Biology subjects

Daley, C. L.

Publications and source records attributed to Daley, C. L..

3 recordsLinked to original sources

bioRxiv2025

Antibiotic dose-response curves can measure antibiotic activity against Mycobacterium abscessus and Mycobacterium peregrinum

Mycobacterium abscessus is a drug-resistant pathogen associated with poor clinical outcomes despite treatment with multidrug antibiotic regimens. Apart from clarithromycin, antimicrobial susceptibility testing (AST) results for Mycobacterium abscessus cannot guide antibiotic selection. AST involves measuring the minimum inhibitory concentration (MIC), which is allowed to span a four-fold range in concentration. This accepted variability of the MIC limits the clinical utility of AST. Antimicrobial dose-response curves, obtained by measuring the growth inhibition of a given organism to increasing concentrations of an antibiotic, can yield metrics of antibiotic activity that are less variable than the MIC. We used Clinical and Laboratory Standards Institute growth conditions for rapid-grower nontuberculous mycobacteria to generate 990 dose-response curves across three time points (72 hours, 96 hours, and 120 hours) for six guideline-recommended (clarithromycin, amikacin, cefoxitin, linezolid, tigecycline, and clofazimine) and five new (omadacycline, tedizolid, SPR719, SQ109, and bedaquiline) antibiotics against Mycobacterium abscessus subspecies abscessus ATCC 19977 and Mycobacterium peregrinum ATCC 700686. We established the fit of the dose-response curve (R2) as a quality control metric. Using the geometric standard deviation and median coefficient of variation, we demonstrated that the IC50 and IC75 (antibiotic concentrations corresponding to 50% and 75% growth inhibition, respectively) are less variable than the MIC. We identified time-dependent changes in dose-response curve metrics that allow the detection of inducible clarithromycin resistance with only five days of incubation. This study demonstrates the potential of dose-response curves in measuring antibiotic activity against Mycobacterium abscessus.

microbiology↗

bioRxiv2023

Synergistic Effects of Sulopenem in Combination with Cefuroxime or Durlobactam against Mycobacterium abscessus

Mycobacterium abscessus (Mab) affects patients with immunosuppression, Cystic Fibrosis (CF), or underlying structural lung diseases. Additionally, Mab poses clinical challenges due to its resistance to multiple antibiotics. Herein, we investigated the synergistic effect of dual {beta}-lactams [sulopenem and cefuroxime (CXM)] or the combination of sulopenem and CXM with a {beta}-lactamase inhibitors [BLI; avibactam (AVI) or durlobactam (DUR)]. The sulopenem-CXM combination yielded low minimum inhibitory concentration MIC values for 54 clinical Mab isolates and ATCC19977 (MIC50 and MIC90 [≤] 0.25 g/mL). Similar synergistic effects were observed in time-kill studies conducted at concentrations achievable in clinical settings. Sulopenem-CXM outperformed monotherapy, yielding [~]1.5 Log10 CFU/mL reduction during 10 days. Addition of BLIs enhanced this antibacterial effect, resulting in additional reduction of CFUs ([~]3 Log10 for sulopenem-CXM and AVI and [~]4 Log10 for sulopenem-DUR). Exploration of the potential mechanisms of the synergy focused on their interactions with L,D-transpeptidases (LDTs; LDTMab1-LDTMab4), Penicillin-Binding-Protein B (PBP-B), and D,D-Carboxypeptidase (DDC). Acyl complexes identified via mass spectrometry analysis, demonstrated the binding of sulopenem with LdtMab2-LdtMab4, DDC, and PBP B, and CXM with LdtMab2 and PBP-B. Molecular docking suggested formation of a covalent adduct between sulopenem and LdtMab2 after the nucleophilic attack of the cysteine residue at the {beta}-lactam carbonyl carbon, leading to the cleavage of the {beta}-lactam ring, and the establishment of a thioester bond linking the LdtMab2 with sulopenem. In conclusion, we demonstrated the biochemical basis of the synergy of sulopenem-CXM with or without BLI. These findings potentially broaden selection of oral therapeutic agents to combat Mab.

microbiology↗

bioRxiv2019

Population Genomics of Nontuberculous Mycobacteria Recovered from United States Cystic Fibrosis Patients

Nontuberculous mycobacteria (NTM) pose a threat to individuals with cystic fibrosis (CF) due to an increased prevalence of pulmonary infections, innate drug resistance of the bacteria, and potential transmission between CF patients. To explore the genetic diversity of NTM isolated from CF patients within the United States (US) and to identify potential transmission events, we sequenced and analyzed the genomes of 341 NTM isolates from 191 CF patients as part of a nationwide surveillance study. The most abundant species in the isolate cohort were Mycobacterium abscessus (59.5%), followed by species in the Mycobacterium avium complex (37.5%). Phylogenomic analyses of the three M. abscessus subspecies revealed that more than half of CF patients had isolates in one of four dominant clones, including two dominant clones of M. abscessus subspecies abscessus and two dominant clones of M. abscessus subspecies massiliense. M. avium isolates from US CF patients, however, do not have dominant clones and are phylogenetically diverse. Longitudinal NTM isolates were compared to determine genome-wide single nucleotide polymorphisms (SNPs) that occur within patients over time. This information was used to compare between and within-patient SNP distributions, to quantitatively define SNP thresholds suggestive of transmission, and calculate a posterior probability of recent transmission given the SNP distance between two isolates from different patients. Out of 114 patients with M. abscessus subspecies, ten clusters of highly similar isolates from 26 patients were identified. Among the 26 patients in the M. abscessus clusters, 12 attended the same CF care centers. No highly similar isolate clusters were observed in M. avium. Our study reveals the contrasting genomic diversity and epidemiology of two major NTM taxa and the potential for between-patient exposure and cross-transmission of these emerging pathogens.

microbiology↗