed in 2009 and 2014. Ten B. pertussis isolates were cultured and characterized. Deficiency in pertactin expression was not observed, and genotyping of the isolates revealed a predominant allelic profile: ptxP3-ptxA1-prn2-fim2-1-fim3-2. CONCLUSION This study demonstrated that pertussis is still present as a cyclical disease in Tunisia, despite high primo-vaccination coverage with a pertussis whole-cell vaccine. The predominant genotype of Tunisian B. pertussis isolates is similar to isolates circulating in countries using the acellular vaccine.
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Affiliation(s)
- Ikram Ben Fraj
- 1University of Tunis El Manar, Children's Hospital of Tunis, Laboratory of Microbiology, UR12ES01, Tunis, Tunisia
| | - Amel Kechrid
- 1University of Tunis El Manar, Children's Hospital of Tunis, Laboratory of Microbiology, UR12ES01, Tunis, Tunisia
| | - Sophie Guillot
- 2Biodiversity and Epidemiology of Bacterial Pathogens Unit, Institut Pasteur, Paris, France
- 3National Reference Center for Whooping Cough and Other Bordetella Infections, Institut Pasteur, Paris, France
| | - Valérie Bouchez
- 2Biodiversity and Epidemiology of Bacterial Pathogens Unit, Institut Pasteur, Paris, France
- 3National Reference Center for Whooping Cough and Other Bordetella Infections, Institut Pasteur, Paris, France
| | - Sylvain Brisse
- 2Biodiversity and Epidemiology of Bacterial Pathogens Unit, Institut Pasteur, Paris, France
- 3National Reference Center for Whooping Cough and Other Bordetella Infections, Institut Pasteur, Paris, France
| | - Nicole Guiso
- 3National Reference Center for Whooping Cough and Other Bordetella Infections, Institut Pasteur, Paris, France
| | - Hanen Smaoui
- 1University of Tunis El Manar, Children's Hospital of Tunis, Laboratory of Microbiology, UR12ES01, Tunis, Tunisia
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Ring N, Abrahams JS, Jain M, Olsen H, Preston A, Bagby S. Resolving the complex Bordetella pertussis genome using barcoded nanopore sequencing. Microb Genom 2018; 4. [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.
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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
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Park YJ, Choi MH, Kim D, Lee K, Kim HO, Jeong SH. An Excel Macro for Determining Allelic and Sequence Types of Bacterial Clones in Multilocus Sequence Typing. Ann Lab Med 2018; 39:183-189. [PMID: 30430781 PMCID: PMC6240524 DOI: 10.3343/alm.2019.39.2.183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Revised: 07/09/2018] [Accepted: 10/16/2018] [Indexed: 11/19/2022] Open
Abstract
Background Multilocus sequence typing (MLST) was designed to overcome the low discriminatory power and poor reproducibility of previous molecular typing schemes, and it is useful for inter-laboratory, inter-regional, and inter-national comparison of pathogenic clones. MLST includes labor-intensive sequencing processes and meticulous allelic/sequence type (ST) determination processes, often prone to error. We developed a free automated MLST determination program (MLST typer) based on the Visual Basic for Applications macro, which runs on Microsoft Excel. Methods MLST typer imports sequence data in the FASTA format, converts reverse complement counterparts of the reverse sequences, assembles forward and reverse-complement converted sequences, and returns allelic numbers for each gene and ST of each isolate. To evaluate the performance of MLST typer, we tested the sequence data from 200 clinical isolates, each consisting of seven housekeeping gene sequences, with a total of 1,400 allelic number determinations. The results were compared with manual assessment. Results MLST typer comprises three worksheets: the Main page, Result page, and Summary page. The Main page console operates the process according to user-specified parameters. The Result and Summary pages provide the allelic type and ST determinations. It took approximately 12 minutes to analyze the sequence data from 200 clinical isolates. Compared with manual assessment, the rate of correct identification was 97.2% (1,361/1,400). Conclusions MLST typer can be widely used for epidemiological studies owing to its thoroughness in repetitive functions, good compatibility with FASTA type data files, and easy-to-understand outputs for allelic and ST determinations.
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Affiliation(s)
- Yu Jin Park
- Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul, Korea.,Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Seoul, Korea
| | - Min Hyuk Choi
- Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul, Korea.,Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Seoul, Korea
| | - Dokyun Kim
- Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul, Korea.,Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Seoul, Korea.
| | - Kwangjun Lee
- Division of Antimicrobial Resistance, National Institute of Health, Centers for Disease Control and Prevention, Cheongju, Korea
| | - Hyun Ok Kim
- Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul, Korea
| | - Seok Hoon Jeong
- Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul, Korea.,Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Seoul, Korea.
