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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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Hao L, Kuttel MM, Ravenscroft N, Thompson A, Prasad AK, Gangolli S, Tan C, Cooper D, Watson W, Liberator P, Pride MW, Jansen KU, Anderson AS, Scully IL. Streptococcus pneumoniae serotype 15B polysaccharide conjugate elicits a cross-functional immune response against serotype 15C but not 15A. Vaccine 2022; 40:4872-4880. [PMID: 35810060 DOI: 10.1016/j.vaccine.2022.06.041] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 06/09/2022] [Accepted: 06/13/2022] [Indexed: 11/25/2022]
Abstract
Protection conferred by pneumococcal polysaccharide conjugate vaccines (PCVs) is associated with PCV-induced antibodies against vaccine-covered serotypes that exhibit functional opsonophagocytic activity (OPA). Structural similarity between capsular polysaccharides of closely related serotypes may result in induction of cross-reactive antibodies with or without a cross-functional activity against a serotype not covered by a PCV, with the former providing an additional protective clinical benefit. Serotypes 15B, 15A, and 15C, in the serogroup 15, are among the most prevalent Streptococcus pneumoniae serotypes associated with invasive pneumococcal disease following the implementation of a 13-valent PCV; in addition, 15B contributes significantly to acute otitis media. Serological discrimination between closely related serotypes such as 15B and 15C is complicated; here, we implemented an algorithm to quickly differentiate 15B from its closely related serotypes 15C and 15A directly from whole-genome sequencing data. In addition, molecular dynamics simulations of serotypes 15A, 15B, and 15C polysaccharides demonstrated that while 15B and 15C polysaccharides assume rigid branched conformation, 15A polysaccharide assumes a flexible linear conformation. A serotype 15B conjugate, included in a 20-valent PCV (PCV20), induced cross-functional OPA serum antibody responses against the structurally similar serotype 15C but not against serotype 15A, both not included in PCV20. In PCV20-vaccinated adults (18-49 years), robust OPA antibody titers were detected against both serotypes 15B (the geometric mean titer [GMT] of 19,334) and 15C (GMTs of 1692 and 2747 for strains PFE344340 and PFE1160, respectively), but were negligible against serotype 15A (GMTs of 10 and 30 for strains PFE593551 and PFE647449, respectively). Cross-functional 15B/C responses were also confirmed using sera from a larger group of older adults (60-64 years).
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Affiliation(s)
- Li Hao
- Pfizer Vaccine Research & Development, 401 N. Middletown Rd, Pearl River, NY 10965, USA
| | - Michelle M Kuttel
- Department of Computer Science, University of Cape Town, Rondebosch 7701, South Africa
| | - Neil Ravenscroft
- Department of Chemistry, University of Cape Town, Rondebosch 7701, South Africa
| | - Allison Thompson
- Pfizer Vaccine Research & Development, 401 N. Middletown Rd, Pearl River, NY 10965, USA
| | - A Krishna Prasad
- Pfizer Vaccine Research & Development, 401 N. Middletown Rd, Pearl River, NY 10965, USA
| | - Seema Gangolli
- Pfizer Vaccine Research & Development, 401 N. Middletown Rd, Pearl River, NY 10965, USA
| | - Charles Tan
- Pfizer Vaccine Research & Development, 401 N. Middletown Rd, Pearl River, NY 10965, USA
| | - David Cooper
- Pfizer Vaccine Research & Development, 401 N. Middletown Rd, Pearl River, NY 10965, USA
| | - Wendy Watson
- Pfizer Vaccine Clinical Research & Development, 500 Arcola Rd, Collegeville, PA 19422, USA
| | - Paul Liberator
- Pfizer Vaccine Research & Development, 401 N. Middletown Rd, Pearl River, NY 10965, USA
| | - Michael W Pride
- Pfizer Vaccine Research & Development, 401 N. Middletown Rd, Pearl River, NY 10965, USA
| | - Kathrin U Jansen
- Pfizer Vaccine Research & Development, 401 N. Middletown Rd, Pearl River, NY 10965, USA
| | - Annaliesa S Anderson
- Pfizer Vaccine Research & Development, 401 N. Middletown Rd, Pearl River, NY 10965, USA
| | - Ingrid L Scully
- Pfizer Vaccine Research & Development, 401 N. Middletown Rd, Pearl River, NY 10965, USA.
