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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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Lee DH, Choi YJ, Kim J, Han E, Bae MH. Pre-Pandemic Distribution of Bacterial Species in Nasopharyngeal Swab Specimens from Pediatric and Adult Patients Detected via RT-PCR Using the Allplex Respiratory Panel. Life (Basel) 2023; 13:1840. [PMID: 37763244 PMCID: PMC10532938 DOI: 10.3390/life13091840] [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: 07/12/2023] [Revised: 08/21/2023] [Accepted: 08/29/2023] [Indexed: 09/29/2023] Open
Abstract
Background: Recently, panel-based molecular diagnostics for the simultaneous detection of respiratory viruses and bacteria in nasopharyngeal swab (NPS) specimens have been highlighted. We identified the distribution of bacterial species in NPS specimens collected from pediatric and adult patients by employing RT-PCR (Allplex respiratory panel 4, RP4, Seegene) to estimate its applicability in a panel-based assay for detecting respiratory viruses. Methods: We used 271 and 173 NPS specimens from pediatric and adult patients, respectively. The results of the Allplex RP4 panel using NPS (NPS-RP4) from adult patients were compared with those of the Seeplex PneumoBacter ACE Detection assay (Seegene), which used sputum for testing (sputum-Seeplex). Results: A total of 147 specimens (54.2%) were positive for the NPS-RP4 panel in pediatric patients. There were 94, 77, 10, 3, 3, and 2 specimens that were positive for Haemophilus influenzae (HI), Streptococcus pneumoniae (SP), Mycoplasma pneumoniae (MP), Chlamydia pneumoniae (CP), Bordetella pertussis (BP), and B. parapertussis (BPP), respectively. Among 173 adult patients, 39 specimens (22.5%) were positive in the NPS-RP4. Thirty specimens were positive for HI, and 13 were positive for SP. One specimen tested positive for both MP and Legionella pneumophila (LP). CP, BP, and BPP results were all negative. However, 126 specimens (72.8%) had positive results with sputum-Seeplex (99 SP, 59 HI, three LP, and two MP), and the overall percentage of agreement between the two assays was 39.3% in the adult patients. Conclusions: Bacterial species in NPS from more than half of pediatric patients were detected. Performing the Allplex RP4 assay with NPS revealed additional respiratory bacteria that are not detected in current clinical practices, which do not include bacterial testing, demanding the use of sputum specimens. However, the use of NPS showed low agreement with standard assays using sputum in adult patients. Thus, more research is needed to develop a reliable RT-PCR method using NPS specimens in adult patients.
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Affiliation(s)
- Dong-Hyun Lee
- Department of Laboratory Medicine, Gyeongsang National University Hospital, Gyeongsang National University School of Medicine, Jinju 52727, Republic of Korea
| | - Young-Jin Choi
- Department of Pediatrics, Hanyang University Guri Hospital, Hanyang University College of Medicine, Guri 11923, Republic of Korea
| | - Jieun Kim
- Division of Infectious Disease, Department of Internal Medicine, Hanyang University Guri Hospital, Hanyang University College of Medicine, Guri 11923, Republic of Korea
| | - Eunhee Han
- Department of Laboratory Medicine, Daejeon St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Seoul 06591, Republic of Korea
| | - Mi-Hyun Bae
- Department of Laboratory Medicine, Hanyang University Guri Hospital, Hanyang University College of Medicine, Guri 11923, Republic of Korea
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Flynn MF, Kelly M, Dooley JSG. Nasopharyngeal Swabs vs. Nasal Aspirates for Respiratory Virus Detection: A Systematic Review. Pathogens 2021; 10:pathogens10111515. [PMID: 34832670 PMCID: PMC8620365 DOI: 10.3390/pathogens10111515] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Revised: 11/10/2021] [Accepted: 11/12/2021] [Indexed: 12/16/2022] Open
Abstract
Nasal pathogen detection sensitivities can be as low as 70% despite advances in molecular diagnostics. This may be linked to the choice of sampling method. A diagnostic test accuracy review for sensitivity was undertaken to compare sensitivity of swabbing to the nasopharynx and extracting nasal aspirates, using the PRISMA protocol, Cochrane rapid review methodology, and QUADAS-2 risk of bias tools, with meta-analysis of included studies. Sensitivities were calculated by a consensus standard of positivity by either method as the ‘gold standard.’ Insufficient sampling methodology, cross sectional study designs, and studies pooling samples across anatomical sites were excluded. Of 13 subsequently eligible studies, 8 had ‘high’ risk of bias, and 5 had ‘high’ applicability concerns. There were no statistical differences in overall sensitivities between collection methods for eight different viruses, and this did not differ with use of PCR, immunofluorescence, or culture. In one study alone, Influenza H1N1(2009) favored nasopharyngeal swabs, with aspirates having 93.3% of the sensitivity of swabs (p > 0.001). Similarly equivocal sensitivities were noted in reports detecting bacteria. The chain of sampling, from anatomical site to laboratory results, features different potential foci along which sensitivity may be lost. A fair body of evidence exists that use of a different sampling method will not yield more respiratory pathogens.