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Zomer A, Otsuka N, Hiramatsu Y, Kamachi K, Nishimura N, Ozaki T, Poolman J, Geurtsen J. Bordetella pertussis population dynamics and phylogeny in Japan after adoption of acellular pertussis vaccines. Microb Genom 2018; 4. [PMID: 29771235 PMCID: PMC5994715 DOI: 10.1099/mgen.0.000180] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Bordetella pertussis, the causative agent of whooping cough, has experienced a resurgence in the past 15 years, despite the existence of both whole-cell and acellular vaccines. Here, we performed whole genome sequencing analysis of 149 clinical strains, provided by the National Institute of Infectious Diseases (NIID), Japan, isolated in 1982–2014, after Japan became the first country to adopt acellular vaccines against B. pertussis. Additionally, we sequenced 39 strains provided by the Konan Kosei Hospital in Aichi prefecture, Japan, isolated in 2008–2013. The genome sequences afforded insight into B. pertussis genome variability and population dynamics in Japan, and revealed that the B. pertussis population in Japan was characterized by two major clades that divided more than 40 years ago. The pertactin gene was disrupted in about 20 % of the 149 NIID isolates, by either a deletion within the signal sequence (ΔSS) or the insertion of IS element IS481 (prn :: IS481). Phylogeny suggests that the parent clones for these isolates originated in Japan. Divergence dating traced the first generation of the pertactin-deficient mutants in Japan to around 1990, and indicated that strains containing the alternative pertactin allele prn2 may have appeared in Japan around 1974. Molecular clock data suggested that observed fluctuations in B. pertussis population size may have coincided with changes in vaccine usage in the country. The continuing failure to eradicate the disease warrants an exploration of novel vaccine compositions.
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Affiliation(s)
- Aldert Zomer
- 1Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Nao Otsuka
- 2Department of Bacteriology II, National Institute of Infectious Diseases, Musashimurayama, Tokyo, Japan
| | - Yukihiro Hiramatsu
- 2Department of Bacteriology II, National Institute of Infectious Diseases, Musashimurayama, Tokyo, Japan.,†Present address: Department of Molecular Bacteriology, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, Japan
| | - Kazunari Kamachi
- 2Department of Bacteriology II, National Institute of Infectious Diseases, Musashimurayama, Tokyo, Japan
| | - Naoko Nishimura
- 3Department of Pediatrics, Konan Kosei Hospital, Takaya-cho, Konan, Aichi, Japan
| | - Takao Ozaki
- 3Department of Pediatrics, Konan Kosei Hospital, Takaya-cho, Konan, Aichi, Japan
| | - Jan Poolman
- 4Janssen Vaccines and Prevention B.V., Leiden, The Netherlands
| | - Jeroen Geurtsen
- 4Janssen Vaccines and Prevention B.V., Leiden, The Netherlands
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Surveillance of Circulating Bordetella pertussis Strains in Europe during 1998 to 2015. J Clin Microbiol 2018; 56:JCM.01998-17. [PMID: 29491017 DOI: 10.1128/jcm.01998-17] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Accepted: 02/23/2018] [Indexed: 12/15/2022] Open
Abstract
One reason for increased pertussis incidence is the adaptation of Bordetella pertussis to vaccine-induced immunity by modulating its genomic structure. This study, EUpert IV, includes 265 isolates collected from nine European countries during 2012 to 2015 (n = 265) and compares the results to previous EUpert I to III studies (1998 to 2009). The analyses included genotyping, serotyping, pulsed-field gel electrophoresis (PFGE), and multilocus variable-number tandem-repeat analysis (MLVA). Genotyping results showed only small variations among the common virulence genes of B. pertussis The frequencies of serotypes Fim2 and Fim3 varied among the four collections. Genomic analyses showed that MLVA type 27 increased to 80% between the periods of 1998 to 2001 and 2012 to 2015. Two PFGE profiles, BpSR3 (29.4%) and BpSR10 (27.2%), constituted more than 50% of the circulating isolates in the present collection. Our study indicates that the European B. pertussis population is changing and became more homogenous after the introduction of acellular pertussis vaccines.
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Screening and Genomic Characterization of Filamentous Hemagglutinin-Deficient Bordetella pertussis. Infect Immun 2018; 86:IAI.00869-17. [PMID: 29358336 DOI: 10.1128/iai.00869-17] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Accepted: 01/18/2018] [Indexed: 11/20/2022] Open
Abstract
Despite high vaccine coverage, pertussis cases in the United States have increased over the last decade. Growing evidence suggests that disease resurgence results, in part, from genetic divergence of circulating strain populations away from vaccine references. The United States employs acellular vaccines exclusively, and current Bordetella pertussis isolates are predominantly deficient in at least one immunogen, pertactin (Prn). First detected in the United States retrospectively in a 1994 isolate, the rapid spread of Prn deficiency is likely vaccine driven, raising concerns about whether other acellular vaccine immunogens experience similar pressures, as further antigenic changes could potentially threaten vaccine efficacy. We developed an electrochemiluminescent antibody capture assay to monitor the production of the acellular vaccine immunogen filamentous hemagglutinin (Fha). Screening 722 U.S. surveillance isolates collected from 2010 to 2016 identified two that were both Prn and Fha deficient. Three additional Fha-deficient laboratory strains were also identified from a historic collection of 65 isolates dating back to 1935. Whole-genome sequencing of deficient isolates revealed putative, underlying genetic changes. Only four isolates harbored mutations to known genes involved in Fha production, highlighting the complexity of its regulation. The chromosomes of two Fha-deficient isolates included unexpected structural variation that did not appear to influence Fha production. Furthermore, insertion sequence disruption of fhaB was also detected in a previously identified pertussis toxin-deficient isolate that still produced normal levels of Fha. These results demonstrate the genetic potential for additional vaccine immunogen deficiency and underscore the importance of continued surveillance of circulating B. pertussis evolution in response to vaccine pressure.
