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Miellet WR, Almeida ST, Trzciński K, Sá-Leão R. Streptococcus pneumoniae carriage studies in adults: Importance, challenges, and key issues to consider when using quantitative PCR-based approaches. Front Microbiol 2023; 14:1122276. [PMID: 36910231 PMCID: PMC9994646 DOI: 10.3389/fmicb.2023.1122276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 01/31/2023] [Indexed: 02/18/2023] Open
Abstract
Streptococcus pneumoniae causes significant morbidity and mortality among older adults. Detection of pneumococcal carriage is an accepted endpoint in pneumococcal conjugate vaccine studies. However, low sensitivity of culture-based approaches and nasopharyngeal samples have hampered adult S. pneumoniae carriage studies in the past. In contrast, detection of adult S. pneumoniae carriers with qPCR-based approaches can achieve high sensitivity and specificity and qPCR-based testing of oral samples improves accuracy of adult carriage detection. In this Viewpoint we outline a strategy for accurate qPCR-based testing. We recommend a dual-target approach for S. pneumoniae qPCR detection as no genetic target is universally present among or solely unique to it. Furthermore, we advise the evaluation of concordance among quantified qPCR targets to improve the accuracy of S. pneumoniae testing and qPCR-based serotyping. We do not recommend omission of qPCR-based oral sample testing as it will likely result in an underestimation of true adult carrier rates.
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Affiliation(s)
- Willem R Miellet
- Department of Pediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht, Netherlands.,Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, Netherlands
| | - Sónia T Almeida
- Laboratory of Molecular Microbiology of Human Pathogens, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Krzysztof Trzciński
- Department of Pediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht, Netherlands
| | - Raquel Sá-Leão
- Laboratory of Molecular Microbiology of Human Pathogens, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
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Miellet WR, van Veldhuizen J, Litt D, Mariman R, Wijmenga-Monsuur AJ, Nieuwenhuijsen T, Christopher J, Thombre R, Eletu S, Bosch T, Rots NY, van Houten MA, Miller E, Fry NK, Sanders EAM, Trzciński K. A spitting image: molecular diagnostics applied to saliva enhance detection of Streptococcus pneumoniae and pneumococcal serotype carriage. Front Microbiol 2023; 14:1156695. [PMID: 37138599 PMCID: PMC10149683 DOI: 10.3389/fmicb.2023.1156695] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 03/27/2023] [Indexed: 05/05/2023] Open
Abstract
Background Despite strong historical records on the accuracy of saliva testing, oral fluids are considered poorly suited for pneumococcal carriage detection. We evaluated an approach for carriage surveillance and vaccine studies that increases the sensitivity and specificity of pneumococcus and pneumococcal serotype detection in saliva samples. Methods Quantitative PCR (qPCR)-based methods were applied to detect pneumococcus and pneumococcal serotypes in 971 saliva samples collected from 653 toddlers and 318 adults. Results were compared with culture-based and qPCR-based detection in nasopharyngeal samples collected from children and in nasopharyngeal and oropharyngeal samples collected from adults. Optimal C q cut-offs for positivity in qPCRs were determined via receiver operating characteristic curve analysis and accuracy of different approaches was assessed using a composite reference for pneumococcal and for serotype carriage based on isolation of live pneumococcus from the person or positivity of saliva samples determined with qPCR. To evaluate the inter-laboratory reproducibility of the method, 229 culture-enriched samples were tested independently in the second center. Results In total, 51.5% of saliva samples from children and 31.8% of saliva samples from adults were positive for pneumococcus. Detection of pneumococcus by qPCR in culture-enriched saliva exhibited enhanced sensitivity and higher agreement with a composite reference compared to diagnostic culture of nasopharyngeal samples in children (Cohen's κ: 0.69-0.79 vs. 0.61-0.73) and in adults (κ: 0.84-0.95 vs. 0.04-0.33) and culture of oropharyngeal samples in adults (κ: 0.84-0.95 vs. -0.12-0.19). Similarly, detection of serotypes with qPCR in culture-enriched saliva exhibited enhanced sensitivity and higher agreement with a composite reference compared to nasopharyngeal culture in children (κ: 0.73-0.82 vs. 0.61-0.73) and adults (κ: 0.90-0.96 vs. 0.00-0.30) and oropharyngeal culture in adults (κ: 0.90-0.96 vs. -0.13 to 0.30). However, results of qPCRs targeting serotype 4, 5, and 17F and serogroups 9, 12, and 35 were excluded due to assays' lack of specificity. We observed excellent quantitative agreement for qPCR-based detection of pneumococcus between laboratories. After exclusion of serotype/serogroup-specific assays with insufficient specificity, moderate agreement (κ 0.68, 95% CI 0.58-0.77) was observed. Conclusion Molecular testing of culture-enriched saliva samples improves the sensitivity of overall surveillance of pneumococcal carriage in children and adults, but limitations of qPCR-based approaches for pneumococcal serotypes carriage detection should be considered.
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Affiliation(s)
- Willem R. Miellet
- Department of Pediatric Immunology and Infectious Diseases, Wilhelmina Children’s Hospital, University Medical Center Utrecht, Utrecht, Netherlands
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, Netherlands
- Willem R. Miellet,
| | - Janieke van Veldhuizen
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, Netherlands
| | - David Litt
- Respiratory and Vaccine Preventable Bacteria Reference Unit (RVPBRU), UK Health Security Agency, London, United Kingdom
| | - Rob Mariman
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, Netherlands
| | - Alienke J. Wijmenga-Monsuur
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, Netherlands
| | - Tessa Nieuwenhuijsen
- Department of Pediatric Immunology and Infectious Diseases, Wilhelmina Children’s Hospital, University Medical Center Utrecht, Utrecht, Netherlands
| | - Jennifer Christopher
- Respiratory and Vaccine Preventable Bacteria Reference Unit (RVPBRU), UK Health Security Agency, London, United Kingdom
| | - Rebecca Thombre
- Respiratory and Vaccine Preventable Bacteria Reference Unit (RVPBRU), UK Health Security Agency, London, United Kingdom
| | - Seyi Eletu
- Respiratory and Vaccine Preventable Bacteria Reference Unit (RVPBRU), UK Health Security Agency, London, United Kingdom
| | - Thijs Bosch
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, Netherlands
| | - Nynke Y. Rots
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, Netherlands
| | | | - Elizabeth Miller
- Department of Infectious Disease Epidemiology, Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Norman K. Fry
- Respiratory and Vaccine Preventable Bacteria Reference Unit (RVPBRU), UK Health Security Agency, London, United Kingdom
- Immunisation and Vaccine Preventable Diseases Division, UK Health Security Agency, London, United Kingdom
| | - Elisabeth A. M. Sanders
- Department of Pediatric Immunology and Infectious Diseases, Wilhelmina Children’s Hospital, University Medical Center Utrecht, Utrecht, Netherlands
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, Netherlands
| | - Krzysztof Trzciński
- Department of Pediatric Immunology and Infectious Diseases, Wilhelmina Children’s Hospital, University Medical Center Utrecht, Utrecht, Netherlands
- *Correspondence: Krzysztof Trzciński,
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Turner P, Sá-Leão R, Greenhill A, Leach A, Satzke C. World Health Organization (WHO) Standard Methods for Pneumococcal Carriage Studies. Clin Infect Dis 2022; 75:924-925. [PMID: 35314867 PMCID: PMC9477444 DOI: 10.1093/cid/ciac221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Paul Turner
- Cambodia Oxford Medical Research Unit, Angkor Hospital for Children, Siem Reap, Cambodia
- Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
| | - Raquel Sá-Leão
- Molecular Microbiology of Human Pathogens Laboratory, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Andrew Greenhill
- Life Sciences, School of Science, Psychology and Sport, Federation University, Churchill, Australia
| | - Amanda Leach
- Child Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, Australia
| | - Catherine Satzke
- Translational Microbiology Group, Murdoch Children’s Research Institute, Royal Children’s Hospital, Parkville, Victoria, Australia
- Department of Paediatrics, University of Melbourne, Parkville, Victoria, Australia
- Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
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4
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Miellet WR, van Veldhuizen J, Litt D, Mariman R, Wijmenga-Monsuur AJ, Badoux P, Nieuwenhuijsen T, Thombre R, Mayet S, Eletu S, Sheppard C, van Houten MA, Rots NY, Miller E, Fry NK, Sanders EAM, Trzciński K. It Takes Two to Tango: Combining Conventional Culture With Molecular Diagnostics Enhances Accuracy of Streptococcus pneumoniae Detection and Pneumococcal Serogroup/Serotype Determination in Carriage. Front Microbiol 2022; 13:859736. [PMID: 35509314 PMCID: PMC9060910 DOI: 10.3389/fmicb.2022.859736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 03/14/2022] [Indexed: 11/16/2022] Open
Abstract
Background The specificity of molecular methods for the detection of Streptococcus pneumoniae carriage is under debate. We propose a procedure for carriage surveillance and vaccine impact studies that increases the accuracy of molecular detection of live pneumococci in polymicrobial respiratory samples. Methods Culture and qPCR methods were applied to detect pneumococcus and pneumococcal serotypes in 1,549 nasopharyngeal samples collected in the Netherlands (n = 972) and England (n = 577) from 946 toddlers and 603 adults, and in paired oropharyngeal samples collected exclusively from 319 Dutch adults. Samples with no live pneumococci isolated at primary diagnostic culture yet generating signal specific for pneumococcus in qPCRs were re-examined with a second, qPCR-guided culture. Optimal Cq cut-offs for positivity in qPCRs were determined via receiver operating characteristic (ROC) curve analysis using isolation of live pneumococci from the primary and qPCR-guided cultures as reference. Results Detection of pneumococcus and pneumococcal serotypes with qPCRs in cultured (culture-enriched) nasopharyngeal samples exhibited near-perfect agreement with conventional culture (Cohen’s kappa: 0.95). Molecular methods displayed increased sensitivity of detection for multiple serotype carriage, and implementation of qPCR-guided culturing significantly increased the proportion of nasopharyngeal and oropharyngeal samples from which live pneumococcus was recovered (p < 0.0001). For paired nasopharyngeal and oropharyngeal samples from adults none of the methods applied to a single sample type exhibited good agreement with results for primary and qPCR-guided nasopharyngeal and oropharyngeal cultures combined (Cohens kappa; 0.13–0.55). However, molecular detection of pneumococcus displayed increased sensitivity with culture-enriched oropharyngeal samples when compared with either nasopharyngeal or oropharyngeal primary cultures (p < 0.05). Conclusion The accuracy of pneumococcal carriage surveillance can be greatly improved by complementing conventional culture with qPCR and vice versa, by using results of conventional and qPCR-guided cultures to interpret qPCR data. The specificity of molecular methods for the detection of live pneumococci can be enhanced by incorporating statistical procedures based on ROC curve analysis. The procedure we propose for future carriage surveillance and vaccine impact studies improves detection of pneumococcal carriage in adults in particular and enhances the specificity of serotype carriage detection.