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Affiliation(s)
- Matthew F. Flynn
- School of Biomedical Sciences, Ulster University, Cromore Road, Coleraine BT52 1SA, UK;
- Altnagelvin Area Hospital, Glenshane Road, Londonderry BT47 6SB, UK;
- Correspondence:
| | - Martin Kelly
- Altnagelvin Area Hospital, Glenshane Road, Londonderry BT47 6SB, UK;
| | - James S. G. Dooley
- School of Biomedical Sciences, Ulster University, Cromore Road, Coleraine BT52 1SA, UK;
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Epidemiology of Human Metapneumovirus-associated Lower Respiratory Tract Infections in African Children: Systematic Review and Meta-analysis. Pediatr Infect Dis J 2021; 40:479-485. [PMID: 33480663 DOI: 10.1097/inf.0000000000003041] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
BACKGROUND Human metapneumovirus (hMPV) has been associated with upper and lower respiratory tract infections (LRTI) in children and adults. This systematic review evaluated the epidemiology of hMPV-associated LRTI, including severe acute respiratory infection (SARI) hospitalization or clinically diagnosed severe pneumonia, in African children under 5 years of age. METHODS We searched Science Direct, PubMed, Cochrane Central, Scopus, and WHO regional databases using the terms "("Human metapneumovirus" AND "Africa") OR ("hMPV" AND "Africa")" up to September 17, 2020. Other sources included ClinicalTrials.gov to obtain unpublished data. Studies were included if children were less than 5 years of age and hospitalized with hMPV-associated LRTI, SARI or if clinically diagnosed with severe pneumonia in the community. The main outcomes were prevalence of hMPV identified among children with hospitalized LRTI or SARI. We further calculated odds ratios for hMPV in cases with LRTI compared with non-LRTI controls. Pooled results were calculated using a random-effects model. RESULTS Thirty studies were eligible for inclusion in the review. The prevalence of hMPV-LRTI/SARI among hospitalized and severe pneumonia cases was 4.7% [95% confidence interval (CI): 3.9-5.6, I2 = 95.0]. The case-control studies indicated that hMPV was 2.0-fold (95% CI: 0.9-4.4) more likely to be identified in LRTI cases (10.3%) than controls (6.0%). Three of 5 studies reported hMPV-associated LRTI case fatality risk, with a pooled estimate of 1.3% (95% CI: 0.3-2.9; I2 = 49). CONCLUSIONS hMPV was associated with approximately 5% of LRTI/SARI hospitalizations or severe pneumonia cases in Africa.
