Genetic Studies of Vibrio cholerae in South West Cameroon-A Phylogenetic Analysis of Isolates from the 2010-2011 Epidemic.
BACKGROUND
During the cholera outbreak from 2010 to 2011 in Cameroon, 33,192 cases with 1,440 deaths (case fatality ratio 4.34%) were reported to the World Health Organization. Of these, the South West Region reported 3,120 clinical cases. This region is in the Equatorial Monsoon climatic subzone of Cameroon, close to the coast, raising questions as to whether cases were linked with development of environmental reservoirs.


METHODS
In an investigation conducted by the Laboratory for Emerging Infectious Diseases, University of Buea, toxigenic V. cholerae O1 were isolated from diarrheal stool samples from 18 patients, with ages ranging from <3 to 70 years. Coordinates for clinical centers at which cases were identified were obtained using a handheld GPS, and were mapped using ArcGIS. Antibiotic susceptibility testing was performed using the Kirby 'Bauer agar disc diffusion method. The full genomes of these strains were sequenced with the Illumina MiSeq platform. De novo assembly of cholera genomes and multiple sequence alignment were carried out using the bioinformatics pipeline developed in the Emerging Pathogens Institute laboratory at the University of Florida.


CONCLUSIONS
Genetic comparisons showed that isolates were closely related, with pairwise p-distances ranging from 2.25 to 14.52 10-5 nt substitutions per site, and no statistically significant correlation between the pairwise genetic distances and the geographic distances among sampling locations. Indeed, the phylogeny of the Cameroonian strains displays the typical star-like topology and intermixing of strains from different locations that are characteristic of an exponential outbreak localized around a relatively restricted area with occasional spillover to other parts of the country, likely mediated by direct human contact and human movement. Findings highlight the utility of whole genome sequencing and phylogenetic analysis in understanding transmission patterns at the local level.
Emerging Pathogens Institute, University of Florida, Gainesville, Florida, USA; Department of Environmental and Global Health, College of Public Health and Health Professions, University of Florida, Gainesville, Florida, USA.
Moise C
MC
Ngwa
Laboratory for Emerging Infectious Diseases, University of Buea, Buea, South West Region, Cameroon.
Thomas
T
Masalla
Laboratory for Emerging Infectious Diseases, University of Buea, Buea, South West Region, Cameroon.
Seraphine
S
Esemu
Laboratory for Emerging Infectious Diseases, University of Buea, Buea, South West Region, Cameroon.
Foche Francis
FF
Fumoloh
Ian
I
Kracalik
Emerging Pathogens Institute, University of Florida, Gainesville, Florida, USA.
Eleonora
E
Cella
Emerging Pathogens Institute, University of Florida, Gainesville, Florida, USA.
Meer Taifur
MT
Alam
Laboratory for Emerging Infectious Diseases, University of Buea, Buea, South West Region, Cameroon.
Jane-Francis
JF
Akoachere
Emerging Pathogens Institute, University of Florida, Gainesville, Florida, USA; Department of Environmental and Global Health, College of Public Health and Health Professions, University of Florida, Gainesville, Florida, USA.
Song
S
Liang
Emerging Pathogens Institute, University of Florida, Gainesville, Florida, USA.
Marco
M
Salemi
Emerging Pathogens Institute, University of Florida, Gainesville, Florida, USA; Department of Medicine, College of Medicine, University of Florida, Gainesville, Florida, USA.
J Glenn
JG
Morris
Emerging Pathogens Institute, University of Florida, Gainesville, Florida, USA; Department of Environmental and Global Health, College of Public Health and Health Professions, University of Florida, Gainesville, Florida, USA.
Afsar
A
Ali
Laboratory for Emerging Infectious Diseases, University of Buea, Buea, South West Region, Cameroon; Department of Microbiology, University of Buea, Buea, South West Region, Cameroon.
Lucy M
LM
Ndip