Chowdhary, A. | Search bioRxiv

bioRxiv2018

Correlation of in vitro susceptibility based on MICs and SQLE mutations with clinical response to terbinafine in patients with tinea corporis/cruris

Recalcitrant dermatophytoses are on the rise and recent publications have documented high minimum inhibitory concentrations (MICs) to TRB and squalene epoxidase (SQLE) mutations. However, literature correlating the laboratory the data with clinical response is lacking.\n\nThis study was conducted to study the clinico-mycological profile of tinea corporis and cruris, including antifungal susceptibility testing (AFST) and SQLE mutation analysis and correlate these with clinical response to TRB. Skin scrapings of patients with tinea corporis with/without tinea cruris were subjected to species identification, AFST and SQLE gene analysis (on 15 isolates). KOH confirmed cases were started on TRB 250mg once a day (OD). If >50% clinical clearance was achieved by 3 weeks; the same dose was continued.(Group 1). If clinical clearance at 3 weeks was <50%, the dose was increased to 250mg twice a day (BD) (Group 2). If the response still remained below 50% after 3 weeks of BD, the patients were treated with itraconazole (ITR)(Group 3). Trichophyton interdigitale was confirmed on all 64 isolates obtained on culture. Forty four (68.7%) isolates had high ([≥]1 g/ml) MICs to TRB. Six isolates were found to have aminoacid substitution Leu393Phe in SQLE protein, while one had the substitution Phe397Leu. The difference in modal MICs to TRB between the 3 clinical response groups (1.5157g/ml, 5.0396 g/ml and 20.1587g/ml respectively for group 1,2 and 3) was highly significant. Clinical response was achieved in 68% of those resistant by MIC data, and 42.8% of SQLE mutation harboring isolates, by increasing drug (TRB) exposure.\n\nWe infer that TRB resistance in dermatophytes has reached alarming proportions in our patients. Though improved outcomes were achieved with higher drug exposure, with the high failure rate seen in the study, the case for shifting to another class of antifungals as first line agent against dermatophytoses is strong.

microbiology↗

bioRxiv2017

Population Genomics Of Cryptococcus neoformans var. grubii Reveals New Biogeographic Relationships And Finely Maps Hybridization

Cryptococcus neoformans var. grubii is the causative agent of cryptococcal meningitis, a significant source of mortality in immunocompromised individuals, typically HIV/AIDS patients from developing countries. Despite the worldwide emergence of this ubiquitous infection, little is known about the global molecular epidemiology of this fungal pathogen. Here we sequence the genomes of 188 diverse isolates and characterized the major subdivisions, their relative diversity and the level of genetic exchange between them. While most isolates of C. neoformans var. grubii belong to one of three major lineages (VNI, VNII, and VNB), some haploid isolates show hybrid ancestry including some that appear to have recently interbred, based on the detection of large blocks of each ancestry across each chromosome. Many isolates display evidence of aneuploidy, which was detected for all chromosomes. In diploid isolates of C. neoformans var. grubii (serotype A/A) and of hybrids with C. neoformans var. neoformans (serotype A/D) such aneuploidies have resulted in loss of heterozygosity, where a chromosomal region is represented by the genotype of only one parental isolate. Phylogenetic and population genomic analyses of isolates from Brazil revealed that the previously African VNB lineage occurs naturally in the South American environment. This suggests migration of the VNB lineage between Africa and South America prior to its diversification, supported by finding ancestral recombination events between isolates from different lineages and regions. The results provide evidence of substantial population structure, with all lineages showing multi-continental distributions demonstrating the highly dispersive nature of this pathogen.\n\nAuthor SummaryCryptococcus neoformans var. grubii is a human fungal pathogen of immunocompromised individuals that has global clinical impact, causing half a million deaths per year. Substantial genetic substructure exists for this pathogen, with two lineages found globally (VNI, VNII) whereas a third has appeared confined to sub-Saharan Africa (VNB). Here, we utilized genome sequencing of a large set of global isolates to examine the genetic diversity, hybridization, and biogeography of these lineages. We found that while the three major lineages are well separated, recombination between the lineages has occurred, notably resulting in hybrid isolates with segmented ancestry across the genome. In addition, we showed that isolates from South America are placed within the VNB lineage, formerly thought to be confined to Africa, and that there is phylogenetic separation between these geographies that substantially expands the diversity of these lineages. Our findings provide a new framework for further studies of the dynamics of natural populations of C. neoformans var. grubii.

genomics↗