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Bedoya-Correa CM, Betancur-Giraldo S, Franco J, Arango-Santander S. Probiotic Effect of Streptococcus dentisani on Oral Pathogens: An In Vitro Study. Pathogens 2024; 13:351. [PMID: 38787203 PMCID: PMC11123734 DOI: 10.3390/pathogens13050351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Revised: 04/15/2024] [Accepted: 04/23/2024] [Indexed: 05/25/2024] Open
Abstract
Probiotics, including Streptococcus dentisani, have been proposed as an alternative to re-establish the ecology of the oral cavity and inhibit the formation of pathogenic biofilms. The main objective of this work was to assess the probiotic ability of S. dentisani against Streptococcus mutans, Streptococcus mitis, and Candida albicans biofilms. The ability of the strains to form a monospecies biofilm and the probiotic potential of S. dentisani using the competition, exclusion, and displacement strategies were determined. All strains were moderate biofilm producers. The ability of S. dentisani to compete with and exclude S. mutans and S. mitis during biofilm formation was not significant. However, S. dentisani significantly reduced pathologic streptococcal biofilms using the displacement strategy. Also S. dentisani reduced the formation of the C. albicans biofilm mainly through competition and displacement. In vitro, S. dentisani exhibited probiotic potential to reduce the formation of potentially pathogenic biofilms. Further investigation is required to understand the biofilm-inhibiting mechanisms exhibited by this probiotic strain.
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Affiliation(s)
- Claudia María Bedoya-Correa
- GIOM Group, Faculty of Dentistry, Universidad Cooperativa de Colombia, Medellin 055421, Colombia; (J.F.); (S.A.-S.)
| | | | - John Franco
- GIOM Group, Faculty of Dentistry, Universidad Cooperativa de Colombia, Medellin 055421, Colombia; (J.F.); (S.A.-S.)
- Salud y Sostenibilidad Group, School of Microbiology, Universidad de Antioquia, Medellin 050010, Colombia
| | - Santiago Arango-Santander
- GIOM Group, Faculty of Dentistry, Universidad Cooperativa de Colombia, Medellin 055421, Colombia; (J.F.); (S.A.-S.)
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Ren Q, Zhang M, Xue R, Liu T, Yang Z, Yang Z. Purification and characterization of a novel low-molecular-weight antimicrobial peptide produced by Lactiplantibacillus plantarum NMGL2. Int J Biol Macromol 2023; 248:125932. [PMID: 37482152 DOI: 10.1016/j.ijbiomac.2023.125932] [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: 03/20/2023] [Revised: 07/18/2023] [Accepted: 07/19/2023] [Indexed: 07/25/2023]
Abstract
The present study aimed to purify and characterize a novel low-molecular-weight antimicrobial peptide (AMP) named as PNMGL2 produced by Lactiplantibacillus plantarum NMGL2. The AMP was effectively separated and purified by ethyl acetate extraction and DEAE-Sepharose anion exchange chromatography. Tricine-SDS-PAGE of the purified AMP showed a major protein band below 1.7 kDa, which was identified by MALDI-TOF MS to be a hexapeptide LNFLKK (761.95 Da), and structurally characterized to be combination of helixes and random coil by a PEP-FOLD 3 De novo approach. The antimicrobial activity of LNFLKK was confirmed by chemical synthesis of the peptide that showed clear inhibition (MIC 7.8 mg/mL) against both Gram-positive bacteria (Staphylococcus aureus and Listeria monocytogenes), and Gram-negative bacteria (Enterobacter sakazakii, Escherichia coli and Shigella flexneri). PNMGL2 was pH resistant (pH 2-9), heat stable (121 °C, 30 min), and protease sensitive. Treatment of UV rays, sodium chloride and organic solvents did not decrease the activity. Sequencing of the whole genome of L. plantarum NMGL2 revealed presence of a bacteriocin gene cluster with two putative bacteriocin genes (ORF4 and ORF5) that were not expressed, confirming the significance of PNMGL2 contributing the antimicrobial activity of the strain. This study demonstrated the low-molecular-weight AMP that was uncharacterized in the relevant available databases, suggesting its potential application as a novel natural food preservative.
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Affiliation(s)
- Qingxia Ren
- Key Laboratory of Geriatric Nutrition and Health of Ministry of Education, Beijing Technology and Business University, Beijing 100048, China; Beijing Engineering and Technology Research Center of Food Additives, Beijing Technology and Business University, Beijing 100048, China
| | - Min Zhang
- Key Laboratory of Agro-Products Primary Processing, Academy of Agricultural Planning and Engineering, Ministry of Agriculture and Rural Affairs, Beijing 100125, China
| | - Rui Xue
- Key Laboratory of Geriatric Nutrition and Health of Ministry of Education, Beijing Technology and Business University, Beijing 100048, China; Beijing Engineering and Technology Research Center of Food Additives, Beijing Technology and Business University, Beijing 100048, China
| | - Tongji Liu
- Key Laboratory of Geriatric Nutrition and Health of Ministry of Education, Beijing Technology and Business University, Beijing 100048, China; Beijing Engineering and Technology Research Center of Food Additives, Beijing Technology and Business University, Beijing 100048, China
| | - Zhennai Yang
- Key Laboratory of Geriatric Nutrition and Health of Ministry of Education, Beijing Technology and Business University, Beijing 100048, China; Beijing Engineering and Technology Research Center of Food Additives, Beijing Technology and Business University, Beijing 100048, China.
| | - Zhang Yang
- Department of Neurology, Affiliated Hospital of Guizhou Medical University, Guiyang 550025, China.
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Colomba C, Garbo V, Boncori G, Albano C, Bagarello S, Condemi A, Giordano S, Canduscio LA, Gallo C, Parrinello G, Cascio A. Streptococcus mitis as a New Emerging Pathogen in Pediatric Age: Case Report and Systematic Review. Antibiotics (Basel) 2023; 12:1222. [PMID: 37508318 PMCID: PMC10376791 DOI: 10.3390/antibiotics12071222] [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: 06/28/2023] [Revised: 07/20/2023] [Accepted: 07/20/2023] [Indexed: 07/30/2023] Open
Abstract
Streptococcus mitis, a normal inhabitant of the oral cavity, is a member of Viridans Group Streptococci (VGS). Generally recognized as a causative agent of invasive diseases in immunocompromised patients, S. mitis is considered to have low pathogenic potential in immunocompetent individuals. We present a rare case of sinusitis complicated by meningitis and cerebral sino-venous thrombosis (CSVT) caused by S. mitis in a previously healthy 12-year-old boy with poor oral health status. With the aim of understanding the real pathogenic role of this microorganism, an extensive review of the literature about invasive diseases due to S. mitis in pediatric patients was performed. Our data define the critical role of this microorganism in invasive infections, especially in immunocompetent children and in the presence of apparently harmful conditions such as sinusitis and caries. Attention should be paid to the choice of therapy because of VGS's emerging antimicrobial resistance patterns.
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Affiliation(s)
- Claudia Colomba
- Department of Health Promotion, Maternal and Infant Care, Internal Medicine and Medical Specialties, University of Palermo, 90100 Palermo, Italy
- Division of Pediatric Infectious Diseases, "G. Di Cristina" Hospital, ARNAS Civico Di Cristina Benfratelli, 90100 Palermo, Italy
| | - Valeria Garbo
- Department of Health Promotion, Maternal and Infant Care, Internal Medicine and Medical Specialties, University of Palermo, 90100 Palermo, Italy
| | - Giovanni Boncori
- Department of Health Promotion, Maternal and Infant Care, Internal Medicine and Medical Specialties, University of Palermo, 90100 Palermo, Italy
| | - Chiara Albano
- Department of Health Promotion, Maternal and Infant Care, Internal Medicine and Medical Specialties, University of Palermo, 90100 Palermo, Italy
| | - Sara Bagarello
- Department of Health Promotion, Maternal and Infant Care, Internal Medicine and Medical Specialties, University of Palermo, 90100 Palermo, Italy
| | - Anna Condemi
- Department of Health Promotion, Maternal and Infant Care, Internal Medicine and Medical Specialties, University of Palermo, 90100 Palermo, Italy
| | - Salvatore Giordano
- Division of Pediatric Infectious Diseases, "G. Di Cristina" Hospital, ARNAS Civico Di Cristina Benfratelli, 90100 Palermo, Italy
| | - Laura A Canduscio
- Division of Pediatric Infectious Diseases, "G. Di Cristina" Hospital, ARNAS Civico Di Cristina Benfratelli, 90100 Palermo, Italy
| | - Cristina Gallo
- Division of Radiology, "G. Di Cristina" Hospital, ARNAS Civico Di Cristina Benfratelli, 90100 Palermo, Italy
| | - Gaspare Parrinello
- Department of Health Promotion, Maternal and Infant Care, Internal Medicine and Medical Specialties, University of Palermo, 90100 Palermo, Italy
| | - Antonio Cascio
- Department of Health Promotion, Maternal and Infant Care, Internal Medicine and Medical Specialties, University of Palermo, 90100 Palermo, Italy
- Infectious and Tropical Diseases Unit, AOU Policlinico "P. Giaccone", 90100 Palermo, Italy
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Lu J, Sha Y, Gao M, Shi W, Lin X, Li K, Bao Q, Feng C. Identification and characterization of a novel aminoglycoside O-nucleotidyltransferase ANT(6)-If from Paenibacillus thiaminolyticus PATH554. Front Microbiol 2023; 14:1184349. [PMID: 37455719 PMCID: PMC10343464 DOI: 10.3389/fmicb.2023.1184349] [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: 03/11/2023] [Accepted: 06/07/2023] [Indexed: 07/18/2023] Open
Abstract
Background Paenibacillus thiaminolyticus, a species of genus Paenibacillus of the family Paenibacillaceae, exists widely in environments and habitats in various plants and worms, and occasionally causes human infections. This work aimed to characterize the function of a novel aminoglycoside O-nucleotidyltransferase resistance gene, designated ant(6)-If, from a P. thiaminolyticus strain PATH554. Methods Molecular cloning, antimicrobial susceptibility testing, enzyme expression and purification, and kinetic analysis were used to validate the function of the novel gene. Whole-genome sequencing and comparative genomic analysis were performed to investigate the phylogenetic relationship of ANT(6)-If and other aminoglycoside O-nucleotidyltransferases, and the synteny of ant(6)-If related sequences. Results The recombinant with the cloned ant(6)-If gene (pMD19-ant(6)-If/DH5α) demonstrated a 128-fold increase of minimum inhibitory concentration level against streptomycin, compared with the control strains (DH5α and pMD19/DH5α). The kinetic parameter kcat/Km of ANT(6)-If for streptomycin was 9.01 × 103 M-1·s-1. Among the function-characterized resistance genes, ANT(6)-If shared the highest amino acid sequence identity of 75.35% with AadK. The ant(6)-If gene was located within a relatively conserved genomic region in the chromosome. Conclusion ant(6)-If conferred resistance to streptomycin. The study of a novel resistance gene in an unusual environmental bacterium in this work contributed to elucidating the resistance mechanisms in the microorganisms.
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Affiliation(s)
- Junwan Lu
- Medical Molecular Biology Laboratory, School of Medicine, Jinhua Polytechnic, Jinhua, China
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, School of Laboratory Medicine and Life Sciences, Institute of Biomedical Informatics, Ministry of Education, Wenzhou Medical University, Wenzhou, China
| | - Yuning Sha
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, School of Laboratory Medicine and Life Sciences, Institute of Biomedical Informatics, Ministry of Education, Wenzhou Medical University, Wenzhou, China
| | - Mengdi Gao
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, School of Laboratory Medicine and Life Sciences, Institute of Biomedical Informatics, Ministry of Education, Wenzhou Medical University, Wenzhou, China
| | - Weina Shi
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, School of Laboratory Medicine and Life Sciences, Institute of Biomedical Informatics, Ministry of Education, Wenzhou Medical University, Wenzhou, China
| | - Xi Lin
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, School of Laboratory Medicine and Life Sciences, Institute of Biomedical Informatics, Ministry of Education, Wenzhou Medical University, Wenzhou, China
| | - Kewei Li
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, School of Laboratory Medicine and Life Sciences, Institute of Biomedical Informatics, Ministry of Education, Wenzhou Medical University, Wenzhou, China
| | - Qiyu Bao
- Medical Molecular Biology Laboratory, School of Medicine, Jinhua Polytechnic, Jinhua, China
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, School of Laboratory Medicine and Life Sciences, Institute of Biomedical Informatics, Ministry of Education, Wenzhou Medical University, Wenzhou, China
| | - Chunlin Feng
- Medical Molecular Biology Laboratory, School of Medicine, Jinhua Polytechnic, Jinhua, China
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, School of Laboratory Medicine and Life Sciences, Institute of Biomedical Informatics, Ministry of Education, Wenzhou Medical University, Wenzhou, China
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Mathieu E, Marquant Q, Chain F, Bouguyon E, Saint-Criq V, Le-Goffic R, Descamps D, Langella P, Tompkins TA, Binda S, Thomas M. An Isolate of Streptococcus mitis Displayed In Vitro Antimicrobial Activity and Deleterious Effect in a Preclinical Model of Lung Infection. Nutrients 2023; 15:nu15020263. [PMID: 36678133 PMCID: PMC9867278 DOI: 10.3390/nu15020263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 12/19/2022] [Accepted: 12/23/2022] [Indexed: 01/06/2023] Open
Abstract
Microbiota studies have dramatically increased over these last two decades, and the repertoire of microorganisms with potential health benefits has been considerably enlarged. The development of next generation probiotics from new bacterial candidates is a long-term strategy that may be more efficient and rapid with discriminative in vitro tests. Streptococcus strains have received attention regarding their antimicrobial potential against pathogens of the upper and, more recently, the lower respiratory tracts. Pathogenic bacterial strains, such as non-typable Haemophilus influenzae (NTHi), Pseudomonas aeruginosa (P. aeruginosa) and Staphylococcus aureus (S. aureus), are commonly associated with acute and chronic respiratory diseases, and it could be interesting to fight against pathogens with probiotics. In this study, we show that a Streptococcus mitis (S. mitis) EM-371 strain, isolated from the buccal cavity of a human newborn and previously selected for promising anti-inflammatory effects, displayed in vitro antimicrobial activity against NTHi, P. aeruginosa or S. aureus. However, the anti-pathogenic in vitro activity was not sufficient to predict an efficient protective effect in a preclinical model. Two weeks of treatment with S. mitis EM-371 did not protect against, and even exacerbated, NTHi lung infection.
