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Peno C, Lin TY, Hislop MS, Yolda-Carr D, Farjado K, York A, Pitzer VE, Weinberger DM, Bei AK, Allicock OM, Wyllie AL. A low-cost culture- and DNA extraction-free method for the molecular detection of pneumococcal carriage in saliva. Microbiol Spectr 2024:e0059124. [PMID: 39028185 DOI: 10.1128/spectrum.00591-24] [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: 03/06/2024] [Accepted: 05/05/2024] [Indexed: 07/20/2024] Open
Abstract
Molecular methods have improved the sensitivity of the detection of pneumococcal carriage in saliva. However, they typically require sample culture enrichment and nucleic acid extraction prior to performing the detection assay and may limit scalability for extensive surveillance of pneumococcus, particularly in low-resource settings. We evaluated the performance of a DNA-extraction-free method for the detection of pneumococcus in saliva. We developed a streamlined qPCR-based protocol for the detection of pneumococcus, omitting culture enrichment and DNA extraction. Using saliva samples collected from children attending childcare centers (New Haven, CT, USA), we evaluated the detection of pneumococcus using saliva lysates as compared to purified DNA extracted from culture-enriched aliquots of the paired samples using qPCR targeting the pneumococcal piaB gene. Of the 759 saliva samples tested from 92 children [median age 3.65 years; IQR (2.46-4.78)], pneumococcus was detected in 358 (47.2%) saliva lysates prepared using the extraction-free protocol and in 369 (48.6%) DNA extracted from culture-enriched samples. We observed near-perfect agreement between the two protocols (Cohen's kappa: 0.92; 95% CI: 0.90-0.95). Despite a high correlation between CT values generated by the two methods (r = 0.93, P < 0.0001), the CT values generated from saliva lysates were higher (lower concentration) than those from culture-enriched samples (ΔCT = 6.69, P < 0.00001). The cost of detecting pneumococcus using saliva lysates was at least fivefold lower (US$2.53) compared to the cost of the culture-enriched method (range: US$13.60-US$19.46). For pneumococcal carriage surveillance in children, our findings suggest that a DNA extraction-free approach may offer a cost-effective alternative to the resource-intensive culture-enrichment method.IMPORTANCESurveillance for carriage of pneumococcus is a key component of evaluating the performance of pneumococcal vaccines and informing new vaccination strategies. To improve the scalability of pneumococcal carriage surveillance, we show that molecular detection of pneumococcus in saliva from children can be performed without culture enrichment and DNA extraction. Our findings show that using the extraction-free method can improve surveillance efforts for pneumococcal carriage in children, overcoming the resource-intensive hurdle that comes with the use of molecular methods, particularly in low-resource settings.
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Affiliation(s)
- Chikondi Peno
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, USA
| | - Tzu-Yi Lin
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, USA
| | - Maikel S Hislop
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, USA
| | - Devyn Yolda-Carr
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, USA
| | - Katherine Farjado
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, USA
| | - Anna York
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, USA
| | - Virginia E Pitzer
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, USA
| | - Daniel M Weinberger
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, USA
| | - Amy K Bei
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, USA
| | - Orchid M Allicock
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, USA
| | - Anne L Wyllie
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, USA
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Howard LM, Grijalva CG. Impact of respiratory viral infections on nasopharyngeal pneumococcal colonization dynamics in children. Curr Opin Infect Dis 2024; 37:170-175. [PMID: 38437245 DOI: 10.1097/qco.0000000000001008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/06/2024]
Abstract
PURPOSE OF REVIEW Prevention of acute respiratory illnesses (ARI) in children is a global health priority, as these remain a leading cause of pediatric morbidity and mortality throughout the world. As new products and strategies to prevent respiratory infections caused by important pathogens such as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), influenza, respiratory syncytial virus and pneumococcus are advancing, increasing evidence suggests that these and other respiratory viruses and pneumococci may exhibit interactions that are associated with altered colonization and disease dynamics. We aim to review recent data evaluating interactions between respiratory viruses and pneumococci in the upper respiratory tract and their potential impact on pneumococcal colonization patterns and disease outcomes. RECENT FINDINGS While interactions between influenza infection and subsequent increased susceptibility and transmissibility of colonizing pneumococci have been widely reported in the literature, emerging evidence suggests that human rhinovirus, SARS-CoV-2, and other viruses may also exhibit interactions with pneumococci and alter pneumococcal colonization patterns. Additionally, colonizing pneumococci may play a role in modifying outcomes associated with respiratory viral infections. Recent evidence suggests that vaccination with pneumococcal conjugate vaccines, and prevention of colonization with pneumococcal serotypes included in these vaccines, may be associated with reducing the risk of subsequent viral infection and the severity of the associated illnesses. SUMMARY Understanding the direction and dynamics of viral-pneumococcal interactions may elucidate the potential effects of existing and emerging viral and bacterial vaccines and other preventive strategies on the health impact of these important respiratory pathogens.
