scholarly journals Mutations in dnaA and a cryptic interaction site increase drug resistance in Mycobacterium tuberculosis

2020 ◽  
Vol 16 (11) ◽  
pp. e1009063
Author(s):  
Nathan D. Hicks ◽  
Samantha R. Giffen ◽  
Peter H. Culviner ◽  
Michael C. Chao ◽  
Charles L. Dulberger ◽  
...  
Keyword(s):  
Drug Resistance ◽  
Mycobacterium Tuberculosis ◽  
Genome Wide Association Study ◽  
Critical Concentration ◽  
Drug Susceptibility ◽  
Interaction Site ◽  
Clinical Strains ◽  
Synonymous Mutations ◽  
Genome Wide ◽  
A Genome

Genomic dissection of antibiotic resistance in bacterial pathogens has largely focused on genetic changes conferring growth above a single critical concentration of drug. However, reduced susceptibility to antibiotics—even below this breakpoint—is associated with poor treatment outcomes in the clinic, including in tuberculosis. Clinical strains of Mycobacterium tuberculosis exhibit extensive quantitative variation in antibiotic susceptibility but the genetic basis behind this spectrum of drug susceptibility remains ill-defined. Through a genome wide association study, we show that non-synonymous mutations in dnaA, which encodes an essential and highly conserved regulator of DNA replication, are associated with drug resistance in clinical M. tuberculosis strains. We demonstrate that these dnaA mutations specifically enhance M. tuberculosis survival during isoniazid treatment via reduced expression of katG, the activator of isoniazid. To identify DnaA interactors relevant to this phenotype, we perform the first genome-wide biochemical mapping of DnaA binding sites in mycobacteria which reveals a DnaA interaction site that is the target of recurrent mutation in clinical strains. Reconstructing clinically prevalent mutations in this DnaA interaction site reproduces the phenotypes of dnaA mutants, suggesting that clinical strains of M. tuberculosis have evolved mutations in a previously uncharacterized DnaA pathway that quantitatively increases resistance to the key first-line antibiotic isoniazid. Discovering genetic mechanisms that reduce drug susceptibility and support the evolution of high-level drug resistance will guide development of biomarkers capable of prospectively identifying patients at risk of treatment failure in the clinic.

scholarly journals Genetic features of persistently antimicrobial drug-susceptible extraintestinal pathogenic Escherichia coli pandemic sequence type 95

2021 ◽  
Author(s):  
Yuan Hu Allegretti ◽  
Reina Yamaji ◽  
Sheila Adams-Sapper ◽  
Lee W Riley
Keyword(s):  
Escherichia Coli ◽  
Drug Resistance ◽  
Resistance Genes ◽  
Genome Wide Association Study ◽  
Drug Susceptibility ◽  
Sequence Type ◽  
Genome Wide Association ◽  
Genome Wide ◽  
A Genome ◽  
Genetic Features

Extraintestinal pathogenic Escherichia coli (ExPEC) belonging to multilocus sequence type 95 (ST95) is one of the most widespread ExPEC lineages associated with bloodstream infections (BSI) and urinary tract infections (UTI). In contrast to other widespread ExPEC sequence types, a large proportion ST95 strains remains susceptible to all antimicrobial agents used to treat BSI or UTI. We aimed to identify genomic features of ST95 associated with persistent drug susceptibility. We conducted a genome-wide association study of 80 ExPEC ST95 isolates from patients with BSI or UTI in Northern California, and 1669 ST95 isolates deposited in the Enterobase database. Of the total of 1749 ST95 isolates, we compared whole-genome sequences of 887 drug-susceptible strains and 862 strains resistant to one or more drugs (defined genotypically as strains harboring drug-resistance genes annotated in the ResFinder database) to identify genetic features associated with strains devoid of drug-resistance genes. By a genome-wide association study of 553 UTI and BSI ST95 isolates, we found 44 accessory genes significantly associated with drug susceptibility, six of which encoded hypothetical proteins. Fifteen of these were not found in any of the WGSs of ST131 ExPEC strains, which are frequently multidrug-resistant, and eight of these genes were annotated to encode transporter or transfer systems. These findings highlight the potential mechanisms by which ST95 strains may resist the acquisition of mobile DNA elements carrying drug-resistance genes.

