title: Hybrid Vibrio cholerae El Tor lacking SXT identified as the cause of a cholera outbreak in the Philippines.
abstract: Cholera continues to be a global threat, with high rates of morbidity and mortality. In 2011, a cholera outbreak occurred in Palawan, Philippines, affecting more than 500 people, and 20 individuals died. Vibrio cholerae O1 was confirmed as the etiological agent. Source attribution is critical in cholera outbreaks for proper management of the disease, as well as to control spread. In this study, three V. cholerae O1 isolates from a Philippines cholera outbreak were sequenced and their genomes analyzed to determine phylogenetic relatedness to V. cholerae O1 isolates from recent outbreaks of cholera elsewhere. The Philippines V. cholerae O1 isolates were determined to be V. cholerae O1 hybrid El Tor belonging to the seventh-pandemic clade. They clustered tightly, forming a monophyletic clade closely related to V. cholerae O1 hybrid El Tor from Asia and Africa. The isolates possess a unique multilocus variable-number tandem repeat analysis (MLVA) genotype (12-7-9-18-25 and 12-7-10-14-21) and lack SXT. In addition, they possess a novel 15-kb genomic island (GI-119) containing a predicted type I restriction-modification system. The CTXΦ-RS1 array of the Philippines isolates was similar to that of V. cholerae O1 MG116926, a hybrid El Tor strain isolated in Bangladesh in 1991. Overall, the data indicate that the Philippines V. cholerae O1 isolates are unique, differing from recent V. cholerae O1 isolates from Asia, Africa, and Haiti. Furthermore, the results of this study support the hypothesis that the Philippines isolates of V. cholerae O1 are indigenous and exist locally in the aquatic ecosystem of the Philippines.
  
  
  OBJECTIVE
  Genetic characterization and phylogenomics analysis of outbreak strains have proven to be critical for probing clonal relatedness to strains isolated in different geographical regions and over time. Recently, extensive genetic analyses of V. cholerae O1 strains isolated in different countries have been done. However, genome sequences of V. cholerae O1 isolates from the Philippines have not been available for epidemiological investigation. In this study, molecular typing and phylogenetic analysis of Vibrio cholerae isolated from both clinical and environmental samples in 2011 confirmed unique genetic features of the Philippines isolates, which are helpful to understand the global epidemiology of cholera.
authors.affiliation: St. Luke's Medical Center, Research and Biotechnology Division, Quezon City, Philippines.
authors.forename: David C
authors.initials: DC
authors.lastname: Klinzing
authors.forename: Seon Young
authors.initials: SY
authors.lastname: Choi
authors.forename: Nur A
authors.initials: NA
authors.lastname: Hasan
authors.affiliation: St. Luke's Medical Center, Research and Biotechnology Division, Quezon City, Philippines.
authors.forename: Ronald R
authors.initials: RR
authors.lastname: Matias
authors.affiliation: National Epidemiology Center, Department of Health, Manila, Philippines.
authors.forename: Enrique
authors.initials: E
authors.lastname: Tayag
authors.affiliation: Research Institute for Tropical Medicine, Alabang, Philippines.
authors.forename: Josefina
authors.initials: J
authors.lastname: Geronimo
authors.affiliation: TMG Biosciences, LLC, Austin, Texas, USA.
authors.forename: Evan
authors.initials: E
authors.lastname: Skowronski
authors.affiliation: Maryland Pathogen Research Institute, University of Maryland, College Park, Maryland, USA.
authors.forename: Shah M
authors.initials: SM
authors.lastname: Rashed
authors.affiliation: St. Luke's Medical Center, Research and Biotechnology Division, Quezon City, Philippines.
authors.forename: Kent
authors.initials: K
authors.lastname: Kawashima
authors.affiliation: U.S. Army Edgewood Chemical Biological Center, Aberdeen, Maryland, USA.
authors.forename: C Nicole
authors.initials: CN
authors.lastname: Rosenzweig
authors.affiliation: U.S. Army Edgewood Chemical Biological Center, Aberdeen, Maryland, USA.
authors.forename: Henry S
authors.initials: HS
authors.lastname: Gibbons
authors.affiliation: St. Luke's Medical Center, Research and Biotechnology Division, Quezon City, Philippines.
authors.forename: Brian C
authors.initials: BC
authors.lastname: Torres
authors.affiliation: St. Luke's Medical Center, Research and Biotechnology Division, Quezon City, Philippines.
authors.forename: Veni
authors.initials: V
authors.lastname: Liles
authors.affiliation: St. Luke's Medical Center, Research and Biotechnology Division, Quezon City, Philippines.
authors.forename: Alicia C
authors.initials: AC
authors.lastname: Alfon
authors.affiliation: St. Luke's Medical Center, Research and Biotechnology Division, Quezon City, Philippines.
authors.forename: Maria Luisa
authors.initials: ML
authors.lastname: Juan
authors.affiliation: St. Luke's Medical Center, Research and Biotechnology Division, Quezon City, Philippines.
authors.forename: Filipinas F
authors.initials: FF
authors.lastname: Natividad
authors.affiliation: Department of Biology, Johns Hopkins University, Baltimore, Maryland, USA.
authors.forename: Thomas A
authors.initials: TA
authors.lastname: Cebula
authors.affiliation: rcolwell@umiacs.umd.edu.
authors.forename: Rita R
authors.initials: RR
authors.lastname: Colwell
mesh_terms: D002771:Cholera / Q000453:epidemiology* / Q000382:microbiology*; D016000:Cluster Analysis; D004196:Disease Outbreaks; D024881:Drug Resistance, Bacterial; D005798:Genes, Bacterial; D016680:Genome, Bacterial; D005838:Genotype; D018598:Minisatellite Repeats; D008969:Molecular Sequence Data; D058889:Molecular Typing; D010679:Philippines / Q000453:epidemiology; D010802:Phylogeny; D011995:Recombination, Genetic; D017422:Sequence Analysis, DNA; D017385:Sequence Homology; D041241:Vibrio cholerae O1 / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification*