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Ankudavicius V, Nikitina D, Lukosevicius R, Tilinde D, Salteniene V, Poskiene L, Miliauskas S, Skieceviciene J, Zemaitis M, Kupcinskas J. Detailed Characterization of the Lung-Gut Microbiome Axis Reveals the Link between PD-L1 and the Microbiome in Non-Small-Cell Lung Cancer Patients. Int J Mol Sci 2024; 25:2323. [PMID: 38396998 PMCID: PMC10889071 DOI: 10.3390/ijms25042323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 01/26/2024] [Accepted: 02/09/2024] [Indexed: 02/25/2024] Open
Abstract
Next-generation sequencing technologies have started a new era of respiratory tract research in recent years. Alterations in the respiratory microbiome between healthy and malignant conditions have been revealed. However, the composition of the microbiome varies among studies, even in similar medical conditions. Also, there is a lack of complete knowledge about lung-gut microbiome interactions in lung cancer patients. The aim of this study was to explore the lung-gut axis in non-small-cell lung cancer (NSCLC) patients and the associations between lung-gut axis microbiota and clinical parameters (CRP, NLR, LPS, CD8, and PD-L1). Lung tissue and fecal samples were used for bacterial 16S rRNA sequencing. The results revealed, for the first time, that the bacterial richness in lung tumor tissue gradually decreased with an increase in the level of PD-L1 expression (p < 0.05). An analysis of β-diversity indicated a significant positive correlation between the genera Romboutsia and Alistipes in both the lung tumor biopsies and stool samples from NSCLC patients (p < 0.05). Survival analysis showed that NSCLC patients with higher bacterial richness in their stool samples had prolonged overall survival (HR: 2.06, 95% CI: 1.025-4.17, p = 0.0426).
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Affiliation(s)
- Vytautas Ankudavicius
- Department of Pulmonology, Lithuanian University of Health Sciences, LT-44307 Kaunas, Lithuania
| | - Darja Nikitina
- Institute for Digestive Research, Lithuanian University of Health Sciences, LT-44307 Kaunas, Lithuania
| | - Rokas Lukosevicius
- Institute for Digestive Research, Lithuanian University of Health Sciences, LT-44307 Kaunas, Lithuania
| | - Deimante Tilinde
- Institute for Digestive Research, Lithuanian University of Health Sciences, LT-44307 Kaunas, Lithuania
| | - Violeta Salteniene
- Institute for Digestive Research, Lithuanian University of Health Sciences, LT-44307 Kaunas, Lithuania
| | - Lina Poskiene
- Department of Pathology, Lithuanian University of Health Sciences, LT-44307 Kaunas, Lithuania
| | - Skaidrius Miliauskas
- Department of Pulmonology, Lithuanian University of Health Sciences, LT-44307 Kaunas, Lithuania
| | - Jurgita Skieceviciene
- Institute for Digestive Research, Lithuanian University of Health Sciences, LT-44307 Kaunas, Lithuania
| | - Marius Zemaitis
- Department of Pulmonology, Lithuanian University of Health Sciences, LT-44307 Kaunas, Lithuania
| | - Juozas Kupcinskas
- Institute for Digestive Research, Lithuanian University of Health Sciences, LT-44307 Kaunas, Lithuania
- Department of Gastroenterology, Lithuanian University of Health Sciences, LT-44307 Kaunas, Lithuania
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Pérez-Cobas AE, Ginevra C, Rusniok C, Jarraud S, Buchrieser C. The respiratory tract microbiome, the pathogen load, and clinical interventions define severity of bacterial pneumonia. Cell Rep Med 2023; 4:101167. [PMID: 37633274 PMCID: PMC10518590 DOI: 10.1016/j.xcrm.2023.101167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 06/18/2023] [Accepted: 08/02/2023] [Indexed: 08/28/2023]
Abstract
Bacterial pneumonia is a considerable problem worldwide. Here, we follow the inter-kingdom respiratory tract microbiome (RTM) of a unique cohort of 38 hospitalized patients (n = 97 samples) with pneumonia caused by Legionella pneumophila. The RTM composition is characterized by diversity drops early in hospitalization and ecological species replacement. RTMs with the highest bacterial and fungal loads show low diversity and pathogen enrichment, suggesting high biomass as a biomarker for secondary and/or co-infections. The RTM structure is defined by a "commensal" cluster associated with a healthy RTM and a "pathogen" enriched one, suggesting that the cluster equilibrium drives the microbiome to recovery or dysbiosis. Legionella biomass correlates with disease severity and co-morbidities, while clinical interventions influence the RTM dynamics. Fungi, archaea, and protozoa seem to contribute to progress of pneumonia. Thus, the interplay of the RTM equilibrium, the pathogen load dynamics, and clinical interventions play a critical role in patient recovery.
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Affiliation(s)
- Ana Elena Pérez-Cobas
- Institut Pasteur, Université Paris Cité, Biologie des Bactéries Intracellulaires, Paris, France; CNRS UMR 6047, 75724 Paris, France.
| | - Christophe Ginevra
- Hospices Civils de Lyon, Centre National de Référence des Légionelles, Bron, France; Centre International de Recherche en Infectiologie, Université Lyon 1, UMR CNRS 5308, U1111 Inserm, École Normale Supérieure de Lyon, Lyon, France
| | - Christophe Rusniok
- Institut Pasteur, Université Paris Cité, Biologie des Bactéries Intracellulaires, Paris, France; CNRS UMR 6047, 75724 Paris, France
| | - Sophie Jarraud
- Hospices Civils de Lyon, Centre National de Référence des Légionelles, Bron, France; Centre International de Recherche en Infectiologie, Université Lyon 1, UMR CNRS 5308, U1111 Inserm, École Normale Supérieure de Lyon, Lyon, France
| | - Carmen Buchrieser
- Institut Pasteur, Université Paris Cité, Biologie des Bactéries Intracellulaires, Paris, France; CNRS UMR 6047, 75724 Paris, France.
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Miellet WR, Almeida ST, Trzciński K, Sá-Leão R. Streptococcus pneumoniae carriage studies in adults: Importance, challenges, and key issues to consider when using quantitative PCR-based approaches. Front Microbiol 2023; 14:1122276. [PMID: 36910231 PMCID: PMC9994646 DOI: 10.3389/fmicb.2023.1122276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 01/31/2023] [Indexed: 02/18/2023] Open
Abstract
Streptococcus pneumoniae causes significant morbidity and mortality among older adults. Detection of pneumococcal carriage is an accepted endpoint in pneumococcal conjugate vaccine studies. However, low sensitivity of culture-based approaches and nasopharyngeal samples have hampered adult S. pneumoniae carriage studies in the past. In contrast, detection of adult S. pneumoniae carriers with qPCR-based approaches can achieve high sensitivity and specificity and qPCR-based testing of oral samples improves accuracy of adult carriage detection. In this Viewpoint we outline a strategy for accurate qPCR-based testing. We recommend a dual-target approach for S. pneumoniae qPCR detection as no genetic target is universally present among or solely unique to it. Furthermore, we advise the evaluation of concordance among quantified qPCR targets to improve the accuracy of S. pneumoniae testing and qPCR-based serotyping. We do not recommend omission of qPCR-based oral sample testing as it will likely result in an underestimation of true adult carrier rates.
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Affiliation(s)
- Willem R Miellet
- Department of Pediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht, Netherlands.,Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, Netherlands
| | - Sónia T Almeida
- Laboratory of Molecular Microbiology of Human Pathogens, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Krzysztof Trzciński
- Department of Pediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht, Netherlands
| | - Raquel Sá-Leão
- Laboratory of Molecular Microbiology of Human Pathogens, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
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Miellet WR, van Veldhuizen J, Litt D, Mariman R, Wijmenga-Monsuur AJ, Badoux P, Nieuwenhuijsen T, Thombre R, Mayet S, Eletu S, Sheppard C, van Houten MA, Rots NY, Miller E, Fry NK, Sanders EAM, Trzciński K. It Takes Two to Tango: Combining Conventional Culture With Molecular Diagnostics Enhances Accuracy of Streptococcus pneumoniae Detection and Pneumococcal Serogroup/Serotype Determination in Carriage. Front Microbiol 2022; 13:859736. [PMID: 35509314 PMCID: PMC9060910 DOI: 10.3389/fmicb.2022.859736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 03/14/2022] [Indexed: 11/16/2022] Open
Abstract
Background The specificity of molecular methods for the detection of Streptococcus pneumoniae carriage is under debate. We propose a procedure for carriage surveillance and vaccine impact studies that increases the accuracy of molecular detection of live pneumococci in polymicrobial respiratory samples. Methods Culture and qPCR methods were applied to detect pneumococcus and pneumococcal serotypes in 1,549 nasopharyngeal samples collected in the Netherlands (n = 972) and England (n = 577) from 946 toddlers and 603 adults, and in paired oropharyngeal samples collected exclusively from 319 Dutch adults. Samples with no live pneumococci isolated at primary diagnostic culture yet generating signal specific for pneumococcus in qPCRs were re-examined with a second, qPCR-guided culture. Optimal Cq cut-offs for positivity in qPCRs were determined via receiver operating characteristic (ROC) curve analysis using isolation of live pneumococci from the primary and qPCR-guided cultures as reference. Results Detection of pneumococcus and pneumococcal serotypes with qPCRs in cultured (culture-enriched) nasopharyngeal samples exhibited near-perfect agreement with conventional culture (Cohen’s kappa: 0.95). Molecular methods displayed increased sensitivity of detection for multiple serotype carriage, and implementation of qPCR-guided culturing significantly increased the proportion of nasopharyngeal and oropharyngeal samples from which live pneumococcus was recovered (p < 0.0001). For paired nasopharyngeal and oropharyngeal samples from adults none of the methods applied to a single sample type exhibited good agreement with results for primary and qPCR-guided nasopharyngeal and oropharyngeal cultures combined (Cohens kappa; 0.13–0.55). However, molecular detection of pneumococcus displayed increased sensitivity with culture-enriched oropharyngeal samples when compared with either nasopharyngeal or oropharyngeal primary cultures (p < 0.05). Conclusion The accuracy of pneumococcal carriage surveillance can be greatly improved by complementing conventional culture with qPCR and vice versa, by using results of conventional and qPCR-guided cultures to interpret qPCR data. The specificity of molecular methods for the detection of live pneumococci can be enhanced by incorporating statistical procedures based on ROC curve analysis. The procedure we propose for future carriage surveillance and vaccine impact studies improves detection of pneumococcal carriage in adults in particular and enhances the specificity of serotype carriage detection.
