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Ren J, Sun P, Wang M, Zhou W, Liu Z. Insights into the role of Streptococcus oralis as an opportunistic pathogen in infectious diseases. Front Cell Infect Microbiol 2024; 14:1480961. [PMID: 39559706 PMCID: PMC11570589 DOI: 10.3389/fcimb.2024.1480961] [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: 08/14/2024] [Accepted: 10/17/2024] [Indexed: 11/20/2024] Open
Abstract
Streptococcus oralis, belonging to the viridans group streptococci (VGS), has been considered a member of normal flora mainly inhabiting the oral cavity. However, more recently, there has been growing recognition of its role as a causative agent in various life-threatening infectious diseases such as infective endocarditis (IE) and meningitis. Additionally, the differences in the prevalence, clinical features, and prognosis of opportunistic infections between S. oralis and other VGS species have been addressed. Particularly the predominance of S. oralis in IE has drawn critical attention. In potentially fatal infections, clinical neglect of S. oralis as an instigating agent might significantly impede early diagnosis and treatment. Nevertheless, to date, the infectious diseases associated with S. oralis have not yet been comprehensively described. Therefore, this review will give an overview of infectious diseases caused by S. oralis to uncover its hidden role as an opportunistic pathogen.
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Affiliation(s)
- Jingyi Ren
- School of Stomatology, Binzhou Medical University, Yantai, China
- Department of Implantology, The Affiliated Yantai Stomatological Hospital, Binzhou Medical University, Yantai, China
| | - Peng Sun
- Department of Spine Surgery, 970 Hospital of the People’s Liberation Army Joint Logistics Support Force (PLA JLSF), Yantai, China
| | - Meijuan Wang
- Department of Implantology, The Affiliated Yantai Stomatological Hospital, Binzhou Medical University, Yantai, China
| | - Wenjuan Zhou
- Department of Implantology, The Affiliated Yantai Stomatological Hospital, Binzhou Medical University, Yantai, China
- Yantai Engineering Research Center for Digital Technology of Stomatology, Yantai, China
- Characteristic Laboratories of Colleges and Universities in Shandong Province for Digital Stomatology, Yantai, China
| | - Zhonghao Liu
- School of Stomatology, Binzhou Medical University, Yantai, China
- Department of Implantology, The Affiliated Yantai Stomatological Hospital, Binzhou Medical University, Yantai, China
- Yantai Engineering Research Center for Digital Technology of Stomatology, Yantai, China
- Characteristic Laboratories of Colleges and Universities in Shandong Province for Digital Stomatology, Yantai, China
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Treerat P, Anderson D, Giacaman RA, Merritt J, Kreth J. Glycerol metabolism supports oral commensal interactions. THE ISME JOURNAL 2023; 17:1116-1127. [PMID: 37169870 PMCID: PMC10284889 DOI: 10.1038/s41396-023-01426-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 04/19/2023] [Accepted: 04/27/2023] [Indexed: 05/13/2023]
Abstract
During oral biofilm development, interspecies interactions drive species distribution and biofilm architecture. To understand what molecular mechanisms determine these interactions, we used information gained from recent biogeographical investigations demonstrating an association of corynebacteria with streptococci. We previously reported that Streptococcus sanguinis and Corynebacterium durum have a close relationship through the production of membrane vesicle and fatty acids leading to S. sanguinis chain elongation and overall increased fitness supporting their commensal state. Here we present the molecular mechanisms of this interspecies interaction. Coculture experiments for transcriptomic analysis identified several differentially expressed genes in S. sanguinis. Due to its connection to fatty acid synthesis, we focused on the glycerol-operon. We further explored the differentially expressed type IV pili genes due to their connection to motility and biofilm adhesion. Gene inactivation of the glycerol kinase glpK had a profound impact on the ability of S. sanguinis to metabolize C. durum secreted glycerol and impaired chain elongation important for their interaction. Investigations on the effect of type IV pili revealed a reduction of S. sanguinis twitching motility in the presence of C. durum, which was caused by a decrease in type IV pili abundance on the surface of S. sanguinis as determined by SEM. In conclusion, we identified that the ability to metabolize C. durum produced glycerol is crucial for the interaction of C. durum and S. sanguinis. Reduced twitching motility could lead to a closer interaction of both species, supporting niche development in the oral cavity and potentially shaping symbiotic health-associated biofilm communities.
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Affiliation(s)
- Puthayalai Treerat
- Department of Restorative Dentistry, School of Dentistry, Oregon Health & Science University (OHSU), Portland, OR, 97239, USA.
| | - David Anderson
- Department of Restorative Dentistry, School of Dentistry, Oregon Health & Science University (OHSU), Portland, OR, 97239, USA
| | - Rodrigo A Giacaman
- Cariology Unit, Department of Oral Rehabilitation, Faculty of Dentistry, University of Talca, Talca, Chile
| | - Justin Merritt
- Department of Restorative Dentistry, School of Dentistry, Oregon Health & Science University (OHSU), Portland, OR, 97239, USA
- Department of Molecular Microbiology and Immunology, School of Medicine, Oregon Health & Science University (OHSU), Portland, OR, 97239, USA
| | - Jens Kreth
- Department of Restorative Dentistry, School of Dentistry, Oregon Health & Science University (OHSU), Portland, OR, 97239, USA.
- Department of Molecular Microbiology and Immunology, School of Medicine, Oregon Health & Science University (OHSU), Portland, OR, 97239, USA.
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Joyce LR, Youngblom MA, Cormaty H, Gartstein E, Barber KE, Akins RL, Pepperell CS, Palmer KL. Comparative Genomics of Streptococcus oralis Identifies Large Scale Homologous Recombination and a Genetic Variant Associated with Infection. mSphere 2022; 7:e0050922. [PMID: 36321824 PMCID: PMC9769543 DOI: 10.1128/msphere.00509-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 10/17/2022] [Indexed: 11/07/2022] Open
Abstract
The viridans group streptococci (VGS) are a large consortium of commensal streptococci that colonize the human body. Many species within this group are opportunistic pathogens causing bacteremia and infective endocarditis (IE), yet little is known about why some strains cause invasive disease. Identification of virulence determinants is complicated by the difficulty of distinguishing between the closely related species of this group. Here, we analyzed genomic data from VGS that were isolated from blood cultures in patients with invasive infections and oral swabs of healthy volunteers and then determined the best-performing methods for species identification. Using whole-genome sequence data, we characterized the population structure of a diverse sample of Streptococcus oralis isolates and found evidence of frequent recombination. We used multiple genome-wide association study tools to identify candidate determinants of invasiveness. These tools gave consistent results, leading to the discovery of a single synonymous single nucleotide polymorphism (SNP) that was significantly associated with invasiveness. This SNP was within a previously undescribed gene that was conserved across the majority of VGS species. Using the growth in the presence of human serum and a simulated infective endocarditis vegetation model, we were unable to identify a phenotype for the enriched allele in laboratory assays, suggesting a phenotype may be specific to natural infection. These data highlighted the power of analyzing natural populations for gaining insight into pathogenicity, particularly for organisms with complex population structures like the VGS. IMPORTANCE The viridians group streptococci (VGS) are a large collection of closely related commensal streptococci, with many being opportunistic pathogens causing invasive diseases, such as bacteremia and infective endocarditis. Little is known about virulence determinants in these species, and there is a distinct lack of genomic information available for the VGS. In this study, we collected VGS isolates from invasive infections and healthy volunteers and performed whole-genome sequencing for a suite of downstream analyses. We focused on a diverse sample of Streptococcus oralis genomes and identified high rates of recombination in the population as well as a single genome variant highly enriched in invasive isolates. The variant lies within a previously uncharacterized gene, nrdM, which shared homology with the anaerobic ribonucleoside triphosphate reductase, nrdD, and was highly conserved among VGS. This work increased our knowledge of VGS genomics and indicated that differences in virulence potential among S. oralis isolates were, at least in part, genetically determined.
