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Choudhury A, Zhang Y, Ma J, Li R, Chamcha R, Akgul A, Stachura N, Follmer T, Newhard W, Jackson G, Herbert J, Nguyen C, Pham H, Nasrin S, McCabe K, Rajam G, Johnson KD, Rouphael N, Cruz SY, Verch T. Qualification of a 21-valent pneumococcal urine antigen detection assay and development of clinical positivity cutoffs. Bioanalysis 2024:1-12. [PMID: 38940371 DOI: 10.1080/17576180.2024.2357030] [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: 02/03/2024] [Accepted: 05/15/2024] [Indexed: 06/29/2024] Open
Abstract
Aim: Serotype-specific assays detecting pneumococcal polysaccharides in bodily fluids are needed to understand the pneumococcal serotype distribution in non-bacteremic pneumonia. Methods: We developed a urine antigen detection assay and using urine samples from adult outpatients without pneumonia developed positivity cutoffs for both a previously published 15-valent and the new 21-valent assay. Clinical sensitivity was confirmed with samples from patients with invasive pneumococcal disease. Results: Total assay precision ranged from 7.6 to 17.8% coefficient of variation while accuracy ranged between 80 and 150% recovery, except for three serotypes where recoveries ranged from 32 to 60%. Clinical sensitivity was 86.4% and specificity was 96.5% across all 30 serotypes. Conclusion: The assay could potentially assess serotype-distribution in non-infected and infected participants with pneumococcal disease.
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Affiliation(s)
| | - Yuhua Zhang
- Merck & Co., Inc., West Point, PA 19486, USA
| | - Junshui Ma
- Merck & Co., Inc., West Point, PA 19486, USA
| | - Ruonan Li
- Merck & Co., Inc., West Point, PA 19486, USA
| | | | - Ali Akgul
- Merck & Co., Inc., West Point, PA 19486, USA
| | | | - Thy Follmer
- Merck & Co., Inc., West Point, PA 19486, USA
| | | | | | | | | | - Huy Pham
- Merck & Co., Inc., West Point, PA 19486, USA
| | | | | | | | | | - Nadine Rouphael
- Department of Medicine, Emory University, Atlanta, 30322,Georgia
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2
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Sari RF, Fadilah F, Maladan Y, Sarassari R, Safari D. A narrative review of genomic characteristics, serotype, immunogenicity, and vaccine development of Streptococcus pneumoniae capsular polysaccharide. Clin Exp Vaccine Res 2024; 13:91-104. [PMID: 38752009 PMCID: PMC11091432 DOI: 10.7774/cevr.2024.13.2.91] [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: 09/29/2023] [Revised: 03/31/2024] [Accepted: 04/05/2024] [Indexed: 05/18/2024] Open
Abstract
This narrative review describes genomic characteristic, serotyping, immunogenicity, and vaccine development of Streptococcus pneumoniae capsular polysaccharide (CPS). CPS is a primary virulence factor of S. pneumoniae. The genomic characteristics of S. pneumoniae CPS, including the role of biosynthetic gene and genetic variation within cps (capsule polysaccharide) locus which may lead to serotype replacement are still being investigated. One hundred unique serotypes of S. pneumoniae have been identified through various methods of serotyping using phenotypic and genotypic approach. The advantages and limitations of each method are various, emphasizing the need for accurate and comprehensive serotyping for effective disease surveillance and vaccine targeting. In addition, we elaborate the critical role of CPS in vaccine development by providing an overview of immunogenicity, ongoing research of pneumococcal vaccines, and the impact on disease burden.
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Affiliation(s)
- Ratna Fathma Sari
- Master’s Programme in Biomedical Sciences, Faculty of Medicine, University of Indonesia, Jakarta, Indonesia
- Eijkman Research Center for Molecular Biology, National Research and Innovation Agency, Cibinong, Indonesia
| | - Fadilah Fadilah
- Medical Chemistry Department, Faculty of Medicine, University of Indonesia, Jakarta, Indonesia
| | - Yustinus Maladan
- Eijkman Research Center for Molecular Biology, National Research and Innovation Agency, Cibinong, Indonesia
| | - Rosantia Sarassari
- Eijkman Research Center for Molecular Biology, National Research and Innovation Agency, Cibinong, Indonesia
| | - Dodi Safari
- Eijkman Research Center for Molecular Biology, National Research and Innovation Agency, Cibinong, Indonesia
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3
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Zhou S, Che J, Wang X, Lin Y, Niu J, Liang W, Xu L, Zhang M, Liao Y, Shao Z, Li Q. Identification of pneumococcal serotypes with individual recognition of vaccine types by a highly multiplexed real-time PCR-based MeltArray approach. JOURNAL OF MICROBIOLOGY, IMMUNOLOGY, AND INFECTION = WEI MIAN YU GAN RAN ZA ZHI 2024; 57:107-117. [PMID: 37919170 DOI: 10.1016/j.jmii.2023.10.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 09/07/2023] [Accepted: 10/24/2023] [Indexed: 11/04/2023]
Abstract
BACKGROUND Pneumococcus serotyping is important for monitoring serotype epidemiology, vaccine-induced serotypes replacement and emerging pathogenic serotypes. However, the lack of high-resolution serotyping tools has hindered its widespread implementation. METHODS We devised a single-step, multiplex real-time polymerase chain reaction (PCR)-based MeltArray approach termed PneumoSero that can identify 92 serotypes with individual recognition of 54 serotypes, including all 24 currently available vaccine types. The limit of detection (LOD) and the ability to coexisting serotypes were studied, followed by analytical evaluation using 92 reference pneumococcal strains and 125 non-pneumococcal strains, and clinical evaluation using 471 pneumococcus isolates and 46 pneumococcus-positive clinical samples. RESULTS The LODs varied with serotypes from 50 to 100 copies per reaction and 10 % of the minor serotypes were detectable in samples containing two mixed serotypes. Analytical evaluation presented 100 % accuracy in both 92 reference pneumococcal strains and 125 non-pneumococcal strains. Clinical evaluation of 471 pneumococcus isolates displayed full concordance with Sanger sequencing results. The 46 clinical specimens yielded 45 typeable results and one untypeable result. Of the 45 typeable samples, 41 were of a single serotype and four were of mixed serotypes, all of which were confirmed by Sanger sequencing or separate PCR assays. CONCLUSION We conclude that the PneumoSero assay can be implemented as a routine tool for pneumococcal serotyping in standard microbiology laboratories and even in clinical settings.
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Affiliation(s)
- Shujuan Zhou
- Engineering Research Centre of Molecular Diagnostics of the Ministry of Education, State Key Laboratory of Cellular Stress Biology, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Life Sciences, Xiamen University, Xiamen, China
| | - Jie Che
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Xuran Wang
- Engineering Research Centre of Molecular Diagnostics of the Ministry of Education, State Key Laboratory of Cellular Stress Biology, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Life Sciences, Xiamen University, Xiamen, China
| | - Yong Lin
- Institute of Infectious Disease, School of Medicine, Xiamen University, Xiamen, China
| | - Jianjun Niu
- Institute of Infectious Disease, School of Medicine, Xiamen University, Xiamen, China
| | - Weitong Liang
- Engineering Research Centre of Molecular Diagnostics of the Ministry of Education, State Key Laboratory of Cellular Stress Biology, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Life Sciences, Xiamen University, Xiamen, China
| | - Li Xu
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Maojun Zhang
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Yiqun Liao
- Engineering Research Centre of Molecular Diagnostics of the Ministry of Education, State Key Laboratory of Cellular Stress Biology, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Life Sciences, Xiamen University, Xiamen, China; School of Public Health, Xiamen University, Xiamen, China.
| | - Zhujun Shao
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China.
| | - Qingge Li
- Engineering Research Centre of Molecular Diagnostics of the Ministry of Education, State Key Laboratory of Cellular Stress Biology, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Life Sciences, Xiamen University, Xiamen, China.
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4
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Henares D, Lo SW, Perez-Argüello A, Redin A, Ciruela P, Garcia-Garcia JJ, Brotons P, Yuste J, Sá-Leão R, Muñoz-Almagro C. Comparison of next generation technologies and bioinformatics pipelines for capsular typing of Streptococcus pneumoniae. J Clin Microbiol 2023; 61:e0074123. [PMID: 38092657 PMCID: PMC10729682 DOI: 10.1128/jcm.00741-23] [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: 06/12/2023] [Accepted: 10/01/2023] [Indexed: 12/20/2023] Open
Abstract
Whole genome sequencing (WGS)-based approaches for pneumococcal capsular typing have become an alternative to serological methods. In silico serotyping from WGS has not yet been applied to long-read sequences produced by third-generation technologies. The objective of the study was to determine the capsular types of pneumococci causing invasive disease in Catalonia (Spain) using serological typing and WGS and to compare the performance of different bioinformatics pipelines using short- and long-read data from WGS. All invasive pneumococcal pediatric isolates collected in Hospital Sant Joan de Déu (Barcelona) from 2013 to 2019 were included. Isolates were assigned a capsular type by serological testing based on anticapsular antisera and by different WGS-based pipelines: Illumina sequencing followed by serotyping with PneumoCaT, SeroBA, and Pathogenwatch vs MinION-ONT sequencing coupled with serotyping by Pathogenwatch from pneumococcal assembled genomes. A total of 119 out of 121 pneumococcal isolates were available for sequencing. Twenty-nine different serotypes were identified by serological typing, with 24F (n = 17; 14.3%), 14 (n = 10; 8.4%), and 15B/C (n = 8; 6.7%) being the most common serotypes. WGS-based pipelines showed initial concordance with serological typing (>91% of accuracy). The main discrepant results were found at the serotype level within a serogroup: 6A/B, 6C/D, 9A/V, 11A/D, and 18B/C. Only one discrepancy at the serogroup level was observed: serotype 29 by serological testing and serotype 35B/D by all WGS-based pipelines. Thus, bioinformatics WGS-based pipelines, including those using third-generation sequencing, are useful for pneumococcal capsular assignment. Possible discrepancies between serological typing and WGS-based approaches should be considered in pneumococcal capsular-type surveillance studies.
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Affiliation(s)
- Desiree Henares
- Department of RDI Microbiology, Hospital Sant Joan de Déu, Barcelona, Spain
- Infectious Diseases and Microbiome, Institut de Recerca Sant Joan de Déu, Barcelona, Spain
- CIBER Center for Epidemiology and Public Health (CIBERESP), Instituto de Salud Carlos III, Madrid, Spain
| | - Stephanie W. Lo
- Parasites and Microbes Programme, Wellcome Sanger Institute, Hinxton, United Kingdom
- Milner Center for Evolution, Life Sciences Department, University of Bath, Bath, United Kingdom
| | - Amaresh Perez-Argüello
- Department of RDI Microbiology, Hospital Sant Joan de Déu, Barcelona, Spain
- Infectious Diseases and Microbiome, Institut de Recerca Sant Joan de Déu, Barcelona, Spain
| | - Alba Redin
- Department of RDI Microbiology, Hospital Sant Joan de Déu, Barcelona, Spain
- Infectious Diseases and Microbiome, Institut de Recerca Sant Joan de Déu, Barcelona, Spain
| | - Pilar Ciruela
- CIBER Center for Epidemiology and Public Health (CIBERESP), Instituto de Salud Carlos III, Madrid, Spain
- Surveillance and Public Health Emergency Response, Public Health Agency of Catalonia (ASPCAT), Barcelona, Spain
| | - Juan Jose Garcia-Garcia
- CIBER Center for Epidemiology and Public Health (CIBERESP), Instituto de Salud Carlos III, Madrid, Spain
- Pediatrics Department, Hospital Sant Joan de Déu, Barcelona, Spain
- Department of Surgery and Medical-Surgical Specialties, Facultat de Medicina i Ciències de la Salut, Universitat de Barcelona, Barcelona, Spain
| | - Pedro Brotons
- Department of RDI Microbiology, Hospital Sant Joan de Déu, Barcelona, Spain
- Infectious Diseases and Microbiome, Institut de Recerca Sant Joan de Déu, Barcelona, Spain
- CIBER Center for Epidemiology and Public Health (CIBERESP), Instituto de Salud Carlos III, Madrid, Spain
- School of Medicine, Universitat Internacional de Catalunya, Barcelona, Spain
| | - Jose Yuste
- Spanish Pneumococcal Reference Laboratory, National Center for Microbiology, Instituto de Salud Carlos III, Madrid, Spain
- CIBER of Respiratory Diseases (CIBERES), Instituto de salud Carlos III, Madrid, Spain
| | - Raquel Sá-Leão
- Laboratory of Molecular Microbiology of Human Pathogens, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), Oeiras, Portugal
| | - Carmen Muñoz-Almagro
- Department of RDI Microbiology, Hospital Sant Joan de Déu, Barcelona, Spain
- Infectious Diseases and Microbiome, Institut de Recerca Sant Joan de Déu, Barcelona, Spain
- CIBER Center for Epidemiology and Public Health (CIBERESP), Instituto de Salud Carlos III, Madrid, Spain
- School of Medicine, Universitat Internacional de Catalunya, Barcelona, Spain
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5
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Kampff Z, van Sinderen D, Mahony J. Cell wall polysaccharides of streptococci: A genetic and structural perspective. Biotechnol Adv 2023; 69:108279. [PMID: 37913948 DOI: 10.1016/j.biotechadv.2023.108279] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 10/04/2023] [Accepted: 10/28/2023] [Indexed: 11/03/2023]
Abstract
The Streptococcus genus comprises both commensal and pathogenic species. Additionally, Streptococcus thermophilus is exploited in fermented foods and in probiotic preparations. The ecological and metabolic diversity of members of this genus is matched by the complex range of cell wall polysaccharides that they present on their cell surfaces. These glycopolymers facilitate their interactions and environmental adaptation. Here, current knowledge on the genetic and compositional diversity of streptococcal cell wall polysaccharides including rhamnose-glucose polysaccharides, exopolysaccharides and teichoic acids is discussed. Furthermore, the species-specific cell wall polysaccharide combinations and specifically highlighting the presence of rhamnose-glucose polysaccharides in certain species, which are replaced by teichoic acids in other species. This review highlights model pathogenic and non-pathogenic species for which there is considerable information regarding cell wall polysaccharide composition, structure and genetic information. These serve as foundations to predict and focus research efforts in other streptococcal species for which such data currently does not exist.
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Affiliation(s)
- Zoe Kampff
- School of Microbiology and APC Microbiome Ireland, University College Cork, Cork T12 YT20, Ireland
| | - Douwe van Sinderen
- School of Microbiology and APC Microbiome Ireland, University College Cork, Cork T12 YT20, Ireland
| | - Jennifer Mahony
- School of Microbiology and APC Microbiome Ireland, University College Cork, Cork T12 YT20, Ireland.
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6
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Duke JA, Avci FY. Emerging vaccine strategies against the incessant pneumococcal disease. NPJ Vaccines 2023; 8:122. [PMID: 37591986 PMCID: PMC10435554 DOI: 10.1038/s41541-023-00715-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 08/01/2023] [Indexed: 08/19/2023] Open
Abstract
The incidence of invasive pneumococcal disease (IPD) caused by infection with the pathogen Streptococcus pneumoniae (Spn) has been on a downward trend for decades due to worldwide vaccination programs. Despite the clinical successes observed, the Center for Disease Control (CDC) reports that the continued global burden of S. pneumoniae will be in the millions each year, with a case-fatality rate hovering around 5%. Thus, it is a top priority to continue developing new Spn vaccination strategies to harness immunological insight and increase the magnitude of protection provided. As emphasized by the World Health Organization (WHO), it is also crucial to broaden the implementation of vaccines that are already obtainable in the clinical setting. This review focuses on the immune mechanisms triggered by existing pneumococcal vaccines and provides an overview of the current and upcoming clinical strategies being employed. We highlight the associated challenges of serotype selectivity and using pneumococcal-derived proteins as alternative vaccine antigens.
