Whole genome sequencing data of Leptospira weilii and Leptospira kirschneri isolated from human subjects of Sri Lanka

Leptospirosis is a re-emerging zoonotic disease. This article reports the complete genome sequences of three novel strains of Genus Leptospira: two from the species Leptospira weilii (FMAS_RT1, FMAS_PD2) and one from Leptospira kirschneri (FMAS_PN5). These isolates were recovered from the blood samples of acute febrile patients in different geographical and climatic zones of Sri Lanka. High-quality genomic DNA was extracted from the three isolates in mid-log phase cultures. Whole genome sequencing was conducted using the PacBio Single Molecule Real-Time (SMRT) platform to identify the species, genome features, and novelty of the strains. The annotation was conducted using RAST (Rapid Annotation Using Subsystem Technology version 2.0) and the NCBI Prokaryotic Genome Annotation Pipeline. The genome sequences of three isolates have been deposited in the Mendeley data repository and the National Center for Biotechnology Information (NCBI) repository. This data will be useful for future researchers when conducting comparative genomic analysis, revealing the exact mechanism of pathogenesis of leptospirosis and developing molecular diagnostic tools for early detection.

Levels of Cytokines in Leptospirosis Patients with Different Serovars and rfb Locus

Leptospirosis has a wide spectrum of clinical manifestations ranging from mild to severe disease. The cytokine response is considered one of the key drivers for this varying manifestation. The different cytokine response observed in patients with leptospirosis could be due to the variation of infecting serovars. Since the rfb locus codes for the lipopolysaccharide synthesis of the bacterial cell wall, which also determines the serovar, this locus may play a role in driving a specific cytokine response in the host. We investigated 12 commonly used cytokine profiles in serum samples of culture, microscopic agglutination test (MAT), or polymerase chain reaction (PCR)-positive patients with leptospirosis. The sequences of the rfb locus in culture-positive samples were generated from whole genome sequencing and serovar status was drawn from original data published. Isolated cultures were subjected to whole genome sequencing using the PacBio RS II system, and the resulting data were used to determine the species. The recovered genomic data were annotated with the Rapid Annotation using Subsystem Technology (RAST) subsystem, and the rfb locus was extracted. The cytokine analysis was carried out using the Qiagen human ELISA kit. Eighteen samples were found to be positive by culture, while the other 7 samples were positive by PCR or MAT. Infections from Leptospira interrogans serovar Autumnalis (5), Pyrogens (3), Icterohaemorrhagiae (1) Leptospira borgpetersenii (all 7 samples clustered in same clonal group with serovar status not determined), Leptospira weilii (1 with serovar status not determined), and Leptospira kirschneri serovar Grippotyphosa (1) were included in the analysis. Three patients [infected with Leptospira interrogansserovar Autumnalis (2) and Pyrogens (1)] and 2 MAT-positive patients (highest titer against serovar Bratislava of L.interrognas) were reported to have severe clinical manifestations, while the rest had mild to moderate symptoms. Although the serum cytokine concentration of patients with severe clinical manifestation was comparatively higher, a statistically significant difference was observed only for interleukin (IL)-1β (P < 0.05). IL-10/tumor necrosis factor-alpha (TNF-α) ratio was high in patients with severe complications. In general, patients infected with L. interrogans showed higher concentration of cytokines compared to L. borgpetersenii.

Knowledge and attitudes on attention deficit hyperactivity disorder (ADHD) among school teachers in Anuradhapura district, Sri Lanka: a descriptive cross-sectional study

OBJECTIVE

This study aimed to assess the knowledge and attitude of school teachers from a rural district in a developing country towards children with attention deficit hyperactivity disorder (ADHD).

DESIGN

A population-based descriptive cross-sectional study was conducted using probability proportionate to size cluster sampling.

SETTING

This study was conducted in 21 government schools in Anuradhapura district, Sri Lanka.

PARTICIPANTS

The study sample consisted of 458 teachers with a mean age of 41 completed years ranging from 24 to 59 years.

MAIN OUTCOME MEASUREMENTS

We assessed knowledge, attitudes and sources of information on ADHD using the self-administered, validated Knowledge of Attention Deficit Disorder Scale (KADD), Teacher Attitudes Towards Inclusion Scale (TAIS) and the Perceived and Actual Sources of Information questionnaires.

RESULTS

The median KADD score was 11 (IQR 8-14) and 45.5% (n=208) of participants lacked sufficient knowledge. Percentages of the correct answers, misconceptions and 'don't know' responses were 28.2%, 24.5% and 45.5%, respectively. The majority of teachers believed that the children with ADHD generally experience more problems in novel situations than in familiar situations (63.5%), a diagnosis of ADHD by itself makes a child eligible for placement in special education (61.1%), and children with ADHD do not often have difficulties organising tasks and activities (61.1%). Some participants (12%) stated that punishment would improve the outcome of the children with ADHD. The attitudes were positive with TAIS 1 and 2 median scores of 46 (IQR 36-58) and 49 (IQR 40-59). The majority of participants relied on informal knowledge gained through their personal experience in the classroom on ADHD (n=337, 76%). The majority of teachers (n=300, 67.7%) preferred to be educated through seminars.

CONCLUSIONS

School teachers possess a positive attitude. However, they have poor knowledge and significant misconceptions regarding ADHD which may affect the identification and management.