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Affiliation(s)
- Willem R Miellet
- Department of Pediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital, University Medical Center Utrecht (UMCU), Utrecht, Netherlands.,Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, Netherlands
| | - Janieke van Veldhuizen
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, Netherlands
| | - David Litt
- Respiratory and Vaccine Preventable Bacterial Reference Unit (RVPBRU), Public Health England - National Infection Service, London, United Kingdom
| | - Rob Mariman
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, Netherlands
| | - Alienke J Wijmenga-Monsuur
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, Netherlands
| | - Paul Badoux
- Regional Laboratory of Public Health (Streeklab) Haarlem, Haarlem, Netherlands
| | - Tessa Nieuwenhuijsen
- Department of Pediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital, University Medical Center Utrecht (UMCU), Utrecht, Netherlands
| | - Rebecca Thombre
- Respiratory and Vaccine Preventable Bacterial Reference Unit (RVPBRU), Public Health England - National Infection Service, London, United Kingdom
| | - Sanaa Mayet
- Respiratory and Vaccine Preventable Bacterial Reference Unit (RVPBRU), Public Health England - National Infection Service, London, United Kingdom
| | - Seyi Eletu
- Respiratory and Vaccine Preventable Bacterial Reference Unit (RVPBRU), Public Health England - National Infection Service, London, United Kingdom
| | - Carmen Sheppard
- Respiratory and Vaccine Preventable Bacterial Reference Unit (RVPBRU), Public Health England - National Infection Service, London, United Kingdom
| | | | - Nynke Y Rots
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, Netherlands
| | - Elizabeth Miller
- Immunisation and Countermeasures Division, Public Health England (PHE) - National Infection Service, London, United Kingdom
| | - Norman K Fry
- Respiratory and Vaccine Preventable Bacterial Reference Unit (RVPBRU), Public Health England - National Infection Service, London, United Kingdom.,Immunisation and Countermeasures Division, Public Health England (PHE) - National Infection Service, London, United Kingdom
| | - Elisabeth A M Sanders
- Department of Pediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital, University Medical Center Utrecht (UMCU), Utrecht, Netherlands.,Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, Netherlands
| | - Krzysztof Trzciński
- Department of Pediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital, University Medical Center Utrecht (UMCU), Utrecht, Netherlands
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5
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Ganaie F, Branche AR, Peasley M, Rosch JW, Nahm MH. Oral streptococci expressing pneumococci-like cross-reactive capsule types can affect WHO recommended pneumococcal carriage procedure. Clin Infect Dis 2021; 75:647-656. [PMID: 34891152 DOI: 10.1093/cid/ciab1003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND Carriage studies are fundamental to assess the effects of pneumococcal vaccines. Since a large proportion of oral streptococci carry homologs of pneumococcal genes, nonculture-based detection and serotyping of upper respiratory tract (URT) samples can be problematic. Herein, we investigated if culture-free molecular methods could differentiate pneumococci from oral streptococci carried by adults in URT. METHODS Paired nasopharyngeal (NP) and oropharyngeal (OP) samples were collected from 100 older adults twice a month for one year. Extracts from the combined NP+OP samples (n=2400) were subjected to lytA real-time PCR. Positive samples were subjected to pure culture isolation followed by species confirmation using multiple approaches. Multibead assay and whole-genome sequencing were used for serotyping. RESULTS lytA-PCR was positive in 301 combined NP+OP extracts, 20 of which grew probable pneumococcal-like colonies based on colony morphology and biochemical tests. Multiple approaches confirmed that four isolates were S. pneumoniae, three were S. psuedopneumoniae, and thirteen were S. mitis. Eight nonpneumococcal strains carried pneumococcus-like cps loci (size: ~18 to 25 kb) that showed >70% of nucleotide identity with their pneumococcal counterparts. While investigating the antigenic profile, we found some S. mitis strains (P066 and P107) reacted with both serotype-specific polyclonal (Type 39 and FS17b) and monoclonal (Hyp10AG1 and Hyp17FM1) antisera, whereas some strains (P063 and P074) reacted only with polyclonal antisera (Type 5 and FS35a). CONCLUSION The extensive capsular overlap suggests that pneumococcal vaccines could reduce carriage of oral streptococci expressing cross-reactive capsules. Further, direct use of culture-free PCR-based methods in URT samples has limited usefulness for carriage studies.
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Affiliation(s)
- Feroze Ganaie
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Angela R Branche
- Department of Medicine, University of Rochester, Rochester, NY, USA
| | - Michael Peasley
- Department of Medicine, University of Rochester, Rochester, NY, USA
| | - Jason W Rosch
- Department of Infectious Diseases, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Moon H Nahm
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
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6
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Nikolaou E, German EL, Blizard A, Howard A, Hitchins L, Chen T, Chadwick J, Pojar S, Mitsi E, Solórzano C, Sunny S, Dunne F, Gritzfeld JF, Adler H, Hinds J, Gould KA, Rylance J, Collins AM, Gordon SB, Ferreira DM. The nose is the best niche for detection of experimental pneumococcal colonisation in adults of all ages, using nasal wash. Sci Rep 2021; 11:18279. [PMID: 34521967 PMCID: PMC8440778 DOI: 10.1038/s41598-021-97807-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 08/10/2021] [Indexed: 11/09/2022] Open
Abstract
Previous studies have suggested that the pneumococcal niche changes from the nasopharynx to the oral cavity with age. We use an Experimental Human Pneumococcal Challenge model to investigate pneumococcal colonisation in different anatomical niches with age. Healthy adults (n = 112) were intranasally inoculated with Streptococcus pneumoniae serotype 6B (Spn6B) and were categorised as young 18-55 years (n = 57) or older > 55 years (n = 55). Colonisation status (frequency and density) was determined by multiplex qPCR targeting the lytA and cpsA-6A/B genes in both raw and culture-enriched nasal wash and oropharyngeal swab samples collected at 2-, 7- and 14-days post-exposure. For older adults, raw and culture-enriched saliva samples were also assessed. 64% of NW samples and 54% of OPS samples were positive for Spn6B in young adults, compared to 35% of NW samples, 24% of OPS samples and 6% of saliva samples in older adults. Many colonisation events were only detected in culture-enriched samples. Experimental colonisation was detected in 72% of young adults by NW and 63% by OPS. In older adults, this was 51% by NW, 36% by OPS and 9% by saliva. The nose, as assessed by nasal wash, is the best niche for detection of experimental pneumococcal colonisation in both young and older adults.
