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Kashiwaya K, Saga T, Ishii Y, Sakata R, Iwata M, Yoshizawa S, Chang B, Ohnishi M, Tateda K. Worldwide Lineages of Clinical Pneumococci in a Japanese Teaching Hospital Identified by DiversiLab System. J Infect Chemother 2016; 22:407-13. [PMID: 27107736 DOI: 10.1016/j.jiac.2016.03.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Revised: 03/11/2016] [Accepted: 03/16/2016] [Indexed: 11/19/2022]
Abstract
Pneumococcal Molecular Epidemiology Network (PMEN) clones are representatives of worldwide-spreading pathogens. DiversiLab system, a repetitive PCR system, has been proposed as a less labor-and time-intensive genotyping platform alternative to conventional methods. However, the utility and analysis parameters of DiversiLab for identifying worldwide lineages was not established. To evaluate and optimize the performance of DiversiLab for identifying worldwide pneumococcal lineages, we examined 245 consecutive isolates of clinical Streptococcus pneumoniae from all age-group patients at a teaching hospital in Japan. The capsular swelling reaction of all isolates yielded 24 different serotypes. Intensive visual observation (VO) of DiversiLab band pattern difference divided all isolates into 73 clusters. Multilocus sequence typing (MLST) of representative 73 isolates from each VO cluster yielded 51 different STs. Among them, PMEN-related lineages accounted for 63% (46/73). Although the serotype of PMEN-related isolates was identical to that of the original PMEN clone in 70% (32/46), CC156-related PMEN lineages, namely Greece(6B)-22 and Colombia(23F)-26, harbored various capsular types discordant to the original PMEN clones. Regarding automated analysis, genotyping by extended Jaccard (XJ) with a 75% similarity index cutoff (SIC) showed the highest correlation with serotyping (adjusted Rand's coefficient, 0.528). Elevating the SIC for XJ to 85% increased the discriminatory power sufficient for distinguishing two major PMEN-related isolates of Taiwan(19F)-14 and Netherlands(3)-31. These results demonstrated a potential utility of DiversiLab for identifying worldwide lineage of pneumococcus. An optimized parameters of automated analysis should be useful especially for comparison for reference strains by "identification" function of DiversiLab.
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Affiliation(s)
- Kiyoshi Kashiwaya
- Department of Microbiology and Infectious Diseases, Toho University School of Medicine, Tokyo, Japan; Department of Clinical Laboratory, Tokyo Metropolitan Cancer and Infectious Diseases Center Komagome Hospital, Tokyo, Japan
| | - Tomoo Saga
- Department of Microbiology and Infectious Diseases, Toho University School of Medicine, Tokyo, Japan; Central Laboratory Division, Akita University Hospital, Akita, Japan.
