TABLE 3.
Identification of genes encoding SHV β-lactamases by a combination of PCR-RFLP and RSI-PCR analysis
| Mutations detected by PCR-RFLP analysis or RSI-PCR witha:
|
blaSHV variants yielding amplimers with various RFLP and RSI profilesc | ||||||||
|---|---|---|---|---|---|---|---|---|---|
| SspI* (8b) | DdeI (35) |
BglI
|
HinfI* (179) | PstI* (205) | NheI (238) | NruI* (240) | |||
| 43 | 156 | 187 | |||||||
| − | − | − | − | − | − | − | − | − | [blaSHV-1], blaSHV-16, dblaSHV-19(173/HaeII), blaSHV-28e |
| + | − | + | − | − | − | − | − | − | blaSHV-14 |
| + | − | + | − | − | − | − | − | + | blaSHV-18 |
| − | − | − | + | − | − | − | − | − | blaSHV-27 |
| − | − | − | − | + | − | − | − | − | blaSHV-26 |
| − | − | − | − | − | + | − | − | − | blaSHV-6, blaSHV-8 (179/BstUI), blaSHV-24 (179/SacII) |
| − | + | − | − | − | − | − | − | − | [blaSHV-11], blaSHV-13 (238/BsrI∗), blaSHV-25 (129/NlaIII) |
| − | + | − | − | − | − | − | + | − | [blaSHV-2a] |
| − | + | − | − | − | − | − | + | + | [blaSHV-12], blaSHV-15 (80/BtsI) |
| − | − | − | − | − | − | − | + | − | [blaSHV-2], blaSHV-20 (173/HaeII), blaSHV-21 (173/HaeII and 122/EcoRI) |
| − | − | − | − | − | − | + | + | − | [blaSHV-3] |
| − | − | − | − | − | − | + | + | + | [blaSHV-4] |
| − | − | + | − | − | − | − | + | + | blaSHVf |
| + | − | + | − | − | − | − | + | + | blaSHV-7 |
| − | − | − | − | − | − | − | + | + | [blaSHV-5], blaSHV-9 (54/NotI), blaSHV-10 (54/NotI and 130/StyI), blaSHV-22 (158/MaeII), blaSHV-23 (122/EcoRI and 188/AvaII) |
Mutations (amino acid positions are shown in parentheses or as subordinate headings) are detected by either PCR-RFLP analysis or RSI-PCR (indicated by asterisks). Symbols −, yielding amplimers with the same PCR-RFLP or RSI-PCR pattern as that of blaSHV-1; +, yielding amplimers with PCR-RFLP or RSI-PCR pattern generated by mutation.
Amino acid position numbering according to Ambler et al. (1).
Brackets indicate the blaSHV genes that are commonly found and can be differentiated by detecting four mutations (DdeI, position 35; PstI, position 205; NheI, position 238, and NruI, position 240) (see text).
Parentheses enclose mutation position and restriction endonuclease for PCR-RFLP or RSI-PCR (indicated by asterisk) analysis that can be applied for further identification of the gene. The gene encoding SHV-16 (Arpin et al., GenBank accession no. AF072684) can be differentiated from that encoding SHV-1 by comparing sizes of their amplimers using a pair of primers identifying the mutation at position 179; the amplimer generated from blaSHV-16 will yield a fragment of 250 bp, whereas that of blaSHV-1 will give a 235-bp fragment.
The gene encoding SHV-28 (Yu et al., GenBank accession no. AF299299) differs from that encoding SHV-1 by an amino acid substitution at position 7 from tyrosine in SHV-1 to phenylalanine in SHV-28. No restriction endonucleases detecting this mutation are available.
This gene was described by Winokur et al. and appears to be identical to SHV-17, which has been withdrawn (see text).