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Kalizang'oma A, Swarthout TD, Mwalukomo TS, Kamng’ona A, Brown C, Msefula J, Demetriou H, Chan JM, Roalfe L, Obolski U, Lourenço J, Goldblatt D, Chaguza C, French N, Heyderman RS. Clonal Expansion of a Streptococcus pneumoniae Serotype 3 Capsule Variant Sequence Type 700 With Enhanced Vaccine Escape Potential After 13-Valent Pneumococcal Conjugate Vaccine Introduction. J Infect Dis 2024; 230:e189-e198. [PMID: 39052729 PMCID: PMC11272040 DOI: 10.1093/infdis/jiae040] [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: 12/13/2022] [Accepted: 01/21/2024] [Indexed: 03/28/2024] Open
Abstract
BACKGROUND Streptococcus pneumoniae serotype 3 remains a problem globally. Malawi introduced 13-valent pneumococcal conjugate vaccine (PCV13) in 2011, but there has been no direct protection against serotype 3 carriage. We explored whether vaccine escape by serotype 3 is due to clonal expansion of a lineage with a competitive advantage. METHODS The distribution of serotype 3 Global Pneumococcal Sequence Clusters (GPSCs) and sequence types (STs) globally was assessed using sequences from the Global Pneumococcal Sequencing Project. Whole-genome sequences of 135 serotype 3 carriage isolates from Blantyre, Malawi (2015-2019) were analyzed. Comparative analysis of the capsule locus, entire genomes, antimicrobial resistance, and phylogenetic reconstructions were undertaken. Opsonophagocytosis was evaluated using serum samples from vaccinated adults and children. RESULTS Serotype 3 GPSC10-ST700 isolates were most prominent in Malawi. Compared with the prototypical serotype 3 capsular polysaccharide locus sequence, 6 genes are absent, with retention of capsule polysaccharide biosynthesis. This lineage is characterized by increased antimicrobial resistance and lower susceptibility to opsonophagocytic killing. CONCLUSIONS A serotype 3 variant in Malawi has genotypic and phenotypic characteristics that could enhance vaccine escape and clonal expansion after post-PCV13 introduction. Genomic surveillance among high-burden populations is essential to improve the effectiveness of next-generation pneumococcal vaccines.
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Affiliation(s)
- Akuzike Kalizang'oma
- NIHR Mucosal Pathogens Research Unit, Research Department of Infection, Division of Infection and Immunity, University College London, London, United Kingdom
- Pneumonia and Meningitis Pathogens Associate Research Group, Malawi-Liverpool-Wellcome Research Programme, Blantyre, Malawi
| | - Todd D Swarthout
- NIHR Mucosal Pathogens Research Unit, Research Department of Infection, Division of Infection and Immunity, University College London, London, United Kingdom
- Pneumonia and Meningitis Pathogens Associate Research Group, Malawi-Liverpool-Wellcome Research Programme, Blantyre, Malawi
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
| | - Thandie S Mwalukomo
- School of Medicine and Oral Health, Kamuzu University of Health Sciences, Blantyre, Malawi
| | - Arox Kamng’ona
- School of Life Sciences and Allied Health Professionals, Kamuzu University of Health Sciences, Blantyre, Malawi
| | - Comfort Brown
- Pneumonia and Meningitis Pathogens Associate Research Group, Malawi-Liverpool-Wellcome Research Programme, Blantyre, Malawi
| | - Jacquline Msefula
- Pneumonia and Meningitis Pathogens Associate Research Group, Malawi-Liverpool-Wellcome Research Programme, Blantyre, Malawi
| | - Hayley Demetriou
- Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
| | - Jia Mun Chan
- NIHR Mucosal Pathogens Research Unit, Research Department of Infection, Division of Infection and Immunity, University College London, London, United Kingdom
| | - Lucy Roalfe
- Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
| | - Uri Obolski
- Porter School of the Environment and Earth Science, Tel-Aviv University, Tel-Aviv, Israel
| | - Jose Lourenço
- Faculdade de Ciências, BioISI, Universidade de Lisboa, Lisbon, Portugal
| | - David Goldblatt
- NIHR Mucosal Pathogens Research Unit, Research Department of Infection, Division of Infection and Immunity, University College London, London, United Kingdom
- Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
| | - Chrispin Chaguza
- NIHR Mucosal Pathogens Research Unit, Research Department of Infection, Division of Infection and Immunity, University College London, London, United Kingdom
- Parasites and Microbes Programme, Wellcome Sanger Institute, Hinxton, United Kingdom
