Biology subjects

Szita, G.

Publications and source records attributed to Szita, G..

4 recordsLinked to original sources

bioRxiv2023

Bacterial colony size growth estimation by deep learning

The bacterial growth rate is important for pathogenicity and food safety. Therefore, the study of bacterial growth rate over time can provide important data from a medical and veterinary point of view. We trained convolutional neural networks (CNNs) on manually annotated solid medium cultures to detect bacterial colonies as accurately as possible. Predictions of bacterial colony size and growth rate were estimated from image sequences of independent Staphylococcus aureus cultures using trained CNNs. A simple linear model for control cultures with less than 150 colonies estimated that the mean growth rate was 60.3 m/h for the first 24 h. Analyzing with a mixed effect model that also takes into account the effect of culture, smaller values of change in colony size were obtained (control: 51.0 m/h, rifampicin pretreated: 36.5m/h). An increase in the number of neighboring colonies clearly reduces the colony growth rate in the control group but less typically in the rifampicin-pretreated group. Based on our results, CNN-based bacterial colony detection and the subsequent analysis of bacterial colony growth dynamics might become an accurate and efficient tool for bacteriological work and research.

bioinformatics↗

bioRxiv2020

A glimpse of antimicrobial resistance gene diversity in kefir and yoghurt

Antimicrobial resistance (AMR) is a global threat gaining more and more practical significance every year. The protection of bacteria against antimicrobials based on antimicrobial resistance genes (ARGs) developed in evolution. One of the essential clinical questions is the origin of ARGs of pathogen bacteria. Since the bacteria can share genetic components by horizontal gene transfer (HGT), all even non-pathogen bacteria may provide ARG to any pathogens when they became close physically. The bacteria of the human gut may make contact with bacteria entered into the body by food. The fermented food contains bacteria in high amount by its nature. Here we studied the diversity of ARG content by a unified metagenomic approach in various kefir and yoghurt products, in grain and isolated bacterial strains. We found numerous ARGs of commonly used fermenting bacteria with diversity characteristics in kefir and yoghurt samples. Even with the strictest filter restrictions we identified ARGs undermining the efficacy of aminocoumarin, aminoglycoside, carbapenem, cephalosporin, cephamycin, diaminopyrimidine, elfamycin, fluoroquinolone, fosfomycin, glycylcycline, lincosamides, macrolide, monobactam, nitrofuran, nitroimidazole, penam, penem, peptide, phenicol, rifamycin, tetracycline and triclosan. In the case of gene lmrD, we detected genetic environment providing mobility of this ARG. Our findings support that theory during the fermentation process the food ARG content can grow by the bacteria multiplication. Results presented suggest that starting culture strains of fermented food should be monitored and selected to decrease the ARG amount intake by nutrition.

genomics↗

bioRxiv2020

Semiautomated Detection Of Pseudomonas aeruginosa From Diverse Water Samples Using Highly Selective Z-Broth And Redoxpotential Monitor

Pseudomonas aeruginosa is a facultative bacterial pathogen with increasing public health risk potential. Contaminated water in hospital environments is a growing cause of multidrug-resistent P. aeruginosa nosocomial infections that are life-threatening and are costly to treat. P. aeruginosa is common in natural water bodies, but it is not unusual in drinking water and has been detected in bottled water, also. Suppliers in Europe must eliminate live forms of the bacterium in drinking water to meet human consumption requirements. Laboratory testing for the presence of viable P. aeruginosa is mostly done manually using culture media but conductance/impedimetry measurements for detection are also available. In order to improve expedience and cost efficiency as well as to automate the detection and the data registration, we applied the highly selective Z-broth culture media and redox potential monitoring to detect P. aeruginosa from water. The Z-broth is based on only a few, stable chemicals that provide consistency of quality and long shelf life. It limits growth to P. aeruginosa and, thus, eliminates the need for subsequent microbiological identification steps of the European Standard procedure defined in ISO 16 266:2006 (2018). A redox potential monitor was used in this work, that simultaneously recorded 64 sample curves and automatically marked positive samples reliably within 24 hours after sample initialization. In comparison, the standard method requires additional tests that prolongs identification to some days. Practical applicability and reliability of the method in this paper was demonstrated by testing a total of 739 water samples of which 222 were tap water, 342 well water and 145 had been taken from swimming pools. It is considered this method is well suited to process large numbers of samples for purposes of detecting P. aeruginosa contamination with relative ease, little cost in shortened time. Using Z-broth in combination with redox potential monitoring can be recommended for central laboratories for routine testing of drinking water for live P. aeruginosa presence. As well, using this method for testing of fluids and surfaces for P. aeruginosa contamination would be advantageous in such environments as the hospital industry, swimming pools and spas, where cleaning routines and P. aeruginosa transmission prevention protocols could be made much more resultful and cost-effective due to ease and speed of processing both spot check and water samples. HighlightsO_LIA method was applied for detection of viable Pseudomonas aeruginosa in 739 water samples. C_LIO_LIRedox potential monitoring of Z-broth cultures exclusively registered growth of P. aeruginosa. C_LIO_LIThe method is highly selective, reliable and partly automated, with lower labor costs. C_LIO_LIThe method is suited for testing of water and hospital environments for P. aeruginosa. C_LI

microbiology↗

bioRxiv2019

Raw milk for human consumption may carry antimicrobial resistance genes

BackgroundThe increasing prevalence of antimicrobial resistance (AMR) is a significant threat to global health. The widespread use of antibiotics is increasingly shortening the time it takes for resistant strains to develop. More and more multi-drug-resistant bacterial strains cause life-threatening infections and the death of tens of thousands of people each year. Beyond disease control animals are often given antibiotics for growth promotion or increased feed efficiency, which further increase the chance of the development of multi-resistant strains. After the consumption of unprocessed animal products, these strains may meet the human bacteriota. Among the foodborne and the human populations, antimicrobial resistance genes (ARGs) may be shared by horizontal gene transfer. This study aims to test the presence of antimicrobial resistance genes in milk metagenome, investigate their genetic position and their linkage to mobile genetic elements. ResultsWe have analyzed raw milk samples from public markets sold for human consumption. The milk samples contained genetic material from various bacterial species and the detailed analysis uncovered the presence of several antimicrobial resistance genes. The samples contained complete ARGs influencing the effectiveness of acridine dye, cephalosporin, cephamycin, fluoroquinolone, penam, peptide antibiotics and tetracycline. One of the ARGs, PC1 beta-lactamase may also be a mobile element that facilitates the transfer of resistance genes to other bacteria, e.g. to the ones living in the human gut. ConclusionBesides the animal products antibiotic residuals, their potentially transmissible antimicrobial resistance gene content may also contribute to the development of human pathogenic bacterias antimicrobial resistance.

genomics↗