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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.
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Risk Factors Associated With Bordetella pertussis Among Infants ≤4 Months of Age in the Pre-Tdap Era: United States, 2002-2005. Pediatr Infect Dis J 2017; 36:726-735. [PMID: 28033240 PMCID: PMC8508157 DOI: 10.1097/inf.0000000000001528] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
BACKGROUND In the United States, infants have the highest reported pertussis incidence and death rates. Improved understanding of infant risk factors is needed to optimize prevention strategies. METHODS We prospectively enrolled infants ≤4 months of age with incident-confirmed pertussis from 4 sites during 2002-2005 (preceding pertussis antigen-containing vaccination recommendations for adolescents/adults); each case-patient was age and site matched with 2 control subjects. Caregivers completed structured interviews. Infants and their contacts ≥11 years of age were offered serologic testing for IgG; being seropositive was defined as ≥94 antipertussis toxin IgG enzyme-linked immunosorbent assay units per milliliter. RESULTS Enrolled subjects (115 case-patients; 230 control subjects) had 4396 contacts during incubation periods; 83 (72%) case-patients had ≥1 contact with prolonged (≥5 days) new cough in primary or secondary households. In multivariable analysis, the odds for pertussis were higher for infants with primary/secondary household contacts who had a prolonged new cough, compared with infants who did not. These contacts included mother [adjusted matched odds ratio (aMOR), 43.8; 95% confidence interval (CI), 6.45-298.0] and ≥1 nonmother contact (aMOR, 20.1; 95% CI, 6.48-62.7). Infants receiving breast milk with 0-1 formula feedings daily had decreased pertussis odds (aMOR, 0.27; 95% CI, 0.08-0.89), compared with those receiving more formula. Of 41 tested case-patients, 37 (90%) were seropositive. CONCLUSIONS Pertussis in infants was associated with prolonged new cough (≥5 days) in infants' household contacts. Findings suggest that breastfeeding protects against pertussis and warrants recommendation with pertussis prevention strategies, which currently include pertussis vaccination of pregnant mothers and infants' close contacts.
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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: 2.0] [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: 1.0] [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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Development of a qualitative assay for screening of Bordetella pertussis isolates for pertussis toxin production. PLoS One 2017; 12:e0175326. [PMID: 28394915 PMCID: PMC5386250 DOI: 10.1371/journal.pone.0175326] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2016] [Accepted: 03/23/2017] [Indexed: 01/28/2023] Open
Abstract
Bordetella pertussis infection has been increasing in the US, with reported cases reaching over 50,000 in 2012, a number last observed in the 1950s. Concurrently, B. pertussis lacking the pertactin protein, one of the immunogens included in the acellular vaccine formulations, has rapidly emerged since 2010, and has become the predominant circulating phenotype. Monitoring the production of the remaining acellular vaccine immunogens, such as pertussis toxin (Pt), is a critical next step. To date, methods for screening Pt have been either through genomic sequencing means or by conventional ELISAs. However, sequencing limits detection to the DNA level, missing potential disruptions in transcription or translation. Conventional ELISAs are beneficial for detecting the protein; however, they can often suffer from poor sensitivity and specificity. Here we describe a rapid, highly sensitive and specific electrochemiluminescent capture ELISA that can detect Pt production in prepared inactivated bacterial suspensions. Over 340 isolates were analyzed and analytical validation parameters, such as precision, reproducibility, and stability, were rigorously tested. Intra-plate and inter-plate variability measured at 9.8% and 11.5%, respectively. Refrigerated samples remained stable for two months and variability was unaffected (coefficient of variation was 12%). Interestingly, despite the intention of being a qualitative method, the assay was sensitive enough to detect a small, but statistically significant, difference in protein production between different pertussis promoter allelic groups of strains, ptxP1 and ptxP3. This technology has the ability to perform screening of multiple antigens at one time, thus, improving testing characteristics while minimizing costs, specimen volume, and testing time.
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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.
