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

A Systematic Review of Zoonotic Disease Prevalence in Sri Lanka (2000-2022)

Background: The burden of zoonotic diseases in developing countries is significantly underestimated, influenced by various factors such as misdiagnosis, underreporting, natural disasters, climate change, resource limitations, rapid unplanned urbanization, poverty, animal migration, travel, ecotourism, and the tropical environmental conditions prevalent in the region. Despite Sri Lanka's provision of a publicly funded free health care system, zoonoses still contribute significantly to the burden of communicable diseases in the country. This study serves as a timely and exhaustive systematic review of zoonoses reported over the past 22 years in Sri Lanka. Materials and Methods: This systematic review adhered to the guidelines provided by the "Preferred Reporting Items for Systematic Reviews and Meta-Analyses" (PRISMA) statement. A systematic literature search was conducted between July and September 2022, utilizing the following databases and sources: Google Scholar, PubMed, Cochrane Library, Weekly Epidemiological Reports, and Rabies Statistical Bulletins published by the Ministry of Health, Sri Lanka. Results: From the initial database search, 1,710 articles were identified. After excluding nonzoonotic diseases, duplicated reports, inaccessible articles, and those not meeting the inclusion criteria, 570 reports were evaluated for eligibility. Of these, 91 reports were selected for data extraction, comprising 58 original research articles, 10 case reports, 16 weekly epidemiological reports, and 7 rabies statistical bulletins. Over the study period (2000-2022), 14 parasitic, 7 bacterial, and 7 viral zoonoses have been reported in Sri Lanka. Notably, leptospirosis emerged as the most reported zoonotic disease in the country. Conclusions: In response to these findings, we strongly recommend the implementation of a tailored, country-specific prevention and control program. To achieve this goal effectively, we emphasize the importance of adopting a country-specific "One Health" approach as a comprehensive framework for managing and controlling zoonotic diseases in Sri Lanka.

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.

Why do Doctors Miss the Diagnosis of Leptospiral Uveitis? Emergence of New Serovars and Challenges in Diagnosis

PURPOSE

Leptospirosis is an endemic disease in India and uveitis is its late complication. Several Indian reports showed diversity of serovars, changing patterns and existence of new serovars. Failure to add new serovars in testing panel result in increased false-negativity in serology.

AIM

To analyse seroprevalence, changing patterns and to discuss the resulting challenges in diagnosis.

METHODS

In this retrospective study covering the period from 1994 to 2020, we analysed data from laboratory records of patients diagnosed with leptospiral uveitis in South India. Microscopic agglutination Test (MAT) and/or Enzyme-Linked Immunosorbent Assay (ELISA) were performed on clinically diagnosed leptospiral uveitis cases from our hospital, as well as on systemic leptospirosis patients from government and private hospitals.

RESULTS

Out of a total of 87 216 new uveitis cases with varying causes over 27 years, 3,658 (4.1%) were clinically diagnosed as leptospiral uveitis. Among them, 1,268 (34.7%) patients were seropositive. In 1994, 92% of clinically diagnosed leptospirosis patients were seropositive in the MAT performed at the Centers for Disease Control and Prevention in Atlanta. However, the positivity rate gradually declined to 35% over the years. The predominant serovars identified were L. autumnalis, L. icterohaemorrhagiae, and L. australis. There were notable variations in the distribution of serovars over the years.

CONCLUSIONS

The data suggest a declining sensitivity of MAT and ELISA, possibly due to the emergence of new serovars. Customizing the panel based on local isolates could enhance the performance of MAT. Critical need is the addition of advanced molecular techniques to improve the diagnosis.

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.

Core genome sequencing and genotyping of Leptospira interrogans in clinical samples by target capture sequencing

BACKGROUND

The life-threatening pathogen Leptospira interrogans is the most common agent of leptospirosis, an emerging zoonotic disease. However, little is known about the strains that are currently circulating worldwide due to the fastidious nature of the bacteria and the difficulty to isolate cultures. In addition, the paucity of bacteria in blood and other clinical samples has proven to be a considerable challenge for directly genotyping the agent of leptospirosis directly from patient material. Our understanding of the genetic diversity of strains during human infection is therefore limited.

METHODS

Here, we carried out hybridization capture followed by Illumina sequencing of the core genome directly from 20 clinical samples that were PCR positive for pathogenic Leptospira to elucidate the genetic diversity of currently circulating Leptospira strains in mainland France.