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Affiliation(s)
- Elissavet Nikolaou
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, 1st Daulby Street, Liverpool, L7 8XZ, UK.
| | - Esther L German
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, 1st Daulby Street, Liverpool, L7 8XZ, UK.
| | - Annie Blizard
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, 1st Daulby Street, Liverpool, L7 8XZ, UK
| | - Ashleigh Howard
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, 1st Daulby Street, Liverpool, L7 8XZ, UK
| | - Lisa Hitchins
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, 1st Daulby Street, Liverpool, L7 8XZ, UK
| | - Tao Chen
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, 1st Daulby Street, Liverpool, L7 8XZ, UK
| | - Jim Chadwick
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, 1st Daulby Street, Liverpool, L7 8XZ, UK
| | - Sherin Pojar
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, 1st Daulby Street, Liverpool, L7 8XZ, UK
| | - Elena Mitsi
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, 1st Daulby Street, Liverpool, L7 8XZ, UK
| | - Carla Solórzano
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, 1st Daulby Street, Liverpool, L7 8XZ, UK
| | - Syba Sunny
- Medical Microbiology, Royal Liverpool University Hospital, Liverpool, UK
| | - Felicity Dunne
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, 1st Daulby Street, Liverpool, L7 8XZ, UK.,Institute of Inflammation and Ageing, University of Birmingham, Birmingham, UK
| | - Jenna F Gritzfeld
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, 1st Daulby Street, Liverpool, L7 8XZ, UK.,Institute of Life Course and Medical Sciences, University of Liverpool, Alder Hey Children's NHS Foundation Trust Hospital, Liverpool, UK
| | - Hugh Adler
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, 1st Daulby Street, Liverpool, L7 8XZ, UK
| | - Jason Hinds
- Infection and Immunity Research Institute, St George's University London, London, UK
| | - Katherine A Gould
- Infection and Immunity Research Institute, St George's University London, London, UK
| | - Jamie Rylance
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, 1st Daulby Street, Liverpool, L7 8XZ, UK
| | - Andrea M Collins
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, 1st Daulby Street, Liverpool, L7 8XZ, UK
| | - Stephen B Gordon
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, 1st Daulby Street, Liverpool, L7 8XZ, UK.,College of Medicine, Queen Elizabeth Central Hospital, Blantyre, Malawi
| | - Daniela M Ferreira
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, 1st Daulby Street, Liverpool, L7 8XZ, UK
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7
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Beall B. Potential Epidemiologic and Historical Implications of Capsular Serotypes Shared by Pneumococci and Their Nonpneumococcal Relatives. J Infect Dis 2021; 222:343-346. [PMID: 31605123 DOI: 10.1093/infdis/jiz457] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Accepted: 09/04/2019] [Indexed: 01/31/2023] Open
Affiliation(s)
- Bernard Beall
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA
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8
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Abstract
Streptococcus pneumoniae (the pneumococcus) carriage is commonly used to measure effects of pneumococcal vaccines. Based on findings from culture-based studies, the World Health Organization recommends both nasopharyngeal (NP) and oropharyngeal (OP) sampling for detecting adult carriage. Given evidence of potential confounding by other streptococci, we evaluated molecular methods for pneumococcal identification and serotyping from 250 OP samples collected from adults in Fiji, using paired NP samples for comparison. Samples were screened using lytA quantitative PCR (qPCR), as well as pneumococcal identification and serotyping conducted by DNA microarray. A subset of OP samples were characterized by latex sweep agglutination and multiplex PCR. Alternate qPCR assays (piaB and bguR) for pneumococcal identification were evaluated. The lytA qPCR was less specific and had poor positive predictive value (PPV) in OP samples (88% and 26%, respectively) compared with NP samples (95% and 64%, respectively). Using additional targets piaB and/or bguR improved qPCR specificity in OP, although the PPV (42 to 53%) was still poor. Using microarray, we found that 102/107 (95%) of OP samples contained nonpneumococcal streptococci with partial or divergent complements of pneumococcal capsule genes. We explored 91 colonies isolated from 11 OP samples using various techniques, including multiplex PCR, latex agglutination, and microarray. We found that nonpneumococcal streptococci contribute to false positives in pneumococcal serotyping and may also contribute to spurious identification by qPCR. Our results highlight that molecular approaches should include multiple loci to minimize false-positive results when testing OP samples. Regardless of method, pneumococcal identification and serotyping results from OP samples should be interpreted with caution.IMPORTANCE Streptococcus pneumoniae (the pneumococcus) is a significant global pathogen. Accurate identification and serotyping are vital. In contrast with World Health Organization recommendations based on culture methods, we demonstrate that pneumococcal identification and serotyping with molecular methods are affected by sample type. Results from oropharyngeal samples from adults were often inaccurate. This is particularly important for assessment of vaccine impact using carriage studies, particularly in low- and middle-income countries where there are significant barriers for disease surveillance.
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9
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Wyllie AL, Pannekoek Y, Bovenkerk S, van Engelsdorp Gastelaars J, Ferwerda B, van de Beek D, Sanders EAM, Trzciński K, van der Ende A. Sequencing of the variable region of rpsB to discriminate between Streptococcus pneumoniae and other streptococcal species. Open Biol 2018; 7:rsob.170074. [PMID: 28931649 PMCID: PMC5627049 DOI: 10.1098/rsob.170074] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Accepted: 08/11/2017] [Indexed: 01/08/2023] Open
Abstract
The vast majority of streptococci colonizing the human upper respiratory tract are commensals, only sporadically implicated in disease. Of these, the most pathogenic is Mitis group member, Streptococcus pneumoniae Phenotypic and genetic similarities between streptococci can cause difficulties in species identification. Using ribosomal S2-gene sequences extracted from whole-genome sequences published from 501 streptococci, we developed a method to identify streptococcal species. We validated this method on non-pneumococcal isolates cultured from cases of severe streptococcal disease (n = 101) and from carriage (n = 103), and on non-typeable pneumococci from asymptomatic individuals (n = 17) and on whole-genome sequences of 1157 pneumococcal isolates from meningitis in the Netherlands. Following this, we tested 221 streptococcal isolates in molecular assays originally assumed specific for S. pneumoniae, targeting cpsA, lytA, piaB, ply, Spn9802, zmpC and capsule-type-specific genes. Cluster analysis of S2-sequences showed grouping according to species in line with published phylogenies of streptococcal core genomes. S2-typing convincingly distinguished pneumococci from non-pneumococcal species (99.2% sensitivity, 100% specificity). Molecular assays targeting regions of lytA and piaB were 100% specific for S. pneumoniae, whereas assays targeting cpsA, ply, Spn9802, zmpC and selected serotype-specific assays (but not capsular sequence typing) showed a lack of specificity. False positive results were over-represented in species associated with carriage, although no particular confounding signal was unique for carriage isolates.
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Affiliation(s)
- Anne L Wyllie
- Department of Paediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Yvonne Pannekoek
- Department of Medical Microbiology, Academic Medical Center, Amsterdam, the Netherlands
| | - Sandra Bovenkerk
- Department of Medical Microbiology, Academic Medical Center, Amsterdam, the Netherlands
| | - Jody van Engelsdorp Gastelaars
- Department of Paediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Bart Ferwerda
- Department of Neurology, Academic Medical Center, Amsterdam Neuroscience, Amsterdam, the Netherlands
| | - Diederik van de Beek
- Department of Neurology, Academic Medical Center, Amsterdam Neuroscience, Amsterdam, the Netherlands
| | - Elisabeth A M Sanders
- Department of Paediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht, the Netherlands.,Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Krzysztof Trzciński
- Department of Paediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Arie van der Ende
- Department of Medical Microbiology, Academic Medical Center, Amsterdam, the Netherlands.,The Netherlands Reference Laboratory for Bacterial Meningitis, Academic Medical Center, Amsterdam, the Netherlands
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10
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Sakai F, Sonaty G, Watson D, Klugman KP, Vidal JE. Development and characterization of a synthetic DNA, NUversa, to be used as a standard in quantitative polymerase chain reactions for molecular pneumococcal serotyping. FEMS Microbiol Lett 2018; 364:4082726. [PMID: 28903467 PMCID: PMC5812490 DOI: 10.1093/femsle/fnx173] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2017] [Accepted: 08/04/2017] [Indexed: 01/18/2023] Open
Abstract
Identification of Streptococcus pneumoniae and its more than 90 serotypes is routinely conducted by culture and Quellung reactions. Quantitative polymerase chain reactions (qPCRs) have been developed for molecular detection, including a pan-pneumococcus lytA assay, and assays targeting 79 serotypes. Reactions require genomic DNA from every target to prepare standards, which can be time consuming. In this study, we have developed a synthetic DNA molecule as a surrogate for genomic DNA and present new single-plex qPCR reactions to increase molecular detection to 94 pneumococcal serotypes. Specificity of these new reactions was confirmed with a limit of detection between 2 and 20 genome equivalents/reaction. A synthetic DNA (NUversa, ∼8.2 kb) was then engineered to contain all available qPCR targets for serotyping and lytA. NUversa was cloned into pUC57-Amp-modified to generate pNUversa (∼10.2 kb). Standards prepared from pNUversa and NUversa were compared against standards made out of genomic DNA. Linearity [NUversa (R2 > 0.982); pNUversa (R2 > 0.991)] and efficiency of qPCR reactions were similar to those utilizing chromosomal DNA (R2 > 0.981). Quantification with plasmid pNUversa was affected, however, whereas quantification with synthetic NUversa was comparable to that of genomic DNA. Therefore, NUversa may be utilized as DNA standard in single-plex assays of the currently known 94 pneumococcal serotypes.
