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Publication Metadata only Epidemiological tracking and population assignment of the non-clonal bacterium, burkholderia pseudomallei(2011-12-01) Julia Dale; Erin P. Price; Heidie Hornstra; Joseph D. Busch; Mark Mayo; Daniel Godoy; Vanaporn Wuthiekanun; Anthony Baker; Jeffrey T. Foster; David M. Wagner; Apichai Tuanyok; Jeffrey Warner; Brian G. Spratt; Sharon J. Peacock; Bart J. Currie; Paul Keim; Talima Pearson; Northern Arizona University; Royal Darwin Hospital; Imperial College London; Mahidol University; James Cook University, Australia; University of Cambridge; Translational Genomics Research InstituteRapid assignment of bacterial pathogens into predefined populations is an important first step for epidemiological tracking. For clonal species, a single allele can theoretically define a population. For non-clonal species such as Burkholderia... (MLST). These populations correlate with the major foci of endemicity (Australia and Southeast Asia). Here, we use multiple Bayesian approaches to evaluate the compositional robustness of these populations, and provide assignment results for MLSTPublication Metadata only Trimethoprim/sulfamethoxazole resistance in clinical isolates of Burkholderia pseudomallei(2005-06-01) Vanaporn Wuthiekanun; Allen C. Cheng; Wirongrong Chierakul; Premjit Amornchai; Direk Limmathurotsakul; Wipada Chaowagul; Andrew J.H. Simpson; Jennifer M. Short; Gumphol Wongsuvan; Bina Maharjan; Nicholas J. White; Sharon J. Peacock; Mahidol University; Menzies School of Health Research; Sappasitthiprasong Hospital; Dstl; Heartlands Hospital; Nuffield Department of Clinical Medicineassigned as 'susceptible' or 'intermediate' by disc diffusion may be viewed as 'susceptible'; those assigned as 'resistant' require further evaluation by MIC methodology. © The Author 2005. Published by Oxford University Press on behalf of the BritishPublication Metadata only Trimethoprim-sulfamethoxazole versus trimethoprimsulfamethoxazole plus doxycycline as oral eradicative treatment for melioidosis (MERTH): A multicentre, double-blind, non-inferiority, randomised controlled trial(2014-01-01) Ploenchan Chetchotisakd; Wirongrong Chierakul; Wipada Chaowagul; Siriluck Anunnatsiri; Kriangsak Phimda; Piroon Mootsikapun; Seksan Chaisuksant; Jiraporn Pilaikul; Bandit Thinkhamrop; Sunchai Phiphitaporn; Wattanachai Susaengrat; Chalongchai Toondee; Surasakdi Wongrattanacheewin; Vanaporn Wuthiekanun; Narisara Chantratita; Janjira Thaipadungpanit; Nicholas P. Day; Direk Limmathurotsakul; Sharon J. Peacock; Faculty of Medicine, Thammasat University; Kaen University; Mahidol University; Sappasitthiprasong Hospital; Udon Thani Center Hospital; Khon Kaen Regional Hospital; Mahasarakam Hospital; Khon Kaen University; University of Oxford; University of Cambridge(aged ≥15 years) from five centres in northeast Thailand with culture-confirmed melioidosis who had received a course of parenteral antimicrobial drugs. Using a computer-generated sequence, we randomly assigned patients to receive TMP-SMX plus placebo... melioidosis, and the non-inferiority margin was a hazard ratio (HR) of 1.7. This study is registered with www.controlled-trials. com, number ISRCTN86140460. Findings We enrolled and randomly assigned 626 patients: 311 to TMP-SMX plus placebo and 315 to TMP-SMXPublication Open Access A single multilocus sequence typing (MLST) scheme for seven pathogenic Leptospira species(2013) Siriphan Boonsilp; ศิริพรรณ บุญศิลป์; Janjira Thaipadungpanit; จันทรจิรา ไทยผดุงพานิช; Premjit Amornchai; เปรมจิตร อมรชัย; Vanaporn Wuthiekanun; วรรณพร วุฒิเอกอนันต์; Bailey, Mark S.; Holden, Matthew T. G.; Zhang, Cuicai; Jiang, Xiugao; Koizumi, Nobuo; Taylor, Kyle; Galloway, Renee; Hoffmaster, Alex R.; Craig, Scott; Smythe, Lee