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Abu-Raya B, Goldfarb DM, Smieja M, Luinstra K, Richard-Greenblatt M, Steenhoff AP, Feemster KA, Arscott-Mills T, Cunningham CK, Shah SS, Patel MZ, Kelly MS, Sadarangani M. The prevalence and clinical characteristics of pertussis-associated pneumonia among infants in Botswana. BMC Pediatr 2019; 19:444. [PMID: 31733643 PMCID: PMC6858628 DOI: 10.1186/s12887-019-1820-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Accepted: 11/04/2019] [Indexed: 02/08/2023] Open
Abstract
Background There are scant data on the prevalence and clinical course of pertussis disease among infants with pneumonia in low- and middle-income countries. While pertussis vaccination coverage is high (≥90%) among infants in Botswana, human immunodeficiency virus (HIV) infection affects nearly one-third of pregnancies. We aimed to evaluate the prevalence and clinical course of pertussis disease in a cohort of HIV-unexposed uninfected (HUU), HIV-exposed uninfected (HEU), and HIV-infected infants with pneumonia in Botswana. Methods We recruited children 1–23 months of age with clinical pneumonia at a tertiary care hospital in Gaborone, Botswana between April 2012 and June 2016. We obtained nasopharyngeal swab specimens at enrollment and tested these samples using a previously validated in-house real-time PCR assay that detects a unique sequence of the porin gene of Bordetella pertussis. Results B. pertussis was identified in 1/248 (0.4%) HUU, 3/110 (2.7%) HEU, and 0/33 (0.0%) HIV-infected children. All pertussis-associated pneumonia cases occurred in infants 1–5 months of age (prevalence, 1.0% [1/103] in HUU and 4.8% [3/62] in HEU infants). No HEU infants with pertussis-associated pneumonia were taking cotrimoxazole prophylaxis at the time of hospital presentation. One HUU infant with pertussis-associated pneumonia required intensive care unit admission for mechanical ventilation, but there were no deaths. Conclusions The prevalence of pertussis was low among infants and young children with pneumonia in Botswana. Although vaccination against pertussis in pregnancy is designed to prevent classical pertussis disease, reduction of pertussis-associated pneumonia might be an important additional benefit.
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Affiliation(s)
- Bahaa Abu-Raya
- Vaccine Evaluation Center, BC Children's Hospital Research Institute, University of British Columbia, 950 West 28th Avenue, Vancouver, BC, V5Z 4H4, Canada. .,Division of Infectious Diseases, Department of Pediatrics, University of British Columbia, Vancouver, BC, Canada.
| | - David M Goldfarb
- Division of Infectious Diseases, Department of Pediatrics, University of British Columbia, Vancouver, BC, Canada.,Botswana-University of Pennsylvania Partnership, Gaborone, Botswana.,Department of Pathology and Laboratory Medicine, BC Children's Hospital, Vancouver, British Columbia, Canada
| | - Marek Smieja
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, Ontario, Canada
| | - Kathy Luinstra
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, Ontario, Canada
| | | | - Andrew P Steenhoff
- Botswana-University of Pennsylvania Partnership, Gaborone, Botswana.,Division of Infectious Diseases, Children's Hospital of Philadelphia, Philadelphia, PA, USA.,Global Health Center, Children's Hospital of Philadelphia, Philadelphia, PA, USA.,Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Kristen A Feemster
- Division of Infectious Diseases, Children's Hospital of Philadelphia, Philadelphia, PA, USA.,Global Health Center, Children's Hospital of Philadelphia, Philadelphia, PA, USA.,Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.,Division of Disease Control, Philadelphia Department of Public Health, Philadelphia, PA, USA
| | - Tonya Arscott-Mills
- Botswana-University of Pennsylvania Partnership, Gaborone, Botswana.,Global Health Center, Children's Hospital of Philadelphia, Philadelphia, PA, USA.,Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Coleen K Cunningham