| | - Yoshikazu Ishii
- Department of Microbiology and Infectious Diseases, Toho University School of Medicine, Tokyo, Japan
| | - Ryuji Sakata
- Department of Microbiology and Infectious Diseases, Toho University School of Medicine, Tokyo, Japan
| | - Morihiro Iwata
- Clinical Laboratory Department, Toho University Omori Medical Center, Tokyo, Japan
| | - Sadako Yoshizawa
- Division of Infection Control, Toho University Omori Medical Center, Tokyo, Japan
| | - Bin Chang
- Department of Bacteriology I, National Institute of Infectious Diseases, Tokyo, Japan
| | - Makoto Ohnishi
- Department of Bacteriology I, National Institute of Infectious Diseases, Tokyo, Japan
| | - Kazuhiro Tateda
- Department of Microbiology and Infectious Diseases, Toho University School of Medicine, Tokyo, Japan; Clinical Laboratory Department, Toho University Omori Medical Center, Tokyo, Japan; Division of Infection Control, Toho University Omori Medical Center, Tokyo, Japan
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Evidence of a clonal expansion of Streptococcus pneumoniae serotype 19A in adults as in children assessed by the DiversiLab® system. Eur J Clin Microbiol Infect Dis 2014; 33:2067-73. [DOI: 10.1007/s10096-014-2148-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2014] [Accepted: 04/28/2014] [Indexed: 11/26/2022]
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Williams TM, Loman NJ, Ebruke C, Musher DM, Adegbola RA, Pallen MJ, Weinstock GM, Antonio M. Genome analysis of a highly virulent serotype 1 strain of Streptococcus pneumoniae from West Africa. PLoS One 2012; 7:e26742. [PMID: 23082106 PMCID: PMC3474768 DOI: 10.1371/journal.pone.0026742] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2011] [Accepted: 10/02/2011] [Indexed: 11/18/2022] Open
Abstract
Streptococcus pneumoniae is a leading cause of pneumonia, meningitis, and bacteremia, estimated to cause 2 million deaths annually. The majority of pneumococcal mortality occurs in developing countries, with serotype 1 a leading cause in these areas. To begin to better understand the larger impact that serotype 1 strains have in developing countries, we characterized virulence and genetic content of PNI0373, a serotype 1 strain from a diseased patient in The Gambia. PNI0373 and another African serotype 1 strain showed high virulence in a mouse intraperitoneal challenge model, with 20% survival at a dose of 1 cfu. The PNI0373 genome sequence was similar in structure to other pneumococci, with the exception of a 100 kb inversion. PNI0373 showed only15 lineage specific CDS when compared to the pan-genome of pneumococcus. However analysis of non-core orthologs of pneumococcal genomes, showed serotype 1 strains to be closely related. Three regions were found to be serotype 1 associated and likely products of horizontal gene transfer. A detailed inventory of known virulence factors showed that some functions associated with colonization were absent, consistent with the observation that carriage of this highly virulent serotype is unusual. The African serotype 1 strains thus appear to be closely related to each other and different from other pneumococci despite similar genetic content.
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Affiliation(s)
- Tiffany M. Williams
- The Genome Institute, Washington University, St. Louis, Missouri, United States of America
| | - Nicholas J. Loman
- Centre for Systems Biology, University of Birmingham, Birmingham, United Kingdom
| | - Chinelo Ebruke
- Bacterial Diseases Programme, Medical Research Council Laboratories, Banjul, The Gambia
| | - Daniel M. Musher
- Infectious Diseases Section, Michael E. DeBakey VA Medical Center, Houston, Texas, United States of America
| | - Richard A. Adegbola
- Bacterial Diseases Programme, Medical Research Council Laboratories, Banjul, The Gambia
| | - Mark J. Pallen
- Centre for Systems Biology, University of Birmingham, Birmingham, United Kingdom
| | - George M. Weinstock
- The Genome Institute, Washington University, St. Louis, Missouri, United States of America
- * E-mail:
| | - Martin Antonio
- Bacterial Diseases Programme, Medical Research Council Laboratories, Banjul, The Gambia
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Okada T, Takada K, Fujita K, Ikemi T, Osgood RC, Childers NK, Michalek SM. Differentiation of banding patterns between Streptococcus mutans and Streptococcus sobrinus isolates in rep-PCR using ERIC primer. J Oral Microbiol 2011; 3:JOM-3-7190. [PMID: 22145074 PMCID: PMC3230236 DOI: 10.3402/jom.v3i0.7190] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2011] [Revised: 11/09/2011] [Accepted: 11/09/2011] [Indexed: 11/18/2022] Open