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Affiliation(s)
- Luke R. Joyce
- Department of Biological Sciences, The University of Texas at Dallas, Richardson, Texas, USA
| | - Madison A. Youngblom
- Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Department of Medical Microbiology and Immunology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Harshini Cormaty
- Department of Biological Sciences, The University of Texas at Dallas, Richardson, Texas, USA
| | - Evelyn Gartstein
- Department of Biological Sciences, The University of Texas at Dallas, Richardson, Texas, USA
| | - Katie E. Barber
- Department of Pharmacy Practice, University of Mississippi School of Pharmacy, University of Mississippi, Jackson, Mississippi, USA
| | | | - Caitlin S. Pepperell
- Department of Medical Microbiology and Immunology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Department of Medicine (Infectious Diseases), School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Kelli L. Palmer
- Department of Biological Sciences, The University of Texas at Dallas, Richardson, Texas, USA
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Abstract
Oral commensal streptococci are primary colonizers of the oral cavity. These streptococci produce many adhesins, metabolites, and antimicrobials that modulate microbial succession and diversity within the oral cavity. Often, oral commensal streptococci antagonize cariogenic and periodontal pathogens such as Streptococcus mutans and Porphyromonas gingivalis, respectively. Mechanisms of antagonism are varied and range from the generation of hydrogen peroxide, competitive metabolite scavenging, the generation of reactive nitrogen intermediates, and bacteriocin production. Furthermore, several oral commensal streptococci have been shown to alter the host immune response at steady state and in response to oral pathogens. Collectively, these features highlight the remarkable ability of oral commensal streptococci to regulate the structure and function of the oral microbiome. In this review, we discuss mechanisms used by oral commensal streptococci to interact with diverse oral pathogens, both physically and through the production of antimicrobials. Finally, we conclude by exploring the critical roles of oral commensal streptococci in modulating the host immune response and maintaining health and homeostasis.
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Affiliation(s)
- Joshua J. Baty
- Department of Microbiology, School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Sara N. Stoner
- Department of Microbiology, School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Jessica A. Scoffield
- Department of Microbiology, School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA
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Streptococcus sputorum, a Novel Member of Streptococcus with Multidrug Resistance, Exhibits Cytotoxicity. Antibiotics (Basel) 2021; 10:antibiotics10121532. [PMID: 34943744 PMCID: PMC8698525 DOI: 10.3390/antibiotics10121532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Revised: 12/03/2021] [Accepted: 12/10/2021] [Indexed: 11/29/2022] Open
Abstract
We describe the genomic and phenotypic characteristics of a novel member of Streptococcus with multidrug resistance (MDR) isolated from hospital samples. Strains SP218 and SP219 were identified as a novel Streptococcus, S. sputorum, using whole-genome sequencing and biochemical tests. Average nucleotide identity values of strains SP218 and SP219 with S. pseudopneumoniae IS7493 and S. pneumoniae ST556 were 94.3% and 93.3%, respectively. Genome-to-genome distance values of strains SP218 and SP219 with S. pseudopneumoniae IS7493 and S. pneumoniae ST556 were 56.70% (54–59.5%) and 56.40% (52.8–59.9%), respectively. The biochemical test results distinguished these strains from S. pseudopneumoniae and S. pneumoniae, particularly hydrolysis of equine urate and utilization of ribose to produce acid. These isolates were resistant to six major classes of antibiotics, which correlated with horizontal gene transfer and mutation. Notably, strain SP219 exhibited cytotoxicity against human lung epithelial cell line A549. Our results indicate the pathogenic potential of S. sputorum, and provide valuable insights into mitis group of streptococci.
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Puccio T, An SS, Schultz AC, Lizarraga CA, Bryant AS, Culp DJ, Burne RA, Kitten T. Manganese transport by Streptococcus sanguinis in acidic conditions and its impact on growth in vitro and in vivo. Mol Microbiol 2021; 117:375-393. [PMID: 34862691 PMCID: PMC8844241 DOI: 10.1111/mmi.14854] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 11/24/2021] [Accepted: 11/30/2021] [Indexed: 02/06/2023]
Abstract
Streptococcus sanguinis is an oral commensal and an etiological agent of infective endocarditis. Previous studies have identified the SsaACB manganese transporter as essential for endocarditis virulence; however, the significance of SsaACB in the oral environment has never been examined. Here we report that a ΔssaACB deletion mutant of strain SK36 exhibits reduced growth and manganese uptake under acidic conditions. Further studies revealed that these deficits resulted from the decreased activity of TmpA, shown in the accompanying paper to function as a ZIP‐family manganese transporter. Transcriptomic analysis of fermentor‐grown cultures of SK36 WT and ΔssaACB strains identified pH‐dependent changes related to carbon catabolite repression in both strains, though their magnitude was generally greater in the mutant. In strain VMC66, which possesses a MntH transporter, loss of SsaACB did not significantly alter growth or cellular manganese levels under the same conditions. Interestingly, there were only modest differences between SK36 and its ΔssaACB mutant in competition with Streptococcus mutans in vitro and in a murine oral colonization model. Our results suggest that the heterogeneity of the oral environment may provide a rationale for the variety of manganese transporters found in S. sanguinis.