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Affiliation(s)
- Elliot Mathieu
- Micalis Institute, Institut National de Recherche pour L’Agriculture, L’Alimentation et L’Environnement (INRAE), AgroParisTech, Université Paris-Saclay, UMR1319, F-78350 Jouy-en-Josas, France
- Paris Center for Microbiome Medicine (PaCeMM) FHU, AP-HP, F-75571 Paris, France
- Correspondence:
| | - Quentin Marquant
- Université Paris-Saclay, INRAE, UVSQ, VIM, F-78350 Jouy-en-Josas, France
- Laboratoire VIM-Suresnes, Hôpital Foch, F-92150 Suresnes, France
| | - Florian Chain
- Micalis Institute, Institut National de Recherche pour L’Agriculture, L’Alimentation et L’Environnement (INRAE), AgroParisTech, Université Paris-Saclay, UMR1319, F-78350 Jouy-en-Josas, France
- Paris Center for Microbiome Medicine (PaCeMM) FHU, AP-HP, F-75571 Paris, France
| | - Edwige Bouguyon
- Université Paris-Saclay, INRAE, UVSQ, VIM, F-78350 Jouy-en-Josas, France
| | - Vinciane Saint-Criq
- Micalis Institute, Institut National de Recherche pour L’Agriculture, L’Alimentation et L’Environnement (INRAE), AgroParisTech, Université Paris-Saclay, UMR1319, F-78350 Jouy-en-Josas, France
- Paris Center for Microbiome Medicine (PaCeMM) FHU, AP-HP, F-75571 Paris, France
| | - Ronan Le-Goffic
- Université Paris-Saclay, INRAE, UVSQ, VIM, F-78350 Jouy-en-Josas, France
| | - Delphyne Descamps
- Université Paris-Saclay, INRAE, UVSQ, VIM, F-78350 Jouy-en-Josas, France
| | - Philippe Langella
- Micalis Institute, Institut National de Recherche pour L’Agriculture, L’Alimentation et L’Environnement (INRAE), AgroParisTech, Université Paris-Saclay, UMR1319, F-78350 Jouy-en-Josas, France
- Paris Center for Microbiome Medicine (PaCeMM) FHU, AP-HP, F-75571 Paris, France
| | | | - Sylvie Binda
- Lallemand Health Solutions, Montreal, QC H4P 2R2, Canada
| | - Muriel Thomas
- Micalis Institute, Institut National de Recherche pour L’Agriculture, L’Alimentation et L’Environnement (INRAE), AgroParisTech, Université Paris-Saclay, UMR1319, F-78350 Jouy-en-Josas, France
- Paris Center for Microbiome Medicine (PaCeMM) FHU, AP-HP, F-75571 Paris, France
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Pham H, Tran TDT, Yang Y, Ahn JH, Hur HG, Kim YH. Analysis of phylogenetic markers for classification of a hydrogen peroxide producing Streptococcus oralis isolated from saliva by a newly devised differential medium. J Microbiol 2022; 60:795-805. [DOI: 10.1007/s12275-022-2261-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 06/22/2022] [Accepted: 06/23/2022] [Indexed: 11/30/2022]
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Vogel V, Fuchs M, Jachmann M, Bitzer A, Mauerer S, Münch J, Spellerberg B. The Role of SilX in Bacteriocin Production of Streptococcus anginosus. Front Microbiol 2022; 13:904318. [PMID: 35875552 PMCID: PMC9298176 DOI: 10.3389/fmicb.2022.904318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 06/07/2022] [Indexed: 12/03/2022] Open
Abstract
Streptococcus anginosus produces the novel antimicrobial peptide Angicin, which inhibits Gram positive microorganisms and is classified as a group IId bacteriocin. Production of Angicin is regulated by the quorum sensing system Sil (Streptococcus invasion locus), which is located adjacent to the bacteriocin gene cluster. Within this genetic region a typical CAAX protease is encoded, which was designated SilX. Nelfinavir, a HIV protease inhibitor, led to a concentration dependent reduction in antimicrobial activity, presumably through the inhibition of SilX. Concentrations exceeding 25 μM Nelfinavir caused a complete abolishment of bacteriocin activity against Listeria monocytogenes. These results are supported by the observation, that a SilX deletion mutant of S. anginosus strain BSU 1211 no longer inhibits the growth of L. monocytogenes. Antimicrobial activity could be restored by addition of synthetically synthesized mature SilCR, implying that SilX may be involved in the export and processing of the signal peptide SilCR. Some CAAX proteases have been reported to provide immunity against bacteriocins. However, in a radial diffusion assay the deletion mutant S. anginosus BSU 1211ΔSilX showed no sensitivity toward Angicin arguing against a role of SilX in the immunity of S. anginosus. The putative processing of the signal peptide SilCR indicates a novel function of the CAAX protease SilX, in the context of S. anginosus bacteriocin production.
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Affiliation(s)
- Verena Vogel
- Institute of Medical Microbiology and Hygiene, Ulm University Medical Center, Ulm, Germany
| | - Miki Fuchs
- Institute of Medical Microbiology and Hygiene, Ulm University Medical Center, Ulm, Germany
| | - Marie Jachmann
- Institute of Medical Microbiology and Hygiene, Ulm University Medical Center, Ulm, Germany
| | - Alina Bitzer
- Institute of Medical Microbiology and Hygiene, Ulm University Medical Center, Ulm, Germany
| | - Stefanie Mauerer
- Institute of Medical Microbiology and Hygiene, Ulm University Medical Center, Ulm, Germany
| | - Jan Münch
- Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany
| | - Barbara Spellerberg
- Institute of Medical Microbiology and Hygiene, Ulm University Medical Center, Ulm, Germany
- *Correspondence: Barbara Spellerberg,
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Alsheikh-Hussain AS, Ben Zakour NL, Forde BM, Silayeva O, Barnes AC, Beatson SA. A high-quality reference genome for the fish pathogen Streptococcus iniae. Microb Genom 2022; 8:000777. [PMID: 35229712 PMCID: PMC9176272 DOI: 10.1099/mgen.0.000777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Fish mortality caused by Streptococcus iniae is a major economic problem in aquaculture in warm and temperate regions globally. There is also risk of zoonotic infection by S. iniae through handling of contaminated fish. In this study, we present the complete genome sequence of S. iniae strain QMA0248, isolated from farmed barramundi in South Australia. The 2.12 Mb genome of S. iniae QMA0248 carries a 32 kb prophage, a 12 kb genomic island and 92 discrete insertion sequence (IS) elements. These include nine novel IS types that belong mostly to the IS3 family. Comparative and phylogenetic analysis between S. iniae QMA0248 and publicly available complete S. iniae genomes revealed discrepancies that are probably due to misassembly in the genomes of isolates ISET0901 and ISNO. Long-range PCR confirmed five rRNA loci in the PacBio assembly of QMA0248, and, unlike S. iniae 89353, no tandemly repeated rRNA loci in the consensus genome. However, we found sequence read evidence that the tandem rRNA repeat existed within a subpopulation of the original QMA0248 culture. Subsequent nanopore sequencing revealed that the tandem rRNA repeat was the most prevalent genotype, suggesting that there is selective pressure to maintain fewer rRNA copies under uncertain laboratory conditions. Our study not only highlights assembly problems in existing genomes, but provides a high-quality reference genome for S. iniae QMA0248, including manually curated mobile genetic elements, that will assist future S. iniae comparative genomic and evolutionary studies.
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Affiliation(s)
- Areej S. Alsheikh-Hussain
- School of Chemistry & Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Queensland, Australia
| | - Nouri L. Ben Zakour
- School of Chemistry & Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Queensland, Australia
- The Westmead Institute for Medical Research and the University of Sydney, Sydney, New South Wales, Australia
| | - Brian M. Forde
- School of Chemistry & Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Queensland, Australia
| | - Oleksandra Silayeva
- School of Biological Science, The University of Queensland, Brisbane, Queensland, Australia
| | - Andrew C. Barnes
- School of Biological Science, The University of Queensland, Brisbane, Queensland, Australia
- *Correspondence: Andrew C. Barnes,
| | - Scott A. Beatson
- School of Chemistry & Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Queensland, Australia
- *Correspondence: Scott A. Beatson,
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Ishikawa Y, Saiki K, Urano-Tashiro Y, Yamanaka Y, Takahashi Y. Expression and diversity of the sialic acid-binding adhesin and its homologs associated with oral streptococcal infection. Microbiol Immunol 2021; 66:59-66. [PMID: 34783072 DOI: 10.1111/1348-0421.12950] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 10/13/2021] [Accepted: 11/06/2021] [Indexed: 11/29/2022]
Abstract
Streptococcus gordonii, one of the early colonizers of oral biofilms, is involved in the development of dental caries, periodontal disease, and infective endocarditis. The Hsa adhesin of S. gordonii DL1 has the ability to bind strongly to the terminal sialic acid groups of host glycoproteins via the binding region, NR2, which is important for the pathogenicity of S. gordonii DL1. Low similarity with the NR2 of Hsa homologs among other streptococcal species has been reported. However, the reports have been limited to certain strains. This study attempted to assess frequency of the expression on the bacterial cell surface and to analyze the diversity of Hsa homologs among different wild strains of oral streptococci. We isolated 186 wild-type strains of oral streptococci from healthy volunteers and analyzed their hemagglutinating activity on human erythrocytes and their Hsa homologs and NR2 homologous regions by dot immunoblotting using anti-Hsa and anti-NR2 antisera, respectively. We found 30 strains reacted with anti-NR2 antiserum (NR2-positive) and determined the sequence of the NR2 regions. Many strains with high hemagglutinating activity were also NR2-positive, suggesting that the NR2 region may be associated with hemagglutinating activity. Among the NR2-positive strains, four different amino acid sequence patterns were observed, demonstrating diversity in the NR2 region. Notably, S. gordonii strains frequently possessed Hsa homologs and NR2-like antigens compared to other streptococci. It is speculated that the possessing frequency of Hsa homologs and the amino acid sequence of NR2 region may vary among streptococcal species. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Yuiko Ishikawa
- Department of Microbiology, The Nippon Dental University School of Life Dentistry at Tokyo, Japan
| | - Keitarou Saiki
- Department of Microbiology, The Nippon Dental University School of Life Dentistry at Tokyo, Japan
| | - Yumiko Urano-Tashiro
- Department of Microbiology, The Nippon Dental University School of Life Dentistry at Tokyo, Japan
| | - Yuki Yamanaka
- Department of Microbiology, The Nippon Dental University School of Life Dentistry at Tokyo, Japan
| | - Yukihiro Takahashi
- Department of Microbiology, The Nippon Dental University School of Life Dentistry at Tokyo, Japan
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Gisch N, Peters K, Thomsen S, Vollmer W, Schwudke D, Denapaite D. Commensal Streptococcus mitis produces two different lipoteichoic acids of type I and type IV. Glycobiology 2021; 31:1655-1669. [PMID: 34314482 DOI: 10.1093/glycob/cwab079] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 06/16/2021] [Accepted: 07/14/2021] [Indexed: 11/14/2022] Open
Abstract
The opportunistic pathogen Streptococcus mitis possesses, like other members of the Mitis group of viridans streptococci, phosphorylcholine (P-Cho)-containing teichoic acids (TAs) in its cell wall. Bioinformatic analyses predicted the presence of TAs that are almost identical with those identified in the pathogen S. pneumoniae, but a detailed analysis of S. mitis lipoteichoic acid (LTA) was not performed to date. Here we determined the structures of LTA from two S. mitis strains, the high-level beta-lactam and multiple antibiotic resistant strain B6 and the penicillin-sensitive strain NCTC10712. In agreement with bioinformatic predictions we found that the structure of one LTA (type IV) was like pneumococcal LTA, except the exchange of a glucose moiety with a galactose within the repeating units. Further genome comparisons suggested that the majority of S. mitis strains should contain the same type IV LTA as S. pneumoniae, providing a more complete understanding of the biosynthesis of these P-Cho-containing TAs in members of the Mitis group of streptococci. Remarkably, we observed besides type IV LTA an additional polymer belonging to LTA type I in both investigated S. mitis strains. This LTA consists of β-galactofuranosyl-(1,3)-diacylglycerol as glycolipid anchor and a poly-glycerol-phosphate chain at the O-6 position of the furanosidic galactose. Hence, these bacteria are capable of synthesizing two different LTA polymers, most likely produced by distinct biosynthesis pathways. Our bioinformatics analysis revealed the prevalence of the LTA synthase LtaS, most probably responsible for the second LTA version (type I), amongst S. mitis and S. pseudopneumoniae strains.
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Affiliation(s)
- Nicolas Gisch
- Division of Bioanalytical Chemistry, Priority Area Infections, Research Center Borstel, Leibniz Lung Center, 23845 Borstel, Germany
| | - Katharina Peters
- Centre for Bacterial Cell Biology, Biosciences Institute, Newcastle University, NE2 4AX Newcastle upon Tyne, UK
| | - Simone Thomsen
- Division of Bioanalytical Chemistry, Priority Area Infections, Research Center Borstel, Leibniz Lung Center, 23845 Borstel, Germany
| | - Waldemar Vollmer
- Centre for Bacterial Cell Biology, Biosciences Institute, Newcastle University, NE2 4AX Newcastle upon Tyne, UK
| | - Dominik Schwudke
- Division of Bioanalytical Chemistry, Priority Area Infections, Research Center Borstel, Leibniz Lung Center, 23845 Borstel, Germany.,German Center for Infection Research (DZIF), Thematic Translational Unit Tuberculosis, Partner Site: Hamburg-Lübeck-Borstel-Riems, 23845 Borstel, Germany.,Airway Research Center North, Member of the German Center for Lung Research (DZL), 23845 Borstel, Germany
| | - Dalia Denapaite
- Department of Microbiology, University of Kaiserslautern, 67663 Kaiserslautern, Germany
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11
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Streptococcal Infections in Marine Mammals. Microorganisms 2021; 9:microorganisms9020350. [PMID: 33578962 PMCID: PMC7916692 DOI: 10.3390/microorganisms9020350] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 01/29/2021] [Accepted: 02/07/2021] [Indexed: 01/28/2023] Open
Abstract
Marine mammals are sentinels for the marine ecosystem and threatened by numerous factors including infectious diseases. One of the most frequently isolated bacteria are beta-hemolytic streptococci. However, knowledge on ecology and epidemiology of streptococcal species in marine mammals is very limited. This review summarizes published reports on streptococcal species, which have been detected in marine mammals. Furthermore, we discuss streptococcal transmission between and adaptation to their marine mammalian hosts. We conclude that streptococci colonize and/or infect marine mammals very frequently, but in many cases, streptococci isolated from marine mammals have not been further identified. How these bacteria disseminate and adapt to their specific niches can only be speculated due to the lack of respective research. Considering the relevance of pathogenic streptococci for marine mammals as part of the marine ecosystem, it seems that they have been neglected and should receive scientific interest in the future.
