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Ding Y, Wang Q, Li D, Li Y, Yao K, Wang T. Differences in the effects of Bordetella pertussis and respiratory syncytial virus infection on the composition of nasopharyngeal flora in neonates. Front Pediatr 2023; 11:1034147. [PMID: 37351319 PMCID: PMC10282602 DOI: 10.3389/fped.2023.1034147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 04/25/2023] [Indexed: 06/24/2023] Open
Abstract
Introduction Bordetella pertussis and respiratory syncytial virus (RSV) are important pathogens causing cough in neonates. Few studies have investigated the differences in the effects of these two specific infections on respiratory flora. The aim of this study was to explore whether infections with Bordetella pertussis and RSV have different effects on respiratory floral composition in neonates. Methods Nasopharyngeal respiratory flora was assessed by 16S ribosomal RNA amplification and V3-V4 region sequencing. Shannon and Simpson indices were calculated to determine the α diversity and principal coordinate analysis was performed to determine the β diversity. Results In total, 111 hospitalized neonates were divided into the pertussis (n = 29), RSV (n = 57), and control groups (n = 25) according to the pathogens detected. The relative abundance of Bordetella was significantly higher in the pertussis group (median: 19.18%, interquartile range: 72.57%). In contrast, this species was not detected in the other two groups. In the RSV group, the relative abundance of Streptococcus (median: 77.15%, interquartile range: 45.84%) was significantly higher than those in the pertussis and control groups (both P < 0.001). The α diversity of the RSV group was significantly lower than that of the control group (P < 0.001). Moreover, no statistically significant differences in the Shannon and Simpson indices were observed between the pertussis and control groups (P = 0.101 and P = 0.202, respectively). Principal coordinate analysis revealed a large overlap between the pertussis and control groups and a significant distance between the RSV and control groups without any overlap. Discussion Thus, the effects of infections with the two species, B. pertussis and RSV, impacted the diversity of nasopharyngeal flora differently. The principles underlying the difference in the effects of different pathogens on microbial flora require further investigation.
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Affiliation(s)
- Yijun Ding
- Department of Neonatology, Beijing Children’s Hospital, Capital Medical University, National Center for Children’s Health, Beijing, China
| | - Qing Wang
- Beijing Pediatric Research Institute, Beijing Children’s Hospital, Capital Medical University, National Center for Children’s Health, Beijing, China
| | - Dongfang Li
- R&D Department, BGI PathoGenesis Pharmaceutical Technology, BGI-Shenzhen, Shenzhen, China
| | - Yue Li
- Beijing Pediatric Research Institute, Beijing Children’s Hospital, Capital Medical University, National Center for Children’s Health, Beijing, China
| | - Kaihu Yao
- Beijing Pediatric Research Institute, Beijing Children’s Hospital, Capital Medical University, National Center for Children’s Health, Beijing, China
| | - Tianyou Wang
- Department of Hematology and Oncology, Beijing Children’s Hospital, Capital Medical University, National Center for Children’s Health, Beijing, China
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Li C, Huang C, Zhang R, Wang H, Tian S, Tang YW, Deng J. Evaluation of BioFire Respiratory Panel 2 plus for Detection of Bordetella pertussis in Nasopharyngeal Swab Specimens from Children with Clinically Suspected Pertussis. Microbiol Spectr 2023; 11:e0180622. [PMID: 36602355 PMCID: PMC9927272 DOI: 10.1128/spectrum.01806-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
The objective of this study was to compare the performances of BioFire Respiratory Panel 2 (RP2) plus, quantitative real-time PCR (qPCR), and culture for the detection of Bordetella pertussis in nasopharyngeal swab (NPS) specimens. Consecutive NPS specimens were collected from patients with clinically suspected pertussis from 1 March 1 to 31 July 2018 in Shenzhen Children's Hospital. All the specimens were tested in parallel by RP2 plus, qPCR, and culture methods. A total of 464 children were enrolled in this study. The positive pertussis rates of culture, RP2 plus, and qPCR were 23.1%, 39.0%, and 38.4%, respectively. Compared to the combined reference standard, the sensitivity, specificity, positive predictive value, and negative predictive values were, respectively, 56.6% (95% confidence