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Affiliation(s)
- Tanya Puccio
- Philips Institute for Oral Health Research, Virginia Commonwealth University School of Dentistry, Richmond, Virginia, USA
| | - Seon-Sook An
- Philips Institute for Oral Health Research, Virginia Commonwealth University School of Dentistry, Richmond, Virginia, USA
| | - Alexander C Schultz
- Department of Oral Biology, University of Florida College of Dentistry, Gainesville, Florida, USA
| | - Claudia A Lizarraga
- Department of Oral Biology, University of Florida College of Dentistry, Gainesville, Florida, USA
| | - Ashley S Bryant
- Department of Oral Biology, University of Florida College of Dentistry, Gainesville, Florida, USA
| | - David J Culp
- Department of Oral Biology, University of Florida College of Dentistry, Gainesville, Florida, USA
| | - Robert A Burne
- Department of Oral Biology, University of Florida College of Dentistry, Gainesville, Florida, USA
| | - Todd Kitten
- Philips Institute for Oral Health Research, Virginia Commonwealth University School of Dentistry, Richmond, Virginia, USA
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Puccio T, Kunka KS, An SS, Kitten T. Contribution of a ZIP-family protein to manganese uptake and infective endocarditis virulence in Streptococcus sanguinis. Mol Microbiol 2021; 117:353-374. [PMID: 34855265 PMCID: PMC8844249 DOI: 10.1111/mmi.14853] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 11/24/2021] [Accepted: 11/30/2021] [Indexed: 01/18/2023]
Abstract
Streptococcus sanguinis is an important cause of infective endocarditis. In strain SK36, the ABC‐family manganese transporter, SsaACB, is essential for virulence. We have now identified a ZIP‐family protein, TmpA, as a secondary manganese transporter. A tmpA mutant had no phenotype, but a ΔssaACB ΔtmpA mutant was more attenuated for serum growth and for virulence in a rabbit model than its ΔssaACB parent. The growth of both mutants was restored by supplemental manganese, but the ΔssaACB ΔtmpA mutant required twenty‐fold more and accumulated less. Although ZIP‐family proteins are known for zinc and iron transport, TmpA‐mediated transport of either metal was minimal. While ssaACB appears ubiquitous in St. sanguinis, tmpA was present in a majority of strains and a mntH gene encoding an NRAMP‐family transporter was identified in relatively few, including VMC66. As in SK36, deletion of ssaACB greatly diminished VMC66 endocarditis virulence and serum growth, and deletion of tmpA from this mutant diminished virulence further. Virulence was not significantly altered by deletion of mntH from either VMC66 or its ΔssaACB mutant. This and the accompanying paper together suggest that SsaACB is of primary importance for endocarditis virulence while secondary transporters TmpA and MntH contribute to growth under differing conditions.
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Affiliation(s)
- Tanya Puccio
- Philips Institute for Oral Health Research, Virginia Commonwealth University School of Dentistry, Richmond, Virginia, USA
| | - Karina S Kunka
- Philips Institute for Oral Health Research, Virginia Commonwealth University School of Dentistry, Richmond, Virginia, USA
| | - Seon-Sook An
- Philips Institute for Oral Health Research, Virginia Commonwealth University School of Dentistry, Richmond, Virginia, USA
| | - Todd Kitten
- Philips Institute for Oral Health Research, Virginia Commonwealth University School of Dentistry, Richmond, Virginia, USA
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Solakyildirim K, Li Y, Bayer AS, Sullam PM, Xiong YQ, Lebrilla CB, Bensing BA. Proteoglycan 4 (lubricin) is a highly sialylated glycoprotein associated with cardiac valve damage in animal models of infective endocarditis. Glycobiology 2021; 31:1582-1595. [PMID: 34459483 DOI: 10.1093/glycob/cwab095] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 07/30/2021] [Accepted: 08/16/2021] [Indexed: 11/12/2022] Open
Abstract
S. gordonii and S. sanguinis are primary colonizers of tooth surfaces, and are generally associated with oral health, but can also cause infective endocarditis (IE). These species express "Siglec-like" adhesins that bind sialylated glycans on host glycoproteins, which can aid the formation of infected platelet-fibrin thrombi (vegetations) on cardiac valve surfaces. We previously determined that the ability of S. gordonii to bind sialyl T-antigen (sTa) increased pathogenicity, relative to recognition of sialylated core 2 O-glycan structures, in an animal model of IE. However, it is unclear when and where the sTa structure is displayed, and which sTa-modified host factors promote valve colonization. In this study, we identified sialylated glycoproteins in the aortic valve vegetations and plasma of rat and rabbit models of this disease. Glycoproteins that display sTa versus core 2 O-glycan structures were identified by using recombinant forms of the streptococcal Siglec-like adhesins for lectin blotting and affinity capture, and the O-linked glycans were profiled by mass spectrometry. Proteoglycan 4 (PRG4), also known as lubricin, was a major carrier of sTa in the infected vegetations. Moreover, plasma PRG4 levels were significantly higher in animals with damaged or infected valves, as compared with healthy animals. The combined results demonstrate that, in addition to platelet GPIbα, PRG4 is a highly sialylated mucin-like glycoprotein found in aortic valve vegetations and may contribute to the persistence of oral streptococci in this protected endovascular niche. Moreover, plasma PRG4 could serve as a biomarker for endocardial injury and infection.
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Affiliation(s)
- Kemal Solakyildirim
- Department of Chemistry, University of California, Davis, California, United States of America.,Department of Chemistry, Erzincan Binali Yildirim University, Erzincan, 24100, Turkey
| | - Yi Li
- Division of Infectious Diseases, Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, California, United States of America
| | - Arnold S Bayer
- Division of Infectious Diseases, Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, California, United States of America.,David Geffen School of Medicine at UCLA, Los Angeles, California, United States of America
| | - Paul M Sullam
- Department of Medicine, San Francisco Veterans Affairs Medical Center and University of California, San Francisco, California, United States of America
| | - Yan Q Xiong
- Division of Infectious Diseases, Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, California, United States of America.,David Geffen School of Medicine at UCLA, Los Angeles, California, United States of America
| | - Carlito B Lebrilla
- Department of Chemistry, University of California, Davis, California, United States of America
| | - Barbara A Bensing
- Department of Medicine, San Francisco Veterans Affairs Medical Center and University of California, San Francisco, California, United States of America
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Isolation and Identification of Optochin-Resistant Viridans Group Streptococci from the Sputum Samples of Adult Patients in Jakarta, Indonesia. Int J Microbiol 2021; 2021:6646925. [PMID: 34335780 PMCID: PMC8294987 DOI: 10.1155/2021/6646925] [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: 12/04/2020] [Revised: 02/20/2021] [Accepted: 07/05/2021] [Indexed: 11/17/2022] Open
Abstract
Aim To investigate optochin-resistant viridans group streptococci (VGS) strains isolated from the sputum sample of adult patients with different clinical symptoms. Materials and Methods Optochin-resistant VGS isolates were identified by matrix-assisted laser desorption ionization time of flight mass spectrometry (MALDI-TOF MS). recA sequencing was used to confirm identified isolates at the genus level by MALDI-TOF MS. Finding. We identified 79% of tested isolates (148/187) at the species-level identification using the MALDI-TOF MS tool. We identified that the most common species isolated from sputum specimens were S. oralis (44.9%) followed by S. mitis (25.7%), S. infantis (9.1%), S. parasanguinis (7.5%), S. peroris (3.7%), S. anginosus (2.7%), and S. sanguinis (2.1%). Discussion. The S. oralis strains were majority of optochin-resistant VGS isolates obtained from sputum of adult patients in Jakarta, Indonesia. MALDI-TOF MS showed potential for the rapid identification tool to identify optochin-resistant VGS isolates. Although there were discrepancies in identifying isolates at the genus/species level, the performance could be improved by expanding its database.
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Barajas-Colon E, Warady BA. Streptococcus salivarius peritonitis in an infant receiving chronic peritoneal dialysis. Perit Dial Int 2020; 41:341-343. [PMID: 33084495 DOI: 10.1177/0896860820964285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Peritonitis is the most common infectious complication of chronic peritoneal dialysis in children and the most common reason for hospitalization. Although the most common organisms responsible for peritonitis are gram-positive bacteria, peritonitis has not previously been reported secondary to Streptococcus salivarius, one of the 26 species in the Streptococcus viridians group. We describe a 4-month-old male who developed S. salivarius peritonitis while receiving automated peritoneal dialysis and who was successfully treated with a 14-day course of intraperitoneal vancomycin. Subtyping episodes of S. viridans-related infection is essential for the identification of S. salivarius.
