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Alcorlo M, Abdullah MR, Steil L, Sotomayor F, López-de Oro L, de Castro S, Velázquez S, Kohler TP, Jiménez E, Medina A, Usón I, Keller LE, Bradshaw JL, McDaniel LS, Camarasa MJ, Völker U, Hammerschmidt S, Hermoso JA. Molecular and structural basis of oligopeptide recognition by the Ami transporter system in pneumococci. PLoS Pathog 2024; 20:e1011883. [PMID: 38838057 PMCID: PMC11192437 DOI: 10.1371/journal.ppat.1011883] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 06/21/2024] [Accepted: 04/30/2024] [Indexed: 06/07/2024] Open
Abstract
ATP-binding cassette (ABC) transport systems are crucial for bacteria to ensure sufficient uptake of nutrients that are not produced de novo or improve the energy balance. The cell surface of the pathobiont Streptococcus pneumoniae (pneumococcus) is decorated with a substantial array of ABC transporters, critically influencing nasopharyngeal colonization and invasive infections. Given the auxotrophic nature of pneumococci for certain amino acids, the Ami ABC transporter system, orchestrating oligopeptide uptake, becomes indispensable in host compartments lacking amino acids. The system comprises five exposed Oligopeptide Binding Proteins (OBPs) and four proteins building the ABC transporter channel. Here, we present a structural analysis of all the OBPs in this system. Multiple crystallographic structures, capturing both open and closed conformations along with complexes involving chemically synthesized peptides, have been solved at high resolution providing insights into the molecular basis of their diverse peptide specificities. Mass spectrometry analysis of oligopeptides demonstrates the unexpected remarkable promiscuity of some of these proteins when expressed in Escherichia coli, displaying affinity for a wide range of peptides. Finally, a model is proposed for the complete Ami transport system in complex with its various OBPs. We further disclosed, through in silico modelling, some essential structural changes facilitating oligopeptide transport into the cellular cytoplasm. Thus, the structural analysis of the Ami system provides valuable insights into the mechanism and specificity of oligopeptide binding by the different OBPs, shedding light on the intricacies of the uptake mechanism and the in vivo implications for this human pathogen.
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Affiliation(s)
- Martín Alcorlo
- Department of Crystallography and Structural Biology, Institute of Physical-Chemistry “Blas Cabrera”, Spanish National Research Council (CSIC), Madrid; Spain
| | - Mohammed R. Abdullah
- Department of Molecular Genetics and Infection Biology, Interfaculty Institute for Genetics and Functional Genomics, Center for Functional Genomics of Microbes, University of Greifswald, Greifswald; Germany
| | - Leif Steil
- Department of Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, Center for Functional Genomics of Microbes, University Medicine Greifswald, Greifswald; Germany
| | - Francisco Sotomayor
- Department of Crystallography and Structural Biology, Institute of Physical-Chemistry “Blas Cabrera”, Spanish National Research Council (CSIC), Madrid; Spain
| | - Laura López-de Oro
- Department of Crystallography and Structural Biology, Institute of Physical-Chemistry “Blas Cabrera”, Spanish National Research Council (CSIC), Madrid; Spain
| | | | | | - Thomas P. Kohler
- Department of Molecular Genetics and Infection Biology, Interfaculty Institute for Genetics and Functional Genomics, Center for Functional Genomics of Microbes, University of Greifswald, Greifswald; Germany
| | - Elisabet Jiménez
- Crystallographic Methods, Institute of Molecular Biology of Barcelona (IBMB-CSIC), Barcelona Science Park, Helix Building, Barcelona; Spain
| | - Ana Medina
- Crystallographic Methods, Institute of Molecular Biology of Barcelona (IBMB-CSIC), Barcelona Science Park, Helix Building, Barcelona; Spain
| | - Isabel Usón
- Crystallographic Methods, Institute of Molecular Biology of Barcelona (IBMB-CSIC), Barcelona Science Park, Helix Building, Barcelona; Spain
- ICREA, Institució Catalana de Recerca i Estudis Avançats, Barcelona; Spain
| | - Lance E. Keller
- Center for Immunology and Microbial Research, University of Mississippi Medical Center, Jackson, Mississippi; United States of America
- Department of Cell and Molecular Biology, University of Mississippi Medical Center, Jackson, Mississippi; United States of America
| | - Jessica L. Bradshaw
- Department of Microbiology and Immunology, University of Mississippi Medical Center, Jackson, Mississippi; United States of America
