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Dorji D, Graham RM, Richmond P, Keil A, Mukkur TK. Biofilm forming potential and antimicrobial susceptibility of newly emerged Western Australian Bordetella pertussis clinical isolates. BIOFOULING 2016; 32:1141-1152. [PMID: 27669900 DOI: 10.1080/08927014.2016.1232715] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2015] [Accepted: 08/30/2016] [Indexed: 05/23/2023]
Abstract
Whooping cough caused by Bordetella pertussis is increasing in several countries despite high vaccine coverage. One potential reason for the resurgence is the emergence of genetic variants of the bacterium. Biofilm formation has recently been associated with the pathogenesis of B. pertussis. Biofilm formation of 21 Western Australian B. pertussis clinical isolates was investigated. All isolates formed thicker biofilms than the reference vaccine strain Tohama I while retaining susceptibility to ampicillin, erythromycin, azithromycin and streptomycin. When two biofilm-forming clinical isolates were compared with Tohama I, minimum bactericidal concentrations of antimicrobial agents increased. Isobaric tags for relative and absolute quantitation (iTRAQ)-based proteomic analysis revealed significant differences in protein expression in B. pertussis biofilms, providing an opportunity for identification of novel biofilm-associated antigens for incorporation in current pertussis vaccines to improve their protective efficacy. The study also highlights the importance of determining antibiograms for biofilms to formulate improved antimicrobial therapeutic regimens.
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Affiliation(s)
- Dorji Dorji
- a School of Biomedical Sciences and Curtin Health Innovation Research Institute (CHIRI) , Curtin University , Perth , Australia
- c Jigme Dorji Wangchuck National Referral Hospital , Khesar Gyalpo University of Medical Sciences of Bhutan , Thimphu , Bhutan
| | - Ross M Graham
- a School of Biomedical Sciences and Curtin Health Innovation Research Institute (CHIRI) , Curtin University , Perth , Australia
| | | | - Anthony Keil
- b Princess Margaret Hospital , Perth , Australia
| | - Trilochan K Mukkur
- a School of Biomedical Sciences and Curtin Health Innovation Research Institute (CHIRI) , Curtin University , Perth , Australia
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202
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Linz B, Ivanov YV, Preston A, Brinkac L, Parkhill J, Kim M, Harris SR, Goodfield LL, Fry NK, Gorringe AR, Nicholson TL, Register KB, Losada L, Harvill ET. Acquisition and loss of virulence-associated factors during genome evolution and speciation in three clades of Bordetella species. BMC Genomics 2016; 17:767. [PMID: 27716057 PMCID: PMC5045587 DOI: 10.1186/s12864-016-3112-5] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2015] [Accepted: 09/23/2016] [Indexed: 11/10/2022] Open
Abstract
Background The genus Bordetella consists of nine species that include important respiratory pathogens such as the ‘classical’ species B. bronchiseptica, B. pertussis and B. parapertussis and six more distantly related and less extensively studied species. Here we analyze sequence diversity and gene content of 128 genome sequences from all nine species with focus on the evolution of virulence-associated factors. Results Both genome-wide sequence-based and gene content-based phylogenetic trees divide the genus into three species clades. The phylogenies are congruent between species suggesting genus-wide co-evolution of sequence diversity and gene content, but less correlated within species, mainly because of strain-specific presence of many different prophages. We compared the genomes with focus on virulence-associated genes and identified multiple clade-specific, species-specific and strain-specific events of gene acquisition and gene loss, including genes encoding O-antigens, protein secretion systems and bacterial toxins. Gene loss was more frequent than gene gain throughout the evolution, and loss of hundreds of genes was associated with the origin of several species, including the recently evolved human-restricted B. pertussis and B. holmesii, B. parapertussis and the avian pathogen B. avium. Conclusions Acquisition and loss of multiple genes drive the evolution and speciation in the genus Bordetella, including large scale gene loss associated with the origin of several species. Recent loss and functional inactivation of genes, including those encoding pertussis vaccine components and bacterial toxins, in individual strains emphasize ongoing evolution. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3112-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Bodo Linz
- Department of Veterinary and Biomedical Sciences, Pennsylvania State University, University Park, PA 16802, USA.
| | - Yury V Ivanov
- Department of Veterinary and Biomedical Sciences, Pennsylvania State University, University Park, PA 16802, USA
| | - Andrew Preston
- The Millner Centre for Evolution and Department of Biology and Biochemistry, University of Bath, Bath, UK
| | | | - Julian Parkhill
- Pathogen Genomics, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | - Maria Kim
- J. Craig Venter Institute, Rockville, MD, USA
| | - Simon R Harris
- Pathogen Genomics, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | - Laura L Goodfield
- Department of Veterinary and Biomedical Sciences, Pennsylvania State University, University Park, PA 16802, USA
| | - Norman K Fry
- Public Health England, Respiratory and Vaccine Preventable Bacteria Reference Unit, London, UK
| | | | - Tracy L Nicholson
- USDA, Agricultural Research Service, National Animal Disease Center, Ames, IA, USA
| | - Karen B Register
- USDA, Agricultural Research Service, National Animal Disease Center, Ames, IA, USA
| | | | - Eric T Harvill
- Department of Veterinary and Biomedical Sciences, Pennsylvania State University, University Park, PA 16802, USA. .,Singapore Centre on Environmental Life Sciences Engineering, Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore 637551, Singapore. .,Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA 30602, USA.
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203
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Effectiveness of acellular pertussis vaccination during childhood (<7 years of age) for preventing pertussis in household contacts 1-9 years old in Catalonia and Navarra (Spain). Eur J Clin Microbiol Infect Dis 2016; 35:2059-2067. [PMID: 27612470 DOI: 10.1007/s10096-016-2766-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Accepted: 08/23/2016] [Indexed: 10/21/2022]
Abstract
Pertussis vaccination with 4-5 doses of acellular vaccines is recommended in Spain to all children at 2 months to 6 years of age. The effectiveness of the acellular pertussis vaccination was assessed in this study by comparing the incidence of secondary pertussis in vaccinated (4-5 doses) and unvaccinated or partially vaccinated (0-3 doses) household contacts 1-9 years old of confirmed cases of pertussis in Spain in 2012-13. Eighty-five percent of contacts had been vaccinated with 4-5 doses of acellular pertussis vaccines. During the 2-year study period, 64 cases of secondary pertussis were detected among 405 household contacts 1-9 years old: 47 among vaccinated and 17 among unvaccinated or partially vaccinated contacts. The effectiveness for preventing secondary pertussis, calculated as 1 minus the relative risk (RR) of secondary pertussis in vaccinated vs. unvaccinated/partially vaccinated contacts, was 50 % [95 % confidence interval (CI): 19-69 %, p < 0.01] when household contacts were vaccinated using DTaP, Tdap, hexavalent or heptavalent vaccines, and it was 51.3 % (95 % CI: 21-70 %, p < 0.01) when they were vaccinated using DTaP or TdaP vaccines. The effectiveness adjusted for age, sex, pertussis chemotherapy and type of household contact was 58.6 % (95 % CI: 17-79 %, p < 0.05) when contacts were vaccinated using available acellular vaccines, and it was 59.6 % (95 % CI: 18-80 %, p < 0.01) when they were vaccinated using DTaP vaccines. Acellular pertussis vaccination during childhood was effective for preventing secondary pertussis in household contacts 1-9 years old of pertussis cases in Catalonia and Navarra, Spain.
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204
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Trent MS, Stead CM, Tran AX, Hankins JV. Invited review: Diversity of endotoxin and its impact on pathogenesis. ACTA ACUST UNITED AC 2016. [DOI: 10.1177/09680519060120040201] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Lipopolysaccharide or LPS is localized to the outer leaflet of the outer membrane and serves as the major surface component of the bacterial cell envelope. This remarkable glycolipid is essential for virtually all Gram-negative organisms and represents one of the conserved microbial structures responsible for activation of the innate immune system. For these reasons, the structure, function, and biosynthesis of LPS has been an area of intense research. The LPS of a number of bacteria is composed of three distinct regions — lipid A, a short core oligosaccharide, and the O-antigen polysaccharide. The lipid A domain, also known as endotoxin, anchors the molecule in the outer membrane and is the bioactive component recognized by TLR4 during human infection. Overall, the biochemical synthesis of lipid A is a highly conserved process; however, investigation of the lipid A structures of various organisms shows an impressive amount of diversity. These differences can be attributed to the action of latent enzymes that modify the canonical lipid A molecule. Variation of the lipid A domain of LPS serves as one strategy utilized by Gram-negative bacteria to promote survival by providing resistance to components of the innate immune system and helping to evade recognition by TLR4. This review summarizes the biochemical machinery required for the production of diverse lipid A structures of human pathogens and how structural modification of endotoxin impacts pathogenesis.
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Affiliation(s)
- M. Stephen Trent
- Department of Microbiology, James H. Quillen College of Medicine, East Tennessee State University, Johnson City, Tennessee, USA,
| | - Christopher M. Stead
- Department of Microbiology, James H. Quillen College of Medicine, East Tennessee State University, Johnson City, Tennessee, USA
| | - An X. Tran
- Department of Microbiology, James H. Quillen College of Medicine, East Tennessee State University, Johnson City, Tennessee, USA
| | - Jessica V. Hankins
- Department of Microbiology, James H. Quillen College of Medicine, East Tennessee State University, Johnson City, Tennessee, USA
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205
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Feasibility of Genome-Wide Screening for Biosafety Assessment of Probiotics: A Case Study of Lactobacillus helveticus MTCC 5463. Probiotics Antimicrob Proteins 2016. [PMID: 26223907 DOI: 10.1007/s12602-015-9199-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Recent years have witnessed an explosion in genome sequencing of probiotic strains for accurate identification and characterization. Regulatory bodies are emphasizing on the need for performing phase I safety studies for probiotics. The main hypothesis of this study was to explore the feasibility of using genome databases for safety screening of strains. In this study, we attempted to develop a framework for the safety assessment of a potential probiotic strain, Lactobacillus helveticus MTCC 5463 based on genome mining for genes associated with antibiotic resistance, production of harmful metabolites, and virulence. The sequencing of MTCC 5463 was performed using GS-FLX Titanium reagents. Genes coding for antibiotic resistance and virulence were identified using Antibiotic Resistance Genes Database and Virulence Factors Database. Results indicated that MTCC 5463 carried antibiotic resistance genes associated with beta-lactam and fluoroquinolone. There is no threat of transfer of these genes to host gut commensals because the genes are not plasmid encoded. The presence of genes for adhesion, biofilm, surface proteins, and stress-related proteins provides robustness to the strain. The presence of hemolysin gene in the genome revealed a theoretical risk of virulence. The results of in silico analysis complemented the in vitro studies and human clinical trials, confirming the safety of the probiotic strain. We propose that the safety assessment of probiotic strains administered live at high doses using a genome-wide screening could be an effective and time-saving tool for identifying prognostic biomarkers of biosafety.
