Structure-guided functional studies of plasmid-encoded dihydrofolate reductases reveal a common mechanism of trimethoprim resistance in Gram-negative pathogens

Krucinska, J.; Lombardo, Michael N.; Erlandsen, Heidi; Estrada, Alexavier; Si, Debjani; Viswanathan, Kishore; Wright, Dennis L.

doi:10.1038/s42003-022-03384-y

Cited by 14 publications

(11 citation statements)

References 72 publications

(62 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…As expected, the majority of the class 1 integron gene cassettes we detected are AMR related. The dihydrofolate reductase encoded by dfrA5 confers high levels of trimethoprim resistance in Gram-negative bacteria . We found an association between the dfrA5 gene cassette and a Comamonadaceae- family host (Figure C).…”

Section: Resultsmentioning

confidence: 72%

“…The dihydrofolate reductase encoded by df rA5 confers high levels of trimethoprim resistance in Gram-negative bacteria. 63 We found an association between the dfrA5 gene cassette and a Comamonadaceae-family host (Figure 2C). The blaOXA 10 gene encodes a class D beta-lactamase that hydrolyses the semisynthetic antibiotic oxacillin.…”

Section: ■ Results and Discussionmentioning

confidence: 82%

See 1 more Smart Citation

Uncovering Bacterial Hosts of Class 1 Integrons in an Urban Coastal Aquatic Environment with a Single-Cell Fusion-Polymerase Chain Reaction Technology

Ghaly

Penesyan

et al. 2023

Environ. Sci. Technol.

View full text Add to dashboard Cite

Horizontal gene transfer (HGT) is a key driver of bacterial evolution via transmission of genetic materials across taxa. Class 1 integrons are genetic elements that correlate strongly with anthropogenic pollution and contribute to the spread of antimicrobial resistance (AMR) genes via HGT. Despite their significance to human health, there is a shortage of robust, culture-free surveillance technologies for identifying uncultivated environmental taxa that harbor class 1 integrons. We developed a modified version of epicPCR (emulsion, paired isolation, and concatenation polymerase chain reaction (PCR)) that links class 1 integrons amplified from single bacterial cells to taxonomic markers from the same cells in emulsified aqueous droplets. Using this single-cell genomic approach and Nanopore sequencing, we successfully assigned class 1 integron gene cassette arrays containing mostly AMR genes to their hosts in coastal water samples that were affected by pollution. Our work presents the first application of epicPCR for targeting variable, multigene loci of interest. We also identified the Rhizobacter genus as novel hosts of class 1 integrons. These findings establish epicPCR as a powerful tool for linking taxa to class 1 integrons in environmental bacterial communities and offer the potential to direct mitigation efforts toward hotspots of class 1 integron-mediated dissemination of AMR.

show abstract

Section: Resultsmentioning

confidence: 72%

Section: ■ Results and Discussionmentioning

confidence: 82%

Uncovering Bacterial Hosts of Class 1 Integrons in an Urban Coastal Aquatic Environment with a Single-Cell Fusion-Polymerase Chain Reaction Technology

Ghaly

Penesyan

et al. 2023

Environ. Sci. Technol.

View full text Add to dashboard Cite

show abstract

“…As expected, the majority of the class 1 integron gene cassettes we detected are AMR related. The dihydrofolate reductase encoded by dfrA5 confers high levels of trimethoprim resistance in Gram-negative bacteria 63 . We found an association between the dfrA5 gene cassette and a Comamonadaceae- family host (Figure 2C).…”

Section: Resultsmentioning

confidence: 99%

“…The dfrA5 gene encodes a dihydrofolate reductase that confers a high level of resistance to trimethoprim in Gram-negative bacteria 63 . It is among the most frequently observed trimethoprim resistance genes found in association with class 1 integrons 64 .…”

Section: Class 1 Gene Cassettes Detected By Epicpcrmentioning

confidence: 99%

Uncovering bacterial hosts of class 1 integrons in an urban coastal aquatic environment with a single-cell fusion-polymerase chain reaction technology