interval [CI], 49.2 to 63.7%), 100% (98.3 to 100%), 100% (95.7 to 100%), and 77.0% (72.2 to 81.2%) for culture, 89.9% (84.5 to 93.7%), 96.0% (92.8 to 97.9%), 93.9% (89.1 to 96.8%), and 93.3% (89.5 to 95.8%) for RP2 plus, and 86.8% (80.9 to 91.1%), 94.9% (91.4 to 97.1%), 92.1% (86.9 to 95.5%), and 91.3% (87.2 to 94.2%) for qPCR. The most prevalent codetected pathogen was human rhinovirus/enterovirus (n = 99, 52.4%), followed by parainfluenza virus (n =32, 16.9%) and respiratory syncytial virus (n = 29, 15.3%), in children with B. pertussis present, which was consistent with the top three pathogens previously found in children with B. pertussis absent. Turnaround times for RP2 plus, qPCR, and culture were 2 h, 8 h, and 120 h, respectively. RP2 plus quickly and accurately detected B. pertussis, providing valuable information for an early clinical diagnosis and optimal choice of therapy. IMPORTANCE In recent years, there have been some epidemic or local outbreaks of pertussis in countries with high vaccination rates. One of the crucial factors in controlling pertussis is early diagnosis, which is based on specific laboratory measurements, including culture, serological tests, and PCR assays. Compared to culture and serological tests, PCR is more suitable for clinical application, with a fast detection speed of several hours independent of the disease stage and individual vaccination status. BioFire Respiratory Panel 2 plus, a multiplex PCR assay for simultaneously detecting 22 respiratory pathogens, facilitates the quick detection of Bordetella pertussis and coinfecting respiratory pathogens. It also provides valuable information for an early clinical diagnosis and optimal choice of therapy for children with clinically suspected pertussis.
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Affiliation(s)
- Chi Li
- Division of Infectious Diseases, Shenzhen Children's Hospital, Shenzhen, China
| | - Chaoying Huang
- Division of Infectious Diseases, Shenzhen Children's Hospital, Shenzhen, China
| | - Ruimu Zhang
- Division of Infectious Diseases, Shenzhen Children's Hospital, Shenzhen, China
| | - Hongmei Wang
- Division of Infectious Diseases, Shenzhen Children's Hospital, Shenzhen, China
- Department of Laboratory Medicine, Memorial Sloan-Kettering Cancer Center, New York, New York, USA
- Department of Internal Medicine, Memorial Sloan-Kettering Cancer Center, New York, New York, USA
| | - Shufeng Tian
- Division of Infectious Diseases, Shenzhen Children's Hospital, Shenzhen, China
| | - Yi-Wei Tang
- Department of Laboratory Medicine, Memorial Sloan-Kettering Cancer Center, New York, New York, USA
- Department of Internal Medicine, Memorial Sloan-Kettering Cancer Center, New York, New York, USA
| | - Jikui Deng
- Division of Infectious Diseases, Shenzhen Children's Hospital, Shenzhen, China
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Okada K, Horikoshi Y, Nishimura N, Ishii S, Nogami H, Motomura C, Miyairi I, Tsumura N, Mori T, Ito K, Honma S, Nagai K, Tanaka H, Hayakawa T, Abe C, Ouchi K. Clinical evaluation of a new rapid immunochromatographic test for detection of Bordetella pertussis antigen. Sci Rep 2022; 12:8069. [PMID: 35577904 PMCID: PMC9109659 DOI: 10.1038/s41598-022-11933-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 05/03/2022] [Indexed: 11/08/2022] Open
Abstract
A more rapid and less complicated test to diagnose pertussis is required in clinical settings. We need to detect Bordetella pertussis, which mainly causes pertussis, as early as possible, because pertussis is more likely to become severe in infants, and people around them can easily become a source of infection due to its strong infectivity. Nevertheless, methods that can detect B. pertussis rapidly and efficiently are lacking. Therefore, we developed a new immunochromatographic antigen kit (ICkit) for the early diagnosis of pertussis. The ICkit detects B. pertussis antigens in a nasopharyngeal swab without equipment and provides the result in about 15 min with a simple procedure. Additionally, a prospective study to evaluate the ICkit was conducted in 11 medical institutions, involving 195 cases with suspected pertussis. Compared with the real-time polymerase chain reaction (rPCR), the sensitivity and specificity of the ICkit were 86.4% (19/22) and 97.1% (168/173), respectively. The ICkit detected the antigen in both children and adults. Furthermore, the ICkit detected the antigen until the 25th day from the onset of cough, when rPCR detected the antigen. Thus, the ICkit demonstrated a high correlation with rPCR and would help diagnose pertussis more rapidly and efficiently.