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206
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Hoonakker ME, Verhagen LM, Pupo E, de Haan A, Metz B, Hendriksen CFM, Han WGH, Sloots A. Vaccine-Mediated Activation of Human TLR4 Is Affected by Modulation of Culture Conditions during Whole-Cell Pertussis Vaccine Preparation. PLoS One 2016; 11:e0161428. [PMID: 27548265 PMCID: PMC4993483 DOI: 10.1371/journal.pone.0161428] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2015] [Accepted: 08/05/2016] [Indexed: 12/01/2022] Open
Abstract
The potency of whole-cell pertussis (wP) vaccines is still determined by an intracerebral mouse protection test. To allow development of suitable in vitro alternatives to this test, insight into relevant parameters to monitor the consistency of vaccine quality is essential. To this end, a panel of experimental wP vaccines of varying quality was prepared by sulfate-mediated suppression of the BvgASR master virulence regulatory system of Bordetella pertussis during cultivation. This system regulates the transcription of a range of virulence proteins, many of which are considered important for the induction of effective host immunity. The protein compositions and in vivo potencies of the vaccines were BvgASR dependent, with the vaccine containing the highest amount of virulence proteins having the highest in vivo potency. Here, the capacities of these vaccines to stimulate human Toll-like receptors (hTLR) 2 and 4 and the role these receptors play in wP vaccine-mediated activation of antigen-presenting cells in vitro were studied. Prolonged BvgASR suppression was associated with a decreased capacity of vaccines to activate hTLR4. In contrast, no significant differences in hTLR2 activation were observed. Similarly, vaccine-induced activation of MonoMac-6 and monocyte-derived dendritic cells was strongest with the highest potency vaccine. Blocking of TLR2 and TLR4 showed that differences in antigen-presenting cell activation could be largely attributed to vaccine-dependent variation in hTLR4 signalling. Interestingly, this BvgASR-dependent decrease in hTLR4 activation coincided with a reduction in GlcN-modified lipopolysaccharides in these vaccines. Accordingly, expression of the lgmA-C genes, required for this glucosamine modification, was significantly reduced in bacteria exposed to sulfate. Together, these findings demonstrate that the BvgASR status of bacteria during wP vaccine preparation is critical for their hTLR4 activation capacity and suggest that including such parameters to assess consistency of newly produced vaccines could bring in vitro testing of vaccine quality a step closer.
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Affiliation(s)
- Marieke E. Hoonakker
- Institute for Translational Vaccinology (Intravacc), Bilthoven, The Netherlands
- Department of Animals in Science and Society, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
- * E-mail:
| | - Lisa M. Verhagen
- Institute for Translational Vaccinology (Intravacc), Bilthoven, The Netherlands
- Centre for Immunology of Infectious Diseases and Vaccines, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Elder Pupo
- Institute for Translational Vaccinology (Intravacc), Bilthoven, The Netherlands
| | - Alex de Haan
- Institute for Translational Vaccinology (Intravacc), Bilthoven, The Netherlands
| | - Bernard Metz
- Institute for Translational Vaccinology (Intravacc), Bilthoven, The Netherlands
| | - Coenraad F. M. Hendriksen
- Institute for Translational Vaccinology (Intravacc), Bilthoven, The Netherlands
- Department of Animals in Science and Society, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Wanda G. H. Han
- Centre for Immunology of Infectious Diseases and Vaccines, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Arjen Sloots
- Institute for Translational Vaccinology (Intravacc), Bilthoven, The Netherlands
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207
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Register KB, Nicholson TL, Brunelle BW. Comparison of ribotyping and sequence-based typing for discriminating among isolates of Bordetella bronchiseptica. J Microbiol Methods 2016; 129:117-126. [PMID: 27542997 DOI: 10.1016/j.mimet.2016.08.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Revised: 08/15/2016] [Accepted: 08/15/2016] [Indexed: 11/16/2022]
Abstract
PvuII ribotyping and MLST are each highly discriminatory methods for genotyping Bordetella bronchiseptica, but a direct comparison between these approaches has not been undertaken. The goal of this study was to directly compare the discriminatory power of PvuII ribotyping and MLST, using a single set of geographically and genetically diverse strains, and to determine whether subtyping based on repeat region sequences of the pertactin gene (prn) provides additional resolution. One hundred twenty-two isolates were analyzed, representing 11 mammalian or avian hosts, sourced from the United States, Europe, Israel and Australia. Thirty-two ribotype patterns were identified; one isolate could not be typed. In comparison, all isolates were typeable by MLST and a total of 30 sequence types was identified. An analysis based on Simpson's Index of Diversity (SID) revealed that ribotyping and MLST are nearly equally discriminatory, with SIDs of 0.920 for ribotyping and 0.919 for MLST. Nonetheless, for ten ribotypes and eight MLST sequence types, the alternative method discriminates among isolates that otherwise type identically. Pairing prn repeat region typing with ribotyping yielded 54 genotypes and increased the SID to 0.954. Repeat region typing combined with MLST resulted in 47 genotypes and an SID of 0.944. Given the technical and practical advantages of MLST over ribotyping, and the nominal difference in their SIDs, we conclude MLST is the preferred primary typing tool. We recommend the combination of MLST and prn repeat region typing as a high-resolution, objective and standardized approach valuable for investigating the population structure and epidemiology of B. bronchiseptica.
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Affiliation(s)
- Karen B Register
- Ruminant Diseases and Immunology Research Unit, USDA/Agricultural Research Service/National Animal Disease Center, 1920 Dayton Avenue, Ames, IA 50010, United States.
| | - Tracy L Nicholson
- Virus and Prion Research Unit, USDA/Agricultural Research Service/National Animal Disease Center, 1920 Dayton Avenue, Ames, IA 50010, United States
| | - Brian W Brunelle
- Food Safety and Enteric Pathogens Research Unit, USDA/Agricultural Research Service/National Animal Disease Center, 1920 Dayton Avenue, Ames, IA 50010, United States
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208
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Saeb ATM. Presence of Bacterial Virulence Gene Homologues in the dibenzo-p-dioxins degrading bacterium Sphingomonas wittichii. Bioinformation 2016; 12:241-248. [PMID: 28197061 PMCID: PMC5290665 DOI: 10.6026/97320630012241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2016] [Revised: 06/22/2016] [Accepted: 06/23/2016] [Indexed: 11/28/2022] Open
Abstract
Sphingomonas wittichii, a close relative of the human pathogen Sphingomonas paucimobilis, is a microorganism of great interest to the bioremediation community for its ability of biodegradation to a large number of toxic polychlorinated dioxins. In the present study we investigated the presence of different virulence factors and genes in S. wittichii. We utilized phylogenetic, comparative genomics and bioinformatics analysis to investigate the potentiality of S. wittichii as a potential virulent pathogen. The 16SrDNA phylogenetic tree showed that the closest bacterial taxon to S. wittichii is Brucella followed by Helicobacter, Campylobacter, Pseudomonas then Legionella. Despite their close phylogenetic relationship, S. wittichii did not share any virulence factors with Helicobacter or Campylobacter. On the contrary, in spite of the phylogenetic divergence between S. wittichii and Pseudomonas spp., they shared many major virulence factors, such as, adherence, antiphagocytosis, Iron uptake, proteases and quorum sensing. S. wittichii contains several major virulence factors resembling Pseudomonas sp., Legionella sp., Brucella sp. and Bordetella sp. virulence factors. Similarity of virulence factors did not match phylogenetic relationships. These findings suggest horizontal gene transfer of virulence factors rather than sharing a common pathogenic ancestor. S. wittichii is a potential virulent bacterium. Another possibility is that reductive evolution process attenuated S. wittichii pathogenic capabilities. Thus plenty of care must be taken when using this bacterium in soil remediation purposes.
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Affiliation(s)
- Amr T. M. Saeb
- Biotechnology Department, Strategic Center for Diabetes Research, College of medicine, King Saud University, Saudi Arabia
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209
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Abstract
The plague bacillus Yersinia pestis is unique among the pathogenic Enterobacteriaceae in utilizing an arthropod-borne transmission route. Transmission by fleabite is a recent evolutionary adaptation that followed the divergence of Y. pestis from the closely related food- and waterborne enteric pathogen Yersinia pseudotuberculosis A combination of population genetics, comparative genomics, and investigations of Yersinia-flea interactions have disclosed the important steps in the evolution and emergence of Y. pestis as a flea-borne pathogen. Only a few genetic changes, representing both gene gain by lateral transfer and gene loss by loss-of-function mutation (pseudogenization), were fundamental to this process. The emergence of Y. pestis fits evolutionary theories that emphasize ecological opportunity in adaptive diversification and rapid emergence of new species.
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210
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Xu T, Qin S, Hu Y, Song Z, Ying J, Li P, Dong W, Zhao F, Yang H, Bao Q. Whole genomic DNA sequencing and comparative genomic analysis of Arthrospira platensis: high genome plasticity and genetic diversity. DNA Res 2016; 23:325-38. [PMID: 27330141 PMCID: PMC4991836 DOI: 10.1093/dnares/dsw023] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2015] [Accepted: 05/12/2016] [Indexed: 11/13/2022] Open
Abstract
Arthrospira platensis is a multi-cellular and filamentous non-N2-fixing cyanobacterium that is capable of performing oxygenic photosynthesis. In this study, we determined the nearly complete genome sequence of A. platensis YZ. A. platensis YZ genome is a single, circular chromosome of 6.62 Mb in size. Phylogenetic and comparative genomic analyses revealed that A. platensis YZ was more closely related to A. platensis NIES-39 than Arthrospira sp. PCC 8005 and A. platensis C1. Broad gene gains were identified between A. platensis YZ and three other Arthrospira speices, some of which have been previously demonstrated that can be laterally transferred among different species, such as restriction-modification systems-coding genes. Moreover, unprecedented extensive chromosomal rearrangements among different strains were observed. The chromosomal rearrangements, particularly the chromosomal inversions, were analysed and estimated to be closely related to palindromes that involved long inverted repeat sequences and the extensively distributed type IIR restriction enzyme in the Arthrospira genome. In addition, species from genus Arthrospira unanimously contained the highest rate of repetitive sequence compared with the other species of order Oscillatoriales, suggested that sequence duplication significantly contributed to Arthrospira genome phylogeny. These results provided in-depth views into the genomic phylogeny and structural variation of A. platensis, as well as provide a valuable resource for functional genomics studies.
