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von Mollendorf C, Mungun T, Ulziibayar M, Skoko P, Boelsen L, Nguyen C, Batsaikhan P, Suuri B, Luvsantseren D, Narangerel D, Tsolmon B, Demberelsuren S, Ortika BD, Pell CL, Wee-Hee A, Nation ML, Hinds J, Dunne EM, Mulholland EK, Satzke C. Effect of pneumococcal conjugate vaccine six years post-introduction on pneumococcal carriage in Ulaanbaatar, Mongolia. Nat Commun 2024; 15:6577. [PMID: 39097620 PMCID: PMC11297977 DOI: 10.1038/s41467-024-50944-3] [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: 03/25/2024] [Accepted: 07/24/2024] [Indexed: 08/05/2024] Open
Abstract
Limited data from Asia are available on long-term effects of pneumococcal conjugate vaccine introduction on pneumococcal carriage. Here we assess the impact of 13-valent pneumococcal conjugate vaccine (PCV13) introduction on nasopharyngeal pneumococcal carriage prevalence, density and antimicrobial resistance. Cross-sectional carriage surveys were conducted pre-PCV13 (2015) and post-PCV13 introduction (2017 and 2022). Pneumococci were detected and quantified by real-time PCR from nasopharyngeal swabs. DNA microarray was used for molecular serotyping and to infer genetic lineage (Global Pneumococcal Sequence Cluster). The study included 1461 infants (5-8 weeks old) and 1489 toddlers (12-23 months old) enrolled from family health clinics. We show a reduction in PCV13 serotype carriage (with non-PCV13 serotype replacement) and a reduction in the proportion of samples containing resistance genes in toddlers six years post-PCV13 introduction. We observed an increase in pneumococcal nasopharyngeal density. Serotype 15 A, the most prevalent non-vaccine-serotype in 2022, was comprised predominantly of GPSC904;9. Reductions in PCV13 serotype carriage will likely result in pneumococcal disease reduction. It is important for ongoing surveillance to monitor serotype changes to potentially inform new vaccine development.
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Affiliation(s)
- Claire von Mollendorf
- Infection, Immunity, and Global Health, Murdoch Children's Research Institute, Melbourne, Australia.
- Department of Paediatrics, The University of Melbourne, Melbourne, Australia.
| | - Tuya Mungun
- National Center of Communicable Diseases, Ulaanbaatar, Mongolia
| | | | - Paige Skoko
- Infection, Immunity, and Global Health, Murdoch Children's Research Institute, Melbourne, Australia
- Department of Paediatrics, The University of Melbourne, Melbourne, Australia
| | - Laura Boelsen
- Infection, Immunity, and Global Health, Murdoch Children's Research Institute, Melbourne, Australia
| | - Cattram Nguyen
- Infection, Immunity, and Global Health, Murdoch Children's Research Institute, Melbourne, Australia
- Department of Paediatrics, The University of Melbourne, Melbourne, Australia
| | | | | | | | | | - Bilegtsaikhan Tsolmon
- National Center of Communicable Diseases, Ulaanbaatar, Mongolia
- Mongolian National University of Medical Sciences, Ulaanbaatar, Mongolia
| | | | - Belinda D Ortika
- Infection, Immunity, and Global Health, Murdoch Children's Research Institute, Melbourne, Australia
| | - Casey L Pell
- Infection, Immunity, and Global Health, Murdoch Children's Research Institute, Melbourne, Australia
| | - Ashleigh Wee-Hee
- Infection, Immunity, and Global Health, Murdoch Children's Research Institute, Melbourne, Australia
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Monica L Nation
- Infection, Immunity, and Global Health, Murdoch Children's Research Institute, Melbourne, Australia
| | - Jason Hinds
- Institute for Infection and Immunity, St George's, University of London, London, UK
- BUGS Bioscience, London Bioscience Innovation Centre, London, UK
| | - Eileen M Dunne
- Infection, Immunity, and Global Health, Murdoch Children's Research Institute, Melbourne, Australia
- Department of Paediatrics, The University of Melbourne, Melbourne, Australia
| | - E Kim Mulholland
- Infection, Immunity, and Global Health, Murdoch Children's Research Institute, Melbourne, Australia
- Department of Paediatrics, The University of Melbourne, Melbourne, Australia
- London School of Hygiene and Tropical Medicine, London, UK
| | - Catherine Satzke
- Infection, Immunity, and Global Health, Murdoch Children's Research Institute, Melbourne, Australia
- Department of Paediatrics, The University of Melbourne, Melbourne, Australia
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
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2
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Siguier P, Rousseau P, Cornet F, Chandler M. A subclass of the IS1202 family of bacterial insertion sequences targets XerCD recombination sites. Plasmid 2023; 127:102696. [PMID: 37302728 DOI: 10.1016/j.plasmid.2023.102696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 05/31/2023] [Accepted: 06/01/2023] [Indexed: 06/13/2023]
Abstract
We describe here a new family of IS which are related to IS1202, originally isolated from Streptococcus pneumoniae in the mid-1990s and previously tagged as an emerging IS family in the ISfinder database. Members of this family have impacted some important properties of their hosts. We describe here another potentially important property of certain family members: specific targeting of xrs recombination sites. The family could be divided into three subgroups based on their transposase sequences and the length on the target repeats (DR) they generate on insertion: subgroup IS1202 (24-29 bp); ISTde1 (15-18 bp); and ISAba32 (5-6 bp). Members of the ISAba32 subgroup were repeatedly found abutting Xer recombinase recombination sites (xrs), separated by an intervening copy of a DR. These xrs sites, present in multiple copies in a number of Acinetobacter plasmids flanking antibiotic resistance genes, were proposed to form a new type of mobile genetic element using the chromosomally-encoded XerCD recombinase for mobility. Transposase alignments identified subgroup-specific indels which may be responsible for the differences in the transposition properties of the three subgroups (i.e. DR length and target specificity). We propose that this collection of IS be classed as a new insertion sequence family: the IS1202 family composed of three subgroups, only one of which specifically targets plasmid-borne xrs. We discuss the implications of xrs targeting for gene mobility.
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Affiliation(s)
- Patricia Siguier
- Laboratoire de Microbiologie et Génétique Moléculaires, Centre de Biologie Integrative, Université de Toulouse, CNRS, UPS, France.
| | - Philippe Rousseau
- Laboratoire de Microbiologie et Génétique Moléculaires, Centre de Biologie Integrative, Université de Toulouse, CNRS, UPS, France
| | - François Cornet
- Laboratoire de Microbiologie et Génétique Moléculaires, Centre de Biologie Integrative, Université de Toulouse, CNRS, UPS, France
| | - Michael Chandler
- Department of Biochemistry and Molecular & Cellular Biology, Georgetown University Medical Center, Washington, DC, USA.
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3
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Nation ML, Manna S, Tran HP, Nguyen CD, Vy LTT, Uyen DY, Phuong TL, Dai VTT, Ortika BD, Wee-Hee AC, Beissbarth J, Hinds J, Bright K, Smith-Vaughan H, Nguyen TV, Mulholland K, Temple B, Satzke C. Impact of COVID-19 Nonpharmaceutical Interventions on Pneumococcal Carriage Prevalence and Density in Vietnam. Microbiol Spectr 2023; 11:e0361522. [PMID: 36645282 PMCID: PMC9927266 DOI: 10.1128/spectrum.03615-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 12/15/2022] [Indexed: 01/17/2023] Open
Abstract
Nonpharmaceutical interventions (NPIs) implemented to contain SARS-CoV-2 have decreased invasive pneumococcal disease. Previous studies have proposed the decline is due to reduced pneumococcal transmission or suppression of respiratory viruses, but the mechanism remains unclear. We undertook a secondary analysis of data collected from a clinical trial to evaluate the impact of NPIs on pneumococcal carriage and density, drivers of transmission and disease, during the COVID-19 pandemic in Ho Chi Minh City, Vietnam. Nasopharyngeal samples from children aged 24 months were assessed in three periods - one pre-COVID-19 period (n = 1,537) and two periods where NPIs were implemented with increasing stringency (NPI period 1 [NPI-1, n = 307], and NPI period 2 [NPI-2, n = 262]). Pneumococci were quantified using lytA quantitative PCR and serotyped by DNA microarray. Overall, capsular, and nonencapsulated pneumococcal carriage and density were assessed in each NPI period compared with the pre-COVID-19 period using unadjusted log-binomial and linear regression. Pneumococcal carriage was generally stable after the implementation of NPIs. In contrast, overall pneumococcal carriage density decreased by 0.44 log10 genome equivalents/mL (95% confidence interval [CI]: 0.19 to 0.69) in NPI-1 and by 0.84 log10 genome equivalents/mL (95% CI: 0.55 to 1.13) in NPI-2 compared with the pre-COVID-19 period. Reductions in overall pneumococcal density were driven by reductions in capsular pneumococci, with no corresponding reduction in nonencapsulated density. As higher pneumococcal density is a risk factor for disease, the decline in density provides a plausible explanation for the reductions in invasive pneumococcal disease that have been observed in many countries in the absence of a substantive reduction in pneumococcal carriage. IMPORTANCE The pneumococcus is a major cause of mortality globally. Implementation of NPIs during the COVID-19 pandemic led to reductions in invasive pneumococcal disease in many countries. However, no studies have conducted a fully quantitative assessment on the impact of NPIs on pneumococcal carriage density, which could explain this reduction. We evaluated the impact of COVID-19 NPIs on pneumococcal carriage prevalence and density in 2,106 children aged 24 months in Vietnam and found pneumococcal carriage density decreased up to 91.5% after NPI introduction compared with the pre-COVID-19 period, which was mainly attributed to capsular pneumococci. Only a minor effect on carriage prevalence was observed. As respiratory viruses are known to increase pneumococcal carriage density, transmission, and disease, this work suggests that interventions targeting respiratory viruses may have the added benefit of reducing invasive pneumococcal disease and explain the reductions observed following NPI implementation.
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Affiliation(s)
- Monica Larissa Nation
- Infection and Immunity, Murdoch Children's Research Institute, Parkville, Victoria, Australia
| | - Sam Manna
- Infection and Immunity, Murdoch Children's Research Institute, Parkville, Victoria, Australia
- Department of Paediatrics, The University of Melbourne, Parkville, Victoria, Australia
- Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Parkville, Victoria, Australia
| | - Hau Phuc Tran
- Department of Disease Control and Prevention, Pasteur Institute of Ho Chi Minh City, Ho Chi Minh City, Vietnam
| | - Cattram Duong Nguyen
- Infection and Immunity, Murdoch Children's Research Institute, Parkville, Victoria, Australia
- Department of Paediatrics, The University of Melbourne, Parkville, Victoria, Australia
| | - Le Thi Tuong Vy
- Department of Disease Control and Prevention, Pasteur Institute of Ho Chi Minh City, Ho Chi Minh City, Vietnam
| | - Doan Y. Uyen
- Department of Disease Control and Prevention, Pasteur Institute of Ho Chi Minh City, Ho Chi Minh City, Vietnam
| | - Tran Linh Phuong
- Clinical Research Center, Pasteur Institute of Ho Chi Minh City, Ho Chi Minh City, Vietnam
| | - Vo Thi Trang Dai
- Department of Microbiology and Immunology, Pasteur Institute of Ho Chi Minh City, Ho Chi Minh City, Vietnam
| | - Belinda Daniela Ortika
- Infection and Immunity, Murdoch Children's Research Institute, Parkville, Victoria, Australia
| | | | - Jemima Beissbarth
- Child Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, Northern Territory, Australia
| | - Jason Hinds
- Institute for Infection and Immunity, St. George's University of London, London, England, United Kingdom
- BUGS Bioscience, London Bioscience Innovation Centre, London, England, United Kingdom
| | - Kathryn Bright
- Infection and Immunity, Murdoch Children's Research Institute, Parkville, Victoria, Australia
| | - Heidi Smith-Vaughan
- Child Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, Northern Territory, Australia
| | - Thuong Vu Nguyen
- Department of Disease Control and Prevention, Pasteur Institute of Ho Chi Minh City, Ho Chi Minh City, Vietnam
| | - Kim Mulholland
- Infection and Immunity, Murdoch Children's Research Institute, Parkville, Victoria, Australia
- Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, England, United Kingdom
| | - Beth Temple
- Infection and Immunity, Murdoch Children's Research Institute, Parkville, Victoria, Australia
- Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, Casuarina, Northern Territory, Australia
| | - Catherine Satzke
- Infection and Immunity, Murdoch Children's Research Institute, Parkville, Victoria, Australia
- Department of Paediatrics, The University of Melbourne, Parkville, Victoria, Australia
- Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Parkville, Victoria, Australia
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4
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Nanayakkara U, Khan MA, Hargun DK, Sivagnanam S, Samarawickrama C. Ocular streptococcal infections: A clinical and microbiological review. Surv Ophthalmol 2023:S0039-6257(23)00036-X. [PMID: 36764397 DOI: 10.1016/j.survophthal.2023.02.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Revised: 01/30/2023] [Accepted: 02/01/2023] [Indexed: 02/11/2023]
Abstract
Streptococcus is a diverse bacterial genus that is part of the ocular surface microbiome implicated in conjunctivitis, keratitis, endophthalmitis, dacryocystitis, and orbital cellulitis which can lead to decreased visual acuity and require surgical intervention. The pathophysiology of S. pneumoniae is well established and the role of the polysaccharide capsule, pneumolysin, neuraminidases, and zinc metalloproteinases in ocular infections described. Additionally, key virulence factors of the viridans group streptococci such as cytolysins and proteases have been outlined, but there is a paucity of research on the remaining streptococcus species. These virulence factors tend to result in aggressive disease. Clinically, S. pneumoniae is implicated in 2.7-41.2% of bacterial conjunctivitis cases, more predominant in the pediatric population, and is implicated in 1.8-10.7% of bacterial keratitis isolates. Streptococcus bacteria are significantly implicated in acute postoperative, post-intravitreal, and bleb-associated endophthalmitis, responsible for 10.3-37.5, 29.4, and 57.1% of cases, respectively. Group A and B streptococcus endogenous endophthalmitis is rare, but has a very poor prognosis. Inappropriate prescription of antibiotics in cases of non-bacterial aetiology has contributed to increasing resistance, and a clinical index is needed to more accurately monitor this. Furthermore, there is an increasing need for prospective, surveillance studies of antimicrobial resistance in ocular pathogens, as well as point-of-care testing using molecular techniques.
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Affiliation(s)
| | | | | | - Shobini Sivagnanam
- Blacktown Hospital, Sydney, Australia; Australian Clinical Labs, Bella Vista, Sydney, Australia
| | - Chameen Samarawickrama
- University of Sydney, Australia; Translational Ocular Research and Immunology Consortium (TORIC), Westmead Institute for Medical Research, Australia.
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5
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Manna S, Spry L, Wee-Hee A, Ortika BD, Boelsen LK, Batinovic S, Mazarakis N, Ford RL, Lo SW, Bentley SD, Russell FM, Blyth CC, Pomat WS, Petrovski S, Hinds J, Licciardi PV, Satzke C. Variants of Streptococcus pneumoniae Serotype 14 from Papua New Guinea with the Potential to Be Mistyped and Escape Vaccine-Induced Protection. Microbiol Spectr 2022; 10:e0152422. [PMID: 35862970 PMCID: PMC9431120 DOI: 10.1128/spectrum.01524-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 06/16/2022] [Indexed: 11/20/2022] Open
Abstract
Streptococcus pneumoniae (the pneumococcus) is a human pathogen of global importance, classified into serotypes based on the type of capsular polysaccharide produced. Serotyping of pneumococci is essential for disease surveillance and vaccine impact measurement. However, the accuracy of serotyping methods can be affected by previously undiscovered variants. Previous studies have identified variants of serotype 14, a highly invasive serotype included in all licensed vaccine formulations. However, the potential of these variants to influence serotyping accuracy and evade vaccine-induced protection has not been investigated. In this study, we screened 1,386 nasopharyngeal swabs from children hospitalized with acute respiratory infection in Papua New Guinea for pneumococci. Swabs containing pneumococci (n = 1,226) were serotyped by microarray to identify pneumococci with a divergent serotype 14 capsule locus. Three serotype 14 variants ('14-like') were isolated and characterized further. The serotyping results of these isolates using molecular methods varied depending on the method, with 3/3 typing as nontypeable (PneumoCaT), 3/3 typing as serotype 14 (seroBA), and 2/3 typing as serotype 14 (SeroCall and quantitative PCR). All three isolates were nontypeable by phenotypic methods (Quellung and latex agglutination), indicating the absence of capsule. Illumina and nanopore sequencing were employed to examine their capsule loci and revealed unique mutations. Lastly, when incubated with sera from vaccinated individuals, the 14-like isolates evaded serotype-specific opsonophagocytic killing. Our study highlights the need for phenotypic testing to validate serotyping data derived from molecular methods. The convergent evolution of capsule loss underscores the importance of studying pneumococcal population biology to monitor the emergence of pneumococci capable of vaccine escape, globally. IMPORTANCE Pneumococcus is a pathogen of major public health importance. Current vaccines have limited valency, targeting a subset (up to 20) of the more than 100 capsule types (serotypes). Precise serotyping methods are therefore essential to avoid mistyping, which can reduce the accuracy of data used to inform decisions around vaccine introduction and/or maintenance of national vaccination programs. In this study, we examine a variant of serotype 14 (14-like), a virulent serotype present in all currently licensed vaccine formulations. Although these 14-like pneumococci no longer produce a serotype 14 capsule, widely used molecular methods can mistype them as serotype 14. Importantly, we show that 14-like pneumococci can evade opsonophagocytic killing mediated by vaccination. Despite the high accuracy of molecular methods for serotyping, our study reemphasizes their limitations. This is particularly relevant in situations where nonvaccine type pneumococci (e.g., the 14-likes in this study) could potentially be misidentified as a vaccine type (e.g., serotype 14).