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Affiliation(s)
- Edgar Barajas-Colon
- Nephrology Department, 61670Hospital Infantil de México Federico Gómez, Mexico City, Mexico
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Lao J, Guédon G, Lacroix T, Charron-Bourgoin F, Libante V, Loux V, Chiapello H, Payot S, Leblond-Bourget N. Abundance, Diversity and Role of ICEs and IMEs in the Adaptation of Streptococcus salivarius to the Environment. Genes (Basel) 2020; 11:genes11090999. [PMID: 32858915 PMCID: PMC7563491 DOI: 10.3390/genes11090999] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 08/20/2020] [Accepted: 08/21/2020] [Indexed: 01/15/2023] Open
Abstract
Streptococcus salivarius is a significant contributor to the human oral, pharyngeal and gut microbiomes that contribute to the maintenance of health. The high genomic diversity observed in this species is mainly caused by horizontal gene transfer. This work aimed to evaluate the contribution of integrative and conjugative elements (ICEs) and integrative and mobilizable elements (IMEs) in S. salivarius genome diversity. For this purpose, we performed an in-depth analysis of 75 genomes of S. salivarius and searched for signature genes of conjugative and mobilizable elements. This analysis led to the retrieval of 69 ICEs, 165 IMEs and many decayed elements showing their high prevalence in S. salivarius genomes. The identification of almost all ICE and IME boundaries allowed the identification of the genes in which these elements are inserted. Furthermore, the exhaustive analysis of the adaptation genes carried by these elements showed that they encode numerous functions such as resistance to stress, to antibiotics or to toxic compounds, and numerous enzymes involved in diverse cellular metabolic pathways. These data support the idea that not only ICEs but also IMEs and decayed elements play an important role in S. salivarius adaptation to the environment.
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Affiliation(s)
- Julie Lao
- Université de Lorraine, INRAE, DynAMic, F-54000 Nancy, France; (J.L.); (G.G.); (F.C.-B.); (V.L.); (S.P.)
- Université Paris-Saclay, INRAE, MaIAGE, 78350 Jouy-en-Josas, France; (T.L.); (V.L.); (H.C.)
| | - Gérard Guédon
- Université de Lorraine, INRAE, DynAMic, F-54000 Nancy, France; (J.L.); (G.G.); (F.C.-B.); (V.L.); (S.P.)
| | - Thomas Lacroix
- Université Paris-Saclay, INRAE, MaIAGE, 78350 Jouy-en-Josas, France; (T.L.); (V.L.); (H.C.)
| | - Florence Charron-Bourgoin
- Université de Lorraine, INRAE, DynAMic, F-54000 Nancy, France; (J.L.); (G.G.); (F.C.-B.); (V.L.); (S.P.)
| | - Virginie Libante
- Université de Lorraine, INRAE, DynAMic, F-54000 Nancy, France; (J.L.); (G.G.); (F.C.-B.); (V.L.); (S.P.)
| | - Valentin Loux
- Université Paris-Saclay, INRAE, MaIAGE, 78350 Jouy-en-Josas, France; (T.L.); (V.L.); (H.C.)
| | - Hélène Chiapello
- Université Paris-Saclay, INRAE, MaIAGE, 78350 Jouy-en-Josas, France; (T.L.); (V.L.); (H.C.)
| | - Sophie Payot
- Université de Lorraine, INRAE, DynAMic, F-54000 Nancy, France; (J.L.); (G.G.); (F.C.-B.); (V.L.); (S.P.)
| | - Nathalie Leblond-Bourget
- Université de Lorraine, INRAE, DynAMic, F-54000 Nancy, France; (J.L.); (G.G.); (F.C.-B.); (V.L.); (S.P.)
- Correspondence: ; Tel.: +33-3-72-74-51-46
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Imai K, Nemoto R, Kodana M, Tarumoto N, Sakai J, Kawamura T, Ikebuchi K, Mitsutake K, Murakami T, Maesaki S, Fujiwara T, Hayakawa S, Hoshino T, Seki M, Maeda T. Rapid and Accurate Species Identification of Mitis Group Streptococci Using the MinION Nanopore Sequencer. Front Cell Infect Microbiol 2020; 10:11. [PMID: 32083020 PMCID: PMC7002467 DOI: 10.3389/fcimb.2020.00011] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Accepted: 01/10/2020] [Indexed: 11/13/2022] Open
Abstract
Differentiation between mitis group streptococci (MGS) bacteria in routine laboratory tests has become important for obtaining accurate epidemiological information on the characteristics of MGS and understanding their clinical significance. The most reliable method of MGS species identification is multilocus sequence analysis (MLSA) with seven house-keeping genes; however, because this method is time-consuming, it is deemed unsuitable for use in most clinical laboratories. In this study, we established a scheme for identifying 12 species of MGS (S. pneumoniae, S. pseudopneumoniae, S. mitis, S. oralis, S. peroris, S. infantis, S. australis, S. parasanguinis, S. sinensis, S. sanguinis, S. gordonii, and S. cristatus) using the MinION nanopore sequencer (Oxford Nanopore Technologies, Oxford, UK) with the taxonomic aligner "What's in My Pot?" (WIMP; Oxford Nanopore's cloud-based analysis platform) and Kraken2 pipeline with the custom database adjusted for MGS species identification. The identities of the species in reference genomes (n = 514), clinical isolates (n = 31), and reference strains (n = 4) were confirmed via MLSA. The nanopore simulation reads were generated from reference genomes, and the optimal cut-off values for MGS species identification were determined. For 31 clinical isolates (S. pneumoniae = 8, S. mitis = 17 and S. oralis = 6) and 4 reference strains (S. pneumoniae = 1, S. mitis = 1, S. oralis = 1, and S. pseudopneumoniae = 1), a sequence library was constructed via a Rapid Barcoding Sequencing Kit for multiplex and real-time MinION sequencing. The optimal cut-off values for the identification of MGS species for analysis by WIMP and Kraken2 pipeline were determined. The workflow using Kraken2 pipeline with a custom database identified all 12 species of MGS, and WIMP identified 8 MGS bacteria except S. infantis, S. australis, S. peroris, and S. sinensis. The results obtained by MinION with WIMP and Kraken2 pipeline were consistent with the MGS species identified by MLSA analysis. The practical advantage of whole genome analysis using the MinION nanopore sequencer is that it can aid in MGS surveillance. We concluded that MinION sequencing with the taxonomic aligner enables accurate MGS species identification and could contribute to further epidemiological surveys.