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Clearance of mixed biofilms of Streptococcus pneumoniae and methicillin-susceptible/resistant Staphylococcus aureus by antioxidants N-acetyl-L-cysteine and cysteamine. Sci Rep 2022; 12:6668. [PMID: 35461321 PMCID: PMC9035182 DOI: 10.1038/s41598-022-10609-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 04/07/2022] [Indexed: 12/01/2022] Open
Abstract
Biofilm-associated infections are of great concern because they are associated with antibiotic resistance and immune evasion. Co-colonization by Staphylococcus aureus and Streptococcus pneumoniae is possible and a threat in clinical practice. We investigated the interaction between S. aureus and S. pneumoniae in mixed biofilms and tested new antibiofilm therapies with antioxidants N-acetyl-l-cysteine (NAC) and cysteamine (Cys). We developed two in vitro S. aureus–S. pneumoniae mixed biofilms in 96-well polystyrene microtiter plates and we treated in vitro biofilms with Cys and NAC analyzing their effect by CV staining and viable plate counting. S. pneumoniae needed a higher proportion of cells in the inoculum and planktonic culture to reach a similar population rate in the mixed biofilm. We demonstrated the effect of Cys in preventing S. aureus biofilms and S. aureus–S. pneumoniae mixed biofilms. Moreover, administration of 5 mg/ml of NAC nearly eradicated the S. pneumoniae population and killed nearly 94% of MSSA cells and 99% of MRSA cells in the mixed biofilms. The methicillin resistance background did not change the antioxidants effect in S. aureus. These results identify NAC and Cys as promising repurposed drug candidates for the prevention and treatment of mixed biofilms by S. pneumoniae and S. aureus.
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Application of multi-omics technology for the elucidation of anti-pneumococcal activity of 3-acyl-2-phenylamino-1,4-dihydroquinolin-4-one (APDQ) derivative against Streptococcus pneumoniae. Sci Rep 2020; 10:20685. [PMID: 33244098 PMCID: PMC7691496 DOI: 10.1038/s41598-020-77694-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Accepted: 11/10/2020] [Indexed: 11/24/2022] Open
Abstract
Streptococcus pneumoniae is one of Gram-positive pathogen that causes invasive pneumococcal disease. Nowadays, many S. pneumoniae strains are resistant to commonly used antibiotics such as β-lactams and macrolides. 3-Acyl-2-phenylamino-1,4-dihydroquinolin-4-one (APDQ) derivatives are known as novel chemicals having anti-pneumococcal activity against S. pneumoniae. The underlying mechanism of the anti-pneumococcal activity of this inhibitor remains unknown. Therefore, we tried to find the anti-pneumococcal mechanism of APDQ230122, one of the APDQ derivatives active against S. pneumoniae. We performed transcriptomic analysis (RNA-Seq) and proteomic analysis (LC–MS/MS analysis) to get differentially expressed genes (DEG) and differentially expressed proteins (DEP) of S. pneumoniae 521 treated with sub-inhibitory concentrations of APDQ230122 and elucidated the comprehensive expression changes of genes and proteins using multi-omics analysis. As a result, genes or proteins of peptidoglycan biosynthesis and DNA replication were significantly down-regulated. Electron microscopy analysis revealed that the structure of peptidoglycan was damaged by APDQ230122 in a chemical concentration-dependent manner. Therefore, we suggest peptidoglycan biosynthesis is a major target of APDQ230122. Multi-omics analysis can provide us useful information to elucidate anti-pneumococcal activity of APDQ230122.
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Dube FS, Ramjith J, Gardner-Lubbe S, Nduru P, Robberts FJL, Wolter N, Zar HJ, Nicol MP. Longitudinal characterization of nasopharyngeal colonization with Streptococcus pneumoniae in a South African birth cohort post 13-valent pneumococcal conjugate vaccine implementation. Sci Rep 2018; 8:12497. [PMID: 30131607 PMCID: PMC6104038 DOI: 10.1038/s41598-018-30345-5] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Accepted: 07/23/2018] [Indexed: 12/28/2022] Open
Abstract
Monitoring changes in pneumococcal carriage is key to understanding vaccination-induced shifts in the ecology of carriage and impact on health. We longitudinally investigated pneumococcal carriage dynamics in infants. Pneumococcal isolates were obtained from nasopharyngeal (NP) swabs collected 2-weekly from 137 infants enrolled from birth through their first year of life. Pneumococci were serotyped by sequetyping, confirmed by Quellung. Pneumococci were isolated from 54% (1809/3331) of infants. Median time to first acquisition was 63 days. Serotype-specific acquisition rates ranged from 0.01 to 0.88 events/child-year and did not differ between PCV13 and non-PCV13 serotypes (0.11 events/child-year [95% CI 0.07-0.18] vs. 0.11 events/child-year [95% CI 0.06-0.18]). There was no difference in carriage duration between individual PCV13 and non-PCV13 serotypes (40.6 days [95% CI 31.9-49.4] vs. 38.6 days [95% CI 35.1-42.1]), however cumulatively the duration of carriage of non-PCV13 serotypes was greater than PCV13 serotypes (141.2 days (95% CI 126.6-155.8) vs. 30.7 days (95% CI 22.3-39.0). Frequently carried PCV13 serotypes included 19F, 9V, 19A and 6A, while non-PCV13 serotypes included 15B/15C, 21, 10A, 16F, 35B, 9N and 15A. Despite high immunization coverage in our setting, PCV13 serotypes remain in circulation in this cohort, comprising 22% of isolates. Individual PCV13 serotypes were acquired, on average, at equivalent rate to non-PCV13 serotypes, and carried for a similar duration, although the most common non-PCV13 serotypes were more frequently acquired than PCV13 serotypes.
