Comparative Genomic Analyses of Streptococcus pseudopneumoniae Provide Insight into Virulence and Commensalism Dynamics

Shahinas, Dea; Thornton, Christina S.; Tamber, Gurdip Singh; Arya, Gitanjali; Wong, A. Y.; Jennifer, H.; Alexander, David C.; Low, Donald E.; Pillai, Dylan R.

doi:10.1371/journal.pone.0065670

Cited by 24 publications

(29 citation statements)

References 62 publications

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“…Comparative genomic hybridization showed that this islet is common among S. pseudopneumoniae strains (13) and among eight sequence types of SMG that have been identified (14, 15). The sequence of lytA is S.…”

Section: Introductionmentioning

confidence: 93%

“…An analysis of the first S. pseudopneumoniae genome of strain IS7493 documented the lack of some pneumococcal virulence factors, such as the capsule biosynthesis genes and the choline-binding proteins PspC, PcpA, and PspA (13). However, it contained the ply-lytA islet.…”

Section: Introductionmentioning

confidence: 99%

“…pseudopneumoniae IS7493 are more similar to PBPs of resistant S. pneumoniae than to the highly conserved PBPs of sensitive strains (13). Since this strain has a decreased susceptibility to beta-lactams, its PBPs might not be representative for this species.…”

Section: Introductionmentioning

confidence: 99%

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Insight into the Diversity of Penicillin-Binding Protein 2x Alleles and Mutations in Viridans Streptococci

Linden

Otten

Bergmann

et al. 2017

Antimicrob Agents Chemother

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The identification of commensal streptococci species is an everlasting problem due to their ability to genetically transform. A new challenge in this respect is the recent description of Streptococcus pseudopneumoniae as a new species, which was distinguished from closely related pathogenic S. pneumoniae and commensal S. mitis by a variety of physiological and molecular biological tests. Forty-one atypical S. pneumoniae isolates have been collected at the German National Reference Center for Streptococci (GNRCS). Multilocus sequence typing (MLST) confirmed 35 isolates as the species S. pseudopneumoniae. A comparison with the pbp2x sequences from 120 commensal streptococci isolated from different continents revealed that pbp2x is distinct among penicillin-susceptible S. pseudopneumoniae isolates. Four penicillin-binding protein x (PBPx) alleles of penicillin-sensitive S. mitis account for most of the diverse sequence blocks in resistant S. pseudopneumoniae, S. pneumoniae, and S. mitis, and S. infantis and S. oralis sequences were found in S. pneumoniae from Japan. PBP2x genes of the family of mosaic genes related to pbp2x in the S. pneumoniae clone Spain23F-1 were observed in S. oralis and S. infantis as well, confirming its global distribution. Thirty-eight sites were altered within the PBP2x transpeptidase domains of penicillin-resistant strains, excluding another 37 sites present in the reference genes of sensitive strains. Specific mutational patterns were detected depending on the parental sequence blocks, in agreement with distinct mutational pathways during the development of beta-lactam resistance. The majority of the mutations clustered around the active site, whereas others are likely to affect stability or interactions with the C-terminal domain or partner proteins.

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Section: Introductionmentioning

confidence: 93%

Section: Introductionmentioning

confidence: 99%

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Insight into the Diversity of Penicillin-Binding Protein 2x Alleles and Mutations in Viridans Streptococci

Linden

Otten

Bergmann

et al. 2017

Antimicrob Agents Chemother

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“…Roman numerals in column "ICE" refers to integration sites (Table S8). ICE, Mega-2 and "other resistances" refer to genotypic resistances; penicillin (Pen) and co-trimoxazole (SXT) refer to phenotypic resistances (Table S7) and references (5, 20, 57-59). ND, not determined due to the presence of pseudogenes/contig breaks; NA, data not available.…”

Section: Resultsmentioning

confidence: 99%

“…Some studies have described the presence of pneumococcal virulence genes in S. pseudopneumoniae (3, 9, 20, 21), but a comprehensive overview of the distribution of known, and potentially new, genes that could promote virulence and colonization in this species is lacking.…”

Section: Introductionmentioning

confidence: 99%

Comparative genomic analysis of the emerging pathogen Streptococcus pseudopneumoniae: novel insights into virulence determinants and identification of a novel species-specific molecular marker