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Affiliation(s)
- Kazuo Imai
- Department of Infectious Disease and Infection Control, Saitama Medical University, Saitama, Japan
- Center for Clinical Infectious Diseases and Research, Saitama Medical University, Saitama, Japan
| | - Rina Nemoto
- Department of Microbiology, Saitama Medical University, Saitama, Japan
| | - Masahiro Kodana
- Department of Laboratory Medicine, Saitama Medical University, Saitama, Japan
| | - Norihito Tarumoto
- Department of Infectious Disease and Infection Control, Saitama Medical University, Saitama, Japan
- Center for Clinical Infectious Diseases and Research, Saitama Medical University, Saitama, Japan
| | - Jun Sakai
- Department of Infectious Disease and Infection Control, Saitama Medical University, Saitama, Japan
- Center for Clinical Infectious Diseases and Research, Saitama Medical University, Saitama, Japan
| | - Toru Kawamura
- Department of Laboratory Medicine, Saitama Medical University, Saitama, Japan
| | - Kenji Ikebuchi
- Department of Laboratory Medicine, Saitama Medical University, Saitama, Japan
| | - Kotaro Mitsutake
- Department of Infectious Diseases and Infection Control, International Medical Center, Saitama Medical University, Saitama, Japan
| | - Takashi Murakami
- Center for Clinical Infectious Diseases and Research, Saitama Medical University, Saitama, Japan
- Department of Microbiology, Saitama Medical University, Saitama, Japan
| | - Shigefumi Maesaki
- Department of Infectious Disease and Infection Control, Saitama Medical University, Saitama, Japan
- Center for Clinical Infectious Diseases and Research, Saitama Medical University, Saitama, Japan
| | - Taku Fujiwara
- Department of Pediatric Dentistry, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Satoshi Hayakawa
- Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, Tokyo, Japan
| | - Tomonori Hoshino
- Division of Pediatric Dentistry, Meikai University School of Dentistry, Sakado, Japan
| | - Mitsuko Seki
- Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, Tokyo, Japan
- Division of Pediatric Dentistry, Meikai University School of Dentistry, Sakado, Japan
| | - Takuya Maeda
- Center for Clinical Infectious Diseases and Research, Saitama Medical University, Saitama, Japan
- Department of Laboratory Medicine, Saitama Medical University, Saitama, Japan
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Bensing BA, Li L, Yakovenko O, Wong M, Barnard KN, Iverson TM, Lebrilla CB, Parrish CR, Thomas WE, Xiong Y, Sullam PM. Recognition of specific sialoglycan structures by oral streptococci impacts the severity of endocardial infection. PLoS Pathog 2019; 15:e1007896. [PMID: 31233555 PMCID: PMC6611644 DOI: 10.1371/journal.ppat.1007896] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Revised: 07/05/2019] [Accepted: 06/05/2019] [Indexed: 11/18/2022] Open
Abstract
Streptococcus gordonii and Streptococcus sanguinis are primary colonizers of the tooth surface. Although generally non-pathogenic in the oral environment, they are a frequent cause of infective endocarditis. Both streptococcal species express a serine-rich repeat surface adhesin that mediates attachment to sialylated glycans on mucin-like glycoproteins, but the specific sialoglycan structures recognized can vary from strain to strain. Previous studies have shown that sialoglycan binding is clearly important for aortic valve infections caused by some S. gordonii, but this process did not contribute to the virulence of a strain of S. sanguinis. However, these streptococci can bind to different subsets of sialoglycan structures. Here we generated isogenic strains of S. gordonii that differ only in the type and range of sialoglycan structures to which they adhere and examined whether this rendered them more or less virulent in a rat model of endocarditis. The findings indicate that the recognition of specific sialoglycans can either enhance or diminish pathogenicity. Binding to sialyllactosamine reduces the initial colonization of mechanically-damaged aortic valves, whereas binding to the closely-related trisaccharide sialyl T-antigen promotes higher bacterial densities in valve tissue 72 hours later. A surprising finding was that the initial attachment of streptococci to aortic valves was inversely proportional to the affinity of each strain for platelets, suggesting that binding to platelets circulating in the blood may divert bacteria away from the endocardial surface. Importantly, we found that human and rat platelet GPIbα (the major receptor for S. gordonii and S. sanguinis on platelets) display similar O-glycan structures, comprised mainly of a di-sialylated core 2 hexasaccharide, although the rat GPIbα has a more heterogenous composition of modified sialic acids. The combined results suggest that streptococcal interaction with a minor O-glycan on GPIbα may be more important than the over-all affinity for GPIbα for pathogenic effects. Infective endocarditis (IE) is a life-threatening infection of heart valves, and streptococci that normally reside in the mouth are a leading cause of this disease. Some oral streptococcal species express a protein on their surface that enables attachment to glycan (sugar) modifications on saliva proteins, an interaction that may be important for colonization of the tooth and other oral surfaces. These "Siglec-like adhesins" are hypervariable in the type and number of glycan structures they bind, ranging from just one to more than six of the structures displayed on the saliva proteins. If streptococci enter into the bloodstream, the Siglec-like adhesin can mediate attachment to similar glycans that decorate platelet or plasma proteins, which can impact the overall virulence of the organism. This study highlights how recognition of a specific type of glycan structure can cause a generally beneficial or neutral microbe to create damage to specific tissues—in this case the heart valves, illustrating one means by which commensal bacteria can become opportunistic or accidental pathogens. The findings further indicate that certain glycan-binding streptococci among the oral microbiota may be predisposed to produce infective endocarditis.
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Affiliation(s)
- Barbara A. Bensing
- Department of Medicine, San Francisco Veterans Affairs Medical Center and University of California, San Francisco, California, United States of America
- * E-mail:
| | - Liang Li
- Los Angeles Biomedical Research Institute, Harbor-UCLA Medical Center, Torrance, California, United States of America
| | - Olga Yakovenko
- Department of Bioengineering, University of Washington, Seattle, Washington, United States of America
| | - Maurice Wong
- Department of Chemistry, University of California, Davis, California, United States of America
| | - Karen N. Barnard
- Baker Institute for Animal Health, Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, New York, United States of America
| | - T. M. Iverson
- Departments of Pharmacology and Biochemistry, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Carlito B. Lebrilla
- Department of Chemistry, University of California, Davis, California, United States of America
| | - Colin R. Parrish
- Baker Institute for Animal Health, Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, New York, United States of America
| | - Wendy E. Thomas
- Department of Bioengineering, University of Washington, Seattle, Washington, United States of America
| | - Yan Xiong
- Los Angeles Biomedical Research Institute, Harbor-UCLA Medical Center, Torrance, California, United States of America
- David Geffen School of Medicine at UCLA, Los Angeles, California, United States of America
| | - Paul M. Sullam
- Department of Medicine, San Francisco Veterans Affairs Medical Center and University of California, San Francisco, California, United States of America
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Alves LA, de Carli TR, Harth-Chu EN, Mariano FS, Höfling JF, Stipp RN, Mattos-Graner RO. Oral streptococci show diversity in resistance to complement immunity. J Med Microbiol 2019; 68:600-608. [PMID: 30843785 DOI: 10.1099/jmm.0.000955] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
PURPOSE Mechanisms underlying systemic infections by oral species of Mitis (Streptococcus mitis, Streptococcus oralis) and Sanguinis (Streptococcus gordonii, Streptococcus sanguinis) commensal streptococci are poorly understood. This study investigates profiles of susceptibility to complement-mediated host immunity in representative strains of these four species, which were isolated from oral sites or from the bloodstream. METHODOLOGY Deposition of complement opsonins (C3b/iC3b), and surface binding to C-reactive protein (CRP) and to IgG antibodies were quantified by flow cytometry in 34 strains treated with human serum (HS), and compared to rates of opsonophagocytosis by human PMN mediated by complement (CR1/3) and/or IgG Fc (FcγRII/III) receptors. RESULTS S. sanguinis strains showed reduced susceptibility to complement opsonization and low binding to CRP and to IgG compared to other species. Surface levels of C3b/iC3b in S. sanguinis strains were 4.5- and 7.8-fold lower than that observed in S. gordonii and Mitis strains, respectively. Diversity in C3b/iC3b deposition was evident among Mitis species, in which C3b/iC3b deposition was significantly associated with CR/FcγR-dependent opsonophagocytosis by PMN (P<0.05). Importantly, S. gordonii and Mitis group strains isolated from systemic infections showed resistance to complement opsonization when compared to oral isolates of the respective species (P<0.05). CONCLUSIONS This study establishes species-specific profiles of susceptibility to complement immunity in Mitis and Sanguinis streptococci, and indicates that strains associated with systemic infections have increased capacity to evade complement immunity. These findings highlight the need for studies identifying molecular functions involved in complement evasion in oral streptococci.
