Staphylococcosis is one of the most important infectious diseases in rabbit medicine, especially in commercial farming. Previous studies revealed the existence of virulent variants adapted to rabbits. Typical and atypical, highly virulent as well as low virulent variants have been isolated and reported from industrial units in all major rabbit-meat-producing countries. Preceding the research focused on detecting defined nucleotide sequences, the genome of these organisms as a whole was rarely subjected to scientific investigations. The authors sequenced 51 Staphylococcus strains originating from industrial rabbit farms in Hungary. Another 12 draft genomes of rabbit isolates were constructed from read sequences available in digital repositories, and were compared based on whole-genome multilocus sequence typing. The clonal origin of highly virulent variants is confirmed, the strains from Hungary were closely related with the strains isolated in the UK, Italy, and Spain. Atypical highly virulent strains are the most prevalent in Hungary, they form a separate clonal cluster. The low virulent strains were genetically similar, but more heterogeneous than the highly virulent (HV) and aHV strains even by the traditional MLST typing scheme. Other “non-aureus” Staphylococcus species were also identified.

Livestock-Associated Methicillin-ResistantStaphylococcus aureus (LA-MRSA) strains of clonal complex (CC) 398 are widely disseminated in pigs and are considered emerging pathogens in human medicine. To investigate the prevalence, genetic characteristics, and zoonotic potential of the pathogen in pig production settings, dust samples were collected from 40 pig operations in Hungary, along with nasal swabs of attending veterinarians and other swine professionals (n=27) in 2019. MRSA isolates were further characterized by performing whole-genome sequencing and susceptibility testing. The whole-genome sequences of 14 human-derived LA-MRSA clinical isolates from the same year were also included in the study. The proportion of positive farms was 83 (33/40), and 70 (19/27) of the swine professionals carried the pathogen. All but one MRSA strain belonged to CC398, including the human clinical isolates. The core genome multilocus sequence typing (cgMLST) analysis revealed clusters of closely-related isolates of both environmental and human origin with a pairwise allelic distance of 24, and both cgMLST and single nucleotide polymorphism (SNP) analyses suggest recent transmission events between the farm environment and humans. Four human clinical isolates harboured the immune-evasion gene cluster, of which one was considered to be closely related to farm isolates. Half of the swine-related strains showed decreased susceptibility to eight or more antimicrobials, and along with human isolates, they carried eight different types of multidrug-resistance genes, including cfr. The results showed a dramatic increase in the occurrence of LA-MRSA in the swine industry in Hungary, compared with the 2 prevalence reported by the European Food Safety Authority baseline study in 2008. The wide range of antimicrobial resistance of the strains, accompanied by the emergence of the pathogen in humans both asymptomatic carriers and diseased call for revision of the risk posed by LA-MRSA to the public health.

The presence of methicillin-resistant Staphylococcus aureus (MRSA) strains in the food chain has been confirmed by several studies in the European Union, but there are only limited data available in Hungary. The objective of the present study was to investigate the antibiotic resistance of Staphylococcus strains isolated from foods, using classical microbiological, molecular biological methods and the MALDI-TOF-MS technique, as well as the multi-locus sequence typing (MLST) of antibiotic resistant strains. During the study, 47 coagulase-positive (CPS) and 30 coagulase-negative (CNS) Staphylococcus isolates were collected. In the course of the MALDI-TOF-MS investigations, all CPS isolates (n=47) were found to be S. aureus species, while 8 different species were identified in the case of the CNS strains. Methicillin resistance was confirmed in two S. aureus strains, one of which had a sequence type not yet known, while the other MRSA strain was type ST398, which is the most common type of MRSA strain isolated from farm animals in the EU/EEA. (The abbreviation “MRSA” is often used in common parlance, but occasionally in the literature to denote “multidrug-resistant Staphylococcus aureus”. In the authors’ manuscript - the methicillin-resistant pathogen is correctly designated as such. Ed.)

