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Mir-Cros A, Moreno-Mingorance A, Martín-Gómez MT, Abad R, Bloise I, Campins M, González-Praetorius A, Gutiérrez MN, Martín-González H, Muñoz-Almagro C, Orellana MÁ, de Pablos M, Roca-Grande J, Rodrigo C, Rodríguez ME, Uriona S, Vidal MJ, Pumarola T, Larrosa MN, González-López JJ. Pertactin-Deficient Bordetella pertussis with Unusual Mechanism of Pertactin Disruption, Spain, 1986-2018. Emerg Infect Dis 2022; 28:967-976. [PMID: 35447067 PMCID: PMC9045434 DOI: 10.3201/eid2805.211958] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Bordetella pertussis not expressing pertactin has increased in countries using acellular pertussis vaccines (ACV). The deficiency is mostly caused by pertactin gene disruption by IS481. To assess the effect of the transition from whole-cell vaccine to ACV on the emergence of B. pertussis not expressing pertactin in Spain, we studied 342 isolates collected during 1986–2018. We identified 93 pertactin-deficient isolates. All were detected after introduction of ACV and represented 38% of isolates collected during the ACV period; 58.1% belonged to a genetic cluster of isolates carrying the unusual prn::del(–292, 1340) mutation. Pertactin inactivation by IS481 insertion was identified in 23.7% of pertactin-deficient isolates, arising independently multiple times and in different phylogenetic branches. Our findings support the emergence and dissemination of a cluster of B. pertussis with an infrequent mechanism of pertactin disruption in Spain, probably resulting from introduction of ACV.
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Abrahams JS, Weigand MR, Ring N, MacArthur I, Etty J, Peng S, Williams MM, Bready B, Catalano AP, Davis JR, Kaiser MD, Oliver JS, Sage JM, Bagby S, Tondella ML, Gorringe AR, Preston A. Towards comprehensive understanding of bacterial genetic diversity: large-scale amplifications in Bordetella pertussis and Mycobacterium tuberculosis. Microb Genom 2022; 8:000761. [PMID: 35143385 PMCID: PMC8942028 DOI: 10.1099/mgen.0.000761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 12/11/2021] [Indexed: 11/18/2022] Open
Abstract
Bacterial genetic diversity is often described solely using base-pair changes despite a wide variety of other mutation types likely being major contributors. Tandem duplication/amplifications are thought to be widespread among bacteria but due to their often-intractable size and instability, comprehensive studies of these mutations are rare. We define a methodology to investigate amplifications in bacterial genomes based on read depth of genome sequence data as a proxy for copy number. We demonstrate the approach with Bordetella pertussis, whose insertion sequence element-rich genome provides extensive scope for amplifications to occur. Analysis of data for 2430 B. pertussis isolates identified 272 putative amplifications, of which 94 % were located at 11 hotspot loci. We demonstrate limited phylogenetic connection for the occurrence of amplifications, suggesting unstable and sporadic characteristics. Genome instability was further described in vitro using long-read sequencing via the Nanopore platform, which revealed that clonally derived laboratory cultures produced heterogenous populations rapidly. We extended this research to analyse a population of 1000 isolates of another important pathogen, Mycobacterium tuberculosis. We found 590 amplifications in M. tuberculosis, and like B. pertussis, these occurred primarily at hotspots. Genes amplified in B. pertussis include those involved in motility and respiration, whilst in M. tuberuclosis, functions included intracellular growth and regulation of virulence. Using publicly available short-read data we predicted previously unrecognized, large amplifications in B. pertussis and M. tuberculosis. This reveals the unrecognized and dynamic genetic diversity of B. pertussis and M. tuberculosis, highlighting the need for a more holistic understanding of bacterial genetics.
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Affiliation(s)
- Jonathan S. Abrahams
- Department of Biology and Biochemistry and Milner Centre for Evolution, University of Bath, Bath, UK
| | - Michael R. Weigand
- Division of Bacterial Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Natalie Ring
- Department of Biology and Biochemistry and Milner Centre for Evolution, University of Bath, Bath, UK
| | - Iain MacArthur
- Department of Biology and Biochemistry and Milner Centre for Evolution, University of Bath, Bath, UK
| | - Joss Etty
- Department of Biology and Biochemistry and Milner Centre for Evolution, University of Bath, Bath, UK
| | - Scott Peng
- Division of Bacterial Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Margaret M. Williams
- Division of Bacterial Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | | | | | | | | | | | | | - Stefan Bagby
- Department of Biology and Biochemistry and Milner Centre for Evolution, University of Bath, Bath, UK
| | - M. Lucia Tondella
- Division of Bacterial Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | | | - Andrew Preston
- Department of Biology and Biochemistry and Milner Centre for Evolution, University of Bath, Bath, UK
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Sadarangani M, Marchant A, Kollmann TR. Immunological mechanisms of vaccine-induced protection against COVID-19 in humans. Nat Rev Immunol 2021; 21:475-484. [PMID: 34211186 PMCID: PMC8246128 DOI: 10.1038/s41577-021-00578-z] [Citation(s) in RCA: 359] [Impact Index Per Article: 119.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/07/2021] [Indexed: 02/06/2023]
Abstract
Most COVID-19 vaccines are designed to elicit immune responses, ideally neutralizing antibodies (NAbs), against the SARS-CoV-2 spike protein. Several vaccines, including mRNA, adenoviral-vectored, protein subunit and whole-cell inactivated virus vaccines, have now reported efficacy in phase III trials and have received emergency approval in many countries. The two mRNA vaccines approved to date show efficacy even after only one dose, when non-NAbs and moderate T helper 1 cell responses are detectable, but almost no NAbs. After a single dose, the adenovirus vaccines elicit polyfunctional antibodies that are capable of mediating virus neutralization and of driving other antibody-dependent effector functions, as well as potent T cell responses. These data suggest that protection may require low levels of NAbs and might involve other immune effector mechanisms including non-NAbs, T cells and innate immune mechanisms. Identifying the mechanisms of protection as well as correlates of protection is crucially important to inform further vaccine development and guide the use of licensed COVID-19 vaccines worldwide.