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Affiliation(s)
- Lívia A Alves
- Department of Oral Diagnosis, Piracicaba Dental School - State University of Campinas, Piracicaba, SP, Brazil
| | - Thaís R de Carli
- Department of Oral Diagnosis, Piracicaba Dental School - State University of Campinas, Piracicaba, SP, Brazil
| | - Erika N Harth-Chu
- Department of Oral Diagnosis, Piracicaba Dental School - State University of Campinas, Piracicaba, SP, Brazil
| | - Flávia S Mariano
- Department of Oral Diagnosis, Piracicaba Dental School - State University of Campinas, Piracicaba, SP, Brazil
| | - José F Höfling
- Department of Oral Diagnosis, Piracicaba Dental School - State University of Campinas, Piracicaba, SP, Brazil
| | - Rafael N Stipp
- Department of Oral Diagnosis, Piracicaba Dental School - State University of Campinas, Piracicaba, SP, Brazil
| | - Renata O Mattos-Graner
- Department of Oral Diagnosis, Piracicaba Dental School - State University of Campinas, Piracicaba, SP, Brazil
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15
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Genomic, Phenotypic, and Virulence Analysis of Streptococcus sanguinis Oral and Infective-Endocarditis Isolates. Infect Immun 2018; 87:IAI.00703-18. [PMID: 30396893 DOI: 10.1128/iai.00703-18] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Accepted: 10/26/2018] [Indexed: 12/22/2022] Open
Abstract
Streptococcus sanguinis, an abundant and benign inhabitant of the oral cavity, is an important etiologic agent of infective endocarditis (IE), particularly in people with predisposing cardiac valvular damage. Although commonly isolated from patients with IE, little is known about the factors that make any particular S. sanguinis isolate more virulent than another or, indeed, whether significant differences in virulence exist among isolates. In this study, we compared the genomes of a collection of S. sanguinis strains comprised of both oral isolates and bloodstream isolates from patients diagnosed with IE. Oral and IE isolates could not be distinguished by phylogenetic analyses, and we did not succeed in identifying virulence genes unique to the IE strains. We then investigated the virulence of these strains in a rabbit model of IE using a variation of the Bar-seq (barcode sequencing) method wherein we pooled the strains and used Illumina sequencing to count unique barcodes that had been inserted into each isolate at a conserved intergenic region. After we determined that several of the genome sequences were misidentified in GenBank, our virulence results were used to inform our bioinformatic analyses, identifying genes that may explain the heterogeneity in virulence. We further characterized these strains by assaying for phenotypes potentially contributing to virulence. Neither strain competition via bacteriocin production nor biofilm formation showed any apparent relationship with virulence. Increased cell-associated manganese was, however, correlated with blood isolates. These results, combined with additional phenotypic assays, suggest that S. sanguinis virulence is highly variable and results from multiple genetic factors.
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16
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Surface proteins involved in the adhesion of Streptococcus salivarius to human intestinal epithelial cells. Appl Microbiol Biotechnol 2018; 102:2851-2865. [PMID: 29442170 PMCID: PMC5847202 DOI: 10.1007/s00253-018-8794-y] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Revised: 01/10/2018] [Accepted: 01/14/2018] [Indexed: 01/08/2023]
Abstract
The adhesion properties of 14 Streptococcus salivarius strains to mucus (HT29-MTX) and non-mucus secreting (Caco-2/TC7) human intestinal epithelial cells were investigated. Ability to adhere to these two eukaryotic cell lines greatly differs between strains. The presence of mucus played a major factor in adhesion, likely due to high adhesiveness to mucins present in the native human mucus layer covering the whole cell surface. Only one S. salivarius strain (F6-1), isolated from the feces of a healthy baby, was found to strongly adhere to HT-29 MTX cells at a level comparable to that of Lactobacillus rhamnosus GG, a probiotic strain considered to be highly adherent. By sequencing the genome of F6-1, we were able to identify 36 genes encoding putative surface proteins. Deletion mutants were constructed for six of them and their adhesion abilities on HT-29 MTX cells were checked. Our study confirmed that four of these genes encode adhesins involved in the adhesion of S. salivarius to host cells. Such adhesins were also identified in other S. salivarius strains.
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17
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Diversity of Integrative and Conjugative Elements of Streptococcus salivarius and Their Intra- and Interspecies Transfer. Appl Environ Microbiol 2017; 83:AEM.00337-17. [PMID: 28432093 DOI: 10.1128/aem.00337-17] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Accepted: 04/12/2017] [Indexed: 01/12/2023] Open
Abstract
Integrative and conjugative elements (ICEs) are widespread chromosomal mobile genetic elements which can transfer autonomously by conjugation in bacteria. Thirteen ICEs with a conjugation module closely related to that of ICESt3 of Streptococcus thermophilus were characterized in Streptococcus salivarius by whole-genome sequencing. Sequence comparison highlighted ICE evolution by shuffling of 3 different integration/excision modules (for integration in the 3' end of the fda, rpsI, or rpmG gene) with the conjugation module of the ICESt3 subfamily. Sequence analyses also pointed out a recombination occurring at oriT (likely mediated by the relaxase) as a mechanism of ICE evolution. Despite a similar organization in two operons including three conserved genes, the regulation modules show a high diversity (about 50% amino acid sequence divergence for the encoded regulators and presence of unrelated additional genes) with a probable impact on the regulation of ICE activity. Concerning the accessory genes, ICEs of the ICESt3 subfamily appear particularly rich in restriction-modification systems and orphan methyltransferase genes. Other cargo genes that could confer a selective advantage to the cell hosting the ICE were identified, in particular, genes for bacteriocin synthesis and cadmium resistance. The functionality of 2 ICEs of S. salivarius was investigated. Autonomous conjugative transfer to other S. salivarius strains, to S. thermophilus, and to Enterococcus faecalis was observed. The analysis of the ICE-fda border sequence in these transconjugants allowed the localization of the DNA cutting site of the ICE integrase.IMPORTANCE The ICESt3 subfamily of ICEs appears to be widespread in streptococci and targets diverse chromosomal integration sites. These ICEs carry diverse cargo genes that can confer a selective advantage to the host strain. The maintenance of these mobile genetic elements likely relies in part on self-encoded restriction-modification systems. In this study, intra- and interspecies transfer was demonstrated for 2 ICEs of S. salivarius Closely related ICEs were also detected in silico in other Streptococcus species (S. pneumoniae and S. parasanguinis), thus indicating that diffusion of ICESt3-related elements probably plays a significant role in horizontal gene transfer (HGT) occurring in the oral cavity but also in the digestive tract, where S. salivarius is present.
