Fungal infections are a global problem imposing considerable disease burden. One of the unmet needs in addressing these infections is rapid, sensitive diagnostics. A promising molecular diagnostic approach is high-resolution melt analysis (HRM). However, there has been little effort in leveraging HRM data for automated, objective identification of fungal species. The purpose of these studies was to assess the utility of distance methods developed for comparison of time series data to classify HRM curves as a means of fungal species identification. Dynamic time warping (DTW), first introduced in the context of speech recognition to identify temporal distortion of similar sounds, is an elastic distance measure that has been successfully applied to a wide range of time series data. Comparison of HRM curves of the rDNA internal transcribed spacer (ITS) region from 51 strains of 18 fungal species using DTW distances allowed accurate classification and clustering of all 51 strains. The utility of DTW distances for species identification was demonstrated by matching HRM curves from 243 previously identified clinical isolates against a database of curves from standard reference strains. The results revealed a number of prior misclassifications, discriminated species that are not resolved by routine phenotypic tests, and accurately identified all 243 test strains. In addition to DTW, several other distance functions, Edit Distance on Real sequence (EDR) and Shape-based Distance (SBD), showed promise. It is concluded that DTW-based distances provide a useful metric for the automated identification of fungi based on HRM curves of the ITS region and that this provides the foundation for a robust and automatable method applicable to the clinical setting.

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Background: Campylobacter infections are typically self-limited, but in cases with severe enteritis, immuno-compromised system and bacteremia, an appropriate antimicrobial treatment is demanding. Our study aim was to determine the isolation rate of Campylobacter among patients with acute enteritis in the capital of North Macedonia and its antimicrobial susceptibility. Material and methods: A total number of 3820 patients clinically diagnosed as acute enteritis, were included in the study. Stool samples were collected and Campylobacter was isolated and identified by classical microbiological methods. Antimicrobial susceptibility of all isolates to Ceftriaxone, Amoxicillin-clavulonic acid, Erythromycin, Ciprofloxacin, Tetracycline and Gentamicin was determined by disc-diffusion technique. Additionally, minimal inhibitory concentrations of all Campylobacter isolates against erythromycin, ciprofloxacin and tetracycline were determined by Epsilon gradient tests. Results: Campylobacter species was isolated in 97 patients. Although the mean isolation rate of Campylobacter spp. during the whole study period was 2.53%, a statistically significant increase was detected in 2016 and 2017, in comparison with the data from previous four years of the study. The isolation rate of Campylobacter spp. didn’t reveal statistically significant difference between males and females (p > 0.05). 46.4 % of patients with Campylobacter enteritis were children at the age under 15 years. Forty-three C. jejuni isolates were susceptible to all six antibiotics, but the remaining 44 isolates revealed resistance to at least one antibiotic. C. coli isolates were resistant to 3 antibiotics simultaneously. Two C. coli isolates only, were susceptible to all 6 antibiotics. 40.90% of C. jejuni and 50% of C. coli isolates were resistant to beta-lactams, fluoroquinolones and tetracyclines, simultaneously. Conclusion: The increase of the isolation rate of Campylobacter from patients with acute enteritis indicates the need for permanent isolation and identification of Campylobacter from every clinically diagnosed patient, as acute enteritis. Erythromicin is the most effective antibiotic for treatment of Campylobacter enteritis in our patients. The high level of Campylobacter resistance to beta-lactams, fluoroquinolones and tetracyclines requires more rational approach in the treatment of Campylobacter enteritis