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12
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Stubbs HE, Bensing BA, Yamakawa I, Sharma P, Yu H, Chen X, Sullam PM, Iverson TM. Tandem sialoglycan-binding modules in a Streptococcus sanguinis serine-rich repeat adhesin create target dependent avidity effects. J Biol Chem 2020; 295:14737-14749. [PMID: 32820052 PMCID: PMC7586212 DOI: 10.1074/jbc.ra120.014177] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Revised: 07/29/2020] [Indexed: 01/07/2023] Open
Abstract
Sialic acid-binding immunoglobulin-like lectins (Siglec)-like domains of streptococcal serine-rich repeat (SRR) adhesins recognize sialylated glycans on human salivary, platelet, and plasma glycoproteins via a YTRY sequence motif. The SRR adhesin from Streptococcus sanguinis strain SK1 has tandem sialoglycan-binding domains and has previously been shown to bind sialoglycans with high affinity. However, both domains contain substitutions within the canonical YTRY motif, making it unclear how they interact with host receptors. To identify how the S. sanguinis strain SK1 SRR adhesin affects interactions with sialylated glycans and glycoproteins, we determined high-resolution crystal structures of the binding domains alone and with purified trisaccharides. These structural studies determined that the ligands still bind at the noncanonical binding motif, but with fewer hydrogen-bonding interactions to the protein than is observed in structures of other Siglec-like adhesins. Complementary biochemical studies identified that each of the two binding domains has a different selectivity profile. Interestingly, the binding of SK1 to platelets and plasma glycoproteins identified that the interaction to some host targets is dominated by the contribution of one binding domain, whereas the binding to other host receptors is mediated by both binding domains. These results provide insight into outstanding questions concerning the roles of tandem domains in targeting host receptors and suggest mechanisms for how pathogens can adapt to the availability of a range of related but nonidentical host receptors. They further suggest that the definition of the YTRY motif should be changed to ϕTRX, a more rigorous description of this sialic acid-recognition motif given recent findings.
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Affiliation(s)
- Haley E. Stubbs
- Graduate Program in Chemical and Physical Biology, Vanderbilt University, Nashville, Tennessee, USA
| | - Barbara A. Bensing
- Department of Medicine, Veterans Affairs Medical Center, San Francisco, California, USA,Department of Medicine, University of California, San Francisco, California, USA
| | - Izumi Yamakawa
- Department of Pharmacology, Vanderbilt University, Nashville, Tennessee, USA
| | - Pankaj Sharma
- Department of Pharmacology, Vanderbilt University, Nashville, Tennessee, USA
| | - Hai Yu
- Department of Chemistry, University of California, Davis, California, USA
| | - Xi Chen
- Department of Chemistry, University of California, Davis, California, USA
| | - Paul M. Sullam
- Department of Medicine, Veterans Affairs Medical Center, San Francisco, California, USA
| | - T. M. Iverson
- Department of Pharmacology, Vanderbilt University, Nashville, Tennessee, USA,Department of Biochemistry, Vanderbilt University, Nashville, Tennessee, USA,Center for Structural Biology, Vanderbilt University, Nashville, Tennessee, USA,For correspondence: T. M. Iverson,
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13
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Afshar D, Rafiee F, Kheirandish M, Ohadian Moghadam S, Azarsa M. Autolysin (lytA) recombinant protein: a potential target for developing vaccines against pneumococcal infections. Clin Exp Vaccine Res 2020; 9:76-80. [PMID: 32864363 PMCID: PMC7445314 DOI: 10.7774/cevr.2020.9.2.76] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 07/28/2020] [Indexed: 11/25/2022] Open
Abstract
Purpose N-acetylmuramoyl-l-alanine amidase known as lytA, is an immunogenic protein that plays an important role in the pathogenesis of Streptococcus pneumoniae. It is highly conserved among S. pneumoniae strains and is absent among other Streptococcus species. In the present study, the level of antibodies against the lytA recombinant protein was evaluated in healthy individuals' sera. Materials and Methods DNA was extracted from S. pneumoniae ATCC 49619 to amplify lytA gene by polymerase chain reaction assay. The lytA amplicon and pET28a vector were separately double digested using Nde-1 and Xho1 restriction enzymes and then ligated together with ligase enzyme. The recombinant plasmid was expressed in Escherichia coli BL21 strain and the lytA recombinant protein purified using nickel-nitrilotriacetic acid affinity chromatography. Western blot was carried to detect lytA recombinant protein. Sixty healthy individual's sera (at three age groups: group 1, <2; group 2, 2–40; and group 3, 60–90 years old) were collected and the titers of anti-lytA antibodies were determined. Results The lytA gene was highly expressed in E. coli BL21 host. The recombinant lytA protein was purified and confirmed by western blotting. Tukey test analysis showed that there were no significant differences among the age groups considering the anti-lytA titer of 10. However, at the anti-lytA titer of 60, significant differences were observed between group 1 vs. group 2 (p<0.001); group 1 vs. group 3 (p=0.003), and group 2 vs. group 3 (p=0.024). Conclusion The lytA protein seems to be a highly immunogenic antigen and a potential target for developing vaccines against pneumococcal infections.
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Affiliation(s)
- Davoud Afshar
- Department of Microbiology and Virology, School of Medicine, Zanjan University of Medical Sciences, Zanjan, Iran
| | - Farzaneh Rafiee
- Department of Microbiology and Virology, School of Medicine, Zanjan University of Medical Sciences, Zanjan, Iran
| | - Mozhgan Kheirandish
- Department of Microbiology and Virology, School of Medicine, Zanjan University of Medical Sciences, Zanjan, Iran
| | | | - Mohammad Azarsa
- Department of Microbiology, Khoy University of Medical Sciences, Khoy, Iran
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14
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Watanabe Y, Nagao Y, Endo H, Yamane I, Hirata M, Hatakeyama K. An intubated 7-month-old infant with a retropharyngeal abscess and multidrug-resistant Streptococcus mitis. Clin Case Rep 2019; 7:2443-2448. [PMID: 31893077 PMCID: PMC6935668 DOI: 10.1002/ccr3.2528] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2019] [Revised: 09/19/2019] [Accepted: 10/09/2019] [Indexed: 12/23/2022] Open
Abstract
The profile of antimicrobial resistance (ie, antibiogram) may be disparate between children and adults. An infant developed severe deep neck infection with a multidrug-resistant microbe. The microbe was more drug-resistant in children than in adults, in our hospital. Treatment of a child should be guided by the antibiogram obtained from children.
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Affiliation(s)
| | - Yoshiro Nagao
- Department of PediatricsFukuoka Tokushukai HospitalKasugaJapan
| | - Hisashi Endo
- Department of PediatricsFukuoka Tokushukai HospitalKasugaJapan
| | - Ichiro Yamane
- Department of PediatricsFukuoka Tokushukai HospitalKasugaJapan
| | - Masaaki Hirata
- Department of PediatricsFukuoka Tokushukai HospitalKasugaJapan
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15
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Identification of Virulence-Associated Properties by Comparative Genome Analysis of Streptococcus pneumoniae, S. pseudopneumoniae, S. mitis, Three S. oralis Subspecies, and S. infantis. mBio 2019; 10:mBio.01985-19. [PMID: 31481387 PMCID: PMC6722419 DOI: 10.1128/mbio.01985-19] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Streptococcus pneumoniae is one of the most important human pathogens but is closely related to Streptococcus mitis, with which humans live in harmony. The fact that the two species evolved from a common ancestor provides a unique basis for studies of both infection-associated properties and properties important for harmonious coexistence with the host. By detailed comparisons of genomes of the two species and other related streptococci, we identified 224 genes associated with virulence and 25 genes unique to the mutualistic species. The exclusive presence of the virulence factors in S. pneumoniae enhances their potential as vaccine components, as a direct impact on beneficial members of the commensal microbiota can be excluded. Successful adaptation of S. mitis and other commensal streptococci to a harmonious relationship with the host relied on genetic stability and properties facilitating life in biofilms. From a common ancestor, Streptococcus pneumoniae and Streptococcus mitis evolved in parallel into one of the most important pathogens and a mutualistic colonizer of humans, respectively. This evolutionary scenario provides a unique basis for studies of both infection-associated properties and properties important for harmonious coexistence with the host. We performed detailed comparisons of 60 genomes of S. pneumoniae, S. mitis, Streptococcus pseudopneumoniae, the three Streptococcus oralis subspecies oralis, tigurinus, and dentisani, and Streptococcus infantis. Nonfunctional remnants of ancestral genes in both S. pneumoniae and in S. mitis support the evolutionary model and the concept that evolutionary changes on both sides were required to reach their present relationship to the host. Confirmed by screening of >7,500 genomes, we identified 224 genes associated with virulence. The striking difference to commensal streptococci was the diversity of regulatory mechanisms, including regulation of capsule production, a significantly larger arsenal of enzymes involved in carbohydrate hydrolysis, and proteins known to interfere with innate immune factors. The exclusive presence of the virulence factors in S. pneumoniae enhances their potential as vaccine components, as a direct impact on beneficial members of the commensal microbiota can be excluded. In addition to loss of these virulence-associated genes, adaptation of S. mitis to a mutualistic relationship with the host apparently required preservation or acquisition of 25 genes lost or absent from S. pneumoniae. Successful adaptation of S. mitis and other commensal streptococci to a harmonious relationship with the host relied on genetic stability and properties facilitating life in biofilms.
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16
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Liu Y, Zeng Y, Huang Y, Gu L, Wang S, Li C, Morrison DA, Deng H, Zhang JR. HtrA-mediated selective degradation of DNA uptake apparatus accelerates termination of pneumococcal transformation. Mol Microbiol 2019; 112:1308-1325. [PMID: 31396996 DOI: 10.1111/mmi.14364] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/06/2019] [Indexed: 02/06/2023]
Abstract
Natural transformation mediates horizontal gene transfer, and thereby promotes exchange of antibiotic resistance and virulence traits among bacteria. Streptococcus pneumoniae, the first known transformable bacterium, rapidly activates and then terminates the transformation state, but it is unclear how the bacterium accomplishes this rapid turn-around at the protein level. This work determined the transcriptomic and proteomic dynamics during the window of pneumococcal transformation. RNA sequencing revealed a nearly uniform temporal pattern of rapid transcriptional activation and subsequent shutdown for the genes encoding transformation proteins. In contrast, mass spectrometry analysis showed that the majority of transformation proteins were substantially preserved beyond the window of transformation. However, ComEA and ComEC, major components of the DNA uptake apparatus for transformation, were completely degraded at the end of transformation. Further mutagenesis screening revealed that the membrane-associated serine protease HtrA mediates selective degradation of ComEA and ComEC, strongly suggesting that breakdown of the DNA uptake apparatus by HtrA is an important mechanism for termination of pneumococcal transformation. Finally, our mutagenesis analysis showed that HtrA inhibits natural transformation of Streptococcus mitis and Streptococcus gordonii. Together, this work has revealed that HtrA regulates the level and duration of natural transformation in multiple streptococcal species.
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Affiliation(s)
- Yanni Liu
- Center for Infectious Disease Research, School of Medicine, Tsinghua University, Beijing, China
| | - Yuna Zeng
- Center for Infectious Disease Research, School of Medicine, Tsinghua University, Beijing, China
| | - Yijia Huang
- Center for Infectious Disease Research, School of Medicine, Tsinghua University, Beijing, China
| | - Lixiao Gu
- School of Life Sciences, Tsinghua University, Beijing, China
| | - Shaolin Wang
- College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Chunhao Li
- Department of Oral and Craniofacial Molecular Biology, School of Dentistry, Virginia Commonwealth University, Richmond, VA, USA
| | - Donald A Morrison
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL, USA
| | - Haiteng Deng
- School of Life Sciences, Tsinghua University, Beijing, China
| | - Jing-Ren Zhang
- Center for Infectious Disease Research, School of Medicine, Tsinghua University, Beijing, China
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17
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Intranasal Immunization with the Commensal Streptococcus mitis Confers Protective Immunity against Pneumococcal Lung Infection. Appl Environ Microbiol 2019; 85:AEM.02235-18. [PMID: 30683742 DOI: 10.1128/aem.02235-18] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Accepted: 01/02/2019] [Indexed: 02/04/2023] Open
Abstract
Streptococcus pneumoniae is a bacterial pathogen that causes various diseases of public health concern worldwide. Current pneumococcal vaccines target the capsular polysaccharide surrounding the cells. However, only up to 13 of more than 90 pneumococcal capsular serotypes are represented in the current conjugate vaccines. In this study, we used two experimental approaches to evaluate the potential of Streptococcus mitis, a commensal that exhibits immune cross-reactivity with S. pneumoniae, to confer protective immunity to S. pneumoniae lung infection in mice. First, we assessed the immune response and protective effect of wild-type S. mitis against lung infection by S. pneumoniae strains D39 (serotype 2) and TIGR4 (serotype 4). Second, we examined the ability of an S. mitis mutant expressing the S. pneumoniae type 4 capsule (S. mitis TIGR4cps) to elicit focused protection against S. pneumoniae TIGR4. Our results showed that intranasal immunization of mice with S. mitis produced significantly higher levels of serum IgG and IgA antibodies reactive to both S. mitis and S. pneumoniae, as well as enhanced production of interleukin 17A (IL-17A), but not gamma interferon (IFN-γ) and IL-4, compared with control mice. The immunization resulted in a reduced bacterial load in respiratory tissues following lung infection with S. pneumoniae TIGR4 or D39 compared with control mice. With S. mitis TIGR4cps, protection upon challenge with S. pneumoniae TIGR4 was superior. Thus, these findings show the potential of S. mitis to elicit natural serotype-independent protection against two pneumococcal serotypes and to provide the benefits of the well-recognized protective effect of capsule-targeting vaccines.IMPORTANCE Streptococcus pneumoniae causes various diseases worldwide. Current pneumococcal vaccines protect against a limited number of more than 90 pneumococcal serotypes, accentuating the urgent need to develop novel prophylactic strategies. S. pneumoniae and the commensal Streptococcus mitis share immunogenic characteristics that make S. mitis an attractive vaccine candidate against S. pneumoniae In this study, we evaluated the potential of S. mitis and its mutant expressing pneumococcal capsule type 4 (S. mitis TIGR4cps) to induce protection against S. pneumoniae lung infection in mice. Our findings show that intranasal vaccination with S. mitis protects against S. pneumoniae strains D39 (serotype 2) and TIGR4 (serotype 4) in a serotype-independent fashion, which is associated with enhanced antibody and T cell responses. Furthermore, S. mitis TIGR4cps conferred additional protection against S. pneumoniae TIGR4, but not against D39. The findings highlight the potential of S. mitis to generate protection that combines both serotype-independent and serotype-specific responses.