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Affiliation(s)
- Teng Xu
- School of Laboratory Medicine and Life Science/Institute of Biomedical Informatics, Wenzhou Medical University, Wenzhou 325035, China
| | - Song Qin
- Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
| | - Yongwu Hu
- School of Laboratory Medicine and Life Science/Institute of Biomedical Informatics, Wenzhou Medical University, Wenzhou 325035, China BGI-Shenzhen, Shenzhen 518083, China
| | - Zhijian Song
- School of Laboratory Medicine and Life Science/Institute of Biomedical Informatics, Wenzhou Medical University, Wenzhou 325035, China
| | - Jianchao Ying
- School of Laboratory Medicine and Life Science/Institute of Biomedical Informatics, Wenzhou Medical University, Wenzhou 325035, China
| | - Peizhen Li
- School of Laboratory Medicine and Life Science/Institute of Biomedical Informatics, Wenzhou Medical University, Wenzhou 325035, China
| | - Wei Dong
- BGI-Shenzhen, Shenzhen 518083, China
| | - Fangqing Zhao
- Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
| | - Huanming Yang
- BGI-Shenzhen, Shenzhen 518083, China James D. Watson Institute of Genome Sciences, Zhejiang University, Hangzhou 310058, China
| | - Qiyu Bao
- School of Laboratory Medicine and Life Science/Institute of Biomedical Informatics, Wenzhou Medical University, Wenzhou 325035, China BGI-Shenzhen, Shenzhen 518083, China
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211
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Bowden KE, Weigand MR, Peng Y, Cassiday PK, Sammons S, Knipe K, Rowe LA, Loparev V, Sheth M, Weening K, Tondella ML, Williams MM. Genome Structural Diversity among 31 Bordetella pertussis Isolates from Two Recent U.S. Whooping Cough Statewide Epidemics. mSphere 2016; 1:e00036-16. [PMID: 27303739 PMCID: PMC4888882 DOI: 10.1128/msphere.00036-16] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Accepted: 04/03/2016] [Indexed: 11/20/2022] Open
Abstract
During 2010 and 2012, California and Vermont, respectively, experienced statewide epidemics of pertussis with differences seen in the demographic affected, case clinical presentation, and molecular epidemiology of the circulating strains. To overcome limitations of the current molecular typing methods for pertussis, we utilized whole-genome sequencing to gain a broader understanding of how current circulating strains are causing large epidemics. Through the use of combined next-generation sequencing technologies, this study compared de novo, single-contig genome assemblies from 31 out of 33 Bordetella pertussis isolates collected during two separate pertussis statewide epidemics and 2 resequenced vaccine strains. Final genome architecture assemblies were verified with whole-genome optical mapping. Sixteen distinct genome rearrangement profiles were observed in epidemic isolate genomes, all of which were distinct from the genome structures of the two resequenced vaccine strains. These rearrangements appear to be mediated by repetitive sequence elements, such as high-copy-number mobile genetic elements and rRNA operons. Additionally, novel and previously identified single nucleotide polymorphisms were detected in 10 virulence-related genes in the epidemic isolates. Whole-genome variation analysis identified state-specific variants, and coding regions bearing nonsynonymous mutations were classified into functional annotated orthologous groups. Comprehensive studies on whole genomes are needed to understand the resurgence of pertussis and develop novel tools to better characterize the molecular epidemiology of evolving B. pertussis populations. IMPORTANCE Pertussis, or whooping cough, is the most poorly controlled vaccine-preventable bacterial disease in the United States, which has experienced a resurgence for more than a decade. Once viewed as a monomorphic pathogen, B. pertussis strains circulating during epidemics exhibit diversity visible on a genome structural level, previously undetectable by traditional sequence analysis using short-read technologies. For the first time, we combine short- and long-read sequencing platforms with restriction optical mapping for single-contig, de novo assembly of 31 isolates to investigate two geographically and temporally independent U.S. pertussis epidemics. These complete genomes reshape our understanding of B. pertussis evolution and strengthen molecular epidemiology toward one day understanding the resurgence of pertussis.
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Affiliation(s)
- Katherine E. Bowden
- Division of Bacterial Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Michael R. Weigand
- Division of Bacterial Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Yanhui Peng
- Division of Bacterial Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Pamela K. Cassiday
- Division of Bacterial Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Scott Sammons
- Biotechnology Core Facility Branch, Division of Scientific Resources, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Kristen Knipe
- Biotechnology Core Facility Branch, Division of Scientific Resources, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Lori A. Rowe
- Biotechnology Core Facility Branch, Division of Scientific Resources, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Vladimir Loparev
- Biotechnology Core Facility Branch, Division of Scientific Resources, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Mili Sheth
- Biotechnology Core Facility Branch, Division of Scientific Resources, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Keeley Weening
- Vermont Department of Health Laboratory, Burlington, Vermont, USA
| | - M. Lucia Tondella
- Division of Bacterial Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Margaret M. Williams
- Division of Bacterial Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
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212
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Bacterial Metabolism in the Host Environment: Pathogen Growth and Nutrient Assimilation in the Mammalian Upper Respiratory Tract. Microbiol Spectr 2016; 3. [PMID: 26185081 DOI: 10.1128/microbiolspec.mbp-0007-2014] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Pathogens evolve in specific host niches and microenvironments that provide the physical and nutritional requirements conducive to their growth. In addition to using the host as a source of food, bacterial pathogens must avoid the immune response to their presence. The mammalian upper respiratory tract is a site that is exposed to the external environment, and is readily colonized by bacteria that live as resident flora or as pathogens. These bacteria can remain localized, descend to the lower respiratory tract, or traverse the epithelium to disseminate throughout the body. By virtue of their successful colonization of the respiratory epithelium, these bacteria obtain the nutrients needed for growth, either directly from host resources or from other microbes. This chapter describes the upper respiratory tract environment, including its tissue and mucosal structure, prokaryotic biota, and biochemical composition that would support microbial life. Neisseria meningitidis and the Bordetella species are discussed as examples of bacteria that have no known external reservoirs but have evolved to obligately colonize the mammalian upper respiratory tract.
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213
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Clayton AL, Jackson DG, Weiss RB, Dale C. Adaptation by Deletogenic Replication Slippage in a Nascent Symbiont. Mol Biol Evol 2016; 33:1957-66. [PMID: 27189544 PMCID: PMC4948707 DOI: 10.1093/molbev/msw071] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
As a consequence of population level constraints in the obligate, host-associated lifestyle, intracellular symbiotic bacteria typically exhibit high rates of molecular sequence evolution and extensive genome degeneration over the course of their host association. While the rationale for genome degeneration is well understood, little is known about the molecular mechanisms driving this change. To understand these mechanisms we compared the genome of Sodalis praecaptivus, a nonhost associated bacterium that is closely related to members of the Sodalis-allied clade of insect endosymbionts, with the very recently derived insect symbiont Candidatus Sodalis pierantonius. The characterization of indel mutations in the genome of Ca. Sodalis pierantonius shows that the replication system in this organism is highly prone to deletions resulting from polymerase slippage events in regions encoding G+C-rich repetitive sequences. This slippage-prone phenotype is mechanistically associated with the loss of certain components of the bacterial DNA recombination machinery at an early stage in symbiotic life and is expected to facilitate rapid adaptation to the novel host environment. This is analogous to the emergence of mutator strains in both natural and laboratory populations of bacteria, which tend to reach high frequencies in clonal populations due to linkage between the mutator allele and the resulting adaptive mutations.
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Affiliation(s)
| | | | | | - Colin Dale
- Department of Biology, University of Utah
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214
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Vandecraen J, Monsieurs P, Mergeay M, Leys N, Aertsen A, Van Houdt R. Zinc-Induced Transposition of Insertion Sequence Elements Contributes to Increased Adaptability of Cupriavidus metallidurans. Front Microbiol 2016; 7:359. [PMID: 27047473 PMCID: PMC4803752 DOI: 10.3389/fmicb.2016.00359] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2015] [Accepted: 03/07/2016] [Indexed: 12/15/2022] Open
Abstract
Bacteria can respond to adverse environments by increasing their genomic variability and subsequently facilitating adaptive evolution. To demonstrate this, the contribution of Insertion Sequence (IS) elements to the genetic adaptation of Cupriavidus metallidurans AE126 to toxic zinc concentrations was determined. This derivative of type strain CH34, devoid of its main zinc resistance determinant, is still able to increase its zinc resistance level. Specifically, upon plating on medium supplemented with a toxic zinc concentration, resistant variants arose in which a compromised cnrYX regulatory locus caused derepression of CnrH sigma factor activity and concomitant induction of the corresponding RND-driven cnrCBA efflux system. Late-occurring zinc resistant variants likely arose in response to the selective conditions, as they were enriched in cnrYX disruptions caused by specific IS elements whose transposase expression was found to be zinc-responsive. Interestingly, deletion of cnrH, and consequently the CnrH-dependent adaptation potential, still enabled adaptation by transposition of IS elements (ISRme5 and IS1086) that provided outward-directed promoters driving cnrCBAT transcription. Finally, adaptation to zinc by IS reshuffling can also enhance the adaptation to subsequent environmental challenges. Thus, transposition of IS elements can be induced by stress conditions and play a multifaceted, pivotal role in the adaptation to these and subsequent stress conditions.
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Affiliation(s)
- Joachim Vandecraen
- Unit of Microbiology, Belgian Nuclear Research Centre (SCK•CEN)Mol, Belgium; Laboratory of Food Microbiology and Leuven Food Science and Nutrition Research Centre, Department of Microbial and Molecular Systems, Faculty of Bioscience Engineering, Katholieke Universiteit LeuvenLeuven, Belgium
| | - Pieter Monsieurs
- Unit of Microbiology, Belgian Nuclear Research Centre (SCK•CEN) Mol, Belgium
| | - Max Mergeay
- Unit of Microbiology, Belgian Nuclear Research Centre (SCK•CEN) Mol, Belgium
| | - Natalie Leys
- Unit of Microbiology, Belgian Nuclear Research Centre (SCK•CEN) Mol, Belgium
| | - Abram Aertsen
- Laboratory of Food Microbiology and Leuven Food Science and Nutrition Research Centre, Department of Microbial and Molecular Systems, Faculty of Bioscience Engineering, Katholieke Universiteit Leuven Leuven, Belgium
| | - Rob Van Houdt
- Unit of Microbiology, Belgian Nuclear Research Centre (SCK•CEN) Mol, Belgium
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215
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Shapiro LR, Scully ED, Straub TJ, Park J, Stephenson AG, Beattie GA, Gleason ML, Kolter R, Coelho MC, De Moraes CM, Mescher MC, Zhaxybayeva O. Horizontal Gene Acquisitions, Mobile Element Proliferation, and Genome Decay in the Host-Restricted Plant Pathogen Erwinia Tracheiphila. Genome Biol Evol 2016; 8:649-64. [PMID: 26992913 PMCID: PMC4824170 DOI: 10.1093/gbe/evw016] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/28/2016] [Indexed: 12/18/2022] Open
Abstract
Modern industrial agriculture depends on high-density cultivation of genetically similar crop plants, creating favorable conditions for the emergence of novel pathogens with increased fitness in managed compared with ecologically intact settings. Here, we present the genome sequence of six strains of the cucurbit bacterial wilt pathogen Erwinia tracheiphila (Enterobacteriaceae) isolated from infected squash plants in New York, Pennsylvania, Kentucky, and Michigan. These genomes exhibit a high proportion of recent horizontal gene acquisitions, invasion and remarkable amplification of mobile genetic elements, and pseudogenization of approximately 20% of the coding sequences. These genome attributes indicate that E. tracheiphila recently emerged as a host-restricted pathogen. Furthermore, chromosomal rearrangements associated with phage and transposable element proliferation contribute to substantial differences in gene content and genetic architecture between the six E. tracheiphila strains and other Erwinia species. Together, these data lead us to hypothesize that E. tracheiphila has undergone recent evolution through both genome decay (pseudogenization) and genome expansion (horizontal gene transfer and mobile element amplification). Despite evidence of dramatic genomic changes, the six strains are genetically monomorphic, suggesting a recent population bottleneck and emergence into E. tracheiphila's current ecological niche.