Abstract
Background Streptococcus mutans and Streptococcus sobrinus are considered to be important bacterial species in the initiation of human dental caries. Therefore, the establishment of a reliable genotyping method to distinguish S. mutans from S. sobrinus is of central importance. Objective We assessed the usefulness of repetitive extragenic palindromic polymerase chain reaction (rep-PCR) using ERIC primer banding patterns in differentiating S. mutans and S. sobrinus. Design Five S. mutans and two S. sobrinus prototype strains and 50 clinical isolates (38 S. mutans serotype c, 4 S. sobrinus serotype d, and 8 S. sobrinus serotype g) were examined. The banding patterns of amplicons generated were compared among the prototype strains and clinical isolates, to find common bands that distinguish S. mutans and S. sobrinus. Results Multiple banding patterns were seen with all strains tested. The representative strains of S. mutans tested revealed six unique, strong bands at 2,000 bp, 1,700 bp, 1,400 bp, 1,100 bp, 850 bp, and 250 bp, whereas S. sobrinus had seven strong bands at 2,000 bp, 1,800 bp, 1,100 bp, 900 bp, 800 bp, 600 bp, and 550 bp. The band at 1,100 bp was the only band that was observed in both S. mutans and S. sobrinus. Furthermore, most clinical S. mutans isolates revealed identical banding patterns. All S. mutans had amplicons at 1,700 bp, 850 bp, and 250 bp, whereas those of S. sobrinus were at 1,100 bp, 900 bp, and 800 bp. Conclusions These results indicate that using rep-PCR with the ERIC primers can distinguish between S. mutans and S. sobrinus.
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Affiliation(s)
- Tamami Okada
- Department of Operative Dentistry, Nihon University School of Dentistry at Matsudo, Matsudo, Japan
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Esteva C, Selva L, de Sevilla MF, Garcia-Garcia JJ, Pallares R, Muñoz-Almagro C. Streptococcus pneumoniae serotype 1 causing invasive disease among children in Barcelona over a 20-year period (1989-2008). Clin Microbiol Infect 2011; 17:1441-4. [PMID: 21729192 DOI: 10.1111/j.1469-0691.2011.03526.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Fifty-six isolates of serotype 1 were identified during a 20-year prospective study (1989-2008), including all children with culture-proven invasive pneumococcal disease (IPD) admitted to a children's hospital in Barcelona. Forty-eight of them (85.7%) were in children aged >2 years. Complicated pneumonia (n = 28) and non-complicated pneumonia (n = 20) were the main clinical presentations. The frequency of serotype 1 IPD increased from 1999-2003 to 2004-2008: 1.2 to 4.4 episodes/100 000 children (p <0.001). The ST306 clone were identified in 70.4% of isolates. As IPD caused by serotype 1 is mainly detected in older children, a vaccination programme for children >2 years should be considered.
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Affiliation(s)
- C Esteva
- Department of Microbiology, Hospital Sant Joan de Deu and University of Barcelona, Esplugues, Spain
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Zähner D, Gudlavalleti A, Stephens DS. Increase in pilus islet 2-encoded pili among Streptococcus pneumoniae isolates, Atlanta, Georgia, USA. Emerg Infect Dis 2010; 16:955-62. [PMID: 20507746 PMCID: PMC3086225 DOI: 10.3201/eid1606.091820] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
PI-2–encoding isolates are potential vaccine candidates. To define the prevalence of pilus islet 2 (PI-2)–encoded pili in Streptococcus pneumoniae in a geographically defined area, we examined 590 S. pneumoniae isolates from population-based surveillance of invasive pneumococcal disease in Atlanta, Georgia, USA, 1994–2006. In 2006, PI-2 was present in 21% of all invasive isolates, including serotypes 1 (100%), 7F (89%), 11A (21%), 19A (40%), and 19F (75%). Only serotype 19F is included in the 7-valent pneumococcal conjugate vaccine that is in use worldwide. In 1999, PI-2-containing isolates were of the same serotypes but accounted for only 3.6% of all invasive isolates. The increase of PI-2 in 2006 resulted predominantly from the emergence of serotype 19A isolates of sequence type 320 and the expansion of serotype 7F isolates. The increase in PI-2-containing isolates and the finding that isolates of all identified serotypes expressed highly conserved PI-2 pili supports their potential as a vaccine candidate.