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18
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Salvadori G, Junges R, Åmdal HA, Chen T, Morrison DA, Petersen FC. High-resolution profiles of the Streptococcus mitis CSP signaling pathway reveal core and strain-specific regulated genes. BMC Genomics 2018; 19:453. [PMID: 29898666 PMCID: PMC6001120 DOI: 10.1186/s12864-018-4802-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Accepted: 05/18/2018] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND In streptococci of the mitis group, competence for natural transformation is a transient physiological state triggered by competence stimulating peptides (CSPs). Although low transformation yields and the absence of a widespread functional competence system have been reported for Streptococcus mitis, recent studies revealed that, at least for some strains, high efficiencies can be achieved following optimization protocols. To gain a deeper insight into competence in this species, we used RNA-seq, to map the global CSP response of two transformable strains: the type strain NCTC12261T and SK321. RESULTS All known genes induced by ComE in Streptococcus pneumoniae, including sigX, were upregulated in the two strains. Likewise, all sets of streptococcal SigX core genes involved in extracellular DNA uptake, recombination, and fratricide were upregulated. No significant differences in the set of induced genes were observed when the type strain was grown in rich or semi-defined media. Five upregulated operons unique to S. mitis with a SigX-box in the promoter region were identified, including two specific to SK321, and one specific to NCTC12261T. Two of the strain-specific operons coded for different bacteriocins. Deletion of the unique S. mitis sigX regulated genes had no effect on transformation. CONCLUSIONS Overall, comparison of the global transcriptome in response to CSP shows the conservation of the ComE and SigX-core regulons in competent S. mitis isolates, as well as species and strain-specific genes. Although some S. mitis exhibit truncations in key competence genes, this study shows that in transformable strains, competence seems to depend on the same core genes previously identified in S. pneumoniae.
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Affiliation(s)
- G Salvadori
- Institute of Oral Biology, Faculty of Dentistry, University of Oslo, Postboks 1052, Blindern, 0316, Oslo, Norway
| | - R Junges
- Institute of Oral Biology, Faculty of Dentistry, University of Oslo, Postboks 1052, Blindern, 0316, Oslo, Norway
| | - H A Åmdal
- Institute of Oral Biology, Faculty of Dentistry, University of Oslo, Postboks 1052, Blindern, 0316, Oslo, Norway
| | - T Chen
- Department of Microbiology, The Forsyth Institute, Cambridge, MA, USA
| | - D A Morrison
- Department of Biological Sciences, College of Liberal Arts and Sciences, University of Illinois at Chicago, Chicago, IL, USA
| | - F C Petersen
- Institute of Oral Biology, Faculty of Dentistry, University of Oslo, Postboks 1052, Blindern, 0316, Oslo, Norway.
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19
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Zhang Q, Lin K, Wang C, Xu Z, Yang L, Ma Q. Identification of Streptococcus mitis321A vaccine antigens based on reverse vaccinology. Mol Med Rep 2018; 17:7477-7486. [PMID: 29620181 PMCID: PMC5983942 DOI: 10.3892/mmr.2018.8799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Accepted: 04/19/2017] [Indexed: 11/23/2022] Open
Abstract
Streptococcus mitis (S. mitis) may transform into highly pathogenic bacteria. The aim of the present study was to identify potential antigen targets for designing an effective vaccine against the pathogenic S. mitis321A. The genome of S. mitis321A was sequenced using an Illumina Hiseq2000 instrument. Subsequently, Glimmer 3.02 and Tandem Repeat Finder (TRF) 4.04 were used to predict genes and tandem repeats, respectively, with DNA sequence function analysis using the Basic Local Alignment Search Tool (BLAST) in the Kyoto Encyclopedia of Genes and Genomes (KEGG) and Cluster of Orthologous Groups of proteins (COG) databases. Putative gene antigen candidates were screened with BLAST ahead of phylogenetic tree analysis. The DNA sequence assembly size was 2,110,680 bp with 40.12% GC, 6 scaffolds and 9 contig. Consequently, 1,944 genes were predicted, and 119 TRF, 56 microsatellite DNA, 10 minisatellite DNA and 154 transposons were acquired. The predicted genes were associated with various pathways and functions concerning membrane transport and energy metabolism. Multiple putative genes encoding surface proteins, secreted proteins and virulence factors, as well as essential genes were determined. The majority of essential genes belonged to a phylogenetic lineage, while 321AGL000129 and 321AGL000299 were on the same branch. The current study provided useful information regarding the biological function of the S. mitis321A genome and recommends putative antigen candidates for developing a potent vaccine against S. mitis.
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Affiliation(s)
- Qiao Zhang
- Institute of Respiratory Disease, Xinqiao Hospital of Third Military Medical University, Chongqing 400037, P.R. China
| | - Kexiong Lin
- Institute of Respiratory Disease, Xinqiao Hospital of Third Military Medical University, Chongqing 400037, P.R. China
| | - Changzheng Wang
- Institute of Respiratory Disease, Xinqiao Hospital of Third Military Medical University, Chongqing 400037, P.R. China
| | - Zhi Xu
- Institute of Respiratory Disease, Xinqiao Hospital of Third Military Medical University, Chongqing 400037, P.R. China
| | - Li Yang
- Institute of Respiratory Disease, Xinqiao Hospital of Third Military Medical University, Chongqing 400037, P.R. China
| | - Qianli Ma
- Institute of Respiratory Disease, Xinqiao Hospital of Third Military Medical University, Chongqing 400037, P.R. China
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20
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Shekhar S, Khan R, Ferreira DM, Mitsi E, German E, Rørvik GH, Berild D, Schenck K, Kwon K, Petersen F. Antibodies Reactive to Commensal Streptococcus mitis Show Cross-Reactivity With Virulent Streptococcus pneumoniae Serotypes. Front Immunol 2018; 9:747. [PMID: 29713324 PMCID: PMC5911667 DOI: 10.3389/fimmu.2018.00747] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Accepted: 03/26/2018] [Indexed: 12/05/2022] Open
Abstract
Current vaccines against Streptococcus pneumoniae, a bacterial species that afflicts people by causing a wide spectrum of diseases, do not protect against all pneumococcal serotypes. Thus, alternative vaccines to fight pneumococcal infections that target common proteins are under investigation. One promising strategy is to take advantage of immune cross-reactivity between commensal and pathogenic microbes for cross-protection. In this study, we examined the antibody-mediated cross-reactivity between S. pneumoniae and Streptococcus mitis, a commensal species closely related to S. pneumoniae. Western blot analysis showed that rabbit antisera raised against S. mitis reacted with multiple proteins of virulent S. pneumoniae strains (6B, TIGR4, and D39). Rabbit anti-S. pneumoniae IgG antibodies also showed binding to S. mitis antigens. Incubation of rabbit antisera raised against S. mitis with heterologous or homologous bacterial lysates resulted in marked inhibition of the developments of bands in the Western blots. Furthermore, plasma IgG antibodies from adult human volunteers intranasally inoculated with S. pneumoniae 6B revealed enhanced S. mitis-specific IgG titers compared with the pre-inoculation samples. Using an on-chip protein microarray representing a number of selected membrane and extracellular S. pneumoniae proteins, we identified choline-binding protein D (CbpD), cell division protein (FtsH), and manganese ABC transporter or manganese-binding adhesion lipoprotein (PsaA) as common targets of the rabbit IgG antibodies raised against S. mitis or S. pneumoniae. Cumulatively, these findings provide evidence on the antibody-mediated cross-reactivity of proteins from S. mitis and S. pneumoniae, which may have implications for development of effective and wide-range pneumococcal vaccines.
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Affiliation(s)
- Sudhanshu Shekhar
- Department of Oral Biology, Faculty of Dentistry, University of Oslo, Oslo, Norway
| | - Rabia Khan
- Department of Oral Biology, Faculty of Dentistry, University of Oslo, Oslo, Norway
| | - Daniela M Ferreira
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | - Elena Mitsi
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | - Esther German
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | | | - Dag Berild
- Faculty of Medicine, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Karl Schenck
- Department of Oral Biology, Faculty of Dentistry, University of Oslo, Oslo, Norway
| | - Keehwan Kwon
- Infectious Diseases Group, J. Craig Venter Institute, Rockville, MD, United States
| | - Fernanda Petersen
- Department of Oral Biology, Faculty of Dentistry, University of Oslo, Oslo, Norway
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21
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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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22
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Damé-Teixeira N, Parolo CCF, Maltz M, Rup AG, Devine DA, Do T. Gene expression of bacterial collagenolytic proteases in root caries. J Oral Microbiol 2018; 10:1424475. [PMID: 34394852 PMCID: PMC5774410 DOI: 10.1080/20002297.2018.1424475] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Accepted: 01/03/2018] [Indexed: 01/22/2023] Open
Abstract
Objective: It is unknown whether bacteria play a role in the collagen matrix degradation that occurs during caries progression. Our aim was to characterize the expression level of genes involved in bacterial collagenolytic proteases in root biofilms with and without caries. Method: we collected samples from active cavitated root caries lesions (RC, n = 30) and from sound root surfaces (SRS, n = 10). Total microbial RNA was isolated and cDNA sequenced on the Illumina Hi-Seq2500. Reads were mapped to 162 oral bacterial reference genomes. Genes encoding putative bacterial collagenolytic proteases were identified. Normalization and differential expression analysis was performed on all metatranscriptomes (FDR<10-3). Result: Genes encoding collagenases were identified in 113 bacterial species the majority were peptidase U32. In RC, Streptococcus mutans and Veillonella parvula expressed the most collagenases. Organisms that overexpressed collagenolytic protease genes in RC (Log2FoldChange>8) but none in SRS were Pseudoramibacter alactolyticus [HMPREF0721_RS02020; HMPREF0721_RS04640], Scardovia inopinata [SCIP_RS02440] and Olsenella uli DSM7084 [OLSU_RS02990]. Conclusion: Our findings suggest that the U32 proteases may be related to carious dentine. The contribution of a small number of species to dentine degradation should be further investigated. These proteases may have potential in future biotechnological and medical applications, serving as targets for the development of therapeutic agents.
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Affiliation(s)
- Nailê Damé-Teixeira
- Faculty of Health Science, Department of Dentistry, University of Brasilia, Brasilia, Brazil
| | | | - Marisa Maltz
- Faculty of Dentistry, Department of Social and Preventive Dentistry, Federal University of Rio Grande do Sul, Porto Alegre, Brazil
| | - Ariel Goulart Rup
- Faculty of Dentistry, Department of Social and Preventive Dentistry, Federal University of Rio Grande do Sul, Porto Alegre, Brazil
| | - Deirdre Ann Devine
- School of Dentistry, Division of Oral Biology, University of Leeds, Leeds, United Kingdom
| | - Thuy Do
- School of Dentistry, Division of Oral Biology, University of Leeds, Leeds, United Kingdom
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Ikryannikova LN, Malakhova MV, Lominadze GG, Karpova IY, Kostryukova ES, Mayansky NA, Kruglov AN, Klimova EA, Lisitsina ES, Ilina EN, Govorun VM. Inhibitory effect of streptococci on the growth of M. catarrhalis strains and the diversity of putative bacteriocin-like gene loci in the genomes of S. pneumoniae and its relatives. AMB Express 2017; 7:218. [PMID: 29236192 PMCID: PMC5729180 DOI: 10.1186/s13568-017-0521-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Accepted: 12/05/2017] [Indexed: 11/18/2022] Open
Abstract
S. pneumoniae is a facultative human pathogen causing a wide range of infections including the life-threatening pneumoniae or meningitis. It colonizes nasopharynx as well as its closest phylogenetic relatives S. pseudopneumoniae and S. mitis. Both the latter, despite the considerable morphological and phenotypic similarity with the pneumococcus, are considerably less pathogenic for humans and cause infections mainly in the immunocompromized hosts. In this work, we compared the inhibitory effect of S. pneumoniae and its relatives on the growth of Moraxella catarrhalis strains using the culture-based antagonistic test. We observed that the inhibitory effect of S. mitis strains is kept when a hydrogen peroxide produced by cells is inactivated by catalase, and even when the live cells are killed in chloroform vapors, in contrast to the pneumococcus whose inhibiting ability disappeared when the cells die. It was suggested that this effect may be due to the production of bacterial antimicrobial peptides by S. mitis, so we examined the genomes of our strains for the presence of bacteriocin-like peptides encoding genes. We observed that a set of bacteriocin-like genes in the genome of S. mitis is greatly poorer in comparison with S. pneumoniae one; moreover, in one S. mitis strain we found no bacteriocin-like genes. It could mean that there are probably some additional opportunities of S. mitis to inhibit the growth of competing neighbors which are still have to be discovered.
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van der Linden M, Rutschmann J, Maurer P, Hakenbeck R. PBP2a in β-Lactam-Resistant Laboratory Mutants and Clinical Isolates: Disruption Versus Reduced Penicillin Affinity. Microb Drug Resist 2017; 24:718-731. [PMID: 29195053 DOI: 10.1089/mdr.2017.0302] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Alterations in PBP2a have been recognized in cefotaxime-resistant laboratory mutants and β-lactam-resistant clinical isolates of Streptococcus pneumoniae. DNA sequencing revealed fundamental differences between these two settings. Internal stop codons in pbp2a occurred in all three laboratory mutants analyzed, caused by a mutation in pbp2a of mutant C604, and tandem duplications within pbp2a resulting in premature stop codons in another two mutants C403 and C406. In contrast, mosaic PBP2a genes were observed in several penicillin-resistant clinical isolates from South Africa, the Czech Republic, Hungary, and in the clone Poland23F-16, with sequence blocks diverging from sensitive strains by over 4%. Most of these pbp2a variants except pbp2a from the South African strain contained sequences related to pbp2a of Streptococcus mitis B6, confirming that this species serves as reservoir for penicillin-resistance determinants.
