Genome-wide identification of genes required for alternative peptidoglycan cross-linking in Escherichia coli revealed unexpected impacts of β-lactams

Voedts, Henri; Kennedy, Sean; Sezonov, Guennadi; Arthur, Michel; Hugonnet, Jean-Emmanuel

doi:10.1038/s41467-022-35528-3

Cited by 16 publications

(12 citation statements)

References 72 publications

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“…Mutations causing accumulation of UndP-O-antigen and UndP-enterobacterial common antigen intermediates in E. coli 55,56 and Shigella exneri 57 are known to cause substantial morphological defects from insu cient peptidoglycan synthesis. While, β-lactam susceptibility has been observed in large-scale screens for disruptions in UndP utilisation pathways in A. baylyi 32 , Vibrio cholerae 76 , P. aeruginosa 77,78 , and E. coli 79 ; we are the rst to validate these interactions with targeted genetic and chemical investigations.…”

Section: Discussionmentioning

confidence: 86%

Profiling cell envelope-antibiotic interactions reveals vulnerabilities to β-lactams in a multidrug-resistant bacterium

Hogan

Natarajan

Maydaniuk

et al. 2023

Preprint

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The cell envelope of the Gram-negative Burkholderia cepacia complex (Bcc) presents unique restrictions to antibiotic penetration. As a consequence, Bcc species are notorious for causing recalcitrant multidrug-resistant infections in immunocompromised individuals, such as those living with cystic fibrosis. To systematically identify cell envelope-associated resistance and susceptibility determinants at the genome level, we constructed a high-density, randomly-barcoded transposon mutant library in the clinical isolate B. cenocepacia K56-2 and exposed it to a panel of more than twenty cell envelope-targeting antibiotics. By quantifying relative mutant fitness with BarSeq, followed by validation with CRISPR-interference, we profiled over a hundred new functional associations and identified novel mediators of antibiotic susceptibility in the Bcc cell envelope. We revealed new connections between β-lactam susceptibility, peptidoglycan synthesis, and blockages in undecaprenyl phosphate metabolism, which highlight a vulnerability in sharing this lipid intermediate. We then show that the clinically relevant synergy of the β-lactam/β-lactamase inhibitor combination ceftazidime/avibactam is primarily mediated by inhibition of the PenB carbapenemase. Importantly, we found that avibactam more strongly potentiates the activity of aztreonam and meropenem than ceftazidime in a panel of Bcc clinical isolates. Finally, we characterize for first time in the Bcc the iron and receptor-dependent activity of the novel siderophore-cephalosporin antibiotic, cefiderocol. Overall, our work has implications for antibiotic target prioritization, and for using additional combinations of β-lactam/β-lactamase inhibitors that can extend the utility of our current clinical arsenal of antibacterial therapies.

show abstract

Section: Discussionmentioning

confidence: 86%

Profiling cell envelope-antibiotic interactions reveals vulnerabilities to β-lactams in a multidrug-resistant bacterium

Hogan

Natarajan

Maydaniuk

et al. 2023

Preprint

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“…We, therefore, identified a set of core mutant PRGs ( n = 131) contributing to high-level resistance evolution through the phenotype-genotype atlas. In addition to the well-characterized ARGs, e.g., pdeR involved in biofilm formation 38 , ycjV involved in efflux pump 35,39 , MJ1187 involved in drug inactivation 40 , yafK involved in target bypass 41,42 , and yjiR involved in transcriptional reprogramming 43 , others may confer high-level resistance via unreported mechanisms, e.g., metH , ynfB , ulaG , ftsK , rtcR , and hflK . By locating these understudied core mutant PRGs in the gene co-fitness interaction network and analyzing the functions of interacted genes, their resistance mechanisms were proposed.…”

Section: Discussionmentioning

confidence: 99%

High-Throughput Evolution Unravels Landscapes of High-Level Antibiotic Resistance Induced by Low-Level Antibiotic Exposure