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18
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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: 32] [Impact Index Per Article: 4.0] [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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Resistance Genes and Genetic Elements Associated with Antibiotic Resistance in Clinical and Commensal Isolates of Streptococcus salivarius. Appl Environ Microbiol 2015; 81:4155-63. [PMID: 25862227 DOI: 10.1128/aem.00415-15] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2015] [Accepted: 04/04/2015] [Indexed: 01/14/2023] Open
Abstract
The diversity of clinical (n = 92) and oral and digestive commensal (n = 120) isolates of Streptococcus salivarius was analyzed by multilocus sequence typing (MLST). No clustering of clinical or commensal strains can be observed in the phylogenetic tree. Selected strains (92 clinical and 46 commensal strains) were then examined for their susceptibilities to tetracyclines, macrolides, lincosamides, aminoglycosides, and phenicol antibiotics. The presence of resistance genes tet(M), tet(O), erm(A), erm(B), mef(A/E), and catQ and associated genetic elements was investigated by PCR, as was the genetic linkage of resistance genes. High rates of erythromycin and tetracycline resistance were observed among the strains. Clinical strains displayed either the erm(B) (macrolide-lincosamide-streptogramin B [MLSB] phenotype) or mef(A/E) (M phenotype) resistance determinant, whereas almost all the commensal strains harbored the mef(A/E) resistance gene, carried by a macrolide efflux genetic assembly (MEGA) element. A genetic linkage between a macrolide resistance gene and genes of Tn916 was detected in 23 clinical strains and 5 commensal strains, with a predominance of Tn3872 elements (n = 13), followed by Tn6002 (n = 11) and Tn2009 (n = 4) elements. Four strains harboring a mef(A/E) gene were also resistant to chloramphenicol and carried a catQ gene. Sequencing of the genome of one of these strains revealed that these genes colocalized on an IQ-like element, as already described for other viridans group streptococci. ICESt3-related elements were also detected in half of the isolates. This work highlights the potential role of S. salivarius in the spread of antibiotic resistance genes both in the oral sphere and in the gut.
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Angeletti S, Dicuonzo G, Avola A, Crea F, Dedej E, Vailati F, Farina C, De Florio L. Viridans Group Streptococci clinical isolates: MALDI-TOF mass spectrometry versus gene sequence-based identification. PLoS One 2015; 10:e0120502. [PMID: 25781023 PMCID: PMC4362942 DOI: 10.1371/journal.pone.0120502] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2014] [Accepted: 01/23/2015] [Indexed: 11/29/2022] Open
Abstract
Viridans Group Streptococci (VGS) species-level identification is fundamental for patients management. Matrix-assisted laser desorption ionization—time of flight mass spectrometry (MALDI-TOF MS) has been used for VGS identification but discrimination within the Mitis group resulted difficult. In this study, VGS identifications with two MALDI-TOF instruments, the Biotyper (Bruker) and the VITEK MS (bioMérieux) have been compared to those derived from tuf, soda and rpoB genes sequencing. VGS isolates were clustered and a dendrogram constructed using the Biotyper 3.0 software (Bruker). RpoB gene sequencing resulted the most sensitive and specific molecular method for S. pneumonia identification and was used as reference method. The sensitivity and the specificity of the VITEK MS in S. pneumonia identification were 100%, while the Biotyper resulted less specific (92.4%). In non pneumococcal VGS strains, the group-level correlation between rpoB and the Biotyper was 100%, while the species-level correlation was 61% after database upgrading (than 37% before upgrading). The group-level correlation between rpoB and the VITEK MS was 100%, while the species-level correlation was 36% and increases at 69% if isolates identified as S. mitis/S. oralis are included. The less accurate performance of the VITEK MS in VGS identification within the Mitis group was due to the inability to discriminate between S. mitis and S. oralis. Conversely, the Biotyper, after the release of the upgraded database, was able to discriminate between the two species. In the dendrogram, VGS strains from the same group were grouped into the same cluster and had a good correspondence with the gene-based clustering reported by other authors, thus confirming the validity of the upgraded version of the database. Data from this study demonstrated that MALDI-TOF technique can represent a rapid and cost saving method for VGS identification even within the Mitis group but improvements of spectra database are still recommended.
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Affiliation(s)
- Silvia Angeletti
- Clinical Pathology and Microbiology Laboratory, University Hospital Campus Bio-Medico of Rome, Rome, Italy
- * E-mail:
| | - Giordano Dicuonzo
- Clinical Pathology and Microbiology Laboratory, University Hospital Campus Bio-Medico of Rome, Rome, Italy
| | - Alessandra Avola
- Clinical Pathology and Microbiology Laboratory, University Hospital Campus Bio-Medico of Rome, Rome, Italy
| | - Francesca Crea
- Clinical Pathology and Microbiology Laboratory, University Hospital Campus Bio-Medico of Rome, Rome, Italy
| | - Etleva Dedej
- Clinical Pathology and Microbiology Laboratory, University Hospital Campus Bio-Medico of Rome, Rome, Italy
| | - Francesca Vailati
- Microbiology Institute, AO ‘Papa Giovanni XXIII’ (formerly AO ‘Ospedali Riuniti’) of Bergamo, Bergamo, Italy
| | - Claudio Farina
- Microbiology Institute, AO ‘Papa Giovanni XXIII’ (formerly AO ‘Ospedali Riuniti’) of Bergamo, Bergamo, Italy
| | - Lucia De Florio
- Clinical Pathology and Microbiology Laboratory, University Hospital Campus Bio-Medico of Rome, Rome, Italy
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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: 110] [Impact Index Per Article: 10.0] [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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Delorme C, Abraham AL, Renault P, Guédon E. Genomics of Streptococcus salivarius, a major human commensal. INFECTION GENETICS AND EVOLUTION 2014; 33:381-92. [PMID: 25311532 DOI: 10.1016/j.meegid.2014.10.001] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2014] [Revised: 09/30/2014] [Accepted: 10/02/2014] [Indexed: 10/24/2022]
Abstract
The salivarius group of streptococci is of particular importance for humans. This group consists of three genetically similar species, Streptococcus salivarius, Streptococcus vestibularis and Streptococcus thermophilus. S. salivarius and S. vestibularis are commensal organisms that may occasionally cause opportunistic infections in humans, whereas S. thermophilus is a food bacterium widely used in dairy production. We developed Multilocus sequence typing (MLST) and comparative genomic analysis to confirm the clear separation of these three species. These analyses also identified a subgroup of four strains, with a core genome diverging by about 10%, in terms of its nucleotide sequence, from that of S. salivarius sensu stricto. S. thermophilus species displays a low level of nucleotide variability, due to its recent emergence with the development of agriculture. By contrast, nucleotide variability is high in the other two species of the salivarius group, reflecting their long-standing association with humans. The species of the salivarius group have genome sizes ranging from the smallest (∼ 1.7 Mb for S. thermophilus) to the largest (∼ 2.3 Mb for S. salivarius) among streptococci, reflecting genome reduction linked to a narrow, nutritionally rich environment for S. thermophilus, and natural, more competitive niches for the other two species. Analyses of genomic content have indicated that the core genes of S. salivarius account for about two thirds of the genome, indicating considerable variability of gene content and differences in potential adaptive features. Furthermore, we showed that the genome of this species is exceptionally rich in genes encoding surface factors, glycosyltransferases and response regulators. Evidence of widespread genetic exchanges was obtained, probably involving a natural competence system and the presence of diverse mobile elements. However, although the S. salivarius strains studied were isolated from several human body-related sites (all levels of the digestive tract, skin, breast milk, and body fluids) and included clinical strains, no genetic or genomic niche-specific features could be identified to discriminate specific group.