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Affiliation(s)
- Jeremy A Duke
- Sanofi, Suite 300, 2501 Discovery Drive, Orlando, FL, 32826, USA
| | - Fikri Y Avci
- Department of Biochemistry, Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA, 30322, USA.
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7
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Azarsa M, Mosadegh M, Habibi Ghahfarokhi S, Pourmand MR. Serotype Distribution and Multi Locus Sequence Type (MLST) of Erythromycin-Resistant Streptococcus Pneumoniae Isolates in Tehran, Iran. Rep Biochem Mol Biol 2023; 12:259-268. [PMID: 38317819 PMCID: PMC10838590 DOI: 10.61186/rbmb.12.2.259] [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: 04/29/2023] [Accepted: 07/04/2023] [Indexed: 02/07/2024]
Abstract
Background The number of erythromycin-resistant Streptococcus pneumoniae has significantly increased around the world. The present study aimed to determine the serotype distribution and molecular epidemiology of the erythromycin-resistant Streptococcus pneumoniae (ERSP) isolated from patients with invasive disease. Methods A total of 44 Streptococcus pneumoniae isolates were tested for susceptibility to several antimicrobial agents. Additionally, the polymerase chain reaction (PCR) was applied to evaluate ERSP isolates in terms of the presence of erythromycin resistance genes (e.g., ermB and mefA). The isolates were serotyped using the sequential multiplex-PCR method, and molecular epidemiology was assessed through the multilocus sequence typing (MLST) analysis. Results The results represented multidrug resistance (MDR) in approximately half of the pneumococcal isolates. Among 22 ERSP isolates, 20 (90.9%) and 12 (56%) ones contained ermB and mefA, respectively. Further, 14 (31.8%), 3 (22.7%), and 19A (18.1%) were the common serotypes among the isolates. No significant correlation was observed between serotypes and erythromycin resistance genes. Furthermore, the MLST results revealed 18 different sequence types (STs), the top ones of which were ST3130 (3 isolates) and ST166 (3 isolates). Population genetic analysis disclosed that CC63 (32%), CC156 (18%), and CC320 (18%) were identified as the predominant clonal complexes. Conclusions The ERSP isolates exhibited high genetic diversity. The large frequency of MDR isolates suggests the emergence of high resistant strains, as well as the need to implement vaccination in the immunization schedule of Iran. These accumulating evidences indicate that 13-valent pneumococcal conjugate vaccines provided higher serotype coverage in the ERSP isolates.
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Affiliation(s)
- Mohammad Azarsa
- Department of Microbiology, Khoy University of Medical Sciences, Khoy, Iran.
| | - Mehrdad Mosadegh
- Department of Pathobiology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran.
| | - Soheila Habibi Ghahfarokhi
- Department of Pathobiology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran.
| | - Mohammad Reza Pourmand
- Department of Pathobiology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran.
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8
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Abdul Rahman NA, Mohd Desa MN, Masri SN, Taib NM, Sulaiman N, Hazman H, John J. The Molecular Approaches and Challenges of Streptococcus pneumoniae Serotyping for Epidemiological Surveillance in the Vaccine Era. Pol J Microbiol 2023; 72:103-115. [PMID: 37314355 DOI: 10.33073/pjm-2023-023] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 05/09/2023] [Indexed: 06/15/2023] Open
Abstract
Streptococcus pneumoniae (pneumococcus) belongs to the Gram-positive cocci. This bacterium typically colonizes the nasopharyngeal region of healthy individuals. It has a distinct polysaccharide capsule - a virulence factor allowing the bacteria to elude the immune defense mechanisms. Consequently, it might trigger aggressive conditions like septicemia and meningitis in immunocompromised or older individuals. Moreover, children below five years of age are at risk of morbidity and mortality. Studies have found 101 S. pneumoniae capsular serotypes, of which several correlate with clinical and carriage isolates with distinct disease aggressiveness. Introducing pneumococcal conjugate vaccines (PCV) targets the most common disease-associated serotypes. Nevertheless, vaccine selection pressure leads to replacing the formerly dominant vaccine serotypes (VTs) by non-vaccine types (NVTs). Therefore, serotyping must be conducted for epidemiological surveillance and vaccine assessment. Serotyping can be performed using numerous techniques, either by the conventional antisera-based (Quellung and latex agglutination) or molecular-based approaches (sequetyping, multiplex PCR, real-time PCR, and PCR-RFLP). A cost-effective and practical approach must be used to enhance serotyping accuracy to monitor the prevalence of VTs and NVTs. Therefore, dependable pneumococcal serotyping techniques are essential to precisely monitor virulent lineages, NVT emergence, and genetic associations of isolates. This review discusses the principles, associated benefits, and drawbacks of the respective available conventional and molecular approaches, and potentially the whole genome sequencing (WGS) to be directed for future exploration.
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Affiliation(s)
- Nurul Asyikin Abdul Rahman
- 1Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Serdang, Malaysia
- 2School of Biology, Faculty of Applied Sciences, Universiti Teknologi MARA, Kuala Pilah, Malaysia
| | - Mohd Nasir Mohd Desa
- 1Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Serdang, Malaysia
| | - Siti Norbaya Masri
- 3Department of Medical Microbiology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Serdang, Malaysia
| | - Niazlin Mohd Taib
- 3Department of Medical Microbiology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Serdang, Malaysia
| | - Nurshahira Sulaiman
- 1Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Serdang, Malaysia
| | - Hazmin Hazman
- 1Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Serdang, Malaysia
| | - James John
- 4Department of Medical Laboratory Technology, School of Allied Health Science, Sathyabama Institute of Science and Technology, Chennai, India
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Chun YY, Tan KS, Yu L, Pang M, Wong MHM, Nakamoto R, Chua WZ, Huee-Ping Wong A, Lew ZZR, Ong HH, Chow VT, Tran T, Yun Wang D, Sham LT. Influence of glycan structure on the colonization of Streptococcus pneumoniae on human respiratory epithelial cells. Proc Natl Acad Sci U S A 2023; 120:e2213584120. [PMID: 36943879 PMCID: PMC10068763 DOI: 10.1073/pnas.2213584120] [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: 08/08/2022] [Accepted: 02/10/2023] [Indexed: 03/23/2023] Open
Abstract
Virtually all living cells are encased in glycans. They perform key cellular functions such as immunomodulation and cell-cell recognition. Yet, how their composition and configuration affect their functions remains enigmatic. Here, we constructed isogenic capsule-switch mutants harboring 84 types of capsular polysaccharides (CPSs) in Streptococcus pneumoniae. This collection enables us to systematically measure the affinity of structurally related CPSs to primary human nasal and bronchial epithelial cells. Contrary to the paradigm, the surface charge does not appreciably affect epithelial cell binding. Factors that affect adhesion to respiratory cells include the number of rhamnose residues and the presence of human-like glycomotifs in CPS. Besides, pneumococcal colonization stimulated the production of interleukin 6 (IL-6), granulocyte-macrophage colony-stimulating factor (GM-CSF), and monocyte chemoattractantprotein-1 (MCP-1) in nasal epithelial cells, which also appears to be dependent on the serotype. Together, our results reveal glycomotifs of surface polysaccharides that are likely to be important for colonization and survival in the human airway.
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Affiliation(s)
- Ye-Yu Chun
- Infectious Diseases Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore117545
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore117545
| | - Kai Sen Tan
- Infectious Diseases Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore117545
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore117545
- Department of Otolaryngology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore117597
| | - Lisa Yu
- Infectious Diseases Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore117545
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore117545
- College of Art and Sciences, Cornell University, Ithaca, NY14853
| | - Michelle Pang
- Infectious Diseases Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore117545
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore117545
| | - Ming Hui Millie Wong
- Infectious Diseases Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore117545
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore117545
| | - Rei Nakamoto
- Infectious Diseases Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore117545
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore117545
| | - Wan-Zhen Chua
- Infectious Diseases Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore117545
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore117545
| | - Amanda Huee-Ping Wong
- Infectious Diseases Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore117545
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore117545
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore117593
| | - Zhe Zhang Ryan Lew
- Infectious Diseases Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore117545
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore117545
| | - Hsiao Hui Ong
- Infectious Diseases Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore117545
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore117545
| | - Vincent T. Chow
- Infectious Diseases Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore117545
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore117545
| | - Thai Tran
- Infectious Diseases Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore117545
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore117545
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore117593
| | - De Yun Wang
- Infectious Diseases Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore117545
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore117545
| | - Lok-To Sham
- Infectious Diseases Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore117545
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore117545
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10
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Huang LD, Yang MJ, Huang YY, Jiang KY, Yan J, Sun AH. Molecular Characterization of Predominant Serotypes, Drug Resistance, and Virulence Genes of Streptococcus pneumoniae Isolates From East China. Front Microbiol 2022; 13:892364. [PMID: 35722327 PMCID: PMC9198556 DOI: 10.3389/fmicb.2022.892364] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Accepted: 04/25/2022] [Indexed: 11/13/2022] Open
Abstract
Streptococcus pneumoniae is a common diplococcus pathogen found worldwide. The characterization of predominant serotypes, drug resistance, and virulence genes of S. pneumoniae isolates prevailing in different areas and countries is clinically important for choice of antibiotics and improvement of vaccines. In this study, pneumonia (78.7%) and meningitis (37.0%) were the predominant diseases observed in the 282 (children) and 27 (adults) S. pneumoniae-infected patients (p < 0.05) from seven hospitals in different areas of East China. Of the 309 pneumococcal isolates, 90.3% were classified by PCR into 15 serotypes, with serotypes 19F (27.2%) and the 6A/B (19.1%) being most predominant (p < 0.05). Importantly, serotypes 15A and 15B/C combined for a total of 10.4% of the isolates, but these serotypes are not included in the 13-valent pneumococcal capsule conjugate vaccine used in China. Antimicrobial susceptibility analysis by the E-test showed that >95% of the 309 pneumococcal isolates were susceptible to moxifloxacin and levofloxacin, as well as 18.4, 85.8, and 81.6% of the isolates displayed susceptibility to penicillin, cefotaxime, and imipenem, respectively. A significant correlation between the prevalence of predominant serotypes and their penicillin resistance was observed (p < 0.05). In particular, >95% of all the pneumococcal isolates showed resistance to erythromycin and azithromycin. Of the nine detected virulence genes, the lytA, ply, hysA, and nanA were the most common with 95–100% positive rates in the 309 pneumococcal isolates, while the pavA and psaA genes displayed a significant correlation with pneumococcal bacteremia and meningitis (p < 0.05). Overall, our data suggested that the predominant serotypes, drug resistance, and virulence genes of the S. pneumoniae isolates prevailing in East China are distinct from those observed in other areas of China and adjacent countries.
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Affiliation(s)
- Li-Dan Huang
- School of Basic Medical Sciences and Forensic Medicine, Hangzhou Medical College, Hangzhou, China
| | - Mei-Juan Yang
- School of Basic Medical Sciences and Forensic Medicine, Hangzhou Medical College, Hangzhou, China
| | - Yan-Ying Huang
- Hangzhou Chest Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Ke-Yi Jiang
- School of Basic Medical Sciences and Forensic Medicine, Hangzhou Medical College, Hangzhou, China
| | - Jie Yan
- Department of Medical Microbiology and Parasitology, Zhejiang University School of Medicine, Hangzhou, China
| | - Ai-Hua Sun
- School of Basic Medical Sciences and Forensic Medicine, Hangzhou Medical College, Hangzhou, China
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Validation of Fourier Transform Infrared Spectroscopy for Serotyping of Streptococcus pneumoniae. J Clin Microbiol 2022; 60:e0032522. [PMID: 35699436 PMCID: PMC9297836 DOI: 10.1128/jcm.00325-22] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Fourier transform infrared (FT-IR) spectroscopy (IR Biotyper; Bruker) allows highly discriminatory fingerprinting of closely related bacterial strains. In this study, FT-IR spectroscopy-based capsular typing of Streptococcus pneumoniae was validated as a rapid, cost-effective, and medium-throughput alternative to the classical phenotypic techniques. A training set of 233 strains was defined, comprising 34 different serotypes and including all 24 vaccine types (VTs) and 10 non-vaccine types (NVTs). The acquired spectra were used to (i) create a dendrogram where strains clustered together according to their serotypes and (ii) train an artificial neural network (ANN) model to predict unknown pneumococcal serotypes. During validation using 153 additional strains, we reached 98.0% accuracy for determining serotypes represented in the training set. Next, the performance of the IR Biotyper was assessed using 124 strains representing 59 non-training set serotypes. In this setting, 42 of 59 serotypes (71.1%) could be accurately categorized as being non-training set serotypes. Furthermore, it was observed that comparability of spectra was affected by the source of the Columbia medium used to grow the pneumococci and that this complicated the robustness and standardization potential of FT-IR spectroscopy. A rigorous laboratory workflow in combination with specific ANN models that account for environmental noise parameters can be applied to overcome this issue in the near future. The IR Biotyper has the potential to be used as a fast, cost-effective, and accurate phenotypic serotyping tool for S. pneumoniae.
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Gaultier GN, Nix EB, Thorgrimson J, Boreham D, McCready W, Ulanova M. Naturally acquired antibodies against 7 Streptococcus pneumoniae serotypes in Indigenous and non-Indigenous adults. PLoS One 2022; 17:e0267051. [PMID: 35421173 PMCID: PMC9009640 DOI: 10.1371/journal.pone.0267051] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 03/31/2022] [Indexed: 12/13/2022] Open
Abstract
Despite the use of pneumococcal conjugate vaccines for pediatric immunization, North American Indigenous populations continue to experience high burden of pneumococcal infections. Naturally acquired antibodies, which can protect unvaccinated adults against pneumococcal infections, have not previously been studied in Canadian Indigenous people. We analysed concentrations of natural serum IgG, IgM and IgA antibodies specific to 7 serotype-specific capsular polysaccharides (3, 6B, 9V, 14, 19A, 19F and 23F) in 141 healthy individuals (age between 18 and 80 years), including Indigenous adults living in 2 geographical different areas of Ontario, Canada, and non-Indigenous residing in northwestern Ontario. Regardless of the geographical area, concentrations of IgG specific to serotypes 6B, 9V, and 14, IgM specific to 9V, and all serotype-specific IgA were significantly higher in Indigenous study participants as compared to non-Indigenous. The differences are likely attributed to an increased exposure of Indigenous individuals to Streptococcus pneumoniae and/or cross-reactive antigens of other microorganisms or plants present in the environment. Although in non-Indigenous adults concentrations of IgM specific to 9V, 19A, 19F, and 23F significantly decreased with age, this was not observed in Indigenous individuals suggesting that Indigenous people may experience continuous exposure to pneumococci and cross-reactive antigens over the life span. Women had generally higher concentrations of natural IgG and IgM concentrations than men, with more striking differences found in Indigenous adults, potentially associated with larger exposure of women to young children, the major reservoir of pneumococci in communities. Our data suggest that increased rates of pneumococcal infections among Indigenous people are unlikely related to deficiency of naturally acquired antibodies, at least those specific to 7 common serotypes. Determining serological correlates of protection for adults will be essential to identify the groups in need of adult pneumococcal immunizations that may prevent excessive burden of the disease among North American Indigenous people.
