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Peng Y, Williams MM, Xiaoli L, Simon A, Fueston H, Tondella ML, Weigand MR. Strengthening Bordetella pertussis genomic surveillance by direct sequencing of residual positive specimens. J Clin Microbiol 2024; 62:e0165323. [PMID: 38445858 PMCID: PMC11005353 DOI: 10.1128/jcm.01653-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Accepted: 02/12/2024] [Indexed: 03/07/2024] Open
Abstract
Whole-genome sequencing (WGS) of microbial pathogens recovered from patients with infectious disease facilitates high-resolution strain characterization and molecular epidemiology. However, increasing reliance on culture-independent methods to diagnose infectious diseases has resulted in few isolates available for WGS. Here, we report a novel culture-independent approach to genome characterization of Bordetella pertussis, the causative agent of pertussis and a paradigm for insufficient genomic surveillance due to limited culture of clinical isolates. Sequencing libraries constructed directly from residual pertussis-positive diagnostic nasopharyngeal specimens were hybridized with biotinylated RNA "baits" targeting B. pertussis fragments within complex mixtures that contained high concentrations of host and microbial background DNA. Recovery of B. pertussis genome sequence data was evaluated with mock and pooled negative clinical specimens spiked with reducing concentrations of either purified DNA or inactivated cells. Targeted enrichment increased the yield of B. pertussis sequencing reads up to 90% while simultaneously decreasing host reads to less than 10%. Filtered sequencing reads provided sufficient genome coverage to perform characterization via whole-genome single nucleotide polymorphisms and whole-genome multilocus sequencing typing. Moreover, these data were concordant with sequenced isolates recovered from the same specimens such that phylogenetic reconstructions from either consistently clustered the same putatively linked cases. The optimized protocol is suitable for nasopharyngeal specimens with diagnostic IS481 Ct < 35 and >10 ng DNA. Routine implementation of these methods could strengthen surveillance and study of pertussis resurgence by capturing additional cases with genomic characterization.
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Affiliation(s)
- Yanhui Peng
- Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Margaret M. Williams
- Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | | | - Ashley Simon
- Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Heather Fueston
- Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Maria L. Tondella
- Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Michael R. Weigand
- Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
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Ding X, Lan W, Li J, Deng M, Li Y, Katayama Y, Gu JD. Metagenomic insight into the pathogenic-related characteristics and resistome profiles within microbiome residing on the Angkor sandstone monuments in Cambodia. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 918:170402. [PMID: 38307295 DOI: 10.1016/j.scitotenv.2024.170402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 01/06/2024] [Accepted: 01/22/2024] [Indexed: 02/04/2024]
Abstract
To reveal the characteristics of indigenous microbiome including the pathogenic-related ones on Angkor monuments in Cambodia and the distribution pattern of resistome at different locations, several sites, namely Angkor Wat, Bayon of Angkor Thom, and Prasat Preah Vihear with different exposure levels to tourists were selected to conduct the metagenomic analysis in this study. The general characteristics of the microbiome on these monuments were revealed, and the association between the environmental geo-ecological feature and the indigenous microbiome was delineated. The most common microbial groups included 6 phyla, namely Acidobacteria, Actinobacteria, Gemmatimonadetes, Nitrospirae, Proteobacteria and Verrucomicrobia on the monuments, but Firmicutes and Chlamydiae were the most dominant phyla found in bats droppings. The taxonomic family of Chitinophagaceae could serve as a signature microbial group for Preah Vihear, the less visited site. More importantly, the pathogenic-related characteristics of the microbiome residing on Angkor monuments were uncovered. A set of specific antibiotic resistance genes (ARGs) with cross-niches dispersal capacity (between the environmental microbiome and the microbiome within warm blood fauna) was identified to be high by the source tracking analysis based on ARGs profile varies in this study. Among the 10 ARG-types detected in this study, 6 of them are confined to resistance mechanism of antibiotic efflux-pump. The findings of this study provide new a new direction on public health management and implication globally at archaeological sites for tourism.
