Characterization of a prophage and a defective integrative conjugative element carrying the optrA gene in linezolid-resistant Streptococcus dysgalactiae subsp. equisimilis isolates from pigs, Italy.

OBJECTIVES To investigate the optrA-carrying genetic elements and their transferability in two linezolid-resistant Streptococcus dysgalactiae subsp. equisimilis (SDSE) strains of swine origin. METHODS SDSE strains (V220 and V1524) were phenotypically and genotypically characterized. Transferability of oxazolidinone resistance genes (filter mating), genetic elements and relatedness between isolates (WGS) were analysed. Excision of the genetic elements was assayed by inverse PCR. RESULTS SDSE isolates were resistant to chloramphenicol, florfenicol and linezolid, but susceptible to tedizolid and both carried the optrA gene.In SDSE V220 optrA was located on a 72.9-kb ICESdyV220 inserted in the 3' end of the chromosomal rum gene. It was 94%-96% identical (coverage, from 31% to 61%) to other optrA-carrying ICEs. In-depth ICESdyV220 sequence analysis revealed that optrA was carried by an IMESdyV220 (17.9 kb), also containing the tet(O/W/32/O) gene. Inverse PCR assays excluded the ICESdyV220 mobility. In SDSE V1524, optrA was carried by the ΦSdyV1524 prophage, integrated near the 5' end of the chromosomal had gene, showing a genetic organization similar to that of other streptococcal phage. Conjugation and transduction assays failed to demonstrate the optrA transferability to streptococcal recipients. V220 and V1524 belonged to two novel sequence types (ST704 and ST634, respectively). CONCLUSIONS To the best of our knowledge, this is the first identification of the optrA gene on a prophage and an ICE in SDSE isolates from swine brain.These findings are consistent with the current belief in the key role of bacteriophages and ICEs in the streptococcal evolution and adaptation.

[1]  C. Schultsz,et al.  Streptococcus suis outbreak caused by an emerging zoonotic strain with acquired multi-drug resistance in Thailand , 2023, Microbial genomics.

[2]  Jiachang Cai,et al.  An Optimized Screening Approach for the Oxazolidinone Resistance Gene optrA Yielded a Higher Fecal Carriage Rate among Healthy Individuals in Hangzhou, China , 2022, Microbiology spectrum.

[3]  S. Schwarz,et al.  Oxazolidinones: mechanisms of resistance and mobile genetic elements involved. , 2022, The Journal of antimicrobial chemotherapy.

[4]  A. R. Fernandes,et al.  Phylogenetic analysis and accessory genome diversity reveal insight into the evolutionary history of Streptococcus dysgalactiae , 2022, Frontiers in microbiology.

[5]  Lennard Epping,et al.  Progressive Lameness of a Greater One-Horned Rhinoceros (Rhinoceros unicornis) Associated with a Retroperitoneal Abscess and Thrombus Caused by Streptococcus dysgalactiae Subspecies equisimilis , 2022, Animals : an open access journal from MDPI.

[6]  Daniel N. Wilson,et al.  Structural basis for PoxtA-mediated resistance to phenicol and oxazolidinone antibiotics , 2021, Nature Communications.

[7]  D. Porcellato,et al.  Whole genome sequencing reveals possible host species adaptation of Streptococcusdysgalactiae , 2021, Scientific Reports.

[8]  Siguo Liu,et al.  Identification of a Streptococcus parasuis isolate co-harbouring the oxazolidinone resistance genes cfr(D) and optrA. , 2021, The Journal of antimicrobial chemotherapy.

[9]  Jianzhong Shen,et al.  Mobile Oxazolidinone Resistance Genes in Gram-Positive and Gram-Negative Bacteria , 2021, Clinical microbiology reviews.

[10]  OUP accepted manuscript , 2021, Journal of Antimicrobial Chemotherapy.

[11]  V. di Pilato,et al.  Detection of Oxazolidinone Resistance Genes and Characterization of Genetic Environments in Enterococci of Swine Origin, Italy , 2020, Microorganisms.

[12]  R. Kaas,et al.  ResFinder 4.0 for predictions of phenotypes from genotypes , 2020, The Journal of antimicrobial chemotherapy.

[13]  S. Ding,et al.  Capsular serotypes, antimicrobial susceptibility, and the presence of transferable oxazolidinone resistance genes in Streptococcus suis isolated from healthy pigs in China. , 2020, Veterinary microbiology.

[14]  Dmitry Antipov,et al.  Using SPAdes De Novo Assembler , 2020, Current protocols in bioinformatics.

[15]  D. Qu,et al.  In vitro evaluation of the antibacterial activities of radezolid and linezolid for Streptococcus agalactiae. , 2019, Microbial pathogenesis.

[16]  Suhua Zhang,et al.  A prophage and two ICESa2603-family integrative and conjugative elements (ICEs) carrying optrA in Streptococcus suis. , 2019, The Journal of antimicrobial chemotherapy.

