Biology subjects

Makrai, L.

Publications and source records attributed to Makrai, L..

11 recordsLinked to original sources

bioRxiv2024

A One Health approach metagenomic study on the antimicrobial resistance traits of canine saliva

According to the One Health concept, physical proximity among pets and their owners facilitates the spread of various bacteria. Interspecies bacterial transfer media include canine saliva that can be transmitted by licking and biting. Antimicrobial resistance genes (ARGs) are the natural constituents of the bacterial genome. However, human activity can increase the prominence of ARGs. To assess factors that may affect the resistome of the canine oral cavity, the shotgun metagenomic sequencing dataset of 1830 canine saliva samples was bioinformatically analyzed and supplemented with survey results of the physical and behavioral traits of the dogs. Bacteriome and resistome associated with the canine saliva samples were described throughout the analysis. Moreover, the subset of higher public health ARGs and ESKAPE pathogen-related (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter species) higher public health ARGs were also collected. Further on, the set and subsets of ARGs were studied considering the surveyed traits of the sampled dogs. Overall, 318 ARG types reached sufficiently high detection rates. These ARGs can affect 31 antibiotic drug classes by various resistance mechanisms. ARGs against tetracyclines and cephalosporins appeared in the highest number of samples. However, surprisingly, another CIA group, peptides were represented by ARGs in the third-highest number of samples. Considering further ARG appearance rates in the samples, Critically Important Antimicrobials (CIAs, WHO), such as aminoglycosides, fluoroquinolones, or macrolides, were among the most frequently affected drug classes by higher public health risk ARGs and ESKAPE pathogen related higher public health risk ARGs. Bacteria in the saliva of white and diluted (merle, gray) color dogs and dogs characterized with decreased activity and decreased aggression more often harbored ARGs. Reduced playfulness could have been specifically associated with higher public health risk ARG presence. Even though the oral microbiome of the owners is unknown, One Health and public health implications of the close human-pet bonds and factors potentially underlying the rise in salivary ARG numbers should be considered, mostly in the light of the presence of ARGs affecting critically important drugs for human medicine.

genomics↗

bioRxiv2023

Apis mellifera filamentous virus from a honey bee gut microbiome survey in Hungary

In Hungary, as part of a nationwide, climatically balanced survey for a next-generation sequencing-based study of the honey bee (Apis mellifera) gut microbiome, repeated sampling was carried out during the honey production season (March and May 2019). Among other findings, the presence of Apis mellifera filamentous virus (AmFV) was detected in all samples, some at very high levels. AmFV-derived reads were more abundant in the March samples than in the May samples. In March, a higher abundance of AmFV-originated reads was identified in samples collected from warmer areas compared to those collected from cooler areas. A lower proportion of AmFV-derived reads were identified in samples collected in March from the wetter areas than those collected from the drier areas. AmFV-read abundance in samples collected in May showed no significant differences between groups based on either environmental temperature or precipitation. The AmFV abundance correlated negatively with Bartonella apihabitans, Bartonella choladocola, and positively with Frischella perrara, Gilliamella apicola, Gilliamella sp. ESL0443, Lactobacillus apis, Lactobacillus kullabergensis, Lactobacillus sp. IBH004. De novo metagenome assembly of four samples resulted in almost the complete AmFV genome. According to phylogenetic analysis based on DNA polymerase, the Hungarian strains are closest to the strain CH-05 isolated in Switzerland.

bioinformatics↗

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↗

bioRxiv2022

Porcine cytomegalovirus detection by nanopore-based metagenomic sequencing in a Hungarian pig farm

The rapid diagnosis of infectious diseases has an essential impact on their control, treatment and recovery. Oxford Nanopore Technologies (ONT) sequencing opens up a new dimension in applying clinical metagenomics. In a large-scale pig farm in Hungary, four fattening and one piglet nasal swab pooled samples were sequenced using ONT for metagenomic analysis. Long reads covering 53.69% of the porcine cytomegalovirus genome were obtained in the piglet sample. The 650 bp long read matching the glycoprotein B gene of the virus is sequentially most similar to Japanese, Chinese and Spanish isolates.

genomics↗

bioRxiv2022

Antimicrobial resistance gene lack in tick-borne pathogenic bacteria

Tick-borne infections, including those of bacterial origin, are significant public health issues. Antimicrobial resistance (AMR), which is one of the most pressing health challenges of our time, is driven by specific genetic determinants, primarily by the antimicrobial resistance genes (ARGs) of bacteria. In our work, we investigated the occurrence of ARGs in the genomes of tick-borne bacterial species that can cause human infections. For this purpose, we processed short/long reads of 1550 bacterial isolates of the genera Anaplasma (n=20), Bartonella (n=131), Borrelia (n=311), Coxiella (n=73), Ehrlichia (n=13), Francisella (n=959) and Rickettsia (n=43) generated by second/third generation sequencing that have been freely accessible at the NCBI SRA repository. From Francisella tularensis, 98.9% of the samples contained the FTU-1 gene, and 16.3% contained additional ARGs. Only 2.2% of isolates from other genera (Bartonella: 2, Coxiella: 8, Ehrlichia: 1, Rickettsia: 2) contained any ARG. We found that the odds of ARG occurrence in Coxiella samples were significantly higher in isolates related to farm animals than from other sources. Our results describe a lack in ARGs in these bacteria and suggest that antibiotic susceptibility testing might be considered before the treatment of tick-borne infections in farm animals.