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Affiliation(s)
- Willem R Miellet
- Department of Pediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital, University Medical Center Utrecht (UMCU), Utrecht, Netherlands.,Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, Netherlands
| | - Janieke van Veldhuizen
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, Netherlands
| | - David Litt
- Respiratory and Vaccine Preventable Bacterial Reference Unit (RVPBRU), Public Health England - National Infection Service, London, United Kingdom
| | - Rob Mariman
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, Netherlands
| | - Alienke J Wijmenga-Monsuur
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, Netherlands
| | - Paul Badoux
- Regional Laboratory of Public Health (Streeklab) Haarlem, Haarlem, Netherlands
| | - Tessa Nieuwenhuijsen
- Department of Pediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital, University Medical Center Utrecht (UMCU), Utrecht, Netherlands
| | - Rebecca Thombre
- Respiratory and Vaccine Preventable Bacterial Reference Unit (RVPBRU), Public Health England - National Infection Service, London, United Kingdom
| | - Sanaa Mayet
- Respiratory and Vaccine Preventable Bacterial Reference Unit (RVPBRU), Public Health England - National Infection Service, London, United Kingdom
| | - Seyi Eletu
- Respiratory and Vaccine Preventable Bacterial Reference Unit (RVPBRU), Public Health England - National Infection Service, London, United Kingdom
| | - Carmen Sheppard
- Respiratory and Vaccine Preventable Bacterial Reference Unit (RVPBRU), Public Health England - National Infection Service, London, United Kingdom
| | | | - Nynke Y Rots
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, Netherlands
| | - Elizabeth Miller
- Immunisation and Countermeasures Division, Public Health England (PHE) - National Infection Service, London, United Kingdom
| | - Norman K Fry
- Respiratory and Vaccine Preventable Bacterial Reference Unit (RVPBRU), Public Health England - National Infection Service, London, United Kingdom.,Immunisation and Countermeasures Division, Public Health England (PHE) - National Infection Service, London, United Kingdom
| | - Elisabeth A M Sanders
- Department of Pediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital, University Medical Center Utrecht (UMCU), Utrecht, Netherlands.,Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, Netherlands
| | - Krzysztof Trzciński
- Department of Pediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital, University Medical Center Utrecht (UMCU), Utrecht, Netherlands
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Abstract
Mitis group Streptococcus are human obligate bacteria residing in the nasopharynx and oral cavity. They comprise both commensal and pathogenic species with the most well-known being Streptococcus pneumoniae – a leading cause of meningitis and pneumonia. A primary difference between the commensal and pathogenic species is the presence of the polysaccharide capsule – a major virulence factor in S. pneumoniae, also present in other commensal species. Our current understanding of the evolutionary divergence of the pathogenic and commensal species has been inferred from extant strains. Ancient genomes can further elucidate streptococcal evolutionary history. We extracted streptococcal genome reads from a 5700-year-old ancient metagenome and worked towards characterizing them. Due to excessive within- and between-species recombination common among streptococci we were unable to parse individual species. Further, the composite reads of the ancient metagenome do not fit within the diversity of any specific extant species. Using a capsular gene database and AT-content analysis we determined that this ancient metagenome is missing polysaccharide synthesis genes integral to streptococcal capsule formation. The presence of multiple zinc metalloproteases suggests that adaptation to host IgA1 had begun and the presence of other virulence factors further implies development of close host–microbe interactions, though the absence of a capsule suggests an inability to cause invasive disease. The presence of specific virulence factors such as pneumolysin implies stable maintenance of such genes through streptococcal evolution that may strengthen their value as anti-pneumococcal vaccine antigens, while maintaining awareness of their potential presence in commensal species. Following from Jensen et al.’s initial analysis we provide historical context for this long time human nasopharyngeal resident, the Mitis group Streptococcus.
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Affiliation(s)
- Sophie Belman
- Department of Genetics, University of Cambridge, Cambridge, UK
- Parasites & Microbes, Wellcome Sanger Institute, Hinxton, UK
| | - Chrispin Chaguza
- Yale School of Medicine, New Haven, CT, USA
- Parasites & Microbes, Wellcome Sanger Institute, Hinxton, UK
| | - Narender Kumar
- Parasites & Microbes, Wellcome Sanger Institute, Hinxton, UK
| | - Stephanie Lo
- Parasites & Microbes, Wellcome Sanger Institute, Hinxton, UK
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Susic DF, Wang L, Roberts LM, Bai M, Gia A, McGovern E, Jiang XT, Davis GK, El-Omar E, Henry A. The P4 Study: Postpartum Maternal and Infant Faecal Microbiome 6 Months After Hypertensive Versus Normotensive Pregnancy. Front Cell Infect Microbiol 2022; 12:646165. [PMID: 35198457 PMCID: PMC8860159 DOI: 10.3389/fcimb.2022.646165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2020] [Accepted: 01/03/2022] [Indexed: 11/13/2022] Open
Abstract
Objective/Hypothesis To explore potential differences in faecal microbiome between women, and their infants, who had normotensive pregnancies (NP) and those who had a hypertensive pregnancy (HP), either gestational hypertension (GH) or preeclampsia (PE). Methods This is a sub study of P4 (Postpartum Physiology, Psychology, and Paediatrics Study) and includes 18 mother-infant pairs: 10 NP and 8 HP (HP as defined by blood pressure > 140/90mmHg; of which 6 had PE, and 2 GH), six months postpartum. The participating mothers collected stool samples from themselves and their infants. 16S rRNA V3-V4 amplicons were used to study the faecal microbiome. Results The sample of women and their infants were mostly primiparous (n =16) with vaginal birth (n = 14). At the time of faecal sampling 8 women were using hormonal contraception, and one HP woman remained on an antihypertensive. All women had blood pressure < 130/80mmHg, and 10 had high BMI (> 30). All infants had started solids, 8 were exclusively breastfed, 1 exclusively formula fed and 9 both. Three infants had been exposed to a course of antibiotics. Six months postpartum, there were no significant differences in alpha or beta diversity between the gut microbiota of HP and NP women (P > 0.05). However, a statistically significant difference was detected in alpha diversity between infants following HP and NP, with lower diversity levels in HP infants (P < 0.05). It was also found that at a genus and species level, the gut microbiota of HP women was enriched with Bifidobacterium and Bifidobacterium sp. and depleted in Barnesiella and Barnesiella intestinihominis when compared to NP women (P < 0.05). Similarly, the gut microbiota of infants born from HP was enriched in Streptococcus infantis and depleted in Sutterella, Sutterella sp., Bacteroides sp. and Clostridium aldenense compared to infants born from NP (P < 0.05). Discussion While our findings are at best preliminary, due to the very small sample size, they do suggest that the presence of hypertension in pregnancy may adversely affect the maternal microbiota postpartum, and that of their infants. Further analysis of postpartum microbiome data from future studies will be important to validate these early findings and provide further evidence about the changes in the microbiota in the offspring of women following hypertensive disorders of pregnancy (HDP), including possible links to the causes of long-term cardiovascular disease, the prevalence of which is increased in women who have experienced HDP.
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Affiliation(s)
- Daniella Frances Susic
- School of Women’s and Children’s Health, Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia
- Microbiome Research Centre, University of New South Wales, Sydney, NSW, Australia
- Department of Womens and Childrens Health, St. George Hospital, Sydney, NSW, Australia
- *Correspondence: Daniella Frances Susic,
| | - Leanne Wang
- Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia
| | - Lynne Margaret Roberts
- Microbiome Research Centre, University of New South Wales, Sydney, NSW, Australia
- Department of Womens and Childrens Health, St. George Hospital, Sydney, NSW, Australia
- St. George and Sutherland Clinical School, University of New South Wales, Sydney, NSW, Australia
| | - Michelle Bai
- Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia
| | - Andrew Gia
- Microbiome Research Centre, University of New South Wales, Sydney, NSW, Australia
| | - Emily McGovern
- Microbiome Research Centre, University of New South Wales, Sydney, NSW, Australia
| | - Xiao-Tao Jiang
- Microbiome Research Centre, University of New South Wales, Sydney, NSW, Australia
| | - Gregory K. Davis
- School of Women’s and Children’s Health, Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia
- Department of Womens and Childrens Health, St. George Hospital, Sydney, NSW, Australia
| | - Emad El-Omar
- Microbiome Research Centre, University of New South Wales, Sydney, NSW, Australia
- St. George and Sutherland Clinical School, University of New South Wales, Sydney, NSW, Australia
| | - Amanda Henry
- School of Women’s and Children’s Health, Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia
- Department of Womens and Childrens Health, St. George Hospital, Sydney, NSW, Australia
- George Institute for Global Health, University of New South Wales, Newtown, NSW, Australia
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Ganaie F, Branche AR, Peasley M, Rosch JW, Nahm MH. Oral streptococci expressing pneumococci-like cross-reactive capsule types can affect WHO recommended pneumococcal carriage procedure. Clin Infect Dis 2021; 75:647-656. [PMID: 34891152 DOI: 10.1093/cid/ciab1003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND Carriage studies are fundamental to assess the effects of pneumococcal vaccines. Since a large proportion of oral streptococci carry homologs of pneumococcal genes, nonculture-based detection and serotyping of upper respiratory tract (URT) samples can be problematic. Herein, we investigated if culture-free molecular methods could differentiate pneumococci from oral streptococci carried by adults in URT. METHODS Paired nasopharyngeal (NP) and oropharyngeal (OP) samples were collected from 100 older adults twice a month for one year. Extracts from the combined NP+OP samples (n=2400) were subjected to lytA real-time PCR. Positive samples were subjected to pure culture isolation followed by species confirmation using multiple approaches. Multibead assay and whole-genome sequencing were used for serotyping. RESULTS lytA-PCR was positive in 301 combined NP+OP extracts, 20 of which grew probable pneumococcal-like colonies based on colony morphology and biochemical tests. Multiple approaches confirmed that four isolates were S. pneumoniae, three were S. psuedopneumoniae, and thirteen were S. mitis. Eight nonpneumococcal strains carried pneumococcus-like cps loci (size: ~18 to 25 kb) that showed >70% of nucleotide identity with their pneumococcal counterparts. While investigating the antigenic profile, we found some S. mitis strains (P066 and P107) reacted with both serotype-specific polyclonal (Type 39 and FS17b) and monoclonal (Hyp10AG1 and Hyp17FM1) antisera, whereas some strains (P063 and P074) reacted only with polyclonal antisera (Type 5 and FS35a). CONCLUSION The extensive capsular overlap suggests that pneumococcal vaccines could reduce carriage of oral streptococci expressing cross-reactive capsules. Further, direct use of culture-free PCR-based methods in URT samples has limited usefulness for carriage studies.
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Affiliation(s)
- Feroze Ganaie
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Angela R Branche
- Department of Medicine, University of Rochester, Rochester, NY, USA
| | - Michael Peasley
- Department of Medicine, University of Rochester, Rochester, NY, USA
| | - Jason W Rosch
- Department of Infectious Diseases, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Moon H Nahm
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
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Czaplewska P, Bogucka AE, Musiał N, Tretiakow D, Skorek A, Stodulski D. Trial Proteomic Qualitative and Quantitative Analysis of the Protein Matrix of Submandibular Sialoliths. Molecules 2021; 26:6725. [PMID: 34771131 DOI: 10.3390/molecules26216725] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 11/01/2021] [Accepted: 11/04/2021] [Indexed: 11/25/2022] Open
Abstract
Our studies aimed to explore the protein components of the matrix of human submandibular gland sialoliths. A qualitative analysis was carried out based on the filter aided sample preparation (FASP) methodology. In the protein extraction process, we evaluated the applicability of the standard demineralization step and the use of a lysis buffer containing sodium dodecyl sulfate (SDS) and dithiothreitol (DTT). The analysis of fragmentation spectra based on the human database allowed for the identification of 254 human proteins present in the deposits. In addition, the use of multi-round search in the PEAKS Studio program against the bacterial base allowed for the identification of 393 proteins of bacterial origin present in the extract obtained from sialolith, which so far has not been carried out for this biological material. Furthermore, we successfully applied the SWATH methodology, allowing for a relative quantitative analysis of human proteins present in deposits. The obtained results correlate with the classification of sialoliths proposed by Tretiakow. The performed functional analysis allowed for the first time the selection of proteins, the levels of which differ between the tested samples, which may suggest the role of these proteins in the calcification process in different types of sialoliths. These are preliminary studies, and drawing specific conclusions requires research on a larger group, but it provides us the basis for the continuation of the work that has already begun.
