Multiplexed Strain Phenotyping Defines Consequences of Genetic Diversity in Mycobacterium tuberculosis for Infection and Vaccination Outcomes

Carey, Allison F.; Wang, Xin; Cicchetti, Nico; Spaulding, Caitlin N.; Liu, Qingyun; Hopkins, Forrest; Brown, J. A.; Sixsmith, Jaimie; Sutiwisesak, Rujapak; Behar, Samuel M.; Ioerger, Thomas R.; Fortune, Sarah M.

doi:10.1128/msystems.00110-22

Cited by 6 publications

(3 citation statements)

References 72 publications

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“…Further, since the drug tolerance spawned by heterogeneity is adaptive, we might anticipate that future work will demonstrate that the production of heterogeneous sub-populations is itself under genetic selection and control. In fact, multiple recent reports already point in that direction ( Bellerose et al., 2019 ; Safi et al., 2019 ; Safi et al., 2020 ; Ma et al., 2021 ; Carey et al., 2022 ; Martini et al., 2022 ).…”

Section: Discussionmentioning

confidence: 96%

The evolving biology of Mycobacterium tuberculosis drug resistance

Jones

Adams

Eldesouky

et al. 2022

Front. Cell. Infect. Microbiol.

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Tuberculosis, caused by Mycobacterium tuberculosis (Mtb) is an ancient disease that has remained a leading cause of infectious death. Mtb has evolved drug resistance to every antibiotic regimen ever introduced, greatly complicating treatment, lowering rates of cure and menacing TB control in parts of the world. As technology has advanced, our understanding of antimicrobial resistance has improved, and our models of the phenomenon have evolved. In this review, we focus on recent research progress that supports an updated model for the evolution of drug resistance in Mtb. We highlight the contribution of drug tolerance on the path to resistance, and the influence of heterogeneity on tolerance. Resistance is likely to remain an issue for as long as drugs are needed to treat TB. However, with technology driving new insights and careful management of newly developed resources, antimicrobial resistance need not continue to threaten global progress against TB, as it has done for decades.

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Section: Discussionmentioning

confidence: 96%

The evolving biology of Mycobacterium tuberculosis drug resistance

Jones

Adams

Eldesouky

et al. 2022

Front. Cell. Infect. Microbiol.

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“…Recently, variant analysis, transcriptional studies and genome-wide transposon sequencing were used to unravel the biological basis of the distinctive phenotypes of Beijing strains. These analyses identified functional genetic changes across multiple stress and host response pathways, suggesting that these adaptive changes may be the reason for the distinct clinical characteristics and epidemiological success of this M. tuberculosis family [ 41 ].…”

Section: Discussionmentioning

confidence: 99%

Clinical Strains of Mycobacterium tuberculosis Representing Different Genotype Families Exhibit Distinct Propensities to Adopt the Differentially Culturable State

Gordhan,

Padarath,

Sewcharran

et al. 2024

Pathogens

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Growing evidence points to the presence of differentially culturable tubercle bacteria (DCTB) in clinical specimens from individuals with active tuberculosis (TB) disease. These bacteria are unable to grow on solid media but can resuscitate in liquid media. Given the epidemiological success of certain clinical genotype families of Mycobacterium tuberculosis, we hypothesize that different strains may have distinct mechanisms of adaptation and tolerance. We used an in vitro carbon starvation model to determine the propensity of strains from lineages 2 and 4 that included the Beijing and LAM families respectively, to generate DCTB. Beijing strains were associated with a greater propensity to produce DCTB compared to LAM strains. Furthermore, LAM strains required culture filtrate (CF) for resuscitation whilst starved Beijing strains were not dependent on CF. Moreover, Beijing strains showed improved resuscitation with cognate CF, suggesting the presence of unique growth stimulatory molecules in this family. Analysis of starved Beijing and LAM strains showed longer cells, which with resuscitation were restored to a shorter length. Cell wall staining with fluorescent D-amino acids identified strain-specific incorporation patterns, indicating that cell surface remodeling during resuscitation was distinct between clinical strains. Collectively, our data demonstrate that M. tuberculosis clinical strains from different genotype lineages have differential propensities to generate DCTB, which may have implications for TB treatment success.