A methicillin-rezisztens Staphylococcus aureus (MRSA) törzsek élelmiszerláncban előforduló jelenlétét számos tanulmány igazolta az Európai Unióban, azonban Magyarországon kevés adat áll rendelkezésünkre ezzel kapcsolatban. Jelen vizsgálat célja az élelmiszerekből izolált Staphylococcus törzsek antibiotikum rezisztenciá-jának vizsgálata klasszikus mikrobiológiai, molekuláris biológiai módszerekkel és MALDI-TOF-MS technikával, továbbá az antibiotikum rezisztens törzsek multilókusz szekvencia tipizálása (MLST). A vizsgálat során 47 koaguláz-pozitív (CPS) és 30 koaguláz-negatív Staphylococcus (CNS) izolátumot gyűjtöttünk. A MALDI-TOF-MS vizsgálat során minden CPS izolátum (n=47) S. aureus fajnak bizonyult, míg a CNS törzsek esetében 8 különböző fajt azonosítottunk. Két S. aureus törzs esetében állapítottunk meg methicillin-rezisztenciát, amelyek közül az egyik izolátum eddig még nem ismert szekvencia típusba, míg a másik MRSA törzs az ST398 típusba tartozott, amely a mezőgazdasági haszonállatokból izolált MRSA törzsek leggyakoribb típusa az EU/EGT területén. (Az „MRSA” rövidítést köznapi szóhasználatban, de esetenként a szakirodalomban is gyakran a „multirezisztens Staphylococcus aureus” megjelölésére használják. A szerzők kéziratában - helyesen a methicillin-rezisztens kórokozót jelölik így. A Szerk.)

Diatoms, eukaryotic algae with silica cell wall have been proved to be reliable bioindicators and are applied in ecological status assessment of aquatic ecosystems using indices calculated from pollution sensitivity and indicator values of species. Traditional method of identification of diatom species is based on morphological features of frustule that requires in-depth taxonomical knowledge and expertise. Metabarcoding that combines barcodes and high-throughput sequencing offers a promising alternative. In this pilot study we tested the applicability of metabarcoding of benthic diatom assemblages for ecological status assessment of water bodies in Hungary comparing its performance to that of morphology-based identification of species. Samples from 78 rivers and streams arranged along a trophic gradient and 14 soda pans representing unique types of habitats were investigated. Sequences of the barcode region of rbcL gene suggested by Vasselon et al. (2017) were acquired revealing 1135 diatom amplicon sequence variants (ASVs) of which 54% could be assigned at species level using Diat.barcode (Rimet et al. 2019) as reference database. Morphological investigation detected more species and intraspecific taxa in the lotic and lentic samples (413 and 78, respectively) than metabarcoding (190 and 75). Correspondence between taxa detected based on morphology and DNA sequences was relatively low (on average 24% in lotic and 26% in lentic samples) but considerably increased (on average 66% and 56%, respectively) when taking into account only the taxa reaching higher than 5% relative abundance in microscopy counting. The differences mainly derived from that a considerable portion (59% and 32%, respectively) of the morphologically identified taxa were not recorded in the reference database. Community structure of samples from both running and standing waters based on microscopy and DNA sequence analysis showed significant correlation as revealed using Mantel test. For rivers and streams diatom index IPS (Specific Pollution Sensitivity Index, (Coste in Cemagref, 1982) for soda pans indices H (Ziemann et al., 2001) and IBD (Indice Biologique Diatomées, Lenoir and Coste, 1996) were calculated from the results of the two aspects. Strong correlation was found between morphology- and sequence-based indices and in about half of the samples, the ecological status class obtained with the two methods coincided. Our results suggest that metabarcoding inheres a great opportunity and could be successfully applied in benthic diatom-based ecological status assessment of Hungarian waters after the reference database is supplemented with taxa frequently occurring in these habitats. References Cemagref, 1982. Etude des méthodes biologiques quantitativesd’appréciation de la qualité des eaux, Rapport Division Qualité des Eaux Lyon. Agence financière de Bassin Rhône-Méditerranée-Corse, Pierre-Bénite, France. Lenoir, A., Coste, M., 1996. Development of a practical diatom index of overall water quality applicable to the French National Water Board Network. Presented at the International symposium, Volksbildungsheim Grilhof Vill, AUT, 17-19 September 1995, Universität Innsbruck, pp. 29–43. Rimet, F., Gusev, E., Kahlert, M., Kelly, M.G., Kulikovskiy, M., Maltsev, Y., Mann, D.G., Pfannkuchen, M., Trobajo, R., Vasselon, V., Zimmermann, J., Bouchez, A., 2019. Diat.barcode, an open-access curated barcode library for diatoms. Sci. Rep. 9, 15116. Vasselon, V., Rimet, F., Tapolczai, K., Bouchez, A., 2017. Assessing ecological status with diatoms DNA metabarcoding: Scaling-up on a WFD monitoring network (Mayotte island, France). Ecol. Indic. 82, 1–12. Ziemann, H., Kies, L., Schulz, C.-J., 2001. Desalinization of running waters: III. Changes in the structure of diatom assemblages caused by a decreasing salt load and changing ion spectra in the river Wipper (Thuringia, Germany). Limnologica 31, 257–280.