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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.
Emergence of Community-Associated Methicillin-Resistant Staphylococcus aureus Associated with Pediatric Infection in Cambodia
Kheng Chheng, Sarah Tarquinio, Vanaporn Wuthiekanun, Lina Sin, Janjira Thaipadungpanit, Premjit Amornchai, Ngoun Chanpheaktra, Sarinna Tumapa, Hor Putchhat, Nicholas P. J. Day, Sharon J. Peacock
PLOS ONE , 2009, DOI: 10.1371/journal.pone.0006630
Abstract: Background The incidence of community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) infection is rising in the developed world but appears to be rare in developing countries. One explanation for this difference is that resource poor countries lack the diagnostic microbiology facilities necessary to detect the presence of CA-MRSA carriage and infection. Methodology and Principal Findings We developed diagnostic microbiology capabilities at the Angkor Hospital for Children, Siem Reap, western Cambodia in January 2006 and in the same month identified a child with severe community-acquired impetigo caused by CA-MRSA. A study was undertaken to identify and describe additional cases presenting between January 2006 and December 2007. Bacterial isolates underwent molecular characterization using multilocus sequence typing, staphylococcal cassette chromosome mec (SCCmec) typing, and PCR for the presence of the genes encoding Panton-Valentine Leukocidin (PVL). Seventeen children were identified with CA-MRSA infection, of which 11 had skin and soft tissue infection and 6 had invasive disease. The majority of cases were unrelated in time or place. Molecular characterization identified two independent MRSA clones; fifteen isolates were sequence type (ST) 834, SCCmec type IV, PVL gene-negative, and two isolates were ST 121, SCCmec type V, PVL gene-positive. Conclusions This represents the first ever report of MRSA in Cambodia, spread of which would pose a significant threat to public health. The finding that cases were mostly unrelated in time or place suggests that these were sporadic infections in persons who were CA-MRSA carriers or contacts of carriers, rather than arising in the context of an outbreak.
A Simple Scoring System to Differentiate between Relapse and Re-Infection in Patients with Recurrent Melioidosis
Direk Limmathurotsakul ,Wipada Chaowagul,Narisara Chantratita,Vanaporn Wuthiekanun,Mayurachat Biaklang,Sarinna Tumapa,Nicholas J. White,Nicholas P. J. Day,Sharon J. Peacock
PLOS Neglected Tropical Diseases , 2008, DOI: 10.1371/journal.pntd.0000327
Abstract: Background Melioidosis is an important cause of morbidity and mortality in East Asia. Recurrent melioidosis occurs in around 10% of patients following treatment either because of relapse with the same strain or re-infection with a new strain of Burkholderia pseudomallei. Distinguishing between the two is important but requires bacterial genotyping. The aim of this study was to develop a simple scoring system to distinguish re-infection from relapse. Methods In a prospective study of 2,804 consecutive adult patients with melioidosis presenting to Sappasithiprasong Hospital, NE Thailand, between1986 and 2005, there were 141 patients with recurrent melioidosis with paired strains available for genotyping. Of these, 92 patients had relapse and 49 patients had re-infection. Variables associated with relapse or re-infection were identified by multivariable logistic regression and used to develop a predictive model. Performance of the scoring system was quantified with respect to discrimination (area under receiver operating characteristic curves, AUC) and categorization (graphically). Bootstrap resampling was used to internally validate the predictors and adjust for over-optimism. Findings Duration of oral antimicrobial treatment, interval between the primary episode and recurrence, season, and renal function at recurrence were independent predictors of relapse or re-infection. A score of <5 correctly identified relapse in 76 of 89 patients (85%), whereas a score ≥5 correctly identified re-infection in 36 of 52 patients (69%). The scoring index had good discriminative power, with a bootstrap bias-corrected AUC of 0.80 (95%CI: 0.73–0.87). Conclusions A simple scoring index to predict the cause of recurrent melioidosis has been developed to provide important bedside information where rapid bacterial genotyping is unavailable.