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Affiliation(s)
- Lori R Shapiro
- Department of Organismic and Evolutionary Biology, Harvard University
| | - Erin D Scully
- Grain, Forage, and Bioenergy Research Unit, USDA-ARS, Lincoln, Nebraska and Department of Agronomy and Horticulture, University of Nebraska-Lincoln
| | | | - Jihye Park
- Graduate Program in Bioinformatics and Genomics, Pennsylvania State University Present address: Department of Pediatrics, Massachusetts General Hospital, Boston, Massachusetts
| | | | - Gwyn A Beattie
- Department of Plant Pathology and Microbiology, Iowa State University
| | - Mark L Gleason
- Department of Plant Pathology and Microbiology, Iowa State University
| | - Roberto Kolter
- Department of Microbiology and Immunology, Harvard Medical School, Boston, Massachusetts
| | - Miguel C Coelho
- Department of Molecular and Cellular Biology, Harvard University
| | | | - Mark C Mescher
- Department of Environmental Systems Science, ETH Zürich, Zürich, Switzerland
| | - Olga Zhaxybayeva
- Department of Biological Sciences, Dartmouth College Department of Computer Science, Dartmouth College
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216
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Lamberti Y, Cafiero JH, Surmann K, Valdez H, Holubova J, Večerek B, Sebo P, Schmidt F, Völker U, Rodriguez ME. Proteome analysis of Bordetella pertussis isolated from human macrophages. J Proteomics 2016; 136:55-67. [DOI: 10.1016/j.jprot.2016.02.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Revised: 02/05/2016] [Accepted: 02/07/2016] [Indexed: 12/13/2022]
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217
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Sealey KL, Belcher T, Preston A. Bordetella pertussis epidemiology and evolution in the light of pertussis resurgence. INFECTION GENETICS AND EVOLUTION 2016; 40:136-143. [PMID: 26932577 DOI: 10.1016/j.meegid.2016.02.032] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Revised: 02/16/2016] [Accepted: 02/25/2016] [Indexed: 11/28/2022]
Abstract
Whooping cough, or pertussis, is resurgent in many countries world-wide. This is linked to switching from the use of whole cell vaccines to acellular vaccines in developed countries. Current evidence suggests that this has resulted in the earlier waning of vaccine-induced immunity, an increase in asymptomatic infection with concomitant increases in transmission and increased selection pressure for Bordetellapertussis variants that are better able to evade vaccine-mediated immunity than older isolates. This review discusses recent findings in B. pertussis epidemiology and evolution in the light of pertussis resurgence, and highlights the important role for genomics-based studies in monitoring B. pertussis adaptation.
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Affiliation(s)
- Katie L Sealey
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, UK
| | - Thomas Belcher
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, UK
| | - Andrew Preston
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, UK.
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218
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Nishikawa S, Shinzawa N, Nakamura K, Ishigaki K, Abe H, Horiguchi Y. Thebvg-repressed genebrtA, encoding biofilm-associated surface adhesin, is expressed during host infection byBordetella bronchiseptica. Microbiol Immunol 2016; 60:93-105. [DOI: 10.1111/1348-0421.12356] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Revised: 12/24/2015] [Accepted: 01/07/2016] [Indexed: 11/30/2022]
Affiliation(s)
- Sayaka Nishikawa
- Department of Molecular Bacteriology, Research Institute for Microbial Diseases; Osaka University; 3-1 Yamada-oka Suita Osaka 565-0871 Japan
| | - Naoaki Shinzawa
- Department of Molecular Bacteriology, Research Institute for Microbial Diseases; Osaka University; 3-1 Yamada-oka Suita Osaka 565-0871 Japan
| | - Keiji Nakamura
- Department of Molecular Bacteriology, Research Institute for Microbial Diseases; Osaka University; 3-1 Yamada-oka Suita Osaka 565-0871 Japan
| | - Keisuke Ishigaki
- Department of Molecular Bacteriology, Research Institute for Microbial Diseases; Osaka University; 3-1 Yamada-oka Suita Osaka 565-0871 Japan
| | - Hiroyuki Abe
- Department of Molecular Bacteriology, Research Institute for Microbial Diseases; Osaka University; 3-1 Yamada-oka Suita Osaka 565-0871 Japan
| | - Yasuhiko Horiguchi
- Department of Molecular Bacteriology, Research Institute for Microbial Diseases; Osaka University; 3-1 Yamada-oka Suita Osaka 565-0871 Japan
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219
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Uncovering Listeria monocytogenes hypervirulence by harnessing its biodiversity. Nat Genet 2016; 48:308-313. [PMID: 26829754 PMCID: PMC4768348 DOI: 10.1038/ng.3501] [Citation(s) in RCA: 454] [Impact Index Per Article: 56.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Accepted: 01/06/2016] [Indexed: 12/17/2022]
Abstract
Microbial pathogenesis studies are typically performed with reference strains, thereby overlooking microbial intra-species virulence heterogeneity. Here we integrated human epidemiological and clinical data with bacterial population genomics to harness the biodiversity of the model foodborne pathogen Listeria monocytogenes and decipher the basis of its neural and placental tropisms. Taking advantage of the clonal structure of this bacterial species, we identify clones epidemiologically associated with either food or human central nervous system (CNS) and maternal-neonatal (MN) listeriosis. The latter are also most prevalent in patients without immunosuppressive comorbidities. Strikingly, CNS and MN clones are hypervirulent in a humanized mouse model of listeriosis. By integrating epidemiological data and comparative genomics, we uncovered multiple novel putative virulence factors and demonstrated experimentally the contribution of the first gene cluster mediating Listeria monocytogenes neural and placental tropisms. This study illustrates the exceptional power of harnessing microbial biodiversity to identify clinically relevant microbial virulence attributes.
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220
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Safarchi A, Octavia S, Wu SZ, Kaur S, Sintchenko V, Gilbert GL, Wood N, McIntyre P, Marshall H, Keil AD, Lan R. Genomic dissection of Australian Bordetella pertussis isolates from the 2008-2012 epidemic. J Infect 2016; 72:468-77. [PMID: 26826518 DOI: 10.1016/j.jinf.2016.01.005] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Revised: 12/15/2015] [Accepted: 01/14/2016] [Indexed: 11/24/2022]
Abstract
OBJECTIVES Despite high pertussis vaccination coverage, Australia experienced a prolonged epidemic in 2008-2012. The predominant Bordetella pertussis genotype harboured pertussis toxin promoter allele, ptxP3, and pertactin gene allele, prn2. The emergence and expansion of prn non-expressing isolates (Prn negative), were also observed. We aimed to investigate the microevolution and genomic diversity of epidemic B. pertussis isolates. METHODS We sequenced 22 B. pertussis isolates collected in 2008-2012 from two states of Australia which are geographically widely separated. Ten of the 22 were Prn negative isolates with three different modes of silencing of prn (prn::IS481F, prn::IS481R and prn::IS1002). Five pre-epidemic isolates were also sequenced for comparison. RESULTS Five single nucleotide polymorphisms were common in the epidemic isolates and differentiated them from pre-epidemic isolates. The Australian epidemic isolates can be divided into five lineages (EL1-EL5) with EL1 containing only Prn negative isolates. Comparison with global isolates showed that three lineages remained geographically and temporally distinct whereas two lineages mixed with isolates from 2012 UK outbreak. CONCLUSION Our results suggest significant diversification and the microevolution of B. pertussis within the 2008-2012 Australian epidemic.
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Affiliation(s)
- Azadeh Safarchi
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Sophie Octavia
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Sunny Z Wu
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Sandeep Kaur
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Vitali Sintchenko
- Centre for Infectious Diseases and Microbiology - Public Health, Institute of Clinical Pathology and Medical Research, Pathology West, Westmead Hospital, New South Wales, Australia; Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, New South Wales, Australia
| | - Gwendolyn L Gilbert
- Centre for Infectious Diseases and Microbiology - Public Health, Institute of Clinical Pathology and Medical Research, Pathology West, Westmead Hospital, New South Wales, Australia; Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, New South Wales, Australia
| | - Nicholas Wood
- National Centre for Immunisation Research and Surveillance of Vaccine Preventable Diseases (NCIRS), The Children's Hospital at Westmead, Westmead, New South Wales 2145, Australia; Discipline of Paediatrics and Child Health, University of Sydney, The Children's Hospital at Westmead, Westmead, New South Wales 2145, Australia; Department of Microbiology and Infectious Diseases, The Children's Hospital at Westmead, New South Wales, Australia
| | - Peter McIntyre
- National Centre for Immunisation Research and Surveillance of Vaccine Preventable Diseases (NCIRS), The Children's Hospital at Westmead, Westmead, New South Wales 2145, Australia; Discipline of Paediatrics and Child Health, University of Sydney, The Children's Hospital at Westmead, Westmead, New South Wales 2145, Australia; Department of Microbiology and Infectious Diseases, The Children's Hospital at Westmead, New South Wales, Australia
| | - Helen Marshall
- Vaccinology and Immunology Research Trials Unit, Women's and Children's Hospital and School of Medicine and Robinson Research Institute, University of Adelaide, South Australia, Australia
| | - Anthony D Keil
- Department of Microbiology, PathWest Laboratory Medicine WA, Princess Margaret Hospital for Children, Perth, Australia
| | - Ruiting Lan
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia.