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Cassiday PK, Skoff TH, Jawahir S, Tondella ML. Changes in Predominance of Pulsed-Field Gel Electrophoresis Profiles of Bordetella pertussis Isolates, United States, 2000-2012. Emerg Infect Dis 2016; 22:442-8. [PMID: 26886905 PMCID: PMC4766905 DOI: 10.3201/eid2203.151136] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
These changes are concurrrent with other recent molecular changes and may be contributing to US pertussis reemergence. To clarify the characteristics of circulating Bordetella pertussis isolates, we used pulsed-field gel electrophoresis (PFGE) to analyze 5,262 isolates collected in the United States during 2000–2012. We found 199 PFGE profiles; 5 profiles accounted for 72% of isolates. The most common profile, CDC013, accounted for 35%–46% of isolates tested from 2000–2009; however, the proportion of isolates of this profile rapidly decreased in 2010. Profile CDC237, first seen in 2009, increased rapidly and accounted for 29% of 2012 isolates. No location bias was observed among profiles during 2000–2010, but differences were observed among isolates from different states during 2012. Predominant profiles match those observed in recent European PFGE studies. PFGE profile changes are concurrent with other recent molecular changes in B. pertussis and may be contributing to the reemergence of pertussis in the United States. Continued PFGE monitoring is critical for understanding the changing epidemiology of pertussis.
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Williams MM, Sen K, Weigand MR, Skoff TH, Cunningham VA, Halse TA, Tondella ML. Bordetella pertussis Strain Lacking Pertactin and Pertussis Toxin. Emerg Infect Dis 2016; 22:319-322. [PMID: 26812174 PMCID: PMC4734536 DOI: 10.3201/eid2202.151332] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [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
A Bordetella pertussis strain lacking 2 acellular vaccine immunogens, pertussis toxin and pertactin, was isolated from an unvaccinated infant in New York State in 2013. Comparison with a French strain that was pertussis toxin–deficient, pertactin wild-type showed that the strains carry the same 28-kb deletion in similar genomes.
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Lega J, Brown HE. Data-driven outbreak forecasting with a simple nonlinear growth model. Epidemics 2016; 17:19-26. [PMID: 27770752 PMCID: PMC5159251 DOI: 10.1016/j.epidem.2016.10.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Revised: 09/20/2016] [Accepted: 10/09/2016] [Indexed: 01/03/2023] Open
Abstract
We present EpiGro, a simple data-driven method to forecast the scope of an ongoing outbreak. We provide general hypotheses for expected model validity and also discuss model limitations. We propose an automated parameter estimation method that can be used for forecasting. We test our approach on 9 different outbreaks and show robustness over multiple systems and over noisy data sets. In the absence of other information or in conjunction with other models, EpiGro may be useful to public health responders.
Recent events have thrown the spotlight on infectious disease outbreak response. We developed a data-driven method, EpiGro, which can be applied to cumulative case reports to estimate the order of magnitude of the duration, peak and ultimate size of an ongoing outbreak. It is based on a surprisingly simple mathematical property of many epidemiological data sets, does not require knowledge or estimation of disease transmission parameters, is robust to noise and to small data sets, and runs quickly due to its mathematical simplicity. Using data from historic and ongoing epidemics, we present the model. We also provide modeling considerations that justify this approach and discuss its limitations. In the absence of other information or in conjunction with other models, EpiGro may be useful to public health responders.
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Vodzak J, Queenan AM, Souder E, Evangelista AT, Long SS. Clinical Manifestations and Molecular Characterization of Pertactin-Deficient and Pertactin-Producing Bordetella pertussis in Children, Philadelphia 2007-2014. Clin Infect Dis 2016; 64:60-66. [PMID: 27624959 DOI: 10.1093/cid/ciw632] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2015] [Accepted: 08/25/2016] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Bordetella pertussis strains lacking expression of pertactin, a bacterial adhesin and vaccine target, are emerging. There are limited data on disease manifestations of mutant strains in children. We sought to compare clinical manifestations of pertactin-deficient and pertactin-producing B. pertussis infection in infants and describe corresponding molecular characteristics. METHODS Molecular characterization of archived B. pertussis isolates (collected January 2007 to March 2014) included Western blot analysis, pulsed-field gel electrophoresis (PFGE), polymerase chain reaction, and pertactin gene sequencing. Medical record review compared epidemiologic and clinical courses of pertactin-producing and pertactin-deficient B. pertussis infections. RESULTS Sixty of 72 B. pertussis isolates were viable for analysis. Within the cohort of infants, the median age was 95 days, 90% received ≤1 dose of vaccine, and 72% were hospitalized. Pertactin deficiency was first noted in 2008, and its prevalence increased over time (68% overall prevalence). There were no statistically significant differences in presenting symptoms or signs, hospitalization, intensive care, respiratory support, or laboratory results related to pertactin expression. Illness length was shorter in pertactin-deficient group (mean difference, 3.2 days; P = .04); no difference was noted in the subgroup of infants <4 months old. Molecular analyses identified 11 PFGE profiles (Centers for Disease Control and Prevention profile No. 002 predominant, 47%). In 41 pertactin-deficient strains, sequencing identified 2 stop codon and 3 IS481 locations disrupting the prn gene. Mutations and nucleotide positions were not unique to PFGE type, nor were they clustered in time. CONCLUSIONS In this cohort of predominantly unimmunized infants, clinical disease did not differ between infection with pertactin-deficient and those with pertactin-producing B. pertussis. Molecular analyses demonstrated remarkable PFGE strain diversity, with multiple mechanisms and molecular sites of pertactin inactivation.