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Affiliation(s)
- Mark van der Linden
- 1 Department of Medical Microbiology, German National Reference Center for Streptococci , Aachen, Germany
| | | | - Patrick Maurer
- 3 School of Engineering, University of Applied Sciences , Saarbrücken, Germany
| | - Regine Hakenbeck
- 4 Department of Microbiology, University of Kaiserslautern , Kaiserslautern, Germany
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25
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Sitkiewicz I. How to become a killer, or is it all accidental? Virulence strategies in oral streptococci. Mol Oral Microbiol 2017; 33:1-12. [PMID: 28727895 DOI: 10.1111/omi.12192] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/17/2017] [Indexed: 01/03/2023]
Abstract
Streptococci are a diverse group of Gram-positive microorganisms sharing common virulence traits and similar strategies to escape the oral niche and establish an infection in other parts of the host organism. Invasive infection with oral streptococci is "a perfect storm" that requires the concerted action of multiple biotic and abiotic factors. Our understanding of streptococcal pathogenicity and infectivity should probably be less mechanistic and driven not only by the identification of novel virulence factors. The observed diversity of the genus, including the range of virulence and pathogenicity mechanisms, is most likely the result of interspecies interactions, a massive horizontal gene transfer between streptococci within a shared oral niche, recombination events, selection of specialized clones, and modification of regulatory circuits. Selective pressure by the host and bacterial communities is a driving force for the selection of virulence traits and shaping the streptococcal genome. Global regulatory events driving niche adaptation and interactions with bacterial communities and the host steer research interests towards attempts to define the oral interactome on the transcriptional level and define signal cross-feeding and co-expression and co-regulation of virulence genes.
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Affiliation(s)
- I Sitkiewicz
- Department of Molecular Microbiology, National Medicines Institute, Warsaw, Poland
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26
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The oral commensal Streptococcus mitis activates the aryl hydrocarbon receptor in human oral epithelial cells. Int J Oral Sci 2017. [PMID: 28621325 PMCID: PMC5709542 DOI: 10.1038/ijos.2017.17] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Streptococcus mitis (S. mitis) is a pioneer commensal bacterial species colonizing many of the surfaces of the oral cavity in healthy individuals. Yet, not much information is available regarding its interaction with the host. We used examination of its transcriptional regulation in oral keratinocytes to elucidate some of its potential roles in the oral cavity. Transcription factor analysis of oral keratinocytes predicted S. mitis-mediated activation of aryl hydrocarbon receptor (AhR). Activation and functionality of AhR was confirmed through nuclear translocation determined by immunofluorescence microscopy and real-time polymerase chain reaction with reverse transcription analysis of CYP1A1, the hallmark gene for AhR activation. Addition of Streptococcus mutans or Streptococcus gordonii did not induce CYP1A1 transcription in the keratinocyte cultures. Introduction of an AhR-specific inhibitor revealed that S. mitis-mediated transcription of CXCL2 and CXCL8 was regulated by AhR. Elevated levels of prostaglandin E2 (enzyme-linked immunosorbent assay) in supernatants from S. mitis-treated oral epithelial cells were also attenuated by inhibition of AhR activity. The observed AhR-regulated activities point to a contribution of S. mitis in the regulation of inflammatory responses and thereby to wound healing in the oral cavity. The concept that the oral commensal microbiota can induce AhR activation is important, also in view of the role that AhR has in modulation of T-cell differentiation and as an anti-inflammatory factor in macrophages.
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27
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Long Persistence of a Streptococcus pneumoniae 23F Clone in a Cystic Fibrosis Patient. mSphere 2017; 2:mSphere00201-17. [PMID: 28596991 PMCID: PMC5463027 DOI: 10.1128/msphere.00201-17] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2017] [Accepted: 05/01/2017] [Indexed: 02/07/2023] Open
Abstract
Streptococcus pneumoniae is a common resident in the human nasopharynx. However, carriage can result in severe diseases due to a unique repertoire of pathogenicity factors that are rare in closely related commensal streptococci. We investigated a penicillin-resistant S. pneumoniae clone of serotype 23F isolated from a cystic fibrosis patient on multiple occasions over an unusually long period of over 3 years that was present without causing disease. Genome comparisons revealed an apparent nonfunctional pneumococcus-specific gene encoding a hyaluronidase, supporting the view that this enzyme adds to the virulence potential of the bacterium. The 23F clone harbored unique mosaic genes encoding penicillin resistance determinants, the product of horizontal gene transfer involving the commensal S. mitis as donor species. Sequences identical to one such mosaic gene were identified in an S. mitis strain from the same patient, suggesting that in this case S. pneumoniae played the role of donor. Streptococcus pneumoniae isolates of serotype 23F with intermediate penicillin resistance were recovered on seven occasions over a period of 37 months from a cystic fibrosis patient in Berlin. All isolates expressed the same multilocus sequence type (ST), ST10523. The genome sequences of the first and last isolates, D122 and D141, revealed the absence of two phage-related gene clusters compared to the genome of another ST10523 strain, D219, isolated earlier at a different place in Germany. Genomes of all three strains carried the same novel mosaic penicillin-binding protein (PBP) genes, pbp2x, pbp2b, and pbp1a; these genes were distinct from those of other penicillin-resistant S. pneumoniae strains except for pbp1a of a Romanian S. pneumoniae isolate. All PBPs contained mutations that have been associated with the penicillin resistance phenotype. Most interestingly, a mosaic block identical to an internal pbp2x sequence of ST10523 was present in pbp2x of Streptococcus mitis strain B93-4, which was isolated from the same patient. This suggests interspecies gene transfer from S. pneumoniae to S. mitis within the host. Nearly all genes expressing surface proteins, which represent major virulence factors of S. pneumoniae and are typical for this species, were present in the genome of ST10523. One exception was the hyaluronidase gene hlyA, which contained a 12-nucleotide deletion within the promoter region and an internal stop codon. The lack of a functional hyaluronidase might contribute to the ability to persist in the host for an unusually long period of time. IMPORTANCEStreptococcus pneumoniae is a common resident in the human nasopharynx. However, carriage can result in severe diseases due to a unique repertoire of pathogenicity factors that are rare in closely related commensal streptococci. We investigated a penicillin-resistant S. pneumoniae clone of serotype 23F isolated from a cystic fibrosis patient on multiple occasions over an unusually long period of over 3 years that was present without causing disease. Genome comparisons revealed an apparent nonfunctional pneumococcus-specific gene encoding a hyaluronidase, supporting the view that this enzyme adds to the virulence potential of the bacterium. The 23F clone harbored unique mosaic genes encoding penicillin resistance determinants, the product of horizontal gene transfer involving the commensal S. mitis as donor species. Sequences identical to one such mosaic gene were identified in an S. mitis strain from the same patient, suggesting that in this case S. pneumoniae played the role of donor.
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28
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Streptococcus mitis and S. oralis Lack a Requirement for CdsA, the Enzyme Required for Synthesis of Major Membrane Phospholipids in Bacteria. Antimicrob Agents Chemother 2017; 61:AAC.02552-16. [PMID: 28223392 PMCID: PMC5404519 DOI: 10.1128/aac.02552-16] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Accepted: 02/04/2017] [Indexed: 11/20/2022] Open
Abstract
Synthesis and integrity of the cytoplasmic membrane are fundamental to cellular life. Experimental evolution studies have hinted at unique physiology in the Gram-positive bacteria Streptococcus mitis and S. oralis These organisms commonly cause bacteremia and infectious endocarditis (IE) but are rarely investigated in mechanistic studies of physiology and evolution. Unlike in other Gram-positive pathogens, high-level (MIC ≥ 256 μg/ml) daptomycin resistance rapidly emerges in S. mitis and S. oralis after a single drug exposure. In this study, we found that inactivating mutations in cdsA are associated with high-level daptomycin resistance in S. mitis and S. oralis IE isolates. This is surprising given that cdsA is an essential gene for life in commonly studied model organisms. CdsA is the enzyme responsible for the synthesis of CDP-diacylglycerol, a key intermediate for the biosynthesis of all major phospholipids in prokaryotes and most anionic phospholipids in eukaryotes. Lipidomic analysis by liquid chromatography-mass spectrometry (LC-MS) showed that daptomycin-resistant strains have an accumulation of phosphatidic acid and completely lack phosphatidylglycerol and cardiolipin, two major anionic phospholipids in wild-type strains, confirming the loss of function of CdsA in the daptomycin-resistant strains. To our knowledge, these daptomycin-resistant streptococci represent the first model organisms whose viability is CdsA independent. The distinct membrane compositions resulting from the inactivation of cdsA not only provide novel insights into the mechanisms of daptomycin resistance but also offer unique opportunities to study the physiological functions of major anionic phospholipids in bacteria.
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Lees JA, Kremer PHC, Manso AS, Croucher NJ, Ferwerda B, Serón MV, Oggioni MR, Parkhill J, Brouwer MC, van der Ende A, van de Beek D, Bentley SD. Large scale genomic analysis shows no evidence for pathogen adaptation between the blood and cerebrospinal fluid niches during bacterial meningitis. Microb Genom 2017; 3:e000103. [PMID: 28348877 PMCID: PMC5361624 DOI: 10.1099/mgen.0.000103] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Accepted: 12/18/2016] [Indexed: 12/26/2022] Open
Abstract
Recent studies have provided evidence for rapid pathogen genome diversification, some of which could potentially affect the course of disease. We have previously described such variation seen between isolates infecting the blood and cerebrospinal fluid (CSF) of a single patient during a case of bacterial meningitis. Here, we performed whole-genome sequencing of paired isolates from the blood and CSF of 869 meningitis patients to determine whether such variation frequently occurs between these two niches in cases of bacterial meningitis. Using a combination of reference-free variant calling approaches, we show that no genetic adaptation occurs in either invaded niche during bacterial meningitis for two major pathogen species, Streptococcus pneumoniae and Neisseria meningitidis. This study therefore shows that the bacteria capable of causing meningitis are already able to do this upon entering the blood, and no further sequence change is necessary to cross the blood–brain barrier. Our findings place the focus back on bacterial evolution between nasopharyngeal carriage and invasion, or diversity of the host, as likely mechanisms for determining invasiveness.
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Affiliation(s)
- John A Lees
- 1Pathogen Genomics, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Philip H C Kremer
- 2Department of Neurology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center, Amsterdam, The Netherlands
| | - Ana S Manso
- 3Department of Genetics, University of Leicester, Leicester, UK
| | - Nicholas J Croucher
- 4Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Bart Ferwerda
- 2Department of Neurology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center, Amsterdam, The Netherlands
| | - Mercedes Valls Serón
- 2Department of Neurology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center, Amsterdam, The Netherlands
| | - Marco R Oggioni
- 3Department of Genetics, University of Leicester, Leicester, UK
| | - Julian Parkhill
- 1Pathogen Genomics, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Matthijs C Brouwer
- 2Department of Neurology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center, Amsterdam, The Netherlands
| | - Arie van der Ende
- 5Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center, Amsterdam, The Netherlands.,6Netherlands Reference Laboratory for Bacterial Meningitis, Academic Medical Center, Amsterdam, The Netherlands
| | - Diederik van de Beek
- 2Department of Neurology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center, Amsterdam, The Netherlands
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30
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Szafrański SP, Winkel A, Stiesch M. The use of bacteriophages to biocontrol oral biofilms. J Biotechnol 2017; 250:29-44. [PMID: 28108235 DOI: 10.1016/j.jbiotec.2017.01.002] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Revised: 01/09/2017] [Accepted: 01/10/2017] [Indexed: 12/15/2022]
Abstract
Infections induced by oral biofilms include caries, as well as periodontal, and peri-implant disease, and may influence quality of life, systemic health, and expenditure. As bacterial biofilms are highly resistant and resilient to conventional antibacterial therapy, it has been difficult to combat these infections. An innovative alternative to the biocontrol of oral biofilms could be to use bacteriophages or phages, the viruses of bacteria, which are specific, non-toxic, self-proliferating, and can penetrate into biofilms. Phages for Actinomyces naeslundii, Aggregatibacter actinomycetemcomitans, Enterococcus faecalis, Fusobacterium nucleatum, Lactobacillus spp., Neisseria spp., Streptococcus spp., and Veillonella spp. have been isolated and characterised. Recombinant phage enzymes (lysins) have been shown to lyse A. naeslundii and Streptococcus spp. However, only a tiny fraction of available phages and their lysins have been explored so far. The unique properties of phages and their lysins make them promising but challenging antimicrobials. The genetics and biology of phages have to be further explored in order to determine the most effective way of applying them. Studying the effect of phages and lysins on multispecies biofilms should pave the way for microbiota engineering and microbiota-based therapy.
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Affiliation(s)
- Szymon P Szafrański
- Lower Saxony Centre for Biomedical Engineering, Implant Research and Development (NIFE), Stadtfelddamm 34, D-30625 Hannover, Germany; Department of Prosthetic Dentistry and Biomedical Materials Science, Hannover Medical School (MHH), Carl-Neuberg-Strasse 1, D-30625 Hannover, Germany.
| | - Andreas Winkel
- Lower Saxony Centre for Biomedical Engineering, Implant Research and Development (NIFE), Stadtfelddamm 34, D-30625 Hannover, Germany; Department of Prosthetic Dentistry and Biomedical Materials Science, Hannover Medical School (MHH), Carl-Neuberg-Strasse 1, D-30625 Hannover, Germany
| | - Meike Stiesch
- Lower Saxony Centre for Biomedical Engineering, Implant Research and Development (NIFE), Stadtfelddamm 34, D-30625 Hannover, Germany; Department of Prosthetic Dentistry and Biomedical Materials Science, Hannover Medical School (MHH), Carl-Neuberg-Strasse 1, D-30625 Hannover, Germany.