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Affiliation(s)
- Sam Manna
- Infection and Immunity, Murdoch Children’s Research Institute, Royal Children's Hospital, Parkville, Victoria, Australia
- Department of Paediatrics, The University of Melbourne, Parkville, Victoria, Australia
- Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Parkville, Victoria, Australia
| | - Leena Spry
- Infection and Immunity, Murdoch Children’s Research Institute, Royal Children's Hospital, Parkville, Victoria, Australia
| | - Ashleigh Wee-Hee
- Infection and Immunity, Murdoch Children’s Research Institute, Royal Children's Hospital, Parkville, Victoria, Australia
| | - Belinda D. Ortika
- Infection and Immunity, Murdoch Children’s Research Institute, Royal Children's Hospital, Parkville, Victoria, Australia
| | - Laura K. Boelsen
- Infection and Immunity, Murdoch Children’s Research Institute, Royal Children's Hospital, Parkville, Victoria, Australia
| | - Steven Batinovic
- Department of Microbiology, Anatomy, Physiology, and Pharmacology, La Trobe University, Bundoora, Victoria, Australia
| | - Nadia Mazarakis
- Infection and Immunity, Murdoch Children’s Research Institute, Royal Children's Hospital, Parkville, Victoria, Australia
| | - Rebecca L. Ford
- Infection and Immunity Unit, Papua New Guinea Institute of Medical Research, Goroka, Eastern Highlands, Papua New Guinea
| | - Stephanie W. Lo
- Parasites and Microbes, Wellcome Sanger Institute, Hinxton, United Kingdom
| | - Stephen D. Bentley
- Parasites and Microbes, Wellcome Sanger Institute, Hinxton, United Kingdom
| | - Fiona M. Russell
- Infection and Immunity, Murdoch Children’s Research Institute, Royal Children's Hospital, Parkville, Victoria, Australia
- Department of Paediatrics, The University of Melbourne, Parkville, Victoria, Australia
| | - Christopher C. Blyth
- Wesfarmers Centre of Vaccines and Infectious Diseases, Telethon Kids Institute and School of Medicine, University of Western Australia, Perth, Australia
- Department of Infectious Diseases, Perth Children’s Hospital, Perth, Australia
- Department of Microbiology, PathWest Laboratory Medicine, Perth, Australia
| | - William S. Pomat
- Infection and Immunity Unit, Papua New Guinea Institute of Medical Research, Goroka, Eastern Highlands, Papua New Guinea
| | - Steve Petrovski
- Department of Microbiology, Anatomy, Physiology, and Pharmacology, La Trobe University, Bundoora, Victoria, Australia
| | - Jason Hinds
- Institute for Infection and Immunity, St. George's, University of London, United Kingdom
- BUGS Bioscience, London Bioscience Innovation Centre, London, United Kingdom
| | - Paul V. Licciardi
- Infection and Immunity, Murdoch Children’s Research Institute, Royal Children's Hospital, Parkville, Victoria, Australia
- Department of Paediatrics, The University of Melbourne, Parkville, Victoria, Australia
| | - Catherine Satzke
- Infection and Immunity, Murdoch Children’s Research Institute, Royal Children's Hospital, Parkville, Victoria, Australia
- Department of Paediatrics, The University of Melbourne, Parkville, Victoria, Australia
- Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Parkville, Victoria, Australia
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6
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Toizumi M, Satoh C, Quilty BJ, Nguyen HAT, Madaniyazi L, Le LT, Ng CFS, Hara M, Iwasaki C, Takegata M, Kitamura N, Nation ML, Satzke C, Kumai Y, Do HT, Bui MX, Mulholland K, Flasche S, Dang DA, Kaneko K, Yoshida LM. Effect of pneumococcal conjugate vaccine on prevalence of otitis media with effusion among children in Vietnam. Vaccine 2022; 40:5366-5375. [PMID: 35934579 DOI: 10.1016/j.vaccine.2022.07.047] [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: 01/12/2022] [Revised: 04/28/2022] [Accepted: 07/29/2022] [Indexed: 10/16/2022]
Abstract
PURPOSE Otitis media with effusion (OME) is common in young children and is associated with Streptococcus pneumoniae infection. We aimed to determine the impact of pneumococcal conjugate vaccine (PCV) introduction on the prevalence of OME and OME associated with vaccine-type (VT) or non-VT. METHODS Population-based cross-sectional surveys were conducted in pre- (2016) and post-PCV periods (2017, 2018, and 2019) at selected communes in Nha Trang, Vietnam. For each survey, we randomly selected 60 children aged 4-11 months and 60 aged 14-23 months from each commune. Nasopharyngeal sample collection and tympanic membrane examination by digital otoscope were performed. S. pneumoniae was detected and serotyped by lytA qPCR and microarray. Odds ratios (OR) and 95% confidence intervals (CIs) were calculated using Firth's logistic regression, stratified by age group. RESULTS Over the four surveys, 2089 children had a bilateral ear examination. Compared to pre-PCV, the prevalence of OME reduced in 2018 (OR 0.51, 95 %CI 0.28-0.93) and in 2019 (OR 0.53, 95 %CI 0.29-0.97) among the <12-month-olds, but no significant reduction among the 12-23-month-olds. The prevalence of OME associated with VT pneumococcus decreased in 2018 and 2019 (2018: OR 0.14, 95 %CI 0.03-0.55; 2019: OR 0.20, 95 %CI 0.05-0.69 in the <12-months-olds, 2018: OR 0.05, 95 %CI 0.00-0.44, 2019: OR 0.41, 95 %CI 0.10-1.61 in the 12-23-months-olds). The prevalence of OME associated with non-VT pneumococcus increased in the 12-23-month-olds in 2017 (OR 3.09, 95 %CI 1.47-7.45) and returned to the pre-PCV level of prevalence in 2018 and 2019 (OR 0.94, 95 %CI 0.40-2.43 and 1.40, 95 %CI 0.63-3.49). CONCLUSION PCV10 introduction was associated with a reduction of OME prevalence in infants but not in older children.
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Affiliation(s)
- Michiko Toizumi
- Department of Pediatric Infectious Diseases, Institute of Tropical Medicine, Nagasaki University, Nagasaki, Japan; School of Tropical Medicine and Global Health, Nagasaki University, Nagasaki, Japan
| | - Chisei Satoh
- Department of Otorhinolaryngology, Nagasaki University Hospital, Nagasaki, Japan
| | - Billy J Quilty
- Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | | | - Lina Madaniyazi
- Department of Pediatric Infectious Diseases, Institute of Tropical Medicine, Nagasaki University, Nagasaki, Japan; School of Tropical Medicine and Global Health, Nagasaki University, Nagasaki, Japan
| | - Lien Thuy Le
- Department of Bacteriology, the Pasteur Institute in Nha Trang, Nha Trang, Viet Nam
| | - Chris Fook Sheng Ng
- School of Tropical Medicine and Global Health, Nagasaki University, Nagasaki, Japan; Department of Global Health Policy, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Minoru Hara
- Department of Otorhinolaryngology, Kamio Memorial Hospital, Tokyo, Japan
| | - Chihiro Iwasaki
- Department of Pediatric Infectious Diseases, Institute of Tropical Medicine, Nagasaki University, Nagasaki, Japan
| | - Mizuki Takegata
- Department of Pediatric Infectious Diseases, Institute of Tropical Medicine, Nagasaki University, Nagasaki, Japan
| | - Noriko Kitamura
- School of Tropical Medicine and Global Health, Nagasaki University, Nagasaki, Japan
| | | | - Catherine Satzke
- Infection and Immunity, Murdoch Children's Research Institute, Melbourne, Australia; Department of Paediatrics, The University of Melbourne, Melbourne, Australia; Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Yoshihiko Kumai
- Department of Otorhinolaryngology, Nagasaki University Hospital, Nagasaki, Japan
| | - Hung Thai Do
- Department of Bacteriology, the Pasteur Institute in Nha Trang, Nha Trang, Viet Nam
| | | | - Kim Mulholland
- Infection and Immunity, Murdoch Children's Research Institute, Melbourne, Australia; Department of Paediatrics, The University of Melbourne, Melbourne, Australia
| | - Stefan Flasche
- Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Duc Anh Dang
- National Institute of Hygiene and Epidemiology, Hanoi, Viet Nam
| | - Kenichi Kaneko
- Department of Otorhinolaryngology, Nagasaki University Hospital, Nagasaki, Japan
| | - Lay-Myint Yoshida
- Department of Pediatric Infectious Diseases, Institute of Tropical Medicine, Nagasaki University, Nagasaki, Japan; School of Tropical Medicine and Global Health, Nagasaki University, Nagasaki, Japan.
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7
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Nagaraj G, Govindan V, Ganaie F, Venkatesha VT, Hawkins PA, Gladstone RA, McGee L, Breiman RF, Bentley SD, Klugman KP, Lo SW, Ravikumar KL. Streptococcus pneumoniae genomic datasets from an Indian population describing pre-vaccine evolutionary epidemiology using a whole genome sequencing approach. Microb Genom 2021; 7. [PMID: 34494953 PMCID: PMC8715438 DOI: 10.1099/mgen.0.000645] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Globally, India has a high burden of pneumococcal disease, and pneumococcal conjugate vaccine (PCV) has been rolled out in different phases across the country since May 2017 in the national infant immunization programme (NIP). To provide a baseline for assessing the impact of the vaccine on circulating pneumococci in India, genetic characterization of pneumococcal isolates detected prior to introduction of PCV would be helpful. Here we present a population genomic study of 480 Streptococcus pneumoniae isolates collected across India and from all age groups before vaccine introduction (2009–2017), including 294 isolates from pneumococcal disease and 186 collected through nasopharyngeal surveys. Population genetic structure, serotype and antimicrobial susceptibility profile were characterized and predicted from whole-genome sequencing data. Our findings revealed high levels of genetic diversity represented by 110 Global Pneumococcal Sequence Clusters (GPSCs) and 54 serotypes. Serotype 19F and GPSC1 (CC320) was the most common serotype and pneumococcal lineage, respectively. Coverage of PCV13 (Pfizer) and 10-valent Pneumosil (Serum Institute of India) serotypes in age groups of ≤2 and 3–5 years were 63–75 % and 60–69 %, respectively. Coverage of PPV23 (Merck) serotypes in age groups of ≥50 years was 62 % (98/158). Among the top five lineages causing disease, GPSC10 (CC230), which ranked second, is the only lineage that expressed both PCV13 (serotypes 3, 6A, 14, 19A and 19F) and non-PCV13 (7B, 13, 10A, 11A, 13, 15B/C, 22F, 24F) serotypes. It exhibited multidrug resistance and was the largest contributor (17 %, 18/103) of NVTs in the disease-causing population. Overall, 42 % (202/480) of isolates were penicillin-resistant (minimum inhibitory concentration ≥0.12 µg ml−1) and 45 % (217/480) were multidrug-resistant. Nine GPSCs (GPSC1, 6, 9, 10, 13, 16, 43, 91, 376) were penicillin-resistant and among them six were multidrug-resistant. Pneumococci expressing PCV13 serotypes had a higher prevalence of antibiotic resistance. Sequencing of pneumococcal genomes has significantly improved our understanding of the biology of these bacteria. This study, describing the pneumococcal disease and carriage epidemiology pre-PCV introduction, demonstrates that 60–75 % of pneumococcal serotypes in children ≤5 years are covered by PCV13 and Pneumosil. Vaccination against pneumococci is very likely to reduce antibiotic resistance. A multidrug-resistant pneumococcal lineage, GPSC10 (CC230), is a high-risk clone that could mediate serotype replacement.
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Affiliation(s)
- Geetha Nagaraj
- Central Research Laboratory, Kempegowda Institute of Medical Sciences, Bangalore, India
| | - Vandana Govindan
- Central Research Laboratory, Kempegowda Institute of Medical Sciences, Bangalore, India
| | - Feroze Ganaie
- Central Research Laboratory, Kempegowda Institute of Medical Sciences, Bangalore, India
| | - V T Venkatesha
- Central Research Laboratory, Kempegowda Institute of Medical Sciences, Bangalore, India
| | - Paulina A Hawkins
- Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | | | - Lesley McGee
- Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Robert F Breiman
- Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | | | - Keith P Klugman
- Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Stephanie W Lo
- Parasites and Microbes, Wellcome Sanger Institute, Hinxton, UK
| | - K L Ravikumar
- Central Research Laboratory, Kempegowda Institute of Medical Sciences, Bangalore, India
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8
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Britton KJ, Pickering JL, Pomat WS, de Gier C, Nation ML, Pell CL, Granland CM, Solomon V, Ford RL, Greenhill A, Hinds J, Moore HC, Richmond PC, Blyth CC, Lehmann D, Satzke C, Kirkham LAS. Lack of effectiveness of 13-valent pneumococcal conjugate vaccination against pneumococcal carriage density in Papua New Guinean infants. Vaccine 2021; 39:5401-5409. [PMID: 34384633 DOI: 10.1016/j.vaccine.2021.07.085] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 07/22/2021] [Accepted: 07/26/2021] [Indexed: 11/17/2022]
Abstract
BACKGROUND Papua New Guinea (PNG) introduced the 13-valent pneumococcal conjugate vaccine (PCV13) in 2014, with administration at 1, 2, and 3 months of age. PCV13 has reduced or eliminated carriage of vaccine types in populations with low pneumococcal carriage prevalence, carriage density and serotype diversity. This study investigated PCV13 impact on serotype-specific pneumococcal carriage prevalence, density, and serotype diversity in PNG infants, who have some of the highest reported rates of pneumococcal carriage and disease in the world. METHODS Nasopharyngeal swabs were collected at 1, 4 and 9 months of age from PCV13-vaccinated infants (n = 57) and age-/season-matched, unvaccinated infants (at approximately 1 month, n = 53; 4 months, n = 57; 9 months, n = 52). Serotype-specific pneumococcal carriage density and antimicrobial resistance genes were identified by qPCR and microarray. RESULTS Pneumococci were present in 89% of swabs, with 60 different serotypes and four non-encapsulated variants detected. Multiple serotype carriage was common (47% of swabs). Vaccine type carriage prevalence was similar between PCV13-vaccinated and unvaccinated infants at 4 and 9 months of age. The prevalence of non-vaccine type carriage was also similar between cohorts, with non-vaccine types present in three-quarters of samples (from both vaccinated and unvaccinated infants) by 4 months of age. The median pneumococcal carriage density was high and similar at each age group (~7.0 log10genome equivalents/mL). PCV13 had no effect on overall pneumococcal carriage density, vaccine type density, non-vaccine type density, or the prevalence of antimicrobial resistance genes. CONCLUSION PNG infants experience dense and diverse pneumococcal colonisation with concurrent serotypes from 1 month of age. PCV13 had no impact on pneumococcal carriage density, even for vaccine serotypes. The low prevalence of vaccine serotypes, high pneumococcal carriage density and abundance of non-vaccine serotypes likely contribute to the lack of PCV13 impact on carriage in PNG infants. Indirect effects of the infant PCV programs are likely to be limited in PNG. Alternative vaccines with broader coverage should be considered.
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Affiliation(s)
- Kathryn J Britton
- Wesfarmers Centre of Vaccines and Infectious Diseases, Telethon Kids Institute, The University of Western Australia, Perth, Australia; Division of Paediatrics, School of Medicine, The University of Western Australia, Perth, Australia.
| | - Janessa L Pickering
- Wesfarmers Centre of Vaccines and Infectious Diseases, Telethon Kids Institute, The University of Western Australia, Perth, Australia.
| | - William S Pomat
- Wesfarmers Centre of Vaccines and Infectious Diseases, Telethon Kids Institute, The University of Western Australia, Perth, Australia; Papua New Guinea Institute of Medical Research, Goroka, Papua New Guinea.
| | - Camilla de Gier
- Wesfarmers Centre of Vaccines and Infectious Diseases, Telethon Kids Institute, The University of Western Australia, Perth, Australia; Division of Paediatrics, School of Medicine, The University of Western Australia, Perth, Australia.
| | - Monica L Nation
- Translational Microbiology Group, Murdoch Children's Research Institute, Melbourne, Australia.
| | - Casey L Pell
- Translational Microbiology Group, Murdoch Children's Research Institute, Melbourne, Australia.
| | - Caitlyn M Granland
- Wesfarmers Centre of Vaccines and Infectious Diseases, Telethon Kids Institute, The University of Western Australia, Perth, Australia.
| | - Vela Solomon
- Papua New Guinea Institute of Medical Research, Goroka, Papua New Guinea.
| | - Rebecca L Ford
- Papua New Guinea Institute of Medical Research, Goroka, Papua New Guinea.
| | - Andrew Greenhill
- School of Health and Life Sciences, Federation University, Victoria, Australia.
| | - Jason Hinds
- Institute for Infection and Immunity, St. George's University of London, London, United Kingdom.
| | - Hannah C Moore
- Wesfarmers Centre of Vaccines and Infectious Diseases, Telethon Kids Institute, The University of Western Australia, Perth, Australia.
| | - Peter C Richmond
- Wesfarmers Centre of Vaccines and Infectious Diseases, Telethon Kids Institute, The University of Western Australia, Perth, Australia; Division of Paediatrics, School of Medicine, The University of Western Australia, Perth, Australia.
| | - Christopher C Blyth
- Wesfarmers Centre of Vaccines and Infectious Diseases, Telethon Kids Institute, The University of Western Australia, Perth, Australia; Division of Paediatrics, School of Medicine, The University of Western Australia, Perth, Australia; Department of Paediatric Infectious Diseases, Perth Children's Hospital, Perth, Australia; Department of Microbiology, PathWest Laboratory Medicine WA, QEII Medical Centre, Perth, Australia.
| | - Deborah Lehmann
- Wesfarmers Centre of Vaccines and Infectious Diseases, Telethon Kids Institute, The University of Western Australia, Perth, Australia.
| | - Catherine Satzke
- Translational Microbiology Group, Murdoch Children's Research Institute, Melbourne, Australia; Department of Paediatrics, The University of Melbourne, Melbourne, Australia; Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia.
| | - Lea-Ann S Kirkham
- Wesfarmers Centre of Vaccines and Infectious Diseases, Telethon Kids Institute, The University of Western Australia, Perth, Australia; Centre for Child Health Research, The University of Western Australia, Perth, Australia.
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9
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D'Aeth JC, van der Linden MPG, McGee L, de Lencastre H, Turner P, Song JH, Lo SW, Gladstone RA, Sá-Leão R, Ko KS, Hanage WP, Breiman RF, Beall B, Bentley SD, Croucher NJ. The role of interspecies recombination in the evolution of antibiotic-resistant pneumococci. eLife 2021; 10:e67113. [PMID: 34259624 PMCID: PMC8321556 DOI: 10.7554/elife.67113] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 04/16/2021] [Indexed: 12/27/2022] Open
Abstract
Multidrug-resistant Streptococcus pneumoniae emerge through the modification of core genome loci by interspecies homologous recombinations, and acquisition of gene cassettes. Both occurred in the otherwise contrasting histories of the antibiotic-resistant S. pneumoniae lineages PMEN3 and PMEN9. A single PMEN3 clade spread globally, evading vaccine-induced immunity through frequent serotype switching, whereas locally circulating PMEN9 clades independently gained resistance. Both lineages repeatedly integrated Tn916-type and Tn1207.1-type elements, conferring tetracycline and macrolide resistance, respectively, through homologous recombination importing sequences originating in other species. A species-wide dataset found over 100 instances of such interspecific acquisitions of resistance cassettes and flanking homologous arms. Phylodynamic analysis of the most commonly sampled Tn1207.1-type insertion in PMEN9, originating from a commensal and disrupting a competence gene, suggested its expansion across Germany was driven by a high ratio of macrolide-to-β-lactam consumption. Hence, selection from antibiotic consumption was sufficient for these atypically large recombinations to overcome species boundaries across the pneumococcal chromosome.