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Affiliation(s)
- Kenji Okada
- Division of Basic Nursing, Fukuoka Nursing College, Fukuoka, Japan
| | - Yuho Horikoshi
- Division of Infectious Diseases, Department of Pediatrics, Tokyo Metropolitan Children's Medical Center, Tokyo, Japan
| | - Naoko Nishimura
- Department of Pediatrics, Konan Kosei Hospital, Aichi, Japan
| | - Shigeki Ishii
- Department of Pediatrics, Miyazaki Prefectural Miyazaki Hospital, Miyazaki, Japan
| | - Hiroko Nogami
- Department of Respiratory Medicine, National Hospital Organization Fukuoka National Hospital, Fukuoka, Japan
| | - Chikako Motomura
- Department of Pediatrics, National Hospital Organization Fukuoka National Hospital, Fukuoka, Japan
| | - Isao Miyairi
- Division of Infectious Diseases, Department of Medical Subspecialties, National Center for Child Health and Development, Tokyo, Japan
| | | | - Toshihiko Mori
- Department of Pediatrics, NTT East Sapporo Hospital, Hokkaido, Japan
| | - Kenta Ito
- Department of General Pediatrics, Aichi Children's Health and Medical Center, Aichi, Japan
| | | | | | - Hiroshi Tanaka
- Sapporo Cough Asthma and Allergy Center, Hokkaido, Japan
| | - Toru Hayakawa
- Diagnostics Department, Asahi Kasei Pharma Corporation, 1-1-2 Yurakucho, Chiyoda-ku, Tokyo, 100-0006, Japan.
| | - Chiharu Abe
- Diagnostics Department, Asahi Kasei Pharma Corporation, 1-1-2 Yurakucho, Chiyoda-ku, Tokyo, 100-0006, Japan
| | - Kazunobu Ouchi
- Department of Medical Welfare for Children, Kawasaki University of Medical Welfare, Okayama, Japan
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Exploring the nasopharyngeal microbiota composition in infants with whooping cough: A test-negative case-control study. PLoS One 2021; 16:e0259318. [PMID: 34714887 PMCID: PMC8555781 DOI: 10.1371/journal.pone.0259318] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 10/16/2021] [Indexed: 01/04/2023] Open
Abstract
Purpose The purpose of this study was to characterize the nasopharyngeal microbiota of infants with possible and confirmed pertussis compared to healthy controls. Methods This prospective study included all infants <1 year with microbiologically confirmed diagnosis of pertussis attended at a University Hospital over a 12-month period. For each confirmed case, up to 2 consecutive patients within the same age range and meeting the clinical case definition of pertussis but testing PCR-negative were included as possible cases. A third group of asymptomatic infants (healthy controls) were also included. Nasopharyngeal microbiota was characterized by sequencing the V3-V4 region of the 16S rRNA gene. Common respiratory DNA/RNA viral co-infection was tested by multiplex PCR. Results Twelve confirmed cases, 21 possible cases and 9 healthy controls were included. Confirmed whooping cough was primarily driven by detection of Bordetella with no other major changes on nasopharyngeal microbiota. Possible cases had limited abundance or absence of Bordetella and a distinctive microbiota with lower bacterial richness and diversity and higher rates of viral co-infection than both confirmed cases and healthy controls. Bordetella reads determined by 16S rRNA gene sequencing were found in all 12 confirmed cases (100%), 3 out of the 21 possible cases (14.3%) but in any healthy control. Conclusion This study supports the usefulness of 16S rRNA gene sequencing for improved sensitivity on pertussis diagnosis compared to real-time PCR and to understand other microbial changes occurring in the nasopharynx in children <1 year old with suspected whooping cough compared to healthy controls.
