Comparative Sequencing of the Serine-Aspartate Repeat-Encoding Region of the Clumping Factor B Gene (clfB) for Resolution within Clonal Groups of Staphylococcus aureus
Moleculartechniques such as spa typing and multilocus sequence typinguse DNA sequence data for differentiating Staphylococcusaureus isolates. Although spa typing is capable ofdetecting both genetic micro- and macrovariation, it has lessdiscriminatory power than the more labor-intensive pulsed-field...
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Published in | Journal of Clinical Microbiology Vol. 43; no. 8; pp. 3985 - 3994 |
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Main Authors | , , , , , , |
Format | Journal Article |
Language | English |
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Washington, DC
American Society for Microbiology
01.08.2005
American Society for Microbiology (ASM) |
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Abstract | Moleculartechniques such as spa typing and multilocus sequence typinguse DNA sequence data for differentiating Staphylococcusaureus isolates. Although spa typing is capable ofdetecting both genetic micro- and macrovariation, it has lessdiscriminatory power than the more labor-intensive pulsed-field gelelectrophoresis (PFGE) and costly genomic DNA microarray analyses. Thislimitation hinders strain interrogation for newly emerging clones andoutbreak investigations in hospital or community settings where robustclones are endemic. To overcome this constraint, we developed a typingsystem using DNA sequence analysis of the serine-aspartate (SD)repeat-encoding region within the gene encoding thekeratin- and fibrinogen-binding clumping factor B (clfBtyping) and tested whether it is capable of discriminating withinclonal groups. We analyzed 116 S. aureus strains, and therepeat region was present in all isolates, varying in sequence and inlength from 420 to 804 bp. In a sample of 36 well-characterizedgenetically diverse isolates, clfB typing subdivided identicalspa and PFGE clusters which had been discriminated bywhole-genome DNA microarray mapping. The combination of spatyping and clfB typing resulted in a discriminatory power(99.5%) substantially higher than that of spa typing alone andclosely approached that of the whole-genome microarray (100.0%).clfB typing also successfully resolved genetic differencesamong isolates differentiated by PFGE that had been collected overshort periods of time from single hospitals and that belonged to themost prevalent S. aureus clone in the United States.clfB typing demonstrated in vivo, in vitro, and interpatienttransmission stability yet revealed that this locus may berecombinogenic in a primarily clonal population structure. Takentogether, these data show that the SD repeat-encoding region ofclfB is a highly stable marker of microvariation, that inconjunction with spa typing it may serve as a DNAsequence-based alternative to PFGE for investigating geneticallysimilar strains, and that it is useful for analyzing collections ofisolates in both long-term population-based and local epidemiologicstudies. |
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AbstractList | Moleculartechniques such as spa typing and multilocus sequence typinguse DNA sequence data for differentiating Staphylococcusaureus isolates. Although spa typing is capable ofdetecting both genetic micro- and macrovariation, it has lessdiscriminatory power than the more labor-intensive pulsed-field gelelectrophoresis (PFGE) and costly genomic DNA microarray analyses. Thislimitation hinders strain interrogation for newly emerging clones andoutbreak investigations in hospital or community settings where robustclones are endemic. To overcome this constraint, we developed a typingsystem using DNA sequence analysis of the serine-aspartate (SD)repeat-encoding region within the gene encoding thekeratin- and fibrinogen-binding clumping factor B (clfBtyping) and tested whether it is capable of discriminating withinclonal groups. We analyzed 116 S. aureus strains, and therepeat region was present in all isolates, varying in sequence and inlength from 420 to 804 bp. In a sample of 36 well-characterizedgenetically diverse isolates, clfB typing subdivided identicalspa and PFGE clusters which had been discriminated bywhole-genome DNA microarray mapping. The combination of spatyping and clfB typing resulted in a discriminatory