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221
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Chen P, Dong J, Yin H, Bao X, Chen L, He Y, Chen R, Wan X, Zhao Y, Hou X. Genome comparison and evolutionary analysis of different industrial lager yeasts (Saccharomyces pastorianus). JOURNAL OF THE INSTITUTE OF BREWING 2016. [DOI: 10.1002/jib.303] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Peng Chen
- State Key Laboratory of Biological Fermentation Engineering of Beer; Tsingtao Brewery Co., Ltd.; Qingdao 266061 People's Republic of China
| | - Jianjun Dong
- State Key Laboratory of Biological Fermentation Engineering of Beer; Tsingtao Brewery Co., Ltd.; Qingdao 266061 People's Republic of China
| | - Hua Yin
- State Key Laboratory of Biological Fermentation Engineering of Beer; Tsingtao Brewery Co., Ltd.; Qingdao 266061 People's Republic of China
| | - Xiaoming Bao
- State Key Laboratory of Microbial Technology; Shandong University; Jinan 250100 People's Republic of China
| | - Lu Chen
- State Key Laboratory of Biological Fermentation Engineering of Beer; Tsingtao Brewery Co., Ltd.; Qingdao 266061 People's Republic of China
| | - Yang He
- State Key Laboratory of Biological Fermentation Engineering of Beer; Tsingtao Brewery Co., Ltd.; Qingdao 266061 People's Republic of China
| | - Rong Chen
- State Key Laboratory of Biological Fermentation Engineering of Beer; Tsingtao Brewery Co., Ltd.; Qingdao 266061 People's Republic of China
| | - Xiujuan Wan
- State Key Laboratory of Biological Fermentation Engineering of Beer; Tsingtao Brewery Co., Ltd.; Qingdao 266061 People's Republic of China
| | - Yuxiang Zhao
- State Key Laboratory of Biological Fermentation Engineering of Beer; Tsingtao Brewery Co., Ltd.; Qingdao 266061 People's Republic of China
| | - Xiaoping Hou
- State Key Laboratory of Biological Fermentation Engineering of Beer; Tsingtao Brewery Co., Ltd.; Qingdao 266061 People's Republic of China
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222
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Basheer SM, Bouchez V, Novikov A, Augusto LA, Guiso N, Caroff M. Structure activity characterization of Bordetella petrii lipid A, from environment to human isolates. Biochimie 2016; 120:87-95. [DOI: 10.1016/j.biochi.2015.07.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Accepted: 07/06/2015] [Indexed: 11/30/2022]
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223
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Clinical characteristics and pertussis costs in cases reported to epidemiological services and cases detected in household contacts in Catalonia (Spain). Eur J Clin Microbiol Infect Dis 2015; 35:285-92. [DOI: 10.1007/s10096-015-2542-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Accepted: 11/29/2015] [Indexed: 10/22/2022]
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224
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Bentley SD, Parkhill J. Genomic perspectives on the evolution and spread of bacterial pathogens. Proc Biol Sci 2015; 282:20150488. [PMID: 26702036 PMCID: PMC4707741 DOI: 10.1098/rspb.2015.0488] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Accepted: 05/19/2015] [Indexed: 12/22/2022] Open
Abstract
Since the first complete sequencing of a free-living organism, Haemophilus influenzae, genomics has been used to probe both the biology of bacterial pathogens and their evolution. Single-genome approaches provided information on the repertoire of virulence determinants and host-interaction factors, and, along with comparative analyses, allowed the proposal of hypotheses to explain the evolution of many of these traits. These analyses suggested many bacterial pathogens to be of relatively recent origin and identified genome degradation as a key aspect of host adaptation. The advent of very-high-throughput sequencing has allowed for detailed phylogenetic analysis of many important pathogens, revealing patterns of global and local spread, and recent evolution in response to pressure from therapeutics and the human immune system. Such analyses have shown that bacteria can evolve and transmit very rapidly, with emerging clones showing adaptation and global spread over years or decades. The resolution achieved with whole-genome sequencing has shown considerable benefits in clinical microbiology, enabling accurate outbreak tracking within hospitals and across continents. Continued large-scale sequencing promises many further insights into genetic determinants of drug resistance, virulence and transmission in bacterial pathogens.
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Affiliation(s)
- Stephen D Bentley
- The Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Julian Parkhill
- The Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
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225
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Izac M, Garnier D, Speck D, Lindley ND. A Functional Tricarboxylic Acid Cycle Operates during Growth of Bordetella pertussis on Amino Acid Mixtures as Sole Carbon Substrates. PLoS One 2015; 10:e0145251. [PMID: 26684737 PMCID: PMC4684311 DOI: 10.1371/journal.pone.0145251] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Accepted: 11/30/2015] [Indexed: 12/31/2022] Open
Abstract
It has been claimed that citrate synthase, aconitase and isocitrate dehydrogenase activities are non-functional in Bordetella pertussis and that this might explain why this bacterium’s growth is sometimes associated with accumulation of polyhydroxybutyrate (PHB) and/or free fatty acids. However, the sequenced genome includes the entire citric acid pathway genes. Furthermore, these genes were expressed and the corresponding enzyme activities detected at high levels for the pathway when grown on a defined medium imitating the amino acid content of complex media often used for growth of this pathogenic microorganism. In addition, no significant PHB or fatty acids could be detected. Analysis of the carbon balance and stoichiometric flux analysis based on specific rates of amino acid consumption, and estimated biomass requirements coherent with the observed growth rate, clearly indicate that a fully functional tricarboxylic acid cycle operates in contrast to previous reports.
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Affiliation(s)
- Marie Izac
- Université de Toulouse; INSA, UPSr, INP, LISBP, Toulouse, France
- INRA, UMR792 Ingénierie des Systèmes Biologiques et des Procédés, Toulouse, France
- CNRS, UMR5504, Toulouse, France
| | | | | | - Nic D Lindley
- Université de Toulouse; INSA, UPSr, INP, LISBP, Toulouse, France
- INRA, UMR792 Ingénierie des Systèmes Biologiques et des Procédés, Toulouse, France
- CNRS, UMR5504, Toulouse, France
- * E-mail:
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226
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Environmental marine pathogen isolation using mesocosm culture of sharpsnout seabream: striking genomic and morphological features of novel Endozoicomonas sp. Sci Rep 2015; 5:17609. [PMID: 26639610 PMCID: PMC4671022 DOI: 10.1038/srep17609] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2015] [Accepted: 11/02/2015] [Indexed: 11/09/2022] Open
Abstract
Aquaculture is a burgeoning industry, requiring diversification into new farmed species, which are often at risk from infectious disease. We used a mesocosm technique to investigate the susceptibility of sharpsnout seabream (Diplodus puntazzo) larvae to potential environmental pathogens in seawater compared to control borehole water. Fish exposed to seawater succumbed to epitheliocystis from 21 days post hatching, causing mortality in a quarter of the hosts. The pathogen responsible was not chlamydial, as is often found in epitheliocystis, but a novel species of the γ-proteobacterial genus Endozoicomonas. Detailed characterisation of this pathogen within the infectious lesions using high resolution fluorescent and electron microscopy showed densely packed rod shaped bacteria. A draft genome sequence of this uncultured bacterium was obtained from preserved material. Comparison with the genome of the Endozoicomonas elysicola type strain shows that the genome of Ca. Endozoicomonas cretensis is undergoing decay through loss of functional genes and insertion sequence expansion, often indicative of adaptation to a new niche or restriction to an alternative lifestyle. These results demonstrate the advantage of mesocosm studies for investigating the effect of environmental bacteria on susceptible hosts and provide an important insight into the genome dynamics of a novel fish pathogen.
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227
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Fingermann M, Hozbor D. Acid tolerance response of Bordetella bronchiseptica in avirulent phase. Microbiol Res 2015; 181:52-60. [DOI: 10.1016/j.micres.2015.09.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Revised: 08/26/2015] [Accepted: 09/01/2015] [Indexed: 01/06/2023]
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228
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Bart MJ, van der Heide HGJ, Zeddeman A, Heuvelman K, van Gent M, Mooi FR. Complete Genome Sequences of 11 Bordetella pertussis Strains Representing the Pandemic ptxP3 Lineage. GENOME ANNOUNCEMENTS 2015; 3:e01394-15. [PMID: 26607899 PMCID: PMC4661318 DOI: 10.1128/genomea.01394-15] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Accepted: 10/16/2015] [Indexed: 01/31/2023]
Abstract
Pathogen adaptation has contributed to the resurgence of pertussis. To facilitate our understanding of this adaptation we report here 11 completely closed and annotated Bordetella pertussis genomes representing the pandemic ptxP3 lineage. Our analyses included six strains which do not produce the vaccine components pertactin and/or filamentous hemagglutinin.
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Affiliation(s)
- Marieke J Bart
- Department of Pediatrics, Laboratory of Pediatric Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands Centre for Infectious Diseases Control (CIb), National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Han G J van der Heide
- Centre for Infectious Diseases Control (CIb), National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Anne Zeddeman
- Department of Pediatrics, Laboratory of Pediatric Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands Centre for Infectious Diseases Control (CIb), National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Kees Heuvelman
- Centre for Infectious Diseases Control (CIb), National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Marjolein van Gent
- Centre for Infectious Diseases Control (CIb), National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Frits R Mooi
- Department of Pediatrics, Laboratory of Pediatric Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands Centre for Infectious Diseases Control (CIb), National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
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229
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Brotons P, de Paz HD, Esteva C, Latorre I, Muñoz-Almagro C. Validation of a loop-mediated isothermal amplification assay for rapid diagnosis of pertussis infection in nasopharyngeal samples. Expert Rev Mol Diagn 2015; 16:125-30. [PMID: 26565672 DOI: 10.1586/14737159.2016.1112741] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
OBJECTIVE To develop and validate a novel loop-mediated amplification (LAMP) assay for rapid diagnosis (<1 hour) of whooping cough in nasopharyngeal samples versus the gold standard: real-time PCR. METHODS The study included all nasopharyngeal samples (n = 213) collected from children with clinical suspicion of pertussis admitted to Children's University Hospital Sant Joan de Déu (Barcelona, Spain) during July-December 2014. Fresh samples were routinely analyzed by real-time PCR and stored for retrospective LAMP analysis, following an easy 30 minute DNA extraction step by Chelex-100. RESULTS Performance results of the LAMP assay were: linearity, 10(5)-10(1) CFU/ml; Limit of Detection, 2 CFU/ml; precision (mean CV), 7.38%; diagnostic sensitivity, 96.55%; diagnostic specificity, 99.46%; time to detection, 12-30 minutes. CONCLUSION The new test was shown to be 2.5-fold faster than real-time PCR while maintaining similar levels of analytical and clinical performance. Therefore it could become a useful diagnostic tool for molecular point-of-care testing.
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Affiliation(s)
- Pedro Brotons
- a Department of Molecular Microbiology , Hospital Sant Joan de Déu, University of Barcelona , Barcelona , Spain
| | - Hector D de Paz
- a Department of Molecular Microbiology , Hospital Sant Joan de Déu, University of Barcelona , Barcelona , Spain
| | - Cristina Esteva
- a Department of Molecular Microbiology , Hospital Sant Joan de Déu, University of Barcelona , Barcelona , Spain
| | - Irene Latorre
- a Department of Molecular Microbiology , Hospital Sant Joan de Déu, University of Barcelona , Barcelona , Spain
| | - Carmen Muñoz-Almagro
- a Department of Molecular Microbiology , Hospital Sant Joan de Déu, University of Barcelona , Barcelona , Spain
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230
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Nicholson TL, Shore SM, Register KB, Bayles DO, Kingsley RA, Brunelle BW. Comparative genomic analysis of the swine pathogen Bordetella bronchisepticastrain KM22. Vet Microbiol 2015; 182:87-94. [PMID: 26711033 PMCID: PMC7117204 DOI: 10.1016/j.vetmic.2015.10.026] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Revised: 10/22/2015] [Accepted: 10/27/2015] [Indexed: 11/01/2022]
Abstract
The well-characterized Bordetella bronchiseptica strain KM22, originally isolated from a pig with atrophic rhinitis, has been used to develop a reproducible swine respiratory disease model. The goal of this study was to identify genetic features unique to KM22 by comparing the genome sequence of KM22 to the laboratory reference strain RB50. To gain a broader perspective of the genetic relationship of KM22 among other B. bronchiseptica strains, selected genes of KM22 were then compared to five other B. bronchiseptica strains isolated from different hosts. Overall, the KM22 genome sequence is more similar to the genome sequences of the strains isolated from animals than the strains isolated from humans. The majority of virulence gene expression in Bordetella is positively regulated by the two-component sensory transduction system BvgAS. bopN, bvgA, fimB, and fimC were the most highly conserved BvgAS-regulated genes present in all seven strains analyzed. In contrast, the BvgAS-regulated genes present in all seven strains with the highest sequence divergence werefimN, fim2, fhaL, andfhaS. A total of eight major fimbrial subunit genes were identified in KM22. Quantitative real-time PCR data demonstrated that seven of the eight fimbrial subunit genes identified in KM22 are expressed and regulated by BvgAS. The annotation of the KM22 genome sequence, coupled with the comparative genomic analyses reported in this study, can be used to facilitate the development of vaccines with improved efficacy towards B. bronchiseptica in swine to decrease the prevalence and disease burden caused by this pathogen.