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Affiliation(s)
- Fuminori Sakai
- Hubert Department of Global Health, Rollins School of Public Health, Emory University, 1518 Clifton Rd NE Room 6007, Atlanta, GA 30322, USA
| | - Griffin Sonaty
- Hubert Department of Global Health, Rollins School of Public Health, Emory University, 1518 Clifton Rd NE Room 6007, Atlanta, GA 30322, USA
| | - David Watson
- Hubert Department of Global Health, Rollins School of Public Health, Emory University, 1518 Clifton Rd NE Room 6007, Atlanta, GA 30322, USA
| | - Keith P Klugman
- Hubert Department of Global Health, Rollins School of Public Health, Emory University, 1518 Clifton Rd NE Room 6007, Atlanta, GA 30322, USA.,Bill and Melinda Gates Foundation, 500 Fifth Avenue North, Seattle, WA 98109, USA
| | - Jorge E Vidal
- Hubert Department of Global Health, Rollins School of Public Health, Emory University, 1518 Clifton Rd NE Room 6007, Atlanta, GA 30322, USA
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11
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Current challenges in the accurate identification of Streptococcus pneumoniae and its serogroups/serotypes in the vaccine era. J Microbiol Methods 2017; 141:48-54. [DOI: 10.1016/j.mimet.2017.07.015] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Revised: 07/30/2017] [Accepted: 07/31/2017] [Indexed: 11/21/2022]
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12
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Pneumococcal nasopharyngeal carriage among children in Brazil prior to the introduction of the 10-valent conjugate vaccine: a culture- and PCR-based survey. Epidemiol Infect 2017; 145:1720-1726. [DOI: 10.1017/s0950268817000449] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
SUMMARYWe performed two different approaches (broth enrichment step prior to culture (BEC) and PCR (BEPCR)) for detecting Streptococcus pneumoniae from nasopharyngeal specimens collected from 242 children aged <6 years attending one hospital (n = 140) and one childcare centre (n = 102) in a major urban area in Brazil. These specimens were collected immediately before the introduction of the 10-valent pneumococcal conjugate vaccine (PCV10) and the 13-valent vaccine (PCV13) for routine use in Brazil. Results were compared with previous findings obtained with direct culture (DC) on a selective medium. Colonisation prevalence was 58·3% (n = 141), being higher among children attending the childcare centre (62·7% vs. 55%). The culture-based methods (DC and BEC) enabled the detection of S. pneumoniae in 119 (49·2%) and 115 (47·5%) children, respectively. The PCR-based method (BEPCR) was more sensitive and 137 (56·6%) carriers were identified. Twenty-six serogroups/serotypes were identified, predominantly 6B, 19F, 14, 6A, 15C and 23F. Multiple colonisation was observed in 13 (5·4%) children. The estimated serotypes coverage of available PCVs was 40·4% for the 10-valent (included in the Brazilian immunisation programme) and 55·8% for the 13-valent (only available in private clinics). The use of robust approaches to obtain a more realistic insight about the asymptomatic carrier status is of paramount importance to estimate and assess the impact of vaccine implementation. The combination between culture-based and molecular methods constitutes a suitable strategy.
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13
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Molecular surveillance of nasopharyngeal carriage of Streptococcus pneumoniae in children vaccinated with conjugated polysaccharide pneumococcal vaccines. Sci Rep 2016; 6:23809. [PMID: 27046258 PMCID: PMC4820691 DOI: 10.1038/srep23809] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Accepted: 03/15/2016] [Indexed: 11/16/2022] Open
Abstract
Following the introduction of pneumococcal conjugate vaccines (PCVs) for infants, surveillance studies on Streptococcus pneumoniae carriage have proven valuable for monitoring vaccine effects. Here, we compared molecular versus conventional diagnostic methods in prospective cross-sectional surveillances in vaccinated infants in the Netherlands. Nasopharyngeal samples (n = 1169) from 11- and 24-month-old children, collected during autumn/winter 2010/2011 and 2012/2013, were tested by conventional culture for S. pneumoniae. DNA extracted from all culture-plate growth was tested by qPCR for pneumococcal-specific genes (lytA/piaB) and selected serotypes (including PCV13-serotypes). qPCR significantly increased the number of carriers detected compared to culture (69% vs. 57%, p < 0.0001). qPCR assays targeting vaccine-serotypes 4 and 5 proved non-specific (results excluded). For serotypes reliably targeted by qPCR, the number of serotype-carriage events detected by qPCR (n = 709) was 1.68× higher compared to culture (n = 422). There was a strong correlation (rho = 0.980; p < 0.0001) between the number of serotypes detected using qPCR and by culture. This study demonstrates the high potential of molecular methods in pneumococcal surveillances, particularly for enhanced serotype detection. We found no evidence of a hidden circulation of vaccine-targeted serotypes, despite vaccine-serotypes still significantly contributing to invasive pneumococcal disease in unvaccinated individuals, supporting the presence of a substantial S. pneumoniae reservoir outside vaccinated children.
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14
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Jauneikaite E, Tocheva AS, Jefferies JMC, Gladstone RA, Faust SN, Christodoulides M, Hibberd ML, Clarke SC. Current methods for capsular typing of Streptococcus pneumoniae. J Microbiol Methods 2015; 113:41-9. [PMID: 25819558 DOI: 10.1016/j.mimet.2015.03.006] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2014] [Revised: 02/21/2015] [Accepted: 03/08/2015] [Indexed: 10/23/2022]
Abstract
Streptococcus pneumoniae is a major respiratory tract pathogen causing pneumococcal disease mainly in children aged less than five years and in the elderly. Ninety-eight different capsular types (serotypes) of pneumococci have been reported, but pneumococcal conjugate vaccines (PCV) include polysaccharide antigens against only 7, 10 or 13 serotypes. It is therefore important to track the emergence of serotypes due to the clonal expansion of non-vaccine serotypes. Increased numbers of carried and disease-causing pneumococci are now being analysed as part of the post-PCV implementation surveillance studies and hence rapid, accurate and cost-effective typing methods are important. Here we describe serotyping methods published prior to 10th November 2014 for pneumococcal capsule typing. Sixteen methods were identified; six were based on serological tests using immunological properties of the capsular epitopes, eight were semi-automated molecular tests, and one describes the identification of capsular type directly from whole genome data, which also allows for further intra and inter-genome analyses. There was no single method that could be recommended for all pneumococcal capsular typing applications. Although the Quellung reaction is still considered to be the gold-standard, laboratories should take into account the number of pneumococcal isolates and the type of samples to be used for testing, the time frame for the results and the resources available in order to select the most appropriate method. Most likely, a combination of phenotypic and genotypic methods would be optimal to monitor and evaluate the impact of pneumococcal conjugate vaccines and to provide information for future vaccine formulations.
