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Battista M, Hoffmann B, Bachelot Y, Zimmermann L, Teuber L, Jost A, Linde S, Westermann M, Müller MM, Slevogt H, Hammerschmidt S, Figge MT, Vilhena C, Zipfel PF. The role of pneumococcal extracellular vesicles on the pathophysiology of the kidney disease hemolytic uremic syndrome. mSphere 2023; 8:e0014223. [PMID: 37358300 PMCID: PMC10449520 DOI: 10.1128/msphere.00142-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 04/20/2023] [Indexed: 06/27/2023] Open
Abstract
Streptococcus pneumoniae-induced hemolytic uremic syndrome (Sp-HUS) is a kidney disease characterized by microangiopathic hemolytic anemia, thrombocytopenia, and acute kidney injury. This disease is frequently underdiagnosed and its pathophysiology is poorly understood. In this work, we compared clinical strains, isolated from infant Sp-HUS patients, with a reference pathogenic strain D39, for host cytotoxicity and further explored the role of Sp-derived extracellular vesicles (EVs) in the pathogenesis of an HUS infection. In comparison with the wild-type strain, pneumococcal HUS strains caused significant lysis of human erythrocytes and increased the release of hydrogen peroxide. Isolated Sp-HUS EVs were characterized by performing dynamic light-scattering microscopy and proteomic analysis. Sp-HUS strain released EVs at a constant concentration during growth, yet the size of the EVs varied and several subpopulations emerged at later time points. The cargo of the Sp-HUS EVs included several virulence factors at high abundance, i.e., the ribosomal subunit assembly factor BipA, the pneumococcal surface protein A, the lytic enzyme LytC, several sugar utilization, and fatty acid synthesis proteins. Sp-HUS EVs strongly downregulated the expression of the endothelial surface marker platelet endothelial cell adhesion molecule-1 and were internalized by human endothelial cells. Sp-HUS EVs elicited the release of pro-inflammatory cytokines (interleukin [IL]-1β, IL-6) and chemokines (CCL2, CCL3, CXCL1) by human monocytes. These findings shed new light on the overall function of Sp-EVs, in the scope of infection-mediated HUS, and suggest new avenues of research for exploring the usefulness of Sp-EVs as therapeutic and diagnostic targets. IMPORTANCE Streptococcus pneumoniae-associated hemolytic uremic syndrome (Sp-HUS) is a serious and underdiagnosed deadly complication of invasive pneumococcal disease. Despite the introduction of the pneumococcal vaccine, cases of Sp-HUS continue to emerge, especially in children under the age of 2. While a lot has been studied regarding pneumococcal proteins and their role on Sp-HUS pathophysiology, little is known about the role of extracellular vesicles (EVs). In our work, we isolate and initially characterize EVs from a reference pathogenic strain (D39) and a strain isolated from a 2-year-old patient suffering from Sp-HUS. We demonstrate that despite lacking cytotoxicity toward human cells, Sp-HUS EVs are highly internalized by endothelial cells and can trigger cytokine and chemokine production in monocytes. In addition, this work specifically highlights the distinct morphological characteristics of Sp-HUS EVs and their unique cargo. Overall, this work sheds new light into potentially relevant players contained in EVs that might elucidate about pneumococcal EVs biogenesis or pose as interesting candidates for vaccine design.
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Affiliation(s)
- Miriana Battista
- Department of Infection Biology, Leibniz Institute for Natural Product Research and Infection Biology, Jena, Germany
| | - Bianca Hoffmann
- Applied Systems Biology, HKI-Center for Systems Biology of Infection, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute (HKI), Jena, Germany
| | - Yann Bachelot
- Applied Systems Biology, HKI-Center for Systems Biology of Infection, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute (HKI), Jena, Germany
| | - Lioba Zimmermann
- Department of Infection Biology, Leibniz Institute for Natural Product Research and Infection Biology, Jena, Germany
| | - Laura Teuber
- Department of Infection Biology, Leibniz Institute for Natural Product Research and Infection Biology, Jena, Germany
| | - Aurélie Jost
- Microverse Imaging Center, Cluster of Excellence “Balance of the Microverse,” Friedrich Schiller University, Jena, Germany
| | - Susanne Linde
- Center for Electron Microscopy, Jena University Hospital, Jena, Germany
| | - Martin Westermann
- Center for Electron Microscopy, Jena University Hospital, Jena, Germany
| | - Mario M. Müller
- Septomics Research Center, Jena University Hospital, Jena, Germany
| | - Hortense Slevogt
- Septomics Research Center, Jena University Hospital, Jena, Germany
| | - Sven Hammerschmidt
- Department of Molecular Genetics and Infection Biology, Interfaculty Institute for Genetics and Functional Genomics, Center for Functional Genomics of Microbes, University of Greifswald, Greifswald, Germany
| | - Marc Thilo Figge
- Applied Systems Biology, HKI-Center for Systems Biology of Infection, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute (HKI), Jena, Germany
- Faculty of Biological Sciences, Institute of Microbiology, Friedrich Schiller University, Jena, Germany
| | - Cláudia Vilhena
- Department of Infection Biology, Leibniz Institute for Natural Product Research and Infection Biology, Jena, Germany
| | - Peter F. Zipfel
- Department of Infection Biology, Leibniz Institute for Natural Product Research and Infection Biology, Jena, Germany
- Faculty of Biological Sciences, Institute of Microbiology, Friedrich Schiller University, Jena, Germany
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Abdul Rahman NA, Mohd Desa MN, Masri SN, Taib NM, Sulaiman N, Hazman H, John J. The Molecular Approaches and Challenges of Streptococcus pneumoniae Serotyping for Epidemiological Surveillance in the Vaccine Era. Pol J Microbiol 2023; 72:103-115. [PMID: 37314355 DOI: 10.33073/pjm-2023-023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 05/09/2023] [Indexed: 06/15/2023] Open
Abstract
Streptococcus pneumoniae (pneumococcus) belongs to the Gram-positive cocci. This bacterium typically colonizes the nasopharyngeal region of healthy individuals. It has a distinct polysaccharide capsule - a virulence factor allowing the bacteria to elude the immune defense mechanisms. Consequently, it might trigger aggressive conditions like septicemia and meningitis in immunocompromised or older individuals. Moreover, children below five years of age are at risk of morbidity and mortality. Studies have found 101 S. pneumoniae capsular serotypes, of which several correlate with clinical and carriage isolates with distinct disease aggressiveness. Introducing pneumococcal conjugate vaccines (PCV) targets the most common disease-associated serotypes. Nevertheless, vaccine selection pressure leads to replacing the formerly dominant vaccine serotypes (VTs) by non-vaccine types (NVTs). Therefore, serotyping must be conducted for epidemiological surveillance and vaccine assessment. Serotyping can be performed using numerous techniques, either by the conventional antisera-based (Quellung and latex agglutination) or molecular-based approaches (sequetyping, multiplex PCR, real-time PCR, and PCR-RFLP). A cost-effective and practical approach must be used to enhance serotyping accuracy to monitor the prevalence of VTs and NVTs. Therefore, dependable pneumococcal serotyping techniques are essential to precisely monitor virulent lineages, NVT emergence, and genetic associations of isolates. This review discusses the principles, associated benefits, and drawbacks of the respective available conventional and molecular approaches, and potentially the whole genome sequencing (WGS) to be directed for future exploration.
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Affiliation(s)
- Nurul Asyikin Abdul Rahman
- 1Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Serdang, Malaysia
- 2School of Biology, Faculty of Applied Sciences, Universiti Teknologi MARA, Kuala Pilah, Malaysia
| | - Mohd Nasir Mohd Desa
- 1Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Serdang, Malaysia
| | - Siti Norbaya Masri
- 3Department of Medical Microbiology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Serdang, Malaysia
| | - Niazlin Mohd Taib
- 3Department of Medical Microbiology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Serdang, Malaysia
| | - Nurshahira Sulaiman
- 1Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Serdang, Malaysia
| | - Hazmin Hazman
- 1Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Serdang, Malaysia
| | - James John
- 4Department of Medical Laboratory Technology, School of Allied Health Science, Sathyabama Institute of Science and Technology, Chennai, India
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Wu SC, Jan HM, Vallecillo-Zúniga ML, Rathgeber MF, Stowell CS, Murdock KL, Patel KR, Nakahara H, Stowell CJ, Nahm MH, Arthur CM, Cummings RD, Stowell SR. Whole microbe arrays accurately predict interactions and overall antimicrobial activity of galectin-8 toward distinct strains of Streptococcus pneumoniae. Sci Rep 2023; 13:5324. [PMID: 37005394 PMCID: PMC10067959 DOI: 10.1038/s41598-023-27964-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 01/10/2023] [Indexed: 04/04/2023] Open
Abstract
Microbial glycan microarrays (MGMs) populated with purified microbial glycans have been used to define the specificity of host immune factors toward microbes in a high throughput manner. However, a limitation of such arrays is that glycan presentation may not fully recapitulate the natural presentation that exists on microbes. This raises the possibility that interactions observed on the array, while often helpful in predicting actual interactions with intact microbes, may not always accurately ascertain the overall affinity of a host immune factor for a given microbe. Using galectin-8 (Gal-8) as a probe, we compared the specificity and overall affinity observed using a MGM populated with glycans harvested from various strains of Streptococcus pneumoniae to an intact microbe microarray (MMA). Our results demonstrate that while similarities in binding specificity between the MGM and MMA are apparent, Gal-8 binding toward the MMA more accurately predicted interactions with strains of S. pneumoniae, including the overall specificity of Gal-8 antimicrobial activity. Taken together, these results not only demonstrate that Gal-8 possesses antimicrobial activity against distinct strains of S. pneumoniae that utilize molecular mimicry, but that microarray platforms populated with intact microbes present an advantageous strategy when exploring host interactions with microbes.
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Affiliation(s)
- Shang-Chuen Wu
- Joint Program in Transfusion Medicine, Department of Pathology, Brigham and Women's Hospital, National Center for Functional Glycomics, 630E New Research Building, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA, 02115, USA
| | - Hau-Ming Jan
- Joint Program in Transfusion Medicine, Department of Pathology, Brigham and Women's Hospital, National Center for Functional Glycomics, 630E New Research Building, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA, 02115, USA
| | - Mary L Vallecillo-Zúniga
- Joint Program in Transfusion Medicine, Department of Pathology, Brigham and Women's Hospital, National Center for Functional Glycomics, 630E New Research Building, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA, 02115, USA
| | - Matthew F Rathgeber
- Joint Program in Transfusion Medicine, Department of Pathology, Brigham and Women's Hospital, National Center for Functional Glycomics, 630E New Research Building, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA, 02115, USA
| | - Caleb S Stowell
- Joint Program in Transfusion Medicine, Department of Pathology, Brigham and Women's Hospital, National Center for Functional Glycomics, 630E New Research Building, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA, 02115, USA
| | - Kaleb L Murdock
- Joint Program in Transfusion Medicine, Department of Pathology, Brigham and Women's Hospital, National Center for Functional Glycomics, 630E New Research Building, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA, 02115, USA
| | - Kashyap R Patel
- Joint Program in Transfusion Medicine, Department of Pathology, Brigham and Women's Hospital, National Center for Functional Glycomics, 630E New Research Building, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA, 02115, USA
| | - Hirotomo Nakahara
- Joint Program in Transfusion Medicine, Department of Pathology, Brigham and Women's Hospital, National Center for Functional Glycomics, 630E New Research Building, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA, 02115, USA
| | - Carter J Stowell
- Joint Program in Transfusion Medicine, Department of Pathology, Brigham and Women's Hospital, National Center for Functional Glycomics, 630E New Research Building, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA, 02115, USA
| | - Moon H Nahm
- Department of Medicine, University of Alabama at Birmingham, 1720 2nd Ave South Birmingham, Alabama, 35294, USA
| | - Connie M Arthur
- Joint Program in Transfusion Medicine, Department of Pathology, Brigham and Women's Hospital, National Center for Functional Glycomics, 630E New Research Building, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA, 02115, USA
| | - Richard D Cummings
- Harvard Glycomics Center, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, 02115, USA
| | - Sean R Stowell
- Joint Program in Transfusion Medicine, Department of Pathology, Brigham and Women's Hospital, National Center for Functional Glycomics, 630E New Research Building, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA, 02115, USA.
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Downs SL, Madhi SA, van der Merwe L, Nunes MC, Olwagen CP. Optimization of a high-throughput nanofluidic real-time PCR to detect and quantify of 15 bacterial species and 92 Streptococcus pneumoniae serotypes. Sci Rep 2023; 13:4588. [PMID: 36944704 PMCID: PMC10030628 DOI: 10.1038/s41598-023-31820-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 03/17/2023] [Indexed: 03/23/2023] Open
Abstract
Sensitive tools for detecting concurrent colonizing pneumococcal serotypes are needed for detailed evaluation of the direct and indirect impact of routine pneumococcal conjugate vaccine (PCV) immunization. A high-throughput quantitative nanofluidic real-time PCR (Standard BioTools 'Fluidigm') reaction-set was developed to detect and quantify 92 pneumococcal serotypes in archived clinical samples. Nasopharyngeal swabs collected in 2009-2011 from South African children ≤ 5 years-old, previously serotyped with standard culture-based methods were used for comparison. The reaction-set within the 'Fluidigm' effectively amplified all targets with high efficiency (90-110%), reproducibility (R2 ≥ 0.98), and at low limit-of-detection (< 102 CFU/ml). A blind analysis of 1 973 nasopharyngeal swab samples showed diagnostic sensitivity > 80% and specificity > 95% compared with the referent standard, culture based Quellung method. The qPCR method was able to serotype pneumococcal types with good discrimination compared with Quellung (ROC-AUC: > 0.73). The high-throughput nanofluidic real-time PCR method simultaneously detects 57 individual serotypes, and 35 serotypes within 16 serogroups in 96 samples (including controls), within a single qPCR run. This method can be used to evaluate the impact of current PCV formulations on vaccine-serotype and non-vaccine-serotype colonization, including detection of multiple concurrently colonizing serotypes. Our qPCR method can allow for monitoring of serotype-specific bacterial load, as well as emergence or ongoing transmission of minor or co-colonizing serotypes that may have invasive disease potential.
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Affiliation(s)
- Sarah L Downs
- South African Medical Research Council, Vaccines and Infectious Diseases Analytics Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
- Department of Science and Technology/National Research Foundation, South African Research Chair Initiative in Vaccine Preventable Diseases, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
| | - Shabir A Madhi
- South African Medical Research Council, Vaccines and Infectious Diseases Analytics Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Department of Science and Technology/National Research Foundation, South African Research Chair Initiative in Vaccine Preventable Diseases, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Lara van der Merwe
- South African Medical Research Council, Vaccines and Infectious Diseases Analytics Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Department of Science and Technology/National Research Foundation, South African Research Chair Initiative in Vaccine Preventable Diseases, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Marta C Nunes
- South African Medical Research Council, Vaccines and Infectious Diseases Analytics Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Department of Science and Technology/National Research Foundation, South African Research Chair Initiative in Vaccine Preventable Diseases, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Courtney P Olwagen
- South African Medical Research Council, Vaccines and Infectious Diseases Analytics Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
- Department of Science and Technology/National Research Foundation, South African Research Chair Initiative in Vaccine Preventable Diseases, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
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de Souza MB, de Carvalho E, Cergole-Novella MC, Molinari DA, Colpas DR, Dos Santos Carmo AM, Dos Santos Menezes Gaiotto Daros V, de Campos IB. Multiplex PCR to Streptococcus pneumoniae serotype identification directly in cerebrospinal fluid samples. Eur J Clin Microbiol Infect Dis 2023; 42:255-266. [PMID: 36662376 PMCID: PMC9854411 DOI: 10.1007/s10096-023-04547-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 01/11/2023] [Indexed: 01/21/2023]
Abstract
Streptococcus pneumoniae causes invasive diseases of significant public health concern, such as meningitis. The culture of cerebrospinal fluid (CSF) samples, the standard technique for meningitis diagnoses, is not always positive. Consequently, meaningful information about the etiological agent is lost, which can compromise effective epidemiological surveillance and the improvement of immunization policies. This study aims to standardize a method to genotype pneumococcus in the CSF samples which could mitigate the absence of isolated strains, and also evaluate the prediction of this assay. We applied eight multiplex PCR (mPCR) assays to CSF samples paired with the Quellung reaction applied to the isolated strains. We also compared different master mix kits in the mPCR. Moreover, a retrospective study was conducted with CSF samples considered pneumococcus positive due to the presence of the lytA gene. Results showed that genotyping by the mPCR correlated 100% with the Quellung reaction, and genotyping was dependent on the master mix applied. In the retrospective study (2014-2020), 73.4% were successfully genotyped. The analyses of the receiver operating characteristic curve showed that the cycle threshold (Ct value) around 30 for the lytA gene had a 75% positive chance of successful genotyping, whereas with a Ct value > 35, the chance was 12.5%. Finally, we observed that genotype 19A was prevalent in the period (12%), information unknown until now due to the lack of isolated strains. Therefore, the mPCR of CSF samples can efficiently predict S. pneumoniae serotypes, especially in the absence of isolated strains, which can be a great tool for pneumococcal serotype surveillance.
