Genetic environment of β-lactamase genes of extended-spectrum β-lactamase-producing Klebsiella pneumoniae isolates from patients with lower respiratory tract infection in China

Background Extended-spectrum β-lactamase (ESBL)-producing Klebsiella pneumoniae (K. pneumoniae) is one of the most popular pathogens that cause refractory respiratory tract infection. The genetic environment, including insertion sequences and the types of promoter, plays a key role in exploration of the mechanism of prevalence and dismission of the ESBL-producing K. pneumoniae isolates. The aim of the investigation was to target analysis the genetic environment and promoter sequences of bla CTX-M, bla SHV and bla TEM, the most popular β-lactamase genes harbored by ESBL-producing K. pneumoniae isolates. Methods From February 2010 to July 2011, 158 of 416 K. pneumoniae isolates producing ESBL from patients with lower respiratory tract infection were collected from seven tertiary hospitals from Beijing, Anhui, Fujian, Liaoning, Hebei and Inner Mongolia Autonomous Region in China. The genetic environment including promoters of 10 types of bla CTX-M, 18 types of bla SHV and 2 types of bla TEM were analyzed by amplification and direct sequencing with various sets of PCR primers. Results ISEcp1 was located upstream of the 5' end of the bla CTX-M gene in 130 (97.0%) out of 134 K. pneumoniae isolates harboring bla CTX-M and provided a conserved promoter to bla CTX-M. A non-coding sequence preceded by kdpC and recF was identified in all of the bla SHV genes except bla SHV-12 and bla SHV-2a. IS26 was also found upstream of 1 bla CTX-M-15, 10 bla SHV-1 strains, 4 bla TEM-1 and all of the bla SHV-2, bla SHV-2a, bla SHV-5 and bla SHV-12. Eighty-seven of 91 strains harboring bla TEM-1 carried a copy of Tn2 and IS26-bla TEM-1 fragments were also detected in 4 strains. With respect to K. pneumoniae, the genetic environment of bla CTX-M-38, bla SHV-142 and bla TEM-135 were firstly elaborated, and four kinds of novel genetic environment of bla CTX-M-3, bla CTX-M-15 and bla TEM-1 have been detected as well. Conclusions Perfective implementation of the genetic environment information of β-lactamase gene needs to be further explored and supplemented. ISEcp1 and IS26 elements are widespread upstream of the bla CTX-M, bla SHV and bla TEM genes and contribute to horizontal transmission and genetic expression.