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Makarewicz O, Lucas M, Brandt C, Herrmann L, Albersmeier A, Rückert C, Blom J, Goesmann A, van der Linden M, Kalinowski J, Pletz MW. Whole Genome Sequencing of 39 Invasive Streptococcus pneumoniae Sequence Type 199 Isolates Revealed Switches from Serotype 19A to 15B. PLoS One 2017; 12:e0169370. [PMID: 28046133 PMCID: PMC5207522 DOI: 10.1371/journal.pone.0169370] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Accepted: 12/15/2016] [Indexed: 11/18/2022] Open
Abstract
Streptococcus pneumoniae is a major pathogen that causes different invasive pneumococcal diseases (IPD). The pneumococcal polysaccharide capsule is a main virulence factor. More than 94 capsule types have been described, but only a limited number of capsule types accounted for the majority of IPD cases before the introduction of pneumococcal vaccines. After the introduction of the conjugated pneumococcal vaccine PCV7, which covered the seven most frequent serotypes in IPD in the USA, an increase in IPD caused by non-vaccine serotypes was observed, and serotype 19A, which belongs to sequence type (ST) 199, was among the most prevalent STs. After the introduction of the extended vaccine PCV13, which includes serotype 19A, serogroup 15B/C increased in IPD. Therefore, whole genome sequences of 39 isolates of ST199 from Germany (collected between 1998 and 2011) with serotype 19A (n = 24) and serogroup 15B/C (n = 15) were obtained using an Illumina platform and were analysed to identify capsular switches within ST199. Two 19A to 15B/C serotype switch events were identified. Both events occurred before the introduction of PCV7, which indicates that a capsular switch from 19A to 15B among ST199 isolates is not unusual and is not directly linked to the vaccination. The observed serotype replacement appears to be the result of a vacant niche due to the displacement of vaccine serotypes that is now successfully occupied by ST199 clones.
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Affiliation(s)
- Oliwia Makarewicz
- Center for Infectious Diseases and Infection Control, Jena University Hospital, Jena, Germany
- * E-mail:
| | - Marie Lucas
- Center for Infectious Diseases and Infection Control, Jena University Hospital, Jena, Germany
| | - Christian Brandt
- Center for Infectious Diseases and Infection Control, Jena University Hospital, Jena, Germany
| | - Leonie Herrmann
- Center for Biotechology, University of Bielefeld, Bielefeld, Germany
| | | | - Christian Rückert
- Center for Biotechology, University of Bielefeld, Bielefeld, Germany
| | - Jochen Blom
- Institute for Bioinformatics and Systems Biology, Justus Liebig University Giessen, Giessen, Germany
| | - Alexander Goesmann
- Institute for Bioinformatics and Systems Biology, Justus Liebig University Giessen, Giessen, Germany
| | - Mark van der Linden
- German National Reference Center of Streptococci, University Hospital RWTH Aachen, Aachen, Germany
| | - Jörn Kalinowski
- Center for Biotechology, University of Bielefeld, Bielefeld, Germany
| | - Mathias W. Pletz
- Center for Infectious Diseases and Infection Control, Jena University Hospital, Jena, Germany
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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: 64] [Impact Index Per Article: 8.0] [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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Martín V, Mediano P, Del Campo R, Rodríguez JM, Marín M. Streptococcal Diversity of Human Milk and Comparison of Different Methods for the Taxonomic Identification of Streptococci. J Hum Lact 2016; 32:NP84-NP94. [PMID: 26261225 DOI: 10.1177/0890334415597901] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
BACKGROUND The genus Streptococcus is 1 of the dominant bacterial groups in human milk, but the taxonomic identification of some species remains difficult. OBJECTIVE The objective of this study was to investigate the discriminatory ability of different methods to identify streptococcal species in order to perform an assessment of the streptococcal diversity of human milk microbiota as accurately as possible. METHODS The identification of 105 streptococcal strains from human milk was performed by 16S rRNA, tuf, and sodA gene sequencing, phylogenetic analysis, and Matrix Assisted Laser Desorption Ionization-Time of Flight (MALDI-TOF) mass spectrometry. RESULTS Streptococcus salivarius, Streptococcus mitis, and Streptococcus parasanguinis were the streptococcal dominant species in the human milk microbiota. Sequencing of housekeeping genes allowed the classification of 96.2% (16S rRNA), 84.8% ( sodA), and 88.6% ( tuf) of the isolates. Phylogenetic analysis showed 3 main streptococcal clusters corresponding with the mitis (73 isolates), salivarius (29), mutans (1)-pyogenic (2) groups, but many of the mitis group isolates (36) could not be assigned to any species. The application of the MALDI-TOF Bruker Biotyper system resulted in the identification of 56 isolates (53.33%) at the species level, but it could not discriminate between S pneumoniae and S mitis isolates, in contrast to the Vitek-MS system. CONCLUSION There was a good agreement among the different methods assessed in this study to identify those isolates of the salivarius, mutans, and pyogenic groups, whereas unambiguous discrimination could not be achieved concerning some species of the mitis group ( S mitis, S pneumoniae, S pseudopneumoniae, S oralis).
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Affiliation(s)
- Virginia Martín
- 1 Departamento de Nutrición, Bromatología y Tecnología de los Alimentos, Universidad Complutense de Madrid, Madrid, Spain
| | - Pilar Mediano
- 1 Departamento de Nutrición, Bromatología y Tecnología de los Alimentos, Universidad Complutense de Madrid, Madrid, Spain
| | - Rosa Del Campo
- 2 Servicio de Microbiología, Hospital Universitario Ramón y Cajal, Madrid, Spain
| | - Juan M Rodríguez
- 1 Departamento de Nutrición, Bromatología y Tecnología de los Alimentos, Universidad Complutense de Madrid, Madrid, Spain
| | - María Marín
- 1 Departamento de Nutrición, Bromatología y Tecnología de los Alimentos, Universidad Complutense de Madrid, Madrid, Spain
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Salvadori G, Junges R, Morrison DA, Petersen FC. Overcoming the Barrier of Low Efficiency during Genetic Transformation of Streptococcus mitis. Front Microbiol 2016; 7:1009. [PMID: 27458432 PMCID: PMC4932118 DOI: 10.3389/fmicb.2016.01009] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Accepted: 06/14/2016] [Indexed: 01/31/2023] Open
Abstract
Objective:Streptococcus mitis is a predominant oral colonizer, but difficulties in genetic manipulation of this species have hampered our understanding of the mechanisms it uses for colonization of oral surfaces. The aim of this study was to reveal optimal conditions for natural genetic transformation in S. mitis and illustrate its application in direct genome editing. Methods: Luciferase reporter assays were used to assess gene expression of the alternative sigma factor (σX) in combination with natural transformation experiments to evaluate the efficiency by which S. mitis activates the competence system and incorporates exogenous DNA. Optimal amounts and sources of donor DNA (chromosomal, amplicon, or replicative plasmid), concentrations of synthetic competence-stimulating peptide, and transformation media were assessed. Results: A semi-defined medium showed much improved results for response to the competence stimulating peptide when compared to rich media. The use of a donor amplicon with large homology flanking regions also provided higher transformation rates. Overall, an increase of transformation efficiencies from 0.001% or less to over 30% was achieved with the developed protocol. We further describe the construction of a markerless mutant based on this high efficiency strategy. Conclusion: We optimized competence development in S. mitis, by use of semi-defined medium and appropriate concentrations of synthetic competence factor. Combined with the use of a large amplicon of donor DNA, this method allowed easy and direct editing of the S. mitis genome, broadening the spectrum of possible downstream applications of natural transformation in this species.
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Affiliation(s)
- Gabriela Salvadori
- Department of Oral Biology, Faculty of Dentistry, University of Oslo Oslo, Norway
| | - Roger Junges
- Department of Oral Biology, Faculty of Dentistry, University of Oslo Oslo, Norway
| | - Donald A Morrison
- Department of Biological Sciences, College of Liberal Arts and Sciences, University of Illinois at Chicago Chicago, IL, USA
| | - Fernanda C Petersen
- Department of Oral Biology, Faculty of Dentistry, University of Oslo Oslo, Norway
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de Vries LE, Hasman H, Jurado Rabadán S, Agersø Y. Sequence-Based Characterization of Tn5801-Like Genomic Islands in Tetracycline-Resistant Staphylococcus pseudintermedius and Other Gram-positive Bacteria from Humans and Animals. Front Microbiol 2016; 7:576. [PMID: 27199912 PMCID: PMC4844618 DOI: 10.3389/fmicb.2016.00576] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2015] [Accepted: 04/08/2016] [Indexed: 01/18/2023] Open
Abstract
Antibiotic resistance in pathogens is often associated with mobile genetic elements, such as genomic islands (GI) including integrative and conjugative elements (ICEs). These can transfer resistance genes within and between bacteria from humans and/or animals. The aim of this study was to investigate whether Tn5801-like GIs carrying the tetracycline resistance gene, tet(M), are common in Staphylococcus pseudintermedius from pets, and to do an overall sequences-based characterization of Tn5801-like GIs detected in Gram-positive bacteria from humans and animals. A total of 27 tetracycline-resistant S. pseudintermedius isolates from Danish pets (1998–2005) were screened for tet(M) by PCR. Selected isolates (13) were screened for GI- or ICE-specific genes (intTn5801 or xisTn916) and their tet(M) gene was sequenced (Sanger-method). Long-range PCR mappings and whole-genome-sequencing (Illumina) were performed for selected S. pseudintermedius-isolates (seven and three isolates, respectively) as well as for human S. aureus isolates (seven and one isolates, respectively) and one porcine Enterococcus faecium isolate known to carry Tn5801-like GIs. All 27 S. pseudintermedius were positive for tet(M). Out of 13 selected isolates, seven contained Tn5801-like GIs and six contained Tn916-like ICEs. Two different Tn5801-like GI types were detected among S. pseudintermedius (Tn5801 and GI6287) - both showed high similarity compared to GenBank sequences from human pathogens. Two distinct Tn5801-like GI types were detected among the porcine E. faecium and human S. aureus isolates (Tn6014 and GI6288). Tn5801-like GIs were detected in GenBank-sequences from Gram-positive bacteria of human, animal or food origin worldwide. Known Tn5801-like GIs were divided into seven types. The results showed that Tn5801-like GIs appear to be relatively common in tetracycline-resistant S. pseudintermedius in Denmark. Almost identical Tn5801-like GIs were identified in different Gram-positive species of pet and human origin, suggesting that horizontal transfer of these elements has occurred between S. pseudintermedius from pets and human pathogens, including S. aureus.
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Affiliation(s)
- Lisbeth E de Vries
- Department of Technology, Metropolitan University College Copenhagen, Denmark
| | - Henrik Hasman
- National Food Institute, Technical University of Copenhagen Lyngby, Denmark
| | | | - Yvonne Agersø
- National Food Institute, Technical University of Copenhagen Lyngby, Denmark
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Utter DR, Mark Welch JL, Borisy GG. Individuality, Stability, and Variability of the Plaque Microbiome. Front Microbiol 2016; 7:564. [PMID: 27148241 PMCID: PMC4840391 DOI: 10.3389/fmicb.2016.00564] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Accepted: 04/04/2016] [Indexed: 01/13/2023] Open
Abstract
Dental plaque is a bacterial biofilm composed of a characteristic set of organisms. Relatively little information from cultivation-independent, high-throughput analyses has been published on the temporal dynamics of the dental plaque microbiome. We used Minimum Entropy Decomposition, an information theory-based approach similar to oligotyping that provides single-nucleotide resolution, to analyze a previously published time series data set and investigate the dynamics of the plaque microbiome at various analytic and taxonomic levels. At both the genus and 97% Operational Taxonomic Unit (OTU) levels of resolution, the range of variation within each individual overlapped that of other individuals in the data set. When analyzed at the oligotype level, however, the overlap largely disappeared, showing that single-nucleotide resolution enables differentiation of individuals from one another without ambiguity. The overwhelming majority of the plaque community in all samples was made up of bacteria from a moderate number of plaque-typical genera, indicating that the overall community framework is shared among individuals. Each of these genera fluctuated in abundance around a stable mean that varied between individuals, with some genera having higher inter-individual variability than others. Thus, at the genus level, differences between individuals lay not in the identity of the major genera but in consistently differing proportions of these genera from mouth to mouth. However, at the oligotype level, we detected oligotype “fingerprints,” a highly individual-specific set of persistently abundant oligotypes fluctuating around a stable mean over time. For example, within the genus Corynebacterium, more than a dozen oligotypes were detectable in each individual, of which a different subset reached high abundance in any given person. This pattern suggests that each mouth contains a subtly different community of organisms. We also compared the Chinese plaque community characterized here to previously characterized Western plaque communities, as represented by analyses of data emerging from the Human Microbiome Project, and found no major differences between Chinese and Western supragingival plaque. In conclusion, we found the plaque microbiome to be highly individualized at the oligotype level and characterized by stability of community membership, with variability in the relative abundance of community members between individuals and over time.
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Affiliation(s)
- Daniel R Utter
- Department of Organismic and Evolutionary Biology, Harvard UniversityCambridge, MA, USA; Department of Microbiology, The Forsyth InstituteCambridge, MA, USA
| | - Jessica L Mark Welch
- Department of Microbiology, The Forsyth InstituteCambridge, MA, USA; Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological LaboratoryWoods Hole, MA, USA
| | - Gary G Borisy
- Department of Microbiology, The Forsyth Institute Cambridge, MA, USA
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Bensing BA, Khedri Z, Deng L, Yu H, Prakobphol A, Fisher SJ, Chen X, Iverson TM, Varki A, Sullam PM. Novel aspects of sialoglycan recognition by the Siglec-like domains of streptococcal SRR glycoproteins. Glycobiology 2016; 26:1222-1234. [PMID: 27037304 DOI: 10.1093/glycob/cww042] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Revised: 03/23/2016] [Accepted: 03/25/2016] [Indexed: 12/15/2022] Open
Abstract
Serine-rich repeat glycoproteins are adhesins expressed by commensal and pathogenic Gram-positive bacteria. A subset of these adhesins, expressed by oral streptococci, binds sialylated glycans decorating human salivary mucin MG2/MUC7, and platelet glycoprotein GPIb. Specific sialoglycan targets were previously identified for the ligand-binding regions (BRs) of GspB and Hsa, two serine-rich repeat glycoproteins expressed by Streptococcus gordonii While GspB selectively binds sialyl-T antigen, Hsa displays broader specificity. Here we examine the binding properties of four additional BRs from Streptococcus sanguinis or Streptococcus mitis and characterize the molecular determinants of ligand selectivity and affinity. Each BR has two domains that are essential for sialoglycan binding by GspB. One domain is structurally similar to the glycan-binding module of mammalian Siglecs (sialic acid-binding immunoglobulin-like lectins), including an arginine residue that is critical for glycan recognition, and that resides within a novel, conserved YTRY motif. Despite low sequence similarity to GspB, one of the BRs selectively binds sialyl-T antigen. Although the other three BRs are highly similar to Hsa, each displayed a unique ligand repertoire, including differential recognition of sialyl Lewis antigens and sulfated glycans. These differences in glycan selectivity were closely associated with differential binding to salivary and platelet glycoproteins. Specificity of sialoglycan adherence is likely an evolving trait that may influence the propensity of streptococci expressing Siglec-like adhesins to cause infective endocarditis.