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Affiliation(s)
- Xinghua Ding
- School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong, China; School of History and Culture, Hunan Normal University, 36 Lushan Road, Changsha 410000, Hunan, People's Republic of China
| | - Wensheng Lan
- Shenzhen R&D Key Laboratory of Alien Pest Detection Technology, The Shenzhen Academy of Inspection and Quarantine, Food Inspection and Quarantine Center of Shenzhen Custom, 1011 Fuqiang Road, Shenzhen 518045, People's Republic of China
| | - Jing Li
- School of Food and Biotechnology, Guangdong Industry Polytechnic, Guangzhou 510300, People's Republic of China
| | - Maocheng Deng
- School of Food and Biotechnology, Guangdong Industry Polytechnic, Guangzhou 510300, People's Republic of China
| | - Yiliang Li
- Department of Earth Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Yoko Katayama
- Tokyo National Research Institute for Cultural Properties, 13-43 Ueno Park, Taito-ku, Tokyo 110-8713, Japan
| | - Ji-Dong Gu
- Environmental Science and Engineering Research Group, Guangdong Technion - Israel Institute of Technology, 241 Daxue Road, Shantou, Guangdong 515063, People's Republic of China; Guangdong Provincial Key Laboratory of Materials and Technologies for Energy Conversion, Guangdong Technion - Israel Institute of Technology, 241 Daxue Road, Shantou, Guangdong 515063, People's Republic of China.
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Koide K, Yao S, Chiang C, Thuy PTB, Nga DTT, Huong DT, Dien TM, Vichit O, Vutthikol Y, Sovannara S, Samnang C, Takayama I, Ainai A, Nakajima N, Otsuka N, Kamachi K, Saitoh A. Genotyping and macrolide-resistant mutation of Bordetella pertussis in East and South-East Asia. J Glob Antimicrob Resist 2022; 31:263-269. [PMID: 36270447 PMCID: PMC9750937 DOI: 10.1016/j.jgar.2022.10.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 10/05/2022] [Accepted: 10/10/2022] [Indexed: 11/09/2022] Open
Abstract
OBJECTIVES Macrolide-resistant Bordetella pertussis (MRBP) has been emerging and prevailing in mainland China since 2011. In this study, we aimed to investigate the genotype and macrolide resistance of circulating B. pertussis in East and Southeast Asia using genetic analyses. METHODS A total of 302 DNA extracts from clinical specimens and isolates from 2010 to 2020 were analyzed: 145 from Vietnam, 76 from Cambodia, 48 from Taiwan, and 33 from Japan. Genotypes were determined by multilocus variable-number tandem-repeat analysis (MLVA). Macrolide-resistant A2047G mutation in B. pertussis 23S rRNA was investigated using the duplex Cycleave real-time polymerase chain reaction (PCR) assay. Whole-genome sequencing was performed on two MRBP isolates that were identified for the first time in Taiwan. RESULTS Overall, 286 DNA extracts (95%) generated a complete MLVA genotype and 283 DNA extracts (94%) yielded a complete result for the A2047G mutation analysis. The A2047G mutation was detected in 18 DNA extracts: fourteen from Vietnam, one from Cambodia, two from Taiwan, and one from Japan. Most of them (78%) showed the genotypes MT104 and MT195, which have previously been reported in Chinese MRBP isolates. Further, the Taiwanese MRBP isolates were classified into the MT104 clade of Chinese MRBP isolates. CONCLUSION After MRBP emerged and spread in mainland China, it may have spread to East and Southeast Asia in the 2010s. Continued surveillance targeting the A2047G mutation of MRBP is needed to prevent further spread of this emerging pathogen.