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Affiliation(s)
- Christine Delorme
- INRA, UMR 1319 Micalis, Domaine de Vilvert, F-78352 Jouy-en-Josas, France; AgroParisTech, UMR MICALIS, Jouy-en-Josas, France
| | - Anne-Laure Abraham
- INRA, UMR 1319 Micalis, Domaine de Vilvert, F-78352 Jouy-en-Josas, France; AgroParisTech, UMR MICALIS, Jouy-en-Josas, France
| | - Pierre Renault
- INRA, UMR 1319 Micalis, Domaine de Vilvert, F-78352 Jouy-en-Josas, France; AgroParisTech, UMR MICALIS, Jouy-en-Josas, France
| | - Eric Guédon
- INRA, UMR 1319 Micalis, Domaine de Vilvert, F-78352 Jouy-en-Josas, France; AgroParisTech, UMR MICALIS, Jouy-en-Josas, France.
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Velusamy SK, Fine DH, Velliyagounder K. Prophylactic effect of human lactoferrin against Streptococcus mutans bacteremia in lactoferrin knockout mice. Microbes Infect 2014; 16:762-7. [PMID: 25124544 PMCID: PMC4252812 DOI: 10.1016/j.micinf.2014.07.009] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2014] [Revised: 07/23/2014] [Accepted: 07/24/2014] [Indexed: 11/19/2022]
Abstract
Streptococcus mutans is the primary agent of dental caries, which is often detected in transient bacteremia. Lactoferrin is a multifunctional glycoprotein showing antibacterial activities against several Streptococcus species. We reported here the prophylactic effect of human lactoferrin (hLF) in a lactoferrin knockout mouse (LFKO-/-) bacteremic model. The hLF treatment significantly cleared S. mutans from the blood and organs of bacteremic mice when compared to the non-hLF treated mice. Further, analysis of serum cytokines, spleen and liver cytokine mRNA levels revealed that hLF prophylaxis modulates their release differently when compared to the non-hLF treated group. C-reactive protein level (P = 0.003) also decreased following hLF prophylaxis in S. mutans induced bacteremic mice. Additional quantitative RT-PCR analysis revealed that hLF prophylaxis significantly decreased the expression level of IFN-γ, TNF-α, IL-1β, IL-6, MPO and iNOS in spleen and liver. These results suggested that the hLF protects the host against S. mutans-induced experimental bacteremia.
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GyrB polymorphisms accurately assign invasive viridans group streptococcal species. J Clin Microbiol 2014; 52:2905-12. [PMID: 24899021 DOI: 10.1128/jcm.01068-14] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Viridans group streptococci (VGS) are a heterogeneous group of medically important bacteria that cannot be accurately assigned to a particular species using conventional phenotypic methods. Although multilocus sequence analysis (MLSA) is considered the gold standard for VGS species-level identification, MLSA is not yet feasible in the clinical setting. Conversely, molecular methods, such as sodA and 16S rRNA gene sequencing, are clinically practical but not sufficiently accurate for VGS species-level identification. Here, we present data regarding the use of an ∼ 400-nucleotide internal fragment of the gene encoding DNA gyrase subunit B (GyrB) for VGS species-level identification. MLSA, internal gyrB, sodA, full-length, and 5' 16S gene sequences were used to characterize 102 unique VGS blood isolates collected from 2011 to 2012. When using the MLSA species assignment as a reference, full-length and 5' partial 16S gene and sodA sequence analyses failed to correctly assign all strains to a species. Precise species determination was particularly problematic for Streptococcus mitis and Streptococcus oralis isolates. However, the internal gyrB fragment allowed for accurate species designations for all 102 strains. We validated these findings using 54 VGS strains for which MLSA, 16S gene, sodA, and gyrB data are available at the NCBI, showing that gyrB is superior to 16S gene and sodA sequence analyses for VGS species identification. We also observed that specific polymorphisms in the 133-amino acid sequence of the internal GyrB fragment can be used to identify invasive VGS species. Thus, the GyrB amino acid sequence may offer a more practical and accurate method for classifying invasive VGS strains to the species level.
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Jakubovics NS, Yassin SA, Rickard AH. Community interactions of oral streptococci. ADVANCES IN APPLIED MICROBIOLOGY 2014; 87:43-110. [PMID: 24581389 DOI: 10.1016/b978-0-12-800261-2.00002-5] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
It is now clear that the most common oral diseases, dental caries and periodontitis, are caused by mixed-species communities rather than by individual pathogens working in isolation. Oral streptococci are central to these disease processes since they are frequently the first microorganisms to colonize oral surfaces and they are numerically the dominant microorganisms in the human mouth. Numerous interactions between oral streptococci and other bacteria have been documented. These are thought to be critical for the development of mixed-species oral microbial communities and for the transition from oral health to disease. Recent metagenomic studies are beginning to shed light on the co-occurrence patterns of streptococci with other oral bacteria. Refinements in microscopy techniques and biofilm models are providing detailed insights into the spatial distribution of streptococci in oral biofilms. Targeted genetic manipulation is increasingly being applied for the analysis of specific genes and networks that modulate interspecies interactions. From this work, it is clear that streptococci produce a range of extracellular factors that promote their integration into mixed-species communities and enable them to form social networks with neighboring taxa. These "community integration factors" include coaggregation-mediating adhesins and receptors, small signaling molecules such as peptides or autoinducer-2, bacteriocins, by-products of metabolism including hydrogen peroxide and lactic acid, and a range of extracellular enzymes. Here, we provide an overview of various types of community interactions between oral streptococci and other microorganisms, and we consider the possibilities for the development of new technologies to interfere with these interactions to help control oral biofilms.
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Affiliation(s)
- Nicholas S Jakubovics
- Oral Biology, School of Dental Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom.
| | - Sufian A Yassin
- Oral Biology, School of Dental Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Alexander H Rickard
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, Michigan, USA
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