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Affiliation(s)
- Felix S Dube
- Department of Molecular and Cell Biology, Faculty of Science, University of Cape Town, Cape Town, South Africa. .,Division of Medical Microbiology, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa. .,Institute for Infectious Diseases and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa.
| | - Jordache Ramjith
- Division of Epidemiology & Biostatistics, School of Public Health & Family Medicine, University of Cape Town, Cape Town, South Africa
| | - Sugnet Gardner-Lubbe
- Department of Statistical Sciences, Faculty of Science, University of Cape Town, Cape Town, South Africa
| | - Polite Nduru
- Department of Paediatrics and Child Health, Red Cross War Memorial Children's Hospital, University of Cape Town, Cape Town, South Africa
| | - F J Lourens Robberts
- Division of Medical Microbiology, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Nicole Wolter
- Centre for Respiratory Diseases and Meningitis (CRDM), National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa.,School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Heather J Zar
- Department of Paediatrics and Child Health, Red Cross War Memorial Children's Hospital, University of Cape Town, Cape Town, South Africa.,SAMRC Unit on Child and Adolescent Health, University of Cape Town, Cape Town, South Africa
| | - Mark P Nicol
- Division of Medical Microbiology, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa.,National Health Laboratory Service, Groote Schuur Hospital, Cape Town, South Africa.,Institute for Infectious Diseases and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
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Molecular characterization of non-vaccine Streptococcus pneumoniae serotypes 11A, 15 B/C and 23A recovered from invasive isolates in Colombia. BIOMEDICA 2017; 37:390-396. [DOI: 10.7705/biomedica.v37i3.3223] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Revised: 11/30/2016] [Indexed: 11/21/2022]
Abstract
Introducción. En Colombia se recolectaron 192 aislamientos invasivos de Streptococcus pneumoniae de los serotipos 11A, 15B/C y 23A (no incluidos en las vacunas conjugadas) entre 1994 y 2014, como parte de las actividades del Sistema de Redes de Vigilancia de los Agentes Responsables de Neumonías y Meningitis Bacterianas (SIREVA II).Objetivo. Determinar las características moleculares de aislamientos invasivos de los serotipos 11A, 15B/C y 23A de S. pneumoniae recolectados en Colombia entre 1994 y 2014. Materiales y métodos. La caracterización molecular de los aislamientos se hizo mediante electroforesis en gel de campo pulsado (Pulse-Field Gel Electrophoresis, PFGE) y por tipificación de secuencias multilocus (Multilocus Sequence Typing, MLST).Resultados. El serotipo 11A mostró un grupo clonal representado por el ST62, en tanto que el serotipo 15B/C se distribuyó en tres grupos asociados con los clones Netherlands15B-37 ST199 (28,75 %), ST8495 (18,75 %) y SLV (variante en un solo locus) de ST193 (21,25 %). Los aislamientos con serotipo 23A se agruparon en tres grupos clonales; 70,21 % de ellos estaban estrechamente relacionados con el ST42, 17,02 % con el Colombia23F-ST338, y 6,38 % con el Netherlands15B-37 ST199.Conclusión. Los clones Colombia23F-ST338 y Netherlands15B-ST199 encontrados en este estudio abarcaron más serotipos de los reportados previamente por otros autores, incluido el serotipo 23A. Estos análisis revelan la importancia de la conmutación (switching) capsular en la expansión de clones exitosos entre los serotipos no vacunales como causa de enfermedad invasiva neumocócica.
