Izumiya, H. | bioRxiv Science

bioRxiv2025

Genetic basis of R-phase H:z27 antigen expression and phylogenetic relationships of Salmonella enterica serovar Senftenberg

Salmonella enterica serovar Senftenberg (S. Senftenberg) is one of the most prevalent Salmonella serovars and can be isolated from various animals and humans. According to the White-Kauffmann-Le Minor (WKL) scheme, the antigenic formula of S. Senftenberg is defined as 1,3,19:g,[s],t:-. Although the antigenic formula 1,3,19:z27:- was formerly designated as serovar Simsbury, this name was later removed from the WKL scheme due to reports of interconvertibility between serovars Senftenberg and Simsbury. The H:z27 antigen is currently recognized as one of the R-phase H antigens of S. Senftenberg. To elucidate the genetic basis of H:z27 antigen expression in S. Senftenberg, we determined the whole-genome sequences of isolates expressing the H:z27 antigen. These isolates belonged to sequence type (ST) 185 and harbored a horizontally acquired chromosomal region containing the fljA, fljB, and pinR genes, which are predicted to encode a translational repressor of fliC mRNA, a phase 2 flagellin, and an invertase, respectively. A deletion mutant lacking this region expressed the H:g,s,t antigen instead of H:z27, as confirmed by serotyping and Western blot analysis. Phylogenetic analysis based on S. Senftenberg genome archives, together with the sequences obtained in this study, suggested that the S. Senftenberg ST185 lineage acquired the fljAB-pinR locus around 1867. In contrast, our broader phylogenetic analysis of Salmonella serovars indicated that S. Senftenberg ST14 is genetically closer to certain other serovars than to ST185, while ST185 shows a closer relationship to a different serovar than to ST14. These findings suggest that S. Senftenberg comprises at least two distinct genomic lineages. IMPORTANCELimited information is available on the genetic basis of R-phase H antigen expression in S. enterica. In this study, we first demonstrated that the R-phase H:z27 antigen of S. Senftenberg is determined by a horizontally acquired chromosomal region. The ST 185 lineage of S. Senftenberg appears to have acquired this chromosomal region around 1867 and subsequently disseminated worldwide. We also demonstrated that S. Senftenberg comprises at least two distinct genomic lineages. The combined use of serotyping and multilocus sequence typing may provide a typing framework that better reflects the disease potential of Salmonella.

microbiology↗

bioRxiv2024

Typhi Mykrobe: fast and accurate lineage identification and antimicrobial resistance genotyping directly from sequence reads for the typhoid fever agent Salmonella Typhi

BackgroundTyphoid fever results from systemic infection with Salmonella enterica serovar Typhi (Typhi) and causes 10 million illnesses annually. Disease control relies on prevention (water, sanitation, and hygiene interventions or vaccination) and effective antimicrobial treatment. Antimicrobial resistant (AMR) Typhi lineages have emerged and become established in many parts of the world. Knowledge of local pathogen populations informed by genomic surveillance, including of lineages (defined by the GenoTyphi scheme) and AMR determinants, is increasingly used to inform local treatment guidelines and to inform vaccination strategy. Current tools for genotyping Typhi require multiple read alignment or assembly steps and have not been validated for analysis of data generated with Oxford Nanopore Technologies (ONT) long-read sequencing devices. Here, we introduce Typhi Mykrobe, a command line software tool for rapid genotyping of Typhi lineages, AMR determinants, and plasmid replicons direct from sequencing reads. ResultsWe validated Typhi Mykrobe lineage genotyping by comparison with the current standard read mapping-based approach and demonstrated 99.8% concordance across nearly 13,000 genomes sequenced with Illumina platforms. For the few isolates with discordant calls, we show that Typhi Mykrobe results are better supported by the evidence from raw sequence read data than the results generated using the mapping-based approach. We also demonstrate 99.9% concordance for detection of AMR determinants compared with the current standard assembly-based approach, with similar results for plasmid marker detection. Typhi Mykrobe predicts clinical resistance categorisation (S/I/R) for eight drug classes, and we show strong agreement with phenotypic categorisations generated from reference laboratory minimum inhibitory concentration (MIC) data for n=1,572 Illumina-sequenced isolates (>99% agreement within one doubling dilution). We show strong concordance (>96% for genotype and >98% for AMR and plasmid) between calls made from ONT reads and those made from Illumina reads for isolates sequenced on both platforms (n =93 genomes). Typhi Mykrobe takes less than a minute per sample and is available at https://github.com/typhoidgenomics/genotyphi. ConclusionsTyphi Mykrobe provides rapid and sensitive genotyping of Typhi genomes direct from Illumina and ONT reads, although lower accuracy was observed for R9 ONT data. It demonstrated accurate assignment of GenoTyphi lineage, detection of AMR determinants and prediction of corresponding AMR phenotypes, and identification of plasmid replicons.

microbiology↗