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Kalizang'oma A, Chaguza C, Gori A, Davison C, Beleza S, Antonio M, Beall B, Goldblatt D, Kwambana-Adams B, Bentley SD, Heyderman RS. Streptococcus pneumoniae serotypes that frequently colonise the human nasopharynx are common recipients of penicillin-binding protein gene fragments from Streptococcus mitis. Microb Genom 2021; 7. [PMID: 34550067 PMCID: PMC8715442 DOI: 10.1099/mgen.0.000622] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Streptococcus pneumoniae is an important global pathogen that causes bacterial pneumonia, sepsis and meningitis. Beta-lactam antibiotics are the first-line treatment for pneumococcal disease, however, their effectiveness is hampered by beta-lactam resistance facilitated by horizontal genetic transfer (HGT) with closely related species. Although interspecies HGT is known to occur among the species of the genus Streptococcus, the rates and effects of HGT between Streptococcus pneumoniae and its close relatives involving the penicillin binding protein (pbp) genes remain poorly understood. Here we applied the fastGEAR tool to investigate interspecies HGT in pbp genes using a global collection of whole-genome sequences of Streptococcus mitis, Streptococcus oralis and S. pneumoniae. With these data, we established that pneumococcal serotypes 6A, 13, 14, 16F, 19A, 19F, 23F and 35B were the highest-ranking serotypes with acquired pbp fragments. S. mitis was a more frequent pneumococcal donor of pbp fragments and a source of higher pbp nucleotide diversity when compared with S. oralis. Pneumococci that acquired pbp fragments were associated with a higher minimum inhibitory concentration (MIC) for penicillin compared with pneumococci without acquired fragments. Together these data indicate that S. mitis contributes to reduced β-lactam susceptibility among commonly carried pneumococcal serotypes that are associated with long carriage duration and high recombination frequencies. As pneumococcal vaccine programmes mature, placing increasing pressure on the pneumococcal population structure, it will be important to monitor the influence of antimicrobial resistance HGT from commensal streptococci such as S. mitis.
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Affiliation(s)
- Akuzike Kalizang'oma
- NIHR Global Health Research Unit on Mucosal Pathogens, Division of Infection & Immunity, University College London, London, UK
| | - Chrispin Chaguza
- Parasites and Microbes, Wellcome Sanger Institute, Hinxton, UK.,Darwin College, University of Cambridge, Silver Street, Cambridge, UK.,Department of Clinical Infection, Microbiology and Immunology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Andrea Gori
- NIHR Global Health Research Unit on Mucosal Pathogens, Division of Infection & Immunity, University College London, London, UK
| | - Charlotte Davison
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - Sandra Beleza
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - Martin Antonio
- Medical Research Council Unit The Gambia at London School of Hygiene & Tropical Medicine, World Health Organization, Collaborating Centre for New Vaccines Surveillance, Banjul, Gambia
| | - Bernard Beall
- Centers for Disease Control and Prevention, National Center for Immunization and Respiratory Diseases, Division of Bacterial Diseases, Atlanta, GA, USA
| | - David Goldblatt
- University College London, Great Ormond Street Institute of Child Health, London, UK
| | - Brenda Kwambana-Adams
- NIHR Global Health Research Unit on Mucosal Pathogens, Division of Infection & Immunity, University College London, London, UK
| | | | - Robert S Heyderman
- NIHR Global Health Research Unit on Mucosal Pathogens, Division of Infection & Immunity, University College London, London, UK
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Hu H, Jin D, Yang Y, Zhang J, Ma C, Qiu Z. Distinct profile of bacterial community and antibiotic resistance genes on microplastics in Ganjiang River at the watershed level. Environ Res 2021; 200:111363. [PMID: 34048747 DOI: 10.1016/j.envres.2021.111363] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 05/18/2021] [Accepted: 05/18/2021] [Indexed: 06/12/2023]
Abstract
Microplastics are of great public concern due to their wide distribution and the potential risk to humans and animals. In this study, the microplastic pollution associated with bacterial communities, human pathogenic bacteria, and antibiotic resistance genes (ARGs) were investigated compared to water, sediment, and natural wood particles. Microplastics were widely distributed in surface water of the Ganjiang River at a watershed level with an average value of 407 particles m-3. The fragment was the main microplastic shape found in the basin. Microplastics had significantly higher observed species and Chao1 index of bacterial communities than those in water, but comparable to wood particles. However, there was no difference in the microplastics pollution and alpha diversity indices of bacterial between different reaches along the Ganjiang River. Flavobacterium, Rhodoferax, Pseudomonas, and Janthinobacterium on the microplastics were all found to be enriched compared with water and sediment. Principal component analysis of the composition and function profile of bacterial communities showed that microplastics provide a new microbial niche in the Ganjiang River, which was distinct from water, sediment, and natural wood. Pseudomonas genus dominated the composition of human pathogenic bacteria on the microplastics, which was significantly different from water and sediment. No difference was observed in the relative abundance of total ARGs among the four media. However, microplastic and wood particles showed similar composition patterns of ARGs compared with water and sediment.
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Affiliation(s)
- Hua Hu
- School of Resources Environmental and Chemical Engineering, Nanchang University, Nanchang, 330031, China; Nanchang Environmental Engineering and Technology, Co., Ltd., Nanchang, 330096, China
| | - Danfeng Jin
- The Institute of Microbiology, Jiangxi Academy of Sciences, Nanchang, 330096, China
| | - Yuyi Yang
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
| | - Jian Zhang
- School of Resources Environmental and Chemical Engineering, Nanchang University, Nanchang, 330031, China
| | - Changpo Ma
- School of Resources Environmental and Chemical Engineering, Nanchang University, Nanchang, 330031, China
| | - Zumin Qiu
- School of Resources Environmental and Chemical Engineering, Nanchang University, Nanchang, 330031, China.
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11
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Gertz RE Jr, Pimenta FC, Chochua S, Larson S, Venero AK, Bigogo G, Milucky J, Carvalho MDG, Beall B. Nonpneumococcal Strains Recently Recovered from Carriage Specimens and Expressing Capsular Serotypes Highly Related or Identical to Pneumococcal Serotypes 2, 4, 9A, 13, and 23A. mBio 2021; 12:e01037-21. [PMID: 34006665 DOI: 10.1128/mBio.01037-21] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The polysaccharide capsule is a key virulence factor of Streptococcus pneumoniae There are numerous epidemiologically important pneumococcal capsular serotypes, and recent findings have demonstrated that several of them are commonly found among nonpathogenic commensal species. Here, we describe 9 nonpneumococcal strains carrying close homologs of pneumococcal capsular biosynthetic (cps) loci that were discovered during recent pneumococcal carriage studies of adults in the United States and Kenya. Two distinct Streptococcus infantis strains cross-reactive with pneumococcal serotype 4 and carrying cps4-like capsular biosynthetic (cps) loci were recovered. Opsonophagocytic killing assays employing rabbit antisera raised against S. infantis US67cps4 revealed serotype 4-specific killing of both pneumococcal and nonpneumococcal strains. An S. infantis strain and two Streptococcus oralis strains, all carrying cps9A-like loci, were cross-reactive with pneumococcal serogroup 9 strains in immunodiffusion assays. Antiserum raised against S. infantis US64cps9A specifically promoted killing of serotype 9A and 9V pneumococcal strains as well as S. oralis serotype 9A strains. Serotype-specific PCR of oropharyngeal specimens from a recent adult carriage study in the United States indicated that such nonpneumococcal strains were much more common in this population than serotype 4 and serogroup 9 pneumococci. We also describe S. oralis and S. infantis strains expressing serotypes identical or highly related to serotypes 2, 13, and 23A. This study has expanded the known overlap of pneumococcal capsular serotypes with related commensal species. The frequent occurrence of nonpneumococcal strains in the upper respiratory tract that share vaccine and nonvaccine capsular serotypes with pneumococci could affect population immunity to circulating pneumococcal strains.IMPORTANCE The distributions and frequencies of individual pneumococcal capsular serotypes among nonpneumococcal strains in the upper respiratory tract are unknown and potentially affect pneumococcal serotype distributions among the population and immunity to circulating pneumococcal strains. Repeated demonstration that these nonpneumococcal strains expressing so-called pneumococcal serotypes are readily recovered from current carriage specimens is likely to be relevant to pneumococcal epidemiology, niche biology, and even to potential strategies of employing commensal live vaccines. Here, we describe multiple distinct nonpneumococcal counterparts for each of the pneumococcal conjugate vaccine (PCV) serotypes 4 and 9V. Additional data from contemporary commensal isolates expressing serotypes 2, 13, and 23A further demonstrate the ubiquity of such strains. Increased focus upon this serological overlap between S. pneumoniae and its close relatives may eventually prove that most, or possibly all, pneumococcal serotypes have counterparts expressed by the common upper respiratory tract commensal species Streptococcus mitis, Streptococcus oralis, and Streptococcus infantis.
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12
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Kalina WV, Souza V, Wu K, Giardina P, McKeen A, Jiang Q, Tan C, French R, Ren Y, Belanger K, McElhiney S, Unnithan M, Cheng H, Mininni T, Giordano-Schmidt D, Gessner BD, Jansen KU, Pride MW. Qualification and Clinical Validation of an Immunodiagnostic Assay for Detecting 11 Additional Streptococcus pneumoniae Serotype-specific Polysaccharides in Human Urine. Clin Infect Dis 2021; 71:e430-e438. [PMID: 32072165 PMCID: PMC7713672 DOI: 10.1093/cid/ciaa158] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Accepted: 02/18/2020] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND Identifying Streptococcus pneumoniae serotypes by urinary antigen detection (UAD) assay is the most sensitive way to evaluate the epidemiology of nonbacteremic community-acquired pneumonia (CAP). We first described a UAD assay to detect the S. pneumoniae serotypes 1, 3, 4, 5, 6A, 6B, 7F, 9V, 14, 18C, 19A, 19F, and 23F, covered by the licensed 13-valent S. pneumoniae conjugate vaccine. To assess the substantial remaining pneumococcal disease burden after introduction of several pneumococcal vaccines, a UAD-2 assay was developed to detect 11 additional serotypes (2, 8, 9N, 10A, 11A, 12F, 15B, 17F, 20, 22F, and 33F) in individuals with radiographically confirmed CAP. METHODS The specificity of the UAD-2 assay was achieved by capturing pneumococcal polysaccharides with serotype-specific monoclonal antibodies, using Luminex technology. Assay qualification was used to assess accuracy, precision, and sample linearity. Serotype positivity was based on cutoffs determined by nonparametric statistical evaluation of urine samples from individuals without pneumococcal disease. The sensitivity and specificity of the positivity cutoffs were assessed in a clinical validation, using urine samples obtained from a large study that measured the proportion of radiographically confirmed CAP caused by S. pneumoniae serotypes in hospitalized US adults. RESULTS The UAD-2 assay was shown to be specific and reproducible. Clinical validation demonstrated assay sensitivity and specificity of 92.2% and 95.9% against a reference standard of bacteremic pneumonia. In addition, the UAD-2 assay identified a S. pneumoniae serotype in 3.72% of nonbacteremic CAP cases obtained from hospitalized US adults. When combined with bacteremic CAP cases, the proportion of pneumonias with a UAD-2 serotype was 4.33%. CONCLUSIONS The qualified/clinically validated UAD-2 method has applicability in understanding the epidemiology of nonbacteremic S. pneumoniae CAP and for assessing the efficacy of future pneumococcal conjugate vaccines that are under development.