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Affiliation(s)
- Mariana Brena de Souza
- Adolfo Lutz Institute, Santo André Regional Center, Av. Ramiro Colleoni, 240 - Vila Dora, Santo André, SP, Zip Code: 09040-160, Brazil
| | - Eneas de Carvalho
- Butantan Institute, Bacteriology Laboratory, Av. Vital Brasil, 1500 - Butantã, São Paulo, SP, Zip Code: 05503-900, Brazil
| | - Maria Cecília Cergole-Novella
- Adolfo Lutz Institute, Santo André Regional Center, Av. Ramiro Colleoni, 240 - Vila Dora, Santo André, SP, Zip Code: 09040-160, Brazil
| | - Delma Aparecida Molinari
- Adolfo Lutz Institute, Santo André Regional Center, Av. Ramiro Colleoni, 240 - Vila Dora, Santo André, SP, Zip Code: 09040-160, Brazil
| | - Daniela Rodrigues Colpas
- Adolfo Lutz Institute, Santo André Regional Center, Av. Ramiro Colleoni, 240 - Vila Dora, Santo André, SP, Zip Code: 09040-160, Brazil
| | - Andréia Moreira Dos Santos Carmo
- Adolfo Lutz Institute, Santo André Regional Center, Av. Ramiro Colleoni, 240 - Vila Dora, Santo André, SP, Zip Code: 09040-160, Brazil
| | | | - Ivana Barros de Campos
- Adolfo Lutz Institute, Santo André Regional Center, Av. Ramiro Colleoni, 240 - Vila Dora, Santo André, SP, Zip Code: 09040-160, Brazil.
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Tabatabaei SR, Shamshiri A, Azimi L, Nazari-Alam A, Karimi A, Mirjavadi SA, Tariverdi M. Co-infection with dual Streptococcus pneumoniae serotypes as a cause of pediatric bacterial meningitis in Iran: a multi-center cross-sectional study. BMC Infect Dis 2022; 22:625. [PMID: 35850636 PMCID: PMC9290261 DOI: 10.1186/s12879-022-07606-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 07/06/2022] [Indexed: 11/19/2022] Open
Abstract
Background Meningitis is considered a life-threatening infection with high mortality all over the world. Hemophilus influenzae (H. influenzae) and Streptococcus pneumoniae (S. pneumoniae) are regarded as the two most common infectious agents causing bacterial meningitis. This study aimed to identify H. influenzae and S. pneumoniae serotypes in blood and cerebrospinal fluid (CSF) of pediatric patients with meningitis, using polymerase chain reaction (PCR). Methods This multi-center cross-sectional study included 284 children with suspected meningitis referred to 4 target hospitals. Overall, 412 samples (128 blood and 284 CSF samples) were obtained from the patients from November 14, 2016 to November 15, 2017. The extracted DNA was examined using multiplex real time PCR to screen for S. pneumoniae and H. influenzae. S. pneumoniae serotyping was also done by multiplex PCR. Results Out of 284 CSF specimens, 22 were positive for ply S. pneumoniae. Of 20 DNA samples meeting the Quality Control (QC) standards for serotyping, 7 (35%), 6 (30%), 2 (10%), 2 (10%), 2 (10%), 1 (5%), 1 (5%), 1 (5%), 1 (5%) and 1 (5%) were positive for serotypes 3, 11A, 6A, 14, 7C, 23F, 23B, 19A, and 19F and 5, respectively. Overall, nine samples were positive for two serotypes, of whom 3 and 11A were the most common from Tehran province. Of note, one of these CSF samples showed a new co-infection with serotypes 7C and 14. Also, 6 samples (30%) were positive for H. influenzae detected by bexA primer. None of the blood samples were positive for S. pneumoniae or H. influenzae. Conclusion Co-infection with S. pneumoniae serotypes can occur in bacterial meningitis and it might be missed if all serotypes are not evaluated in CSF specimens.
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Affiliation(s)
- Sedigheh Rafiei Tabatabaei
- Pediatric Infections Research Center, Research Institute for Children's Health, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Ahmadreza Shamshiri
- Department of Epidemiology and Biostatistics, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Leila Azimi
- Pediatric Infections Research Center, Research Institute for Children's Health, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Ali Nazari-Alam
- Infectious Diseases Research Center, Kashan University of Medical Sciences, Kashan, Iran
| | - Abdollah Karimi
- Pediatric Infections Research Center, Research Institute for Children's Health, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | | | - Marjan Tariverdi
- Department of Pediatric Infectious Diseases, Faculty of Medicine, Children's Clinical Research Development Center, Hormozgan University of Medical Sciences, Bandar Abbas, Iran.
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Pneumococcal Serotype Identification by Capsular Sequence Typing (CST): A Modified Novel Approach for Serotyping Directly in Clinical Samples. Diagnostics (Basel) 2021; 11:diagnostics11122353. [PMID: 34943589 PMCID: PMC8700394 DOI: 10.3390/diagnostics11122353] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 12/10/2021] [Accepted: 12/10/2021] [Indexed: 11/16/2022] Open
Abstract
As almost 60-70% of Invasive Pneumococcal Disease (IPD) is identified by nonculture methods in Greece, serotyping is of high importance for the better monitoring of pneumococcal serotypes due to the availability of conjugate vaccines. The aim of the study was the modification and direct application of the Capsular Sequence Typing (CST) assay in clinical samples in order to serotype Streptococcus pneumoniae culture-negative, Polymerase Chain Reaction (PCR_-positive samples, followed by CST group specific single-tube PCR assays. A two-step PCR modified assay was applied on a total of 306 samples (such as CSF, blood, pleural and middle ear fluids, isolates) obtained from 283 patients with IPD. The overall performance permits a rapid, accurate and cost-effective method for nonculture pneumococcal serotyping. As the management of IPD is closely related to the continuous monitoring of pneumococcal serotypes, the proposed approach proved to be a valuable tool for the typing and epidemiological monitoring of S. pneumoniae, for the evaluation of the overall impact of vaccination programs in the era of pneumococcal conjugate vaccines, in order to initiate the appropriate vaccination strategy.
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Ji Y, Wang P, Xu T, Zhou Y, Chen R, Zhu H, Zhou K. Development of a One-Step Multiplex PCR Assay for Differential Detection of Four species ( Enterobacter cloacae, Enterobacter hormaechei, Enterobacter roggenkampii, and Enterobacter kobei) Belonging to Enterobacter cloacae Complex With Clinical Significance. Front Cell Infect Microbiol 2021; 11:677089. [PMID: 34095000 PMCID: PMC8169972 DOI: 10.3389/fcimb.2021.677089] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 04/06/2021] [Indexed: 11/13/2022] Open
Abstract
Enterobacter cloacae complex (ECC) is composed of multiple species and the taxonomic status is consecutively updated. In last decades ECC is frequently associated with multidrug resistance and become an important nosocomial pathogen. Currently, rapid and accurate identification of ECC to the species level remains a technical challenge, thus impedes our understanding of the population at the species level. Here, we aimed to develop a simple, reliable, and economical method to distinguish four epidemiologically prevalent species of ECC with clinical significance, i.e., E. cloacae, E. hormaechei, E. roggenkampii, and E. kobei. A total of 977 ECC genomes were retrieved from the GenBank, and unique gene for each species was obtained by core-genome comparisons. Four pairs of species-specific primers were designed based on the unique genes. A total of 231 ECC clinical strains were typed both by hsp60 typing and by species-specific PCRs. The specificity and sensitivity of the four species-specific PCRs ranged between 96.56% and 100% and between 76.47% and 100%, respectively. The PCR for E. cloacae showed the highest specificity and sensitivity. A one-step multiplex PCR was subsequently established by combining the species-specific primers. Additional 53 hsp60-typed ECC and 20 non-ECC isolates belonging to six species obtained from samples of patients, sewage water and feces of feeding animals were tested by the multiplex PCR. The identification results of both techniques were concordant. The multiplex PCR established in this study provides an accurate, expeditious, and cost-effective way for routine diagnosis and molecular surveillance of ECC strains at species level.
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Affiliation(s)
- Yang Ji
- Shenzhen Institute of Respiratory Diseases, Second Clinical Medical College, Jinan University (Shenzhen People's Hospital); The First Affiliated Hospital, Southern University of Science and Technology (Shenzhen People's Hospital), Shenzhen, China
| | - Peihong Wang
- State Key Laboratory for Turbulence and Complex Systems and Department of Biomedical Engineering, College of Engineering, Peking University, Beijing, China.,Center for Quantitative Biology, Peking University, Beijing, China
| | - Tingting Xu
- Shenzhen Institute of Respiratory Diseases, Second Clinical Medical College, Jinan University (Shenzhen People's Hospital); The First Affiliated Hospital, Southern University of Science and Technology (Shenzhen People's Hospital), Shenzhen, China
| | - Yanzi Zhou
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Rongchang Chen
- Shenzhen Institute of Respiratory Diseases, Second Clinical Medical College, Jinan University (Shenzhen People's Hospital); The First Affiliated Hospital, Southern University of Science and Technology (Shenzhen People's Hospital), Shenzhen, China
| | - Huaiqiu Zhu
- State Key Laboratory for Turbulence and Complex Systems and Department of Biomedical Engineering, College of Engineering, Peking University, Beijing, China.,Center for Quantitative Biology, Peking University, Beijing, China
| | - Kai Zhou
- Shenzhen Institute of Respiratory Diseases, Second Clinical Medical College, Jinan University (Shenzhen People's Hospital); The First Affiliated Hospital, Southern University of Science and Technology (Shenzhen People's Hospital), Shenzhen, China
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Tsang RSW. A Narrative Review of the Molecular Epidemiology and Laboratory Surveillance of Vaccine Preventable Bacterial Meningitis Agents: Streptococcus pneumoniae, Neisseria meningitidis, Haemophilus influenzae and Streptococcus agalactiae. Microorganisms 2021; 9:449. [PMID: 33671611 PMCID: PMC7926440 DOI: 10.3390/microorganisms9020449] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 02/16/2021] [Accepted: 02/16/2021] [Indexed: 12/23/2022] Open
Abstract
This narrative review describes the public health importance of four most common bacterial meningitis agents, Streptococcus pneumoniae, Neisseria meningitidis, Haemophilus influenzae, and S. agalactiae (group B Streptococcus). Three of them are strict human pathogens that normally colonize the nasopharynx and may invade the blood stream to cause systemic infections and meningitis. S. agalactiae colonizes the genito-gastrointestinal tract and is an important meningitis agent in newborns, but also causes invasive infections in infants or adults. These four bacteria have polysaccharide capsules that protect them against the host complement defense. Currently licensed conjugate vaccines (against S. pneumoniae, H. influenza, and N. meningitidis only but not S. agalactiae) can induce protective serum antibodies in infants as young as two months old offering protection to the most vulnerable groups, and the ability to eliminate carriage of homologous serotype strains in vaccinated subjects lending further protection to those not vaccinated through herd immunity. However, the serotype-specific nature of these vaccines have driven the bacteria to adapt by mechanisms that affect the capsule antigens through either capsule switching or capsule replacement in addition to the possibility of unmasking of strains or serotypes not covered by the vaccines. The post-vaccine molecular epidemiology of vaccine-preventable bacterial meningitis is discussed based on findings obtained with newer genomic laboratory surveillance methods.
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Affiliation(s)
- Raymond S W Tsang
- Laboratory for Vaccine Preventable Bacterial Diseases, National Microbiology Laboratory, Public Health Agency of Canada, 1015 Arlington Street, Winnipeg, MB R3E 3R2, Canada
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10
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Abstract
PURPOSE OF REVIEW Pneumonia is the main global cause of sepsis, and has been associated with high morbidity and high short and long-term mortality rates. As it may be caused by a wide spectrum of microorganisms, microbial diagnosis is challenging and the choice of adequate therapy remains an important problem. This review focuses on recently published studies of microbiological diagnostic tests and clinical assessments for pneumonia, including community-acquired pneumonia, hospital-acquired pneumonia, and ventilator-associated pneumonia. RECENT FINDINGS Over the past decade, the microbiological diagnosis of pneumonia has improved significantly - thanks to the development and implementation of molecular diagnostic tests for identifying the most frequent pathogens causing pneumonia and for determining their patterns of resistance. Molecular methods for the diagnosis of pneumonia focus on multiple target detection systems and pathogen detection arrays, and, more recently, have been used in combination with mass spectrometry. SUMMARY The implementation of rapid diagnostic techniques in routine clinical practice able to identify and determine the resistance patterns of the causative microbes may transform the management of pneumonia, improving the selection and administration of antimicrobial therapies especially in critically ill patients. The validation of new diagnostic technology platforms is crucial in order to assess their usefulness and to guide antimicrobial treatment in this population.
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11
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Tzani-Tzanopoulou P, Skliros D, Megremis S, Xepapadaki P, Andreakos E, Chanishvili N, Flemetakis E, Kaltsas G, Taka S, Lebessi E, Doudoulakakis A, Papadopoulos NG. Interactions of Bacteriophages and Bacteria at the Airway Mucosa: New Insights Into the Pathophysiology of Asthma. FRONTIERS IN ALLERGY 2021; 1:617240. [PMID: 35386933 PMCID: PMC8974763 DOI: 10.3389/falgy.2020.617240] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Accepted: 12/29/2020] [Indexed: 12/16/2022] Open
Abstract
The airway epithelium is the primary site where inhaled and resident microbiota interacts between themselves and the host, potentially playing an important role on allergic asthma development and pathophysiology. With the advent of culture independent molecular techniques and high throughput technologies, the complex composition and diversity of bacterial communities of the airways has been well-documented and the notion of the lungs' sterility definitively rejected. Recent studies indicate that the microbial composition of the asthmatic airways across the spectrum of disease severity, differ significantly compared with healthy individuals. In parallel, a growing body of evidence suggests that bacterial viruses (bacteriophages or simply phages), regulating bacterial populations, are present in almost every niche of the human body and can also interact directly with the eukaryotic cells. The triptych of airway epithelial cells, bacterial symbionts and resident phages should be considered as a functional and interdependent unit with direct implications on the respiratory and overall homeostasis. While the role of epithelial cells in asthma pathophysiology is well-established, the tripartite interactions between epithelial cells, bacteria and phages should be scrutinized, both to better understand asthma as a system disorder and to explore potential interventions.
