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Prevalence of genotypic HIV-1 drug resistance in Thailand, 2002
Ekachai Jenwitheesuk, Chotip Watitpun, Asda Vibhagool, Wasun Chantratita
Annals of Clinical Microbiology and Antimicrobials , 2003, DOI: 10.1186/1476-0711-2-4
Abstract: Genotypic resistance testing was performed on samples collected in 2002 from 88 HIV-1 infected individuals. Automated DNA sequencing was used to genotype the HIV-1 polymerase gene isolated from patients' plasma.Resistance to protease inhibitors, nucleoside and non-nucleoside reverse transcriptase inhibitors were found in 10 (12%), 42 (48%) and 19 (21%) patients, respectively. The most common drug resistance mutations in the protease gene were at codon 82 (8%), 90 (7%) and 54 (6%), whereas resistant mutations at codon 215 (45%), 67 (40%), 41 (38%) and 184 (27%) were commonly found in the RT gene. This finding indicates that genotypic resistance to nucleoside reverse transcriptase inhibitors was prevalent in 2002. The frequency of resistant mutations corresponding to non-nucleoside reverse transcriptase inhibitors was three times higher-, while resistant mutation corresponding to protease inhibitors was two times lower than those frequencies determined in 2001.This study shows that the frequencies of RT inhibitor resistance mutations have been increased after the reduction in the price of RT inhibitors since December 2001. We believe that this was an important factor that influenced the mutation patterns of HIV-1 protease and RT genes in Thailand.During the last decade, the prevalence of human immunodeficiency virus type 1 (HIV-1) drug resistance has increased in developed countries as a result of widespread antiretroviral therapy [1-9]. Genotypic evidence of resistance for any drug was found in fewer than 2% of cases in one study from 1989 [4], increased to 10%-16% in cohorts recruited after 1995 [2,3], and attained between 20% and 26% in studies performed since 1997 [5-9]. Overall, several studies show rates of primary genotypic drug resistance between 10% and 18% for nucleoside reverse transcriptase inhibitors (NRTIs), of none to 13% for non-nucleoside reverse transcriptase inhibitors (NNRTIs), and of 3% to 7% for protease inhibitors (PIs) [1-9].In July 2002, S Sir
ParallABEL: an R library for generalized parallelization of genome-wide association studies
Unitsa Sangket, Surakameth Mahasirimongkol, Wasun Chantratita, Pichaya Tandayya, Yurii S Aulchenko
BMC Bioinformatics , 2010, DOI: 10.1186/1471-2105-11-217
Abstract: Most components of GWA analysis can be divided into four groups based on the types of input data and statistical outputs. The first group contains statistics computed for a particular Single Nucleotide Polymorphism (SNP), or trait, such as SNP characterization statistics or association test statistics. The input data of this group includes the SNPs/traits. The second group concerns statistics characterizing an individual in a study, for example, the summary statistics of genotype quality for each sample. The input data of this group includes individuals. The third group consists of pair-wise statistics derived from analyses between each pair of individuals in the study, for example genome-wide identity-by-state or genomic kinship analyses. The input data of this group includes pairs of SNPs/traits. The final group concerns pair-wise statistics derived for pairs of SNPs, such as the linkage disequilibrium characterisation. The input data of this group includes pairs of individuals. We developed the ParallABEL library, which utilizes the Rmpi library, to parallelize these four types of computations. ParallABEL library is not only aimed at GenABEL, but may also be employed to parallelize various GWA packages in R. The data set from the North American Rheumatoid Arthritis Consortium (NARAC) includes 2,062 individuals with 545,080, SNPs' genotyping, was used to measure ParallABEL performance. Almost perfect speed-up was achieved for many types of analyses. For example, the computing time for the identity-by-state matrix was linearly reduced from approximately eight hours to one hour when ParallABEL employed eight processors.Executing genome-wide association analysis using the ParallABEL library on a computer cluster is an effective way to boost performance, and simplify the parallelization of GWA studies. ParallABEL is a user-friendly parallelization of GenABEL.GWA analysis [1] is a well established and powerful method for identifying loci associated with variations of c
