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Bai F, Cai C, Zhang T, Wang P, Shi L, Zhai L, Li H, Zhang L, Yao S. Genome-Based Analysis of Aspergillus niger Aggregate Species from China and Their Potential for Fumonisin B 2 and Ochratoxin A Production. Curr Microbiol 2022; 79:193. [PMID: 35579721 DOI: 10.1007/s00284-022-02876-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 04/11/2022] [Indexed: 11/30/2022]
Abstract
Based on entire genome sequencing, this study focused on the classification of Aspergillus niger aggregation species and investigated their potential for fumonisin B2 (FB2) and ochratoxin A (OTA) production. In the current study, 22 strains were used, namely 17 A. niger strains, four A. welwitschiae strains, and one A. lacticoffeatus (a synonym of A. niger) strain. Traditional multigene phylogenetic analysis, average nucleotide identity analysis (ANI), and the whole-genome single-nucleotide polymorphism (SNP) analyses were used to reconfirm the taxonomic status of A. niger, A. welwitschiae, and A. lacticoffeatus. The ability of A. niger to produce FB2 and OTA on five culture substrates was determined, and the association between FB2 and OTA gene clusters and toxin-producing abilities was explored. The results revealed that the ANI method could distinguish A. niger from A. welwitschiae, with an ANI value of < 98%. The SNP-based phylogenetic analysis suggested that A. niger and A. welwitschiae were two independent phylogenetic species. The ANI, SNP, and multigene phylogenetic analysis supported previous findings that A. lacticoffeatus was a synonymous species of A. niger. Aspergillus niger strains exhibited the varied potential of producing FB2 and OTA on different culture media. The A. niger genome sequence analysis revealed no significant difference in fumonisin gene clusters between FB2-nonproducing isolates and FB2-producing isolates, and the integrity of the ochratoxin biosynthesis genes cluster was clearly associated with OTA production. In conclusion, gene sequencing can be useful in assessing A. niger's ability to produce OTA, but it cannot reliably predict its ability to produce FB2.
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Affiliation(s)
- Feirong Bai
- China Center of Industrial Culture Collection (CICC), China National Research Institute of Food and Fermentation Industries Co., Ltd, Beijing, 100015, China
| | - Chengshan Cai
- China Center of Industrial Culture Collection (CICC), China National Research Institute of Food and Fermentation Industries Co., Ltd, Beijing, 100015, China
| | - Tianci Zhang
- China Center of Industrial Culture Collection (CICC), China National Research Institute of Food and Fermentation Industries Co., Ltd, Beijing, 100015, China
| | - Penghui Wang
- China Center of Industrial Culture Collection (CICC), China National Research Institute of Food and Fermentation Industries Co., Ltd, Beijing, 100015, China
| | - Liang Shi
- China Center of Industrial Culture Collection (CICC), China National Research Institute of Food and Fermentation Industries Co., Ltd, Beijing, 100015, China
| | - Lei Zhai
- China Center of Industrial Culture Collection (CICC), China National Research Institute of Food and Fermentation Industries Co., Ltd, Beijing, 100015, China
| | - Hui Li
- China Center of Industrial Culture Collection (CICC), China National Research Institute of Food and Fermentation Industries Co., Ltd, Beijing, 100015, China
| | - Lu Zhang
- China Center of Industrial Culture Collection (CICC), China National Research Institute of Food and Fermentation Industries Co., Ltd, Beijing, 100015, China
| | - Su Yao
- China Center of Industrial Culture Collection (CICC), China National Research Institute of Food and Fermentation Industries Co., Ltd, Beijing, 100015, China.
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2
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Labbé G, Kruczkiewicz P, Robertson J, Mabon P, Schonfeld J, Kein D, Rankin MA, Gopez M, Hole D, Son D, Knox N, Laing CR, Bessonov K, Taboada EN, Yoshida C, Ziebell K, Nichani A, Johnson RP, Van Domselaar G, Nash JHE. Rapid and accurate SNP genotyping of clonal bacterial pathogens with BioHansel. Microb Genom 2021; 7. [PMID: 34554082 PMCID: PMC8715432 DOI: 10.1099/mgen.0.000651] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Hierarchical genotyping approaches can provide insights into the source, geography and temporal distribution of bacterial pathogens. Multiple hierarchical SNP genotyping schemes have previously been developed so that new isolates can rapidly be placed within pre-computed population structures, without the need to rebuild phylogenetic trees for the entire dataset. This classification approach has, however, seen limited uptake in routine public health settings due to analytical complexity and the lack of standardized tools that provide clear and easy ways to interpret results. The BioHansel tool was developed to provide an organism-agnostic tool for hierarchical SNP-based genotyping. The tool identifies split k-mers that distinguish predefined lineages in whole genome sequencing (WGS) data using SNP-based genotyping schemes. BioHansel uses the Aho-Corasick algorithm to type isolates from assembled genomes or raw read sequence data in a matter of seconds, with limited computational resources. This makes BioHansel ideal for use by public health agencies that rely on WGS methods for surveillance of bacterial pathogens. Genotyping results are evaluated using a quality assurance module which identifies problematic samples, such as low-quality or contaminated datasets. Using existing hierarchical SNP schemes for Mycobacterium tuberculosis and Salmonella Typhi, we compare the genotyping results obtained with the k-mer-based tools BioHansel and SKA, with those of the organism-specific tools TBProfiler and genotyphi, which use gold-standard reference-mapping approaches. We show that the genotyping results are fully concordant across these different methods, and that the k-mer-based tools are significantly faster. We also test the ability of the BioHansel quality assurance module to detect intra-lineage contamination and demonstrate that it is effective, even in populations with low genetic diversity. We demonstrate the scalability of the tool using a dataset of ~8100 S. Typhi public genomes and provide the aggregated results of geographical distributions as part of the tool’s output. BioHansel is an open source Python 3 application available on PyPI and Conda repositories and as a Galaxy tool from the public Galaxy Toolshed. In a public health context, BioHansel enables rapid and high-resolution classification of bacterial pathogens with low genetic diversity.
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Affiliation(s)
- Geneviève Labbé
- National Microbiology Laboratory, Public Health Agency of Canada, Guelph, Ontario, Canada
| | | | - James Robertson
- National Microbiology Laboratory, Public Health Agency of Canada, Guelph, Ontario, Canada
| | - Philip Mabon
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Justin Schonfeld
- National Microbiology Laboratory, Public Health Agency of Canada, Guelph, Ontario, Canada
| | - Daniel Kein
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Marisa A Rankin
- National Microbiology Laboratory, Public Health Agency of Canada, Guelph, Ontario, Canada
| | - Matthew Gopez
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Darian Hole
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - David Son
- National Microbiology Laboratory, Public Health Agency of Canada, Guelph, Ontario, Canada
| | - Natalie Knox
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada.,Department of Medical Microbiology & Infectious Diseases, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Chad R Laing
- National Centres for Animal Disease Lethbridge Laboratory, Canadian Food Inspection Agency, Lethbridge, AB, Canada
| | - Kyrylo Bessonov
- National Microbiology Laboratory, Public Health Agency of Canada, Guelph, Ontario, Canada
| | - Eduardo N Taboada
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Catherine Yoshida
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Kim Ziebell
- National Microbiology Laboratory, Public Health Agency of Canada, Guelph, Ontario, Canada
| | - Anil Nichani
- National Microbiology Laboratory, Public Health Agency of Canada, Guelph, Ontario, Canada
| | - Roger P Johnson
- National Microbiology Laboratory, Public Health Agency of Canada, Guelph, Ontario, Canada
| | - Gary Van Domselaar
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada.,National Centres for Animal Disease Lethbridge Laboratory, Canadian Food Inspection Agency, Lethbridge, AB, Canada
| | - John H E Nash
- National Microbiology Laboratory, Public Health Agency of Canada, Toronto, Ontario, Canada
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3
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Sharma NC, Anandan S, Devanga Ragupathi NK, Muthuirulandi Sethuvel DP, Vasudevan K, Kumar D, Gupta SK, Sangal L, Veeraraghavan B. Genetic Diversity of Clinical Bordetella Pertussis ST2 Strains in comparison with Vaccine Reference Strains of India. J Genomics 2021; 9:38-42. [PMID: 34527084 PMCID: PMC8437686 DOI: 10.7150/jgen.58823] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Accepted: 05/11/2021] [Indexed: 11/12/2022] Open
Abstract
Objectives: Pertussis is a highly contagious disease of the respiratory tract caused by Bordetella pertussis, a bacterium that lives in the mouth, nose, and throat. Current study reports the highly accurate complete genomes of two clinical B. pertussis strains from India for the first time. Methods: Complete genome sequencing was performed for two B. pertussis strains using Ion Torrent PGM and Oxford nanopore sequencing method. Data was assembled de novo and the sequence annotation was performed through PATRIC and NCBI server. Downstream analyses of the isolates were performed using CGE server databases for antimicrobial resistance genes, plasmids, and sequence types. The phylogenetic analysis was performed using Roary. Results: The analysis revealed insertional elements flanked by IS481, which has been previously regarded as the important component for bacterial evolution. The two B. pertussis clinical strains exhibited diversity through genome degradation when compared to whole-cell vaccine reference strains of India. These isolates harboured multiple genetic virulence traits and toxin subunits, which belonged to sequence type ST2. Conclusion: The genome information of Indian clinical B. pertussis strains will serve as a baseline data to decipher more information on the genome evolution, virulence factors and their role in pathogenesis for effective vaccine strategies.