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Affiliation(s)
- Joshua C D'Aeth
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College LondonLondonUnited Kingdom
| | - Mark PG van der Linden
- Institute for Medical Microbiology, National Reference Center for Streptococci, University Hospital RWTH AachenAachenGermany
| | - Lesley McGee
- Respiratory Diseases Branch, Centers for Disease Control and PreventionAtlantaUnited States
| | - Herminia de Lencastre
- Laboratory of Molecular Genetics, Instituto de Tecnologia Química e Biológica, Universidade Nova de LisboaOeirasPortugal
- Laboratory of Microbiology and Infectious Diseases, The Rockefeller UniversityNew YorkUnited States
| | - Paul Turner
- Cambodia Oxford Medical Research Unit, Angkor Hospital for ChildrenSiem ReapCambodia
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of OxfordOxfordUnited Kingdom
| | - Jae-Hoon Song
- Department of Molecular Cell Biology, Sungkyunkwan University School of MedicineSuwonRepublic of Korea
| | - Stephanie W Lo
- Parasites & Microbes, Wellcome Sanger Institute, Wellcome Genome CampusHinxtonUnited Kingdom
| | - Rebecca A Gladstone
- Parasites & Microbes, Wellcome Sanger Institute, Wellcome Genome CampusHinxtonUnited Kingdom
| | - Raquel Sá-Leão
- Laboratory of Molecular Microbiology of Human Pathogens, Instituto de Tecnologia Química e Biológica, Universidade Nova de LisboaOeirasPortugal
| | - Kwan Soo Ko
- Department of Molecular Cell Biology, Sungkyunkwan University School of MedicineSuwonRepublic of Korea
| | - William P Hanage
- Center for Communicable Disease Dynamics, Harvard T.H. Chan School of Public HealthBostonUnited States
| | - Robert F Breiman
- Department of Global Health, Rollins School of Public Health, Emory UniversityAtlantaUnited States
| | - Bernard Beall
- Respiratory Diseases Branch, Centers for Disease Control and PreventionAtlantaUnited States
| | - Stephen D Bentley
- Parasites & Microbes, Wellcome Sanger Institute, Wellcome Genome CampusHinxtonUnited Kingdom
| | - Nicholas J Croucher
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College LondonLondonUnited Kingdom
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10
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Mohamed YH, Toizumi M, Uematsu M, Nguyen HAT, Le LT, Takegata M, Iwasaki C, Kitamura N, Nation ML, Dunne EM, Hinds J, Do HT, Vien MQ, Satzke C, Flasche S, Mulholland K, Dang DA, Kitaoka T, Yoshida LM. Prevalence of Streptococcus pneumoniae in conjunctival flora and association with nasopharyngeal carriage among children in a Vietnamese community. Sci Rep 2021; 11:337. [PMID: 33431887 PMCID: PMC7801475 DOI: 10.1038/s41598-020-79175-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Accepted: 11/30/2020] [Indexed: 11/22/2022] Open
Abstract
Conjunctival pneumococcal serotypes among members of a community have not been investigated well. We determined the prevalence and association of Streptococcus pneumoniae in the nasopharynx and conjunctiva among children in a community before pneumococcal conjugate vaccine introduction. In October 2016, conjunctival and nasopharyngeal swabs were collected from children (< 24 months old) and nasopharyngeal swabs from mothers in Nha Trang, Vietnam. Quantitative lytA PCR and DNA microarray were performed to detect and serotype S. pneumoniae. The association between S. pneumoniae in the nasopharynx and conjunctiva was evaluated using multivariable logistic regression model. Among 698 children, 62 (8.9%, 95% CI 6.9-11.2%) were positive for S. pneumoniae in the conjunctiva. Non-encapsulated S. pneumoniae were most commonly identified, followed by serotypes 6A, 6B, and 14. Nasopharyngeal and conjunctival detection were positively associated (aOR 47.30, 95% CI 24.07-92.97). Low birth-weight, day-care attendance, and recent eye symptoms were independently associated with S. pneumoniae detection in the conjunctiva (aOR 11.14, 95% CI 3.76-32.98, aOR 2.19, 95% CI 1.45-3.31, and aOR 3.59, 95% CI 2.21-5.84, respectively). Serotypes and genotypes in the conjunctiva and nasopharynx matched in 87% of the children. Three mothers' nasopharyngeal pneumococcal samples had matched serotype and genotype with their child's in the conjunctiva and nasopharynx. S. pneumoniae presence in nasopharynx and conjunctiva were strongly associated. The high concordance of serotypes suggests nasopharyngeal carriage may be a source of transmission to the conjunctiva.
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Affiliation(s)
- Yasser Helmy Mohamed
- Department of Ophthalmology and Visual Sciences, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan
| | - Michiko Toizumi
- Department of Pediatric Infectious Diseases, Institute of Tropical Medicine, Nagasaki University, 1-12-4 Sakamoto, Nagasaki, 852-8523, Japan
| | - Masafumi Uematsu
- Department of Ophthalmology and Visual Sciences, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan
| | | | - Lien Thuy Le
- Pasteur Institute in Nha Trang, Nha Trang, Vietnam
| | - Mizuki Takegata
- Department of Pediatric Infectious Diseases, Institute of Tropical Medicine, Nagasaki University, 1-12-4 Sakamoto, Nagasaki, 852-8523, Japan
| | - Chihiro Iwasaki
- Department of Pediatric Infectious Diseases, Institute of Tropical Medicine, Nagasaki University, 1-12-4 Sakamoto, Nagasaki, 852-8523, Japan
| | - Noriko Kitamura
- Department of Pediatric Infectious Diseases, Institute of Tropical Medicine, Nagasaki University, 1-12-4 Sakamoto, Nagasaki, 852-8523, Japan
| | - Monica L Nation
- Infection and Immunity, Murdoch Children's Research Institute, Parkville, VIC, Australia
| | - Eileen M Dunne
- Infection and Immunity, Murdoch Children's Research Institute, Parkville, VIC, Australia
| | - Jason Hinds
- Institute for Infection and Immunity, St. George's, University of London, London, UK
- London Bioscience Innovation Centre, BUGS Bioscience, London, UK
| | - Hung Thai Do
- Pasteur Institute in Nha Trang, Nha Trang, Vietnam
| | | | - Catherine Satzke
- Infection and Immunity, Murdoch Children's Research Institute, Parkville, VIC, Australia
- Department of Paediatrics, The University of Melbourne, Parkville, VIC, Australia
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Parkville, VIC, Australia
| | - Stefan Flasche
- Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, UK
| | - Kim Mulholland
- Infection and Immunity, Murdoch Children's Research Institute, Parkville, VIC, Australia
| | - Duc-Anh Dang
- National Institute of Hygiene and Epidemiology, Hanoi, Vietnam
| | - Takashi Kitaoka
- Department of Ophthalmology and Visual Sciences, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan
| | - Lay-Myint Yoshida
- Department of Pediatric Infectious Diseases, Institute of Tropical Medicine, Nagasaki University, 1-12-4 Sakamoto, Nagasaki, 852-8523, Japan.
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11
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Zhang Z, Yu YX, Wang YG, Liu X, Wang LF, Zhang H, Liao MJ, Li B. Complete genome analysis of a virulent Vibrio scophthalmi strain VSc190401 isolated from diseased marine fish half-smooth tongue sole, Cynoglossus semilaevis. BMC Microbiol 2020; 20:341. [PMID: 33176689 PMCID: PMC7661262 DOI: 10.1186/s12866-020-02028-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2020] [Accepted: 10/30/2020] [Indexed: 12/12/2022] Open
Abstract
Background Vibrio scophthalmi is an opportunistic bacterial pathogen, which is widely distributed in the marine environment. Earlier studies have suggested that it is a normal microorganism in the turbot gut. However, recent studies have confirmed that this bacterial strain can cause diseases in many different marine animals. Therefore, it is necessary to investigate its whole genome for better understanding its physiological and pathogenic mechanisms. Results In the present study, we obtained a pathogenic strain of V. scophthalmi from diseased half-smooth tongue sole (Cynoglossus semilaevis) and sequenced its whole genome. Its genome contained two circular chromosomes and two plasmids with a total size of 3,541,838 bp, which harbored 3185 coding genes. Among these genes, 2648, 2298, and 1915 genes could be found through annotation information in COG, Blast2GO, and KEGG databases, respectively. Moreover, 10 genomic islands were predicted to exist in the chromosome I through IslandViewer online system. Comparison analysis in VFDB and PHI databases showed that this strain had 334 potential virulence-related genes and 518 pathogen-host interaction-related genes. Although it contained genes related to four secretion systems of T1SS, T2SS, T4SS, and T6SS, there was only one complete T2SS secretion system. Based on CARD database blast results, 180 drug resistance genes belonging to 27 antibiotic resistance categories were found in the whole genome of such strain. However, there were many differences between the phenotype and genotype of drug resistance. Conclusions Based on the whole genome analysis, the pathogenic V. scophthalmi strain contained many types of genes related to pathogenicity and drug resistance. Moreover, it showed inconsistency between phenotype and genotype on drug resistance. These results suggested that the physiological mechanism seemed to be complex. Supplementary Information The online version contains supplementary material available at 10.1186/s12866-020-02028-7.
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Affiliation(s)
- Zheng Zhang
- Key Laboratory of Maricultural Organism Disease Control, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academic of Fishery Sciences, Qingdao, Shandong, 266071, PR China. .,Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, Shandong, 266237, PR China.
| | - Yong-Xiang Yu
- Key Laboratory of Maricultural Organism Disease Control, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academic of Fishery Sciences, Qingdao, Shandong, 266071, PR China
| | - Yin-Geng Wang
- Key Laboratory of Maricultural Organism Disease Control, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academic of Fishery Sciences, Qingdao, Shandong, 266071, PR China. .,Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, Shandong, 266237, PR China.
| | - Xiao Liu
- Key Laboratory of Maricultural Organism Disease Control, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academic of Fishery Sciences, Qingdao, Shandong, 266071, PR China
| | - Li-Fang Wang
- Key Laboratory of Maricultural Organism Disease Control, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academic of Fishery Sciences, Qingdao, Shandong, 266071, PR China
| | - Hao Zhang
- Key Laboratory of Maricultural Organism Disease Control, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academic of Fishery Sciences, Qingdao, Shandong, 266071, PR China
| | - Mei-Jie Liao
- Key Laboratory of Maricultural Organism Disease Control, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academic of Fishery Sciences, Qingdao, Shandong, 266071, PR China.,Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, Shandong, 266237, PR China
| | - Bin Li
- Key Laboratory of Maricultural Organism Disease Control, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academic of Fishery Sciences, Qingdao, Shandong, 266071, PR China
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12
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Häfner S. Streptococcal oddity: Article highlight based on "pspK acquisition contributes to the loss of capsule in pneumococci: molecular characterisation of non-encapsulated pneumococci" by Takeaki Wajima et al. Microbes Infect 2020; 22:392-396. [PMID: 32693303 DOI: 10.1016/j.micinf.2020.07.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2020] [Accepted: 07/06/2020] [Indexed: 10/23/2022]
Affiliation(s)
- Sophia Häfner
- University of Copenhagen, BRIC Biotech Research & Innovation Centre, Lund Group, 2200 Copenhagen, Denmark.
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13
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Neal EFG, Nguyen CD, Ratu FT, Dunne EM, Kama M, Ortika BD, Boelsen LK, Kado J, Tikoduadua L, Devi R, Tuivaga E, Reyburn RC, Satzke C, Rafai E, Mulholland EK, Russell FM. Factors associated with pneumococcal carriage and density in children and adults in Fiji, using four cross-sectional surveys. PLoS One 2020; 15:e0231041. [PMID: 32236150 PMCID: PMC7112956 DOI: 10.1371/journal.pone.0231041] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 03/13/2020] [Indexed: 01/26/2023] Open
Abstract
This study describes predictors of pneumococcal nasopharyngeal carriage and density in Fiji. We used data from four annual (2012-2015) cross-sectional surveys, pre- and post-introduction of ten-valent pneumococcal conjugate vaccine (PCV10) in October 2012. Infants (5-8 weeks), toddlers (12-23 months), children (2-6 years), and their caregivers participated. Pneumococci were detected and quantified using lytA qPCR, with molecular serotyping by microarray. Logistic and quantile regression were used to determine predictors of pneumococcal carriage and density, respectively. There were 8,109 participants. Pneumococcal carriage was negatively associated with years post-PCV10 introduction (global P<0.001), and positively associated with indigenous iTaukei ethnicity (aOR 2.74 [95% CI 2.17-3.45] P<0.001); young age (infant, toddler, and child compared with caregiver participant groups) (global P<0.001); urban residence (aOR 1.45 [95% CI 1.30-2.57] P<0.001); living with ≥2 children <5 years of age (aOR 1.42 [95% CI 1.27-1.59] P<0.001); low family income (aOR 1.44 [95% CI 1.28-1.62] P<0.001); and upper respiratory tract infection (URTI) symptoms (aOR 1.77 [95% CI 1.57-2.01] P<0.001). Predictors were similar for PCV10 and non-PCV10 carriage, except PCV10 carriage was negatively associated with PCV10 vaccination (0.58 [95% CI 0.41-0.82] P = 0.002) and positively associated with exposure to household cigarette smoke (aOR 1.21 [95% CI 1.02-1.43] P = 0.031), while there was no association between years post-PCV10 introduction and non-PCV10 carriage. Pneumococcal density was positively associated with URTI symptoms (adjusted median difference 0.28 [95% CI 0.16, 0.40] P<0.001) and toddler and child, compared with caregiver, participant groups (global P = 0.008). Predictors were similar for PCV10 and non-PCV10 density, except infant, toddler, and child participant groups were not associated with PCV10 density. PCV10 introduction was associated with reduced the odds of overall and PCV10 pneumococcal carriage in Fiji. However, after adjustment iTaukei ethnicity was positively associated with pneumococcal carriage compared with Fijians of Indian Descent, despite similar PCV10 coverage rates.
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Affiliation(s)
- Eleanor F. G. Neal
- Infection & Immunity, Murdoch Children’s Research Institute, Royal Children’s Hospital, Parkville, VIC, Australia
- Department of Paediatrics, The University of Melbourne, Parkville, Australia
- * E-mail:
| | - Cattram D. Nguyen
- Infection & Immunity, Murdoch Children’s Research Institute, Royal Children’s Hospital, Parkville, VIC, Australia
- Department of Paediatrics, The University of Melbourne, Parkville, Australia
| | | | - Eileen M. Dunne
- Infection & Immunity, Murdoch Children’s Research Institute, Royal Children’s Hospital, Parkville, VIC, Australia
- Department of Paediatrics, The University of Melbourne, Parkville, Australia
| | - Mike Kama
- Ministry of Health and Medical Services, Suva, Fiji
| | - Belinda D. Ortika
- Infection & Immunity, Murdoch Children’s Research Institute, Royal Children’s Hospital, Parkville, VIC, Australia
| | - Laura K. Boelsen
- Infection & Immunity, Murdoch Children’s Research Institute, Royal Children’s Hospital, Parkville, VIC, Australia
| | - Joseph Kado
- Telethon Kids Institute, University of Western Australia, Western Australia, Australia
- College of Medicine Nursing and Health Sciences, Fiji National University, Suva, Fiji
| | | | - Rachel Devi
- Ministry of Health and Medical Services, Suva, Fiji
| | | | - Rita C. Reyburn
- Infection & Immunity, Murdoch Children’s Research Institute, Royal Children’s Hospital, Parkville, VIC, Australia
| | - Catherine Satzke
- Infection & Immunity, Murdoch Children’s Research Institute, Royal Children’s Hospital, Parkville, VIC, Australia
- Department of Paediatrics, The University of Melbourne, Parkville, Australia
| | - Eric Rafai
- Ministry of Health and Medical Services, Suva, Fiji
| | - E. Kim Mulholland
- Infection & Immunity, Murdoch Children’s Research Institute, Royal Children’s Hospital, Parkville, VIC, Australia
- Department of Paediatrics, The University of Melbourne, Parkville, Australia
- Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Fiona M. Russell
- Infection & Immunity, Murdoch Children’s Research Institute, Royal Children’s Hospital, Parkville, VIC, Australia
- Department of Paediatrics, The University of Melbourne, Parkville, Australia
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14
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Müller A, Salmen A, Aebi S, de Gouveia L, von Gottberg A, Hathaway LJ. Pneumococcal serotype determines growth and capsule size in human cerebrospinal fluid. BMC Microbiol 2020; 20:16. [PMID: 31959125 PMCID: PMC6971925 DOI: 10.1186/s12866-020-1700-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2019] [Accepted: 01/09/2020] [Indexed: 12/02/2022] Open
Abstract
Background The polysaccharide capsule is a major virulence factor of S. pneumoniae in diseases such as meningitis. While some capsular serotypes are more often found in invasive disease, high case fatality rates are associated with those serotypes more commonly found in asymptomatic colonization. We tested whether growth patterns and capsule size in human cerebrospinal fluid depends on serotype using a clinical isolate of S. pneumoniae and its capsule switch mutants. Results We found that the growth pattern differed markedly from that in culture medium by lacking the exponential and lysis phases. Growth in human cerebrospinal fluid was reduced when strains lost their capsules. When a capsule was present, growth was serotype-specific: high carriage serotypes (6B, 9 V, 19F and 23F) grew better than low carriage serotypes (7F, 14, 15B/C and 18C). Growth correlated with the case-fatality rates of serotypes reported in the literature. Capsule size in human cerebrospinal fluid also depended on serotype. Conclusions We propose that serotype-specific differences in disease severity observed in meningitis patients may, at least in part, be explained by differences in growth and capsule size in human cerebrospinal fluid. This information could be useful to guide future vaccine design.
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Affiliation(s)
- Annelies Müller
- Institute for Infectious Diseases, Faculty of Medicine, University of Bern, Friedbühlstrasse 51, CH-3001, Bern, Switzerland.,Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Anke Salmen
- Department of Neurology, Inselspital, University Hospital Bern and University of Bern, Bern, Switzerland
| | - Suzanne Aebi
- Institute for Infectious Diseases, Faculty of Medicine, University of Bern, Friedbühlstrasse 51, CH-3001, Bern, Switzerland
| | - Linda de Gouveia
- National Institute for Communicable Diseases: Division of the National Health Laboratory Service, Johannesburg, South Africa
| | - Anne von Gottberg
- National Institute for Communicable Diseases: Division of the National Health Laboratory Service, Johannesburg, South Africa.,Faculty of Health Sciences, School of Pathology, University of Witwatersrand, Johannesburg, South Africa
| | - Lucy J Hathaway
- Institute for Infectious Diseases, Faculty of Medicine, University of Bern, Friedbühlstrasse 51, CH-3001, Bern, Switzerland.