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Claassen-Weitz S, Lim KYL, Mullally C, Zar HJ, Nicol MP. The association between bacteria colonizing the upper respiratory tract and lower respiratory tract infection in young children: a systematic review and meta-analysis. Clin Microbiol Infect 2021; 27:1262-1270. [PMID: 34111578 PMCID: PMC8437050 DOI: 10.1016/j.cmi.2021.05.034] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 05/21/2021] [Accepted: 05/22/2021] [Indexed: 11/28/2022]
Abstract
BACKGROUND Bacteria colonizing the upper respiratory tract (URT) of young children play a key role in the pathogenesis of lower respiratory tract infection (LRTI). OBJECTIVES To systematically review the literature on the association between bacteria colonizing the URT and LRTI among young children. DATA SOURCES MEDLINE, Academic Search Premier, Africa-Wide Information and CINAHL, Scopus and Web of Science. STUDY ELIGIBILITY CRITERIA Studies published between 1923 and 2020, investigating URT bacteria from LRTI cases and controls. PARTICIPANTS Children under 5 years with and without acute LRTI. METHODS Three reviewers independently screened titles, abstracts and full texts. Meta-analysis was done using Mantel-Haenszel fixed- or random-effects models. RESULTS Most eligible studies (41/50) tested nasopharyngeal specimens when investigating URT bacteria. Most studies were of cross-sectional design (44/50). Twenty-four studies were performed in children in lower- or lower-middle-income countries (LMICs). There was higher prevalence of Haemophilus influenzae (pooled OR 1.60; 95% CI 1.23-2.07) and Klebsiella spp. (pooled OR 2.04; 95% CI 1.17-3.55) from URT specimens of cases versus controls. We observed a positive association between the detection of Streptococcus pneumoniae from URT specimens and LRTI after excluding studies where there was more antibiotic treatment prior to sampling in cases vs. controls (pooled OR 1.41; 95% CI 1.04-1.90). High density colonization with S. pneumoniae (>6.9 log10 copies/mL) was associated with an increased risk for LRTI. The associations between both Streptococcus and Haemophilus URT detection and LRTI were supported, at genus level, by 16S rRNA sequencing. Evidence for the role of Moraxella catarrhalis and Staphylococcus aureus was inconclusive. CONCLUSIONS Detection of H. influenzae or Klebsiella spp. in the URT was associated with LRTI, while evidence for association with S. pneumoniae was less conclusive. Longitudinal studies assessing URT microbial communities, together with environmental and host factors are needed to better understand pathogenesis of childhood LRTI.
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Affiliation(s)
- Shantelle Claassen-Weitz
- Division of Medical Microbiology, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa.
| | - Katherine Y L Lim
- Marshall Centre for Infectious Diseases Research and Training, School of Biomedical Sciences, University of Western Australia, Perth, Australia
| | - Christopher Mullally
- Marshall Centre for Infectious Diseases Research and Training, School of Biomedical Sciences, University of Western Australia, Perth, Australia
| | - Heather J Zar
- Department of Paediatrics and Child Health, Red Cross War Memorial Children's Hospital, Cape Town, South Africa; SAMRC Unit on Child & Adolescent Health, University of Cape Town, Cape Town, South Africa; Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Mark P Nicol
- Division of Medical Microbiology, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa; Division of Infection and Immunity, School of Biomedical Sciences, University of Western Australia, Perth, Australia
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Multicenter Performance Evaluation of the Simplexa Bordetella Direct Kit in Nasopharyngeal Swab Specimens. J Clin Microbiol 2020; 59:JCM.01041-20. [PMID: 33055187 DOI: 10.1128/jcm.01041-20] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 10/07/2020] [Indexed: 11/20/2022] Open
Abstract
Detection of Bordetella pertussis and Bordetella parapertussis using molecular methods is sensitive and specific with a short turnaround time compared to other diagnostic methods. In this multicenter study, we compared the performance of the Simplexa Bordetella Direct kit to those of other molecular assays in detecting and differentiating B. pertussis and B. parapertussis in nasopharyngeal swab specimens. The limits of detection (LODs) were 150 CFU/ml or 3 fg/μl of DNA for B. pertussis and 1,500 CFU/ml or 10 fg/μl of DNA for B. parapertussis A total of 1,103 fresh and residual frozen specimens from eight clinical sites were tested. Combining the data from individual clinical sites using different comparative assays, the overall positive percent agreement (PPA) and negative percent agreement (NPA) for B. pertussis were 98.7% and 97.3%, respectively. The overall PPA and NPA for B. parapertussis were 96.7% and 100%, respectively. For prospective fresh specimens, the overall PPA and NPA for both targets were 97.7% and 99.3%, respectively. For retrospective frozen specimens, the overall PPA and NPA for both targets were 92.6% and 93.2%, respectively. The percentage of invalid results was 1.0%. A cross-reactivity study using 74 non-Bordetella bacterial species and five yeast species revealed that the Simplexa Bordetella Direct kit was 100% specific. The hands-on time and assay run time of the Simplexa Bordetella Direct kit are favorable compared to those of other commercial and laboratory-developed tests. In summary, the Simplexa Bordetella Direct kit has a performance comparable to those of other molecular assays for the detection of B. pertussis and B. parapertussis.
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