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Affiliation(s)
| | - Shalini Anandan
- Department of Clinical Microbiology, Christian Medical College, Vellore - 632 004, India
| | - Naveen Kumar Devanga Ragupathi
- Department of Clinical Microbiology, Christian Medical College, Vellore - 632 004, India.,Department of Chemical and Biological Engineering, The University of Sheffield, Sheffield, United Kingdom
| | | | - Karthick Vasudevan
- Department of Clinical Microbiology, Christian Medical College, Vellore - 632 004, India
| | - Dhirendra Kumar
- Maharishi Valmiki Infectious Diseases Hospital, New Delhi - 110009, India
| | - Sushil Kumar Gupta
- Maharishi Valmiki Infectious Diseases Hospital, New Delhi - 110009, India
| | - Lucky Sangal
- World Health Organization, Country Office, New Delhi - 110029, India
| | - Balaji Veeraraghavan
- Department of Clinical Microbiology, Christian Medical College, Vellore - 632 004, India
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4
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Wang Y, Liang Q, Lu B, Shen H, Liu S, Shi Y, Leptihn S, Li H, Wei J, Liu C, Xiao H, Zheng X, Liu C, Chen H. Whole-genome analysis of probiotic product isolates reveals the presence of genes related to antimicrobial resistance, virulence factors, and toxic metabolites, posing potential health risks. BMC Genomics 2021; 22:210. [PMID: 33761872 PMCID: PMC7988973 DOI: 10.1186/s12864-021-07539-9] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 03/15/2021] [Indexed: 11/10/2022] Open
Abstract
Background Safety issues of probiotic products have been reported frequently in recent years. Ten bacterial strains isolated from seven commercial probiotic products on market were evaluated for their safety, by whole-genome analysis. Results We found that the bacterial species of three probiotic products were incorrectly labeled. Furthermore, six probiotic product isolates (PPS) contained genes for the production of toxic metabolites, while another three strains contained virulence genes, which might pose a potential health risk. In addition, three of them have drug-resistance genes, among which two strains potentially displayed multidrug resistance. One isolate has in silico predicted transferable genes responsible for toxic metabolite production, and they could potentially transfer to human gut microflora or environmental bacteria. Isolates of Lactobacillus rhamnosus and Bifidobacterium animalis subsp. lactis are associated with low risk for human consumption. Based on a comparative genome analysis, we found that the isolated Enterococcus faecium TK-P5D clustered with a well-defined probiotic strain, while E. faecalis TK-P4B clustered with a pathogenic strain. Conclusions Our work clearly illustrates that whole-genome analysis is a useful method to evaluate the quality and safety of probiotic products. Regulatory quality control and stringent regulations on probiotic products are needed to ensure safe consumption and protect human health. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07539-9.
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Affiliation(s)
- Ying Wang
- Key laboratory of Microbial technology and Bioinformatics of Zhejiang Province, Zhejiang Institute of Microbiology, Hangzhou, 310012, Zhejiang, China
| | - Qian Liang
- Key laboratory of Microbial technology and Bioinformatics of Zhejiang Province, Zhejiang Institute of Microbiology, Hangzhou, 310012, Zhejiang, China
| | - Bian Lu
- Xiaoshan Center for Disease Control and Prevention, Hangzhou, 311201, Zhejiang, China
| | - Hong Shen
- NMPA Key laboratory for Testing and Risk Warning of Pharmaceutical Microbiology, Biological Inspection Department, Zhejiang Institute for Food and Drug Control, Hangzhou, 310052, Zhejiang, China
| | - Shuyan Liu
- Dalian Customs District, Dalian, 116001, Liaoning, China
| | - Ya Shi
- Key laboratory of Microbial technology and Bioinformatics of Zhejiang Province, Zhejiang Institute of Microbiology, Hangzhou, 310012, Zhejiang, China
| | - Sebastian Leptihn
- Zhejiang University-University of Edinburgh Institute, School of Medicine, Zhejiang University, Hangzhou, 310058, Zhejiang, China
| | - Hong Li
- China National Accreditation Institute for Conformity Assessment, Beijing, 100062, China
| | - Jin Wei
- Nordkapp Medical Group, Hangzhou, 311121, Zhejiang, China
| | - Chengzhi Liu
- Key laboratory of Microbial technology and Bioinformatics of Zhejiang Province, Zhejiang Institute of Microbiology, Hangzhou, 310012, Zhejiang, China
| | - Hailong Xiao
- Hangzhou Institute for Food and Drug Control, Hangzhou, 310018, Zhejiang, China
| | - Xiaoling Zheng
- NMPA Key laboratory for Testing and Risk Warning of Pharmaceutical Microbiology, Biological Inspection Department, Zhejiang Institute for Food and Drug Control, Hangzhou, 310052, Zhejiang, China
| | - Chao Liu
- Department of Orthopaedics, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, 310009, Zhejiang, China.
| | - Huan Chen
- Key laboratory of Microbial technology and Bioinformatics of Zhejiang Province, Zhejiang Institute of Microbiology, Hangzhou, 310012, Zhejiang, China.
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5
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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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6
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Emerging Bordetella pertussis Strains Induce Enhanced Signaling of Human Pattern Recognition Receptors TLR2, NOD2 and Secretion of IL-10 by Dendritic Cells. PLoS One 2017; 12:e0170027. [PMID: 28076445 PMCID: PMC5226795 DOI: 10.1371/journal.pone.0170027] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2016] [Accepted: 12/26/2016] [Indexed: 01/04/2023] Open
Abstract
Vaccines against pertussis have been available for more than 60 years. Nonetheless, this highly contagious disease is reemerging even in countries with high vaccination coverage. Genetic changes of Bordetella pertussis over time have been suggested to contribute to the resurgence of pertussis, as these changes may favor escape from vaccine-induced immunity. Nonetheless, studies on the effects of these bacterial changes on the immune response are limited. Here, we characterize innate immune recognition and activation by a collection of genetically diverse B. pertussis strains isolated from Dutch pertussis patients before and after the introduction of the pertussis vaccines. For this purpose, we used HEK-Blue cells transfected with human pattern recognition receptors TLR2, TLR4, NOD2 and NOD1 as a high throughput system for screening innate immune recognition of more than 90 bacterial strains. Physiologically relevant human monocyte derived dendritic cells (moDC), purified from peripheral blood of healthy donors were also used. Findings indicate that, in addition to inducing TLR2 and TLR4 signaling, all B. pertussis strains activate the NOD-like receptor NOD2 but not NOD1. Furthermore, we observed a significant increase in TLR2 and NOD2, but not TLR4, activation by strains circulating after the introduction of pertussis vaccines. When using moDC, we observed that the recently circulating strains induced increased activation of these cells with a dominant IL-10 production. In addition, we observed an increased expression of surface markers including the regulatory molecule PD-L1. Expression of PD-L1 was decreased upon blocking TLR2. These in vitro findings suggest that emerging B. pertussis strains have evolved to dampen the vaccine-induced inflammatory response, which would benefit survival and transmission of this pathogen. Understanding how this disease has resurged in a highly vaccinated population is crucial for the design of improved vaccines against pertussis.