Genome-Wide Association Study in Thai Tsunami Survivors Identified Risk Alleles for Posttraumatic Stress Disorder  [PDF]
Nuntika Thavichachart, Taisei Mushiroda, Thongchai Thavichachart, Ongart Charoensook, Anchalee Prasansuklab, Prathan Rutchatajumroon, Sookjaroen Tangwongchai, Puangsoi Worakul, Buranee Kanchanatawan, Siriluck Suppapitiporn, Atapol Sughondhabirom, Chutima Roomruangwong, Wasun Chantratita, Atsushi Takahashi, Michiaki Kubo, Naoyuki Kamatani, Yusuke Nakamura
Open Journal of Genetics (OJGen) , 2015, DOI: 10.4236/ojgen.2015.52004
Abstract: Posttraumatic stress disorder (PTSD) is a psychiatric disorder found in individuals afflicted by a traumatic event. Multiple environmental and genetic factors can contribute to PTSD susceptibility. Since it is rare to find members of the same family afflicted by the same catastrophic event, it is not practical to determine PTSD susceptibility genes by a gene linkage analysis. A natural disaster, such as the 2004 Tsunami, provided us with a rare chance for a genetic analysis of PTSD. To identify SNPs associated with PTSD susceptibility, we conducted a genome-association study (GWAS) in Thai-Tsunami survivors. Initial phase of the study with 396 chronic PTSD patients and 457 controls, we identified top ninety SNPs (P < 1 × 10-4), which were further assessed in the second phase with 395 chronic PTSD patients and 798 controls. Two SNPs (rs267950 and rs954406), were identified in the second phase, and subjected to fine mapping using a data set from both phases. SNP rs267943 showed the strongest association with PTSD susceptibility and was in complete linkage disequilibrium with SNP rs267950 with P = 6.15 × 10-8, OR = 1.46 and 95% CI = 1.19 - 1.79, reaching genome-wide significance. SNP rs267943 is located on chromosome 5 in the intron of the death-associated protein 1 (DAP1) gene and, when linked to a synthetic promoter, could regulate transcription. To our knowledge, this is the first GWAS for PTSD susceptibility in an Asian population which could provide an important insight into the genetic contribution of PTSD and may lead to new treatment strategies for PTSD.
Influence of DAP1 Genotype and Psychosocial Factors on Posttraumatic Stress Disorder in Thai Tsunami Survivors: A GxE Approach  [PDF]
Nuntika Thavichachart, Prathan Rutchatajumroon, Taisei Mushiroda, Anchalee Prasansuklab, Sookjaroen Tangwongchai, Puangsoi Worakul, Buranee Kanchanatawan, Siriluck Suppapitiporn, Atapol Sughondhabirom, Chutima Roomruangwong, Ongart Charoensook, Wasun Chantratita, Atsushi Takahashi, Michiaki Kubo, Naoyuki Kamatani, Yusuke Nakamura
Open Journal of Genetics (OJGen) , 2019, DOI: 10.4236/ojgen.2019.93005
Abstract: Background: Posttraumatic Stress Disorder (PTSD) is a psychiatric disorder found in individuals afflicted by a traumatic event including the natural disaster. “Tsunami” occurred in Andaman coast of Thailand on December 26, 2004, in which 33.6% of survivors were diagnosed as PTSD. This study aimed to explore the single nucleotide polymorphism (SNP). rs267943 genotype is located on chromosome 5 in the intron of the death-associated protein 1 (DAP1) gene and psychosocial factors for PTSD. Methods: Participants (N = 1970) were recruited from volunteers who have complete data both of DAP1 gene and psychosocial factor. Results: Using a binary logistic regression model, significant gene-environment interactions were found for the single nucleotide polymorphism (SNP) rs267943 and psychosocial factors including depression (adj. OR = 6.0, 95% CI = 4.29 - 8.39), neurotic personality (adj. OR = 2.73, 95% CI = 2.18 - 3.42), planning (adj. OR = 1.52, 95% CI = 1.20 - 1.93), use of emotional support (adj. OR = 1.32, 95% CI = 1.21 - 1.94) with statistical significant p < 0.001 and self-distraction (adj. OR = 1.52, 95% CI = 1.15 - 1.85) with statistical significant p < 0.05. Conclusion: This study demonstrated that GxE studies can be utilized to shed light on the origins of PTSD.