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Affiliation(s)
- Leigh M Howard
- Department of Pediatrics, Division of Infectious Diseases
| | - Carlos G Grijalva
- Departments of Health Policy and Biomedical Informatics, Division of Pharmacoepidemiology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
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Keeley AJ, Groves D, Armitage EP, Senghore E, Jagne YJ, Sallah HJ, Drammeh S, Angyal A, Hornsby H, de Crombrugghe G, Smeesters PR, Rossi O, Carducci M, Peno C, Bogaert D, Kampmann B, Marks M, Shaw HA, Turner CR, de Silva TI. Streptococcus pyogenes Colonization in Children Aged 24-59 Months in the Gambia: Impact of Live Attenuated Influenza Vaccine and Associated Serological Responses. J Infect Dis 2023; 228:957-965. [PMID: 37246259 PMCID: PMC10547459 DOI: 10.1093/infdis/jiad153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 03/02/2023] [Accepted: 05/11/2023] [Indexed: 05/30/2023] Open
Abstract
BACKGROUND Immunity to Streptococcus pyogenes in high burden settings is poorly understood. We explored S. pyogenes nasopharyngeal colonization after intranasal live attenuated influenza vaccine (LAIV) among Gambian children aged 24-59 months, and resulting serological response to 7 antigens. METHODS A post hoc analysis was performed in 320 children randomized to receive LAIV at baseline (LAIV group) or not (control). S. pyogenes colonization was determined by quantitative polymerase chain reaction (qPCR) on nasopharyngeal swabs from baseline (day 0), day 7, and day 21. Anti-streptococcal IgG was quantified, including a subset with paired serum before/after S. pyogenes acquisition. RESULTS The point prevalence of S. pyogenes colonization was 7%-13%. In children negative at day 0, S. pyogenes was detected at day 7 or 21 in 18% of LAIV group and 11% of control group participants (P = .12). The odds ratio (OR) for colonization over time was significantly increased in the LAIV group (day 21 vs day 0 OR, 3.18; P = .003) but not in the control group (OR, 0.86; P = .79). The highest IgG increases following asymptomatic colonization were seen for M1 and SpyCEP proteins. CONCLUSIONS Asymptomatic S. pyogenes colonization appears modestly increased by LAIV, and may be immunologically significant. LAIV could be used to study influenza-S. pyogenes interactions. Clinical Trials Registration. NCT02972957.
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Affiliation(s)
- Alexander J Keeley
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
- Department of Infection, Immunity, and Cardiovascular Disease, Medical School, University of Sheffield, Sheffield, United Kingdom
- Vaccines and Immunity Theme, Medical Research Council Unit The Gambia at London School of Hygiene and Tropical Medicine, Banjul, The Gambia
| | - Danielle Groves
- Department of Infection, Immunity, and Cardiovascular Disease, Medical School, University of Sheffield, Sheffield, United Kingdom
| | - Edwin P Armitage
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
- Vaccines and Immunity Theme, Medical Research Council Unit The Gambia at London School of Hygiene and Tropical Medicine, Banjul, The Gambia
| | - Elina Senghore
- Vaccines and Immunity Theme, Medical Research Council Unit The Gambia at London School of Hygiene and Tropical Medicine, Banjul, The Gambia
| | - Ya Jankey Jagne
- Vaccines and Immunity Theme, Medical Research Council Unit The Gambia at London School of Hygiene and Tropical Medicine, Banjul, The Gambia
| | - Hadijatou J Sallah
- Vaccines and Immunity Theme, Medical Research Council Unit The Gambia at London School of Hygiene and Tropical Medicine, Banjul, The Gambia
| | - Sainabou Drammeh
- Vaccines and Immunity Theme, Medical Research Council Unit The Gambia at London School of Hygiene and Tropical Medicine, Banjul, The Gambia
| | - Adri Angyal
- Department of Infection, Immunity, and Cardiovascular Disease, Medical School, University of Sheffield, Sheffield, United Kingdom
| | - Hailey Hornsby
- Department of Infection, Immunity, and Cardiovascular Disease, Medical School, University of Sheffield, Sheffield, United Kingdom
| | - Gabrielle de Crombrugghe
- Molecular Bacteriology Laboratory, Université Libre de Bruxelles, Brussels, Belgium
- Department of Pediatrics, Hôpital Universitaire des Enfants Reine Fabiola, Université Libre de BruxellesBrussels, Belgium
| | - Pierre R Smeesters
- Molecular Bacteriology Laboratory, Université Libre de Bruxelles, Brussels, Belgium
- Department of Pediatrics, Hôpital Universitaire des Enfants Reine Fabiola, Université Libre de BruxellesBrussels, Belgium
| | - Omar Rossi
- GSK Vaccines Institute for Global Health, Siena, Italy
| | | | - Chikondi Peno
- Centre for Inflammation Research, Queen's Medical Research Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - Debby Bogaert
- Centre for Inflammation Research, Queen's Medical Research Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - Beate Kampmann
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
- Vaccines and Immunity Theme, Medical Research Council Unit The Gambia at London School of Hygiene and Tropical Medicine, Banjul, The Gambia
- Charité Centre for Global Health and Institut für Internationale Gesundheit, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Michael Marks
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