RESULTS

Capture with RNA probes covering the L. interrogans core genome resulted in a 72 to 13,000-fold increase in pathogen reads relative to standard sequencing without capture. Variant analysis of the genomes sequenced from the biological samples using 273 Leptospira reference genomes was then carried out to determine the genotype of the infecting strain. For samples with sufficient coverage (19/20 samples with coverage > 8×), we could unambiguously identify L. interrogans serovars Icterohaemorrhagiae and Copenhageni (14 samples), L. kirschneri serovar Grippotyphosa (4 samples), and L. interrogans serovar Pyrogenes (1 sample) as the infecting strains.

CONCLUSIONS

We obtained high-quality genomic data with suitable coverage for confident core genome genotyping of the agent of leptospirosis for most of our clinical samples. The recovery of the genome of the serovars Icterohaemorrhagiae and Copenhageni directly from multiple clinical samples revealed low adaptive diversification of the core genes during human infection. The ability to generate culture-free genomic data opens new opportunities for better understanding of the epidemiology of this fastidious pathogen and pathogenesis of this neglected disease.

Leptospirosis: A Potential Culprit for Chronic Kidney Disease of Uncertain Etiology

PURPOSE

Chronic kidney disease of uncertain etiology (CKDu) is an environmental nephropathy in which the etiological factors are yet uncertain. Leptospirosis, a spirochetal infection that is common among agricultural communities, has been identified as a potential etiology for CKDu beyond environmental nephropathy. Although CKDu is a chronic kidney disease, in endemic regions, an increasing number of cases are reported with features suggestive of acute interstitial nephritis without any known reason (AINu), with or without background CKD. The study hypothesizes that exposure to pathogenic leptospires is one of the causative factors for the occurrence of AINu.

METHOD

This study was carried out using 59 clinically diagnosed AINu patients, 72 healthy controls from CKDu endemic region (endemic controls [ECs]), and 71 healthy controls from CKDu non-endemic region (non-endemic controls [NECs]).

RESULTS

The seroprevalence of 18.6, 6.9, and 7.0% was observed in the AIN (or AINu), EC, and NEC groups, respectively, from the rapid IgM test. Among 19 serovars tested, the highest seroprevalence was observed at 72.9, 38.9, and 21.1% in the AIN (AINu), EC, and NEC groups, respectively, by microscopic agglutination test (MAT), particularly for serovar Leptospira santarosai serovar Shermani. This emphasizes the presence of infection in AINu patients, and this also suggests that Leptospira exposure might play an important role in AINu.

CONCLUSION

These data suggest that exposure to Leptospira infection could be one of the possible causative factors for the occurrence of AINu, which may lead to CKDu in Sri Lanka.

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 multilocus 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 intraspecies, 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 nonpathogenic 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. This assay holds considerable promise in the clinical setting, and for routine epidemiological and environmental surveillance studies. IMPORTANCE Leptospirosis is caused by a diverse group of pathogenic spirochetes comprising over 200 different serotypes. Some are widely reported and of public health importance owing to their propensity to produce severe, fatal disease in humans. Apart from their tedium and expense, current serotyping approaches require isolation of the organisms in culture media-a protracted and incredibly inefficient process-rendering them useless clinically and limiting their utilization in prospective studies or outbreak investigations. The unavailability of culture-independent assays capable of distinguishing Leptospira serotypes remains a crucial gap in the field. The 11108 qPCR-assay overcomes this barrier to progress via direct taxonomic and serotype classification of Leptospira from urine and serum samples, and hence, is the first qPCR-based prognostic test for human leptospirosis.

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.

A global one health perspective on leptospirosis in humans and animals

Leptospirosis is a quintessential one health disease of humans and animals caused by pathogenic spirochetes of the genus Leptospira. Intra- and interspecies transmission is dependent on 1) reservoir host animals in which organisms replicate and are shed in urine over long periods of time, 2) the persistence of spirochetes in the environment, and 3) subsequent human-animal-environmental interactions. The combination of increased flooding events due to climate change, changes in human-animal-environmental interactions as a result of the pandemic that favor a rise in the incidence of leptospirosis, and under-recognition of leptospirosis because of nonspecific clinical signs and severe signs that resemble COVID-19 represents a "perfect storm" for resurgence of leptospirosis in people and domestic animals. Although often considered a disease that occurs in warm, humid climates with high annual rainfall, pathogenic Leptospira spp have recently been associated with disease in animals and humans that reside in semiarid regions like the southwestern US and have impacted humans that have a wide spectrum of socioeconomic backgrounds. Therefore, it is critical that physicians, veterinarians, and public health experts maintain a high index of suspicion for the disease regardless of geographic and socioeconomic circumstances and work together to understand outbreaks and implement appropriate control measures. Over the last decade, major strides have been made in our understanding of the disease because of improvements in diagnostic tests, molecular epidemiologic tools, educational efforts on preventive measures, and vaccines. These novel approaches are highlighted in the companion Currents in One Health by Sykes et al, AJVR, September 2022.

