Data on the phylogenetic typing, integron gene cassette array analysis, multi-drug resistance analysis and correlation between antimicrobial resistance determinants in Klebsiella strains

The antimicrobial resistance of Klebsiella species in the poultry industry is becoming a public concern. In support our recent publication “Characterization of antimicrobial resistance in Klebsiella species isolated from chicken broilers” (Wu et al., 2016) [1], multilocus sequence typing (MLST) and gyrA PCR-RFLP assays were conducted to identify the genetic relationships between and phylogenetic groups of the 90 antimicrobial resistant Klebsiella species isolated from a commercial broiler slaughter plant in Shandong, China. In addition, PCR-RFLP was performed to identify different gene cassette arrays in class 1 and 2 integrons, and the correlations between different antimicrobial resistance determinants were analyzed.


a b s t r a c t
The antimicrobial resistance of Klebsiella species in the poultry industry is becoming a public concern. In support our recent publication "Characterization of antimicrobial resistance in Klebsiella species isolated from chicken broilers" (Wu et al., 2016) [1], multilocus sequence typing (MLST) and gyrA PCR-RFLP assays were conducted to identify the genetic relationships between and phylogenetic groups of the 90 antimicrobial resistant Klebsiella species isolated from a commercial broiler slaughter plant in Shandong, China. In addition, PCR-RFLP was performed to identify different gene cassette arrays in class 1 and 2 integrons, and the correlations between different antimicrobial resistance determinants were analyzed. &

Data accessibility
The data is available with this article

Value of the data
The gyrA PCR-RFLP assay and MLST analysis in the Klebsiella isolates indicate the relationship of epidemiology of drug resistant bacteria in between clinical and poultry industry.
The PCR-PFLP by EcoRII can be applied as a tool for detection of gene cassette arrays of integron 1 or 2.
The statistical data and finding of a significant association of antimicrobial resistance determinants can be used as references for the investigation of other drug resistant bacteria.

Data
MLST was performed using seven housekeeping genes (rpoB, gapA, mdh, pgi, phoE, infB, and tonB), and primers of those genes for PCR amplification and sequencing were designed (Table 1) [2]. gyrA PCR-RFLP profiles showed nearly all (89/90) of the isolates were identified as KpI-type and only one isolate was KpIII (Fig. 1). Antimicrobial susceptibility to nine antimicrobial agents was tested for the 90 Klebsiella isolates [1]. Among the isolates, 96.7% of them were resistant to more than three tested antimicrobial agents as well as 91.1% were resistant to more than three beta-lactam antibiotics (Fig. 2). A significant association between different antimicrobial resistance determinants was analyzed (Table 2). PCR-PFLP patterns of gene cassette arrays for integron 1 or 2 were performed (Fig. 3), and the detailed description was in the original article [1].

PCR Program
PCRs were prepared as follows: a final volume of 25 μl containing 1 μM of each primer, 0.2 mM dNTPs, 1.5 mM MgCl 2 , and 1 unit of Taq polymerase (TransGen Biotech, Beijing, China). The conditions used for amplification were as described by the original article [1].

Primers designed for the MLST analysis of Klebsiella isolates
The primer pairs for seven housekeeping genes (rpoB, gapA, mdh, pgi, phoE, infB, and tonB) were designed for PCR amplification and sequencing (Table 1), as described previously [2].

Molecular identification by PCR-RFLP analysis of the gyrA gene
gyrA PCR-RFLP patterns were obtained by the restriction analysis of a 441-bp PCR fragment of the gyrA gene using the restriction enzymes HincII, TaqI, or HaeIII (Fig. 1) [3,4]. According to this approach, Klebsiella strains can be classified into the KpI, KpII, and KpIII phylogenetic groups.

Statistics analysis
According to the prevalence of antimicrobial resistance genes among 90 Klebsiella isolates [1], the number of antimicrobial resistance strains (Fig. 2a) and the percentage of tested strains resistant to  were the sequencing primers for pgi and infB, respectively.  different numbers of beta-lactam antibiotic groups were analyzed (Fig. 2b). Also the statistical analysis of the correlation between different antimicrobial resistance determinants was performed by chi-square tests using SPSS (SPSS 19.0 for Windows; SPSS Inc., Chicago, IL, USA), and a p-value o0.05 was considered to be statistically significant ( Table 2).

Identification of integron gene cassette arrays
The gene cassette arrays of class 1 and 2 integrons were analyzed (Fig. 3) by a PCR-RFLP method as described previously [5].