- Division of Pediatric Infectious Diseases, Duke University Medical Center, Durham, NC, USA
| | - Samir S Shah
- Divisions of Hospital Medicine and Infectious Diseases, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Mohamed Zaakir Patel
- Department of Paediatrics and Adolescent Health, University of Botswana School of Medicine, Gaborone, Botswana
| | - Matthew S Kelly
- Botswana-University of Pennsylvania Partnership, Gaborone, Botswana.,Global Health Center, Children's Hospital of Philadelphia, Philadelphia, PA, USA.,Division of Pediatric Infectious Diseases, Duke University Medical Center, Durham, NC, USA
| | - Manish Sadarangani
- Vaccine Evaluation Center, BC Children's Hospital Research Institute, University of British Columbia, 950 West 28th Avenue, Vancouver, BC, V5Z 4H4, Canada.,Division of Infectious Diseases, Department of Pediatrics, University of British Columbia, Vancouver, BC, Canada
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Wang L, Yang S, Yan X, Liu T, Feng Z, Li G. Comparing the yield of oropharyngeal swabs and sputum for detection of 11 common pathogens in hospitalized children with lower respiratory tract infection. Virol J 2019; 16:84. [PMID: 31234918 PMCID: PMC6591818 DOI: 10.1186/s12985-019-1177-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Accepted: 05/07/2019] [Indexed: 12/01/2022] Open
Abstract
Background Advances in molecular laboratory techniques are changing the prospects for the diagnosis of viral infectious diseases. Multiplex polymerase chain reaction assay (multiplex-PCR) can detect dozens of pathogens simultaneously, greatly reducing turnaround time (TAT) and improving detection sensitivity. But as a double-edged sword, due to the high sensitivity of PCR, the type of respiratory specimens is critical to diagnosis. In this work, we performed a head-to-head comparison to evaluate the multiplex-PCR yields between two samples, sputum and flocked oropharyngeal swabs (OPS). Methods Eleven common respiratory pathogens were tested in hospitalized children< 13 years of age who met the criteria for lower respiratory tract infection by GeXP-based multiplex-PCR of paired OPS and sputum. Results From January to June 2018, 440 children with paired OPS and sputum were tested. The positive rate was 84% (369/440) for OPS and 88% (386/440) for sputum (p = .007). The frequency of detection of HRV, RSV, Influenza A virus, HMPV, parainfluenza virus, adenovirus, M. pneumoniae, coronavirus, bocavirus and C. pneumoniae in sputa was higher than that of OPSs (all p < .001). Both types of specimens had similarly very good kappa values for most of pathogens, except for Mycoplasma pneumonia (κ = 0.61) and Chlamydia pneumoniae (κ = 0.24). Additionally, 79.3% (349/440) of cases showed consistent results between the two types of samples, and they were significantly younger than patients with inconsistent results (p = .002). Conclusions Flocked oropharyngeal swabs and sputum performed similarly for the detection of common respiratory pathogens in hospitalized children by multiplex-PCR, except for Mycoplasma pneumoniae and Chlamydia pneumoniae. Young patients are likely to have consistent results between the two specimens. Electronic supplementary material The online version of this article (10.1186/s12985-019-1177-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Le Wang
- Institute of Pediatric Research, Children's Hospital of Hebei Province, Shijiazhuang, 050031, China
| | - Shuo Yang
- Institute of Pediatric Research, Children's Hospital of Hebei Province, Shijiazhuang, 050031, China
| | - Xiaotong Yan
- Institute of Pediatric Research, Children's Hospital of Hebei Province, Shijiazhuang, 050031, China
| | - Teng Liu
- Institute of Pediatric Research, Children's Hospital of Hebei Province, Shijiazhuang, 050031, China
| | - Zhishan Feng
- Hebei General Hospital, Shijiazhuang, 050000, China.
| | - Guixia Li
- Institute of Pediatric Research, Children's Hospital of Hebei Province, Shijiazhuang, 050031, China.