Microbial Protein Binding to gC1qR Drives PLA2G1B-Induced CD4 T-Cell Anergy

The origin of the impaired CD4 T-cell response and immunodeficiency of HIV-infected patients is still only partially understood. We recently demonstrated that PLA2G1B phospholipase synergizes with the HIV gp41 envelope protein in HIV viremic plasma to induce large abnormal membrane microdomains (aMMDs) that trap and inactivate physiological receptors, such as those for IL-7. However, the mechanism of regulation of PLA2G1B activity by the cofactor gp41 is not known. Here, we developed an assay to directly follow PLA2G1B enzymatic activity on CD4 T-cell membranes. We demonstrated that gp41 directly binds to PLA2G1B and increases PLA2G1B enzymatic activity on CD4 membrane. Furthermore, we show that the conserved 3S sequence of gp41, known to bind to the innate sensor gC1qR, increases PLA2G1B activity in a gC1qR-dependent manner using gC1qR KO cells. The critical role of the 3S motif and gC1qR in the inhibition of CD4 T-cell function by the PLA2G1B/cofactor system in HIV-infected patients led us to screen additional microbial proteins for 3S-like motifs and to study other proteins known to bind to the gC1qR to further investigate the role of the PLA2G1B/cofactor system in other infectious diseases and carcinogenesis. We have thus extended the PLA2G1B/cofactor system to HCV and Staphylococcus aureus infections and additional pathologies where microbial proteins with 3S-like motifs also increase PLA2G1B enzymatic activity. Notably, the bacteria Porphyromonas gingivalis, which is associated with pancreatic ductal adenocarcinoma (PDAC), encodes such a cofactor protein and increased PLA2G1B activity in PDAC patient plasma inhibits the CD4 response to IL-7. Our findings identify PLA2G1B/cofactor system as a CD4 T-cell inhibitor. It involves the gC1qR and disease-specific cofactors which are gC1qR-binding proteins that can contain 3S-like motifs. This mechanism involved in HIV-1 immunodeficiency could play a role in pancreatic cancer and several other diseases. These observations suggest that the PLA2G1B/cofactor system is a general CD4 T-cell inhibitor and pave the way for further studies to better understand the role of CD4 T-cell anergy in infectious diseases and tumor escape.

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.

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.

Time series models for prediction of leptospirosis in different climate zones in Sri Lanka

In tropical countries such as Sri Lanka, where leptospirosis—a deadly disease with a high mortality rate—is endemic, prediction is required for public health planning and resource allocation. Routinely collected meteorological data may offer an effective means of making such predictions. This study included monthly leptospirosis and meteorological data from January 2007 to April 2019 from Sri Lanka. Factor analysis was first used with rainfall data to classify districts into meteorological zones. We used a seasonal autoregressive integrated moving average (SARIMA) model for univariate predictions and an autoregressive distributed lag (ARDL) model for multivariable analysis of leptospirosis with monthly average rainfall, temperature, relative humidity (RH), solar radiation (SR), and the number of rainy days/month (RD). Districts were classified into wet (WZ) and dry (DZ) zones, and highlands (HL) based on the factor analysis of rainfall data. The WZ had the highest leptospirosis incidence; there was no difference in the incidence between the DZ and HL. Leptospirosis was fluctuated positively with rainfall, RH and RD, whereas temperature and SR were fluctuated negatively. The best-fitted SARIMA models in the three zones were different from each other. Despite its known association, rainfall was positively significant in the WZ only at lag 5 (P = 0.03) but was negatively associated at lag 2 and 3 (P = 0.04). RD was positively associated for all three zones. Temperature was positively associated at lag 0 for the WZ and HL (P < 0.009) and was negatively associated at lag 1 for the WZ (P = 0.01). There was no association with RH in contrast to previous studies. Based on altitude and rainfall data, meteorological variables could effectively predict the incidence of leptospirosis with different models for different climatic zones. These predictive models could be effectively used in public health planning purposes.