Biology subjects

Eladawy, M.

Publications and source records attributed to Eladawy, M..

4 recordsLinked to original sources

bioRxiv2025

Growth of Gram-negative uropathogens in human urine under hypoxic conditions produces clinically relevant metabolomic profiles

BackgroundMuch work on uropathogens is done in rich laboratory media that do not reflect the nutrient availability of urine. Also, the environment of the bladder is microaerobic ([~]5 % O2) but routine laboratory work with uropathogens is done under aerobic conditions. AimsTo understand the influence of oxygen conditions (aerobic, microaerobic) and physiologically relevant growth substrates (artificial urine, human urine) on the ability of bacteria isolated from catheter-associated urinary tract infections (CAUTIs) to form biofilms, and to begin to define the CAUTI bacterial metabolome. MethodsBiofilm assays were conducted in rich lab medium (tryptone soy broth supplemented with glucose), and commercially available artificial and pooled human urine for 29 well-characterized uropathogens representing five different genera of Gram-negative bacteria. Spent media were collected and analysed using 400 MHz 1H-NMR, to quantify major metabolites produced by uropathogens in artificial urine and human urine. FindingsThere was a significant decrease in biofilm formation for all uropathogens when grown in physiologically relevant growth substrates. Untargeted metabolomic analyses of artificial and human urine showed the artificial urine used in this study did not recapitulate the complexity of major metabolites present in human urine. Further analyses of spent human urine highlighted significant increases in acetate production by the uropathogens when they were grown under microaerobic compared with aerobic conditions. ConclusionsGrowth of uropathogenic Enterobacteriaceae under physiologically relevant conditions (i.e. human urine, 5 % O2) generates data more relevant to clinical disease and is an important consideration for future work on bacteria causing urinary tract infections.

microbiology↗

bioRxiv2025

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

Catheter-associated urinary tract infections (CAUTIs) are among the most common healthcare-associated infections in low- and middle-income countries (LMICs). In this study, phenotypic (EUCAST AMR profiles) and genomic data were generated for 132 isolates (67 Escherichia coli, 14 Pseudomonas aeruginosa, 11 Klebsiella pneumoniae, 9 Proteus mirabilis, 8 Providencia spp., 5 Enterobacter hormaechei, and 18 rare uropathogens) recovered from CAUTIs in an Egyptian hospital. Among the Escherichia coli isolates, phylogroup B2 was most represented (53.7 %), followed by B1 (19.4 %), A (11.9 %), D (7.4 %), F (5.9 %) and C (1.4 %). Several (22/132, 16.6 %) isolates were multidrug-resistant, while almost half (62/132, 46.9 %) were extensively drug-resistant. Comparison of phenotypic data with genotypic data from three different AMR-profiling tools (ResFinder, CARD, AMRFinder) highlighted phenotype-genotype discordance as an important consideration in resistome studies in Egypt, with a total concordance of 91.1 %, 85.7 %, and 80.3 % 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. In addition to the findings from our comparative analyses, new AMR variants are reported for Egypt for Pseudomonas (OXA-486, OXA-488, OXA-905, IMP-43, PDC-35, PDC-45, PDC-201) and Escherichia coli (TEM-176, TEM-190). In summary, we show 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.

microbiology↗

bioRxiv2023

Phenotypic and genomic characterization of Pseudomonas aeruginosa isolates recovered from catheter-associated urinary tract infections in an Egyptian hospital

Catheter-associated urinary tract infections (CAUTIs) represent one of the major healthcare-associated infections, and Pseudomonas aeruginosa is a common Gram-negative bacterium associated with catheter infections in Egyptian clinical settings. The present study describes the phenotypic and genotypic characteristics of 31 P. aeruginosa isolates recovered from CAUTIs in an Egyptian hospital over a 3-month period. Genomes of isolates were of good quality and were confirmed to be P. aeruginosa by comparison to the type strain (average nucleotide identity, phylogenetic analysis). Clonal diversity among the isolates was determined; eight different sequence types were found (STs 244, 357, 381, 621, 773, 1430, 1667 and 3765), of which 357 and 773 are considered high-risk clones. Antimicrobial resistance (AMR) testing according to EUCAST guidelines showed the isolates were highly resistant to quinolones [ciprofloxacin (12/31, 38.7 %) and levofloxacin (9/31, 29 %) followed by tobramycin (10/31, 32.5 %)], and cephalosporins (7/31, 22.5 %). Genotypic analysis of resistance determinants predicted all isolates to encode a range of AMR genes, including those conferring resistance to aminoglycosides, {beta}-lactamases, fluoroquinolones, fosfomycin, sulfonamides, tetracyclines and chloramphenicol. One isolate was found to carry a 422,938 bp pBT2436-like megaplasmid encoding OXA-520, the first report from Egypt of this emerging family of clinically important mobile genetic elements. All isolates were able to form biofilms, and were predicted to encode virulence genes associated with adherence, antimicrobial activity, antiphagocytosis, phospholipase enzymes, iron uptake, proteases, secretion systems, and toxins. The present study shows how phenotypic analysis alongside genomic analysis may help us understand the AMR and virulence profiles of P. aeruginosa contributing to CAUTIs in Egypt.

microbiology↗

bioRxiv2023

Phage vB_KmiS-Kmi2C infects members of the Klebsiella oxytoca complex and represents a novel genus of lytic bacteriophage

AIMSThis study aimed to characterise the lytic phage vB_KmiS-Kmi2C, isolated from sewage water on a GES-positive strain of Klebsiella michiganensis. METHODS AND RESULTSComparative phylogenetic and network-based analyses were used to characterise the genome of phage vB_KmiS-Kmi2C (circular genome of 42,234 bp predicted to encode 55 genes), demonstrating it shared little similarity with other known phages. The phage was lytic on clinical strains of K. oxytoca (n=2) and K. michiganensis (n=4), and was found to both prevent biofilm formation and disrupt established biofilms produced by these strains. CONCLUSIONSWe have identified a phage capable of killing clinically relevant members of the Klebsiella oxytoca complex (KoC). The phage represents a novel virus family (proposed name Dilsviridae) and genus (proposed name Dilsvirus). SIGNIFICANCE AND IMPACT OF THE STUDYIdentification a novel lytic phage active against clinically relevant strains of the KoC provides an alternative to antibiotics to treat these increasingly antimicrobial-resistant opportunistic pathogens. The unusual way in which the phage can disrupt established biofilms may allow us to identify novel phage-based approaches for biofilm remediation in the future.

microbiology↗