Supplementary material for Phylogenomic analysis supports Mycobacterium tuberculosis transmission between humans and elephants

Supplementary information: Table S1: Detailed information on the 94 whole genomes retrieved from GenBank and used in this study.Peer reviewe

Phylogenomic analysis supports Mycobacterium tuberculosis transmission between humans and elephants

[Introduction]: Tuberculosis is an infectious disease caused by a group of acid-fast bacilli known as Mycobacterium tuberculosis complex (MTC), which has a major impact on humans. Transmission of MTC across the human-animal interface has been demonstrated by several studies. However, the reverse zoonotic transmission from humans to animals (zooanthroponosis) has often been neglected.[Methods]: In this study, we used Nanopore MinION and Illumina MiSeq approaches to sequence the whole genome of M. tuberculosis strains isolated from two deceased Asian elephants (Elephas maximus) and one human in Chitwan, Nepal. The evolutionary relationships and drug resistance capacity of these strains were assessed using the whole genome data generated by the stand-alone tool Tb-Profiler. Phylogenomic trees were also constructed using a non-synonymous SNP alignment of 2,596 bp, including 94 whole genome sequences representative of the previously described M. tuberculosis lineages from elephants worldwide (lineages 1 and 4) and from humans in Nepal (lineages 1, 2 and 3).[Results and discussion]: The new genomes achieved an average coverage of 99.6%, with an average depth of 55.67x. These M. tuberculosis strains belong to lineage 1 (elephant DG), lineage 2 (elephant PK) and lineage 4 (human), and none of them were found to have drug-resistant variants. The elephant-derived isolates were evolutionarily closely related to human-derived isolates previously described in Nepal, both in lineages 1 and 2, providing additional support for zooanthroponosis or bidirectional transmission between humans and elephants. The human-derived isolate clustered together with other published human isolates from Argentina, Russia and the United Kingdom in the lineage 4 clade. This complex multi-pathogen, multi-host system is challenging and highlights the need for a One Health approach to tuberculosis prevention and control at human-animal interface, particularly in regions where human tuberculosis is highly endemic.This work was supported by National Funds through FCT-Fundação para a Ciência e a Tecnologia in the scope of the project UIDP/50027/2020.Peer reviewe

Prevalence and factors associated with depression, anxiety and stress symptoms among construction workers in Nepal.

IntroductionThe construction industry in Nepal, which employs a significant proportion of the population, ranks as one of the largest industries in the country. Construction work is physically demanding and can be risky due to the use of heavy machinery and the presence of intense physical labor. However, the physical and mental health of construction workers in Nepal is often neglected. This study aimed to assess psychological distress (depression, anxiety, and stress symptoms) and its association with socio-demographic, lifestyle, and occupational factors among construction workers in Kavre district, Nepal.MethodsWe conducted a cross-sectional study from 1st October 2019 to 15th January 2020 among 402 construction workers in Banepa, and Panauti municipalities of Kavre district, Nepal. We collected data with face-to-face interviews using a structured questionnaire consisting of a) socio-demographic characteristics; b) lifestyle and occupational characteristics; and c) depression, anxiety and stress symptoms. We collected data using electronic forms in KoboToolbox and imported them into R version 3.6.2 for statistical analysis. We present parametric numerical variables as mean and standard deviation, and categorical variables as percentage and frequency. The confidence interval around proportion was estimated with the Clopper-Pearson method. We applied univariate and multivariable logistic regression to determine factors associated with depression symptoms, anxiety, and stress. The result of logistic regression was presented as crude odds ratio, adjusted odds ratio (AOR), and their 95% confidence interval (CI).ResultsThe prevalence of depression, anxiety and stress symptoms were 17.1% (95%CI: 13.6-21.2), 19.2% (95%CI: 15.5-23.4) and 16.4% (95%CI: 12.9-20.4), respectively. In multivariable logistic regression analysis, depression symptom was positively associated with poor sleep quality (AOR = 3.51; 95%CI: 1.5-8.19; p-value: 0.004); stress symptom was positively associated with Brahmin ethnicity (AOR = 3.76; 95%CI:1.34-10.58; p-value: 0.012) and current smoking (AOR = 2.0; 95%CI: 1.11-3.82 p-value: 0.022). But anxiety symptoms were not associated with any of the variables.ConclusionsThe prevalence of depression, anxiety, and stress symptoms were high among construction workers. Developing evidence-based and appropriate community-based mental health prevention programs among laborers and construction workers is recommended

Rapid genomic surveillance of SARS-CoV-2 in a dense urban community of Kathmandu Valley using sewage samples

Understanding disease burden and transmission dynamics in resource-limited, low-income countries like Nepal are often challenging due to inadequate surveillance systems. These issues are exacerbated by limited access to diagnostic and research facilities throughout the country. Nepal has one of the highest COVID-19 case rates (915 cases per 100,000 people) in South Asia, with densely-populated Kathmandu experiencing the highest number of cases. Swiftly identifying case clusters (hotspots) and introducing effective intervention programs is crucial to mounting an effective containment strategy. The rapid identification of circulating SARS-CoV-2 variants can also provide important information on viral evolution and epidemiology. Genomic-based environmental surveillance can help in the early detection of outbreaks before clinical cases are recognized and identify viral micro-diversity that can be used for designing real-time risk-based interventions. This research aimed to develop a genomic-based environmental surveillance system by detecting and characterizing SARS-CoV-2 in sewage samples of Kathmandu using portable next-generation DNA sequencing devices. Out of 22 sites in the Kathmandu Valley from June to August 2020, sewage samples from 16 (80%) sites had detectable SARS-CoV-2. A heatmap was created to visualize the presence of SARS-CoV-2 infection in the community based on viral load intensity and corresponding geospatial data. Further, 47 mutations were observed in the SARS-CoV-2 genome. Some detected mutations (n = 9, 22%) were novel at the time of data analysis and yet to be reported in the global database, with one indicating a frameshift deletion in the spike gene. SNP analysis revealed possibility of assessing circulating major/minor variant diversity on environmental samples based on key mutations. Our study demonstrated the feasibility of rapidly obtaining vital information on community transmission and disease dynamics of SARS-CoV-2 using genomic-based environmental surveillance