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Hiller NL, Orihuela CJ. Biological puzzles solved by using Streptococcus pneumoniae: a historical review of the pneumococcal studies that have impacted medicine and shaped molecular bacteriology. J Bacteriol 2024:e0005924. [PMID: 38809015 DOI: 10.1128/jb.00059-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2024] Open
Abstract
The major human pathogen Streptococcus pneumoniae has been the subject of intensive clinical and basic scientific study for over 140 years. In multiple instances, these efforts have resulted in major breakthroughs in our understanding of basic biological principles as well as fundamental tenets of bacterial pathogenesis, immunology, vaccinology, and genetics. Discoveries made with S. pneumoniae have led to multiple major public health victories that have saved the lives of millions. Studies on S. pneumoniae continue today, where this bacterium is being used to dissect the impact of the host on disease processes, as a powerful cell biology model, and to better understand the consequence of human actions on commensal bacteria at the population level. Herein we review the major findings, i.e., puzzle pieces, made with S. pneumoniae and how, over the years, they have come together to shape our understanding of this bacterium's biology and the practice of medicine and modern molecular biology.
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Affiliation(s)
- N Luisa Hiller
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, USA
| | - Carlos J Orihuela
- Department of Microbiology, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA
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Zeng Y, Song Y, Cui L, Wu Q, Wang C, Coelho AC, Zhang G, Wei D, Li C, Zhang J, Corbeil J, Li Y, Feng J. Phylogenomic insights into evolutionary trajectories of multidrug resistant S. pneumoniae CC271 over a period of 14 years in China. Genome Med 2023; 15:46. [PMID: 37403170 DOI: 10.1186/s13073-023-01200-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 05/31/2023] [Indexed: 07/06/2023] Open
Abstract
BACKGROUND Streptococcus pneumoniae is a gram-positive opportunistic pathogen, and infection risks of S. pneumoniae can be profoundly augmented by its acquired multidrug-resistance (MDR). The rapid development of MDR in S. pneumoniae was attributed to the international dissemination of a small number of multidrug-resistant "clones." Clonal complex (CC) 271 is a prevalent MDR CC in the world and the most prevalent CC in China. However, the evolutionary trajectories of multidrug-resistant S. pneumoniae CC271 in China still are largely unknown. METHODS We investigated a collection of 1312 S. pneumoniae isolates collected from 28 tertiary hospitals in China from 2007 to 2020. Recombination prediction and recombination-masked phylogenetic analysis were combined to determine the population structure and mode of evolution of CC271. Data from the Global Pneumococcal Sequencing program (GPS) were combined to understand the global distribution of clones identified in this study. Bayesian analysis were recruited to analysis the evolutionary dynamics of dominant clones within CC271 in China. RESULTS The phylogenomic analysis resulted in the discovery of two globally distributed clones, ST271-A and ST271-B. ST271-A was a derivative of ST236 and an ancestor of ST271-B and ST320, refining the internal phylogenetic relationship of CC271. ST271-B was the most dominant clone in China, with higher β-lactam resistance especially for cephalosporins comparing to other MDR clones. Bayesian skyline plot showed a rapid expansion of 19F ST271-B from 1995 to 2000, which correlates with the widespread use of cephalosporins in the 1990s in China. 19A ST320, a vaccine-escape clone, is the second largest population in China. The Bayesian skyline plot showed that the 19A ST320 began to expand rapidly around 2001, which appeared to coincide with the prevalence of 19A after application of PCV7 in 2000 in the USA. We also observed frequent transmission of 19A ST320 between countries. It suggests that mass vaccination in some countries could affect the prevalence of clones in unvaccinated countries in the context of high-frequency international transmission. CONCLUSIONS Our results refined the internal phylogenetic relationship of CC271, showing that the 19F ST271-B and 19A ST320 evolved independently from ST271-A, with different histories and driving forces for their evolution and dissemination in China.
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Affiliation(s)
- Yuan Zeng
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- College of Life Science, University of Chinese Academy of Sciences, Beijing, China
| | - Yuqin Song
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Lanqing Cui
- Institute of Clinical Pharmacology, Peking University First Hospital, Beijing, China
| | - Qi Wu
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Chao Wang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Adriano Cappellazzo Coelho
- Departamento de Biologia Animal, Instituto de Biologia, Universidade Estadual de Campinas (UNICAMP), Campinas, Brazil
| | - Gang Zhang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Dawei Wei
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Chao Li
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Jingren Zhang
- Center for Infectious Disease Research, Department of Basic Medical Science, School of Medicine, Tsinghua University, Beijing, China
| | - Jacques Corbeil
- Department of Molecular Medicine, Big Data Research Centre, Nutrition Health and Society Centre (NUTRISS), INAF Institute Intelligence and Data, Laval University, Québec, Canada
| | - Yun Li
- Institute of Clinical Pharmacology, Peking University First Hospital, Beijing, China.
| | - Jie Feng
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.
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Puzia W, Gawor J, Gromadka R, Skoczyńska A, Sadowy E. Comparative genomic analysis of two ST320 Streptococcus pneumoniae isolates, representing serotypes 19A and 19F. BMC Genom Data 2023; 24:19. [PMID: 37032356 PMCID: PMC10084702 DOI: 10.1186/s12863-023-01118-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 03/03/2023] [Indexed: 04/11/2023] Open
Abstract
BACKGROUND Streptococcus pneumoniae (pneumococcus) represents an important human pathogen, responsible for respiratory and invasive infections in the community. The efficacy of polysaccharide conjugate vaccines formulated against pneumococci is reduced by the phenomenon of serotype replacement in population of this pathogen. The aim of the current study was to obtain and compare complete genomic sequences of two pneumococcal isolates, both belonging to ST320 but differing by the serotype. RESULTS Here, we report genomic sequences of two isolates of important human pathogen, S. pneumoniae. Genomic sequencing resulted in complete sequences of chromosomes of both isolates, 2,069,241 bp and 2,103,144 bp in size, and confirmed the presence of cps loci specific for serotypes 19A and 19F. The comparative analysis of these genomes revealed several instances of recombination, which involved not only S. pneumoniae but also presumably other streptococci as donors. CONCLUSIONS We report the complete genomic sequences of two S. pneumoniae isolates of ST320 and serotypes 19A and 19F. The detailed comparative analysis of these genomes revealed the history of several recombination events, clustered in the region including the cps locus.
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Affiliation(s)
- Weronika Puzia
- Department of Epidemiology and Clinical Microbiology, National Medicines Institute, Warsaw, Poland
- DNA Sequencing and Synthesis Facility, Institute of Biochemistry and Biophysics PAS, Warsaw, Poland
| | - Jan Gawor
- DNA Sequencing and Synthesis Facility, Institute of Biochemistry and Biophysics PAS, Warsaw, Poland
| | - Robert Gromadka
- DNA Sequencing and Synthesis Facility, Institute of Biochemistry and Biophysics PAS, Warsaw, Poland
| | - Anna Skoczyńska
- Department of Epidemiology and Clinical Microbiology, National Medicines Institute, Warsaw, Poland
- National Reference Centre for Bacterial Meningitis, National Medicines Institute, Warsaw, Poland
| | - Ewa Sadowy
- Department of Molecular Microbiology, National Medicines Institute, Ul. Chelmska 30/34, 00-725, Warsaw, Poland.
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Whole-genome analysis-based phylogeographic investigation of Streptococcus pneumoniae serotype 19A sequence type 320 isolates in Japan. Antimicrob Agents Chemother 2021; 66:e0139521. [PMID: 34930035 PMCID: PMC8846463 DOI: 10.1128/aac.01395-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
After the introduction of the seven-valent pneumococcal conjugate vaccine, the global spread of multidrug-resistant serotype 19A-sequence type 320 (ST320) strains of Streptococcus pneumoniae became a public health concern. In Japan, the main genotype of serotype 19A was ST3111, and the identification rate of ST320 was low. Although the isolates were sporadically detected in both adults and children, their origin remains unknown. Thus, by combining pneumococcal isolates collected in three nationwide pneumococcal surveillance studies conducted in Japan between 2008 and 2020, we analyzed 56 serotype 19A-ST320 isolates along with 931 global isolates, using whole-genome sequencing to uncover the transmission route of the globally distributed clone in Japan. The clone was frequently detected in Okinawa Prefecture, where the United States returned to Japan in 1972. Phylogenetic analysis demonstrated that the isolates from Japan were genetically related to those from the United States; therefore, the common ancestor may have originated in the United States. In addition, Bayesian analysis suggested that the time to the most recent common ancestor of the isolates from Japan and the U.S. was approximately the 1990s to 2000, suggesting the possibility that the common ancestor could have already spread in the United States before the Taiwan 19F-14 isolate was first identified in a Taiwanese hospital in 1997. The phylogeographical analysis supported the transmission of the clone from the United States to Japan, but the analysis could be influenced by sampling bias. These results suggested the possibility that the serotype 19A-ST320 clone had already spread in the United States before being imported into Japan.
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Riley LW. Distinguishing Pathovars from Nonpathovars: Escherichia coli. Microbiol Spectr 2020; 8:10.1128/microbiolspec.ame-0014-2020. [PMID: 33385193 PMCID: PMC10773148 DOI: 10.1128/microbiolspec.ame-0014-2020] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Indexed: 02/07/2023] Open
Abstract
Escherichia coli is one of the most well-adapted and pathogenically versatile bacterial organisms. It causes a variety of human infections, including gastrointestinal illnesses and extraintestinal infections. It is also part of the intestinal commensal flora of humans and other mammals. Groups of E. coli that cause diarrhea are often described as intestinal pathogenic E. coli (IPEC), while those that cause infections outside of the gut are called extraintestinal pathogenic E. coli (ExPEC). IPEC can cause a variety of diarrheal illnesses as well as extraintestinal syndromes such as hemolytic-uremic syndrome. ExPEC cause urinary tract infections, bloodstream infection, sepsis, and neonatal meningitis. IPEC and ExPEC have thus come to be referred to as pathogenic variants of E. coli or pathovars. While IPEC can be distinguished from commensal E. coli based on their characteristic virulence factors responsible for their associated clinical manifestations, ExPEC cannot be so easily distinguished. IPEC most likely have reservoirs outside of the human intestine but it is unclear if ExPEC represent nothing more than commensal E. coli that breach a sterile barrier to cause extraintestinal infections. This question has become more complicated by the advent of whole genome sequencing (WGS) that has raised a new question about the taxonomic characterization of E. coli based on traditional clinical microbiologic and phylogenetic methods. This review discusses how molecular epidemiologic approaches have been used to address these questions, and how answers to these questions may contribute to our better understanding of the epidemiology of infections caused by E. coli. *This article is part of a curated collection.
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Affiliation(s)
- Lee W Riley
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, CA 94720
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Zhu Z, Surujon D, Ortiz-Marquez JC, Huo W, Isberg RR, Bento J, van Opijnen T. Entropy of a bacterial stress response is a generalizable predictor for fitness and antibiotic sensitivity. Nat Commun 2020; 11:4365. [PMID: 32868761 PMCID: PMC7458919 DOI: 10.1038/s41467-020-18134-z] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Accepted: 08/06/2020] [Indexed: 02/07/2023] Open
Abstract
Current approaches explore bacterial genes that change transcriptionally upon stress exposure as diagnostics to predict antibiotic sensitivity. However, transcriptional changes are often specific to a species or antibiotic, limiting implementation to known settings only. While a generalizable approach, predicting bacterial fitness independent of strain, species or type of stress, would eliminate such limitations, it is unclear whether a stress-response can be universally captured. By generating a multi-stress and species RNA-Seq and experimental evolution dataset, we highlight the strengths and limitations of existing gene-panel based methods. Subsequently, we build a generalizable method around the observation that global transcriptional disorder seems to be a common, low-fitness, stress response. We quantify this disorder using entropy, which is a specific measure of randomness, and find that in low fitness cases increasing entropy and transcriptional disorder results from a loss of regulatory gene-dependencies. Using entropy as a single feature, we show that fitness and quantitative antibiotic sensitivity predictions can be made that generalize well beyond training data. Furthermore, we validate entropy-based predictions in 7 species under antibiotic and non-antibiotic conditions. By demonstrating the feasibility of universal predictions of bacterial fitness, this work establishes the fundamentals for potentially new approaches in infectious disease diagnostics.
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Affiliation(s)
- Zeyu Zhu
- Biology Department, Boston College, Chestnut Hill, MA, 02467, USA
| | - Defne Surujon
- Biology Department, Boston College, Chestnut Hill, MA, 02467, USA
| | | | - Wenwen Huo
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, MA, 02111, USA
| | - Ralph R Isberg
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, MA, 02111, USA
| | - José Bento
- Computer Science Department, Boston College, Chestnut Hill, MA, 02467, USA
| | - Tim van Opijnen
- Biology Department, Boston College, Chestnut Hill, MA, 02467, USA.
