Understanding the Relationship Between Non-Tuberculous Mycobacteria and Climate
Non-tuberculous mycobacteria (NTM) are diverse microorganisms present in various environments, with some species causing severe diseases in humans. The incidence of NTM-related infections has been on the rise globally, potentially influenced by climate change. Factors such as soil, water sources, and contaminated medical equipment contribute to NTM transmission. Studying the impact of climate variables on NTM growth and prevalence is crucial for public health interventions.
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Non-Tuberculous Mycobacteria and Climate This is a real research project! Expected answers and experiment success is NOT guaranteed Experiment results may change the structure of the course add new experiments, change schedule, etc. Negative results are common in research. Do not get discourage by this!! Use this as a learning opportunity. Your grade will not depend on experiment results. You can drive the project! Do you have an idea for an experiment you think would add to the project? Do you have a research question related to the project? You will be guided by the instructor to create protocols, draft hypothesis, troubleshoot, etc. Questions are welcomed! And encouraged! Your peer mentors can help you too!
Optional: Include graphs and data from the Sixth assessment report. Present and discuss with students: https://www.ipcc.ch/report/ar6/wg1/figures/summary-for- policymakers
Microorganisms and climate have a strong relationship What climate variables do you think are associated with microbial growth? Temperature pH acidification Precipitation/draught Land use Light
Microorganisms and climate have a strong relationship Present and discuss manuscript and particularly Figure 4b from Carlos A. Guerra et al (2021): https://onlinelibrary.wiley.com/doi/full/10.1111/geb.13273
What are NTMs Non-Tuberculous Mycobacteria >190 species and subspecies Environmental mycobacteria (mostly innocuous) but some opportunistic species can cause severe pulmonary disease and other manifestations. M. avium complex (MAC) M. avium, M. intracellulare, M. chimaera M. kansasii M. xenopi M. abscessus (Rapid grower) Sub-species: abscessus, bolletti, massiliense Other species which cause disease only occasionally (i.e. M. gordonae) Opportunistic disease most common in patients with underlying lung conditions (Cystic fibrosis, COPD)
Why studying NTMs and climate change NTMs are ubiquitous in the environment Incidence and prevalence of NTMs has been increasing throughout the world. NTM disease prevalence rose from 2.4 cases/100,000 in the early 1980s to 15.2 cases/100,000 in 2013 in the US. Is climate change behind this rise? Soil Natural and drinking water Sewage water Decaying vegetation MAC Source of infection is thought to be drinking water and tap aerosols Nosocomial infections (i.e. M. chimerae) are due to contaminated medical equipment.
NTMs physiology Slow growers: 20-24h doubling time. Rapid growers: 8-12h doubling time High lipid content cell wall Intrinsic resistant to disinfectants, high temperatures and UV light. Hard to treat! Can form biofilms (i.e. pipes and medical devices) Each specie may have specific characteristics in regards to antibiotic resistance, cell wall components, etc. Show a representative figure of Mycobacteria cell wall
Studies on NTM diversity and environment variability Roguet et al, 2018 Microb Ecol 49 urban and semi-urban lakes in and around Paris, France Sampled once for two consecutive years One lake sampled every month. Mycobacteria density measure by real time QPCR of the atpE gene NTM DNA found in all lakes, with variable mycobacterial densities (measured as genome units per liter) No association found between nutrient availability, but pH and iron availability had some correlation with mycobacterial densities.
Studies on NTM diversity and environment variability Walsh et al 2019 Appl Environ Microbiol 16S rRNA and hsp65 sequencing of 143 soil samples from a range of ecosystems Mycobacteria sequences found in 133 soil samples M. avium complex found only in 15 samples (in wet, acidic samples) Mycobacterial abundances higher in acidic soils and cooler climates
Studies on NTM diversity and environment variability Bland et al, 2005 Appl Environ Microbiol 7 sites along the Rio Grande were sampled once per month for ~1yr Samples were decontaminated and plated into selective media Pathogenic species identified M. avium, M. intracellulare Choose representative figure from manuscript
Outline of the project Identify research question Create NTM stock Plate and isolate NTMS Identify species by hsp65 sequencing Map NTM diversity in soil and water samples Soil and water samples Develop hypothesis for experimental testing Correlate findings to environmental variables 16S rRNA and hsp65 Next Generation Sequencing Total gDNA extraction Compare and contrast soil vs w ter microbiome Compare and contrast microbiomes with high NTM content
Examples of questions generated in previous semesters Isolated species vary from season to season? Is this related to specific sampling site? Are there any differences in temperature of isolation between seasons? Some location have no culturable NTMs Could this be related to specific sampling site? Are variables associated with lack of NTMs? Are these sample enriched for other bacteria? Do these sites have a low microbial abundance in general? Specific climate events may have an effect on results Early snowfall, wildfires and ash accumulation in water and top soil.
Important notes! We have a google doc with data from previous semesters. All of you will contribute and maintain a proper database. You can also use data from previous semesters to compare results, environmental variables, etc. For sample storage (i.e. soil, DNA, glycerol stocks), always label the tubes with date, initials and content. Make sure the notebook includes this information as well.
What is next? Next class: Review good practices for notebook keeping, Biosafety procedures (i.e. how to use a Biosafety Cabinet, autoclave, the importance of disinfection contact time), how to prepare a poster. Next week: Before we gest started, we need to draft a research hypothesis and question. All of you will pick a manuscript to review. We will discuss as a group the different manuscripts. When reading the manuscript keep in mind potential research questions that can complement results from previous semesters. Also make notes of any methods that may be useful for the project. Come prepared to give a brief summary of your manuscript, and any potential research questions (within the context of NTMs and climate!)