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Affiliation(s)
| | - Eli B. Nix
- NOSM University, Thunder Bay, ON, Canada
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13
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Romaru J, Bahuaud M, Lejeune G, Hentzien M, Berger JL, Robbins A, Lebrun D, N’Guyen Y, Bani-Sadr F, Batteux F, Servettaz A. Single-Dose 13-Valent Conjugate Pneumococcal Vaccine in People Living With HIV – Immunological Response and Protection. Front Immunol 2021; 12:791147. [PMID: 34987514 PMCID: PMC8721113 DOI: 10.3389/fimmu.2021.791147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 11/29/2021] [Indexed: 11/26/2022] Open
Abstract
Background Patients living with HIV (PLHIV) are prone to invasive pneumococcal disease. The 13-valent conjugated pneumococcal vaccine (PCV13) is currently recommended for all PLHIV, followed in most guidelines by a 23-valent polysaccharide pneumococcal vaccine. Data are scarce concerning the immunological efficacy of PCV13 among PLHIV. Objective To assess the immunological response at one month, and the immunological protection at 1-, 6-, and 12 months in PLHIV with a CD4 cell count above 200 cells/µl after a single dose of PCV13, as measured by both ELISA and opsonophagocytic assay (OPA). Methods PLHIV with CD4 cell count >200 cells/µl were included. Specific IgG serum concentrations for eight serotypes by ELISA and seven serotypes by OPA were measured at baseline, 1-, 6-, and 12 months after the PCV13 vaccination. Global response was defined as a two-fold increase from baseline of specific IgG antibody levels (μg/ml) assayed by ELISA or as a four-fold increase in OPA titer from baseline, for at least five serotypes targeted by PCV13. Global protection was defined as an IgG-concentration ≥1 µg/ml by ELISA or as an opsonization titer ≥LLOQ by OPA for at least five tested serotypes targeted by PCV13. Factors associated with global response and global protection were assessed using logistic regression. Results Of the 38 PLHIV included, 57.9% and 63.2% were global responders, 92.1% and 78.9% were globally protected at one month, and 64.7% and 55.9% were still protected at 12 months, by ELISA and OPA respectively. A CD4/CD8 ratio of >0.8 was significantly associated with a better global response by OPA (OR=6.11, p=0.02), and a CD4 nadir <200 was significantly associated with a poorer global response by ELISA (OR=0.22, p=0.04). A CD4 cell count nadir <200 and age over 50 years were associated with poorer global protection by OPA at M1 (OR=0.18, p=0.04) and M12 (OR= 0.15, p=0.02), respectively. Plasma HIV RNA viral load <40 copies/ml was significantly associated with a better global protection at M1 by ELISA and OPA (OR=21.33, p=0.025 and OR=8.40, p=0.04) Conclusion Vaccination with PCV13 in these patients induced immunological response and protection at one month. At one year, more than half of patients were still immunologically protected.
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Affiliation(s)
- Juliette Romaru
- Department of Internal Medicine, Clinical Immunology and Infectious Diseases, Reims University Hospital, Reims, France
| | - Mathilde Bahuaud
- Plateforme d’Immunomonitoring Vaccinal, Laboratory of Immunology, Cochin Hospital and University Paris-Descartes, APHP, Paris, France
| | - Gauthier Lejeune
- Department of Internal Medicine, Clinical Immunology and Infectious Diseases, Reims University Hospital, Reims, France
- Department of Internal Medicine and Infectious Diseases, CH de Charleville-Mézières, Charleville-Mézières, France
| | - Maxime Hentzien
- Department of Internal Medicine, Clinical Immunology and Infectious Diseases, Reims University Hospital, Reims, France
- *Correspondence: Maxime Hentzien,
| | - Jean-Luc Berger
- Department of Internal Medicine, Clinical Immunology and Infectious Diseases, Reims University Hospital, Reims, France
| | - Ailsa Robbins
- Department of Internal Medicine, Clinical Immunology and Infectious Diseases, Reims University Hospital, Reims, France
- Laboratory of Immunology, EA7509 IRMAIC, University of Reims Champagne-Ardenne (URCA), Reims, France
| | - Delphine Lebrun
- Department of Internal Medicine and Infectious Diseases, CH de Charleville-Mézières, Charleville-Mézières, France
| | - Yohan N’Guyen
- Department of Internal Medicine, Clinical Immunology and Infectious Diseases, Reims University Hospital, Reims, France
| | - Firouzé Bani-Sadr
- Department of Internal Medicine, Clinical Immunology and Infectious Diseases, Reims University Hospital, Reims, France
| | - Frédéric Batteux
- Plateforme d’Immunomonitoring Vaccinal, Laboratory of Immunology, Cochin Hospital and University Paris-Descartes, APHP, Paris, France
| | - Amélie Servettaz
- Department of Internal Medicine, Clinical Immunology and Infectious Diseases, Reims University Hospital, Reims, France
- Laboratory of Immunology, EA7509 IRMAIC, University of Reims Champagne-Ardenne (URCA), Reims, France
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Beca Martínez MT, Morey Montalvo M, Santos Sanz S, Barrio Cortes J, Cañellas Llabrés S, Lasheras Carbajo MD. [Evaluation of the change in pneumococcal vaccination in 2018 in adults in the Community of Madrid]. Semergen 2021; 47:240-247. [PMID: 33865695 DOI: 10.1016/j.semerg.2021.01.006] [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: 11/05/2020] [Revised: 12/21/2020] [Accepted: 01/02/2021] [Indexed: 11/30/2022]
Abstract
BACKGROUND In the Community of Madrid since 2005 vaccination against pneumococcus in adults from 60 years of age has been carried out with pneumococcal polysaccharide vaccine (PPV23). In January 2018, the guideline changed in favor of pneumococcal conjugate vaccine (PCV13). The objective of this study was to analyze the data of pneumococcal vaccination and to evaluate the implementation of the new guideline of vaccination against pneumococcus in adults in the Community of Madrid. METHODS Cross-sectional study to estimate vaccine coverage by a retrospective review of the record of vaccination history of people ≥60 years resident in the Community of Madrid. RESULTS In the Community of Madrid until 2018, 83% of the population were vaccinated with PPV23, 6% with PCV13 and 11% with both vaccines. 96.5% came from Primary Care records. The doses administered of PCV13 surpassed those of PPV23 in ≥60 years in all age groups. 78,660 people ≥60 years were vaccinated with PCV13 (19.5% without risk factors, 67.3% with chronic diseases, 2.5% of the high-risk group and 10.7% belonging to both groups). CONCLUSIONS In 2018, following Community of Madrid recommendations, 6,639 people were not properly vaccinated with PCV13 and 72,021 (91.6%) were properly vaccinated. The greatest confusion occurred in people ≥60 years without risk factors who had a previous PPV23 and did not require another vaccine but received a PCV13 without complying with the recommended schedule.
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Affiliation(s)
- M T Beca Martínez
- Servicio de Medicina Preventiva, Hospital Virgen de la Salud, Complejo Hospitalario de Toledo, Toledo, España.
| | - M Morey Montalvo
- Servicio de Prevención de la Enfermedad, Subdirección General de Promoción, Prevención y Educación para la Salud, Dirección General de Salud Pública, Consejería de Sanidad, Madrid, España
| | - S Santos Sanz
- Servicio de Prevención de la Enfermedad, Subdirección General de Promoción, Prevención y Educación para la Salud, Dirección General de Salud Pública, Consejería de Sanidad, Madrid, España
| | - J Barrio Cortes
- Unidad de Investigación, Gerencia Asistencial de Atención Primaria, Madrid, España; Fundación para la Investigación e Innovación Biosanitaria en Atención Primaria, Madrid, España
| | - S Cañellas Llabrés
- Servicio de Prevención de la Enfermedad, Subdirección General de Promoción, Prevención y Educación para la Salud, Dirección General de Salud Pública, Consejería de Sanidad, Madrid, España
| | - M D Lasheras Carbajo
- Servicio de Prevención de la Enfermedad, Subdirección General de Promoción, Prevención y Educación para la Salud, Dirección General de Salud Pública, Consejería de Sanidad, Madrid, España
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Romero-Cordero S, Kirwan R, Noguera-Julian A, Cardellach F, Fortuny C, Morén C. A Mitocentric View of the Main Bacterial and Parasitic Infectious Diseases in the Pediatric Population. Int J Mol Sci 2021; 22:3272. [PMID: 33806981 PMCID: PMC8004694 DOI: 10.3390/ijms22063272] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 03/13/2021] [Accepted: 03/16/2021] [Indexed: 01/04/2023] Open
Abstract
Infectious diseases occur worldwide with great frequency in both adults and children. Both infections and their treatments trigger mitochondrial interactions at multiple levels: (i) incorporation of damaged or mutated proteins to the complexes of the electron transport chain, (ii) mitochondrial genome (depletion, deletions, and point mutations) and mitochondrial dynamics (fusion and fission), (iii) membrane potential, (iv) apoptotic regulation, (v) generation of reactive oxygen species, among others. Such alterations may result in serious adverse clinical events with great impact on children's quality of life, even resulting in death. As such, bacterial agents are frequently associated with loss of mitochondrial membrane potential and cytochrome c release, ultimately leading to mitochondrial apoptosis by activation of caspases-3 and -9. Using Rayyan QCRI software for systematic reviews, we explore the association between mitochondrial alterations and pediatric infections including (i) bacterial: M. tuberculosis, E. cloacae, P. mirabilis, E. coli, S. enterica, S. aureus, S. pneumoniae, N. meningitidis and (ii) parasitic: P. falciparum. We analyze how these pediatric infections and their treatments may lead to mitochondrial deterioration in this especially vulnerable population, with the intention of improving both the understanding of these diseases and their management in clinical practice.
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Affiliation(s)
- Sonia Romero-Cordero
- Faculty of Medicine, Pompeu Fabra University and Universitat Autònoma de Barcelona, 08002 Barcelona, Spain;
| | - Richard Kirwan
- School of Biological and Environmental Sciences, Liverpool John Moores University, Liverpool L2 2QP, UK
| | - Antoni Noguera-Julian
- Malalties Infeccioses i Resposta Inflamatòria Sistèmica en Pediatria, Unitat d’Infeccions, Servei de Pediatria, Institut de Recerca Pediàtrica Hospital Sant Joan de Déu, 08950 Barcelona, Spain; (A.N.-J.); (C.F.)
- Faculty of Medicine and Health Sciences, University of Barcelona, 08036 Barcelona, Spain;
- Centro de Investigación Biomédica en Red de Epidemiología y Salud Pública (CIBERESP), 28029 Madrid, Spain
- Red de Investigación Translacional en Infectología Pediátrica (RITIP), 28029 Madrid, Spain
| | - Francesc Cardellach
- Faculty of Medicine and Health Sciences, University of Barcelona, 08036 Barcelona, Spain;
- Muscle Research and Mitochondrial Function Laboratory, Cellex-IDIBAPS, Faculty of Medicine and Health Sciences, University of Barcelona, 08036 Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER) (ISCIII), 28029 Madrid, Spain
- Internal Medicine Department-Hospital Clínic of Barcelona (HCB), 08036 Barcelona, Spain
| | - Clàudia Fortuny
- Malalties Infeccioses i Resposta Inflamatòria Sistèmica en Pediatria, Unitat d’Infeccions, Servei de Pediatria, Institut de Recerca Pediàtrica Hospital Sant Joan de Déu, 08950 Barcelona, Spain; (A.N.-J.); (C.F.)
- Faculty of Medicine and Health Sciences, University of Barcelona, 08036 Barcelona, Spain;
- Centro de Investigación Biomédica en Red de Epidemiología y Salud Pública (CIBERESP), 28029 Madrid, Spain
- Red de Investigación Translacional en Infectología Pediátrica (RITIP), 28029 Madrid, Spain
| | - Constanza Morén
- Faculty of Medicine and Health Sciences, University of Barcelona, 08036 Barcelona, Spain;
- Muscle Research and Mitochondrial Function Laboratory, Cellex-IDIBAPS, Faculty of Medicine and Health Sciences, University of Barcelona, 08036 Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER) (ISCIII), 28029 Madrid, Spain
- Internal Medicine Department-Hospital Clínic of Barcelona (HCB), 08036 Barcelona, Spain
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Sharew B, Moges F, Yismaw G, Mihret A, Abebe W, Fentaw S, Tessema B. Serotype Distribution of Streptococcus pneumoniae Isolates Causing Invasive and Non-Invasive Infections Using Whole-Genome Sequencing in Ethiopia. Infect Drug Resist 2021; 14:787-794. [PMID: 33688213 PMCID: PMC7936710 DOI: 10.2147/idr.s293578] [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: 11/25/2020] [Accepted: 02/18/2021] [Indexed: 11/23/2022] Open
Abstract
Background In Ethiopia, pneumococcal conjugate vaccine 10 (PCV10) was introduced in 2011 in the national vaccination program. This study was aimed to assess serotype distribution of invasive and non-invasive Streptococcus pneumoniae isolates using whole-genome sequencing. Methods A hospital-based prospective study was conducted from 2018 to 2019 at Addis Ababa and Amhara region referral hospitals, from all patients. Clinical Samples were collected and initially cultured onto 5% sheep blood agar at 37°C in a 5% CO2 atmosphere. Sequencing was done using the Illumina NextSeq 500 and SeroBA was used to predict serotypes from whole-genome sequencing raw data. Results Of the 57 S. pneumoniae isolates, there were 32 circulating serotypes. The most common serotypes were 15A/B/C (n=5, 8.8%), 6A (n=4, 7.0%), 10A/F (n=4, 7.0%), 23A (n=4, 7.0%) and 7C (n=3, 5.3%). The serotype coverage of PCV10 and PCV13 were 12.3% and 26.3% respectively. The most common invasive serotypes were 15A/B/C (n=5, 8.8%) and 6A (n=4, 7.0%), and non-invasive serotypes were 23A (n=4, 7.0%) and 10A/F (n=3, 5.3%). The most prevalent serotype obtained from PCV10 eligible children was 3 (n=2, 3.5%). The prevalent serotype obtained from PCV10 non-eligible patients were type 23A (n=4, 7%) and type 6A (n=3, 5.2%). The most common serotypes among children ≤18 years old were 10A/F, 7C, 35A/B, 16F, 19A, 3 and 38. However, the proportions of some non-vaccine serotypes (11A/B and 15A/B/C) were higher in adult patients. Conclusion In this study a shift in the distribution of non-vaccinated S. pneumoniae serotypes increases in the population, and PCV10 serotype coverage was reduced as compared to PCV13. Therefore, it is important to continue monitoring serotype changes among all patients in addition to assessing the impact and effectiveness brought by vaccines and provides a foundation for prevention strategies and vaccine policies.