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“…However, we have previously found that higher epidemiologic fitness of L2.2 strains correlates with slower growth in mice. 50 Therefore, we sought to assess the epidemiologic fitness of the L1 subclade strains. Terminal branch lengths (TBLs), determined by the number of SNPs derived from the most recent branching point of each strain, serves as a proxy for the maximum evolutionary time after transmission.…”

Section: Mtb L1 Clade Is Associated With Poor Clinical Outcomes and I...mentioning

confidence: 99%

High-throughput phenogenotypingof Mycobacteria tuberculosisclinical strains reveals bacterial determinants of treatment outcomes

Stanley

Spaulding

Liu

et al. 2023

Preprint

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Background: Combatting the tuberculosis (TB) epidemic caused by Mycobacterium tuberculosis (Mtb) necessitates a better understanding of the factors contributing to patient clinical outcomes and transmission. While host and environmental factors have been evaluated, the impact of Mtb genetic background and phenotypic diversity is underexplored. Previous work has made associations between Mtb genetic lineages and some clinical and epidemiological features, but the bacterial traits underlying these connections are largely unknown. Methods: We developed a high-throughput functional genomics platform for defining genotype-phenotype relationships across a panel of Mtb clinical isolates. These phenotypic fitness profiles function as intermediate traits which can be linked to Mtb genetic variants and associated with clinical and epidemiological outcomes. We applied this approach to a collection of 158 Mtb strains from a study of Mtb transmission in Ho Chi Minh City, Vietnam. Mtb strains were genetically tagged in multiplicate, which allowed us to pool the strains and assess in vitro competitive fitness using deep sequencing across a set of 14 host-relevant antibiotic and metabolic conditions. Phylogenetic and monogenic associations with these intermediate traits were identified and then associated with clinical outcomes. Findings: Mtb clinical strains have a broad range of growth and drug response dynamics that can be clustered by their phylogenetic relationships. We identified novel monogenic associations with Mtb fitness in various metabolic and antibiotic conditions. Among these, we find that mutations in Rv1339, a phosphodiesterase, which were identified through their association with slow growth in glycerol, are further associated with treatment failure. We also identify a previously uncharacterized subclade of Lineage 1 strains (L1.1.1.1) that is phenotypically distinguished by slow growth under most antibiotic and metabolic stress conditions in vitro. This clade is associated with cavitary disease, treatment failure, and demonstrates increased transmission potential. Interpretation: High-throughput phenogenotyping of Mtb clinical strains enabled bacterial intermediate trait identification that can provide a mechanistic link between Mtb genetic variation and patient clinical outcomes. Mtb strains associated with cavitary disease, treatment failure, and transmission potential display intermediate phenotypes distinguished by slow growth under various antibiotic and metabolic conditions. These data suggest that Mtb growth regulation is an adaptive advantage for host bacterial success in human populations, in at least some circumstances. These data further suggest markers for the underlying bacterial processes that govern these clinical outcomes.

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Multiplexed Strain Phenotyping Defines Consequences of Genetic Diversity in Mycobacterium tuberculosis for Infection and Vaccination Outcomes

Cited by 6 publications

References 72 publications

The evolving biology of Mycobacterium tuberculosis drug resistance

The evolving biology of Mycobacterium tuberculosis drug resistance

Clinical Strains of Mycobacterium tuberculosis Representing Different Genotype Families Exhibit Distinct Propensities to Adopt the Differentially Culturable State

High-throughput phenogenotypingof Mycobacteria tuberculosisclinical strains reveals bacterial determinants of treatment outcomes

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