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Affiliation(s)
- Panagiota Tzani-Tzanopoulou
- Allergy and Clinical Immunology Unit, 2nd Pediatric Clinic, National and Kapodistrian University of Athens, Athens, Greece
| | - Dimitrios Skliros
- Laboratory of Molecular Biology, Department of Biotechnology, School of Food, Biotechnology and Development, Agricultural University of Athens, Athens, Greece
| | - Spyridon Megremis
- Division of Evolution and Genomic Sciences, University of Manchester, Manchester, United Kingdom
| | - Paraskevi Xepapadaki
- Allergy and Clinical Immunology Unit, 2nd Pediatric Clinic, National and Kapodistrian University of Athens, Athens, Greece
| | - Evangelos Andreakos
- Center for Clinical, Experimental Surgery and Translational Research of the Biomedical Research Foundation of the Academy of Athens, Athens, Greece
| | - Nina Chanishvili
- Laboratory for Genetics of Microorganisms and Bacteriophages, Eliava Institute of Bacteriophage, Microbiology & Virology, Tbilisi, GA, United States
| | - Emmanouil Flemetakis
- Laboratory of Molecular Biology, Department of Biotechnology, School of Food, Biotechnology and Development, Agricultural University of Athens, Athens, Greece
| | - Grigoris Kaltsas
- Department of Electrical and Electronic Engineering, University of West Attica, Athens, Greece
| | - Styliani Taka
- Allergy and Clinical Immunology Unit, 2nd Pediatric Clinic, National and Kapodistrian University of Athens, Athens, Greece
| | - Evangelia Lebessi
- Department of Microbiology, P. & A. Kyriakou Children's Hospital, Athens, Greece
| | | | - Nikolaos G Papadopoulos
- Allergy and Clinical Immunology Unit, 2nd Pediatric Clinic, National and Kapodistrian University of Athens, Athens, Greece.,Division of Evolution and Genomic Sciences, University of Manchester, Manchester, United Kingdom
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12
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A Choline-Recognizing Monomeric Lysin, ClyJ-3m, Shows Elevated Activity against Streptococcus pneumoniae. Antimicrob Agents Chemother 2020; 64:AAC.00311-20. [PMID: 32958710 DOI: 10.1128/aac.00311-20] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Accepted: 09/10/2020] [Indexed: 12/29/2022] Open
Abstract
Streptococcus pneumoniae is a leading pathogen for bacterial pneumonia, which can be treated with bacteriophage lysins harboring a conserved choline binding module (CBM). Such lysins regularly function as choline-recognizing dimers. Previously, we reported a pneumococcus-specific lysin ClyJ comprising the binding domain from the putative endolysin gp20 from the Streptococcus phage SPSL1 and the CHAP (cysteine, histidine-dependent amidohydrolase/peptidase) catalytic domain from the PlyC lysin. A variant of ClyJ with a shortened linker, i.e., ClyJ-3, shows improved activity and reduced cytotoxicity. Resembling typical CBM-containing lysins, ClyJ-3 dimerized upon binding with choline. Herein, we further report a choline-recognizing variant of ClyJ-3, i.e., ClyJ-3m, constructed by deleting its C-terminal tail. Biochemical characterization showed that ClyJ-3m remains a monomer after it binds to choline yet exhibits improved bactericidal activity against multiple pneumococcal strains with different serotypes. In an S. pneumoniae-infected bacteremia model, a single intraperitoneal administration of 2.32 μg/mouse of ClyJ-3m showed 70% protection, while only 20% of mice survived in the group receiving an equal dose of ClyJ-3 (P < 0.05). A pharmacokinetic analysis following single intravenously doses of 0.29 and 1.16 mg/kg of ClyJ-3 or ClyJ-3m in BALB/c mice revealed that ClyJ-3m shows a similar half-life but less clearance and a greater area under curve than ClyJ-3. Taken together, the choline-recognizing monomer ClyJ-3m exhibited enhanced bactericidal activity and improved pharmacokinetic proprieties compared to those of its parental ClyJ-3 lysin. Our study also provides a new way for rational design and programmed engineering of lysins targeting S. pneumoniae.
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13
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Kovács E, Sahin-Tóth J, Tóthpál A, van der Linden M, Tirczka T, Dobay O. Co-carriage of Staphylococcus aureus, Streptococcus pneumoniae, Haemophilus influenzae and Moraxella catarrhalis among three different age categories of children in Hungary. PLoS One 2020; 15:e0229021. [PMID: 32032364 PMCID: PMC7006921 DOI: 10.1371/journal.pone.0229021] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Accepted: 01/28/2020] [Indexed: 11/21/2022] Open
Abstract
Background The nasopharynx can from time to time accommodate otherwise pathogenic bacteria. This phenomenon is called asymptomatic carriage. However, in case of decreased immunity, viral infection or any other enhancing factors, severe disease can develop. Our aim in this study was to survey the nasal carriage rates of four important respiratory pathogens in three different age groups of children attending nurseries, day-care centres and primary schools. This is the first study from Hungary about the asymptomatic carriage of H. influenzae and M. catarrhalis. Methods Altogether 580 asymptomatic children were screened in three Hungarian cities. Samples were collected from both nostrils with cotton swabs. The identification was based on both colony morphology and species-specific PCRs. Serotyping was performed for S. pneumoniae, H. influenzae and M. catarrhalis. Antibiotic susceptibility was determined with agar dilution, according to the EUCAST guidelines. Clonality was examined by PFGE. Results and conclusions Whereas the carriage rates of S. pneumoniae, H. influenzae and M. catarrhalis clearly decreased with age, that of S. aureus showed an opposite tendency. Multiple carriage was least prevalent if S. aureus was one of the participants. The negative association between this bacterium and the others was statistically significant. For pneumococcus, the overall carriage rate was lower compared to earlier years, and PCV13 serotypes were present in only 6.2% of the children. The majority of H. influenzae isolates was non-typeable and no type b was detected; serotype A was dominant among M. catarrhalis. All four bacteria were more sensitive to antibiotics compared to clinical isolates. No MRSAs were detected, but we found three mupirocin resistant strains. The positive effect of Hib- and PCV-vaccination is undoubted. Continued surveillance of these pathogens is required.
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Affiliation(s)
- Eszter Kovács
- Institute of Medical Microbiology, Semmelweis University, Budapest, Hungary
| | - Judit Sahin-Tóth
- Institute of Medical Microbiology, Semmelweis University, Budapest, Hungary
| | - Adrienn Tóthpál
- Institute of Medical Microbiology, Semmelweis University, Budapest, Hungary
| | - Mark van der Linden
- German National Reference Center for Streptococci, Department of Medical Microbiology, University Hospital RWTH Aachen, Aachen, Germany
| | | | - Orsolya Dobay
- Institute of Medical Microbiology, Semmelweis University, Budapest, Hungary
- * E-mail:
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14
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Park DC, Kim SH, Yong D, Suh IB, Kim YR, Yi J, Song W, Song SA, Moon HW, Lee HK, Park KU, Kim S, Jeong SH, Lee J, Jeong J, Kim YK, Lee M, Cho J, Kim JW, Shin KS, Hwang SH, Chung JW, Woo HI, Lee CH, Ryoo N, Chang CL, Kim HS, Kim J, Shin JH, Kim SH, Lee MK, Lee SG, Jang SJ, Lee K, Suh H, Sohn YH, Kwon MJ, Lee HJ, Hong KH, Woo KS, Park CM, Shin JH. Serotype Distribution and Antimicrobial Resistance of Invasive and Noninvasive Streptococcus pneumoniae Isolates in Korea between 2014 and 2016. Ann Lab Med 2019; 39:537-544. [PMID: 31240881 PMCID: PMC6660335 DOI: 10.3343/alm.2019.39.6.537] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Revised: 04/14/2019] [Accepted: 06/13/2019] [Indexed: 12/14/2022] Open
Abstract
Background Several factors contribute to differences in Streptococcus pneumoniae serotype distribution. We investigated the serotype distribution and antimicrobial resistance of S. pneumoniae isolated between 2014 and 2016 in Korea. Methods We collected a total of 1,855 S. pneumoniae isolates from 44 hospitals between May 2014 and May 2016, and analyzed the serotypes by sequential multiplex PCR. We investigated the distribution of each serotype by patient age, source of the clinical specimen, and antimicrobial resistance pattern. Results The most common serotypes were 11A (10.1%), followed by 19A (8.8%), 3 (8.5%), 34 (8.1%), 23A (7.3%), and 35B (6.2%). The major invasive serotypes were 3 (12.6%), 19A (7.8%), 34 (7.8%), 10A (6.8%), and 11A (6.8%). Serotypes 10A, 15B, 19A, and 12F were more common in patients ≤5 years old, while serotype 3 was more common in patients ≥65 years old compared with the other age groups. The coverage rates of pneumococcal conjugate vaccine (PCV)7, PCV10, PCV13, and pneumococcal polysaccharide vaccine 23 were 11.8%, 12.12%, 33.3%, and 53.6%, respectively. Of the 1,855 isolates, 857 (46.2%) were multi-drug resistant (MDR), with serotypes 11A and 19A predominant among the MDR strains. The resistance rates against penicillin, cefotaxime, and levofloxacin were 22.8%, 12.5%, and 9.4%, respectively. Conclusions There were significant changes in the major S. pneumoniae serotypes in the community. Non-PCV13 serotypes increased in patients ≤5 years old following the introduction of national immunization programs with the 10- and 13-polyvalent vaccines.
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Affiliation(s)
- Dong Chul Park
- Department of Laboratory Medicine, Inje University College of Medicine, Busan, Korea
| | - Si Hyun Kim
- Department of Clinical Laboratory Science, Semyung University, Jecheon, Korea
| | - Dongeun Yong
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Seoul, Korea
| | - In Bum Suh
- Department of Laboratory Medicine, Kangwon National University College of Medicine, Chuncheon, Korea
| | - Young Ree Kim
- Department of Laboratory Medicine, School of Medicine, Jeju National University, Jeju, Korea
| | - Jongyoun Yi
- Department of Laboratory Medicine, Pusan National University School of Medicine, Busan, Korea
| | - Wonkeun Song
- Department of Laboratory Medicine, Hallym University College of Medicine, Chuncheon, Korea
| | - Sae Am Song
- Department of Laboratory Medicine, Inje University College of Medicine, Busan, Korea
| | - Hee Won Moon
- Department of Laboratory Medicine, Konkuk University School of Medicine, Seoul, Korea
| | - Hae Kyung Lee
- Department of Laboratory Medicine, Uijeongbu St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Kyoung Un Park
- Department of Laboratory Medicine, Seoul National University College of Medicine, Seoul, Korea
| | - Sunjoo Kim
- Department of Laboratory Medicine, Gyeongsang National University College of Medicine, Jinju, Korea
| | - Seok Hoon Jeong
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Seoul, Korea
| | - Jaehyeon Lee
- Department of Laboratory Medicine, Chonbuk National University Medical School and Hospital, Jeonju, Korea
| | - Joseph Jeong
- Department of Laboratory Medicine, Ulsan University Hospital, University of Ulsan College of Medicine, Ulsan, Korea
| | - Yu Kyung Kim
- Department of Laboratory Medicine, School of Medicine, Kyungpook National University, Daegu, Korea
| | - Miae Lee
- Department of Laboratory Medicine, Ewha Womans University College of Medicine, Seoul, Korea
| | - Jihyun Cho
- Department of Laboratory Medicine, Wonkwang University College of Medicine, Iksan, Korea
| | - Jong Wan Kim
- Department of Laboratory Medicine, Dankook University College of Medicine, Cheonan, Korea
| | - Kyeong Seob Shin
- Department of Laboratory Medicine, Chungbuk National University College of Medicine, Cheongju, Korea
| | - Sang Hyun Hwang
- Department of Laboratory Medicine, University of Ulsan College of Medicine and Asan Medical Center, Seoul, Korea
| | - Jae Woo Chung
- Department of Laboratory Medicine, Dongguk University College of Medicine, Ilsan, Korea
| | - Hye In Woo
- Department of Laboratory Medicine and Genetics, Samsung Medical Hospital, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Chae Hoon Lee
- Department of Laboratory Medicine, College of Medicine, Yeungnam University, Daegu, Korea
| | - Namhee Ryoo
- Department of Laboratory Medicine, Keimyung University School of Medicine, Daegu, Korea
| | - Chulhun L Chang
- Department of Laboratory Medicine, Pusan National University School of Medicine, Busan, Korea
| | - Hyun Soo Kim
- Department of Laboratory Medicine, Hallym University College of Medicine, Chuncheon, Korea
| | - Jayoung Kim
- Department of Laboratory Medicine, International St. Mary's Hospital, College of Medicine, Catholic Kwandong University, Incheon, Korea
| | - Jong Hee Shin
- Department of Laboratory Medicine, Chonnam National University Medical School, Gwangju, Korea
| | - Soo Hyun Kim
- Department of Laboratory Medicine, Chonnam National University Medical School, Gwangju, Korea
| | - Mi Kyung Lee
- Department of Laboratory Medicine, Chung-Ang University College of Medicine, Seoul, Korea
| | - Seong Gyu Lee
- Department of Laboratory Medicine, Bundang Jesaeng General Hospital, Seongnam, Korea
| | - Sook Jin Jang
- Department of Laboratory Medicine, College of Medicine, Chosun University, Gwangju, Korea
| | - Kyutaeg Lee
- Department of Laboratory Medicine, Cheju Halla General Hospital, Jeju, Korea
| | - HunSuk Suh
- Department of Laboratory Medicine, Daegu Catholic University School of Medicine, Daegu, Korea
| | - Yong Hak Sohn
- Department of Laboratory Medicine, Eulji University School of Medicine, Daejeon, Korea
| | - Min Jung Kwon
- Department of Laboratory Medicine and Genetics, Samsung Medical Hospital, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Hee Joo Lee
- Department of Laboratory Medicine, School of Medicine, Kyung Hee University, Seoul, Korea
| | - Ki Ho Hong
- Department of Laboratory Medicine, Seoul Medical Center, Seoul, Korea
| | - Kwang Sook Woo
- Department of Laboratory Medicine, Dong-A University College of Medicine, Busan, Korea
| | - Chul Min Park
- Department of Laboratory Medicine, Dongnam Institute of Radiological & Medical Sciences, Busan, Korea
| | - Jeong Hwan Shin
- Department of Laboratory Medicine, Inje University College of Medicine, Busan, Korea.,Paik Institute for Clinical Research, Inje University College of Medicine, Busan, Korea.
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15
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Identification of Pneumococcal Serotypes by PCR-Restriction Fragment Length Polymorphism. Diagnostics (Basel) 2019; 9:diagnostics9040196. [PMID: 31752204 PMCID: PMC6963424 DOI: 10.3390/diagnostics9040196] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [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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16
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Gonzales-Siles L, Salvà-Serra F, Degerman A, Nordén R, Lindh M, Skovbjerg S, Moore ERB. Identification and capsular serotype sequetyping of Streptococcus pneumoniae strains. J Med Microbiol 2019; 68:1173-1188. [PMID: 31268417 DOI: 10.1099/jmm.0.001022] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
PURPOSE Correct serotype identification of Streptococcus pneumoniae (pneumococcus) is important for monitoring disease epidemiology and assessing the impacts of pneumococcal vaccines. Furthermore, correct identification and differentiation of the pathogenic S. pneumoniae from closely related commensal species of the mitis group of the genus Streptococcus are essential for correct serotype identification. METHODOLOGY A new protocol for determining the existing 98 serotypes of pneumococcus was developed, applying two PCR amplifications and amplicon sequencing, using newly designed internal primers. The new protocol was validated using S. pneumoniae genome sequences, reference strains with confirmed serotypes and clinical isolates, and comparing the results with those from the traditional Quellung reaction or antiserum panel gel precipitation, in addition to real-time PCR analysis. The taxonomic identifications of 422 publicly available (GenBank) genome sequences of S. pneumoniae, Streptococcus pseudopneumoniae and Streptococcus mitis were assessed by whole-genome sequence average nucleotide identity based on blast (ANIb) analysis. RESULTS The proposed sequetyping protocol generates a 1017 bp whole cpsB region sequence, increasing resolution for serotype identification in pneumococcus isolates. The identifications of all GenBank genome sequences of S. pneumoniae were confirmed, whereas most of the S. pseudopneumoniae and almost all of the S. mitis genome sequences did not fulfil the ANIb thresholds for species-level identification. The housekeeping biomarker gene, groEL, correctly identified S. pneumoniae but often misclassified S. pseudopneumoniae and S. mitis as S. pneumoniae. CONCLUSIONS These studies affirm the importance of applying reliable identification protocols for S. pneumoniae before serotyping; our protocols provide reliable diagnostic tools, as well as an improved workflow, for serotype identification of pneumococcus and differentiation of serogroup 6 types.