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Affiliation(s)
- Bekele Sharew
- Department of Medical Microbiology, School of Biomedical and Laboratory Sciences, College of Medicine and Health Sciences, University of Gondar, Gondar, Ethiopia.,Department of Medical Laboratory Sciences, College of Medicine and Health Sciences, Wollo University, Dessie, Ethiopia
| | - Feleke Moges
- Department of Medical Microbiology, School of Biomedical and Laboratory Sciences, College of Medicine and Health Sciences, University of Gondar, Gondar, Ethiopia
| | - Gizachew Yismaw
- Department of Medical Microbiology, School of Biomedical and Laboratory Sciences, College of Medicine and Health Sciences, University of Gondar, Gondar, Ethiopia
| | - Adane Mihret
- Armauer Hansen Research Institute, Addis Ababa, Ethiopia
| | - Wondiwossen Abebe
- Department of Medical Microbiology, School of Biomedical and Laboratory Sciences, College of Medicine and Health Sciences, University of Gondar, Gondar, Ethiopia
| | - Surafal Fentaw
- Ethiopian Public Health Institute, Addis Ababa, Ethiopia
| | - Belay Tessema
- Department of Medical Microbiology, School of Biomedical and Laboratory Sciences, College of Medicine and Health Sciences, University of Gondar, Gondar, Ethiopia
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Perret C, Le Corre N, Castro-Rodriguez JA. Emergent Pneumonia in Children. Front Pediatr 2021; 9:676296. [PMID: 34222146 PMCID: PMC8247473 DOI: 10.3389/fped.2021.676296] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 05/21/2021] [Indexed: 12/11/2022] Open
Abstract
In recent decades there have been multiple pathogens, viruses and bacteria, which have emerged as causal agents of pneumonia affecting adults, albeit less frequently, to children. For the purposes of this article we have classified emerging pathogens as follows: True emerging, to pathogens identified for the very first time affecting human population (SARS-CoV-1, SARS-CoV-2, MERS-CoV, avian influenza, and hantavirus); Re-emerging, to known pathogens which circulation was controlled once, but they have reappeared (measles, tuberculosis, antimicrobial resistant bacteria such as CA-MRSA, Mycoplasma pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, Stenotrophomonas maltophilia, and new serotypes of post-vaccine pneumococcal); and finally, those that we have called old known with new presentations, including common pathogens that, in particular condition, have changed their form of presentation (rhinovirus, and non-SARS coronavirus). We will review for each of them their epidemiology, forms of presentation, therapy, and prognosis in children compared to the adult with the aim of being able to recognize them to establish appropriate therapy, prognostics, and effective control measures.
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Affiliation(s)
- Cecilia Perret
- Department of Pediatric Infectious Diseases and Immunology, School of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Nicole Le Corre
- Department of Pediatric Infectious Diseases and Immunology, School of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Jose A Castro-Rodriguez
- Department of Pediatric Pulmonology and Cardiology, School of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile
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Wouters I, Desmet S, Van Heirstraeten L, Herzog SA, Beutels P, Verhaegen J, Goossens H, Van Damme P, Malhotra-Kumar S, Theeten H. How nasopharyngeal pneumococcal carriage evolved during and after a PCV13-to-PCV10 vaccination programme switch in Belgium, 2016 to 2018. ACTA ACUST UNITED AC 2020; 25. [PMID: 32046817 PMCID: PMC7014673 DOI: 10.2807/1560-7917.es.2020.25.5.1900303] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Background The current carriage study was set up to reinforce surveillance during/after the PCV13-to-PCVC10 switch in Belgium. Aim This observational study monitored carriage of Streptococcus pneumoniae (Sp) serotypes, particularly those no longer covered (3, 6A, 19A), as well as Haemophilus influenzae (Hi), because PCV10 contains the non-typeable Hi protein D. Methods A total of 2,615 nasopharyngeal swabs from children (6–30 months old) attending day care were collected in three periods over 2016–2018. Children’s demographic and clinical characteristics and vaccination status were obtained through a questionnaire. Sp and Hi were identified by culture and PCR. Pneumococcal strains were tested for antimicrobial (non-)susceptibility by disc diffusion and serotyped by Quellung-reaction (Quellung-reaction and PCR for serotypes 3, 6A, 19A). Results The carriage prevalence of Sp (> 75%) remained stable over the successive periods but that of Hi increased (87.4%, 664 Hi-carriers/760 in 2016 vs 93.9%, 895/953 in 2017–2018). The proportion of non-PCV13 vaccine serotypes decreased (94.6%, 438 isolates/463 in 2016 vs 89.7%, 599/668 in 2017–2018) while that of PCV13-non-PCV10 vaccine serotypes (3 + 6A + 19A) increased (0.9%, 4 isolates/463 in 2016 vs 7.8%, 52/668 in 2017–2018), with serotype 19A most frequently identified (87.9%, 58/66 isolates). Non-susceptibility of pneumococci against any of the tested antibiotics was stable over the study period (> 44%). Conclusions During and after the PCV13-to-PCV10 vaccine switch, the proportion of non-PCV13 serotypes decreased, mainly due to a serotype 19A carriage prevalence increase. These results complement invasive pneumococcal disease surveillance data, providing further basis for pneumococcal vaccination programme policy making.
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Affiliation(s)
- Ine Wouters
- Centre for the Evaluation of Vaccination, Vaccine and Infectious Disease Institute, University of Antwerp, Wilrijk, Belgium
| | - Stefanie Desmet
- Reference Centre for Pneumococci, University Hospitals Leuven, Leuven, Belgium
| | - Liesbet Van Heirstraeten
- Laboratory of Medical Microbiology, Vaccine and Infectious Disease Institute, University of Antwerp, Wilrijk, Belgium
| | - Sereina A Herzog
- Centre for Health Economics Research and Modelling Infectious Diseases, University of Antwerp, Wilrijk, Belgium
| | - Philippe Beutels
- Centre for Health Economics Research and Modelling Infectious Diseases, University of Antwerp, Wilrijk, Belgium
| | - Jan Verhaegen
- Reference Centre for Pneumococci, University Hospitals Leuven, Leuven, Belgium
| | - Herman Goossens
- Laboratory of Medical Microbiology, Vaccine and Infectious Disease Institute, University of Antwerp, Wilrijk, Belgium
| | - Pierre Van Damme
- Centre for the Evaluation of Vaccination, Vaccine and Infectious Disease Institute, University of Antwerp, Wilrijk, Belgium
| | - Surbhi Malhotra-Kumar
- Laboratory of Medical Microbiology, Vaccine and Infectious Disease Institute, University of Antwerp, Wilrijk, Belgium
| | - Heidi Theeten
- Centre for the Evaluation of Vaccination, Vaccine and Infectious Disease Institute, University of Antwerp, Wilrijk, Belgium
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- The members of the NPcarriage Study Group are listed at the end of the article
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Raguindin PF. The changing epidemiology of pneumococcal diseases: new challenges after widespread routine immunization. Int J Public Health 2020; 65:709-710. [DOI: 10.1007/s00038-020-01403-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2020] [Revised: 05/20/2020] [Accepted: 05/27/2020] [Indexed: 10/24/2022] Open
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20
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SERS-based immunocapture and detection of pathogenic bacteria using a boronic acid-functionalized polydopamine-coated Au@Ag nanoprobe. Mikrochim Acta 2020; 187:290. [DOI: 10.1007/s00604-020-04248-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 03/30/2020] [Indexed: 10/24/2022]
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Abdoli S, Safamanesh S, Khosrojerdi M, Azimian A. Molecular Detection and Serotyping of Streptococcus pneumoniae in Children with Suspected Meningitis in Northeast Iran. IRANIAN JOURNAL OF MEDICAL SCIENCES 2020; 45:125-133. [PMID: 32210489 PMCID: PMC7071549 DOI: 10.30476/ijms.2019.45423] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Background: To date, more than 90 Streptococcus pneumoniae (S. pneumoniae) capsular serotypes are known. The prevalence of these serotypes varies
according to the geographical area and the regional vaccination program. Due to the lack of regular vaccination programs for S. pneumoniae in developing countries,
serotyping of the prevalent isolates is useful in selecting the correct vaccine. The present study aimed to evaluate common serotypes of pneumococcal meningitis in Bojnurd, Iran. Methods: All cerebrospinal fluid (CFS) samples suspected for bacterial meningitis were analyzed. The samples were collected during 2014-2018 in the Laboratory of Imam Reza Hospital
(Bojnurd, Iran). Due to the high rate of false-negative cultures, polymerase chain reaction (PCR) was used for the detection of lytA and psaA genes of S. pneumoniae.
In addition, the modified Marimon’s PCR method was used for serotyping the bacteria. The data were analyzed using Pearson’s Chi-square test. Results: Out of the 901 CSF samples, 106 cases tested positive for S. pneumoniae using the PCR method, while only 92 cases tested positive using the conventional methods.
Based on the Marimon’s PCR method, serotypes 23F, 19F, 19A, 1, 14, and serogroup 6A/B were the most common types. Serogroups 18C, 15A/F, 15B/C, 9A/V, 7A/F, 11A/D/F, and 22A/F were
also detected in isolates. Note that 2.8% of the samples were non-typable (NT). Conclusion: The results showed that only 13 serotypes were responsible for all meningitis cases. Pneumococcal capsular vaccine-13 (PCV-13) is the preferred choice against common serotypes of S. pneumoniae in northeast Iran. The abstract was presented in Iran’s 19th International Congress of Microbiology, as a poster and published in the congress abstracts book.
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Affiliation(s)
- Sepideh Abdoli
- Department of Biotechnology and Molecular Sciences, School of Medicine, North Khorasan University of Medical Sciences, Bojnurd, Iran
| | - Saghar Safamanesh
- Department of Pathobiology and Laboratory Sciences, School of Medicine, North Khorasan University of Medical Sciences, Bojnurd, Iran.,Vector-borne Diseases Research Center, North Khorasan University of Medical Sciences, Bojnurd, Iran
| | - Mahsa Khosrojerdi
- Department of Pediatrics, School of Medicine, Semnan University of Medical Sciences, Semnan, Iran
| | - Amir Azimian
- Department of Pathobiology and Laboratory Sciences, School of Medicine, North Khorasan University of Medical Sciences, Bojnurd, Iran.,Vector-borne Diseases Research Center, North Khorasan University of Medical Sciences, Bojnurd, Iran
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Nakamura A, Kawakami K, Wakana A, Folaranmi TA, Iino T. A Japanese nationwide survey of 23-valent pneumococcal capsular polysaccharide vaccine (PPSV23) revaccination coverage rate among elderly adults aged 65 and older and physician's attitude. Hum Vaccin Immunother 2020; 16:2292-2299. [PMID: 32045317 PMCID: PMC7553671 DOI: 10.1080/21645515.2020.1717184] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
In July 2017, the Japanese Association for Infectious Diseases issued guidance for the administration of the PPSV23 revaccination. Despite increasing recognition of its protective benefits, levels of PPSV23 revaccination coverage rate in Japanese elderly population are unclear at present. Here, we report the results of a survey to know PPSV23 revaccination rates among elderly patients aged 65 and older. We asked an array of questions related to PPSV23 revaccination to Elderly adults and doctors across Japan via Web-based surveys in June 2018. The sampled population consisted of 5,085 men and women aged 65 and older. The PPSV23 revaccination coverage rate was estimated by survey questions regarded vaccination counts, intervals, and vaccine type. In addition, 400 internal medicine physicians were surveyed and asked about their reasons for recommending PPSV23 revaccination to elderly patients. In total, 1,648 elderly adults had received at least one PPSV23 dose; of these, 58 had received it at least twice (revaccination coverage rate: 3.5%). The most commonly cited justification for revaccination with PPSV23 among the surveyed physicians was that the benefits of revaccination exceed the risks of revaccination. In addition, multivariate analysis showed revaccinated status was most strongly associated with recommendations from peers (e.g. spouse, family, friends) among elderly subjects. This study reports PPSV23 revaccination coverage rate among Japanese adults aged 65 and older for the first time and concludes that the coverage rate is very low.
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Affiliation(s)
| | - Kenji Kawakami
- Medical Division, NTT East Izu Hospital , Shizuoka, Japan
| | - Akira Wakana
- Biostatistics&Research Decision Sciences, Japan Development, MSD K.K ., Tokyo, Japan
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Habibi Ghahfarokhi S, Mosadegh M, Ahmadi A, Pourmand MR, Azarsa M, Rahbar M, Nikmanesh B. Serotype Distribution and Antibiotic Susceptibility of Streptococcus pneumoniae Isolates in Tehran, Iran: A Surveillance Study. Infect Drug Resist 2020; 13:333-340. [PMID: 32099424 PMCID: PMC7007777 DOI: 10.2147/idr.s234295] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2019] [Accepted: 01/23/2020] [Indexed: 11/23/2022] Open
Abstract
Introduction Encapsulated Streptococcus pneumoniae strains cause high morbidity and mortality, mainly in countries with no pneumococcal conjugate vaccines (PCVs) immunization program. This study investigated the epidemiological changes of S. pneumoniae isolates including serotype distribution and antimicrobial susceptibility in Tehran, Iran. Methods A total of 80 S. pneumoniae samples were collected from patients admitted to Shariati hospital over two periods. Half of the isolates were collected from February to September 2017 and the other half from July 2018 to March 2019. The antimicrobial susceptibility testing and PCV-13 serotype coverage of S. pneumoniae isolates were evaluated among patients with invasive and non-invasive infections. Results The most common serotypes were 23F (17.5%), 14 (16.3%), 3 (16.3%) 19F (12.5%), and 19A (12.5%) in the present study. The vaccine coverage rates of PCV-7, PCV-10 and PCV-13 were 52.6%, 52.6%, and 83.7%, respectively. S. pneumoniae isolates with the serotype of the PCV-13 showed an increasing trend during the study. Nearly half of the S. pneumoniae strains were MDR, while MDR serotype 19A increased (40%) during the study periods. A small minority of isolates (16%) belonged to non-vaccine serotypes, 65% of which were assigned to MDR. In general, the frequency of penicillin resistant and MDR strains were estimated about 27.5% and 51%, respectively. An increase was observed in resistance to erythromycin and co-trimoxazole. Conclusion The results showed that majority of the circulating serotypes in our study are related to PCV-13 serotypes. The use of conjugate vaccine in the immunization program and surveillance of antimicrobial resistance can be effective in reducing the pneumococcal clinical burden.
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Affiliation(s)
- Soheila Habibi Ghahfarokhi
- Department of Pathobiology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Mehrdad Mosadegh
- Department of Pathobiology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Ali Ahmadi
- Molecular Biology Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Mohammad Reza Pourmand
- Department of Pathobiology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Mohammad Azarsa
- Department of Microbiology, Khoy University of Medical Sciences, Khoy, Iran
| | - Mohammad Rahbar
- Department of Microbiology, Reference Health Laboratories Research Center, Ministry of Health and Medical Education, Tehran, Iran
| | - Bahram Nikmanesh
- Department of Medical Laboratory Sciences, School of Allied Medical Sciences, Tehran University of Medical Sciences, Tehran, Iran
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24
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The strategy for correcting interference from water in Fourier transform infrared spectrum based bacterial typing. Talanta 2020; 208:120347. [DOI: 10.1016/j.talanta.2019.120347] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2019] [Revised: 09/09/2019] [Accepted: 09/10/2019] [Indexed: 11/18/2022]
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25
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Silva SM, Rodrigues ICG, Santos RDS, Ternes YMF. The direct and indirect effects of the pneumococcal conjugated vaccine on carriage rates in children aged younger than 5 years in Latin America and the Caribbean: a systematic review. EINSTEIN-SAO PAULO 2019; 18:eRW4890. [PMID: 31778464 PMCID: PMC6896659 DOI: 10.31744/einstein_journal/2020rw4890] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Accepted: 06/25/2019] [Indexed: 11/24/2022] Open
Abstract
Objective To demonstrate the impact of pneumococcal conjugate vaccine in Streptococcus pneumoniae carriage status in children younger than 5 years in Latin America and the Caribbean. Methods A systematic literature review was carried out on the direct and indirect effects of pneumococcal vaccine in the carriage status, after implementation in childhood immunization programs. Studies carried out in children younger than 5 years were selected from the PubMed® and Virtual Health Library databases, and data collected after implementation of pneumococcal vaccine in Latin America and the Caribbean, between 2008 and 2018. Results From 1,396 articles identified, 738 were selected based on titles and abstracts. After duplicate removal, 31 studies were eligible for full-text reading, resulting in 6 publications for analysis. All selected publications were observational studies and indicated a decrease in the carriage and vaccine types, and an increase in the circulation of non-vaccine serotypes, such as 6A, 19A, 35B, 21 and 38. We did not identify changes in the antimicrobial resistance after vaccine implementation. Conclusion A decrease in the carriage status of vaccine types and non-vaccine types was detected. The continuous monitoring of pneumococcal vaccine effect is fundamental to demonstrate the impact of the carriage status and, consequently, of invasive pneumococcal disease, allowing better targeting approaches in countries that included pneumococcal vaccine in their immunization programs. Our study protocol was registered in PROSPERO (www.crd.york.ac.uk/prospero) under number CRD42018096719.
