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I am doing an undergraduate research project that involves blaZ gene typing for different strain types of Staphylococcus aureus bacteria; for reference, here are some of papers on this topic that explore resistance abilities of the blaZ gene and four different beta-lactamases that can be produced:

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3421557/

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC188454/

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC106017/

Right now, I need to be able to align blaZ gene sequences in plasmids (or chromosomal regions, when looking at type B blaZ genes) of different S. aureus strains to the four blaZ gene type (A, B, C, and D) reference strains as mentioned in the first paper. The first paper provides the following strains as "reference strains": type A, PC1; type B, 22260; type C, RN98; and type D, FAR19. However, I can only find the nucleotide sequence for PC1 and the partial sequence for 22260 on Genbank; when I search for RN98 or FAR19, no relevant results come up. Even though these gene type sequences should only be distinguishable by several SNPs, it's important that I have references for all four for the most accurate strain typing.

In the last paper, I noticed they provide some of the differences between all four blaZ gene type nucleotide sequences, but not in a "from start to finish" order (i.e. the numbering above the nucleotides is not sequential and the sequence comparison length overall is less than 846, which is the length of the PC1 coding regions). Please advise, as after countless searches on Genbank I still do not have the specific sequencing information I need for each blaZ type.

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  • $\begingroup$ The sequences from that first paper probably weren't submitted to any database. If you want those specific sequences, you could try contacting the corresponding author. $\endgroup$
    – canadianer
    Jun 21, 2020 at 21:13

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You might have already tried this, but how about doing a BLAST search using one of the sequences you do have, and perhaps limiting the organism to Staph a.

More info: The below article did a similar comparison and mentions types RN9 and FAR10, perhaps these are related (or misspelled originally) See below.

"Real-Time PCR Assay for Detection of blaZ Genes in Staphylococcus aureus Clinical Isolates" at https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3993521/ mentions: "type A, PC1(pI254) and NCTC 9789; type B, 22260 and ST79/741; type C, 3804(pII3804), RN9(pII147), and V137; and type D, FAR10"

In any case I highly recommend going to your original article of interest, and use the "cited by" function to find more recent papers.

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  • $\begingroup$ Thank you! I tried this and a list of S. aureus strains with significant alignments were produced. Unfortunately none of them contained the reference sequence strain types as mentioned in the paper, i.e. RN98 or FAR19, but another paper I found gave some information on the types of differences (and number of differences) between amino acid sequences in each one, so I might be able to look into that as well for deducing sequence differences. $\endgroup$
    – CinnamonKittyLover
    Jun 21, 2020 at 17:52

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