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7
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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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8
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Wagner B, Melzer H, Freymüller G, Stumvoll S, Rendi-Wagner P, Paulke-Korinek M, Repa A, Mooi FR, Kollaritsch H, Mittermayer H, Kessler HH, Stanek G, Steinborn R, Duchêne M, Wiedermann U. Genetic Variation of Bordetella pertussis in Austria. PLoS One 2015; 10:e0132623. [PMID: 26182210 PMCID: PMC4504479 DOI: 10.1371/journal.pone.0132623] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Accepted: 06/16/2015] [Indexed: 02/07/2023] Open
Abstract
In Austria, vaccination coverage against Bordetella pertussis infections during infancy is estimated at around 90%. Within the last years, however, the number of pertussis cases has increased steadily, not only in children but also in adolescents and adults, indicating both insufficient herd immunity and vaccine coverage. Waning immunity in the host and/or adaptation of the bacterium to the immunised hosts could contribute to the observed re-emergence of pertussis. In this study we therefore addressed the genetic variability in B. pertussis strains from several Austrian cities. Between the years 2002 and 2008, 110 samples were collected from Vienna (n = 32), Linz (n = 63) and Graz (n = 15) by nasopharyngeal swabs. DNA was extracted from the swabs, and bacterial sequence polymorphisms were examined by MLVA (multiple-locus variable number of tandem repeat analysis) (n = 77), by PCR amplification and conventional Sanger sequencing of the polymorphic regions of the prn (pertactin) gene (n = 110), and by amplification refractory mutation system quantitative PCR (ARMS-qPCR) (n = 110) to directly address polymorphisms in the genes encoding two pertussis toxin subunits (ptxA and ptxB), a fimbrial adhesin (fimD), tracheal colonisation factor (tcfA), and the virulence sensor protein (bvgS). Finally, the ptxP promoter region was screened by ARMS-qPCR for the presence of the ptxP3 allele, which has been associated with elevated production of pertussis toxin. The MLVA analysis revealed the highest level of polymorphisms with an absence of MLVA Type 29, which is found outside Austria. Only Prn subtypes Prn1/7, Prn2 and Prn3 were found with a predominance of the non-vaccine type Prn2. The analysis of the ptxA, ptxB, fimD, tcfA and bvgS polymorphisms showed a genotype mixed between the vaccine strain Tohama I and a clinical isolate from 2006 (L517). The major part of the samples (93%) displayed the ptxP3 allele. The consequences for the vaccination strategy are discussed.
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Affiliation(s)
- Birgit Wagner
- Institute of Specific Prophylaxis and Tropical Medicine, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria
| | - Helen Melzer
- Institute of Specific Prophylaxis and Tropical Medicine, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria
- Astellas Pharma, Vienna, Austria
| | - Georg Freymüller
- Genomics Core Facility, VetCore, University of Veterinary Medicine, Vienna, Austria
| | - Sabine Stumvoll
- Department of Hygiene, Microbiology and Tropical Medicine, Elisabethinen Hospital, Linz, Austria
- analyse BioLab, Linz, Austria
| | - Pamela Rendi-Wagner
- Institute of Specific Prophylaxis and Tropical Medicine, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria
- Federal Ministry of Health, Vienna, Austria
| | - Maria Paulke-Korinek
- Institute of Specific Prophylaxis and Tropical Medicine, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria
- Federal Ministry of Health, Vienna, Austria
| | - Andreas Repa
- Department of Pediatrics and Adolescent Medicine, Medical University of Vienna, Vienna, Austria
| | - Frits R. Mooi
- Centre for Infectious Diseases Control, National Institute of Public Health and the Environment, Bilthoven, The Netherlands
| | - Herwig Kollaritsch
- Institute of Specific Prophylaxis and Tropical Medicine, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria
| | - Helmut Mittermayer
- Department of Hygiene, Microbiology and Tropical Medicine, Elisabethinen Hospital, Linz, Austria
- analyse BioLab, Linz, Austria
| | - Harald H. Kessler
- Department of Hygiene, Microbiology and Environmental Medicine, Medical University Graz, Graz, Austria
| | - Gerold Stanek
- Institute for Hygiene and Applied Immunology, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria
| | - Ralf Steinborn
- Genomics Core Facility, VetCore, University of Veterinary Medicine, Vienna, Austria
| | - Michael Duchêne
- Institute of Specific Prophylaxis and Tropical Medicine, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria
- * E-mail:
| | - Ursula Wiedermann
- Institute of Specific Prophylaxis and Tropical Medicine, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria
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9
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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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10
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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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11
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Studying Bordetella pertussis populations by use of SNPeX, a simple high-throughput single nucleotide polymorphism typing method. J Clin Microbiol 2015; 53:838-46. [PMID: 25568442 DOI: 10.1128/jcm.02995-14] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Large outbreaks of pertussis occur despite vaccination. A first step in the analyses of outbreaks is strain typing. However, the typing of Bordetella pertussis, the causative agent of pertussis, is problematic because the available assays are insufficiently discriminatory, not unequivocal, time-consuming, and/or costly. Here, we describe a single nucleotide primer extension assay for the study of B. pertussis populations, SNPeX (single nucleotide primer extension), which addresses these problems. The assay is based on the incorporation of fluorescently labeled dideoxynucleotides (ddNTPs) at the 3' end of allele-specific poly(A)-tailed primers and subsequent analysis with a capillary DNA analyzer. Each single nucleotide polymorphism (SNP) primer has a specific length, and as a result, up to 20 SNPs can be determined in one SNPeX reaction. Importantly, PCR amplification of target DNA is not required. We selected 38 SNPeX targets from the whole-genome sequencing data of 74 B. pertussis strains collected from across the world. The SNPeX-based phylogenetic trees preserved the general tree topology of B. pertussis populations based on whole-genome sequencing, with a minor loss of details. We envisage a strategy whereby SNP types (SnpTs) are quickly identified with the SNPeX assay during an outbreak, followed by whole-genome sequencing (WGS) of a limited number of isolates representing predominant SnpTs and the incorporation of novel SNPs in the SNPeX assay. The flexibility of the SNPeX assay allows the method to evolve along with the pathogen, making it a promising method for studying outbreaks of B. pertussis and other pathogens.
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van Gent M, Heuvelman CJ, van der Heide HG, Hallander HO, Advani A, Guiso N, Wirsing von Kőnig CH, Vestrheim DF, Dalby T, Fry NK, Pierard D, Detemmerman L, Zavadilova J, Fabianova K, Logan C, Habington A, Byrne M, Lutyńska A, Mosiej E, Pelaz C, Gröndahl-Yli-Hannuksela K, Barkoff AM, Mertsola J, Economopoulou A, He Q, Mooi FR. Analysis of Bordetella pertussis clinical isolates circulating in European countries during the period 1998-2012. Eur J Clin Microbiol Infect Dis 2014; 34:821-30. [PMID: 25527446 PMCID: PMC4365279 DOI: 10.1007/s10096-014-2297-2] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2014] [Accepted: 12/07/2014] [Indexed: 12/31/2022]
Abstract
Despite more than 50 years of vaccination, pertussis is still an endemic disease, with regular epidemic outbreaks. With the exception of Poland, European countries have replaced whole-cell vaccines (WCVs) by acellular vaccines (ACVs) in the 1990s. Worldwide, antigenic divergence in vaccine antigens has been found between vaccine strains and circulating strains. In this work, 466 Bordetella pertussis isolates collected in the period 1998–2012 from 13 European countries were characterised by multi-locus antigen sequence typing (MAST) of the pertussis toxin promoter (ptxP) and of the genes coding for proteins used in the ACVs: pertussis toxin (Ptx), pertactin (Prn), type 2 fimbriae (Fim2) and type 3 fimbriae (Fim3). Isolates were further characterised by fimbrial serotyping, multi-locus variable-number tandem repeat analysis (MLVA) and pulsed-field gel electrophoresis (PFGE). The results showed a very similar B. pertussis population for 12 countries using ACVs, while Poland, which uses a WCV, was quite distinct, suggesting that ACVs and WCVs select for different B. pertussis populations. This study forms a baseline for future studies on the effect of vaccination programmes on B. pertussis populations.