Ghaly

Penesyan

et al. 2023

Preprint

View full text Add to dashboard Cite

Horizontal gene transfer (HGT) drives bacterial evolution via transmission of genetic materials across taxa. Class 1 integrons are mobile genetic elements that correlate strongly with anthropogenic pollution and contribute to the spread of antimicrobial resistance (AMR) genes via HGT. Despite their significance to human health, there is a shortage of robust, culture-free surveillance technologies for identifying uncultivated environmental taxa that harbour class 1 integrons. We developed a modified version of the epicPCR (emulsion, paired isolation and concatenation PCR) technology that links class 1 integrons amplified from single bacterial cells to taxonomic markers from the same cells in emulsified aqueous droplets. Using this single-cell genomic approach and Nanopore long-read sequencing, we successfully assigned class 1 integron gene cassette arrays containing mostly AMR genes to their hosts in coastal water samples that were affected by urban pollution. Our work presents the first application of epicPCR for targeting variable, multi-gene loci of interest. We also identified theRhizobactergenus as novel hosts of class 1 integrons. These findings establish epicPCR as a powerful tool for linking bacterial taxa to class 1 integrons in environmental bacterial communities and offer the potential to direct mitigation efforts towards hotspots of class 1 integron-mediated dissemination of AMR.

show abstract

“…Owing to the growing drug resistance to some of the available DHFR inhibitors, research for the discovery of new and selective DHFR inhibitors has been intensely increased, using molecular modeling, synthetic techniques, in vivo and in vitro biological investigation, mechanistic studies, and structure-activity relationships [ 10 , 11 , 12 ].…”

Section: Introductionmentioning

confidence: 99%

Unveiling the Efficacy of Sesquiterpenes from Marine Sponge Dactylospongia elegans in Inhibiting Dihydrofolate Reductase Using Docking and Molecular Dynamic Studies

et al. 2023

View full text Add to dashboard Cite

Dihydrofolate reductase (DHFR) is a crucial enzyme that maintains the levels of 5,6,7,8-tetrahydrofolate (THF) required for the biological synthesis of the building blocks of DNA, RNA, and proteins. Over-activation of DHFR results in the progression of multiple pathological conditions such as cancer, bacterial infection, and inflammation. Therefore, DHFR inhibition plays a major role in treating these illnesses. Sesquiterpenes of various types are prime metabolites derived from the marine sponge Dactylospongia elegans and have demonstrated antitumor, anti-inflammation, and antibacterial capacities. Here, we investigated the in silico potential inhibitory effects of 87 D. elegans metabolites on DHFR and predicted their ADMET properties. Compounds were prepared computationally for molecular docking into the selected crystal structure of DHFR (PDB: 1KMV). The docking scores of metabolites 34, 28, and 44 were the highest among this series (gscore values of −12.431, −11.502, and −10.62 kcal/mol, respectively), even above the co-crystallized inhibitor SRI-9662 score (−10.432 kcal/mol). The binding affinity and protein stability of these top three scored compounds were further estimated using molecular dynamic simulation. Compounds 34, 28, and 44 revealed high binding affinity to the enzyme and could be possible leads for DHFR inhibitors; however, further in vitro and in vivo investigations are required to validate their potential.

show abstract

Structure-guided functional studies of plasmid-encoded dihydrofolate reductases reveal a common mechanism of trimethoprim resistance in Gram-negative pathogens

Cited by 14 publications

References 72 publications

Uncovering Bacterial Hosts of Class 1 Integrons in an Urban Coastal Aquatic Environment with a Single-Cell Fusion-Polymerase Chain Reaction Technology

Uncovering Bacterial Hosts of Class 1 Integrons in an Urban Coastal Aquatic Environment with a Single-Cell Fusion-Polymerase Chain Reaction Technology

Uncovering bacterial hosts of class 1 integrons in an urban coastal aquatic environment with a single-cell fusion-polymerase chain reaction technology

Unveiling the Efficacy of Sesquiterpenes from Marine Sponge Dactylospongia elegans in Inhibiting Dihydrofolate Reductase Using Docking and Molecular Dynamic Studies

Contact Info

Product

Resources

About