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Affiliation(s)
- Barbara A Bensing
- Department of Medicine, The San Francisco Veterans Affairs Medical Center, and the University of California, San Francisco, San Francisco, CA 94121, USA
| | - Zahra Khedri
- The Glycobiology Research and Training Center, and the Department of Cellular and Molecular Medicine, University of California, San Diego, San Diego, CA 92093, USA
| | - Lingquan Deng
- The Glycobiology Research and Training Center, and the Department of Cellular and Molecular Medicine, University of California, San Diego, San Diego, CA 92093, USA
| | - Hai Yu
- Department of Chemistry, University of California, Davis, Davis, CA 95616, USA
| | - Akraporn Prakobphol
- Department of Obstetrics, Gynecology and Reproductive Sciences, The University of California, San Francisco, San Francisco, CA 94143, USA
| | - Susan J Fisher
- Department of Obstetrics, Gynecology and Reproductive Sciences, The University of California, San Francisco, San Francisco, CA 94143, USA
| | - Xi Chen
- Department of Chemistry, University of California, Davis, Davis, CA 95616, USA
| | - Tina M Iverson
- Department of Pharmacology, Vanderbilt University, Nashville, TN 27232, USA
| | - Ajit Varki
- The Glycobiology Research and Training Center, and the Department of Cellular and Molecular Medicine, University of California, San Diego, San Diego, CA 92093, USA
| | - Paul M Sullam
- Department of Medicine, The San Francisco Veterans Affairs Medical Center, and the University of California, San Francisco, San Francisco, CA 94121, USA
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Simões AS, Tavares DA, Rolo D, Ardanuy C, Goossens H, Henriques-Normark B, Linares J, de Lencastre H, Sá-Leão R. lytA-based identification methods can misidentify Streptococcus pneumoniae. Diagn Microbiol Infect Dis 2016; 85:141-8. [PMID: 27107535 DOI: 10.1016/j.diagmicrobio.2016.03.018] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Revised: 02/19/2016] [Accepted: 03/20/2016] [Indexed: 02/01/2023]
Abstract
During surveillance studies we detected, among over 1500 presumptive pneumococci, 11 isolates displaying conflicting or novel results when characterized by widely accepted phenotypic (optochin susceptibility and bile solubility) and genotypic (lytA-BsaAI-RFLP and MLST) identification methods. We aimed to determine the genetic basis for the unexpected results given by lytA-BsaAI-RFLP and investigate the accuracy of the WHO recommended lytA real-time PCR assay to classify these 11 isolates. Three novel lytA-BsaAI-RFLP signatures were found (one in pneumococcus and two in S. mitis). In addition, one pneumococcus displayed the atypical lytA-BsaAI-RFLP signature characteristic of non-pneumococci and two S. pseudopneumoniae displayed the typical lytA-BsaAI-RFLP pattern characteristic of pneumococci. lytA real-time PCR misidentified these three isolates. In conclusion, identification of pneumococci by lytA real-time PCR, and other lytA-based methodologies, may lead to false results. This is of particular relevance in the increasingly frequent colonization studies relying solely on culture-independent methods.
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Affiliation(s)
- Alexandra S Simões
- Laboratory of Molecular Microbiology of Human Pathogens, Instituto de Tecnologia Química e Biológica António Xavier (ITQB), Universidade Nova de Lisboa (UNL), Oeiras, Portugal
| | - Débora A Tavares
- Laboratory of Molecular Microbiology of Human Pathogens, Instituto de Tecnologia Química e Biológica António Xavier (ITQB), Universidade Nova de Lisboa (UNL), Oeiras, Portugal
| | - Dora Rolo
- Microbiology Department, Hospital Universitari de Bellvitge, Universitat de Barcelona-IDIBELL, L'Hospitalet de Llobregat, Barcelona, Spain; CIBERES (Ciber de Enfermedades Respiratorias), ISCIII, Madrid, Spain
| | - Carmen Ardanuy
- Microbiology Department, Hospital Universitari de Bellvitge, Universitat de Barcelona-IDIBELL, L'Hospitalet de Llobregat, Barcelona, Spain; CIBERES (Ciber de Enfermedades Respiratorias), ISCIII, Madrid, Spain
| | - Herman Goossens
- Department of Medical Microbiology, University of Antwerp, Antwerp, Belgium; Vaccine and Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
| | - Birgitta Henriques-Normark
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden; Department of Laboratory Medicine, Division of Clinical Microbiology, Karolinska University Hospital, Stockholm, Sweden
| | - Josefina Linares
- Microbiology Department, Hospital Universitari de Bellvitge, Universitat de Barcelona-IDIBELL, L'Hospitalet de Llobregat, Barcelona, Spain; CIBERES (Ciber de Enfermedades Respiratorias), ISCIII, Madrid, Spain
| | - Hermínia de Lencastre
- Laboratory of Molecular Genetics, ITQB, UNL, 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 (ITQB), Universidade Nova de Lisboa (UNL), Oeiras, Portugal.
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Highly Variable Streptococcus oralis Strains Are Common among Viridans Streptococci Isolated from Primates. mSphere 2016; 1:mSphere00041-15. [PMID: 27303717 PMCID: PMC4863584 DOI: 10.1128/msphere.00041-15] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Accepted: 02/06/2016] [Indexed: 12/11/2022] Open
Abstract
Streptococcus pneumoniae is a rare example of a human-pathogenic bacterium among viridans streptococci, which consist of commensal symbionts, such as the close relatives Streptococcus mitis and S. oralis. We have shown that S. oralis can frequently be isolated from primates and a variety of other viridans streptococci as well. Genes and genomic islands which are known pneumococcal virulence factors are present in S. oralis and S. mitis, documenting the widespread occurrence of these compounds, which encode surface and secreted proteins. The frequent occurrence of CRISP-Cas gene clusters and a surprising variation of a set of small noncoding RNAs are factors to be considered in future research to further our understanding of mechanisms involved in the genomic diversity driven by horizontal gene transfer among viridans streptococci. Viridans streptococci were obtained from primates (great apes, rhesus monkeys, and ring-tailed lemurs) held in captivity, as well as from free-living animals (chimpanzees and lemurs) for whom contact with humans is highly restricted. Isolates represented a variety of viridans streptococci, including unknown species. Streptococcus oralis was frequently isolated from samples from great apes. Genotypic methods revealed that most of the strains clustered on separate lineages outside the main cluster of human S. oralis strains. This suggests that S. oralis is part of the commensal flora in higher primates and evolved prior to humans. Many genes described as virulence factors in Streptococcus pneumoniae were present also in other viridans streptococcal genomes. Unlike in S. pneumoniae, clustered regularly interspaced short palindromic repeat (CRISPR)–CRISPR-associated protein (Cas) gene clusters were common among viridans streptococci, and many S. oralis strains were type PI-2 (pilus islet 2) variants. S. oralis displayed a remarkable diversity of genes involved in the biosynthesis of peptidoglycan (penicillin-binding proteins and MurMN) and choline-containing teichoic acid. The small noncoding cia-dependent small RNAs (csRNAs) controlled by the response regulator CiaR might contribute to the genomic diversity, since we observed novel genomic islands between duplicated csRNAs, variably present in some isolates. All S. oralis genomes contained a β-N-acetyl-hexosaminidase gene absent in S. pneumoniae, which in contrast frequently harbors the neuraminidases NanB/C, which are absent in S. oralis. The identification of S. oralis-specific genes will help us to understand their adaptation to diverse habitats. IMPORTANCEStreptococcus pneumoniae is a rare example of a human-pathogenic bacterium among viridans streptococci, which consist of commensal symbionts, such as the close relatives Streptococcus mitis and S. oralis. We have shown that S. oralis can frequently be isolated from primates and a variety of other viridans streptococci as well. Genes and genomic islands which are known pneumococcal virulence factors are present in S. oralis and S. mitis, documenting the widespread occurrence of these compounds, which encode surface and secreted proteins. The frequent occurrence of CRISP-Cas gene clusters and a surprising variation of a set of small noncoding RNAs are factors to be considered in future research to further our understanding of mechanisms involved in the genomic diversity driven by horizontal gene transfer among viridans streptococci.
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Diversity and Evolution of the Tn5801-tet(M)-Like Integrative and Conjugative Elements among Enterococcus, Streptococcus, and Staphylococcus. Antimicrob Agents Chemother 2016; 60:1736-46. [PMID: 26729505 DOI: 10.1128/aac.01864-15] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Accepted: 12/27/2015] [Indexed: 12/11/2022] Open
Abstract
This work describes the diversity and evolution of Tn5801 among enterococci, staphylococci, and streptococci based on analysis of the 5,073 genomes of these bacterial groups available in gene databases. We also examined 610 isolates of Enterococcus (from 10 countries, 1987 to 2010) for the presence of this and other known CTn-tet(M) elements due to the scarcity of data about Tn5801 among enterococci. Genome location (by ICeu-I-pulsed-field gel electrophoresis [PFGE] hybridization/integration site identification), conjugation and fitness (by standard methods), Tn5801 characterization (by long-PCR mapping/sequencing), and clonality (by PFGE/multilocus sequence typing [MLST]) were studied. Twenty-three Tn5801 variants (17 unpublished) clustered in two groups, designated "A" (25 kb; n = 14; predominant in Staphylococcus aureus) and "B" (20 kb; n = 9; predominant in Streptococcus agalactiae). The percent GC content of the common backbone suggests a streptococcal origin of Tn5801 group B, with further acquisition of a 5-kb fragment that resulted in group A. Deep sequence analysis allowed identification of variants associated with clonal lineages of S. aureus (clonal complex 8 [CC8], sequence type 239 [ST239]), S. agalactiae (CC17), Enterococcus faecium (ST17/ST18), or Enterococcus faecalis (ST8), local variants, or variants located in different species and geographical areas. All Tn5801 elements were chromosomally located upstream of the guaA gene, which serves as an integration hot spot. Transferability was demonstrated only for Tn5801 type B among E. faecalis clonal backgrounds, which eventually harbored another Tn5801 copy. The study documents early acquisition of Tn5801 by Enterococcus, Staphylococcus, and Streptococcus. Clonal waves of these pathogens seem to have contributed to the geographical spread and local evolution of the transposon. Horizontal transfer, also demonstrated, could explain the variability observed, with the isolates often containing sequences of different origins.
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Gisch N, Schwudke D, Thomsen S, Heß N, Hakenbeck R, Denapaite D. Lipoteichoic acid of Streptococcus oralis Uo5: a novel biochemical structure comprising an unusual phosphorylcholine substitution pattern compared to Streptococcus pneumoniae. Sci Rep 2015; 5:16718. [PMID: 26577602 PMCID: PMC4649388 DOI: 10.1038/srep16718] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Accepted: 10/14/2015] [Indexed: 02/06/2023] Open
Abstract
Members of the Mitis group of streptococci possess teichoic acids (TAs) as integral components of their cell wall that are unique among Gram-positive bacteria. Both, lipoteichoic (LTA) and wall teichoic acid, are formed by the same biosynthetic pathway, are of high complexity and contain phosphorylcholine (P-Cho) residues. These residues serve as anchors for choline-binding proteins (CBPs), some of which have been identified as virulence factors of the human pathogen Streptococcus pneumoniae. We investigated the LTA structure of its close relative Streptococcus oralis. Our analysis revealed that S. oralis Uo5 LTA has an overall architecture similar to pneumococcal LTA (pnLTA) and can be considered as a subtype of type IV LTA. Its structural complexity is even higher than that of pnLTA and its composition differs in number and type of carbohydrate moieties, inter-residue connectivities and especially the P-Cho substitution pattern. Here, we report the occurrence of a saccharide moiety substituted with two P-Cho residues, which is unique as yet in bacterial derived surface carbohydrates. Finally, we could link the observed important structural variations between S. oralis and S. pneumoniae LTA to the divergent enzymatic repertoire for their TA biosynthesis.
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Affiliation(s)
- Nicolas Gisch
- Division of Bioanalytical Chemistry, Priority Area Infections, Research Center Borstel, Leibniz-Center for Medicine and Biosciences, Parkallee 1-40, 23845 Borstel, Germany
| | - Dominik Schwudke
- Division of Bioanalytical Chemistry, Priority Area Infections, Research Center Borstel, Leibniz-Center for Medicine and Biosciences, Parkallee 1-40, 23845 Borstel, Germany
| | - Simone Thomsen
- Division of Bioanalytical Chemistry, Priority Area Infections, Research Center Borstel, Leibniz-Center for Medicine and Biosciences, Parkallee 1-40, 23845 Borstel, Germany
| | - Nathalie Heß
- Department of Microbiology, University of Kaiserslautern, Paul-Ehrlich Straße 24, 67663 Kaiserslautern, Germany
| | - Regine Hakenbeck
- Department of Microbiology, University of Kaiserslautern, Paul-Ehrlich Straße 24, 67663 Kaiserslautern, Germany
| | - Dalia Denapaite
- Department of Microbiology, University of Kaiserslautern, Paul-Ehrlich Straße 24, 67663 Kaiserslautern, Germany
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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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Commensal streptococci serve as a reservoir for β-lactam resistance genes in Streptococcus pneumoniae. Antimicrob Agents Chemother 2015; 59:3529-40. [PMID: 25845880 DOI: 10.1128/aac.00429-15] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2015] [Accepted: 03/31/2015] [Indexed: 11/20/2022] Open
Abstract
Streptococcus pneumoniae is a leading cause of pneumonia, meningitis, septicemia, and middle ear infections. The incidence of S. pneumoniae isolates that are not susceptible to penicillin has risen worldwide and may be above 20% in some countries. Beta-lactam antibiotic resistance in pneumococci is associated with significant sequence polymorphism in penicillin-binding proteins (PBPs). Commensal streptococci, especially S. mitis and S. oralis, have been identified as putative donors of mutated gene fragments. However, no studies have compared sequences of the involved pbp genes in large collections of commensal streptococci with those of S. pneumoniae. We therefore investigated the sequence diversity of the transpeptidase region of the three pbp genes, pbp2x, pbp2b, and pbp1a in 107, 96, and 88 susceptible and nonsusceptible strains of commensal streptococci, respectively, at the nucleotide and amino acid levels to determine to what extent homologous recombination between commensal streptococci and S. pneumoniae plays a role in the development of beta-lactam resistance in S. pneumoniae. In contrast to pneumococci, extensive sequence variation in the transpeptidase region of pbp2x, pbp2b, and pbp1a was observed in both susceptible and nonsusceptible strains of commensal streptococci, conceivably reflecting the genetic diversity of the many evolutionary lineages of commensal streptococci combined with the recombination events occurring with intra- and interspecies homologues. Our data support the notion that resistance to beta-lactam antibiotics in pneumococci is due to sequences acquired from commensal Mitis group streptococci, especially S. mitis. However, several amino acid alterations previously linked to beta-lactam resistance in pneumococci appear to represent species signatures of the donor strain rather than being causal of resistance.