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Affiliation(s)
- Warren V Kalina
- Vaccine Research and Development,Pfizer Research, Pearl River, New York, USA
| | - Victor Souza
- Vaccine Research and Development,Pfizer Research, Pearl River, New York, USA
| | - Kangjian Wu
- Vaccine Research and Development,Pfizer Research, Pearl River, New York, USA
| | - Peter Giardina
- Vaccine Research and Development,Pfizer Research, Pearl River, New York, USA
| | - Andrew McKeen
- Early Clinical Development, Pfizer Research, Pearl River, New York, USA
| | - Qin Jiang
- Global Clinical Affairs, Pfizer, Collegeville, Pennsylvania, USA
| | - Charles Tan
- Early Clinical Development, Pfizer Research, Pearl River, New York, USA
| | - Roger French
- Early Clinical Development, Pfizer Research, Pearl River, New York, USA
| | - Yanhua Ren
- Vaccine Research and Development,Pfizer Research, Pearl River, New York, USA
| | - Kelly Belanger
- Vaccine Research and Development,Pfizer Research, Pearl River, New York, USA
| | - Susan McElhiney
- Vaccine Research and Development,Pfizer Research, Pearl River, New York, USA
| | - Manu Unnithan
- Vaccine Research and Development,Pfizer Research, Pearl River, New York, USA
| | - Huiming Cheng
- Vaccine Research and Development,Pfizer Research, Pearl River, New York, USA
| | - Terri Mininni
- Vaccine Research and Development,Pfizer Research, Pearl River, New York, USA
| | | | | | - Kathrin U Jansen
- Vaccine Research and Development,Pfizer Research, Pearl River, New York, USA
| | - Michael W Pride
- Vaccine Research and Development,Pfizer Research, Pearl River, New York, USA
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13
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Shekhar S, Åmdal HA, Petersen FC. Vaccination With the Commensal Streptococcus mitis Expressing Pneumococcal Serotype 5 Capsule Elicits IgG/IgA and Th17 Responses Against Streptococcus pneumoniae. Front Immunol 2021; 12:676488. [PMID: 33953733 PMCID: PMC8089380 DOI: 10.3389/fimmu.2021.676488] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 03/30/2021] [Indexed: 01/20/2023] Open
Abstract
Recent studies have identified a clinical isolate of the commensal Streptococcus mitis that expresses Streptococcus pneumoniae serotype 5 capsule (S. mitis serotype 5) and shows serospecificity toward pneumococcal serotype 5. However, it remains unknown whether S. mitis serotype 5 induces protective immunity against pneumococcal serotype 5. In this study, we evaluated the ability of S. mitis serotype 5 to generate protective immunity in a mouse model of lung infection with pneumococcal serotype 5. Upon challenge infection with S. pneumoniae serotype 5, mice intranasally immunized with S. mitis serotype 5 exhibited reduced pneumococcal loads in the lungs, nasal wash, and bronchoalveolar lavage fluid compared with those receiving PBS (control). The immunized mice displayed significantly higher levels of IgG and IgA antibodies reactive to S. mitis serotype 5, S. pneumoniae serotype 5 or S. pneumoniae serotype 4 than the antibody levels in control mice. In vaccinated mice, the IgG/IgA antibody levels reactive to S. mitis serotype 5 or S. pneumoniae serotype 5 were higher than the levels reactive to S. pneumoniae serotype 4. Furthermore, in-vitro restimulation of the lung-draining mediastinal lymph node cells and splenocytes from immunized mice with killed S. mitis serotype 5, S. pneumoniae serotype 5 or S. pneumoniae serotype 4 showed enhanced Th17, but not Th1 and Th2, responses. Overall, our findings show that mucosal immunization with S. mitis serotype 5 protects against S. pneumoniae serotype 5 infection and induces Th17 and predominant serotype-specific IgG/IgA antibody responses against pneumococcal infection.
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Affiliation(s)
| | - Heidi A Åmdal
- Institute of Oral Biology, University of Oslo, Oslo, Norway
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14
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Wei Y, Joyce LR, Wall AM, Guan Z, Palmer KL. Streptococcus pneumoniae, S. mitis, and S. oralis Produce a Phosphatidylglycerol-Dependent, ltaS-Independent Glycerophosphate-Linked Glycolipid. mSphere 2021; 6:e01099-20. [PMID: 33627509 DOI: 10.1128/mSphere.01099-20] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Lipoteichoic acid (LTA) is a Gram-positive bacterial cell surface polymer that participates in host-microbe interactions. It was previously reported that the major human pathogen Streptococcus pneumoniae and the closely related oral commensals S. mitis and S. oralis produce type IV LTAs. Herein, using liquid chromatography/mass spectrometry-based lipidomic analysis, we found that in addition to type IV LTA biosynthetic precursors, S. mitis, S. oralis, and S. pneumoniae also produce glycerophosphate (Gro-P)-linked dihexosyl (DH)-diacylglycerol (DAG), which is a biosynthetic precursor of type I LTA. cdsA and pgsA mutants produce DHDAG but lack (Gro-P)-DHDAG, indicating that the Gro-P moiety is derived from phosphatidylglycerol (PG), whose biosynthesis requires these genes. S. mitis, but not S. pneumoniae or S. oralis, encodes an ortholog of the PG-dependent type I LTA synthase, ltaS. By heterologous expression analyses, we confirmed that S. mitisltaS confers poly(Gro-P) synthesis in both Escherichia coli and Staphylococcus aureus and that S. mitisltaS can rescue the growth defect of an S. aureusltaS mutant. However, we do not detect a poly(Gro-P) polymer in S. mitis using an anti-type I LTA antibody. Moreover, Gro-P-linked DHDAG is still synthesized by an S. mitisltaS mutant, demonstrating that S. mitis LtaS does not catalyze Gro-P transfer to DHDAG. Finally, an S. mitisltaS mutant has increased sensitivity to human serum, demonstrating that ltaS confers a beneficial but currently undefined function in S. mitis. Overall, our results demonstrate that S. mitis, S. pneumoniae, and S. oralis produce a Gro-P-linked glycolipid via a PG-dependent, ltaS-independent mechanism. IMPORTANCE The cell wall is a critical structural component of bacterial cells that confers important physiological functions. For pathogens, it is a site of host-pathogen interactions. In this work, we analyze the glycolipids synthesized by the mitis group streptococcal species, S. pneumoniae, S. oralis, and S. mitis. We find that all produce the glycolipid, glycerophosphate (Gro-P)-linked dihexosyl (DH)-diacylglycerol (DAG), which is a precursor for the cell wall polymer type I lipoteichoic acid in other bacteria. We investigate whether the known enzyme for type I LTA synthesis, LtaS, plays a role in synthesizing this molecule in S. mitis. Our results indicate that a novel mechanism is responsible. Our results are significant because they identify a novel feature of S. pneumoniae, S. oralis, and S. mitis glycolipid biology.
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15
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Beall B. Potential Epidemiologic and Historical Implications of Capsular Serotypes Shared by Pneumococci and Their Nonpneumococcal Relatives. J Infect Dis 2021; 222:343-346. [PMID: 31605123 DOI: 10.1093/infdis/jiz457] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Accepted: 09/04/2019] [Indexed: 01/31/2023] Open
Affiliation(s)
- Bernard Beall
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA
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16
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van der Kamp I, Draper LA, Smith MK, Buttimer C, Ross RP, Hill C. A New Phage Lysin Isolated from the Oral Microbiome Targeting Streptococcus pneumoniae. Pharmaceuticals (Basel) 2020; 13:ph13120478. [PMID: 33352708 PMCID: PMC7767030 DOI: 10.3390/ph13120478] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2020] [Revised: 12/15/2020] [Accepted: 12/17/2020] [Indexed: 12/22/2022] Open
Abstract
Streptococcus pneumoniae is highly pathogenic and causes several mucosal and invasive infections. Due to the rising number of multidrug-resistant (MDR) strains of S. pneumoniae, new antimicrobials with alternative mechanisms of action are urgently needed. In this study, we identified two new Streptococcal phages from the oral microbiome, 23TH and SA01. Their lysins, 23TH_48 and SA01_53, were recombinantly expressed, characterized and tested for their lethality. SA01_53 was found to only lyse its host strain of S. anginosus, while 23TH_48 was found to possess a broader lytic activity beyond its host strain of S. infantis, with several S. pneumoniae isolates sensitive to its lytic activity. 23TH_48 at a concentration of five activity units per mL (U/mL) was found to reduce cell counts of S. pneumoniae DSM 24048 by 4 log10 colony forming units per mL (CFU/mL) within 1 h and effectively prevented and destroyed biofilms of S. pneumoniae R6 at concentrations of 228.8 ng/µL and 14.3 ng/µL, respectively. Given its high lytic activity, 23TH_48 could prove to be a promising candidate to help combat pneumococcal infections.
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Affiliation(s)
- Imme van der Kamp
- APC Microbiome Ireland, University College Cork, T12 YT20 Cork, Ireland; (I.v.d.K.); (L.A.D.); (M.K.S.); (C.B.); (R.P.R.)
| | - Lorraine A. Draper
- APC Microbiome Ireland, University College Cork, T12 YT20 Cork, Ireland; (I.v.d.K.); (L.A.D.); (M.K.S.); (C.B.); (R.P.R.)
| | - Muireann K. Smith
- APC Microbiome Ireland, University College Cork, T12 YT20 Cork, Ireland; (I.v.d.K.); (L.A.D.); (M.K.S.); (C.B.); (R.P.R.)
| | - Colin Buttimer
- APC Microbiome Ireland, University College Cork, T12 YT20 Cork, Ireland; (I.v.d.K.); (L.A.D.); (M.K.S.); (C.B.); (R.P.R.)
| | - R. Paul Ross
- APC Microbiome Ireland, University College Cork, T12 YT20 Cork, Ireland; (I.v.d.K.); (L.A.D.); (M.K.S.); (C.B.); (R.P.R.)
| | - Colin Hill
- APC Microbiome Ireland, University College Cork, T12 YT20 Cork, Ireland; (I.v.d.K.); (L.A.D.); (M.K.S.); (C.B.); (R.P.R.)
- School of Microbiology, University College Cork, T12 YN60 Cork, Ireland
- Correspondence:
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17
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Lawrence H, Pick H, Baskaran V, Daniel P, Rodrigo C, Ashton D, Edwards-Pritchard RC, Sheppard C, Eletu SD, Litt D, Fry NK, Rose S, Trotter C, McKeever TM, Lim WS. Effectiveness of the 23-valent pneumococcal polysaccharide vaccine against vaccine serotype pneumococcal pneumonia in adults: A case-control test-negative design study. PLoS Med 2020; 17:e1003326. [PMID: 33095759 PMCID: PMC7584218 DOI: 10.1371/journal.pmed.1003326] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Accepted: 08/31/2020] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND Vaccination with the 23-valent pneumococcal polysaccharide vaccine (PPV23) is available in the United Kingdom to adults aged 65 years or older and those in defined clinical risk groups. We evaluated the vaccine effectiveness (VE) of PPV23 against vaccine-type pneumococcal pneumonia in a cohort of adults hospitalised with community-acquired pneumonia (CAP). METHODS AND FINDINGS Using a case-control test-negative design, a secondary analysis of data was conducted from a prospective cohort study of adults (aged ≥16 years) with CAP hospitalised at 2 university teaching hospitals in Nottingham, England, from September 2013 to August 2018. The exposure of interest was PPV23 vaccination at any time point prior to the index admission. A case was defined as PPV23 serotype-specific pneumococcal pneumonia and a control as non-PPV23 serotype pneumococcal pneumonia or nonpneumococcal pneumonia. Pneumococcal serotypes were identified from urine samples using a multiplex immunoassay or from positive blood cultures. Multivariable logistic regression was used to derive adjusted odds of case status between vaccinated and unvaccinated individuals; VE estimates were calculated as (1 - odds ratio) × 100%. Of 2,357 patients, there were 717 PPV23 cases (48% vaccinated) and 1,640 controls (54.5% vaccinated). The adjusted VE (aVE) estimate against PPV23 serotype disease was 24% (95% CI 5%-40%, p = 0.02). Estimates were similar in analyses restricted to vaccine-eligible patients (n = 1,768, aVE 23%, 95% CI 1%-40%) and patients aged ≥65 years (n = 1,407, aVE 20%, 95% CI -5% to 40%), but not in patients aged ≥75 years (n = 905, aVE 5%, 95% CI -37% to 35%). The aVE estimate in relation to PPV23/non-13-valent pneumococcal conjugate vaccine (PCV13) serotype pneumonia (n = 417 cases, 43.7% vaccinated) was 29% (95% CI 6%-46%). Key limitations of this study are that, due to high vaccination rates, there was a lack of power to reject the null hypothesis of no vaccine effect, and that the study was not large enough to allow robust subgroup analysis in the older age groups. CONCLUSIONS In the setting of an established national childhood PCV13 vaccination programme, PPV23 vaccination of clinical at-risk patient groups and adults aged ≥65 years provided moderate long-term protection against hospitalisation with PPV23 serotype pneumonia. These findings suggest that PPV23 vaccination may continue to have an important role in adult pneumococcal vaccine policy, including the possibility of revaccination of older adults.