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Affiliation(s)
| | - Sarah M Shore
- National Animal Disease Center, ARS, USDA, Ames, IA, United States
| | - Karen B Register
- National Animal Disease Center, ARS, USDA, Ames, IA, United States
| | - Darrell O Bayles
- National Animal Disease Center, ARS, USDA, Ames, IA, United States
| | - Robert A Kingsley
- The Wellcome Trust Sanger Institute, the Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Brain W Brunelle
- National Animal Disease Center, ARS, USDA, Ames, IA, United States
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231
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Type Six Secretion System of Bordetella bronchiseptica and Adaptive Immune Components Limit Intracellular Survival During Infection. PLoS One 2015; 10:e0140743. [PMID: 26485303 PMCID: PMC4618060 DOI: 10.1371/journal.pone.0140743] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2015] [Accepted: 09/30/2015] [Indexed: 11/19/2022] Open
Abstract
The Type Six Secretion System (T6SS) is required for Bordetella bronchiseptica cytotoxicity, cytokine modulation, infection, and persistence. However, one-third of recently sequenced Bordetella bronchiseptica strains of the predominantly human-associated Complex IV have lost their T6SS through gene deletion or degradation. Since most human B. bronchiseptica infections occur in immunocompromised patients, we determine here whether loss of Type Six Secretion is beneficial to B. bronchiseptica during infection of immunocompromised mice. Infection of mice lacking adaptive immunity (Rag1-/- mice) with a T6SS-deficient mutant results in a hypervirulent phenotype that is characterized by high numbers of intracellular bacteria in systemic organs. In contrast, wild-type B. bronchiseptica kill their eukaryotic cellular hosts via a T6SS-dependent mechanism that prevents survival in systemic organs. High numbers of intracellular bacteria recovered from immunodeficient mice but only low numbers from wild-type mice demonstrates that B. bronchiseptica survival in an intracellular niche is limited by B and T cell responses. Understanding the nature of intracellular survival during infection, and its effects on the generation and function of the host immune response, are important to contain and control the spread of Bordetella-caused disease.
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232
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Park J, Zhang Y, Chen C, Dudley EG, Harvill ET. Diversity of secretion systems associated with virulence characteristics of the classical bordetellae. MICROBIOLOGY-SGM 2015; 161:2328-40. [PMID: 26459829 DOI: 10.1099/mic.0.000197] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Secretion systems are key virulence factors, modulating interactions between pathogens and the host's immune response. Six potential secretion systems (types 1-6; T1SS-T6SS) have been discussed in classical bordetellae, respiratory commensals/pathogens of mammals. The prototypical Bordetella bronchiseptica strain RB50 genome seems to contain all six systems, whilst two human-restricted subspecies, Bordetella parapertussis and Bordetella pertussis, have lost different subsets of these. This implicates secretion systems in the divergent evolutionary histories that have led to their success in different niches. Based on our previous work demonstrating that changes in secretion systems are associated with virulence characteristics, we hypothesized there would be substantial divergence of the loci encoding each amongst sequenced strains. Here, we describe extensive differences in secretion system loci; 10 of the 11 sequenced strains had lost subsets of genes or one entire secretion system locus. These loci contained genes homologous to those present in the respective loci in distantly related organisms, as well as genes unique to bordetellae, suggesting novel and/or auxiliary functions. The high degree of conservation of the T3SS locus, a complex machine with interdependent parts that must be conserved, stands in dramatic contrast to repeated loss of T5aSS 'autotransporters', which function as an autonomous unit. This comparative analysis provided insights into critical aspects of each pathogen's adaptation to its different niche, and the relative contributions of recombination, mutation and horizontal gene transfer. In addition, the relative conservation of various secretion systems is an important consideration in the ongoing search for more highly conserved protective antigens for the next generation of pertussis vaccines.
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Affiliation(s)
- Jihye Park
- 1 Department of Veterinary and Biomedical Sciences, Pennsylvania State University, University Park, PA, USA 2 Graduate Program in Bioinformatics and Genomics, Pennsylvania State University, University Park, PA, USA
| | - Ying Zhang
- 1 Department of Veterinary and Biomedical Sciences, Pennsylvania State University, University Park, PA, USA
| | - Chun Chen
- 3 Department of Food Science, Pennsylvania State University, University Park, PA, USA
| | - Edward G Dudley
- 3 Department of Food Science, Pennsylvania State University, University Park, PA, USA
| | - Eric T Harvill
- 1 Department of Veterinary and Biomedical Sciences, Pennsylvania State University, University Park, PA, USA 4 Singapore Centre on Environmental Life Sciences Engineering, Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
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233
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Abstract
The introduction of vaccination in the 1950s significantly reduced the morbidity and mortality of pertussis. However, since the 1990s, a resurgence of pertussis has been observed in vaccinated populations, and a number of causes have been proposed for this phenomenon, including improved diagnostics, increased awareness, waning immunity, and pathogen adaptation. The resurgence of pertussis highlights the importance of standardized, sensitive, and specific laboratory diagnoses, the lack of which is responsible for the large differences in pertussis notifications between countries. Accurate laboratory diagnosis is also important for distinguishing between the several etiologic agents of pertussis-like diseases, which involve both viruses and bacteria. If pertussis is diagnosed in a timely manner, antibiotic treatment of the patient can mitigate the symptoms and prevent transmission. During an outbreak, timely diagnosis of pertussis allows prophylactic treatment of infants too young to be (fully) vaccinated, for whom pertussis is a severe, sometimes fatal disease. Finally, reliable diagnosis of pertussis is required to reveal trends in the (age-specific) disease incidence, which may point to changes in vaccine efficacy, waning immunity, and the emergence of vaccine-adapted strains. Here we review current approaches to the diagnosis of pertussis and discuss their limitations and strengths. In particular, we emphasize that the optimal diagnostic procedure depends on the stage of the disease, the age of the patient, and the vaccination status of the patient.
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Affiliation(s)
- Anneke van der Zee
- Molecular Diagnostics Unit, Maasstad Hospital, Rotterdam, The Netherlands
| | | | - Frits R Mooi
- National Institute for Public Health and the Environment, Bilthoven, The Netherlands Laboratory of Pediatric Infectious Diseases, Department of Pediatrics, Radboud University Medical Centre, Nijmegen, The Netherlands
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234
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Carbonetti NH. Contribution of pertussis toxin to the pathogenesis of pertussis disease. Pathog Dis 2015; 73:ftv073. [PMID: 26394801 DOI: 10.1093/femspd/ftv073] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/16/2015] [Indexed: 12/19/2022] Open
Abstract
Pertussis toxin (PT) is a multisubunit protein toxin secreted by Bordetella pertussis, the bacterial agent of the disease pertussis or whooping cough. PT in detoxified form is a component of all licensed acellular pertussis vaccines, since it is considered to be an important virulence factor for this pathogen. PT inhibits G protein-coupled receptor signaling through Gi proteins in mammalian cells, an activity that has led to its widespread use as a cell biology tool. But how does this activity of PT contribute to pertussis, including the severe respiratory symptoms of this disease? In this minireview, the contribution of PT to the pathogenesis of pertussis disease will be considered based on evidence from both human infections and animal model studies. Although definitive proof of the role of PT in humans is lacking, substantial evidence supports the idea that PT is a major contributor to pertussis pathology, including the severe respiratory symptoms associated with this disease.
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Affiliation(s)
- Nicholas H Carbonetti
- Department of Microbiology and Immunology, University of Maryland Medical School, Baltimore, MD 21201, USA
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235
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Single Amino Acid Polymorphisms of Pertussis Toxin Subunit S2 (PtxB) Affect Protein Function. PLoS One 2015; 10:e0137379. [PMID: 26375454 PMCID: PMC4573519 DOI: 10.1371/journal.pone.0137379] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2014] [Accepted: 08/17/2015] [Indexed: 11/19/2022] Open
Abstract
Whooping cough due to Bordetella pertussis is increasing in incidence, in part due to accumulation of mutations which increase bacterial fitness in highly vaccinated populations. Polymorphisms in the pertussis toxin, ptxA and ptxB genes, and the pertactin, prn genes of clinical isolates of Bordetella pertussis collected in Cincinnati from 1989 through 2005 were examined. While the ptxA and prn genotypes were variable, all 48 strains had the ptxB2 genotype; ptxB1 encodes glycine at amino acid 18 of the S2 subunit of pertussis toxin, while ptxB2 encodes serine. We investigated antigenic and functional differences of PtxB1 and PtxB2. The S2 protein was not very immunogenic. Only a few vaccinated or individuals infected with B. pertussis developed antibody responses to the S2 subunit, and these sera recognized both polymorphic forms equally well. Amino acid 18 of S2 is in a glycan binding domain, and the PtxB forms displayed differences in receptor recognition and toxicity. PtxB1 bound better to the glycoprotein, fetuin, and Jurkat T cells in vitro, but the two forms were equally effective at promoting CHO cell clustering. To investigate in vivo activity of Ptx, one μg of Ptx was administered to DDY mice and blood was collected on 4 days after injection. PtxB2 was more effective at promoting lymphocytosis in mice.
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236
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Interspecies variations in Bordetella catecholamine receptor gene regulation and function. Infect Immun 2015; 83:4639-52. [PMID: 26371128 DOI: 10.1128/iai.00787-15] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Accepted: 09/10/2015] [Indexed: 11/20/2022] Open
Abstract
Bordetella bronchiseptica can use catecholamines to obtain iron from transferrin and lactoferrin via uptake pathways involving the BfrA, BfrD, and BfrE outer membrane receptor proteins, and although Bordetella pertussis has the bfrD and bfrE genes, the role of these genes in iron uptake has not been demonstrated. In this study, the bfrD and bfrE genes of B. pertussis were shown to be functional in B. bronchiseptica, but neither B. bronchiseptica bfrD nor bfrE imparted catecholamine utilization to B. pertussis. Gene fusion analyses found that expression of B. bronchiseptica bfrA was increased during iron starvation, as is common for iron receptor genes, but that expression of the bfrD and bfrE genes of both species was decreased during iron limitation. As shown previously for B. pertussis, bfrD expression in B. bronchiseptica was also dependent on the BvgAS virulence regulatory system; however, in contrast to the case in B. pertussis, the known modulators nicotinic acid and sulfate, which silence Bvg-activated genes, did not silence expression of bfrD in B. bronchiseptica. Further studies using a B. bronchiseptica bvgAS mutant expressing the B. pertussis bvgAS genes revealed that the interspecies differences in bfrD modulation are partly due to BvgAS differences. Mouse respiratory infection experiments determined that catecholamine utilization contributes to the in vivo fitness of B. bronchiseptica and B. pertussis. Additional evidence of the in vivo importance of the B. pertussis receptors was obtained from serologic studies demonstrating pertussis patient serum reactivity with the B. pertussis BfrD and BfrE proteins.