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26
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Identification of Pneumococcal Serotypes by PCR-Restriction Fragment Length Polymorphism. Diagnostics (Basel) 2019; 9:diagnostics9040196. [PMID: 31752204 PMCID: PMC6963424 DOI: 10.3390/diagnostics9040196] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Revised: 11/13/2019] [Accepted: 11/15/2019] [Indexed: 11/30/2022] Open
Abstract
Streptococcus pneumoniae shows more than 90 capsular serotypes that can be distinguished by their reactivity against antisera. The main objective of this work was the development of a molecular method for serotyping without the use of antisera. A computer program containing an algorithm was used to search in a database for potentially useful enzymes for Restriction Fragment Length Polymorphism-RFLP typing, in order to maximize the discrimination between different serotypes. DNA sequences of 90 serotypes for the region between dexB and aliA genes were compiled, and a computer screening of restriction enzymes was performed. The wzg–wzh–wzd–wze region and Sse9I restriction predicted unique PCR-RFLP patterns for 39 serotypes and eight serogroups. A second restriction enzyme resolved fragment specific patterns for 25 serotypes. The method was tested with 98 serotype-unknown clinical isolates. PCR-RFLP analysis deduced correct serotypes that were confirmed by Quellung reaction for 78.5% of the isolates.
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27
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Martinez-Vega R, Jauneikaite E, Thoon KC, Chua HY, Huishi Chua A, Khong WX, Tan BH, Low Guek Hong J, Venkatachalam I, Anantharajah Tambyah P, Hibberd ML, Clarke SC, Ng OT. Risk factor profiles and clinical outcomes for children and adults with pneumococcal infections in Singapore: A need to expand vaccination policy? PLoS One 2019; 14:e0220951. [PMID: 31618204 PMCID: PMC6795432 DOI: 10.1371/journal.pone.0220951] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2019] [Accepted: 07/27/2019] [Indexed: 11/18/2022] Open
Abstract
Invasive pneumococcal infection is a major cause of morbidity and mortality worldwide despite the availability of pneumococcal vaccines. The aim of this study was to re-evaluate the clinical syndromes, prognostic factors and outcomes for pneumococcal disease in adults and children in Singapore during the period before and after the introduction of the pneumococcal vaccine. We retrospectively analyzed a large cohort of patients admitted to the four main public hospitals in Singapore with S. pneumoniae infection between 1997 and 2013. A total of 889 (64% of all isolates identified in the clinical laboratories) cases were included in the analysis; 561 (63.1%) were adult (≥16 years) cases with a median age of 62 years and 328 (36.9%) were paediatric cases with a median age of 3 years. Bacteraemic pneumonia was the most common syndrome in both groups (69.3% vs. 44.2%), followed by primary bacteraemia without pneumonia (14.3% vs. 13.4%), meningitis (6.4% vs. 7.6%) and non-bacteraemic pneumonia (5.2% vs. 21%). The major serotypes in adults were 3, 4, 6B, 14, 19F and 23F whereas in children they were 14, 6B and 19F, accounting both for nearly half of pneumococcal disease cases. No particular serotype was associated with mortality or severity of the pneumococcal disease. Overall mortality rate was 18.5% in adults and 3% in children. Risk factors for mortality included acute cardiac events in adults, meningitis in children and critical illness and bilateral pulmonary infiltrates in both adults and children. Penicillin resistance was not associated with increased mortality. Our results agree with global reports that the course of pneumococcal disease and its clinical outcome were more severe in adults than in children. The main serotypes causing invasive disease were mostly covered by the vaccines in use. The high mortality rates reflect an urgent need to increase vaccination coverage in both adults and children to tackle this vaccine-preventable infection.
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Affiliation(s)
| | - Elita Jauneikaite
- Infectious Diseases, Genome Institute of Singapore, Singapore, Singapore
- Faculty of Medicine and Institute of Life Sciences, University of Southampton, Southampton, United Kingdom
| | - Koh Cheng Thoon
- Infectious Disease Service, Department of Paediatrics, KK Women’s and Children’s Hospital, Singapore, Singapore
- Duke-NUS Graduate Medical School, Singapore, Singapore
| | - Hui Ying Chua
- Department of Infectious Diseases, Tan Tock Seng Hospital, Singapore, Singapore
| | - Amanda Huishi Chua
- Department of Infectious Diseases, Tan Tock Seng Hospital, Singapore, Singapore
| | - Wei Xin Khong
- Department of Infectious Diseases, Tan Tock Seng Hospital, Singapore, Singapore
| | - Ban Hock Tan
- Department of Infectious Diseases, Singapore General Hospital, Singapore, Singapore
| | - Jenny Low Guek Hong
- Department of Infectious Diseases, Singapore General Hospital, Singapore, Singapore
| | | | | | - Martin L. Hibberd
- Infectious Diseases, Genome Institute of Singapore, Singapore, Singapore
| | - Stuart C. Clarke
- Faculty of Medicine and Institute of Life Sciences, University of Southampton, Southampton, United Kingdom
| | - Oon Tek Ng
- Department of Infectious Diseases, Tan Tock Seng Hospital, Singapore, Singapore
- National Centre for Infectious Diseases (NCID), Singapore, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
- * E-mail:
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28
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Development for Clinical Use of a Multiplexed Immunoassay Using Sputum Samples for Streptococcus pneumoniae: a Non-Culture-Based Approach for Serotype-Specific Detection. J Clin Microbiol 2019; 57:JCM.01782-18. [PMID: 31340989 DOI: 10.1128/jcm.01782-18] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Accepted: 07/16/2019] [Indexed: 11/20/2022] Open
Abstract
The multiplexed immunoassay (MIA) is an automated, monoclonal antibody-based serotyping assay that uses culture lysates of Streptococcus pneumoniae This study describes the development and validation of applying MIA directly to sputum samples for the serotype-specific detection of S. pneumoniae Sputum optimization involved liquefaction and fractionation. The subjects included 173 adult patients from whom both pneumococcal isolates cultured from sputum samples and the corresponding sputum samples were available at the Korea University Hospital from March 2012 to June 2015. Pneumococcal lysates and the sputum fraction were separately evaluated by MIA with a set A reaction to identify 27 serotypes (24 vaccine serotypes and serotypes 6C, 6D, and 11E). MIA results were validated by multiplex PCR (mPCR). Among the 173 patients analyzed, the pneumococcal isolate MIA detected a single set A serotype in 104 patients, and the corresponding sputum MIA showed concordant results with additional multiple serotypes in 21 patients. For the remaining 69 patients whose pneumococcal isolates were not determined to be set A serotypes by the pneumococcal isolate MIA, the corresponding sputum MIA identified additional set A serotypes (single serotypes, n = 17; multiple serotypes, n = 4). Serotypes 3 and 11A/D/F were the most commonly detected serotypes in both the pneumococcal isolate and sputum MIA analyses. However, serotype 8 was the most prevalent serotype detected only by the sputum MIA. The results of mPCR, performed for validation, showed a high concordance with the results of the sputum MIA. In conclusion, MIA using sputum samples enables the accurate, rapid, direct, and serotype-specific detection of S. pneumoniae, which may improve postvaccination serotype surveillance.
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Sutcliffe CG, Shet A, Varghese R, Veeraraghavan B, Manoharan A, Wahl B, Chandy S, Sternal J, Khan R, Singh RK, Santosham M, Arora NK. Nasopharyngeal carriage of Streptococcus pneumoniae serotypes among children in India prior to the introduction of pneumococcal conjugate vaccines: a cross-sectional study. BMC Infect Dis 2019; 19:605. [PMID: 31291902 PMCID: PMC6621985 DOI: 10.1186/s12879-019-4254-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Accepted: 07/03/2019] [Indexed: 01/24/2023] Open
Abstract
BACKGROUND Streptococcus pneumoniae is a major cause of pneumonia, meningitis, and other serious infections among children in India. India introduced the 13-valent pneumococcal conjugate vaccine (PCV) in several states in 2017, and is expected to expand to nationwide coverage in the near future. To establish a baseline for measuring the impact of PCV in India, we assessed overall and serotype-specific nasopharyngeal carriage in two pediatric populations. METHODS A cross-sectional study was conducted in Palwal District, Haryana, from December 2016 to July 2017, prior to vaccine introduction. Children 2-59 months of age with clinical pneumonia seeking healthcare and those in the community with no clear illness were targeted for enrollment. A nasopharyngeal swab was collected and tested for pneumococcus using conventional culture and sequential multiplex PCR. Isolates were tested for antimicrobial resistance using an E test. Children were considered colonized if pneumococcus was isolated by culture or PCR. The prevalence of pneumococcal and serotype-specific colonization was compared between groups of children using log-binomial regression. RESULTS Among 601 children enrolled, 91 had clinical pneumonia and 510 were community children. The proportion colonized with S. pneumoniae was 74.7 and 54.5% among children with clinical pneumonia and community children, respectively (adjusted prevalence ratio: 1.38; 95% confidence interval: 1.19, 1.60). The prevalence of PCV13 vaccine-type colonization was similar between children with clinical pneumonia (31.9%) and community children (28.0%; p = 0.46). The most common colonizing serotypes were 6A, 6B, 14, 19A, 19F, and 23F, all of which are included in the PCV13 vaccine product. Antimicrobial resistance to at least one drug was similar between isolates from children with clinical pneumonia (66.1%) and community children (61.5%; p = 0.49); while resistance to at least two drugs was more common among isolates from children with clinical pneumonia (25.8% vs. 16.4%; p = 0.08). Resistance for all drugs was consistently higher for PCV13 vaccine-type serotypes compared to non-vaccine serotypes in both groups. CONCLUSION This study provides baseline information on the prevalence of serotype-specific pneumococcal colonization among children prior to the introduction of PCV in India. Our results suggest a role for pneumococcal vaccines in reducing pneumococcal colonization and antimicrobial resistant isolates circulating in India.
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Affiliation(s)
- Catherine G Sutcliffe
- Johns Hopkins Bloomberg School of Public Health, 615 N. Wolfe Street, Baltimore, MD, 21205, USA.
| | - Anita Shet
- Johns Hopkins Bloomberg School of Public Health, 615 N. Wolfe Street, Baltimore, MD, 21205, USA
| | - Rosemol Varghese
- Christian Medical College, Ida Scudder Road, Vellore, Tamil Nadu, 632004, India
| | | | - Anand Manoharan
- The CHILDS Trust Medical Research Foundation, 12-A Nageswara Road, Nungambakkam, Chennai, 600034, India
| | - Brian Wahl
- Johns Hopkins Bloomberg School of Public Health, 615 N. Wolfe Street, Baltimore, MD, 21205, USA
| | - Sara Chandy
- The CHILDS Trust Medical Research Foundation, 12-A Nageswara Road, Nungambakkam, Chennai, 600034, India
| | - Jack Sternal
- Johns Hopkins Bloomberg School of Public Health, 615 N. Wolfe Street, Baltimore, MD, 21205, USA
| | - Raziuddin Khan
- The INCLEN Trust International, F-1/5, 2nd Floor, Okhla Industrial Area Phase - 1, New Delhi, 110020, India
| | - Rakesh Kumar Singh
- The INCLEN Trust International, F-1/5, 2nd Floor, Okhla Industrial Area Phase - 1, New Delhi, 110020, India
| | - Mathuram Santosham
- Johns Hopkins Bloomberg School of Public Health, 615 N. Wolfe Street, Baltimore, MD, 21205, USA
| | - Narendra K Arora
- The INCLEN Trust International, F-1/5, 2nd Floor, Okhla Industrial Area Phase - 1, New Delhi, 110020, India.
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30
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Gonzales-Siles L, Salvà-Serra F, Degerman A, Nordén R, Lindh M, Skovbjerg S, Moore ERB. Identification and capsular serotype sequetyping of Streptococcus pneumoniae strains. J Med Microbiol 2019; 68:1173-1188. [PMID: 31268417 DOI: 10.1099/jmm.0.001022] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
PURPOSE Correct serotype identification of Streptococcus pneumoniae (pneumococcus) is important for monitoring disease epidemiology and assessing the impacts of pneumococcal vaccines. Furthermore, correct identification and differentiation of the pathogenic S. pneumoniae from closely related commensal species of the mitis group of the genus Streptococcus are essential for correct serotype identification. METHODOLOGY A new protocol for determining the existing 98 serotypes of pneumococcus was developed, applying two PCR amplifications and amplicon sequencing, using newly designed internal primers. The new protocol was validated using S. pneumoniae genome sequences, reference strains with confirmed serotypes and clinical isolates, and comparing the results with those from the traditional Quellung reaction or antiserum panel gel precipitation, in addition to real-time PCR analysis. The taxonomic identifications of 422 publicly available (GenBank) genome sequences of S. pneumoniae, Streptococcus pseudopneumoniae and Streptococcus mitis were assessed by whole-genome sequence average nucleotide identity based on blast (ANIb) analysis. RESULTS The proposed sequetyping protocol generates a 1017 bp whole cpsB region sequence, increasing resolution for serotype identification in pneumococcus isolates. The identifications of all GenBank genome sequences of S. pneumoniae were confirmed, whereas most of the S. pseudopneumoniae and almost all of the S. mitis genome sequences did not fulfil the ANIb thresholds for species-level identification. The housekeeping biomarker gene, groEL, correctly identified S. pneumoniae but often misclassified S. pseudopneumoniae and S. mitis as S. pneumoniae. CONCLUSIONS These studies affirm the importance of applying reliable identification protocols for S. pneumoniae before serotyping; our protocols provide reliable diagnostic tools, as well as an improved workflow, for serotype identification of pneumococcus and differentiation of serogroup 6 types.