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15
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Mohale T, Wolter N, Allam M, Nzenze SA, Madhi SA, du Plessis M, von Gottberg A. Genomic differences among carriage and invasive nontypeable pneumococci circulating in South Africa. Microb Genom 2019; 5. [PMID: 31617841 PMCID: PMC6861859 DOI: 10.1099/mgen.0.000299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Most pneumococci express a polysaccharide capsule, a key virulence factor and target for pneumococcal vaccines. However, pneumococci showing no serological evidence of capsule expression [nontypeable pneumococci (NTPn)] are more frequently isolated from carriage studies than in invasive disease. Limited data exist about the population structure of carriage NTPn from the African continent. We aimed to characterize carriage NTPn and compare them to previously described invasive NTPn. Carriage and invasive NTPn isolates were obtained from South African cross-sectional studies (2009 and 2012) and laboratory-based surveillance for invasive pneumococcal disease (2003–2013), respectively. Isolates were characterized by capsular locus sequence analysis, multilocus sequence typing, antimicrobial non-susceptibility patterns and phylogenetic analysis. NTPn represented 3.7 % (137/3721) of carriage isolates compared to 0.1 % (39/32 824) of invasive isolates (P<0.001), and 24 % (33/137) of individuals were co-colonized with encapsulated pneumococci. Non-susceptibility to cotrimoxazole [84 % (112/133) vs 44 % (17/39)], penicillin [77 % (102/133) vs 36 % (14/39)], erythromycin [53 % (70/133) vs 31 % (12/39)] and clindamycin [36 % (48/133) vs 18 % (7/39)] was higher (P=0.03) among carriage than invasive NTPn. Ninety-one per cent (124/137) of carriage NTPn had complete deletion of the capsular locus and 9 % (13/137) had capsule genes, compared to 44 % (17/39) and 56 % (22/39) of invasive NTPn, respectively. Carriage NTPn were slightly less diverse [Simpson’s diversity index (D)=0.92] compared to invasive NTPn [D=0.97]. Sixty-seven per cent (92/137) of carriage NTPn belonged to a lineage exclusive to NTPn strains compared to 23 % (9/39) of invasive NTPn. We identified 293 and 275 genes that were significantly associated with carriage and invasive NTPn, respectively. NTPn isolates detected in carriage differed from those causing invasive disease, which may explain their success in colonisation or in causing invasive disease.
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Affiliation(s)
- Thabo Mohale
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa.,Clinical Microbiology and Infectious Diseases, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Nicole Wolter
- Clinical Microbiology and Infectious Diseases, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.,Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa
| | - Mushal Allam
- Sequencing Core Facility, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa
| | - Susan A Nzenze
- Department of Science and Technology/National Research Foundation: Vaccine Preventable Diseases Research Chair, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.,Medical Research Council: Respiratory and Meningeal Pathogens Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Shabir A Madhi
- Department of Science and Technology/National Research Foundation: Vaccine Preventable Diseases Research Chair, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.,Medical Research Council: Respiratory and Meningeal Pathogens Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Mignon du Plessis
- Clinical Microbiology and Infectious Diseases, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.,Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa
| | - Anne von Gottberg
- Clinical Microbiology and Infectious Diseases, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.,Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa
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16
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Neal EFG, Nguyen C, Ratu FT, Matanitobua S, Dunne EM, Reyburn R, Kama M, Devi R, Jenkins KM, Tikoduadua L, Kado J, Rafai E, Satzke C, Mulholland EK, Russell FM. A Comparison of Pneumococcal Nasopharyngeal Carriage in Very Young Fijian Infants Born by Vaginal or Cesarean Delivery. JAMA Netw Open 2019; 2:e1913650. [PMID: 31626319 PMCID: PMC6813584 DOI: 10.1001/jamanetworkopen.2019.13650] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
IMPORTANCE Pneumococcal nasopharyngeal carriage is a prerequisite for pneumococcal disease. The main transmission route is from toddlers, who commonly carry pneumococci. However, neonatal pneumococcal disease case reports suggest that vertical pneumococcal transmission may also occur. OBJECTIVE To describe and compare pneumococcal nasopharyngeal carriage and density by infant mode of delivery in young Fijian infants. DESIGN, SETTING, AND PARTICIPANTS Annual cross-sectional surveys were performed in Suva, Fiji, before the introduction of 10-valent pneumococcal conjugate vaccine (PCV10), from September 14 to December 20, 2012, and after PCV10 was introduced, from July 11 to November 19, 2013; July 15 to December 9, 2014; and August 13 to November 19, 2015. Caregivers of 2006 infants aged 5 to 8 weeks participated in the surveys. Statistical analysis was performed from May 24, 2018, to August 12, 2019. EXPOSURES Caregivers provided data on infant mode of delivery and demographics via interviewer-led survey. MAIN OUTCOMES AND MEASURES Pneumococci in swab samples were detected and quantified by lytA quantitative polymerase chain reaction with molecular serotyping by microarray. Pneumococci were categorized as PCV10 or non-PCV10 serotypes. RESULTS Of the 2006 infants (976 girls and 1030 boys; mean [SD] age, 6.1 [0.02] weeks]), 1742 (86.8%) were born vaginally and 264 were born by cesarean delivery. Infants delivered vaginally, compared with those born by cesarean delivery, had a higher prevalence of overall pneumococcal nasopharyngeal carriage (470 of 1722 [27.3%; 95% CI, 25.2%-29.4%] vs 47 of 260 [18.1%; 95% CI, 13.6%-23.3%]; P = .002), PCV10 carriage (113 of 1698 [6.7%; 95% CI, 5.5%-7.9%] vs 8 of 256 [3.1%; 95% CI, 1.4%-6.1%]; P = .03), and non-PCV10 carriage (355 of 1698 [20.9%; 95% CI, 19.0%-22.9%] vs 38 of 256 [14.8%; 95% CI, 10.7%-19.8%]; P = .02), and had higher median densities of overall pneumococci (4.9 log10 genome equivalents [GE]/mL [interquartile range, 4.8-5.0 log10 GE/mL] vs 4.5 log10 GE/mL [interquartile range, 4.1-4.6 log10 GE/mL]; P = .01) and non-PCV10 pneumococci (4.9 log10 GE/mL [interquartile range, 4.7-5.0 log10 GE/mL] vs 4.4 log10 GE/mL [interquartile range, 4.0-4.7 log10 GE/mL]; P = .01). Vaginal delivery was associated with overall (adjusted odds ratio, 1.57 [95% CI, 1.10-2.23]; P = .01) and non-PCV10 (adjusted odds ratio, 1.49 [95% CI, 1.01-2.20]; P = .04]) pneumococcal nasopharyngeal carriage. Vaginal delivery was not associated with PCV10 carriage (adjusted odds ratio, 1.67 [95% CI, 0.80-3.51]; P = .17). After adjustment, vaginal delivery was not associated with density. CONCLUSIONS AND RELEVANCE Pneumococcal nasopharyngeal carriage prevalence and density were higher in infants delivered vaginally compared with those delivered by cesarean birth. After adjustment, vaginal delivery was associated with pneumococcal carriage. Differences in carriage by mode of delivery may be due to differential exposure to the vaginal microbiota during delivery and the effect of intrapartum antibiotics during cesarean delivery on the infant microbiome. Our findings also raise the hypothesis that vertical transmission may contribute to pneumococcal acquisition.
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Affiliation(s)
- Eleanor Frances Georgina Neal
- Infection and Immunity, Murdoch Children’s Research Institute, Royal Children’s Hospital, Parkville, Victoria, Australia
- Department of Paediatrics, The University of Melbourne, Parkville, Victoria, Australia
- Centre for International Child Health, Department of Paediatrics, The University of Melbourne, Parkville, Victoria, Australia
| | - Cattram Nguyen
- Infection and Immunity, Murdoch Children’s Research Institute, Royal Children’s Hospital, Parkville, Victoria, Australia
- Department of Paediatrics, The University of Melbourne, Parkville, Victoria, Australia
| | | | | | - Eileen Margaret Dunne
- Infection and Immunity, Murdoch Children’s Research Institute, Royal Children’s Hospital, Parkville, Victoria, Australia
- Department of Paediatrics, The University of Melbourne, Parkville, Victoria, Australia
| | - Rita Reyburn
- Infection and Immunity, Murdoch Children’s Research Institute, Royal Children’s Hospital, Parkville, Victoria, Australia
| | - Mike Kama
- Ministry of Health and Medical Services, Suva, Fiji
| | - Rachel Devi
- Ministry of Health and Medical Services, Suva, Fiji
| | | | | | - Joseph Kado
- College of Medicine Nursing and Health Sciences, Fiji National University, Suva, Fiji
- Telethon Kids Institute, University of Western Australia, Nedlands, Western Australia, Australia
| | - Eric Rafai
- Ministry of Health and Medical Services, Suva, Fiji
| | - Catherine Satzke
- Infection and Immunity, Murdoch Children’s Research Institute, Royal Children’s Hospital, Parkville, Victoria, Australia
- Department of Paediatrics, The University of Melbourne, Parkville, Victoria, Australia
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Parkville, Victoria, Australia
| | - Edward Kim Mulholland
- Infection and Immunity, Murdoch Children’s Research Institute, Royal Children’s Hospital, Parkville, Victoria, Australia
- Department of Paediatrics, The University of Melbourne, Parkville, Victoria, Australia
- Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Fiona Mary Russell
- Infection and Immunity, Murdoch Children’s Research Institute, Royal Children’s Hospital, Parkville, Victoria, Australia
- Department of Paediatrics, The University of Melbourne, Parkville, Victoria, Australia
- Centre for International Child Health, Department of Paediatrics, The University of Melbourne, Parkville, Victoria, Australia
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17
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Murad C, Dunne EM, Sudigdoadi S, Fadlyana E, Tarigan R, Pell CL, Watts E, Nguyen CD, Satzke C, Hinds J, Dewi MM, Dhamayanti M, Sekarwana N, Rusmil K, Mulholland EK, Kartasasmita C. Pneumococcal carriage, density, and co-colonization dynamics: A longitudinal study in Indonesian infants. Int J Infect Dis 2019; 86:73-81. [DOI: 10.1016/j.ijid.2019.06.024] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Revised: 06/19/2019] [Accepted: 06/20/2019] [Indexed: 02/06/2023] Open
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18
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Takeuchi N, Ohkusu M, Wada N, Kurosawa S, Miyabe A, Yamaguchi M, Nahm MH, Ishiwada N. Molecular typing, antibiotic susceptibility, and biofilm production in nonencapsulated Streptococcus pneumoniae isolated from children in Japan. J Infect Chemother 2019; 25:750-757. [PMID: 31235348 DOI: 10.1016/j.jiac.2019.02.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Revised: 02/04/2019] [Accepted: 02/10/2019] [Indexed: 10/26/2022]
Abstract
The prevalence of nonencapsulated Streptococcus pneumoniae (NESp) has increased with the introduction of pneumococcal conjugate vaccines in children; however, the bacteriological characteristics of NESp have not been sufficiently clarified. In this study, NESp strains isolated from the nasopharyngeal carriage of children from four nursery schools in Japan were analyzed for molecular type, antibiotic susceptibility, and biofilm productivity. A total of 152 putative S. pneumoniae strains were identified by optochin-susceptibility analysis, of which 21 were not serotypeable by slide agglutination, quellung reaction, or multiplex PCR. Among these 21 strains, three were lytA-negative and, therefore, not S. pneumoniae. The remaining 18 strains were positive for lytA, ply, pspK, and bile solubility and were confirmed as NESp. Therefore, the isolation rate of NESp in the S. pneumoniae strains in this study was 12.0% (18/149). Molecular-typing analyses classified five strains as two existing sequence types (STs; ST7502 and ST7786), and 13 strains formed four novel STs. Horizontal spread was suspected, because strains with the same ST were often isolated from the same nursery school. The NESp isolates were generally susceptible to most antimicrobials, with the exception of macrolides; however, all isolates possessed more than one abnormal penicillin-binding protein gene. Furthermore, NESp strains were more effective than encapsulated counterparts at forming biofilms, which showed obvious differences in morphology. These data indicated that NESp strains should be continuously monitored as emerging respiratory pathogens.
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Affiliation(s)
- Noriko Takeuchi
- Department of Infectious Diseases, Medical Mycology Research Center, Chiba University, Chiba, Japan.
| | - Misako Ohkusu
- Department of Infectious Diseases, Medical Mycology Research Center, Chiba University, Chiba, Japan
| | | | - Satoko Kurosawa
- Kurosawa Children's and Internal Medicine Clinic, Tokyo, Japan
| | - Akiko Miyabe
- Division of Laboratory Medicine and Clinical Genetics, Chiba University Hospital, Chiba, Japan
| | | | - Moon H Nahm
- Division of Pulmonary, Allergy & Critical Care Medicine, Department of Medicine, The University of Alabama at Birmingham, Birmingham, AL, USA
| | - Naruhiko Ishiwada
- Department of Infectious Diseases, Medical Mycology Research Center, Chiba University, Chiba, Japan
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19
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van Tonder AJ, Gladstone RA, Lo SW, Nahm MH, du Plessis M, Cornick J, Kwambana-Adams B, Madhi SA, Hawkins PA, Benisty R, Dagan R, Everett D, Antonio M, Klugman KP, von Gottberg A, Breiman RF, McGee L, Bentley SD. Putative novel cps loci in a large global collection of pneumococci. Microb Genom 2019; 5. [PMID: 31184299 PMCID: PMC6700660 DOI: 10.1099/mgen.0.000274] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The pneumococcus produces a polysaccharide capsule, encoded by the cps locus, that provides protection against phagocytosis and determines serotype. Nearly 100 serotypes have been identified with new serotypes still being discovered, especially in previously understudied regions. Here we present an analysis of the cps loci of more than 18 000 genomes from the Global Pneumococcal Sequencing (GPS) project with the aim of identifying novel cps loci with the potential to produce previously unrecognized capsule structures. Serotypes were assigned using whole genome sequence data and 66 of the approximately 100 known serotypes were included in the final dataset. Closer examination of each serotype’s sequences identified nine putative novel cps loci (9X, 11X, 16X, 18X1, 18X2, 18X3, 29X, 33X and 36X) found in ~2.6 % of the genomes. The large number and global distribution of GPS genomes provided an unprecedented opportunity to identify novel cps loci and consider their phylogenetic and geographical distribution. Nine putative novel cps loci were identified and examples of each will undergo subsequent structural and immunological analysis.
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Affiliation(s)
- Andries J van Tonder
- Parasites and Microbes, The Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Rebecca A Gladstone
- Parasites and Microbes, The Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Stephanie W Lo
- Parasites and Microbes, The Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Moon H Nahm
- Division of Pulmonary Medicine, Departments of Medicine and Microbiology, The University of Alabama at Birmingham, Birmingham, AL, USA
| | - Mignon du Plessis
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, Johannesburg, South Africa.,School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | | | | | - Shabir A Madhi
- Medical Research Council: Respiratory and Meningeal Pathogens Research Unit, University of the Witwatersrand, Johannesburg, South Africa
| | - Paulina A Hawkins
- Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Rachel Benisty
- Faculty of Health Sciences, Ben-Gurion University of the Negev, Beersheeba, Beer-Sheva, Israel
| | - Ron Dagan
- Faculty of Health Sciences, Ben-Gurion University of the Negev, Beersheeba, Beer-Sheva, Israel
| | - Dean Everett
- Queens Research Institute, University of Edinburgh, Edinburgh EH8 9YL, UK
| | - Martin Antonio
- Vaccines and Immunity Theme, MRC Unit, Banjul, The Gambia
| | - Keith P Klugman
- Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Anne von Gottberg
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, Johannesburg, South Africa.,School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Robert F Breiman
- Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA.,Queens Research Institute, University of Edinburgh, Edinburgh EH8 9YL, UK
| | - Lesley McGee
- Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Stephen D Bentley
- Parasites and Microbes, The Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK.,Emory Global Health Institute, Emory University, Atlanta, GA, USA
| | -
- https://www.pneumogen.net/gps/
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20
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von Mollendorf C, Dunne EM, La Vincente S, Ulziibayar M, Suuri B, Luvsantseren D, Narangerel D, Ortika BD, Pell CL, Nation ML, Alamrousi A, Hinds J, Demberelsuren S, Nguyen C, Mungun T, Mulholland EK, Satzke C. Pneumococcal carriage in children in Ulaanbaatar, Mongolia before and one year after the introduction of the 13-valent pneumococcal conjugate vaccine. Vaccine 2019; 37:4068-4075. [PMID: 31174939 DOI: 10.1016/j.vaccine.2019.05.078] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Revised: 05/24/2019] [Accepted: 05/26/2019] [Indexed: 11/27/2022]
Abstract
BACKGROUND Nasopharyngeal carriage of Streptococcus pneumoniae precedes disease, is the source of pneumococcal community spread, and the mechanism for herd protection provided by pneumococcal conjugate vaccines (PCVs). There are few PCV impact studies in low- and middle-income countries, particularly in Asia. In 2016, Mongolia introduced the 13-valent PCV (PCV13) in a phased manner using a 2 + 1 schedule, with catch-up. We aimed to assess the impact of PCV13 introduction on nasopharyngeal pneumococcal carriage and density in children in Mongolia. METHODS We conducted two cross-sectional carriage surveys (pre- and one year post-PCV) at community health clinics in two districts of the capital city, Ulaanbaatar in both May-July 2015 and 2017. The study analysis included 961 children too young to be vaccinated (5-8 weeks old) and 989 children eligible for vaccination (12-23 months old). Pneumococci were detected by quantitative real-time PCR and molecular serotyping performed using DNA microarray. FINDINGS One year post-PCV introduction, PCV13 serotype carriage reduced by 52% in 12-23 month olds (adjusted prevalence ratio [aPR] 0.48 [95% confidence interval [CI] 0.39-0.59]), with evidence of non-PCV13 serotype replacement (aPR 1.55 [95% CI 1.30-1.85]), compared with the pre-PCV period. In 5-8 week olds, PCV13 serotype carriage reduced by 51% (aPR 0.49 [95% CI 0.33-0.73]) with no significant change in non-PCV13 serotype carriage (aPR 1.10 [95% CI 0.83-1.46]). An increase was observed in both PCV13 and non-PCV13 pneumococcal density post-PCV introduction. Antimicrobial resistance (AMR) genes were common, with 82.3% of samples containing at least one of the 10 AMR genes assessed. CONCLUSION This study demonstrates substantive PCV13 impact on pneumococcal carriage one year post-vaccine introduction in Mongolia. The reductions in PCV13 serotype carriage are likely to result in reductions in pneumococcal disease including indirect effects. Increases in non-PCV13 serotypes require further monitoring.