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Affiliation(s)
- M van Gent
- Centre for Infectious Disease Control (CIb), National Institute for Public Health and the Environment (RIVM), P.O. Box 1, 3720 BA, Bilthoven, The Netherlands,
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13
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Bordetella pertussis naturally occurring isolates with altered lipooligosaccharide structure fail to fully mature human dendritic cells. Infect Immun 2014; 83:227-38. [PMID: 25348634 DOI: 10.1128/iai.02197-14] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Bordetella pertussis is a Gram-negative bacterium and the causative agent of whooping cough. Despite high vaccination coverage, outbreaks are being increasingly reported worldwide. Possible explanations include adaptation of this pathogen, which may interfere with recognition by the innate immune system. Here, we describe innate immune recognition and responses to different B. pertussis clinical isolates. By using HEK-Blue cells transfected with different pattern recognition receptors, we found that 3 out of 19 clinical isolates failed to activate Toll-like receptor 4 (TLR4). These findings were confirmed by using the monocytic MM6 cell line. Although incubation with high concentrations of these 3 strains resulted in significant activation of the MM6 cells, it was found to occur mainly through interaction with TLR2 and not through TLR4. When using live bacteria, these 3 strains also failed to activate TLR4 on HEK-Blue cells, and activation of MM6 cells or human monocyte-derived dendritic cells was significantly lower than activation induced by the other 16 strains. Mass spectrum analysis of the lipid A moieties from these 3 strains indicated an altered structure of this molecule. Gene sequence analysis revealed mutations in genes involved in lipid A synthesis. Findings from this study indicate that B. pertussis isolates that do not activate TLR4 occur naturally and that this phenotype may give this bacterium an advantage in tempering the innate immune response and establishing infection. Knowledge on the strategies used by this pathogen in evading the host immune response is essential for the improvement of current vaccines or for the development of new ones.
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Aflitos S, Schijlen E, de Jong H, de Ridder D, Smit S, Finkers R, Wang J, Zhang G, Li N, Mao L, Bakker F, Dirks R, Breit T, Gravendeel B, Huits H, Struss D, Swanson-Wagner R, van Leeuwen H, van Ham RCHJ, Fito L, Guignier L, Sevilla M, Ellul P, Ganko E, Kapur A, Reclus E, de Geus B, van de Geest H, Te Lintel Hekkert B, van Haarst J, Smits L, Koops A, Sanchez-Perez G, van Heusden AW, Visser R, Quan Z, Min J, Liao L, Wang X, Wang G, Yue Z, Yang X, Xu N, Schranz E, Smets E, Vos R, Rauwerda J, Ursem R, Schuit C, Kerns M, van den Berg J, Vriezen W, Janssen A, Datema E, Jahrman T, Moquet F, Bonnet J, Peters S. Exploring genetic variation in the tomato (Solanum section Lycopersicon) clade by whole-genome sequencing. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2014; 80:136-48. [PMID: 25039268 DOI: 10.1111/tpj.12616] [Citation(s) in RCA: 228] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2014] [Revised: 06/23/2014] [Accepted: 07/01/2014] [Indexed: 05/20/2023]
Abstract
We explored genetic variation by sequencing a selection of 84 tomato accessions and related wild species representative of the Lycopersicon, Arcanum, Eriopersicon and Neolycopersicon groups, which has yielded a huge amount of precious data on sequence diversity in the tomato clade. Three new reference genomes were reconstructed to support our comparative genome analyses. Comparative sequence alignment revealed group-, species- and accession-specific polymorphisms, explaining characteristic fruit traits and growth habits in the various cultivars. Using gene models from the annotated Heinz 1706 reference genome, we observed differences in the ratio between non-synonymous and synonymous SNPs (dN/dS) in fruit diversification and plant growth genes compared to a random set of genes, indicating positive selection and differences in selection pressure between crop accessions and wild species. In wild species, the number of single-nucleotide polymorphisms (SNPs) exceeds 10 million, i.e. 20-fold higher than found in most of the crop accessions, indicating dramatic genetic erosion of crop and heirloom tomatoes. In addition, the highest levels of heterozygosity were found for allogamous self-incompatible wild species, while facultative and autogamous self-compatible species display a lower heterozygosity level. Using whole-genome SNP information for maximum-likelihood analysis, we achieved complete tree resolution, whereas maximum-likelihood trees based on SNPs from ten fruit and growth genes show incomplete resolution for the crop accessions, partly due to the effect of heterozygous SNPs. Finally, results suggest that phylogenetic relationships are correlated with habitat, indicating the occurrence of geographical races within these groups, which is of practical importance for Solanum genome evolution studies.
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15
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Zeddeman A, van Gent M, Heuvelman CJ, van der Heide HG, Bart MJ, Advani A, Hallander HO, Wirsing von Konig CH, Riffelman M, Storsaeter J, Vestrheim DF, Dalby T, Krogfelt KA, Fry NK, Barkoff AM, Mertsola J, He Q, Mooi F. Investigations into the emergence of pertactin-deficient Bordetella pertussis isolates in six European countries, 1996 to 2012. ACTA ACUST UNITED AC 2014; 19. [PMID: 25166348 DOI: 10.2807/1560-7917.es2014.19.33.20881] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Pathogen adaptation has been proposed to contribute to the resurgence of pertussis. A striking recent example is the emergence of isolates deficient in the vaccine component pertactin (Prn). This study explores the emergence of such Prn-deficient isolates in six European countries. During 2007 to 2009, 0/83 isolates from the Netherlands, 0/18 from the United Kingdom, 0/17 Finland, 0/23 Denmark, 4/99 Sweden and 5/20 from Norway of the isolates collected were Prn-deficient. In the Netherlands and Sweden, respectively 4/146 and 1/8 were observed in a later period (2010–12). The Prn-deficient isolates were genetically diverse and different mutations were found to inactivate the prn gene. These are indications that Prn-deficiency is subject to positive selective pressure. We hypothesise that the switch from whole cell to acellular pertussis vaccines has affected the balance between ‘costs and benefits’ of Prn production by Bordetella pertussis to the extent that isolates that do not produce Prn are able to expand. The absence of Prn-deficient isolates in some countries may point to ways to prevent or delay the spread of Prn-deficient strains. In order to substantiate this hypothesis, trends in the European B. pertussis population should be monitored continuously.