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The Pneumococcal Serotype 15C Capsule Is Partially O-Acetylated and Allows for Limited Evasion of 23-Valent Pneumococcal Polysaccharide Vaccine-Elicited Anti-Serotype 15B Antibodies. CLINICAL AND VACCINE IMMUNOLOGY : CVI 2017. [PMID: 28637806 DOI: 10.1128/cvi.00099-17] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
As a species, Streptococcus pneumoniae (the pneumococcus) utilizes a diverse array of capsular polysaccharides to evade the host. In contrast to large variations in sugar composition and linkage formation, O-acetylation is a subtle capsular modification that nonetheless has a large impact on capsular shielding and recognition of the capsule by vaccine-elicited antibodies. Serotype 15B, which is included in the 23-valent pneumococcal polysaccharide vaccine (PPV23), carries the putative O-acetyltransferase gene wciZ The coding sequence of wciZ contains eight consecutive TA repeats [(TA)8]. Replication slippage is thought to result in the addition or loss of TA repeats, subsequently causing frameshift and truncation of WciZ to yield a nonacetylated serotype, 15C. Using sensitive serological tools, we show that serotype 15C isolates whose wciZ contains seven or nine TA repeats retain partial O-acetylation, while serotype 15C isolates whose wciZ contains six TA repeats have barely detectable O-acetylation. We confirmed by inhibition enzyme-linked immunosorbent assay that (TA)7 serotype 15C is ∼0.1% as acetylated as serotype 15B, while serotype 15X is nonacetylated. To eliminate the impact of genetic background, we created isogenic serotype 15B, (TA)7 serotype 15C, and 15BΔwciZ (15X) strains and found that reduction or absence of WciZ-mediated O-acetylation did not affect capsular shielding from phagocytes, biofilm formation, adhesion to nasopharyngeal cells, desiccation tolerance, or murine colonization. Sera from PPV23-immunized persons opsonized serotype 15B significantly but only slightly better than serotypes 15C and 15X; thus, PPV23 may not result in expansion of serotype 15C.
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Gladstone RA, Devine V, Jones J, Cleary D, Jefferies JM, Bentley SD, Faust SN, Clarke SC. Pre-vaccine serotype composition within a lineage signposts its serotype replacement - a carriage study over 7 years following pneumococcal conjugate vaccine use in the UK. Microb Genom 2017; 3:e000119. [PMID: 29026652 PMCID: PMC5628697 DOI: 10.1099/mgen.0.000119] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Accepted: 05/08/2017] [Indexed: 11/18/2022] Open
Abstract
Serotype replacement has been reported in carriage and disease after pneumococcal conjugate vaccine (PCV) introductions in the UK and globally. We previously described concurrent expansion and decline of sequence types associated with serotype replacement over 5 years following PCV introductions in the UK. Here we use whole-genome sequencing to fully characterise the population structure of pneumococcal isolates collected over seven winters encompassing PCV7 and PCV13 introductions in the UK, investigating the importance of lineages in serotype replacement. We analysed 672 pneumococcal genomes from colonised children of 4 years old or less. The temporal prevalence of 20 lineages, defined by hierarchical Bayesian analysis of population structure (BAPS), was assessed in the context of serotype replacement. Multiple serotypes were detected in the primary winter of sampling within three vaccine-type (VT) lineages BAPS4, BAPS10 and BAPS11, in which serotype replacement were observed. In contrast, serotype replacement was not seen in the remaining three VT lineages (BAPS1, BAPS13 and BAPS14), that expressed a single serotype (6B, 6A and 3, respectively) in the primary winter. One lineage, BAPS1 serotype 6B was undetectable in the population towards the end of the study period. The dynamics of serotype replacement, in this UK population, was preceded by the presence or absence of multiple serotypes within VT lineages, in the pre-PCV population. This observation could help predict which non-vaccine types (NVTs) may be involved in replacement in future PCV introductions here and elsewhere. It could further indicate whether any antibiotic resistance associated with the lineages is likely to be affected by replacement.
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Affiliation(s)
- Rebecca A. Gladstone
- Infection Genomics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Vanessa Devine
- Faculty of Medicine and Institute for Life Sciences, University of Southampton, UK
| | - Jessica Jones
- Faculty of Medicine and Institute for Life Sciences, University of Southampton, UK
| | - David Cleary
- Faculty of Medicine and Institute for Life Sciences, University of Southampton, UK
| | - Johanna M. Jefferies
- Faculty of Medicine and Institute for Life Sciences, University of Southampton, UK
- Southampton NIHR Respiratory Biomedical Research Unit, University Hospital Southampton Foundation NHS Trust, Southampton, UK
| | - Stephen D. Bentley
- Infection Genomics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Saul N. Faust
- Faculty of Medicine and Institute for Life Sciences, University of Southampton, UK
- Southampton NIHR Respiratory Biomedical Research Unit, University Hospital Southampton Foundation NHS Trust, Southampton, UK
- NIHR Wellcome Trust Clinical Research, Manchester Royal Infirmary, Grafton St, Manchester M13 9WL, UK
| | - Stuart C. Clarke
- Faculty of Medicine and Institute for Life Sciences, University of Southampton, UK
- Southampton NIHR Respiratory Biomedical Research Unit, University Hospital Southampton Foundation NHS Trust, Southampton, UK
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Kapatai G, Sheppard CL, Al-Shahib A, Litt DJ, Underwood AP, Harrison TG, Fry NK. Whole genome sequencing of Streptococcus pneumoniae: development, evaluation and verification of targets for serogroup and serotype prediction using an automated pipeline. PeerJ 2016; 4:e2477. [PMID: 27672516 PMCID: PMC5028725 DOI: 10.7717/peerj.2477] [Citation(s) in RCA: 101] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Accepted: 08/23/2016] [Indexed: 11/25/2022] Open
