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Alexandrova AS, Setchanova LP, Pencheva DR, Mitov IG. Phenotypic and genotypic characterization of serogroup 6 Streptococcus pneumoniae isolates collected during 10-valent pneumococcal conjugate vaccine era in Bulgaria. Acta Microbiol Immunol Hung 2020; 67:91-99. [PMID: 31813257 DOI: 10.1556/030.66.2019.039] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Accepted: 10/01/2019] [Indexed: 11/19/2022]
Abstract
Serogroup 6 remains common in the pneumococcal-conjugated vaccine era in Bulgaria; therefore, we investigated its clonal and serotype dynamics. The antibiotic susceptibilities were assessed by broth microdilution. Strains identified as serogroup 6 with latex agglutination method were subjected to serotype-specific PCRs. Erythromycin-resistant strains were analyzed by PCR for presence of ermB and mefE genes. MLST was performed to define clonal composition of the sequence types (STs). Serogroup 6 was represented by 40 (13.3%) from 301 invasive and non-invasive Streptococcus pneumoniae isolates. Molecular serotyping revealed new emerging serotype 6C (6.6%), not detected in pre-vaccine era. Among unvaccinated patients, mostly we observed serotypes 6А (57.1%) and 6В (28.6%). Serotype 6C was distinctive for vaccinated children (64%), followed by 6A (24%). Penicillin and ceftriaxone non-susceptible serogroup 6 strains were 65% and 5%, respectively; erythromycin- and clindamycin-resistant were 70.0% and 52.5%, respectively. Multidrug-resistant strains were 57.5%. Prevalent genetic determinant for macrolide resistance was ermB gene (75%). MLST revealed 17 STs into 5 clonal complexes and 7 singletons. Predominant genetic lineage was CC386, represented by MDR-6C non-invasive strains. Serotype 6B, principally responsible for invasive diseases in the pre-vaccine era, retreated this position to serotype 6A.
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Affiliation(s)
| | - Lena Petrova Setchanova
- Department of Medical Microbiology, Medical Faculty, Medical University of Sofia, Sofia, Bulgaria
| | - Daniela Rosenova Pencheva
- Molecular Medicine Center, Department of Medical Chemistry and Biochemistry, Medical Faculty, Medical University of Sofia, Sofia, Bulgaria
| | - Ivan Gergov Mitov
- Department of Medical Microbiology, Medical Faculty, Medical University of Sofia, Sofia, Bulgaria
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Draft Genome Sequences of Clinical Isolates of Serotype 6E Streptococcus pneumoniae from Five Asian Countries. GENOME ANNOUNCEMENTS 2017; 5:5/10/e01728-16. [PMID: 28280026 PMCID: PMC5347246 DOI: 10.1128/genomea.01728-16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Although serotype 6E Streptococcus pneumoniae consistently expresses capsules of either vaccine-serotype 6A or 6B, certain genetic variants of serotype 6E may evade vaccine induced immunity. Thus, draft genome sequences from five clinical isolates of serotype 6E from each of five different Asian countries have been generated to provide insight into the genomic diversity in serotype 6E strains.
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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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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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Marimón JM, Ercibengoa M, Tamayo E, Alonso M, Pérez-Trallero E. Long-Term Epidemiology of Streptococcus pneumoniae Serogroup 6 in a Region of Southern Europe with Special Reference to Serotype 6E. PLoS One 2016; 11:e0149047. [PMID: 26863305 PMCID: PMC4749257 DOI: 10.1371/journal.pone.0149047] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2015] [Accepted: 01/26/2016] [Indexed: 11/25/2022] Open
Abstract
Streptococcus pneumoniae serotype 6E has recently been described, but its long-term epidemiology is not well known. From 1981–2013, 704 serogroup 6 clinical isolates were obtained in Gipuzkoa, Basque Country, Spain. All invasive and one in four non-invasive isolates were included. Overall, 75, 97, 51 and 45 serotypes 6A, 6B, 6C and 6E isolates, respectively, were detected. No serotype 6D isolates were identified. The prevalence of serotypes 6E and 6B, but not that of serotypes 6A and 6C, declined after the introduction of pneumococcal conjugate vaccines. Serotype 6E isolates showed the highest resistance rate. Most serotype 6E isolates were ST90.