Wang,

Lu,

Jiang

et al. 2023

Preprint

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Potential pathogens exposed to low-level environmental antibiotics could develop high-level clinically relevant antibiotic resistance detrimental to the health of the general population. However, the underlying evolutionary landscapes remain poorly understood. We conducted a high-throughput experimental evolution study by exposing an environmentally isolated pathogenicEscherichia colistrain to 96 typical antibiotics at 10 μg l−1for 20 days. Antibiotic resistance phenotypic (IC90against 8 clinically used antibiotics) and genetic changes of the evolved populations were systematically investigated, revealing a universal increase in antibiotic resistance (up to 349-fold), and mutations in 2,432 genes. Transposon sequencing was further employed to verify genes potentially associated with resistance. A core set of mutant genes conferring high-level resistance was analyzed to elucidate their resistance mechanisms by analyzing the functions of interacted genes within the gene co-fitness network and performing gene knockout validations. We developed machine-learning models to predict antibiotic resistance phenotypes from antibiotic structures and genomic mutations, enabling the resistance predictions for another 569 antibiotics. Importantly, 14.6% of the 481 key mutations were observed in clinical and environmentalE. coliisolates retrieved from the NCBI database, and several were over-represented in clinical isolates. Deciphering the evolutionary landscapes underlying resistance exposed to low-level environmental antibiotics is crucial for evaluating the emergence and risks of environment-originated clinical antibiotic resistance.

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“…Mutations causing accumulation of UndP-O-antigen and UndP-enterobacterial common antigen intermediates in E. coli [55, 56] and Shigella flexneri [57] are known to cause substantial morphological defects from insufficient peptidoglycan synthesis. While, β-lactam susceptibility has been observed in large-scale screens for disruptions in UndP utilisation pathways in A. baylyi [32], Vibrio cholerae [76], P. aeruginosa [77, 78], and E. coli [79]; we are the first to validate these interactions with targeted genetic and chemical investigations.…”

Section: Discussionmentioning

confidence: 99%

Profiling cell envelope-antibiotic interactions reveals vulnerabilities to β-lactams in a multidrug-resistant bacterium

Hogan

Maydaniuk

Natarajan

et al. 2022

Preprint

View full text Add to dashboard Cite

The cell envelope of the Gram-negativeBurkholderia cepaciacomplex (Bcc) presents unique restrictions to antibiotic penetration. As a consequence, Bcc species are notorious for causing recalcitrant multidrug-resistant infections in immunocompromised individuals, such as those living with cystic fibrosis. To systematically identify cell envelope-associated resistance and susceptibility determinants at the genome level, we constructed a high-density, randomly-barcoded transposon mutant library in the clinical isolateB. cenocepaciaK56-2 and exposed it to a panel of more than twenty cell envelope-targeting antibiotics. By quantifying relative mutant fitness with BarSeq, followed by validation with CRISPR-interference, we profiled over a hundred new chemical-genetic interactions and identified novel mediators of antibiotic susceptibility in the Bcc cell envelope. We first reveal new connections between broad-spectrum β-lactam susceptibility, peptidoglycan synthesis, and blockages in undecaprenyl phosphate metabolism, highlighting a β-lactam critical vulnerability associated with sharing this common lipid intermediate. We then show that the clinically relevant synergy of the β-lactam/ β-lactamase inhibitor combination ceftazidime/avibactam is primarily mediated by inhibition of the PenB carbapenemase, over more than twenty other putative β-lactamases. Importantly, avibactam more strongly potentiates the activity of aztreonam and meropenem than ceftazidime in a panel of Bcc clinical isolates. Finally, we characterize for first time in the Bcc the iron and receptor-dependent activity of the novel siderophore cephalosporin antibiotic, cefiderocol. Overall, our work has implications for antibiotic target prioritization, and for using additional combinations of β-lactam/ β-lactamase inhibitors that can extend the utility of our current clinical arsenal of antibacterial therapies.

show abstract

Genome-wide identification of genes required for alternative peptidoglycan cross-linking in Escherichia coli revealed unexpected impacts of β-lactams

Cited by 16 publications

References 72 publications

Profiling cell envelope-antibiotic interactions reveals vulnerabilities to β-lactams in a multidrug-resistant bacterium

Profiling cell envelope-antibiotic interactions reveals vulnerabilities to β-lactams in a multidrug-resistant bacterium

High-Throughput Evolution Unravels Landscapes of High-Level Antibiotic Resistance Induced by Low-Level Antibiotic Exposure

Profiling cell envelope-antibiotic interactions reveals vulnerabilities to β-lactams in a multidrug-resistant bacterium

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