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Affiliation(s)
- Lucia Gonzales-Siles
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy of the University of Gothenburg, Gothenburg, Sweden.,Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Gothenburg, Sweden
| | - Francisco Salvà-Serra
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy of the University of Gothenburg, Gothenburg, Sweden.,Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Gothenburg, Sweden.,Culture Collection University of Gothenburg (CCUG), Department of Clinical Microbiology, Sahlgrenska University Hospital, Gothenburg, Sweden.,Microbiology, Department of Biology, University of the Balearic Islands, Palma de Mallorca, Spain
| | - Anna Degerman
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy of the University of Gothenburg, Gothenburg, Sweden
| | - Rickard Nordén
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy of the University of Gothenburg, Gothenburg, Sweden
| | - Magnus Lindh
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy of the University of Gothenburg, Gothenburg, Sweden
| | - Susann Skovbjerg
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy of the University of Gothenburg, Gothenburg, Sweden.,Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Gothenburg, Sweden
| | - Edward R B Moore
- Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Gothenburg, Sweden.,Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy of the University of Gothenburg, Gothenburg, Sweden.,Culture Collection University of Gothenburg (CCUG), Department of Clinical Microbiology, Sahlgrenska University Hospital, Gothenburg, Sweden
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17
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Silva-Costa C, Brito MJ, Pinho MD, Friães A, Aguiar SI, Ramirez M, Melo-Cristino J. Pediatric Complicated Pneumonia Caused by Streptococcus pneumoniae Serotype 3 in 13-Valent Pneumococcal Conjugate Vaccinees, Portugal, 2010-2015. Emerg Infect Dis 2019; 24:1307-1314. [PMID: 29912700 PMCID: PMC6038763 DOI: 10.3201/eid2407.180029] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Despite use of 7-valent pneumococcal conjugate vaccine, incidence of pleural effusion and empyema (pediatric complicated pneumococcal pneumonia [PCPP]) is reportedly increasing globally. We cultured and performed PCR on 152 pleural fluid samples recovered from pediatric patients in Portugal during 2010–2015 to identify and serotype Streptococcus pneumoniae. We identified only 17 cases by culture, but molecular methods identified S. pneumoniae in 68% (92/135) of culture-negative samples. The most frequent serotypes were 3, 1, and 19A, together accounting for 62% (68/109) of cases. Nineteen cases attributable to 13-valent pneumococcal conjugate vaccine (PCV13) serotypes (mostly serotype 3) were detected among 22 children age-appropriately vaccinated with PCV13. The dominance of the additional serotypes included in PCV13 among PCPP cases in Portugal continues, even with PCV13 available on the private market (without reimbursement) since 2010 and with average annual coverage of 61% among age-eligible children. Our data suggest reduced effectiveness of PCV13 against serotype 3 PCPP.
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MESH Headings
- Adolescent
- Child
- Child, Preschool
- Female
- History, 21st Century
- Humans
- Immunization, Secondary
- Infant
- Male
- Pneumococcal Vaccines/administration & dosage
- Pneumococcal Vaccines/adverse effects
- Pneumococcal Vaccines/immunology
- Pneumonia, Pneumococcal/epidemiology
- Pneumonia, Pneumococcal/etiology
- Pneumonia, Pneumococcal/history
- Pneumonia, Pneumococcal/prevention & control
- Portugal/epidemiology
- Serogroup
- Streptococcus pneumoniae/classification
- Streptococcus pneumoniae/immunology
- Vaccination
- Vaccines, Conjugate/administration & dosage
- Vaccines, Conjugate/adverse effects
- Vaccines, Conjugate/immunology
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Ercibengoa M, Alonso M, Vicente D, Morales M, Garcia E, Marimón JM. Utility of MALDI-TOF MS as a new tool for Streptococcus pneumoniae serotyping. PLoS One 2019; 14:e0212022. [PMID: 30753210 PMCID: PMC6372175 DOI: 10.1371/journal.pone.0212022] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Accepted: 01/15/2019] [Indexed: 02/06/2023] Open
Abstract
Nowadays, more than 95 different Streptococcus pneumoniae serotypes are known, being less than one third responsible for the majority of severe pneumococcal infections. After the introduction of conjugate vaccines, a change in the epidemiology of the serotypes causing invasive pneumococcal disease has been observed making the surveillance of circulating serotypes especially relevant. Some recent studies have used matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) technology to identify the most frequent pneumococcal serotypes that cause invasive disease. The objectives of this study were to evaluate the efficacy of previously described discriminatory peaks determined by MALDI-TOF MS for the identification of serotypes 6B, 19F, 19A and 35B using reference and clinical isolates and to try to identify other discriminatory peaks for serotypes 11A, 19F and 19A using transformed pneumococcal strains. Most of the proposed peaks defined in the literature for the identification of serotypes 6B, 19F, 19A, 35B were not found in the spectra of the 10 reference isolates nor in those of the 60 clinical isolates tested corresponding to these four serotypes. The analysis and comparison of the mass spectra of genetically modified pneumococci (transformed strains) did not allow the establishment of new discriminatory peaks for serotypes 11A, 19F, and 19A. MALDI-TOF MS in the usual range of 2,000 to 20,000 m/z did not prove to be a valid technique for direct S. pneumoniae serotyping.
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Affiliation(s)
- María Ercibengoa
- Hospital Universitario Donostia–Instituto de Investigación Sanitaria Biodonostia, San Sebastián, Spain
- CIBER de Enfermedades Respiratorias–CIBERES, Madrid, Spain
- Preventive Medicine and Health Public Department, University of Basque Country UPV/EHU, San Sebastián, Spain
- * E-mail:
| | - Marta Alonso
- Hospital Universitario Donostia–Instituto de Investigación Sanitaria Biodonostia, San Sebastián, Spain
- CIBER de Enfermedades Respiratorias–CIBERES, Madrid, Spain
| | - Diego Vicente
- Hospital Universitario Donostia–Instituto de Investigación Sanitaria Biodonostia, San Sebastián, Spain
- CIBER de Enfermedades Respiratorias–CIBERES, Madrid, Spain
- Preventive Medicine and Health Public Department, University of Basque Country UPV/EHU, San Sebastián, Spain
| | - Maria Morales
- CIBER de Enfermedades Respiratorias–CIBERES, Madrid, Spain
- Departamento de Biotecnología Microbiana y de Plantas, Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Ernesto Garcia
- CIBER de Enfermedades Respiratorias–CIBERES, Madrid, Spain
- Departamento de Biotecnología Microbiana y de Plantas, Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Jose María Marimón
- Hospital Universitario Donostia–Instituto de Investigación Sanitaria Biodonostia, San Sebastián, Spain
- CIBER de Enfermedades Respiratorias–CIBERES, Madrid, Spain
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19
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Kovács E, Sahin-Tóth J, Tóthpál A, Kristóf K, van der Linden M, Tirczka T, Dobay O. Vaccine-driven serotype-rearrangement is seen with latency in clinical isolates: Comparison of carried and clinical pneumococcal isolates from the same time period in Hungary. Vaccine 2019; 37:99-108. [DOI: 10.1016/j.vaccine.2018.11.026] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Revised: 11/08/2018] [Accepted: 11/12/2018] [Indexed: 01/09/2023]
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20
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Assessment of Postvaccine Immunity against Streptococcus pneumoniae in Patients with Asplenia, including an Analysis of Its Impact on Bacterial Flora of the Upper Respiratory Tract and Incidence of Infections. J Immunol Res 2018; 2018:1691347. [PMID: 30687764 PMCID: PMC6330813 DOI: 10.1155/2018/1691347] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Accepted: 11/29/2018] [Indexed: 11/29/2022] Open
Abstract
S. pneumoniae is a microorganism that may cause a serious threat in postsplenectomy patients due to a potentially invasive course of infection. In order to assess a protective activity after vaccination with the 23-valent vaccine, we made an analysis of the level of antibodies in patients with asplenia compared to a control group of healthy donors. Additionally, colonization by potentially pathogenic microorganisms of the upper respiratory tract was analyzed to determine the carrier state by strains with vaccine serotype. No such strains were found in the research, yet three non-vaccine-serotype strains were found. Colonization of the upper respiratory tract by potentially pathogenic microorganisms may be connected with increased susceptibility observed and incidence of infections in patients with asplenia. However, colonization by S. pneumoniae may not have an effect on the level of specific antibodies with the 23-valent vaccine against S. pneumoniae (PPV23) in postsplenectomy patients and healthy people. The response to vaccination against S. pneumoniae showed a lower level of specific antibodies in patients with splenectomy performed more than 2 years before the test than in patients with a recently removed spleen, i.e., from 1 month to 2 years before the test. Vaccination against pneumococci also has positive effects on incidence of other etiology infections, which is of high significance in the prophylaxis of infectious diseases in this group of patients.
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21
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Shen M, Yao R, Yue H, Zhang J, Chen M, Zhang W, Liu D, Wu K. Serotype prevalence and antibiotic susceptibility patterns of pneumococcal isolates in Zunyi city, China. Saudi Med J 2018; 38:1243-1249. [PMID: 29209675 PMCID: PMC5787637 DOI: 10.15537/smj.2017.12.21090] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
OBJECTIVES To assess the serotype distribution and antimicrobial susceptibility of pneumococci isolated from inpatients of all ages suspected of having bacterial infections. METHODS In this retrospective study, pneumococcal isolates were consecutively collected from the Third Affiliated Hospital of Zunyi Medical University, in Zunyi city, China, between January 2014 and December 2016. Pneumococci were identified using routine microbiological assays. We performed antimicrobial susceptibility analyses using the bacteria identification/susceptibility system VITEK2 and E-tests. Capsular types of all isolates were determined by multiplex polymerase chain reaction. RESULTS We identified 778 pneumococcal isolates. Serotypes 19F, 6A/6B, 19A, 23F, and 15B/15C were the most prevalent strains, accounting for 71.5% (556/778) of all isolates. Data show that 409 (70.4%) isolates could be covered by the PCV13 vaccine in children less than 2 years old. Irrespective of serotypes, 747 (96%) isolates were sensitive to penicillin, while 720 to 778 (90% to 100%) isolates were not susceptible to erythromycin, tetracycline, and trimethoprim/sulfamethoxazole. For isolates resistant to penicillin, ceftriaxone, cefotaxime, and meropenem, 22 to 39 (70% to 81.25%) strains belonged to PCV13 serotypes. CONCLUSION We found a substantial increase in the annual number of pneumococcal isolates since 2014. The theoretical impact of PCV13 was high in children less than 2 years old, and penicillin might be effective against pneumococcal infections in this region.
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Affiliation(s)
- Meijing Shen
- Department of Laboratory Medicine, The Third Affiliated Hospital of Zunyi Medical University, Zunyi, China. E-mail.
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22
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Streptococcus pneumoniae Serotyping by a Single Polymerase Chain Reaction–Based Multiplex Assay. INFECTIOUS DISEASES IN CLINICAL PRACTICE 2018. [DOI: 10.1097/ipc.0000000000000554] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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23
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Gillis HD, Demczuk WHB, Griffith A, Martin I, Warhuus M, Lang ALS, ElSherif M, McNeil SA, LeBlanc JJ. PCR-based discrimination of emerging Streptococcus pneumoniae serotypes 22F and 33F. J Microbiol Methods 2017; 144:99-106. [PMID: 29162393 DOI: 10.1016/j.mimet.2017.11.017] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Revised: 11/17/2017] [Accepted: 11/17/2017] [Indexed: 11/30/2022]
Abstract
Serotyping of Streptococcus pneumoniae is important to monitor disease epidemiology and assess the impact of pneumococcal vaccines. Traditionally, the Quellung reaction used serotype-specific antibodies to classify S. pneumoniae based on differences in capsular antigens. More recently, PCR-based serotype deduction relying on serotype-specific capsule biosynthesis genes has been broadly applied for pneumococcal surveillance. However, PCR-based serotyping lacks discrimination for certain S. pneumoniae serotypes, including the differentiation of serotype 22F from 22A, and serotype 33F from 33A and 37. Serotypes 22F and 33F are emerging serotypes that are absent in the currently licensed 13-valent pneumococcal conjugate vaccine, but present in the new candidate 15-valent formulation. This study validated novel PCR reactions to detect and discriminate S. pneumoniae serotypes 22F and 33F. In order to differentiate S. pneumoniae serotypes 22F or 33F from genetically similar serotypes, two novel PCR reactions were designed and validated. The specificity of all PCR targets was evaluated using all 92 different S. pneumoniae serotypes, as well as 32 other streptococci. Reproducibility was evaluated using geographically and genetically diverse strains of S. pneumoniae serotypes 22F and 22A, or serotypes 33F, 33A, and 37 that were previously characterized by reputable reference laboratories. Overall, S. pneumoniae serotypes 22F and 33F could be accurately and reproducibly be detected and discriminated using PCR alone. Such a molecular serotyping approach provides a valuable diagnostic tool that is feasible in any molecular laboratory, to enable pneumococcal serotype surveillance and subsequent assessment of the impact of the new 15-valent candidate pneumococcal vaccine.
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Affiliation(s)
- Hayley D Gillis
- Canadian Center for Vaccinology (CCfV), Dalhousie University, Halifax, Nova Scotia (NS), Canada; Nova Scotia Health Authority (NSHA), Halifax, Nova Scotia (NS), Canada
| | | | - Averil Griffith
- National Microbiology Laboratory (NML), Winnipeg, MB, Canada
| | - Irene Martin
- National Microbiology Laboratory (NML), Winnipeg, MB, Canada
| | - Michelle Warhuus
- Canadian Center for Vaccinology (CCfV), Dalhousie University, Halifax, Nova Scotia (NS), Canada
| | - Amanda L S Lang
- Canadian Center for Vaccinology (CCfV), Dalhousie University, Halifax, Nova Scotia (NS), Canada; Nova Scotia Health Authority (NSHA), Halifax, Nova Scotia (NS), Canada
| | - May ElSherif
- Canadian Center for Vaccinology (CCfV), Dalhousie University, Halifax, Nova Scotia (NS), Canada; Nova Scotia Health Authority (NSHA), Halifax, Nova Scotia (NS), Canada
| | - Shelly A McNeil
- Canadian Center for Vaccinology (CCfV), Dalhousie University, Halifax, Nova Scotia (NS), Canada; Nova Scotia Health Authority (NSHA), Halifax, Nova Scotia (NS), Canada
| | - Jason J LeBlanc
- Canadian Center for Vaccinology (CCfV), Dalhousie University, Halifax, Nova Scotia (NS), Canada; Nova Scotia Health Authority (NSHA), Halifax, Nova Scotia (NS), Canada.
