Biology subjects

Agampodi, S. B.

Publications and source records attributed to Agampodi, S. B..

3 recordsLinked to original sources

bioRxiv2024

Genomic Analysis of Human-infecting Leptospira borgpetersenii isolates in Sri Lanka expanded PF07598 gene family repertoire, less overall genome reduction than bovine isolates

Leptospira borgpetersenii commonly causes human leptospirosis, including severe disease. The first published analysis of L. borgpetersenii, performed on two strains of serovar Hardjo (L550 and JB197), concluded that the L. borgpetersenii genome is in the process of genome decay with functional consequences leading to a more obligately host-dependent life cycle. Yet whole genome analysis has only been carried out on few strains of L. borgpetersenii, with limited closed genomes and comprehensive analysis. Herein we report the complete, circularized genomes of seven non-Hardjo Leptospira borgpetersenii isolates from human leptospirosis patients in Sri Lanka. These isolates (all ST144) were found to be nearly identical by whole genome analysis; serotyping showed they are a novel serovar. We show that the L. borgpetersenii isolated from humans in Sri Lanka are less genomically decayed than previously reported isolates: fewer pseudogenes (N=141) and Insertion Sequence (IS) elements (N=46) compared to N=248, N=270, and N=400 pseudogenes, and N=121 and N=116 IS elements in published L. borgpetersenii Hardjo genomes (L550, JB197 and TC112). Compared to previously published L. borgpetersenii whole genome analyses showing two to three VM proteins in L. borgpetersenii isolates from cattle, rats and humans, we found that all of the human L. borgpetersenii isolates from Sri Lanka, including previously reported serovar Piyasena, have 4 encoded VM proteins, one ortholog of L. interrogans Copenhageni LIC12339 and 3 orthologs of LIC12844. Our findings of fewer pseudogenes, IS elements and expansion of the LIC12844 homologs of the PF07598 family in these human isolates suggests that this newly identified L. borgpetersenii serovar from Sri Lanka has unique pathogenicity. Comparative genome analysis and experimental studies of these L. borgpetersenii isolates will enable deeper insights into the molecular and cellular mechanisms of leptospirosis pathogenesis. Author SummaryLeptospirosis is an emerging bacterial zoonosis worldwide. Leptospira borgpetersenii predominates as the cause of human leptospirosis in some agricultural contexts. We address here the relatively neglected comparative genome analysis of L. borgpetersenii. We show here that L. borgpetersenii isolated from humans in Sri Lanka have less genome reduction compared to available cattle isolates and have novel virulence characteristics compared to isolates from other animals including cattle and rats.

microbiology↗

bioRxiv2022

Culture-Independent Detection and Identification of Leptospira Serovars

Pathogenic Leptospira, the causative agents of leptospirosis, comprise >200 serotypes (called serovars). Most have a restricted reservoir-host range, and some, e.g., serovar Copenhageni, are cosmopolitan and of public health importance owing to their propensity to produce severe, fatal disease in humans. Available serotyping approaches--such as multi-locus sequence typing, core genome sequence typing, pulsed-field gel electrophoresis, and the cross-agglutination absorption test--are tedious and expensive, and require isolation of the organisms in culture media--a protracted and incredibly inefficient process-- precluding their use in prospective studies or outbreak investigations. The unavailability of culture-independent assays capable of distinguishing Leptospira serotypes remains a crucial gap in the field. Here, we have developed a simple yet specific real-time qPCR assay--targeting a Leptospira-unique gene encoding a putative polysaccharide flippase--that provides intra-species, serotype-defining (i.e., epidemiologically useful) information, and improves upon the sensitivity of preferred lipL32-based qPCR-based diagnostic tests. The assay, dubbed RAgI ("rage one"), is rapid and affordable, and reliably and specifically detects group I pathogenic Leptospira in culture, serum and urine, with no detectable off-target amplification--even of the genetically related but low virulence group II pathogenic (formerly "intermediate") or non-pathogenic Leptospira. It retained 100% diagnostic specificity when tested against difficult sample types, including field-collected dog urine-samples and environmental samples containing varied and complex microbial species-consortia. And holds considerable promise in the clinical setting, and for routine epidemiological and environmental surveillance studies.

microbiology↗

bioRxiv2018

Suicidal ideation and intentional self-harm in pregnancy as neglected agenda in maternal health; an experience from rural Sri Lanka

BackgroundSuicide only present the tip of the iceberg of maternal mental health issues. Only a fraction of pregnant women with suicidal ideation proceeds to intentional self-harm (ISH) and even a smaller proportion are fatal. The purpose of the present study was to determine the prevalence of depression, suicidal ideation (present and past) and history of ISH among pregnant mothers in rural Sri Lanka.\n\nMethodsWe have conducted a hospital based cross sectional study in the third largest hospital in Sri Lanka and a another tertiary care center. Pregnant women admitted to hospital at term were included as study participants. The Edinburgh Postpartum Depression Scale (EPDS), a self-administered questionnaire for demographic and clinical data and a data extraction sheet to get pregnancy related data from the pregnancy record was used.\n\nResultsThe study sample consisted of 475 pregnant women in their third trimester. For the tenth question of EPDS \"the thought of harming myself has occurred to me during last seven days\" was answered as \"yes quite a lot\" by four (0.8%), \"yes sometimes\" by eleven (2.3%) and hardly ever by 13 (2.7%). Two additional pregnant women reported that they had suicidal ideation during the early part of the current pregnancy period though they are not having it now. Four (0.8%) pregnant women reported having a history of ISH during the current pregnancy. History of ISH prior to this pregnancy was reported by eight women and five of them were reported to hospitals, while others were managed at home. Of the 475 pregnant females included in the study, 126 (26.5%) had an EPDS score more than nine, showing probable anxiety and depression. Pregnant women who had primary/post-primary or tertiary education compared to those who were in-between those two categories were at higher risk of high EPDS with a OR of 1.94 (95% CI 1.1-3.3). Reported suicidal ideation prior to pregnancy had a OR of 6.4 (95% CI 2.3-17.5).\n\nConclusionsBased on our data, we conservatively estimate around 3000 ISH annually in Sri Lanka, which should be considered as a high priority for an urgent intervention.\n\nPlain English SummaryMental disturbances are common during pregnancy. Most of the time, these are normal. However, these disturbances may become serious and lead to self-harm and suicide. In this study, we estimated the proportion of pregnant women who had depression and idea of self-harming during pregnancy.\n\nRespondents were pregnant women admitted to two large hospitals for the childbirth. They answered a list o questions about the thought of self-harm and attempts of self-harm during the present as well as past pregnancies.\n\nRespondents included 475 pregnant women. Of them, 3.1% reported that \"the thought of self-harming has occurred to them during last seven days quite a lot (0.8%) or sometimes\" (2.3%). Four (0.8%) pregnant women reported that they actually did it to some extent. Of the 475 pregnant women included in the study, 126 (26.5%) had symptoms of anxiety/depression. Level of education seemed to have an association with anxiety and depression. When women reported that they had thought of self-harm prior to pregnancy, they were about 6.4 times more likely to have depression/anxiety during the pregnancy. Adding a simple screening question (as we used in this study) during the initial pregnancy assessment to detect history of suicidal thoughts will be helpful in identification of high-risk mothers for depression and suicide.

epidemiology↗