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Open Access Research article

A unified approach to molecular epidemiology investigations: tools and patterns in California as a case study for endemic shigellosis

Sawsan Al-Nimri1, Woutrina A Miller2*, Barbara A Byrne2, Gerry Guibert3 and Lily Chen1

Author Affiliations

1 Biology Department, San Francisco State University, 1600 Holloway Ave, San Francisco, CA, 94132, USA

2 Pathology, Microbiology & Immunology Department, School of Veterinary Medicine, University of California, Davis, CA, 95616, USA

3 Monterey County Public Health Department, 1270 Natividad Rd, Salinas, CA, 93906, USA

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BMC Infectious Diseases 2009, 9:184  doi:10.1186/1471-2334-9-184

Published: 24 November 2009



Shigellosis causes diarrheal disease in humans from both developed and developing countries, and multi-drug resistance is an emerging problem. The objective of this study is to present a unified approach that can be used to characterize endemic and outbreak patterns of shigellosis using use a suite of epidemiologic and molecular techniques. The approach is applied to a California case study example of endemic shigellosis at the population level.


Epidemiologic patterns were evaluated with respect to demographics, multi-drug resistance, antimicrobial resistance genes, plasmid profiles, and pulsed-field gel electrophoresis (PFGE) fingerprints for the 43 Shigella isolates obtained by the Monterey region health departments over the two year period from 2004-2005.


The traditional epidemiologic as well as molecular epidemiologic findings were consistent with endemic as compared to outbreak shigellosis in this population. A steady low level of cases was observed throughout the study period and high diversity was observed among strains. In contrast to most studies in developed countries, the predominant species was Shigella flexneri (51%) followed closely by S. sonnei (49%). Over 95% of Shigella isolates were fully resistant to three or more antimicrobial drug subclasses, and 38% of isolates were resistant to five or more subclasses. More than half of Shigella strains tested carried the tetB, catA, or blaTEM genes for antimicrobial resistance to tetracycline, chloramphenicol, and ampicillin, respectively.


This study shows how epidemiologic patterns at the host and bacterial population levels can be used to investigate endemic as compared to outbreak patterns of shigellosis in a community. Information gathered as part of such investigations will be instrumental in identifying emerging antimicrobial resistance, for developing treatment guidelines appropriate for that community, and to provide baseline data with which to compare outbreak strains in the future.