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Affiliation(s)
- Claire von Mollendorf
- New Vaccines, Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, Australia; Department of Paediatrics, The University of Melbourne, Parkville, Australia.
| | - Eileen M Dunne
- New Vaccines, Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, Australia; Department of Paediatrics, The University of Melbourne, Parkville, Australia
| | - Sophie La Vincente
- New Vaccines, Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, Australia
| | - Mukhchuluun Ulziibayar
- National Center of Communicable Diseases (NCCD), Ministry of Health, Ulaanbaatar, Mongolia
| | - Bujinlkham Suuri
- National Center of Communicable Diseases (NCCD), Ministry of Health, Ulaanbaatar, Mongolia
| | | | | | - Belinda D Ortika
- New Vaccines, Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, Australia
| | - Casey L Pell
- New Vaccines, Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, Australia
| | - Monica L Nation
- New Vaccines, Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, Australia
| | - Ahmed Alamrousi
- New Vaccines, Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, Australia
| | - Jason Hinds
- Institute for Infection and Immunity, St George's, University of London, London, UK; BUGS Bioscience, London Bioscience Innovation Centre, London, UK
| | | | - Cattram Nguyen
- New Vaccines, Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, Australia; Department of Paediatrics, The University of Melbourne, Parkville, Australia
| | - Tuya Mungun
- National Center of Communicable Diseases (NCCD), Ministry of Health, Ulaanbaatar, Mongolia
| | - E Kim Mulholland
- New Vaccines, Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, Australia; Department of Paediatrics, The University of Melbourne, Parkville, Australia; Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, UK
| | - Catherine Satzke
- New Vaccines, Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, Australia; Department of Paediatrics, The University of Melbourne, Parkville, Australia; Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Parkville, Australia
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21
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Negash AA, Asrat D, Abebe W, Hailemariam T, Gebre M, Verhaegen J, Aseffa A, Vaneechoutte M. Pneumococcal Carriage, Serotype Distribution, and Risk Factors in Children With Community-Acquired Pneumonia, 5 Years After Introduction of the 10-Valent Pneumococcal Conjugate Vaccine in Ethiopia. Open Forum Infect Dis 2019; 6:ofz259. [PMID: 31263735 PMCID: PMC6592415 DOI: 10.1093/ofid/ofz259] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Accepted: 05/30/2019] [Indexed: 12/18/2022] Open
Abstract
Background There is a scarcity of data on pneumococcal serotypes carried by children in Ethiopia. We studied pneumococcal nasopharyngeal carriage rate, serotypes, and risk factors among children with community acquired pneumonia (CAP). Methods A prospective observational cohort study was performed in children with CAP, aged 0–15 years, in 2 pediatric emergency departments in Addis Ababa, Ethiopia. Nasopharyngeal swabs were cultured, and serotypes of Streptococcus pneumoniae were determined by sequencing the cpsB gene and by the Quellung reaction. Risk factors were analyzed by using binary logistic regression. Results Nasopharyngeal swabs were collected from 362 children with CAP. Pneumococcal carriage rate was 21.5% (78 of 362). The most common serotypes were 19A (27%), 16F (8.5%), and 6A (4.9%). In addition, 8.5% of the pneumococcal isolates were nontypeable. In bivariate analysis, children with a parent that smokes were more likely to carry pneumococci (crude odds ratio, 3.9; 95% confidence interval [CI], 1.2–12.3; P = .023) than those with parents that do not smoke. In multivariable analysis, living in a house with ≥2 rooms (adjusted odds ratio [AOR], 0.48; 95% CI, 0.28–0.82; P = .007) and vaccination with ≥2 doses of 10-valent pneumococcal conjugate vaccine (PCV10) (AOR, 0.37; 95% CI, 0.15–0.92; P = .033) were protective of pneumococcal carriage. Conclusions Five years after introduction of PCV10 in Ethiopia, the vaccine-related serotype 19A was predominant in the nasopharynx of children with CAP. Continued evaluation of the direct and indirect impact of PCV10 on pneumococcal serotype distribution in Ethiopia is warranted.
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Affiliation(s)
- Abel Abera Negash
- Armauer Hansen Research Institute, Addis Ababa, Ethiopia.,Laboratory Bacteriology Research, Department of Diagnostic Sciences, Faculty of Medicine and Health Sciences, Ghent University, Belgium
| | - Daniel Asrat
- Department of Microbiology and Immunology, School of Medicine, Addis Ababa University, Ethiopia
| | - Workeabeba Abebe
- Department of Pediatrics and Child Health, School of Medicine, Addis Ababa University, Ethiopia
| | - Tewodros Hailemariam
- Department of Pediatrics and Child Health, Yekatit 12 Medical College, Addis Ababa, Ethiopia
| | - Meseret Gebre
- Armauer Hansen Research Institute, Addis Ababa, Ethiopia
| | - Jan Verhaegen
- Pneumococcal Reference Laboratory, Universitair Ziekenhuis, Katholieke Universiteit Leuven, Belgium
| | - Abraham Aseffa
- Armauer Hansen Research Institute, Addis Ababa, Ethiopia
| | - Mario Vaneechoutte
- Laboratory Bacteriology Research, Department of Diagnostic Sciences, Faculty of Medicine and Health Sciences, Ghent University, Belgium
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22
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Rendueles O, de Sousa JAM, Bernheim A, Touchon M, Rocha EPC. Genetic exchanges are more frequent in bacteria encoding capsules. PLoS Genet 2018; 14:e1007862. [PMID: 30576310 PMCID: PMC6322790 DOI: 10.1371/journal.pgen.1007862] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Revised: 01/07/2019] [Accepted: 11/29/2018] [Indexed: 12/12/2022] Open
Abstract
Capsules allow bacteria to colonize novel environments, to withstand numerous stresses, and to resist antibiotics. Yet, even though genetic exchanges with other cells should be adaptive under such circumstances, it has been suggested that capsules lower the rates of homologous recombination and horizontal gene transfer. We analysed over one hundred pan-genomes and thousands of bacterial genomes for the evidence of an association between genetic exchanges (or lack thereof) and the presence of a capsule system. We found that bacteria encoding capsules have larger pan-genomes, higher rates of horizontal gene transfer, and higher rates of homologous recombination in their core genomes. Accordingly, genomes encoding capsules have more plasmids, conjugative elements, transposases, prophages, and integrons. Furthermore, capsular loci are frequent in plasmids, and can be found in prophages. These results are valid for Bacteria, independently of their ability to be naturally transformable. Since we have shown previously that capsules are commonly present in nosocomial pathogens, we analysed their co-occurrence with antibiotic resistance genes. Genomes encoding capsules have more antibiotic resistance genes, especially those encoding efflux pumps, and they constitute the majority of the most worrisome nosocomial bacteria. We conclude that bacteria with capsule systems are more genetically diverse and have fast-evolving gene repertoires, which may further contribute to their success in colonizing novel niches such as humans under antibiotic therapy. Previous works showed that bacteria encoding capsules are better colonizers and are dominant in most environments suggesting a positive role for capsules in the genetic diversification of bacteria. Yet, it has been repeatedly suggested, based almost exclusively studies in few model species, that such bacteria are less diverse and engage in fewer genetic exchanges. Here, we reverse the current paradigm and show that bacteria encoding capsules have larger and more diverse gene repertoires, which change faster by horizontal gene transfer and recombination. Our study alters the traditional view of the capsule as a barrier to gene flow and raises novel questions about the role of capsules in bacterial adaptation.
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Affiliation(s)
- Olaya Rendueles
- Microbial Evolutionary Genomics, Institut Pasteur, Paris, France
- UMR 3525, CNRS, Paris, France
- * E-mail:
| | - Jorge A. Moura de Sousa
- Microbial Evolutionary Genomics, Institut Pasteur, Paris, France
- UMR 3525, CNRS, Paris, France
| | - Aude Bernheim
- Microbial Evolutionary Genomics, Institut Pasteur, Paris, France
- UMR 3525, CNRS, Paris, France
| | - Marie Touchon
- Microbial Evolutionary Genomics, Institut Pasteur, Paris, France
- UMR 3525, CNRS, Paris, France
| | - Eduardo P. C. Rocha
- Microbial Evolutionary Genomics, Institut Pasteur, Paris, France
- UMR 3525, CNRS, Paris, France
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23
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Satzke C, Dunne EM, Choummanivong M, Ortika BD, Neal EFG, Pell CL, Nation ML, Fox KK, Nguyen CD, Gould KA, Hinds J, Chanthongthip A, Xeuatvongsa A, Mulholland EK, Sychareun V, Russell FM. Pneumococcal carriage in vaccine-eligible children and unvaccinated infants in Lao PDR two years following the introduction of the 13-valent pneumococcal conjugate vaccine. Vaccine 2018; 37:296-305. [PMID: 30502068 DOI: 10.1016/j.vaccine.2018.10.077] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Revised: 10/11/2018] [Accepted: 10/23/2018] [Indexed: 01/27/2023]
Abstract
Pneumococcal carriage is a prerequisite for disease, and underpins herd protection provided by pneumococcal conjugate vaccines (PCVs). There are few data on the impact of PCVs in lower income settings, particularly in Asia. In 2013, the Lao People's Democratic Republic (Lao PDR) introduced 13-valent PCV (PCV13) as a 3 + 0 schedule (doses at 6, 10 and 14 weeks of age) with limited catch-up vaccination. We conducted two cross-sectional carriage surveys (pre- and two years post-PCV) to assess the impact of PCV13 on nasopharyngeal pneumococcal carriage in 5-8 week old infants (n = 1000) and 12-23 month old children (n = 1010). Pneumococci were detected by quantitative real-time PCR, and molecular serotyping was performed using DNA microarray. Post PCV13, there was a 23% relative reduction in PCV13-type carriage in children aged 12-23 months (adjusted prevalence ratio [aPR] 0.77 [0.61-0.96]), and no significant change in non-PCV13 serotype carriage (aPR 1.11 [0.89-1.38]). In infants too young to be vaccinated, there was no significant change in carriage of PCV13 serotypes (aPR 0.74 [0.43-1.27]) or non-PCV13 serotypes (aPR 1.29 [0.85-1.96]), although trends were suggestive of indirect effects. Over 70% of pneumococcal-positive samples contained at least one antimicrobial resistance gene, which were more common in PCV13 serotypes (p < 0.001). In 12-23 month old children, pneumococcal density of both PCV13 serotypes and non-PCV13 serotypes was higher in PCV13-vaccinated compared with undervaccinated children (p = 0.004 and p < 0.001, respectively). This study provides evidence of PCV13 impact on carriage in a population without prior PCV7 utilisation, and provides important data from a lower-middle income setting in Asia. The reductions in PCV13 serotype carriage in vaccine-eligible children are likely to result in reductions in pneumococcal transmission and disease in Lao PDR.
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Affiliation(s)
- Catherine Satzke
- Pneumococcal Research, Murdoch Children's Research Institute, Royal Children's Hospital, Flemington Road, Parkville, Australia; Department of Paediatrics, The University of Melbourne, Parkville, Australia; Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Parkville, Australia.
| | - Eileen M Dunne
- Pneumococcal Research, Murdoch Children's Research Institute, Royal Children's Hospital, Flemington Road, Parkville, Australia; Department of Paediatrics, The University of Melbourne, Parkville, Australia
| | | | - Belinda D Ortika
- Pneumococcal Research, Murdoch Children's Research Institute, Royal Children's Hospital, Flemington Road, Parkville, Australia
| | - Eleanor F G Neal
- Pneumococcal Research, Murdoch Children's Research Institute, Royal Children's Hospital, Flemington Road, Parkville, Australia; Department of Paediatrics, The University of Melbourne, Parkville, Australia; Centre for International Child Health, Department of Paediatrics, The University of Melbourne, Parkville, Australia
| | - Casey L Pell
- Pneumococcal Research, Murdoch Children's Research Institute, Royal Children's Hospital, Flemington Road, Parkville, Australia
| | - Monica L Nation
- Pneumococcal Research, Murdoch Children's Research Institute, Royal Children's Hospital, Flemington Road, Parkville, Australia
| | - Kimberley K Fox
- Expanded Programme on Immunization, World Health Organization Regional Office for the Western Pacific, Manila, Philippines
| | - Cattram D Nguyen
- Pneumococcal Research, Murdoch Children's Research Institute, Royal Children's Hospital, Flemington Road, Parkville, Australia; Department of Paediatrics, The University of Melbourne, Parkville, Australia
| | - Katherine A Gould
- Institute for Infection and Immunity, St. George's, University of London, London, UK; BUGS Bioscience, London Bioscience Innovation Centre, London, UK
| | - Jason Hinds
- Institute for Infection and Immunity, St. George's, University of London, London, UK; BUGS Bioscience, London Bioscience Innovation Centre, London, UK
| | - Anisone Chanthongthip
- Laos-Oxford-Mahosot Hospital Wellcome Trust Research Unit, Vientiane, Lao People's Democratic Republic
| | | | - E Kim Mulholland
- Pneumococcal Research, Murdoch Children's Research Institute, Royal Children's Hospital, Flemington Road, Parkville, Australia; Department of Paediatrics, The University of Melbourne, Parkville, Australia; Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, UK
| | | | - Fiona M Russell
- Pneumococcal Research, Murdoch Children's Research Institute, Royal Children's Hospital, Flemington Road, Parkville, Australia; Department of Paediatrics, The University of Melbourne, Parkville, Australia; Centre for International Child Health, Department of Paediatrics, The University of Melbourne, Parkville, Australia
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24
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The Role of Pneumococcal Virulence Factors in Ocular Infectious Diseases. Interdiscip Perspect Infect Dis 2018; 2018:2525173. [PMID: 30538741 PMCID: PMC6257906 DOI: 10.1155/2018/2525173] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Accepted: 11/07/2018] [Indexed: 12/24/2022] Open
Abstract
Streptococcus pneumoniae is a gram-positive, facultatively anaerobic pathogen that can cause severe infections such as pneumonia, meningitis, septicemia, and middle ear infections. It is also one of the top pathogens contributing to bacterial keratitis and conjunctivitis. Though two pneumococcal vaccines exist for the prevention of nonocular diseases, they do little to fully prevent ocular infections. This pathogen has several virulence factors that wreak havoc on the conjunctiva, cornea, and intraocular system. Polysaccharide capsule aids in the evasion of host complement system. Pneumolysin (PLY) is a cholesterol-dependent cytolysin that acts as pore-forming toxin. Neuraminidases assist in adherence and colonization by exposing cell surface receptors to the pneumococcus. Zinc metalloproteinases contribute to evasion of the immune system and disease severity. The main purpose of this review is to consolidate the multiple studies that have been conducted on several pneumococcal virulence factors and the role each plays in conjunctivitis, keratitis, and endophthalmitis.
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25
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Manna S, Dunne EM, Ortika BD, Pell CL, Kama M, Russell FM, Mungun T, Mulholland EK, Hinds J, Satzke C. Discovery of a Streptococcus pneumoniae serotype 33F capsular polysaccharide locus that lacks wcjE and contains a wcyO pseudogene. PLoS One 2018; 13:e0206622. [PMID: 30395578 PMCID: PMC6218050 DOI: 10.1371/journal.pone.0206622] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2018] [Accepted: 10/16/2018] [Indexed: 12/25/2022] Open
Abstract
As part of large on-going vaccine impact studies in Fiji and Mongolia, we identified 25/2750 (0.9%) of nasopharyngeal swabs by microarray that were positive for Streptococcus pneumoniae contained pneumococci with a divergent 33F capsular polysaccharide locus (designated ‘33F-1’). We investigated the 33F-1 capsular polysaccharide locus to better understand the genetic variation and its potential impact on serotyping results. Whole genome sequencing was conducted on ten 33F-1 pneumococcal isolates. Initially, sequence reads were used for molecular serotyping by PneumoCaT. Phenotypic typing of 33F-1 isolates was then performed using the Quellung reaction and latex agglutination. Genome assemblies were used in phylogenetic analyses of each gene in the capsular locus to investigate genetic divergence. All ten pneumococcal isolates with the 33F-1 cps locus typed as 33F by Quellung and latex agglutination. Unlike the reference 33F capsule locus sequence, DNA microarray and PneumoCaT analyses found that 33F-1 pneumococci lack the wcjE gene, and instead contain wcyO with a frameshift mutation. Phylogenetic analyses found the wzg, wzh, wzd, wze, wchA, wciG and glf genes in the 33F-1 cps locus had higher DNA sequence similarity to homologues from other serotypes than to the 33F reference sequence. We have discovered a novel genetic variant of serotype 33F, which lacks wcjE and contains a wcyO pseudogene. This finding adds to the understanding of molecular epidemiology of pneumococcal serotype diversity, which is poorly understood in low and middle-income countries.
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Affiliation(s)
- Sam Manna
- Pneumococcal Research, Murdoch Children’s Research Institute, Royal Children's Hospital, Parkville, VIC, Australia
- * E-mail:
| | - Eileen M. Dunne
- Pneumococcal Research, Murdoch Children’s Research Institute, Royal Children's Hospital, Parkville, VIC, Australia
- Department of Paediatrics, The University of Melbourne, Parkville, VIC, Australia
| | - Belinda D. Ortika
- Pneumococcal Research, Murdoch Children’s Research Institute, Royal Children's Hospital, Parkville, VIC, Australia
| | - Casey L. Pell
- Pneumococcal Research, Murdoch Children’s Research Institute, Royal Children's Hospital, Parkville, VIC, Australia
| | - Mike Kama
- Ministry of Health and Medical Services, Suva, Fiji
| | - Fiona M. Russell
- Department of Paediatrics, The University of Melbourne, Parkville, VIC, Australia
- Centre for International Child Health, Royal Children’s Hospital, Melbourne, Australia
| | - Tuya Mungun
- National Center for Communicable Diseases, Ministry of Health, Ulaanbaatar, Mongolia
| | - E. Kim Mulholland
- Pneumococcal Research, Murdoch Children’s Research Institute, Royal Children's Hospital, Parkville, VIC, Australia
- Department of Paediatrics, The University of Melbourne, Parkville, VIC, Australia
- Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Jason Hinds
- Institute for Infection and Immunity, St. George's, University of London, London, United Kingdom
- BUGS Bioscience, London Bioscience Innovation Centre, London, United Kingdom
| | - Catherine Satzke
- Pneumococcal Research, Murdoch Children’s Research Institute, Royal Children's Hospital, Parkville, VIC, Australia
- Department of Paediatrics, The University of Melbourne, Parkville, VIC, Australia
- Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Parkville, VIC, Australia
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26
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Molecular characterisation of multidrug-resistant pneumococcal clones colonising healthy children in Mérida, Venezuela. J Glob Antimicrob Resist 2018; 14:45-50. [DOI: 10.1016/j.jgar.2018.02.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Revised: 01/25/2018] [Accepted: 02/05/2018] [Indexed: 11/18/2022] Open
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27
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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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28
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Dunne EM, Murad C, Sudigdoadi S, Fadlyana E, Tarigan R, Indriyani SAK, Pell CL, Watts E, Satzke C, Hinds J, Dewi NE, Yani FF, Rusmil K, Mulholland EK, Kartasasmita C. Carriage of Streptococcus pneumoniae, Haemophilus influenzae, Moraxella catarrhalis, and Staphylococcus aureus in Indonesian children: A cross-sectional study. PLoS One 2018; 13:e0195098. [PMID: 29649269 PMCID: PMC5896896 DOI: 10.1371/journal.pone.0195098] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Accepted: 03/18/2018] [Indexed: 11/30/2022] Open
Abstract
Streptococcus pneumoniae is an important cause of infection and commonly colonizes the nasopharynx of young children, along with other potentially pathogenic bacteria. The objectives of this study were to estimate the carriage prevalence of S. pneumoniae, Haemophilus influenzae, Moraxella catarrhalis, and Staphylococcus aureus in young children in Indonesia, and to examine interactions between these bacterial species. 302 healthy children aged 12–24 months were enrolled in community health centers in the Bandung, Central Lombok, and Padang regions. Nasopharyngeal swabs were collected and stored according to World Health Organization recommendations, and bacterial species detected by qPCR. Pneumococcal serotyping was conducted by microarray and latex agglutination/Quellung. Overall carriage prevalence was 49.5% for S. pneumoniae, 27.5% for H. influenzae, 42.7% for M. catarrhalis, and 7.3% for S. aureus. Prevalence of M. catarrhalis and S. pneumoniae, as well as pneumococcal serotype distribution, varied by region. Positive associations were observed for S. pneumoniae and M. catarrhalis (OR 3.07 [95%CI 1.91–4.94]), and H. influenzae and M. catarrhalis (OR 2.34 [95%CI 1.40–3.91]), and a negative association was found between M. catarrhalis and S. aureus (OR 0.06 [95%CI 0.01–0.43]). Densities of S. pneumoniae, H. influenzae, and M. catarrhalis were positively correlated when two of these species were present. Prior to pneumococcal vaccine introduction, pneumococcal carriage prevalence and serotype distribution varies among children living in different regions of Indonesia. Positive associations in both carriage and density identified among S. pneumoniae, H. influenzae, and M. catarrhalis suggest a synergistic relationship among these species with potential clinical implications.