| | - Larry S. McDaniel
- Center for Immunology and Microbial Research, University of Mississippi Medical Center, Jackson, Mississippi; United States of America
- Department of Cell and Molecular Biology, University of Mississippi Medical Center, Jackson, Mississippi; United States of America
| | | | - Uwe Völker
- Department of Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, Center for Functional Genomics of Microbes, University Medicine Greifswald, Greifswald; Germany
| | - Sven Hammerschmidt
- Department of Molecular Genetics and Infection Biology, Interfaculty Institute for Genetics and Functional Genomics, Center for Functional Genomics of Microbes, University of Greifswald, Greifswald; Germany
| | - Juan A. Hermoso
- Department of Crystallography and Structural Biology, Institute of Physical-Chemistry “Blas Cabrera”, Spanish National Research Council (CSIC), Madrid; Spain
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2
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Kanojiya P, Saroj SD. Effect of respiratory tract co-colonizers on initial attachment of Neisseria meningitidis. Arch Microbiol 2023; 205:273. [PMID: 37400657 DOI: 10.1007/s00203-023-03612-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 06/16/2023] [Accepted: 06/19/2023] [Indexed: 07/05/2023]
Abstract
Respiratory tract is a complex system comprising of unique microbiota inhabitants. Neisseria meningitidis, Staphylococcus aureus, Streptococcus pyogenes, Pseudomonas aeruginosa and Klebsiella pneumoniae are few prevalent bacteria in the community composition during lung infections. Although, N. meningitidis resides asymptomatically in nasopharynx of the human host, it can cause fatal infections like meningitis. However, factors affecting transit from carriage to symptomatic infection are not well understood. Various host metabolites and environmental conditions affect the virulence of bacteria. Here, we report that presence of co-colonizers significantly reduces the initial attachment of N. meningitidis to A549 nasopharyngeal epithelial cells. Further, significant decrease in invasion to A549 nasopharyngeal epithelial cells was observed. Moreover, survival in J774A.1 murine macrophage also increases significantly when conditioned media (CM) from S. pyogenes and L. rhamnosus is used for culturing N. meningitidis. The increase in survival could be attributed to increased capsule synthesis. The gene expression studies revealed increased expression of siaC and ctrB in CM prepared from the growth S. pyogenes and L. rhamnosus. Overall, the results suggest change in the virulence of N. meningitidis is assisted by lung microbiota.
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Affiliation(s)
- Poonam Kanojiya
- Symbiosis School of Biological Sciences, Symbiosis International (Deemed University), Lavale, Pune, Maharashtra, 412115, India
| | - Sunil D Saroj
- Symbiosis School of Biological Sciences, Symbiosis International (Deemed University), Lavale, Pune, Maharashtra, 412115, India.
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3
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AmiA and AliA peptide ligands are secreted by Klebsiella pneumoniae and inhibit growth of Streptococcus pneumoniae. Sci Rep 2022; 12:22268. [PMID: 36564446 PMCID: PMC9789142 DOI: 10.1038/s41598-022-26838-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 12/21/2022] [Indexed: 12/24/2022] Open
Abstract
Streptococcus pneumoniae colonizes the human nasopharynx, a multi-species microbial niche. Pneumococcal Ami-AliA/AliB oligopeptide permease is an ABC transporter involved in environmental sensing with peptides AKTIKITQTR, FNEMQPIVDRQ, and AIQSEKARKHN identified as ligands of its substrate binding proteins AmiA, AliA, and AliB, respectively. These sequences match ribosomal proteins of multiple bacterial species, including Klebsiella pneumoniae. By mass spectrometry, we identified such peptides in the Klebsiella pneumoniae secretome. AmiA and AliA peptide ligands suppressed pneumococcal growth, but the effect was dependent on peptide length. Growth was suppressed for diverse pneumococci, including antibiotic-resistant strains, but not other bacterial species tested, with the exception of Streptococcus pseudopneumoniae, whose growth was suppressed by the AmiA peptide ligand. By multiple sequence alignments and protein and peptide binding site predictions, for AmiA we have identified the location of an amino acid in the putative binding site whose mutation appears to result in loss of response to the peptide. Our results indicate that pneumococci sense the presence of Klebsiella pneumoniae peptides in the environment.