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Affiliation(s)
- Lucia Gonzales-Siles
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy of the University of Gothenburg, Gothenburg, Sweden.,Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Gothenburg, Sweden
| | - Francisco Salvà-Serra
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy of the University of Gothenburg, Gothenburg, Sweden.,Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Gothenburg, Sweden.,Culture Collection University of Gothenburg (CCUG), Department of Clinical Microbiology, Sahlgrenska University Hospital, Gothenburg, Sweden.,Microbiology, Department of Biology, University of the Balearic Islands, Palma de Mallorca, Spain
| | - Anna Degerman
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy of the University of Gothenburg, Gothenburg, Sweden
| | - Rickard Nordén
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy of the University of Gothenburg, Gothenburg, Sweden
| | - Magnus Lindh
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy of the University of Gothenburg, Gothenburg, Sweden
| | - Susann Skovbjerg
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy of the University of Gothenburg, Gothenburg, Sweden.,Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Gothenburg, Sweden
| | - Edward R B Moore
- Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Gothenburg, Sweden.,Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy of the University of Gothenburg, Gothenburg, Sweden.,Culture Collection University of Gothenburg (CCUG), Department of Clinical Microbiology, Sahlgrenska University Hospital, Gothenburg, Sweden
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Varghese R, Neeravi A, Subramanian N, Pavithra B, Kavipriya A, Kumar JL, Girish Kumar CP, Jeyraman Y, Karthik G, Verghese VP, Veeraraghavan B. Clonal similarities and sequence-type diversity of invasive and carriage Streptococcus pneumoniae in India among children under 5 Years. Indian J Med Microbiol 2019; 37:358-362. [PMID: 32003333 DOI: 10.4103/ijmm.ijmm_19_348] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
Background Pneumococcal pneumonia is one of the major causes of mortality in children less than 5 years in Asia, especially in India. Available PCVs have less serotype coverage in India compared to western countries. Moreover, the baseline pneumococcal serotype and sequence type data is limited and available data doesn't represent the entire India. With this background we aimed to characterize invasive and carriage isolates of S. pneumoniae from a tertiary care hospital in South India. Materials and Methods A total of 221 S. pneumoniae isolates, invasive (n=138) and carriage (n=83) between the time period of 2012-2018 were included. Isolates was identified and confirmed using standard laboratory protocols. Serotyping was performed by Customized sequential multiplex PCR and MLST as described in www.pubmlst.org. Results The major serotypes were 19F, 6B, 14, 6A and 19A and the sequence types (ST) were ST63, 236 and 230. Predominant STs in invasive was ST 63 whereas in carriage were ST4894 and 1701. High level ST diversity in carriage was observed. Majority of the STs were SLVs or DLVs of previously reported STs or PMEN clones. Phylogenetic analyses of the STs revealed gradual expansion of three PMEN CCs CC320, 63 and 230. Conclusion The vaccine serotypes were the predominant ones found to be associated with IPD, PMEN clones, new STs and antimicrobial resistance. Accordingly, PCV13 is expected to provide invasive serotype coverage of 75% in Indian children less than 5 years. This study provides baseline serotype and sequence type data prior to the introduction of PCV in South India.
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Affiliation(s)
- Rosemol Varghese
- Department of Clinical Microbiology, Christian Medical College, Vellore, Tamil Nadu, India
| | - Ayyanraj Neeravi
- Department of Clinical Microbiology, Christian Medical College, Vellore, Tamil Nadu, India
| | - Nithya Subramanian
- Department of Paediatrics, Christian Medical College, Chennai, Tamil Nadu, India
| | - B Pavithra
- Department of Clinical Microbiology, Christian Medical College, Vellore, Tamil Nadu, India
| | - A Kavipriya
- Department of Clinical Microbiology, Christian Medical College, Vellore, Tamil Nadu, India
| | - Jones Lionel Kumar
- Department of Clinical Microbiology, Christian Medical College, Vellore, Tamil Nadu, India
| | - C P Girish Kumar
- ICMR, National Institute of Epidemiology, Chennai, Tamil Nadu, India
| | - Yuvraj Jeyraman
- ICMR, National Institute of Epidemiology, Chennai, Tamil Nadu, India
| | - G Karthik
- Department of Medicine, Christian Medical College, Vellore, Tamil Nadu, India
| | - Valsan P Verghese
- Department of Paediatrics, Christian Medical College, Chennai, Tamil Nadu, India
| | - Balaji Veeraraghavan
- Department of Clinical Microbiology, Christian Medical College, Vellore, Tamil Nadu, India
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Sanz JC, de Luis R, Del Río S, Gamen S, Cercenado E, Orellana MA, Yuste J. Direct identification of pneumococcal serotypes in blood cultures by a PCR-reverse-hybridisation technique. Enferm Infecc Microbiol Clin 2019; 38:170-173. [PMID: 31248724 DOI: 10.1016/j.eimc.2019.04.010] [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: 02/19/2019] [Revised: 04/26/2019] [Accepted: 04/29/2019] [Indexed: 10/26/2022]
Abstract
INTRODUCTION The objective of this study was to assess the performance of a technique (S. PneumoStrip test) based on PCR followed by reverse strip hybridisation for the detection of Streptococcus pneumoniae serotypes directly in blood culture vials. METHODS One hundred and ten (110) pairs of isolated strains and their corresponding original blood cultures vials were studied in parallel. Pure isolated strains were conventionally serotyped using latex agglutination and the Quellung reaction. The S. PneumoStrip test was carried out directly in the original blood culture samples. RESULTS In 102 cases (92.7%), results of the serotype obtained by Quellung coincided with their corresponding original blood cultures typed by S. PneumoStrip. CONCLUSIONS S. PneumoStrip test is a good alternative technique for direct pneumococcal serotyping in blood culture clinical samples.
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Affiliation(s)
- Juan Carlos Sanz
- Unidad de Microbiología Clínica, Laboratorio Regional de Salud Pública, Dirección General de Salud Pública, Comunidad de Madrid, Centro de Especialidades Médicas Vicente Soldevilla, Madrid, Spain; CIBER de Epidemiología y Salud Pública (CIBERESP), Madrid, Spain.
| | | | | | | | - Emilia Cercenado
- Servicio de Microbiología, Hospital General Universitario Gregorio Marañón, Madrid, Spain
| | | | - Jose Yuste
- Laboratorio de Referencia de Neumococo, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain; CIBER de Enfermedades Respiratorias (CIBERES), Madrid, Spain
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33
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Ercibengoa M, Alonso M, Vicente D, Morales M, Garcia E, Marimón JM. Utility of MALDI-TOF MS as a new tool for Streptococcus pneumoniae serotyping. PLoS One 2019; 14:e0212022. [PMID: 30753210 PMCID: PMC6372175 DOI: 10.1371/journal.pone.0212022] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Accepted: 01/15/2019] [Indexed: 02/06/2023] Open
Abstract
Nowadays, more than 95 different Streptococcus pneumoniae serotypes are known, being less than one third responsible for the majority of severe pneumococcal infections. After the introduction of conjugate vaccines, a change in the epidemiology of the serotypes causing invasive pneumococcal disease has been observed making the surveillance of circulating serotypes especially relevant. Some recent studies have used matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) technology to identify the most frequent pneumococcal serotypes that cause invasive disease. The objectives of this study were to evaluate the efficacy of previously described discriminatory peaks determined by MALDI-TOF MS for the identification of serotypes 6B, 19F, 19A and 35B using reference and clinical isolates and to try to identify other discriminatory peaks for serotypes 11A, 19F and 19A using transformed pneumococcal strains. Most of the proposed peaks defined in the literature for the identification of serotypes 6B, 19F, 19A, 35B were not found in the spectra of the 10 reference isolates nor in those of the 60 clinical isolates tested corresponding to these four serotypes. The analysis and comparison of the mass spectra of genetically modified pneumococci (transformed strains) did not allow the establishment of new discriminatory peaks for serotypes 11A, 19F, and 19A. MALDI-TOF MS in the usual range of 2,000 to 20,000 m/z did not prove to be a valid technique for direct S. pneumoniae serotyping.
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Affiliation(s)
- María Ercibengoa
- Hospital Universitario Donostia–Instituto de Investigación Sanitaria Biodonostia, San Sebastián, Spain
- CIBER de Enfermedades Respiratorias–CIBERES, Madrid, Spain
- Preventive Medicine and Health Public Department, University of Basque Country UPV/EHU, San Sebastián, Spain
- * E-mail:
| | - Marta Alonso
- Hospital Universitario Donostia–Instituto de Investigación Sanitaria Biodonostia, San Sebastián, Spain
- CIBER de Enfermedades Respiratorias–CIBERES, Madrid, Spain
| | - Diego Vicente
- Hospital Universitario Donostia–Instituto de Investigación Sanitaria Biodonostia, San Sebastián, Spain
- CIBER de Enfermedades Respiratorias–CIBERES, Madrid, Spain
- Preventive Medicine and Health Public Department, University of Basque Country UPV/EHU, San Sebastián, Spain
| | - Maria Morales
- CIBER de Enfermedades Respiratorias–CIBERES, Madrid, Spain
- Departamento de Biotecnología Microbiana y de Plantas, Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Ernesto Garcia
- CIBER de Enfermedades Respiratorias–CIBERES, Madrid, Spain
- Departamento de Biotecnología Microbiana y de Plantas, Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Jose María Marimón
- Hospital Universitario Donostia–Instituto de Investigación Sanitaria Biodonostia, San Sebastián, Spain
- CIBER de Enfermedades Respiratorias–CIBERES, Madrid, Spain
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Abstract
Streptococcus pneumoniae is one of the commonest bacteria that cause morbidity and mortality in children and the elderly. The two extremes of age and individuals with underlying disease are particularly at risk of developing pneumococcal disease. The pneumococcus is responsible for a wide range of infectious diseases, ranging from mild, non-invasive infections such as otitis media and sinusitis, to more severe infections including pneumonia, septicemia, and meningitis. Despite the licensure of highly effective pneumococcal conjugate vaccines, the control of pneumococcal disease is still challenging. Here we describe the critical role of Streptococcus pneumoniae in public health.
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Affiliation(s)
- Godwin Oligbu
- Paediatric Infectious Diseases Research Group, Institute for Infection and Immunity, St. George's, University of London, London, UK. .,Immunisation and Countermeasures Division, National Infection Service, Public Health England, London, UK.
| | - Norman K Fry
- Immunisation and Countermeasures Division, National Infection Service, Public Health England, London, UK.,Respiratory and Vaccine Preventable Bacterial Reference Unit (RVPBRU), National Infection Service Laboratories, Public Health England, London, UK
| | - Shamez N Ladhani
- Paediatric Infectious Diseases Research Group, Institute for Infection and Immunity, St. George's, University of London, London, UK.,Immunisation and Countermeasures Division, National Infection Service, Public Health England, London, UK
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35
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Novais Â, Freitas AR, Rodrigues C, Peixe L. Fourier transform infrared spectroscopy: unlocking fundamentals and prospects for bacterial strain typing. Eur J Clin Microbiol Infect Dis 2018; 38:427-448. [DOI: 10.1007/s10096-018-3431-3] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Accepted: 11/11/2018] [Indexed: 01/25/2023]
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36
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Voß F, Kohler TP, Meyer T, Abdullah MR, van Opzeeland FJ, Saleh M, Michalik S, van Selm S, Schmidt F, de Jonge MI, Hammerschmidt S. Intranasal Vaccination With Lipoproteins Confers Protection Against Pneumococcal Colonisation. Front Immunol 2018; 9:2405. [PMID: 30405609 PMCID: PMC6202950 DOI: 10.3389/fimmu.2018.02405] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Accepted: 09/28/2018] [Indexed: 12/29/2022] Open
Abstract
Streptococcus pneumoniae is endowed with a variety of surface-exposed proteins representing putative vaccine candidates. Lipoproteins are covalently anchored to the cell membrane and highly conserved among pneumococcal serotypes. Here, we evaluated these lipoproteins for their immunogenicity and protective potential against pneumococcal colonisation. A multiplex-based immunoproteomics approach revealed the immunogenicity of selected lipoproteins. High antibody titres were measured in sera from mice immunised with the lipoproteins MetQ, PnrA, PsaA, and DacB. An analysis of convalescent patient sera confirmed the immunogenicity of these lipoproteins. Examining the surface localisation and accessibility of the lipoproteins using flow cytometry indicated that PnrA and DacB were highly abundant on the surface of the bacteria. Mice were immunised intranasally with PnrA, DacB, and MetQ using cholera toxin subunit B (CTB) as an adjuvant, followed by an intranasal challenge with S. pneumoniae D39. PnrA protected the mice from pneumococcal colonisation. For the immunisation with DacB and MetQ, a trend in reducing the bacterial load could be observed, although this effect was not statistically significant. The reduction in bacterial colonisation was correlated with the increased production of antigen-specific IL-17A in the nasal cavity. Immunisation induced high systemic IgG levels with a predominance for the IgG1 isotype, except for DacB, where IgG levels were substantially lower compared to MetQ and PnrA. Our results indicate that lipoproteins are interesting targets for future vaccine strategies as they are highly conserved, abundant, and immunogenic.
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Affiliation(s)
- Franziska Voß
- Department of Molecular Genetics and Infection Biology, Center for Functional Genomics of Microbes, Interfaculty Institute of Genetics and Functional Genomics, University of Greifswald, Greifswald, Germany
| | - Thomas P Kohler
- Department of Molecular Genetics and Infection Biology, Center for Functional Genomics of Microbes, Interfaculty Institute of Genetics and Functional Genomics, University of Greifswald, Greifswald, Germany
| | - Tanja Meyer
- Department of Functional Genomics, Center for Functional Genomics of Microbes, Interfaculty Institute of Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Mohammed R Abdullah
- Department of Molecular Genetics and Infection Biology, Center for Functional Genomics of Microbes, Interfaculty Institute of Genetics and Functional Genomics, University of Greifswald, Greifswald, Germany
| | - Fred J van Opzeeland
- Section Pediatric Infectious Diseases, Laboratory of Medical Immunology, Radboud Center for Infectious Diseases, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
| | - Malek Saleh
- Department of Molecular Genetics and Infection Biology, Center for Functional Genomics of Microbes, Interfaculty Institute of Genetics and Functional Genomics, University of Greifswald, Greifswald, Germany
| | - Stephan Michalik
- Department of Functional Genomics, Center for Functional Genomics of Microbes, Interfaculty Institute of Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Saskia van Selm
- Section Pediatric Infectious Diseases, Laboratory of Medical Immunology, Radboud Center for Infectious Diseases, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
| | - Frank Schmidt
- Department of Functional Genomics, Center for Functional Genomics of Microbes, Interfaculty Institute of Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany.,ZIK-FunGene, Department of Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Marien I de Jonge
- Section Pediatric Infectious Diseases, Laboratory of Medical Immunology, Radboud Center for Infectious Diseases, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
| | - Sven Hammerschmidt
- Department of Molecular Genetics and Infection Biology, Center for Functional Genomics of Microbes, Interfaculty Institute of Genetics and Functional Genomics, University of Greifswald, Greifswald, Germany
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Schembri J, Gillis HD, Lang ALS, Warhuus M, Martin I, Demczuk W, ElSherif M, McNeil SA, LeBlanc JJ. Multi-target plasmid controls for conventional and real-time PCR-based serotyping of Streptococcus pneumoniae. Plasmid 2018; 98:45-51. [PMID: 30217467 DOI: 10.1016/j.plasmid.2018.09.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Revised: 09/10/2018] [Accepted: 09/10/2018] [Indexed: 11/28/2022]
Abstract
BACKGROUND Serotyping of Streptococcus pneumoniae is an integral part of disease surveillance, with over 92 serotypes characterized to date using traditional serotyping. To identify the most predominant disease causing serotypes, molecular serotyping methods are now increasingly being used, like conventional and real-time multiplex PCR (cmPCR and rmPCR, respectively). Given that cmPCR consists of eight reactions spanning 41 targets, and rmPCR consists of seven triplex reactions, standardizing positive controls for these assays is challenging. As such, a 43-target plasmid for cmPCR (pSpn-CM1) and a 23 target plasmid for rmPCR (pSpn-RM1) were designed and validated. METHODS Plasmid pSpn-RM1 was designed and synthesized as chimeric DNA sequences to include all PCR target primer binding sites sequences for cmPCR. Plasmid pSpn-RM1 consisted of all primer and probe sequences required for rmPCR. Additional targets (lytA and cpsA) were included in both plasmids for quantification, following their propagation and purification from Escherichia coli. RESULTS When tested using the cmPCR reactions, all targets could be reproducibly be detected using pSpn-CM1 as template, with good amplicon visibility at a concentration of 1.4 (± 0.3) × 105 copies/ml was used. For the rmPCR reactions, all targets were reproducibly amplified with a concentration of 1.1 (± 0.2) × 104 copies/ml of pSpn-RM1, and the PCR efficiency for each target was equivalent to DNA extracted from representative S. pneumoniae serotypes. CONCLUSIONS These quantifiable multi-target plasmids simplify the preparation of controls for PCR-based serotyping of S. pneumoniae, and methods herein could be extended to other highly multiplexed PCR assays.