Complete genome sequences of twelve strains of Leptospira interrogans isolated from humans in Sri Lanka

Leptospirosis, a major zoonotic disease caused by pathogenic Leptospira spp. is recognized globally as an emerging zoonotic disease. Whole-genome sequencing reveals hidden messages about Leptospira's pathogenesis. We used Single Molecule Real-Time (SMRT) sequencing to obtain complete genome sequences of twelve L. interrogans isolates from febrile patients from Sri Lanka for a comparative whole genome sequencing study. The sequence data generated 12 genomes with a coverage greater than X600 with sizes ranging from 4.62 Mb to 5.16 Mb, and a G + C content ranging from 35.00% to 35.42%. The total number of coding sequences predicted by the NCBI (National Center for Biotechnology Information) genome assembly platform ranged from 3845 to 4621 for the twelve strains. Leptospira serogroup with similar-sized LPS biosynthetic loci that belonged to the same clade had a close relationship in the phylogenetic analysis. Nonetheless, variations in the genes encoding sugar biosynthesis were found in the serovar determinant region (rfb locus). Type I and Type III CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) systems were found in all of the strains. Genome BLAST Distance Phylogeny of these sequences allowed for detailed genomic strain typing. These findings may help us better understand the pathogenesis, develop a tools for early diagnosis, comparative genomic analysis and evolution of Leptospira.

Incorporating early pregnancy mental health screening and management into routine maternal care: experience from the Rajarata Pregnancy Cohort (RaPCo), Sri Lanka

Early identification of mental health problems in pregnancy in low-income and middle-income countries is scarcely reported. We present the experience of a programme assimilating screening and management of antenatal anxiety and depression in conjunction with the Rajarata Pregnancy Cohort, in Sri Lanka. We adopted a two-stage screening approach to identify the symptoms and the reasons for anxiety and depression. Pregnant women (n=3074), less than 13 weeks of period of gestation underwent screening with the Edinburgh Postnatal Depression Scale (EPDS). Scores were positive among 23% and 14% of women in the first and second trimesters, respectively. Clinical (telephone) interviews (n=78, response 56.9%) were held for women having high EPDS scores to screen for clinical depression using the 'mental health GAP' tool. Targeted interventions including counselling, financial and social support and health education were employed. The procedure was repeated in the second trimester with in-person clinical interviews and inquiry into intentional self-harm. Our findings indicated that (1) the majority of mental health problems in early pregnancy were anxiety related to early pregnancy-associated conditions manageable at the primary healthcare level, (2) coupling mental health screening using psychometric tools with clinical interviews facilitates targeted patient-centred care, (3) the majority of intentional self-harm during pregnancy is not in the routine health surveillance system and (4) promoting women to attend the psychiatry clinic in tertiary care hospital has been difficult. Following the experience, we propose a model for mental health service provision in routine pregnancy care programme starting from early pregnancy.

SARIMA and ARDL models for predicting leptospirosis in Anuradhapura district Sri Lanka

Leptospirosis is considered a neglected tropical disease despite its considerable mortality and morbidity. Lack of prediction remains a major reason for underestimating the disease. Although many models have been developed, most of them focused on the districts situated in the wet zone due to higher case numbers in that region. However, leptospirosis remains a major disease even in the dry zone of Sri Lanka. The objective of this study is to develop a time series model to predict leptospirosis in the Anuradhapura district situated in the dry zone of Sri Lanka. Time series data on monthly leptospirosis incidences from January 2008 to December 2018 and monthly rainfall, rainy days, temperature, and relative humidity were considered in model fitting. The first 72 months (55%) were used to fit the model, and the subsequent 60 months(45%) were used to validate the model. The log-transformed dependent variable was employed for fitting the Univariate seasonal ARIMA model. Based on the stationarity of the mean of the five variables, the ARDL model was selected as the multivariate time series technique. Residuals analysis was performed on normality, heteroskedasticity, and serial correlation to validate the model. The lowest AIC and MAPE were used to select the best model. Univariate models could not be fitted without adjusting the outliers. Adjusting seasonal outliers yielded better results than the models without adjustments. Best fitted Univariate model was ARIMA(1,0,0)(0,1,1)₁₂,(AIC-1.08, MAPE-19.8). Best fitted ARDL model was ARDL(1, 3, 2, 1, 0),(AIC-2.04,MAPE-30.4). The number of patients reported in the previous month, rainfall, rainy days, and temperature showed a positive association, while relative humidity was negatively associated with leptospirosis. Multivariate models fitted better than univariate models for the original data. Best-fitted models indicate the necessity of including other explanatory variables such as patient, host, and epidemiological factors to yield better results.

Demographic, exposure, clinical, biochemical and diagnostic data of febrile patients recruited for the largest field study on leptospirosis in Sri Lanka

This dataset includes data from febrile patients recruited for a large hospital-based study in Sri Lanka from 2016 to 2019. The variables include primary socio-demographic data, exposure data, clinical data, biochemical and investigation data. Some of these data are available as serial data from admission to discharge daily. Microscopic agglutination test, quantitative PCR of whole blood, urine and serum and culture isolation was performed to diagnose the patients with leptospirosis.

Non-Alcoholic Fatty Liver Disease Among Pregnant Women With Metabolic Syndrome: Should Nutritional Intervention Be a Priority? A Cross Sectional Study in Rural Sri Lanka

Objectives

Although non-alcoholic fatty liver disease (NAFLD) is the hepatic manifestation of metabolic syndrome (MetS), the prevalence data of NAFLD in MetS are scarce in literature, especially in south Asian populations. Knowledge regarding NAFLD in Mets is important as both conditions can be controlled using Nutritional interventions. This study aims to compare the proportions of NAFLD among first trimester pregnant mothers with MetS and without MetS in Anuradhapura District, Sri Lanka.

