Session:

Infectious Disease Surveillance

Abstract No.:

41.026

Title:

Genome sequencing of Vibrio cholerae isolates from an outbreak in the Philippines: unique genome structure and mobile elements

Author(s):

D. Klinzing¹, R. Matias¹, S. Y. Choi², N. Hasan², B. Torres¹, V. Liles¹, M. L. Juan¹, M. Alvarez¹, R. Capistrano³, M. E. J. Villareal³, J. Geronimo⁴, J. Lopez³, M. C. Mapue³, F. Alberto⁵, H. Gibbons⁶, N. Rosenzweig⁶, T. Cebula², E. Tayag³, F. Natividad¹, R. Colwell², E. Skowronski⁷; ¹St. Luke's Medical Center, Research and Biotechnology Division, Quezon City/PH, ²CosmosID, Pathogen Diagnostics, College Park, MD/US, ³Department of Health, National Epidemiology Center, Manila/PH, ⁴Department of Health, Research Institute for Tropical Medicine, Muntinlupa City/PH, ⁵Department of Health, Center for Health and Development IV-B, Quezon City/PH, ⁶Edgewood Chemical Biological Center, Biosciences, Aberdeen Proving Ground, MD/US, ⁷Tahoe Research Initiative, Global Biosurveillance, Incline Village, NV/US

Abstract:

Background: Cholera is a leading cause of severe diarrhoeal disease. Investigation by the Department of Health of the Philippines of an outbreak of diarrhoeal disease in Palawan in 2011 identified Vibrio cholerae as a putative causative agent.
Methods: Three microbial isolates, one environmental and two clinical samples, were characterized biochemically by The Research Institute for Tropical Medicine (RITM) and sent to St. Luke's Medical Center (SLMC) for whole genome sequencing. Extracted genomic DNA was sequenced using a Roche GSjr following standard Roche protocols. Sequencing reads were assembled into contigs using Roche Assembler and compared to Genbank entries using BLAST. Annotation was performed by both RAST and the annotation engine of the Institute for Genome Sciences in Maryland.
Results: Analysis of the shotgun genome data of all three isolates revealed that the Philippines strains are members of the 7th pandemic clade of O1 cholerae and are a hybrid of El Tor and Classical biotypes. The environmental strain was very closely related to one clinical isolate, indicating a possible source of the infection. However, the other clinical isolate differed significantly from the other two isolates. A novel 15kB genomic element containing a predicted type II restriction-modification system was identified in all three isolates. PCR was done to determine toxin gene and prophage genome structure.
Conclusion: The Philippines cholerae strains contain a unique configuration of elements, previously seen only in O1 El Tor MG-116926, isolated in Bangladesh in 1991. In addition, the Philippines strains contain elements and structure similar to the MO10 strain, a type O139 strain, from Africa. These data are the first Vibrio genome sequences generated from Philippines isolates and demonstrate the divergent and unique nature of the microbial diversity in the Philippines.