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Affiliation(s)
- Kentaro Koide
- Department of Bacteriology II, National Institute of Infectious Diseases, Tokyo, Japan
| | - ShuMan Yao
- Centre for Diagnostics and Vaccine Development, Centres for Disease Control, Taipei, Taiwan
| | - Chuen‑Sheue Chiang
- Centre for Diagnostics and Vaccine Development, Centres for Disease Control, Taipei, Taiwan
| | - Phung Thi Bich Thuy
- Department of Molecular Biology for Infectious Disease, Vietnam National Children's Hospital, Hanoi, Vietnam
| | - Do Thi Thuy Nga
- Division of General Internal Medicine, Centre for Tropical Diseases, Vietnam National Children's Hospital, Hanoi, Vietnam
| | - Do Thu Huong
- Division of General Internal Medicine, Centre for Tropical Diseases, Vietnam National Children's Hospital, Hanoi, Vietnam
| | - Tran Minh Dien
- Surgical Intensive Care Unit, Vietnam National Children's Hospital, Hanoi, Vietnam
| | - Ork Vichit
- National Immunization Program, Ministry of Health, Cambodia
| | - Yong Vutthikol
- National Immunization Program, Ministry of Health, Cambodia
| | | | - Chham Samnang
- Vaccine-Preventable Diseases and Immunization, World Health Organization, Cambodia
| | - Ikuyo Takayama
- Research Centre for Influenza and Respiratory Viruses, National Institute of Infectious Diseases, Tokyo, Japan
| | - Akira Ainai
- Department of Pathology, National Institute of Infectious Diseases, Tokyo, Japan
| | - Noriko Nakajima
- Department of Pathology, National Institute of Infectious Diseases, Tokyo, Japan
| | - Nao Otsuka
- Department of Bacteriology II, National Institute of Infectious Diseases, Tokyo, Japan
| | - Kazunari Kamachi
- Department of Bacteriology II, National Institute of Infectious Diseases, Tokyo, Japan,Corresponding author. Mailing address: Department of Bacteriology II, National Institute of Infectious Diseases, 4-7-1 Gakuen, Musashimurayama, Tokyo 208-0011, Japan.
| | - Akihiko Saitoh
- Department of Pediatrics, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
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Ivaska L, Barkoff AM, Mertsola J, He Q. Macrolide Resistance in Bordetella pertussis: Current Situation and Future Challenges. Antibiotics (Basel) 2022; 11:1570. [PMID: 36358225 PMCID: PMC9686491 DOI: 10.3390/antibiotics11111570] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 10/31/2022] [Accepted: 11/05/2022] [Indexed: 01/19/2024] Open
Abstract
Pertussis is a highly contagious respiratory infection caused by Bordetella pertussis bacterium. The mainstay of treatment is macrolide antibiotics that reduce transmissibility, shorten the duration of symptoms and decrease mortality in infants. Recently, the macrolide resistance of B. pertussis has been reported globally but is especially widespread in mainland China. In this review, we aim to summarise the current understanding of the epidemiology, resistance mechanisms and clinical implications of B. pertussis macrolide resistance. Since the first appearance of macrolide-resistant B. pertussis in Arizona, USA, in 1994, only sporadic cases have been reported outside China. In certain parts of China, on the other hand, up to 70-100% of the recent clinical isolates have been found to be macrolide resistant. Reasons for macrolide resistance being centred upon China during the last decade can only be speculated on, but the dominant B. pertussis lineage is different between China and most of the high-income countries. It seems evident that efforts to increase awareness, guide molecular epidemiological surveillance and carry out systematic screening of B. pertussis positive samples for macrolide resistance should be implemented globally. In addition, practices to improve the clinical care of infants with pertussis caused by resistant strains should be studied vigorously.