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Ouennane S, Leprohon P, Moineau S. Diverse virulent pneumophages infect Streptococcus mitis. PLoS One 2015; 10:e0118807. [PMID: 25692983 PMCID: PMC4334900 DOI: 10.1371/journal.pone.0118807] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2014] [Accepted: 01/23/2015] [Indexed: 01/01/2023] Open
Abstract
Streptococcus mitis has emerged as one of the leading causes of bacterial endocarditis and is related to Streptococcus pneumoniae. Antibiotic resistance has also increased among strains of S. mitis and S. pneumoniae. Phages are being reinvestigated as alternatives to antibiotics for managing infections. In this study, the two virulent phages Cp-1 (Podoviridae) and Dp-1 (Siphoviridae), previously isolated from S. pneumoniae, were found to also infect S. mitis. Microbiological assays showed that both pneumophages could not only replicate in S. mitis but also produced more visible plaques on this host. However, the burst size and phage adsorption data were lower in S. mitis as compared to S. pneumoniae. A comparison of the genomes of each phage grown on both hosts produced identical nucleotide sequences, confirming that the same phages infect both bacterial species. We also discovered that the genomic sequence of podophage Cp-1 of the Félix d'Hérelle collection is different than the previously reported sequence and thus renamed SOCP.
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Affiliation(s)
- Siham Ouennane
- Département de Biochimie, Microbiologie et Bio-Informatique, Faculté des Sciences et de Génie, Groupe de Recherche en Écologie Buccale, Félix d’Hérelle Reference Center for Bacterial Viruses, Faculté de Médecine Dentaire, Université Laval, Québec City, Québec, Canada
| | - Philippe Leprohon
- Département de Microbiologie, Infectiologie et Immunologie, Faculté de Médecine, Université Laval, Québec City, Québec, Canada
| | - Sylvain Moineau
- Département de Biochimie, Microbiologie et Bio-Informatique, Faculté des Sciences et de Génie, Groupe de Recherche en Écologie Buccale, Félix d’Hérelle Reference Center for Bacterial Viruses, Faculté de Médecine Dentaire, Université Laval, Québec City, Québec, Canada
- * E-mail:
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Chancey ST, Agrawal S, Schroeder MR, Farley MM, Tettelin H, Stephens DS. Composite mobile genetic elements disseminating macrolide resistance in Streptococcus pneumoniae. Front Microbiol 2015; 6:26. [PMID: 25709602 PMCID: PMC4321634 DOI: 10.3389/fmicb.2015.00026] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2014] [Accepted: 01/08/2015] [Indexed: 01/17/2023] Open
Abstract
Macrolide resistance in Streptococcus pneumoniae emerged in the U.S. and globally during the early 1990's. The RNA methylase encoded by erm(B) and the macrolide efflux genes mef(E) and mel were identified as the resistance determining factors. These genes are disseminated in the pneumococcus on mobile, often chimeric elements consisting of multiple smaller elements. To better understand the variety of elements encoding macrolide resistance and how they have evolved in the pre- and post-conjugate vaccine eras, the genomes of 121 invasive and ten carriage isolates from Atlanta from 1994 to 2011 were analyzed for mobile elements involved in the dissemination of macrolide resistance. The isolates were selected to provide broad coverage of the genetic variability of antibiotic resistant pneumococci and included 100 invasive isolates resistant to macrolides. Tn916-like elements carrying mef(E) and mel on the Macrolide Genetic Assembly (Mega) and erm(B) on the erm(B) element and Tn917 were integrated into the pneumococcal chromosome backbone and into larger Tn5253-like composite elements. The results reported here include identification of novel insertion sites for Mega and characterization of the insertion sites of Tn916-like elements in the pneumococcal chromosome and in larger composite elements. The data indicate that integration of elements by conjugation was infrequent compared to recombination. Thus, it appears that conjugative mobile elements allow the pneumococcus to acquire DNA from distantly related bacteria, but once integrated into a pneumococcal genome, transformation and recombination is the primary mechanism for transmission of novel DNA throughout the pneumococcal population.
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Affiliation(s)
- Scott T Chancey
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine Atlanta, GA, USA ; Laboratories of Microbial Pathogenesis, Department of Veterans Affairs Medical Center Atlanta, GA, USA
| | - Sonia Agrawal
- Institute for Genome Sciences, University of Maryland School of Medicine Baltimore, MD, USA
| | - Max R Schroeder
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine Atlanta, GA, USA ; Laboratories of Microbial Pathogenesis, Department of Veterans Affairs Medical Center Atlanta, GA, USA
| | - Monica M Farley
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine Atlanta, GA, USA ; Laboratories of Microbial Pathogenesis, Department of Veterans Affairs Medical Center Atlanta, GA, USA
| | - Hervé Tettelin
- Institute for Genome Sciences, University of Maryland School of Medicine Baltimore, MD, USA ; Department of Microbiology and Immunology, University of Maryland School of Medicine Baltimore, MD, USA
| | - David S Stephens
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine Atlanta, GA, USA ; Laboratories of Microbial Pathogenesis, Department of Veterans Affairs Medical Center Atlanta, GA, USA
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Alvarez-Sieiro P, Redruello B, Ladero V, Cañedo E, Martin MC, Fernández M, Alvarez MA. Solubilization of gliadins for use as a source of nitrogen in the selection of bacteria with gliadinase activity. Food Chem 2015; 168:439-44. [DOI: 10.1016/j.foodchem.2014.07.085] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2014] [Revised: 06/11/2014] [Accepted: 07/15/2014] [Indexed: 01/08/2023]
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RecFOR is not required for pneumococcal transformation but together with XerS for resolution of chromosome dimers frequently formed in the process. PLoS Genet 2015; 11:e1004934. [PMID: 25569614 PMCID: PMC4287498 DOI: 10.1371/journal.pgen.1004934] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2014] [Accepted: 12/02/2014] [Indexed: 11/19/2022] Open
Abstract
Homologous recombination (HR) is required for both genome maintenance and generation of diversity in eukaryotes and prokaryotes. This process initiates from single-stranded (ss) DNA and is driven by a universal recombinase, which promotes strand exchange between homologous sequences. The bacterial recombinase, RecA, is loaded onto ssDNA by recombinase loaders, RecBCD and RecFOR for genome maintenance. DprA was recently proposed as a third loader dedicated to genetic transformation. Here we assessed the role of RecFOR in transformation of the human pathogen Streptococcus pneumoniae. We firstly established that RecFOR proteins are not required for plasmid transformation, strongly suggesting that DprA ensures annealing of plasmid single-strands internalized in the process. We then observed no reduction in chromosomal transformation using a PCR fragment as donor, contrasting with the 10,000-fold drop in dprA- cells and demonstrating that RecFOR play no role in transformation. However, a ∼1.45-fold drop in transformation was observed with total chromosomal DNA in recFOR mutants. To account for this limited deficit, we hypothesized that transformation with chromosomal DNA stimulated unexpectedly high frequency (>30% of cells) formation of chromosome dimers as an intermediate in the generation of tandem duplications, and that RecFOR were crucial for dimer resolution. We validated this hypothesis, showing that the site-specific recombinase XerS was also crucial for dimer resolution. An even higher frequency of dimer formation (>80% of cells) was promoted by interspecies transformation with Streptococcus mitis chromosomal DNA, which contains numerous inversions compared to pneumococcal chromosome, each potentially promoting dimerization. In the absence of RecFOR and XerS, dimers persist, as confirmed by DAPI staining, and can limit the efficiency of transformation, since resulting in loss of transformant chromosome. These findings strengthen the view that different HR machineries exist for genome maintenance and transformation in pneumococci. These observations presumably apply to most naturally transformable species. Homologous recombination (HR) is a widespread process which maintains genome integrity and promotes diversity. In bacteria, HR mends damaged DNA to ensure genome integrity and is also involved in transformation, a mechanism of horizontal gene transfer allowing acquisition of new genetic traits. HR is driven by recombinases, which are loaded onto single-stranded DNA by the recombinase loaders RecBCD and RecFOR for genome maintenance. DprA was recently proposed as another loader dedicated to transformation. During transformation, foreign DNA is taken up as single strands and integrated into the chromosome by HR. In this study, we show that RecFOR is not involved in transformation in Streptococcus pneumoniae. These results provide further support to the existence of different HR machineries dedicated to genetic transformation and genome maintenance in this pathogen. In addition, we show that transformation with chromosomal DNA generates chromosome dimers with unexpectedly high frequency, and that their resolution requires RecFOR and the site-specific recombinase XerS. In cells lacking these proteins, dimers persist and have a detrimental effect on the efficiency of transformation. Since the HR mechanisms leading to dimer formation are most likely conserved, this effect is presumably general to naturally transformable species.
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48
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Shelburne SA, Sahasrabhojane P, Saldana M, Yao H, Su X, Horstmann N, Thompson E, Flores AR. Streptococcus mitis strains causing severe clinical disease in cancer patients. Emerg Infect Dis 2014; 20:762-71. [PMID: 24750901 PMCID: PMC4012796 DOI: 10.3201/eid2005.130953] [Citation(s) in RCA: 103] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The genetically diverse viridans group streptococci (VGS) are increasingly recognized as the
cause of a variety of human diseases. We used a recently developed multilocus sequence analysis
scheme to define the species of 118 unique VGS strains causing bacteremia in patients with cancer;
Streptococcus mitis (68 patients) and S. oralis (22 patients) were
the most frequently identified strains. Compared with patients infected with non–S.
mitis strains, patients infected with S. mitis strains were more likely to
have moderate or severe clinical disease (e.g., VGS shock syndrome). Combined with the sequence
data, whole-genome analyses showed that S. mitis strains may more precisely be
considered as >2 species. Furthermore, we found that multiple S.
mitis strains induced disease in neutropenic mice in a dose-dependent fashion. Our data
define the prominent clinical effect of the group of organisms currently classified as S.
mitis and lay the groundwork for increased understanding of this understudied pathogen.
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49
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Identification of proteins in Streptococcus pneumoniae by reverse vaccinology and genetic diversity of these proteins in clinical isolates. Appl Biochem Biotechnol 2014; 175:2124-65. [PMID: 25448632 DOI: 10.1007/s12010-014-1375-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2014] [Accepted: 11/10/2014] [Indexed: 10/24/2022]
Abstract
Streptococcus pneumoniae is a major cause of morbidity and mortality worldwide. Virulence-associated proteins common and conserved among all capsular types now represent the best strategy to combat pneumococcal infections. Our aim was to identify conserved targets in pneumococci that showed positive prediction for lipoprotein and extracellular subcellular location using bioinformatics programs and verify the distribution and the degree of conservation of these targets in pneumococci. These targets can be considered potential vaccine candidate to be evaluated in the future. A set of 13 targets were analyzed and confirmed the presence in all pneumococci tested. These 13 genes were highly conserved showing around >96 % of amino acid and nucleotide identity, but they were also present and show high identity in the closely related species Streptococcus mitis, Streptococcus oralis, and Streptococcus pseudopneumoniae. S. oralis clusters away from S. pneumoniae, while S. pseudopneumoniae and S. mitis cluster closer. The divergence between the selected targets was too small to be observed consistently in phylogenetic groups between the analyzed genomes of S. pneumoniae. The proteins analyzed fulfill two of the initial criteria of a vaccine candidate: targets are present in a variety of different pneumococci strains including different serotypes and are conserved among the samples evaluated.
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50
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Croucher NJ, Coupland PG, Stevenson AE, Callendrello A, Bentley SD, Hanage WP. Diversification of bacterial genome content through distinct mechanisms over different timescales. Nat Commun 2014; 5:5471. [PMID: 25407023 PMCID: PMC4263131 DOI: 10.1038/ncomms6471] [Citation(s) in RCA: 142] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Accepted: 10/03/2014] [Indexed: 12/16/2022] Open
Abstract
Bacterial populations often consist of multiple co-circulating lineages. Determining how such population structures arise requires understanding what drives bacterial diversification. Using 616 systematically sampled genomes, we show that Streptococcus pneumoniae lineages are typically characterized by combinations of infrequently transferred stable genomic islands: those moving primarily through transformation, along with integrative and conjugative elements and phage-related chromosomal islands. The only lineage containing extensive unique sequence corresponds to a set of atypical unencapsulated isolates that may represent a distinct species. However, prophage content is highly variable even within lineages, suggesting frequent horizontal transmission that would necessitate rapidly diversifying anti-phage mechanisms to prevent these viruses sweeping through populations. Correspondingly, two loci encoding Type I restriction-modification systems able to change their specificity over short timescales through intragenomic recombination are ubiquitous across the collection. Hence short-term pneumococcal variation is characterized by movement of phage and intragenomic rearrangements, with the slower transfer of stable loci distinguishing lineages. Populations of the pathogenic bacterium Streptococcus pneumoniae consist of distinct co-circulating lineages. Here, the authors show lineages are characterized by particular combinations of stable genomic islands, whereas prophage and restriction-modification systems vary over short timescales.
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Affiliation(s)
- Nicholas J Croucher
- 1] Centre for Communicable Disease Dynamics, Harvard School of Public Health, 677 Huntington Avenue, Boston, Massachusetts 02115, USA [2] Department of Infectious Disease Epidemiology, St. Mary's Campus, Imperial College, London W2 1PG, UK
| | - Paul G Coupland
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Abbie E Stevenson
- Centre for Communicable Disease Dynamics, Harvard School of Public Health, 677 Huntington Avenue, Boston, Massachusetts 02115, USA
| | - Alanna Callendrello
- Centre for Communicable Disease Dynamics, Harvard School of Public Health, 677 Huntington Avenue, Boston, Massachusetts 02115, USA
| | - Stephen D Bentley
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - William P Hanage
- Centre for Communicable Disease Dynamics, Harvard School of Public Health, 677 Huntington Avenue, Boston, Massachusetts 02115, USA
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