Methods

A community based cross-sectional comparative study was conducted among randomly selected first trimester pregnant mothers (less than 12 weeks of gestational age), in Anuradhapura district, Sri Lanka. Detailed clinical examination, biochemical investigations, and ultrasound scan(USS) to diagnose fatty liver were performed at the time of recruitment. MetS was defined according to the criteria by International Diabetes Federation, American Heart Association, and World Health Organization. NAFLD was categorized as fatty liver grades (FLG) 0, I, II and III by ultrasound criteria.

Results

Of the 634 mothers recruited, 30 (4.7%) were categorized as metabolic syndrome. The proportion of NAFLD among MetS group was 80% (n = 24/30) while it was 49.8% (n = 300/604) in none- MetS group. (Chi-sq = 10.4, p = 0.001). The proportion of FLG 0, FLG I, FLG II among MetS participants were 6(20%), 8(26.7%), 16(53.3%) respectively while they were 302(50.2%), 226(37.5%), 74(12.5%) respectively in non -MetS participants. (Chi-sq = 40, P < 0.000) None of the mothers were categorized as FLG III. The mean Gamma glutamyl transferase level and the Alanine aminotransferase levels were significantly higher (P < 0.025) in the MetS group, while no significant difference was observed in the Aspartate aminotransferase level. The mean dome to pole length of the liver among the MetS group was significantly higher (13.9 vs. 13.0 cm) in the MetS group. (t = 3.8, p = 0.001).

Conclusions

The proportion of NAFLD in pregnant mothers with MetS was significantly higher. Therefore, promising nutritional interventions are recommended to control the disease and minimize adverse pregnancy outcomes.

Funding Sources

Accelerating Higher Education Expansion and Development (AHEAD) grant (Grant number: DOR STEM HEMS [6026-LK/8743-LK]), a World Bank-funded project through the University grant commission, Sri Lanka.

Diagnostic method-based underestimation of leptospirosis in clinical and research settings; an experience from a large prospective study in a high endemic setting

Background

Leptospirosis has globally significant human mortality and morbidity, yet estimating the clinical and public health burden of leptospirosis is challenging because timely diagnosis remains limited. The goal of the present study was to evaluate leptospirosis undercounting by current standard methods in both clinical and epidemiological study settings.

Methodology/Principal findings

A prospective hospital-based study was conducted in multiple hospitals in Sri Lanka from 2016 to 2019. Culture, whole blood, and urine samples were collected from clinically suspected leptospirosis cases and patients with undifferentiated fever. Analysis of biological samples from 1,734 subjects confirmed 591 (34.1%) cases as leptospirosis and 297 (17.1%) were classified as “probable” leptospirosis cases. Whole blood quantitative PCR (qPCR) did identify the most cases (322/540(60%)) but missed 40%. Cases missed by each method include; urine qPCR, 70% (153/220); acute sample microscopic agglutination test (MAT), 80% (409/510); paired serum sample MAT, 58% (98/170); and surveillance clinical case definition, 53% (265/496). qPCR of negative culture samples after six months of observation was of diagnostic value retrospectively with but missed 58% of positives (109/353).

Conclusion

Leptospirosis disease burden estimates should consider the limitations of standard diagnostic tests. qPCR of multiple sample types should be used as a leading standard test for diagnosing acute leptospirosis.

Diagnostics of leptospirosis have not been optimised yet and is considered as a significant limiting factor for estimating the disease burden. This prospective hospital-based study, including 1734 clinically suspected leptospirosis cases and undifferentiated febrile patients, revealed that a minimum of 40% of cases would be missed by using any of the following tests individually. (Whole blood qPCR, single or paired-sample MAT, Urine qPCR, culture, culture qPCR, surveillance case definition). Therefore, we conclude that whole blood qPCR should be the standard test for diagnosing leptospirosis for clinical purposes until day 10 of the reported disease. MAT should be limited to places where the serological diagnosis has an epidemiological interest. qPCR testing of microscopically-negative cultures should be done before discarding to increase the yield in research settings.

The variable presence of Leptospira in the environment; an epidemiological explanation based on serial analysis of water samples

Human leptospirosis involves the classic epidemiological triad (agent, host and environment); hence the investigations should include the knowledge on Leptospira within the animals and the environment. The objectives of this study are to explore the abundance of Leptospira in different climate zones of Sri Lanka and to describe the presence of Leptospira in the same water source at serial time points. First, water and soil samples were collected from different parts of Sri Lanka (Component-1); second, water sampling continued only in the dry zone (Component-2). Finally, serial water sampling from ten open wells was performed at five different time points (Component-3). Quantitative PCR of water and metagenomic sequencing of soil were performed to detect Leptospira. Three replicates for each sample were used for PCR testing, and positive result of two or more replicates was defined as 'strongly positive,' and one positive replicate was defined as positive. In the water and soil sample analysis in the whole country (Component-1), two out of 12 water sites were positive, and both were situated in the wet zone. Very small quantities of the genus Leptospira were detected by 16 amplicon analysis of soil in all 11 sites. In the dry zone water sample analysis (Component-2), only samples from 6 out of 26 sites were positive, of which one site was strongly positive. In the serial sample analysis (Component-3), Six, five, four, five, and six wells were positive in serial measurements. All wells were positive for at least one time point, while only one well was positive for all five time points. Proximity to the tank and greater distances from the main road were associated with strong positive results for Leptospira (P<0.05). The presence of Leptospira was not consistent, indicating the variable abundance of Leptospira in the natural environment. This intermittent nature of positivity could be explained by the repetitive contamination by animal urine.