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Affiliation(s)
- Lauri Ivaska
- Department of Paediatrics and Adolescent Medicine, Turku University Hospital and University of Turku, 20521 Turku, Finland
- InFLAMES Research Flagship Center, University of Turku, 20520 Turku, Finland
| | - Alex-Mikael Barkoff
- Institute of Biomedicine, Centre for Infections and Immunity, University of Turku, 20520 Turku, Finland
| | - Jussi Mertsola
- Department of Paediatrics and Adolescent Medicine, Turku University Hospital and University of Turku, 20521 Turku, Finland
- Institute of Biomedicine, Centre for Infections and Immunity, University of Turku, 20520 Turku, Finland
| | - Qiushui He
- InFLAMES Research Flagship Center, University of Turku, 20520 Turku, Finland
- Institute of Biomedicine, Centre for Infections and Immunity, University of Turku, 20520 Turku, Finland
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Fong W, Timms V, Sim E, Pey K, Nguyen T, Sintchenko V. Genomic and transcriptomic variation in Bordetella spp. following induction of erythromycin resistance. J Antimicrob Chemother 2022; 77:3016-3025. [PMID: 35971665 PMCID: PMC9616548 DOI: 10.1093/jac/dkac272] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 07/19/2022] [Indexed: 11/23/2022] Open
Abstract
Background The emergence of macrolide resistance in Bordetella pertussis, the causative agent of pertussis, due to mutations in the 23S rRNA gene has been recently recognized. However, resistance mechanisms to macrolides in Bordetella parapertussis and Bordetella holmesii remain unknown. Objectives This study investigated genomic changes induced by in vitro exposure to erythromycin in these three main pathogens responsible for pertussis-like disease. Methods A set of 10 clinical and reference strains of B. pertussis, B. parapertussis and B. holmesii was exposed to erythromycin for 15 weeks or 30 subculture passages. Antibiotic pressure was achieved by growth on the selective media with erythromycin Etest strips or impregnated discs. Genome polymorphisms and transcriptomic profiles were examined by short- and long-read sequencing of passaged isolates. Results B. parapertussis and B. holmesii isolates developed significant in vitro resistance to erythromycin (MIC >256 mg/L) within 2 to 7 weeks and at 5 to 12 weeks, respectively. B. pertussis remained phenotypically susceptible to the antibiotic following 15 weeks of exposure, with the MIC between 0.032 to 0.38 mg/L. Genomic analysis revealed that B. holmesii developed resistance due to mutations in the 23S rRNA gene. The resistance mechanism in B. parapertussis was hypothesized as being due to upregulation of an efflux pump mechanism. Conclusions These findings indicate that both B. holmesii and B. parapertussis can be more prone to induced resistance following exposure to treatment with erythromycin than B. pertussis. The surveillance of macrolide resistance in Bordetella isolates recovered from patients with pertussis, especially persistent disease, is warranted.
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Affiliation(s)
- Winkie Fong
- Centre for Infectious Diseases and Microbiology-Public Health, Westmead Hospital, Westmead, New South Wales, Australia
| | - Verlaine Timms
- Centre for Infectious Diseases and Microbiology-Public Health, Westmead Hospital, Westmead, New South Wales, Australia.,Neilan Laboratory of Microbial and Molecular Diversity, College of Engineering, Science and Environment, The University of Newcastle, Newcastle, New South Wales, Australia
| | - Eby Sim
- Centre for Infectious Diseases and Microbiology-Public Health, Westmead Hospital, Westmead, New South Wales, Australia.,Microbial Genomics Reference Laboratory, Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, NSW Health Pathology, Westmead, New South Wales, Australia
| | - Keenan Pey
- Centre for Infectious Diseases and Microbiology-Public Health, Westmead Hospital, Westmead, New South Wales, Australia.,Sydney Institute of Infectious Diseases, The University of Sydney, Camperdown, New South Wales, Australia
| | - Trang Nguyen
- Microbial Genomics Reference Laboratory, Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, NSW Health Pathology, Westmead, New South Wales, Australia
| | - Vitali Sintchenko
- Centre for Infectious Diseases and Microbiology-Public Health, Westmead Hospital, Westmead, New South Wales, Australia.,Microbial Genomics Reference Laboratory, Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, NSW Health Pathology, Westmead, New South Wales, Australia.,Sydney Institute of Infectious Diseases, The University of Sydney, Camperdown, New South Wales, Australia
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Zhang J, Zhang D, Wang X, Wei X, Li H. Macrolide susceptibility and molecular characteristics of Bordetella pertussis. J Int Med Res 2022; 50:3000605221078782. [PMID: 35225710 PMCID: PMC8894965 DOI: 10.1177/03000605221078782] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Objective To analyse macrolide resistance and molecular characteristics of Bordetella pertussis clinical isolates from western China, and to explore the relationship between macrolide-resistance and genotypes. Methods Susceptibilities of B. pertussis clinical isolates to erythromycin, azithromycin and clarithromycin were determined by epsilometer test (E-test). Isolated strains were sequenced to ascertain the presence of the 23S rRNA gene A2047G mutation. Strains were typed using multilocus antigen sequence typing, multilocus variable-number tandem-repeat analysis (MLVA) and pulsed-field gel electrophoresis (PFGE). Results Of 58 B. pertussis strains isolated in this study, 46 were macrolide-resistant and 12 were macrolide sensitive. All macrolide-resistant strains carried the A2047G mutation and were the prn1/ptxP1/ptxA1/fim3-1/fim2-1 genotype; the MLVA types were MT195 (19/58), MT55 (13/58) and MT104 (14/58), and the PFGE profiles were classified into BpSR23 (17/58) and BpFINR9 (29/58) types. None of the macrolide-sensitive strains carried the A2047G mutation; genotypes were (prn9 or prn2)/ptxP3/ptxA1/fim3-1/fim2-1, and all were MT27. PFGE profiles differed from the macrolide-resistant strains. Conclusions B. pertussis clinical isolates from western China were severely resistant to macrolides. Genotypes differed between macrolide-resistant and macrolide-sensitive strains, and there may be a correlation between acquisition of macrolide resistance and changes in specific molecular types.