[17]  Liping Wang,et al.  Characterization of a Linezolid- and Vancomycin-Resistant Streptococcus suis Isolate That Harbors optrA and vanG Operons , 2019, Front. Microbiol..

[18]  Liping Wang,et al.  Identification and pathogenicity of an XDR Streptococcus suis isolate that harbours the phenicol-oxazolidinone resistance genes optrA and cfr, and the bacitracin resistance locus bcrABDR. , 2019, International journal of antimicrobial agents.

[19]  R. Gutiérrez-Ríos,et al.  BLAST-XYPlot Viewer: A Tool for Performing BLAST in Whole-Genome Sequenced Bacteria/Archaea and Visualize Whole Results Simultaneously , 2018, G3: Genes, Genomes, Genetics.

[20]  Jia Gu,et al.  fastp: an ultra-fast all-in-one FASTQ preprocessor , 2018, bioRxiv.

[21]  N. Leblond-Bourget,et al.  The Obscure World of Integrative and Mobilizable Elements, Highly Widespread Elements that Pirate Bacterial Conjugative Systems , 2017, Genes.

[22]  V. Burrus,et al.  Mechanisms of stabilization of integrative and conjugative elements. , 2017, Current opinion in microbiology.

[23]  João André Carriço,et al.  Beta-hemolytic Streptococcus dysgalactiae strains isolated from horses are a genetically distinct population within the Streptococcus dysgalactiae taxon , 2016, Scientific Reports.

[24]  X. Xia,et al.  A novel gene, optrA, that confers transferable resistance to oxazolidinones and phenicols and its presence in Enterococcus faecalis and Enterococcus faecium of human and animal origin. , 2015, The Journal of antimicrobial chemotherapy.

[25]  Andrew J. Page,et al.  Roary: rapid large-scale prokaryote pan genome analysis , 2015, bioRxiv.

[26]  M. Mingoia,et al.  Transduction of the Streptococcus pyogenes bacteriophage Φm46.1, carrying resistance genes mef(A) and tet(O), to other Streptococcus species , 2014, Front. Microbiol..

[27]  Torsten Seemann,et al.  Prokka: rapid prokaryotic genome annotation , 2014, Bioinform..

[28]  N. Leblond-Bourget,et al.  Conjugative and mobilizable genomic islands in bacteria: evolution and diversity. , 2014, FEMS microbiology reviews.

[29]  T. Kirikae,et al.  Complete Genome Sequence of Streptococcus dysgalactiae subsp. equisimilis 167 Carrying Lancefield Group C Antigen and Comparative Genomics of S. dysgalactiae subsp. equisimilis Strains , 2013, Genome biology and evolution.

[30]  Jianzhong Shen,et al.  First Report of the Multiresistance Gene cfr in Streptococcus suis , 2013, Antimicrobial Agents and Chemotherapy.

[31]  Alexey A. Gurevich,et al.  QUAST: quality assessment tool for genome assemblies , 2013, Bioinform..

[32]  D. Petrelli,et al.  Two Distinct Genetic Elements Are Responsible for erm(TR)-Mediated Erythromycin Resistance in Tetracycline-Susceptible and Tetracycline-Resistant Strains of Streptococcus pyogenes , 2011, Antimicrobial Agents and Chemotherapy.

[33]  P. Varaldo,et al.  Different Genetic Elements Carrying the tet(W) Gene in Two Human Clinical Isolates of Streptococcus suis , 2010, Antimicrobial Agents and Chemotherapy.

[34]  Paramvir S. Dehal,et al.  FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments , 2010, PloS one.

[35]  Armanda Pugnaloni,et al.  Φm46.1, the Main Streptococcus pyogenes Element Carrying mef(A) and tet(O) Genes , 2009, Antimicrobial Agents and Chemotherapy.

[36]  M. P. Montanari,et al.  Genetic Elements Responsible for Erythromycin Resistance in Streptococci , 2008, Antimicrobial Agents and Chemotherapy.

[37]  J. Melo-Cristino,et al.  DNA Methylase Activity as a Marker for the Presence of a Family of Phage-Like Elements Conferring Efflux-Mediated Macrolide Resistance in Streptococci , 2006, Antimicrobial Agents and Chemotherapy.

[38]  M. Vecchi,et al.  Prophage association of mef(A) elements encoding efflux-mediated erythromycin resistance in Streptococcus pyogenes. , 2005, The Journal of antimicrobial chemotherapy.

[39]  Jun Yu,et al.  VFDB: a reference database for bacterial virulence factors , 2004, Nucleic Acids Res..

[40]  J. Musser,et al.  Structure and distribution of an unusual chimeric genetic element encoding macrolide resistance in phylogenetically diverse clones of group A Streptococcus. , 2003, The Journal of infectious diseases.

[41]  E. Boyd,et al.  Common themes among bacteriophage-encoded virulence factors and diversity among the bacteriophages involved. , 2002, Trends in microbiology.

[42]  J. Musser,et al.  The fundamental contribution of phages to GAS evolution, genome diversification and strain emergence. , 2002, Trends in microbiology.