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Toda H, Tanaka Y, Satoh K, Komatsu M, Wada Y, Tobe T, Kamisako T. Epidemiological and molecular characterization of invasive Streptococcus pneumoniae isolated following introduction of 7-valent conjugate vaccine in Kinki region, Japan, 2008-2013. J Infect Chemother 2019; 26:451-458. [PMID: 31870586 DOI: 10.1016/j.jiac.2019.11.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 09/14/2019] [Accepted: 11/27/2019] [Indexed: 11/24/2022]
Abstract
Streptococcus pneumoniae is one of the most common bacteria causing community-acquired pneumonia and meningitis. The use of 7-valent pneumococcal conjugate vaccine (PCV7) has reduced the incidence of pneumococcal disease while changing pneumococcal population through herd immunity and non-vaccine pneumococci replacement. This study investigated molecular epidemiologic characteristics of pneumococcal strains in the Kinki region of Japan from 2008 to 2013. A total of 159 invasive pneumococcal isolates were characterized by serotyping, antibiotic susceptibility testing, PCR analysis of penicillin-binding protein genes, multilocus sequence typing (MLST), and pulsed-field gel electrophoresis (PFGE). In adult populations, pediatric PCV7 introduction decreased isolates expressing PCV7 serotypes via herd immunity and increased isolates expressing non-PCV7 serotypes. The rate of penicillin resistance and isolates with alterations in all three pbp genes was higher in PCV7 type isolates than in non-PCV7 type isolates. In MLST analysis, all of serotype 19F isolates were of the same sequence type, ST236, which is the antimicrobial-resistant clone Taiwan19F-14, and the majority of serotypes 23F and 19A isolates were of ST1437 and ST3111 respectively, which are the predominant clones of antimicrobial-resistant pneumococci in Japan. In PFGE profiles, serotype 6B-ST2224, serotype 19F-ST236, serotype 19A-ST3111, and serotype 23F-ST1437 formed six separate clusters composed of genetically identical strains, and genetically identical serotype 22F-ST433 formed two different clusters between the pre- and post-PCV7 period. The results of molecular analysis suggest the spread and persistence of these identical antimicrobial resistant clones in the Kinki region and genetic changes of epidemic clone serotype 22F-ST433 before and after pediatric PCV7 introduction.
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Affiliation(s)
- Hirofumi Toda
- Department of Clinical Laboratory, Kindai University Hospital, Japan; Laboratory of Molecular Medical Microbiology, Department of Biomedical Informatics, Osaka University Graduate School of Medicine, Japan.
| | - Yuji Tanaka
- Department of Clinical Laboratory Medicine, Kindai University Faculty of Medicine, Japan
| | - Kaori Satoh
- Clinical Research Center, Kindai University Hospital, Japan
| | - Masaru Komatsu
- Department of Clinical Laboratory Science, Tenri Health Care University, Japan
| | - Yasunao Wada
- Department of Clinical Laboratory, Hyogo Medical University Hospital, Japan
| | - Toru Tobe
- Laboratory of Molecular Medical Microbiology, Department of Biomedical Informatics, Osaka University Graduate School of Medicine, Japan
| | - Toshinori Kamisako
- Department of Clinical Laboratory Medicine, Kindai University Faculty of Medicine, Japan
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High Frequency of Macrolide-Resistant Streptococcus pneumoniae Colonization in Respiratory Tract of Healthy Children in Ardabil, Iran. TANAFFOS 2019; 18:118-125. [PMID: 32440299 PMCID: PMC7230131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
BACKGROUND Streptococcus pneumoniae (S. pneumoniae) is one of the most common causes of human diseases in young children. Macrolides are commonly antibiotics used for empirical treatment of community-acquired respiratory infections. The purpose of this study was to determine antibiotic resistance pattern as well as the relationship between macrolide resistance and the major mechanisms of resistance in pneumococci isolated from healthy children. MATERIALS AND METHODS In this cross-sectional study, 43 isolates of S. pneumoniae were collected from healthy children in Ardabil. Resistance pattern against tested antibiotics was determined using the disk diffusion method. The Minimum Inhibitory Concentration (MIC) of erythromycin was determined using the E-test strips. The mefA/E and ermB gene were detected in erythromycin-resistant isolates using the specific primers and Polymerase Chain Reaction (PCR) technique. RESULTS According to antimicrobial susceptibility testing, 74.4 % of the isolates were resistant to erythromycin, 95.3 % to penicillin, 81.3 % to co-trimoxazole, 72 % to azithromycin, 41.8 % to tetracycline, 27.9 % to clindamycin, and 16.2 % to chloramphenicol. All isolates were susceptible to levofloxacin and vancomycin. In the case of rifampin, 95.3% of the isolates were sensitive and 4.6% semi-sensitive. The MIC of erythromycin for resistant isolates was between 1.5 and ≥ 256 μg/ml. PCR results revealed that 100% of erythromycin-resistant isolates contained mefA/E gene and 81.25 % contained both the ermB and mefA/E genes. CONCLUSION The prevalence of antibiotic-resistant strains of S. pneumoniae, especially resistance to macrolides, was high among healthy children in Ardabil. According to the results of this study, we suggest using levofloxacin, rifampin and vancomycin antibiotics as an appropriate prophylactic regimen in pneumococcal infections.
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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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Žemličková H, Mališová L, Španělová P, Jakubů V, Kozáková J, Musílek M, Medvecký M. Molecular characterization of serogroup 19 Streptococcus pneumoniae in the Czech Republic in the post-vaccine era. J Med Microbiol 2018; 67:1003-1011. [PMID: 29856703 PMCID: PMC6152367 DOI: 10.1099/jmm.0.000765] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Accepted: 05/08/2018] [Indexed: 11/18/2022] Open
Abstract
Purpose. The aim of this study was to characterize serogroup 19 isolates resistant to macrolides and/or penicillin found among pneumococci recovered from cases of invasive and respiratory tract disease in the Czech Republic in 2014.Methods. Pneumococcal isolates of serotypes 19A (n=26) and 19F (n=10) that were non-susceptible to penicillin and/or macrolides and had been collected in 2014 were analysed using multi-locus sequence typing (MLST). Four isolates representing the major clones were subjected to whole-genome sequencing (WGS).Results. The penicillin-susceptible macrolide-resistant isolates of serotype 19A were mainly associated with sequence type (ST) 416 belonging to clonal complex (CC) 199, and the penicillin-resistant isolates were of serotype 19F belonging to ST1464 (CC 320). WGS revealed the presence of pilus 1, in association with pilus 2, in serotype19F isolates belonging to CC 320. Another adhesin, pneumococcal serine-rich protein (PsrP), was only present in serotype 19A isolates of ST416. Analysis of the penicillin-binding proteins (PBPs) of serotype 19F penicillin-resistant isolates (ST1464 and ST271) performed on PBP1a, 2b and 2x identified a large number of mutations in comparison to the reference strain, R6. Both isolates contained a unique PBP profile; however, they were highly similar to PBP sequences of the Taiwan19F-14 reference strain. The Pbp2b sequences of both 19F isolates showed the lowest similarity to those of the Taiwan19F-14 strain (91 % similarity), while they were also found to be distantly related to each other (94 % similarity).Conclusions. WGS revealed specific virulence factors in antibiotic-resistant pneumococcal clones that spread rapidly in the post-vaccine era in the Czech Republic.
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Affiliation(s)
- Helena Žemličková
- Centre for Epidemiology and Microbiology, National Institute of Public Health, Prague, Czech Republic
- Department of Clinical Microbiology, Faculty of Medicine and University Hospital, Charles University, Hradec Kralove, Czech Republic
| | - Lucia Mališová
- Centre for Epidemiology and Microbiology, National Institute of Public Health, Prague, Czech Republic
| | - Petra Španělová
- Centre for Epidemiology and Microbiology, National Institute of Public Health, Prague, Czech Republic
| | - Vladislav Jakubů
- Centre for Epidemiology and Microbiology, National Institute of Public Health, Prague, Czech Republic
| | - Jana Kozáková
- Centre for Epidemiology and Microbiology, National Institute of Public Health, Prague, Czech Republic
| | - Martin Musílek
- Centre for Epidemiology and Microbiology, National Institute of Public Health, Prague, Czech Republic
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Oodate M, Kimura K, Banno H, Yokoyama S, Jin W, Wachino JI, Hasegawa Y, Arakawa Y. Predominance of Serogroup 19 CC320/271 among Penicillin-Nonsusceptible Streptococcus pneumoniae Isolates after Introduction of the PCV7 Vaccine in Several Regions of Japan. Jpn J Infect Dis 2017; 71:14-20. [PMID: 29093321 DOI: 10.7883/yoken.jjid.2017.236] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Multidrug-resistant Streptococcus pneumoniae serogroup 19, including serotypes 19A and 19F, associated with clonal complex 320/271 (CC320/271), has been previously shown to be predominant in many countries after introduction of a 7-valent pneumococcal conjugate vaccine (PCV7). However, in Japan there has been no epidemiological research focused on penicillin-nonsusceptible isolates after this event. Therefore, we aimed to characterize penicillin-nonsusceptible S. pneumoniae (PNSSP; penicillin minimum inhibitory concentration [MIC] ≥ 4.0 μg/ml) after the introduction of PCV7 in Japan. Throughout Japan, we collected 1,057 pneumococcal isolates from 2010 to 2014. We then evaluated MICs and performed serotyping, multilocus sequence typing, and sequencing of penicillin-binding protein genes in 51 isolates (penicillin MIC ≥ 2.0 μg/ml). Twenty-three isolates (2.2%) showed penicillin nonsusceptibility (penicillin MIC ≥ 4.0 μg/ml). Serotypes 19F (14 isolates, 60.9%) and 23F (4 isolates, 17.4%), which are covered by the vaccine, were predominant among PNSSP strains. Only 3 isolates belonged to nonvaccine serotype 19A. Among the PNSSP isolates, CC320/271 (16/23 strains, 69.6%) was the most prevalent clone. Moreover, CC320/271 clones showed high MIC values of a third-generation cephalosporin. Thus, we demonstrated clonal predominance of serogroup 19 CC320/271 with strong resistance to β-lactams including a third-generation cephalosporin among PNSSP isolates.
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Affiliation(s)
- Mitsuru Oodate
- Department of Bacteriology, Nagoya University Graduate School of Medicine.,Department of Respiratory Medicine, Nagoya University Graduate School of Medicine
| | - Kouji Kimura
- Department of Bacteriology, Nagoya University Graduate School of Medicine
| | - Hirotsugu Banno
- Department of Bacteriology, Nagoya University Graduate School of Medicine
| | - Satoru Yokoyama
- Department of Bacteriology, Nagoya University Graduate School of Medicine
| | - Wanchun Jin
- Department of Bacteriology, Nagoya University Graduate School of Medicine
| | - Jun-Ichi Wachino
- Department of Bacteriology, Nagoya University Graduate School of Medicine
| | - Yoshinori Hasegawa
- Department of Respiratory Medicine, Nagoya University Graduate School of Medicine
| | - Yoshichika Arakawa
- Department of Bacteriology, Nagoya University Graduate School of Medicine
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Jensen PA, Zhu Z, van Opijnen T. Antibiotics Disrupt Coordination between Transcriptional and Phenotypic Stress Responses in Pathogenic Bacteria. Cell Rep 2017; 20:1705-1716. [PMID: 28813680 PMCID: PMC5584877 DOI: 10.1016/j.celrep.2017.07.062] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Revised: 06/28/2017] [Accepted: 07/23/2017] [Indexed: 01/19/2023] Open
Abstract
Bacterial genes that change in expression upon environmental disturbance have commonly been seen as those that must also phenotypically matter. However, several studies suggest that differentially expressed genes are rarely phenotypically important. We demonstrate, for Gram-positive and Gram-negative bacteria, that these seemingly uncoordinated gene sets are involved in responses that can be linked through topological network analysis. However, the level of coordination is stress dependent. While a well-coordinated response is triggered in response to nutrient stress, antibiotics trigger an uncoordinated response in which transcriptionally and phenotypically important genes are neither linked spatially nor in their magnitude. Moreover, a gene expression meta-analysis reveals that genes with large fitness changes during stress have low transcriptional variation across hundreds of other conditions, and vice versa. Our work suggests that cellular responses can be understood through network models that incorporate regulatory and genetic relationships, which could aid drug target predictions and genetic network engineering.
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Affiliation(s)
- Paul A Jensen
- Biology Department, Boston College, Chestnut Hill, MA, USA.
| | - Zeyu Zhu
- Biology Department, Boston College, Chestnut Hill, MA, USA.