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Affiliation(s)
- A Zeddeman
- Centre for Infectious Diseases Research, Diagnostics and Screening (IDS), Centre for Infectious Diseases Control (CIb), National Institute of Public Health and the Environment (RIVM), the Netherlands
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16
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Sequence variation in virulence-related genes of Bordetella pertussis isolates from Poland in the period 1959–2013. Eur J Clin Microbiol Infect Dis 2014; 34:147-152. [DOI: 10.1007/s10096-014-2216-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2014] [Accepted: 07/17/2014] [Indexed: 02/07/2023]
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17
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Bart MJ, Harris SR, Advani A, Arakawa Y, Bottero D, Bouchez V, Cassiday PK, Chiang CS, Dalby T, Fry NK, Gaillard ME, van Gent M, Guiso N, Hallander HO, Harvill ET, He Q, van der Heide HGJ, Heuvelman K, Hozbor DF, Kamachi K, Karataev GI, Lan R, Lutyńska A, Maharjan RP, Mertsola J, Miyamura T, Octavia S, Preston A, Quail MA, Sintchenko V, Stefanelli P, Tondella ML, Tsang RSW, Xu Y, Yao SM, Zhang S, Parkhill J, Mooi FR. Global population structure and evolution of Bordetella pertussis and their relationship with vaccination. mBio 2014; 5:e01074. [PMID: 24757216 PMCID: PMC3994516 DOI: 10.1128/mbio.01074-14] [Citation(s) in RCA: 197] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2014] [Accepted: 03/19/2014] [Indexed: 11/20/2022] Open
Abstract
Bordetella pertussis causes pertussis, a respiratory disease that is most severe for infants. Vaccination was introduced in the 1950s, and in recent years, a resurgence of disease was observed worldwide, with significant mortality in infants. Possible causes for this include the switch from whole-cell vaccines (WCVs) to less effective acellular vaccines (ACVs), waning immunity, and pathogen adaptation. Pathogen adaptation is suggested by antigenic divergence between vaccine strains and circulating strains and by the emergence of strains with increased pertussis toxin production. We applied comparative genomics to a worldwide collection of 343 B. pertussis strains isolated between 1920 and 2010. The global phylogeny showed two deep branches; the largest of these contained 98% of all strains, and its expansion correlated temporally with the first descriptions of pertussis outbreaks in Europe in the 16th century. We found little evidence of recent geographical clustering of the strains within this lineage, suggesting rapid strain flow between countries. We observed that changes in genes encoding proteins implicated in protective immunity that are included in ACVs occurred after the introduction of WCVs but before the switch to ACVs. Furthermore, our analyses consistently suggested that virulence-associated genes and genes coding for surface-exposed proteins were involved in adaptation. However, many of the putative adaptive loci identified have a physiological role, and further studies of these loci may reveal less obvious ways in which B. pertussis and the host interact. This work provides insight into ways in which pathogens may adapt to vaccination and suggests ways to improve pertussis vaccines. IMPORTANCE Whooping cough is mainly caused by Bordetella pertussis, and current vaccines are targeted against this organism. Recently, there have been increasing outbreaks of whooping cough, even where vaccine coverage is high. Analysis of the genomes of 343 B. pertussis isolates from around the world over the last 100 years suggests that the organism has emerged within the last 500 years, consistent with historical records. We show that global transmission of new strains is very rapid and that the worldwide population of B. pertussis is evolving in response to vaccine introduction, potentially enabling vaccine escape.
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Affiliation(s)
| | - Simon R. Harris
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Abdolreza Advani
- Swedish Institute for Communicable Disease Control (SMI), Solna, Sweden
| | | | - Daniela Bottero
- Laboratorio VacSal, Instituto de Biotecnología y Biología Molecular, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, CONICET, La Plata, Argentina
| | | | - Pamela K. Cassiday
- National Center for Immunization and Respiratory Diseases (NCIRD), Centers for Disease Control and Prevention (CDC), Atlanta, Georgia, USA
| | | | - Tine Dalby
- Microbiology & Infection Control, Statens Serum Institut, Copenhagen, Denmark
| | - Norman K. Fry
- Public Health England—Respiratory and Vaccine Preventable Bacteria Reference Unit, Colindale, United Kingdom
| | - María Emilia Gaillard
- Laboratorio VacSal, Instituto de Biotecnología y Biología Molecular, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, CONICET, La Plata, Argentina
| | - Marjolein van Gent
- Centre for Infectious Diseases Research, Diagnostics and Screening (IDS), Centre for Infectious Diseases Control (CIb), National Institute of Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | | | - Hans O. Hallander
- Swedish Institute for Communicable Disease Control (SMI), Solna, Sweden
| | - Eric T. Harvill
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, Pennsylvania, USA
| | - Qiushui He
- Department of Infectious Disease Surveillance and Control, National Institute for Health and Welfare, Finland
| | - Han G. J. van der Heide
- Centre for Infectious Diseases Research, Diagnostics and Screening (IDS), Centre for Infectious Diseases Control (CIb), National Institute of Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Kees Heuvelman
- Centre for Infectious Diseases Research, Diagnostics and Screening (IDS), Centre for Infectious Diseases Control (CIb), National Institute of Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Daniela F. Hozbor
- Laboratorio VacSal, Instituto de Biotecnología y Biología Molecular, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, CONICET, La Plata, Argentina
| | - Kazunari Kamachi
- National Institute of Infectious Diseases, Shinjuku-ku, Tokyo, Japan
| | - Gennady I. Karataev
- Gamaleya Research Institute for Epidemiology and Microbiology, Ministry of Health Russian Federation, Moscow, Russian Federation
| | - Ruiting Lan
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia
| | - Anna Lutyńska
- National Institute of Public Health, National Institute of Hygiene, Warsaw, Poland
| | - Ram P. Maharjan
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia
| | - Jussi Mertsola
- Department of Pediatrics, Turku University Hospital, Turku, Finland
| | - Tatsuo Miyamura
- National Institute of Infectious Diseases, Shinjuku-ku, Tokyo, Japan
| | - Sophie Octavia
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia
| | - Andrew Preston
- Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom
| | - Michael A. Quail
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | | | - Paola Stefanelli
- Department of Infectious, Parasitic & Immune-Mediated Diseases, Istituto Superiore di Sanita, Rome, Italy
| | - M. Lucia Tondella
- National Center for Immunization and Respiratory Diseases (NCIRD), Centers for Disease Control and Prevention (CDC), Atlanta, Georgia, USA
| | - Raymond S. W. Tsang
- Laboratory for Syphilis Diagnostics and Vaccine Preventable Bacterial Diseases, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Yinghua Xu
- National Institute for Food and Drug Control, Beijing, Republic of China
| | - Shu-Man Yao
- Centers for Disease Control, Taipei, Taiwan, Republic of China
| | - Shumin Zhang
- National Institute for Food and Drug Control, Beijing, Republic of China
| | - Julian Parkhill
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
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Abstract
Over the course of the past several decades, rapid advancements in molecular technologies have revolutionized the practice of public health microbiology, and have fundamentally changed the nature, accuracy, and timeliness of laboratory data for outbreak investigation and response. Whole-genome sequencing, in particular, is becoming an increasingly feasible and cost-effective approach for near real-time high-resolution strain typing, genomic characterization, and comparative analyses. This review discusses the current state of the art in bacterial strain typing for outbreak investigation and infectious disease surveillance, and the impact of emerging genomic technologies on the field of public health microbiology.
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Affiliation(s)
- Duncan MacCannell
- National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, 1600 Clifton Road Northeast, MS-C12, Atlanta, GA 30333, USA.
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19
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Poolman JT, Hallander H, Halperin SA. Pertussis vaccines: where to now? Expert Rev Vaccines 2014; 10:1497-500. [DOI: 10.1586/erv.11.147] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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20
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van der Ark AAJ, Hozbor DF, Boog CJP, Metz B, van den Dobbelsteen GPJM, van Els CACM. Resurgence of pertussis calls for re-evaluation of pertussis animal models. Expert Rev Vaccines 2014; 11:1121-37. [DOI: 10.1586/erv.12.83] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
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21
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de Gouw D, Hermans PWM, Bootsma HJ, Zomer A, Heuvelman K, Diavatopoulos DA, Mooi FR. Differentially expressed genes in Bordetella pertussis strains belonging to a lineage which recently spread globally. PLoS One 2014; 9:e84523. [PMID: 24416242 PMCID: PMC3885589 DOI: 10.1371/journal.pone.0084523] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2013] [Accepted: 11/14/2013] [Indexed: 01/20/2023] Open
Abstract
Pertussis is a highly contagious, acute respiratory disease in humans caused by the Gram-negative pathogen Bordetella pertussis. Pertussis has resurged in the face of intensive vaccination and this has coincided with the emergence of strains carrying a particular allele for the pertussis toxin promoter, ptxP3, which is associated with higher levels of pertussis toxin (Ptx) production. Within 10 to 20 years, ptxP3 strains have nearly completely replaced the previously dominant ptxP1 strains resulting in a worldwide selective sweep. In order to identify B. pertussis genes associated with the selective sweep, we compared the expression of genes in ptxP1 and ptxP3 strains that are under control of the Bordetella master virulence regulatory locus (bvgASR). The BvgAS proteins comprise a two component sensory transduction system which is regulated by temperature, nicotinic acid and sulfate. By increasing the sulfate concentration, it is possible to change the phase of B. pertussis from virulent to avirulent. Until recently, the only distinctive phenotype of ptxP3 strains was a higher Ptx production. Here we identify additional phenotypic differences between ptxP1 and ptxP3 strains which may have contributed to its global spread by comparing global transcriptional responses under sulfate-modulating conditions. We show that ptxP3 strains are less sensitive to sulfate-mediated gene suppression, resulting in an increased production of the vaccine antigens pertactin (Prn) and Ptx and a number of other virulence genes, including a type III secretion toxin, Vag8, a protein involved in complement resistance, and lpxE involved in lipid A modification. Furthermore, enhanced expression of the vaccine antigens Ptx and Prn by ptxP3 strains was confirmed at the protein level. Identification of genes differentially expressed between ptxP1 and ptxP3 strains may elucidate how B. pertussis has adapted to vaccination and allow the improvement of pertussis vaccines by identifying novel vaccine candidates.