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Affiliation(s)
- Elita Jauneikaite
- Faculty of Medicine and Institute for Life Sciences, University of Southampton, Southampton SO16 6YD, UK; Infectious Diseases, Genome Institute of Singapore, 138672, Singapore
| | - Anna S Tocheva
- Faculty of Medicine and Institute for Life Sciences, University of Southampton, Southampton SO16 6YD, UK
| | - Johanna M C Jefferies
- Faculty of Medicine and Institute for Life Sciences, University of Southampton, Southampton SO16 6YD, UK; NIHR Southampton Respiratory Biomedical Research Unit, University Hospital Southampton NHS Foundation Trust, Southampton SO16 6YD, UK
| | - Rebecca A Gladstone
- Faculty of Medicine and Institute for Life Sciences, University of Southampton, Southampton SO16 6YD, UK
| | - Saul N Faust
- Faculty of Medicine and Institute for Life Sciences, University of Southampton, Southampton SO16 6YD, UK; NIHR Southampton Respiratory Biomedical Research Unit, University Hospital Southampton NHS Foundation Trust, Southampton SO16 6YD, UK; NIHR Wellcome Trust Clinical Research Facility, University Hospital Southampton NHS Foundation Trust, Southampton SO16 6YD, UK
| | - Myron Christodoulides
- Faculty of Medicine and Institute for Life Sciences, University of Southampton, Southampton SO16 6YD, UK
| | - Martin L Hibberd
- Infectious Diseases, Genome Institute of Singapore, 138672, Singapore; London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK
| | - Stuart C Clarke
- Faculty of Medicine and Institute for Life Sciences, University of Southampton, Southampton SO16 6YD, UK; NIHR Southampton Respiratory Biomedical Research Unit, University Hospital Southampton NHS Foundation Trust, Southampton SO16 6YD, UK.
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15
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Single-plex quantitative assays for the detection and quantification of most pneumococcal serotypes. PLoS One 2015; 10:e0121064. [PMID: 25798884 PMCID: PMC4370668 DOI: 10.1371/journal.pone.0121064] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2014] [Accepted: 01/27/2015] [Indexed: 12/04/2022] Open
Abstract
Streptococcus pneumoniae globally kills more children than any other infectious disease every year. A prerequisite for pneumococcal disease and transmission is colonization of the nasopharynx. While the introduction of pneumococcal conjugate vaccines has reduced the burden of pneumococcal disease, understanding the impact of vaccination on nasopharyngeal colonization has been hampered by the lack of sensitive quantitative methods for the detection of >90 known S. pneumoniae serotypes. In this work, we developed 27 new quantitative (q)PCR reactions and optimized 26 for a total of 53 qPCR reactions targeting pneumococcal serotypes or serogroups, including all vaccine types. Reactions proved to be target-specific with a limit of detection of 2 genome equivalents per reaction. Given the number of probes required for these assays and their unknown shelf-life, the stability of cryopreserved reagents was evaluated. Our studies demonstrate that two-year cryopreserved probes had similar limit of detection as freshly-diluted probes. Moreover, efficiency and limit of detection of 1-month cryopreserved, ready-to-use, qPCR reaction mixtures were similar to those of freshly prepared mixtures. Using these reactions, our proof-of-concept studies utilizing nasopharyngeal samples (N=30) collected from young children detected samples containing ≥2 serotypes/serogroups. Samples colonized by multiple serotypes/serogroups always had a serotype that contributes at least 50% of the pneumococcal load. In addition, a molecular approach called S6-q(PCR)2 was developed and proven to individually detect and quantify epidemiologically-important serogroup 6 strains including 6A, 6B, 6C and 6D. This technology will be useful for epidemiological studies, diagnostic platforms and to study the pneumobiome.
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16
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Krone CL, Wyllie AL, van Beek J, Rots NY, Oja AE, Chu MLJN, Bruin JP, Bogaert D, Sanders EAM, Trzciński K. Carriage of Streptococcus pneumoniae in aged adults with influenza-like-illness. PLoS One 2015; 10:e0119875. [PMID: 25789854 PMCID: PMC4366201 DOI: 10.1371/journal.pone.0119875] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2014] [Accepted: 02/03/2015] [Indexed: 01/03/2023] Open
Abstract
Incidence of pneumococcal disease is disproportionally high in infants and elderly. Nasopharyngeal colonisation by Streptococcus pneumoniae is considered a prerequisite for disease but unlike in children, carriage in elderly is rarely detected. Here, we tested for S. pneumoniae in nasopharyngeal and saliva samples collected from community-dwelling elderly with influenza-like-illness (ILI). Trans-nasal nasopharyngeal, trans-oral nasopharyngeal and saliva samples (n = 270 per sample type) were collected during winter/spring 2011/2012 from 135 persons aged 60–89 at onset of ILI and 7–9 weeks later following recovery. After samples were tested for pneumococci by conventional culture, all plate growth was collected. DNA extracted from plate harvests was tested by quantitative-PCRs (qPCR) specific for S. pneumoniae and serotypes included in the 13-valent pneumococcal conjugated vaccine (PCV13). Pneumococci were cultured from 14 of 135 (10%) elderly with none of the sampled niches showing superiority in carriage detection. With 76/270 (28%) saliva, 31/270 (11%) trans-oral and 13/270 (5%) trans-nasal samples positive by qPCR, saliva was superior to nasopharyngeal swabs (p<0.001) in qPCR-based carriage detection. Overall, from all methods used in the study, 65 of 135 (48%) elderly carried pneumococci at least once and 26 (19%) at both study time points. The difference between carriage prevalence at ILI (n = 49 or 36%) versus recovery (n = 42 or 31%) was not significant (p = 0.38). At least 23 of 91 (25%) carriage events in 19 of 65 (29%) carriers were associated with PCV13-serotypes. We detected a large reservoir of pneumococci in saliva of elderly, with PCV13-serotype distribution closely resembling the contemporary carriage of serotypes reported in the Netherlands for PCV-vaccinated infants.
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Affiliation(s)
- Cassandra L. Krone
- Paediatric Immunology and Infectious Diseases, Wilhelmina Children’s Hospital, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Anne L. Wyllie
- Paediatric Immunology and Infectious Diseases, Wilhelmina Children’s Hospital, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Josine van Beek
- Centre for Infectious Disease Control Netherlands, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Nynke Y. Rots
- Centre for Infectious Disease Control Netherlands, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Anna E. Oja
- Paediatric Immunology and Infectious Diseases, Wilhelmina Children’s Hospital, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Mei Ling J. N. Chu
- Paediatric Immunology and Infectious Diseases, Wilhelmina Children’s Hospital, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Jacob P. Bruin
- Regional Laboratory of Public Health, Haarlem, The Netherlands
| | - Debby Bogaert
- Paediatric Immunology and Infectious Diseases, Wilhelmina Children’s Hospital, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Elisabeth A. M. Sanders
- Paediatric Immunology and Infectious Diseases, Wilhelmina Children’s Hospital, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Krzysztof Trzciński
- Paediatric Immunology and Infectious Diseases, Wilhelmina Children’s Hospital, University Medical Center Utrecht, Utrecht, The Netherlands
- * E-mail:
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17
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Ramirez M. Streptococcus pneumoniae. MOLECULAR MEDICAL MICROBIOLOGY 2015:1529-1546. [DOI: 10.1016/b978-0-12-397169-2.00086-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
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18
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Direct detection and prediction of all pneumococcal serogroups by target enrichment-based next-generation sequencing. J Clin Microbiol 2014; 52:4244-52. [PMID: 25274995 DOI: 10.1128/jcm.02397-14] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Despite the availability of standard methods for pneumococcal serotyping, there is room for improvement in the available methods, in terms of throughput, multiplexing capacity, and the number of serotypes identified. We describe a target enrichment-based next-generation sequencing method applied to nasopharyngeal samples for direct detection and serogroup prediction of all known serotypes of Streptococcus pneumoniae, 32 to the serotype level and the rest to the closely related serogroup level. The method was applied to detect and to predict the serogroups of pneumococci directly in clinical samples and from sweeps of primary culture DNA, with increased detection rates versus culture-based identification and agreement with the serotypes/serogroups determined by conventional serotyping methods. We propose this method, in conjunction with traditional serotyping methods, as an alternative to rapid detection and serotyping of pneumococci.
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19
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Satzke C, Turner P, Virolainen-Julkunen A, Adrian PV, Antonio M, Hare KM, Henao-Restrepo AM, Leach AJ, Klugman KP, Porter BD, Sá-Leão R, Scott JA, Nohynek H, O'Brien KL. Standard method for detecting upper respiratory carriage of Streptococcus pneumoniae: updated recommendations from the World Health Organization Pneumococcal Carriage Working Group. Vaccine 2014; 32:165-79. [PMID: 24331112 DOI: 10.1016/j.vaccine.2013.08.062] [Citation(s) in RCA: 328] [Impact Index Per Article: 32.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2013] [Revised: 07/25/2013] [Accepted: 08/23/2013] [Indexed: 11/29/2022]
Abstract
In 2003 the World Health Organization (WHO) convened a working group and published a set of standard methods for studies measuring nasopharyngeal carriage of Streptococcus pneumoniae (the pneumococcus). The working group recently reconvened under the auspices of the WHO and updated the consensus standard methods. These methods describe the collection, transport and storage of nasopharyngeal samples, as well as provide recommendations for the identification and serotyping of pneumococci using culture and non-culture based approaches. We outline the consensus position of the working group, the evidence supporting this position, areas worthy of future research, and the epidemiological role of carriage studies. Adherence to these methods will reduce variability in the conduct of pneumococcal carriage studies undertaken in the context of pneumococcal vaccine trials, implementation studies, and epidemiology studies more generally so variability in methodology does not confound the interpretation of study findings.
