Importance of whole genome sequencing for the assessment of outbreaks in diagnostic laboratories: analysis of a case series of invasive Streptococcus pyogenes infections

• Published in: European journal of clinical microbiology & infectious diseases Vol. 36; no. 7; pp. 1173 - 1180
• Main Authors: Tagini, F., Aubert, B., Troillet, N., Pillonel, T., Praz, G., Crisinel, P. A., Prod’hom, G., Asner, S., Greub, G.
• Format: Journal Article
• Language: English
• Published: Berlin/Heidelberg Springer Berlin Heidelberg 01-07-2017; Springer Nature B.V
• Subjects: Adolescent; Aged; Antibiotic resistance; Antibiotics; Bacteriological Techniques - methods; Biomedical and Life Sciences; Biomedicine; Child; Child, Preschool; Diagnostic systems; Disease Outbreaks; Drug Resistance, Bacterial; Female; Gene sequencing; Genes; Genomes; Genotype; Health risks; Humans; Hygiene; Infant; Infections; Internal Medicine; Male; Medical Microbiology; Middle Aged; Molecular Diagnostic Techniques - methods; Molecular Typing - methods; Multilocus sequence typing; Mutation; Original; Original Article; Outbreaks; Polymorphism; Public health; Regulators; Single-nucleotide polymorphism; Streptococcal Infections - diagnosis; Streptococcal Infections - epidemiology; Streptococcus; Streptococcus infections; Streptococcus pyogenes - isolation & purification; Switzerland - epidemiology; Transcription; Virulence; Virulence Factors - genetics; Whole Genome Sequencing - methods; Emm-typing; Streptococcus pyogenes; Outbreak; MLST; Whole genome sequencing; Group a streptococcus
• ISSN: 0934-9723; 1435-4373
• DOI: 10.1007/s10096-017-2905-z

Outbreaks of
Streptococcus pyogenes
hypervirulent clones are constant public health threats. In western Switzerland, an increase of severe cases of
S. pyogenes
invasive infections was observed between December 2015 and March 2016. Our aim was (i) to investigate these cases by the use of Whole Genome Sequencing (WGS) and (ii) to determine the specific virulome and resistome of each isolate in order to undertake adequate public health measures. Eleven
Streptococcus pyogenes
strains isolated from 11 patients with severe invasive infections between December 13, 2015 and March 12, 2016 were included in our study. Practically,
emm
-typing, MLST and WGS were used to investigate the relatedness between the isolates. The presence of virulence and antibiotic resistance genes as well as mutations in transcriptional regulators of virulence and in genes encoding for antibiotic targets were assessed. Three and two groups of isolates shared the same
emm
-type and ST type, respectively. Single Nucleotide Polymorphism (SNP) analysis revealed 14 to 32 SNPs between the strains of the same
emm
-type group, ruling out the possibility of a clonal outbreak. Mutations found in
covS
and
rocA
could partially explain an increased virulence. As these reassuring results were obtained in less than 10 days, no specific hospital hygiene and no dedicated public health measures had to be undertaken. WGS is a powerful technique to discriminate between closely related strains, excluding an outbreak in less than 10 days. Moreover, WGS provided extensive data on the virulome and resistome of all these strains.