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Fu P, Li Y, Qin J, Xie L, Yang C, Wang C. Molecular epidemiology and genomic features of Bordetella parapertussis in Shanghai, China, 2017-2022. Front Microbiol 2024; 15:1428766. [PMID: 39044958 PMCID: PMC11263204 DOI: 10.3389/fmicb.2024.1428766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Accepted: 06/28/2024] [Indexed: 07/25/2024] Open
Abstract
Background Pertussis is a highly contagious respiratory illness mainly caused by Bordetella pertussis (BP). Bordetella parapertussis (BPP) can induce symptoms compatible with pertussis, but has been underdiagnosed and underreported. The current pertussis vaccines offer low protection against BPP. Herein, we aim to reveal the epidemiology and genomic evolution of BPP in Shanghai, China. Methods Children diagnosed with BPP infection from January 2017 to December 2022 in Shanghai, China were enrolled. We performed antimicrobial susceptibility testing (AST), multiple locus variable-number tandem repeat analysis (MLVA), and whole genome sequencing (WGS) analysis. A total of 260 international BPP genomes were chosen for comparison to investigate the genomic diversity and phylogenetic characteristics of Chinese strains within a global context. Results Sixty patients were diagnosed with BPP infection by culture, with the positive ratio of 3.5‰ (60/17337) for BPP in nasopharyngeal swap samples. The average age of patients was 4.5 ± 0.3 years. BPPs contained four MLVA types including MT6 (65.0%), MT4 (26.7%), untype-1 (6.7%) and MT5 (1.7%), and none of strains showed resistance to macrolides. All strains carried virulence genotype of ptxP37/ptxA13/ptxB3/ptxC3/ptxD3/ptxE3/fim2-2/fim3-10. MT4 and MT5 strains carried prn54, whereas MT6 and untype-1 BPPs expressed prn101. We identified two outbreaks after 2020 caused by MT4 and MT6 strains, each corresponding to distinct WGS-based phylogenetic lineages. The MT4-lineage is estimated to have originated around 1991 and has since spread globally, being introduced to China between 2005 and 2010. In contrast, the MT6-lineage was exclusively identified in China and is inferred to have originated around 2002. Conclusion We revealed the genomic diversity of BPPs circulating in Shanghai, China, and reported the outbreaks of MT6 and MT4 BPPs after 2020. This is the first report on the emergence and regional outbreak of MT6 BPPs in the world, indicating that continuous surveillance on BPPs are thus required.
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Affiliation(s)
- Pan Fu
- Laboratory of Microbiology, Department of Clinical Laboratory, Children’s Hospital of Fudan University, National Children's Medical Center, Shanghai, China
- Nosocomial Infection Control Department, Children’s Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Yijia Li
- Laboratory of Microbiology, Department of Clinical Laboratory, Children’s Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Jie Qin
- Laboratory of Microbiology, Department of Clinical Laboratory, Children’s Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Li Xie
- CAS Key Laboratory of Molecular Virology and Immunology, The Center for Microbes, Development and Health, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai, China
| | - Chao Yang
- CAS Key Laboratory of Molecular Virology and Immunology, The Center for Microbes, Development and Health, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai, China
| | - Chuanqing Wang
- Laboratory of Microbiology, Department of Clinical Laboratory, Children’s Hospital of Fudan University, National Children's Medical Center, Shanghai, China
- Nosocomial Infection Control Department, Children’s Hospital of Fudan University, National Children's Medical Center, Shanghai, China
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Cardoso MJ, Rouhani D, Cabal Rosel A, Daza Prieto B, Hopfgartner M, Stöger A, Hasenberger P, Stadlbauer S, Moesenbacher T, Hyden P, Wiedermann U, Schmid D, Ruppitsch W. Complete genome sequence of Bordetella parapertussis strain 400431-b, isolated from a protracted course of whooping cough in Austria, 2023. Microbiol Resour Announc 2024; 13:e0097623. [PMID: 38018846 DOI: 10.1128/mra.00976-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Accepted: 10/26/2023] [Indexed: 11/30/2023] Open
Abstract
Here, we report the complete genome of Bordetella parapertussis strain 400431-b isolated from a nasopharyngeal swab from a 4-year-old patient presenting with a protracted course of whooping cough, vaccinated with three doses of diphtheria-tetanus-acellular pertussis-hepatitis B-poliomyelitis-Haemophilus influenzae type b vaccine.