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237
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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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238
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Trainor EA, Nicholson TL, Merkel TJ. Bordetella pertussis transmission. Pathog Dis 2015; 73:ftv068. [PMID: 26374235 DOI: 10.1093/femspd/ftv068] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/17/2015] [Indexed: 11/14/2022] Open
Abstract
Bordetella pertussis and B. bronchiseptica are Gram-negative bacterial respiratory pathogens. Bordetella pertussis is the causative agent of whooping cough and is considered a human-adapted variant of B. bronchiseptica. Bordetella pertussis and B. bronchiseptica share mechanisms of pathogenesis and are genetically closely related. However, despite the close genetic relatedness, these Bordetella species differ in several classic fundamental aspects of bacterial pathogens such as host range, pathologies and persistence. The development of the baboon model for the study of B. pertussis transmission, along with the development of the swine and mouse model for the study of B. bronchiseptica, has enabled the investigation of different aspects of transmission including the route, attack rate, role of bacterial and host factors, and the impact of vaccination on transmission. This review will focus on B. pertussis transmission and how animal models of B. pertussis transmission and transmission models using the closely related B. bronchiseptica have increased our understanding of B. pertussis transmission.
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Affiliation(s)
- Elizabeth A Trainor
- Division of Bacterial, Parasitic and Allergenic Products, Center for Biologics Evaluation and Research, FDA, Bethesda, MD 20892, USA
| | - Tracy L Nicholson
- National Animal Disease Center, Agricultural Research Service, USDA, Ames, IA 50010, USA
| | - Tod J Merkel
- Division of Bacterial, Parasitic and Allergenic Products, Center for Biologics Evaluation and Research, FDA, Bethesda, MD 20892, USA
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239
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Transposase interaction with the β sliding clamp: effects on insertion sequence proliferation and transposition rate. Sci Rep 2015; 5:13329. [PMID: 26306550 PMCID: PMC4549789 DOI: 10.1038/srep13329] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Accepted: 07/23/2015] [Indexed: 01/05/2023] Open
Abstract
Insertion sequences (ISs) are ubiquitous and abundant mobile genetic elements in prokaryotic genomes. ISs often encode only one protein, the transposase, which catalyzes their transposition. Recent studies have shown that transposases of many different IS families interact with the β sliding clamp, a DNA replication factor of the host. However, it was unclear to what extent this interaction limits or favors the ability of ISs to colonize a chromosome from a phylogenetically-distant organism, or if the strength of this interaction affects the transposition rate. Here we describe the proliferation of a member of the IS1634 family in Acidiphilium over ~600 generations of cultured growth. We demonstrate that the purified transposase binds to the β sliding clamp of Acidiphilium, Leptospirillum and E. coli. Further, we also demonstrate that the Acidiphilium IS1634 transposase binds to the archaeal sliding clamp (PCNA) from Methanosarcina, and that the transposase encoded by Methanosarcina IS1634 binds to Acidiphilium β. Finally, we demonstrate that increasing the strength of the interaction between β and transposase results in a higher transposition rate in vivo. Our results suggest that the interaction could determine the potential of ISs to be mobilized in bacterial populations and also their ability to proliferate within chromosomes.
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240
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Belcher T, Preston A. Bordetella pertussis evolution in the (functional) genomics era. Pathog Dis 2015; 73:ftv064. [PMID: 26297914 DOI: 10.1093/femspd/ftv064] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/20/2015] [Indexed: 11/12/2022] Open
Abstract
The incidence of whooping cough caused by Bordetella pertussis in many developed countries has risen dramatically in recent years. This has been linked to the use of an acellular pertussis vaccine. In addition, it is thought that B. pertussis is adapting under acellular vaccine mediated immune selection pressure, towards vaccine escape. Genomics-based approaches have revolutionized the ability to resolve the fine structure of the global B. pertussis population and its evolution during the era of vaccination. Here, we discuss the current picture of B. pertussis evolution and diversity in the light of the current resurgence, highlight import questions raised by recent studies in this area and discuss the role that functional genomics can play in addressing current knowledge gaps.
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Affiliation(s)
- Thomas Belcher
- Department of Biology and Biochemistry, University of Bath, Bath BA2 7AY, UK
| | - Andrew Preston
- Department of Biology and Biochemistry, University of Bath, Bath BA2 7AY, UK
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241
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Xu Y, Liu B, Gröndahl-Yli-Hannuksila K, Tan Y, Feng L, Kallonen T, Wang L, Peng D, He Q, Wang L, Zhang S. Whole-genome sequencing reveals the effect of vaccination on the evolution of Bordetella pertussis. Sci Rep 2015; 5:12888. [PMID: 26283022 PMCID: PMC4539551 DOI: 10.1038/srep12888] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Accepted: 07/10/2015] [Indexed: 12/11/2022] Open
Abstract
Herd immunity can potentially induce a change of circulating viruses. However, it remains largely unknown that how bacterial pathogens adapt to vaccination. In this study, Bordetella pertussis, the causative agent of whooping cough, was selected as an example to explore possible effect of vaccination on the bacterial pathogen. We sequenced and analysed the complete genomes of 40 B. pertussis strains from Finland and China, as well as 11 previously sequenced strains from the Netherlands, where different vaccination strategies have been used over the past 50 years. The results showed that the molecular clock moved at different rates in these countries and in distinct periods, which suggested that evolution of the B. pertussis population was closely associated with the country vaccination coverage. Comparative whole-genome analyses indicated that evolution in this human-restricted pathogen was mainly characterised by ongoing genetic shift and gene loss. Furthermore, 116 SNPs were specifically detected in currently circulating ptxP3-containing strains. The finding might explain the successful emergence of this lineage and its spread worldwide. Collectively, our results suggest that the immune pressure of vaccination is one major driving force for the evolution of B. pertussis, which facilitates further exploration of the pathogenicity of B. pertussis.
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Affiliation(s)
- Yinghua Xu
- Key Laboratory of the Ministry of Health for Research on Quality and Standardization of Biotech Products, National Institutes of Food and Drug Control, Beijing 100050, P. R. China
| | - Bin Liu
- 1] TEDA School of Biological Sciences and Biotechnology, Nankai University, Tianjin 300457, P.R. China [2] Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, 23 Hongda Street, Tianjin 300457, P. R. China
| | | | - Yajun Tan
- Key Laboratory of the Ministry of Health for Research on Quality and Standardization of Biotech Products, National Institutes of Food and Drug Control, Beijing 100050, P. R. China
| | - Lu Feng
- 1] TEDA School of Biological Sciences and Biotechnology, Nankai University, Tianjin 300457, P.R. China [2] Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, 23 Hongda Street, Tianjin 300457, P. R. China
| | - Teemu Kallonen
- Department of Medical Microbiology and Immunology, Turku University, Turku 20520, Finland
| | - Lichan Wang
- Key Laboratory of the Ministry of Health for Research on Quality and Standardization of Biotech Products, National Institutes of Food and Drug Control, Beijing 100050, P. R. China
| | - Ding Peng
- 1] TEDA School of Biological Sciences and Biotechnology, Nankai University, Tianjin 300457, P.R. China [2] Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, 23 Hongda Street, Tianjin 300457, P. R. China
| | - Qiushui He
- 1] Department of Medical Microbiology and Immunology, Turku University, Turku 20520, Finland [2] Department of Infectious Disease Surveillance and Control, National Institute for Health and Welfare, Turku 20520, Finland [3] Department of Medical Microbiology, Capital Medical University, Beijing 100069, P. R. China
| | - Lei Wang
- 1] TEDA School of Biological Sciences and Biotechnology, Nankai University, Tianjin 300457, P.R. China [2] Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, 23 Hongda Street, Tianjin 300457, P. R. China [3] State Key Laboratory of Medicinal Chemical Biology, Nankai University 300457, Tianjin, P. R. China
| | - Shumin Zhang
- Key Laboratory of the Ministry of Health for Research on Quality and Standardization of Biotech Products, National Institutes of Food and Drug Control, Beijing 100050, P. R. China
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242
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Arias-Palomo E, Berger JM. An Atypical AAA+ ATPase Assembly Controls Efficient Transposition through DNA Remodeling and Transposase Recruitment. Cell 2015; 162:860-71. [PMID: 26276634 PMCID: PMC4537775 DOI: 10.1016/j.cell.2015.07.037] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2015] [Revised: 04/21/2015] [Accepted: 06/24/2015] [Indexed: 01/27/2023]
Abstract
Transposons are ubiquitous genetic elements that drive genome rearrangements, evolution, and the spread of infectious disease and drug-resistance. Many transposons, such as Mu, Tn7, and IS21, require regulatory AAA+ ATPases for function. We use X-ray crystallography and cryo-electron microscopy to show that the ATPase subunit of IS21, IstB, assembles into a clamshell-shaped decamer that sandwiches DNA between two helical pentamers of ATP-associated AAA+ domains, sharply bending the duplex into a 180° U-turn. Biochemical studies corroborate key features of the structure and further show that the IS21 transposase, IstA, recognizes the IstB•DNA complex and promotes its disassembly by stimulating ATP hydrolysis. Collectively, these studies reveal a distinct manner of higher-order assembly and client engagement by a AAA+ ATPase and suggest a mechanistic model where IstB binding and subsequent DNA bending primes a selected insertion site for efficient transposition.
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Affiliation(s)
- Ernesto Arias-Palomo
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - James M Berger
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
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243
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Abe A, Nishimura R, Tanaka N, Kurushima J, Kuwae A. The Bordetella Secreted Regulator BspR Is Translocated into the Nucleus of Host Cells via Its N-Terminal Moiety: Evaluation of Bacterial Effector Translocation by the Escherichia coli Type III Secretion System. PLoS One 2015; 10:e0135140. [PMID: 26247360 PMCID: PMC4527748 DOI: 10.1371/journal.pone.0135140] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2015] [Accepted: 07/17/2015] [Indexed: 11/27/2022] Open
Abstract
Bordetella bronchiseptica is genetically related to B. pertussis and B. parapertussis, which cause respiratory tract infections in humans. These pathogens possess a large number of virulence factors, including the type III secretion system (T3SS), which is required for the delivery of effectors into the host cells. In a previous study, we identified a transcriptional regulator, BspR, that is involved in the regulation of the T3SS-related genes in response to iron-starved conditions. A unique feature of BspR is that this regulator is secreted into the extracellular milieu via the T3SS. To further characterize the role of BspR in extracellular localization, we constructed various truncated derivatives of BspR and investigated their translocation into the host cells using conventional translocation assays. In this study, the effector translocation was evaluated by the T3SS of enteropathogenic E. coli (EPEC), since the exogenous expression of BspR triggers severe repression of the Bordetella T3SS expression. The results of the translocation assays using the EPEC T3SS showed that the N-terminal 150 amino acid (aa) residues of BspR are sufficient for translocation into the host cells in a T3SS-dependent manner. In addition, exogenous expression of BspR in HeLa cells demonstrated that the N-terminal 100 aa residues are involved in the nuclear localization. In contrast, the N-terminal 54 aa residues are sufficient for the extracellular secretion into the bacterial culture supernatant via the EPEC T3SS. Thus, BspR is not only a transcriptional regulator in bacteria cytosol, but also functions as an effector that translocates into the nuclei of infected host cells.
