Jonathan C Thomas | Search PubMed

PubMed2025

Phenotype-genotype discordance in antimicrobial resistance profiles of Gram-negative uropathogens recovered from catheter-associated urinary tract infections in Egypt.

OBJECTIVES: Catheter-associated urinary tract infections (CAUTIs) are among the most common healthcare-associated infections in low- and middle-income countries (LMICs), but there are few resistome data available for relevant uropathogens. The goal of this study was to characterize the antimicrobial resistance (AMR) phenotypes and genotypes of a large collection of Gram-negative bacteria recovered from CAUTIs in a hospital in Mansoura, Egypt. METHODS: Phenotypic AMR profiles and whole-genome sequence data were generated for 132 isolates. Resistomes were predicted using ResFinder, CARD and AMRFinder. Similarity of uropathogen genomic data was determined using sourmash (kmer signatures). Escherichia coli genomic data were subject to a pangenome analysis using Panaroo. RESULTS: Sixty-seven E. coli (Phylogroup B2; 53.7%, 36/67), 14 Pseudomonas aeruginosa, 11 Klebsiella pneumoniae, 9 Proteus mirabilis, 8 Providencia spp., 5 Enterobacter hormaechei and 18 rare CAUTI-associated isolates were identified. Several (22/132) isolates were multidrug-resistant, while almost half (62/132) were extensively drug-resistant. Phenotype-genotype discordance was found to be an important consideration in resistome studies in Egypt, with a total concordance of 91% (1115/1225), 85.7% (1273/1485) and 80.5% (1196/1485) for ResFinder, CARD and AMRFinder, respectively. Pseudomonas, at the species level, exhibited the greatest discordance. At the antimicrobial level, meropenem was subject to greatest discordance. New AMR variants were found for Egypt for Pseudomonas (blaOXA-486, blaOXA-488, blaOXA-905, blaIMP-43, blaPDC-35, blaPDC-45, blaPDC-201) and E. coli (blaTEM-176, blaTEM-190). CONCLUSIONS: This study shows that there is phenotype-genotype discordance in AMR profiling among CAUTI isolates, highlighting the need for comprehensive approaches in resistome studies. We also show the genomic diversity of Gram-negative uropathogens contributing to disease burden in a little-studied LMIC setting.

Egypt↗

PubMed2006

Improved multilocus sequence typing scheme for Staphylococcus epidermidis.

We evaluated three multilocus sequence typing (MLST) schemes for Staphylococcus epidermidis and selected the seven most discriminatory loci for the formation of a new, more powerful MLST scheme. This improved scheme gave 31 sequence types (STs) and 5 clonal complexes (CCs), whereas the other schemes delineate 16 to 24 STs and 1 to 3 CCs.

Algorithms↗

PubMed2005

In vitro activity of a novel compound, the metal ion chelating agent AQ+, against clinical isolates of Staphylococcus aureus.

OBJECTIVES: To determine the efficacy of a novel antimicrobial compound, AQ+, against a genetically heterogeneous collection comprising 213 Staphylococcus aureus isolates from global sources. AQ+ is an aqueous preparation containing 0.5% 8-hydroxyquinoline. METHODS: MICs were found for all the isolates tested using the BSAC microdilution method. Time-kill studies were performed according to NCCLS guidelines. Transmission electron microscopy (TEM) was used to view the ultrastructural effects of AQ+. RESULTS: AQ+ was shown to strongly inhibit the growth of all isolates with a median MIC of 0.25% at a pH optimum of 9.2. Lowering the pH to 7.5 gave an approximately 4-fold reduction in efficacy and at pH 5.5 there was an approximately 8-fold reduction in efficacy. Methicillin-resistant S. aureus (MRSA) as well as vancomycin-intermediate S. aureus were shown to be as equally susceptible to AQ+ as methicillin-susceptible S. aureus. Time-kill curves for AQ+ were similar to those for gentamicin. TEM showed that AQ+ actively disrupts the cell wall of S. aureus leading to cell lysis. CONCLUSIONS: These results suggest that AQ+ has strong antimicrobial activity and may be useful in preparations to reduce nasal and skin carriage of MRSA.

Anti-Bacterial Agents↗