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Affiliation(s)
- Maria João Cardoso
- Institute of Medical Microbiology and Hygiene, Austrian Agency for Health and Food Safety , Vienna, Austria
- ECDC Fellowship Programme, Public Health Microbiology path (EUPHEM), European Centre for Disease Prevention and Control (ECDC) , Stockholm, Sweden
| | | | - Adriana Cabal Rosel
- Institute of Medical Microbiology and Hygiene, Austrian Agency for Health and Food Safety , Vienna, Austria
| | - Beatriz Daza Prieto
- Institute of Medical Microbiology and Hygiene, Austrian Agency for Health and Food Safety , Vienna, Austria
- Institute of Chemical, Environmental, and Bioscience Engineering, Research Area of Biochemical Technology, Technical University of Vienna , Vienna, Austria
| | - Miriam Hopfgartner
- Institute of Medical Microbiology and Hygiene, Austrian Agency for Health and Food Safety , Vienna, Austria
| | - Anna Stöger
- Institute of Medical Microbiology and Hygiene, Austrian Agency for Health and Food Safety , Vienna, Austria
| | - Petra Hasenberger
- Institute of Medical Microbiology and Hygiene, Austrian Agency for Health and Food Safety , Vienna, Austria
| | - Silke Stadlbauer
- Institute of Medical Microbiology and Hygiene, Austrian Agency for Health and Food Safety , Vienna, Austria
| | - Tobias Moesenbacher
- Institute of Medical Microbiology and Hygiene, Austrian Agency for Health and Food Safety , Vienna, Austria
| | - Patrick Hyden
- Institute of Medical Microbiology and Hygiene, Austrian Agency for Health and Food Safety , Vienna, Austria
| | - Ursula Wiedermann
- Institute of Specific Prophylaxis and Tropical Medicine, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna , Vienna, Austria
| | - Daniela Schmid
- Division of Infection Diagnosis and Infectious Disease Epidemiology, Center of Pathophysiology, Infectiology and Immunology, Medical University of Vienna , Vienna, Austria
| | - Werner Ruppitsch
- Institute of Medical Microbiology and Hygiene, Austrian Agency for Health and Food Safety , Vienna, Austria
- Department of Biotechnology, University of Natural Resources and Life Sciences , Vienna, Austria
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Shuai X, Zhou Z, Ba X, Lin Y, Lin Z, Liu Z, Yu X, Zhou J, Zeng G, Ge Z, Chen H. Bacteriophages: Vectors of or weapons against the transmission of antibiotic resistance genes in hospital wastewater systems? WATER RESEARCH 2024; 248:120833. [PMID: 37952327 DOI: 10.1016/j.watres.2023.120833] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 10/26/2023] [Accepted: 11/03/2023] [Indexed: 11/14/2023]
Abstract
Antimicrobial resistance poses a serious threat to human health and is responsible for the death of millions of people annually. Hospital wastewater is an important hotspot for antibiotic-resistance genes (ARGs) and antibiotic-resistant bacteria (ARB). However, little is known about the relationship between phages and ARGs in hospital wastewater systems (HWS). In the present study, the viral diversity of 12 HWSs using data from public metagenomic databases was investigated. Viruses were widely found in both the influent and effluent of each HWS. A total of 45 unique ARGs were carried by 85 viral contigs, which accounted for only 0.14% of the total viral populations, implying that ARGs were not commonly present in phages. Three efflux pump genes were identified as shared between phages and bacterial genomes. However, the predominant types of ARGs in HWS such as aminoglycoside- and beta-lactam-resistance genes were rarely found in phages. Based on CRISPR spacer and tRNA matches, interactions between 171 viral contigs and 60 antibiotic-resistant genomes were predicted, including interactions involving phages and vancomycin-resistant Enterococcus_B faecium or beta-lactam-resistant Klebsiella pneumoniae. More than half (56.1%) of these viral contigs indicated lytic and none of them carried ARGs. As the vOTUs in this study had few ARGs and were primarily lytic, HWS may be a valuable source for phage discovery. Future studies will be able to experimentally validate these sequence-based results to confirm the suitability of HWS phages for pathogen control measures in wastewater.
