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

Overview

Journal Animals (Basel)

Date 2020 Jul 8

PMID 32630808

Citations 3

Authors

Zoltan Nemet

Ervin Albert

Adam Dan

Gyula Balka

Aron Szenes

Rita Sipos

Szabolcs Bodizs

Imre Biksi

Affiliations

Soon will be listed here.

Abstract

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 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" species were also identified.

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References

Devriese L . A simplified system for biotyping Staphylococcus aureus strains isolated from animal species. J Appl Bacteriol. 1984; 56(2):215-20. DOI: 10.1111/j.1365-2672.1984.tb01341.x. View

Brettin T, Davis J, Disz T, Edwards R, Gerdes S, Olsen G . RASTtk: a modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes. Sci Rep. 2015; 5:8365. PMC: 4322359. DOI: 10.1038/srep08365. View

Nemet Z, Albert E, Nagy K, Csuka E, Dan A, Szenci O . Virulence type and tissue tropism of Staphylococcus strains originating from Hungarian rabbit farms. Vet Microbiol. 2016; 193:1-6. DOI: 10.1016/j.vetmic.2016.08.005. View

Roisin S, Gaudin C, de Mendonca R, Bellon J, Van Vaerenbergh K, De Bruyne K . Pan-genome multilocus sequence typing and outbreak-specific reference-based single nucleotide polymorphism analysis to resolve two concurrent Staphylococcus aureus outbreaks in neonatal services. Clin Microbiol Infect. 2016; 22(6):520-6. DOI: 10.1016/j.cmi.2016.01.024. View

Matuszewska M, Murray G, Harrison E, Holmes M, Weinert L . The Evolutionary Genomics of Host Specificity in Staphylococcus aureus. Trends Microbiol. 2020; 28(6):465-477. DOI: 10.1016/j.tim.2019.12.007. View

Viana D, Selva L, Segura P, Penades J, Corpa J . Genotypic characterization of Staphylococcus aureus strains isolated from rabbit lesions. Vet Microbiol. 2007; 121(3-4):288-98. DOI: 10.1016/j.vetmic.2006.12.003. View

Vancraeynest D, Hermans K, Haesebrouck F . Prevalence of genes encoding exfoliative toxins, leucotoxins and superantigens among high and low virulence rabbit Staphylococcus aureus strains. Vet Microbiol. 2006; 117(2-4):211-8. DOI: 10.1016/j.vetmic.2006.05.009. View

Holmes M, Harrison E, Fisher E, Graham E, Parkhill J, Foster G . Genomic Analysis of Companion Rabbit Staphylococcus aureus. PLoS One. 2016; 11(3):e0151458. PMC: 4786088. DOI: 10.1371/journal.pone.0151458. View

Satta G, Ling C, Cunningham E, McHugh T, Hopkins S . Utility and limitations of Spa-typing in understanding the epidemiology of Staphylococcus aureus bacteraemia isolates in a single University Hospital. BMC Res Notes. 2013; 6:398. PMC: 3850082. DOI: 10.1186/1756-0500-6-398. View

10.

Nurk S, Bankevich A, Antipov D, Gurevich A, Korobeynikov A, Lapidus A . Assembling single-cell genomes and mini-metagenomes from chimeric MDA products. J Comput Biol. 2013; 20(10):714-37. PMC: 3791033. DOI: 10.1089/cmb.2013.0084. View

11.

Hermans K, Devriese L, Haesebrouck F . Rabbit staphylococcosis: difficult solutions for serious problems. Vet Microbiol. 2002; 91(1):57-64. DOI: 10.1016/s0378-1135(02)00260-2. View

12.

Schurch A, Arredondo-Alonso S, Willems R, Goering R . Whole genome sequencing options for bacterial strain typing and epidemiologic analysis based on single nucleotide polymorphism versus gene-by-gene-based approaches. Clin Microbiol Infect. 2018; 24(4):350-354. DOI: 10.1016/j.cmi.2017.12.016. View

13.

Jolley K, Bray J, Maiden M . Open-access bacterial population genomics: BIGSdb software, the PubMLST.org website and their applications. Wellcome Open Res. 2018; 3:124. PMC: 6192448. DOI: 10.12688/wellcomeopenres.14826.1. View

14.

Vancraeynest D, Hermans K, Haesebrouck F . Genotypic and phenotypic screening of high and low virulence Staphylococcus aureus isolates from rabbits for biofilm formation and MSCRAMMs. Vet Microbiol. 2004; 103(3-4):241-7. DOI: 10.1016/j.vetmic.2004.09.002. View

15.

Wattam A, Davis J, Assaf R, Boisvert S, Brettin T, Bun C . Improvements to PATRIC, the all-bacterial Bioinformatics Database and Analysis Resource Center. Nucleic Acids Res. 2016; 45(D1):D535-D542. PMC: 5210524. DOI: 10.1093/nar/gkw1017. View

16.

Argemi X, Hansmann Y, Prola K, Prevost G . Coagulase-Negative Staphylococci Pathogenomics. Int J Mol Sci. 2019; 20(5). PMC: 6429511. DOI: 10.3390/ijms20051215. View

17.

Rao Q, Shang W, Hu X, Rao X . Staphylococcus aureus ST121: a globally disseminated hypervirulent clone. J Med Microbiol. 2015; 64(12):1462-1473. DOI: 10.1099/jmm.0.000185. View

18.

Harmsen D, Claus H, Witte W, Rothganger J, Claus H, Turnwald D . Typing of methicillin-resistant Staphylococcus aureus in a university hospital setting by using novel software for spa repeat determination and database management. J Clin Microbiol. 2003; 41(12):5442-8. PMC: 309029. DOI: 10.1128/JCM.41.12.5442-5448.2003. View

19.

Attili A, Nebbia P, Bellato A, Galosi L, Papeschi C, Rossi G . The Effect of Age and Sampling Site on the Outcome of Infection in a Rabbit () Farm in Italy. Animals (Basel). 2020; 10(5). PMC: 7278480. DOI: 10.3390/ani10050774. View

20.

Vancraeynest D, Haesebrouck F, Deplano A, Denis O, Godard C, Wildemauwe C . International dissemination of a high virulence rabbit Staphylococcus aureus clone. J Vet Med B Infect Dis Vet Public Health. 2006; 53(9):418-22. DOI: 10.1111/j.1439-0450.2006.00977.x. View