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Affiliation(s)
- Hannah Lawrence
- Department of Respiratory Medicine, Nottingham University Hospitals NHS Trust, Nottingham, United Kingdom
- Division of Epidemiology and Public Health, University of Nottingham, Nottingham, United Kingdom
| | - Harry Pick
- Department of Respiratory Medicine, Nottingham University Hospitals NHS Trust, Nottingham, United Kingdom
| | - Vadsala Baskaran
- Department of Respiratory Medicine, Nottingham University Hospitals NHS Trust, Nottingham, United Kingdom
- Division of Epidemiology and Public Health, University of Nottingham, Nottingham, United Kingdom
- NIHR Nottingham Biomedical Research Centre, Queen’s Medical Centre, Nottingham, United Kingdom
| | - Priya Daniel
- Department of Respiratory Medicine, University Hospitals of Derby and Burton NHS Foundation Trust, Derby, United Kingdom
| | - Chamira Rodrigo
- Department of Respiratory Medicine, Nottingham University Hospitals NHS Trust, Nottingham, United Kingdom
| | - Deborah Ashton
- Department of Respiratory Medicine, Nottingham University Hospitals NHS Trust, Nottingham, United Kingdom
| | | | - Carmen Sheppard
- Respiratory and Vaccine Preventable Bacteria Reference Unit, Public Health England–National Infection Service, Colindale, London, United Kingdom
| | - Seyi D. Eletu
- Respiratory and Vaccine Preventable Bacteria Reference Unit, Public Health England–National Infection Service, Colindale, London, United Kingdom
| | - David Litt
- Respiratory and Vaccine Preventable Bacteria Reference Unit, Public Health England–National Infection Service, Colindale, London, United Kingdom
| | - Norman K. Fry
- Respiratory and Vaccine Preventable Bacteria Reference Unit, Public Health England–National Infection Service, Colindale, London, United Kingdom
- Immunisation and Countermeasures Division, Public Health England Colindale–National Infection Service, London, United Kingdom
| | - Samuel Rose
- Respiratory and Vaccine Preventable Bacteria Reference Unit, Public Health England–National Infection Service, Colindale, London, United Kingdom
| | - Caroline Trotter
- Disease Dynamic Unit, Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Tricia M. McKeever
- Division of Epidemiology and Public Health, University of Nottingham, Nottingham, United Kingdom
- NIHR Nottingham Biomedical Research Centre, Queen’s Medical Centre, Nottingham, United Kingdom
| | - Wei Shen Lim
- Department of Respiratory Medicine, Nottingham University Hospitals NHS Trust, Nottingham, United Kingdom
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18
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Farrar JL, Odiembo H, Odoyo A, Bigogo G, Kim L, Lessa FC, Feikin DR, Breiman RF, Whitney CG, Carvalho MG, Pimenta FC. Limited Added Value of Oropharyngeal Swabs for Detecting Pneumococcal Carriage in Adults. Open Forum Infect Dis 2020; 7:ofaa368. [PMID: 32995349 PMCID: PMC7505525 DOI: 10.1093/ofid/ofaa368] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Accepted: 08/13/2020] [Indexed: 11/14/2022] Open
Abstract
We compared pneumococcal isolation rates and evaluated the benefit of using oropharyngeal (OP) specimens in addition to nasopharyngeal (NP) specimens collected from adults in rural Kenya. Of 846 adults, 52.1% were colonized; pneumococci were detected from both NP and OP specimens in 23.5%, NP only in 22.9%, and OP only in 5.7%. Ten-valent pneumococcal conjugate vaccine strains were detected from both NP and OP in 3.4%, NP only in 4.1%, and OP only in 0.7%. Inclusion of OP swabs increased carriage detection by 5.7%; however, the added cost of collecting and processing OP specimens may justify exclusion from future carriage studies among adults.
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Affiliation(s)
- Jennifer L Farrar
- Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Herine Odiembo
- Global Disease Detection Division (GDD) and International Emerging Infections Program (IEIP), Kenya Medical Research Institute (KEMRI)/CDC Public Health and Research Collaboration, Kisumu, Kenya
| | - Arthur Odoyo
- Global Disease Detection Division (GDD) and International Emerging Infections Program (IEIP), Kenya Medical Research Institute (KEMRI)/CDC Public Health and Research Collaboration, Kisumu, Kenya
| | - Godfrey Bigogo
- Global Disease Detection Division (GDD) and International Emerging Infections Program (IEIP), Kenya Medical Research Institute (KEMRI)/CDC Public Health and Research Collaboration, Kisumu, Kenya
| | - Lindsay Kim
- Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Fernanda C Lessa
- Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Daniel R Feikin
- Global Disease Detection Division (GDD) and International Emerging Infections Program (IEIP), Kenya Medical Research Institute (KEMRI)/CDC Public Health and Research Collaboration, Kisumu, Kenya
| | - Robert F Breiman
- Emory Global Health Institute, Emory University, Atlanta, Georgia, USA
| | - Cynthia G Whitney
- Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Maria G Carvalho
- Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Fabiana C Pimenta
- Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
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19
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Chen L, Collij V, Jaeger M, van den Munckhof ICL, Vich Vila A, Kurilshikov A, Gacesa R, Sinha T, Oosting M, Joosten LAB, Rutten JHW, Riksen NP, Xavier RJ, Kuipers F, Wijmenga C, Zhernakova A, Netea MG, Weersma RK, Fu J. Gut microbial co-abundance networks show specificity in inflammatory bowel disease and obesity. Nat Commun 2020; 11:4018. [PMID: 32782301 PMCID: PMC7419557 DOI: 10.1038/s41467-020-17840-y] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Accepted: 07/20/2020] [Indexed: 02/07/2023] Open
Abstract
The gut microbiome is an ecosystem that involves complex interactions. Currently, our knowledge about the role of the gut microbiome in health and disease relies mainly on differential microbial abundance, and little is known about the role of microbial interactions in the context of human disease. Here, we construct and compare microbial co-abundance networks using 2,379 metagenomes from four human cohorts: an inflammatory bowel disease (IBD) cohort, an obese cohort and two population-based cohorts. We find that the strengths of 38.6% of species co-abundances and 64.3% of pathway co-abundances vary significantly between cohorts, with 113 species and 1,050 pathway co-abundances showing IBD-specific effects and 281 pathway co-abundances showing obesity-specific effects. We can also replicate these IBD microbial co-abundances in longitudinal data from the IBD cohort of the integrative human microbiome (iHMP-IBD) project. Our study identifies several key species and pathways in IBD and obesity and provides evidence that altered microbial abundances in disease can influence their co-abundance relationship, which expands our current knowledge regarding microbial dysbiosis in disease. Gut microbiome alterations have been linked to inflammatory bowel disease (IBD) and obesity. Here, the authors characterize the metagenomes of four large human cohorts and perform co-abundance network analysis showing that dysbiosis in disease is marked by the altered co-abundance relationships, suggesting that pathway coabundance networks are more heterogeneous than species network.
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Affiliation(s)
- Lianmin Chen
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands.,Department of Pediatrics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Valerie Collij
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands.,Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Martin Jaeger
- Department of Internal Medicine and Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Inge C L van den Munckhof
- Department of Internal Medicine and Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Arnau Vich Vila
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands.,Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Alexander Kurilshikov
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Ranko Gacesa
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands.,Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Trishla Sinha
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Marije Oosting
- Department of Internal Medicine and Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Leo A B Joosten
- Department of Internal Medicine and Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands.,Department of Medical Genetics, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Joost H W Rutten
- Department of Internal Medicine and Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Niels P Riksen
- Department of Internal Medicine and Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Ramnik J Xavier
- Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.,Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Folkert Kuipers
- Department of Pediatrics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands.,Department of Laboratory Medicine, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Cisca Wijmenga
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands.,University of Groningen, Groningen, the Netherlands
| | - Alexandra Zhernakova
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Mihai G Netea
- Department of Internal Medicine and Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands.,Department for Genomics & Immunoregulation, Life and Medical Sciences Institute, University of Bonn, 53115, Bonn, Germany.,Human Genomics Laboratory, Craiova University of Medicine and Pharmacy, Craiova, Romania
| | - Rinse K Weersma
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Jingyuan Fu
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands. .,Department of Pediatrics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands.
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20
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Boelsen LK, Dunne EM, Gould KA, Ratu FT, Vidal JE, Russell FM, Mulholland EK, Hinds J, Satzke C. The Challenges of Using Oropharyngeal Samples To Measure Pneumococcal Carriage in Adults. mSphere 2020; 5:e00478-20. [PMID: 32727860 DOI: 10.1128/mSphere.00478-20] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Streptococcus pneumoniae (the pneumococcus) carriage is commonly used to measure effects of pneumococcal vaccines. Based on findings from culture-based studies, the World Health Organization recommends both nasopharyngeal (NP) and oropharyngeal (OP) sampling for detecting adult carriage. Given evidence of potential confounding by other streptococci, we evaluated molecular methods for pneumococcal identification and serotyping from 250 OP samples collected from adults in Fiji, using paired NP samples for comparison. Samples were screened using lytA quantitative PCR (qPCR), as well as pneumococcal identification and serotyping conducted by DNA microarray. A subset of OP samples were characterized by latex sweep agglutination and multiplex PCR. Alternate qPCR assays (piaB and bguR) for pneumococcal identification were evaluated. The lytA qPCR was less specific and had poor positive predictive value (PPV) in OP samples (88% and 26%, respectively) compared with NP samples (95% and 64%, respectively). Using additional targets piaB and/or bguR improved qPCR specificity in OP, although the PPV (42 to 53%) was still poor. Using microarray, we found that 102/107 (95%) of OP samples contained nonpneumococcal streptococci with partial or divergent complements of pneumococcal capsule genes. We explored 91 colonies isolated from 11 OP samples using various techniques, including multiplex PCR, latex agglutination, and microarray. We found that nonpneumococcal streptococci contribute to false positives in pneumococcal serotyping and may also contribute to spurious identification by qPCR. Our results highlight that molecular approaches should include multiple loci to minimize false-positive results when testing OP samples. Regardless of method, pneumococcal identification and serotyping results from OP samples should be interpreted with caution.IMPORTANCE Streptococcus pneumoniae (the pneumococcus) is a significant global pathogen. Accurate identification and serotyping are vital. In contrast with World Health Organization recommendations based on culture methods, we demonstrate that pneumococcal identification and serotyping with molecular methods are affected by sample type. Results from oropharyngeal samples from adults were often inaccurate. This is particularly important for assessment of vaccine impact using carriage studies, particularly in low- and middle-income countries where there are significant barriers for disease surveillance.
