Antibiotic resistance, multidrug resistance and enterobacterial repetitive intergenic consensus polymerase chain reaction profiles of clinically important Klebsiella species
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Reservoirs of drug resistant bacterial genomes and extrachromosomal DNA segments are a growing problem and cause emergence of new multidrug resistant (MDR) strains [1]. Antibiotic resistance of Klebsiella infections are causing increasing morbidity and mortality, and an increase in health care costs worldwide.
In epidemiological research, not only phenotypical analysis, but also genotypical analysis is conducted by using various molecular typing methods such as plasmid profiling, ribotyping, and polymerase chain reaction (PCR) to find genetic relationships between clinically important bacterial species [2, 3]. Our present study focused on prevalence of five Klebsiella spp. (K. pneumoniae, K. ornithinolytica, K. oxytoca, K. terrigena, and K. rhinoscleromatis) found in clinical materials. We examined antibiotic resistance and multidrug resistant strains and determined enterobacterial repetitive intergenic consensus (ERIC) PCR profiles for all Klebsiella spp.
Materials and methods
Bacterial strains
We used 5 different Klebsiella spp. (K. ornithinolytica, K. pneumoniae, K. oxytoca, K. terrigena, and K. rhinoscleromatis) that had been isolated in a previous study [4].
Antibiotic resistance testing and antibiotyping
The antibiotic resistance of Klebsiella species to six different antibiotics and combinations (SXT: trimethoprim-sulfamethoxazole (1.25/23.75 μg), SAM: ampicillin-sulbactam (10/10 μg), IPM: imipenem (10 μg), TZP: piperacillin tazobactam (100/10 μg), CIP: ciprofloxacin (5 μg), CZ: ceftizoxime (30 g)) were assessed using a Kirby–Bauer disc diffusion method. Klebsiella spp. that showed the same antibiotic resistance pattern, were grouped in the same antibiotype. MDR was defined as being resistant to at least three or more of antimicrobial classes [5].
Genomic DNA Extraction
The genomic DNA of Klebsiella spp. was extracted from bacterial cultures by using a bacterial DNA extraction kit (BioBasic, East Markham, Ontario, Canada) and isolated DNA was stored at -20°C.
Fingerprinting by enterobacterial repetitive intergenic consensus polymerase chain reaction
We determined the genomic fingerprint of Klebsiella spp. using enterobacterial repetitive intergenic consensus (ERIC) polymerase chain reaction (PCR) by using ERIC1 (5-ATG TAA GCT CCT GGG GAT TCA C-3′) and ERIC2 (5′-AAG TAA GTG ACT GGG GTG AGC G-3′) primers [6]. The reaction mix contained 50 ng template of DNA, 1 × PCR buffer (10 mM Tris-HCl, pH 8.3, 50 mM KCl, 1.5 mM, MgCl2, 0.1% Triton X-100), 2.5 mM dNTP, 2.5 U Taq polymerase (Roche Diagnostics, Mannheim, Germany) and 5 mM of each primer (ERIC1 and ERIC2) in a final volume of 50 μl [7]. The amplification procedure consisted of the following cycling steps: initial denaturation at 95°C for 2 min, followed by 40 cycles of denaturation at 94°C for 1 min, annealing at 52°C for 1 min, and extension at 72°C for 2 min. The final extension step was performed at 72°C for 2 min.
Gel electrophoresis and data analysis
We analyzed PCR products using 1.8% agarose gel electrophoresis (Scie-Plas; Warwickshire, UK) by using TBE 1× buffer (0.9 M Tris, 0.9 M Boric acid, and 20 mM EDTA, pH 8.3) at 90 V for 5 h. Agarose gels were documented using a Gel Logic 200 Molecular Imaging System (Kodak; Rochester, NY, USA). To analyze the profiles of Klebsiella strains, NTSYSpc (version 2.1; Applied Biostatistics, Port Jefferson, N Y, USA) Numerical Taxonomy and Multivariate Analysis System was used and a dendrogram was constructed using an unweighted pair group method with arithmetic mean and by using Dice coefficients of similarity. Klebsiella sp. strains with a similarity coefficient of 70% were grouped in a genotype.
Ethical considerations
This study was designed to fully protect the anonymity of patients using unlinked anonymized samples and was conducted in compliance with the principles of the contemporary version of the Declaration of Helsinki. The protocol was approved by the Hacettepe University Scientific Research Projects Coordination Unit (project No. 08D11601001).
Results
We found that the urine samples and the urology service unit were the source of most Klebsiella spp. isolated with K. pneumoniae, K. ornithinolytica, and K. terrigena species being the most frequent (Figures 1 and 2).