Bird Diversity Relative to Forest Types and Physical Factors at Tung Salang Luang National Park, Thailand
Auttpol Nakwa,Narit Sitasuwan,Araya Jatisatein,Porntip Chantaramongkol,Wasun Pupichit,Pornchai Srisakb
Research Journal of Biological Sciences , 2012,
Abstract: A survey of bird diversity was carried out at Tung Salang Luang National Park in three forest types i.e. mixed forest (seasonal evergreen forest mixed with deciduous dipterocarp forest), seasonal evergreen forest and deciduous dipterocarp forest, during March 2004 to February 2005. The point count mixed line transect methods were used for data collection. The survey found 6,697 birds in total from 140 sp., 35 families and 11 orders occurring in the mixed forest, seasonal evergreen forest and deciduous dipterocarp forest were as follows: 107, 100 and 94 sp. The quantitative bird communities have a negative correlation with climatic changes, as a result, the dynamic pattern of bird populations in the 3 habitats during a year were similar. The fewest species numbers and individual numbers were found during the rainy season and slightly high during the late rainy to early cool seasons. The highest bird populations were found during cool season. Similarity index values of birds in both mixed forest and seasonal evergreen forest were the greatest similar, while both mixed forest and deciduous dipterocarp forest were fewest less similar. The 72.6-78.3% qualitative similarity index values of bird species between study sites was done. Mixed forest had the highest Shannon diversity index 3.9507, followed by deciduous dipterocarp and seasonal evergreen forest were 3.6387 and 3.6025, respectively. The pattern observed suggest that the structure and dynamics of the Tung Salang Luang bird community are strongly liked to physical factors and habitat heterogeneity. Two particular species of bird were observed in this study: Aviceda jerdoni (Jerdon` Baza) and Coracina javensis (Javan Cuckooshrike).
Burkholderia pseudomallei Is Genetically Diverse in Agricultural Land in Northeast Thailand
Vanaporn Wuthiekanun,Direk Limmathurotsakul,Narisara Chantratita,Edward J. Feil,Nicholas P. J. Day,Sharon J. Peacock
PLOS Neglected Tropical Diseases , 2009, DOI: 10.1371/journal.pntd.0000496
Abstract: Background The soil-dwelling Gram-negative bacterium Burkholderia pseudomallei is the cause of melioidosis. Extreme structuring of genotype and genotypic frequency has been demonstrated for B. pseudomallei in uncultivated land, but its distribution and genetic diversity in agricultural land where most human infections are probably acquired is not well defined. Methods Fixed-interval soil sampling was performed in a rice paddy in northeast Thailand in which 100 grams of soil was sampled at a depth of 30 cm from 10×10 sampling points each measuring 2.5 m by 2.5 m. Soil was cultured for the presence of B. pseudomallei and genotyping of colonies present on primary culture plates was performed using a combination of pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing (MLST). Principal Findings B. pseudomallei was cultured from 28/100 samples. Genotyping of 630 primary colonies drawn from 11 sampling points demonstrated 10 PFGE banding pattern types, which on MLST were resolved into 7 sequence types (ST). Overlap of genotypes was observed more often between sampling points that were closely positioned. Two sampling points contained mixed B. pseudomallei genotypes, each with a numerically dominant genotype and one or more additional genotypes present as minority populations. Conclusions Genetic diversity and structuring of B. pseudomallei exists despite the effects of flooding and the physical and chemical processes associated with farming. These findings form an important baseline for future studies of environmental B. pseudomallei.