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Lee HY, Wu TL, Su LH, Li HC, Janapatla RP, Chen CL, Chiu CH. Invasive pneumococcal disease caused by ceftriaxone-resistant Streptococcus pneumoniae in Taiwan. JOURNAL OF MICROBIOLOGY, IMMUNOLOGY, AND INFECTION = WEI MIAN YU GAN RAN ZA ZHI 2017; 51:500-509. [PMID: 28690025 DOI: 10.1016/j.jmii.2016.12.004] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2016] [Revised: 10/26/2016] [Accepted: 12/03/2016] [Indexed: 11/17/2022]
Abstract
BACKGROUND Invasive pneumococcal disease (IPD) was associated with mortality, but the risk factors associated with mortality remains controversial. METHODS A retrospective cohort study was designed. All patients with IPD from 2011 to 2013 admitted in a medical center were screened and collected for their clinical presentations and laboratory characteristics. RESULTS Approximately half of the 134 IPD isolates derived from these patients belonged to three major serotypes (19A, 6A and 3), which are included in 13-valent pneumococcal conjugate vaccine (PCV13), but not in 7-valent pneumococcal conjugate vaccine (PCV7). Ceftriaxone resistance according to non-meningitis criteria was identified in 38% of the IPD isolates, and was the major independent risk factor associated with inappropriate initial therapy that subsequently contributed to mortality of the patients. Infection by serotype 6A, 15B, 19A, 19F, or 23F was the major independent risk factor associated with ceftriaxone resistance (non-meningitis criteria). 77.6% of these isolates belonged to additional PCV13 serotypes, with more than 40% expressing resistance to ceftriaxone. In terms of serotype coverage, PCV13 covered 94.1% of the IPD isolates with ceftriaxone resistance, in comparison to 21.6% only by PCV7. CONCLUSIONS The increase of ceftriaxone resistance in pneumococci in part driven by PCV7 vaccination in Taiwan is worrisome. The use of PCV13 in children as well as in the elderly population is likely to offer protection from the infection caused by ceftriaxone-resistant pneumococci. It is important to give an effective drug such as penicillin, fluoroquinolones or vancomycin in 2 days for improving outcome of IPD patients.
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Affiliation(s)
- Hao-Yuan Lee
- Department of Nursing, Jen-Teh Junior College of Medicine, Nursing and Management, Miaoli, Taiwan; Molecular Infectious Disease Research Center, Chang Gung Memorial Hospital, Taoyuan, Taiwan; School of Medicine, College of Medicine, Fu Jen Catholic University, New Taipei, Taiwan
| | - Tsu-Lan Wu
- Department of Laboratory Medicine, Chang Gung Memorial Hospital, Taoyuan, Taiwan; Department of Medical Biotechnology and Laboratory Science, Chang Gung University, Taoyuan, Taiwan
| | - Lin-Hui Su
- Molecular Infectious Disease Research Center, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Hsin-Chieh Li
- Molecular Infectious Disease Research Center, Chang Gung Memorial Hospital, Taoyuan, Taiwan; Department of Laboratory Medicine, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | | | - Chyi-Liang Chen
- Molecular Infectious Disease Research Center, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Cheng-Hsun Chiu
- Molecular Infectious Disease Research Center, Chang Gung Memorial Hospital, Taoyuan, Taiwan; Department of Pediatrics, Chang Gung Children's Hospital, Chang Gung University College of Medicine, Taoyuan, Taiwan.
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14
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van Opijnen T, Dedrick S, Bento J. Strain Dependent Genetic Networks for Antibiotic-Sensitivity in a Bacterial Pathogen with a Large Pan-Genome. PLoS Pathog 2016; 12:e1005869. [PMID: 27607357 PMCID: PMC5015961 DOI: 10.1371/journal.ppat.1005869] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Accepted: 08/15/2016] [Indexed: 11/19/2022] Open
Abstract
The interaction between an antibiotic and bacterium is not merely restricted to the drug and its direct target, rather antibiotic induced stress seems to resonate through the bacterium, creating selective pressures that drive the emergence of adaptive mutations not only in the direct target, but in genes involved in many different fundamental processes as well. Surprisingly, it has been shown that adaptive mutations do not necessarily have the same effect in all species, indicating that the genetic background influences how phenotypes are manifested. However, to what extent the genetic background affects the manner in which a bacterium experiences antibiotic stress, and how this stress is processed is unclear. Here we employ the genome-wide tool Tn-Seq to construct daptomycin-sensitivity profiles for two strains of the bacterial pathogen Streptococcus pneumoniae. Remarkably, over half of the genes that are important for dealing with antibiotic-induced stress in one strain are dispensable in another. By confirming over 100 genotype-phenotype relationships, probing potassium-loss, employing genetic interaction mapping as well as temporal gene-expression experiments we reveal genome-wide conditionally important/essential genes, we discover roles for genes with unknown function, and uncover parts of the antibiotic's mode-of-action. Moreover, by mapping the underlying genomic network for two query genes we encounter little conservation in network connectivity between strains as well as profound differences in regulatory relationships. Our approach uniquely enables genome-wide fitness comparisons across strains, facilitating the discovery that antibiotic responses are complex events that can vary widely between strains, which suggests that in some cases the emergence of resistance could be strain specific and at least for species with a large pan-genome less predictable.
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Affiliation(s)
- Tim van Opijnen
- Boston College, Biology Department, Chestnut Hill, Massachusetts, United States of America
| | - Sandra Dedrick
- Boston College, Biology Department, Chestnut Hill, Massachusetts, United States of America
| | - José Bento
- Boston College, Computer Science Department, Massachusetts, United States of America
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15
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Kim L, McGee L, Tomczyk S, Beall B. Biological and Epidemiological Features of Antibiotic-Resistant Streptococcus pneumoniae in Pre- and Post-Conjugate Vaccine Eras: a United States Perspective. Clin Microbiol Rev 2016; 29:525-52. [PMID: 27076637 PMCID: PMC4861989 DOI: 10.1128/cmr.00058-15] [Citation(s) in RCA: 169] [Impact Index Per Article: 21.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Streptococcus pneumoniae inflicts a huge disease burden as the leading cause of community-acquired pneumonia and meningitis. Soon after mainstream antibiotic usage, multiresistant pneumococcal clones emerged and disseminated worldwide. Resistant clones are generated through adaptation to antibiotic pressures imposed while naturally residing within the human upper respiratory tract. Here, a huge array of related commensal streptococcal strains transfers core genomic and accessory resistance determinants to the highly transformable pneumococcus. β-Lactam resistance is the hallmark of pneumococcal adaptability, requiring multiple independent recombination events that are traceable to nonpneumococcal origins and stably perpetuated in multiresistant clonal complexes. Pneumococcal strains with elevated MICs of β-lactams are most often resistant to additional antibiotics. Basic underlying mechanisms of most pneumococcal resistances have been identified, although new insights that increase our understanding are continually provided. Although all pneumococcal infections can be successfully treated with antibiotics, the available choices are limited for some strains. Invasive pneumococcal disease data compiled during 1998 to 2013 through the population-based Active Bacterial Core surveillance program (U.S. population base of 30,600,000) demonstrate that targeting prevalent capsular serotypes with conjugate vaccines (7-valent and 13-valent vaccines implemented in 2000 and 2010, respectively) is extremely effective in reducing resistant infections. Nonetheless, resistant non-vaccine-serotype clones continue to emerge and expand.
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Affiliation(s)
- Lindsay Kim
- Epidemiology Section, Respiratory Diseases Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Lesley McGee
- Streptococcus Laboratory, Respiratory Diseases Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Sara Tomczyk
- Epidemiology Section, Respiratory Diseases Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Bernard Beall
- Streptococcus Laboratory, Respiratory Diseases Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
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16
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Addiction of Hypertransformable Pneumococcal Isolates to Natural Transformation for In Vivo Fitness and Virulence. Infect Immun 2016; 84:1887-1901. [PMID: 27068094 DOI: 10.1128/iai.00097-16] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Accepted: 04/06/2016] [Indexed: 12/25/2022] Open
Abstract
Natural genetic transformation of Streptococcus pneumoniae, an important human pathogen, mediates horizontal gene transfer for the development of drug resistance, modulation of carriage and virulence traits, and evasion of host immunity. Transformation frequency differs greatly among pneumococcal clinical isolates, but the molecular basis and biological importance of this interstrain variability remain unclear. In this study, we characterized the transformation frequency and other associated phenotypes of 208 S. pneumoniae clinical isolates representing at least 30 serotypes. While the vast majority of these isolates (94.7%) were transformable, the transformation frequency differed by up to 5 orders of magnitude between the least and most transformable isolates. The strain-to-strain differences in transformation frequency were observed among many isolates producing the same capsule types, indicating no general association between transformation frequency and serotype. However, a statistically significant association was observed between the levels of transformation and colonization fitness/virulence in the hypertransformable isolates. Although nontransformable mutants of all the selected hypertransformable isolates were significantly attenuated in colonization fitness and virulence in mouse infection models, such mutants of the strains with relatively low transformability had no or marginal fitness phenotypes under the same experimental settings. This finding strongly suggests that the pneumococci with high transformation capability are "addicted" to a "hypertransformable" state for optimal fitness in the human host. This work has thus provided an intriguing hint for further investigation into how the competence system impacts the fitness, virulence, and other transformation-associated traits of this important human pathogen.
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17
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Liu EYM, Chang JC, Lin JC, Chang FY, Fung CP. Important Mutations Contributing to High-Level Penicillin Resistance in Taiwan 19F-14, Taiwan 23F-15, and Spain 23F-1 of Streptococcus pneumoniae Isolated from Taiwan. Microb Drug Resist 2016; 22:646-654. [PMID: 27042760 DOI: 10.1089/mdr.2015.0261] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Penicillin-resistant Streptococcus pneumoniae is a serious concern worldwide. In this study, we analyzed the cause of β-lactam resistance in pandemic multidrug-resistant clones. A total of 41 penicillin-nonsusceptible clinical isolates were collected from 1996 to 2012. Sero- and molecular typing confirmed that these isolates were clonal types of Taiwan19F-14, Taiwan23F-15, and Spain23F-1. Sero-switching was found in four isolates. All isolates were multidrug resistant. Sequencing analysis of the penicillin binding proteins (PBPs) was performed on PBP1a, 2b, and 2x, and a large number of mutations were identified in comparing to clinical penicillin-susceptible isolates and the recipient strain R6 used for homologous recombination. The T451A substitution was the key amino acid in PBP2b that contributed to penicillin resistance. T338A in PBP2x played a role in resistance and reached the highest level of resistance when combined with other mutations in PBP2x. High-level penicillin resistance could not be obtained without the combination of mutations in PBP1a with PBP2b and 2x. The amino acid substitutions in PBP1a, 2b, and 2x were the crucial factors for β-lactam resistance.
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Affiliation(s)
- Esther Yip-Mei Liu
- 1 Institute of Clinical Medicine, School of Medicine, National Yang-Ming University , Taipei, Taiwan
| | - Jen-Chang Chang
- 2 Institute of Infectious Diseases and Vaccinology, National Health Research Institutes , Zhunan, Taiwan
| | - Jung-Chung Lin
- 3 Division of Infectious Diseases and Tropical Medicine, Department of Internal Medicine, Tri-Service General Hospital, National Defense Medical Center , Taipei, Taiwan
| | - Feng-Yee Chang
- 3 Division of Infectious Diseases and Tropical Medicine, Department of Internal Medicine, Tri-Service General Hospital, National Defense Medical Center , Taipei, Taiwan
| | - Chang-Phone Fung
- 1 Institute of Clinical Medicine, School of Medicine, National Yang-Ming University , Taipei, Taiwan .,4 Division of Infectious Diseases, Department of Medicine, Taipei Veterans General Hospital and National Yang-Ming University , Taipei, Taiwan
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18
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Pan F, Han L, Huang W, Tang J, Xiao S, Wang C, Qin H, Zhang H. Serotype Distribution, Antimicrobial Susceptibility, and Molecular Epidemiology of Streptococcus pneumoniae Isolated from Children in Shanghai, China. PLoS One 2015; 10:e0142892. [PMID: 26571373 PMCID: PMC4646667 DOI: 10.1371/journal.pone.0142892] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2015] [Accepted: 10/28/2015] [Indexed: 11/19/2022] Open
Abstract
OBJECTIVE Streptococcus pneumoniae is a common pathogenic cause of pediatric infections. This study investigated the serotype distribution, antimicrobial susceptibility, and molecular epidemiology of pneumococci before the introduction of conjugate vaccines in Shanghai, China. METHODS A total of 284 clinical pneumococcal isolates (270, 5, 4,3, and 2 of which were isolated from sputum, bronchoalveolar lavage fluid, blood, cerebral spinal fluid, and ear secretions, respectively) from children less than 14 years of age who had not been vaccinated with a conjugate vaccine, were collected between January and December in 2013. All isolates were serotyped by multiplex polymerase chain reaction or quellung reactions and antimicrobial susceptibility testing was performed using the broth microdilution method. The molecular epidemiology of S.pneumoniae was analyzed by multilocus sequence typing (MLST). RESULTS Among the 284 pneumococcal isolates, 19F (33.5%), 19A (14.1%), 23F (12.0%), and 6A (8.8%) were the most common serotypes and the coverage rates of the 7-, 10-, and 13-valent pneumococcal conjugate vaccines (PCV7, PCV10, and PCV13) were 58.6%, 59.4% and 85.1%, respectively. Antimicrobial susceptibility showed that the prevalence rates of S.pneumoniae resistance to penicillin were 11.3% (32/284). Approximately 88.0% (250/284) of the isolates exhibited multi-drug resistance. MLST analysis revealed a high level of diversity, with 65 sequence types (STs) among 267 isolates. Specifically, the four predominant STs were ST271 (24.3%, 65/267), ST320 (11.2%, 30/267), ST81 (9.7%, 26/267), and ST3173 (5.2%, 14/267), which were mainly associated with serotypes 19F, 19A, 23F, and 6A, respectively. CONCLUSIONS The prevalent serotypes among clinical isolates from children were 19F, 19A, 23F, and 6A and these isolates showed high resistance rates to β-lactams and macrolides. The Taiwan19F-14 clone played a predominant role in the dissemination of pneumococcal isolates in Shanghai, China. Therefore, continued and regional surveillance on pneumococcal isolates may be necessary.