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4
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Ganaie F, Branche AR, Peasley M, Rosch JW, Nahm MH. Oral streptococci expressing pneumococci-like cross-reactive capsule types can affect WHO recommended pneumococcal carriage procedure. Clin Infect Dis 2021; 75:647-656. [PMID: 34891152 DOI: 10.1093/cid/ciab1003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND Carriage studies are fundamental to assess the effects of pneumococcal vaccines. Since a large proportion of oral streptococci carry homologs of pneumococcal genes, nonculture-based detection and serotyping of upper respiratory tract (URT) samples can be problematic. Herein, we investigated if culture-free molecular methods could differentiate pneumococci from oral streptococci carried by adults in URT. METHODS Paired nasopharyngeal (NP) and oropharyngeal (OP) samples were collected from 100 older adults twice a month for one year. Extracts from the combined NP+OP samples (n=2400) were subjected to lytA real-time PCR. Positive samples were subjected to pure culture isolation followed by species confirmation using multiple approaches. Multibead assay and whole-genome sequencing were used for serotyping. RESULTS lytA-PCR was positive in 301 combined NP+OP extracts, 20 of which grew probable pneumococcal-like colonies based on colony morphology and biochemical tests. Multiple approaches confirmed that four isolates were S. pneumoniae, three were S. psuedopneumoniae, and thirteen were S. mitis. Eight nonpneumococcal strains carried pneumococcus-like cps loci (size: ~18 to 25 kb) that showed >70% of nucleotide identity with their pneumococcal counterparts. While investigating the antigenic profile, we found some S. mitis strains (P066 and P107) reacted with both serotype-specific polyclonal (Type 39 and FS17b) and monoclonal (Hyp10AG1 and Hyp17FM1) antisera, whereas some strains (P063 and P074) reacted only with polyclonal antisera (Type 5 and FS35a). CONCLUSION The extensive capsular overlap suggests that pneumococcal vaccines could reduce carriage of oral streptococci expressing cross-reactive capsules. Further, direct use of culture-free PCR-based methods in URT samples has limited usefulness for carriage studies.
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Affiliation(s)
- Feroze Ganaie
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Angela R Branche
- Department of Medicine, University of Rochester, Rochester, NY, USA
| | - Michael Peasley
- Department of Medicine, University of Rochester, Rochester, NY, USA
| | - Jason W Rosch
- Department of Infectious Diseases, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Moon H Nahm
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
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5
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Bradshaw JL, Rafiqullah IM, Robinson DA, McDaniel LS. Transformation of nonencapsulated Streptococcus pneumoniae during systemic infection. Sci Rep 2020; 10:18932. [PMID: 33144660 PMCID: PMC7641166 DOI: 10.1038/s41598-020-75988-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 10/16/2020] [Indexed: 11/24/2022] Open
Abstract
Streptococcus pneumoniae (pneumococcus) is a principal cause of bacterial middle ear infections, pneumonia, and meningitis. Capsule-targeted pneumococcal vaccines have likely contributed to increased carriage of nonencapsulated S. pneumoniae (NESp). Some NESp lineages are associated with highly efficient DNA uptake and transformation frequencies. However, NESp strains lack capsule that may increase disease severity. We tested the hypothesis that NESp could acquire capsule during systemic infection and transform into more virulent pneumococci. We reveal that NESp strains MNZ67 and MNZ41 are highly transformable and resistant to multiple antibiotics. Natural transformation of NESp when co-administered with heat-killed encapsulated strain WU2 in a murine model of systemic infection resulted in encapsulation of NESp and increased virulence during bacteremia. Functional capsule production increased the pathogenic potential of MNZ67 by significantly decreasing complement deposition on the bacterial surface. However, capsule acquisition did not further decrease complement deposition on the relatively highly pathogenic strain MNZ41. Whole genome sequencing of select transformants demonstrated that recombination of up to 56.7 kbp length occurred at the capsule locus, along with additional recombination occurring at distal sites harboring virulence-associated genes. These findings indicate NESp can compensate for lack of capsule production and rapidly evolve into more virulent strains.
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Affiliation(s)
- Jessica L Bradshaw
- Department of Microbiology and Immunology, University of Mississippi Medical Center, Jackson, MS, USA.,Department of Physiology and Anatomy, University of North Texas Health Science Center, Fort Worth, TX, USA
| | - Iftekhar M Rafiqullah
- Department of Microbiology and Immunology, University of Mississippi Medical Center, Jackson, MS, USA
| | - D Ashley Robinson
- Department of Microbiology and Immunology, University of Mississippi Medical Center, Jackson, MS, USA
| | - Larry S McDaniel
- Department of Microbiology and Immunology, University of Mississippi Medical Center, Jackson, MS, USA.