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Affiliation(s)
| | - Anne Marie Queenan
- Infectious Diseases & Vaccines, Janssen, Research & Development, Raritan, New Jersey
| | - Emily Souder
- Department of Pediatrics, Section of Infectious Diseases
| | - Alan T Evangelista
- Department of Pathology and Laboratory Medicine, St Christopher's Hospital for Children and Drexel University College of Medicine, Philadelphia, Pennsylvania
| | - Sarah S Long
- Department of Pediatrics, Section of Infectious Diseases
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Register KB, Nicholson TL, Brunelle BW. Comparison of ribotyping and sequence-based typing for discriminating among isolates of Bordetella bronchiseptica. J Microbiol Methods 2016; 129:117-126. [PMID: 27542997 DOI: 10.1016/j.mimet.2016.08.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Revised: 08/15/2016] [Accepted: 08/15/2016] [Indexed: 11/16/2022]
Abstract
PvuII ribotyping and MLST are each highly discriminatory methods for genotyping Bordetella bronchiseptica, but a direct comparison between these approaches has not been undertaken. The goal of this study was to directly compare the discriminatory power of PvuII ribotyping and MLST, using a single set of geographically and genetically diverse strains, and to determine whether subtyping based on repeat region sequences of the pertactin gene (prn) provides additional resolution. One hundred twenty-two isolates were analyzed, representing 11 mammalian or avian hosts, sourced from the United States, Europe, Israel and Australia. Thirty-two ribotype patterns were identified; one isolate could not be typed. In comparison, all isolates were typeable by MLST and a total of 30 sequence types was identified. An analysis based on Simpson's Index of Diversity (SID) revealed that ribotyping and MLST are nearly equally discriminatory, with SIDs of 0.920 for ribotyping and 0.919 for MLST. Nonetheless, for ten ribotypes and eight MLST sequence types, the alternative method discriminates among isolates that otherwise type identically. Pairing prn repeat region typing with ribotyping yielded 54 genotypes and increased the SID to 0.954. Repeat region typing combined with MLST resulted in 47 genotypes and an SID of 0.944. Given the technical and practical advantages of MLST over ribotyping, and the nominal difference in their SIDs, we conclude MLST is the preferred primary typing tool. We recommend the combination of MLST and prn repeat region typing as a high-resolution, objective and standardized approach valuable for investigating the population structure and epidemiology of B. bronchiseptica.
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Affiliation(s)
- Karen B Register
- Ruminant Diseases and Immunology Research Unit, USDA/Agricultural Research Service/National Animal Disease Center, 1920 Dayton Avenue, Ames, IA 50010, United States.
| | - Tracy L Nicholson
- Virus and Prion Research Unit, USDA/Agricultural Research Service/National Animal Disease Center, 1920 Dayton Avenue, Ames, IA 50010, United States
| | - Brian W Brunelle
- Food Safety and Enteric Pathogens Research Unit, USDA/Agricultural Research Service/National Animal Disease Center, 1920 Dayton Avenue, Ames, IA 50010, United States
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Concordancia entre las técnicas de IFD, PCR y ELISA para determinar la frecuencia de Bordetella parapertussis y Bordetella pertussis en un brote de tos ferina en el departamento de Antioquia (Colombia) en 2013. INFECTIO 2016. [DOI: 10.1016/j.infect.2015.10.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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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: 2.6] [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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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.