Temporal Variation and Factors Associated with Allergic Rhinitis in a Cohort of Rural Preschool Children from Sri Lanka

BACKGROUND

Allergic rhinitis is a common chronic childhood disease with a low diagnosis rate, causing poor quality of life, absenteeism, decreased school performance and significant healthcare cost. However, data on the prevalence of allergic rhinitis is sparse in preschoolers of rural geography, especially in developing countries.

AIM

To describe the epidemiology of allergic rhinitis in preschoolers from a rural geography of a developing country.

METHODS

A population-based cross-sectional study was conducted in Anuradhapura district, Sri Lanka using the WHO-30 cluster methodology with probability proportionate to size sampling. The International Study of Asthma and Allergy in Childhood questionnaire was used to assess symptomatology.

RESULTS

The response rate was 91.8%, with 548 (51.7%) male and 512 (48.3%) female participants. The mean age was 4.4 (± 0.7) years. Allergic rhinitis was reported in 123 (11.6%; 95% CI 9.7-13.5), and eye symptoms were reported in 41 (3.9%; 95% CI 2.8-5.2) children. Activities of daily living were disturbed due to nasal symptoms in 113 (10.7%; 95% CI 8.8-12.5). Allergic rhinitis was independently associated with severe asthma (OR 6.26; 95% CI 3.54-11.06), sleeping on the floor (OR 4.79; 95% CI 1.33-17.25) and having cats in the households (OR 1.86; 95% CI 1.18-2.91). Nasal symptoms were more common in January and August to October months. The standardized local highest monthly temperature, lowest monthly temperature, highest monthly humidity and dew point strongly predicted allergic rhinitis symptom exacerbation (F=4.8, p=0.036, adjusted R square=57.8%, VIF≤2.259, DW=2.1).

CONCLUSIONS

Allergic rhinitis affects 1 in 10 preschool children of rural Sri Lanka. The factors associated and environmental factor model developed to predict symptom exacerbation could be used to prevent allergic rhinitis exacerbations.

Neglecting the neglected during the COVID-19 pandemic: the case of leptospirosis in Sri Lanka

The coronavirus disease 2019 (COVID-19) pandemic has disrupted global health systems and affected the transmission dynamics as well as the surveillance of other infectious diseases. This study described the probable effect of the COVID-19 pandemic on the surveillance and control of leptospirosis in Sri Lanka. With 8,579 reported cases and more than 800 estimated deaths, the Sri Lankan public health surveillance system documented the largest outbreak of leptospirosis in Sri Lankan history in 2020. This was the worst infectious disease outbreak Sri Lanka experienced in 2020, but it was neglected, primarily due to the COVID-19 pandemic.

Clinical spectrum of endemic leptospirosis in relation to cytokine response

OBJECTIVES

To describe the clinical spectrum and the cytokine response of leptospirosis patients in an endemic setting of Sri Lanka.

METHODS

Patients presenting to the university teaching hospital, Anuradhapura, Sri Lanka with a leptospirosis-compatible illness were recruited over a period of 12 months starting from June 2012. Daily clinical and biochemical parameters of the patients were prospectively assessed with a follow-up of 14 days after discharge. A magnetic bead-based multiplex cytokine kit was used to detect 17 cytokines.

RESULTS

Of the 142 clinically suspected leptospirosis patients recruited, 47 were confirmed and, 29 cases were labeled as "probable." Thrombocytopenia and leukocytosis were observed at least once during the hospital stay among 76(54%) and 39(28%) patients, respectively. Acute kidney injury was observed in 31 patients (22%) and it was significantly higher among confirmed and probable cases. Hu TNF-α and IL-1β were detected only in patients without complications. Hu MIP-1b levels were significantly higher among patients with complications. During the convalescence period, all tested serum cytokine levels were lower compared to the acute sample, except for IL-8. The cytokine response during the acute phase clustered in four different groups. High serum creatinine was associated GM-CSF, high IL-5 and IL-6 level were correlates with lung involvement and saturation drop. The patients with high billirubin (direct)>7 mmol/l had high IL-13 levels.

CONCLUSIONS

Results of this study confirms that the knowledge on cytokine response in leptospirosis could be more complex than other similar tropical disease, and biosignatures that provide diagnostic and prognostic information for human leptospirosis remain to be discovered.

Epidemiology of wheeze among preschool children: a population-based cross-sectional study from rural Sri Lanka

OBJECTIVES

To assess the prevalence of wheeze and factors associated with its severity among 3-6 years old children.

METHODOLOGY

DESIGN: A population-based, cross-sectional study using the WHO 30 cluster methodology with probability proportionate to size sampling.

SETTING

36 preschools registered at the divisional secretariat offices of Anuradhapura district, Sri Lanka.

PARTICIPANTS

We recruited 1060 preschool children from 36 preschools aged 3-6 years.

MAIN OUTCOME MEASUREMENTS

We used the International Study of Asthma and Allergy in Childhood questionnaire to assess the prevalence, symptomatology and associated factors of wheeze.