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21
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Sadowy E, Hryniewicz W. Identification of Streptococcus pneumoniae and other Mitis streptococci: importance of molecular methods. Eur J Clin Microbiol Infect Dis 2020; 39:2247-2256. [PMID: 32710352 PMCID: PMC7669753 DOI: 10.1007/s10096-020-03991-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 07/15/2020] [Indexed: 02/06/2023]
Abstract
The Mitis group of streptococci includes an important human pathogen, Streptococcus pneumoniae (pneumococcus) and about 20 other related species with much lower pathogenicity. In clinical practice, some representatives of these species, especially Streptococcus pseudopneumoniae and Streptococcus mitis, are sometimes mistaken for S. pneumoniae based on the results of classical microbiological methods, such as optochin susceptibility and bile solubility. Several various molecular approaches that address the issue of correct identification of pneumococci and other Mitis streptococci have been proposed and are discussed in this review, including PCR- and gene sequencing-based tests as well as new developments in the genomic field that represents an important advance in our understanding of relationships within the Mitis group.
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Affiliation(s)
- Ewa Sadowy
- Department of Molecular Microbiology, National Medicines Institute, Chełmska 30/34, 00-725, Warsaw, Poland.
| | - Waleria Hryniewicz
- Department of Epidemiology and Clinical Microbiology, National Medicines Institute, Chełmska 30/34, 00-725, Warsaw, Poland
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22
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Nahm MH, Brissac T, Kilian M, Vlach J, Orihuela CJ, Saad JS, Ganaie F. Pneumococci Can Become Virulent by Acquiring a New Capsule From Oral Streptococci. J Infect Dis 2020; 222:372-380. [PMID: 31605125 PMCID: PMC7457184 DOI: 10.1093/infdis/jiz456] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Accepted: 09/05/2019] [Indexed: 12/20/2022] Open
Abstract
Pneumococcal conjugate vaccines have been successful, but their use has increased infections by nonvaccine serotypes. Oral streptococci often harbor capsular polysaccharide (PS) synthesis loci (cps). Although this has not been observed in nature, if pneumococcus can replace its cps with oral streptococcal cps, it may increase its serotype repertoire. In the current study, we showed that oral Streptococcus strain SK95 and pneumococcal strain D39 both produce structurally identical capsular PS, and their genetic backgrounds influence the amount of capsule production and shielding from nonspecific killing. SK95 is avirulent in a well-established in vivo mouse model. When acapsular pneumococcus was transformed with SK95 cps, the transformant became virulent and killed all mice. Thus, cps from oral Streptococcus strains can make acapsular pneumococcus virulent, and interspecies cps transfer should be considered a potential mechanism of serotype replacement. Our findings, along with publications from the US Centers for Disease Control and Prevention, highlight potential limitations of the 2013 World Health Organization criterion for studying pneumococcal serotypes carried without isolating bacteria. We show that an oral streptococcal strain, SK95, and a pneumococcal strain, D39, both produce chemically identical capsular PS. We also show that transferring SK95 cps into noncapsulated, avirulent pneumococcus gave it the capacity for virulence in a mouse model.
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Affiliation(s)
- Moon H Nahm
- Department of Medicine, University of Alabama at Birmingham, Birmingham, USA
| | - Terry Brissac
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Mogens Kilian
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | - Jiri Vlach
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Carlos J Orihuela
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Jamil S Saad
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Feroze Ganaie
- Department of Medicine, University of Alabama at Birmingham, Birmingham, USA
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23
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Ganaie F, Saad JS, McGee L, van Tonder AJ, Bentley SD, Lo SW, Gladstone RA, Turner P, Keenan JD, Breiman RF, Nahm MH. A New Pneumococcal Capsule Type, 10D, is the 100th Serotype and Has a Large cps Fragment from an Oral Streptococcus. mBio 2020; 11:e00937-20. [PMID: 32430472 DOI: 10.1128/mBio.00937-20] [Citation(s) in RCA: 190] [Impact Index Per Article: 47.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The polysaccharide capsule is essential for the pathogenicity of pneumococcus, which is responsible for millions of deaths worldwide each year. Currently available pneumococcal vaccines are designed to elicit antibodies to the capsule polysaccharides of the pneumococcal isolates commonly causing diseases, and the antibodies provide protection only against the pneumococcus expressing the vaccine-targeted capsules. Since pneumococci can produce different capsule polysaccharides and therefore reduce vaccine effectiveness, it is important to track the appearance of novel pneumococcal capsule types and how these new capsules are created. Herein, we describe a new and the 100th pneumococcal capsule type with unique chemical and serological properties. The capsule type was named 10D for its serologic similarity to 10A. Genetic studies provide strong evidence that pneumococcus created 10D capsule polysaccharide by capturing a large genetic fragment from an oral streptococcus. Such interspecies genetic exchanges could greatly increase diversity of pneumococcal capsules and complicate serotype shifts. Streptococcus pneumoniae (pneumococcus) is a major human pathogen producing structurally diverse capsular polysaccharides. Widespread use of highly successful pneumococcal conjugate vaccines (PCVs) targeting pneumococcal capsules has greatly reduced infections by the vaccine types but increased infections by nonvaccine serotypes. Herein, we report a new and the 100th capsule type, named serotype 10D, by determining its unique chemical structure and biosynthetic roles of all capsule synthesis locus (cps) genes. The name 10D reflects its serologic cross-reaction with serotype 10A and appearance of cross-opsonic antibodies in response to immunization with 10A polysaccharide in a 23-valent pneumococcal vaccine. Genetic analysis showed that 10D cps has three large regions syntenic to and highly homologous with cps loci from serotype 6C, serotype 39, and an oral streptococcus strain (S. mitis SK145). The 10D cps region syntenic to SK145 is about 6 kb and has a short gene fragment of wciNα at the 5′ end. The presence of this nonfunctional wciNα fragment provides compelling evidence for a recent interspecies genetic transfer from oral streptococcus to pneumococcus. Since oral streptococci have a large repertoire of cps loci, widespread PCV usage could facilitate the appearance of novel serotypes through interspecies recombination.
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24
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Ganaie F, Saad JS, McGee L, van Tonder AJ, Bentley SD, Lo SW, Gladstone RA, Turner P, Keenan JD, Breiman RF, Nahm MH. A New Pneumococcal Capsule Type, 10D, is the 100th Serotype and Has a Large cps Fragment from an Oral Streptococcus. mBio 2020; 11. [PMID: 32430472 DOI: 10.1128/mBio.00937-20] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023] Open
Abstract
Streptococcus pneumoniae (pneumococcus) is a major human pathogen producing structurally diverse capsular polysaccharides. Widespread use of highly successful pneumococcal conjugate vaccines (PCVs) targeting pneumococcal capsules has greatly reduced infections by the vaccine types but increased infections by nonvaccine serotypes. Herein, we report a new and the 100th capsule type, named serotype 10D, by determining its unique chemical structure and biosynthetic roles of all capsule synthesis locus (cps) genes. The name 10D reflects its serologic cross-reaction with serotype 10A and appearance of cross-opsonic antibodies in response to immunization with 10A polysaccharide in a 23-valent pneumococcal vaccine. Genetic analysis showed that 10D cps has three large regions syntenic to and highly homologous with cps loci from serotype 6C, serotype 39, and an oral streptococcus strain (S. mitis SK145). The 10D cps region syntenic to SK145 is about 6 kb and has a short gene fragment of wciNα at the 5' end. The presence of this nonfunctional wciNα fragment provides compelling evidence for a recent interspecies genetic transfer from oral streptococcus to pneumococcus. Since oral streptococci have a large repertoire of cps loci, widespread PCV usage could facilitate the appearance of novel serotypes through interspecies recombination.IMPORTANCE The polysaccharide capsule is essential for the pathogenicity of pneumococcus, which is responsible for millions of deaths worldwide each year. Currently available pneumococcal vaccines are designed to elicit antibodies to the capsule polysaccharides of the pneumococcal isolates commonly causing diseases, and the antibodies provide protection only against the pneumococcus expressing the vaccine-targeted capsules. Since pneumococci can produce different capsule polysaccharides and therefore reduce vaccine effectiveness, it is important to track the appearance of novel pneumococcal capsule types and how these new capsules are created. Herein, we describe a new and the 100th pneumococcal capsule type with unique chemical and serological properties. The capsule type was named 10D for its serologic similarity to 10A. Genetic studies provide strong evidence that pneumococcus created 10D capsule polysaccharide by capturing a large genetic fragment from an oral streptococcus. Such interspecies genetic exchanges could greatly increase diversity of pneumococcal capsules and complicate serotype shifts.
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25
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Clark SE. Commensal bacteria in the upper respiratory tract regulate susceptibility to infection. Curr Opin Immunol 2020; 66:42-49. [PMID: 32416468 DOI: 10.1016/j.coi.2020.03.010] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Revised: 03/12/2020] [Accepted: 03/16/2020] [Indexed: 12/11/2022]
Abstract
The human body is host to several distinct microbial communities. Disruption of these communities increases susceptibility to a wide range of diseases, including respiratory tract infections. While commensal bacteria in the gut contribute to this effect, recent studies point to a role for commensals occupying the upper respiratory tract through direct pathogen killing and by modifying nasal and lung immune homeostasis. Clinical trials exploring 'probiotic' respiratory tract commensals are an exciting development in this area. Upper respiratory tract microbiome sequencing has revealed that destabilization of this community precedes infection, indicating that microbiome profiling of individuals has predictive value. Further investigation of respiratory tract commensal-host interactions will be critical to translate bacterial-mediated protection toward new therapeutic approaches for respiratory tract disease.
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Affiliation(s)
- Sarah E Clark
- Department of Otolaryngology, University of Colorado School of Medicine, Aurora, CO, United States.
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26
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Arguedas A, Trzciński K, O'Brien KL, Ferreira DM, Wyllie AL, Weinberger D, Danon L, Pelton SI, Azzari C, Hammitt LL, Sá-Leão R, Brandileone MCC, Saha S, Suaya J, Isturiz R, Jodar L, Gessner BD. Upper respiratory tract colonization with Streptococcus pneumoniae in adults. Expert Rev Vaccines 2020; 19:353-366. [PMID: 32237926 DOI: 10.1080/14760584.2020.1750378] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
INTRODUCTION Most of the current evidence regarding pneumococcal upper respiratory colonization in adults suggests that despite high disease burden, carriage prevalence is low. Contemporary studies on adult pneumococcal colonization have largely followed the pediatric approach by which samples are obtained mostly from the nasopharynx and bacterial detection is evaluated by routine culture alone. Recent evidence suggests that the 'pediatric approach' may be insufficient in adults and pneumococcal detection in this population may be improved by longitudinal studies that include samples from additional respiratory sites combined with more extensive laboratory testing. AREAS COVERED In this article, relevant literature published in peer review journals on adult pneumococcal colonization, epidemiology, detection methods, and recommendations were reviewed. EXPERT OPINION Respiratory carriage of Streptococcus pneumoniae has been underestimated in adults. Contemporary pneumococcal carriage studies in adults that collect samples from alternative respiratory sites such as the oropharynx, saliva, or nasal wash; are culture-enriched for pneumococcus; and use molecular diagnostic methods designed to target two pneumococcal DNA sequences should enhance pneumococcal detection in the adult respiratory tract. This finding may have implications for the interpretation of dynamics of pneumococcal transmission and vaccination.
