Yohan, you can identify serovars by serotyping only. 16S sequencing is not suitable for such task, even for MLST, you can expect to see only some correlation between DNA and serovars, and it will depend on your set of isolates.

Thank you Alex, if the serotyping is the only solution for this I have 75 samples to analyse. So are there any commercial companies for doing serotyping?  Because we have no such facilities....

xMAP ® Salmonella serotyping test kit and service from Luminex

https://www.luminexcorp.com/eu/research/applied-markets/salmonella-serotyping-assay/

SALMONELLA TEST KIT from Oxoid http://www.oxoid.com/UK/blue/prod_detail/prod_detail.asp?pr=DR1108&c=UK&lang=EN&org=&minfo=Y&print=Y

SSI Salmonella antisera from Statens Serum Institut http://www.ssi.dk/~/media/Admin/Diagnostica%20Downloads/Downloads%20UK/Brochures/BrochureSalmonella%20antisera%20ver%202%20high14112011145552.ashx

Antisera from BIO-RAD http://www.bio-rad.com/webroot/web/pdf/fsd/literature/FSD_14-0699.pdf

Premi®Test Salmonella http://www.oie.int/fileadmin/home/eng/our_scientific_expertise/docs/pdf/usersmanual_pts_june11.pdf

I guess that most of producers have commercial service for testing...

Thank you for your instant reply alex. I will try to contact them also...

Yohan, Salmonella serotyping can be done by procuring the antisera from BD Difco. They products are quite costly but worth the penny spent. You may aslo try the ones mentioned by Alex.. Serotyping is the best way to identify Salmonella serovars. Best wishes

 Thank you suganthi, ok I will try to contact BD also....

PCR identification screening using specific primers has been developed for some major and important serovars. Other molecular methods include DNA-microarray-based approaches, e.g.  serogenotyping, Cheers!

serotyping is cost effective...and equally good./././.

I have found PCR based specific identification of genes, depending on typhoidal or non-typhoidal salmonellae (identified after biochemical characterization) cost effective and reliable. For serotyping you got to have all the antisera required.  

Please check following - my publications: 

1. Early diagnosis of typhoid fever by nested PCR for flagellin gene of Salmonella enterica serotype Typhi. Indian J Med Res 136(5):850–854.

2. Detection of Salmonella in Blood by PCR using iroB gene. J Clin Diagn Res. 2014 Nov; 8(11): DC01–DC03.

Technically serotyping defines serovars but is expensive, objective and can be unreliable. In general MLST will allow the vast majority of isolates to be types into a serovar and can, in the case of S. Typhiumurium for example, further differentiate into STs that may have distinctly different infection biology. It is worth noting all human isolates in England and Wales are whole genome sequenced routinely now.

 Thank you for giving several ideas for my problem ....Kayode, Sayan, Dr. Godfred and Paul.....

I meant to say serotyping can be subjective and needs good controls. As Alex points out 16S is not  a good approach as the variance is small. I would argue MLST largely overcomes this-certainly MArk Achtamann's work would suggest this.

I guess it dependent what you need the results for... Before you read my answer, I have to admit that I have done identification with Listeria and not Salmonella, although I have worked with Salmonella for years... 

16S rRNA sequencing is used for identification of bacteria to species and/or genus level ie fx Salmonella enterica but not saying if you work with Salmonella enterica serovar Typhimurium or Dublin.

Serotyping is a phenotypic typing method where you by use of antisera differentiate between the different serotypes of Salmonella ie Typhimurium or Dublin.

MLST is a molecular typing method where you by sequencing of seven genes different between different molecular subtypes of Salmonella also called sequence types.

There is some correlation between serotyping and MLST sequence types ie ST1 is mainly Typhimurium. Achtman et al (2012; Plos Pathogens 8:e1002776) published about this.

Serovar determination according to Kaufmann-White requires serology. The results do not correlate necessarily with genotyping.