Abstract
Streptococcus pneumoniae typically express one of 92 serologically distinct capsule polysaccharide (cps) types (serotypes). Some of these serotypes are closely related to each other; using the commercially available typing antisera, these are assigned to common serogroups containing types that show cross-reactivity. In this serotyping scheme, factor antisera are used to allocate serotypes within a serogroup, based on patterns of reactions. This serotyping method is technically demanding, requires considerable experience and the reading of the results can be subjective. This study describes the analysis of the S. pneumoniae capsular operon genetic sequence to determine serotype distinguishing features and the development, evaluation and verification of an automated whole genome sequence (WGS)-based serotyping bioinformatics tool, PneumoCaT (Pneumococcal Capsule Typing). Initially, WGS data from 871 S. pneumoniae isolates were mapped to reference cps locus sequences for the 92 serotypes. Thirty-two of 92 serotypes could be unambiguously identified based on sequence similarities within the cps operon. The remaining 60 were allocated to one of 20 ‘genogroups’ that broadly correspond to the immunologically defined serogroups. By comparing the cps reference sequences for each genogroup, unique molecular differences were determined for serotypes within 18 of the 20 genogroups and verified using the set of 871 isolates. This information was used to design a decision-tree style algorithm within the PneumoCaT bioinformatics tool to predict to serotype level for 89/94 (92 + 2 molecular types/subtypes) from WGS data and to serogroup level for serogroups 24 and 32, which currently comprise 2.1% of UK referred, invasive isolates submitted to the National Reference Laboratory (NRL), Public Health England (June 2014–July 2015). PneumoCaT was evaluated with an internal validation set of 2065 UK isolates covering 72/92 serotypes, including 19 non-typeable isolates and an external validation set of 2964 isolates from Thailand (n = 2,531), USA (n = 181) and Iceland (n = 252). PneumoCaT was able to predict serotype in 99.1% of the typeable UK isolates and in 99.0% of the non-UK isolates. Concordance was evaluated in UK isolates where further investigation was possible; in 91.5% of the cases the predicted capsular type was concordant with the serologically derived serotype. Following retesting, concordance increased to 99.3% and in most resolved cases (97.8%; 135/138) discordance was shown to be caused by errors in original serotyping. Replicate testing demonstrated that PneumoCaT gave 100% reproducibility of the predicted serotype result. In summary, we have developed a WGS-based serotyping method that can predict capsular type to serotype level for 89/94 serotypes and to serogroup level for the remaining four. This approach could be integrated into routine typing workflows in reference laboratories, reducing the need for phenotypic immunological testing.
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Affiliation(s)
- Georgia Kapatai
- Respiratory and Vaccine Preventable Bacterial Reference Unit, Public Health England, London, United Kingdom
| | - Carmen L Sheppard
- Respiratory and Vaccine Preventable Bacterial Reference Unit, Public Health England, London, United Kingdom
| | - Ali Al-Shahib
- Infectious Disease Informatics, Public Health England, London, United Kingdom
| | - David J Litt
- Respiratory and Vaccine Preventable Bacterial Reference Unit, Public Health England, London, United Kingdom
| | - Anthony P Underwood
- Infectious Disease Informatics, Public Health England, London, United Kingdom
| | - Timothy G Harrison
- Respiratory and Vaccine Preventable Bacterial Reference Unit, Public Health England, London, United Kingdom
| | - Norman K Fry
- Respiratory and Vaccine Preventable Bacterial Reference Unit, Public Health England, London, United Kingdom
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Liyanapathirana V, Nelson EAS, Ang I, Subramanian R, Ma H, Ip M. Emergence of serogroup 15 Streptococcus pneumoniae of diverse genetic backgrounds following the introduction of pneumococcal conjugate vaccines in Hong Kong. Diagn Microbiol Infect Dis 2014; 81:66-70. [PMID: 25445117 DOI: 10.1016/j.diagmicrobio.2014.09.028] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2014] [Revised: 09/26/2014] [Accepted: 09/29/2014] [Indexed: 10/24/2022]
Abstract
Serogroup 15 pneumococcal isolates from nasopharyngeal carriage of hospitalized children admitted to a teaching hospital in Hong Kong from April 2009 to September 2013 were characterized by pulse-field gel electrophoresis (PFGE), multilocus sequence typing, and antimicrobial non-susceptibility testing. The overall proportion of serogroup 15 isolates in the pre-PCV7 and post-PCV13 periods rose from 5.7% to 20.0%. The increase in trend for serotype 15B/C was statistically significant among children presented with pneumonia; bronchiolitis; upper respiratory tract infection; and febrile, non-respiratory diseases and for serotype 15A/F, among children with bronchiolitis and febrile, non-respiratory diseases. The predominant PFGE cluster of serotype 15B/C belonged to sequence type (ST) 199. Replacement of this more susceptible cluster (Ery and Tet non-susceptibilities of 32.2% and 25.4%) with the non-susceptible cluster, ST8859 (Ery and Tet non-susceptibilities of 91.7% and 87.5%) was noted. ST63 was the predominant serotype 15A cluster (Ery and Tet non-susceptibilities of 97.4% and 92.3%). Serogroup 15 subtypes have emerged in the post-PCV13 era, and these non-susceptible clusters warrant closer monitoring as candidates for incorporation to future pneumococcal vaccines.