RESULTS

The study sample consisted of 548 (51.70%) male and 512 (48.30%) female children with a mean age of 4.41 (±0.66) years. At least one wheezing episode ever was reported in 323 (30.47%; 95% CI 27.71% to 33.34%) children and 247 (23.30%; 95% CI 20.79% to 25.97%) children had a wheezing attack in the preceding year. Severe episodes of wheezing were reported in 76 (7.17%; 95% CI 5.69% to 8.89%) participants. However, only 27 (35.53%; 95% CI 24.88% to 47.34%) children with severe wheezing had been diagnosed as asthmatics by a clinician. The identified independent risk factors for severe wheeze were allergic rhinitis (OR 6.90; 95% CI 3.84 to 12.40), domestic dog(s) (OR 2.34; 95% CI 1.01 to 5.40), frequent consumption of skipjack tuna (OR 1.94; 95% CI 1.11 to 3.39) and passive smoking (OR 1.70; 95% CI 0.93 to 3.11) while living in a house with a cement floor is a protective factor (OR 0.41; 95% CI 0.21 to 0.80).

CONCLUSION

Wheezing commonly affects one-fourth of preschool children in rural Sri Lanka. Severe wheezing is often not diagnosed as asthma despite frequent symptoms, probably due to hesitancy in labelling preschool children as asthmatics. Allergic rhinitis, domestic dogs, frequent consumption of Skipjack tuna fish and exposure to passive smoking were independent risk factors for severe wheeze.

Optimizing the microscopic agglutination test (MAT) panel for the diagnosis of Leptospirosis in a low resource, hyper-endemic setting with varied microgeographic variation in reactivity

The microscopic agglutination test (MAT) is the standard serological reference test for the diagnosis of leptospirosis, despite being a technically demanding and laborious procedure. The use of a locally optimised MAT panel is considered essential for proper performance and interpretation of results. This paper describes the procedure of selecting such an optimised panel for Sri Lanka, a country hyper-endemic for leptospirosis. MAT was performed using 24 strains on 1132 serum samples collected from patients presenting with acute undifferentiated fever. Of 24 strains, 15 were selected as the optimised panel, while only 11% of serum samples showed positivity. A geographical variation in predominantly reactive serovars was observed, whereas reactivity was low with the saprophytic strain Patoc. Testing with paired sera yielded a higher sensitivity but provided only a retrospective diagnosis. Serological tests based on ELISA with complementary molecular diagnosis using PCR are a feasible and robust alternative approach to diagnose leptospirosis in countries having a higher burden of the disease.

Barriers for early initiation and exclusive breastfeeding up to six months in predominantly rural Sri Lanka: a need to strengthen policy implementation

Background

Sri Lanka was named as the first-ever ‘Green’ breastfeeding nation status by the World Breastfeeding Trends Initiative (WBTi) in January 2020. However, improvements are still needed. This study aims to identify barriers and facilitators for early initiation of breastfeeding and exclusive breastfeeding for 6 months in rural Sri Lanka.

Methods

We conducted in-depth interviews with 16 mothers with infants, who had been unable to practice early initiation of breastfeeding and/or exclusive breastfeeding (EBF), in six child-welfare clinics in Anuradhapura, Sri Lanka. Three focus group discussions were held with public health midwives (PHMs). Initial thematic analysis that built upon force field and social learning theories was performed.

Results

Main barriers for EBF were clustered at three time periods; during the first 2–3 days, 2–3 weeks, and 4–5 months postpartum. Early barriers included cesarean section pain, poor breast latch, maternal exhaustion, suboptimal maternity ward environment, and lack of support for breastfeeding. Around 2–3 weeks postpartum mothers introduced water or infant formula due to social norms and poor support. On-demand feeding was misunderstood. Around 4 and 5 months postpartum, EBF ended due to return to work. PHMs reported a heavy workload limiting their time to support breastfeeding.

Conclusion

EBF interruption was due to diverse individual- and environnmental- level barriers that varied across the first 6 months. To improve EBF, Sri Lanka should focus on strengthening policies for reducing the excessive rates of cesarean section, improving support in maternity ward facilities, fostering on-demand breastfeeding, enhancing support for working mothers and reducing the work load of PHMs.

Supplementary Information

The online version contains supplementary material available at 10.1186/s13006-021-00378-0.

12 Novel clonal groups of Leptospira infecting humans in multiple contrasting epidemiological contexts in Sri Lanka

Leptospirosis is a ubiquitous zoonotic disease and a major clinical challenge owing to the multitude of clinical presentations and manifestations that are possibly attributable to the diversity of Leptospira, the understanding of which is key to study the epidemiology of this emerging global disease threat. Sri Lanka is a hotspot for leptospirosis with high levels of endemicity as well as annual epidemics. We carried out a prospective study of Leptospira diversity in Sri Lanka, covering the full range of climatic zones, geography, and clinical severity. Samples were collected for leptospiral culture from 1,192 patients from 15 of 25 districts in Sri Lanka over two and half years. Twenty-five isolates belonging to four pathogenic Leptospira species were identified: L. interrogans, L. borgpetersenii, L. weilii, and L. kirschneri. At least six serogroups were identified among the isolates: Autumnalis (6), Pyrogenes (4), Icterohaemorrhagiae (2), Celledoni (1), Grippotyphosa (2) and Bataviae (1). Seven isolates did not agglutinate using available antisera panels, suggesting new serogroups. Isolates were sequenced using an Illumina platform. These data add 25 new core genome sequence types and were clustered in 15 clonal groups, including 12 new clonal groups. L. borgpetersenii was found only in the dry zone and L. weilii only in the wet zone. Acute kidney injury and cardiovascular involvement were seen only with L. interrogans infections. Thrombocytopenia and liver impairment were seen in both L. interrogans and L. borgpetersenii infections. The inadequate sensitivity of culture isolation to identify infecting Leptospira species underscores the need for culture-independent typing methods for Leptospira.