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Affiliation(s)
- Xinyi Shuai
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Zhenchao Zhou
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Xiaoliang Ba
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Yanhan Lin
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Zejun Lin
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Zhe Liu
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Xi Yu
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Jinyu Zhou
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Guangshu Zeng
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Ziye Ge
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Hong Chen
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China; International Cooperation Base of Environmental Pollution and Ecological Health, Science and Technology Agency of Zhejiang, Zhejiang University, China; Key Laboratory of Environment Remediation and Ecological Health, Ministry of Education, College of Environmental Resource Sciences, Zhejiang University, Hangzhou, China.
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Yılmaz Çolak Ç, Tefon Öztürk BE. Bordetella pertussis and outer membrane vesicles. Pathog Glob Health 2023; 117:342-355. [PMID: 36047634 PMCID: PMC10177744 DOI: 10.1080/20477724.2022.2117937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022] Open
Abstract
Bordetella pertussis is the causative agent of a respiratory infection called pertussis (whooping cough) that can be fatal in newborns and infants. The pathogen produces a variety of antigenic compounds which alone or simultaneously can damage various host cells. Despite the availability of pertussis vaccines and high vaccination coverage around the world, a resurgence of the disease has been observed in many countries. Reasons for the increase in pertussis cases may include increased awareness, improved diagnostic techniques, low vaccine efficacy, especially acellular vaccines, and waning immunity. Many efforts have been made to develop more effective strategies to fight against B. pertussis and one of the strategies is the use of outer membrane vesicles (OMVs) in vaccine formulations. OMVs are attracting great interest as vaccine platforms since they can carry immunogenic structures such as toxins and LPS. Many studies have been carried out with OMVs from different B. pertussis strains and they revealed promising results in the animal challenge and human preclinical model. However, the composition of OMVs differs in terms of isolation and purification methods, strains, culture, and stress conditions. Although the vesicles from B. pertussis represent an attractive pertussis vaccine candidate, further studies are needed to advance clinical research for next-generation pertussis vaccines. This review summarizes general information about pertussis, the history of vaccines against the disease, and the immune response to these vaccines, with a focus on OMVs. We discuss progress in developing an OMV-based pertussis vaccine platform and highlight successful applications as well as potential challenges and gaps.
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Safarchi A, Saedi S, Tay CY, Lamichhane B, Nakhost Lotfi M, Shahcheraghi F. Genome Characteristic of Bordetella parapertussis Isolated from Iran. Curr Microbiol 2022; 79:314. [PMID: 36088519 PMCID: PMC9464130 DOI: 10.1007/s00284-022-03009-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 08/23/2022] [Indexed: 11/28/2022]
Abstract
AbstractPertussis also known as whooping cough is a respiratory infection in humans particularly with severe symptoms in infants and usually caused by Bordetella pertussis. However, Bordetella parapertussis can also cause a similar clinical syndrome. During 2012 to 2015, from nasal swabs sent from different provinces to the pertussis reference laboratory of Pasture Institute of Iran for pertussis confirmation, seven B. parapertussis isolates were identified by bacterial culture, biochemical tests, and the presence of IS1001 insertion in the genome. The expression of pertactin (Prn) as one the major virulence factor for bacterial adhesion was investigated using western blot. Moreover, the genomic characteristic of one recently collected isolate, IRBP134, from a seven-month infant was investigated using Illumina NextSeq sequencing protocol. The results revealed the genome with G+C content 65% and genome size 4.7 Mbp. A total of 81 single nucleotide polymorphisms and 13 short insertions and deletions were found in the genome compared to the B. parapertussis 12822 as a reference genome showing ongoing evolutionary changes. A phylogeny relationship of IRBP134 was also investigated using global B. parapertussis available genomes.