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24
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Kapatai G, Sheppard CL, Troxler LJ, Litt DJ, Furrer J, Hilty M, Fry NK. Pneumococcal 23B Molecular Subtype Identified Using Whole Genome Sequencing. Genome Biol Evol 2017; 9:2122-2135. [PMID: 28910966 PMCID: PMC5581491 DOI: 10.1093/gbe/evx092] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/09/2017] [Indexed: 01/20/2023] Open
Abstract
The polysaccharide capsule is a major virulence factor of Streptococcus pneumoniae and the target of all currently licensed pneumococcal vaccines. At present, there are 92 serologically distinct pneumococcal serotypes. Structural and antigenic variation of capsular types is the result of genetic variation within the capsular polysaccharide synthesis (CPS) locus; however, genetic variation may not always result in phenotypic differences which produce novel serotypes. With the introduction of high throughput whole genome sequencing, discovery of novel genotypic variants is not unexpected and this study describes a novel variant of the serotype 23B CPS operon. This novel variant was characterized as a novel genotypic subtype (23B1) with ∼70% homology to the published 23B CPS sequence. High sequence variability was determined in eight cps genes involved in sugar biosynthesis. However, there was no distinction between the classic 23B serotype and 23B1 serologically or in terms of polysaccharide structure. Phylogenetic and eBURST analysis revealed a distinct lineage for 23B1 with multiple clones (UK, Thailand, and USA) that arose at different points during pneumococcal evolution. Analysis of the UK S. pneumoniae isolates (n = 121) revealed an upsurge of 23B1 ST2372 in 2011, after which this previously unseen ST increased to reach 50% proportion of the 23B sequenced isolates from 2013 and remained prevalent within our sequenced isolates from later years. Therefore, although the 23B1 variant appears to have no phenotypic impact and cannot be considered as novel serotype, it appears to have led to a genetic restructuring of the UK serotype 23B population.
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Affiliation(s)
- Georgia Kapatai
- Respiratory and Vaccine Preventable Bacteria Reference Unit, Public Health England, National Infection Service, London, United Kingdom
| | - Carmen L Sheppard
- Respiratory and Vaccine Preventable Bacteria Reference Unit, Public Health England, National Infection Service, London, United Kingdom
| | - Lukas J Troxler
- Institute for Infectious Diseases, University of Bern, Switzerland
| | - David J Litt
- Respiratory and Vaccine Preventable Bacteria Reference Unit, Public Health England, National Infection Service, London, United Kingdom
| | - Julien Furrer
- Department of Chemistry and Biochemistry, University of Bern, Switzerland
| | - Markus Hilty
- Institute for Infectious Diseases, University of Bern, Switzerland.,Department of Infectious Diseases, Bern University Hospital, Inselspital, University of Bern, Switzerland
| | - Norman K Fry
- Respiratory and Vaccine Preventable Bacteria Reference Unit, Public Health England, National Infection Service, London, United Kingdom
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25
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Marimón JM, Morales M, Gamen S, Manrique A, Ercibengoa M, Cilla G. A reverse-hybridization test for the identification of 76 pneumococcal serotypes, 42 individually and 34 in pairs. J Microbiol Methods 2017; 143:13-16. [PMID: 28818600 DOI: 10.1016/j.mimet.2017.08.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Revised: 08/01/2017] [Accepted: 08/12/2017] [Indexed: 10/19/2022]
Abstract
The S. PneumoStrip test is a recently developed reverse hybridization strip-based commercial assay that allows for the identification of 76 pneumococcal serotypes, 42 individually and 34 in pairs, according to their specific gene sequences. The test was validated with reference strains of 92 different pneumococcal serotypes and with a selection of 75 clinical isolates representing 55 serotypes, showing 100% sensitivity and specificity. The test was also applied to 64 pneumococcal invasive isolates (23 different serotypes) consecutively collected between June 2016 and March 2017, with 60 (93.8%) being serotyped. Four isolates belonging to serotypes 13, 29, and 35B (2 isolates), which are not included in the test, did not produce a hybridization signal with serotype specific probes. The identification of most serotypes causing invasive pneumococcal disease together with the simplicity of performance and results interpretation, and the use of routine laboratory equipment make this test very suitable for most clinical and research laboratories.
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Affiliation(s)
- José M Marimón
- Microbiology Department, Hospital Universitario Donostia-Instituto de Investigación Sanitaria Biodonostia, San Sebastián, Spain; Biomedical Research Center Network for Respiratory Diseases (CIBERES), Madrid, Spain.
| | - María Morales
- Biomedical Research Center Network for Respiratory Diseases (CIBERES), Madrid, Spain
| | | | | | - María Ercibengoa
- Biomedical Research Center Network for Respiratory Diseases (CIBERES), Madrid, Spain
| | - Gustavo Cilla
- Microbiology Department, Hospital Universitario Donostia-Instituto de Investigación Sanitaria Biodonostia, San Sebastián, Spain; Biomedical Research Center Network for Respiratory Diseases (CIBERES), Madrid, Spain
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26
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Abundance and co-occurrence of extracellular capsules increase environmental breadth: Implications for the emergence of pathogens. PLoS Pathog 2017; 13:e1006525. [PMID: 28742161 PMCID: PMC5542703 DOI: 10.1371/journal.ppat.1006525] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Revised: 08/03/2017] [Accepted: 07/12/2017] [Indexed: 02/06/2023] Open
Abstract
Extracellular capsules constitute the outermost layer of many bacteria, are major virulence factors, and affect antimicrobial therapies. They have been used as epidemiological markers and recently became vaccination targets. Despite the efforts to biochemically serotype capsules in a few model pathogens, little is known of their taxonomic and environmental distribution. We developed, validated, and made available a computational tool, CapsuleFinder, to identify capsules in genomes. The analysis of over 2500 prokaryotic genomes, accessible in a database, revealed that ca. 50% of them—including Archaea—encode a capsule. The Wzx/Wzy-dependent capsular group was by far the most abundant. Surprisingly, a fifth of the genomes encode more than one capsule system—often from different groups—and their non-random co-occurrence suggests the existence of negative and positive epistatic interactions. To understand the role of multiple capsules, we queried more than 6700 metagenomes for the presence of species encoding capsules and showed that their distribution varied between environmental categories and, within the human microbiome, between body locations. Species encoding capsules, and especially those encoding multiple capsules, had larger environmental breadths than the other species. Accordingly, capsules were more frequent in environmental bacteria than in pathogens and, within the latter, they were more frequent among facultative pathogens. Nevertheless, capsules were frequent in clinical samples, and were usually associated with fast-growing bacteria with high infectious doses. Our results suggest that capsules increase the environmental range of bacteria and make them more resilient to environmental perturbations. Capsules might allow opportunistic pathogens to profit from empty ecological niches or environmental perturbations, such as those resulting from antibiotic therapy, to colonize the host. Capsule-associated virulence might thus be a by-product of environmental adaptation. Understanding the role of capsules in natural environments might enlighten their function in pathogenesis. Extracellular capsules protect bacterial cells from external aggressions such as antibiotics or desiccation, but can also be targeted by vaccines. Since little was known about their frequency across Prokaryotes, we created and made freely available a computational tool, CapsuleFinder, to identify them from genomic data. Surprisingly, its use showed that many bacterial strains, especially those with the largest genomes, encode several capsules. The frequencies of the different combinations of capsule groups depended strongly on the phyla and the groups themselves, suggesting the existence of epistatic interactions between capsules. Bacteria encoding capsule systems were found in many natural environments, and were frequent in the human microbiome. In contrast to their frequent association with virulence, we found many more capsules in non-pathogens or facultative pathogens than among obligatory pathogens. We suggest that capsules increase the environmental breadth of bacteria thereby facilitating host colonization by opportunistic pathogens.
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27
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Nagaraj G, Ganaie F, Govindan V, Ravikumar KL. Development of PCRSeqTyping-a novel molecular assay for typing of Streptococcus pneumoniae. Pneumonia (Nathan) 2017; 9:8. [PMID: 28702310 PMCID: PMC5471960 DOI: 10.1186/s41479-017-0032-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Accepted: 05/01/2017] [Indexed: 11/25/2022] Open
Abstract
Background Precise serotyping of pneumococci is essential for vaccine development, to better understand the pathogenicity and trends of drug resistance. Currently used conventional and molecular methods of serotyping are expensive and time-consuming, with limited coverage of serotypes. An accurate and rapid serotyping method with complete coverage of serotypes is an urgent necessity. This study describes the development and application of a novel technology that addresses this need. Methods Polymerase chain reaction (PCR) was performed, targeting 1061 bp cpsB region, and the amplicon was subjected to sequencing. The sequence data was analyzed using the National Centre for Biotechnology Information database. For homologous strains, a second round of PCR, sequencing, and data analysis was performed targeting 10 group-specific genes located in the capsular polysaccharide region. Ninety-one pneumococcal reference strains were analyzed with PCRSeqTyping and compared with Quellung reaction using Pneumotest Kit (SSI, Denmark). Results A 100% correlation of PCRSeqTyping results was observed with Pneumotest results. Fifty-nine reference strains were uniquely identified in the first step of PCRSeqTyping. The remaining 32 homologous strains out of 91 were also uniquely identified in the second step. Conclusion This study describes a PCRSeqTyping assay that is accurate and rapid, with high reproducibility. This assay is amenable for clinical testing and does not require culturing of the samples. It is a significant improvement over other methods because it covers all pneumococcal serotypes, and it has the potential for use in diagnostic laboratories and surveillance studies.
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Affiliation(s)
- Geetha Nagaraj
- Central Research Laboratory, KIMS Hospital and Research Centre, KR Road, VV Purum, Bangalore, Karnataka 560 004 India
| | - Feroze Ganaie
- Central Research Laboratory, KIMS Hospital and Research Centre, KR Road, VV Purum, Bangalore, Karnataka 560 004 India
| | - Vandana Govindan
- Central Research Laboratory, KIMS Hospital and Research Centre, KR Road, VV Purum, Bangalore, Karnataka 560 004 India
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28
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Diamantino-Miranda J, Aguiar SI, Carriço JA, Melo-Cristino J, Ramirez M. Clonal and serotype dynamics of serogroup 6 isolates causing invasive pneumococcal disease in Portugal: 1999-2012. PLoS One 2017; 12:e0170354. [PMID: 28152029 PMCID: PMC5289433 DOI: 10.1371/journal.pone.0170354] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Accepted: 01/03/2017] [Indexed: 11/18/2022] Open
Abstract
Although serogroup 6 was among the first to be recognized among Streptococcus pneumoniae, several new serotypes were identified since the introduction of pneumococcal conjugate vaccines (PCVs). A decrease of the 6B-2 variant among invasive pneumococcal disease (IPD), but not 6B-1, was noted post conjugate vaccine introduction, underpinned by a decrease of CC273 isolates. Serotype 6C was associated with adult IPD and increased in this age group representing two lineages (CC315 and CC395), while the same lineages expressed other serogroup 6 serotypes in children. Taken together, these findings suggest a potential cross-protection of PCVs against serotype 6C IPD among vaccinated children but not among adults. Serotype 6A became the most important serogroup 6 serotype in children but it decreased in adult IPD. No other serogroup 6 serotypes were detected, so available phenotypic or simple genotypic assays remain adequate for distinguishing serotypes within serogroup 6 isolates.
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Affiliation(s)
- Jorge Diamantino-Miranda
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Av. Prof. Egas Moniz, Lisboa, Portugal
| | - Sandra Isabel Aguiar
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Av. Prof. Egas Moniz, Lisboa, Portugal
| | - João André Carriço
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Av. Prof. Egas Moniz, Lisboa, Portugal
| | - José Melo-Cristino
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Av. Prof. Egas Moniz, Lisboa, Portugal
| | - Mário Ramirez
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Av. Prof. Egas Moniz, Lisboa, Portugal
- * E-mail:
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29
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Park C, Kwon EY, Choi SM, Cho SY, Byun JH, Park JY, Lee DG, Kang JH, Shin J, Kim H. Comparative evaluation of a newly developed 13-valent pneumococcal conjugate vaccine in a mouse model. Hum Vaccin Immunother 2016; 13:1169-1176. [PMID: 27960627 PMCID: PMC5443391 DOI: 10.1080/21645515.2016.1261772] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Animal models facilitate evaluation of vaccine efficacy at relatively low cost. This study was a comparative evaluation of the immunogenicity and protective efficacy of a new 13-valent pneumococcal conjugate vaccine (PCV13) with a control vaccine in a mouse model. After vaccination, anti-capsular antibody levels were evaluated by pneumococcal polysaccharide (PnP) enzyme-linked immunosorbent assay (ELISA) and opsonophagocytic killing assay (OPA). Also, mice were challenged intraperitoneally with 100-fold of the 50% lethal dose of Streptococcus pneumoniae. The anti-capsular IgG levels against serotypes 1, 4, 7F, 14, 18C, 19A, and 19F were high (quartile 2 >1,600), while those against the other serotypes were low (Q2 ≤ 800). Also, the OPA titres were similar to those determined by PnP ELISA. Comparative analysis between new PCV13 and control vaccination group in a mouse model exhibited significant differences in serological immunity of a few serotypes and the range of anti-capsular IgG in the population. Challenge of wild-type or neutropenic mice with serotypes 3, 5, 6A, 6B, and 9V showed protective immunity despite of induced relatively low levels of anti-capsular antibodies. With comparison analysis, a mouse model should be adequate for evaluating serological efficacy and difference in the population level as preclinical trial.
