Biology subjects

Huse, K. K.

Publications and source records attributed to Huse, K. K..

3 recordsLinked to original sources

bioRxiv2023

Characterization of the RofA regulon in the pandemic M1global and emergent M1UK lineages of Streptococcus pyogenes

Background & AimsThe standalone regulator RofA is a positive regulator of the pilus locus in Streptococcus pyogenes. Found in only certain emm genotypes, RofA has been reported to regulate other virulence factors, although its role in the globally dominant emm1 S. pyogenes is unclear. Given the recent emergence of a new emm1 (M1UK) toxigenic lineage that is distinguished by three non-synonymous SNPs in rofA, we characterized the rofA regulon in six emm1 strains, that are representative of the two contemporary major emm1 lineages (M1global and M1UK) using RNAseq analysis, and then determined the specific role of the M1UK-specific rofA SNPs. ResultsDeletion of rofA in three M1global strains led to altered expression of 14 genes, including six non-pilus locus genes. In M1UK strains, deletion of rofA led to altered expression of 16 genes, including 9 genes that were unique to M1UK. Only the pilus locus genes were common to the RofA regulons of both lineages, while transcriptomic changes varied between strains even within the same lineage. Although introduction of the 3 SNPs into rofA did not impact gene expression in an M1global strain, reversal of 3 SNPs in an M1UK strain led to an unexpected number of transcriptomic changes that in part recapitulated transcriptomic changes seen when deleting RofA in the same strain. Computational analysis predicted interactions with a key histidine residue in the PRD domain of RofA would differ between M1UK and M1global. SummaryRofA is a positive regulator of the pilus locus in all emm1 strains but effects on other genes are strain- and lineage-specific, with no clear, common DNA binding motif. The SNPs in rofA that characterize M1UK may impact regulation of RofA; whether they alter phosphorylation of the RofA PRD domain requires further investigation. Author summaryRofA belongs to the group of "mga-like" bacterial regulatory proteins that comprise a DNA binding domain as well as a phosphorylation domain (PRD) that is responsive to changes in sugar availability. In certain emm genotypes of Streptococcus pyogenes, rofA sits upstream of the pilus locus, to act as a positive regulator. The recent emergence of a SpeA exotoxin-producing sublineage of emm1 S. pyogenes, (M1UK) has focused attention on the role of RofA; M1UK and its associated sublineages are characterized by 3 non-synonymous SNPs in rofA, that include adjacent SNPs in the PRD domain. Here, we determine the impact of rofA deletion and the 3 rofA SNPs in both the widely disseminated M1global clone and the newly emergent M1UK clone. While production of SpeA undoubtedly contributes to infection pathogenesis, the evolution of M1UK points to a role for metabolic regulatory rewiring in success of this lineage.

microbiology↗

bioRxiv2023

Tricontinental detection of Streptococcus pyogenes M1UK: A call for wider research and active surveillance.

The Streptococcus pyogenes M1UK lineage, characterised by an intrinsic ability to express SpeA toxin and defined by 27 single nucleotide polymorphisms in the core genome, dominates the population of emm1 S. pyogenes isolates throughout Europe, Canada, South America, Japan and Oceania. While not the sole deterministic factor, enhanced SpeA expression is likely to have contributed to M1UK lineage expansion, but was not sufficient to support expansion of intermediate lineage M123SNP, that expresses SpeA at a similar level to M1UK. A single nucleotide polymorphism (SNP) in the ssrA leader sequence upstream of speA is one of a limited number of SNPs that distinguish intermediate sublineages that differ in SpeA production. It was recently shown that this SNP leads to increased ssrA terminator read-through, and consequent increased transcription of speA, which lies downstream of ssrA. In this work, introduction of the ssrA SNP into representative isolates of the widely disseminated M1global clone and the intermediate M113SNP lineage, that cannot otherwise produce readily-detectable SpeA in culture, resulted in SpeA expression, confirming the importance of the ssrA SNP to SpeA phenotype. Consistent with this, correction of the ssrA SNP in M1UK abrogated SpeA expression. However, RNAseq analysis of 8 emm1 clinical pharyngitis strains showed that presence of the SNP was not invariably linked to read-through from the ssrA leader sequence or SpeA expression. Read-through was observed in isolates that did not possess the ssrA SNP. Critical review of existing data suggests that speA mRNA transcript length may be impacted by the two-component regulator CovRS, pointing to a complex regulatory network interaction between the bacterial chromosome and phage-encoded superantigens.

microbiology↗

bioRxiv2022

Ongoing emergence of M1UK lineage among invasive group A streptococcus isolates in 2020 and use of allele-specific PCR

BackgroundAn increasing burden of invasive group A streptococcal infections is reported in multiple countries, notably England, where scarlet fever cases are also abundant. In England, increased scarlet fever and invasive infections have been associated with emergence of a sublineage of emm1 Streptococcus pyogenes that expresses increased SpeA scarlet fever erythrogenic toxin. Wider surveillance for toxigenic Streptococcus pyogenes lineage M1UK is much needed however, to date, lineage assignment has required genome sequencing limiting surveillance to those centres with access to such facilities. MethodsTo circumvent the requirement for genome sequencing, an allele-specific PCR was developed to distinguish M1UK from other emm1 strains. Additional PCR assays were developed to distinguish M1UK from two intermediate lineages that were detected previously. The assay was evaluated using DNA from genome-sequenced upper respiratory tract emm1 S. pyogenes strains and a further set of 16 genome-sequenced invasive S. pyogenes isolates that included the two intermediate lineages. The assay was then applied to DNA from all 305 invasive emm1 isolates that had been submitted to the reference laboratory in the one pear period Jan 1-Dec 31 2020, in order to assign lineage. ResultsThe allele specific PCR was 100% accurate when compared with genome sequencing, correctly identifying M1UK, two intermediate sublineages, and other emm1 strains. The assay demonstrated the M1UK lineage to be dominant among emm1 invasive isolates in England, representing 278/305 (91%) of invasive emm1 isolates by end of 2020. ImplicationsEmm1 S. pyogenes have a prominent role in invasive infections; any emm1 lineage that demonstrates enhanced fitness within the population is of public health concern. The allele specific PCR provides a readily available method to subtype emm1 isolates and does not require access to complex sequencing facilities. The data confirm that the M1UK lineage has persisted and further expanded in England underlining the importance of wider global surveillance.

microbiology↗