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Affiliation(s)
- Juansheng Zhang
- Microbiology laboratory, Xi'an Centre for Disease Control and Prevention, Xi'an, Shaanxi Province, China
| | - Diqiang Zhang
- Department of Obstetrics and Gynaecology, Pingchuan District People's Hospital, Baiyin, Gansu Province, China
| | - Xiaoqiang Wang
- Microbiology laboratory, Xi'an Centre for Disease Control and Prevention, Xi'an, Shaanxi Province, China
| | - Xiaoguang Wei
- Microbiology laboratory, Xi'an Centre for Disease Control and Prevention, Xi'an, Shaanxi Province, China
| | - Hao Li
- Microbiology laboratory, Xi'an Centre for Disease Control and Prevention, Xi'an, Shaanxi Province, China
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Liu D, Cheng X, Wei S, Yuan L, Chen C, Yao K. Decline of serologic immunity to diphtheria, tetanus and pertussis with age suggested a full life vaccination in mainland China. Hum Vaccin Immunother 2021; 17:1757-1762. [PMID: 33517831 DOI: 10.1080/21645515.2020.1840253] [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: 10/22/2022] Open
Abstract
Background: Diphtheria-tetanus-pertussis (DTP) vaccine has already been involved in national vaccination program for several decades in China. The immunity against these diseases in the people of all ages is not well investigated.Materials and methods: Serum samples were tested for IgG antibodies to diphtheria toxoid (DT), tetanus toxoid (TT) and pertussis toxin (PT) by using commercial ELISA kits.Results: A total of 666 sera of patients from 1 day to 89 years of age was collected from 2018 to 2019. The protective rates of diphtheria, tetanus and pertussis were 45.5%, 54.4% and 4.7%, respectively. Only 4.7% of the study population had seropositivity against three of the diseases. Young infant (<3 m) and adult (>18y) were generally lack of protective antibody against diphtheria (81.7% and 58.3%) and tetanus (91.5% and 86.2%). An obvious increase in immunity level of diphtheria and tetanus was observed at 3 m-3y, but there was no significant increase of immunity to pertussis at any age group. All age groups showed low immunity to pertussis.Conclusions: The present results revealed the susceptibility to diphtheria and tetanus in young infants and adults, and the susceptibility to pertussis over the ages, which highlight the need to improve the current vaccination program.