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Affiliation(s)
- Jack Schembri
- Canadian Center for Vaccinology (CCfV) Dalhousie University, IWK Health Centre, and Nova Scotia Health Authority (NSHA), Halifax, Nova Scotia, Canada
| | - Hayley D Gillis
- Canadian Center for Vaccinology (CCfV) Dalhousie University, IWK Health Centre, and Nova Scotia Health Authority (NSHA), Halifax, Nova Scotia, Canada
| | - Amanda L S Lang
- Canadian Center for Vaccinology (CCfV) Dalhousie University, IWK Health Centre, and Nova Scotia Health Authority (NSHA), Halifax, Nova Scotia, Canada
| | - Michelle Warhuus
- Canadian Center for Vaccinology (CCfV) Dalhousie University, IWK Health Centre, and Nova Scotia Health Authority (NSHA), Halifax, Nova Scotia, Canada
| | - Irene Martin
- Streptococci and STI Unit, National Microbiology Laboratory (NML), Public Health Agency of Canada (PHAC), Winnipeg, Manitoba, Canada
| | - Walter Demczuk
- Streptococci and STI Unit, National Microbiology Laboratory (NML), Public Health Agency of Canada (PHAC), Winnipeg, Manitoba, Canada
| | - May ElSherif
- Canadian Center for Vaccinology (CCfV) Dalhousie University, IWK Health Centre, and Nova Scotia Health Authority (NSHA), Halifax, Nova Scotia, Canada
| | - Shelly A McNeil
- Canadian Center for Vaccinology (CCfV) Dalhousie University, IWK Health Centre, and Nova Scotia Health Authority (NSHA), Halifax, Nova Scotia, Canada
| | - Jason J LeBlanc
- Canadian Center for Vaccinology (CCfV) Dalhousie University, IWK Health Centre, and Nova Scotia Health Authority (NSHA), Halifax, Nova Scotia, Canada.
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38
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Epping L, van Tonder AJ, Gladstone RA, The Global Pneumococcal Sequencing Consortium, Bentley SD, Page AJ, Keane JA. SeroBA: rapid high-throughput serotyping of Streptococcus pneumoniae from whole genome sequence data. Microb Genom 2018; 4. [PMID: 29870330 PMCID: PMC6113868 DOI: 10.1099/mgen.0.000186] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Streptococcus pneumoniae is responsible for 240 000–460 000 deaths in children under 5 years of age each year. Accurate identification of pneumococcal serotypes is important for tracking the distribution and evolution of serotypes following the introduction of effective vaccines. Recent efforts have been made to infer serotypes directly from genomic data but current software approaches are limited and do not scale well. Here, we introduce a novel method, SeroBA, which uses a k-mer approach. We compare SeroBA against real and simulated data and present results on the concordance and computational performance against a validation dataset, the robustness and scalability when analysing a large dataset, and the impact of varying the depth of coverage on sequence-based serotyping. SeroBA can predict serotypes, by identifying the cps locus, directly from raw whole genome sequencing read data with 98 % concordance using a k-mer-based method, can process 10 000 samples in just over 1 day using a standard server and can call serotypes at a coverage as low as 15–21×. SeroBA is implemented in Python3 and is freely available under an open source GPLv3 licence from: https://github.com/sanger-pathogens/seroba
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Affiliation(s)
- Lennard Epping
- 2Microbial Genomics, Robert Koch Institute, Berlin, Germany.,1Pathogen Informatics, Wellcome Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Andries J van Tonder
- 3Infection Genomics, Wellcome Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Rebecca A Gladstone
- 3Infection Genomics, Wellcome Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, UK
| | | | - Stephen D Bentley
- 3Infection Genomics, Wellcome Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Andrew J Page
- 1Pathogen Informatics, Wellcome Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, UK.,4Quadram Institute, Norwich Research Park, Norwich, UK
| | - Jacqueline A Keane
- 1Pathogen Informatics, Wellcome Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, UK
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39
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Kim HJ, Kim N, Shum D, Huddar S, Park CM, Jang S. Identification of Antipneumococcal Molecules Effective Against Different Streptococcus pneumoniae Serotypes Using a Resazurin-Based High-Throughput Screen. Assay Drug Dev Technol 2018; 15:198-209. [PMID: 28723269 DOI: 10.1089/adt.2017.789] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Streptococcus pneumoniae is a major human pathogen, causing around 1.6 million deaths worldwide each year. By optimizing a resazurin-based assay to detect S. pneumoniae growth in 384-well microplates, we developed a new high-throughput screening (HTS) system for the discovery of antipneumococcal molecules, which was unsuccessful using conventional absorbance measurements. Before applying our protocol to a large-scale screen, we validated the system through a pilot screen targeting about 7,800 bioactive molecules using three different S. pneumoniae serotypes. Primary screenings of a further 27,000 synthetic small molecules facilitated the identification of 3-acyl-2-phenylamino-1,4-dihydropquinolin-4-one (APDQ) derivatives that inhibited growth of S. pneumoniae with MIC90 values <1 μM (0.03-0.81 μM). Five selected APDQ derivatives were also active against Staphylococcus aureus but neither Klebsiella pneumoniae nor Pseudomonas aeruginosa, suggesting that APDQ may act specifically against Gram-positive bacteria. Our results both validated and demonstrated the utility of the resazurin-based HTS system for the identification of new antipneumococcal molecules. Moreover, the identified new antipneumococcal molecules in this study may have potential to be further developed as new antibiotics.
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Affiliation(s)
- Hyung Jun Kim
- 1 Antibacterial Resistance Research Laboratory, Discovery Biology Department, Institut Pasteur Korea , Seongnam-si, Korea
| | - Namyoul Kim
- 2 Assay Development and Screening Group, Screening Sciences and Novel Assay Technologies Department, Institut Pasteur Korea , Seongnam-si, Korea
| | - David Shum
- 2 Assay Development and Screening Group, Screening Sciences and Novel Assay Technologies Department, Institut Pasteur Korea , Seongnam-si, Korea
| | - Srigouri Huddar
- 3 Center for Convergent Research of Emerging Virus Infection, Korea Research Institute of Chemical Technology , Daejeon, Korea.,4 Korea University of Science and Technology , Daejeon, Korea
| | - Chul Min Park
- 3 Center for Convergent Research of Emerging Virus Infection, Korea Research Institute of Chemical Technology , Daejeon, Korea
| | - Soojin Jang
- 1 Antibacterial Resistance Research Laboratory, Discovery Biology Department, Institut Pasteur Korea , Seongnam-si, Korea
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40
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Fong IW, Shlaes D, Drlica K. Antimicrobial Resistance Among Streptococcus pneumoniae. ANTIMICROBIAL RESISTANCE IN THE 21ST CENTURY 2018:13-38. [PMCID: PMC7122384 DOI: 10.1007/978-3-319-78538-7_2] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Antibiotic resistance in Streptococcus pneumoniae (pneumococcus), the main pathogen responsible for community-acquired pneumonia (CAP), meningitis, bacteremia, and otitis media, is a major concern for clinicians. This pathogen is associated with high rates of morbidity and mortality, especially among children under 2 years old, immunocompromised persons, and the elderly population. The major anti-pneumococcus agents are β-lactams and macrolides, with fluoroquinolones ranking third. The emergence of antibiotic-resistant pneumococcus due to overuse of antibiotics is a global concern. While the discovery of novel classes of antibiotics for the pneumococcus is at a standstill, significant progress in reducing the problem of resistance is associated with antibacterial vaccines. Nevertheless, the World Health Organization recently considered drug-resistant S. pneumoniae as ranking among the 12 bacteria, for which there is an urgent need for new treatments. A challenge is to slow the evolution of new strains that are resistant to the vaccines.
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Affiliation(s)
- I. W. Fong
- Department of Medicine, University of Toronto, Toronto, ON Canada
| | - David Shlaes
- Anti-infectives Consulting, LLC, Stonington, CT USA
| | - Karl Drlica
- Public Health Research Institute, New Jersey Medical School, Rutgers Biomedical and Health Sciences, Newark, NJ USA
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41
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Streptococcus pneumoniae Serotyping by a Single Polymerase Chain Reaction–Based Multiplex Assay. INFECTIOUS DISEASES IN CLINICAL PRACTICE 2018. [DOI: 10.1097/ipc.0000000000000554] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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42
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Inghammar M, By Y, Farris C, Phe T, Borand L, Kerleguer A, Goyet S, Saphonn V, Phoeung C, Vong S, Rammaert B, Mayaud C, Guillard B, Yasuda C, Kasper MR, Ford G, Newell SW, An US, Sokhal B, Touch S, Turner P, Jacobs J, Messaoudi M, Komurian-Pradel F, Tarantola A. Serotype Distribution of Clinical Streptococcus pneumoniae Isolates before the Introduction of the 13-Valent Pneumococcal Conjugate Vaccine in Cambodia. Am J Trop Med Hyg 2018; 98:791-796. [PMID: 29313476 PMCID: PMC5930902 DOI: 10.4269/ajtmh.17-0692] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Childhood vaccination with the 13-valent pneumococcal conjugate vaccine (PCV13) was introduced in Cambodia in January 2015. Baseline data regarding circulating serotypes are scarce. All microbiology laboratories in Cambodia were contacted for identification of stored isolates of Streptococcus pneumoniae from clinical specimens taken before the introduction of PCV13. Available isolates were serotyped using a multiplex polymerase chain reaction method. Among 166 identified isolates available for serotyping from patients with pneumococcal disease, 4% were isolated from upper respiratory samples and 80% were from lower respiratory samples, and 16% were invasive isolates. PCV13 serotypes accounted for 60% (95% confidence interval [CI] 52–67) of all isolates; 56% (95% CI 48–64) of noninvasive and 77% (95% CI 57–89) of invasive isolates. Antibiotic resistance was more common among PCV13 serotypes. This study of clinical S. pneumoniae isolates supports the potential for high reduction in pneumococcal disease burden and may serve as baseline data for future monitoring of S. pneumoniae serotypes circulation after implementation of PCV13 childhood vaccination in Cambodia.
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Affiliation(s)
- Malin Inghammar
- Section for Infection Medicine, Department of Clinical Sciences Lund, Lund University, Skane University Hospital, Lund, Sweden.,Institut Pasteur du Cambodge, Phnom Penh, Cambodia
| | - Youlet By
- University of Health Science, Phnom Pen, Cambodia.,Fondation Mérieux, Phnom Penh, Cambodia
| | | | - Thong Phe
- Sihanouk Hospital Center of Hope, Phnom Penh, Cambodia
| | | | | | - Sophie Goyet
- Institut Pasteur du Cambodge, Phnom Penh, Cambodia
| | | | | | - Sirenda Vong
- Institut Pasteur du Cambodge, Phnom Penh, Cambodia
| | - Blandine Rammaert
- CHU de Poitiers, Service de Maladies Infectieuses et Tropicales, INSERM U1070, Université de Poitiers, Poitiers, France
| | | | | | | | | | - Gavin Ford
- Naval Medical Research Unit No. 2, Phnom Penh, Cambodia
| | | | - Ung Sam An
- Cambodian National Laboratory of Public Health, Phnom Penh, Cambodia
| | - Buth Sokhal
- Cambodian National Laboratory of Public Health, Phnom Penh, Cambodia
| | - Sok Touch
- Cambodian Communicable Disease Control Department, Phnom Penh, Cambodia
| | - Paul Turner
- Nuffield Department of Medicine, Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, United Kingdom.,Cambodia Oxford Medical Research Unit, Siem Reap, Cambodia
| | - Jan Jacobs
- Department of Microbiology and Immunology, KU Leuven, Leuven, Belgium.,Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium.,Sihanouk Hospital Center of Hope, Phnom Penh, Cambodia
| | - Mélina Messaoudi
- Emerging Pathogens Laboratory, Fondation Mérieux, Centre International de Recherche en Infectiologie, INSERM U1111, Lyon, France
| | - Florence Komurian-Pradel
- Emerging Pathogens Laboratory, Fondation Mérieux, Centre International de Recherche en Infectiologie, INSERM U1111, Lyon, France
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Mauffrey F, Fournier É, Demczuk W, Martin I, Mulvey M, Martineau C, Lévesque S, Bekal S, Domingo MC, Doualla-Bell F, Longtin J, Lefebvre B. Comparison of sequential multiplex PCR, sequetyping and whole genome sequencing for serotyping of Streptococcus pneumoniae. PLoS One 2017; 12:e0189163. [PMID: 29236737 PMCID: PMC5728576 DOI: 10.1371/journal.pone.0189163] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Accepted: 11/20/2017] [Indexed: 01/22/2023] Open
Abstract
Streptococcus pneumoniae is one of the major causes of pneumonia, meningitis and other pneumococcal infections in young children and elders. Determination of circulating S. pneumoniae serotypes is an essential service by public health laboratories for the monitoring of putative serotype replacement following the introduction of pneumococcal conjugate vaccines (PCVs) and of the efficacy of the immunization program. The Quellung method remains the gold standard for typing S. pneumoniae. Although this method is very effective, it is also costly, time consuming and not totally reliable due to its subjective nature. The objectives of this study were to test and evaluate the efficiency of 3 different molecular methods compared to the Quellung method. Sequential multiplex PCR, sequetyping and whole genome sequencing (WGS) were chosen and tested using a set of diverse S. pneumoniae. One-hundred and eighteen isolates covering 83 serotypes were subjected to multiplex PCR and sequetyping while 88 isolates covering 53 serotypes were subjected to WGS. Sequential multiplex PCR allowed the identification of a significant proportion (49%) of serotypes at the serogroup or subset level but only 27% were identified at the serotype level. Using WGS, 55% to 60% of isolates were identified at the serotype level depending on the analysis strategy used. Finally, sequetyping demonstrated the lowest performance, with 17% of misidentified serotypes. The use of Jin cpsB database instead of the GenBank database slightly improved results but did not significantly impact the efficiency of sequetyping. Although none of these molecular methods may currently replace the Quellung method, WGS remains the most promising molecular pneumococcal serotyping method.
