Biology subjects

Chilambi, G. S.

Publications and source records attributed to Chilambi, G. S..

3 recordsLinked to original sources

bioRxiv2026

Excessive sample reagent incubation time increases the risk of false rifampin resistance results in Xpert(R) MTB/RIF Ultra tests performed on paucibacillary Mycobacterium tuberculosis sputum.

A high rate of false rifampicin resistance (RIF-R) was recently reported in paucibacillary sputum samples tested with the Xpert(R) MTB/RIF Ultra (Ultra) assay. However, 96% of the studied facilities started the test 8 - 12 hours after addition of sample reagent (SR), exceeding the manufacturers recommended limit of 4 hours. Assessed whether excessive long SR incubation could lead to similar false RIF-R results in paucibacillary samples in a reference laboratory setting. We evaluated the performance of the Ultra assay following incubation of TB-negative sputum spiked with 300 CFU/mL and 100,000 CFU/mL levels of Mycobacterium tuberculosis (Mtb) H37Rv in SR for different durations (15 min to 24hrs.) at different temperatures (-20 to 370C) to determine the effect on RIF result calls. No false RIF-R results were observed in these samples with 105 CFU/mL Mtb at any of the conditions tested, even when they deviated largely from recommended limits. Similarly, freezing the 300 CFU/mL SR treated samples at minus 200C for 18 h also prevented the development of false RIF-R results. However, sputum spiked with 300 CFU/ml Mtb, produced false RIF-R calls at longer incubation times and higher incubation temperatures than are recommended by the manufacturer. Approximately half of the results displayed melt patterns consistent with hetero-resistance, indicating SR-induced mutagenesis in a wild-type background. This study demonstrates that extended off-label SR incubation of paucibacillary specimens beyond the recommended 4-hour limit can generate false RIF-R results. Freezing paucibacillary specimens in SR may mitigate this risk although it is not yet an approved procedure.

microbiology↗

bioRxiv2021

Differential ampicillin/ceftriaxone susceptibility among diverse Enterococcus faecalis from infective endocarditis

Enterococcus faecalis is a leading cause of infective endocarditis (IE), especially among older patients with comorbidities. Here we investigated the genomic diversity and antimicrobial susceptibility of 33 contemporary E. faecalis isolates from definite or probable IE cases at the University of Pittsburgh Medical Center (UPMC) between 2018 and 2020. Isolates belonging to two multi-locus sequence types (STs), ST6 and ST179, were isolated from nearly 40% of IE patients. Both of these dominant STs carried known beta-lactam resistance-associated mutations affecting the low-affinity penicillin-binding protein 4 (PBP4). We assessed the ability of ampicillin and ceftriaxone (AC) both alone and in combination to inhibit genetically diverse E. faecalis IE isolates in checkerboard synergy assays and an in vitro one-compartment pharmacokinetic-pharmacodynamic (PK-PD) model of AC treatment. ST6 isolates as well as an isolate with a mutation in the PP2C-type protein phosphatase IreP had higher ceftriaxone MICs compared to other isolates, and showed diminished in vitro synergy of AC. Additionally, both ST6 and ST179 isolates exhibited regrowth after 48 hours of humanized exposures to AC. Overall, we found evidence for diminished in vitro AC activity among E. faecalis IE isolates with PBP4 and IreP mutations. This study highlights the need to evaluate alternate antibiotic combinations in clinical practice against diverse contemporary E. faecalis IE isolates.

microbiology↗

bioRxiv2020

Genomic and phenotypic diversity of Enterococcus faecalis isolated from endophthalmitis

Enterococcus faecalis are hospital-associated opportunistic pathogens and also causative agents of post-operative endophthalmitis. Patients with enterococcal endophthalmitis often have poor visual outcomes, despite appropriate antibiotic therapy. Here we investigated the genomic and phenotypic characteristics of E. faecalis isolates collected from 13 patients treated at the University of Pittsburgh Medical Center Eye Center over 19 years. Comparative genomic analysis indicated that patients were infected with E. faecalis of diverse multi-locus sequence types (STs) previously associated with clinical, commensal, and environmental sources. We identified known E. faecalis virulence factors and antibiotic resistance genes in each genome, including genes conferring resistance to aminoglycosides, erythromycin, and tetracyclines. We assessed all isolates for their cytolysin production, biofilm formation, and antibiotic susceptibility, and observed phenotypic differences between isolates. Fluoroquinolone and cephalosporin susceptibilities were particularly variable, as were biofilm formation and cytolysin production. In addition, we found evidence of E. faecalis adaptation during recurrent endophthalmitis by identifying genetic variants that arose in sequential isolates sampled over eight-months from the same patient. We identified a mutation in the DNA mismatch repair gene mutS that was associated with a hypermutator phenotype in the final isolate from the patient, which was also more resistant to ceftazidime. Overall this study documents the genomic and phenotypic variability among E. faecalis causing endophthalmitis, as well as possible adaptive mechanisms underlying bacterial persistence during recurrent ocular infection. IMPORTANCEBacterial endophthalmitis is a sight-threatening infection of the inside of the eye. Enterococcus faecalis cause endophthalmitis occasionally, but when they do the infections are often severe. Here we investigated the genomes, antibiotic susceptibilities, and virulence-associated traits among E. faecalis collected from 13 patients with post-operative endophthalmitis. We wondered whether there were common bacterial factors that might explain why enterococcal endophthalmitis is so destructive to ocular tissues. Instead we found that E. feacalis isolated from endophthalmitis were genetically and phenotypically diverse; isolates belonged to a variety of genetic lineages and showed varying levels of antibiotic resistance and biofilm formation. We also undertook further characterization of three closely related E. faecalis isolates from a patient with recurrent endophthalmitis, and found that a hypermutator strain emerged during persistent infection. Hypermutators have been found in a variety of other infection contexts; here we describe what we believe is the first case of a hypermutator arising during ocular infection.

microbiology↗