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Affiliation(s)
| | - E Anthony S Nelson
- Department of Paediatrics, Faculty of Medicine, the Chinese University of Hong Kong, Hong Kong
| | - Irene Ang
- Department of Microbiology, the Chinese University of Hong Kong, Hong Kong
| | - Reema Subramanian
- Department of Microbiology, the Chinese University of Hong Kong, Hong Kong
| | - Helen Ma
- Department of Microbiology, the Chinese University of Hong Kong, Hong Kong
| | - Margaret Ip
- Department of Microbiology, the Chinese University of Hong Kong, Hong Kong.
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11
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McElligott M, Vickers I, Cafferkey M, Cunney R, Humphreys H. Non-invasive pneumococcal serotypes and antimicrobial susceptibilities in a paediatric hospital in the era of conjugate vaccines. Vaccine 2014; 32:3495-500. [PMID: 24795223 DOI: 10.1016/j.vaccine.2014.04.047] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2013] [Revised: 04/09/2014] [Accepted: 04/17/2014] [Indexed: 11/15/2022]
Abstract
To evaluate the effects of 7-valent pneumococcal conjugate vaccine (PCV7) introduction to the routine childhood immunisation schedule in 2008 and its replacement by PCV13 in 2010 in Ireland, we surveyed the serotypes and antimicrobial susceptibilities of 339 pneumococci associated with carriage and non-invasive infection (NII) in a Dublin paediatric hospital from 2009 to 2012. Furthermore, we compared the distribution of pneumococcal serotypes collected from 2009 to 2012 to 105 NII pneumococci isolated in 2007, the year before conjugate vaccine introduction. PCV7 serotypes declined from 2007 to 2012 as follows: carriage, 67-23% (p=0.0004); conjunctivitis, 58-0% (p<0.0001); non-bacteraemic lower respiratory tract infection, 50-19% (p=0.0363) and otitis media 54-27%. Notably, antimicrobial resistant (AMR) PCV7 serotypes showed a significant decrease by the end of the study period (i.e. 2012) (p<0.0001). Compared with 2007 the overall occurrence of serotype 19A increased from 1.9 to 10% in 2010 (p=0.0132) and to 15% in 2011 (p=0.0005). Importantly, serotype 19A declined significantly from 2011 levels to an overall prevalence of 4.8% in 2012 (p=0.0243). Most striking was the significant reduction of AMR 19A (p=0.0195). Conversely, increases were observed in non-vaccine type (NVT) pneumococci in 2009-2012, of which serotypes 11A (n=30), 15B/C (n=17), 22F (n=14), 35Bn=13), non-typeable pneumococci (n=13) and 23A (n=12) were the most prevalent. Moreover, an increase in NVT non-susceptible to at least one antimicrobial in 2009-2012 was noted, attributable to serotypes 35B (n=10) and 15A (n=7). In summary, this study has shown that PCV7 and PCV13 introduction has had a positive impact on their target serotypes and antimicrobial resistance amongst pneumococci within a paediatric hospital within a short time period. However, the increase in NVT prevalence highlights the need for continued surveillance.
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Affiliation(s)
- Martha McElligott
- Epidemiology and Molecular Biology Unit and Irish Meningococcal and Meningitis Reference Laboratory, Temple Street Children's University Hospital, Dublin, Ireland; Department of Clinical Microbiology, RCSI Education and Research Centre, Beaumont Hospital, Dublin, Ireland.
