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1. The impact of frequently neglected model violations on bacterial recombination rate estimation: a case study in Mycobacterium canettii and Mycobacterium tuberculosis

   https://doi.org/10.1093/g3journal/jkac055  

   Sabin, Susanna ; Morales-Arce, Ana Y ; Pfeifer, Susanne P ; Jensen, Jeffrey D ( March 2022 , G3 Genes|Genomes|Genetics)

   Wong, A (Ed.)

   Abstract Mycobacterium canettii is a causative agent of tuberculosis in humans, along with the members of the Mycobacterium tuberculosis complex. Frequently used as an outgroup to the M. tuberculosis complex in phylogenetic analyses, M. canettii is thought to offer the best proxy for the progenitor species that gave rise to the complex. Here, we leverage whole-genome sequencing data and biologically relevant population genomic models to compare the evolutionary dynamics driving variation in the recombining M. canettii with that in the nonrecombining M. tuberculosis complex, and discuss differences in observed genomic diversity in the light of expected levels of Hill–Robertson interference. In doing so, we highlight the methodological challenges of estimating recombination rates through traditional population genetic approaches using sequences called from populations of microorganisms and evaluate the likely mis-inference that arises owing to a neglect of common model violations including purifying selection, background selection, progeny skew, and population size change. In addition, we compare performance when full within-host polymorphism data are utilized, versus the more common approach of basing analyses on within-host consensus sequences. 

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2. Zinc limitation triggers anticipatory adaptations in Mycobacterium tuberculosis

   https://doi.org/10.1371/journal.ppat.1009570  

   Dow, Allexa ; Sule, Preeti ; O’Donnell, Timothy J. ; Burger, Andrew ; Mattila, Joshua T. ; Antonio, Brandi ; Vergara, Kevin ; Marcantonio, Endrei ; Adams, L. Garry ; James, Nicholas ; et al ( May 2021 , PLOS Pathogens)

   Sassetti, Christopher M. (Ed.)

   Mycobacterium tuberculosis ( Mtb ) has complex and dynamic interactions with the human host, and subpopulations of Mtb that emerge during infection can influence disease outcomes. This study implicates zinc ion (Zn 2+ ) availability as a likely driver of bacterial phenotypic heterogeneity in vivo . Zn 2+ sequestration is part of “nutritional immunity”, where the immune system limits micronutrients to control pathogen growth, but this defense mechanism seems to be ineffective in controlling Mtb infection. Nonetheless, Zn 2+ -limitation is an environmental cue sensed by Mtb , as calprotectin triggers the zinc uptake regulator (Zur) regulon response in vitro and co-localizes with Zn 2+ -limited Mtb in vivo . Prolonged Zn 2+ limitation leads to numerous physiological changes in vitro , including differential expression of certain antigens, alterations in lipid metabolism and distinct cell surface morphology. Furthermore, Mtb enduring limited Zn 2+ employ defensive measures to fight oxidative stress, by increasing expression of proteins involved in DNA repair and antioxidant activity, including well described virulence factors KatG and AhpC, along with altered utilization of redox cofactors. Here, we propose a model in which prolonged Zn 2+ limitation defines a population of Mtb with anticipatory adaptations against impending immune attack, based on the evidence that Zn 2+ -limited Mtb are more resistant to oxidative stress and exhibit increased survival and induce more severe pulmonary granulomas in mice. Considering that extracellular Mtb may transit through the Zn 2+ -limited caseum before infecting naïve immune cells or upon host-to-host transmission, the resulting phenotypic heterogeneity driven by varied Zn 2+ availability likely plays a key role during early interactions with host cells. 

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3. Comparative survival of environmental and clinical Mycobacterium abscessus isolates in a variety of diverse host cells

   https://doi.org/10.1111/jam.15416  

   Vang, Charmie K. ; Dawrs, Stephanie N. ; Oberlag, Nicole M. ; Gilmore, Anah E. ; Hasan, Nabeeh A. ; Honda, Jennifer R. ( April 2022 , Journal of Applied Microbiology)

   Mycobacterium abscessus subsp. abscessus (MABS) is an emerging, opportunistic pathogen found globally in freshwater biofilms and soil. Typically, isolates are treated as a uniform group of organisms and very little is known about their comparative survival in healthy host cells. We posit that environmentally- and clinically derived isolates, show differential infectivity in immune cells and resistance to innate defenses.

   Six MABS isolates were tested including three water biofilm/soil and three sputum-derived isolates. A clinical MABS type strain and an environmental isolate of Arthrobacter were also included. MABS counts were significantly higher compared to Arthrobacter after co-culture with Acanthamoeba lenticulata, BEAS-2B epithelial cells, alveolar macrophages and the THP-1 macrophage cell line. A rough sputum-derived MABS isolate emerged as an isolate with higher virulence compared to others tested, as both a pellicle and cord former, survivor in the human cell models tested, inducer of high and prolonged production of pro-inflammatory cytokines, and the capacity to evade LL-37.

   Findings support intraspecies variation between MABS isolates.

   These data indicate subversion of host immune defenses by environmental and clinical MABS isolates is nuanced and maybe isolate dependent, providing new information regarding the pathogenesis of NTM infections.

    

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4. Defining the Transcriptional and Post-transcriptional Landscapes of Mycobacterium smegmatis in Aerobic Growth and Hypoxia

   https://doi.org/10.3389/fmicb.2019.00591  

   Martini, M. Carla ; Zhou, Ying ; Sun, Huaming ; Shell, Scarlet S. ( March 2019 , Frontiers in Microbiology)
5. Structural insights into the functional divergence of WhiB-like proteins in Mycobacterium tuberculosis

   https://doi.org/10.1016/j.molcel.2021.06.002  

   Wan, Tao ; Horová, Magdaléna ; Beltran, Daisy Guiza ; Li, Shanren ; Wong, Huey-Xian ; Zhang, Li-Mei ( June 2021 , Molecular Cell)

   null (Ed.)