TABLE 2.

Details of discrepancies between conventional PCR plus DNA sequencing results and Check KPC/ESBL genotyping results

Strain	Source or reference	Gene identified by PCR and DNA sequencing	Gene identified by Check KPC/ESBL genotyping	Comment(s)
E. coli DH10B	This study	blaSHV-38	SHV-non-ESBL	Rare chromosomal genotype found in a single K. pneumoniae isolate (18); mutation conferring ESBL phenotype not assayed with current microarray primers
K. pneumoniae VA-361a	4	blaKPC-2, blaTEM-1, blaSHV-11	KPC, TEM-non-ESBL, SHV-ESBL	Possible production of an SHV-ESBL (e.g., SHV-5/SHV-12)
K. pneumoniae VA-388	4	blaKPC-3, blaTEM-1, blaSHV-11	KPC, TEM-non-ESBL	SHV genes were not detected
K. pneumoniae VA-392a	4	blaKPC-3, blaTEM-1, blaSHV-11	KPC, TEM-non-ESBL, SHV-ESBL	Possible production of an SHV-ESBL (e.g., SHV-5/SHV-12)
K. pneumoniae VA-412a	4	blaKPC-2, blaTEM-1, blaSHV-11	KPC, TEM-non-ESBL, SHV-ESBL	Possible production of an SHV-ESBL (e.g., SHV-5/SHV-12)
K. pneumoniae VA-414	4	blaKPC-3, blaTEM-1, blaSHV-11	KPC, TEM-non-ESBL, SHV-ESBL	SHV-11 is not an ESBL
K. pneumoniae 111b	15	blaTEM-10-like, blaSHV-1-like	TEM-ESBL, SHV-ESBL	SHV-1 is not an ESBL
K. pneumoniae 438b	15	blaTEM-2-like, blaSHV-1-like	TEM-non-ESBL, SHV-ESBL	SHV-1 is not an ESBL
E. coli 25	This study	blaCTX-M-9-like	CTX-M-(IV),c TEM-non-ESBL	blaTEM genes were not detected by PCR analysis (including using internal primers); aIEF showed only one β-lactamase band at a pI of 6.7, possibly related to the CTX-M enzyme expression

^aAnalytical isoelectric focusing (aIEF) revealed β-lactamase bands with pIs of 7.6 and 8.2 and initial standard DNA sequencing of bla_SHV showed double spikes in amino acid position 238 and/or 240 (4).

^bPartial DNA sequencing (i.e., from amino acid 35 to 274 for TEMs and from 8 to 249 for SHVs). The bla_SHV and bla_TEM sequences did not show substitutions conferring an ESBL phenotype.

^cNumber in parentheses following CTX-M designation indicates the family group for CTX-M-type ESBLs (16).