- Hospital for Tropical Diseases, University College London Hospital, London, United Kingdom
- Division of Infection and Immunity, University College London, London, United Kingdom
| | - Helen A Shaw
- Vaccines Division, Scientific Research and Innovation Group, Medicines and Healthcare Products Regulatory Agency, Potters Bar, United Kingdom
| | - Claire R Turner
- School of Biosciences, University of Sheffield, Sheffield, United Kingdom
| | - Thushan I de Silva
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
- Department of Infection, Immunity, and Cardiovascular Disease, Medical School, University of Sheffield, Sheffield, United Kingdom
- Vaccines and Immunity Theme, Medical Research Council Unit The Gambia at London School of Hygiene and Tropical Medicine, Banjul, The Gambia
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Stein RA, Bianchini EC. Bacterial-Viral Interactions: A Factor That Facilitates Transmission Heterogeneities. FEMS MICROBES 2022. [DOI: 10.1093/femsmc/xtac018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Abstract
The transmission of infectious diseases is characterized by heterogeneities that are shaped by the host, the pathogen, and the environment. Extreme forms of these heterogeneities are called super-spreading events. Transmission heterogeneities are usually identified retrospectively, but their contribution to the dynamics of outbreaks makes the ability to predict them valuable for science, medicine, and public health. Previous studies identified several factors that facilitate super-spreading; one of them is the interaction between bacteria and viruses within a host. The heightened dispersal of bacteria colonizing the nasal cavity during an upper respiratory viral infection, and the increased shedding of HIV-1 from the urogenital tract during a sexually transmitted bacterial infection, are among the most extensively studied examples of transmission heterogeneities that result from bacterial-viral interactions. Interrogating these transmission heterogeneities, and elucidating the underlying cellular and molecular mechanisms, are part of much-needed efforts to guide public health interventions, in areas that range from predicting or controlling the population transmission of respiratory pathogens, to limiting the spread of sexually transmitted infections, and tailoring vaccination initiatives with live attenuated vaccines.
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Affiliation(s)
- Richard A Stein
- NYU Tandon School of Engineering Department of Chemical and Biomolecular Engineering 6 MetroTech Center Brooklyn , NY 11201 USA
| | - Emilia Claire Bianchini
- NYU Tandon School of Engineering Department of Chemical and Biomolecular Engineering 6 MetroTech Center Brooklyn , NY 11201 USA
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Desheva Y, Leontieva G, Kramskaya T, Losev I, Petkova N, Rekstin A, Suvorov A. Associated virus-bacterial vaccine based on seasonal LAIV and S. pneumoniae chimeric peptide provide protection against post-influenza pneumococcal infection in mouse model. Virulence 2022; 13:558-568. [PMID: 35266442 PMCID: PMC8920162 DOI: 10.1080/21505594.2022.2049496] [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] [Indexed: 11/01/2022] Open
Abstract
Severe influenza complications are often caused by Streptococcus pneumoniae infection, which presents the most common cause of community-acquired pneumonia. We evaluated in a mouse model an associated virus-bacterial vaccine based on seasonal live influenza vaccines (LAIV) and S. pneumoniae chimeric protein comprising flagellin (PSPF). Intranasal immunization of mice with a complex of trivalent LAIV and PSPF caused an increased release of early cytokines in the lungs of mice. The immunogenicity of LAIV and PSPF in the associated vaccine composition was sometimes decreased compared to each vaccine preparation alone. Nevertheless, only vaccination of mice with LAIV+PSPF significantly reduced lethality and the bacterial load in the lungs in a model of post-influenza bacterial pneumonia. The study of the interactions of influenza viruses with bacterial peptides is important during the development of associated virus-bacterial vaccines intended for the prevention of severe post-influenza bacterial complications.
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Affiliation(s)
- Yulia Desheva
- Virology Department, FSBSI «Institute of Experimental Medicine», Saint Petersburg, Russian Federation
| | - Galina Leontieva
- Molecular Microbiology Department, FSBSI «Institute of Experimental Medicine», Saint Petersburg, Russian Federation
| | - Tatiana Kramskaya
- Molecular Microbiology Department, FSBSI «Institute of Experimental Medicine», Saint Petersburg, Russian Federation
| | - Igor Losev
- Virology Department, FSBSI «Institute of Experimental Medicine», Saint Petersburg, Russian Federation
| | - Nadezhda Petkova
- Virology Department, FSBSI «Institute of Experimental Medicine», Saint Petersburg, Russian Federation
| | - Andrey Rekstin
- Virology Department, FSBSI «Institute of Experimental Medicine», Saint Petersburg, Russian Federation
| | - Alexander Suvorov
- Molecular Microbiology Department, FSBSI «Institute of Experimental Medicine», Saint Petersburg, Russian Federation
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