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6
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Nasher F, Kwun MJ, Croucher NJ, Heller M, Hathaway LJ. Peptide Occurring in Enterobacteriaceae Triggers Streptococcus pneumoniae Cell Death. Front Cell Infect Microbiol 2019; 9:320. [PMID: 31552200 PMCID: PMC6748166 DOI: 10.3389/fcimb.2019.00320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Accepted: 08/26/2019] [Indexed: 11/15/2022] Open
Abstract
Non-encapsulated Streptococcus pneumoniae often possess two genes, aliB-like ORF 1 and aliB-like ORF 2, in place of capsule genes. AliB-like ORF 1 is thought to encode a substrate binding protein of an ABC transporter which binds peptide SETTFGRDFN, found in 50S ribosomal subunit protein L4 of Enterobacteriaceae. Here, we investigated the effect of binding of AliB-like ORF 1 peptide on the transcriptome and proteome of non-encapsulated pneumococci. We found upregulation of gene expression of a metacaspase and a gene encoding N-acetylmuramoyl-L-alanine amidase, both of which are proposed to be involved in programmed cell death in prokaryotic cells. Proteome profiling indicated upregulation of transcriptional regulators and downregulation of metabolism-associated genes. Exposure to the peptide specifically triggered death in pneumococci which express AliB-like ORF 1, with the bacteria having an apoptotic appearance by electron microscopy. We propose that binding of the AliB-like ORF 1 peptide ligand by the pneumococcus signals a challenging environment with hostile bacterial species leading to death of a proportion of the pneumococcal population.
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Affiliation(s)
- Fauzy Nasher
- Institute for Infectious Diseases, Faculty of Medicine, University of Bern, Bern, Switzerland.,Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Min Jung Kwun
- Department of Infectious Disease Epidemiology, MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, United Kingdom
| | - Nicholas J Croucher
- Department of Infectious Disease Epidemiology, MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, United Kingdom
| | - Manfred Heller
- Proteomics and Mass Spectrometry Core Facility, Department for BioMedical Research, University of Bern, Bern, Switzerland
| | - Lucy J Hathaway
- Institute for Infectious Diseases, Faculty of Medicine, University of Bern, Bern, Switzerland
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7
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Hathaway LJ. New Virulence Factors Identified in Pneumococcal Meningitis. Trends Microbiol 2019; 27:895-896. [PMID: 31506191 DOI: 10.1016/j.tim.2019.08.008] [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: 08/08/2019] [Accepted: 08/26/2019] [Indexed: 11/15/2022]
Abstract
Streptococcus pneumoniae causes bacterial meningitis with a high fatality rate globally. Patients who survive have a significant risk of lasting disabilities. Schmidt et al. have identified bacterial proteins that play a crucial role in pneumococcal meningitis: AliB, part of an oligopeptide transporter, and ComDE of the competence regulator.
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Affiliation(s)
- Lucy J Hathaway
- Institute for Infectious Diseases, Faculty of Medicine, University of Bern, Friedbühlstrasse 51, CH-3001 Bern, Switzerland.
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8
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Nasher F, Aguilar F, Aebi S, Hermans PWM, Heller M, Hathaway LJ. Peptide Ligands of AmiA, AliA, and AliB Proteins Determine Pneumococcal Phenotype. Front Microbiol 2018; 9:3013. [PMID: 30568648 PMCID: PMC6290326 DOI: 10.3389/fmicb.2018.03013] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Accepted: 11/21/2018] [Indexed: 12/13/2022] Open
Abstract
The Ami-AliA/AliB oligopeptide permease of Streptococcus pneumoniae has been suggested to play a role in environmental sensing and colonisation of the nasopharynx by this human bacterial pathogen by binding peptides derived from bacterial neighbours of other species in the microbiota. Here, we investigated the effects of the peptide ligands of the permease’s substrate binding proteins AmiA, AliA, and AliB on pneumococcal phenotype. AmiA and AliA ligands reduced pneumococcal growth, increased biofilm production and reduced capsule size. In contrast, AliB ligand increased growth and greatly increased bacterial chain length. A decrease in transformation rate was observed in response to all three peptides. Changes in protein expression were also observed, particularly those associated with metabolism and cell wall synthesis. Understanding interspecies bacterial communication and its effect on development of colonising versus invasive phenotypes has the potential to reveal new targets to tackle and prevent pneumococcal infections.
