Molecular Characterization of Candida auris Isolates at a Major Tertiary Care Center in Lebanon.

BACKGROUND: The globally emerging Candida auris pathogens poses heavy burden to the healthcare system. Their molecular analyses assist in understanding their epidemiology, dissemination, treatment, and control. This study was warranted to describe the genomic features and drug resistance profiles using whole genome sequencing (WGS) among C. auris isolates from Lebanon. METHODS: A total of 28 C. auris clinical isolates, from different hospital units, were phenotypically identified by matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) and tested for antifungal resistance using Vitek-2 system and E test. The complete genomes were determined by WGS using long reads sequencing (PacBio) to reveal the clade distribution and antifungal resistance genes. RESULTS: Candida auris revealed uniform resistance to fluconazole and amphotericin B, with full susceptibility to echinocandins. Among key resistance genes studied, only two mutations were detected: Y132F in ERG11 gene and a novel mutation, D709E, found in CDR1 gene encoding for an ABC efflux pump. Phylogenetically, C. auris genomes belonged to South Asian clade I and showed limited genetic diversity, suggesting person to person transmission. CONCLUSION: This characterization of C. auris isolates from Lebanon revealed the exclusivity of clade I lineage together with uniform resistance to fluconazole and amphotericin B. The control of such highly resistant pathogen necessitates an appropriate and rapid recovery and identification to contain spread and outbreaks.

A reflection on bacterial resistance to antimicrobial agents at a major tertiary care center in Lebanon over a decade.

BACKGROUND: Antimicrobial resistance has been inflecting deleterious health and economic consequences locally and globally. This study addresses the patterns and trends of bacterial resistance to antimicrobial agents over a decade, at a major tertiary care center in Beirut. METHODS: Data on bacterial susceptibility patterns at the CAP accredited Clinical Microbiology Laboratory is analyzed from January 2000 to November 2011, along with related different studies conducted during this period. RESULTS: Increasing rates of ESBL-producing isolates were noted for Escherichia coli, Klebsiella pneumoniae, Salmonella spp. and Shigella spp. Resistance to carbapenems remains problematic in Acinetobacter spp, and Pseudomonas aeruginosa, and started emerging in E. coli and K. pneumoniae. Tigecycline and colistin maintained excellent activity against most ESBL and carbapenem resistant bacteria relevant to the treatment by these agents. Resistance to quinolones is being encountered in Streptococcus pneumoniae, Haemophilus influenzae, Salmonella spp. and Shigella spp. Methicillin resistant Staphylococcus aureus (MRSA), though remaining relatively high, showed decreasing trends of resistance, while vancomycin maintain uniform activity. Rare and sporadic vancomycin resistant strains in enterococci are encountered. Macrolide and clindamycin increasing rates of resistance is noted in S. pneumoniae, group A streptococci, S. aureus, viridans streptococci and some others. CONCLUSION: Physicians should be aware of the local epidemiology of antimicrobial resistance to properly guide the initial therapy. These resistance problems can be attributed to uncontrolled use of antimicrobial agents, thus, highlighting the need for antimicrobial stewardship to curb this threat.