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Affiliation(s)
- Daan de Gouw
- Department of Pediatrics, Laboratory of Pediatric Infectious Diseases, Radboud University Medical Centre, Nijmegen, The Netherlands
- Nijmegen Institute for Infection, Inflammation and Immunity, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Peter W. M. Hermans
- Department of Pediatrics, Laboratory of Pediatric Infectious Diseases, Radboud University Medical Centre, Nijmegen, The Netherlands
- Nijmegen Institute for Infection, Inflammation and Immunity, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Hester J. Bootsma
- Department of Pediatrics, Laboratory of Pediatric Infectious Diseases, Radboud University Medical Centre, Nijmegen, The Netherlands
- Nijmegen Institute for Infection, Inflammation and Immunity, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Aldert Zomer
- Department of Pediatrics, Laboratory of Pediatric Infectious Diseases, Radboud University Medical Centre, Nijmegen, The Netherlands
- Nijmegen Institute for Infection, Inflammation and Immunity, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Kees Heuvelman
- Netherlands Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Dimitri A. Diavatopoulos
- Department of Pediatrics, Laboratory of Pediatric Infectious Diseases, Radboud University Medical Centre, Nijmegen, The Netherlands
- Nijmegen Institute for Infection, Inflammation and Immunity, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Frits R. Mooi
- Department of Pediatrics, Laboratory of Pediatric Infectious Diseases, Radboud University Medical Centre, Nijmegen, The Netherlands
- Nijmegen Institute for Infection, Inflammation and Immunity, Radboud University Medical Centre, Nijmegen, The Netherlands
- Netherlands Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
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van der Maas NAT, Mooi FR, de Greeff SC, Berbers GAM, Spaendonck MAECV, de Melker HE. Pertussis in the Netherlands, is the current vaccination strategy sufficient to reduce disease burden in young infants? Vaccine 2013; 31:4541-7. [PMID: 23933365 DOI: 10.1016/j.vaccine.2013.07.060] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2013] [Revised: 07/02/2013] [Accepted: 07/25/2013] [Indexed: 10/26/2022]
Abstract
BACKGROUND Pertussis has resurged in the Netherlands since 1996. Several measures, i.e. acceleration of the schedule, introduction of a preschool acellular pertussis booster and change from an infant whole cell to an acellular pertussis combination vaccine were implemented in the National Immunisation Programme to decrease disease burden, in particular among very young infants who have the highest morbidity and mortality of pertussis. Nevertheless, a large outbreak occurred in 2011-2012. METHODS 1996-2010 was divided in 3-year-periods to assess the impact of the measures taken, using notifications and hospitalisations. These results were compared with 2011-2012. Mean Incidence rates (IRs) per 100,000 were calculated. RESULTS Although the measures taken resulted in decreased IRs among the targeted age groups after implementation, overall mean IRs of notifications increased from 32 (1996-2004) to 37 (2005-2010) and 63 (2011-2012). Young infants, not yet vaccinated, did not benefit; during the 2011-2012 outbreak, IR in 0-2-month-olds amounted to 259.6. IR among persons over 9 years of age increased from 6.8 (1996-1999) to 59.1 (2011-2012) For hospitalisations overall mean IRs decreased from 1.95 per 100,000 (1997-2004) to 0.88 (2005-2010) and 0.76 (2011). CONCLUSION The measures taken reduced IRs of notifications and hospitalisations among groups eligible for vaccination, but had no effect on the increasing IRs in adolescents and adults. This trend is also observed in other countries. The high IRs in 2012 in adolescents and adults probably resulted in increased transmission to infants, who are at risk for contracting severe pertussis. Therefore, additional measures to protect this group should be considered.
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Affiliation(s)
- Nicoline A T van der Maas
- Epidemiology and Surveillance, Centre for Infectious Disease Control, National Institute for Public Health and the Environment, 3720BA Bilthoven, The Netherlands.
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23
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King AJ, van der Lee S, Mohangoo A, van Gent M, van der Ark A, van de Waterbeemd B. Genome-wide gene expression analysis of Bordetella pertussis isolates associated with a resurgence in pertussis: elucidation of factors involved in the increased fitness of epidemic strains. PLoS One 2013; 8:e66150. [PMID: 23776625 PMCID: PMC3679012 DOI: 10.1371/journal.pone.0066150] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2013] [Accepted: 05/01/2013] [Indexed: 12/11/2022] Open
Abstract
Bordetella pertussis (B. pertussis) is the causative agent of whooping cough, which is a highly contagious disease in the human respiratory tract. Despite vaccination since the 1950s, pertussis remains the most prevalent vaccine-preventable disease in developed countries. A recent resurgence pertussis is associated with the expansion of B. pertussis strains with a novel allele for the pertussis toxin (ptx) promoter ptxP3 in place of resident ptxP1 strains. The recent expansion of ptxP3 strains suggests that these strains carry mutations that have increased their fitness. Compared to the ptxP1 strains, ptxP3 strains produce more Ptx, which results in increased virulence and immune suppression. In this study, we investigated the contribution of gene expression changes of various genes on the increased fitness of the ptxP3 strains. Using genome-wide gene expression profiling, we show that several virulence genes had higher expression levels in the ptxP3 strains compared to the ptxP1 strains. We provide the first evidence that wildtype ptxP3 strains are better colonizers in an intranasal mouse infection model. This study shows that the ptxP3 mutation and the genetic background of ptxP3 strains affect fitness by contributing to the ability to colonize in a mouse infection model. These results show that the genetic background of ptxP3 strains with a higher expression of virulence genes contribute to increased fitness.