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Affiliation(s)
- Dandan Liu
- Key Laboratory of Major Diseases in Children, Ministry of Education, National Key Discipline of Pediatrics (Capital Medical University), Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
| | - Xiaoping Cheng
- Clinical Laboratory, Youyang County People's Hospital, Chongqing, China
| | - Shi Wei
- Key Laboratory of Major Diseases in Children, Ministry of Education, National Key Discipline of Pediatrics (Capital Medical University), Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
| | | | - Changhui Chen
- Department of Pediatrics, Youyang County People's Hospital, Chongqing, China
| | - Kaihu Yao
- Key Laboratory of Major Diseases in Children, Ministry of Education, National Key Discipline of Pediatrics (Capital Medical University), Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
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Cimolai N. Pharmacotherapy for Bordetella pertussis infection. I. A synthesis of laboratory sciences. Int J Antimicrob Agents 2020; 57:106258. [PMID: 33310116 DOI: 10.1016/j.ijantimicag.2020.106258] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 11/09/2020] [Accepted: 11/28/2020] [Indexed: 11/15/2022]
Abstract
There is considerable history and practice experience both with laboratory susceptibility testing for Bordetella pertussis and clinical treatment. This two-part narrative review provides a synthesis of the laboratory and clinical sciences as they apply to this bacterium and the clinical consequences of treating infection. It is generally held that antibiotic susceptibility testing for B. pertussis is not sufficiently standardised, but there has not been an urgent need to consolidate the same given the lack global experience with major resistance profiles. Experience in China, however, has provided concern for high-level macrolide resistance. The nature of and frequency of such resistance has raised the bar for reconsideration of susceptibility testing given that first-line treatment may be regionally compromised. Disk diffusion and Etest susceptibility testing can be recommended for screening resistance among individual isolates of B. pertussis and on an ad hoc manner. Disk diffusion, Etest and/or critical agar dilution testing can be recommended for large-scale studies. Standards for inoculum, growth atmosphere, timing of interpretation, preferred testing media and controls can be extrapolated from the publications to date. Such methods should be able to detect high-level resistance to several antibiotics, but especially macrolides. Concern for intermediate-susceptible categories requires consideration as well as the correlation with bacteriological and clinical outcomes. Provisional standards can be applied at this time, and modification or fine-tuning of any such standards are open to future investigation.
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Affiliation(s)
- Nevio Cimolai
- Department of Pathology and Laboratory Medicine, The University of British Columbia, Vancouver, British Columbia, Canada; Department of Pathology and Laboratory Medicine, Children's and Women's Health Centre of British Columbia, 4480 Oak Street, Vancouver, British Columbia, V6H3V4 Canada.
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Dominguez DC. A profile of the Simplexa™ Bordetella Direct assay for the detection and differentiation of Bordetella pertussis and Bordetella parapertussis in nasopharyngeal swabs. Expert Rev Mol Diagn 2020; 20:889-894. [PMID: 32885709 DOI: 10.1080/14737159.2020.1819240] [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: 10/23/2022]
Abstract
INTRODUCTION Pertussis is a highly contagious respiratory infection caused by Bordetella pertussis and to minor extent B. parapertussis. Despite high vaccination coverage, epidemics persist worldwide. Laboratory testing with the capacity to support increasing demand and generate fast and accurate results is needed to promptly provide treatment to mitigate symptoms, prevent transmission, and thus impact infection control and disease surveillance. AREAS COVERED This review will describe the features of the Simplexa™ Bordetella Direct Assay and compare this technology with other existing assays. Unmet needs and future directions will be discussed. EXPERT COMMENTARY Resurgence of pertussis highlights the importance of reliable and accurate diagnosis. The Simplexa™ Bordetella Direct Assay provides an easy workflow, reduced hand-on time, less risk of contamination, and rapid turnaround time. The use of efficient molecular assays in routine clinical laboratory is valuable for increasing demand, improvement of infection control, and surveillance.