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Affiliation(s)
- Adriano Arguedas
- Vaccines Medical Development & Scientific/Clinical Affairs, Pfizer Inc , Collegeville, PA, USA
| | - Krzysztof Trzciński
- Department of Pediatric Immunology and Infectious Diseases, Wilhelmina's Children Hospital, University Medical Centre Utrecht , Utrecht, The Netherlands
| | - Katherine L O'Brien
- Department of International Health, Johns Hopkins Bloomberg School of Public Health , Baltimore, MD, USA
| | | | - Anne L Wyllie
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health , New Haven, CT, USA
| | - Daniel Weinberger
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health , New Haven, CT, USA
| | | | - Stephen I Pelton
- Pediatric Infectious Diseases, Department of Pediatrics, Maxwell Finland Laboratory for Infectious Diseases, Boston Medical Center , Boston, MA, USA
| | - Chiara Azzari
- Meyer Children's Hospital and University of Florence , Florence, Italy
| | - Laura L Hammitt
- Department of International Health, Johns Hopkins Bloomberg School of Public Health , Baltimore, MD, USA
| | - Raquel Sá-Leão
- Instituto De Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa , Oeiras, Portugal
| | | | - Samir Saha
- Child Health Research Foundation , Matuail, Dhaka, Bangladesh
| | - Jose Suaya
- Vaccines Medical Development & Scientific/Clinical Affairs, Pfizer Inc , New York, NY, USA
| | - Raul Isturiz
- Vaccines Medical Development & Scientific/Clinical Affairs, Pfizer Inc , Collegeville, PA, USA
| | - Luis Jodar
- Vaccines Medical Development & Scientific/Clinical Affairs, Pfizer Inc , Collegeville, PA, USA
| | - Bradford D Gessner
- Vaccines Medical Development & Scientific/Clinical Affairs, Pfizer Inc , Collegeville, PA, USA
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27
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Stedman A, van Vliet AHM, A Chambers M, Gutierrez-Merino J. Gut commensal bacteria show beneficial properties as wildlife probiotics. Ann N Y Acad Sci 2020; 1467:112-132. [PMID: 32026493 DOI: 10.1111/nyas.14302] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 12/19/2019] [Accepted: 01/02/2020] [Indexed: 01/04/2023]
Abstract
Probiotics are noninvasive, environmentally friendly alternatives for reducing infectious diseases in wildlife species. Our aim in the present study was to evaluate the potential of gut commensals such as lactic acid bacteria (LAB) as wildlife probiotics. The LAB selected for our analyses were isolated from European badgers (Meles meles), a wildlife reservoir of bovine tuberculosis, and comprised four different genera: Enterococcus, Weissella, Pediococcus, and Lactobacillus. The enterococci displayed a phenotype and genotype that included the production of antibacterial peptides and stimulation of antiviral responses, as well as the presence of virulence and antibiotic resistance genes; Weissella showed antimycobacterial activity owing to their ability to produce lactate and ethanol; and lactobacilli and pediococci modulated proinflammatory phagocytic responses that associate with protection against pathogens, responses that coincide with the presence of immunomodulatory markers in their genomes. Although both lactobacilli and pediococci showed resistance to antibiotics, this was naturally acquired, and almost all isolates demonstrated a phylogenetic relationship with isolates from food and healthy animals. Our results show that LAB display probiotic benefits that depend on the genus, and that lactobacilli and pediococci are probably the most obvious candidates as probiotics against infectious diseases in wildlife because of their food-grade status and ability to modulate protective innate immune responses.
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Affiliation(s)
- Anna Stedman
- School of Biosciences and Medicine, University of Surrey-Nutritional Sciences, Guildford, United Kingdom.,The Pirbright Institute, Surrey, United Kingdom
| | | | - Mark A Chambers
- School of Veterinary Medicine, University of Surrey, Guildford, United Kingdom.,Bacteriology Department, Animal and Plant Health Agency, Addlestone, United Kingdom
| | - Jorge Gutierrez-Merino
- School of Biosciences and Medicine, University of Surrey-Nutritional Sciences, Guildford, United Kingdom
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28
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Eletu SD, Sheppard CL, Rose S, Smith K, Andrews N, Lim WS, Litt DJ, Fry NK. Re-validation and update of an extended-specificity multiplex assay for detection of Streptococcus pneumoniae capsular serotype/serogroup-specific antigen and cell-wall polysaccharide in urine specimens. Access Microbiol 2020; 2:acmi000094. [PMID: 32974571 PMCID: PMC7470314 DOI: 10.1099/acmi.0.000094] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Accepted: 01/08/2020] [Indexed: 12/27/2022] Open
Abstract
National surveillance of pneumococcal disease at the serotype level is essential to assess the effectiveness of vaccination programmes. We previously developed a highly sensitive extended-specificity multiplex immunoassay for detection of Streptococcus pneumoniae serotype-specific antigen in urine in the absence of isolates. The assay uses human mAbs that detect the 24 pneumococcal serotype/groups targeted by the pneumococcal conjugate vaccines (PCVs) and pneumococcal polysaccharide vaccine (PPV-23) plus some cross-reactive types and the pneumococcal cell-wall polysaccharide. However, the previous assay had some limitations, namely the reduced specificity of the serotype 7F, 20 and 22F assays, for which non-specific binding in urine samples was observed. Here we report on the further development and re-validation of a new version of the assay (version 2.1), which offers improved sensitivity towards serotypes 7F, 18C and 19F and increased specificity for serotypes 7F, 20 and 22F by replacement of some of the antibody clones with new clones. Using a panel of urine specimens from patients diagnosed with community-acquired pneumonia or pneumococcal disease, the overall clinical sensitivity of this version of the assay based on isolation of S. pneumoniae from a normally sterile site is 94.3 % and the clinical specificity is 93.6 %, in comparison with clinical sensitivity and specificity values of 96.2 % and 89.9 % in the previous assay.
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Affiliation(s)
- Seyi D Eletu
- Vaccine Preventable Bacteria Section, Public Health England - National Infection Service, Colindale Avenue, London, NW9 5EQ, UK
| | - Carmen L Sheppard
- Vaccine Preventable Bacteria Section, Public Health England - National Infection Service, Colindale Avenue, London, NW9 5EQ, UK
| | - Samuel Rose
- Vaccine Preventable Bacteria Section, Public Health England - National Infection Service, Colindale Avenue, London, NW9 5EQ, UK
| | - Kenneth Smith
- Oklahoma Medical Research Foundation, 825 NE 13th Street, Oklahoma City, OK 73104, USA
| | - Nick Andrews
- Statistics, Modelling and Economics Department, Public Health England - National Infection Service, Colindale Avenue, London, NW9 5EQ, UK
| | - Wei Shen Lim
- Department of Respiratory Medicine, Nottingham University Hospitals NHS Trust, Nottingham, UK
| | - David J Litt
- Vaccine Preventable Bacteria Section, Public Health England - National Infection Service, Colindale Avenue, London, NW9 5EQ, UK
| | - Norman K Fry
- Vaccine Preventable Bacteria Section, Public Health England - National Infection Service, Colindale Avenue, London, NW9 5EQ, UK.,Immunisation and Countermeasures Division, Public Health England - National Infection Service, Colindale Avenue, London, NW9 5EQ, UK
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29
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García-Suárez MDM, González-Rodríguez I, Cima-Cabal MD, Yuste JE, Vazquez F, Santiago E. Identification of Pneumococcal Serotypes by PCR-Restriction Fragment Length Polymorphism. Diagnostics (Basel) 2019; 9:E196. [PMID: 31752204 DOI: 10.3390/diagnostics9040196] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Revised: 11/13/2019] [Accepted: 11/15/2019] [Indexed: 11/30/2022] Open
Abstract
Streptococcus pneumoniae shows more than 90 capsular serotypes that can be distinguished by their reactivity against antisera. The main objective of this work was the development of a molecular method for serotyping without the use of antisera. A computer program containing an algorithm was used to search in a database for potentially useful enzymes for Restriction Fragment Length Polymorphism-RFLP typing, in order to maximize the discrimination between different serotypes. DNA sequences of 90 serotypes for the region between dexB and aliA genes were compiled, and a computer screening of restriction enzymes was performed. The wzg–wzh–wzd–wze region and Sse9I restriction predicted unique PCR-RFLP patterns for 39 serotypes and eight serogroups. A second restriction enzyme resolved fragment specific patterns for 25 serotypes. The method was tested with 98 serotype-unknown clinical isolates. PCR-RFLP analysis deduced correct serotypes that were confirmed by Quellung reaction for 78.5% of the isolates.
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Harth-Chu EN, Alves LA, Theobaldo JD, Salomão MF, Höfling JF, King WF, Smith DJ, Mattos-Graner RO. PcsB Expression Diversity Influences on Streptococcus mitis Phenotypes Associated With Host Persistence and Virulence. Front Microbiol 2019; 10:2567. [PMID: 31798545 PMCID: PMC6861525 DOI: 10.3389/fmicb.2019.02567] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Accepted: 10/23/2019] [Indexed: 12/31/2022] Open
Abstract
S. mitis is an abundant member of the commensal microbiota of the oral cavity and pharynx, which has the potential to promote systemic infections. By analyzing a collection of S. mitis strains isolated from the oral cavity at commensal states or from systemic infections (blood strains), we established that S. mitis ubiquitously express the surface immunodominant protein, PcsB (also called GbpB), required for binding to sucrose-derived exopolysaccharides (EPS). Immuno dot blot assays with anti-PcsB antibodies and RT-qPCR transcription analyses revealed strain-specific profiles of PcsB production associated with diversity in pcsB transcriptional activities. Additionally, blood strains showed significantly higher levels of PcsB expression compared to commensal isolates. Because Streptococcus mutans co-colonizes S. mitis dental biofilms, and secretes glucosyltransferases (GtfB/C/D) for the synthesis of highly insoluble EPS from sucrose, profiles of S. mitis binding to EPS, biofilm formation and evasion of the complement system were assessed in sucrose-containing BHI medium supplemented or not with filter-sterilized S. mutans culture supernatants. These analyses showed significant S. mitis binding to EPS and biofilm formation in the presence of S. mutans supernatants supplemented with sucrose, compared to BHI or BHI-sucrose medium. In addition, these phenotypes were abolished if strains were grown in culture supernatants of a gtfBCD-defective S. mutans mutant. Importantly, GtfB/C/D-associated phenotypes were enhanced in high PcsB-expressing strains, compared to low PcsB producers. Increased PcsB expression was further correlated with increased resistance to deposition of C3b/iC3b of the complement system after exposure to human serum, when strains were previously grown in the presence of S. mutans supernatants. Finally, analyses of PcsB polymorphisms and bioinformatic prediction of epitopes with significant binding to MHC class II alleles revealed that blood isolates harbor PcsB polymorphisms in its functionally conserved CHAP-domain, suggesting antigenic variation. These findings reveal important roles of PcsB in S. mitis-host interactions under commensal and pathogenic states, highlighting the need for studies to elucidate mechanisms regulating PcsB expression in this species.