There is a huge diversity in pathogenic Leptospira species worldwide, and our knowledge of the currently circulating species is deficient owing to limited isolation and identification of Leptospira species from endemic countries. This prospective study reveals the wide pathogen diversity that causes human leptospirosis in Sri Lanka, representing four species, more than six serogroups, and fifteen clonal groups. Further, the different geographic and climatic zone distributions and clinical manifestations observed underscores the need for prospective studies to expand the molecular epidemiological approaches to combat leptospirosis.

Improving the leptospirosis disease burden assessment by including ambulatory patients from outpatient departments: a cross-sectional study

Background: In Sri Lanka, the disease burden of leptospirosis is estimated based on a routine notification system, which is predominated by patients ill enough to be hospitalized. The notification system does not function well with ambulatory patients in outpatient departments (OPDs). The objective of this study was to determine the proportion of leptospirosis in an OPD setting in a regional public hospital in Sri Lanka to provide further estimation of disease burden.

Methods: This study was conducted in the OPD of the Rathnapura Provincial General Hospital from August to September 2017. Suspected leptospirosis patients were recruited based on standardized criteria and tested using the microscopic agglutination test and quantitative polymerase chain reaction. The number of OPD patients was compared with the reported patient numbers with leptospirosis from the hospital during the same period as the denominator, and the 95% confidence interval was calculated for the proportions using Poisson distribution.

Results: During the study period, of 2,960 fever patients presenting to the OPD, 33 (1.1%) were suspected to have leptospirosis; 8/33 suspected (22.3%) cases were confirmed as being due to leptospirosis. There were 82 notifications of leptospirosis cases from hospital inpatients during the same period, none from the OPD. The total missing proportion from the surveillance system was 28.6% (95% CI, 19.4-40.4%). Among OPD patients, 12 (36.4%) had been given antibiotics from a primary care center prior to the OPD visit. No OPD patient was admitted to the hospital for inward care.

Conclusions: More than 25% of cases of leptospirosis were not identified because they were not sick enough to be admitted nor subjected to routine leptospirosis diagnostic testing.These data have public health implications if the sources of leptospirosis transmission are to be controlled.

The Rajarata Pregnancy Cohort (RaPCo): study protocol

Background

Ending preventable maternal deaths remains a global priority and in the later stages of obstetric transition, identifying the social determinants of maternal health outcomes is essential to address stagnating maternal mortality rates. Countries would hardly achieve the Sustainable Development Goal (SGD) targets on maternal health, unless the complex and context-specific socio-economic aetiologies associated with maternal mental health and suicide are identified. The Rajarata Pregnancy Cohort (RaPCo) is a prospective cohort study, designed to explore the interactions between social determinants and maternal mental health in determining pregnancy and new-born outcomes.

Methods

The study will recruit all eligible pregnant women in the maternal care programme of Anuradhapura district, Sri Lanka from July to September 2019. The estimated sample size is 2400. We will assess the socio-demographic and economic status, social capital, gender-based violence and mental health, including a clinical examination and biochemical investigations during the first trimester. Participants will undergo four follow-ups at 2nd and 3rd trimesters, at delivery and in early postpartum. The new-borns will be followed up at birth, neonatal period, at 6 six months and at 1 year. Pregnancy and child outcome data will be collected using direct contact. Qualitative studies will be carried out to understand the complex social factors and behavioural dimensions related to abortion, antenatal depression, maternal deaths and near misses.

Discussion

This is the first reported maternal cohort in Sri Lanka focusing on social determinants and mental health. As a country in stage four of obstetric transition, these findings will provide generalizable evidence on achieving SGD targets in low- and middle-income countries. The study will be conducted in a district with multi-cultural, multi-ethnic and diverse community characteristics; thus, will enable the evidence generated to be applied in many different contexts. The study also possesses the strength of using direct participant contact, data collection, measurement, examination and biochemical testing to minimise errors in routinely collected data. The RaPCo study will be able to generate evidence to strengthen policies to further reduce maternal deaths in the local, regional and global contexts particularly focusing on social factors and mental health, which are not optimally addressed in the global agenda.

Female Obesity: An Emerging Threat in Sri Lanka

Objectives

Emerging body of evidence clearly shows a transgenerational effect of obesity. The maternal health programme in low- and middle-income countries are typically focusing on undernutrition, while the burden of overweight and obesity are mostly overlooked. The objective of this study was to evaluate the burden of malnutrition in a cohort of pregnant mothers in Sri Lanka.

Methods

A cross sectional analysis was conducted as a part of an ongoing cohort of all pregnant women registered in the public health system and having a period of gestation less than 12 weeks in Anuradhapura district, Sri Lanka were recruited over three months period during 2019. Clinical and anthropometric assessments were done in 240 dedicated clinics.