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Affiliation(s)
- Chulmin Park
- a Vaccine Bio Research Institute , College of Medicine, The Catholic University of Korea , Seoul , the Republic of Korea
| | - Eun-Young Kwon
- a Vaccine Bio Research Institute , College of Medicine, The Catholic University of Korea , Seoul , the Republic of Korea
| | - Su-Mi Choi
- b Division of Infectious Diseases , Department of Internal Medicine, College of Medicine, The Catholic University of Korea , Seoul , the Republic of Korea
| | - Sung-Yeon Cho
- a Vaccine Bio Research Institute , College of Medicine, The Catholic University of Korea , Seoul , the Republic of Korea.,b Division of Infectious Diseases , Department of Internal Medicine, College of Medicine, The Catholic University of Korea , Seoul , the Republic of Korea
| | - Ji-Hyun Byun
- a Vaccine Bio Research Institute , College of Medicine, The Catholic University of Korea , Seoul , the Republic of Korea
| | - Jung Yeon Park
- a Vaccine Bio Research Institute , College of Medicine, The Catholic University of Korea , Seoul , the Republic of Korea
| | - Dong-Gun Lee
- a Vaccine Bio Research Institute , College of Medicine, The Catholic University of Korea , Seoul , the Republic of Korea.,b Division of Infectious Diseases , Department of Internal Medicine, College of Medicine, The Catholic University of Korea , Seoul , the Republic of Korea
| | - Jin Han Kang
- a Vaccine Bio Research Institute , College of Medicine, The Catholic University of Korea , Seoul , the Republic of Korea.,c Department of Pediatrics , College of Medicine, The Catholic University of Korea , Seoul , the Republic of Korea
| | - Jinhwan Shin
- d School of Pharmacy , Sungkyunkwan University , Suwon , the Republic of Korea.,e SK Chemicals Co. Ltd ., Seongnam , Gynuggi-do , the Republic of Korea
| | - Hun Kim
- e SK Chemicals Co. Ltd ., Seongnam , Gynuggi-do , the Republic of Korea
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30
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Kapatai G, Sheppard CL, Al-Shahib A, Litt DJ, Underwood AP, Harrison TG, Fry NK. Whole genome sequencing of Streptococcus pneumoniae: development, evaluation and verification of targets for serogroup and serotype prediction using an automated pipeline. PeerJ 2016; 4:e2477. [PMID: 27672516 PMCID: PMC5028725 DOI: 10.7717/peerj.2477] [Citation(s) in RCA: 99] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Accepted: 08/23/2016] [Indexed: 11/25/2022] Open
Abstract
Streptococcus pneumoniae typically express one of 92 serologically distinct capsule polysaccharide (cps) types (serotypes). Some of these serotypes are closely related to each other; using the commercially available typing antisera, these are assigned to common serogroups containing types that show cross-reactivity. In this serotyping scheme, factor antisera are used to allocate serotypes within a serogroup, based on patterns of reactions. This serotyping method is technically demanding, requires considerable experience and the reading of the results can be subjective. This study describes the analysis of the S. pneumoniae capsular operon genetic sequence to determine serotype distinguishing features and the development, evaluation and verification of an automated whole genome sequence (WGS)-based serotyping bioinformatics tool, PneumoCaT (Pneumococcal Capsule Typing). Initially, WGS data from 871 S. pneumoniae isolates were mapped to reference cps locus sequences for the 92 serotypes. Thirty-two of 92 serotypes could be unambiguously identified based on sequence similarities within the cps operon. The remaining 60 were allocated to one of 20 ‘genogroups’ that broadly correspond to the immunologically defined serogroups. By comparing the cps reference sequences for each genogroup, unique molecular differences were determined for serotypes within 18 of the 20 genogroups and verified using the set of 871 isolates. This information was used to design a decision-tree style algorithm within the PneumoCaT bioinformatics tool to predict to serotype level for 89/94 (92 + 2 molecular types/subtypes) from WGS data and to serogroup level for serogroups 24 and 32, which currently comprise 2.1% of UK referred, invasive isolates submitted to the National Reference Laboratory (NRL), Public Health England (June 2014–July 2015). PneumoCaT was evaluated with an internal validation set of 2065 UK isolates covering 72/92 serotypes, including 19 non-typeable isolates and an external validation set of 2964 isolates from Thailand (n = 2,531), USA (n = 181) and Iceland (n = 252). PneumoCaT was able to predict serotype in 99.1% of the typeable UK isolates and in 99.0% of the non-UK isolates. Concordance was evaluated in UK isolates where further investigation was possible; in 91.5% of the cases the predicted capsular type was concordant with the serologically derived serotype. Following retesting, concordance increased to 99.3% and in most resolved cases (97.8%; 135/138) discordance was shown to be caused by errors in original serotyping. Replicate testing demonstrated that PneumoCaT gave 100% reproducibility of the predicted serotype result. In summary, we have developed a WGS-based serotyping method that can predict capsular type to serotype level for 89/94 serotypes and to serogroup level for the remaining four. This approach could be integrated into routine typing workflows in reference laboratories, reducing the need for phenotypic immunological testing.
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Affiliation(s)
- Georgia Kapatai
- Respiratory and Vaccine Preventable Bacterial Reference Unit, Public Health England, London, United Kingdom
| | - Carmen L Sheppard
- Respiratory and Vaccine Preventable Bacterial Reference Unit, Public Health England, London, United Kingdom
| | - Ali Al-Shahib
- Infectious Disease Informatics, Public Health England, London, United Kingdom
| | - David J Litt
- Respiratory and Vaccine Preventable Bacterial Reference Unit, Public Health England, London, United Kingdom
| | - Anthony P Underwood
- Infectious Disease Informatics, Public Health England, London, United Kingdom
| | - Timothy G Harrison
- Respiratory and Vaccine Preventable Bacterial Reference Unit, Public Health England, London, United Kingdom
| | - Norman K Fry
- Respiratory and Vaccine Preventable Bacterial Reference Unit, Public Health England, London, United Kingdom
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Gharailoo Z, Mousavi SF, Halvani N, Feizabadi MM. Antimicrobial Resistant Pattern and Capsular Typing of Streptococcus Pneumoniae Isolated from Children in Sistan -Baluchestan. MAEDICA 2016; 11:203-207. [PMID: 28694854 PMCID: PMC5486161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
BACKGROUND Ankyloglossia is an anatomic developmental anomaly determining by thick and short, fi brotic ferenum. Tongue changes have severe eff ects on occlusion and oropharyngeal structures. The aim of this study was to evaluate the position of hyoid in children 7-11 years` old with ankyloglossia in lateral cephalometric radiographs. MATERIALS AND METHOD In this study 260 nasopharyngeal swabs were taken from non-vaccinated healthy children between 6 months to 6 years old at medical centers in Sistan-Baluchestan during August 2013 to January 2014. These samples were cultured on blood agar. Primary identifi cation of bacterial isolated was determined by biochemical analysis and molecular tests. Capsular typing was performed by Multiplex PCR using primers targeting cps locus that is highly conserved among diff erent capsular types. The master mixes for PCR were grouped them into six multiplex reactions. RESULTS Out of 260 nasopharyngeal swabs, 42 isolates of Streptococcus pneumoniae were detected and identifi ed. The overall pneumococcal carriage rate was 16.1%. The most frequently isolated capsular types were: 6A/B, 19A, 19F and 23F. These capsular types accounted for 49.9% of all strains detected. CONCLUSION We found that the prevalence of pneumococcal carriage among non-vaccinated children under six years old is about 16%. Our study provides much data about carriage rate and pneumococcal capsular types in preschool children, which is necessary for predicting the diff erent valent pneumococcal conjugated vaccines in Iran.
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Affiliation(s)
- Zahra Gharailoo
- Department of Microbiology, School of Medicine, Tehran University of Medical Science, Tehran, Iran
| | - Seyed Fazlollah Mousavi
- Department of Bacteriology and Microbiology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Niloofar Halvani
- Faculty of Dentistry, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | - Mohammad Mehdi Feizabadi
- Department of Microbiology, School of Medicine, Tehran University of Medical Science, Tehran, Iran
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Application of capsular sequence typing (CST) to serotype non-viable Streptococcus pneumoniae isolates from an old collection. Eur J Clin Microbiol Infect Dis 2016; 35:2025-2031. [PMID: 27580910 DOI: 10.1007/s10096-016-2755-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Accepted: 08/09/2016] [Indexed: 10/21/2022]
Abstract
Serotyping of Streptococcus pneumoniae is essential for monitoring changes in the pneumococcal population and the impact of vaccines. Recently, various DNA-based methods have become available and are increasingly used because they are cheaper and easier to perform than the Quellung reaction. Our aim was to apply a DNA-based method, capsular sequence typing (CST), to a collection of non-viable lyophilized pneumococcal isolates dating from the 1980s to elucidate the serotypes circulating in Italy 30 years ago. As a preliminary evaluation of the method, CST was applied to 68 recent pneumococcal isolates representative of the most common serotypes circulating in Italy in invasive pneumococcal disease (IPD) previously serotyped by the Quellung reaction. CST was then applied to 132 lyophilized non-viable isolates. A serotype-specific polymerase chain reaction (PCR), using primers suggested by the Centers for Disease Control and Prevention (CDC), was performed when CST did not yield a univocal serotype. Considering the control isolates, CST concordance with the Quellung reaction was 95.6 %. For the non-viable lyophilized isolates, CST identified a univocal serotype for 59.4 % of the isolates. This percentage increased to 78.1 % if CST was combined with serotype-specific PCR. The most frequent serotypes in the collection of non-viable strains were: 3 (15.6 %), 14 (11.7 %), 35B (5.5 %), 19A (5.5 %), and 8 (4.7 %). CST proved to be a valid method for serotyping pneumococcal strains and provided information about pneumococcal serotypes present in Italy 30 years ago. The combination of CST with serotype-specific PCR was an effective strategy to identify pneumococcal serotypes that can be suggested also for routine laboratories.
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The blp Locus of Streptococcus pneumoniae Plays a Limited Role in the Selection of Strains That Can Cocolonize the Human Nasopharynx. Appl Environ Microbiol 2016; 82:5206-15. [PMID: 27316956 DOI: 10.1128/aem.01048-16] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Accepted: 06/10/2016] [Indexed: 12/18/2022] Open
Abstract
UNLABELLED Nasopharyngeal colonization is important for Streptococcus pneumoniae evolution, providing the opportunity for horizontal gene transfer when multiple strains co-occur. Although colonization with more than one strain of pneumococcus is common, the factors that influence the ability of strains to coexist are not known. A highly variable blp (bacteriocin-like peptide) locus has been identified in all sequenced strains of S. pneumoniae This locus controls the regulation and secretion of bacteriocins, small peptides that target other bacteria. In this study, we analyzed a series of cocolonizing isolates to evaluate the impact of the blp locus on human colonization to determine whether competitive phenotypes of bacteriocin secretion restrict cocolonization. We identified a collection of 135 nasopharyngeal samples cocolonized with two or more strains, totaling 285 isolates. The blp locus of all strains was characterized genetically with regard to pheromone type, bacteriocin/immunity content, and potential for locus functionality. Inhibitory phenotypes of bacteriocin secretion and locus activity were assessed through overlay assays. Isolates from single colonizations (n = 298) were characterized for comparison. Cocolonizing strains had a high diversity of blp cassettes; approximately one-third displayed an inhibitory phenotype in vitro Despite in vitro evidence of competition, pneumococci cocolonized the subjects independently of blp pheromone type (P = 0.577), bacteriocin/immunity content, blp locus activity (P = 0.798), and inhibitory phenotype (P = 0.716). In addition, no significant differences were observed when single and cocolonizing strains were compared. Despite clear evidence of blp-mediated competition in experimental models, the results of our study suggest that the blp locus plays a limited role in restricting pneumococcal cocolonization in humans. IMPORTANCE Nasopharyngeal colonization with Streptococcus pneumoniae (pneumococcus) is important for pneumococcal evolution, as the nasopharynx represents the major site for horizontal gene transfer when multiple strains co-occur, a phenomenon known as cocolonization. Understanding how pneumococcal strains interact within the competitive environment of the nasopharynx is of chief importance in the context of pneumococcal ecology. In this study, we used an unbiased collection of naturally co-occurring pneumococcal strains and showed that a biological process frequently used by bacteria for competition-bacteriocin production-is not decisive in the coexistence of pneumococci in the host, in contrast to what has been shown in experimental models.
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Single-Step Multiplex PCR Assay for Determining 92 Pneumococcal Serotypes. J Clin Microbiol 2016; 54:2197-200. [PMID: 27280423 DOI: 10.1128/jcm.01156-16] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Accepted: 06/03/2016] [Indexed: 12/31/2022] Open
Abstract
For pneumococcal disease surveillance, simple and cost-effective methods capable of determining all serotypes are needed. Combining a single-tube multiplex PCR with fluorescently labeled primers followed by amplicon analysis using automated fluorescent capillary electrophoresis, each serotype of 92 reference isolates and 297 recently collected clinical isolates was successfully determined.
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Bahy RH, Hamouda HM, Shahat AS, Yassin AS, Amin MA. Emergence of Neoteric Serotypes Among Multidrug Resistant Strains of Streptococcus pneumoniae Prevalent in Egypt. Jundishapur J Microbiol 2016; 9:e30708. [PMID: 27303614 PMCID: PMC4902850 DOI: 10.5812/jjm.30708] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2015] [Revised: 01/25/2016] [Accepted: 02/13/2016] [Indexed: 01/30/2023] Open
Abstract
Background Streptococcus pneumoniae is still one of the major causes of morbidity and mortality worldwide. The prevalent serotype distribution had shown variation along different studies conducted at different time intervals. In order to efficiently assess the epidemiology of the diseases for effective preventive and treatment strategies, serotype prevalence need to be periodically reassessed. Objectives Conducting a reassessment of the prevalent S. pneumoniae serotypes in Egypt as an essential step in the search for a regional vaccine. In addition, monitoring the antibiotic susceptibility patterns of pneumococcal strains currently causing infections as an evaluation of therapeutic strategies applied. Materials and Methods A total of 100 specimens of different sources were collected in Cairo, Egypt, from 2011 to 2013, representing almost all different types of diseases caused by S. pneumoniae such as meningitis, pneumonia, otitis media and sinusitis. Conventional and molecular identification methods were performed, the antimicrobial susceptibility patterns were assessed and serotyping was done using PCR assays to identify the most prevalent types. In addition, detection of certain virulence genes for the most prevalent serotypes was carried out. Results Our results revealed that in Egypt, currently, the most prevalent serotypes were serogroup 6 and serotype 19F as they represented 58% of all isolates. High rates of resistance were found to different antibiotic classes. The lytA and psaA genes were found to be more sensitive for S. pneumoniae identification than ply. Conclusions Our study illustrates the importance of constantly monitoring the prevalent serotypes in any region in order to aid in the development of more effective vaccines.
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Affiliation(s)
- Rehab H Bahy
- Department of Microbiology, National Organization for Drug Control and Research, Giza, Egypt
| | - Hayam M Hamouda
- Department of Microbiology, National Organization for Drug Control and Research, Giza, Egypt
| | - Amal S Shahat
- Department of Biochemistry, National Organization for Drug Control and Research (NODCAR), Giza, Egypt
| | - Aymen S Yassin
- Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Cairo, Egypt
- Corresponding author: Aymen S Yassin, Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Cairo, Egypt. Tel: +20-1009610341, Fax: +20-23620122. E-mail:
| | - Magdy A Amin
- Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Cairo, Egypt
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Simões AS, Tavares DA, Rolo D, Ardanuy C, Goossens H, Henriques-Normark B, Linares J, de Lencastre H, Sá-Leão R. lytA-based identification methods can misidentify Streptococcus pneumoniae. Diagn Microbiol Infect Dis 2016; 85:141-8. [PMID: 27107535 DOI: 10.1016/j.diagmicrobio.2016.03.018] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Revised: 02/19/2016] [Accepted: 03/20/2016] [Indexed: 02/01/2023]
Abstract
During surveillance studies we detected, among over 1500 presumptive pneumococci, 11 isolates displaying conflicting or novel results when characterized by widely accepted phenotypic (optochin susceptibility and bile solubility) and genotypic (lytA-BsaAI-RFLP and MLST) identification methods. We aimed to determine the genetic basis for the unexpected results given by lytA-BsaAI-RFLP and investigate the accuracy of the WHO recommended lytA real-time PCR assay to classify these 11 isolates. Three novel lytA-BsaAI-RFLP signatures were found (one in pneumococcus and two in S. mitis). In addition, one pneumococcus displayed the atypical lytA-BsaAI-RFLP signature characteristic of non-pneumococci and two S. pseudopneumoniae displayed the typical lytA-BsaAI-RFLP pattern characteristic of pneumococci. lytA real-time PCR misidentified these three isolates. In conclusion, identification of pneumococci by lytA real-time PCR, and other lytA-based methodologies, may lead to false results. This is of particular relevance in the increasingly frequent colonization studies relying solely on culture-independent methods.
