Comparison of two rapid test kits with real time polymerase chain reaction for early diagnosis of dengue in Sri Lanka.

Dengue is among the deadliest insect-borne diseases circulating in Sri Lanka. Most of the infections that are diagnosed early are manageable. However, delays in diagnosis may cause fatalities. We evaluated the dengue NS1 antigen card and NS1 SD kit for early diagnosis of dengue using samples from 116 RT-PCR-positive patients admitted within 5 days of the fever onset. RT-PCR tests were performed as standard tests. IgM and IgG ELISA tests were carried out to identify primary and secondary infections. Of the 116 patients who tested positive for dengue using PCR, 48 were positive using NS1 antigen card and 45 were positive using NS1 SD. Patients with 100 copies or higher viral load showed a higher sensitivity in both antigen card and NS1 SD. Of 34 primary infections evaluated, 23 were positive by NS1 antigen card, while the positivity was 21 by NS1 SD. Of the 30 secondary infections evaluated, 15 were positive by NS1 antigen card while 14 by NS1 SD. Our findings showed that while the rapid tests are convenient and much easier to use than PCR, they are less sensitive and need improvement. Until then, clinical diagnosis should have more emphasis on the early diagnosis of dengue.

Burkholderia pseudomallei in soil and natural water bodies in rural Sri Lanka: A hidden threat to public health.

Burkholderia pseudomallei is the causative agent of the potentially fatal infection, melioidosis. This study provides the first evidence for the presence of B. pseudomallei in soil and water in Sri Lanka. Targeted sampling of soil and natural water sources was done between November 2019 and October 2020 over eight field visits encompassing the neighborhood of 28 culture and/or antibody-positive melioidosis patients in northwestern, western and southern Sri Lanka. A total of eight environmental isolates of B. pseudomallei (BPs-env1 to BPs-env8) were cultured from 116 soil and 117 natural water samples collected from 72 locations. The presence of B. pseudomallei in soil and natural water in these areas poses a risk of melioidosis for populations cultivating crops in such soils and using untreated water from these sources for drinking, bathing, and other domestic purposes. Identifying sites positive for B. pseudomallei may help to mitigate risk by raising public awareness of contaminated environmental sources and allowing soil and water remediation.

Biogeography and genetic diversity of clinical isolates of Burkholderia pseudomallei in Sri Lanka.

BACKGROUND: Melioidosis is a potentially fatal infectious disease caused by Burkholderia pseudomallei and the disease is endemic in Southeast Asia and Northern Australia. It has been confirmed as endemic in Sri Lanka. Genomic epidemiology of B. pseudomallei in Sri Lanka is largely unexplored. This study aims to determine the biogeography and genetic diversity of clinical isolates of B. pseudomallei and the phylogenetic and evolutionary relationship of Sri Lankan sequence types (STs) to those found in other endemic regions of Southeast Asia and Oceania. METHODS: The distribution of variably present genetic markers [Burkholderia intracellular motility A (bimA) gene variants bimABP/bimABM, filamentous hemagglutinin 3 (fhaB3), Yersinia-like fimbrial (YLF) and B. thailandensis-like flagellum and chemotaxis (BTFC) gene clusters and lipopolysaccharide O-antigen type A (LPS type A)] was examined among 310 strains. Multilocus sequence typing (MLST) was done for 84 clinical isolates. The phylogenetic and evolutionary relationship of Sri Lankan STs within Sri Lanka and in relation to those found in other endemic regions of Southeast Asia and Oceania were studied using e BURST, PHYLOViZ and minimum evolutionary analysis. RESULTS: The Sri Lankan B. pseudomallei population contained a large proportion of the rare BTFC clade (14.5%) and bimABM allele variant (18.5%) with differential geographic distribution. Genotypes fhaB3 and LPSA were found in 80% and 86% respectively. This study reported 43 STs (including 22 novel). e-BURST analysis which include all Sri Lankan STs (71) resulted in four groups, with a large clonal group (group 1) having 46 STs, and 17 singletons. ST1137 was the commonest ST. Several STs were shared with India, Bangladesh and Cambodia. CONCLUSION: This study demonstrates the usefulness of high-resolution molecular typing to locate isolates within the broad geographical boundaries of B. pseudomallei at a global level and reveals that Sri Lankan isolates are intermediate between Southeast Asia and Oceania.

Nonclonal Burkholderia pseudomallei Population in Melioidosis Case Cluster, Sri Lanka.

A melioidosis case cluster of 10 blood culture-positive patients occurred in eastern Sri Lanka after an extreme weather event. Four infections were caused by Burkholderia pseudomallei isolates of sequence type 594. Whole-genome analysis showed that the isolates were genetically diverse and the case cluster was nonclonal.

Whole-Genome Sequences of Eight Clinical Isolates of Burkholderia pseudomallei from Melioidosis Patients in Eastern Sri Lanka.

Here, we report whole-genome sequences (WGS) of eight clinical isolates of Burkholderia pseudomallei obtained from melioidosis patients with sepsis in eastern Sri Lanka.

Oceanotoga teriensis gen. nov., sp. nov., a thermophilic bacterium isolated from offshore oil-producing wells.

A novel, moderately thermophilic, chemo-organotrophic bacterium was isolated from formation fluid samples from an offshore oil-production well head at Bombay High (Western India). Cells were rod-shaped with a sheath-like outer structure ('toga'); the cells appeared singly, in pairs or in short chains. Cells grew at 25-70 °C (optimum 55-58 °C), pH 5.5-9.0 (optimum pH 7.3-7.8) and 0-12  % (w/v) NaCl (optimum 4.0-4.5  %). The isolate was able to grow on various carbohydrates or complex proteinaceous substances. The isolate reduced thiosulfate and elemental sulfur. The major end products of glucose fermentation were acetate, H2 and CO2. The DNA G+C content of the genomic DNA was 26.8 mol%. Phylogenetic analysis of the 16S rRNA gene placed the strain within the order Thermotogales in the bacterial domain. On the basis of 16S rRNA gene sequence comparisons and in combination with morphological and physiological characteristics, the isolate represents a novel species of new genus, for which the name Oceanotoga teriensis gen. nov., sp. nov. is proposed. The type strain of the type species is OCT74(T) (=JCM 15580(T)=LMG 24865(T)).