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Affiliation(s)
- Fen Pan
- Department of Clinical Laboratory, Shanghai Children’s Hospital, Shanghai Jiaotong University, Shanghai, China
| | - Lizhong Han
- Department of Clinical Microbiology, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Weichun Huang
- Shanghai Children’s Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Jin Tang
- Shanghai Sixth People's Hospital, Shanghai Jiaotong University, Shanghai, China
| | - Shuzhen Xiao
- Department of Clinical Microbiology, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Chun Wang
- Department of Clinical Laboratory, Shanghai Children’s Hospital, Shanghai Jiaotong University, Shanghai, China
| | - Huihong Qin
- Department of Clinical Laboratory, Shanghai Children’s Hospital, Shanghai Jiaotong University, Shanghai, China
| | - Hong Zhang
- Department of Clinical Laboratory, Shanghai Children’s Hospital, Shanghai Jiaotong University, Shanghai, China
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19
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Draft Genome Sequences of Two Streptococcus pneumoniae Serotype 19F Sequence Type 271 Clinical Isolates with Low- and High-Level Cefotaxime Resistance. GENOME ANNOUNCEMENTS 2015; 3:3/3/e00605-15. [PMID: 26067956 PMCID: PMC4463520 DOI: 10.1128/genomea.00605-15] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
We report here the draft genomes of two pneumococcal isolates in Hong Kong, CU_SPNE1_05 and CU_SPNE32_06. Strain CU_SPNE1_05 had a cefotaxime MIC of 1 µg/ml, and CU_SPNE32_06 had an MIC of 32 µg/ml. Both strains belong to the multidrug-resistant serogroup 19, sequence type 271 (clonal complex 3200/271).
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20
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Genetic analyses of penicillin binding protein determinants in multidrug-resistant Streptococcus pneumoniae serogroup 19 CC320/271 clone with high-level resistance to third-generation cephalosporins. Antimicrob Agents Chemother 2015; 59:4040-5. [PMID: 25918136 DOI: 10.1128/aac.00094-15] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2015] [Accepted: 04/19/2015] [Indexed: 11/20/2022] Open
Abstract
We describe the dissemination of a multidrug-resistant (MDR) serogroup 19 pneumococcal clone of representative multilocus sequence type 271 (ST271) with high-level resistance to cefotaxime in Hong Kong and penicillin binding protein (pbp) genes and its relationships to Taiwan(19F)-14 and the prevalent multidrug-resistant 19A clone (MDR19A-ST320). A total of 472 nonduplicate isolates from 2006 and 2011 were analyzed. Significant increases in the rates of nonsusceptibility to penicillin (PEN) (MIC ≥ 4.0 μg/ml; 9.9 versus 23.3%; P = 0.0005), cefotaxime (CTX) (MIC ≥ 2.0 μg/ml; 12.2 versus 30.3%; P < 0.0001 [meningitis MIC ≥ 1.0 μg/ml; 30.2 versus 48.7%; P = 0.0001]), and erythromycin (ERY) (69.2 versus 84.0%; P = 0.0003) were noted when rates from 2006 and 2011 were compared. The CTX-resistant isolates with MICs of 8 μg/ml in 2011 were of serotype 19F, belonging to ST271. Analyses of the penicillin binding protein 2x (PBP2x) amino acid sequences in relation to the corresponding sequences of the R6 strain revealed M339F, E378A, M400T, and Y595F substitutions found within the ST271 clone but not present in Taiwan(19F)-14 or MDR19A. In addition, PBP2bs of ST271 strains and that of the Taiwan(19F)-14 clone were characterized by a unique amino acid substitution, E369D, while ST320 possessed the unique amino acid substitution K366N, as does that of MDR19A in the United States. We hypothesize that ST271 originated from the Taiwan(19F)-14 lineage, which had disseminated in Hong Kong in the early 2000s, and conferred higher-level β-lactam and cefotaxime resistance through acquisitions of 19 additional amino acid substitutions in PBP2b (amino acid [aa] positions 538 to 641) and altered PBP2x via recombination events. The serogroup 19 MDR CC320/271 clone warrants close monitoring to evaluate its effect after the switch to expanded conjugate vaccines.
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21
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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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22
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Croucher NJ, Hanage WP, Harris SR, McGee L, van der Linden M, de Lencastre H, Sá-Leão R, Song JH, Ko KS, Beall B, Klugman KP, Parkhill J, Tomasz A, Kristinsson KG, Bentley SD. Variable recombination dynamics during the emergence, transmission and 'disarming' of a multidrug-resistant pneumococcal clone. BMC Biol 2014; 12:49. [PMID: 24957517 PMCID: PMC4094930 DOI: 10.1186/1741-7007-12-49] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2014] [Accepted: 06/12/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Pneumococcal β-lactam resistance was first detected in Iceland in the late 1980s, and subsequently peaked at almost 25% of clinical isolates in the mid-1990s largely due to the spread of the internationally-disseminated multidrug-resistant PMEN2 (or Spain6B-2) clone of Streptococcus pneumoniae. RESULTS Whole genome sequencing of an international collection of 189 isolates estimated that PMEN2 emerged around the late 1960s, developing resistance through multiple homologous recombinations and the acquisition of a Tn5253-type integrative and conjugative element (ICE). Two distinct clades entered Iceland in the 1980s, one of which had acquired a macrolide resistance cassette and was estimated to have risen sharply in its prevalence by coalescent analysis. Transmission within the island appeared to mainly emanate from Reykjavík and the Southern Peninsular, with evolution of the bacteria effectively clonal, mainly due to a prophage disrupting a gene necessary for genetic transformation in many isolates. A subsequent decline in PMEN2's prevalence in Iceland coincided with a nationwide campaign that reduced dispensing of antibiotics to children in an attempt to limit its spread. Specific mutations causing inactivation or loss of ICE-borne resistance genes were identified from the genome sequences of isolates that reverted to drug susceptible phenotypes around this time. Phylogenetic analysis revealed some of these occurred on multiple occasions in parallel, suggesting they may have been at least temporarily advantageous. However, alteration of 'core' sequences associated with resistance was precluded by the absence of any substantial homologous recombination events. CONCLUSIONS PMEN2's clonal evolution was successful over the short-term in a limited geographical region, but its inability to alter major antigens or 'core' gene sequences associated with resistance may have prevented persistence over longer timespans.
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Affiliation(s)
- Nicholas J Croucher
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard School of Public Health, 677 Huntington Avenue, Boston MA 02115, USA
- Pathogen Genomics, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
- Department of Infectious Disease Epidemiology, Imperial College, Norfolk Place, London W2 1NY, UK
| | - William P Hanage
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard School of Public Health, 677 Huntington Avenue, Boston MA 02115, USA
| | - Simon R Harris
- Pathogen Genomics, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Lesley McGee
- Respiratory Diseases Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Mark van der Linden
- Institute for Medical Microbiology, National Reference Center for Streptococci, University Hospital, RWTH Aachen, Pauwelsstrasse 30, Aachen, Germany
| | - Herminia de Lencastre
- Laboratory of Molecular Genetics, Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, Portugal
- Laboratory of Microbiology, The Rockefeller University, New York, New York, USA
| | - Raquel Sá-Leão
- Laboratory of Molecular Genetics, Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Jae-Hoon Song
- Samsung Medical Centre, Sungkyunkwan University School of Medicine and Asia Pacific Foundation for Infectious Disease, Seoul, South Korea
| | - Kwan Soo Ko
- Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine, Suwon, South Korea
| | - Bernard Beall
- Respiratory Diseases Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Keith P Klugman
- Hubert Department of Global Health, Rollins School of Public Health and Division of Infectious Diseases, School of Medicine, Emory University, Atlanta, Georgia, USA
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, Gauteng, South Africa
| | - Julian Parkhill
- Pathogen Genomics, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Alexander Tomasz
- Laboratory of Microbiology, The Rockefeller University, New York, New York, USA
| | - Karl G Kristinsson
- Clinical Microbiology Department, Landspitali University Hospital and University of Iceland, Reykjavík, Iceland
| | - Stephen D Bentley
- Pathogen Genomics, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
- Department of Medicine, University of Cambridge, Addenbrooke’s Hospital, Cambridge CB2 0SP, UK
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23
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Jefferies JM, Mohd Yusof MY, Devi Sekaran S, Clarke SC. Novel clones of Streptococcus pneumoniae causing invasive disease in Malaysia. PLoS One 2014; 9:e97912. [PMID: 24941079 PMCID: PMC4062404 DOI: 10.1371/journal.pone.0097912] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2013] [Accepted: 04/25/2014] [Indexed: 11/19/2022] Open
Abstract
Although Streptococcus pneumoniae is a leading cause of childhood disease in South East Asia, little has previously been reported regarding the epidemiology of invasive pneumococcal disease in Malaysia and very few studies have explored pneumococcal epidemiology using multilocus sequence typing (MLST). Here we describe serotype, multilocus sequence type (ST), and penicillin susceptibility of thirty pneumococcal invasive disease isolates received by the University of Malaya Medical Centre between February 2000 and January 2007 and relate this to the serotypes included in current pneumococcal conjugate vaccines. A high level of diversity was observed; fourteen serotypes and 26 sequence types (ST), (11 of which were not previously described) were detected from 30 isolates. Penicillin non-susceptible pneumococci accounted for 33% of isolates. The extent of molecular heterogeneity within carried and disease-causing Malaysian pneumococci remains unknown. Larger surveillance and epidemiological studies are now required in this region to provide robust evidence on which to base future vaccine policy.
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Affiliation(s)
- Johanna M. Jefferies
- Faculty of Medicine and Institute of Life Sciences, University of Southampton, Southampton, United Kingdom
- NIHR Southampton Respiratory Biomedical Research Unit, Southampton, United Kingdom
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Mohd Yasim Mohd Yusof
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Shamala Devi Sekaran
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Stuart C. Clarke
- Faculty of Medicine and Institute of Life Sciences, University of Southampton, Southampton, United Kingdom
- NIHR Southampton Respiratory Biomedical Research Unit, Southampton, United Kingdom
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
- Public Health England, Southampton, United Kingdom
- University of Southampton Malaysia Campus, Nusajaya, Malaysia
- * E-mail:
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24
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Croucher NJ, Chewapreecha C, Hanage WP, Harris SR, McGee L, van der Linden M, Song JH, Ko KS, de Lencastre H, Turner C, Yang F, Sá-Leão R, Beall B, Klugman KP, Parkhill J, Turner P, Bentley SD. Evidence for soft selective sweeps in the evolution of pneumococcal multidrug resistance and vaccine escape. Genome Biol Evol 2014; 6:1589-602. [PMID: 24916661 PMCID: PMC4122920 DOI: 10.1093/gbe/evu120] [Citation(s) in RCA: 74] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
The multidrug-resistant Streptococcus pneumoniae Taiwan19F-14, or PMEN14, clone was first observed with a 19F serotype, which is targeted by the heptavalent polysaccharide conjugate vaccine (PCV7). However, “vaccine escape” PMEN14 isolates with a 19A serotype became an increasingly important cause of disease post-PCV7. Whole genome sequencing was used to characterize the recent evolution of 173 pneumococci of, or related to, PMEN14. This suggested that PMEN14 is a single lineage that originated in the late 1980s in parallel with the acquisition of multiple resistances by close relatives. One of the four detected serotype switches to 19A generated representatives of the sequence type (ST) 320 isolates that have been highly successful post-PCV7. A second produced an ST236 19A genotype with reduced resistance to β-lactams owing to alteration of pbp1a and pbp2x sequences through the same recombination that caused the change in serotype. A third, which generated a mosaic capsule biosynthesis locus, resulted in serotype 19A ST271 isolates. The rapid diversification through homologous recombination seen in the global collection was similarly observed in the absence of vaccination in a set of isolates from the Maela refugee camp in Thailand, a collection that also allowed variation to be observed within carriage through longitudinal sampling. This suggests that some pneumococcal genotypes generate a pool of standing variation that is sufficiently extensive to result in “soft” selective sweeps: The emergence of multiple mutants in parallel upon a change in selection pressure, such as vaccine introduction. The subsequent competition between these mutants makes this phenomenon difficult to detect without deep sampling of individual lineages.
