Hi Maytham,

So first of all and as mention before you need to sequence the entire 16S to identify the genus and species of your strain. With this result you could then determine if it is a new species or genus. If it is the case, you will then need to describe your strain and find a species name according with its characteristics. Concerning the STRAIN name, usually you keep the name you gave it in your lab (like A22_HD or RW25).

You can have a look for articles in the "International Journal of Systematic and Evolutionary Microbiology" to see how you could describe your strains.

Hope this helps,

Best.

sequence 16S rRNA gene

What kind of identification you used? as suggested above, to obtain the strain code better to do sequencing for 16S rRNA 

thanks

16SrRNA sequencing can specify bacterial strain into their genus and species groups.

Hi Maytham,

So first of all and as mention before you need to sequence the entire 16S to identify the genus and species of your strain. With this result you could then determine if it is a new species or genus. If it is the case, you will then need to describe your strain and find a species name according with its characteristics. Concerning the STRAIN name, usually you keep the name you gave it in your lab (like A22_HD or RW25).

You can have a look for articles in the "International Journal of Systematic and Evolutionary Microbiology" to see how you could describe your strains.

Hope this helps,

Best.

Well, when it comes to strain determination, one usually has to perform imological tests with antisera specific against H or O antigens. This applies, for example, to strains of Salmonella and E. coli. Usually, reference laboratories do that for you, once you have identified the species. I don´t think a 16S sequencing will give you the strain specificities since determining the sequence of this gene can only give you limited information. 

Hi,

    currently I am working with 24 bacterial isolates, I did 16sRNA sequence it gave info about genus, it also gave species information for few. 16sRNA sequence is not the ultimate but best.

Good luck :)

Hello,

Thank you very much for all answers. I would like clear one point, I Identified Klebsiella pneumoniae ssp pneumonia in two phase, first one based on morphology, Microscopic examination and Biochemical tests. The result show only genus and species name (Klebsiella pneumoniae) but second phase done with VITEK® 2 Compact and the result show only genus, species and subsp (pneumonia), further I sequenced CTX-M15 gene from this bacteria and I aligned It's nucleotides in NCBI/gene bank database and the result show 99% matching and there are strains names for this bacterial appear from other studies.

I concluded from (Qiao Ma , AbdelRahman Zueter , Hung King Tiong Cendrella Lepleux and Bhagya C T ) I can use strain names demonstrated by other researchers studies. In other hands, Uelinton Pinto suggested uses one more experiment or technique.

My further question is; How can I determine bacterial strain? Is it fair if I used bacterial strain name demonstrated by other researcher as shown in NCBI\GenBank identical to my bacterial gene sequence? or I have to do one more experiment ? or simply just I have to write name of bacteria as in my Lab ?

Kindly I need more information …

Thank you

The naming after your name can be done if you modify/mutate the strain belong to others. You can  name your isolated strains after your name. Example can be found at https://www.researchgate.net/profile/Hung_Tiong/publications (page 19, "H2O2")

Dear Hung King Tiong ,

Do you mean, if the bacterial strain got mutation should has new! strain name ?otherwise the name should stay as mentioned by the researcher first one find out this type of bacteria... 

Thank you

Yes, for example in the thesis we refer to strep. Pneumonia still remains the same genus and species, the only difference is we name it to our name of favor, eg.SP# was assigned for our pnumococcal lab strains which we have introduced mutation in them.

Dear Patrick Druggan,

    First of all thank you for the answer. I believed that the result of Vitek trustfully but it limited only for subspecies . I need to know how can I give strains names for bacterial isolates in formal way that will appear in NCBI database and publication journals ?

  I found some answers in Google that is strains refer to bacterial name in my lab but not from trust sources.

Thank you  

Dear Cendrella Lepleux,

   I agree totally with your opinion  because I found some related information support  your answer in Google but not from trusted sources I request  you kindly supply me a paper  say this to use it as a reference because I unable to find such paper even in the journal you suggested. Thank very much I appreciated your help too much.