scholarly journals Genome-wide association study of resistance to Mycobacterium tuberculosis infection identifies a locus at 10q26.2 in three distinct populations

2020 ◽  
Author(s):  
Jocelyn Quistrebert ◽  
Marianna Orlova ◽  
Gaspard Kerner ◽  
Le Thi Ton ◽  
Nguyen Trong Luong ◽  
...  
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Association Study ◽  
Genome Wide Association Study ◽  
Tuberculosis Infection ◽  
Genome Wide Association ◽  
Mycobacterium Tuberculosis Infection ◽  
Endemic Region ◽  
Th17 Lymphocytes ◽  
Genome Wide ◽  
A Genome

The natural history of tuberculosis (TB) is characterized by a large inter-individual outcome variability after exposure to Mycobacterium tuberculosis. Specifically, some highly exposed individuals remain resistant to M. tuberculosis infection, as inferred by tuberculin skin test (TST) or interferon-gamma release assays (IGRAs). We performed a genome-wide association study of resistance to M. tuberculosis infection in an endemic region of Southern Vietnam. We enrolled household contacts (HHC) of pulmonary TB cases and compared subjects who were negative for both TST and IGRA (n=185) with infected individuals (n=353) who were either positive for both TST and IGRA or had a diagnosis of TB. We found a genome-wide significant locus on chromosome 10q26.2 with a cluster of variants associated with strong protection against M. tuberculosis infection (OR=0.42, 95%CI 0.35-0.49, P = 3.71x10-8, for the genotyped variant rs17155120). The locus was replicated in a French multi-ethnic HHC cohort and a familial admixed cohort from a hyper-endemic area of South Africa, with an overall OR for rs17155120 estimated at 0.50 (95%CI 0.45-0.55, P = 1.26x10-9) . The variants are located in intronic regions and upstream of C10orf90, a tumor suppressor gene which encodes an ubiquitin ligase activating the transcription factor p53. In silico analysis showed that the protective alleles were associated with a decreased expression in monocytes of the nearby gene ADAM12 which could lead to an enhanced response of Th17 lymphocytes. Our results reveal a novel locus controlling resistance to M. tuberculosis infection across different populations.

scholarly journals Genome-wide association study of resistance to Mycobacterium tuberculosis infection identifies a locus at 10q26.2 in three distinct populations

PLoS Genetics ◽  
2021 ◽  
Vol 17 (3) ◽  
pp. e1009392 ◽  
Author(s):  
Jocelyn Quistrebert ◽  
Marianna Orlova ◽  
Gaspard Kerner ◽  
Le Thi Ton ◽  
Nguyễn Trong Luong ◽  
...  
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Association Study ◽  
Genome Wide Association Study ◽  
Suppressor Gene ◽  
Genome Wide Association ◽  
Mycobacterium Tuberculosis Infection ◽  
Endemic Region ◽  
Th17 Lymphocytes ◽  
Genome Wide ◽  
A Genome