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Affiliation(s)
- Dorothea Zähner
- Department of Medicine, Division of Infectious Diseases, Emory University School of Medicine, Atlanta, Georgia 30322, USA.
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Rodrigues F, Nunes S, Sá-Leão R, Gonçalves G, Lemos L, Lencastre HD. Streptococcus pneumoniaeNasopharyngeal Carriage in Children Attending Day-Care Centers in the Central Region of Portugal, In the Era of 7-Valent Pneumococcal Conjugate Vaccine. Microb Drug Resist 2009; 15:269-77. [DOI: 10.1089/mdr.2009.0043] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Fernanda Rodrigues
- Infectious Diseases Unit, Pediatric Hospital of Coimbra, Coimbra, Portugal
| | - Sónia Nunes
- Laboratory of Molecular Genetics, Institute of Chemical and Biological Technology, New University of Lisbon, Oeiras, Portugal
| | - Raquel Sá-Leão
- Laboratory of Molecular Genetics, Institute of Chemical and Biological Technology, New University of Lisbon, Oeiras, Portugal
- Center of Mathematics and Fundamental Applications, University of Lisbon, Lisbon, Portugal
| | - Guilherme Gonçalves
- Abel Salazar Institute of Biomedical Sciences (ICBAS), University of Porto, Porto, Portugal
| | - Luís Lemos
- Infectious Diseases Unit, Pediatric Hospital of Coimbra, Coimbra, Portugal
| | - Hermínia de Lencastre
- Laboratory of Molecular Genetics, Institute of Chemical and Biological Technology, New University of Lisbon, Oeiras, Portugal
- The Rockefeller University, New York, New York
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Chiou AC, Andrade SS, Almeida SCG, Zanella RC, Andrade AL, Brandileone MCDC. Molecular assessment of invasive Streptococcus pneumoniae serotype 1 in Brazil: evidence of clonal replacement. J Med Microbiol 2008; 57:839-844. [DOI: 10.1099/jmm.0.47612-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
| | | | | | | | - Ana-Lúcia Andrade
- Institute of Tropical Pathology and Public Health, Federal University of Goiás, Brazil
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Harrington SM, Stock F, Kominski AL, Campbell JD, Hormazabal JC, Livio S, Rao L, Kotloff KL, Sow SO, Murray PR. Genotypic analysis of invasive Streptococcus pneumoniae from Mali, Africa, by semiautomated repetitive-element PCR and pulsed-field gel electrophoresis. J Clin Microbiol 2007; 45:707-14. [PMID: 17192418 PMCID: PMC1829114 DOI: 10.1128/jcm.01871-06] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2006] [Revised: 10/26/2006] [Accepted: 12/13/2006] [Indexed: 12/30/2022] Open
Abstract
As part of a large, ongoing study of invasive infections in pediatric patients in Bamako, Mali, 106 cases of invasive pneumococcal disease were identified from June 2002 to July 2003 (J. D. Campbell et al., Pediatr. Infect. Dis. J. 23:642-649, 2004). Of the 12 serotypes present, the majority of isolates were not contained in PCV7 (the 7-valent pneumococcal conjugate vaccine), including 1 isolate that was serotype 1, 12 isolates that were serotype 2, 58 isolates that were serotype 5, 7 isolates that were serotype 7F, and 1 isolate that was serotype 12F. To determine whether clonal dissemination of the predominant serotypes had taken place, genotyping was performed on 100 S. pneumoniae isolates by using two methods: pulsed-field gel electrophoresis (PFGE) of SmaI-digested genomic DNA, and the Bacterial Barcodes repetitive-element PCR (rep-PCR) method. Criteria for delineating rep-PCR genotypes were established such that isolates of different serotypes were generally not grouped together. The two methods were equally discriminatory within a given pneumococcal serotype. PFGE separated the isolates into 15 genotypes and 7 subtypes; rep-PCR separated isolates into 15 genotypes and 6 subtypes. Using either method, isolates within serotypes 2, 5, and 7 formed three large, separate clusters containing 1 genotype each. Both methods further distinguished related subtypes within serotypes 2 and 5. Interestingly, one of the PFGE subtypes of serotype 5 is indistinguishable from the Columbia(5)-19 clone circulating in Latin America since 1994. The data support that serotypes 2 and 5 were likely to be the result of dissemination of particular clones, some of which are responsible for invasive disease over a broad population range.