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Affiliation(s)
- Fauzy Nasher
- Institute for Infectious Diseases, Faculty of Medicine, University of Bern, Bern, Switzerland.,Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Fernando Aguilar
- Institute for Infectious Diseases, Faculty of Medicine, University of Bern, Bern, Switzerland
| | - Suzanne Aebi
- Institute for Infectious Diseases, Faculty of Medicine, University of Bern, Bern, Switzerland
| | - Peter W M Hermans
- Janssen Vaccines and Prevention, Leiden, Netherlands.,Julius Center, UMC Utrecht, Utrecht, Netherlands
| | - Manfred Heller
- Proteomics and Mass Spectrometry Core Facility, Department for BioMedical Research (DBMR), University of Bern, Bern, Switzerland
| | - Lucy J Hathaway
- Institute for Infectious Diseases, Faculty of Medicine, University of Bern, Bern, Switzerland
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9
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Nasher F, Förster S, Yildirim EC, Grandgirard D, Leib SL, Heller M, Hathaway LJ. Foreign peptide triggers boost in pneumococcal metabolism and growth. BMC Microbiol 2018; 18:23. [PMID: 29580217 PMCID: PMC5870813 DOI: 10.1186/s12866-018-1167-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Accepted: 03/15/2018] [Indexed: 01/19/2023] Open
Abstract
Background Nonencapsulated Streptococcus pneumoniae bacteria are successful colonizers of the human nasopharynx and often possess genes aliB-like ORF 1 and 2 in place of capsule genes. AliB-like ORF 2 binds peptide FPPQSV, found in Prevotella species, resulting in enhanced colonization. How this response is mediated is so far unknown. Results Here we show that the peptide increases expression of genes involved in release of host carbohydrates, carbohydrate uptake and carbohydrate metabolism. In particular, the peptide increased expression of 1,5-anhydro-D-fructose reductase, a metabolic enzyme of an alternative starch and glycogen degrading pathway found in many organisms, in both transcriptomic and proteomic data. The peptide enhanced pneumococcal growth giving a competitive advantage to a strain with aliB-like ORF 2, over its mutant lacking the gene. Possession of aliB-like ORF 2 did not affect release of inflammatory cytokine CXCL8 from epithelial cells in culture and the nonencapsulated wild type strain was not able to establish disease or inflammation in an infant rat model of meningitis. Conclusions We propose that AliB-like ORF 2 confers an advantage in colonization by enhancing carbohydrate metabolism resulting in a boost in growth. This may explain the widespread presence of aliB-like ORF 2 in the nonencapsulated pneumococcal population in the human nasopharynx. Electronic supplementary material The online version of this article (10.1186/s12866-018-1167-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Fauzy Nasher
- 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
| | - Sunniva Förster
- 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.,Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland
| | - Efe C Yildirim
- Institute for Infectious Diseases, Faculty of Medicine, University of Bern, Friedbühlstrasse 51, CH-3001, Bern, Switzerland
| | - Denis Grandgirard
- Institute for Infectious Diseases, Faculty of Medicine, University of Bern, Friedbühlstrasse 51, CH-3001, Bern, Switzerland
| | - Stephen L Leib
- Institute for Infectious Diseases, Faculty of Medicine, University of Bern, Friedbühlstrasse 51, CH-3001, Bern, Switzerland
| | - Manfred Heller
- Proteomics and Mass Spectrometry Core Facility, Department for BioMedical Research, University of Bern, CH-3010, Bern, Switzerland
| | - Lucy J Hathaway
- Institute for Infectious Diseases, Faculty of Medicine, University of Bern, Friedbühlstrasse 51, CH-3001, Bern, Switzerland.
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10
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Mucosal Infections and Invasive Potential of Nonencapsulated Streptococcus pneumoniae Are Enhanced by Oligopeptide Binding Proteins AliC and AliD. mBio 2018; 9:mBio.02097-17. [PMID: 29339428 PMCID: PMC5770551 DOI: 10.1128/mbio.02097-17] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Nonencapsulated Streptococcus pneumoniae (NESp) is an emerging human pathogen that colonizes the nasopharynx and is associated with noninvasive diseases such as otitis media (OM), conjunctivitis, and nonbacteremic pneumonia. Since capsule expression was previously thought to be necessary for establishment of invasive pneumococcal disease (IPD), serotype-specific polysaccharide capsules are targeted by currently licensed pneumococcal vaccines. Yet, NESp expressing oligopeptide binding proteins AliC and AliD have been isolated during IPD. Thus, we hypothesize AliC and AliD are major NESp virulence determinants that facilitate persistence and development of IPD. Our study reveals that NESp expressing AliC and AliD have intensified virulence compared to isogenic mutants. Specifically, we demonstrate AliC and AliD enhance murine nasopharyngeal colonization and pulmonary infection and are required for OM in a chinchilla model. Furthermore, AliC and AliD increase pneumococcal survival in chinchilla whole blood and aid in resistance to killing by human leukocytes. Comparative proteome analysis revealed significant alterations in protein levels when AliC and AliD were absent. Virulence-associated proteins, including a pneumococcal surface protein C variant (CbpAC), were significantly downregulated, while starvation response indicators were upregulated in the double mutant relative to wild-type levels. We also reveal that differentially expressed CbpAC was essential for NESp adherence to epithelial cells, virulence during OM, reduction of C3b deposition on the NESp surface, and binding to nonspecific IgA. Altogether, the rise in NESp prevalence urges the need to understand how NESp establishes disease and persists in a host. This study highlights the roles of AliC, AliD, and CbpAC in the pathogenesis of NESp. Despite the effective, widespread use of licensed pneumococcal vaccines over many decades, pneumococcal infections remain a worldwide burden resulting in high morbidity and mortality. NESp subpopulations are rapidly rising in the wake of capsule-targeted vaccine strategies, yet there is very little knowledge on NESp pathogenic potential and virulence mechanisms. Although NESp lacks a protective capsule, NESp lineages expressing AliC and AliD have been associated with systemic infections. Furthermore, higher antibiotic resistance rates and transformation efficiencies associated with emerging NESp threaten treatment strategies needed to control pneumococcal infections and transmission. Elucidating how NESp survives within a host and establishes disease is necessary for development of broadened pneumococcal prevention methods. Our study identifies virulence determinants and host survival mechanisms employed by NESp with a high pathogenic potential. Moreover, our study also identifies virulence determinants shared by NESp and encapsulated strains that may serve as broad prevention and therapeutic targets.