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Affiliation(s)
- Katherine E. Bowden
- Division of Bacterial Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Michael R. Weigand
- Division of Bacterial Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Yanhui Peng
- Division of Bacterial Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Pamela K. Cassiday
- Division of Bacterial Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Scott Sammons
- Biotechnology Core Facility Branch, Division of Scientific Resources, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Kristen Knipe
- Biotechnology Core Facility Branch, Division of Scientific Resources, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Lori A. Rowe
- Biotechnology Core Facility Branch, Division of Scientific Resources, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Vladimir Loparev
- Biotechnology Core Facility Branch, Division of Scientific Resources, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Mili Sheth
- Biotechnology Core Facility Branch, Division of Scientific Resources, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Keeley Weening
- Vermont Department of Health Laboratory, Burlington, Vermont, USA
| | - M. Lucia Tondella
- Division of Bacterial Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Margaret M. Williams
- Division of Bacterial Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
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Breakwell L, Kelso P, Finley C, Schoenfeld S, Goode B, Misegades LK, Martin SW, Acosta AM. Pertussis Vaccine Effectiveness in the Setting of Pertactin-Deficient Pertussis. Pediatrics 2016; 137:peds.2015-3973. [PMID: 27244813 DOI: 10.1542/peds.2015-3973] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 02/17/2016] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND In the United States, the proportion of Bordetella pertussis isolates lacking pertactin, a component of acellular pertussis vaccines, increased from 14% in 2010 to 85% in 2012. The impact on vaccine effectiveness (VE) is unknown. METHODS We conducted 2 matched case-control evaluations in Vermont to assess VE of the 5-dose diphtheria, tetanus, and acellular pertussis vaccine (DTaP) series among 4- to 10-year-olds, and tetanus, diphtheria, and acellular pertussis vaccine (Tdap) among 11- to 19-year-olds. Cases reported during 2011 to 2013 were included. Three controls were matched to each case by medical home, and additionally by birth year for the Tdap evaluation. Vaccination history was obtained from medical records and parent interviews. Odds ratios (OR) were calculated by using conditional logistic regression; VE was estimated as (1-OR) × 100%. Pertactin status was determined for cases with available isolates. RESULTS Overall DTaP VE was 84% (95% confidence interval [CI] 58%-94%). VE within 12 months of dose 5 was 90% (95% CI 71%-97%), declining to 68% (95% CI 10%-88%) by 5-7 years post-vaccination. Overall Tdap VE was 70% (95% CI 54%-81%). Within 12 months of Tdap vaccination, VE was 76% (95% CI 60%-85%), declining to 56% (95% CI 16%-77%) by 2-4 years post-vaccination. Of cases with available isolates, >90% were pertactin-deficient. CONCLUSIONS Our DTaP and Tdap VE estimates remain similar to those found in other settings, despite high prevalence of pertactin deficiency in Vermont, suggesting these vaccines continue to be protective against reported pertussis disease.
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Affiliation(s)
- Lucy Breakwell
- Epidemic Intelligence Service, Scientific Education and Professional Development Program Office, Meningitis and Vaccine Preventable Diseases Branch, Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, and
| | - Patsy Kelso
- Vermont Department of Health, Burlington, Vermont
| | | | | | - Brant Goode
- Vermont Department of Health, Burlington, Vermont Career Epidemiology Field Officer Program, Division of State and Local Readiness, Office of Public Health Preparedness and Response, Centers for Disease Control and Prevention, Atlanta, Georgia; and
| | - Lara K Misegades
- Meningitis and Vaccine Preventable Diseases Branch, Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, and
| | - Stacey W Martin
- Meningitis and Vaccine Preventable Diseases Branch, Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, and
| | - Anna M Acosta
- Meningitis and Vaccine Preventable Diseases Branch, Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, and
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Qin X, Zerr DM, Kronman MP, Adler AL, Berry JE, Rich S, Buccat AM, Xu M, Englund JA. Comparison of molecular detection methods for pertussis in children during a state-wide outbreak. Ann Clin Microbiol Antimicrob 2016; 15:28. [PMID: 27121506 PMCID: PMC4847268 DOI: 10.1186/s12941-016-0142-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Accepted: 04/17/2016] [Indexed: 11/10/2022] Open
Abstract
A state-wide pertussis outbreak occurred in Washington during the winter–spring months of 2012, concurrent with respiratory viral season. We compared performance characteristics of a laboratory-developed pertussis PCR (LD-PCR for Bordetella pertussis, Bordetella parapertussis, and Bordetella holmesii) and rapid multiplex PCR (RM-PCR) for respiratory viruses (FilmArray™, BioFire, B. pertussis data unblinded following FDA approval post outbreak). We analyzed three cohorts of patients using physician testing orders as a proxy for clinical suspicion for pertussis or respiratory viruses: Cohort 1, tested by LD-PCR for pertussis pathogens only by nasopharyngeal swab; Cohort 2, by RM-PCR for respiratory viruses only by mid-nasal turbinate swab; and Cohort 3, by both methods. B. pertussis was detected in a total of 25 of the 490 patients in Cohort 3 in which LD-PCR detected 20/25 (80 %) cases and the RM-PCR detected 24/25 (96 %; p = 0.2). Pertussis pathogens were detected in 21/584 (3.6 %) of samples from Cohort 1 where clinicians had a relatively strong suspicion for pertussis. In contrast, B. pertussis was detected in only 4/3071 (0.1 %) specimens from Cohort 2 where suspicion for pertussis was lower (p < 0.001 for comparison with Cohort 1). In summary, the two laboratory methods were comparable for the detection of B. pertussis.