D.; Hartskeerl, Rudy A.; Day, Nicholas P.; Narisara Chantratita; นริศรา จันทราทิตย์; Feil, Edward J.; Aanensen, David M.; Spratt, Brian G.; Peacock, Sharon J.; Janjira Thaipadungpanit; Mahidol University. Faculty of Tropical Medicine. Mahidol-Oxford Tropical Medicine Research Unit; Mahidol University. Faculty of Tropical Medicine. Department of Microbiology and Immunologydiscrete clade, and that no strains were misclassified at the species level. Comparison between genotype and serovar was possible for 254 isolates. Of the 31 sequence types (STs) represented by at least two isolates, 18 STs included isolates assigned... between human disease and specific maintenance hosts was demonstrated. CONCLUSION: The new MLST scheme, supported by an updated MLST website, allows the characterization and species assignment of isolates of the seven major pathogenic speciesPublication Metadata only A Single Multilocus Sequence Typing (MLST) Scheme for Seven Pathogenic Leptospira Species(2013-01-01) Siriphan Boonsilp; Janjira Thaipadungpanit; Premjit Amornchai; Vanaporn Wuthiekanun; Mark S. Bailey; Matthew T G Holden; Cuicai Zhang; Xiugao Jiang; Nobuo Koizumi; Kyle Taylor; Renee Galloway; Alex R. Hoffmaster; Scott Craig; Lee D. Smythe; Rudy A. Hartskeerl; Nicholas P. Day; Narisara Chantratita; Edward J. Feil; David M. Aanensen; Brian G. Spratt; Sharon J. Peacock; Mahidol University; Heartlands Hospital; Wellcome Trust Sanger Institute; Chinese Center for Disease Control and Prevention; National Institute of Infectious Diseases; Hokkaido University; National Center for Emerging and Zoonotic Infectious Diseases; Queensland Health; Royal Tropical Institute - KIT; Nuffield Department of Clinical Medicine; University of Bath; Imperial College London; University of Cambridgediscrete clade, and that no strains were misclassified at the species level. Comparison between genotype and serovar was possible for 254 isolates. Of the 31 sequence types (STs) represented by at least two isolates, 18 STs included isolates assigned to two... disease and specific maintenance hosts was demonstrated. Conclusion: The new MLST scheme, supported by an updated MLST website, allows the characterization and species assignment of isolates of the seven major pathogenic species associatedPublication Metadata only Emergence of community-associated methicillin-resistant Staphylococcus aureus carriage in children in Cambodia(2011-02-01) Emma K. Nickerson; Vanaporn Wuthiekanun; Varun Kumar; Premjit Amornchai; Nattavut Wongdeethai; Kheng Chheng; Narisara Chantratita; Hor Putchhat; Janjira Thaipadungpanit; Nicholas P. Day; Sharon J. Peacock; Addenbrooke's Hospital; Mahidol University; Angkor Hospital for Children; University of Cambridge. Most (91%) isolates were assigned to sequence type 834. Only 28 (32%) of 87 MRSA carriers identified in the outpatient department had no history of recent healthcare contact. The study findings have important implications for healthcare in a settingPublication Open Access Genome sequencing defines phylogeny and spread of methicillin-resistant Staphylococcus aureus in a high transmission setting.(2015-01) Tong, Steven Y.C.; Holden, Matthew T.G.; Nickerson, Emma K.; Cooper, Ben S.; Köser, Claudio U.; Cori, Anne; Jombart, Thibaut; Cauchemez, Simon; Fraser, Christophe; Vanaporn Wuthiekanun; วรรณพร วุฒิเอกอนันต์; Janjira Thaipadungpanit; จันทร์จิรา ไทยผดุงพานิช; Maliwan Hongsuwan; มะลิวัลย์ หงษ์สุวรรณ; Day, Nicholas P.; Direk Limmathurotsakul; ดิเรก ลิ้มมธุรสกุล; Parkhill, Julian; Peacock, Sharon J.; Peacock, Sharon J.; Mahidol University. Faculty of Tropical Medicine. Mahidol-Oxford Tropical Medicine Research Unit.Methicillin-resistant Staphylococcus aureus (MRSA) is a major cause of nosocomial infection. Whole-genome sequencing of