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Affiliation(s)
- Nicholas J Croucher
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard School of Public Health, Boston, MassachusettsPathogen Genomics, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Claire Chewapreecha
- Pathogen Genomics, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - William P Hanage
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts
| | - Simon R Harris
- Pathogen Genomics, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Lesley McGee
- Respiratory Diseases Branch, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Mark van der Linden
- Institute for Medical Microbiology, National Reference Center for Streptococci, University Hospital, RWTH Aachen, Aachen, Germany
| | - Jae-Hoon Song
- Samsung Medical Centre, Sungkyunkwan University School of Medicine and Asia Pacific Foundation for Infectious Disease, Seoul, South Korea
| | - Kwan Soo Ko
- Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine, Suwon, South Korea
| | - Herminia de Lencastre
- Laboratory of Molecular Genetics, Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, PortugalLaboratory of Microbiology, The Rockefeller University, New York, New York
| | - Claudia Turner
- Shoklo Malaria Research Unit, Mahidol Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, ThailandMahidol Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, ThailandCentre for Tropical Medicine, Nuffield Department of Medicine, University of Oxford, United Kingdom
| | - Fan Yang
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, China
| | - Raquel Sá-Leão
- Laboratory of Molecular Genetics, Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Bernard Beall
- Respiratory Diseases Branch, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Keith P Klugman
- Hubert Department of Global Health, Rollins School of Public Health and Division of Infectious Diseases, School of Medicine, Emory UniversityCentre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, Gauteng, South Africa
| | - Julian Parkhill
- Pathogen Genomics, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Paul Turner
- Shoklo Malaria Research Unit, Mahidol Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, ThailandMahidol Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, ThailandCentre for Tropical Medicine, Nuffield Department of Medicine, University of Oxford, United Kingdom
| | - Stephen D Bentley
- Pathogen Genomics, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United KingdomDepartment of Medicine, University of Cambridge, Addenbrooke's Hospital, United Kingdom
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Figueira M, Moschioni M, De Angelis G, Barocchi M, Sabharwal V, Masignani V, Pelton SI. Variation of pneumococcal Pilus-1 expression results in vaccine escape during Experimental Otitis Media [EOM]. PLoS One 2014; 9:e83798. [PMID: 24421906 PMCID: PMC3885439 DOI: 10.1371/journal.pone.0083798] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2013] [Accepted: 11/08/2013] [Indexed: 11/18/2022] Open
Abstract
UNLABELLED The pneumococcal Pilus-1 enhances attachment to epithelial cells in the respiratory tract and subsequent invasion. Pilus-1 expression is bi-stable and positively regulated by the RlrA transcriptional regulator. To delineate the role of pilus-1 in Experimental Otitis Media (EOM), we evaluated colonization and disease due to a Streptococcus pneumoniae (SP) wild type strain (Taiwan19F-14 wt) and its otherwise isogenic pilus-1 and pilus-2 deficient mutant (Taiwan19F-14 ΔPI-1/PI-2-) as well as potential for a chimeric protein (RrgB321) vaccine candidate for prevention of middle ear (ME) disease. METHODS Chinchillas were challenged intranasally with either Taiwan19F-14 wt or Taiwan19F-14PI-1/PI-2 deficient mutant. ME status was assessed and direct cultures performed. New cohorts of animals were immunized with RrgB321 or alum. Intranasal challenge with Taiwan19F-14 wt [erythromycin susceptible E(S)] was performed. Subsequently, a second cohort of animals was immunized and challenged with either Taiwan19F-14 wt or a Pilus-1 over-expressing mutant [Taiwan19F-14+pMU1328_Pc-rlrA mutant; E resistant (R)] strain. Pilus-1 expression was analyzed in SP isolated from nasopharynx (NP) and ME fluids by flow cytometry. RESULTS Culture positive EOM developed following challenge with either wild type SP (Taiwan19F-14) or its pilus-1 deficient mutant. Culture positive EOM developed following challenge with wild type in both RrgB321 immunized and control animals. Pilus-1 expression in ME fluids was significantly higher in controls compared to immunized chinchillas. In second cohort of immunized and control animals challenged with the over-expressing Pilus-1 mutant, delayed development of EOM in the immunized animals was observed. Pneumococci recovered from ME fluid of immunized animals were no longer E(R) signifying the loss of the pMU1328_Pc-rlrA plasmid. CONCLUSION Pneumococcal pilus-1 was not essential for EOM. Regulation of Pilus-1 expression in ME fluids in the presence of anti RrgB321 antibody was essential for survival of S. pneumoniae. Pneumococci have evolved mechanisms of regulation of non-essential surface proteins to evade host defenses.
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Affiliation(s)
- Marisol Figueira
- Section of Pediatric Infectious Diseases, Maxwell Finland Laboratory for Infectious Diseases, Boston Medical Center, Boston, Massachusetts, United States of America
- * E-mail:
| | | | | | | | - Vishakha Sabharwal
- Section of Pediatric Infectious Diseases, Maxwell Finland Laboratory for Infectious Diseases, Boston Medical Center, Boston, Massachusetts, United States of America
| | | | - Stephen I. Pelton
- Section of Pediatric Infectious Diseases, Maxwell Finland Laboratory for Infectious Diseases, Boston Medical Center, Boston, Massachusetts, United States of America
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Ramos V, Parra EL, Duarte C, Moreno J. Characterization of Streptococcus pneumoniae invasive serotype 19A isolates recovered in Colombia. Vaccine 2013; 32:755-8. [PMID: 24374499 DOI: 10.1016/j.vaccine.2013.12.024] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2013] [Revised: 11/01/2013] [Accepted: 12/10/2013] [Indexed: 10/25/2022]
Abstract
The aim of this study was to determine the molecular characterization of invasive penicillin non-susceptible Streptococcus pneumoniae serotype 19A isolates, collected in Colombia between 1994 and 2012. A total of 115 isolates serotype 19A were analyzed. Genetic relationship of 80 isolates with minimal inhibitory concentration (MIC) to penicillin ≥0.125 μg/was determined by pulsed-field gel electrophoresis (PFGE) and selected strains were studied by multilocus sequence typing (MLST). Among the 115 isolates, resistance to penicillin in meningitis was 64.2%, in non-meningitis 32.2% were intermediate and 1.1% were high resistance. The most frequent sequence types were ST320 (33.7%), ST276 (21.5%), and ST1118 (11.2%). Five isolates were associated with the Spain(9V)-ST156 clone, and two isolates were related to Colombia(23F)-ST338 clone. S. pneumoniae serotype 19A increased in Colombia was associated with the spread of isolates genetically related to ST320 and ST276, and emergence of capsular variants of worldwide-disseminated clones.
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Affiliation(s)
- Viviana Ramos
- Grupo de Microbiología. Instituto Nacional de Salud, Avenida calle 26 No. 51-20, Bogotá, Colombia
| | - Eliana L Parra
- Grupo de Microbiología. Instituto Nacional de Salud, Avenida calle 26 No. 51-20, Bogotá, Colombia
| | - Carolina Duarte
- Grupo de Microbiología. Instituto Nacional de Salud, Avenida calle 26 No. 51-20, Bogotá, Colombia
| | - Jaime Moreno
- Grupo de Microbiología. Instituto Nacional de Salud, Avenida calle 26 No. 51-20, Bogotá, Colombia.
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Hsieh YC, Lin TL, Chang KY, Huang YC, Chen CJ, Lin TY, Wang JT. Expansion and evolution of Streptococcus pneumoniae serotype 19A ST320 clone as compared to its ancestral clone, Taiwan19F-14 (ST236). J Infect Dis 2013; 208:203-10. [PMID: 23559465 DOI: 10.1093/infdis/jit145] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND The Streptococcus pneumoniae serotype 19A sequence type (ST) 320 clone, derived from an international Taiwan(19F)-14 (ST236) clone, has become prevalent in many countries. METHODS The dynamics of invasive pneumococcal disease (IPD) were determined using the database of the National Notifiable Disease Surveillance System in Taiwan. The virulence of 19A ST320 and Taiwan(19F)-14 (ST236) were assessed in mice. By constructing an isogenic serotype 19F variant of the 19A ST320 strain (19F ST320), we analyzed the role of capsular type and genetic background on the difference in virulence between 19A ST320 and Taiwan(19F)-14 (ST236). RESULTS Between 2008 and 2011, IPD due to serotype 19A increased from 2.1 to 10.2 cases per 100 000 population (P < .001); IPD due to any serotype also significantly increased (P = .01). Most serotype 19A isolates belonged to ST320. Using competition experiments in a murine model of colonization, we demonstrated that 19A ST320 outcompeted Taiwan(19F)-14 (ST236; competitive index, 20.3; P = .001). 19F ST320 was 2-fold less competitive than the 19A ST320 parent (competitive index, 0.47; P = .04) but remained 14-fold more competitive than Taiwan(19F)-14 (ST236; competitive index, 14.7; P < .001). CONCLUSIONS Genetic evolution of pneumococcal clones from Taiwan(19F)-14 (ST236) to 19A ST320 has made this pneumococcus better able to colonize of the nasopharynx. This evolution reflects not only a switch in capsular serotype but also changes in other loci.
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Affiliation(s)
- Yu-Chia Hsieh
- Department of Pediatrics, Chang Gung Children's Hospital, Chang Gung Memorial Hospital, Chang Gung University, College of Medicine, Taiwan
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Spread of multidrug-resistant clonal complex 271 of serotype 19F Streptococcus pneumoniae in Beijing, China: characterization of serotype 19F. Epidemiol Infect 2013; 141:2492-6. [PMID: 23481266 DOI: 10.1017/s0950268813000514] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
We investigated the genetic structure of 120 isolates of serotype 19F Streptococcus pneumoniae from Chinese children with acute respiratory infections collected from 1997 to 2006, and 2010. All strains were susceptible to vancomycin and levofloxacin, and only five strains were not susceptible to penicillin. The non-susceptibility rate to cephalosporins increased from 1997 to 2010. Of 119 erythromycin-resistant strains, 60 carried both ermB and mefA genes. The percentage of clonal complex 271 (CC271) increased from 14.3% in 1997-1998 to 92% in 2010, whereas that of CC983 decreased from 64.3% to 0%. CC271 had a higher non-susceptibility rate to β-lactam antibiotics than CC983 and other CCs. The increased non-susceptibility rate to β-lactam antibiotics in serotype 19F pneumococci was found to be associated with the spread of the international resistant clone CC271 presumably caused by antibiotic pressure. Long-term surveys of serotype 19F S. pneumoniae are required to monitor CC prevalence and trends in antimicrobial resistance.
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Everett DB, Cornick J, Denis B, Chewapreecha C, Croucher N, Harris S, Parkhill J, Gordon S, Carrol ED, French N, Heyderman RS, Bentley SD. Genetic characterisation of Malawian pneumococci prior to the roll-out of the PCV13 vaccine using a high-throughput whole genome sequencing approach. PLoS One 2012; 7:e44250. [PMID: 22970189 PMCID: PMC3438182 DOI: 10.1371/journal.pone.0044250] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2012] [Accepted: 07/31/2012] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Malawi commenced the introduction of the 13-valent pneumococcal conjugate vaccine (PCV13) into the routine infant immunisation schedule in November 2011. Here we have tested the utility of high throughput whole genome sequencing to provide a high-resolution view of pre-vaccine pneumococcal epidemiology and population evolutionary trends to predict potential future change in population structure post introduction. METHODS One hundred and twenty seven (127) archived pneumococcal isolates from randomly selected adults and children presenting to the Queen Elizabeth Central Hospital, Blantyre, Malawi underwent whole genome sequencing. RESULTS The pneumococcal population was dominated by serotype 1 (20.5% of invasive isolates) prior to vaccine introduction. PCV13 is likely to protect against 62.9% of all circulating invasive pneumococci (78.3% in under-5-year-olds). Several Pneumococcal Molecular Epidemiology Network (PMEN) clones are now in circulation in Malawi which were previously undetected but the pandemic multidrug resistant PMEN1 lineage was not identified. Genome analysis identified a number of novel sequence types and serotype switching. CONCLUSIONS High throughput genome sequencing is now feasible and has the capacity to simultaneously elucidate serotype, sequence type and as well as detailed genetic information. It enables population level characterization, providing a detailed picture of population structure and genome evolution relevant to disease control. Post-vaccine introduction surveillance supported by genome sequencing is essential to providing a comprehensive picture of the impact of PCV13 on pneumococcal population structure and informing future public health interventions.
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Affiliation(s)
- Dean B Everett
- Malawi-Liverpool-Wellcome Clinical Research Programme, Chichiri, Blantyre 3, Malawi.