I think you can design for sequence of 16sRNA

Dear Maytham,

The strain numbers for the isolates can be given according to your wish. Usually in each lab they follow a particular pattern for giving the strain numbers. If your lab does not have any such pattern you can start now by taking some initials which abbreviate your lab name or department name etc. followed by a number (which changes from isolate from isolate in a serial order). Hope this information will help you. All the best.  

Dear Maytham,

As far as I know, usually when you describe a strain you affiliate it to its genus species (and sub-species if so) and for the strain you keep the name you give it in your collection/lab.To my opinion it is really hard to differentiate at the strain level as it more a matter of tiny mutations and bacteria are evolving so fast.

You can have a look in reference collection database like the DSMZ (http://www.dsmz.de/catalogues/catalogue-microorganisms.html) where you can see all the different strain names for one type strain for example. Also in "BacDive", "NCBI" or "Strain info" you can also see that usually you can have several strain name for one type strain.

I am not sure there is any paper which statued on strictly strain names but you can have a look in the following paper which gives you general rules for describing a strain. The author is an expert in this taxonomy field so I guess you could also contact him for more specific questions, he might also have some idea about the reference you are looking for.

http://www.ncbi.nlm.nih.gov/pubmed/19700448

Best.

Morphological structure (Gram stain) +  Biochemical test + sequence16S rRNA gene

You must carry out the partial sequencing of 16SrDNA and then do the local ungapped alignment and find out the homologies pairwise. From this you will get the phylogenetic tree and you can then see where all the strains of yours get located. 

Hi Maytham,

I suggest you, if possible, to send you sample to Accugenix 

http://www.criver.com/products-services/rapid-micro/accugenix-microbial-identification-strain-typing

Biolog Inc. has a very easy system for Microbial identification with a database of over 2,500 species.  Please let me know if you have any questions.

http://www.biolog.com/products-static/microbial_identification_overview.php

Shalem is right. Every time you isolate a bacterium from a sample, it is a new strain (or isolate) and should have its own name, which you yourself supply. To do otherwise is incorrect. If you want to classify your isolates beyond the species level, I would recommend MLST. 

Go for 16S rRNA gene sequencing

I agree go for 16S DNA sequencing, folllowed by phylogenetics

d'abord vous devez commencer par les tests physiologiques ( forme, catalase, oxydase, Gram) et après vous pouvez allez aux tests biochimiques et à la fin vous pouvez utiliser les tests moléculaires pour plus de crédibilité comme ARN 16s, 

I agree go for 16S DNA sequencing

You can go for 16S DNA sequencing, then make a phylogenetic tree.

You can do 16SrRNA sequencing and phylogenetic tree.

The new trend is to follow up with multilocus sequence analysis (MLSA) using a number of housekeeping genes, followed by a concatenated tree.

16S DNA sequencing is best method

My opinion determine the isolate by VITEK 2 too easy and not expensive ... just sure the bacteria gram negative or positive or what then use the sutible card

VITEK 2 avilable at central health laboratory of Najaf and also at pharmacy college /kufa

Yes you can when you will do the 16SrRNA sequencing and then the homology analysis using simple tools like BLAST.

To be more accurate, 16SrRNA some time can mislead you.Preferably do the whole genome sequencing and then do the homology studies to be more precise.

The gold-standard method for strain determination is multilocus sequence typing (MLST). However, this requires that the method has been established for the species you are working with. This ought not to be a problem with UTI isolates.

For strain determination, I think using MLST typing for a specific genes of your target bacteria has more higher accuracy than 16s rRNA sequencing.

https://www.nature.com/articles/srep39200

Hope this link be helpful ~

An initial approach is 16S sequencing followed by phylogentic tree

However depending on the strain and coverage this might not be that accurate in many cases.

Full genome sequencing is definitely better approach it is much cheaper now to utilise these technologies.

Bioinformatics pipeline are much user friendly these for whole genome sequencing.