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, Yale University, New Haven, Connecticut, USA
- Yale Institute for Global Health, Yale University, New Haven, Connecticut, USA
| | - Neil French
- Institute of Infection, Veterinary and Ecological Sciences, Department of Clinical Infection, Microbiology and Immunology, University of Liverpool, Liverpool, United Kingdom
| | - Robert S Heyderman
- NIHR Mucosal Pathogens Research Unit, Research Department of Infection, Division of Infection and Immunity, University College London, London, United Kingdom
- Pneumonia and Meningitis Pathogens Associate Research Group, Malawi-Liverpool-Wellcome Research Programme, Blantyre, Malawi
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2
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Köndgen S, Calvignac-Spencer S, Grützmacher K, Keil V, Mätz-Rensing K, Nowak K, Metzger S, Kiyang J, Lübke-Becker A, Deschner T, Wittig RM, Lankester F, Leendertz FH. Evidence for Human Streptococcus pneumoniae in wild and captive chimpanzees: A potential threat to wild populations. Sci Rep 2017; 7:14581. [PMID: 29109465 PMCID: PMC5674046 DOI: 10.1038/s41598-017-14769-z] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Accepted: 10/11/2017] [Indexed: 11/09/2022] Open
Abstract
Habituation of wild great apes for tourism and research has had a significant positive effect on the conservation of these species. However, risks associated with such activities have been identified, specifically the transmission of human respiratory viruses to wild great apes, causing high morbidity and, occasionally, mortality. Here, we investigate the source of bacterial-viral co-infections in wild and captive chimpanzee communities in the course of several respiratory disease outbreaks. Molecular analyses showed that human respiratory syncytial viruses (HRSV) and human metapneumoviruses (HMPV) were involved in the etiology of the disease. In addition our analysis provide evidence for coinfection with Streptococcus (S.) pneumoniae. Characterisation of isolates from wild chimpanzees point towards a human origin of these bacteria. Transmission of these bacteria is of concern because - in contrast to HRSV and HMPV - S. pneumoniae can become part of the nasopharyngeal flora, contributing to the severity of respiratory disease progression. Furthermore these bacteria have the potential to spread to other individuals in the community and ultimately into the population. Targeted vaccination programs could be used to vaccinate habituated great apes but also human populations around great ape habitats, bringing health benefits to both humans and wild great apes.
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Affiliation(s)
- Sophie Köndgen
- Epidemiology of highly pathogenic microorganisms, Robert Koch-Institute, 13353, Berlin, Germany.,Institute of Medical Virology, Charité - Universitätsmedizin Berlin, 10117, Berlin, Germany
| | | | - Kim Grützmacher
- Epidemiology of highly pathogenic microorganisms, Robert Koch-Institute, 13353, Berlin, Germany
| | - Verena Keil
- Epidemiology of highly pathogenic microorganisms, Robert Koch-Institute, 13353, Berlin, Germany
| | | | - Kathrin Nowak
- Epidemiology of highly pathogenic microorganisms, Robert Koch-Institute, 13353, Berlin, Germany.,Department for Infectious Disease Epidemiology, Robert-Koch-Institute, 13353, Berlin, Germany
| | - Sonja Metzger
- Max Planck Institute for Evolutionary Anthropology, Department of Primatology, 04103, Leipzig, Germany.,Evolutionary Ecology, Leipniz Institute for Zoo and Wildlife Research, 10315, Berlin, Germany
| | - John Kiyang
- Limbe Wildlife Centre, Limbe, SW Region, Cameroon
| | - Antina Lübke-Becker
- Berlin Institute of Microbiology and Epizootics, Freie Universität Berlin, 14163, Berlin, Germany
| | - Tobias Deschner
- Max Planck Institute for Evolutionary Anthropology, Department of Primatology, 04103, Leipzig, Germany
| | - Roman M Wittig
- Max Planck Institute for Evolutionary Anthropology, Department of Primatology, 04103, Leipzig, Germany.,Taï Chimpanzee Project, Centre Suisse de Recherches Scientifiques, 01 BP 1303, Abidjan, Ivory Coast
| | - Felix Lankester
- Limbe Wildlife Centre, Limbe, SW Region, Cameroon.,Paul G. Allen School for Global Animal Health, Washington State University, Pullman, WA, 99164, USA
| | - Fabian H Leendertz
- Epidemiology of highly pathogenic microorganisms, Robert Koch-Institute, 13353, Berlin, Germany.
