Consequences of Climate Change on the Emergence of Pathogenic, Environmentally Acquired Nontuberculous Mycobacteria

Abstract

Background: Climate change, manifested by global warming, unpredictable precipitation, and increased frequency and severity of catastrophic weather, is a growing health threat. However, the impact that climate changes pose to environmental bacteria is not fully recognized.

Methods: To understand pathogen response to climate change, we interrogated nontuberculous mycobacteria (NTM) on a continental scale using open-source data products including Surface water microbe community composition data, soil microbe community composition data, and 16S ribosomal RNA (rRNA) gene sequences provided by the National Ecological Observatory Network (NEON) between 2015 and 2018.

Results: Of 6343 soil and water samples, 81.8% were positive for mycobacteria; soil samples had a higher positivity rate. NTM were also identified among a subset of 31 archived DNA samples, albeit in low proportion (6.5% [n = 2]). Viable Mycobacterium chelonae and Mycobacterium arabiense were recovered from 3.7% (3 of 81) biobanked NEON soil and aquatic sediment samples. Finally, using geographic coordinates of NTM from work in Hawai'i (a geographic hot spot for NTM infections), we modeled habitat associations during current and future climates. We found that the potential ranges for NTM are forecast to increase under future climate conditions and are strongly associated with increases in temperature, with pathogenic species accounting for most of the predicted surge.

Conclusions: Very little is known of the possible negative climate impacts on the emergence of disease due to environmental microbes. These data support the notion that NTM prevalence may be heavily augmented by climate change resulting in expansion into new geographic niches and posing new clinical consequences for humans.

Keywords: NEON; climate change; infectious disease; natural environment; nontuberculous mycobacteria.

Figure 1.

Sequencing data for the 16S ribosomal RNA (rRNA) gene reveal mycobacteria at National Ecological Observatory Network (NEON) sites. Existing NEON 16S rRNA gene sequencing data from 1 November 2015 and 31 October 2018 were analyzed for mycobacteria. The percentage of samples in which mycobacteria were detected are shown. Sites with no sequencing data between 1 November 2015 and 31 October 2018 are denoted by gray symbols. NEON sites in Hawai’i, Alaska, and Puerto Rico are not displayed. NEON ecological domain boundaries are included.

Figure 2.

Increases in average annual temperatures (B) and decreases in temperature isothermality (a measure of how consistent the temperature range is throughout the year compared with the temperature range within a single day) (D) under future climatic conditions, compared with current conditions (A and C, respectively), meaning that temperatures will generally be higher throughout the year and will fluctuate less during the course of the day.

Figure 3.

More suitable habitats for pathogenic NTM are predicted to emerge under future climate conditions. Maxent modeling predicts that multiple NTM—including Mycobacterium chimaera, Mycobacterium gordonae, Mycobacterium chelonae, and Mycobacterium abscessus—will thrive under hotter future climates (A) and less fluctuating future temperatures (B), especially M chimaera, and that habitat suitability will increase under future climate conditions for all species studied (C). Gray vertical dotted and dashed lines in A and B represent current (dashed) and future (dotted) average conditions in Hawai’i. As indicated, the average annual temperature is predicted to increase in the future, whereas temperature isothermality (a measure of how consistent the temperature range is throughout the year compared with the temperature range within a single day) is predicted to decrease. See Supplementary Materials and Methods for more description of these variables.

Figure 4.

More suitable habitats emerge for rapid- and slow-growing NTM species under future climate conditions. A–D, Habitat suitability for rapid-growing, pathogenic Mycobacterium chelonae and Mycobacterium abscessus under current (A, C) and future (B, D) climates in Hawai’i. Habitat suitability scores range from 0 (most unsuitable) to 1 (most suitable). E–H, Habitat suitability for slow-growing Mycobacterium chimaera (pathogenic) and Mycobacterium gordonae (nonpathogenic) under current (E, G) and future (F, H) climates in Hawai’i.