Garriss

Nannapaneni

Simões

et al. 2018

Preprint

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31Streptococcus pseudopneumoniae is a close relative of the major human pathogen S. 32 pneumoniae. While initially considered as a commensal species, it has been increasingly 33 associated with lower-respiratory tract infections and high prevalence of antimicrobial 34 resistance (AMR). S. pseudopneumoniae is difficult to identify using traditional typing 35 methods due to similarities with S. pneumoniae and other members of the mitis group (SMG). 36 Using phylogenetic and comparative genomic analyses of SMG genomes, we identified a new 37 molecular marker specific for S. pseudopneumoniae and absent from any other bacterial 38 genome sequenced to date. We found that a large number of known virulence and 39 colonization genes are present in the core S. pseudopneumoniae genome and we reveal the 40 impressive number of known and new surface-exposed proteins encoded by this species. 41 Phylogenetic analyses of S. pseudopneumoniae show that specific clades are associated with 42 allelic variants of core proteins. Resistance to tetracycline and macrolides, the two most 43 common resistances, were encoded by Tn916-like integrating conjugative elements and 44 Mega-2. Overall, we found a tight association of genotypic determinants of AMR as well as 45 phenotypic AMR with a specific lineage of S. pseudopneumoniae. Taken together, our results 46 sheds light on the distribution in S. pseudopneumoniae of genes known to be important during 47 invasive disease and colonization and provide insight into features that could contribute to 48 virulence, colonization and adaptation. 50Importance 51 S. pseudopneumoniae is an overlooked pathogen emerging as the causative agent of lower-52 respiratory tract infections and associated with chronic obstructive pulmonary disease 53 (COPD) and exacerbation of COPD. However, much remains unknown on its clinical 54 importance and epidemiology, mainly due to the lack of specific means to distinguish it from 55 S. pneumoniae. Here, we provide a new molecular marker entirely specific for S. 56 pseudopneumoniae. Furthermore, our research provides a deep analysis of the presence of 57 virulence and colonization genes, as well as AMR determinants in this species. Our results 58 provide crucial information and pave the way for further studies aiming at understanding the 59 pathogenesis and epidemiology of S. pseudopneumoniae. 61 62Streptococcus pseudopneumoniae is a close relative of the human pathogen 64 Streptococcus pneumoniae. It was first described in 2004 (1), and belongs to the mitis group 65 which includes 13 other species of which some are the most common colonizers of the oral 66 cavity, such as S. mitis, S. sanguinis, S. oralis and S. gordonii (2). An increasing number of 67 reports indicate that S. pseudopneumoniae is a potential pathogen, usually associated with 68 underlying conditions (3-5), and that it can be isolated from both invasive and non-invasive 69 sites (6-9). It has been shown to be virulent in a mouse peritonitis/sepsis model (10), and to be 70 the probable ca...

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Characterization of the salivary microbiome before and after antibiotic therapy via separation technique

Pauter-Iwicka

Railean-Plugaru

Złoch

et al. 2023

Appl Microbiol Biotechnol

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In the present research, the MALDI-TOF MS technique was applied as a tool to rapidly identify the salivary microbiome. In this fact, it has been monitored the changes occurred in molecular profiles under different antibiotic therapy. Significant changes in the composition of the salivary microbiota were noticed not only in relation to the non antibiotic (non-AT) and antibiotic treatment (AT) groups, but also to the used media, the antibiotic therapy and co-existed microbiota. Each antibiotic generates specific changes in molecular profiles. The highest number of bacterial species was isolated in the universal culture medium (72%) followed by the selective medium (48% and 38%). In the case of non-AT patients, the prevalence of Streptococcus salivarius (25%), Streptococcus vestibularis (19%), Streptococcus oralis (13%), and Staphylococcus aureus (6%) was identified while in the case of AT, Streptococcus salivarius (11%), Streptococcus parasanguinis (11%), Staphylococcus epidermidis (12%), Enterococcus faecalis (9%), Staphylococcus hominis (8%), and Candida albicans (6%) were identified. Notable to specified that the Candida albicans was noticed only in AT samples, indicating a negative impact on the antibiotic therapy. The accuracy of the MALDI-TOF MS technique was performed by the 16S rRNA gene sequencing analysis—as a reference method. Conclusively, such an approach highlighted in the present study can help in developing the methods enabling a faster diagnosis of disease changes at the cellular level before clinical changes occur. Once the MALDI tool allows for the distinguishing of the microbiota of non-AT and AT, it may enable to monitor the diseases treatment and develop a treatment regimen for individual patients in relation to each antibiotic. Key points The salivary microbiota of antibiotic-treated patients was more bacteria variety MALDI-TOF MS is a promising tool for recording of reproducible molecular profiles Our data can allow to monitor the treatment of bacterial diseases for patients

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Comparative Genomic Analyses of Streptococcus pseudopneumoniae Provide Insight into Virulence and Commensalism Dynamics

Cited by 24 publications

References 62 publications

Insight into the Diversity of Penicillin-Binding Protein 2x Alleles and Mutations in Viridans Streptococci

Insight into the Diversity of Penicillin-Binding Protein 2x Alleles and Mutations in Viridans Streptococci

Comparative genomic analysis of the emerging pathogen Streptococcus pseudopneumoniae: novel insights into virulence determinants and identification of a novel species-specific molecular marker

Characterization of the salivary microbiome before and after antibiotic therapy via separation technique

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