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11
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Nasher F, Heller M, Hathaway LJ. Streptococcus pneumoniae Proteins AmiA, AliA, and AliB Bind Peptides Found in Ribosomal Proteins of Other Bacterial Species. Front Microbiol 2018; 8:2688. [PMID: 29379482 PMCID: PMC5775242 DOI: 10.3389/fmicb.2017.02688] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Accepted: 12/26/2017] [Indexed: 11/13/2022] Open
Abstract
The nasopharynx is frequently colonized by both commensal and pathogenic bacteria including Streptococcus pneumoniae (pneumococcus). Pneumococcus is an important pathogen responsible for bacterial meningitis and community acquired pneumonia but is also commonly an asymptomatic colonizer of the nasopharynx. Understanding interactions between microbes may provide insights into pathogenesis. Here, we investigated the ability of the three oligopeptide-binding proteins AmiA, AliA, and AliB of an ATP-binding cassette transporter of pneumococcus to detect short peptides found in other bacterial species. We found three possible peptide ligands for AmiA and four each for AliA and AliB of which two for each protein matched ribosomal proteins of other bacterial species. Using synthetic peptides we confirmed the following binding: AmiA binds peptide AKTIKITQTR, matching 50S ribosomal subunit protein L30, AliA binds peptide FNEMQPIVDRQ, matching 30S ribosomal protein S20, and AliB binds peptide AIQSEKARKHN, matching 30S ribosomal protein S20, without excluding the possibility of binding of the other peptides. These Ami-AliA/AliB peptide ligands are found in multiple species in the class of Gammaproteobacteria which includes common colonizers of the nostrils and nasopharynx. Binding such peptides may enable pneumococcus to detect and respond to neighboring species in its environment and is a potential mechanism for interspecies communication and environmental surveillance.
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Affiliation(s)
- Fauzy Nasher
- Institute for Infectious Diseases, Faculty of Medicine, University of Bern, Bern, Switzerland.,Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Manfred Heller
- Department of Clinical Research, Proteomics and Mass Spectrometry Core Facility, University of Bern, Bern, Switzerland
| | - Lucy J Hathaway
- Institute for Infectious Diseases, Faculty of Medicine, University of Bern, Bern, Switzerland
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12
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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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Schenck LP, Surette MG, Bowdish DME. Composition and immunological significance of the upper respiratory tract microbiota. FEBS Lett 2016; 590:3705-3720. [PMID: 27730630 PMCID: PMC7164007 DOI: 10.1002/1873-3468.12455] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Revised: 09/30/2016] [Accepted: 10/07/2016] [Indexed: 11/13/2022]
Abstract
The intestinal microbiota is essential for nutrient acquisition, immune development, and exclusion of invading pathogens. The upper respiratory tract (URT) microbiota is less well studied and does not appear to abide by many of the paradigms of the gastrointestinal tract. Decades of carriage studies in children have demonstrated that microbe–microbe competition and collusion occurs in the URT. Whether colonization with common pathogens (e.g., Staphylococcus aureus and Streptococcus pneumoniae) alters immune development or susceptibility to respiratory conditions is just beginning to be understood. Herein, we discuss the biogeography of the URT microbiota, the succession and evolution of the microbiota through the life course, and discuss the evidence for microbe–microbe interactions in colonization and infection.