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Changing trends in antimicrobial susceptibility of Streptococcus pneumoniae isolates in Taiwan, 2006–2007. JOURNAL OF MICROBIOLOGY, IMMUNOLOGY, AND INFECTION = WEI MIAN YU GAN RAN ZA ZHI 2012; 45:305-10. [DOI: 10.1016/j.jmii.2011.12.012] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2011] [Revised: 07/01/2011] [Accepted: 08/22/2011] [Indexed: 11/18/2022]
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VASOO SHAWN, SINGH KAMALJIT, HSU LIYANG, CHIEW YOKEFONG, CHOW CAROL, LIN RAYMONDT, TAMBYAH PAULA. Increasing antibiotic resistance in Streptococcus pneumoniae colonizing children attending day-care centres in Singapore. Respirology 2011; 16:1241-8. [DOI: 10.1111/j.1440-1843.2011.02036.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Comparison of genotypes of Streptococcus pneumoniae serotypes 6A and 6B before and after the introduction of PCV7 vaccination in Korea. Diagn Microbiol Infect Dis 2011; 69:370-5. [DOI: 10.1016/j.diagmicrobio.2010.10.019] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2010] [Revised: 10/13/2010] [Accepted: 10/24/2010] [Indexed: 11/19/2022]
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Beall BW, Gertz RE, Hulkower RL, Whitney CG, Moore MR, Brueggemann AB. Shifting genetic structure of invasive serotype 19A pneumococci in the United States. J Infect Dis 2011; 203:1360-8. [PMID: 21398395 DOI: 10.1093/infdis/jir052] [Citation(s) in RCA: 136] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Following 7-valent conjugate vaccine introduction in the United States in 2000, invasive serotype (sero19A) pneumococcal disease (IPD) emerged rapidly. Sero19A IPD incidence increased slightly during 2005-2008 (from 2.3 cases to 2.5 cases per 100,000 population), whereas sero19A penicillin resistance (defined as a minimum inhibitor concentration [MIC] ≥2 μg/mL) increased significantly (from 28.7% to 43.7%). To better understand changes, we characterized sero19A isolates recovered during 2004-2008. METHODS We performed antimicrobial susceptibility testing on all 2767 sero19A IPD isolates identified through the Centers for Disease Control Active Bacterial Core surveillance during 2004-2008. We genotyped 1804 (96.3%) of 1874 sero19A isolates recovered during 2005-2007 and all 148 year 2008 sero19A isolates from children <5 years of age. RESULTS Resistant clonal complex (CC) 320/271(19A) increased from 20.9% (115 of 550) to 32.9% (208 of 633; P < .001) of IPD isolates during 2005-2007, which paralleled increased sero19A penicillin resistance (from 28.7% [163 of 567 isolates] to 39.5% [261 of 661 isolates]; P < .001). Total IPD due to 320/271(19A) increased during 2005-2007 and increased from 2.1 to 3.6 cases per 100,000 population during 2005-2008 in children <5 years of age. The penicillin-susceptible/intermediate, putative vaccine-escape CC695(19A) increased from 7.5% (41 of 550) to 13.6% (85 of 633) of sero19A isolates during 2005-2007 (P = .002). CONCLUSIONS Sero19A rates may have plateaued; however, clonal shifts are increasing resistance. Increased IPD caused by CC320/271(19A) and CC695(19A) could reflect additional selective advantages in addition to resistance.
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Affiliation(s)
- Bernard W Beall
- Respiratory Diseases Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA.
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Sequence types and antimicrobial susceptibility of invasive streptococcus pneumoniae isolates from a region with high antibiotic selective pressure and suboptimal vaccine coverage. Pediatr Infect Dis J 2010; 29:467-9. [PMID: 20027125 DOI: 10.1097/inf.0b013e3181cb45f3] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Multilocus sequence typing was carried out on 95 invasive pneumococcal isolates belonging to the most common 7 serotypes currently circulating in Taiwan. The study confirmed continued prevalence in Taiwan of a few global clones and sequence types (STs) since the mid-1990s and identified the recent emergence of ST320 (19A) and ST902 (6A). Antimicrobial nonsusceptibility was common in the predominant STs of serotypes 14, 19A, 19F, and 23F.
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National survey of invasive pneumococcal diseases in Taiwan under partial PCV7 vaccination in 2007: emergence of serotype 19A with high invasive potential. Vaccine 2009; 27:5513-8. [PMID: 19615960 DOI: 10.1016/j.vaccine.2009.06.091] [Citation(s) in RCA: 93] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2009] [Revised: 06/10/2009] [Accepted: 06/29/2009] [Indexed: 11/20/2022]
Abstract
We conducted an active, population-based laboratory surveillance study to evaluate the epidemiologic features of invasive pneumococcal disease (IPD) in Taiwan. Concurrently, nasopharyngeal colonization of Streptococcus pneumoniae was evaluated among 1128 healthy children aged <or=5 years. The overall incidence was highest among children aged 2-4 years (15.6/100,000). Serotype 19A, which had never been reported in Taiwan previously, caused a substantial fraction of the invasive diseases (OR, 9.6; 95% CI, 3.1-29.4) among children aged 2-4 years. Comparing serotype distributions of the isolates from nasopharyngeal colonization among children aged <or=5 years, serotypes 14 (OR, 17.3; 95% CI, 5.2-57.9) and 19A (OR, 14.9; 95% CI, 1.9-117) had the highest invasive potential. The study found that serotype 19A expanded in Taiwan, a country with a low 7-valent conjugate pneumococcal vaccine coverage. The 7-valent conjugate pneumococcal vaccines covered 73% of cases in children aged between 2 and 4 years, and 64.7% of cases in children aged <2 years. Among patients aged >or=65 years, the 23-valent pneumococcal polysaccharide vaccine covered 70.4% of cases. In the future, a broader pneumococcal vaccine is needed.
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Ardanuy C, Rolo D, Fenoll A, Tarrago D, Calatayud L, Liñares J. Emergence of a multidrug-resistant clone (ST320) among invasive serotype 19A pneumococci in Spain. J Antimicrob Chemother 2009; 64:507-10. [PMID: 19535383 DOI: 10.1093/jac/dkp210] [Citation(s) in RCA: 80] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
OBJECTIVES Multidrug-resistant Streptococcus pneumoniae isolates of serotype 19A have emerged all over the world in recent years. The aim of this study was to characterize highly penicillin-resistant pneumococcal strains of the 19A serotype, collected in Spain from 1997 to 2007 from patients with invasive disease. METHODS Antibiotic susceptibility was studied by microdilution. All penicillin-resistant pneumococci were typed by PFGE and selected strains were studied by multilocus sequence typing (MLST). The presence of genes related to the Tn916 family of transposons was investigated by PCR. RESULTS From a total of 1197 invasive pneumococcal isolates of serotype 19A received at the Spanish Reference Laboratory between 1997 and 2007, 51 (4.3%) strains showed high-level resistance to penicillin (MICs of 2-4 mg/L). These 51 isolates belonged to three multiresistant clones related to sequence type (ST)81 (n = 21), ST320 (n = 19) and ST276 (n = 11). All 51 serotype 19A pneumococci were tetracycline-resistant and had the tet(M) gene, and 41 strains were macrolide-resistant, harbouring the erm(B) gene. The presence of int and xis genes was detected in all strains associated with other genes of the Tn916 family. CONCLUSIONS The rise in penicillin-resistant serotype 19A invasive pneumococci in Spain was associated with the emergence and clonal spread of two worldwide-disseminated multiresistant clones (ST276 and ST320). The Spain(23F)-1-19A (ST81) clone remained stable throughout the study period. Multidrug resistance was associated with transposons of the Tn916 family.
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Affiliation(s)
- Carmen Ardanuy
- Microbiology Department, Hospital Universitari de Bellvitge, 08907 L'Hospitalet de Llobregat, Barcelona, Spain.
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Hsieh YC, Huang YC, Lin HC, Ho YH, Chang KY, Huang LM, Hsueh PR. Characterization of invasive isolates of Streptococcus pneumoniae among Taiwanese children. Clin Microbiol Infect 2009; 15:991-6. [PMID: 19392891 DOI: 10.1111/j.1469-0691.2009.02743.x] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Accurate molecular surveillance is important in monitoring the dynamics of Streptococcus pneumoniae. A prospective study was conducted to collect invasive isolates of S. pneumoniae from children for genetic analysis from January 2004 to December 2006 in Taiwan. PCRs were performed to detect the zmpC and zmpD genes, both encoding a metalloprotease virulence factor in pneumococci, among these invasive isolates. During the study period, 68 invasive isolates of S. pneumoniae were obtained for analysis. Serotype 14 was the most common type isolated from children with invasive disease and was significantly associated with pneumonia (OR 3.1; 95% CI] 1.1-8.8; p 0.035). Serotype 23F was significantly associated with bacteraemia (OR 7.5; 95% CI 1.8-31.3; p 0.006). The seven-valent conjugate vaccine covered 83.8% of invasive isolates, but non-vaccine serotypes were more frequently isolated from patients with underlying diseases than from patients without underlying diseases (p 0.007 by Fisher's exact test). Clonal complexes related to international clones Spain23F ST81, Spain6B ST95, England14 ST9, Taiwan19F ST236, Taiwan23F ST242 and Colombia23F ST338 accounted for 52.9% of invasive isolates. Dissemination of the penicillin-resistant clones ST876, ST46, ST76 and ST2889, which were first identified in Taiwan, was also found; 1.5% of these invasive isolates carried the zmpC gene, and 47.1% of these invasive isolates carried the zmpD gene. In conclusion, the spread of certain international clones and some domestic antibiotic-resistant clones resulted in invasive diseases among Taiwanese children.
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Affiliation(s)
- Y-C Hsieh
- Division of Paediatric Infectious Diseases, Department of Paediatrics, Chang Gung Children's Hospital, Chang Gung University College of Medicine, Taoyuan
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Albarracín Orio AG, Cortes PR, Tregnaghi M, Piñas GE, Argentinean Network Pneumococcus Study Group, Echenique JR. A new serotype 14 variant of the pneumococcal Spain9V-3 international clone detected in the central region of Argentina. J Med Microbiol 2008; 57:992-999. [PMID: 18628501 DOI: 10.1099/jmm.0.2008/000505-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The penicillin-resistant Spain(9V)-3 clone of Streptococcus pneumoniae is widespread and presents different serotype variants originating from recombination of the capsular genes. In this work, the genetic relatedness of 29 invasive pneumococci isolated from the central region of Argentina (Cordoba, Buenos Aires, Santa Fe and La Pampa provinces) was assessed by multilocus sequence typing (MLST). All of the penicillin-non-susceptible isolates studied (21/29) belonged to a serotype 14 variant of the Spain(9V)-3 clone. This clone was predominant, suggesting that it was responsible for the penicillin resistance spread in this region. Interestingly, this serotype 14 variant (named Cordoba S14V) could be differentiated from the European one by its pbp1a gene, suggesting a different recombinational replacement of the capsular genes. The putative recombination sites were analysed, resulting in the proximal crossover point being clearly localized in the spr0309 gene, with the distal site restricted to the recU gene, confirming a different recombination event. Analysis of the dexB, cpsB, aliA and pbp1a genes from these strains showed a high similarity with the corresponding genes of the Spain(14)-5 clone, suggesting that the capsular genes were provided by this international clone. Analysis of the genetic polymorphisms of the pbp1a (nt 1473-1922) and spr0309 (nt 1-790) genes is proposed as an epidemiological tool to help recognize the Cordoba S14V of the Spain(9V)-3 clone. On the other hand, BOX-repeat-based PCR and MLST analyses of serotype 14 strains revealed a divergent epidemiology of the Cordoba S14V, suggesting a non-recent dissemination in the paediatric population. It is suggested that this molecular epidemiology work will be a reference for monitoring the evolution of S14Vs of Spain(9V)-3, the emergence of new clones and the impact of pneumococcal vaccination programmes in Argentina.
