Abstract
The aspiration these days is to apply rapid methods for parallel analysis of bacteriome and resistome of food samples to increase food safety and prevent antibiotic resistance genes (ARGs) spreading. In this work, we used nanopore sequencing (NS) to determine the diversity and dynamics of the microbiome and resistome in two types of bean sprouts. We proved that NS provided an easy, quick, and reliable way to identify the microbiome and resistome of a food sample also. The species diversity obtained by NS and by cultivation methods with MALDI-TOF MS identification was comparable. In both samples, before and after cultivation (30 °C, 48 h), the dominant part of bacteriome formed Gammaproteobacteria (Enterobacteriaceae, Erwiniaceae, Pseudomonadaceae, Moraxellaceae) and then Firmicutes (Streptococcaceae). The diversity and abundance of single ARGs groups were comparable for both samples despite bacteriome differences. More than 50% of the detected ARGs alignments were mutations conferring resistance to aminoglycosides (16S rRNA), resistance to fluoroquinolones (gyrA, gyrB, parC, parD) and elfamycin (EF-Tu). ARGs encoding efflux pumps formed more than 30% of the detected alignments. Beta-lactamases were represented by many variants, but were less abundant.
Highlights
IntroductionAntibiotic resistance has adverse effects on human, and on livestock, health care, agriculture, and the environment
The spread of antibiotic resistance has become a serious problem
The current trend to reduce the incidence of antibiotic-resistant bacteria (ARB) is the supervision of the appropriate use of antibiotics and the development of new methods to improve the detection of ARB and especially genes encoding antibiotic resistance genes (ARGs) [1]
Summary
Antibiotic resistance has adverse effects on human, and on livestock, health care, agriculture, and the environment. ARB and ARGs can be found in the environment (soil, water), human or animal feces, food, and the gastrointestinal tract, which can serve as their reservoirs (hot spots). The food can be contaminated with ARB and ARGs in several ways. ARB may be present in primary food products (raw meat, milk, fermented dairy products) [6] due to the usage of antibiotics (ATB) in agricultural production (e.g., animal medications) or using ARB contaminated water for irrigation or fertilizers [7]. ARGs can circulate through the food chain, increasing the amount of ARGs in pathogenic bacteria and in the human bacteriome [9,10]
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