Systems-level analysis of NalD mutation, a recurrent driver of rapid drug resistance in acute Pseudomonas aeruginosa infection

Abstract

Pseudomonas aeruginosa, a main cause of human infection, can gain resistance to the antibiotic aztreonam through a mutation in NalD, a transcriptional repressor of cellular efflux. Here we combine computational analysis of clinical isolates, transcriptomics, metabolic modeling and experimental validation to find a strong association between NalD mutations and resistance to aztreonam-as well as resistance to other antibiotics-across P. aeruginosa isolated from different patients. A detailed analysis of one patient's timeline shows how this mutation can emerge in vivo and drive rapid evolution of resistance while the patient received cancer treatment, a bone marrow transplantation, and antibiotics up to the point of causing the patient's death. Transcriptomics analysis confirmed the primary mechanism of NalD action-a loss-of-function mutation that caused constitutive overexpression of the MexAB-OprM efflux system-which lead to aztreonam resistance but, surprisingly, had no fitness cost in the absence of the antibiotic. We constrained a genome-scale metabolic model using the transcriptomics data to investigate changes beyond the primary mechanism of resistance, including adaptations in major metabolic pathways and membrane transport concurrent with aztreonam resistance, which may explain the lack of a fitness cost. We propose that metabolic adaptations may allow resistance mutations to endure in the absence of antibiotics and could be targeted by future therapies against antibiotic resistant pathogens.

Compilation of longitudinal microbiota data and hospitalome from hematopoietic cell transplantation patients

“…6 ). This risk may be specific to transplant recipients damaged by conditioning regimen with injury to the intestinal barrier that could facilitate the translocation of pathogens from the gut into the blood 40 . Still, allo-HCT patients provide a unique opportunity to study microbiota dynamics in such extreme situations.…”

An atlas of the binding specificities of transcription factors in Pseudomonas aeruginosa directs prediction of novel regulators in virulence

“…Using a crystal violet assay, we confirmed that the depletion of known regulators such as AmrZ, FleQ or PA0191 significantly affected biofilm formation (Figure 2-figure supplement 4B). Similar to other prokaryotic TFs, both activating or repressing phenotypes could be observed upon manipulating TF binding in P. aeruginosa (73,(84)(85)(86)(87)(88)(89)(90)(91). However, we observed that most mutant strains did not show an overt biofilm-associated phenotype, even those of some previously known positive TFs such as RsaL (92), CprR (46), AlgB (76,93), CdpR (75), BqsR (Synonym: CarR) (71, 72) and PA3782 (63).…”

“…Using a crystal violet assay, we confirmed that the depletion of known regulators such as AmrZ, FleQ, or PA0191 significantly affected biofilm formation ( Figure 2—figure supplement 4B ). Similar to other prokaryotic TFs, both activating and repressing phenotypes could be observed upon manipulating TF binding in P. aeruginosa ( Yang et al, 2019 ; Poole et al, 1996 ; Kawalek et al, 2019 ; Ha et al, 2004 ; Wu and Jin, 2005 ; Jin et al, 2011 ; Daddaoua et al, 2017 ; Chugani et al, 2001 ; Yan et al, 2019 ). However, we observed that most mutant strains did not show an overt biofilm-associated phenotype, even some of those previously known biofilm-regulatory TFs such as RsaL ( Rampioni et al, 2009 ), CprR ( Badal et al, 2020 ), AlgB ( Chand et al, 2012 ; Mukherjee et al, 2019 ), CdpR ( Zhao et al, 2016 ), BqsR (Synonym: CarR) ( Guragain et al, 2016 ; Sarkisova et al, 2005 ), and PA3782 ( Finelli et al, 2003 ).…”

Coming from the Wild: Multidrug Resistant Opportunistic Pathogens Presenting a Primary, Not Human-Linked, Environmental Habitat

“…For instance, mutations in genes encoding regulators of MDR efflux pumps can lead to the overexpression of the latter and, as a consequence, a more efficient extrusion of drugs. In the case of mexAB-oprM, overexpression may be due to mutations in the gene that encodes its local repressor, MexR, or in genes encoding other secondary regulators, NalC or NalD, events that have been reported in vivo [ 63 , 64 ]. Similarly, mexCD-oprJ and mexXY-oprM overexpression could be driven by spontaneous mutations in genes encoding their repressors, NfxB and MexZ, respectively [ 63 , 65 ].…”