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Affiliation(s)
- Catherine Satzke
- Pneumococcal Research, Murdoch Childrens Research Institute, Royal Children's Hospital, Parkville, VIC, Australia; Centre for International Child Health, Murdoch Childrens Research Institute, Royal Children's Hospital, Parkville, VIC, Australia; Department of Microbiology and Immunology, The University of Melbourne, Parkville, VIC, Australia.
| | - Paul Turner
- Microbiology Department, Angkor Hospital for Children, Siem Reap, Kingdom of Cambodia; Centre for Tropical Medicine, University of Oxford, Oxford, United Kingdom
| | - Anni Virolainen-Julkunen
- Department of Infectious Disease Surveillance and Control, National Institute for Health and Welfare, Helsinki, Finland
| | - Peter V Adrian
- MRC/Wits Respiratory and Meningeal Pathogens Research Unit, University of the Witwatersrand, Johannesburg, South Africa
| | | | - Kim M Hare
- Child Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, NT, Australia
| | | | - Amanda J Leach
- Child Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, NT, Australia
| | - Keith P Klugman
- Rollins School of Public Health, Emory University, Atlanta, GA, USA; Respiratory and Meningeal Pathogens Research Unit, University of Witwatersrand, Johannesburg, South Africa
| | - Barbara D Porter
- Pneumococcal Research, Murdoch Childrens Research Institute, Royal Children's Hospital, Parkville, VIC, Australia
| | - Raquel Sá-Leão
- Laboratory of Molecular Microbiology of Human Pathogens, Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, Portugal
| | - J Anthony Scott
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya; London School of Hygiene & Tropical Medicine, London, UK
| | - Hanna Nohynek
- Vaccine Programme Unit, National Institute for Health and Welfare, Helsinki, Finland
| | - Katherine L O'Brien
- Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
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20
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Wyllie AL, Chu MLJN, Schellens MHB, van Engelsdorp Gastelaars J, Jansen MD, van der Ende A, Bogaert D, Sanders EAM, Trzciński K. Streptococcus pneumoniae in saliva of Dutch primary school children. PLoS One 2014; 9:e102045. [PMID: 25013895 PMCID: PMC4094488 DOI: 10.1371/journal.pone.0102045] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2014] [Accepted: 06/13/2014] [Indexed: 11/19/2022] Open
Abstract
While nasopharyngeal sampling is the gold standard for the detection of Streptococcus pneumoniae carriage, historically seen, saliva sampling also seems highly sensitive for pneumococcal detection. We investigated S. pneumoniae carriage in saliva from fifty schoolchildren by conventional and molecular methods. Saliva was first culture-enriched for pneumococci, after which, DNA was extracted from all bacterial growth and tested by quantitative-PCR (qPCR) for pneumococcus-specific genes lytA and piaA. Next, serotype composition of the samples was determined by serotype-specific qPCRs, conventional-PCRs (cPCR) and sequencing of cPCR amplicons. Although only 2 (4%) of 50 samples were positive by conventional diagnostic culture, 44 (88%) were positive for pneumococci by qPCR. In total, we detected the presence of at least 81 pneumococcal strains representing 20 serotypes in samples from 44 carriers with 23 carriers (52%) positive for multiple (up to 6) serotypes. The number of serotypes detected per sample correlated with pneumococcal abundance. This study shows that saliva could be used as a tool for future pneumococcal surveillance studies. Furthermore, high rates of pneumococcal carriage and co-carriage of multiple pneumococcal strains together with a large number of serotypes in circulation suggests a ubiquitous presence of S. pneumoniae in saliva of school-aged children. Our results also suggest that factors promoting pneumococcal carriage within individual hosts may weaken competitive interactions between S. pneumoniae strains.
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Affiliation(s)
- Anne L. Wyllie
- Department of Paediatric Immunology and Infectious Diseases, Wilhelmina's Children Hospital, University Medical Centre Utrecht, Utrecht, The Netherlands
| | - Mei Ling J. N. Chu
- Department of Paediatric Immunology and Infectious Diseases, Wilhelmina's Children Hospital, University Medical Centre Utrecht, Utrecht, The Netherlands
| | - Mariëlle H. B. Schellens
- Department of Paediatric Immunology and Infectious Diseases, Wilhelmina's Children Hospital, University Medical Centre Utrecht, Utrecht, The Netherlands
| | - Jody van Engelsdorp Gastelaars
- Department of Paediatric Immunology and Infectious Diseases, Wilhelmina's Children Hospital, University Medical Centre Utrecht, Utrecht, The Netherlands
| | - Marc D. Jansen
- Brain Center Rudolf Magnus, Department of Neurology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Arie van der Ende
- Department of Medical Microbiology and the Netherlands Reference Laboratory for Bacterial Meningitis, Academic Medical Center, Amsterdam, The Netherlands
| | - Debby Bogaert
- Department of Paediatric Immunology and Infectious Diseases, Wilhelmina's Children Hospital, University Medical Centre Utrecht, Utrecht, The Netherlands
| | - Elisabeth A. M. Sanders
- Department of Paediatric Immunology and Infectious Diseases, Wilhelmina's Children Hospital, University Medical Centre Utrecht, Utrecht, The Netherlands
| | - Krzysztof Trzciński
- Department of Paediatric Immunology and Infectious Diseases, Wilhelmina's Children Hospital, University Medical Centre Utrecht, Utrecht, The Netherlands
- * E-mail:
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21
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Wolter N, Tempia S, Cohen C, Madhi SA, Venter M, Moyes J, Walaza S, Malope-Kgokong B, Groome M, du Plessis M, Magomani V, Pretorius M, Hellferscee O, Dawood H, Kahn K, Variava E, Klugman KP, von Gottberg A. High nasopharyngeal pneumococcal density, increased by viral coinfection, is associated with invasive pneumococcal pneumonia. J Infect Dis 2014; 210:1649-57. [PMID: 24907383 DOI: 10.1093/infdis/jiu326] [Citation(s) in RCA: 140] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND We identified factors associated with pneumococcal colonization, high colonization density, and invasive pneumococcal pneumonia among patients hospitalized with acute lower respiratory tract infections (ALRTIs). METHODS In 2010, 4025 cases were enrolled in surveillance in South Africa. A total of 969 of 4025 systematically selected nasopharyngeal-oropharyngeal specimens (24%) were tested for respiratory viruses and Streptococcus pneumoniae by real-time polymerase chain reaction. Of these, 749 (77%) had blood tested for S. pneumoniae. RESULTS Pneumococcal colonization was detected in 55% of cases (534 of 969). On multivariable analysis that controlled for age and tuberculosis treatment, infection with influenza virus (adjusted odds ratio [OR], 2.2; 95% confidence interval [CI], 1.1-4.5), adenovirus (adjusted OR, 1.7; 95% CI, 1.1-2.7), rhinovirus (adjusted OR, 1.6; 95% CI, 1.1-2.3), and human immunodeficiency virus (HIV; adjusted OR, 1.6; 95% CI, 1.1-2.4) were associated with pneumococcal colonization. High colonization density was associated with respiratory virus coinfection (adjusted OR, 1.7; 95% CI, 1.1-2.6) and invasive pneumococcal pneumonia (adjusted OR, 2.3; 95% CI, 1.3-4.0), after adjustment for age and sex. Seven percent (52 of 749) had pneumococci detected in blood. On multivariable analysis among colonized cases, invasive pneumococcal pneumonia was associated with HIV (adjusted OR, 3.2; 95% CI, 1.4-7.5), influenza virus (adjusted OR, 8.2; 95% CI, 2.7-25.0), high colonization density (adjusted OR, 18.7; 95% CI, 2.3-155.1), and ≥5 days of hospitalization (adjusted OR, 3.7; 95% CI, 1.7-8.2). CONCLUSIONS Respiratory virus infection was associated with elevated colonization density and, in turn, invasive pneumococcal pneumonia.