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Affiliation(s)
- Eileen M. Dunne
- Pneumococcal Research, Murdoch Children’s Research Institute, Parkville, Victoria, Australia
- Department of Paediatrics, The University of Melbourne, Parkville, Victoria, Australia
| | - Chrysanti Murad
- Department of Biomedical Sciences, Division of Microbiology, Faculty of Medicine, Universitas Padjadjaran, Bandung, West Java, Indonesia
| | - Sunaryati Sudigdoadi
- Department of Biomedical Sciences, Division of Microbiology, Faculty of Medicine, Universitas Padjadjaran, Bandung, West Java, Indonesia
| | - Eddy Fadlyana
- Department of Child Health, Universitas Padjadjaran/Hasan Sadikin General Hospital, Bandung, West Java, Indonesia
| | - Rodman Tarigan
- Department of Child Health, Universitas Padjadjaran/Hasan Sadikin General Hospital, Bandung, West Java, Indonesia
| | | | - Casey L. Pell
- Pneumococcal Research, Murdoch Children’s Research Institute, Parkville, Victoria, Australia
| | - Emma Watts
- Pneumococcal Research, Murdoch Children’s Research Institute, Parkville, Victoria, Australia
| | - Catherine Satzke
- Pneumococcal Research, Murdoch Children’s Research Institute, Parkville, Victoria, Australia
- Department of Paediatrics, The University of Melbourne, Parkville, Victoria, Australia
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Parkville, Victoria, Australia
| | - Jason Hinds
- Institute for Infection and Immunity, St. George’s University of London, London, United Kingdom
- BUGS Bioscience, London Bioscience Innovation Centre, London, United Kingdom
| | - Nurhandini Eka Dewi
- District Health Office of Central Lombok, Praya, West Nusa Tenggara, Indonesia
| | - Finny Fitry Yani
- Department of Child Health, Universitas Andalas, Padang, West Sumatra, Indonesia
| | - Kusnandi Rusmil
- Department of Child Health, Universitas Padjadjaran/Hasan Sadikin General Hospital, Bandung, West Java, Indonesia
| | - E. Kim Mulholland
- Department of Paediatrics, The University of Melbourne, Parkville, Victoria, Australia
- Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Cissy Kartasasmita
- Department of Child Health, Universitas Padjadjaran/Hasan Sadikin General Hospital, Bandung, West Java, Indonesia
- * E-mail:
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29
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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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30
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Gene Acquisition by a Distinct Phyletic Group within Streptococcus pneumoniae Promotes Adhesion to the Ocular Epithelium. mSphere 2017; 2:mSphere00213-17. [PMID: 29085912 PMCID: PMC5656748 DOI: 10.1128/msphere.00213-17] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Accepted: 09/14/2017] [Indexed: 11/20/2022] Open
Abstract
Streptococcus pneumoniae (pneumococcus) displays broad tissue tropism and infects multiple body sites in the human host. However, infections of the conjunctiva are limited to strains within a distinct phyletic group with multilocus sequence types ST448, ST344, ST1186, ST1270, and ST2315. In this study, we sequenced the genomes of six pneumococcal strains isolated from eye infections. The conjunctivitis isolates are grouped in a distinct phyletic group together with a subset of nasopharyngeal isolates. The keratitis (infection of the cornea) and endophthalmitis (infection of the vitreous body) isolates are grouped with the remainder of pneumococcal strains. Phenotypic characterization is consistent with morphological differences associated with the distinct phyletic group. Specifically, isolates from the distinct phyletic group form aggregates in planktonic cultures and chain-like structures in biofilms grown on abiotic surfaces. To begin to investigate the association between genotype and epidemiology, we focused on a predicted surface-exposed adhesin (SspB) encoded exclusively by this distinct phyletic group. Phylogenetic analysis of the gene encoding SspB in the context of a streptococcal species tree suggests that sspB was acquired by lateral gene transfer from Streptococcus suis. Furthermore, an sspB deletion mutant displays decreased adherence to cultured cells from the ocular epithelium compared to the isogenic wild-type and complemented strains. Together these findings suggest that acquisition of genes from outside the species has contributed to pneumococcal tissue tropism by enhancing the ability of a subset of strains to infect the ocular epithelium causing conjunctivitis. IMPORTANCE Changes in the gene content of pathogens can modify their ability to colonize and/or survive in different body sites in the human host. In this study, we investigate a gene acquisition event and its role in the pathogenesis of Streptococccus pneumoniae (pneumococcus). Our findings suggest that the gene encoding the predicted surface protein SspB has been transferred from Streptococcus suis (a distantly related streptococcal species) into a distinct set of pneumococcal strains. This group of strains distinguishes itself from the remainder of pneumococcal strains by extensive differences in genomic composition and by the ability to cause conjunctivitis. We find that the presence of sspB increases adherence of pneumococcus to the ocular epithelium. Thus, our data support the hypothesis that a subset of pneumococcal strains has gained genes from neighboring species that enhance their ability to colonize the epithelium of the eye, thus expanding into a new niche.
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31
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Mostowy RJ, Croucher NJ, De Maio N, Chewapreecha C, Salter SJ, Turner P, Aanensen DM, Bentley SD, Didelot X, Fraser C. Pneumococcal Capsule Synthesis Locus cps as Evolutionary Hotspot with Potential to Generate Novel Serotypes by Recombination. Mol Biol Evol 2017; 34:2537-2554. [PMID: 28595308 PMCID: PMC5850285 DOI: 10.1093/molbev/msx173] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Diversity of the polysaccharide capsule in Streptococcus pneumoniae-main surface antigen and the target of the currently used pneumococcal vaccines-constitutes a major obstacle in eliminating pneumococcal disease. Such diversity is genetically encoded by almost 100 variants of the capsule biosynthesis locus, cps. However, the evolutionary dynamics of the capsule remains not fully understood. Here, using genetic data from 4,519 bacterial isolates, we found cps to be an evolutionary hotspot with elevated substitution and recombination rates. These rates were a consequence of relaxed purifying selection and positive, diversifying selection acting at this locus, supporting the hypothesis that the capsule has an increased potential to generate novel diversity compared with the rest of the genome. Diversifying selection was particularly evident in the region of wzd/wze genes, which are known to regulate capsule expression and hence the bacterium's ability to cause disease. Using a novel, capsule-centered approach, we analyzed the evolutionary history of 12 major serogroups. Such analysis revealed their complex diversification scenarios, which were principally driven by recombination with other serogroups and other streptococci. Patterns of recombinational exchanges between serogroups could not be explained by serotype frequency alone, thus pointing to nonrandom associations between co-colonizing serotypes. Finally, we discovered a previously unobserved mosaic serotype 39X, which was confirmed to carry a viable and structurally novel capsule. Adding to previous discoveries of other mosaic capsules in densely sampled collections, these results emphasize the strong adaptive potential of the bacterium by its ability to generate novel antigenic diversity by recombination.
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Affiliation(s)
- Rafał J. Mostowy
- Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, United Kingdom
| | - Nicholas J. Croucher
- Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, United Kingdom
| | - Nicola De Maio
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
- Institute for Emerging Infections, Oxford Martin School, Oxford, United Kingdom
| | - Claire Chewapreecha
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom
- Bioinformatics and Systems Biology Program, School of Bioresources and Technology, King Mongkut’s University of Technology Thonburi, Bangkok, Thailand
| | - Susannah J. Salter
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Paul Turner
- Nuffield Department of Medicine, Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, United Kingdom
- Cambodia-Oxford Medical Research Unit, Angkor Hospital for Children, Siem Reap, Cambodia
| | - David M. Aanensen
- Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, United Kingdom
- Centre for Genomic Pathogen Surveillance, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Stephen D. Bentley
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Xavier Didelot
- Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, United Kingdom
| | - Christophe Fraser
- Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, United Kingdom
- Nuffield Department of Medicine, Li Ka Shing Centre for Health Information and Discovery, Oxford Big Data Institute, University of Oxford, Oxford, United Kingdom
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Current challenges in the accurate identification of Streptococcus pneumoniae and its serogroups/serotypes in the vaccine era. J Microbiol Methods 2017; 141:48-54. [DOI: 10.1016/j.mimet.2017.07.015] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Revised: 07/30/2017] [Accepted: 07/31/2017] [Indexed: 11/21/2022]
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Development of Serotype-Specific PCR Assays for Typing of Haemophilus parasuis Isolates Circulating in Southern China. J Clin Microbiol 2017; 55:3249-3257. [PMID: 28878007 DOI: 10.1128/jcm.00688-17] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2017] [Accepted: 09/01/2017] [Indexed: 11/20/2022] Open
Abstract
The bacterium Haemophilus parasuis is the specific pathogenic cause of Glässer's disease in swine. Fifteen serotypes of H. parasuis have been reported. A method to serotype H. parasuis isolates accurately would help to prevent and control Glässer's disease outbreaks through appropriate vaccination and to understand the epidemiology in specific geographic areas. However, according to traditional serotyping, the rate of nontypeable (NT) strains is 10 to 40%, which gives low accuracy. In the present study, we developed a set of PCR assays that are able to identify all the currently known H. parasuis serotypes, with a detection limit of 5 CFU. This PCR method is particularly useful to distinguish serotype 5 from serotype 12. We then surveyed the serotype prevalence of H. parasuis isolates from southern China using both the traditional indirect hemagglutination (IHA) and current PCR methods. Of the 298 isolates tested, 228 (76.51%) and 281 (94.30%) were serotyped by the IHA and PCR tests, respectively, with a concordance rate of 80.87% (241/298). The most prevalent serotypes obtained by PCR were 4, 5, 12, 13, NT, and 2, and the most prevalent obtained by IHA were NT, 5, 4, 12, 13, and 2. In conclusion, the PCR assays developed in this study provide a rapid and specific method for the molecular serotyping of H. parasuis.
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Kwarteng A, Amuasi J, Annan A, Ahuno S, Opare D, Nagel M, Vinnemeier C, May J, Owusu-Dabo E. Current meningitis outbreak in Ghana: Historical perspectives and the importance of diagnostics. Acta Trop 2017; 169:51-56. [PMID: 28122199 DOI: 10.1016/j.actatropica.2017.01.014] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Revised: 01/14/2017] [Accepted: 01/16/2017] [Indexed: 01/07/2023]
Abstract
Bacterial meningitis continues to be one of the most dreaded infections in sub-Saharan Africa and other countries that fall in the "meningitis belt" due to recurrent nature of the infection and the sequel of deliberating effects among survivors even after treatment. Ghana has had recurrent epidemics in the past but has been free from high mortality levels. Whereas reasons for the low reported number of deaths in the past are unclear, we hypothesize that it may be due to increased vaccination from expanded program on immunization (EPI) and consequent herd immunity of the general population. As at the end of February, 2016, 100 individuals were reported to have died out of 500 recorded cases. The infection may cause severe brain damage and kills at least 1 out of 10 individuals if quick interventions are not provided. The Ghana Health Service (GHS) and the Ministry of Health (MoH), together with other local and international stakeholders are working intensely to control the spread of the infection in affected communities with treatment and other health management programmes. This review presents a quick overview of meningitis in Ghana with emphasis on S. pneumoniae (responsible for about 70% of cases in the recent epidemic) together with some recommendations aimed at ensuring a "meningitis-free Ghana".
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Zheng H, Qiu X, Roy D, Segura M, Du P, Xu J, Gottschalk M. Genotyping and investigating capsular polysaccharide synthesis gene loci of non-serotypeable Streptococcus suis isolated from diseased pigs in Canada. Vet Res 2017; 48:10. [PMID: 28219415 PMCID: PMC5322794 DOI: 10.1186/s13567-017-0417-6] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2016] [Accepted: 01/20/2017] [Indexed: 11/13/2022] Open
Abstract
Streptococcus suis (S. suis) is an important swine pathogen and an emerging zoonotic agent. Most clinical S. suis strains express capsular polysaccharides (CPS), which can be typed by antisera using the coagglutination test. In this study, 79 S. suis strains recovered from diseased pigs in Canada and which could not be typed using antisera were further characterized by capsular gene typing and sequencing. Four patterns of cps locus were observed: (1) fifteen strains were grouped into previously reported serotypes but presented several mutations in their cps loci, when compared to available data from reference strains; (2) seven strains presented a complete deletion of the cps locus, which would result in an inability to synthesize capsule; (3) forty-seven strains were classified in recently described novel cps loci (NCLs); and (4) ten strains carried novel NCLs not previously described. Different virulence gene profiles (based on the presence of mrp, epf, and/or sly) were observed in these non-serotypeable strains. This study provides further insight in understanding the genetic characteristics of cps loci in non-serotypeable S. suis strains recovered from diseased animals. When using a combination of the previously described 35 serotypes and the complete NCL system, the number of untypeable strains recovered from diseased animals in Canada would be significantly reduced.
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Affiliation(s)
- Han Zheng
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing, China
| | - Xiaotong Qiu
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing, China
| | - David Roy
- Faculty of Veterinary Medicine, Swine and Poultry Infectious Diseases Research Center, University of Montreal, Quebec, Canada
| | - Mariela Segura
- Faculty of Veterinary Medicine, Swine and Poultry Infectious Diseases Research Center, University of Montreal, Quebec, Canada
| | - Pengchen Du
- Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing Key Laboratory of Emerging Infectious Diseases, Beijing, People's Republic of China
| | - Jianguo Xu
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing, China
| | - Marcelo Gottschalk
- Faculty of Veterinary Medicine, Swine and Poultry Infectious Diseases Research Center, University of Montreal, Quebec, Canada.
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Wyres KL, Wick RR, Gorrie C, Jenney A, Follador R, Thomson NR, Holt KE. Identification of Klebsiella capsule synthesis loci from whole genome data. Microb Genom 2016; 2:e000102. [PMID: 28348840 PMCID: PMC5359410 DOI: 10.1099/mgen.0.000102] [Citation(s) in RCA: 267] [Impact Index Per Article: 33.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Accepted: 12/06/2016] [Indexed: 12/14/2022] Open
Abstract
Klebsiella pneumoniae is a growing cause of healthcare-associated infections for which multi-drug resistance is a concern. Its polysaccharide capsule is a major virulence determinant and epidemiological marker. However, little is known about capsule epidemiology since serological typing is not widely accessible and many isolates are serologically non-typeable. Molecular typing techniques provide useful insights, but existing methods fail to take full advantage of the information in whole genome sequences. We investigated the diversity of the capsule synthesis loci (K-loci) among 2503 K. pneumoniae genomes. We incorporated analyses of full-length K-locus nucleotide sequences and also clustered protein-encoding sequences to identify, annotate and compare K-locus structures. We propose a standardized nomenclature for K-loci and present a curated reference database. A total of 134 distinct K-loci were identified, including 31 novel types. Comparative analyses indicated 508 unique protein-encoding gene clusters that appear to reassort via homologous recombination. Extensive intra- and inter-locus nucleotide diversity was detected among the wzi and wzc genes, indicating that current molecular typing schemes based on these genes are inadequate. As a solution, we introduce Kaptive, a novel software tool that automates the process of identifying K-loci based on full locus information extracted from whole genome sequences (https://github.com/katholt/Kaptive). This work highlights the extensive diversity of Klebsiella K-loci and the proteins that they encode. The nomenclature, reference database and novel typing method presented here will become essential resources for genomic surveillance and epidemiological investigations of this pathogen.
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Affiliation(s)
- Kelly L. Wyres
- Centre for Systems Genomics, University of Melbourne, Parkville, Australia
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Australia
| | - Ryan R. Wick
- Centre for Systems Genomics, University of Melbourne, Parkville, Australia
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Australia
| | - Claire Gorrie
- Centre for Systems Genomics, University of Melbourne, Parkville, Australia
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Australia
| | - Adam Jenney
- Infectious Diseases and Microbiology Unit, The Alfred Hospital, Melbourne, Australia
| | | | - Nicholas R. Thomson
- The Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK
- London School of Hygiene and Tropical Medicine, Keppel Street, London, UK
| | - Kathryn E. Holt
- Centre for Systems Genomics, University of Melbourne, Parkville, Australia
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Australia
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Capsular Polysaccharide Expression in Commensal Streptococcus Species: Genetic and Antigenic Similarities to Streptococcus pneumoniae. mBio 2016; 7:mBio.01844-16. [PMID: 27935839 PMCID: PMC5111408 DOI: 10.1128/mbio.01844-16] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Expression of a capsular polysaccharide is considered a hallmark of most invasive species of bacteria, including Streptococcus pneumoniae, in which the capsule is among the principal virulence factors and is the basis for successful vaccines. Consequently, it was previously assumed that capsule production distinguishes S. pneumoniae from closely related commensals of the mitis group streptococci. Based on antigenic and genetic analyses of 187 mitis group streptococci, including 90 recognized serotypes of S. pneumoniae, we demonstrated capsule production by the Wzy/Wzx pathway in 74% of 66 S. mitis strains and in virtually all tested strains of S. oralis (subspecies oralis, dentisani, and tigurinus) and S. infantis. Additional analyses of genomes of S. cristatus, S. parasanguinis, S. australis, S. sanguinis, S. gordonii, S. anginosus, S. intermedius, and S. constellatus revealed complete capsular biosynthesis (cps) loci in all strains tested. Truncated cps loci were detected in three strains of S. pseudopneumoniae, in 26% of S. mitis strains, and in a single S. oralis strain. The level of sequence identities of cps locus genes confirmed that the structural polymorphism of capsular polysaccharides in S. pneumoniae evolved by import of cps fragments from commensal Streptococcus species, resulting in a mosaic of genes of different origins. The demonstrated antigenic identity of at least eight of the numerous capsular polysaccharide structures expressed by commensal streptococci with recognized serotypes of S. pneumoniae raises concerns about potential misidentifications in addition to important questions concerning the consequences for vaccination and host-parasite relationships both for the commensals and for the pathogen. Expression of a capsular polysaccharide is among the principal virulence factors of Streptococcus pneumoniae and is the basis for successful vaccines against infections caused by this important pathogen. Contrasting with previous assumptions, this study showed that expression of capsular polysaccharides by the same genetic mechanisms is a general property of closely related species of streptococci that form a significant part of our commensal microbiota. The demonstrated antigenic identity of many capsular polysaccharides expressed by commensal streptococci and S. pneumoniae raises important questions concerning the consequences for vaccination and host-parasite relationships both for the commensals and the pathogen.
