Comparative Genomics of Carriage and Disease Isolates of Streptococcus pneumoniae Serotype 22F Reveals Lineage-Specific Divergence and Niche Adaptation
Streptococcus pneumoniae is a major cause of meningitis, sepsis, and pneumonia worldwide. Pneumococcal conjugate vaccines have been part of the United Kingdom's childhood immunization program since 2006 and have significantly reduced the incidence of disease due to vaccine efficacy in reducing...
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Published in | Genome biology and evolution Vol. 8; no. 4; pp. 1243 - 1251 |
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Main Authors | , , , , , , , |
Format | Journal Article |
Language | English |
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Oxford University Press
01.04.2016
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Abstract | Streptococcus pneumoniae is a major cause of meningitis, sepsis, and pneumonia worldwide. Pneumococcal conjugate vaccines have been part of the United Kingdom's childhood immunization program since 2006 and have significantly reduced the incidence of disease due to vaccine efficacy in reducing carriage in the population. Here we isolated two clones of 22F (an emerging serotype of clinical concern, multilocus sequence types 433 and 698) and conducted comparative genomic analysis on four isolates, paired by Sequence Type (ST) with one of each pair being derived from carriage and the other disease (sepsis). The most compelling observation was of nonsynonymous mutations in pgdA, encoding peptidoglycan N-acetylglucosamine deacetylase A, which was found in the carriage isolates of both ST433 and 698. Deacetylation of pneumococcal peptidoglycan is known to enable resistance to lysozyme upon invasion. Althought no other clear genotypic signatures related to disease or carriage could be determined, additional intriguing comparisons between the two STs were possible. These include the presence of an intact prophage, in addition to numerous additional phage insertions, within the carriage isolate of ST433. Contrasting gene repertoires related to virulence and colonization, including bacteriocins, lantibiotics, and toxin--antitoxin systems, were also observed. |
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AbstractList | Streptococcus pneumoniae is a major cause of meningitis, sepsis, and pneumonia worldwide. Pneumococcal conjugate vaccines have been part of the United Kingdom's childhood immunization program since 2006 and have significantly reduced the incidence of disease due to vaccine efficacy in reducing carriage in the population. Here we isolated two clones of 22F (an emerging serotype of clinical concern, multilocus sequence types 433 and 698) and conducted comparative genomic analysis on four isolates, paired by Sequence Type (ST) with one of each pair being derived from carriage and the other disease (sepsis). The most compelling observation was of nonsynonymous mutations in pgdA, encoding peptidoglycan N-acetylglucosamine deacetylase A, which was found in the carriage isolates of both ST433 and 698. Deacetylation of pneumococcal peptidoglycan is known to enable resistance to lysozyme upon invasion. Althought no other clear genotypic signatures related to disease or carriage could be determined, additional intriguing comparisons between the two STs were possible. These include the presence of an intact prophage, in addition to numerous additional phage insertions, within the carriage isolate of ST433. Contrasting gene repertoires related to virulence and colonization, including bacteriocins, lantibiotics, and toxin--antitoxin systems, were also observed. Streptococcus pneumoniae is a major cause of meningitis, sepsis, and pneumonia worldwide. Pneumococcal conjugate vaccines have been part of the United Kingdom’s childhood immunization program since 2006 and have significantly reduced the incidence of disease due to vaccine efficacy in reducing carriage in the population. Here we isolated two clones of 22F (an emerging serotype of clinical concern, multilocus sequence types 433 and 698) and conducted comparative genomic analysis on four isolates, paired by Sequence Type (ST) with one of each pair being derived from carriage and the other disease (sepsis). The most compelling observation was of nonsynonymous mutations in pgdA , encoding peptidoglycan N -acetylglucosamine deacetylase A, which was found in the carriage isolates of both ST433 and 698. Deacetylation of pneumococcal peptidoglycan is known to enable resistance to lysozyme upon invasion. Althought no other clear genotypic signatures related to disease or carriage could be determined, additional intriguing comparisons between the two STs were possible. These include the presence of an intact prophage, in addition to numerous additional phage insertions, within the carriage isolate of ST433. Contrasting gene repertoires related to virulence and colonization, including bacteriocins, lantibiotics, and toxin-–antitoxin systems, were also observed. |
Author | Devine, Vanessa T Clarke, Stuart C Faust, Saul N Cleary, David W Bentley, Stephen D Gladstone, Rebecca A Webb, Jeremy S Jefferies, Johanna M C |
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Cites_doi | 10.1093/nar/gkr485 10.1371/journal.pone.0011289 10.1016/j.plasmid.2006.12.006 10.1086/374624 10.1016/j.vaccine.2015.03.012 10.1126/science.1198545 10.1128/JB.137.2.735-739.1979 10.1128/IAI.00814-15 10.1093/nar/gkt1226 10.1186/gb-2010-11-10-r107 10.1128/IAI.00316-06 10.1093/bioinformatics/btu153 10.1093/bioinformatics/btv421 10.1016/S0140-6736(12)61728-0 10.1111/j.1469-0691.2010.03183.x 10.3389/fmicb.2014.00677 10.1099/mic.0.056580-0 10.1038/ng.2625 10.1128/IAI.70.12.7176-7178.2002 10.1128/IAI.70.8.3985-3993.2002 10.1128/JB.00474-07 10.1016/S0140-6736(09)61204-6 10.1038/ncomms6471 10.1016/j.vaccine.2011.04.004 10.1007/978-1-4939-0554-6_12 10.1016/j.vaccine.2007.04.088 10.1128/JB.01272-08 10.1371/journal.pone.0019650 10.1093/nar/gkr846 10.1186/s13073-014-0090-6 10.1146/annurev.micro.61.080706.093501 10.1128/IAI.72.3.1587-1593.2004 10.1128/JCM.01485-09 10.1186/1471-2164-12-402 10.1371/journal.pmed.1001517 10.1128/JB.00690-07 10.1371/journal.pone.0064731 |
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Keywords | genome sequencing invasive pneumococcal disease Streptococcus pneumoniae |
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SubjectTerms | Amidohydrolases - genetics Anti-Bacterial Agents - pharmacology Bacterial Proteins - genetics Child Drug Resistance, Microbial Female Genome Report Genome, Bacterial Genomic Islands Genomics Genomics - methods Humans Male Middle Aged Mutation Pneumococcal Infections - drug therapy Pneumococcal Infections - microbiology Streptococcus infections Streptococcus pneumoniae - drug effects Streptococcus pneumoniae - genetics Streptococcus pneumoniae - isolation & purification Streptococcus pneumoniae - pathogenicity Virulence Factors - genetics |
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Title | Comparative Genomics of Carriage and Disease Isolates of Streptococcus pneumoniae Serotype 22F Reveals Lineage-Specific Divergence and Niche Adaptation |
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