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Affiliation(s)
- Nicole Wolter
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, National Health Laboratory Service Faculty of Health Sciences Medical Research Council: Respiratory and Meningeal Pathogens Research Unit
| | - Stefano Tempia
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, National Health Laboratory Service Influenza Division, Centers for Disease Control and Prevention
| | - Cheryl Cohen
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, National Health Laboratory Service Faculty of Health Sciences
| | - Shabir A Madhi
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, National Health Laboratory Service Medical Research Council: Respiratory and Meningeal Pathogens Research Unit Department of Science and Technology/National Research Foundation: Vaccine-Preventable Diseases
| | - Marietjie Venter
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, National Health Laboratory Service Zoonoses Research Unit, Department of Medical Virology, University of Pretoria
| | - Jocelyn Moyes
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, National Health Laboratory Service
| | - Sibongile Walaza
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, National Health Laboratory Service
| | - Babatyi Malope-Kgokong
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, National Health Laboratory Service
| | - Michelle Groome
- Department of Science and Technology/National Research Foundation: Vaccine-Preventable Diseases
| | - Mignon du Plessis
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, National Health Laboratory Service Faculty of Health Sciences Medical Research Council: Respiratory and Meningeal Pathogens Research Unit
| | - Victoria Magomani
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, National Health Laboratory Service Medical Research Council: Respiratory and Meningeal Pathogens Research Unit
| | - Marthi Pretorius
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, National Health Laboratory Service
| | - Orienka Hellferscee
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, National Health Laboratory Service
| | - Halima Dawood
- Pietermaritzburg Metropolitan Hospitals University of KwaZulu Natal
| | - Kathleen Kahn
- MRC/Wits Rural Public Health and Health Transition Research Unit Research Unit (Agincourt), Faculty of Health Sciences, University of the Witwatersrand, Johannesburg Centre for Global Health Research, Umeå University, Sweden INDEPTH Network, Accra, Ghana
| | | | - Keith P Klugman
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, National Health Laboratory Service Hubert Department of Global Health, Rollins School of Public Health Division of Infectious Diseases, School of Medicine, Emory University, Atlanta, Georgia
| | - Anne von Gottberg
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, National Health Laboratory Service Faculty of Health Sciences Medical Research Council: Respiratory and Meningeal Pathogens Research Unit
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Almeida ST, Nunes S, Santos Paulo AC, Valadares I, Martins S, Breia F, Brito-Avô A, Morais A, de Lencastre H, Sá-Leão R. Low prevalence of pneumococcal carriage and high serotype and genotype diversity among adults over 60 years of age living in Portugal. PLoS One 2014; 9:e90974. [PMID: 24604030 PMCID: PMC3946249 DOI: 10.1371/journal.pone.0090974] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2013] [Accepted: 02/06/2014] [Indexed: 11/27/2022] Open
Abstract
Pneumococcal disease is frequent at the extremes of age. While several studies have looked at colonization among young children, much less is known among the elderly. We aimed to evaluate pneumococcal carriage among elderly adults living in Portugal. Between April 2010 and December 2012, nasopharyngeal and oropharyngeal swabs of adults over 60 years of age, living in an urban area (n = 1,945) or in a rural area (n = 1,416), were obtained. Pneumococci were isolated by culture-based standard procedures, identified by optochin susceptibility, bile solubility and PCR screening for lytA and cpsA, and characterized by antibiotype, serotype, and MLST. Associations between pneumococcal carriage, socio-demographic and clinical characteristics were evaluated by univariate analysis and multiple logistic regression. The global prevalence of carriage was 2.3% (95% CI: 1.8-2.8). In the multiple logistic regression analysis, smoking, being at a retirement home, and living in a rural area increased the odds of being a pneumococcal carrier by 4.4-fold (95% CI: 1.9-9.2), 2.0-fold (95% CI: 1.1-3.6) and 2.0-fold (95% CI: 1.2-3.5), respectively. Among the 77 pneumococcal isolates, 26 serotypes and 40 STs were identified. The most prevalent serotypes were (in decreasing order) 19A, 6C, 22F, 23A, 35F, 11A, and 23B, which accounted, in total, for 60.0% of the isolates. Most isolates (93.5%) had STs previously described in the MLST database. Resistance to macrolides, non-susceptibility to penicillin and multidrug resistance were found in 19.5%, 11.7%, and 15.6% of the isolates, respectively. We conclude that the prevalence of pneumococcal carriage in the elderly, in Portugal, as determined by culture-based methods, is low. Serotype and genotype diversity is high. Living in a rural area, in a retirement home, and being a smoker increased the risk of pneumococcal carriage. This study contributes to the establishment of a baseline that may be used to monitor how novel pneumococcal vaccines impact on colonization among the elderly.
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Affiliation(s)
- Sónia T. Almeida
- Laboratory of Molecular Microbiology of Human Pathogens, Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Sónia Nunes
- Laboratory of Molecular Microbiology of Human Pathogens, Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Ana Cristina Santos Paulo
- Laboratory of Molecular Microbiology of Human Pathogens, Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Idalina Valadares
- Agrupamento de Centros de Saúde Oeiras - Carnaxide, Oeiras, Portugal
| | - Sara Martins
- Agrupamento de Centros de Saúde Oeiras - Carnaxide, Oeiras, Portugal
| | - Fátima Breia
- Agrupamento de Centros de Saúde Alentejo Central II, Évora, Portugal
| | - António Brito-Avô
- Agrupamento de Centros de Saúde Oeiras - Carnaxide, Oeiras, Portugal
| | - Ana Morais
- Agrupamento de Centros de Saúde Oeiras - Carnaxide, Oeiras, Portugal
| | - Hermínia de Lencastre
- Laboratory of Molecular Genetics, Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, Portugal
- Laboratory of Microbiology of Infectious Diseases, The Rockefeller University, New York, New York, United States of America
| | - Raquel Sá-Leão
- Laboratory of Molecular Microbiology of Human Pathogens, Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, Portugal
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23
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Field evaluation of culture plus latex sweep serotyping for detection of multiple pneumococcal serotype colonisation in infants and young children. PLoS One 2013; 8:e67933. [PMID: 23844133 PMCID: PMC3699458 DOI: 10.1371/journal.pone.0067933] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2013] [Accepted: 05/23/2013] [Indexed: 11/19/2022] Open
Abstract
Background Nasopharyngeal swab (NPS) culture by World Health Organisation (WHO) methodology underestimates multiple pneumococcal serotype colonisation compared to a simple culture and latex sweep method. The impacts of this on descriptions of pneumococcal serotype distributions and colonisation dynamics in infancy are not clear. Methods 8,736 NPS collected from infants enrolled into a longitudinal study were processed to evaluate the field utility of the latex sweep method. 1,107 had previously been cultured by WHO methodology. Additionally, colonisation results were compared in 100 matched pairs of infants, where swabs from an individual were cultured either by WHO or latex sweep method. Results In 1,107 swabs cultured by both methods, the latex sweep method was three times more likely to detect colonisation with multiple pneumococcal serotypes than the WHO method (p<0.001). At least one common serotype was identified in 91.2% of swabs from which typeable pneumococci were detected by both methods. Agreement improved with increasing colonisation density (p = 0.03). Estimates of age at first pneumococcal acquisition and colonisation duration were not affected by culture/serotyping method. However, a greater number of serotype carriage episodes were detected in infants cultured by latex sweep (p = 0.03). The overall rate of non-vaccine type pneumococcal acquisition was also greater in infants cultured by latex sweep (p = 0.04). Conclusions Latex sweep serotyping was feasible to perform on a large specimen collection. Multiple serotype colonisation detection was significantly improved compared with WHO methodology. However, use of the latex sweep method is unlikely to significantly alter colonisation study serotype distribution or colonisation dynamics results.