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Affiliation(s)
- Louis Patrick Schenck
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Canada.,Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Canada
| | - Michael G Surette
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Canada.,Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Canada.,Department of Medicine, McMaster University, Hamilton, Canada
| | - Dawn M E Bowdish
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Canada.,Department of Pathology and Molecular Medicine, McMaster University, Hamilton, Canada
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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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Streptococcus pneumoniae Colonization Disrupts the Microbial Community within the Upper Respiratory Tract of Aging Mice. Infect Immun 2016; 84:906-16. [PMID: 26787714 DOI: 10.1128/iai.01275-15] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Accepted: 01/06/2016] [Indexed: 12/21/2022] Open
Abstract
Nasopharyngeal colonization by the Gram-positive bacterium Streptococcus pneumonia is a prerequisite for pneumonia and invasive pneumococcal diseases. Colonization is asymptomatic, involving dynamic and complex interplay between commensals, the host immune system, and environmental factors. The elderly are at an increased risk of developing pneumonia, which might be due to changes in the respiratory microbiota that would impact bacterial colonization and persistence within this niche. We hypothesized that the composition of the upper respiratory tract (URT) microbiota changes with age and subsequently can contribute to sustained colonization and inefficient clearance of S. pneumoniae To test this, we used a mouse model of pneumococcal colonization to compare the composition of the URT microbiota in young, middle-aged, and old mice in the naive state and during the course of colonization using nasal pharyngeal washes. Sequencing of variable region 3 (V3) of the 16S rRNA gene was used to identify changes occurring with age and throughout the course of S. pneumonia colonization. We discovered that age affects the composition of the URT microbiota and that colonization with S. pneumoniae is more disruptive of preexisting communities in older mice. We have further shown that host-pathogen interactions followingS. pneumonia colonization can impact the populations of resident microbes, including Staphylococcus and Haemophilus. Together, our findings indicate alterations to the URT microbiota could be detrimental to the elderly, resulting in increased colonization of S. pneumonia and decreased efficiency in its clearance.
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16
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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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Fontaine L, Wahl A, Fléchard M, Mignolet J, Hols P. Regulation of competence for natural transformation in streptococci. INFECTION GENETICS AND EVOLUTION 2015; 33:343-60. [DOI: 10.1016/j.meegid.2014.09.010] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2014] [Revised: 08/28/2014] [Accepted: 09/07/2014] [Indexed: 02/02/2023]
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18
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Hilty M, Wüthrich D, Salter SJ, Engel H, Campbell S, Sá-Leão R, de Lencastre H, Hermans P, Sadowy E, Turner P, Chewapreecha C, Diggle M, Pluschke G, McGee L, Eser ÖK, Low DE, Smith-Vaughan H, Endimiani A, Küffer M, Dupasquier M, Beaudoing E, Weber J, Bruggmann R, Hanage WP, Parkhill J, Hathaway LJ, Mühlemann K, Bentley SD. Global phylogenomic analysis of nonencapsulated Streptococcus pneumoniae reveals a deep-branching classic lineage that is distinct from multiple sporadic lineages. Genome Biol Evol 2014; 6:3281-94. [PMID: 25480686 PMCID: PMC4986459 DOI: 10.1093/gbe/evu263] [Citation(s) in RCA: 43] [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] [Accepted: 11/25/2014] [Indexed: 01/08/2023] Open
Abstract
The surrounding capsule of Streptococcus pneumoniae has been identified as a major virulence factor and is targeted by pneumococcal conjugate vaccines (PCV). However, nonencapsulated S. pneumoniae (non-Ec-Sp) have also been isolated globally, mainly in carriage studies. It is unknown if non-Ec-Sp evolve sporadically, if they have high antibiotic nonsusceptiblity rates and a unique, specific gene content. Here, whole-genome sequencing of 131 non-Ec-Sp isolates sourced from 17 different locations around the world was performed. Results revealed a deep-branching classic lineage that is distinct from multiple sporadic lineages. The sporadic lineages clustered with a previously sequenced, global collection of encapsulated S. pneumoniae (Ec-Sp) isolates while the classic lineage is comprised mainly of the frequently identified multilocus sequences types (STs) ST344 (n = 39) and ST448 (n = 40). All ST344 and nine ST448 isolates had high nonsusceptiblity rates to β-lactams and other antimicrobials. Analysis of the accessory genome reveals that the classic non-Ec-Sp contained an increased number of mobile elements, than Ec-Sp and sporadic non-Ec-Sp. Performing adherence assays to human epithelial cells for selected classic and sporadic non-Ec-Sp revealed that the presence of a integrative conjugative element (ICE) results in increased adherence to human epithelial cells (P = 0.005). In contrast, sporadic non-Ec-Sp lacking the ICE had greater growth in vitro possibly resulting in improved fitness. In conclusion, non-Ec-Sp isolates from the classic lineage have evolved separately. They have spread globally, are well adapted to nasopharyngeal carriage and are able to coexist with Ec-Sp. Due to continued use of PCV, non-Ec-Sp may become more prevalent.