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Affiliation(s)
- X Qin
- Microbiology Laboratory, Seattle Children's Hospital, Seattle, WA, USA.
| | - D M Zerr
- Division of Pediatric Infectious Diseases, Department of Pediatrics, Seattle Children's Hospital, University of Washington, Seattle, WA, USA
| | - M P Kronman
- Division of Pediatric Infectious Diseases, Department of Pediatrics, Seattle Children's Hospital, University of Washington, Seattle, WA, USA
| | - A L Adler
- Division of Pediatric Infectious Diseases, Department of Pediatrics, Seattle Children's Hospital, University of Washington, Seattle, WA, USA
| | - J E Berry
- Microbiology Laboratory, Seattle Children's Hospital, Seattle, WA, USA
| | - S Rich
- Microbiology Laboratory, Seattle Children's Hospital, Seattle, WA, USA
| | - A M Buccat
- Microbiology Laboratory, Seattle Children's Hospital, Seattle, WA, USA
| | - M Xu
- Microbiology Laboratory, Seattle Children's Hospital, Seattle, WA, USA.,Department of Laboratory Medicine, Seattle Children's Hospital, University of Washington, Seattle, WA, USA
| | - J A Englund
- Division of Pediatric Infectious Diseases, Department of Pediatrics, Seattle Children's Hospital, University of Washington, Seattle, WA, USA
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Sali M, Buttinelli G, Fazio C, Vacca P, La Sorda M, Carannante A, Spanu T, Valentini P, Stefanelli P. Pertussis in infants less than 6 months of age and household contacts, Italy, April 2014. Hum Vaccin Immunother 2016; 11:1173-4. [PMID: 25874559 DOI: 10.1080/21645515.2015.1019190] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
Abstract
We report pertussis cases in 4 infants less than 6 months admitted with symptoms compatible with pertussis to the intensive care unit of the Università Cattolica del Sacro Cuore in Rome, April 2014. Realtime PCR confirmed pertussis diagnosis for the 4 infants, 2 of them were cousins, and for the household contacts of 1 of them. Analysis of pertussis toxin, its promoter and pertactin was also performed. First of all, this report emphasizes the need to investigate household contact of infants with pertussis; secondly, to evaluate the selective vaccination of household members of newborns as an effective program to reduce pertussis in infants.
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Affiliation(s)
- Michela Sali
- a Institute of Microbiology; Università Cattolica del Sacro Cuore ; Rome , Italy
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43
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Carbonetti NH. Contribution of pertussis toxin to the pathogenesis of pertussis disease. Pathog Dis 2015; 73:ftv073. [PMID: 26394801 DOI: 10.1093/femspd/ftv073] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/16/2015] [Indexed: 12/19/2022] Open
Abstract
Pertussis toxin (PT) is a multisubunit protein toxin secreted by Bordetella pertussis, the bacterial agent of the disease pertussis or whooping cough. PT in detoxified form is a component of all licensed acellular pertussis vaccines, since it is considered to be an important virulence factor for this pathogen. PT inhibits G protein-coupled receptor signaling through Gi proteins in mammalian cells, an activity that has led to its widespread use as a cell biology tool. But how does this activity of PT contribute to pertussis, including the severe respiratory symptoms of this disease? In this minireview, the contribution of PT to the pathogenesis of pertussis disease will be considered based on evidence from both human infections and animal model studies. Although definitive proof of the role of PT in humans is lacking, substantial evidence supports the idea that PT is a major contributor to pertussis pathology, including the severe respiratory symptoms associated with this disease.
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Affiliation(s)
- Nicholas H Carbonetti
- Department of Microbiology and Immunology, University of Maryland Medical School, Baltimore, MD 21201, USA
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Bouchez V, Hegerle N, Strati F, Njamkepo E, Guiso N. New Data on Vaccine Antigen Deficient Bordetella pertussis Isolates. Vaccines (Basel) 2015; 3:751-70. [PMID: 26389958 PMCID: PMC4586476 DOI: 10.3390/vaccines3030751] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Revised: 08/25/2015] [Accepted: 09/02/2015] [Indexed: 01/01/2023] Open
Abstract
Evolution of Bordetella pertussis is driven by natural and vaccine pressures. Isolates circulating in regions with high vaccination coverage present multiple allelic and antigenic variations as compared to isolates collected before introduction of vaccination. Furthermore, during the last epidemics reported in regions using pertussis acellular vaccines, isolates deficient for vaccine antigens, such as pertactin (PRN), were reported to reach high proportions of circulating isolates. More sporadic filamentous hemagglutinin (FHA) or pertussis toxin (PT) deficient isolates were also collected. The whole genome of some recent French isolates, deficient or non-deficient in vaccine antigens, were analyzed. Transcription profiles of the expression of the main virulence factors were also compared. The invasive phenotype in an in vitro human tracheal epithelial (HTE) cell model of infection was evaluated. Our genomic analysis focused on SNPs related to virulence genes known to be more likely to present allelic polymorphism. Transcriptomic data indicated that isolates circulating since the introduction of pertussis vaccines present lower transcription levels of the main virulence genes than the isolates of the pre-vaccine era. Furthermore, isolates not producing FHA present significantly higher expression levels of the entire set of genes tested. Finally, we observed that recent isolates are more invasive in HTE cells when compared to the reference strain, but no multiplication occurs within cells.
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Affiliation(s)
- Valérie Bouchez
- Molecular Prevention and Therapy of Human Diseases, Institut Pasteur, 25 rue du Dr Roux, Paris 75015, France.
