<i>Salmonella</i> ’s lost phenotype: implications of sequence-based serotyping on the characterization of lipopolysaccharide-deficient <i>Salmonella</i> isolates

<i>Salmonella</i> serotyping is shifting from slide agglutination toward whole-genome sequencing (WGS). While WGS allows for comprehensive analyses, phenotypic information about lipopolysaccharide-deficient ("LPS-rough") isolates obtained from slide agglutination is lost. This discrepancy represents a challenge for <i>Salmonella</i> control in livestock because in the European Union, LPS-rough <i>Salmonella</i> isolated from food-producing animals that are untypable using slide agglutination alone are not subject to control measures, whereas isolates of certain serovars in certain matrices would be, when based on geno-serotyping. Here, we provide an account of the relevance of this phenotype in the context of routine diagnostics and food safety by characterizing the occurrence, diversity, and isolation matrices of LPS-rough isolates among non-human <i>Salmonella enterica</i> subsp. <i>enterica</i> isolates from Germany. Using available WGS data, we examined phylogenetic relationships and associations with certain genomic features. On average, 5% of isolates exhibited an LPS-rough phenotype across 46 serovars, but clonal distribution of this phenotype along the food chain was not evident. LPS-rough isolates were more commonly found in <i>S</i>. Choleraesuis isolated from wild boar and in <i>S</i>. Typhimurium isolated from pork products, compared with other matrices. We also found associations with two virulence factors, an AMR gene, and a plasmid marker. The present work lays the foundation for future research into the role of certain matrices, environments, or genomic factors in the development of LPS-rough <i>Salmonella</i> isolates and will facilitate the elucidation of the genomic basis of this phenotype, which may improve recommendations regarding risk management and control measures.IMPORTANCEThe present work highlights some of the challenges associated with the recent shift from serology- to sequence-based typing of <i>Salmonella enterica</i> serovars and provides a national perspective on the presence and relevance of the lipopolysaccharide-deficient ("LPS-rough") phenotype in samples obtained from food, animals, and the environment, including considerations regarding the choice of typing method. We provide evidence that clonal distribution of isolates with this phenotype is unlikely, but that certain environments may favor its development, and certain genomic factors may increase survival rates of LPS-rough isolates when exposed to environmental stressors. These findings could have important implications for regulations regarding the surveillance and management of <i>Salmonella</i> isolated from food, feed, and animals in the future, in particular in the context of using different typing methods, and warrant further detailed research.