Results

Total of 3190 mothers were recruited with full anthropometric profile with mean age of 28.3 years (SD 5.6). Prevalence of overweight, obesity grade I, II and III according to Asian cut off limits were 15.3% (n = 520), 31.4%(n = 1065), 1.5% (n = 51) and 2% (n = 7) respectively. Prevalence of underweight was only 15.9%. Waist circumference &gt;80 cm was reported among 1189 (35%) mothers. A marked spatial distribution of obesity was observed with ranging from 23% to 46%. As a more important and unbiased factor in the first trimester of pregnancy, we looked at the predictors of WC &gt;80. After the adjustment for POA and age, living environment variables indicating higher level of financial status such as using electricity as main cooking fuel (OR 2.276), having a wooden floor (OR 1.688), floor tiles (OR 1.377), three-wheeler (OR 1.22) or other vehicle ownership (OR 1.287) were associated with central obesity. Higher education level of women and lower educational level of husband were also identified as predictors. Women from moor ethnic group were also at a higher risk compared to others.

Conclusions

Context specific strategies are required to tackle the double burden of malnutrition and the observed gross micro geographical variation in obesity needs further studies.

Funding Sources

Accelerating Higher Education Expansion And Development (AHEAD) Operation.

Strengths and Barriers in Achieving “Green Status” of Breastfeeding; The Story of Frontline Health Care Workers in Sri Lanka

Objectives

The achievements in breastfeeding in Sri Lanka are due to multiple factors and the work of frontline health care workers: public health midwives (PHMs) was crucial. Objective of this study is to explore the strengths and constraints of PHMs in optimizing breastfeeding practices in the Sri Lankan community.

Methods

We conducted a series of focus group discussions with PHMs in three different areas in Anuradhapura district Sri Lanka. Transcribed data were analyzed thematically to identify the types of strengths and constraints.

Results

Thirty six PHMs participated in the focus groups conducted. The well-established public health system that introduces and reinforce knowledge and skills on breastfeeding assured that mothers will adhere to the current recommendations on EBF. PHMs agreed on the support given by the hospital labor room, theatres and Lactation Management Center on early initiation and EBF. However, emphasis on attachment to breast rather than discharging a newborn on cup feeding was mentioned. PHMs devotion on establishing proper breastfeeding during the early postpartum home visits, the respect and acceptance of PHM by the mother and the community and the knowledge and skills they possess on breastfeeding counseling were highlighted. Irrational prescription of formula by medical practitioners, negative verbal comments by in-laws and unfavorable attitudes of mothers of high social class were seen as social obstacles to promote EBF. The PHMs seem to work with many barriers which could compromise care provision for mothers and children. Inability to attend for the home visit early due to scheduled work, the increased time needed to spent to counsel mothers and subsequent restriction of the daily duties, high population density and having to cover the vacant areas through out, excessive documentation work were problems needed to be addressed with regard to service enhancement.

Conclusions

The PHMs role is inevitable and Sri Lanka needs to enhance and facilitate service provision of grass root level health workers to optimize promotion, protection and support for EBF.

Funding Sources

No funding source.

Sri Lanka; The First Ever Only “Green Nation” in the World for Breastfeeding; Yet Lessons to Learn Through Exploring Maternal Perspectives

Objectives

Sri Lanka has been awarded the first-ever ‘Green’ breastfeeding (BF) nation status by the World Breastfeeding Trends Initiative (WBTi) in January 2020. Our objective was to explore the maternal perceptions of unrevealed barriers for the provision of promotion, protection and support of optimal exclusive breast feeding (EBF) up to six months.

Methods

We used in-depth interviews with 16 mothers with infants completed six months, who had been unable to practice EBF, attending six child-welfare clinics in Anuradhapura, Sri Lanka. Initial thematic analysis built upon force field and social learning theories were conducted to identify the barriers for optimal EBF practices during the first six months life.

Results

Main challenges to EBF were notably clustered at three occasions over the six months and first during the first 2–3 days after the delivery. Factors related to child birth influencing self-efficacy and confidence on establishing breastfeeding included cesarean section, pain and poor positioning due to pain, exhaustion, and perceived “inadequate milk”. Suboptimal policies on ward environment and practice of health staff that could lead to maternal worry and maternal stress related to demand for EBF were also identified as key barriers. Despite the early challenges, mothers who interrupted EBF within the first few days, desired to go back to EBF and was able to do so. The second occasion of cessation of EBF occurred around 2–3 weeks postpartum by introducing water or infant formula. These mothers lacked family support for BF leading to physical and mental exhaustion. Additionally, the mother's perception that “healthy infants should be chubby” also led to introduction of infant formula. On-demand feeding was reported to be a challenge due to misconceptions such as feeding according to a time table. Working mother reported ending EBF between 4 and 5 months, and they lacked self-efficacy, resulting from the lack of enabling environments and social support to express and continue only breast milk.

Conclusions

Although Sri Lanka has attained the “green” breastfeeding top status, interventions are needed to better the support the BF needs of mothers after cesarean section and to practice on-demand feeding and to improve the support for mothers that are employed in order to optimize EBF until completion of six months.

Funding Sources

No funding source.

Complete Genome Sequence of Leptospira interrogans Strains FMAS_KW1, FMAS_KW2 and FMAS_AW1 Isolated from Leptospirosis Patients from Karawanalla and Awissawella, Sri Lanka

Leptospirosis is an important cause of acute undifferentiated fever and complex multisystem febrile diseases in the tropics and subtropics. Understanding the evolution of Leptospira especially as related to the clinical pathogenesis of leptospirosis is facilitated by systematic comparative genomic analysis of human-infecting isolates. Here, we announce the complete genome sequences of three Leptospira strains that were isolated from blood of humans with undifferentiated fever in Sri Lanka.

