Genome-based Salmonella serotyping as the new gold standard

Abstract

Salmonella enterica is the second most reported bacterial cause of food-borne infections in europe. therefore molecular surveillance activities based on pathogen subtyping are an important measure of controlling Salmonellosis by public health agencies. In Germany, at the federal level, this work is carried out by the national Reference center for Salmonella and other Bacterial enteric pathogens (nRc). With rise of next generation sequencing techniques, the NRC has introduced whole-genome-based typing methods for S. enterica in 2016. In this study we report on the feasibility of genome-based in silico serotyping in the German setting using raw sequence reads. We found that SeqSero and seven gene MLST showed 98% and 95% concordance, respectively, with classical serotyping for the here evaluated serotypes, including the most common German serotypes S. enteritidis and S. typhimurium as well as less frequently found serotypes. the level of concordance increased to >99% when the results of both in silico methods were combined. However, both tools exhibited misidentification of monophasic variants, in particular monophasic S. Typhimurium and therefore need to be fine-tuned for reliable detection of this epidemiologically important variant. We conclude that with adjustments Salmonella genomebased serotyping might become the new gold standard.Subtyping of bacterial enteric pathogens, such as Salmonella enterica, traditionally relies on serotyping. The species Salmonella enterica is divided into six subspecies and consists of more than 2600 serovars, which are classified according to the White-Kauffmann-Le Minor Scheme 1 . Serotyping is based on determination of somatic O antigens and flagellin H antigens by reaction with specific antisera. Most S. enterica serovars have two alternately expressed H antigens, also referred to as 'phases' . The phase-1 and phase-2 flagellin proteins are encoded by fliC and fljB, respectively. The phase switch is regulated by the invertase hin and the fliC repressor gene fljA 2 . Therefore, the specific antigenic formula consists of three positions: the first position represents the O antigens, the second and third positions the two different flagellin H antigens. Each antigen position is separated by a colon, i.e. O:H1:H2. The antigenic formula for S. Typhimurium for example is accordingly 1,4,[5],12:i:1,2. There are variants of S. Typhimurium, which express only one flagellin and which therefore are referred to as monophasic S. Typhimurium. S. Enteritidis on the other hand does not possess a second flagellin per se, which is reflected in the antigenic formula: 1,9,12:g,m:-. It should be noted that some serovars share the same antigenic formula and require additional testing for unambiguous identification, e.g. the clinically important serovar S. Chloeraesuis shares its antigenic formula 6,7:c:1,5 with serovars S. Paratyphi C and S. Typhisuis. A differentiation is possible based on biochemical characteristics or PCR 3 .With rise of next generation sequencing (NGS) techniques, genomic typing ...

Peer Review #1 of "Genomic characterization and phylogenetic analysis of Salmonella enterica serovar Javiana (v0.2)"

“…Javiana is polyphyletic, we constructed minimal spanning trees based on cgMLST allele distances of all available Salmonella ser. Javiana strains and of other Salmonella serovars previously described as polyphyletic (Derby, Kentucky, Mississippi, Montevideo, Newport, Saintpaul, and Senftenberg (Achtman et al, 2012;Banerji et al, 2020;Cao et al, 2013;Sangal et al, 2010;Sévellec et al, 2018;Tang et al, 2019;Timme et al, 2013;Vosik et al, 2018;Zhang et al, 2019b)) (Figure 4; Figure S2). The branch length between the two ecBG clusters on the ser.…”

Genomic characterization and phylogenetic analysis ofSalmonella entericaserovar Javiana

“…Javiana is polyphyletic, we constructed minimal spanning trees based on cgMLST allele distances of all available Salmonella ser. Javiana strains and of other Salmonella serovars previously described as polyphyletic (Derby, Kentucky, Mississippi, Montevideo, Newport, Saintpaul, and Senftenberg ( Achtman et al, 2012 ; Alikhan et al, 2018 ; Banerji et al, 2020 ; Cao et al, 2013 ; Sangal et al, 2010 ; Sévellec et al, 2018 ; Tang et al, 2019 ; Timme et al, 2013 ; Vosik et al, 2018 ; Zhang, Payne & Lan, 2019 )) ( Fig. 4 ; Fig.…”

“…ceBGs are equivalent to eBurstGroups (eBGs; in legacy 7-gene MLST), which have been shown to correspond to serovar designations ( EnteroBase Team, 2018 ; Zhou et al, 2019 ). Typically, monophyletic serovar isolates will belong to a single eBG, while polyphyletic serovar isolates will belong to multiple eBGs ( Achtman et al, 2012 ; Alikhan et al, 2018 ; Banerji et al, 2020 ).The observation that the global clinical Salmonella ser. Javiana isolates consisted of multiple major clusters and two ceBGs suggests that this serovar may be polyphyletic.…”

SeroTools: a Python package for Salmonella serotype data analysis

“…SeqSero (a Salmonella-specific tool) and other in silico serovar designation tools have been adopted by U.S. public health agencies as an alternative to serological testing and for quality control applications (Dowdy, 2017;Timme, Sanchez Leon, & Allard, 2019). The advent of new methodologies for serovar determination has engendered a need for method-comparison studies, and has sparked a growing collection of recent publications comparing various laboratory-based and in silico serovar predictions (Banerji, Simon, Tille, Fruth, & Flieger, 2020;Cooper et al, 2020;Diep et al, 2019;Ibrahim & Morin, 2018;Tang et al, 2019;Yachison et al, 2017;Zhang et al, 2019Zhang et al, , 2015. In light of the growing interest in in silico serovar prediction and serotyping method-comparison studies, SeroTools provides unique tools which fill multiple gaps in the analysis process.…”