RESUMO
Epidemiology of shigellosis has drastically changed in recent years due to globalization and sexual risk behaviors. Here, through whole-genome sequencing, we characterized two ESBL-producing Shigella sonnei strains (ShSoBUH1 and ShSoBUH2) carrying a blaCTX-M-15 among men who have sex with men (MSM), who had not recently traveled and presented sexual risk behaviors. Both strains harbored IncB/O/K/Z and IncFII plasmids, which carry aadA1, aadA5, sul1, sul2, dfrA1, dfrA17, mph(A), erm(B), tet(B), qacE and blaCTX-M-15 genes conferring resistance to 2nd and 3rd generation cephalosporins, cotrimoxazole, erythromycin, azithromycin and quinolones. IncFII plasmids containing blaCTX-M-15 from ShSoBUH1 and ShSoBUH2 presented 99,8-99,9% similarity with plasmids from another five CTX-M-15 S. sonnei strains detected in Belgium and Switzerland. A single-nucleotide polymorphism (SNP) analysis determined that the study strains differed by 361 SNPs, belonging to different clusters. To the best of our knowledge, this is the first report describing two extensively drug-resistant (XDR) CTX-M-15 S. sonnei strains in MSM.
RESUMO
PURPOSE: With the rise of the different Variants of Concern (VOC) and Variants of Interest (VOI) in order to control the SARS-CoV-2 pandemic, strategies for accurately tracking these different variants have been developed. While most of these strategies rely heavily on specific PCRs targeting the characteristic mutations of some lineages, several approaches using the alterations at the cycle threshold (Ct) of different commercial PCR diagnostic tests have been described. The objective of this study is to analyse the use of the Ct difference at the Allplex™ SARS-CoV-2/FluA/FluB/RSV Assay (Seegene, Korea) between the Nucleocapside (N) and the Spike (S) or RNA-dependent RNA polymerase (RdRP) genes as a preliminary screening for variant tracking. METHODS: The samples analysed with the Allplex™ SARS-CoV-2/FluA/FluB/RSV Assay from 1st of March 2021 to 26th of December 2021 were selected. The Ct values for N, S, RdRP were collected, and the differences between N and S (ΔS) and N and RdRP (ΔRdRP) were calculated. Using ΔS and ΔRdRP a diagnostic test was designed and these results were compared to the routine Variant assessment. RESULTS: The mean ΔS and ΔRdRP were characteristic for Alpha and Delta. This difference was statistically significant. For Every analysed Variant the diagnostic test achieved a higher than 90% sensitivity with a noteworthy performance with the Omicron variant (97% sensitivity and 90% specificity). CONCLUSIONS: The analysis of the Ct alterations at the Allplex™ SARS-CoV-2/FluA/FluB/RSV Assay may be a suitable method for an early approach to SARS-CoV-2 variant assessment.