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3
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A tetracycline-inducible integrative expression system for Streptococcus pneumoniae. FEMS Microbiol Lett 2017; 364:3038572. [DOI: 10.1093/femsle/fnx044] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Accepted: 02/20/2017] [Indexed: 12/12/2022] Open
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Laux A, Sexauer A, Sivaselvarajah D, Kaysen A, Brückner R. Control of competence by related non-coding csRNAs in Streptococcus pneumoniae R6. Front Genet 2015; 6:246. [PMID: 26257773 PMCID: PMC4507080 DOI: 10.3389/fgene.2015.00246] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Accepted: 07/06/2015] [Indexed: 02/03/2023] Open
Abstract
The two-component regulatory system CiaRH of Streptococcus pneumoniae is involved in β-lactam resistance, maintenance of cell integrity, bacteriocin production, host colonization, virulence, and competence. The response regulator CiaR controls, among other genes, expression of five highly similar small non-coding RNAs, designated csRNAs. These csRNAs control competence development by targeting comC, encoding the precursor of the competence stimulating peptide, which is essential to initiate the regulatory cascade leading to competence. In addition, another gene product of the CiaR regulon, the serine protease HtrA, is also involved in competence control. In the absence of HtrA, five csRNAs could suppress competence, but one csRNA alone was not effective. To determine if all csRNAs are needed, reporter gene fusions to competence genes were used to monitor competence gene expression in the presence of different csRNAs. These experiments showed that two csRNAs were not enough to prevent competence, but combinations of three csRNAs, csRNA1,2,3, or csRNA1,2,4 were sufficient. In S. pneumoniae strains expressing only csRNA5, a surprising positive effect was detected on the level of early competence gene expression. Hence, the role of the csRNAs in competence regulation is more complex than anticipated. Mutations in comC (comC8) partially disrupting predicted complementarity to the csRNAs led to competence even in the presence of all csRNAs. Reconstitution of csRNA complementarity to comC8 restored competence suppression. Again, more than one csRNA was needed. In this case, even two mutated csRNAs complementary to comC8, csRNA1–8 and csRNA2–8, were suppressive. In conclusion, competence in S. pneumoniae is additively controlled by the csRNAs via post-transcriptional regulation of comC.
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Affiliation(s)
- Anke Laux
- Department of Microbiology, University of Kaiserslautern Kaiserslautern, Germany
| | - Anne Sexauer
- Department of Microbiology, University of Kaiserslautern Kaiserslautern, Germany
| | | | - Anne Kaysen
- Department of Microbiology, University of Kaiserslautern Kaiserslautern, Germany
| | - Reinhold Brückner
- Department of Microbiology, University of Kaiserslautern Kaiserslautern, Germany
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5
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Todorova K, Maurer P, Rieger M, Becker T, Bui NK, Gray J, Vollmer W, Hakenbeck R. Transfer of penicillin resistance from Streptococcus oralis to Streptococcus pneumoniae identifies murE as resistance determinant. Mol Microbiol 2015; 97:866-80. [PMID: 26010014 DOI: 10.1111/mmi.13070] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/21/2015] [Indexed: 01/26/2023]
Abstract
Beta-lactam resistant clinical isolates of Streptococcus pneumoniae contain altered penicillin-binding protein (PBP) genes and occasionally an altered murM, presumably products of interspecies gene transfer. MurM and MurN are responsible for the synthesis of branched lipid II, substrate for the PBP catalyzed transpeptidation reaction. Here we used the high-level beta-lactam resistant S. oralis Uo5 as donor in transformation experiments with the sensitive laboratory strain S. pneumoniae R6 as recipient. Surprisingly, piperacillin-resistant transformants contained no alterations in PBP genes but carried murEUo5 encoding the UDP-N-acetylmuramyl tripeptide synthetase. Codons 83-183 of murEUo5 were sufficient to confer the resistance phenotype. Moreover, the promoter of murEUo5 , which drives a twofold higher expression compared to that of S. pneumoniae R6, could also confer increased resistance. Multiple independent transformations produced S. pneumoniae R6 derivatives containing murEUo5 , pbp2xUo5 , pbp1aUo5 and pbp2bUo5 , but not murMUo5 sequences; however, the resistance level of the donor strain could not be reached. S. oralis Uo5 harbors an unusual murM, and murN is absent. Accordingly, the peptidoglycan of S. oralis Uo5 contained interpeptide bridges with one L-Ala residue only. The data suggest that resistance in S. oralis Uo5 is based on a complex interplay of distinct PBPs and other enzymes involved in peptidoglycan biosynthesis.