genomics↗

bioRxiv2022

A climatically representative analysis of Hungarian Ixodes ricinus tick bacteriome

BackgroundThe microbial communities of disease vectors may represent a key feature in several biological functions and thus deserve special attention in light of climate change and the consequent need to develop novel control strategies. Nevertheless, vector-borne microbial networks are still poorly understood. Assessing vectors microbial interactions and climatic dependencies may contribute to better-estimating pathogen transmission characteristics, public health risks and the urgency for control steps to be taken. MethodsIn a climatically representative country-wide survey, Ixodes ricinus ticks were collected from 17 locations in Hungary. Using shotgun metagenomic sequencing, the bacteriome composition was analyzed by investigating the relationship between the abundances of nymphs and females in various climatic environments. ResultsBacterial composition on the genus level revealed a significant difference between the samples from females and nymphs. Within the core bacteriome, females and nymphs showed significant variation in the following genera: Arsenophonus, Bacillus, Candidatus Midichloria, Rhodococcus, Sphingomonas, Staphylococcus, Wolbachia. Among females, according to temperature strata, the following were found differentiating: Curtobacterium, Pseudomonas, Sphingomonas. There was no genus with a significant difference in precipitation categories for females. In the nymphs, Curtobacterium showed significant variation between temperature and Bacillus and Curtobacterium for various precipitation levels. Based on the full sample set, Arsenophonus and Wolbachia correlated positively which we assumed to have occurred due to the presence of I. hookeri. ConclusionsThe composition of vector-borne bacteriome members showed significant alterations at sampling points with different climatic conditions and development stages of the tick hosts. Our findings not only pave the way towards understanding tick-borne bacterial networks and interdependencies but also shed light on the high potential for the presence of a possible biological tick control species, the tick parasitoid, Ixodiphagus hookeri based on related bacteriome patterns. The results of conscious tick microbiome assessment studies may contribute to precision tick control strategies of the future.

genomics↗

bioRxiv2022

Canine saliva is a source of interspecies antimicrobial resistance gene transfer

While the One Health issues of intensive animal farming are commonly discussed, keeping companion animals is less associated with the interspecies headway of antimicrobial resistance. With the constant advance of veterinary standards, antibiotics are regularly applied in companion animal medicine. Due to the close coexsistance of dogs and humans, dog bites and other casual encounters with dog saliva (e.g. licking the owner) are common. According to our metagenome studies based on 26 new generation sequencing canine saliva datasets from 2020 and 2021 reposited in NCBI SRA by The 10,000 Dog Genome Consortium and the Broad Institute within Darwins Ark project, canine saliva is rich in bacteria with predictably transferable antimicrobial resistance genes (ARGs). In the genom of potentially pathogenic Bacteroides, Capnocytophaga, Corynebacterium, Fusobacterium, Pasteurella, Porphyromonas, Staphylococcus and Streptococcus species, that are some of the most relevant bacteria in dog bite infections, ARGs against aminoglycosides, carbapenems, cephalosporins, glycylcyclines, lincosamides, macrolides, oxazolidinone, penams, phenicols, pleuromutilins, streptogramins, sulfonamides and tetracyclines could be identfied. Several ARGs, including ones against amoxicillin-clavulanate, the most commonly applied antibiotic by dog bites, was predicted to be potentially transferable based on their association with mobile genetic elements (e.g. plasmids, phages, integrated mobile genetic elements). According to our findings canine saliva may be a source of transfer of ARG-rich bacteria, that can either colonize the human body or transport ARGs to the host bacteriota and thus can be considered as a risk in the spread of antimicrobial resistance.

genomics↗

bioRxiv2021

Natural diversity of honey bee (Apis mellifera) gut bacteriome in various climatic and seasonal states

As pollinators and producers of numerous human consumed products, honey bees have great ecological, economic and health importance. The composition of their bacteriota, for which the available knowledge is limited, is essential for their bodys functioning. Based on our survey, we performed a metagenomic analysis of samples collected by repeated sampling. We used geolocations that represent the climatic types of the study area over two nutritionally extreme periods (March and May) of the collection season. In bacteriome composition, significant (p=0.002) difference was found between the samples from March and May. The samples bacteriome from March showed a significant (p=0.02) composition difference between cooler and the warmer regions. However, there were no significant bacteriome composition differences among the climatic classes of samples taken in May. Based on our results, one may conclude that the composition of healthy core bacteriome in honey bees varies depending on the climatic and seasonal conditions. This is likely due to climatic factors and vegetation states determining the availability and nutrient content of flowering plants. The results of our study prove that in order to gain a thorough understanding of a microbiomes natural diversity, we need to obtain the necessary information from extreme ranges within the hosts health state.

genomics↗

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↗