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Affiliation(s)
- Akio Abe
- Laboratory of Bacterial Infection, Graduate School of Infection Control Sciences, Kitasato University, Tokyo 108-8641, Japan
- * E-mail:
| | - Ryutaro Nishimura
- Laboratory of Bacterial Infection, Graduate School of Infection Control Sciences, Kitasato University, Tokyo 108-8641, Japan
| | - Naomichi Tanaka
- Laboratory of Bacterial Infection, Graduate School of Infection Control Sciences, Kitasato University, Tokyo 108-8641, Japan
| | - Jun Kurushima
- Laboratory of Bacterial Infection, Graduate School of Infection Control Sciences, Kitasato University, Tokyo 108-8641, Japan
| | - Asaomi Kuwae
- Laboratory of Bacterial Infection, Graduate School of Infection Control Sciences, Kitasato University, Tokyo 108-8641, Japan
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244
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Bouchez V, Guiso N. Bordetella pertussis,B. parapertussis, vaccines and cycles of whooping cough. Pathog Dis 2015; 73:ftv055. [DOI: 10.1093/femspd/ftv055] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/20/2015] [Indexed: 11/12/2022] Open
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245
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Evaluation of MALDI-ToF as a method for the identification of bacteria in the veterinary diagnostic laboratory. Res Vet Sci 2015; 101:42-9. [DOI: 10.1016/j.rvsc.2015.05.018] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Revised: 04/30/2015] [Accepted: 05/30/2015] [Indexed: 11/23/2022]
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246
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McMahon G, Ring SM, Davey-Smith G, Timpson NJ. Genome-wide association study identifies SNPs in the MHC class II loci that are associated with self-reported history of whooping cough. Hum Mol Genet 2015; 24:5930-9. [PMID: 26231221 PMCID: PMC4581602 DOI: 10.1093/hmg/ddv293] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2015] [Accepted: 07/17/2015] [Indexed: 11/23/2022] Open
Abstract
Whooping cough is currently seeing resurgence in countries despite high vaccine coverage. There is considerable variation in subject-specific response to infection and vaccine efficacy, but little is known about the role of human genetics. We carried out a case–control genome-wide association study of adult or parent-reported history of whooping cough in two cohorts from the UK: the ALSPAC cohort and the 1958 British Birth Cohort (815/758 cases and 6341/4308 controls, respectively). We also imputed HLA alleles using dense SNP data in the MHC region and carried out gene-based and gene-set tests of association and estimated the amount of additive genetic variation explained by common SNPs. We observed a novel association at SNPs in the MHC class II region in both cohorts [lead SNP rs9271768 after meta-analysis, odds ratio [95% confidence intervals (CIs)] 1.47 (1.35, 1.6), P-value 1.21E − 18]. Multiple strong associations were also observed at alleles at the HLA class II loci. The majority of these associations were explained by the lead SNP rs9271768. Gene-based and gene-set tests and estimates of explainable common genetic variation could not establish the presence of additional associations in our sample. Genetic variation at the MHC class II region plays a role in susceptibility to whooping cough. These findings provide additional perspective on mechanisms of whooping cough infection and vaccine efficacy.
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Affiliation(s)
| | - Susan M Ring
- School of Social and Community Medicine and MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
| | - George Davey-Smith
- School of Social and Community Medicine and MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
| | - Nicholas J Timpson
- School of Social and Community Medicine and MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
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247
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Bolotin S, Deeks SL, Marchand-Austin A, Rilkoff H, Dang V, Walton R, Hashim A, Farrell D, Crowcroft NS. Correlation of Real Time PCR Cycle Threshold Cut-Off with Bordetella pertussis Clinical Severity. PLoS One 2015; 10:e0133209. [PMID: 26186564 PMCID: PMC4505870 DOI: 10.1371/journal.pone.0133209] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2014] [Accepted: 06/24/2015] [Indexed: 11/18/2022] Open
Abstract
Bordetella pertussis testing performed using real-time polymerase chain reaction (RT-PCR) is interpreted based on a cycle threshold (Ct) value. At Public Health Ontario Laboratories (PHOL), a Ct value <36 is reported as positive, and Ct values ≥36 and <40 are reported as indeterminate. PHOL reported indeterminate results to physicians and public health units until May 2012, after which these results were only reported to physicians. We investigated the association between Ct value and disease symptom and severity to examine the significance of indeterminate results clinically, epidemiologically and for public health reporting. B. pertussis positive and indeterminate RT-PCR results were linked to pertussis cases reported in the provincial Integrated Public Health Information System (iPHIS), using deterministic linkage. Patients with positive RT-PCR results had a lower median age of 10.8 years compared to 12.0 years for patients with indeterminate results (p = 0.24). Hospitalized patients had significantly lower Ct values than non-hospitalized patients (median Ct values of 20.7 vs. 31.6, p<0.001). The proportion of patients reporting the most indicative symptoms of pertussis did not differ between patients with positive vs. indeterminate RT-PCR results. Taking the most indicative symptoms of pertussis as the gold-standard, the positive predictive value of the RT-PCR test was 68.1%. RT-PCR test results should be interpreted in the context of the clinical symptoms, age, vaccination status, prevalence, and other factors. Further information on interpretation of indeterminate RT-PCR results may be needed, and the utility of reporting to public health practitioners should be re-evaluated.
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Affiliation(s)
- Shelly Bolotin
- Public Health Ontario, Toronto, Ontario, Canada
- Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada
| | - Shelley L. Deeks
- Public Health Ontario, Toronto, Ontario, Canada
- Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada
| | - Alex Marchand-Austin
- Public Health Ontario, Toronto, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | | | - Vica Dang
- Public Health Ontario, Toronto, Ontario, Canada
| | - Ryan Walton
- Public Health Ontario, Toronto, Ontario, Canada
| | | | - David Farrell
- Public Health Ontario, Toronto, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Natasha S. Crowcroft
- Public Health Ontario, Toronto, Ontario, Canada
- Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
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248
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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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249
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Hester SE, Goodfield LL, Park J, Feaga HA, Ivanov YV, Bendor L, Taylor DL, Harvill ET. Host Specificity of Ovine Bordetella parapertussis and the Role of Complement. PLoS One 2015; 10:e0130964. [PMID: 26158540 PMCID: PMC4497623 DOI: 10.1371/journal.pone.0130964] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2014] [Accepted: 05/27/2015] [Indexed: 11/30/2022] Open
Abstract
The classical bordetellae are comprised of three subspecies that differ from broad to very limited host specificity. Although several lineages appear to have specialized to particular host species, most retain the ability to colonize and grow in mice, providing a powerful common experimental model to study their differences. One of the subspecies, Bordetella parapertussis, is composed of two distinct clades that have specialized to different hosts: one to humans (Bpphu), and the other to sheep (Bppov). While Bpphu and the other classical bordetellae can efficiently colonize mice, Bppov strains are severely defective in their ability to colonize the murine respiratory tract. Bppov genomic analysis did not reveal the loss of adherence genes, but substantial mutations and deletions of multiple genes involved in the production of O-antigen, which is required to prevent complement deposition on B. bronchiseptica and Bpphu strains. Bppov lacks O-antigen and, like O-antigen mutants of other bordetellae, is highly sensitive to murine complement-mediated killing in vitro. Based on these results, we hypothesized that Bppov failed to colonize mice because of its sensitivity to murine complement. Consistent with this, the Bppov defect in the colonization of wild type mice was not observed in mice lacking the central complement component C3. Furthermore, Bppov strains were highly susceptible to killing by murine complement, but not by sheep complement. These data demonstrate that the failure of Bppov to colonize mice is due to sensitivity to murine, but not sheep, complement, providing a mechanistic example of how specialization that accompanies expansion in one host can limit host range.
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Affiliation(s)
- Sara E. Hester
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, Pennsylvania, United States of America
- Graduate Program in Biochemistry, Microbiology and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Laura L. Goodfield
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, Pennsylvania, United States of America
- Graduate Program in Immunology and Infectious Disease, The Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Jihye Park
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, Pennsylvania, United States of America
- Graduate Program in Bioinformatics and Genomics, The Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Heather A. Feaga
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, Pennsylvania, United States of America
- Graduate Program in Biochemistry, Microbiology and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Yury V. Ivanov
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Liron Bendor
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, Pennsylvania, United States of America
- Graduate Program in Genetics, The Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Dawn L. Taylor
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Eric T. Harvill
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, Pennsylvania, United States of America
- * E-mail:
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250
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Andrade BGN, Marin MFA, Cambuy DD, Fonseca EL, Souza NF, Vicente ACP. Complete genome sequence of a clinical Bordetella pertussis isolate from Brazil. Mem Inst Oswaldo Cruz 2015; 109:972-4. [PMID: 25411007 PMCID: PMC4296508 DOI: 10.1590/0074-0276140288] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2014] [Accepted: 10/07/2014] [Indexed: 11/26/2022] Open
Abstract
There has been a resurgence in the number of pertussis cases in Brazil and around the
world. Here, the genome of a clinical Bordetella pertussis strain (Bz181) that was
recently isolated in Brazil is reported. Analysis of the virulence-associated genes
defining the pre- and post-vaccination lineages revealed the presence of the
prn2-ptxS1A-fim3B-ptxP3 allelic profile in Bz181, which is characteristic of the
current pandemic lineage. A putative metallo-β-lactamase gene presenting all of the
conserved zinc-binding motifs that characterise the catalytic site was identified, in
addition to a multidrug efflux pump of the RND family that could confer resistance to
erythromycin, which is the antibiotic of choice for treating pertussis disease.
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Affiliation(s)
- Bruno Gabriel N Andrade
- Laboratório de Genética Molecular de Microorganismos, Instituto Oswaldo Cruz-Fiocruz, Rio de Janeiro, RJ, Brasil
| | - Michel F Abanto Marin
- Laboratório de Genética Molecular de Microorganismos, Instituto Oswaldo Cruz-Fiocruz, Rio de Janeiro, RJ, Brasil
| | - Diego Duque Cambuy
- Laboratório de Genética Molecular de Microorganismos, Instituto Oswaldo Cruz-Fiocruz, Rio de Janeiro, RJ, Brasil
| | - Erica Lourenço Fonseca
- Laboratório de Genética Molecular de Microorganismos, Instituto Oswaldo Cruz-Fiocruz, Rio de Janeiro, RJ, Brasil
| | | | - Ana Carolina P Vicente
- Laboratório de Genética Molecular de Microorganismos, Instituto Oswaldo Cruz-Fiocruz, Rio de Janeiro, RJ, Brasil
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