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Affiliation(s)
- José M. Marimón
- Microbiology Department, Hospital Universitario Donostia-Instituto Biodonostia, San Sebastián, Spain
- Biomedical Research Center Network for Respiratory Diseases (CIBERES), San Sebastián, Spain
- * E-mail:
| | - María Ercibengoa
- Biomedical Research Center Network for Respiratory Diseases (CIBERES), San Sebastián, Spain
| | - Esther Tamayo
- Biomedical Research Center Network for Respiratory Diseases (CIBERES), San Sebastián, Spain
| | - Marta Alonso
- Microbiology Department, Hospital Universitario Donostia-Instituto Biodonostia, San Sebastián, Spain
| | - Emilio Pérez-Trallero
- Microbiology Department, Hospital Universitario Donostia-Instituto 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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Pneumococcus with the "6E" cps Locus Produces Serotype 6B Capsular Polysaccharide. J Clin Microbiol 2016; 54:967-71. [PMID: 26818670 DOI: 10.1128/jcm.03194-15] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Accepted: 01/15/2016] [Indexed: 11/20/2022] Open
Abstract
Genetic studies of serogroup 6 isolates ofStreptococcus pneumoniaeidentified putative serotype 6E. Although its capsular polysaccharide structure has not been elucidated, putative serotype 6E is described in an increasing number of studies as a potentially new serotype. We show here that SPEC6B, which is widely used as a target strain for serotype 6B opsonophagocytosis assays, has the genetic features of the putative serotype 6E but produces capsular polysaccharide identical to 6B capsular polysaccharide as determined by one-dimensional (1D) and 2D nuclear magnetic resonance (NMR). Thus, putative serotype 6E is a mere genetic variant of serotype 6B. Also, SPEC6B is appropriate as a target strain for serotype 6B opsonophagocytosis assays. This example illustrates the difficulties of assigning new bacterial serotypes based on genetic findings alone.
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Baek JY, Park IH, So TMK, Lalitha MK, Shimono N, Yasin RM, Carlos CC, Perera J, Thamlikitkul V, Hsueh PR, Van PH, Shibl AM, Song JH, Ko KS. Prevalence and characteristics of Streptococcus pneumoniae "putative serotype 6E" isolates from Asian countries. Diagn Microbiol Infect Dis 2015; 80:334-7. [PMID: 25439447 DOI: 10.1016/j.diagmicrobio.2014.08.017] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2014] [Revised: 08/26/2014] [Accepted: 08/31/2014] [Indexed: 11/26/2022]
Abstract
The prevalence, antimicrobial susceptibility, and genotypes of Streptococcus pneumoniae “putative serotype 6E” isolates from Asian countries were investigated. A total of 244 S. pneumoniae serogroup 6 isolates obtained from 11 Asian countries were included in this study. Of the 244 serogroup 6 isolates, 101 (41.4%) were typed as "putative serotype 6E," followed by serotypes 6A, 6B, 6C, and 6D (27.0, 20.1, 5.7, and 5.7%, respectively). Multilocus sequence typing revealed that clonal complex (CC) 90, including ST90 and its variants, was the most prevalent clonal group of "putative serotype 6E" isolates (n = 63; 62.4%). CC146 and CC315 were also found frequently in some of the countries. Most of the "putative serotype 6E" isolates showed very high resistance rates against cefuroxime, erythromycin, azithromycin, clarithromycin, clindamycin, and trimethoprim/sulfamethoxazole, probably due to their highly resistant to antimicrobials clone, CC90. Our results indicate that “putative serotype 6E” is prevalent in Asian countries. The clonal dissemination of "putative serotype 6E" isolates was also identified.
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Kawaguchiya M, Urushibara N, Kobayashi N. High prevalence of genotype 6E (putative serotype 6E) among noninvasive/colonization isolates of Streptococcus pneumoniae in northern Japan. Microb Drug Resist 2014; 21:209-14. [PMID: 25361198 DOI: 10.1089/mdr.2014.0181] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Serogroup 6 of Streptococcus pneumoniae contains four established serotypes (6A-6D). Recently, putative serotype 6E (genotype 6E) was proposed as a novel type, which is cross-reactive with 6B-specific antiserum, but its capsular polysaccharide synthesis (cps) locus is genetically distinct from those of serotypes 6A and 6B. In the present study, prevalence of genotype 6E was analyzed by a newly designed multiplex polymerase chain reaction (PCR) for noninvasive or colonizing S. pneumoniae isolates in northern Japan assigned to serogroup 6 in our previous study by the sequential multiplex PCR developed by Pai et al. Among the isolates previously assigned to 6A and 6B, 2.2% (1/45) and 77.3% (140/181) of isolates, respectively, were revealed to have cps genes of genotype 6E. Eight 6E isolates selected for further analysis were found to have identical or highly similar sequences of cps genes (wzg, wzh, wze, wciN, wciP, and wzy) to those of strains previously reported as putative serotype 6E, and all the isolates were classified into sequence type 90 (ST90). Reanalysis of genetic traits on penicillin and macrolide resistance clarified significantly higher rates of three pbp mutations (gPRSP) and ermB in genotype 6E than in serotypes 6A and 6B. These findings suggested a need for detection of genotype 6E in the surveillance of S. pneumoniae serotypes.
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Affiliation(s)
- Mitsuyo Kawaguchiya
- Department of Hygiene, School of Medicine, Sapporo Medical University , Sapporo, Japan
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