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Affiliation(s)
- Azadeh Safarchi
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052 Australia
- Department of Bacteriology, Pasteur Institute of Iran, Tehran, 1316943551 Islamic Republic of Iran
| | - Samaneh Saedi
- Department of Bacteriology, Pasteur Institute of Iran, Tehran, 1316943551 Islamic Republic of Iran
| | - Chin Yen Tay
- The Marshal Centre for Infectious Disease Research and Training, University of Western Australia, Perth, WA 6009 Australia
| | - Binit Lamichhane
- The Marshal Centre for Infectious Disease Research and Training, University of Western Australia, Perth, WA 6009 Australia
| | - Masoumeh Nakhost Lotfi
- Department of Bacteriology, Pasteur Institute of Iran, Tehran, 1316943551 Islamic Republic of Iran
| | - Fereshteh Shahcheraghi
- Department of Bacteriology, Pasteur Institute of Iran, Tehran, 1316943551 Islamic Republic of Iran
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Kamachi K, Otsuka N, Fumimoto R, Ozawa K, Yao SM, Chiang CS, Luu LDW, Lan R, Shibayama K, Watanabe M. A novel multilocus variable-number tandem repeat analysis for Bordetella parapertussis. J Med Microbiol 2019; 68:1671-1676. [PMID: 31613204 DOI: 10.1099/jmm.0.001095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Purpose. Human-adapted Bordetella parapertussis is one of the causative agents of whooping cough; however, there are currently no genotyping systems with high discriminatory power for this bacterial pathogen. We therefore aimed to develop a multilocus variable-number tandem repeat analysis (MLVA) for human-adapted B. parapertussis.Methodology. Four highly polymorphic variable number tandem repeat (VNTR) loci in the B. parapertussis genome were selected and amplified by multiplex PCR. MLVA was performed based on the number of tandem repeats at VNTR loci. The discriminatory power of MLVA was evaluated with three laboratory reference strains and 50 human isolates of B. parapertussis.Results. Multiplex PCR-based MLVA characterized 53 B. parapertussis reference strains and isolates into 25 MLVA types and the Simpson diversity index was 0.91 (95 % confidence interval, 0.86-0.97). The three reference strains exhibited different MLVA types. Thirty-one Japanese isolates, ten French isolates and three Taiwanese isolates belonged to fourteen, nine and three MLVA types, respectively. In contrast, all five Australian isolates belonged to the same type. Two Japanese isolates collected from patients with known epidemiological links had the same type.Conclusion. Our novel MLVA method has high discriminatory power for genotyping human B. parapertussis. Regarding this organism, this genotyping system is a promising tool for epidemiological surveillance and investigating outbreaks.
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Affiliation(s)
- Kazunari Kamachi
- Department of Bacteriology II, National Institute of Infectious Diseases, Tokyo, Japan
| | - Nao Otsuka
- Department of Bacteriology II, National Institute of Infectious Diseases, Tokyo, Japan
| | - Rei Fumimoto
- Department of Pediatrics, St Marianna University School of Medicine, Kawasaki, Japan.,Department of Bacteriology II, National Institute of Infectious Diseases, Tokyo, Japan
| | - Kensuke Ozawa
- R & D Center for Diagnostic Reagents, Denka Seiken, Niigata, Japan
| | - Shu-Man Yao
- Center for Diagnostics and Vaccine Development, Centers for Disease Control, Taipei, Taiwan, ROC
| | - Chuen-Sheue Chiang
- Center for Diagnostics and Vaccine Development, Centers for Disease Control, Taipei, Taiwan, ROC
| | - Laurence Don Wai Luu
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia
| | - Ruiting Lan
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia
| | - Keigo Shibayama
- Department of Bacteriology II, National Institute of Infectious Diseases, Tokyo, Japan
| | - Mineo Watanabe
- Present address: Division of Microbiology and Molecular Cell Biology, Nihon Pharmaceutical University, Saitama, Japan.,Graduate School of Infection Control Sciences, Kitasato University, Tokyo, Japan
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