power(99.5%) substantially higher than that of spa typing alone andclosely approached that of the whole-genome microarray (100.0%).clfB typing also successfully resolved genetic differencesamong isolates differentiated by PFGE that had been collected overshort periods of time from single hospitals and that belonged to themost prevalent S. aureus clone in the United States.clfB typing demonstrated in vivo, in vitro, and interpatienttransmission stability yet revealed that this locus may berecombinogenic in a primarily clonal population structure. Takentogether, these data show that the SD repeat-encoding region ofclfB is a highly stable marker of microvariation, that inconjunction with spa typing it may serve as a DNAsequence-based alternative to PFGE for investigating geneticallysimilar strains, and that it is useful for analyzing collections ofisolates in both long-term population-based and local epidemiologicstudies. Molecular techniques such as spa typing and multilocus sequence typing use DNA sequence data for differentiating Staphylococcus aureus isolates. Although spa typing is capable of detecting both genetic micro- and macrovariation, it has less discriminatory power than the more labor-intensive pulsed-field gel electrophoresis (PFGE) and costly genomic DNA microarray analyses. This limitation hinders strain interrogation for newly emerging clones and outbreak investigations in hospital or community settings where robust clones are endemic. To overcome this constraint, we developed a typing system using DNA sequence analysis of the serine-aspartate (SD) repeat-encoding region within the gene encoding the keratin- and fibrinogen-binding clumping factor B (clfB typing) and tested whether it is capable of discriminating within clonal groups. We analyzed 116 S. aureus strains, and the repeat region was present in all isolates, varying in sequence and in length from 420 to 804 bp. In a sample of 36 well-characterized genetically diverse isolates, clfB typing subdivided identical spa and PFGE clusters which had been discriminated by whole-genome DNA microarray mapping. The combination of spa typing and clfB typing resulted in a discriminatory power (99.5%) substantially higher than that of spa typing alone and closely approached that of the whole-genome microarray (100.0%). clfB typing also successfully resolved genetic differences among isolates differentiated by PFGE that had been collected over short periods of time from single hospitals and that belonged to the most prevalent S. aureus clone in the United States. clfB typing demonstrated in vivo, in vitro, and interpatient transmission stability yet revealed that this locus may be recombinogenic in a primarily clonal population structure. Taken together, these data show that the SD repeat-encoding region of clfB is a highly stable marker of microvariation, that in conjunction with spa typing it may serve as a DNA sequence-based alternative to PFGE for investigating genetically similar strains, and that it is useful for analyzing collections of isolates in both long-term population-based and local epidemiologic studies. Article Usage Stats Services JCM Citing Articles Google Scholar PubMed Related Content Social Bookmarking CiteULike Delicious Digg Facebook Google+ Mendeley Reddit StumbleUpon Twitter current issue JCM About JCM Subscribers Authors Reviewers Advertisers Inquiries from the Press Permissions & Commercial Reprints ASM Journals Public Access Policy JCM RSS Feeds 1752 N Street N.W. • Washington DC 20036 202.737.3600 • 202.942.9355 fax • journals@asmusa.org Print ISSN: 0095-1137 Online ISSN: 1098-660X Copyright © 2014 by the American Society for Microbiology. For an alternate route to JCM .asm.org, visit: JCM Molecular techniques such as spa typing and multilocus sequence typing use DNA sequence data for differentiating Staphylococcus aureus isolates. Although spa typing is capable of detecting both genetic micro- and macrovariation, it has less discriminatory power than the more labor-intensive pulsed-field gel electrophoresis (PFGE) and costly genomic DNA microarray analyses. This limitation hinders strain interrogation for newly emerging clones and outbreak investigations in hospital or community settings where robust clones are endemic. To overcome this constraint, we developed a typing system using DNA sequence analysis of the serine-aspartate (SD) repeat-encoding region within