The natural history of tuberculosis (TB) is characterized by a large inter-individual outcome variability after exposure to Mycobacterium tuberculosis. Specifically, some highly exposed individuals remain resistant to M. tuberculosis infection, as inferred by tuberculin skin test (TST) or interferon-gamma release assays (IGRAs). We performed a genome-wide association study of resistance to M. tuberculosis infection in an endemic region of Southern Vietnam. We enrolled household contacts (HHC) of pulmonary TB cases and compared subjects who were negative for both TST and IGRA (n = 185) with infected individuals (n = 353) who were either positive for both TST and IGRA or had a diagnosis of TB. We found a genome-wide significant locus on chromosome 10q26.2 with a cluster of variants associated with strong protection against M. tuberculosis infection (OR = 0.42, 95%CI 0.35–0.49, P = 3.71×10−8, for the genotyped variant rs17155120). The locus was replicated in a French multi-ethnic HHC cohort and a familial admixed cohort from a hyper-endemic area of South Africa, with an overall OR for rs17155120 estimated at 0.50 (95%CI 0.45–0.55, P = 1.26×10−9). The variants are located in intronic regions and upstream of C10orf90, a tumor suppressor gene which encodes an ubiquitin ligase activating the transcription factor p53. In silico analysis showed that the protective alleles were associated with a decreased expression in monocytes of the nearby gene ADAM12 which could lead to an enhanced response of Th17 lymphocytes. Our results reveal a novel locus controlling resistance to M. tuberculosis infection across different populations.

scholarly journals Pyrazinamide action is driven by the cell envelope stress response in Mycobacterium tuberculosis

2021 ◽  
Author(s):  
Joshua M. Thiede ◽  
Nicholas A. Dillon ◽  
Michael D. Howe ◽  
Ranee Aflakpui ◽  
Samuel J. Modlin ◽  
...  
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Stress Response ◽  
Antimicrobial Agents ◽  
Cell Envelope ◽  
Drug Susceptibility ◽  
Beta Lactams ◽  
Genome Wide ◽  
A Genome ◽  
Envelope Stress ◽  
Important Drug

ABSTRACTPyrazinamide (PZA) plays a crucial role in first-line tuberculosis drug therapy. Unlike other antimicrobial agents, PZA is only active against Mycobacterium tuberculosis at low pH. The basis for this conditional drug susceptibility remains undefined. In this study, we utilized a genome-wide approach to interrogate potentiation of PZA action. We find that mutations in numerous genes involved in central metabolism as well as cell envelope maintenance and stress response are associated with PZA resistance. Further, we demonstrate that constitutive activation of the cell envelope stress response can drive PZA susceptibility independent of environmental pH. Consequently, treatment with peptidoglycan synthesis inhibitors, such as beta-lactams and D-cycloserine, potentiate PZA action through triggering this response. These findings illuminate a regulatory mechanism for conditional PZA susceptibility and reveals new avenues for enhancing potency of this important drug through targeting activation of the cell envelope stress response.

scholarly journals Bacterial Genome-Wide Association Identifies Novel Factors That Contribute to Ethionamide and Prothionamide Susceptibility in Mycobacterium tuberculosis

mBio ◽  
2019 ◽  
Vol 10 (2) ◽  
Author(s):  
Nathan D. Hicks ◽  
Allison F. Carey ◽  
Jian Yang ◽  
Yanlin Zhao ◽  
Sarah M. Fortune
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Antibiotic Susceptibility ◽  
Experimental Validation ◽  
Genome Wide Association ◽  
Genome Wide Association Studies ◽  
Second Line ◽  
Content Type ◽  
Clinical Strains ◽  
Genome Wide ◽  
A Genome