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Affiliation(s)
- Delfina C Dominguez
- Clinical Laboratory Science/Public Health Sciences, The University of Texas at El Paso , El Paso, TX, USA
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Wang Z, Luan Y, Du Q, Shu C, Peng X, Wei H, Hou T, Liu Y, Liu X, Li Y. The global prevalence ptxP3 lineage of Bordetella pertussis was rare in young children with the co-purified aPV vaccination: a 5 years retrospective study. BMC Infect Dis 2020; 20:615. [PMID: 32814558 PMCID: PMC7437160 DOI: 10.1186/s12879-020-05332-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Accepted: 08/10/2020] [Indexed: 11/16/2022] Open
Abstract
Background The global prevalent ptxP3 strains varies from about 10% to about 50% of circulating B. pertussis population in different areas of China. Methods To investigate the difference of vaccination status between different genotypes in the circulating B. pertussis after 10 years of acellular pertussis vaccine (aPV) used in China. The nasopharyngeal swabs and isolates of B. pertussis from these patients were used to perform genotyping of antigen genes. We use antibiotic susceptibility test against erythromycin and sequencing methods for site 2047 of 23S rRNA to determine the resistance status. Results The ptxP1 allele with erythromycin resistant (ER) B. pertussis infection (total of 449 subjects) consisted of 84.70 to 96.70% from 2012 to 2016 in this study. Vaccinated with co-purified aPV was found in 133(133/403,33.0%), 1(1/9,11.1%) and 2(2/21,9.5%) in ptxP1/fhaB3-ER, ptxP1/fhaB2-ES and ptxP3/fhaB2-ES B. pertussis infected children each, which showed a significant difference (χ2 = 6.87, P = 0.032). Conclusions The ptxP3-ES B. pertussis was rare while the ptxP1-ER B. pertussis was steadily increased in Xi’an, China from 2012 to 2016, where co-purified aPV was prevalent used. This pose a hypothesis that the co-purified aPV might protect against ptxP3 strains more efficient, which generated a rare chance for ptxP3 strains to be under the antibiotic pressure and further developed to be erythromycin resistance. A further cohort study and the mechanisms of the additional antigen proteins of co-purified aPV protected against B. pertussis should be consideration.
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Affiliation(s)
- Zengguo Wang
- Xi'an Children's Hospital, 69 Xijunyuan Road, Xi'an, 710002, Shaanxi Province, China.
| | - Yang Luan
- Xi'an Center for Disease Control and Prevention, 599 Xiying Road, Xi'an, 710054, China
| | - Quanli Du
- Xi'an Center for Disease Control and Prevention, 599 Xiying Road, Xi'an, 710054, China
| | - Chang Shu
- Xi'an Children's Hospital, 69 Xijunyuan Road, Xi'an, 710002, Shaanxi Province, China
| | - Xiaokang Peng
- Xi'an Children's Hospital, 69 Xijunyuan Road, Xi'an, 710002, Shaanxi Province, China
| | - Huijing Wei
- Xi'an Children's Hospital, 69 Xijunyuan Road, Xi'an, 710002, Shaanxi Province, China
| | - Tiejun Hou
- Xi'an Center for Disease Control and Prevention, 599 Xiying Road, Xi'an, 710054, China
| | - Ying Liu
- Xi'an Center for Disease Control and Prevention, 599 Xiying Road, Xi'an, 710054, China
| | - Xiaoguai Liu
- Xi'an Children's Hospital, 69 Xijunyuan Road, Xi'an, 710002, Shaanxi Province, China.
| | - Yarong Li
- Xi'an Children's Hospital, 69 Xijunyuan Road, Xi'an, 710002, Shaanxi Province, China.
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Xu Z, Wang Z, Luan Y, Li Y, Liu X, Peng X, Octavia S, Payne M, Lan R. Genomic epidemiology of erythromycin-resistant Bordetella pertussis in China. Emerg Microbes Infect 2019; 8:461-470. [PMID: 30898080 PMCID: PMC6455148 DOI: 10.1080/22221751.2019.1587315] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
Macrolides such as erythromycin are the empirical treatment of Bordetella pertussis infections. China has experienced an increase in erythromycin-resistant B. pertussis isolates since they were first reported in 2013. Here, we undertook a genomic study on Chinese B. pertussis isolates from 2012 to 2015 to elucidate the origins and phylogenetic relationships of erythromycin-resistant B. pertussis isolates in China. A total of 167 Chinese B. pertussis isolates were used for antibiotic sensitivity testing and multiple locus variable-number tandem repeat (VNTR) analysis (MLVA). All except four isolates were erythromycin-resistant and of the four erythromycin-sensitive isolates, three were non-ptxP1. MLVA types (MT), MT55, MT104 and MT195 were the predominant types. Fifty of those isolates were used for whole genome sequencing and phylogenetic analysis. Genome sequencing and phylogenetic analysis revealed three independent erythromycin-resistant lineages and all resistant isolates carried a mutation in the 23S rRNA gene. A novel fhaB3 allele was found uniquely in Chinese ptxP1 isolates and these Chinese ptxP1-ptxA1-fhaB3 had a 5-fold higher mutation rate than the global ptxP1-ptxA1 B. pertussis population. Our results suggest that the evolution of Chinese B. pertussis is likely to be driven by selection pressure from both vaccination and antibiotics. The emergence of the new non-vaccine fhaB3 allele in Chinese B. pertussis population may be a result of selection from vaccination, whereas the expansion of ptxP1-fhaB3 lineages was most likely to be the result of selection pressure from antibiotics. Further monitoring of B. pertussis in China is required to better understand the evolution of the pathogen.