Effect of colony morphology variation of Burkholderia pseudomallei on intracellular survival and resistance to antimicrobial environments in human macrophages in vitro
Sarunporn Tandhavanant, Aunchalee Thanwisai, Direk Limmathurotsakul, Sunee Korbsrisate, Nicholas PJ Day, Sharon J Peacock, Narisara Chantratita
BMC Microbiology , 2010, DOI: 10.1186/1471-2180-10-303
Abstract: Morphotype was associated with survival in the presence of H2O2 and antimicrobial peptide LL-37, but not with susceptibility to acid, acidified sodium nitrite, or resistance to lysozyme, lactoferrin, human neutrophil peptide-1 or human beta defensin-2. Incubation under anaerobic conditions was a strong driver for switching of type III to an alternative morphotype. Differences were noted in the survival and replication of the three types following uptake by human macrophages, but marked strain-to strain-variability was observed. Uptake of type III alone was associated with colony morphology switching.Morphotype is associated with phenotypes that alter the ability of B. pseudomallei to survive in adverse environmental conditions.Burkholderia pseudomallei is an environmental Gram-negative bacterium that causes a severe and often fatal disease called melioidosis. This is an important cause of sepsis in south-east Asia and northern Australia, a geographic distribution that mirrors the presence of B. pseudomallei in the environment [1]. Melioidosis may develop following bacterial inoculation or inhalation and occurs most often in people with regular contact with contaminated soil and water [1]. Clinical manifestations of melioidosis are highly variable and range from fulminant septicemia to mild localized infection. The overall mortality rate is 40% in northeast Thailand (rising to 90% in patients with severe sepsis) and 20% in northern Australia [1,2].A major feature of melioidosis is that bacterial eradication is difficult to achieve. Fever clearance time is often prolonged (median 8 days), antimicrobial therapy is required for 12-20 weeks, and relapse occurs in around 10% of patients despite an appropriate course of antimicrobial therapy [3,4]. The basis for persistence in the infected human host is unknown, although several observations made to date may be relevant to the clinical behaviour of this organism [2,5]. B. pseudomallei can resist the action of bactericidal
Burkholderia pseudomallei Is Spatially Distributed in Soil in Northeast Thailand
Direk Limmathurotsakul ,Vanaporn Wuthiekanun,Narisara Chantratita,Gumphol Wongsuvan,Premjit Amornchai,Nicholas P. J. Day,Sharon J. Peacock
PLOS Neglected Tropical Diseases , 2010, DOI: 10.1371/journal.pntd.0000694
Abstract: Background Melioidosis is a frequently fatal infectious disease caused by the soil dwelling Gram-negative bacterium Burkholderia pseudomallei. Environmental sampling is important to identify geographical distribution of the organism and related risk of infection to humans and livestock. The aim of this study was to evaluate spatial distribution of B. pseudomallei in soil and consider the implications of this for soil sampling strategies. Methods and Findings A fixed-interval sampling strategy was used as the basis for detection and quantitation by culture of B. pseudomallei in soil in two environmental sites (disused land covered with low-lying scrub and rice field) in northeast Thailand. Semivariogram and indicator semivariogram were used to evaluate the distribution of B. pseudomallei and its relationship with range between sampling points. B. pseudomallei was present on culture of 80/100 sampling points taken from the disused land and 28/100 sampling points from the rice field. The median B. pseudomallei cfu/gram from positive sampling points was 378 and 700 for the disused land and the rice field, respectively (p = 0.17). Spatial autocorrelation of B. pseudomallei was present, in that samples taken from areas adjacent to sampling points that were culture positive (negative) for B. pseudomallei were also likely to be culture positive (negative), and samples taken from areas adjacent to sampling points with a high (low) B. pseudomallei count were also likely to yield a high (low) count. Ranges of spatial autocorrelation in quantitative B. pseudomallei count were 11.4 meters in the disused land and 7.6 meters in the rice field. Conclusions We discuss the implications of the uneven distribution of B. pseudomallei in soil for future environmental studies, and describe a range of established geostatistical sampling approaches that would be suitable for the study of B. pseudomallei that take account of our findings.