the gene encoding the keratin- and fibrinogen-binding clumping factor B ( clfB typing) and tested whether it is capable of discriminating within clonal groups. We analyzed 116 S. aureus strains, and the repeat region was present in all isolates, varying in sequence and in length from 420 to 804 bp. In a sample of 36 well-characterized genetically diverse isolates, clfB typing subdivided identical spa and PFGE clusters which had been discriminated by whole-genome DNA microarray mapping. The combination of spa typing and clfB typing resulted in a discriminatory power (99.5%) substantially higher than that of spa typing alone and closely approached that of the whole-genome microarray (100.0%). clfB typing also successfully resolved genetic differences among isolates differentiated by PFGE that had been collected over short periods of time from single hospitals and that belonged to the most prevalent S. aureus clone in the United States. clfB typing demonstrated in vivo, in vitro, and interpatient transmission stability yet revealed that this locus may be recombinogenic in a primarily clonal population structure. Taken together, these data show that the SD repeat-encoding region of clfB is a highly stable marker of microvariation, that in conjunction with spa typing it may serve as a DNA sequence-based alternative to PFGE for investigating genetically similar strains, and that it is useful for analyzing collections of isolates in both long-term population-based and local epidemiologic studies. |
Author | Kreiswirth, Barry N Koreen, Larry Koreen, Irina V Graviss, Edward A Ramaswamy, Srinivas V Naidich, Steven Graff, Gavin R |
AuthorAffiliation | New Jersey Medical School and Graduate School of Biomedical Sciences, University of Medicine and Dentistry of New Jersey, Newark, New Jersey 07103, 1 Public Health Research Institute, International Center for Public Health, Newark, New Jersey 07103, 2 Department of Pathology, Baylor College of Medicine, Houston, Texas 77030, 3 eGenomics, New York, New York 10013, 4 Department of Pediatrics, Penn State College of Medicine, Hershey, Pennsylvania 17033 5 |
AuthorAffiliation_xml | – name: New Jersey Medical School and Graduate School of Biomedical Sciences, University of Medicine and Dentistry of New Jersey, Newark, New Jersey 07103, 1 Public Health Research Institute, International Center for Public Health, Newark, New Jersey 07103, 2 Department of Pathology, Baylor College of Medicine, Houston, Texas 77030, 3 eGenomics, New York, New York 10013, 4 Department of Pediatrics, Penn State College of Medicine, Hershey, Pennsylvania 17033 5 |
Author_xml | – sequence: 1 fullname: Koreen, Larry – sequence: 2 fullname: Ramaswamy, Srinivas V – sequence: 3 fullname: Naidich, Steven – sequence: 4 fullname: Koreen, Irina V – sequence: 5 fullname: Graff, Gavin R – sequence: 6 fullname: Graviss, Edward A – sequence: 7 fullname: Kreiswirth, Barry N |
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Snippet | Moleculartechniques such as spa typing and multilocus sequence typinguse DNA sequence data for differentiating Staphylococcusaureus isolates. Although spa... Article Usage Stats Services JCM Citing Articles Google Scholar PubMed Related Content Social Bookmarking CiteULike Delicious Digg Facebook Google+ Mendeley... Molecular techniques such as spa typing and multilocus sequence typing use DNA sequence data for differentiating Staphylococcus aureus isolates. Although spa... Molecular techniques such as spa typing and multilocus sequence typing use DNA sequence data for differentiating Staphylococcus aureus isolates. Although spa... |
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SubjectTerms | Adhesins, Bacterial - chemistry Adhesins, Bacterial - genetics Amino Acid Sequence Aspartic Acid Bacterial Typing Techniques Bacteriology Base Sequence Biological and medical sciences Epidemiology Evolution, Molecular Fundamental and applied biological sciences. Psychology Infectious diseases Medical sciences Microbiology Miscellaneous Molecular Sequence Data Repetitive Sequences, Amino Acid Reproducibility of Results Serine Staphylococcus aureus - classification Staphylococcus aureus - genetics |
Title | Comparative Sequencing of the Serine-Aspartate Repeat-Encoding Region of the Clumping Factor B Gene (clfB) for Resolution within Clonal Groups of Staphylococcus aureus |
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