MRSA has been used to define phylogeny and transmission in well-resourced healthcare settings, yet the greatest burden of nosocomial infection occurs in resource-restricted settings where barriers to transmission are lower. Here, we study the flux and genetic diversity of MRSA on ward and individual patient levels in a hospital where transmission was common. We repeatedly screened all patients on two intensive care units for MRSA carriage over a 3-mo period. All MRSA belonged to multilocus sequence type 239 (ST 239). We defined the population structure and charted the spread of MRSA by sequencing 79 isolates from 46 patients and five members of staff, including the first MRSA-positive screen isolates and up to two repeat isolates where available. Phylogenetic analysis identified a flux of distinct ST 239 clades over time in each intensive care unit. In total, five main clades were identified, which varied in the carriage of plasmids encoding antiseptic and antimicrobial resistance determinants. Sequence data confirmed intra- and interwards transmission events and identified individual patients who were colonized by more than one clade. One patient on each unit was the source of numerous transmission events, and deep sampling of one of these cases demonstrated colonization with a "cloud" of related MRSA variants. The application of whole-genome sequencing and analysis provides novel insights into the transmission of MRSA in under-resourced healthcare settings and has relevance to wider global health.Publication Open Access Comparison of two multilocus sequence based genotyping schemes for Leptospira species.(2011-11) Ahmed, Ahmed; Janjira Thaipadungpanit; จันทร์จิรา ไทยผดุงพานิช; Siriphan Boonsilp; ศิริพรรณ บุญศิลป์; Vanaporn Wuthiekanun; วรรณพร วุฒิเอกอนันต์; Nalam, Kishore; Spratt, Brian G.; Aanensen, David M.; Smythe, Lee D.; Ahmed, Niyaz; Feil, Edward J.; Hartskeer, Rudy A.; Peacock, Sharon J.; Ahmed, Ahmed; Mahidol University. Faculty of Tropical Medicine. Department of Microbiology and Immunology.; Mahidol University. Faculty of Tropical Medicine. Mahidol-Oxford Tropical Medicine Research Unit.; Mahidol Univeristy. Faculty of Medicine Siriraj Hospital. Medical Proteomics Unit, Office for Research and Development.BACKGROUND: Several sequence based genotyping schemes have been developed for Leptospira spp. The objective of this study was to genotype a collection of clinical and reference isolates using the two most commonly used schemes and compare and contrast the results. METHODS AND FINDINGS: A total of 48 isolates consisting of L. interrogans (n = 40) and L. kirschneri (n = 8) were typed by the 7 locus MLST scheme described by Thaipadungpanit et al., and the 6 locus genotyping scheme described by Ahmed et al., (termed 7L and 6L, respectively). Two L. interrogans isolates were not typed using 6L because of a deletion of three nucleotides in lipL32. The remaining 46 isolates were resolved into 21 sequence types (STs) by 7L, and 30 genotypes by 6L. Overall nucleotide diversity (based on concatenated sequence) was 3.6% and 2.3% for 7L and 6L, respectively. The D value (discriminatory ability) of 7L and 6L were comparable, i.e. 92.0 (95% CI 87.5-96.5) vs. 93.5 (95% CI 88.6-98.4). The dN/dS ratios calculated for each locus indicated that none were under positive selection. Neighbor joining trees were reconstructed based on the concatenated sequences for each scheme. Both trees showed two distinct groups corresponding to L. interrogans and L. kirschneri, and both identified two clones containing 10 and 7 clinical isolates, respectively. There were six instances in which 6L split single STs as defined by 7L into closely related clusters. We noted two discrepancies between the trees in which the genetic relatedness between two pairs of strains were more closely related by 7L than by 6L. CONCLUSIONS: This genetic analysis indicates that the two schemes are comparable. We discuss their practical advantages and disadvantages.Publication Open Access Clinical and molecular epidemiology of Staphylococcus argenteus infections in Thailand.