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Affiliation(s)
- Andrea G Albarracín Orio
- Departamento de Bioquimica Clinica-CIBICI (CONICET), Facultad de Ciencias Quimicas, Universidad Nacional de Cordoba, Cordoba, Argentina
| | - Paulo R Cortes
- Hospital Pediatrico del Niño Jesus, Cordoba, Argentina.,Centro de Desarrollo de Proyectos Avanzados en Pediatria (CEDEPAP), Cordoba, Argentina.,Departamento de Bioquimica Clinica-CIBICI (CONICET), Facultad de Ciencias Quimicas, Universidad Nacional de Cordoba, Cordoba, Argentina
| | - Miguel Tregnaghi
- Centro de Desarrollo de Proyectos Avanzados en Pediatria (CEDEPAP), Cordoba, Argentina
| | - German E Piñas
- Departamento de Bioquimica Clinica-CIBICI (CONICET), Facultad de Ciencias Quimicas, Universidad Nacional de Cordoba, Cordoba, Argentina
| | | | - José R Echenique
- Departamento de Bioquimica Clinica-CIBICI (CONICET), Facultad de Ciencias Quimicas, Universidad Nacional de Cordoba, Cordoba, Argentina
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39
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Yang F, Xu XG, Yang MJ, Zhang YY, Klugman KP, McGee L. Antimicrobial susceptibility and molecular epidemiology of Streptococcus pneumoniae isolated from Shanghai, China. Int J Antimicrob Agents 2008; 32:386-91. [PMID: 18723327 DOI: 10.1016/j.ijantimicag.2008.05.004] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2008] [Revised: 05/11/2008] [Accepted: 05/12/2008] [Indexed: 11/26/2022]
Abstract
In this study, the antimicrobial resistance profiles of pneumococci isolated from respiratory specimens of patients from Shanghai, China, in 2004 and 2005 are described. Non-susceptible rates to penicillin and erythromycin among paediatric isolates (n=122) were 63.1% and 94.3%, respectively, whilst those of adult isolates (n=39) were 20.5% and 69.2%, respectively (P<0.0001 and P<0.0002). Nineteen serotypes were identified among 103 tested strains, 73.8% of which belonged to 19F, 14, 23F, 6B and 19A. The erm(B) gene was detected in 51 erythromycin-resistant strains (52.6%), the mef(E) gene in 5 strains (5.2%) and both erm(B) and mef(E) in 41 strains (42.3%). Among 45 sequence types (STs) determined by multilocus sequence typing (MLST) in these 103 isolates, 25 STs were new assignments and 9 STs contained 10 new alleles. On the other hand, 46 (68.7%) of 67 penicillin-non-susceptible S. pneumoniae and 51 (52.6%) of 97 macrolide-resistant S. pneumoniae were characterised as belonging to four international resistant clonal complexes, Taiwan(19F)-14, Spain(23F)-1, Spain(6B)-2 and Taiwan(23F)-15. Our findings indicate that the spread of international resistant clones played a predominant role in the emergence and increase of resistance in Shanghai. Conjugate vaccination may be a promising method to prevent the increase in pneumococcal resistance.
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Affiliation(s)
- Fan Yang
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai 200040, China
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40
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Mavroidi A, Paraskakis I, Pangalis A, Kirikou E, Charisiadou A, Athanasiou T, Tassios P, Tzouvelekis L. Spread of the Streptococcus pneumoniae Taiwan19F-14 clone among children in Greece. Clin Microbiol Infect 2007; 13:1213-6. [DOI: 10.1111/j.1469-0691.2007.01837.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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41
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Sjöström K, Blomberg C, Fernebro J, Dagerhamn J, Morfeldt E, Barocchi MA, Browall S, Moschioni M, Andersson M, Henriques F, Albiger B, Rappuoli R, Normark S, Henriques-Normark B. Clonal success of piliated penicillin nonsusceptible pneumococci. Proc Natl Acad Sci U S A 2007; 104:12907-12. [PMID: 17644611 PMCID: PMC1929012 DOI: 10.1073/pnas.0705589104] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Antibiotic resistance in pneumococci is due to the spread of strains belonging to a limited number of clones. The Spain(9V)-3 clone of sequence type (ST)156 is one of the most successful clones with reduced susceptibility to penicillin [pneumococci nonsusceptible to penicillin (PNSP)]. In Sweden during 2000-2003, a dramatic increase in the number of PNSP isolates was observed. Molecular characterization of these isolates showed that a single clone of sequence type ST156 increased from 40% to 80% of all serotype 14, thus causing the serotype expansion. Additionally, during the same time period, we examined the clonal composition of two serotypes 9V and 19F: all 9V and 20% of 19F isolates belonged to the clonal cluster of ST156, and overall approximately 50% of all PNSP belonged to the ST156 clonal cluster. Moreover, microarray and PCR analysis showed that all ST156 isolates, irrespective of capsular type, carried the rlrA pilus islet. This islet was also found to be present in the penicillin-sensitive ST162 clone, which is believed to be the drug-susceptible ancestor of ST156. Competitive experiments between related ST156 serotype 19F strains confirmed that those containing the rlrA pilus islet were more successful in an animal model of carriage. We conclude that the pilus island is an important biological factor common to ST156 isolates and other successful PNSP clones. In Sweden, a country where the low antibiotic usage does not explain the spread of resistant strains, at least 70% of all PNSP isolates collected during year 2003 carried the pilus islet.
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Affiliation(s)
- K. Sjöström
- *Department of Bacteriology, Swedish Institute for Infectious Disease Control, SE-171 82 Solna, Sweden
- Department of Microbiology, Tumor Biology, and Cell Biology, Karolinska Institutet, SE-171 77 Stockholm, Sweden
| | - C. Blomberg
- *Department of Bacteriology, Swedish Institute for Infectious Disease Control, SE-171 82 Solna, Sweden
- Department of Microbiology, Tumor Biology, and Cell Biology, Karolinska Institutet, SE-171 77 Stockholm, Sweden
| | - J. Fernebro
- *Department of Bacteriology, Swedish Institute for Infectious Disease Control, SE-171 82 Solna, Sweden
- Department of Microbiology, Tumor Biology, and Cell Biology, Karolinska Institutet, SE-171 77 Stockholm, Sweden
| | - J. Dagerhamn
- *Department of Bacteriology, Swedish Institute for Infectious Disease Control, SE-171 82 Solna, Sweden
- Department of Microbiology, Tumor Biology, and Cell Biology, Karolinska Institutet, SE-171 77 Stockholm, Sweden
| | - E. Morfeldt
- *Department of Bacteriology, Swedish Institute for Infectious Disease Control, SE-171 82 Solna, Sweden
| | | | - S. Browall
- *Department of Bacteriology, Swedish Institute for Infectious Disease Control, SE-171 82 Solna, Sweden
| | | | - M. Andersson
- *Department of Bacteriology, Swedish Institute for Infectious Disease Control, SE-171 82 Solna, Sweden
| | - F. Henriques
- *Department of Bacteriology, Swedish Institute for Infectious Disease Control, SE-171 82 Solna, Sweden
| | - B. Albiger
- Department of Microbiology, Tumor Biology, and Cell Biology, Karolinska Institutet, SE-171 77 Stockholm, Sweden
- Department of Clinical Microbiology, Lund University, SE-221 00 Malmö, Sweden
| | - Rino Rappuoli
- Novartis Vaccines, 53100 Siena, Italy; and
- To whom correspondence may be addressed. E-mail: or
| | - S. Normark
- *Department of Bacteriology, Swedish Institute for Infectious Disease Control, SE-171 82 Solna, Sweden
- Department of Microbiology, Tumor Biology, and Cell Biology, Karolinska Institutet, SE-171 77 Stockholm, Sweden
| | - B. Henriques-Normark
- *Department of Bacteriology, Swedish Institute for Infectious Disease Control, SE-171 82 Solna, Sweden
- Department of Microbiology, Tumor Biology, and Cell Biology, Karolinska Institutet, SE-171 77 Stockholm, Sweden
- To whom correspondence may be addressed. E-mail: or
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42
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Watson M, Brett M, Brown M, Stewart MG, Warren S. Pneumococci responsible for invasive disease and discharging ears in children in Sydney, Australia. J Med Microbiol 2007; 56:819-823. [PMID: 17510269 DOI: 10.1099/jmm.0.47057-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The serotypes and molecular clones of penicillin-nonsusceptible Streptococcus pneumoniae (PNSP) responsible for invasive pneumococcal disease (IPD) and discharging ears in metropolitan New South Wales were characterized to form a baseline prior to introduction of the heptavalent conjugate pneumococcal vaccine in Australia. Pneumococci isolated between 1 July 2000 and 30 June 2003 in Sydney from children <15 years were tested for antibiotic susceptibilities and serotyped. Penicillin-nonsusceptible pneumococci were typed by multilocus sequence typing and BOX PCR. During this period, 97 (13.9 %) of 698 pneumococci from IPD that were serotyped were penicillin-nonsusceptible. Of 607 pneumococci from discharging ears, 157 (26.1 %) were penicillin-nonsusceptible. Serotype 14 was the predominant serotype responsible for IPD and serotype 19F predominated from discharging ears. The heptavalent vaccine serotypes accounted for 613 (87.8 %) of all invasive isolates and 420 (69.8 %) of all isolates from discharging ears. Representatives of the major international clones were present among the PNSP. The majority of serotypes and clones that showed penicillin-nonsusceptibility are present within the vaccine. Serotype switching was also noted to have occurred prior to introduction of the vaccine. This study provides a characterization of the pneumococcal serotypes associated with IPD and discharging ears that will be useful for detecting potential selective effects of the vaccine. This surveillance should be continued, as it will be important to monitor the frequency and distribution of serotypes in the post-vaccine era.
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Affiliation(s)
- Michael Watson
- The New South Wales Pneumococcal Reference Laboratory, The Children's Hospital at Westmead, Department of Microbiology, Westmead, New South Wales, Australia
| | - Maggie Brett
- The New South Wales Pneumococcal Reference Laboratory, The Children's Hospital at Westmead, Department of Microbiology, Westmead, New South Wales, Australia
| | - Mitchell Brown
- The New South Wales Pneumococcal Reference Laboratory, The Children's Hospital at Westmead, Department of Microbiology, Westmead, New South Wales, Australia
| | - Marianne G Stewart
- The New South Wales Pneumococcal Reference Laboratory, The Children's Hospital at Westmead, Department of Microbiology, Westmead, New South Wales, Australia
| | - Shirley Warren
- The New South Wales Pneumococcal Reference Laboratory, The Children's Hospital at Westmead, Department of Microbiology, Westmead, New South Wales, Australia
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43
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Rantala M, Nyberg S, Lindgren M, Huovinen P, Jalava J, Skyttä R, Teirilä L, Vainio A, Virolainen-Julkunen A, Kaijalainen T. Molecular Epidemiology of Telithromycin-Resistant Pneumococci in Finland. Antimicrob Agents Chemother 2007; 51:1885-7. [PMID: 17325224 PMCID: PMC1855529 DOI: 10.1128/aac.00187-07] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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44
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Olvera A, Cerdà-Cuéllar M, Aragon V. Study of the population structure of Haemophilus parasuis by multilocus sequence typing. MICROBIOLOGY-SGM 2007; 152:3683-3690. [PMID: 17159221 DOI: 10.1099/mic.0.29254-0] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Haemophilus parasuis is the aetiological agent of Glässer's disease in swine. In addition, this bacterium causes other clinical outcomes and can also be isolated from the upper respiratory tract of healthy pigs. Isolates of H. parasuis differ in phenotypic features (e.g. protein profiles, colony morphology or capsule production) and pathogenic capacity. Differences among strains have also been demonstrated at the genetic level. Several typing methods have been used to classify H. parasuis field strains, but they had resolution or implementation problems. To overcome these limitations, a multilocus sequence typing (MLST) system, using partial sequences of the house-keeping genes mdh, 6pgd, atpD, g3pd, frdB, infB and rpoB, was developed. Eleven reference strains and 120 field strains were included in this study. The number of alleles per locus ranged from 14 to 41, 6pgd being the locus with the highest diversity. The high genetic heterogeneity of this bacterium was confirmed with MLST, since the strains were divided into 109 sequence types, and only 13 small clonal complexes were detected by the Burst algorithm. Further analysis by unweighted-pair group method with arithmetic mean (UPGMA) identified six clusters. When the clinical background of the isolates was examined, one cluster was statistically associated with nasal isolation (putative non-virulent), while another cluster showed a significant association with isolation from clinical lesions (putative virulent). The remaining clusters did not show a statistical association with the clinical background of the isolates. Finally, although recombination among H. parasuis strains was detected, two divergent branches were found when a neighbour-joining tree was constructed with the concatenated sequences. Interestingly, one branch included almost all isolates of the putative virulent UPGMA cluster.
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Affiliation(s)
- Alex Olvera
- Centre de Recerca en Sanitat Animal (CReSA), Campus de Bellaterra-Universitat Autònoma de Barcelona, 08193-Bellaterra, Barcelona, Spain
| | - Marta Cerdà-Cuéllar
- Centre de Recerca en Sanitat Animal (CReSA), Campus de Bellaterra-Universitat Autònoma de Barcelona, 08193-Bellaterra, Barcelona, Spain
| | - Virginia Aragon
- Centre de Recerca en Sanitat Animal (CReSA), Campus de Bellaterra-Universitat Autònoma de Barcelona, 08193-Bellaterra, Barcelona, Spain
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45
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Sadowy E, Izdebski R, Skoczynska A, Grzesiowski P, Gniadkowski M, Hryniewicz W. Phenotypic and molecular analysis of penicillin-nonsusceptible Streptococcus pneumoniae isolates in Poland. Antimicrob Agents Chemother 2007; 51:40-7. [PMID: 17043125 PMCID: PMC1797676 DOI: 10.1128/aac.01072-06] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2006] [Accepted: 10/03/2006] [Indexed: 11/20/2022] Open
Abstract
beta-Lactams are the drugs of choice for the treatment of infections caused by the important bacterial pathogen Streptococcus pneumoniae. The recent growth of resistance of this organism to penicillin observed worldwide is of the highest concern. In this study, using 887 surveillance pneumococcal isolates recovered in Poland from 1998 to 2002, we observed the increase in penicillin nonsusceptibility from 8.7% to 20.3%. All of the 109 penicillin-nonsusceptible S. pneumoniae (PNSP) isolates identified, together with 22 archival PNSP isolates from 1995 to 1997, were subsequently analyzed by susceptibility testing, serotyping, profiling of pbp genes, pulsed-field gel electrophoresis, and multilocus sequence typing (MLST). Four predominant serotypes, serotypes 6B, 9V, 14, and 23F, characterized 85.5% of the isolates. MLST revealed the presence of 34 sequence types, 15 of which were novel types. Representatives of seven multiresistant international clones (Spain(23F)-1, Spain(6B)-2, Spain(9V)-3, Taiwan(23F)-15, Poland(23F)-16, Poland(6B)-20, and Sweden(15A)-25) or their closely related variants comprised the majority of the study isolates. The spread of Spain(9V)-3 and its related clone of serotype 14/ST143 has remarkably contributed to the recent increase in penicillin resistance in pneumococci in the country.