- URAS-CNRS 3012, Paris 75015, France.
| | - Nicolas Hegerle
- Molecular Prevention and Therapy of Human Diseases, Institut Pasteur, 25 rue du Dr Roux, Paris 75015, France.
- URAS-CNRS 3012, Paris 75015, France.
| | - Francesco Strati
- Molecular Prevention and Therapy of Human Diseases, Institut Pasteur, 25 rue du Dr Roux, Paris 75015, France.
- URAS-CNRS 3012, Paris 75015, France.
| | - Elisabeth Njamkepo
- Molecular Prevention and Therapy of Human Diseases, Institut Pasteur, 25 rue du Dr Roux, Paris 75015, France.
- URAS-CNRS 3012, Paris 75015, France.
| | - Nicole Guiso
- Molecular Prevention and Therapy of Human Diseases, Institut Pasteur, 25 rue du Dr Roux, Paris 75015, France.
- URAS-CNRS 3012, Paris 75015, France.
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Draft Genome Sequence of a Bordetella pertussis Strain with the Virulence-Associated Allelic Variant ptxP3, Isolated in Italy. GENOME ANNOUNCEMENTS 2015; 3:3/5/e00944-15. [PMID: 26358588 PMCID: PMC4566170 DOI: 10.1128/genomea.00944-15] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Despite a universal immunization program, pertussis has persisted and resurged, and is of particular concern for infants in terms of morbidity and mortality. Here, we report the genome sequence of a Bordetella pertussis strain with the virulence-associated allelic variant ptxP3, isolated from a 45-day-old infant.
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Abstract
Despite implementation of a successful vaccination program, pertussis remains a significant health problem. Although the incidence of pertussis in the United States is reduced by approximately 80% compared with incidence before the introduction of vaccination in the 1940s, deaths still occur and the unrecognized disease burden remains high, with 1 million Bordetella pertussis infections annually in the United States estimated by serologic surveys. Reasons for the resurgence and current prevalence of pertussis may be multifactorial and include waning vaccine-induced protection as well as lower vaccine effectiveness, failure to vaccinate, and changes in the organism itself.
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Affiliation(s)
- Emily Souder
- Section of Infectious Diseases, Department of Pediatrics, St. Christopher's Hospital for Children, Drexel University College of Medicine, 160 East Erie Avenue, Philadelphia, PA 19134, USA.
| | - Sarah S Long
- Section of Infectious Diseases, Department of Pediatrics, St. Christopher's Hospital for Children, Drexel University College of Medicine, 160 East Erie Avenue, Philadelphia, PA 19134, USA
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47
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Barkoff AM, Gröndahl-Yli-Hannuksela K, He Q. Seroprevalence studies of pertussis: what have we learned from different immunized populations. Pathog Dis 2015. [PMID: 26208655 DOI: 10.1093/femspd/ftv050] [Citation(s) in RCA: 75] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Bordetella pertussis is a pathogen-causing whooping cough (pertussis) in humans. Although vaccination against the disease is effective, the bacterium is still circulating among population and can even cause death. Especially young infants, who lack protection, are vulnerable. The laboratory diagnostic methods to detect B. pertussis are culture, PCR and ELISA serology. Reported cases of the disease vary among countries but usually the incidence rates are low, <1 to 10/100 000. However, pertussis often goes unrecognized among patients as it presents itself like the common cold, especially in adults and elders who are often the source of the infection. This makes pertussis difficult to monitor and control. Serological surveillance is an easy manner to estimate the real burden of the disease among population. Furthermore, to have reliable results, anti-PT IgG antibodies should be measured, as PT is the only specific antigen to B. pertussis. This review aims to evaluate available pertussis seroprevalence studies throughout the world, and to compare the findings from countries with different vaccination histories and strategies. Estimation of the real burden of pertussis is compared to reported numbers. In addition, future aspects in seroprevalence studies are considered.
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Affiliation(s)
- Alex-Mikael Barkoff
- Department of Medical Microbiology and Immunology, University of Turku, Turku, Finland
| | | | - Qiushui He
- Department of Medical Microbiology and Immunology, University of Turku, Turku, Finland
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48
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Mooi FR, Zeddeman A, van Gent M. The pertussis problem: classical epidemiology and strain characterization should go hand in hand. JORNAL DE PEDIATRIA (VERSÃO EM PORTUGUÊS) 2015. [DOI: 10.1016/j.jpedp.2015.04.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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Mooi FR, Zeddeman A, van Gent M. The pertussis problem: classical epidemiology and strain characterization should go hand in hand. J Pediatr (Rio J) 2015; 91:315-7. [PMID: 25704450 DOI: 10.1016/j.jped.2015.02.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
- Frits R Mooi
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, Netherlands.
| | - Anne Zeddeman
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, Netherlands
| | - Marjolein van Gent
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, Netherlands
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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: 1.7] [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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