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Affiliation(s)
- Alexandra S Simões
- Laboratory of Molecular Microbiology of Human Pathogens, Instituto de Tecnologia Química e Biológica António Xavier (ITQB), Universidade Nova de Lisboa (UNL), Oeiras, Portugal
| | - Débora A Tavares
- Laboratory of Molecular Microbiology of Human Pathogens, Instituto de Tecnologia Química e Biológica António Xavier (ITQB), Universidade Nova de Lisboa (UNL), Oeiras, Portugal
| | - Dora Rolo
- Microbiology Department, Hospital Universitari de Bellvitge, Universitat de Barcelona-IDIBELL, L'Hospitalet de Llobregat, Barcelona, Spain; CIBERES (Ciber de Enfermedades Respiratorias), ISCIII, Madrid, Spain
| | - Carmen Ardanuy
- Microbiology Department, Hospital Universitari de Bellvitge, Universitat de Barcelona-IDIBELL, L'Hospitalet de Llobregat, Barcelona, Spain; CIBERES (Ciber de Enfermedades Respiratorias), ISCIII, Madrid, Spain
| | - Herman Goossens
- Department of Medical Microbiology, University of Antwerp, Antwerp, Belgium; Vaccine and Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
| | - Birgitta Henriques-Normark
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden; Department of Laboratory Medicine, Division of Clinical Microbiology, Karolinska University Hospital, Stockholm, Sweden
| | - Josefina Linares
- Microbiology Department, Hospital Universitari de Bellvitge, Universitat de Barcelona-IDIBELL, L'Hospitalet de Llobregat, Barcelona, Spain; CIBERES (Ciber de Enfermedades Respiratorias), ISCIII, Madrid, Spain
| | - Hermínia de Lencastre
- Laboratory of Molecular Genetics, ITQB, UNL, Oeiras, Portugal; Laboratory of Microbiology and Infectious Diseases, The Rockefeller University, New York, NY, USA
| | - Raquel Sá-Leão
- Laboratory of Molecular Microbiology of Human Pathogens, Instituto de Tecnologia Química e Biológica António Xavier (ITQB), Universidade Nova de Lisboa (UNL), Oeiras, Portugal.
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Messaoudi M, Milenkov M, Albrich WC, van der Linden MPG, Bénet T, Chou M, Sylla M, Barreto Costa P, Richard N, Klugman KP, Endtz HP, Paranhos-Baccalà G, Telles JN. The Relevance of a Novel Quantitative Assay to Detect up to 40 Major Streptococcus pneumoniae Serotypes Directly in Clinical Nasopharyngeal and Blood Specimens. PLoS One 2016; 11:e0151428. [PMID: 26986831 PMCID: PMC4795784 DOI: 10.1371/journal.pone.0151428] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Accepted: 02/28/2016] [Indexed: 12/25/2022] Open
Abstract
For epidemiological and surveillance purposes, it is relevant to monitor the distribution and dynamics of Streptococcus pneumoniae serotypes. Conventional serotyping methods do not provide rapid or quantitative information on serotype loads. Quantitative serotyping may enable prediction of the invasiveness of a specific serotype compared to other serotypes carried. Here, we describe a novel, rapid multiplex real-time PCR assay for identification and quantification of the 40 most prevalent pneumococcal serotypes and the assay impacts in pneumonia specimens from emerging and developing countries. Eleven multiplex PCR to detect 40 serotypes or serogroups were optimized. Quantification was enabled by reference to standard dilutions of known bacterial load. Performance of the assay was evaluated to specifically type and quantify S. pneumoniae in nasopharyngeal and blood samples from adult and pediatric patients hospitalized with pneumonia (n = 664) from five different countries. Serogroup 6 was widely represented in nasopharyngeal specimens from all five cohorts. The most frequent serotypes in the French, South African, and Brazilian cohorts were 1 and 7A/F, 3 and 19F, and 14, respectively. When both samples were available, the serotype in blood was always present as carriage with other serotypes in the nasopharynx. Moreover, the ability of a serotype to invade the bloodstream may be linked to its nasopharyngeal load. The mean nasopharyngeal concentration of the serotypes that moved to the blood was 3 log-fold higher than the ones only found in the nasopharynx. This novel, rapid, quantitative assay may potentially predict some of the S. pneumoniae serotypes invasiveness and assessment of pneumococcal serotype distribution.
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Affiliation(s)
- Melina Messaoudi
- Emerging Pathogens Laboratory, Fondation Mérieux - Centre International de Recherche en Infectiologie (CIRI), Lyon, France
| | - Milen Milenkov
- Emerging Pathogens Laboratory, Fondation Mérieux - Centre International de Recherche en Infectiologie (CIRI), Lyon, France
| | - Werner C. Albrich
- Department of Infectious Diseases and Hospital Epidemiology, Kantonsspital St. Gallen, St. Gallen, Switzerland
- Medical Research Council Respiratory and Meningeal Pathogens Research Unit, University of the Witwatersrand, Johannesburg, South Africa
| | - Mark P. G. van der Linden
- National Reference Center for Streptococci, Institute of Medical Microbiology, University Hospital RWTH Aachen, Aachen, Germany
| | - Thomas Bénet
- Service d'Hygiène, Epidémiologie et Prévention, Hôpital Edouard Herriot - Hospices Civils de Lyon, France
| | - Monidarin Chou
- Faculty of Pharmacy, University of Health Sciences, Phnom Penh, Cambodia
| | | | - Patricia Barreto Costa
- Laboratório de vírus respiratórios e do sarampo, Instituto Oswaldo Cruz/Fiocruz, Rio de Janeiro, Brazil
| | - Nathalie Richard
- Service de Réanimation Pédiatrique Médico-Chirurgicale, HFME, Groupement Hospitalier Est, Bron, France
| | - Keith P. Klugman
- Medical Research Council Respiratory and Meningeal Pathogens Research Unit, University of the Witwatersrand, Johannesburg, South Africa
- Hubert Department of Global Health and Division of Infectious Diseases, Emory University, Atlanta, Georgia, United States of America
| | - Hubert P. Endtz
- Emerging Pathogens Laboratory, Fondation Mérieux - Centre International de Recherche en Infectiologie (CIRI), Lyon, France
- Departement of Medical Microbiology & Infectious Diseases Erasmus MC, Rotterdam, The Netherlands
| | - Gláucia Paranhos-Baccalà
- Emerging Pathogens Laboratory, Fondation Mérieux - Centre International de Recherche en Infectiologie (CIRI), Lyon, France
| | - Jean-Noël Telles
- Emerging Pathogens Laboratory, Fondation Mérieux - Centre International de Recherche en Infectiologie (CIRI), Lyon, France
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Abstract
Streptococcus pneumoniae (the pneumococcus) is an important human pathogen. Its virulence is largely due to its polysaccharide capsule, which shields it from the host immune system, and because of this, the capsule has been extensively studied. Studies of the capsule led to the identification of DNA as the genetic material, identification of many different capsular serotypes, and identification of the serotype-specific nature of protection by adaptive immunity. Recent studies have led to the determination of capsular polysaccharide structures for many serotypes using advanced analytical technologies, complete elucidation of genetic basis for the capsular types, and the development of highly effective pneumococcal conjugate vaccines. Conjugate vaccine use has altered the serotype distribution by either serotype replacement or switching, and this has increased the need to serotype pneumococci. Due to great advances in molecular technologies and our understanding of the pneumococcal genome, molecular approaches have become powerful tools to predict pneumococcal serotypes. In addition, more-precise and -efficient serotyping methods that directly detect polysaccharide structures are emerging. These improvements in our capabilities will greatly enhance future investigations of pneumococcal epidemiology and diseases and the biology of colonization and innate immunity to pneumococcal capsules.
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Epidemiological analysis of pneumococcal serotype 19A in healthy children following PCV7 vaccination. Epidemiol Infect 2015; 144:1563-73. [PMID: 26548594 DOI: 10.1017/s0950268815002757] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
After the introduction of conjugate vaccines, a strong rearrangement of pneumococcal serotypes was observed globally. Probably most concerning was the emergence of serotype 19A, which has not only high invasive disease potential, but also high antibiotic resistance. In the current study we focused on the increased prevalence of serotype 19A after the PCV vaccination rate became widely used in Hungary. A total of 2262 children aged 3-6 years were screened for pneumococcus carriage using nasal swabs. Children were divided into two groups according to the vaccination rates, low level (group 1) vs. high level (group 2). While the carriage rate did not change over time (average 32·9%), the serotype distribution differed greatly in the two groups. The prevalence of serotype 19A increased >eightfold. Almost all 19A isolates had high-level macrolide resistance and elevated penicillin minimum inhibitory concentrations. Genotyping methods revealed that these new 19A isolates are different from the previously frequent Hungary19A-6 PMEN clone. Both the carriage rate and the overall penicillin and macrolide resistance remained stable over time, but while several serotypes were represented in group 1, serotype 19A alone was clearly dominant in group 2.
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Dube FS, van Mens SP, Robberts L, Wolter N, Nicol P, Mafofo J, Africa S, Zar HJ, Nicol MP. Comparison of a Real-Time Multiplex PCR and Sequetyping Assay for Pneumococcal Serotyping. PLoS One 2015; 10:e0137349. [PMID: 26335454 PMCID: PMC4559314 DOI: 10.1371/journal.pone.0137349] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2015] [Accepted: 08/14/2015] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Pneumococcal serotype identification is essential to monitor pneumococcal vaccine effectiveness and serotype replacement. Serotyping by conventional serological methods are costly, labour-intensive, and require significant technical expertise. We compared two different molecular methods to serotype pneumococci isolated from the nasopharynx of South African infants participating in a birth cohort study, the Drakenstein Child Health Study, in an area with high 13-valent pneumococcal conjugate vaccine (PCV13) coverage. METHODS A real-time multiplex PCR (rmPCR) assay detecting 21 different serotypes/-groups and a sequetyping assay, based on the sequence of the wzh gene within the pneumococcal capsular locus, were compared. Forty pneumococcal control isolates, with serotypes determined by the Quellung reaction, were tested. In addition, 135 pneumococcal isolates obtained from the nasopharynx of healthy children were tested by both serotyping assays and confirmed by Quellung testing. Discordant results were further investigated by whole genome sequencing of four isolates. RESULTS Of the 40 control isolates tested, 25 had a serotype covered by the rmPCR assay. These were all correctly serotyped/-grouped. Sequetyping PCR failed in 7/40 (18%) isolates. For the remaining isolates, sequetyping assigned the correct serotype/-group to 29/33 (88%) control isolates. Of the 132/135 (98%) nasopharyngeal pneumococcal isolates that could be typed, 69/132 (52%) and 112/132 (85%) were assigned the correct serotype/-group by rmPCR and sequetyping respectively. The serotypes of 63/132 (48%) isolates were not included in the rmPCR panel. All except three isolates (serotype 25A and 38) were theoretically amplified and differentiated into the correct serotype/-group with some strains giving ambigous results (serotype 13/20, 17F/33C, and 11A/D/1818F). Of the pneumococcal serotypes detected in this study, 69/91 (76%) were not included in the current PCV13. The most frequently identified serotypes were 11A, 13, 15B/15C, 16F and 10A. CONCLUSION The rmPCR assay performed well for the 21 serotypes/-groups included in the assay. However, in our study setting, a large proportion of serotypes were not detected by rmPCR. The sequetyping assay performed well, but did misassign specific serotypes. It may be useful for regions where vaccine serotypes are less common, however confirmatory testing is advisable.
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Affiliation(s)
- Felix S. Dube
- Division of Medical Microbiology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Suzan P. van Mens
- Division of Medical Microbiology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
- Department of Medical Microbiology and Immunology, St Antonius Hospital, Nieuwegein, the Netherlands
| | - Lourens Robberts
- Division of Medical Microbiology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Nicole Wolter
- Centre for Respiratory Diseases and Meningitis (CRDM), National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
- School of Pathology, Faculty of Health Sciences, University of the Witswatersrand, Johannesburg, South Africa
| | - Paul Nicol
- The State Agricultural Biotechnology Centre, Murdoch University, Murdoch, Australia
| | - Joseph Mafofo
- Centre for Proteomic and Genomic Research (CPGR), Cape Town, South Africa
| | - Samantha Africa
- Division of Medical Microbiology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Heather J. Zar
- Department of Paediatrics and Child Health, Red Cross War Memorial Children’s Hospital, Cape Town, South Africa
- MRC Unit on Child and Adolesscent Health, University of Cape Town, Cape Town, South Africa
| | - Mark P. Nicol
- Division of Medical Microbiology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
- National Health Laboratory Service, Groote Schuur Hospital, Cape Town, South Africa
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Marimón JM, Morales M, Cilla G, Vicente D, Pérez-Trallero E. Detection of bacteria and viruses in the pleural effusion of children and adults with community-acquired pneumonia. Future Microbiol 2015; 10:909-15. [DOI: 10.2217/fmb.14.143] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
ABSTRACT Aim: To study the etiology and the utility of new molecular methods in the diagnosis of complicated pneumonia with empyema. Materials & methods: Bacteria and viruses detection was performed by several traditional and molecular methods in the pleural fluid (PF) of 60 patients (38 children) with community-acquired pneumonia (CAP). Results: Despite prior antimicrobial therapy in 49 (81.7%) CAP patients, an etiological diagnosis could be established in 41 (68.3%), 35 being (58.3%) Streptococcus pneumoniae. PF culture was positive in only 6 patients but each molecular test detected more than 82% of cases. Conclusion: Traditional culture methods have poor diagnostic sensitivity in PF because most CAP patients are under antimicrobial therapy when it is obtained. S. pneumoniae detection by molecular methods highly improves diagnosis.
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Affiliation(s)
- José María Marimón
- Microbiology Department, Hospital Universitario Donostia-IIS-Biodonostia, San Sebastián, Spain
- Biomedical Research Center Network for Respiratory Diseases (CIBERES), San Sebastián, Spain
| | - María Morales
- Biomedical Research Center Network for Respiratory Diseases (CIBERES), San Sebastián, Spain
| | - Gustavo Cilla
- Microbiology Department, Hospital Universitario Donostia-IIS-Biodonostia, San Sebastián, Spain
- Biomedical Research Center Network for Respiratory Diseases (CIBERES), San Sebastián, Spain
| | - Diego Vicente
- Microbiology Department, Hospital Universitario Donostia-IIS-Biodonostia, San Sebastián, Spain
- Biomedical Research Center Network for Respiratory Diseases (CIBERES), San Sebastián, Spain
| | - Emilio Pérez-Trallero
- Microbiology Department, Hospital Universitario Donostia-IIS-Biodonostia, San Sebastián, Spain
- Biomedical Research Center Network for Respiratory Diseases (CIBERES), San Sebastián, Spain
- Faculty of Medicine, University of the Basque Country (UPV/EHU), San Sebastián, Spain
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Jauneikaite E, Tocheva AS, Jefferies JMC, Gladstone RA, Faust SN, Christodoulides M, Hibberd ML, Clarke SC. Current methods for capsular typing of Streptococcus pneumoniae. J Microbiol Methods 2015; 113:41-9. [PMID: 25819558 DOI: 10.1016/j.mimet.2015.03.006] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2014] [Revised: 02/21/2015] [Accepted: 03/08/2015] [Indexed: 10/23/2022]
Abstract
Streptococcus pneumoniae is a major respiratory tract pathogen causing pneumococcal disease mainly in children aged less than five years and in the elderly. Ninety-eight different capsular types (serotypes) of pneumococci have been reported, but pneumococcal conjugate vaccines (PCV) include polysaccharide antigens against only 7, 10 or 13 serotypes. It is therefore important to track the emergence of serotypes due to the clonal expansion of non-vaccine serotypes. Increased numbers of carried and disease-causing pneumococci are now being analysed as part of the post-PCV implementation surveillance studies and hence rapid, accurate and cost-effective typing methods are important. Here we describe serotyping methods published prior to 10th November 2014 for pneumococcal capsule typing. Sixteen methods were identified; six were based on serological tests using immunological properties of the capsular epitopes, eight were semi-automated molecular tests, and one describes the identification of capsular type directly from whole genome data, which also allows for further intra and inter-genome analyses. There was no single method that could be recommended for all pneumococcal capsular typing applications. Although the Quellung reaction is still considered to be the gold-standard, laboratories should take into account the number of pneumococcal isolates and the type of samples to be used for testing, the time frame for the results and the resources available in order to select the most appropriate method. Most likely, a combination of phenotypic and genotypic methods would be optimal to monitor and evaluate the impact of pneumococcal conjugate vaccines and to provide information for future vaccine formulations.
