Streptococcus dysgalactiae subsp. equisimilis from invasive and non-invasive infections in Spain: combining epidemiology, molecular characterization, and genetic diversity.

The purpose of this study was to characterize the antibiotic resistance, virulence, and genetic diversity among invasive and non-invasive Streptococcus dysgalactiae subsp. equisimilis (SDSE) isolates. SDSE were isolated from clinical samples of outpatients and inpatients cares in La Rioja region (Spain) during 2012-2015. The analyses performed were susceptibility testing by disc diffusion, resistance and virulence genes by PCR, emm typing by PCR and sequencing, and other molecular typing by SmaI-PFGE and MLST. Forty-two SDSE isolates were recovered (64.3% non-invasive, 35.7% invasive) that were grouped in 31 PFGE patterns, 17 ST, and 14 emm types, being stC1400, stG6792, and stG62647 the most frequent, and stC74a and stC5345 exclusive in invasive SDSE. Twenty-one SDSE were resistant to at least one antibiotic. The erm(TR) and erm(B) genes were linked with resistance to macrolides; tet(M) and tet(T) to tetracycline; dfrF to trimethoprim; ant(6)-Ia and aph(3')-IIIa to aminoglycosides; and the substitutions Asp80Ala in GyrA and Ser79Phe in ParC with resistance to levofloxacin. The sagA, slo, scpA, and ska virulence genes were amplified in 93% SDSE. Streptococcal superantigenic speGdys gene was identified in 80% of invasive and 63% of non-invasive SDSE and correlated with certain emm types (e.g., stG62647 or stG6792). SDSE invasive infections were most frequent in elderly patients, and half of our SDSE were resistant to at least one antibiotic tested. This work is the first detection of tet(T), dfrF, and new substitution in GyrA protein in SDSE. A high diversity of circulating genetic lineages was found among our SDSE.

Two novel variants in the ATM gene causing ataxia-telangiectasia, including a duplication of 90 kb: Utility of targeted next-generation sequencing in detection of copy number variation.

Ataxia-telangiectasia (A-T) is a rare autosomal recessive neurodegenerative disorder characterized by progressive cerebellar ataxia, ocular apraxia, immunodeficiency, telangiectasia, elevated serum α-fetoprotein concentration, radiosensitivity and cancer predisposition. Classical A-T is caused by biallelic variants on ATM (ataxia telangiectasia mutated) gene, leading to a loss of function of the protein kinase ATM, involved in DNA damage repair. Atypical presentations can be found in A-T-like disease or in Nijmegen breakage syndrome, caused by deficiency of mre11 or nibrin proteins, respectively. In this report, we present the genetic characterization of a 4-year-old female with clinical diagnosis of A-T. Next-generation sequencing (NGS) revealed two novel heterozygous mutations in the ATM gene: a single-nucleotide variant (SNV) at exon 47 (NM_000051.3:c.6899G > C; p.Trp2300Ser) and ∼90 kb genomic duplication spanning exons 17-61, NG_009830.1:g.(41245_49339)_(137044_147250)dup. These findings were validated by Sanger sequencing and MLPA (multiplex ligation-dependent probe amplification) analysis respectively. Familial segregation study confirmed that the two variants are inherited, and the infant is a compound heterozygote. Thus, our study expands the spectrum of ATM pathogenic variants and demonstrates the utility of targeted NGS in the detection of copy number variation.