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Pertussis in Low and Medium Income Countries: A Pragmatic Approach. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1183:137-149. [DOI: 10.1007/5584_2019_409] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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Soofie N, Nunes MC, Kgagudi P, van Niekerk N, Makgobo T, Agosti Y, Hwinya C, Pathirana J, Madhi SA. The Burden of Pertussis Hospitalization in HIV-Exposed and HIV-Unexposed South African Infants. Clin Infect Dis 2016; 63:S165-S173. [PMID: 27838669 PMCID: PMC5106620 DOI: 10.1093/cid/ciw545] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND There are limited data on pertussis in African children, including among human immunodeficiency virus (HIV)-exposed infants. We conducted population-based hospital surveillance to determine the incidence and clinical presentation of Bordetella pertussis-associated hospitalization in perinatal HIV-exposed and -unexposed infants. METHODS Children <12 months of age hospitalized with any sign or symptom of respiratory illness (including suspected sepsis or apnea in neonates) were enrolled from 1 January 2015 to 31 December 2015. Detailed clinical and demographic information was recorded and respiratory samples were tested by polymerase chain reaction (PCR). RESULTS The overall B. pertussis PCR positivity was 2.3% (42/1839), of which 86% (n = 36) occurred in infants <3 months of age. Bordetella pertussis was detected in 2.1% (n = 26/1257) of HIV-unexposed and 2.7% (n = 16/599) of HIV-exposed infants. The incidence (per 1000) of B. pertussis-associated hospitalization was 2.9 (95% confidence interval [CI], 1.8-4.5) and 1.9 (95% CI, 1.3-2.6) in HIV-exposed and HIV-unexposed infants, respectively (P = .09). The overall in-hospital case fatality ratio among the cases was 4.8% (2/42), both deaths of which occurred in HIV-exposed infants <3 months of age. Among cases, presence of cough ≥14 days (20.5%) and paroxysmal coughing spells (33.3%) at diagnosis were uncommon. Only 16 (38%) B. pertussis-associated hospitalizations fulfilled the Centers for Diseases Control and Prevention case definition of "definite" pertussis. CONCLUSIONS Bordetella pertussis contributed to a modest proportion of all-cause respiratory illness hospitalization among black-African children, with a trend for higher incidence among HIV-exposed than HIV-unexposed infants. Maternal vaccination of pregnant women should be considered to reduce the burden of pertussis hospitalization in this population.
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Affiliation(s)
- Nasiha Soofie
- Department of Science and Technology/National Research Foundation, Vaccine Preventable Diseases
- Medical Research Council, Respiratory and Meningeal Pathogens Research Unit, University of the Witwatersrand
| | - Marta C Nunes
- Department of Science and Technology/National Research Foundation, Vaccine Preventable Diseases
- Medical Research Council, Respiratory and Meningeal Pathogens Research Unit, University of the Witwatersrand
| | - Prudence Kgagudi
- Department of Science and Technology/National Research Foundation, Vaccine Preventable Diseases
- Medical Research Council, Respiratory and Meningeal Pathogens Research Unit, University of the Witwatersrand
| | - Nadia van Niekerk
- Department of Science and Technology/National Research Foundation, Vaccine Preventable Diseases
- Medical Research Council, Respiratory and Meningeal Pathogens Research Unit, University of the Witwatersrand
| | - Tselane Makgobo
- Department of Science and Technology/National Research Foundation, Vaccine Preventable Diseases
- Medical Research Council, Respiratory and Meningeal Pathogens Research Unit, University of the Witwatersrand
| | - Yasmeen Agosti
- Department of Science and Technology/National Research Foundation, Vaccine Preventable Diseases
- Medical Research Council, Respiratory and Meningeal Pathogens Research Unit, University of the Witwatersrand
| | - Cleopas Hwinya
- Department of Science and Technology/National Research Foundation, Vaccine Preventable Diseases
- Medical Research Council, Respiratory and Meningeal Pathogens Research Unit, University of the Witwatersrand
| | - Jayani Pathirana
- Department of Science and Technology/National Research Foundation, Vaccine Preventable Diseases
- Medical Research Council, Respiratory and Meningeal Pathogens Research Unit, University of the Witwatersrand
| | - Shabir A Madhi
- Department of Science and Technology/National Research Foundation, Vaccine Preventable Diseases
- Medical Research Council, Respiratory and Meningeal Pathogens Research Unit, University of the Witwatersrand
- National Institute for Communicable Diseases, National Health Laboratory Service, Centre for Respiratory Diseases and Meningitis, Johannesburg, South Africa
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