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Affiliation(s)
- Erika N Harth-Chu
- Department of Oral Diagnosis, Piracicaba Dental School, UNICAMP, Piracicaba, Brazil
| | - Lívia A Alves
- Department of Oral Diagnosis, Piracicaba Dental School, UNICAMP, Piracicaba, Brazil
| | - Jéssica D Theobaldo
- Department of Oral Diagnosis, Piracicaba Dental School, UNICAMP, Piracicaba, Brazil
| | - Mariana F Salomão
- Department of Oral Diagnosis, Piracicaba Dental School, UNICAMP, Piracicaba, Brazil
| | - José F Höfling
- Department of Oral Diagnosis, Piracicaba Dental School, UNICAMP, Piracicaba, Brazil
| | - William F King
- Department of Immunology and Infectious Disease, The Forsyth Institute, Cambridge, MA, United States
| | - Daniel J Smith
- Department of Immunology and Infectious Disease, The Forsyth Institute, Cambridge, MA, United States
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Kilian M, Tettelin H. 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:e01985-19. [PMID: 31481387 DOI: 10.1128/mBio.01985-19] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [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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Sutcliffe CG, Shet A, Varghese R, Veeraraghavan B, Manoharan A, Wahl B, Chandy S, Sternal J, Khan R, Singh RK, Santosham M, Arora NK. Nasopharyngeal carriage of Streptococcus pneumoniae serotypes among children in India prior to the introduction of pneumococcal conjugate vaccines: a cross-sectional study. BMC Infect Dis 2019; 19:605. [PMID: 31291902 PMCID: PMC6621985 DOI: 10.1186/s12879-019-4254-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Accepted: 07/03/2019] [Indexed: 01/24/2023] Open
Abstract
BACKGROUND Streptococcus pneumoniae is a major cause of pneumonia, meningitis, and other serious infections among children in India. India introduced the 13-valent pneumococcal conjugate vaccine (PCV) in several states in 2017, and is expected to expand to nationwide coverage in the near future. To establish a baseline for measuring the impact of PCV in India, we assessed overall and serotype-specific nasopharyngeal carriage in two pediatric populations. METHODS A cross-sectional study was conducted in Palwal District, Haryana, from December 2016 to July 2017, prior to vaccine introduction. Children 2-59 months of age with clinical pneumonia seeking healthcare and those in the community with no clear illness were targeted for enrollment. A nasopharyngeal swab was collected and tested for pneumococcus using conventional culture and sequential multiplex PCR. Isolates were tested for antimicrobial resistance using an E test. Children were considered colonized if pneumococcus was isolated by culture or PCR. The prevalence of pneumococcal and serotype-specific colonization was compared between groups of children using log-binomial regression. RESULTS Among 601 children enrolled, 91 had clinical pneumonia and 510 were community children. The proportion colonized with S. pneumoniae was 74.7 and 54.5% among children with clinical pneumonia and community children, respectively (adjusted prevalence ratio: 1.38; 95% confidence interval: 1.19, 1.60). The prevalence of PCV13 vaccine-type colonization was similar between children with clinical pneumonia (31.9%) and community children (28.0%; p = 0.46). The most common colonizing serotypes were 6A, 6B, 14, 19A, 19F, and 23F, all of which are included in the PCV13 vaccine product. Antimicrobial resistance to at least one drug was similar between isolates from children with clinical pneumonia (66.1%) and community children (61.5%; p = 0.49); while resistance to at least two drugs was more common among isolates from children with clinical pneumonia (25.8% vs. 16.4%; p = 0.08). Resistance for all drugs was consistently higher for PCV13 vaccine-type serotypes compared to non-vaccine serotypes in both groups. CONCLUSION This study provides baseline information on the prevalence of serotype-specific pneumococcal colonization among children prior to the introduction of PCV in India. Our results suggest a role for pneumococcal vaccines in reducing pneumococcal colonization and antimicrobial resistant isolates circulating in India.
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Affiliation(s)
- Catherine G Sutcliffe
- Johns Hopkins Bloomberg School of Public Health, 615 N. Wolfe Street, Baltimore, MD, 21205, USA.
| | - Anita Shet
- Johns Hopkins Bloomberg School of Public Health, 615 N. Wolfe Street, Baltimore, MD, 21205, USA
| | - Rosemol Varghese
- Christian Medical College, Ida Scudder Road, Vellore, Tamil Nadu, 632004, India
| | | | - Anand Manoharan
- The CHILDS Trust Medical Research Foundation, 12-A Nageswara Road, Nungambakkam, Chennai, 600034, India
| | - Brian Wahl
- Johns Hopkins Bloomberg School of Public Health, 615 N. Wolfe Street, Baltimore, MD, 21205, USA
| | - Sara Chandy
- The CHILDS Trust Medical Research Foundation, 12-A Nageswara Road, Nungambakkam, Chennai, 600034, India
| | - Jack Sternal
- Johns Hopkins Bloomberg School of Public Health, 615 N. Wolfe Street, Baltimore, MD, 21205, USA
| | - Raziuddin Khan
- The INCLEN Trust International, F-1/5, 2nd Floor, Okhla Industrial Area Phase - 1, New Delhi, 110020, India
| | - Rakesh Kumar Singh
- The INCLEN Trust International, F-1/5, 2nd Floor, Okhla Industrial Area Phase - 1, New Delhi, 110020, India
| | - Mathuram Santosham
- Johns Hopkins Bloomberg School of Public Health, 615 N. Wolfe Street, Baltimore, MD, 21205, USA
| | - Narendra K Arora
- The INCLEN Trust International, F-1/5, 2nd Floor, Okhla Industrial Area Phase - 1, New Delhi, 110020, India.
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Garriss G, Nannapaneni P, Simões AS, Browall S, Subramanian K, Sá-Leão R, Goossens H, de Lencastre H, Henriques-Normark B. Genomic Characterization of the Emerging Pathogen Streptococcus pseudopneumoniae. mBio 2019; 10:e01286-19. [PMID: 31239383 DOI: 10.1128/mBio.01286-19] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
S. pseudopneumoniae is an overlooked pathogen emerging as the causative agent of lower-respiratory-tract infections and associated with chronic obstructive pulmonary disease (COPD) and exacerbation of COPD. However, much remains unknown on its clinical importance and epidemiology, mainly due to the lack of specific markers to distinguish it from S. pneumoniae. Here, we provide a new molecular marker entirely specific for S. pseudopneumoniae and offer a comprehensive view of the virulence and colonization genes found in this species. Finally, our results pave the way for further studies aiming at understanding the pathogenesis and epidemiology of S. pseudopneumoniae. Streptococcus pseudopneumoniae is a close relative of the major human pathogen S. pneumoniae. It is increasingly associated with lower-respiratory-tract infections (LRTI) and a high prevalence of antimicrobial resistance (AMR). S. pseudopneumoniae is difficult to identify using traditional typing methods due to similarities with S. pneumoniae and other members of the mitis group (SMG). Using whole-genome sequencing of LRTI isolates and a comparative genomic approach, we found that a large number of pneumococcal virulence and colonization genes are present in the core S. pseudopneumoniae genome. We also reveal an impressive number of novel surface-exposed proteins encoded by the genome of this species. In addition, we propose a new and entirely specific molecular marker useful for the identification of S. pseudopneumoniae. Phylogenetic analyses of S. pseudopneumoniae show that specific clades are associated with allelic variants of core proteins. Resistance to tetracycline and macrolides, the two most common types of resistance, were found to be encoded by Tn916-like integrating conjugative elements and Mega-2. Overall, we found a tight association of genotypic determinants of AMR and phenotypic AMR with a specific lineage of S. pseudopneumoniae. Taken together, our results shed light on the distribution in S. pseudopneumoniae of genes known to be important during invasive disease and colonization and provide insight into features that could contribute to virulence, colonization, and adaptation.
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German EL, Solórzano C, Sunny S, Dunne F, Gritzfeld JF, Mitsi E, Nikolaou E, Hyder-Wright AD, Collins AM, Gordon SB, Ferreira DM. Protective effect of PCV vaccine against experimental pneumococcal challenge in adults is primarily mediated by controlling colonisation density. Vaccine 2019; 37:3953-3956. [PMID: 31176540 PMCID: PMC6611220 DOI: 10.1016/j.vaccine.2019.05.080] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Revised: 05/20/2019] [Accepted: 05/28/2019] [Indexed: 11/03/2022]
Abstract
Widespread use of Pneumococcal Conjugate Vaccines (PCV) has reduced vaccine-type nasopharyngeal colonisation and invasive pneumococcal disease. In a double-blind, randomised controlled trial using the Experimental Human Pneumococcal Challenge (EHPC) model, PCV-13 (Prevenar-13) conferred 78% protection against colonisation acquisition and reduced bacterial intensity (AUC) as measured by classical culture. We used a multiplex qPCR assay targeting lytA and pneumococcal serotype 6A/B cpsA genes to re-assess the colonisation status of the same volunteers. Increase in detection of low-density colonisation resulted in reduced PCV efficacy against colonisation acquisition (29%), compared to classical culture (83%). For experimentally colonised volunteers, PCV had a pronounced effect on decreasing colonisation density. These results obtained in adults suggest that the success of PCV vaccination could primarily be mediated by the control of colonisation density. Studies assessing the impact of pneumococcal vaccines should allow for density measurements in their design.
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Affiliation(s)
- E L German
- Liverpool School of Tropical Medicine, Liverpool, United Kingdom.
| | - C Solórzano
- Liverpool School of Tropical Medicine, Liverpool, United Kingdom.
| | - S Sunny
- Liverpool School of Tropical Medicine, Liverpool, United Kingdom.
| | - F Dunne
- Liverpool School of Tropical Medicine, Liverpool, United Kingdom.
| | - J F Gritzfeld
- Liverpool School of Tropical Medicine, Liverpool, United Kingdom.
| | - E Mitsi
- Liverpool School of Tropical Medicine, Liverpool, United Kingdom.
| | - E Nikolaou
- Liverpool School of Tropical Medicine, Liverpool, United Kingdom.
| | | | - A M Collins
- Liverpool School of Tropical Medicine, Liverpool, United Kingdom.
| | - S B Gordon
- Liverpool School of Tropical Medicine, Liverpool, United Kingdom.
| | - D M Ferreira
- Liverpool School of Tropical Medicine, Liverpool, United Kingdom.
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Salvadori G, Junges R, Morrison DA, Petersen FC. Competence in Streptococcus pneumoniae and Close Commensal Relatives: Mechanisms and Implications. Front Cell Infect Microbiol 2019; 9:94. [PMID: 31001492 PMCID: PMC6456647 DOI: 10.3389/fcimb.2019.00094] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Accepted: 03/15/2019] [Indexed: 12/21/2022] Open
Abstract
The mitis group of streptococci comprises species that are common colonizers of the naso-oral-pharyngeal tract of humans. Streptococcus pneumoniae and Streptococcus mitis are close relatives and share ~60–80% of orthologous genes, but still present striking differences in pathogenic potential toward the human host. S. mitis has long been recognized as a reservoir of antibiotic resistance genes for S. pneumoniae, as well as a source for capsule polysaccharide variation, leading to resistance and vaccine escape. Both species share the ability to become naturally competent, and in this context, competence-associated killing mechanisms such as fratricide are thought to play an important role in interspecies gene exchange. Here, we explore the general mechanism of natural genetic transformation in the two species and touch upon the fundamental clinical and evolutionary implications of sharing similar competence, fratricide mechanisms, and a large fraction of their genomic DNA.
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Affiliation(s)
- Gabriela Salvadori
- Faculty of Dentistry, Institute of Oral Biology, University of Oslo, Oslo, Norway
| | - Roger Junges
- Faculty of Dentistry, Institute of Oral Biology, 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, United States
| | - Fernanda C Petersen
- Faculty of Dentistry, Institute of Oral Biology, University of Oslo, Oslo, Norway
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