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Typing Staphylococcus aureus Using the spa Gene and Novel Distance Measures

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Typing Staphylococcus aureus Using the spa Gene and Novel Distance Measures

Content Provider	ACM Digital Library
Author	Agius, Phaedra Bennett, Kristin Kreiswirth, Barry Naidich, Steve
Abstract	We developed an approach for identifying groups or families of Staphylococcus aureus bacteria based on genotype data. With the emergence of drug resistant strains, S. aureus represents a significant human health threat. Identifying the family types efficiently and quickly is crucial in community settings. Here, we develop a hybrid sequence algorithm approach to type this bacterium using only its spa gene. Two of the sequence algorithms we used are well established, while the third, the Best Common Gap-Weighted Sequence (BCGS), is novel. We combined the sequence algorithms with a weighted match/mismatch algorithm for the spa sequence ends. Normalized similarity scores and distances between the sequences were derived and used within unsupervised clustering methods. The resulting spa groupings correlated strongly with the groups defined by the well-established Multi locus sequence typing (MLST) method. Spa typing is preferable to MLST typing which types seven genes instead of just one. Furthermore, our spa clustering methods can be fine-tuned to be more discriminative than MLST, identifying new strains that the MLST method may not. Finally, we performed a multidimensional scaling of our distance matrices to visualize the relationship between isolates. The proposed methodology provides a promising new approach to molecular epidemiology.
Starting Page	693
Ending Page	704
Page Count	12
File Format	PDF
ISSN	15455963
DOI	10.1109/tcbb.2007.1053
Volume Number	4
Issue Number	4
Journal	IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Language	English
Publisher	Association for Computing Machinery (ACM)
Publisher Date	2007-10-01
Access Restriction	One Nation One Subscription (ONOS)
Subject Keyword	Clustering, sequence algorithms, genotyping, staphylococcus aureus, moleuclar epidemiology
Content Type	Text
Resource Type	Article
Subject	Genetics Biotechnology Applied Mathematics

Sl.	Authority	Responsibilities	Communication Details
1	Ministry of Education (GoI), Department of Higher Education	Sanctioning Authority	https://www.education.gov.in/ict-initiatives
2	Indian Institute of Technology Kharagpur	Host Institute of the Project: The host institute of the project is responsible for providing infrastructure support and hosting the project	https://www.iitkgp.ac.in
3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
5	Website/Portal (Helpdesk)	Queries regarding NDLI and its services	support@ndl.gov.in
6	Contents and Copyright Issues	Queries related to content curation and copyright issues	content@ndl.gov.in
7	National Digital Library of India Club (NDLI Club)	Queries related to NDLI Club formation, support, user awareness program, seminar/symposium, collaboration, social media, promotion, and outreach	clubsupport@ndl.gov.in
8	Digital Preservation Centre (DPC)	Assistance with digitizing and archiving copyright-free printed books	dpc@ndl.gov.in
9	IDR Setup or Support	Queries related to establishment and support of Institutional Digital Repository (IDR) and IDR workshops	idr@ndl.gov.in

Typing Staphylococcus aureus Using the spa Gene and Novel Distance Measures

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Typing Staphylococcus aureus Using the spa Gene and Novel Distance Measures

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Typing Staphylococcus aureus Using the spa Gene and Novel Distance Measures

Spa typing and enterotoxin gene profile of staphylococcus aureus.

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Spa typing of Staphylococcus aureus Isolated from Clinical Specimens from Outpatients in Iraq.

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Typing Staphylococcus aureus Using the spa Gene and Novel Distance Measures