| | - Imelda Vickers
- Epidemiology and Molecular Biology Unit and Irish Meningococcal and Meningitis Reference Laboratory, Temple Street Children's University Hospital, Dublin, Ireland; Department of Clinical Microbiology, RCSI Education and Research Centre, Beaumont Hospital, Dublin, Ireland
| | - Mary Cafferkey
- Epidemiology and Molecular Biology Unit and Irish Meningococcal and Meningitis Reference Laboratory, Temple Street Children's University Hospital, Dublin, Ireland; Department of Clinical Microbiology, RCSI Education and Research Centre, Beaumont Hospital, Dublin, Ireland
| | - Robert Cunney
- Epidemiology and Molecular Biology Unit and Irish Meningococcal and Meningitis Reference Laboratory, Temple Street Children's University Hospital, Dublin, Ireland; Health Protection Surveillance Centre, Dublin, Ireland
| | - Hilary Humphreys
- Department of Clinical Microbiology, RCSI Education and Research Centre, Beaumont Hospital, Dublin, Ireland; Department of Microbiology, Beaumont Hospital, Dublin, Ireland
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12
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Domenech M, Araújo-Bazán L, García E, Moscoso M. In vitro biofilm formation by Streptococcus pneumoniae as a predictor of post-vaccination emerging serotypes colonizing the human nasopharynx. Environ Microbiol 2014; 16:1193-201. [PMID: 24373136 DOI: 10.1111/1462-2920.12370] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2013] [Accepted: 12/14/2013] [Indexed: 11/29/2022]
Abstract
The increasing use of the 7-valent pneumococcal conjugate vaccine has been accompanied by the rise of non-vaccine serotypes colonizing the human nasopharynx. The vast majority of infections are caused by microorganisms that grow in biofilms. It has recently been shown that the formation of Streptococcus pneumoniae biofilms in vivo and in vitro is hindered by the presence of capsular polysaccharide. The biofilm-forming capacity of pneumococcal clinical isolates with different types of capsular polysaccharide and various isogenic transformants was examined. Strains of serotypes 19A and 19F, but not 19B and 19C, formed ≥ 80% of the quantity of biofilm associated with a non-encapsulated control strain. Strains of serogroup 6 also showed significant biofilm-forming capacity. The capsules of serotypes 19A and 19F, and serogroup 6 contain the disaccharides α-D-Glcp-(1→2)-α-L-Rhap-(1→ and α-D-Glcp-(1→3)-α-L-Rhap-(1→. Serotype 18A and serotypes 18B/18C have very similar capsular disaccharides: α-D-GlcpNAc-(1→3)-β-L-Rhap-(1→ and α-D-Glcp-(1→3)-β-L-Rhap-(1→ respectively. However, the strains of serogroup 18 showed impaired biofilm formation. These results indicate that the chemical composition/structure of the capsular polysaccharide is crucial to the biofilm-forming capacity of pneumococcal serotypes. Testing of the in vitro biofilm-forming ability of isogenic transformants expressing different capsular polysaccharides may help predict the emergence of colonizing, non-vaccine serotypes.
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Affiliation(s)
- Mirian Domenech
- Departamento de Microbiología Molecular y Biología de las Infecciones, Centro de Investigaciones Biológicas (CIB-CSIC), Madrid, Spain; CIBER de Enfermedades Respiratorias (CIBERES), Madrid, Spain
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13
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Murphy TF, Chonmaitree T, Barenkamp S, Kyd J, Nokso-Koivisto J, Patel JA, Heikkinen T, Yamanaka N, Ogra P, Swords WE, Sih T, Pettigrew MM. Panel 5: Microbiology and immunology panel. Otolaryngol Head Neck Surg 2013; 148:E64-89. [PMID: 23536533 DOI: 10.1177/0194599812459636] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
OBJECTIVE The objective is to perform a comprehensive review of the literature from January 2007 through June 2011 on the virology, bacteriology, and immunology related to otitis media. DATA SOURCES PubMed database of the National Library of Medicine. REVIEW METHODS Three subpanels with co-chairs comprising experts in the virology, bacteriology, and immunology of otitis media were formed. Each of the panels reviewed the literature in their respective fields and wrote draft reviews. The reviews were shared with all panel members, and a second draft was created. The entire panel met at the 10th International Symposium on Recent Advances in Otitis Media in June 2011 and discussed the review and refined the content further. A final draft was created, circulated, and approved by the panel. CONCLUSION Excellent progress has been made in the past 4 years in advancing an understanding of the microbiology and immunology of otitis media. Advances include laboratory-based basic studies, cell-based assays, work in animal models, and clinical studies. IMPLICATIONS FOR PRACTICE The advances of the past 4 years formed the basis of a series of short-term and long-term research goals in an effort to guide the field. Accomplishing these goals will provide opportunities for the development of novel interventions, including new ways to better treat and prevent otitis media.
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Affiliation(s)
- Timothy F Murphy
- Clinical and Translational Research Center, University at Buffalo, State University of New York, Buffalo, New York 14203, USA.