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Affiliation(s)
- Audrey J. King
- National Institute for Public Health and the Environment (RIVM), Laboratory for Infectious Diseases and Screening (LIS) Centre for Infectious Disease Control, Bilthoven, The Netherlands
- * E-mail:
| | - Saskia van der Lee
- National Institute for Public Health and the Environment (RIVM), Laboratory for Infectious Diseases and Screening (LIS) Centre for Infectious Disease Control, Bilthoven, The Netherlands
| | - Archena Mohangoo
- National Institute for Public Health and the Environment (RIVM), Laboratory for Infectious Diseases and Screening (LIS) Centre for Infectious Disease Control, Bilthoven, The Netherlands
| | - Marjolein van Gent
- National Institute for Public Health and the Environment (RIVM), Laboratory for Infectious Diseases and Screening (LIS) Centre for Infectious Disease Control, Bilthoven, The Netherlands
| | - Arno van der Ark
- National Institute for Public Health and the Environment (RIVM), Department of Vaccinology, Bilthoven, The Netherlands
| | - Bas van de Waterbeemd
- National Institute for Public Health and the Environment (RIVM), Department of Vaccinology, Bilthoven, The Netherlands
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Pertussis resurgence: waning immunity and pathogen adaptation - two sides of the same coin. Epidemiol Infect 2013; 142:685-94. [PMID: 23406868 DOI: 10.1017/s0950268813000071] [Citation(s) in RCA: 202] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
Pertussis or whooping cough has persisted and resurged in the face of vaccination and has become one of the most prevalent vaccine-preventable diseases in Western countries. The high circulation rate of Bordetella pertussis poses a threat to infants that have not been (completely) vaccinated and for whom pertussis is a severe, life-threatening, disease. The increase in pertussis is mainly found in age groups in which immunity has waned and this has resulted in the perception that waning immunity is the main or exclusive cause for the resurgence of pertussis. However, significant changes in B. pertussis populations have been observed after the introduction of vaccinations, suggesting a role for pathogen adaptation in the persistence and resurgence of pertussis. These changes include antigenic divergence with vaccine strains and increased production of pertussis toxin. Antigenic divergence will affect both memory recall and the efficacy of antibodies, while higher levels of pertussis toxin may increase suppression of the innate and acquired immune system. We propose these adaptations of B. pertussis have decreased the period in which pertussis vaccines are effective and thus enhanced the waning of immunity. We plead for a more integrated approach to the pertussis problem which includes the characteristics of the vaccines, the B. pertussis populations and the interaction between the two.
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25
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26
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Development of a temperature-switch PCR-based SNP typing method for Mycobacterium ulcerans. PLoS Negl Trop Dis 2012; 6:e1904. [PMID: 23166851 PMCID: PMC3499370 DOI: 10.1371/journal.pntd.0001904] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2012] [Accepted: 10/01/2012] [Indexed: 11/19/2022] Open
Abstract
Mycobacterium ulcerans (M. ulcerans), the causative agent of the devastating skin disease Buruli ulcer (BU), is characterized by an extremely low level of genetic diversity. Recently, we have reported the first discrimination of closely related M. ulcerans variants in the BU endemic Densu River Valley of Ghana. In the study real-time PCR-based single nucleotide polymorphism (SNP) typing at 89 predefined loci revealed the presence of ten M. ulcerans haplotypes circulating in the BU endemic region. Here we describe the development of temperature-switch PCR (TSP) assays that allow distinguishing these haplotypes by conventional agarose gel-based analysis of the PCR products. After validation of the accuracy of typing results, the TSP assays were successfully established in a reference laboratory in Ghana. Development of the cost-effective and rapid TSP-based genetic fingerprinting method will thus allow investigating the spread of M. ulcerans clones by regular genetic monitoring in BU endemic countries.
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van Gent M, Bart MJ, van der Heide HGJ, Heuvelman KJ, Mooi FR. Small mutations in Bordetella pertussis are associated with selective sweeps. PLoS One 2012; 7:e46407. [PMID: 23029513 PMCID: PMC3460923 DOI: 10.1371/journal.pone.0046407] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2012] [Accepted: 08/31/2012] [Indexed: 01/31/2023] Open
Abstract
Bordetella pertussis is the causative agent of pertussis, a highly contagious disease of the human respiratory tract. Despite high vaccination coverage, pertussis has resurged and has become one of the most prevalent vaccine-preventable diseases in developed countries. We have proposed that both waning immunity and pathogen adaptation have contributed to the persistence and resurgence of pertussis. Allelic variation has been found in virulence-associated genes coding for the pertussis toxin A subunit (ptxA), pertactin (prn), serotype 2 fimbriae (fim2), serotype 3 fimbriae (fim3) and the promoter for pertussis toxin (ptxP). In this study, we investigated how more than 60 years of vaccination has affected the Dutch B. pertussis population by combining data from phylogeny, genomics and temporal trends in strain frequencies. Our main focus was on the ptxA, prn, fim3 and ptxP genes. However, we also compared the genomes of 11 Dutch strains belonging to successful lineages. Our results showed that, between 1949 and 2010, the Dutch B. pertussis population has undergone as least four selective sweeps that were associated with small mutations in ptxA, prn, fim3 and ptxP. Phylogenetic analysis revealed a stepwise adaptation in which mutations accumulated clonally. Genomic analysis revealed a number of additional mutations which may have a contributed to the selective sweeps. Five large deletions were identified which were fixed in the pathogen population. However, only one was linked to a selective sweep. No evidence was found for a role of gene acquisition in pathogen adaptation. Our results suggest that the B. pertussis gene repertoire is already well adapted to its current niche and required only fine tuning to persist in the face of vaccination. Further, this work shows that small mutations, even single SNPs, can drive large changes in the populations of bacterial pathogens within a time span of six to 19 years.
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Affiliation(s)
- Marjolein van Gent
- Laboratory for Infectious Diseases and Screening, Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Marieke J. Bart
- Laboratory for Infectious Diseases and Screening, Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Han G. J. van der Heide
- Laboratory for Infectious Diseases and Screening, Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Kees J. Heuvelman
- Laboratory for Infectious Diseases and Screening, Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Frits R. Mooi
- Laboratory for Infectious Diseases and Screening, Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
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28
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Litt DJ, Jauneikaite E, Tchipeva D, Harrison TG, Fry NK. Direct molecular typing of Bordetella pertussis from clinical specimens submitted for diagnostic quantitative (real-time) PCR. J Med Microbiol 2012; 61:1662-1668. [PMID: 22918864 DOI: 10.1099/jmm.0.049585-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Molecular typing of Bordetella pertussis is routinely performed on bacterial isolates, but not on DNA extracted from nasopharyngeal aspirates or pernasal swabs submitted for diagnostic real-time PCR (qPCR). We investigated whether these DNA extracts were suitable for multilocus variable-number tandem repeat analysis (MLVA) and DNA sequence-based typing. We analysed all the available qPCR-positive samples received by our laboratory from patients <1 year of age between January 2008 and August 2010. Eighty-one per cent (106/131) of these generated a complete MLVA profile. This rose to 92 % (105/114) if only samples positive for both of the two targets used for the B. pertussis PCR (insertion element IS481 and pertussis toxin promoter ptxP) were analysed. Sequence-based typing of the pertactin, pertussis toxin S1 subunit and pertussis promoter regions (prn, ptxA and ptxP) was attempted on 89 of the DNA extracts that had generated a full MLVA profile. Eighty-three (93 %) of these produced complete sequences for all three targets. Comparison of molecular typing data from the 89 extracts with those from 111 contemporary bacterial isolates showed that the two sources yielded the same picture of the B. pertussis population [dominated by the MLVA-27 prn(2) ptxA(1) ptxP(3) clonal type]. There was no significant difference in MLVA type distribution or diversity between the two sample sets. This suggests that clinical extracts can be used in place of, or to complement, bacterial cultures for typing purposes (at least, in this age group). With small modifications to methodology, generating MLVA and sequence-based typing data from qPCR-positive clinical DNA extracts is likely to generate a complete dataset in the majority of samples from the <1 year age group. Its success with samples from older subjects remains to be seen. However, our data suggest that it is suitable for inclusion in molecular epidemiological studies of the B. pertussis population or as a tool in outbreak investigations.
