Mycobacterium tuberculosis lineage 4 comprises globally distributed and geographically restricted sublineages

Generalist and specialist species differ in the breadth of their ecological niches. Little is known about the niche width of obligate human pathogens. Here we analyzed a global collection of Mycobacterium tuberculosis lineage 4 clinical isolates, the most geographically widespread cause of human tuberculosis. We show that lineage 4 comprises globally distributed and geographically restricted sublineages, suggesting a distinction between generalists and specialists. Population genomic analyses showed that, whereas the majority of human T cell epitopes were conserved in all sublineages, the proportion of variable epitopes was higher in generalists. Our data further support a European origin for the most common generalist sublineage. Hence, the global success of lineage 4 reflects distinct strategies adopted by different sublineages and the influence of human migration.We thank S. Lecher, S. Li and J. Zallet for technical support. Calculations were performed at the sciCORE scientific computing core facility at the University of Basel. This work was supported by the Swiss National Science Foundation (grants 310030_166687 (S.G.) and 320030_153442 (M.E.) and Swiss HIV Cohort Study grant 740 to L.F.), the European Research Council (309540-EVODRTB to S.G.), TB-PAN-NET (FP7-223681 to S.N.), PathoNgenTrace projects (FP7-278864-2 to S.N.), SystemsX.ch (S.G.), the German Center for Infection Research (DZIF; S.N.), the Novartis Foundation (S.G.), the Natural Science Foundation of China (91631301 to Q.G.), and the National Institute of Allergy and Infectious Diseases (5U01-AI069924-05) of the US National Institutes of Health (M.E.)

Etablierung und Anwendung der CRISPR/Cas-Technologie in nicht-tuberkulösen Mykobakterien (NTM)

Non-tuberculous mycobacteria (NTM) are increasingly recognized for their impact on human health, causing infections, especially in individuals with compromised immune systems or underlying lung conditions. Unlike the well-known Mycobacterium tuberculosis (MTB), NTM's intrinsic resistance to common antibiotics poses treatment challenges. Diagnosing NTM infections is complicated due to nonspecific symptoms, often confused with other diseases. Understanding NTM biology is crucial for improved diagnostics and treatments. The adoption of CRISPRi (Clustered Regularly Interspaced Short Palindromic Repeats interference) and CRISPR/Cas9 in NTM represents a significant breakthrough for advancing NTM research and treatment. The study applied the CRISPRi/dCas9 system to NTM species (M. smegmatis, M. abscessus, and M. avium), using a reporter eGFP gene for functional analysis. CRISPRi led to significant downregulation of eGFP in M. smegmatis and M. abscessus. In M. avium, reduced fluorescence, even without sgRNA, suggested the need for further optimization. CRISPRi proved effective for gene knockdown in M. abscessus. CRISPR/Cas9 was employed to knockout the eGFP gene, resulting in loss of fluorescence in M. smegmatis and M. avium but not in M. abscessus. Assessing the system on the mps1 gene in M. abscessus revealed defects in Glycopeptidolipid synthesis, causing morphotype transition. Evaluation on endogenous genes (porin, ppiA, erm-41, and whiB7) showed successful knockout for porin and ppiA. However, targeting erm-41 and whiB7 indicated the need for system optimization. The successful establishment of CRISPRi and CRISPR/Cas9 in NTM signifies a milestone, offering new avenues for research and potential therapies. These technologies enable precise genomic manipulation, enhancing our understanding of NTM biology and facilitating the development of more effective NTM infection treatments.Nicht-tuberkulöse Mykobakterien (NTM) werden zunehmend für ihre Auswirkungen auf die menschliche Gesundheit erkannt, da sie Infektionen verursachen, insbesondere bei Personen mit geschwächtem Immunsystem oder zugrunde liegenden Lungenerkrankungen. Im Gegensatz zum bekannten Mycobacterium tuberculosis (MTB) stellt die intrinsische Resistenz von NTM gegen gängige Antibiotika eine Herausforderung für die Behandlung dar. Die Diagnose von NTM-Infektionen ist aufgrund unspezifischer Symptome, die häufig mit anderen Krankheiten verwechselt werden, kompliziert. Das Verständnis der NTM-Biologie ist für eine verbesserte Diagnose und Behandlung von entscheidender Bedeutung. Die Einführung von CRISPRi (Clustered Regularly Interspaced Short Palindromic Repeats Interference) und CRISPR/Cas9 bei NTM stellt einen bedeutenden Durchbruch für die Weiterentwicklung der NTM-Forschung und -Behandlung dar. Die Studie wendete das CRISPRi/dCas9-System auf NTM-Arten (M. smegmatis, M. abscessus und M. avium) an und verwendete ein Reporter-eGFP-Gen für die Funktionsanalyse. CRISPRi führte zu einer signifikanten Herunterregulierung von eGFP bei M. smegmatis und M. abscessus. Bei M. avium deutete die verringerte Fluoreszenz, auch ohne sgRNA, auf die Notwendigkeit einer weiteren Optimierung hin. CRISPRi erwies sich als wirksam für den Gen-Knockdown bei M. abscessus. CRISPR/Cas9 wurde eingesetzt, um das eGFP-Gen auszuschalten, was zu einem Fluoreszenzverlust bei M. smegmatis und M. avium führte, nicht jedoch bei M. abscessus. Die Untersuchung des Systems auf dem mps1-Gen in M. abscessus ergab Defekte in der Glycopeptidolipid-Synthese, die einen Morphotypübergang verursachten. Die erfolgreiche Etablierung von CRISPRi und CRISPR/Cas9 in der NTM stellt einen Meilenstein dar und eröffnet neue Wege für die Forschung und mögliche Therapien. Diese Technologien ermöglichen eine präzise Genommanipulation, verbessern unser Verständnis der NTM-Biologie und erleichtern die Entwicklung wirksamerer NTM-Infektionsbehandlungen

Assessing the Impact of Water Salinity on Women’s health in Coastal Areas: An Analysis Based on the Right to Water and Sanitation

This paper critically examines the human rights situations of women in coastal areas of Bangladesh with a special focus on the harmful effects of water salinity on health. Coastal areas in Bangladesh are particularly susceptible to climate change-induced challenges, including salinization of water sources. Our analysis investigates the intersectionality of environmental degradation and human rights, emphasizing the disproportionate impact on women\u27s health. Based on the human rights framework, our study explores how saline water worsens existing inequalities, limiting women\u27s access to clean drinking water, adequate sanitation facilities, and essential healthcare services. By centering human rights principles, we highlight the interconnectedness between environmental degradation and violations of women\u27s rights to water and sanitation, emphasizing the right to health, and safe living conditions. As Bangladesh struggles with escalating sea-level rise, with projections indicating a substantial increase by 2100, the prevalence of water salinity poses a grave threat to coastal communities\u27 well-being and rights. About 73 percent of the population is deprived of drinking water in coastal areas (BEDS, 2020). About 20 million people have already faced the crisis of drinking water in the salinity areas of Bangladesh (World Bank, 2020). Our analysis underscores the urgent need for comprehensive interventions that address this issue\u27s human rights dimensions. While existing research has studied various health consequences of water salinity, our study fills a gap by focusing on the violations of human rights—the right to water and sanitation. Coastal women disproportionately bear the burden of water salinity and face heightened risks due to their reliance on contaminated water sources for daily activities. By highlighting the right to water and sanitation principles, our analysis provides valuable insights for policymakers, advocates, and practitioners to develop inclusive and rights-based strategies aimed at mitigating the adverse effects of water salinity on women\u27s health and well-being in coastal regions