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Affiliation(s)
- Elita Jauneikaite
- Faculty of Medicine and Institute for Life Sciences, University of Southampton, Southampton SO16 6YD, UK; Infectious Diseases, Genome Institute of Singapore, 138672, Singapore
| | - Anna S Tocheva
- Faculty of Medicine and Institute for Life Sciences, University of Southampton, Southampton SO16 6YD, UK
| | - Johanna M C Jefferies
- Faculty of Medicine and Institute for Life Sciences, University of Southampton, Southampton SO16 6YD, UK; NIHR Southampton Respiratory Biomedical Research Unit, University Hospital Southampton NHS Foundation Trust, Southampton SO16 6YD, UK
| | - Rebecca A Gladstone
- Faculty of Medicine and Institute for Life Sciences, University of Southampton, Southampton SO16 6YD, UK
| | - Saul N Faust
- Faculty of Medicine and Institute for Life Sciences, University of Southampton, Southampton SO16 6YD, UK; NIHR Southampton Respiratory Biomedical Research Unit, University Hospital Southampton NHS Foundation Trust, Southampton SO16 6YD, UK; NIHR Wellcome Trust Clinical Research Facility, University Hospital Southampton NHS Foundation Trust, Southampton SO16 6YD, UK
| | - Myron Christodoulides
- Faculty of Medicine and Institute for Life Sciences, University of Southampton, Southampton SO16 6YD, UK
| | - Martin L Hibberd
- Infectious Diseases, Genome Institute of Singapore, 138672, Singapore; London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK
| | - Stuart C Clarke
- Faculty of Medicine and Institute for Life Sciences, University of Southampton, Southampton SO16 6YD, UK; NIHR Southampton Respiratory Biomedical Research Unit, University Hospital Southampton NHS Foundation Trust, Southampton SO16 6YD, UK.
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43
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Tóthpál A, Kardos S, Laub K, Nagy K, Tirczka T, van der Linden M, Dobay O. Radical serotype rearrangement of carried pneumococci in the first 3 years after intensive vaccination started in Hungary. Eur J Pediatr 2015; 174:373-81. [PMID: 25178897 DOI: 10.1007/s00431-014-2408-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/16/2014] [Revised: 08/06/2014] [Accepted: 08/19/2014] [Indexed: 11/25/2022]
Abstract
UNLABELLED Streptococcus pneumoniae is responsible for a significant amount of morbidity and mortality worldwide. Healthy carriers, mainly young children, are the most important sources of infections. In the current study, we aimed to determine the changes that have occurred since the introduction of PCV-7 in Hungary. Nasal specimens were collected from 1,022 healthy children aged 3-6 years attending day-care centres. After thorough identification, pneumococcal isolates were serotyped, and their antibiotic sensitivity was determined. The carriage rate was found to be 34.9%. A huge serotype rearrangement was detected compared to earlier results, with the previously leading serotype 14 having completely disappeared. Serotypes 11A, 35F, 19A, 6B, 15B, 3 and 38 were most prevalent, and 29 different types were identified in total. The PCV-7 types were responsible for 16.5% of all serotypes, and 36.0% are not covered by any pneumococcal vaccines. The isolates were sensitive to most tested antibiotics, except erythromycin (resistance was 21.6%). Only one penicillin-resistant strain was found. The newly and rapidly emerging non-vaccine serotypes are much more sensitive, except serotype 19A. CONCLUSION Due to PCV vaccination, a complete serotype arrangement occurred also in Hungary. The old "paediatric" serotypes were replaced by serotypes 11A, 35F, 19A, 6B, 15B, 3 and 38.
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Affiliation(s)
- Adrienn Tóthpál
- Institute of Medical Microbiology, Semmelweis University, Budapest, Nagyvárad tér 4, 1089, Hungary,
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Ramirez M. Streptococcus pneumoniae. MOLECULAR MEDICAL MICROBIOLOGY 2015:1529-1546. [DOI: 10.1016/b978-0-12-397169-2.00086-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
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Shakrin NNSM, Masri SN, Taib NM, Nordin SA, Jamal F, Desa MNM. Genotypic characterization of Malaysian human isolates of Streptococcus pneumoniae from carriage and clinical sources. Comp Immunol Microbiol Infect Dis 2014; 37:347-54. [DOI: 10.1016/j.cimid.2014.10.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2014] [Revised: 10/08/2014] [Accepted: 10/20/2014] [Indexed: 10/24/2022]
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46
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Khoshdel A, Rastabi RI, Doosti A, Askari S, Hafizi M. Prevalence of Heptavalent Vaccine-related Pneumococcal Serotypes in Nasopharyngeal carrier in children under five years old in Shahrekord, Iran by Multiplex-PCR during 2010- 2011. J Clin Diagn Res 2014; 8:PC01-4. [PMID: 25584276 DOI: 10.7860/jcdr/2014/8970.5104] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2014] [Accepted: 09/05/2014] [Indexed: 11/24/2022]
Abstract
BACKGROUND Heptavalent pneumococcal vaccine which included pneumococcal serotypes 4, 6B, 9V,14, 18C, 19F and 23F has been regularly used and is effective on preventing invasive pneumococcal infection. This study aimed to determine vaccine-related serotype distribution in nasopharyngeal carrier and healthy children under five years old. MATERIALS AND METHODS In this cross-sectional study from September 2010 to September 2011, 363 nasopharyngeal specimens were collected from healthy children in day care centers. In positive cultures of streptococcus pneumoniae (S. pneumonia) distribution, serotypes were detected by Multiplex polymerase chain reaction (PCR). Electrophoresis of PCR products was used for detection of serotypes of S. pneumoniae. RESULTS The carrier rate of S. pneumoniae was 29.5% with 95% confidence interval as 24.8- 34.5%. Electrophoresis of PCR products for detection of serotypes of S. pneumonia revealed 430, 220, 753, 189, 573, 304, and 384 bp (s) for 4, 6B, 9V, 14, 18C, 19F, and 23F serotypes of S. pneumoniae, respectively. The frequency of 23F, 6B, 19F, and 18C serotypes were 43%, 34%, 18%, and 5% respectively, but other serotypes (4, 9V and 14) were not detected. CONCLUSION Based on the 30% carrier rate and high prevalence of most of heptavalent pneumococcal conjugate vaccine serotypes in our study, this vaccine should be used for prevention of invasive infection in Iranian children.
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Affiliation(s)
- Abolfazl Khoshdel
- Pediatrics Infectious Diseases Specialist, Department of Pediatrics, Shahrekord University of Medical Sciences , Shahrekord, Iran
| | - Reza Imani Rastabi
- Infectious & Tropical Diseases Specialist, Department of Infectious & Tropical Diseases, Faculty of Medicine, Shahrekord University of Medical Sciences , Shahrekord, Iran
| | - Abbas Doosti
- Molecular Genetic Ph.D, Biotechnology Research Centre, Islamic Azad University , Shahrekord Branch, Shahrekord, Iran
| | - Shahin Askari
- General Practitioner, Department of Internal Medicine, Shahrekord University of Medical Sciences , Shahrekord, Iran
| | - Masoud Hafizi
- Infectious & Tropical Diseases Specialist, Department of Infectious & Tropical Diseases, Faculty of Medicine, Shahrekord University of Medical Sciences , Shahrekord, Iran
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47
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Changes in the incidence of Streptococcus pneumoniae bacteremia and its serotypes over 10 years in one hospital in South Korea. Vaccine 2014; 32:6403-7. [DOI: 10.1016/j.vaccine.2014.09.062] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2014] [Revised: 09/11/2014] [Accepted: 09/26/2014] [Indexed: 11/17/2022]
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Krishnappa L, Marie M, John J, Dabwan K, Shashidhar P. Serological and molecular capsular typing, antibiotic susceptibility of Streptococcus pneumoniae isolates from invasive and non-invasive infections. Acta Microbiol Immunol Hung 2014; 61:173-9. [PMID: 24939685 DOI: 10.1556/amicr.61.2014.2.7] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Streptococcus pneumoniae causes life threatening infections and necessitate for impediment and controlling disease; to conquer this, information is needed about serotype distribution and patterns of antibiotic resistance. The present study was to determine the serotype distribution of S. pneumoniae isolated from the entire age group individual and to correlate this distribution with susceptibility. Cases of pneumococcal infections have been reviewed for serotyping and antibiotic susceptibility. Out of 117 pneumococcal isolates 45 (39%) were penicillin-resistant, 84 (72%) were erythromycin-resistant and 100% were co-trimoxazole resistant. The most frequently isolated serotypes were 23F, 19F, 14, 6B, 5, 6A, 19A and 9V. PCV7, PCV10 and PCV13 coverage was 68%, 79%, 87%, respectively. Similarly, there was similarity in PCV7 coverage for non invasive isolates (64.5%) and invasive isolates (72.2%). The study state that common pneumococcal serotypes were present in similar ways as reported in literature. A continuous survey of pneumococcal infected population is requirement and necessity for success of vaccination.
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Affiliation(s)
- Lakshmana Krishnappa
- 1 King Saud University Department of Clinical Laboratory Sciences, College of Applied Medical Sciences Po Box 10219 Riyadh 11433 Saudi Arabia
| | - Mohammed Marie
- 1 King Saud University Department of Clinical Laboratory Sciences, College of Applied Medical Sciences Po Box 10219 Riyadh 11433 Saudi Arabia
| | - James John
- 2 Loyola College (Autonomous) Department of Zoology and Advance Biotechnology Chennai India
| | - Khaled Dabwan
- 1 King Saud University Department of Clinical Laboratory Sciences, College of Applied Medical Sciences Po Box 10219 Riyadh 11433 Saudi Arabia
| | - Pradeep Shashidhar
- 1 King Saud University Department of Clinical Laboratory Sciences, College of Applied Medical Sciences Po Box 10219 Riyadh 11433 Saudi Arabia
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Howie SRC, Morris GAJ, Tokarz R, Ebruke BE, Machuka EM, Ideh RC, Chimah O, Secka O, Townend J, Dione M, Oluwalana C, Njie M, Jallow M, Hill PC, Antonio M, Greenwood B, Briese T, Mulholland K, Corrah T, Lipkin WI, Adegbola RA. Etiology of severe childhood pneumonia in the Gambia, West Africa, determined by conventional and molecular microbiological analyses of lung and pleural aspirate samples. Clin Infect Dis 2014; 59:682-5. [PMID: 24867789 PMCID: PMC4130311 DOI: 10.1093/cid/ciu384] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Molecular analyses of lung aspirates from Gambian children with severe pneumonia detected pathogens more frequently than did culture and showed a predominance of bacteria, principally Streptococcuspneumoniae, >75% being of serotypes covered by current pneumococcal conjugate vaccines. Multiple pathogens were detected frequently, notably Haemophilus influenzae (mostly nontypeable) together with S. pneumoniae.
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Affiliation(s)
| | | | - Rafal Tokarz
- Center for Infection and Immunity, Columbia University, New York, New York
| | | | | | - Readon C Ideh
- Medical Research Council Unit, Fajara, Republic of The Gambia
| | - Osaretin Chimah
- Medical Research Council Unit, Fajara, Republic of The Gambia
| | - Ousman Secka
- Medical Research Council Unit, Fajara, Republic of The Gambia
| | - John Townend
- Medical Research Council Unit, Fajara, Republic of The Gambia
| | - Michel Dione
- Medical Research Council Unit, Fajara, Republic of The Gambia
| | | | - Malick Njie
- Ministry of Health and Social Welfare, Banjul, Republic of The Gambia
| | - Mariatou Jallow
- Ministry of Health and Social Welfare, Banjul, Republic of The Gambia
| | - Philip C Hill
- Centre for International Health, University of Otago, Dunedin, New Zealand
| | - Martin Antonio
- Medical Research Council Unit, Fajara, Republic of The Gambia
| | - Brian Greenwood
- London School of Hygiene and Tropical Medicine, United Kingdom
| | - Thomas Briese
- Center for Infection and Immunity, Columbia University, New York, New York
| | - Kim Mulholland
- London School of Hygiene and Tropical Medicine, United Kingdom
| | - Tumani Corrah
- Medical Research Council Unit, Fajara, Republic of The Gambia
| | - W Ian Lipkin
- Center for Infection and Immunity, Columbia University, New York, New York
| | - Richard A Adegbola
- Medical Research Council Unit, Fajara, Republic of The Gambia GlaxoSmithKline Vaccines, Wavre, Belgium
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50
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Burr SE, Milne S, Jafali J, Bojang E, Rajasekhar M, Hart J, Harding-Esch EM, Holland MJ, Mabey DCW, Sillah A, Bailey RL, Roca A. Mass administration of azithromycin and Streptococcus pneumoniae carriage: cross-sectional surveys in the Gambia. Bull World Health Organ 2014; 92:490-8. [PMID: 25110374 DOI: 10.2471/blt.13.133462] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2013] [Revised: 02/25/2014] [Accepted: 03/02/2014] [Indexed: 01/23/2023] Open
Abstract
OBJECTIVE To evaluate the effect of repeated mass drug administration (MDA) of azithromycin in the Gambia on the nasopharyngeal carriage of Streptococcus pneumoniae and on the emergence of antibiotic-resistant strains. METHODS This study involved villages that participated in a cluster randomized trial comparing the effect of one versus three azithromycin MDA rounds on the prevalence of trachoma. Only villages in which most children received 7-valent pneumococcal conjugate vaccine were included. Three cross-sectional surveys were performed in two villages that received three annual MDA rounds: the first immediately before the third MDA round and the second and third, 1 and 6 months, respectively, after the third MDA round. The third survey also covered six villages that had received one MDA round 30 months previously. Pneumococcal carriage was assessed using nasopharyngeal swabs and azithromycin resistance was detected using the Etest. FINDINGS The prevalence of pneumococcal carriage decreased from 43.4% to 19.2% between the first and second surveys (P < 0.001) but rebounded by the third survey (45.8%; P = 0.591). Being a carrier at the first survey was a risk factor for being a carrier at the second (odds ratio: 3.71; P < 0.001). At the third survey, the prevalence of carriage was similar after one and three MDA rounds (50.3% versus 45.8%, respectively; P = 0.170), as was the prevalence of azithromycin resistance (0.3% versus 0.9%, respectively; P = 0.340). CONCLUSION Three azithromycin MDA rounds did not increase the prevalence of nasopharyngeal carriage of azithromycin-resistant S. pneumoniae strains compared with one round.
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Affiliation(s)
- Sarah E Burr
- Department of Clinical Research, London School of Hygiene & Tropical Medicine, Keppel Street, London, WC1E 7HT, England
| | - Sally Milne
- Faculty of Life Sciences, University of Manchester, Manchester, England
| | - James Jafali
- Medical Research Council Unit, Fajara, Banjul, Gambia
| | - Ebrima Bojang
- Medical Research Council Unit, Fajara, Banjul, Gambia
| | - Megha Rajasekhar
- Department of Clinical Research, London School of Hygiene & Tropical Medicine, Keppel Street, London, WC1E 7HT, England
| | - John Hart
- Department of Clinical Research, London School of Hygiene & Tropical Medicine, Keppel Street, London, WC1E 7HT, England
| | | | - Martin J Holland
- Department of Clinical Research, London School of Hygiene & Tropical Medicine, Keppel Street, London, WC1E 7HT, England
| | - David C W Mabey
- Department of Clinical Research, London School of Hygiene & Tropical Medicine, Keppel Street, London, WC1E 7HT, England
| | - Ansumana Sillah
- National Eye Health Programme, Ministry of Health and Social Welfare, Kanifing, Gambia
| | - Robin L Bailey
- Department of Clinical Research, London School of Hygiene & Tropical Medicine, Keppel Street, London, WC1E 7HT, England
| | - Anna Roca
- Medical Research Council Unit, Fajara, Banjul, Gambia
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