(2015-03) Janjira Thaipadungpanit; จันทร์จิรา ไทยผดุงพานิช; Premjit Amornchai; เปรมจิตร อมรชัย; Nickerson, Emma K.; Gumphol Wongsuvan; กำพล วงศ์สุวรรณ; Vanaporn Wuthiekanun; วรรณพร วุฒิเอกอนันต์; Direk Limmathurotsakul; ดิเรก ลิ้มมธุรสกุล; Peacock, Sharon J.; Janjira Thaipadungpanit; Mahidol University. Faculty of Tropical Medicine. Mahidol-Oxford Tropical Medicine Research Unit.; Mahidol University. Faculty of Tropical Medicine. Department of Tropical Medicine and Hygiene.; Mahidol University. Faculty of Tropical Medicine. Department of Microbiology and Immunology.Molecular typing of 246 Staphylococcus aureus isolates from unselected patients in Thailand showed that 10 (4.1%) were actually Staphylococcus argenteus. Contrary to the suggestion that S. argenteus is less virulent than S. aureus, we demonstrated comparable rates of morbidity, death, and health care-associated infection in patients infected with either of these two species.Publication Open Access Systematic review and consensus guidelines for environmental sampling of Burkholderia pseudomallei(2013-03) Direk Limmathurotsakul; ดิเรก ลิ้มมธุรสกุล; Dance, David A. B.; Vanaporn Wuthiekanun; Kaestli, Mirjam; Mayo, Mark; Warner, Jeffrey; Wagner, David M.; Apichai Tuanyok; Wertheim, Heiman; Cheng, Tan Yoke; Mukhopadhyay, Chiranjay; Puthucheary, Savithiri; Day,Nicholas P. J.; Steinmetz, Ivo; Currie, Bart J.; Peacock, Sharon J.; Direk Limmathurotsakul; Mahidol University. Faculty of Tropical Medicine. Department of Tropical Hygiene; Mahidol University. Faculty of Tropical Medicine. Mahidol-Oxford Tropical Medicine Research Unit; Mahidol University. Faculty of Tropical Medicine. Department of Microbiology and ImmunologyBACKGROUND: Burkholderia pseudomallei, a Tier 1 Select Agent and the cause of melioidosis, is a Gram-negative bacillus present in the environment in many tropical countries. Defining the global pattern of B. pseudomallei distribution underpins efforts to prevent infection, and is dependent upon robust environmental sampling methodology. Our objective was to review the literature on the detection of environmental B. pseudomallei, update the risk map for melioidosis, and propose international consensus guidelines for soil sampling. METHODS/PRINCIPAL FINDINGS: An international working party (Detection of Environmental Burkholderia pseudomallei Working Party (DEBWorP)) was formed during the VIth World Melioidosis Congress in 2010. PubMed (January 1912 to December 2011) was searched using the following MeSH terms: pseudomallei or melioidosis. Bibliographies were hand-searched for secondary references. The reported geographical distribution of B. pseudomallei in the environment was mapped and categorized as definite, probable, or possible. The methodology used for detecting environmental B. pseudomallei was extracted and collated. We found that global coverage was patchy, with a lack of studies in many areas where melioidosis is suspected to occur. The sampling strategies and bacterial identification methods used were highly variable, and not all were robust. We developed consensus guidelines with the goals of reducing the probability of false-negative results, and the provision of affordable and 'low-tech' methodology that is applicable in both developed and developing countries. CONCLUSIONS/SIGNIFICANCE: The proposed consensus guidelines provide the basis for the development of an accurate and comprehensive global map of environmental B. pseudomallei.