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Affiliation(s)
- Markus Hilty
- Institute for Infectious Diseases, University of Bern, Switzerland Department of Infectious Diseases, Inselspital, Bern University Hospital and University of Bern, Switzerland
| | - Daniel Wüthrich
- Interfaculty Bioinformatics Unit, University of Bern, Switzerland Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | | | - Hansjürg Engel
- Institute for Infectious Diseases, University of Bern, Switzerland
| | - Samuel Campbell
- Institute for Infectious Diseases, University of Bern, Switzerland
| | - Raquel Sá-Leão
- Instituto de Tecnologia Química e Biológica, University of Lisbon, Portugal
| | - Hermínia de Lencastre
- Instituto de Tecnologia Química e Biológica, University of Lisbon, Portugal Laboratory of Microbiology and Infectious Diseases, The Rockefeller University
| | - Peter Hermans
- Laboratory of Pediatric Infectious Diseases, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Ewa Sadowy
- National Medicines Institute, Warsaw, Poland
| | - Paul Turner
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand Centre for Tropical Medicine, Nuffield Department of Medicine, University of Oxford, United Kingdom
| | - Claire Chewapreecha
- Wellcome Trust Sanger Institute, Hinxton, United Kingdom Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand
| | - Mathew Diggle
- Clinical Microbiology Department, Queens Medical Centre, Nottingham, United Kingdom
| | - Gerd Pluschke
- Swiss Tropical and Public Health Institute, University of Basel, Switzerland
| | - Lesley McGee
- Respiratory Diseases Branch, Centers for Disease Control and Prevention, Georgia, Atlanta
| | - Özgen Köseoğlu Eser
- Department of Microbiology, Medical Faculty, Hacettepe University, Ankara, Turkey
| | - Donald E Low
- Mt Sinai Hospital & Public Health Laboratories, Toronto, Ontario, Canada
| | | | - Andrea Endimiani
- Institute for Infectious Diseases, University of Bern, Switzerland
| | - Marianne Küffer
- Institute for Infectious Diseases, University of Bern, Switzerland
| | | | | | - Johann Weber
- Centre for Integrative Genomics, University of Lausanne, Switzerland
| | - Rémy Bruggmann
- Interfaculty Bioinformatics Unit, University of Bern, Switzerland Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - William P Hanage
- Department of Epidemiology, Center for Communicable Disease Dynamics, Harvard School of Public Health
| | | | - Lucy J Hathaway
- Institute for Infectious Diseases, University of Bern, Switzerland
| | - Kathrin Mühlemann
- Institute for Infectious Diseases, University of Bern, Switzerland Department of Infectious Diseases, Inselspital, Bern University Hospital and University of Bern, Switzerland
| | - Stephen D Bentley
- Wellcome Trust Sanger Institute, Hinxton, United Kingdom Department of Medicine, Addenbrookes Hospital, University of Cambridge, United Kingdom
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Abstract
Within Gram-positive bacteria, the expression of target genes is controlled at the population level via signaling peptides, also known as pheromones. Pheromones control a wide range of functions, including competence, virulence, and others that remain unknown. Until now, their role in bacterial gene regulation has probably been underestimated; indeed, bacteria are able to produce, by ribosomal synthesis or surface protein degradation, an extraordinary variety of peptides which are released outside bacteria and among which, some are pheromones that mediate cell-to-cell communication. The review aims at giving an updated overview of these peptide-dependant communication pathways. More specifically, it follows the whole peptide circuit from the peptide production and secretion in the extracellular medium to its interaction with sensors at bacterial surface or re-import into the bacteria where it plays its regulation role. In recent years, as we have accumulated more knowledge about these systems, it has become apparent that they are more complex than they first appeared. For this reason, more research on peptide-dependant pathways is needed to develop new strategies for controlling functions of interest in Gram-positive bacteria. In particular, such research could lead to alternatives to the use of antibiotics against pathogenic bacteria. In perspective, the review identifies new research questions that emerge in this field and that have to be addressed.
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Affiliation(s)
| | | | - Rozenn Gardan
- a INRA, MICALIS, Domaine de Vilvert , Jouy-en-Josas , France
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