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Affiliation(s)
- David J Litt
- Respiratory and Systemic Infection Laboratory, Health Protection Agency, 61 Colindale Avenue, London NW9 5EQ, UK
| | - Elita Jauneikaite
- Respiratory and Systemic Infection Laboratory, Health Protection Agency, 61 Colindale Avenue, London NW9 5EQ, UK
| | - Draga Tchipeva
- Department of Biomedical Sciences, School of Life Sciences, University of Westminster, London W1W 6UW, UK.,Respiratory and Systemic Infection Laboratory, Health Protection Agency, 61 Colindale Avenue, London NW9 5EQ, UK
| | - Timothy G Harrison
- Respiratory and Systemic Infection Laboratory, Health Protection Agency, 61 Colindale Avenue, London NW9 5EQ, UK
| | - Norman K Fry
- Respiratory and Systemic Infection Laboratory, Health Protection Agency, 61 Colindale Avenue, London NW9 5EQ, UK
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29
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Sibley CD, Peirano G, Church DL. Molecular methods for pathogen and microbial community detection and characterization: current and potential application in diagnostic microbiology. INFECTION GENETICS AND EVOLUTION 2012; 12:505-21. [PMID: 22342514 PMCID: PMC7106020 DOI: 10.1016/j.meegid.2012.01.011] [Citation(s) in RCA: 105] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/10/2011] [Revised: 01/10/2012] [Accepted: 01/12/2012] [Indexed: 12/25/2022]
Abstract
Clinical microbiology laboratories worldwide have historically relied on phenotypic methods (i.e., culture and biochemical tests) for detection, identification and characterization of virulence traits (e.g., antibiotic resistance genes, toxins) of human pathogens. However, limitations to implementation of molecular methods for human infectious diseases testing are being rapidly overcome allowing for the clinical evaluation and implementation of diverse technologies with expanding diagnostic capabilities. The advantages and limitation of molecular techniques including real-time polymerase chain reaction, partial or whole genome sequencing, molecular typing, microarrays, broad-range PCR and multiplexing will be discussed. Finally, terminal restriction fragment length polymorphism (T-RFLP) and deep sequencing are introduced as technologies at the clinical interface with the potential to dramatically enhance our ability to diagnose infectious diseases and better define the epidemiology and microbial ecology of a wide range of complex infections.
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Affiliation(s)
- Christopher D. Sibley
- Department of Microbiology, Immunology & Infectious Diseases, Faculty of Medicine, University of Calgary, Calgary, Alta, Canada
| | - Gisele Peirano
- Division of Microbiology, Calgary Laboratory Services, Calgary, Alta, Canada
| | - Deirdre L. Church
- Department of Pathology & Laboratory Medicine, Faculty of Medicine, University of Calgary, Calgary, Alta, Canada
- Department of Medicine, Faculty of Medicine, University of Calgary, Calgary, Alta, Canada
- Division of Microbiology, Calgary Laboratory Services, Calgary, Alta, Canada
- Corresponding author. Address: c/o Calgary Laboratory Services, 9-3535 Research Rd. N.W., Calgary, Alta, Canada T2L 2K8. Tel.: +1 403 770 3281; fax: +1 403 770 3347.
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30
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Lam C, Octavia S, Bahrame Z, Sintchenko V, Gilbert GL, Lan R. Selection and emergence of pertussis toxin promoter ptxP3 allele in the evolution of Bordetella pertussis. INFECTION GENETICS AND EVOLUTION 2012; 12:492-5. [PMID: 22293463 DOI: 10.1016/j.meegid.2012.01.001] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2011] [Revised: 12/20/2011] [Accepted: 01/04/2012] [Indexed: 11/17/2022]
Abstract
Evolutionary studies using single nucleotide polymorphisms (SNPs) have separated Bordetella pertussis isolates into six major clusters, with recent isolates forming cluster I. The expansion of cluster I isolates was characterised by changes in genes encoding antigenic components in acellular vaccines, including pertactin (Prn). Here, we determined the initial emergence of the pertussis toxin promoter allele, ptxP3, from an evolutionary perspective. This allele was previously shown in a study from the Netherlands to be associated with increased pertussis toxin production as a result of a single base mutation in the ptxP. The ptxP region of 313 worldwide isolates was sequenced, including 208 isolates from Australia collected over a 40 year period. Eight alleles were identified, of which only two predominated: ptxP1 and ptxP3. One novel allele was also found. ptxP3 was only found in SNP cluster I of B. pertussis and its emergence is concurrent with the change to the non-vaccine prn2 allele. Our results suggest that the globally distributed cluster I of B. pertussis has the ability to evade vaccine induced selection pressure.
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Affiliation(s)
- Connie Lam
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia
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31
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Schürch AC, Kremer K, Hendriks ACA, Freyee B, McEvoy CRE, van Crevel R, Boeree MJ, van Helden P, Warren RM, Siezen RJ, van Soolingen D. SNP/RD typing of Mycobacterium tuberculosis Beijing strains reveals local and worldwide disseminated clonal complexes. PLoS One 2011; 6:e28365. [PMID: 22162765 PMCID: PMC3230589 DOI: 10.1371/journal.pone.0028365] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2011] [Accepted: 11/07/2011] [Indexed: 02/04/2023] Open
Abstract
The Beijing strain is one of the most successful genotypes of Mycobacterium tuberculosis worldwide and appears to be highly homogenous according to existing genotyping methods. To type Beijing strains reliably we developed a robust typing scheme using single nucleotide polymorphisms (SNPs) and regions of difference (RDs) derived from whole-genome sequencing data of eight Beijing strains. SNP/RD typing of 259 M. tuberculosis isolates originating from 45 countries worldwide discriminated 27 clonal complexes within the Beijing genotype family. A total of 16 Beijing clonal complexes contained more than one isolate of known origin, of which two clonal complexes were strongly associated with South African origin. The remaining 14 clonal complexes encompassed isolates from different countries. Even highly resolved clonal complexes comprised isolates from distinct geographical sites. Our results suggest that Beijing strains spread globally on multiple occasions and that the tuberculosis epidemic caused by the Beijing genotype is at least partially driven by modern migration patterns. The SNPs and RDs presented in this study will facilitate future molecular epidemiological and phylogenetic studies on Beijing strains.
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Affiliation(s)
- Anita C. Schürch
- Tuberculosis Reference Laboratory, National Institute for Public Health and the Environment (RIVM), Centre for Infectious Disease Control, (CIb/LIS, pb 22), Bilthoven, The Netherlands
- Radboud University Nijmegen Medical Centre/NCMLS, Centre for Molecular and Biomolecular Informatics, Nijmegen, The Netherlands
| | - Kristin Kremer
- Tuberculosis Reference Laboratory, National Institute for Public Health and the Environment (RIVM), Centre for Infectious Disease Control, (CIb/LIS, pb 22), Bilthoven, The Netherlands
| | - Amber C. A. Hendriks
- Tuberculosis Reference Laboratory, National Institute for Public Health and the Environment (RIVM), Centre for Infectious Disease Control, (CIb/LIS, pb 22), Bilthoven, The Netherlands
| | - Benthe Freyee
- Tuberculosis Reference Laboratory, National Institute for Public Health and the Environment (RIVM), Centre for Infectious Disease Control, (CIb/LIS, pb 22), Bilthoven, The Netherlands
| | - Christopher R. E. McEvoy
- Department of Science and Technology, National Research Foundation Centre of Excellence in Biomedical Tuberculosis Research, Medical Research Council Centre for Molecular and Cellular Biology, Stellenbosch University, Tygerberg, Cape Town, South Africa
- Department of Microbiology and Immunology, University of Melbourne, Victoria, Australia
| | - Reinout van Crevel
- Department of Medicine, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
| | - Martin J. Boeree
- Department of Pulmonary Diseases, Radboud University Nijmegen Medical Centre/University Lung Centre Dekkerswald, Nijmegen, The Netherlands
| | - Paul van Helden
- Department of Science and Technology, National Research Foundation Centre of Excellence in Biomedical Tuberculosis Research, Medical Research Council Centre for Molecular and Cellular Biology, Stellenbosch University, Tygerberg, Cape Town, South Africa
| | - Robin M. Warren
- Department of Science and Technology, National Research Foundation Centre of Excellence in Biomedical Tuberculosis Research, Medical Research Council Centre for Molecular and Cellular Biology, Stellenbosch University, Tygerberg, Cape Town, South Africa
| | - Roland J. Siezen
- Radboud University Nijmegen Medical Centre/NCMLS, Centre for Molecular and Biomolecular Informatics, Nijmegen, The Netherlands
| | - Dick van Soolingen
- Tuberculosis Reference Laboratory, National Institute for Public Health and the Environment (RIVM), Centre for Infectious Disease Control, (CIb/LIS, pb 22), Bilthoven, The Netherlands
- Department of Pulmonary Diseases, Radboud University Nijmegen Medical Centre/University Lung Centre Dekkerswald, Nijmegen, The Netherlands
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