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38
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Ndlangisa KM, du Plessis M, Allam M, Wolter N, Mohale T, de Gouveia L, Birkhead M, Klugman KP, von Gottberg A. Two cases of serotypeable and non-serotypeable variants of Streptococcus pneumoniae detected simultaneously during invasive disease. BMC Microbiol 2016; 16:126. [PMID: 27342074 PMCID: PMC4921036 DOI: 10.1186/s12866-016-0745-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2015] [Accepted: 06/15/2016] [Indexed: 01/13/2023] Open
Abstract
Background More than 94 serotypes of Streptococcus pneumoniae have been described to date, however the majority of disease is caused by approximately 20 serotypes. Some pneumococci do not react with commercially available antisera used for serotyping and are thus regarded as non-serotypeable (NT). These pneumococci are commonly isolated during carriage studies and very rarely cause invasive disease. Colonization may occur with more than one serotype however disease with more than one serotype is rarely detected. Thus there are limited data describing cases of pneumococcal disease caused by more than one isolate. Results In two cases of invasive pneumococcal disease in South Africa, a non-serotypeable and a serotypeable isolate were co-detected during routine serotyping. A serotype 1 and 18C isolate were each co-detected with a non-serotypeable isolate in 2009 (case A) and 2010 (case B), from cerebrospinal fluid and blood, respectively. Both patients were 10–14 years old. For case A, the serotypeable isolate could not be obtained due to low representation in the mixed culture. Using electron microscopy we confirmed lack of capsule for the non-serotypeable isolates. Comparison of the case A non-serotypeable isolate with a serotype 1 genome revealed only the presence of the rhamnose biosynthesis genes (rmlA, B, C and D) in the capsular locus, all other capsular genes were absent. Nonetheless it had a multilocus sequence type (ST) associated with serotype 1 (ST217 and ribosomal ST3462) and its core genome clustered with other ST217 isolates. The case B non-serotypeable isolate had all serotype 18C capsular genes except for variation in the wchA and wze genes, compared to the 18C isolate. Both case B isolates were ST9817 and their core genomes were identical. Conclusions The ability of pneumococci to alter capsule production is a potential vaccine escape mechanism and therefore non-serotypeable pneumococci should be monitored as such organisms may increase under vaccine pressure. Electronic supplementary material The online version of this article (doi:10.1186/s12866-016-0745-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Kedibone M Ndlangisa
- Centre for Respiratory Diseases and Meningitis (CRDM), National Institute for Communicable Diseases (NICD), a division of the National Health Laboratory Service, Johannesburg, South Africa. .,School of Pathology, University of the Witwatersrand, Johannesburg, South Africa.
| | - Mignon du Plessis
- Centre for Respiratory Diseases and Meningitis (CRDM), National Institute for Communicable Diseases (NICD), a division of the National Health Laboratory Service, Johannesburg, South Africa.,School of Pathology, University of the Witwatersrand, Johannesburg, South Africa
| | - Mushal Allam
- Centre for Respiratory Diseases and Meningitis (CRDM), National Institute for Communicable Diseases (NICD), a division of the National Health Laboratory Service, Johannesburg, South Africa
| | - Nicole Wolter
- Centre for Respiratory Diseases and Meningitis (CRDM), National Institute for Communicable Diseases (NICD), a division of the National Health Laboratory Service, Johannesburg, South Africa.,School of Pathology, University of the Witwatersrand, Johannesburg, South Africa
| | - Thabo Mohale
- Centre for Respiratory Diseases and Meningitis (CRDM), National Institute for Communicable Diseases (NICD), a division of the National Health Laboratory Service, Johannesburg, South Africa.,School of Pathology, University of the Witwatersrand, Johannesburg, South Africa
| | - Linda de Gouveia
- Centre for Respiratory Diseases and Meningitis (CRDM), National Institute for Communicable Diseases (NICD), a division of the National Health Laboratory Service, Johannesburg, South Africa
| | - Monica Birkhead
- Centre for Emerging and Zoonotic Diseases, National Institute for Communicable Diseases (NICD), a division of the National Health Laboratory Service, Johannesburg, South Africa
| | - Keith P Klugman
- Hubert Department of Global Health, Rollins School of Public Health, and Division of Infectious Diseases, School of Medicine, Emory University, Atlanta, GA, USA
| | - Anne von Gottberg
- Centre for Respiratory Diseases and Meningitis (CRDM), National Institute for Communicable Diseases (NICD), a division of the National Health Laboratory Service, Johannesburg, South Africa.,School of Pathology, University of the Witwatersrand, Johannesburg, South Africa
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39
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Genomic analysis of nontypeable pneumococci causing invasive pneumococcal disease in South Africa, 2003-2013. BMC Genomics 2016; 17:470. [PMID: 27334470 PMCID: PMC4928513 DOI: 10.1186/s12864-016-2808-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Accepted: 05/27/2016] [Indexed: 01/18/2023] Open
Abstract
Background The capsular polysaccharide is the principal virulence factor of Streptococcus pneumoniae and a target for current pneumococcal vaccines. However, some pathogenic pneumococci are serologically nontypeable [nontypeable pneumococci (NTPn)]. Due to their relative rarity, NTPn are poorly characterized, and, as such, limited data exist which describe these organisms. We aimed to describe disease and genotypically characterize NTPn causing invasive pneumococcal disease in South Africa. Results Isolates were detected through national, laboratory-based surveillance for invasive pneumococcal disease in South Africa and characterized by whole genome analysis. We predicted ancestral serotypes (serotypes from which NTPn may have originated) for Group I NTPn using multilocus sequence typing and capsular region sequence analyses. Antimicrobial resistance patterns and mutations potentially causing nontypeability were identified. From 2003–2013, 39 (0.1 %, 39/32,824) NTPn were reported. Twenty-two (56 %) had partial capsular genes (Group I) and 17 (44 %) had complete capsular deletion of which 15 had replacement by other genes (Group II). Seventy-nine percent (31/39) of our NTPn isolates were derived from encapsulated S. pneumoniae. Ancestral serotypes 1 (27 %, 6/22) and 8 (14 %, 3/22) were most prevalent, and 59 % (13/22) of ancestral serotypes were serotypes included in the 13-valent pneumococcal conjugate vaccine. We identified a variety of mutations within the capsular region of Group I NTPn, some of which may be responsible for the nontypeable phenotype. Nonsusceptibility to tetracycline and erythromycin was higher in NTPn than encapsulated S. pneumoniae. Conclusions NTPn are currently a rare cause of invasive pneumococcal disease in South Africa and represent a genetically diverse collection of isolates. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2808-x) contains supplementary material, which is available to authorized users.
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40
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Valente C, Hinds J, Gould KA, Pinto FR, de Lencastre H, Sá-Leão R. Impact of the 13-valent pneumococcal conjugate vaccine on Streptococcus pneumoniae multiple serotype carriage. Vaccine 2016; 34:4072-8. [PMID: 27325351 DOI: 10.1016/j.vaccine.2016.06.017] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Revised: 05/22/2016] [Accepted: 06/02/2016] [Indexed: 02/02/2023]
Abstract
INTRODUCTION Pneumococcal multiple serotype carriage is important for evolution of the species and to understand how the pneumococcal population is changing with vaccination. We aimed to determine the impact of the 13-valent pneumococcal conjugate vaccine (PCV13) on multiple serotype carriage. METHODS AND MATERIALS Nasopharyngeal samples from fully vaccinated pneumococcal carriers (4 doses of PCV13, n=141, aged 18-72months) or from non-vaccinated pneumococcal carriers (0 doses of any PCV, n=140, same age group) were analyzed. Multiple serotype carriage was evaluated by DNA hybridization with a molecular serotyping microarray that detects all known serotypes. RESULTS Vaccinated children had a lower prevalence of multiple serotype carriage than the non-vaccinated group (20.6% vs 29.3%, p=0.097), and a significantly lower proportion of PCV13 serotypes (6.4% vs 38.5%, p=0.0001). PCV13 serotypes found among vaccinated children were mostly detected as a minor serotype in co-colonization with a more abundant non-vaccine serotype. Vaccinated children were colonized by a significantly higher proportion of commensal non-pneumococcal Streptococcus spp. (58.2% vs 42.8%, p=0.012). In vaccinated children there were significantly less non-vaccine type (NVT) co-colonization events than expected based on the distribution of these serotypes in non-vaccinated children. CONCLUSIONS The results suggest that vaccinated children have lower pneumococcal multiple serotype carriage prevalence due to higher competitive abilities of non-vaccine serotypes expanding after PCV13 use. This might represent an additional benefit of PCV13, as decreased co-colonization rates translate into decreased opportunities for horizontal gene transfer and might have implications for the evolution and virulence of pneumococci.
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Affiliation(s)
- Carina Valente
- Laboratory of Molecular Microbiology of Human Pathogens, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Jason Hinds
- Institute for Infection and Immunity, St. George's, University of London, London, UK; BUGS Bioscience, London Bioscience Innovation Centre, London, UK
| | - Katherine A Gould
- Institute for Infection and Immunity, St. George's, University of London, London, UK; BUGS Bioscience, London Bioscience Innovation Centre, London, UK
| | - Francisco R Pinto
- BioISI - Biosystems & Integrative Sciences Institute, Faculdade de Ciências da Universidade de Lisboa, Lisbon, Portugal
| | - Hermínia de Lencastre
- Laboratory of Molecular Genetics, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal; Laboratory of Microbiology and Infectious Diseases, The Rockefeller University, New York, NY, USA
| | - Raquel Sá-Leão
- Laboratory of Molecular Microbiology of Human Pathogens, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal.
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Cleary DW, Devine VT, Jefferies JMC, Webb JS, Bentley SD, Gladstone RA, Faust SN, Clarke SC. Comparative Genomics of Carriage and Disease Isolates of Streptococcus pneumoniae Serotype 22F Reveals Lineage-Specific Divergence and Niche Adaptation. Genome Biol Evol 2016; 8:1243-51. [PMID: 27016484 PMCID: PMC4860696 DOI: 10.1093/gbe/evw066] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Streptococcus pneumoniae is a major cause of meningitis, sepsis, and pneumonia worldwide. Pneumococcal conjugate vaccines have been part of the United Kingdom’s childhood immunization program since 2006 and have significantly reduced the incidence of disease due to vaccine efficacy in reducing carriage in the population. Here we isolated two clones of 22F (an emerging serotype of clinical concern, multilocus sequence types 433 and 698) and conducted comparative genomic analysis on four isolates, paired by Sequence Type (ST) with one of each pair being derived from carriage and the other disease (sepsis). The most compelling observation was of nonsynonymous mutations in pgdA, encoding peptidoglycan N-acetylglucosamine deacetylase A, which was found in the carriage isolates of both ST433 and 698. Deacetylation of pneumococcal peptidoglycan is known to enable resistance to lysozyme upon invasion. Althought no other clear genotypic signatures related to disease or carriage could be determined, additional intriguing comparisons between the two STs were possible. These include the presence of an intact prophage, in addition to numerous additional phage insertions, within the carriage isolate of ST433. Contrasting gene repertoires related to virulence and colonization, including bacteriocins, lantibiotics, and toxin-–antitoxin systems, were also observed.
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Affiliation(s)
- David W Cleary
- Academic Unit of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom Institute for Life Sciences, University of Southampton, Southampton, United Kingdom
| | - Vanessa T Devine
- Academic Unit of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Johanna M C Jefferies
- Academic Unit of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom Institute for Life Sciences, University of Southampton, Southampton, United Kingdom
| | - Jeremy S Webb
- Institute for Life Sciences, University of Southampton, Southampton, United Kingdom Southampton NIHR Respiratory Biomedical Research Unit, University Hospital Southampton Foundation NHS Trust, Southampton, United Kingdom Centre for Biological Sciences, Faculty of Natural and Environmental Sciences, University of Southampton, Southampton, United Kingdom
| | - Stephen D Bentley
- Pathogen Genomics, Wellcome Trust Sanger Institute, Cambridge, United Kingdom
| | - Rebecca A Gladstone
- Pathogen Genomics, Wellcome Trust Sanger Institute, Cambridge, United Kingdom
| | - Saul N Faust
- Academic Unit of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom Southampton NIHR Respiratory Biomedical Research Unit, University Hospital Southampton Foundation NHS Trust, Southampton, United Kingdom NIHR Southampton Wellcome Trust Clinical Research Facility, University Hospital Southampton NHS Foundation Trust, Southampton, United Kingdom
| | - Stuart C Clarke
- Academic Unit of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom Institute for Life Sciences, University of Southampton, Southampton, United Kingdom Southampton NIHR Respiratory Biomedical Research Unit, University Hospital Southampton Foundation NHS Trust, Southampton, United Kingdom NIHR Southampton Wellcome Trust Clinical Research Facility, University Hospital Southampton NHS Foundation Trust, Southampton, United Kingdom
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Abstract
While significant protection from pneumococcal disease has been achieved by the use of polysaccharide and polysaccharide-protein conjugate vaccines, capsule-independent protection has been limited by serotype replacement along with disease caused by nonencapsulated Streptococcus pneumoniae (NESp). NESp strains compose approximately 3% to 19% of asymptomatic carriage isolates and harbor multiple antibiotic resistance genes. Surface proteins unique to NESp enhance colonization and virulence despite the lack of a capsule even though the capsule has been thought to be required for pneumococcal pathogenesis. Genes for pneumococcal surface proteins replace the capsular polysaccharide (cps) locus in some NESp isolates, and these proteins aid in pneumococcal colonization and otitis media (OM). NESp strains have been isolated from patients with invasive and noninvasive pneumococcal disease, but noninvasive diseases, specifically, conjunctivitis (85%) and OM (8%), are of higher prevalence. Conjunctival strains are commonly of the so-called classical NESp lineages defined by multilocus sequence types (STs) ST344 and ST448, while sporadic NESp lineages such as ST1106 are more commonly isolated from patients with other diseases. Interestingly, sporadic lineages have significantly higher rates of recombination than classical lineages. Higher rates of recombination can lead to increased acquisition of antibiotic resistance and virulence factors, increasing the risk of disease and hindering treatment. NESp strains are a significant proportion of the pneumococcal population, can cause disease, and may be increasing in prevalence in the population due to effects on the pneumococcal niche caused by pneumococcal vaccines. Current vaccines are ineffective against NESp, and further research is necessary to develop vaccines effective against both encapsulated and nonencapsulated pneumococci.
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Yahara K, Didelot X, Jolley KA, Kobayashi I, Maiden MCJ, Sheppard SK, Falush D. The Landscape of Realized Homologous Recombination in Pathogenic Bacteria. Mol Biol Evol 2016; 33:456-71. [PMID: 26516092 PMCID: PMC4866539 DOI: 10.1093/molbev/msv237] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Recombination enhances the adaptive potential of organisms by allowing genetic variants to be tested on multiple genomic backgrounds. Its distribution in the genome can provide insight into the evolutionary forces that underlie traits, such as the emergence of pathogenicity. Here, we examined landscapes of realized homologous recombination of 500 genomes from ten bacterial species and found all species have "hot" regions with elevated rates relative to the genome average. We examined the size, gene content, and chromosomal features associated with these regions and the correlations between closely related species. The recombination landscape is variable and evolves rapidly. For example in Salmonella, only short regions of around 1 kb in length are hot whereas in the closely related species Escherichia coli, some hot regions exceed 100 kb, spanning many genes. Only Streptococcus pyogenes shows evidence for the positive correlation between GC content and recombination that has been reported for several eukaryotes. Genes with function related to the cell surface/membrane are often found in recombination hot regions but E. coli is the only species where genes annotated as "virulence associated" are consistently hotter. There is also evidence that some genes with "housekeeping" functions tend to be overrepresented in cold regions. For example, ribosomal proteins showed low recombination in all of the species. Among specific genes, transferrin-binding proteins are recombination hot in all three of the species in which they were found, and are subject to interspecies recombination.
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Affiliation(s)
- Koji Yahara
- Biostatistics Center, Kurume University, Kurume, Fukuoka, Japan College of Medicine, Institute of Life Science, Swansea University, Swansea, United Kingdom
| | - Xavier Didelot
- Department of Infectious Disease Epidemiology, Imperial College London, London, United Kingdom
| | - Keith A Jolley
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Ichizo Kobayashi
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, University of Tokyo, Tokyo, Japan
| | | | - Samuel K Sheppard
- College of Medicine, Institute of Life Science, Swansea University, Swansea, United Kingdom Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Daniel Falush
- College of Medicine, Institute of Life Science, Swansea University, Swansea, United Kingdom Department of Medical Genome Sciences, Graduate School of Frontier Sciences, University of Tokyo, Tokyo, Japan
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Abstract
Streptococcus pneumoniae (the pneumococcus) is an important human pathogen. Its virulence is largely due to its polysaccharide capsule, which shields it from the host immune system, and because of this, the capsule has been extensively studied. Studies of the capsule led to the identification of DNA as the genetic material, identification of many different capsular serotypes, and identification of the serotype-specific nature of protection by adaptive immunity. Recent studies have led to the determination of capsular polysaccharide structures for many serotypes using advanced analytical technologies, complete elucidation of genetic basis for the capsular types, and the development of highly effective pneumococcal conjugate vaccines. Conjugate vaccine use has altered the serotype distribution by either serotype replacement or switching, and this has increased the need to serotype pneumococci. Due to great advances in molecular technologies and our understanding of the pneumococcal genome, molecular approaches have become powerful tools to predict pneumococcal serotypes. In addition, more-precise and -efficient serotyping methods that directly detect polysaccharide structures are emerging. These improvements in our capabilities will greatly enhance future investigations of pneumococcal epidemiology and diseases and the biology of colonization and innate immunity to pneumococcal capsules.