Figure 1
Klebsiella species found in various clinical materials.
Figure 2
Klebsiella species found in various service units URO, urology; SIC, surgical intensive care unit; PTR, physical treatment and rehabilitation unit; IM, internal medicine; EM, emergency medicine; NEU, neurology unit; O, otorhinolaryngology
The greatest resistance was observed against trimethoprim-sulfamethoxazole (88%), the least resistance was against imipenem (12%) as shown in Table 1.
Antibiotic resistance of Klebsiella species
Antibiotics
K. pneumoniae
K. ornithinolytica
K. oxytoca
K. rhinoscleromatis
K. terrigena All Klebsiella spp. (%)
Ciprofloxacin
16%
13%
13%
20%
0% 13%
Imipenem
12%
22%
0%
20%
0% 12%
Ampicillin-sulbactam
24%
35%
0%
20%
50% 28%
Piperacillin-tazobactam
20%
35%
38%
20%
50% 31%
Ceftizoxime
16%
13%
0%
20%
50% 18%
Trimethoprim-sulfamethoxazole
84%
87%
100%
20%
100% 88%
Eleven different antibiotypes were generated. AI was the most frequently observed antibiotype, AVII and AVIII were only observed in K. pneumoniae, AIII and AV I were only observed in K. ornithinolytica, AX was only observed in K. rhinoscleromatis, and AIX was only observed in K. oxytoca. (Figure 3).
Accordingly, 25% of all Klebsiella spp. strains were found as MDR and 65% of these were isolated from urine. MDR strains were mostly isolated from the species of K. ornithinolytica (35%) followed by K. pneumoniae (29%) and they grouped in AV antibiotype profile (53%).
Genotyping performed by using ERIC/PCR grouped Klebsiella spp. strains into 23 different genotypes with a similarity coefficient of 70% (Figure 4). Only 43% of all genotypes included MDR strains. Accordingly, 50% of the strains in the 4th genotype (K31, K32, K36, K38) were found as MDR and all of the MDR strains of K. terrigena were grouped in the AV antibiotype profile. In the 9th genotype, there were only two MDR strains (K5, K10) and they belonged to K. ornithinolytica (Figure 4).
Figure 4
Cluster analysis of the profiles obtained from five different Klebsiella species by ERIC-PCR analysis
Discussion
Klebsiella spp. are known as an important opportunistic pathogens among the members of the Enterobacteriaceae [1, 8-11]. Accordingly, Klebsiella spp. are the second most causative agent of urinary tract infections (UTIs) after Escherichia coli. They represent 6%–17% of all nosocomial UTIs and 7% of all nosocomial infections [9, 12, 13]. Additionally, Klebsiella sp. are known as major agents complicating symptomatic or asymptomatic catheter-acquired UTIs; especially in hospitalized patients [14]. We identified the major foci where these infections occurred and were able to institute defensive procedures against additional spread. As consistent with previously published findings, we found that Klebsiella infections were widespread in samples of urine and in UTIs when compared with other clinical materials [9, 10, 15, 16]. We also found that the most effective antibiotic against Klebsiella spp. was imipenem. The least effective antibiotic was trimethoprim-sulfamethoxazole, and that the overall pattern of imipenem resistance was low: 0% [17], 2% [18], 5.4% [19], 13.9%, [10], and 16% [20]. Additionally, we found 25% of all Klebsiella sp. in the present study to be MDR and that strains that belong to K. ornithinolytica (35%) were predominantly MDR, followed by K. pneumoniae (29%). Previously, K. pneumoniae was found to be the predominant MDR species [21].
Various molecular typing methods, especially PCR fingerprinting assays, are now increasingly being used to identify strains in clinical practice [22]. ERIC/PCR showed that there was heterogeneity between genotypes of Klebsiella spp. strains and that there was no correlation between different species according to their ERIC/PCR profiles. Similarly, phylogenetic analysis of Klebsiella in a previous study showed taxonomic heterogeneity among the species [23]. Electrophoretic analysis of K. pneumoniae also showed genotypical heterogeneity [24-26]. It is therefore not surprising to find genotypical heterogeneity among our five different Klebsiella species, which were isolated from various clinical materials and service units, and grouped in 11 different antibiotypes.
Conclusions
Imipenem was the most effective antibiotic against Klebsiella spp. in our geographical region of Turkey. MDR strains are widespread among Klebsiella spp., especially among K. ornithinolytica and K. pneumoniae. Genotypical heterogeneity exists among Klebsiella spp. It is important to be vigilant for nosocomial infections and to take precautions against the transmission of infectious microorganisms between hospitalized patients to prevent the emergence of MDR strains.
