Genomic Analysis of Staphylococcus aureus Strains Originating from Hungarian Rabbit Farms Reinforce the Clonal Origin of Various Virulence Types

Abstract

<jats:p>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.</jats:p>

Analysis of the Antibiotic Resistance Profiles in Methicillin-Sensitive S. aureus Pathotypes Isolated on a Commercial Rabbit Farm in Italy

“…In recent years, the presence of MRSAs in Italian rabbit breeding and the relationship between antibiotic use in farms and resistance have been evaluated [ 9 , 10 ]. High virulent strains (HV) were detected in Belgium, France, Greece, Italy, Portugal, Spain, and Hungary [ 8 , 11 , 12 ]. On the other hand, a recent study by Nemet et al [ 12 ] provided evidence that low virulent (LV) strains can act as pathogens in rabbits.…”

“…High virulent strains (HV) were detected in Belgium, France, Greece, Italy, Portugal, Spain, and Hungary [ 8 , 11 , 12 ]. On the other hand, a recent study by Nemet et al [ 12 ] provided evidence that low virulent (LV) strains can act as pathogens in rabbits.…”

The influence of antibiotics on transitory resistome during gut colonization with CTX-M-15 and OXA-162 producing Klebsiella pneumoniae ST15

“…The quality and quantity of isolated DNA was assessed by measurements using a Qubit 4.0 fluorometer (Invitrogen, Waltham, USA) and Tapestation 4150 systems (Agilent, Santa Clara, USA). The NGS libraries were prepared using the Nextera DNA Flex Library Prep Kit (Illumina, Eindhoven, The Netherlands) with Nextera DNA CD Indexes 45 . The NGS libraries were sequenced on an Illumina MiSeq instrument using the MiSeq Reagent Kit v2 using paired end 250 bp reads at the Genomics Resource Center at the Biomi Ltd.…”

“…The NGS libraries were sequenced on an Illumina MiSeq instrument using the MiSeq Reagent Kit v2 using paired end 250 bp reads at the Genomics Resource Center at the Biomi Ltd. The fastq files were imported directly from Illumina BaseSpace to the BioNumerics version 7.6 software’s (Applied Maths NV, Belgium) cloud-based calculation engine 45 . De novo sequence assemblies were made with the SPAdes de novo genome assembler (version 3.7.1).…”

High Prevalence of Livestock-Associated Methicillin-Resistant Staphylococcus aureus in Hungarian Pig Farms and Genomic Evidence for the Spillover of the Pathogen to Humans

“…Te resulting Illumina reads were transferred to BIOMI Ltd., Gödöllő, Hungary, for further bioinformatic investigation. Wholegenome multilocus sequence typing (MLST) analysis was performed on assembly free (AF) datasets using the BioNumerics software package version 8.0 (Applied Maths NV, Belgium), as described previously [15]. Ten, distance matrices were generated by selecting the subset of 1861 core genome (cg) loci of each isolate.…”