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Affiliation(s)
- Ewa Sadowy
- Department of Molecular Microbiology, National Institute of Public Health, Ul. Chełmska 30/34, 00-725 Warsaw, Poland.
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46
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Lin WJ, Lo WT, Chou CY, Chen YY, Tsai SY, Chu ML, Wang CC. Antimicrobial resistance patterns and serotype distribution of invasive Streptococcus pneumoniae isolates from children in Taiwan from 1999 to 2004. Diagn Microbiol Infect Dis 2006; 56:189-96. [PMID: 16725302 DOI: 10.1016/j.diagmicrobio.2006.03.016] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2005] [Revised: 03/13/2006] [Accepted: 03/26/2006] [Indexed: 11/18/2022]
Abstract
Streptococcus pneumoniae causes substantial morbidity and mortality worldwide. Because only limited data are available for the antibiotic resistance patterns and seroepidemiology of invasive S. pneumoniae isolates in Taiwanese children, this national surveillance of invasive pneumococcal infections in children was conducted during a 5-year period. Invasive isolates of S. pneumoniae were obtained from sterile sites (yielding blood and cerebrospinal, pleural, and intra-articular fluids) in children (aged < or =14 years) at a total of 40 regional hospitals and medical centers distributed throughout Taiwan. The collection period was between July 1999 and June 2004, with a total of 286 isolates (including 30 cerebrospinal fluids) collected. All the samples were sent to the Center for Disease Control in Taipei for serotyping and susceptibility testing. Of the 286 S. pneumoniae isolates studied, the 5 most common serotypes were 14 (28.3%), 23F (21.0%), 6B (17.1%), 19F (13.6%), and 3 (4.9%). Intermediate- and high-level penicillin resistance was determined for 50.7% and 25.5% of the isolates, respectively. Isolate resistance was demonstrated to erythromycin (93%), tetracycline (82.2%), trimethoprim/sulfamethoxazole (79.4%), cefotaxime (11.2%), and levofloxacin (0.3%). Multiple drug resistance was found for each serotype, but mostly in types 14, 23F, 6B, and 19F. Overall, 85.0% of the serotypes, 90.8% of the penicillin-nonsusceptible S. pneumoniae (PNSSP), and 90.1% of the multiple drug-resistant (MDR) isolates were covered by the heptavalent pneumococcal conjugated vaccine (PCV7). In this study, we found a diverse pulse-field gel electrophoresis pattern among MDR isolates: a high prevalence of drug resistance and a continued increasing trend in penicillin resistance among nationwide pneumococcal isolates from children in Taiwan. The highest prevalence of invasive pneumococcal disease was in children aged 2 to 5 years, and the highest PNSSP prevalence and highest PCV7 coverage were in children aged <2 years. In terms of reducing the risk of invasive pneumococcal illness in Taiwan, the use of PCV7 is likely to have a beneficial effect similar to that obtained in countries that have used it.
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Affiliation(s)
- Wei-Jen Lin
- Department of Pediatrics, Tri-Service General Hospital, National Defense Medical Center, Neihu 114 Taipei, Taiwan
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47
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Chen YY, Yao SM, Chou CY, Chang YC, Shen PW, Huang CT, Su HP, Li SY. Surveillance of invasive Streptococcus pneumoniae in Taiwan, 2002–2003. J Med Microbiol 2006; 55:1109-1114. [PMID: 16849732 DOI: 10.1099/jmm.0.46530-0] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A total of 522 Streptococcus pneumoniae invasive isolates from diverse sources were collected from January 2002 to December 2003 in Taiwan in order to understand the serotype distribution of invasive isolates in Taiwan. The most frequently isolated serotypes of S. pneumoniae were types 14 (18.4 %), 23F (15.1 %), 3 (13.8 %), 19F (13.4 %), 6B (8.2 %), 9V (3.6 %) and 4 (2.5 %). The majority of cases were either under 5 years of age (24.1 %) or older than 65 years (36.6 %). Serotype distribution in adults aged over 14 years and children aged under 2 years was similar, except for that of type 3, which was more prevalent in adults. Penicillin-non-susceptible strains accounted for 67.7 % of all strains and were the predominant strains of serotypes 23F, 19F, 6B and 14. Most strains were susceptible to cephem drug, 85.7 % of isolates were susceptible to cefotaxime and 92.9 % were susceptible to ceftriaxone. A total of 72.6 % (379/522) of the isolates were resistant to at least two antibiotics. The 23-valent vaccine in the current commercial market would cover 87.2 % of the serotypes and 100 % of the penicillin-non-susceptible serotypes of S. pneumoniae in Taiwan. The coverage of 7- and 11-valent protein conjugate vaccines of the serotypes in children under 2 years of age would be 78.8 and 86.5 %, respectively. These results will help to assess the adequacy of the vaccine formulations marketed in Taiwan.
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Affiliation(s)
- Ying-Yan Chen
- Laboratory for Bacteriology and Mycology, Division of Laboratory Research and Development, Center for Disease Control, No. 161, Kun-Yang Street, Taipei, Taiwan
| | - Shu-Man Yao
- Laboratory for Bacteriology and Mycology, Division of Laboratory Research and Development, Center for Disease Control, No. 161, Kun-Yang Street, Taipei, Taiwan
| | - Chen-Ying Chou
- Laboratory for Bacteriology and Mycology, Division of Laboratory Research and Development, Center for Disease Control, No. 161, Kun-Yang Street, Taipei, Taiwan
| | - Yi-Ching Chang
- Laboratory for Bacteriology and Mycology, Division of Laboratory Research and Development, Center for Disease Control, No. 161, Kun-Yang Street, Taipei, Taiwan
| | - Pei-Wun Shen
- Laboratory for Bacteriology and Mycology, Division of Laboratory Research and Development, Center for Disease Control, No. 161, Kun-Yang Street, Taipei, Taiwan
| | - Chung-Ter Huang
- Laboratory for Bacteriology and Mycology, Division of Laboratory Research and Development, Center for Disease Control, No. 161, Kun-Yang Street, Taipei, Taiwan
| | - Hsun-Pi Su
- Laboratory for Bacteriology and Mycology, Division of Laboratory Research and Development, Center for Disease Control, No. 161, Kun-Yang Street, Taipei, Taiwan
| | - Shu-Ying Li
- Laboratory for Bacteriology and Mycology, Division of Laboratory Research and Development, Center for Disease Control, No. 161, Kun-Yang Street, Taipei, Taiwan
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Žemličková H, Melter O, Urbášková P. Epidemiological relationships among penicillin non-susceptible Streptococcus pneumoniae strains recovered in the Czech Republic. J Med Microbiol 2006; 55:437-442. [PMID: 16533992 DOI: 10.1099/jmm.0.46270-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Since 1986, penicillin non-susceptible pneumococci (PNSP) have been found in the Czech Republic. As documented by a nationwide study, the proportion of invasive strains with reduced susceptibility to penicillin has fluctuated around 5 % in the past decade. Although the level of resistance to penicillin remains stable, the contribution of different capsular serotypes among the PNSP population varies. Whereas serotype 19A was predominantly associated with penicillin resistance until 1997, serotype 9V became most common among PNSP strains in 1998. In a collection of PNSP strains (n=225) isolated from 2000 to 2002, the most frequent serotype was 9V (n=91, 40.4 %), followed by 19F (n=30, 13.3 %) and 14 (n=25, 11.5 %). PFGE and multilocus sequence typing were used to characterize a set of PNSP of the currently predominant serotypes 9V (n=42), 14 (n=15) and 19F (n=14). The Spain(9V)-3 clone [sequence type (ST) 156] was responsible for a large proportion (100 % of serotype 9V strains, n=42; 93.3 % of serotype 14 strains, n=14) of the analysed strains. A representative of the Taiwan(19F)-14 clone (ST 236) was also recovered in the Czech Republic (a single isolate of serotype 19F). These findings confirm the spread of the major penicillin-resistant clones in the Czech Republic.
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Affiliation(s)
- Helena Žemličková
- National Institute of Public Health, Šrobárova 48, 100 42 Prague 10, Czech Republic
| | - Oto Melter
- National Institute of Public Health, Šrobárova 48, 100 42 Prague 10, Czech Republic
| | - Pavla Urbášková
- National Institute of Public Health, Šrobárova 48, 100 42 Prague 10, Czech Republic
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Zemlicková H, Crisóstomo MI, Brandileone MC, Camou T, Castañeda E, Corso A, Echániz-Aviles G, Pásztor M, Tomasz A. Serotypes and clonal types of penicillin-susceptible streptococcus pneumoniae causing invasive disease in children in five Latin American countries. Microb Drug Resist 2005; 11:195-204. [PMID: 16201921 DOI: 10.1089/mdr.2005.11.195] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
We used multilocus sequencing typing (MLST) to determine the genetic backgrounds of 185 recent penicillin susceptible Streptococcus pneumoniae isolates with serotypes that most frequently cause invasive disease in preschool age children in five Latin American countries-Argentina, Brazil, Colombia, Mexico, and Uruguay. Most of the isolates were associated with pneumonia (90/185), meningitis (74/185), and bacteremia (17/185). The collection of strains included seven serotypes-14, 6B, 5, 1, 23 F-which represent the serotypes of S. pneumoniae most frequently associated with sterile site infections in children. Also included were strains expressing serotypes 7F and 3. Comparison of serotype and multilocus sequence type allowed division of the isolates into two groups: strains expressing serotypes 1, 5, 3, and 7 were represented by a relatively few sequence types while strains expressing serotypes 6B, 14, and 23 F showed great genetic diversity. The genetic diversity of serotypes 14, 6B, and 23 F may be related to the capacity of these serotypes to colonize the nasopharynx of healthy carriers during which opportunities for diversification through genetic exchanges can occur. The findings present an interesting contrast with the results of an earlier study in which over 80% of invasive penicillin- resistant serotype 14 and 23 isolates from the same countries were found to belong to as few as two pandemic clones of S. pneumoniae.
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50
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Littauer P, Sangvik M, Caugant DA, Høiby EA, Simonsen GS, Sundsfjord A. Molecular epidemiology of macrolide-resistant isolates of Streptococcus pneumoniae collected from blood and respiratory specimens in Norway. J Clin Microbiol 2005; 43:2125-32. [PMID: 15872231 PMCID: PMC1153744 DOI: 10.1128/jcm.43.5.2125-2132.2005] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Norway has a low prevalence of antimicrobial resistance, including macrolide-resistant Streptococcus pneumoniae (MRSP). In a nationwide surveillance program, a total of 2,200 S. pneumoniae isolates were collected from blood cultures and respiratory tract specimens. Macrolide resistance was detected in 2.7%. M-type macrolide resistance was found in 60% of resistant isolates, and these were mainly mef(A)-positive, serotype-14 invasive isolates. The erm(B)-encoded macrolide-lincosamide-streptogramin B (MLS(B)) type dominated among the noninvasive isolates. One strain had an A2058G mutation in the 23S rRNA gene. Coresistance to other antibiotics was seen in 96% of the MLS(B)-type isolates, whereas 92% of the M-type isolates were susceptible to other commonly used antimicrobial agents. Serotypes 14, 6B, and 19F accounted for 84% of the macrolide-resistant isolates, with serotype 14 alone accounting for 67% of the invasive isolates. A total of 29 different sequence types (STs) were detected by multilocus sequence typing. Twelve STs were previously reported international resistant clones, and 75% of the macrolide-resistant isolates had STs identical or closely related to these clones. Eleven isolates displayed 10 novel STs, and 7/11 of these "Norwegian strains" coexpressed MLS(B) and tetracycline resistance, indicating the presence of Tn1545. The invasive serotype-14 isolates were all classified as ST9 or single-locus variants of this clone. ST9 is a mef-positive M-type clone, commonly known as England(14)-9, reported from several European countries. These observations suggest that the import of major international MRSP clones and the local spread of Tn1545 are the major mechanisms involved in the evolution and dissemination of MRSP in Norway.
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Affiliation(s)
- P Littauer
- University Hospital of North Norway (UNN), Department of Microbiology and Virology, Faculty of Medicine, Institute for Medical Biology, University of Tromsø, N-9037 Tromsø, Norway
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