Study protocol: characterising the clinical, epidemiological and aetiological aspects of leptospirosis in Sri Lanka: a hospital based clinico-epidemiological study

INTRODUCTION

Sri Lanka has one of the highest incidences of leptospirosis worldwide. We hypothesised that different geographical locations and patient context will have a distinct molecular epidemiology of leptospirosis, based on microgeographical characteristics related to regiona-specific Leptospira predominance. Our objective is to characterise the clinical, epidemiological and molecular aspects of leptospirosis in Sri Lanka to understand disease progression, risk factors and obtain isolates of Leptospira.

METHODS AND ANALYSIS

We designed a multicentre prospective study in Sri Lanka to recruit undifferentiated febrile patients and conduct follow-ups during hospital stays. Patients will be recruited from outpatient departments and medical wards. This study will be conducted at two main sites (Anuradhapura and Peradeniya) and several additional sites (Awissawella, Ratnapura and Polonnaruwa). Blood and urine will be collected from patients on the day of admission to the ward or presentation to the outpatient department. Bedside inoculation of 2-4 drops of venous blood will be performed with Ellinghausen-McCullough-Johnson-Harris (EMJH) semisolid media supplemented with antibiotics. Regionally optimised microscopic agglutination test, culture and qPCR-evidence will be performed to confirm the presence of Leptospira in blood which in turn will confirm the presence of disease. Whole genome sequencing will be carried out for all isolates recovered from patients. Multilocus sequence typing (MLST) will be used for the genotyping of new isolates. Sri Lankan isolates will be identified using three published MLST schemes for Leptospira.

ETHICS AND DISSEMINATION

Ethical clearance for the study was obtained from Ethics Review Committees (ERC), Medicine and Allied Sciences (FMAS), Rajarata University of Sri Lanka (RUSL) and University of Peradeniya. All genomic data generated through this project will be available at GenBank. Anonymised data will be deposited at the ERC, FMAS, RUSL.

Correction to: A Case-Control Study of Environmental and Occupational Risks of Leptospirosis in Sri Lanka

The original version of this article unfortunately contained a mistake in one of the co-author's family name. The correct name should be Janith Warnasekara instead of Janith Warnasuriya. The original article has been corrected.

A Case-Control Study of Environmental and Occupational Risks of Leptospirosis in Sri Lanka

Sri Lanka has one of the highest incidences of human leptospirosis worldwide. Outbreaks of this zoonotic infection are related to the monsoons and flooding. The study investigates risk factors associated with environmental, animal and occupational exposure while acknowledging the potential bias due to hanta viral infections in the study samples. Data were obtained from structured interviews with 483 patients (276 cases and 207 controls). Risk exposures were studied for the entire population and for two stratified occupational groups: non-paddy workers and paddy workers. A higher odds ratio (OR) of leptospirosis transmission for paddy workers was observed compared to non-paddy workers (OR 1.905, 95% CI 1.274-2.856). Rat exposure was not associated with a significant higher risk for any of the groups. Instead, cattle and household animals seemed to be important for transmission of leptospirosis to humans, especially among non-paddy workers (OR 10.655, 95% CI 1.213-93.582). Leptospirosis in paddy workers was associated with environmental factors linked to contamination and wetness in paddy fields. Interestingly, abandoned paddy fields were found to have a protective effect against transmission to paddy workers (OR 0.421, 95% CI 0.237-0.748). Keeping animals on these dryer fields may act as a boundary for contamination of paddy fields with infectious animal urine. This finding may be considered as a public health intervention targeting leptospirosis among paddy workers.

Estimating the burden of leptospirosis in Sri Lanka; a systematic review

Background

Although the assessment of disease burden should be a priority for allocating resources, leptospirosis is grossly underestimated despite its true burden in Sri Lanka. This study aimed to assess the morbidity and mortality of leptospirosis based on routine surveillance data, hospital reported data and scientific publications from Sri Lanka.

Method

A systematic review was carried out, and Pub Med, MEDLINE®, BIOSIS Previews, Zoological Record, Web of Science Core Collection, Current Contents Connect, KCI-Korean Journal Database, BIOSIS Citation Index, Data Citation Index, SciELO Citation Index and Google Scholar databases were searched. Quarterly epidemiological bulletin (QEB), indoor morbidity & mortality returns (IMMR) and hand searches of local literature were performed in local libraries. Forty-two relevant full texts, 32 QEBs, and 8 IMMR were included in the full text review. Adjustments were made for under diagnosis, underreporting and chance variability.

Results

The estimated annual caseload of leptospirosis in Sri Lanka from 2008 to 2015, was 10,423, and the cumulative annual incidence of leptospirosis that required hospitalization was 52.1 (95% CI 51.7–52.6) per 100,000 people. The estimated number of annual deaths due to leptospirosis was approximately 730 (95% CI 542–980), with an estimated pooled case fatality ratio of 7.0% (95% CI 5.2–9.4). The most common organs involved were the kidney, liver and heart, with median rates of 48.7, 30, and 14.2%, respectively.

Conclusion

Our systematic review shows gross underestimation of the true leptospirosis burden in the national statistics of Sri Lanka, and the hospitalization rates estimated in our study were compatible with the total burden estimate of 300·6 (95% CI 96·54–604·23) per 100,000 people published previously.

Electronic supplementary material

The online version of this article (10.1186/s12879-018-3655-y) contains supplementary material, which is available to authorized users.