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Affiliation(s)
- S M Harrington
- Department of Laboratory Medicine, National Institutes of Health, Bethesda, Maryland, USA.
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Byington CL, Korgenski K, Daly J, Samore MH, Pavia AT. Reply to Calbo and Garau. Clin Infect Dis 2005. [DOI: 10.1086/498314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Affiliation(s)
| | - Kent Korgenski
- Department of Intermountain Health Care, Salt Lake City, Utah
| | - Judy Daly
- Department of Intermountain Health Care, Salt Lake City, Utah
| | - Matthew H. Samore
- Department of Internal Medicine, University of Utah, Salt Lake City, Utah
- Salt Lake Informatics, Decision Enhancement, and Surveillance Center, Veterans Affairs Health Care System, Salt Lake City, Utah
| | - Andrew T. Pavia
- Department of Pediatrics, University of Utah, Salt Lake City, Utah
- Department of Internal Medicine, University of Utah, Salt Lake City, Utah
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Byington CL, Samore MH, Stoddard GJ, Barlow S, Daly J, Korgenski K, Firth S, Glover D, Jensen J, Mason EO, Shutt CK, Pavia AT. Temporal Trends of Invasive Disease Due to Streptococcus pneumoniae among Children in the Intermountain West: Emergence of Nonvaccine Serogroups. Clin Infect Dis 2005; 41:21-9. [PMID: 15937758 DOI: 10.1086/430604] [Citation(s) in RCA: 197] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2004] [Accepted: 02/08/2005] [Indexed: 11/03/2022] Open
Abstract
BACKGROUND Use of the heptavalent pneumococcal conjugate vaccine (PCV-7 [Prevnar]) has been associated with decreased a incidence of invasive pneumococcal disease (IPD) among children in the United States. METHODS Cases of IPD in children < 18 years of age insured by or receiving health care from Intermountain Health Care during 1996-2003 were identified. Isolates of S. pneumoniae from children with IPD treated at Primary Children's Medical Center (PCMC; Salt Lake City, UT) during 1997-2003 were serogrouped. Temporal trends of IPD, serogroup distribution of pneumococci, and antibiotic resistance among pneumococci were analyzed. RESULTS A total of 1535 cases of IPD were identified. The rate of IPD decreased 27% after the introduction of PCV7. Among children with IPD who were cared for at PCMC, disease in 73% was caused by PCV7 serogroups in 1997-2000, compared with 50% in 2001-2003 (P < .001), and the percentage of isolates resistant to penicillin decreased from 34% in 1997-2000 to 22% in 2001-2003 (P = .04). The percentage of IPD cases that were empyema increased from 16% to 30% (P = .015), and the percentage of severe cases of IPD increased from 57% to 71% (P = .026). Children with IPD due to non-PCV7 serogroups were older, were more likely to have parapneumonic empyema, and had longer hospital stays. CONCLUSIONS The incidence of IPD in the IMW decreased by 27% after the introduction of the PCV7 vaccine. During the postvaccine period (2001-2003), there were significant decreases in the proportion of cases of IPD caused by PCV7 and antibiotic-resistant serogroups. These benefits were accompanied by a significant increase in the proportion of IPD cases due to non-PCV7 serogroups, with increases in the incidence of empyema and severe IPD.
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Affiliation(s)
- Carrie L Byington
- Department of Pediatrics, University of Utah, Salt Lake City, UT 84132, USA.
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