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Affiliation(s)
- Manish Sadarangani
- Vaccine Evaluation Center, BC Children's Hospital, Vancouver, British Columbia, Canada.
- Department of Pediatrics, University of British Columbia, Vancouver, British Columbia, Canada.
| | - Arnaud Marchant
- Institute for Medical Immunology, Université libre de Bruxelles, Charleroi, Belgium
| | - Tobias R Kollmann
- Telethon Kids Institute, Perth Children's Hospital, University of Western Australia, Nedlands, Western Australia, Australia
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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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Xu Z, Octavia S, Luu LDW, Payne M, Timms V, Tay CY, Keil AD, Sintchenko V, Guiso N, Lan R. Pertactin-Negative and Filamentous Hemagglutinin-Negative Bordetella pertussis, Australia, 2013-2017. Emerg Infect Dis 2019; 25:1196-1199. [PMID: 31107218 PMCID: PMC6537726 DOI: 10.3201/eid2506.180240] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
During the 2008–2012 pertussis epidemic in Australia, pertactin (Prn)–negative Bordetella pertussis emerged. We analyzed 78 isolates from the 2013–2017 epidemic and documented continued expansion of Prn-negative ptxP3 B. pertussis strains. We also detected a filamentous hemagglutinin-negative and Prn-negative B. pertussis isolate.
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Weigand MR, Peng Y, Batra D, Burroughs M, Davis JK, Knipe K, Loparev VN, Johnson T, Juieng P, Rowe LA, Sheth M, Tang K, Unoarumhi Y, Williams MM, Tondella ML. Conserved Patterns of Symmetric Inversion in the Genome Evolution of Bordetella Respiratory Pathogens. mSystems 2019; 4:e00702-19. [PMID: 31744907 PMCID: PMC6867878 DOI: 10.1128/msystems.00702-19] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Accepted: 11/01/2019] [Indexed: 12/11/2022] Open
Abstract
Whooping cough (pertussis), primarily caused by Bordetella pertussis, has resurged in the United States, and circulating strains exhibit considerable chromosome structural fluidity in the form of rearrangement and deletion. The genus Bordetella includes additional pathogenic species infecting various animals, some even causing pertussis-like respiratory disease in humans; however, investigation of their genome evolution has been limited. We studied chromosome structure in complete genome sequences from 167 Bordetella species isolates, as well as 469 B. pertussis isolates, to gain a generalized understanding of rearrangement patterns among these related pathogens. Observed changes in gene order primarily resulted from large inversions and were only detected in species with genomes harboring multicopy insertion sequence (IS) elements, most notably B. holmesii and B. parapertussis While genomes of B. pertussis contain >240 copies of IS481, IS elements appear less numerous in other species and yield less chromosome structural diversity through rearrangement. These data were further used to predict all possible rearrangements between IS element copies present in Bordetella genomes, revealing that only a subset is observed among circulating strains. Therefore, while it appears that rearrangement occurs less frequently in other species than in B. pertussis, these clinically relevant respiratory pathogens likely experience similar mutation of gene order. The resulting chromosome structural fluidity presents both challenges and opportunity for the study of Bordetella respiratory pathogens.IMPORTANCE Bordetella pertussis is the primary agent of whooping cough (pertussis). The Bordetella genus includes additional pathogens of animals and humans, including some that cause pertussis-like respiratory illness. The chromosome of B. pertussis has previously been shown to exhibit considerable structural rearrangement, but insufficient data have prevented comparable investigation in related species. In this study, we analyze chromosome structure variation in several Bordetella species to gain a generalized understanding of rearrangement patterns in this genus. Just as in B. pertussis, we observed inversions in other species that likely result from common mutational processes. We used these data to further predict additional, unobserved inversions, suggesting that specific genome structures may be preferred in each species.
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Affiliation(s)
- Michael R Weigand
- Division of Bacterial Disease, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Yanhui Peng
- Division of Bacterial Disease, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Dhwani Batra
- Division of Scientific Resources, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Mark Burroughs
- Division of Scientific Resources, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Jamie K Davis
- Division of Scientific Resources, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Kristen Knipe
- Division of Scientific Resources, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Vladimir N Loparev
- Division of Scientific Resources, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Taccara Johnson
- Division of Bacterial Disease, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Phalasy Juieng
- Division of Scientific Resources, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Lori A Rowe
- Division of Scientific Resources, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Mili Sheth
- Division of Scientific Resources, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Kevin Tang
- Division of Scientific Resources, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Yvette Unoarumhi
- Division of Scientific Resources, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Margaret M Williams
- Division of Bacterial Disease, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - M Lucia Tondella
- Division of Bacterial Disease, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
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8
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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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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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