ABSTRACT In Mycobacterium tuberculosis, recent genome-wide association studies have identified a novel constellation of mutations that are correlated with high-level drug resistances. Interpreting the functional importance of the new resistance-associated mutations has been complicated, however, by a lack of experimental validation and a poor understanding of the epistatic factors influencing these correlations, including strain background and programmatic variation in treatment regimens. Here we perform a genome-wide association analysis in a panel of Mycobacterium tuberculosis strains from China to identify variants correlated with resistance to the second-line prodrug ethionamide (ETH). Mutations in a bacterial monooxygenase, Rv0565c, are significantly associated with ETH resistance. We demonstrate that Rv0565c is a novel activator of ETH, independent of the two known activators, EthA and MymA. Clinically prevalent mutations abrogate Rv0565c function, and deletion of Rv0565c confers a consistent fitness benefit on M. tuberculosis in the presence of partially inhibitory doses of ETH. Interestingly, Rv0565c activity affects susceptibility to prothionamide (PTH), the ETH analog used in China, to a greater degree. Further, clinical isolates vary in their susceptibility to both ETH and PTH, to an extent that correlates with the total expression of ETH/PTH activators (EthA, MymA, and Rv0565c). These results suggest that clinical strains considered susceptible to ETH/PTH are not equally fit during treatment due to both Rv0565c mutations and more global variation in the expression of the prodrug activators. IMPORTANCE Phenotypic antibiotic susceptibility testing in Mycobacterium tuberculosis is slow and cumbersome. Rapid molecular diagnostics promise to help guide therapy, but such assays rely on complete knowledge of the molecular determinants of altered antibiotic susceptibility. Recent genomic studies of antibiotic-resistant M. tuberculosis have identified several candidate loci beyond those already known to contribute to antibiotic resistance; however, efforts to provide experimental validation have lagged. Our study identifies a gene (Rv0565c) that is associated with resistance to the second-line antibiotic ethionamide at a population level. We then use bacterial genetics to show that the variants found in clinical strains of M. tuberculosis improve bacterial survival after ethionamide exposure.

scholarly journals Genome-wide association studies reveal the complex genetic architecture of DMI fungicide resistance in Cercospora beticola

2020 ◽  
Author(s):  
Rebecca Spanner ◽  
Demetris Taliadoros ◽  
Jonathan Richards ◽  
Viviana Rivera-Varas ◽  
Jonathan Neubauer ◽  
...  
Keyword(s):  
Fungicide Resistance ◽  
Genome Wide Association Study ◽  
Selective Sweep ◽  
Association Studies ◽  
Genome Wide Association ◽  
Cercospora Beticola ◽  
Genome Wide Association Studies ◽  
Synonymous Mutations ◽  
Genome Wide ◽  
A Genome

AbstractCercospora leaf spot is the most important disease of sugar beet worldwide. The disease is caused by the fungus Cercospora beticola and is managed principally by timely application of fungicides including those of the sterol demethylation inhibitor (DMI) class. However, reliance on DMIs has caused an increase in resistance to this class of fungicides in multiple C. beticola populations. To better understand the genetic and evolutionary basis for resistance in C. beticola, a genome-wide association study (GWAS) and selective sweep analysis were conducted for the first time in this fungal plant pathogen. We performed whole genome resequencing of 190 C. beticola isolates predominantly from North Dakota and Minnesota that were phenotyped for sensitivity to tetraconazole, the most widely used DMI fungicide in this region. GWAS identified mutations in genes associated with DMI fungicide resistance including a Regulator of G-protein Signaling (RGS) protein, an ATP-binding cassette (ABC) pleiotropic drug resistance transporter, a dual-specificity tyrosine phosphorylation-regulated kinase (DYRK), and a gene annotated as a hypothetical protein. A SNP upstream of CbCYP51, the gene encoding the target of DMI fungicides, was also identified via GWAS. Haplotype analysis of CbCYP51 identified a synonymous mutation (E170) in high linkage disequilibrium with the upstream SNP, and multiple non-synonymous mutations (L144F, I387M and Y464S) associated with DMI resistance. Additionally, a putative codon bias effect for the L144F substitution was identified that generated different resistance potentials. We also identified a CbCYP51 paralog in C. beticola, CbCYP51-like, with high protein homology to CYP51C found uniquely in Fusarium species but CbCYP51-like does not appear to influence DMI sensitivity. Genome-wide scans of selection showed that several of the GWAS mutations for fungicide resistance resided in regions that have recently undergone a selective sweep. Using radial plate growth on selected media as a fitness proxy, we did not find a trade-off associated with DMI fungicide resistance suggesting that resistance mutations can persist in C. beticola populations. Taken together, we show that population genomic data from a crop pathogen can allow the identification of mutations conferring fungicide resistance and inform about their origins in the pathogen population.

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