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Affiliation(s)
- Zheng Xu
- a School of Biotechnology and Biomolecular Sciences , University of New South Wales , Sydney , Australia
| | - Zengguo Wang
- b Xi'an Center for Disease Prevention and Control , Xi'an , People's Republic of China.,c Department of Infectious Diseases , Xi'an Children's Hospital , Xi'an , People's Republic of China
| | - Yang Luan
- b Xi'an Center for Disease Prevention and Control , Xi'an , People's Republic of China
| | - Yarong Li
- c Department of Infectious Diseases , Xi'an Children's Hospital , Xi'an , People's Republic of China
| | - Xiaoguai Liu
- c Department of Infectious Diseases , Xi'an Children's Hospital , Xi'an , People's Republic of China
| | - Xiaokang Peng
- c Department of Infectious Diseases , Xi'an Children's Hospital , Xi'an , People's Republic of China
| | - Sophie Octavia
- a School of Biotechnology and Biomolecular Sciences , University of New South Wales , Sydney , Australia
| | - Michael Payne
- a School of Biotechnology and Biomolecular Sciences , University of New South Wales , Sydney , Australia
| | - Ruiting Lan
- a School of Biotechnology and Biomolecular Sciences , University of New South Wales , Sydney , Australia
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Molecular Epidemiology of Bordetella pertussis. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1183:19-33. [PMID: 31342459 DOI: 10.1007/5584_2019_402] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Although vaccination has been effective, Bordetella pertussis is increasingly causing epidemics, especially in industrialized countries using acellular vaccines (aPs). One factor behind the increased circulation is the molecular changes on the pathogen level. After pertussis vaccinations were introduced, changes in the fimbrial (Fim) serotype of the circulating strains was observed. When bacterial typing methods improved, further changes between the vaccine and circulating strains, especially among the common virulence genes including pertussis toxin (PT) and pertactin (PRN) were noticed. Moreover, development of genome based techniques including pulsed-field gel electrophoresis (PFGE), multiple-locus variable number tandem repeat analysis (MLVA) and whole-genome sequencing (WGS) have offered a better resolution to monitor B. pertussis strains. After the introduction of aP vaccines, B. pertussis strains that are deficient to vaccine antigens, especially PRN, have appeared widely. On the other hand, antimicrobial resistance to first line drugs (macrolides) against B. pertussis is still low in many countries and therefore no globally evaluated antimicrobial susceptibility test values have been recommended. In this review, we focus on the molecular changes in the bacteria, which have or may have affected the past and current epidemiology of pertussis.
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Lönnqvist E, Barkoff AM, Mertsola J, He Q. Antimicrobial susceptibility testing of Finnish Bordetella pertussis isolates collected during 2006–2017. J Glob Antimicrob Resist 2018; 14:12-16. [DOI: 10.1016/j.jgar.2018.02.012] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Revised: 01/31/2018] [Accepted: 02/18/2018] [Indexed: 10/18/2022] Open
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Antimicrobial Susceptibility and Molecular Detection of Pertactin-producing and Pertactin-Deficient Bordetella pertussis. Pediatr Infect Dis J 2017; 36:119-121. [PMID: 27956730 DOI: 10.1097/inf.0000000000001366] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Resurgence of Bordetella pertussis in recent years in the United States has coincided with a dramatic rise in pertactin-deficient strains. Limited data exist on detectability by nucleic acid amplification testing and antimicrobial susceptibility of pertactin-deficient B. pertussis. This study compares 15 pertactin-producing and 15 pertactin-deficient B. pertussis isolates. Pertactin-producing and pertactin-deficient strains were equally detected by nucleic acid amplification testing and were susceptible to antibiotics.
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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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