Burkholderia pseudomallei genome plasticity associated with genomic island variation
Sarinna Tumapa, Matthew TG Holden, Mongkol Vesaratchavest, Vanaporn Wuthiekanun, Direk Limmathurotsakul, Wirongrong Chierakul, Edward J Feil, Bart J Currie, Nicholas PJ Day, William C Nierman, Sharon J Peacock
BMC Genomics , 2008, DOI: 10.1186/1471-2164-9-190
Abstract: Five islands from B. pseudomallei strain K96243 were chosen as representatives of different types of genomic islands present in this strain, and their presence investigated in other B. pseudomallei. In silico analysis of 10 B. pseudomallei genome sequences provided evidence for the variable presence of these regions, together with micro-evolutionary changes that generate GI diversity. The diversity of GIs in 186 isolates from NE Thailand (83 environmental and 103 clinical isolates) was investigated using multiplex PCR screening. The proportion of all isolates positive by PCR ranged from 12% for a prophage-like island (GI 9), to 76% for a metabolic island (GI 16). The presence of each of the five GIs did not differ between environmental and disease-associated isolates (p > 0.05 for all five islands). The cumulative number of GIs per isolate for the 186 isolates ranged from 0 to 5 (median 2, IQR 1 to 3). The distribution of cumulative GI number did not differ between environmental and disease-associated isolates (p = 0.27). The presence of GIs was defined for the three largest clones in this collection (each defined as a single sequence type, ST, by multilocus sequence typing); these were ST 70 (n = 15 isolates), ST 54 (n = 11), and ST 167 (n = 9). The rapid loss and/or acquisition of gene islands was observed within individual clones. Comparisons were drawn between isolates obtained from the environment and from patients with melioidosis in order to examine the role of genomic islands in virulence and clinical associations. There was no reproducible association between the individual or cumulative presence of five GIs and a range of clinical features in 103 patients with melioidosis.Horizontal gene transfer of mobile genetic elements can rapidly alter the gene repertoire of B. pseudomallei. This study confirms the utility of a range of approaches in defining the presence and significance of genomic variation in natural populations of B. pseudomallei.Burkholderia pseu
Burkholderia Hep_Hag autotransporter (BuHA) proteins elicit a strong antibody response during experimental glanders but not human melioidosis
Rachaneeporn Tiyawisutsri, Matthew TG Holden, Sarinna Tumapa, Sirirat Rengpipat, Simon R Clarke, Simon J Foster, William C Nierman, Nicholas PJ Day, Sharon J Peacock
BMC Microbiology , 2007, DOI: 10.1186/1471-2180-7-19
Abstract: Using bacteriophage-mediated immunoscreening we identified genes expressed in vivo during experimental equine glanders infection. A family of immunodominant antigens were identified that share protein domain architectures with hemagglutinins and invasins. These have been designated Burkholderia Hep_Hag autotransporter (BuHA) proteins. A total of 110/207 positive clones (53%) of a B. mallei expression library screened with sera from two infected horses belonged to this family. This contrasted with 6/189 positive clones (3%) of a B. pseudomallei expression library screened with serum from 21 patients with culture-proven melioidosis.Members of the BuHA proteins are found in other Gram-negative bacteria and have been shown to have important roles related to virulence. Compared with other bacterial species, the genomes of both B. mallei and B. pseudomallei contain a relative abundance of this family of proteins. The domain structures of these proteins suggest that they function as multimeric surface proteins that modulate interactions of the cell with the host and environment. Their effect on the cellular immune response to B. mallei and their potential as diagnostics for glanders requires further study.Burkholderia mallei is the causative agent of glanders, a serious Gram-negative infection that predominantly affects horses and other equines [1]. Natural B. mallei infection has largely been eradicated and human infection is extremely rare, but renewed interest in this organism parallels its classification as a category B biothreat agent. There is a need to develop an effective vaccine for individuals at risk of exposure from deliberate release, and understanding the immune response elicited during infection with B. mallei is central to this process. The relative importance of cellular versus humoral responses in the development of protective immunity against B. mallei is under investigation. Experimental evidence indicates that both play a role, but that stimulation of
Genomic acquisition of a capsular polysaccharide virulence cluster by non-pathogenic Burkholderia isolates
Bernice Meng Qi Sim, Narisara Chantratita, Wen Fong Ooi, Tannistha Nandi, Ryan Tewhey, Vanaporn Wuthiekanun, Janjira Thaipadungpanit, Sarinna Tumapa, Pramila Ariyaratne, Wing-Kin Sung, Xiao Hui Sem, Hui Hoon Chua, Kalpana Ramnarayanan, Chi Ho Lin, Yichun Liu, Edward J Feil, Mindy B Glass, Gladys Tan, Sharon J Peacock, Patrick Tan
Genome Biology , 2010, DOI: 10.1186/gb-2010-11-8-r89
Abstract: Of 39 genomic regions variably present across the B. thailandensis strains, 13 regions corresponded to known genomic islands, while 26 regions were novel. Variant B. thailandensis isolates exhibited isolated acquisition of a capsular polysaccharide biosynthesis gene cluster (B. pseudomallei-like capsular polysaccharide) closely resembling a similar cluster in B. pseudomallei that is essential for virulence in mammals; presence of this cluster was confirmed by whole genome sequencing of a representative variant strain (B. thailandensis E555). Both whole-genome microarray and multi-locus sequence typing analysis revealed that the variant strains formed part of a phylogenetic subgroup distinct from the ancestral B. thailandensis population and were associated with atypical isolation sources when compared to the majority of previously described B. thailandensis strains. In functional assays, B. thailandensis E555 exhibited several B. pseudomallei-like phenotypes, including colony wrinkling, resistance to human complement binding, and intracellular macrophage survival. However, in murine infection assays, B. thailandensis E555 did not exhibit enhanced virulence relative to other B. thailandensis strains, suggesting that additional factors are required to successfully colonize and infect mammals.The discovery of such novel variant strains demonstrates how unbiased genomic surveys of non-pathogenic isolates can reveal insights into the development and emergence of new pathogenic species.The evolution of pathogen virulence is a complex process involving macrogenomic processes, such as large-scale gene acquisition and loss, combined with more subtle modifications of existing genes and regulatory pathways. Previous studies have shown that microbial pathogens can employ a variety of molecular factors to enable human and animal infection, such as type III toxin secretion systems, adhesins, and modulators of host signaling pathways [1-4]. As the compendium of virulence factors i
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