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 [Formula: see text] 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 [Formula: see text], rifampicin pretreated: 36.5[Formula: see text]). 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.

Annotated dataset for deep-learning-based bacterial colony detection.

Quantifying bacteria per unit mass or volume is a common task in various fields of microbiology (e.g., infectiology and food hygiene). Most bacteria can be grown on culture media. The unicellular bacteria reproduce by dividing into two cells, which increases the number of bacteria in the population. Methodologically, this can be followed by culture procedures, which mostly involve determining the number of bacterial colonies on the solid culture media that are visible to the naked eye. However, it is a time-consuming and laborious professional activity. Addressing the automation of colony counting by convolutional neural networks in our work, we have cultured 24 bacteria species of veterinary importance with different concentrations on solid media. A total of 56,865 colonies were annotated manually by bounding boxes on the 369 digital images of bacterial cultures. The published dataset will help developments that use artificial intelligence to automate the counting of bacterial colonies.

Antimicrobial resistance genes in raw milk for human consumption.

The increasing prevalence of antimicrobial resistance (AMR) is a significant threat to global health. More and more multi-drug-resistant bacterial strains cause life-threatening infections and the death 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. We have analyzed raw milk samples from public markets sold for human consumption. The milk samples contained genetic material from various bacterial species and the in-depth 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.

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 main determinants of AMR are the antimicrobial resistance genes (ARGs). Since bacteria can share genetic components via horizontal gene transfer, even non-pathogenic bacteria may provide ARG to any pathogens which they become physically close to (e.g. in the human gut). In addition, fermented food naturally contains bacteria in high amounts. In this study, we examined the diversity of ARG content in various kefir and yoghurt samples (products, grains, bacterial strains) using a unified metagenomic approach. We found numerous ARGs of commonly used fermenting bacteria. Even with the strictest filter restrictions, we identified ARGs undermining the efficacy of aminocoumarins, aminoglycosides, carbapenems, cephalosporins, cephamycins, diaminopyrimidines, elfamycins, fluoroquinolones, fosfomycins, glycylcyclines, lincosamides, macrolides, monobactams, nitrofurans, nitroimidazoles, penams, penems, peptides, phenicols, rifamycins, tetracyclines and triclosan. In the case of gene lmrD, we detected genetic environment providing mobility of this ARG. Our findings support the theory that during the fermentation process, the ARG content of foods can grow due to bacterial multiplication. The results presented suggest that the starting culture strains of fermented foods should be monitored and selected in order to decrease the intake of ARGs via foods.

Alteration of avian hepatic cytochrome P450 gene expression and activity by certain feed additives.

We investigated the effect of four feed additives, namely ß-glucan, a drinking water acidifier (DWA), a sanguinarine-containing product (SN) and fulvic acid, on hepatic cytochrome P450 (CYP) mRNA expression and CYP enzyme activity in chickens. The test substances were given to the chickens in the recommended dose or in tenfold dose. The administration of 5 mg/kg body weight (bw) ß-glucan and 0.1 ml/kg bw DWA for five days decreased the relative gene expression of CYP1A4 and CYP2C23a. The dosing of 50 mg/kg bw ß-glucan, 5 and 50 mg/kg bw SN, 1 ml/kg bw DWA and 250 mg/kg bw fulvic acid doubled the hepatic CYP1A4 activity. The activity of CYP2C and CYP3A remained unchanged. Avoidance of CYP1A-mediated feed-drug interactions requires accurate dosing of ß-glucan, DWA and fulvic acid. According to our results, no treatment resulted in excessive or less CYP2C and CYP3A protein formation, which reduces the risk of potential feed additive-drug interactions in chickens. However, the administration of feed additive SN containing a plant alkaloid should be avoided concomitantly with CYP1A-metabolised medicines.

Alteration in Inflammatory Responses and Cytochrome P450 Expression of Porcine Jejunal Cells by Drinking Water Supplements.

The intestinal epithelium is the first determining barrier to the drugs administered per os. Cytochrome P450 (CYP) enzymes are substantial in the initial step of xenobiotic metabolism; therefore, intestinal CYP enzyme activities could be an important influencing factor of the oral utilization of xenobiotic substances. In this study, the effect of four drinking water supplements on CYP mRNA levels of porcine intestinal epithelial cells was examined. Further goal of the study is to describe the effect of these feed additives on the proinflammatory response of the LPS-treated enterocytes. The nontransformed porcine intestinal epithelial cells (IPEC-J2) were grown on six-well polyester membrane inserts. Cell cultures were treated with LPS (10 µg/ml), ß-glucan (5 and 50 µg/ml), sanguinarine-containing additive (5 and 50 µg/ml), drinking water acidifier (0.1 and 1 µl/ml), and fulvic acid (25 and 250 µg/ml) for 1 hour. Cells were washed with culture medium and incubated for additional 1 h before total RNA isolation. IL-6, IL-8, TNF-α, HSP70, CYP1A1, CYP1A2, and CYP3A29 mRNA levels were measured. The LPS treatment upregulated the gene expression of IL-8 and TNF-α. The relative gene expression of IL-6 remained unchanged and TNF-α and HSP70 were downregulated after the treatment with each feed additive. CYP1A1 and CYP1A2 expressions increased after sanguinarine-containing solution, fulvic acid, and drinking water acidifier treatment. None of the treatments changed the gene expression of CYP3A29, responsible for the metabolism of the majority of drug substances used in swine industry. The feed additive substances inhibited the expression of proinflammatory mediators HSP70 and TNF-α; however, ß-glucan and fulvic acid elevated the production of the chemokine IL-8 mRNA in endotoxin-treated enterocytes. All acidic supplements increased the expression of CYP1A1 gene; their constituents may serve as a ligand of CYP1A1 nuclear receptors.

Rapid in-house detection method of Campylobacter spp. from food by redox potential monitoring combined with real-time PCR.

The rapid detection of Campylobacter spp. is of utmost importance for the reduction of infections in humans by contaminated food products. The standard culturing method (ISO 10272-1:2006) involves a high time and labour demand. In this paper, we present a method that reduces the detection time of Campylobacter spp. to or below one third as compared to the ISO method, at a reduced cost per test. We used redox potential change of enrichment cultures (Bolton broth with Bolton selective supplement) for reliably selecting Campylobacter-contaminated raw milk and broiler meat samples. Identification of Campylobacter spp. in the contaminated samples was done by real-time PCR method. Culturing time to conclusive redox monitoring varied between 6 and 24 h for positive samples, depending on the contamination rate, in contrast to 136 h with the standard culturing process. However, now the Campylobacter-negative majority of food samples will not need to be tested by real-time PCR because redox potential monitoring can identify them in the selective enrichment phase. This method could be potentially used as a faster alternative to the current standard ISO 10272-1:2006, for nonregulatory monitoring purposes.

Listeria monocytogenes food monitoring data and incidence of human listeriosis in Hungary, 2004.

Food samples were monitored for contamination with Listeria monocytogenes, and the incidence of human listeriosis was evaluated according to the data obtained in Hungary in the year 2004. Of the food samples tested, the bacterium was most often detectable in milk and dairy products, as 72.1% of all L. monocytogenes strains were isolated from these samples. The food samples most commonly yielded strains of serotype 1/2a (45.1%) and 4b (27.0%). In 2004, 3 perinatal and 14 nonperinatal human listeriosis cases were diagnosed in Hungary. These disease cases were most often caused by strains belonging to serotype 4b (52.8%) and serotype 1/2a (23.5%). On the basis of the antibiotic sensitivity test results of strains isolated from the disease cases, penicillin and aminoglycoside antibiotics or a combination thereof were found to be effective.