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Sabharwal V, Figueira M, Pelton SI, Pettigrew MM. Virulence of Streptococcus pneumoniae serotype 6C in experimental otitis media. Microbes Infect 2012; 14:712-8. [PMID: 22414497 DOI: 10.1016/j.micinf.2012.02.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2011] [Revised: 02/15/2012] [Accepted: 02/17/2012] [Indexed: 10/28/2022]
Abstract
Increases in colonization with serotypes of Streptococcus pneumoniae not contained within the 7-valent pneumococcal conjugate vaccine (PCV) have been reported among children following introduction. Serotype 6C has emerged as prevalent in nasopharyngeal colonization and acute otitis media (AOM), though it is uncommonly recovered from children with invasive pneumococcal disease. Vaccine serotypes within PCV7 have been replaced by nonvaccine serotypes without significant changes in the overall carriage rate. We hypothesize 1) that serotypes vary in their ability to evade host defenses and establish AOM following colonization and 2) the observed reduction in pneumococcal otitis results from a reduced disease potential by some 'replacement serotypes'. We compared the capacity of S. pneumoniae serotypes 6C and 19A to produce experimental otitis media (EOM) in a chinchilla model. The proportion of chinchillas that developed culture positive EOM and density of middle ear infection was evaluated. EOM was found in 28/82 (34%) ears challenged with 6C compared to 13/18(72.2%) with 19A [p = 0.0003]. When disease due to 6C did occur, it was characterized by low-density infection. Our findings demonstrate that challenge with serotype 6C results in EOM less frequently than 19A. These data support the need for greater knowledge regarding differences among serotypes to produce AOM.
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Affiliation(s)
- Vishakha Sabharwal
- Section of Pediatric Infectious Diseases, Maxwell Finland Laboratory for Infectious Diseases, Boston Medical Center, 670 Albany Street, 6th Floor, Boston, MA 02118, USA.
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Thomas JC, Figueira M, Fennie KP, Laufer AS, Kong Y, Pichichero ME, Pelton SI, Pettigrew MM. Streptococcus pneumoniae clonal complex 199: genetic diversity and tissue-specific virulence. PLoS One 2011; 6:e18649. [PMID: 21533186 PMCID: PMC3077395 DOI: 10.1371/journal.pone.0018649] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2010] [Accepted: 03/14/2011] [Indexed: 11/19/2022] Open
Abstract
Streptococcus pneumoniae is an important cause of otitis media and invasive disease. Since introduction of the heptavalent pneumococcal conjugate vaccine, there has been an increase in replacement disease due to serotype 19A clonal complex (CC)199 isolates. The goals of this study were to 1) describe genetic diversity among nineteen CC199 isolates from carriage, middle ear, blood, and cerebrospinal fluid, 2) compare CC199 19A (n = 3) and 15B/C (n = 2) isolates in the chinchilla model for pneumococcal disease, and 3) identify accessory genes associated with tissue-specific disease among a larger collection of S. pneumoniae isolates. CC199 isolates were analyzed by comparative genome hybridization. One hundred and twenty-seven genes were variably present. The CC199 phylogeny split into two main clades, one comprised predominantly of carriage isolates and another of disease isolates. Ability to colonize and cause disease did not differ by serotype in the chinchilla model. However, isolates from the disease clade were associated with faster time to bacteremia compared to carriage clade isolates. One 19A isolate exhibited hypervirulence. Twelve tissue-specific genes/regions were identified by correspondence analysis. After screening a diverse collection of 326 isolates, spr0282 was associated with carriage. Four genes/regions, SP0163, SP0463, SPN05002 and RD8a were associated with middle ear isolates. SPN05002 also associated with blood and CSF, while RD8a associated with blood isolates. The hypervirulent isolate's genome was sequenced using the Solexa paired-end sequencing platform and compared to that of a reference serotype 19A isolate, revealing the presence of a novel 20 kb region with sequence similarity to bacteriophage genes. Genetic factors other than serotype may modulate virulence potential in CC199. These studies have implications for the long-term effectiveness of conjugate vaccines. Ideally, future vaccines would target common proteins to effectively reduce carriage and disease in the vaccinated population.
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Affiliation(s)
- Jonathan C. Thomas
- Division of Epidemiology of Microbial Diseases, Yale School of Public Health, Yale University School of Medicine, New Haven, Connecticut, United States of America
- Department of Microbiology, University of Mississippi Medical Center, Jackson, Mississippi, United States of America
| | - Marisol Figueira
- Boston University School of Medicine and Public Health, Boston Medical Center, Boston, Massachusetts, United States of America
| | - Kristopher P. Fennie
- Yale University School of Nursing, New Haven, Connecticut, United States of America
| | - Alison S. Laufer
- Division of Epidemiology of Microbial Diseases, Yale School of Public Health, Yale University School of Medicine, New Haven, Connecticut, United States of America
| | - Yong Kong
- Department of Molecular Biophysics and Biochemistry, W. M. Keck Foundation Biotechnology Resource Laboratory, New Haven, Connecticut, United States of America
| | - Michael E. Pichichero
- Rochester General Hospital Research Institute, Rochester, New York, United States of America
| | - Stephen I. Pelton
- Boston University School of Medicine and Public Health, Boston Medical Center, Boston, Massachusetts, United States of America
| | - Melinda M. Pettigrew
- Division of Epidemiology of Microbial Diseases, Yale School of Public Health, Yale University School of Medicine, New Haven, Connecticut, United States of America
- * E-mail:
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