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Affiliation(s)
- Florian Mauffrey
- Laboratoire de santé publique du Québec, Institut national de santé publique du Québec, Sainte-Anne-de-Bellevue, Québec, Canada
| | - Éric Fournier
- Laboratoire de santé publique du Québec, Institut national de santé publique du Québec, Sainte-Anne-de-Bellevue, Québec, Canada
| | - Walter Demczuk
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Irene Martin
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Michael Mulvey
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Christine Martineau
- Laboratoire de santé publique du Québec, Institut national de santé publique du Québec, Sainte-Anne-de-Bellevue, Québec, Canada
| | - Simon Lévesque
- Laboratoire de santé publique du Québec, Institut national de santé publique du Québec, Sainte-Anne-de-Bellevue, Québec, Canada
| | - Sadjia Bekal
- Laboratoire de santé publique du Québec, Institut national de santé publique du Québec, Sainte-Anne-de-Bellevue, Québec, Canada
| | - Marc-Christian Domingo
- Laboratoire de santé publique du Québec, Institut national de santé publique du Québec, Sainte-Anne-de-Bellevue, Québec, Canada
| | - Florence Doualla-Bell
- Laboratoire de santé publique du Québec, Institut national de santé publique du Québec, Sainte-Anne-de-Bellevue, Québec, Canada
| | - Jean Longtin
- Laboratoire de santé publique du Québec, Institut national de santé publique du Québec, Sainte-Anne-de-Bellevue, Québec, Canada
| | - Brigitte Lefebvre
- Laboratoire de santé publique du Québec, Institut national de santé publique du Québec, Sainte-Anne-de-Bellevue, Québec, Canada
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44
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Development of an Extended-Specificity Multiplex Immunoassay for Detection of Streptococcus pneumoniae Serotype-Specific Antigen in Urine by Use of Human Monoclonal Antibodies. CLINICAL AND VACCINE IMMUNOLOGY : CVI 2017; 24:CVI.00262-17. [PMID: 28978509 DOI: 10.1128/cvi.00262-17] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Accepted: 09/30/2017] [Indexed: 11/20/2022]
Abstract
Current pneumococcal vaccines cover the 10 to 23 most common serotypes of the 92 presently described. However, with the increased usage of pneumococcal-serotype-based vaccines, the risk of serotype replacement and an increase in disease caused by nonvaccine serotypes remains. Serotype surveillance of pneumococcal infections relies heavily on culture techniques, which are known to be insensitive, particularly in cases of noninvasive disease. Pneumococcal-serotype-specific urine assays offer an alternative method of serotyping for both invasive and noninvasive disease. However, the assays described previously cover mainly conjugate vaccine serotypes, give little information about circulating nonvaccine serotypes, and are currently available only in one or two specialist laboratories. Our laboratory has developed a Luminex-based extended-range antigen capture assay to detect pneumococcal-serotype-specific antigens in urine samples. The assay targets 24 distinct serotypes/serogroups plus the cell wall polysaccharide (CWP) and some cross-reactive serotypes. We report that the assay is capable of detecting all the targeted serotypes and the CWP at 0.1 ng/ml, while some serotypes are detected at concentrations as low as 0.3 pg/ml. The analytical serotype specificity was determined to be 98.4% using a panel of polysaccharide-negative urine specimens spiked with nonpneumococcal bacterial antigens. We also report clinical sensitivities of 96.2% and specificities of 89.9% established using a panel of urine specimens from patients diagnosed with community-acquired pneumonia or pneumococcal disease. This assay can be extended for testing other clinical samples and has the potential to greatly improve serotype-specific surveillance in the many cases of pneumococcal disease in which a culture is never obtained.
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45
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Ktari S, Jmal I, Mroua M, Maalej S, Ben Ayed NE, Mnif B, Rhimi F, Hammami A. Serotype distribution and antibiotic susceptibility of Streptococcus pneumoniae strains in the south of Tunisia: A five-year study (2012–2016) of pediatric and adult populations. Int J Infect Dis 2017; 65:110-115. [DOI: 10.1016/j.ijid.2017.10.015] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Revised: 10/19/2017] [Accepted: 10/20/2017] [Indexed: 10/18/2022] Open
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46
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Hare KM, Leach AJ, Smith-Vaughan HC, Chang AB, Grimwood K. Streptococcus pneumoniae and chronic endobronchial infections in childhood. Pediatr Pulmonol 2017; 52:1532-1545. [PMID: 28922566 DOI: 10.1002/ppul.23828] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Accepted: 08/06/2017] [Indexed: 01/03/2023]
Abstract
Streptococcus pneumoniae (pneumococcus) is the main cause of bacterial pneumonia worldwide and has been studied extensively in this context. However, its role in chronic endobronchial infections and accompanying lower airway neutrophilic infiltration has received little attention. Severe and recurrent pneumonia are risk factors for chronic suppurative lung disease (CSLD) and bronchiectasis; the latter causes considerable morbidity and, in some populations, premature death in children and adults. Protracted bacterial bronchitis (PBB) is another chronic endobronchial infection associated with substantial morbidity. In some children, PBB may progress to bronchiectasis. Although nontypeable Haemophilus influenzae is the main pathogen in PBB, CSLD and bronchiectasis, pneumococci are isolated commonly from the lower airways of children with these diagnoses. Here we review what is known currently about pneumococci in PBB, CSLD and bronchiectasis, including the importance of pneumococcal nasopharyngeal colonization and how persistence in the lower airways may contribute to the pathogenesis of these chronic pulmonary disorders. Antibiotic treatments, particularly long-term azithromycin therapy, are discussed together with antibiotic resistance and the impact of pneumococcal conjugate vaccines. Important areas requiring further investigation are identified, including immune responses associated with pneumococcal lower airway infection, alone and in combination with other respiratory pathogens, and microarray serotyping to improve detection of carriage and infection by multiple serotypes. Genome wide association studies of pneumococci from the upper and lower airways will help identify virulence and resistance determinants, including potential therapeutic targets and vaccine antigens to treat and prevent endobronchial infections. Much work is needed, but the benefits will be substantial.
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Affiliation(s)
- Kim M Hare
- Child Health Division, Menzies School of Health Research, Darwin, Northern Territory, Australia
| | - Amanda J Leach
- Child Health Division, Menzies School of Health Research, Darwin, Northern Territory, Australia
| | - Heidi C Smith-Vaughan
- Child Health Division, Menzies School of Health Research, Darwin, Northern Territory, Australia.,School of Medicine, Griffith University, Gold Coast, Queensland, Australia
| | - Anne B Chang
- Child Health Division, Menzies School of Health Research, Darwin, Northern Territory, Australia.,Department of Respiratory Medicine, Lady Cilento Children's Hospital, Brisbane, Queensland, Australia.,Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Keith Grimwood
- School of Medicine, Griffith University, Gold Coast, Queensland, Australia.,Menzies Health Institute Queensland, Griffith University, Gold Coast, Queensland, Australia.,Gold Coast Health, Gold Coast, Queensland, Australia
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47
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Gillis HD, Demczuk WHB, Griffith A, Martin I, Warhuus M, Lang ALS, ElSherif M, McNeil SA, LeBlanc JJ. PCR-based discrimination of emerging Streptococcus pneumoniae serotypes 22F and 33F. J Microbiol Methods 2017; 144:99-106. [PMID: 29162393 DOI: 10.1016/j.mimet.2017.11.017] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Revised: 11/17/2017] [Accepted: 11/17/2017] [Indexed: 11/30/2022]
Abstract
Serotyping of Streptococcus pneumoniae is important to monitor disease epidemiology and assess the impact of pneumococcal vaccines. Traditionally, the Quellung reaction used serotype-specific antibodies to classify S. pneumoniae based on differences in capsular antigens. More recently, PCR-based serotype deduction relying on serotype-specific capsule biosynthesis genes has been broadly applied for pneumococcal surveillance. However, PCR-based serotyping lacks discrimination for certain S. pneumoniae serotypes, including the differentiation of serotype 22F from 22A, and serotype 33F from 33A and 37. Serotypes 22F and 33F are emerging serotypes that are absent in the currently licensed 13-valent pneumococcal conjugate vaccine, but present in the new candidate 15-valent formulation. This study validated novel PCR reactions to detect and discriminate S. pneumoniae serotypes 22F and 33F. In order to differentiate S. pneumoniae serotypes 22F or 33F from genetically similar serotypes, two novel PCR reactions were designed and validated. The specificity of all PCR targets was evaluated using all 92 different S. pneumoniae serotypes, as well as 32 other streptococci. Reproducibility was evaluated using geographically and genetically diverse strains of S. pneumoniae serotypes 22F and 22A, or serotypes 33F, 33A, and 37 that were previously characterized by reputable reference laboratories. Overall, S. pneumoniae serotypes 22F and 33F could be accurately and reproducibly be detected and discriminated using PCR alone. Such a molecular serotyping approach provides a valuable diagnostic tool that is feasible in any molecular laboratory, to enable pneumococcal serotype surveillance and subsequent assessment of the impact of the new 15-valent candidate pneumococcal vaccine.
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Affiliation(s)
- Hayley D Gillis
- Canadian Center for Vaccinology (CCfV), Dalhousie University, Halifax, Nova Scotia (NS), Canada; Nova Scotia Health Authority (NSHA), Halifax, Nova Scotia (NS), Canada
| | | | - Averil Griffith
- National Microbiology Laboratory (NML), Winnipeg, MB, Canada
| | - Irene Martin
- National Microbiology Laboratory (NML), Winnipeg, MB, Canada
| | - Michelle Warhuus
- Canadian Center for Vaccinology (CCfV), Dalhousie University, Halifax, Nova Scotia (NS), Canada
| | - Amanda L S Lang
- Canadian Center for Vaccinology (CCfV), Dalhousie University, Halifax, Nova Scotia (NS), Canada; Nova Scotia Health Authority (NSHA), Halifax, Nova Scotia (NS), Canada
| | - May ElSherif
- Canadian Center for Vaccinology (CCfV), Dalhousie University, Halifax, Nova Scotia (NS), Canada; Nova Scotia Health Authority (NSHA), Halifax, Nova Scotia (NS), Canada
| | - Shelly A McNeil
- Canadian Center for Vaccinology (CCfV), Dalhousie University, Halifax, Nova Scotia (NS), Canada; Nova Scotia Health Authority (NSHA), Halifax, Nova Scotia (NS), Canada
| | - Jason J LeBlanc
- Canadian Center for Vaccinology (CCfV), Dalhousie University, Halifax, Nova Scotia (NS), Canada; Nova Scotia Health Authority (NSHA), Halifax, Nova Scotia (NS), Canada.
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48
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Kapatai G, Sheppard CL, Troxler LJ, Litt DJ, Furrer J, Hilty M, Fry NK. Pneumococcal 23B Molecular Subtype Identified Using Whole Genome Sequencing. Genome Biol Evol 2017; 9:2122-2135. [PMID: 28910966 PMCID: PMC5581491 DOI: 10.1093/gbe/evx092] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/09/2017] [Indexed: 01/20/2023] Open
Abstract
The polysaccharide capsule is a major virulence factor of Streptococcus pneumoniae and the target of all currently licensed pneumococcal vaccines. At present, there are 92 serologically distinct pneumococcal serotypes. Structural and antigenic variation of capsular types is the result of genetic variation within the capsular polysaccharide synthesis (CPS) locus; however, genetic variation may not always result in phenotypic differences which produce novel serotypes. With the introduction of high throughput whole genome sequencing, discovery of novel genotypic variants is not unexpected and this study describes a novel variant of the serotype 23B CPS operon. This novel variant was characterized as a novel genotypic subtype (23B1) with ∼70% homology to the published 23B CPS sequence. High sequence variability was determined in eight cps genes involved in sugar biosynthesis. However, there was no distinction between the classic 23B serotype and 23B1 serologically or in terms of polysaccharide structure. Phylogenetic and eBURST analysis revealed a distinct lineage for 23B1 with multiple clones (UK, Thailand, and USA) that arose at different points during pneumococcal evolution. Analysis of the UK S. pneumoniae isolates (n = 121) revealed an upsurge of 23B1 ST2372 in 2011, after which this previously unseen ST increased to reach 50% proportion of the 23B sequenced isolates from 2013 and remained prevalent within our sequenced isolates from later years. Therefore, although the 23B1 variant appears to have no phenotypic impact and cannot be considered as novel serotype, it appears to have led to a genetic restructuring of the UK serotype 23B population.
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Affiliation(s)
- Georgia Kapatai
- Respiratory and Vaccine Preventable Bacteria Reference Unit, Public Health England, National Infection Service, London, United Kingdom
| | - Carmen L Sheppard
- Respiratory and Vaccine Preventable Bacteria Reference Unit, Public Health England, National Infection Service, London, United Kingdom
| | - Lukas J Troxler
- Institute for Infectious Diseases, University of Bern, Switzerland
| | - David J Litt
- Respiratory and Vaccine Preventable Bacteria Reference Unit, Public Health England, National Infection Service, London, United Kingdom
| | - Julien Furrer
- Department of Chemistry and Biochemistry, University of Bern, Switzerland
| | - Markus Hilty
- Institute for Infectious Diseases, University of Bern, Switzerland.,Department of Infectious Diseases, Bern University Hospital, Inselspital, University of Bern, Switzerland
| | - Norman K Fry
- Respiratory and Vaccine Preventable Bacteria Reference Unit, Public Health England, National Infection Service, London, United Kingdom
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49
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Tagini F, Greub G. Bacterial genome sequencing in clinical microbiology: a pathogen-oriented review. Eur J Clin Microbiol Infect Dis 2017; 36:2007-2020. [PMID: 28639162 PMCID: PMC5653721 DOI: 10.1007/s10096-017-3024-6] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Accepted: 05/22/2017] [Indexed: 12/11/2022]
Abstract
In recent years, whole-genome sequencing (WGS) has been perceived as a technology with the potential to revolutionise clinical microbiology. Herein, we reviewed the literature on the use of WGS for the most commonly encountered pathogens in clinical microbiology laboratories: Escherichia coli and other Enterobacteriaceae, Staphylococcus aureus and coagulase-negative staphylococci, streptococci and enterococci, mycobacteria and Chlamydia trachomatis. For each pathogen group, we focused on five different aspects: the genome characteristics, the most common genomic approaches and the clinical uses of WGS for (i) typing and outbreak analysis, (ii) virulence investigation and (iii) in silico antimicrobial susceptibility testing. Of all the clinical usages, the most frequent and straightforward usage was to type bacteria and to trace outbreaks back. A next step toward standardisation was made thanks to the development of several new genome-wide multi-locus sequence typing systems based on WGS data. Although virulence characterisation could help in various particular clinical settings, it was done mainly to describe outbreak strains. An increasing number of studies compared genotypic to phenotypic antibiotic susceptibility testing, with mostly promising results. However, routine implementation will preferentially be done in the workflow of particular pathogens, such as mycobacteria, rather than as a broadly applicable generic tool. Overall, concrete uses of WGS in routine clinical microbiology or infection control laboratories were done, but the next big challenges will be the standardisation and validation of the procedures and bioinformatics pipelines in order to reach clinical standards.
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Affiliation(s)
- F Tagini
- Institute of Microbiology, Department of Laboratory, University of Lausanne & University Hospital, Lausanne, Switzerland
| | - G Greub
- Institute of Microbiology, Department of Laboratory, University of Lausanne & University Hospital, Lausanne, Switzerland.
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50
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External Quality Assurance for Laboratory Identification and Capsular Typing of Streptococcus pneumoniae. Sci Rep 2017; 7:13280. [PMID: 29038446 PMCID: PMC5643306 DOI: 10.1038/s41598-017-13605-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Accepted: 09/26/2017] [Indexed: 12/20/2022] Open
Abstract
An external quality assessment (EQA) scheme for pneumococcal serotype identification has been performed over a period of 11 years, by a network of European pneumococcal reference laboratories. We report the results from the EQA, and present an assessment of the acceptability and utility of the EQA scheme. Reports from 22 EQA panels distributed in 2005-2016 were analysed. Each EQA panel consisted of seven isolates. A questionnaire including seven questions related to the acceptability and utility of the EQA scheme was distributed to all participating laboratories. Altogether, 154 pneumococcal isolates were tested. Of the 92 serologically distinct serotypes currently defined, 49 serotypes were included in the rounds. Discrepant results were observed in eight EQA rounds, involving 11 isolates (7.1%, 95% CI: 4% to 12%). All participating laboratories reported that the EQA scheme was useful for quality assurance purposes. Our results show that comparable serotyping data can be obtained in different laboratories. The EQA participation helps to keep the typing procedures at a high standard and provides data for accreditation purposes. The EQA is helpful when new technologies are introduced, and reveal limitations of both genotypic and phenotypic methods. Continuation of the presented EQA scheme is planned.
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