Diversity of Xenorhabdus and Photorhabdus spp. and Their Symbiotic Entomopathogenic Nematodes from Thailand
Aunchalee Thanwisai,Sarunporn Tandhavanant,Natnaree Saiprom,Nick R. Waterfield,Phan Ke Long,Helge B. Bode,Sharon J. Peacock,Narisara Chantratita
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0043835
Abstract: Xenorhabdus and Photorhabdus spp. are bacterial symbionts of entomopathogenic nematodes (EPNs). In this study, we isolated and characterized Xenorhabdus and Photorhabdus spp. from across Thailand together with their associated nematode symbionts, and characterized their phylogenetic diversity. EPNs were isolated from soil samples using a Galleria-baiting technique. Bacteria from EPNs were cultured and genotyped based on recA sequence. The nematodes were identified based on sequences of 28S rDNA and internal transcribed spacer regions. A total of 795 soil samples were collected from 159 sites in 13 provinces across Thailand. A total of 126 EPNs isolated from samples taken from 10 provinces were positive for Xenorhabdus (n = 69) or Photorhabdus spp. (n = 57). Phylogenetic analysis separated the 69 Xenorhabdus isolates into 4 groups. Groups 1, 2 and 3 consisting of 52, 13 and 1 isolates related to X. stockiae, and group 4 consisting of 3 isolates related to X. miraniensis. The EPN host for isolates related to X. stockiae was S. websteri, and for X. miraniensis was S. khoisanae. The Photorhabdus species were identified as P. luminescens (n = 56) and P. asymbiotica (n = 1). Phylogenenic analysis divided P. luminescens into five groups. Groups 1 and 2 consisted of 45 and 8 isolates defined as subspecies hainanensis and akhurstii, respectively. One isolate was related to hainanensis and akhurstii, two isolates were related to laumondii, and one isolate was the pathogenic species P. asymbiotica subsp. australis. H. indica was the major EPN host for Photorhabdus. This study reveals the genetic diversity of Xenorhabdus and Photorhabdus spp. and describes new associations between EPNs and their bacterial symbionts in Thailand.
Genetic Diversity and Microevolution of Burkholderia pseudomallei in the Environment
Narisara Chantratita equal contributor,Vanaporn Wuthiekanun equal contributor,Direk Limmathurotsakul,Mongkol Vesaratchavest,Aunchalee Thanwisai,Premjit Amornchai,Sarinna Tumapa,Edward J. Feil,Nicholas P. Day,Sharon J. Peacock
PLOS Neglected Tropical Diseases , 2008, DOI: 10.1371/journal.pntd.0000182
Abstract: Background The soil dwelling Gram-negative pathogen Burkholderia pseudomallei is the cause of melioidosis. The diversity and population structure of this organism in the environment is poorly defined. Methods and Findings We undertook a study of B. pseudomallei in soil sampled from 100 equally spaced points within 237.5 m2 of disused land in northeast Thailand. B. pseudomallei was present on direct culture of 77/100 sampling points. Genotyping of 200 primary plate colonies from three independent sampling points was performed using a combination of pulsed field gel electrophoresis (PFGE) and multilocus sequence typing (MLST). Twelve PFGE types and nine sequence types (STs) were identified, the majority of which were present at only a single sampling point. Two sampling points contained four STs and the third point contained three STs. Although the distance between the three sampling points was low (7.6, 7.9, and 13.3 meters, respectively), only two STs were present in more than one sampling point. Each of the three samples was characterized by the localized expansion of a single B. pseudomallei clone (corresponding to STs 185, 163, and 93). Comparison of PFGE and MLST results demonstrated that two STs contained strains with variable PFGE banding pattern types, indicating geographic structuring even within a single MLST-defined clone. Conclusions We discuss the implications of this extreme structuring of genotype and genotypic frequency in terms of micro-evolutionary dynamics and ecology, and how our results may inform future sampling strategies.
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