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Morales M, Martín-Galiano AJ, Domenech M, García E. Insights into the Evolutionary Relationships of LytA Autolysin and Ply Pneumolysin-Like Genes in Streptococcus pneumoniae and Related Streptococci. Genome Biol Evol 2015; 7:2747-61. [PMID: 26349755 PMCID: PMC4607534 DOI: 10.1093/gbe/evv178] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Streptococcus pneumoniae (pneumococcus) is a major human pathogen. The main pneumococcal autolysin LytA and the pneumolysin Ply are two of the bacterium's most important virulence factors. The lytA- and ply-related genes are also found in other streptococci of the Mitis group (SMG). The precise characteristics of the lytA-related-but not the ply-related-genes of SMG and their prophages have been previously described. A search of the more than 400 SMG genomic sequences available in public databases (ca. 300 for S. pneumoniae), showed Streptococcus pseudopneumoniae IS7493 to harbor four ply-related genes, two of which (plyA and plyB) have 98% identical nucleotides. The plyA homolog of S. pseudopneumoniae is conserved in all S. pneumoniae strains, and seems to be included in a pathogenicity island together with the lytA gene. However, only nonencapsulated S. pneumoniae strains possess a plyB gene, which is part of an integrative and conjugative element. Notably, the existence of a bacterial lytA-related gene in a genome is linked to the presence of plyA and vice versa. The present analysis also shows there are eight main types of plyA-lytA genomic islands. A possible stepwise scenario for the evolution of the plyA-lytA island in S. pneumoniae is proposed.
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Affiliation(s)
- María Morales
- Departamento de Microbiología Molecular y Biología de las Infecciones, Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain Unidad de Genética Bacteriana, Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - Antonio J Martín-Galiano
- Unidad de Genética Bacteriana, Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III (ISCIII), Madrid, Spain Centro Nacional de Microbiología, ISCIII, Majadahonda, Madrid, Spain
| | - Mirian Domenech
- Departamento de Microbiología Molecular y Biología de las Infecciones, Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain Unidad de Genética Bacteriana, Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - Ernesto García
- Departamento de Microbiología Molecular y Biología de las Infecciones, Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain Unidad de Genética Bacteriana, Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III (ISCIII), Madrid, Spain
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Kamng'ona AW, Hinds J, Bar-Zeev N, Gould KA, Chaguza C, Msefula C, Cornick JE, Kulohoma BW, Gray K, Bentley SD, French N, Heyderman RS, Everett DB. High multiple carriage and emergence of Streptococcus pneumoniae vaccine serotype variants in Malawian children. BMC Infect Dis 2015; 15:234. [PMID: 26088623 PMCID: PMC4474563 DOI: 10.1186/s12879-015-0980-2] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2014] [Accepted: 06/08/2015] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Carriage of either single or multiple pneumococcal serotypes (multiple carriage) is a prerequisite for developing invasive pneumococcal disease. However, despite the reported high rates of pneumococcal carriage in Malawi, no data on carriage of multiple serotypes has been reported previously. Our study provides the first description of the prevalence of multiple pneumococcal carriage in Malawi. METHODS The study was conducted in Blantyre and Karonga districts in Malawi, from 2008 to 2012. We recruited 116 children aged 0-13 years. These children were either HIV-infected (N = 44) or uninfected (N = 72). Nasopharyngeal samples were collected using sterile swabs. Pneumococcal serotypes in the samples were identified by microarray. Strains that could not be typed by microarray were sequenced to characterise possible genetic alterations within the capsular polysaccharide (CPS) locus. RESULTS The microarray identified 179 pneumococcal strains (from 116 subjects), encompassing 43 distinct serotypes and non-typeable (NT) strains. Forty per cent (46/116) of children carried multiple serotypes. Carriage of vaccine type (VT) strains was higher (p = 0.028) in younger (0-2 years) children (71 %, 40/56) compared to older (3-13 years) children (50 %, 30/60). Genetic variations within the CPS locus of known serotypes were observed in 19 % (34/179) of the strains identified. The variants included 13-valent pneumococcal conjugate vaccine (PCV13) serotypes 6B and 19A, and the polysaccharide vaccine serotype 20. Serotype 6B variants were the most frequently isolated (47 %, 16/34). Unlike the wild type, the CPS locus of the 6B variants contained an insertion of the licD-family phosphotransferase gene. The CPS locus of 19A- and 20-variants contained an inversion in the sugar-biosynthesis (rmlD) gene and a 717 bp deletion within the transferase (whaF) gene, respectively. CONCLUSIONS The high multiple carriage in Malawian children provides opportunities for genetic exchange through horizontal gene transfer. This may potentially lead to CPS locus variants and vaccine escape. Variants reported here occurred naturally, however, PCV13 introduction could exacerbate the CPS genetic variations. Further studies are therefore recommended to assess the invasive potential of these variants and establish whether PCV13 would offer cross-protection. We have shown that younger children (0-2 years) are a reservoir of VT serotypes, which makes them an ideal target for vaccination.
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Affiliation(s)
- Arox W Kamng'ona
- Microbes, Immunity and Vaccines, Malawi Liverpool Wellcome Trust Clinical Research Programme, Blantyre, Malawi. .,Biochemistry Department, University of Malawi, College of Medicine, Blantyre, Malawi. .,Institute of Infection and Global Health, University of Liverpool, Liverpool, UK.
| | - Jason Hinds
- Division of Clinical Sciences, St George's, University of London, London, UK.
| | - Naor Bar-Zeev
- Microbes, Immunity and Vaccines, Malawi Liverpool Wellcome Trust Clinical Research Programme, Blantyre, Malawi. .,Institute of Infection and Global Health, University of Liverpool, Liverpool, UK.
| | - Katherine A Gould
- Division of Clinical Sciences, St George's, University of London, London, UK.
| | - Chrispin Chaguza
- Microbes, Immunity and Vaccines, Malawi Liverpool Wellcome Trust Clinical Research Programme, Blantyre, Malawi. .,Institute of Infection and Global Health, University of Liverpool, Liverpool, UK.
| | - Chisomo Msefula
- Microbes, Immunity and Vaccines, Malawi Liverpool Wellcome Trust Clinical Research Programme, Blantyre, Malawi. .,Microbiology Department, University of Malawi, College of Medicine, Blantyre, Malawi.
| | - Jennifer E Cornick
- Microbes, Immunity and Vaccines, Malawi Liverpool Wellcome Trust Clinical Research Programme, Blantyre, Malawi. .,Institute of Infection and Global Health, University of Liverpool, Liverpool, UK.
| | - Benard W Kulohoma
- Microbes, Immunity and Vaccines, Malawi Liverpool Wellcome Trust Clinical Research Programme, Blantyre, Malawi. .,Institute of Infection and Global Health, University of Liverpool, Liverpool, UK. .,International Centre for Insect Physiology and Ecology, Nairobi, Kenya.
| | - Katherine Gray
- Biochemistry Department, University of Malawi, College of Medicine, Blantyre, Malawi.
| | - Stephen D Bentley
- Pathogen Genomics, Wellcome Trust Sanger Institute, Cambridge, UK. .,Department of Medicine, University of Cambridge, Cambridge, UK.
| | - Neil French
- Microbes, Immunity and Vaccines, Malawi Liverpool Wellcome Trust Clinical Research Programme, Blantyre, Malawi. .,Institute of Infection and Global Health, University of Liverpool, Liverpool, UK. .,Malawi Epidemiology and Intervention Research Unit (MEIRU), Karonga, Malawi.
| | - Robert S Heyderman
- Microbes, Immunity and Vaccines, Malawi Liverpool Wellcome Trust Clinical Research Programme, Blantyre, Malawi. .,Liverpool School of Tropical Medicine, Liverpool, UK.
| | - Dean B Everett
- Microbes, Immunity and Vaccines, Malawi Liverpool Wellcome Trust Clinical Research Programme, Blantyre, Malawi. .,Institute of Infection and Global Health, University of Liverpool, Liverpool, UK.
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Structures of Capsular Polysaccharide Serotypes 35F and 35C of Streptococcus pneumoniae Determined by Nuclear Magnetic Resonance and Their Relation to Other Cross-Reactive Serotypes. J Bacteriol 2015; 197:2762-9. [PMID: 26055112 DOI: 10.1128/jb.00207-15] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Accepted: 05/30/2015] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED The structures of Streptococcus pneumoniae capsular polysaccharides (CPSs) are essential for defining the antigenic as well as genetic relationships between CPS serotypes. The four serotypes that comprise CPS serogroup 35 (i.e., types 35F, 35A, 35B, and 35C) are known to cross-react with genetically related type 20, 29, 34, 42, or 47F. While the structures of CPS serotype 35A (CPS35A) and CPS35B are known, those of CPS35F and CPS35C are not. In the present study, the serotypes of CPS35F and CPS35C were characterized by high-resolution heteronuclear magnetic resonance (NMR) spectroscopy and glycosyl composition analyses to reveal the following repeat unit structures: [Formula: see text] where OAc indicates O-acetylated. Importantly, CPS35F, the immunizing serotype for the production of group 35 serum, more closely resembles CPS34 and CPS47F than other members of serogroup 35. Moreover, CPS35C is distinct from either CPS35F or CPS35B but closely related to CPS35A and identical to de-O-acetylated CPS42. The findings provide a comprehensive view of the structural and genetic relations that exist between the members of CPS serogroup 35 and other cross-reactive serotypes. IMPORTANCE Cross-reactions of diagnostic rabbit antisera with Streptococcus pneumoniae capsular polysaccharide serotypes are generally limited to members of the same serogroup. Exceptions do, however, occur, most notably among a group of nonvaccine serotypes that includes the members of serogroup 35 (i.e., types 35F, 35A, 35B, and 35C) and other genetically related types. The presently determined structures of S. pneumoniae serotypes 35F and 35C complete the structural characterization of serogroup 35 and thereby provide the first comprehensive description of how different members of this serogroup are related to each other and to types 29, 34, 42, and 47F. The structural and genetic features of these serotypes suggest the existence of three distinct capsular polysaccharide subgroups that presumably emerged by immune selection in the human host.
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Croucher NJ, Kagedan L, Thompson CM, Parkhill J, Bentley SD, Finkelstein JA, Lipsitch M, Hanage WP. Selective and genetic constraints on pneumococcal serotype switching. PLoS Genet 2015; 11:e1005095. [PMID: 25826208 PMCID: PMC4380333 DOI: 10.1371/journal.pgen.1005095] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2014] [Accepted: 02/23/2015] [Indexed: 11/19/2022] Open
Abstract
Streptococcus pneumoniae isolates typically express one of over 90 immunologically distinguishable polysaccharide capsules (serotypes), which can be classified into “serogroups” based on cross-reactivity with certain antibodies. Pneumococci can alter their serotype through recombinations affecting the capsule polysaccharide synthesis (cps) locus. Twenty such “serotype switching” events were fully characterised using a collection of 616 whole genome sequences from systematic surveys of pneumococcal carriage. Eleven of these were within-serogroup switches, representing a highly significant (p < 0.0001) enrichment based on the observed serotype distribution. Whereas the recombinations resulting in between-serogroup switches all spanned the entire cps locus, some of those that caused within-serogroup switches did not. However, higher rates of within-serogroup switching could not be fully explained by either more frequent, shorter recombinations, nor by genetic linkage to genes involved in β–lactam resistance. This suggested the observed pattern was a consequence of selection for preserving serogroup. Phenotyping of strains constructed to express different serotypes in common genetic backgrounds was used to test whether genotypes were physiologically adapted to particular serogroups. These data were consistent with epistatic interactions between the cps locus and the rest of the genome that were specific to serotype, but not serogroup, meaning they were unlikely to account for the observed distribution of capsule types. Exclusion of these genetic and physiological hypotheses suggested future work should focus on alternative mechanisms, such as host immunity spanning multiple serotypes within the same serogroup, which might explain the observed pattern. Streptococcus pneumoniae is a major respiratory pathogen responsible for a high burden of morbidity and mortality worldwide. Current anti-pneumococcal vaccines target the bacterium’s polysaccharide capsule, of which at least 95 different variants (‘serotypes’) are known, which are classified into ‘serogroups’. Bacteria can change their serotype through genetic recombination, termed ‘switching’, which can allow strains to evade vaccine-induced immunity. By combining epidemiological data with whole genome sequencing, this work finds a robust and unexpected pattern of serotype switching in a sample of bacteria collected following the introduction of routine anti-pneumococcal vaccination: switching was much more likely to exchange one serotype for another within the same serogroup than expected by chance. Several hypotheses are presented and tested to explain this pattern, including limitations of genetic recombination, interactions between the genes that determine serotype and the rest of the genome, and the constraints imposed by bacterial metabolism. This provides novel information on the evolution of S. pneumoniae, particularly regarding how the bacterium might diversify as newer vaccines are introduced.
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Affiliation(s)
- Nicholas J. Croucher
- Department of Infectious Disease Epidemiology, Imperial College London, London, United Kingdom
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, United States of America
- * E-mail:
| | - Lisa Kagedan
- Department of Epidemiology and Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, United States of America
| | - Claudette M. Thompson
- Department of Epidemiology and Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, United States of America
| | - Julian Parkhill
- Pathogen Genomics, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Stephen D. Bentley
- Pathogen Genomics, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Jonathan A. Finkelstein
- Department of Population Medicine, Harvard Medical School and Harvard Pilgrim Health Care Institute, Boston, Massachusetts, United States of America
- Division of General Pediatrics, Boston Children’s Hospital, Boston, Massachusetts, United States of America
| | - Marc Lipsitch
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, United States of America
- Department of Epidemiology and Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, United States of America
| | - William P. Hanage
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, United States of America
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Jauneikaite E, Tocheva AS, Jefferies JMC, Gladstone RA, Faust SN, Christodoulides M, Hibberd ML, Clarke SC. Current methods for capsular typing of Streptococcus pneumoniae. J Microbiol Methods 2015; 113:41-9. [PMID: 25819558 DOI: 10.1016/j.mimet.2015.03.006] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2014] [Revised: 02/21/2015] [Accepted: 03/08/2015] [Indexed: 10/23/2022]
Abstract
Streptococcus pneumoniae is a major respiratory tract pathogen causing pneumococcal disease mainly in children aged less than five years and in the elderly. Ninety-eight different capsular types (serotypes) of pneumococci have been reported, but pneumococcal conjugate vaccines (PCV) include polysaccharide antigens against only 7, 10 or 13 serotypes. It is therefore important to track the emergence of serotypes due to the clonal expansion of non-vaccine serotypes. Increased numbers of carried and disease-causing pneumococci are now being analysed as part of the post-PCV implementation surveillance studies and hence rapid, accurate and cost-effective typing methods are important. Here we describe serotyping methods published prior to 10th November 2014 for pneumococcal capsule typing. Sixteen methods were identified; six were based on serological tests using immunological properties of the capsular epitopes, eight were semi-automated molecular tests, and one describes the identification of capsular type directly from whole genome data, which also allows for further intra and inter-genome analyses. There was no single method that could be recommended for all pneumococcal capsular typing applications. Although the Quellung reaction is still considered to be the gold-standard, laboratories should take into account the number of pneumococcal isolates and the type of samples to be used for testing, the time frame for the results and the resources available in order to select the most appropriate method. Most likely, a combination of phenotypic and genotypic methods would be optimal to monitor and evaluate the impact of pneumococcal conjugate vaccines and to provide information for future vaccine formulations.
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Affiliation(s)
- Elita Jauneikaite
- Faculty of Medicine and Institute for Life Sciences, University of Southampton, Southampton SO16 6YD, UK; Infectious Diseases, Genome Institute of Singapore, 138672, Singapore
| | - Anna S Tocheva
- Faculty of Medicine and Institute for Life Sciences, University of Southampton, Southampton SO16 6YD, UK
| | - Johanna M C Jefferies
- Faculty of Medicine and Institute for Life Sciences, University of Southampton, Southampton SO16 6YD, UK; NIHR Southampton Respiratory Biomedical Research Unit, University Hospital Southampton NHS Foundation Trust, Southampton SO16 6YD, UK
| | - Rebecca A Gladstone
- Faculty of Medicine and Institute for Life Sciences, University of Southampton, Southampton SO16 6YD, UK
| | - Saul N Faust
- Faculty of Medicine and Institute for Life Sciences, University of Southampton, Southampton SO16 6YD, UK; NIHR Southampton Respiratory Biomedical Research Unit, University Hospital Southampton NHS Foundation Trust, Southampton SO16 6YD, UK; NIHR Wellcome Trust Clinical Research Facility, University Hospital Southampton NHS Foundation Trust, Southampton SO16 6YD, UK
| | - Myron Christodoulides
- Faculty of Medicine and Institute for Life Sciences, University of Southampton, Southampton SO16 6YD, UK
| | - Martin L Hibberd
- Infectious Diseases, Genome Institute of Singapore, 138672, Singapore; London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK
| | - Stuart C Clarke
- Faculty of Medicine and Institute for Life Sciences, University of Southampton, Southampton SO16 6YD, UK; NIHR Southampton Respiratory Biomedical Research Unit, University Hospital Southampton NHS Foundation Trust, Southampton SO16 6YD, UK.
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50
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Mutations in pneumococcal cpsE generated via in vitro serial passaging reveal a potential mechanism of reduced encapsulation utilized by a conjunctival isolate. J Bacteriol 2015; 197:1781-91. [PMID: 25777672 DOI: 10.1128/jb.02602-14] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2014] [Accepted: 03/05/2015] [Indexed: 12/27/2022] Open
Abstract
UNLABELLED The polysaccharide capsule of Streptococcus pneumoniae is required for nasopharyngeal colonization and for invasive disease in the lungs, blood, and meninges. In contrast, the vast majority of conjunctival isolates are acapsular. The first serotype-specific gene in the capsule operon, cpsE, encodes the initiating glycosyltransferase and is one of the few serotype-specific genes that can tolerate null mutations. This report characterizes a spontaneously arising TIGR4 mutant exhibiting a reduced capsule, caused by a 6-nucleotide duplication in cpsE which results in duplication of Ala and Ile at positions 45 and 46. This strain (AI45dup) possessed more exposed phosphorylcholine and was hypersusceptible to C3 complement deposition compared to the wild type. Accordingly, the mutant was significantly better at forming abiotic biofilms and binding epithelial cells in vitro but was avirulent in a sepsis model. In vitro serial passaging of the wild-type strain failed to reproduce the AI45dup mutation but instead led to a variety of mutants with reduced capsule harboring single nucleotide polymorphisms (SNPs) in cpsE. A single passage in the sepsis model after high-dose inoculation readily yielded revertants of AI45dup with restored wild-type capsule level, but the majority of SNP alleles of cpsE could not revert, suppress, or bypass. Analysis of cpsE in conjunctival isolates revealed a strain with a single missense mutation at amino acid position 377, which was responsible for reduced encapsulation. This study supports the hypothesis that spontaneous, nonreverting mutations in cpsE serve as a form of adaptive mutation by providing a selective advantage to S. pneumoniae in niches where expression of capsule is detrimental. IMPORTANCE While the capsule of Streptococcus pneumoniae is required for colonization and invasive disease, most conjunctival isolates are acapsular by virtue of deletion of the entire capsular operon. We show that spontaneous acapsular mutants isolated in vitro harbor mostly nonrevertible single nucleotide polymorphism (SNP) null mutations in cpsE, encoding the initiating glycosyltransferase. From a small collection of acapsular conjunctival isolates, we identified one strain with a complete capsular operon but containing a SNP in cpsE that we show is responsible for the acapsular phenotype. We propose that acapsular conjunctival isolates may arise initially from such nonreverting SNP null mutations in cpsE, which can be followed later by deletion of portions or all of the cps operon.
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