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Carvalho MDG, Pimenta FC, Moura I, Roundtree A, Gertz RE, Li Z, Jagero G, Bigogo G, Junghae M, Conklin L, Feikin DR, Breiman RF, Whitney CG, Beall BW. Non-pneumococcal mitis-group streptococci confound detection of pneumococcal capsular serotype-specific loci in upper respiratory tract. PeerJ 2013; 1:e97. [PMID: 23825797 PMCID: PMC3698467 DOI: 10.7717/peerj.97] [Citation(s) in RCA: 80] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2013] [Accepted: 06/10/2013] [Indexed: 11/20/2022] Open
Abstract
We performed culture-based and PCR-based tests for pneumococcal identification and serotyping from carriage specimens collected in rural and urban Kenya. Nasopharyngeal specimens from 237 healthy children <5 years old (C-NPs) and combined nasopharyngeal/oropharyngeal specimens from 158 adults (A-NP/OPs, 118 HIV-positive) were assessed using pneumococcal isolation (following broth culture enrichment) with Quellung-based serotyping, real-time lytA-PCR, and conventional multiplexed PCR-serotyping (cmPCR). Culture-based testing from C-NPs, HIV-positive A-NP/OPs, and HIV-negative A-NP/OPs revealed 85.2%, 40.7%, and 12.5% pneumococcal carriage, respectively. In contrast, cmPCR serotypes were found in 93.2%, 98.3%, and 95.0% of these sets, respectively. Two of 16 lytA-negative C-NPs and 26 of 28 lytA-negative A-NP/OPs were cmPCR-positive for 1–10 serotypes (sts) or serogroups (sgs). A-NP/OPs averaged 5.5 cmPCR serotypes/serogroups (5.2 in HIV-positive, 7.1 in HIV-negative) and C-NPs averaged 1.5 cmPCR serotypes/serogroups. cmPCR serotypes/serogroups from lytA-negative A-NP/OPs included st2, st4, sg7F/7A, sg9N/9L, st10A, sg10F/10C/33C, st13, st17F, sg18C/18A/18B/18F, sg22F/22A, and st39. Nine strains of three non-pneumococcal species (S. oralis, S. mitis, and S. parasanguinis) (7 from A-OP, 1 from both A-NP and A-OP, and 1 from C-NP) were each cmPCR-positive for one of 7 serotypes/serogroups (st5, st13, sg15A/15F, sg10F/10C/33C, sg33F/33A/37, sg18C/18A/18B/18F, sg12F/12A/12B/ 44/46) with amplicons revealing 83.6–99.7% sequence identity to pneumococcal references. In total, 150 cmPCR amplicons from carriage specimens were sequenced, including 25 from lytA-negative specimens. Amplicon sequences derived from specimens yielding a pneumococcal isolate with the corresponding serotype were identical or highly conserved (>98.7%) with the reference cmPCR amplicon for the st, while cmPCR amplicons from lytA-negative specimens were generally more divergent. Separate testing of 56 A-OPs and 56 A-NPs revealed that ∼94% of the positive cmPCR results from A-NP/OPs were from OP microbiota. In contrast, A-NPs yielded >2-fold more pneumococcal isolates than A-OPs. Verified and suspected non-pneumococcal cmPCR serotypes/serogroups appeared to be relatively rare in C-NPs and A-NPs compared to A-OPs. Our findings indicate that non-pneumococcal species can confound serotype-specific PCR and other sequence-based assays due to evolutionarily conserved genes most likely involved in biosynthesis of surface polysaccharide structures.
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Affiliation(s)
- Maria da Gloria Carvalho
- National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention , Atlanta , USA
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25
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Expression of Streptococcus pneumoniae Virulence-Related Genes in the Nasopharynx of Healthy Children. PLoS One 2013; 8:e67147. [PMID: 23825636 PMCID: PMC3688971 DOI: 10.1371/journal.pone.0067147] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2013] [Accepted: 05/13/2013] [Indexed: 11/19/2022] Open
Abstract
Colonization and persistence in the human nasopharynx are prerequisites for Streptococcus pneumoniae disease and carriage acquisition, which normally occurs during early childhood. Animal models and in vitro studies (i.e. cell adhesion and cell cytotoxicity assays) have revealed a number of colonization and virulence factors, as well as regulators, implicated in nasopharyngeal colonization and pathogenesis. Expression of genes encoding these factors has never been studied in the human nasopharynx. Therefore, this study analyzed expression of S. pneumoniae virulence-related genes in human nasopharyngeal samples. Our experiments first demonstrate that a density of ≥10(4) CFU/ml of S. pneumoniae cells in the nasopharynx provides enough DNA and RNA to amplify the lytA gene by conventional PCR and to detect the lytA message, respectively. A panel of 21 primers that amplified S. pneumoniae sequences was designed, and their specificity for S. pneumoniae sequences was analyzed in silico and validated against 20 related strains inhabitants of the human upper respiratory tract. These primers were utilized in molecular reactions to find out that all samples contained the genes ply, pavA, lytC, lytA, comD, codY, and mgrA, whereas nanA, nanB, pspA, and rrgB were present in ∼91-98% of the samples. Gene expression studies of these 11 targets revealed that lytC, lytA, pavA and comD were the most highly expressed pneumococcal genes in the nasopharynx whereas the rest showed a moderate to low level of expression. This is the first study to evaluate expression of virulence- and, colonization-related genes in the nasopharynx of healthy children and establishes the foundation for future gene expression studies during human pneumococcal disease.
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Ansaldi F, de Florentiis D, Canepa P, Ceravolo A, Rappazzo E, Iudici R, Martini M, Botti G, Orsi A, Icardi G, Durando P. Carriage of Streptoccoccus pneumoniae in healthy adults aged 60 years or over in a population with very high and long-lasting pneumococcal conjugate vaccine coverage in children: rationale and perspectives for PCV13 implementation. Hum Vaccin Immunother 2013; 9:614-20. [PMID: 23292052 DOI: 10.4161/hv.23253] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
A serial cross-sectional study of nasopharyngeal carriage among adults aged 60 y or over was conducted in winter-spring 2012 with the aim to describe circulating Streptococcus pneumoniae in an area, Liguria Administrative Region, where the vaccine was implemented for a decade and coverage in pediatric age group reached a value close to 100% for more than 5 y, determining a picture of very high vaccine immunological pressure. The serotype-specific carriage picture in adults was compared with that observed in children by means of a cross-sectional study performed one year before using the same sampling and laboratory methods. Cluster sampling enrolled 283 adults, representative of the open population. Detection of multi-serotype carriage was performed using, real-time PCR and primer specific PCRs. Carriage prevalence of participants with at least one positive sample adjusted for age, i.e., period prevalence, was 18.7%, considering the Ligurian population as standard population, showing that the pneumococcal carriage in the elderly is not a rare event as emerged in other surveys. The long-term use of PCV7 has resulted in strong decrease of vaccine types carriage among adults and children. A multivariate analysis showed that age class and contact with children attending day care covariates were strongly associated with Streptococcus pneumoniae carriage. A strong link between the picture observed in < 5-y-old children and ≥ 60-y-old adults emerged: a strong correlation of specific-serotype prevalence between adults and children and risk factor analysis supported the role played by inter-age-group transmission.
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Affiliation(s)
- Filippo Ansaldi
- I.R.C.C.S. "A.O.U. San Martino-IST"; Genoa, Italy; Department of Health Sciences; University of Genoa; Genoa, Italy
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27
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Sequential triplex real-time PCR assay for detecting 21 pneumococcal capsular serotypes that account for a high global disease burden. J Clin Microbiol 2012; 51:647-52. [PMID: 23224094 DOI: 10.1128/jcm.02927-12] [Citation(s) in RCA: 107] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We developed and validated a real-time PCR assay consisting of 7 triplexed reactions to identify 11 individual serotypes plus 10 small serogroups representing the majority of disease-causing isolates of Streptococcus pneumoniae. This assay targets the 13 serotypes included within the 13-valent conjugate vaccine and 8 additional key serotypes or serogroups. Advantages over other serotyping assays are described. The assay will be expanded to 40 serotypes/serogroups. We will provide periodic updates at our protocol website.
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28
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Gladstone RA, Jefferies JM, Faust SN, Clarke SC. Sampling methods for the study of pneumococcal carriage: a systematic review. Vaccine 2012; 30:6738-44. [PMID: 22981760 DOI: 10.1016/j.vaccine.2012.08.080] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2012] [Revised: 08/20/2012] [Accepted: 08/31/2012] [Indexed: 10/27/2022]
Abstract
Streptococcus pneumoniae is an important pathogen worldwide. Accurate sampling of S. pneumoniae carriage is central to surveillance studies before and following conjugate vaccination programmes to combat pneumococcal disease. Any bias introduced during sampling will affect downstream recovery and typing. Many variables exist for the method of collection and initial processing, which can make inter-laboratory or international comparisons of data complex. In February 2003, a World Health Organisation working group published a standard method for the detection of pneumococcal carriage for vaccine trials to reduce or eliminate variability. We sought to describe the variables associated with the sampling of S. pneumoniae from collection to storage in the context of the methods recommended by the WHO and those used in pneumococcal carriage studies since its publication. A search of published literature in the online PubMed database was performed on the 1st June 2012, to identify published studies that collected pneumococcal carriage isolates, conducted after the publication of the WHO standard method. After undertaking a systematic analysis of the literature, we show that a number of differences in pneumococcal sampling protocol continue to exist between studies since the WHO publication. The majority of studies sample from the nasopharynx, but the choice of swab and swab transport media is more variable between studies. At present there is insufficient experimental data that supports the optimal sensitivity of any standard method. This may have contributed to incomplete adoption of the primary stages of the WHO detection protocol, alongside pragmatic or logistical issues associated with study design. Consequently studies may not provide a true estimate of pneumococcal carriage. Optimal sampling of carriage could lead to improvements in downstream analysis and the evaluation of pneumococcal vaccine impact and extrapolation to pneumococcal disease control therefore further in depth comparisons would be of value.
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Affiliation(s)
- R A Gladstone
- Academic Unit of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, UK
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