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Affiliation(s)
- Katya Todorova
- Department of Microbiology, University of Kaiserslautern, Kaiserslautern, Germany
| | - Patrick Maurer
- Department of Microbiology, University of Kaiserslautern, Kaiserslautern, Germany
| | - Martin Rieger
- Department of Microbiology, University of Kaiserslautern, Kaiserslautern, Germany
| | - Tina Becker
- Department of Microbiology, University of Kaiserslautern, Kaiserslautern, Germany
| | - Nhat Khai Bui
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, NE2 4AX, UK
| | - Joe Gray
- Institute for Cell and Molecular Biosciences, Pinnacle Laboratory, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Waldemar Vollmer
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, NE2 4AX, UK
| | - Regine Hakenbeck
- Department of Microbiology, University of Kaiserslautern, Kaiserslautern, Germany
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Schnorpfeil A, Kranz M, Kovács M, Kirsch C, Gartmann J, Brunner I, Bittmann S, Brückner R. Target evaluation of the non-coding csRNAs reveals a link of the two-component regulatory system CiaRH to competence control in Streptococcus pneumoniae R6. Mol Microbiol 2013; 89:334-49. [PMID: 23710838 DOI: 10.1111/mmi.12277] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/22/2013] [Indexed: 11/30/2022]
Abstract
The two-component regulatory system CiaRH of Streptococcus pneumoniae controls 25 genes, five of which specify homologous small non-coding csRNAs (cia-dependent small RNAs). The csRNAs were predicted to act regulatory as base-pairing sRNAs, but their targets have not been identified. By csRNA gene inactivations we established that the major phenotypes associated with a hyperactive CiaRH system, enhanced β-lactam resistance and prevention of genetic competence, are dependent on the csRNAs. Computational target predictions and evaluations by translational fusions identified six genes to be under csRNA control: spr0081, spr0371, spr0159, spr0551, spr1097 and spr2043(comC). Measuring the effect of single csRNAs on three targets indicated that they acted additively. One of the targets, comC(spr2043), encoding the precursor of the competence stimulating pheromone CSP, constitutes a link of CiaRH to competence control. Partially disrupting predicted csRNA-comC complementarity led to strongly diminished repression by the csRNAs and to transformability in a strain with a hyperactive CiaRH. Thus, a hyperactive CiaRH system prevents competence development by csRNA-dependent post-transcriptional repression of CSP production. The csRNAs are also involved in competence regulation in the wild-type strain R6, but their activity is only apparent in the absence of the protease gene htrA, another CiaRH regulon member.
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Affiliation(s)
- Anke Schnorpfeil
- Department of Microbiology, University of Kaiserslautern, D-67663, Kaiserslautern, Germany
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Calvignac-Spencer S, Leendertz SAJ, Gillespie TR, Leendertz FH. Wild great apes as sentinels and sources of infectious disease. Clin Microbiol Infect 2012; 18:521-7. [PMID: 22448813 DOI: 10.1111/j.1469-0691.2012.03816.x] [Citation(s) in RCA: 83] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Emerging zoonotic infectious diseases pose a serious threat to global health. This is especially true in relation to the great apes, whose close phylogenetic relationship with humans results in a high potential for microorganism exchange. In this review, we show how studies of the microorganisms of wild great apes can lead to the discovery of novel pathogens of importance for humans. We also illustrate how these primates, living in their natural habitats, can serve as sentinels for outbreaks of human disease in regions with a high likelihood of disease emergence. Greater sampling efforts and improvements in sample preservation and diagnostic capacity are rapidly improving our understanding of the diversity and distribution of microorganisms in wild great apes. Linking non-invasive diagnostic data with observational health data from great apes habituated to human presence is a promising approach for the discovery of pathogens of high relevance for humans.
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