But Werner, although this is the case, it does not mean it is the best way forward. Serotyping relies on variation in expression of a small number of LPS and flagella genes. The actual phenotype of the isolate is governed by 4500 genes and how they are expressed. WGS approaches will replace serotyping and given the cost (and frequent unreliability) of serotyping, it is time as PHE in the UK have done to move forward from this.  As a low cost option I would use MLST as it may give a few servers the same ST but this may actually mean more than the same serotype.  

Paul, I argue from a medical point of view. For diagnosis it is sufficient to name S. enterica serovars by means of O- and H- antigens. For all other purposes which require clonal analysis, WGS or MLST will be the future.

 In response to Michael Ganzle

Yes several people have developed PCR-based serotyping for Salmonella but it is a bit laborious given that you may need to identify up to 4 variations of O antigens and 2  H for each serovar. It is reasonably easy to get to serogroup level. It's when you look at Group D Salmonella where you begin to see where serotyping can go wrong as Enteritidis, Dublin and Gallinarum/Pullorum share the same O antigenic formulae but differ slightly in H antigens-not surprising when you look at the genomic relationship but does lead to mistyping especially if the reaction to the H antigen is weak.  Furthermore the issue of biphasic flagella in many serovars makes typing challenging. Serotyping tends to be best done in dedicated and experienced labs, but there is a lot of anecdotal evidence of different labs typing the same isolate as different servers.

Werner

For diagnosis of a standard diarrheal non-typhoidal Salmonella in humans I would agree. Almost certainly an antibiogram would be as important as knowing serotype. Where genomic approaches, especially WGS, have an advantage is in invasive NTS and identifying unusual variants such ST313 S. Typhimurium.  In poultry identifying the avian adapted serotypes is pretty important as they tend to wipe out flocks.

John

I agree entirely-access to NGS for whole genomes may be an issue for some (which is why MLST still has a place for now), but in terms of epidemiological investigation it blows anything else out-of -the water and tells us so much (including likely resistance and some indication of pathogenicity/likely epidemic isolates).  Some of the work Sharon Peacock has done using WGS in epidemiology (albeit not for Salmonella) shows the power as does the PNAS paper on Enteritidis/Gallinarum evolution and host adaptation. As we begin to better understand the infection biology genomic variation brings  I think we will soon be in a better position to predict and intervene in outbreaks in humans and livestock.

Thank you for all 

John, If I go for a WGS method, May I know the cost per sample. I think it little bit expensive and I want to know  about Institutes/Universities which are doing WGS commercially, because I have 75 samples to analyse.

I have NTS isolates which i want to serotype and do WGS. Where can i get these services? What is the cost per isolate? My NTS are from Humans and Livestock. I am from Kenya.

I sent my Salmonella isolates to World Health Organization (WHO) National Salmonella and Shigella Centre in Bangkok. I think if you can contact them they will give you the service. For WGS contact macrogen korea.

Until now, there is no research uses the 16S rRNA sequences to serotype Salmonella strains. you can use only serotyping by agglutination test.

Of cause 16S rRNA not enough to identification of serovars level....Finally I did my identification using serotyping method but serotyping service not available in some countries. But if we can do whole genome sequencing that may advantage for future works.

I agree with all Paul and John wrote. Of course, MLST would be the method of choice, given it is available at place with reliable Quality. If you have to make a rapid diagnosis based on clinical symptoms, serology is sufficient (I agree, expensive). Sample tourism to reference labs is also expensive and time-consuming.

Yohan, did you get to the answer you were looking at?

Of cause Sir Werner....I took the service of serotyping from WHO Salmonella and Shigella Centre in Thailand. Sir, Do you have any information about any other laboratory doing serotyping and cost per sample?

What is the purpose of 16Sr RNA sequence for Salmonella because it is still very popular and have a lot of sequence data at the NCBI database.

But that is not accurate than Serotyping for the identification of Serovars.