Abstract
To investigate the molecular epidemiology of aminoglycosides resistance among Klebsiella pneumonia in hospitals in China, the antibiotics resistance and the possession of extended-spectrum β-lactamases (ESBLs) from 162 isolates were examined using Kirby-Bauer disk diffusion and PCR sequencing. Overall, 47.5% (77/162) of strains showed an ESBL phenotype. According to antibiotics resistance, ESBLs-positive K. pneumoniae showed significantly higher resistance to most antibiotics than ESBLs-negative strains (P<0.05). Moreover, 162 strains harboured aminoglycoside-modifying enzymes genes (AMEs) including aac (3)-II (n = 49), aac (6’)-Ib (n = 32), ant (3”)-I (n = 22) and ant (2”)-I (n = 7). Overall, 11.1% (18/162) and 6.2% (10/162) of isolates carried 16S rRNA methylase genes (armA and rmtB), in which the aminoglycoside MIC was more than 256 μg/ml. In conclusion, our study characterised aminoglycosides resistance among K. pneumoniae strains in China hospitals and revealed antibiotic resistance and the increased presence of AMEs and 16S rRNA methylase genes in K. pneumonia, enabling the prevalence of aminoglycosides resistance of K. pneumoniae to be tracked from patients.
Keywords: Aminoglycosides resistance, AMEs, 16S rRNA methylase, Klebsiella pneumonia
Introduction
Recently, Klebsiella pneumonia has become one of the most important conditional pathogenic bacteria in nosocomial infections. Accordingly, antimicrobial therapy continues to be a widely available tool for the prevention and control of this infection. However, owing to the overuse of antimicrobials, especially β-lactams or aminoglycosides, resistance has become increasingly prevalent, thus compromising their therapeutic efficacy. Indeed, the emergence and prevalence of antimicrobial-resistant K. pneumoniae strains has been described in many countries [1-3]. The underlying mechanism of β-lactam resistance is dominated by the expression of extended-spectrum β-lactamase (ESBLs) [1]. Moreover, the mechanisms of resistance to aminoglycosides also include enzymatic modification of this drug, modification of the ribosomal target and decreased intracellular antibiotic accumulation by alterations of the outer membrane permeability, decreased inner membrane transport or active efflux [4]. Among them, the production of aminoglycoside-modifying enzymes is the most common mechanism of resistance to aminoglycosides. Modification of 16S rRNA by these enzymes reduces binding to aminoglycosides, leading to high-level resistance to aminoglycosides, including arbekacin, amikacin and, kanamycin [5,6]. Currently, seven 16S rRNA methylase genes have been identified (armA, rmtA, rmtB, rmtC, rmtD, rmtE and npmA) [1-3].
The goals of the present study were to investigate the state of antibiotic resistance and the prevalence of ESBLs and the aminoglycoside resistance genes in K. pneumoniae strains, in order to assess which resistance mechanisms might contribute to the observed aminoglycosides resistance in K. pneumoniae.
Materials and methods
Bacterial isolates
Between October 2009 and December 2010, a total of 162 K. pneumoniae field strains were isolated from patients in the Third Affiliated Hospital of Sun Yat-sen University. These isolates were identified by conventional biochemical methods and the MicroScan Wa1kAway-40 automatic bacteria identification system.
Antimicrobial susceptibility testing
The antibiotic susceptibility of K. pneumoniae to 22 common antibiotics was determined using K-B disk diffusion method according to CLSI [7]. Twenty-two common antibiotics were used, including: Ampicillin (AMP, 10 μg), Ampicillin/sulbactam (SAM, 10 μg/10 μg), Piperacillin (PIP, 100 μg), Piperacillin/tazobactam (TZP, 100 μg/10 μg), Amoxycillin/clavulanic acid (AMC, 20 μg/10 μg), Ticarcillin/clavulanic acid (TLC, 75 μg/10 μg), Cefazolin (CZL, 30 μg), Cefotaxime (CTX, 30 μg), Ceftriaxone (CRO, 30 μg), Ceftazidime (CAZ, 30 μg), Cefepime (FEP, 30 μg), Cefoxitin (FOX, 30 μg), Aztreonam (ATM, 30 μg), Imipenem (IMP, 10 μg), Ciprofloxacin (CIP, 5 μg), Levofloxacin (LEV, 5 μg), Sulphamethoxazole/trimethoprim (SXT, 1.25 μg/23.75 μg), Amikacin (AMK, 30 μg), Gentamycin (GM, 10 μg), Tobramycin (TOB, 10 μg), Cefotaxime/clavulanic (CTX/CA, 30 μg/10 μg) and, Ceftazidime/clavulanic acid (CAZ/CA, 30 μg/10 μg). Generally, the breakpoints for the antimicrobial agents for K. pneumoniae were according to CLSI [7].
Moreover, minimal inhibitory concentrations (MICs) of amikacin, gentamycin and tobramycin to K. pneumoniae were detected. The reference strains Escherichia coli ATCC 25922, Escherichia coli ATCC 35218 and K. pneumoniae ATCC 700603 served as quality control strains for the determination of antibiotics susceptibility.
The ESBLs phenotypic confirmation
Confirmatory tests for ESBLs of 162 K. pneumoniae clinical isolates were performed by adopting the Kirby-Bauer diffusions method, according to CLSI [7].
Screening for aminoglycosides resistance genes
The isolates were selected for further molecular characterisation of aminoglycosides resistance by polymerase chain reaction (PCR) using ExTaq DNA polymerase (TAKARA, Dalian, China), and specific oligonucleotide primers, as previously described [1,8-10]. The aminoglycosides resistance genes included aac (3)-II, aac (6’)-Ib, ant (3”)-I, ant (2”)-I, aac (3)-I, aac (6’)-II, aac (6’)-Iad and 16S rRNA methylase genes (armA, rmtA, rmtB, rmtC, rmtD, npmA). The DNA templates of all 162 K. pneumoniae strains were prepared using the standard boiling method [11]. The PCR amplicons were cloned into pMD-19T vectors (TaKaRa Inc., China) and sequenced by the Applied Biosystems 3730 sequence analyser (Applied Biosystems Inc., USA).
Statistical analysis
We used the SPSS13.0 statistics software package for analysis. The data was described as x̅±s. The differences between groups were compared by the chi-square test (P<0.05 for statistical significance).
Results and discussion
Bacterial isolates
A total of 162 clinical isolates of K. pneumoniae were isolated from sputum (49.4%), plasma (16.0%) and bile (9.9%) sample (Table 1). For the sources of the samples, the top three departments were the intensive care unit (ICU) (22.8%), hepatic surgery (14.8%) and the neurosurgery department (11.7%) (Table 2). Over the past 10 years, a progressive increase has been seen on a worldwide scale [12,13]. In the USA, this phenomenon in K. pneumoniae was first described in North Carolina in 1996 [12], and the new emerging nosocomial pathogen is probably best known for an outbreak in Israel that began around 2006 within the healthcare system there [13].
Table 1.
The distribution of specimens of K. pneumoniae (n = 162)
| Specimens | Strains (n) | Rate (%) |
|---|---|---|
| Sputum | 80 | 49.4 |
| Blood | 26 | 16.0 |
| Bile | 16 | 9.9 |
| Urine | 13 | 8.0 |
| Cutaneous mucous secretions | 12 | 7.4 |
| Throat swab | 6 | 3.7 |
| Hydrothorax and ascites | 5 | 3.1 |
| Others | 4 | 2.5 |
Table 2.
The distribution of K. pneumoniae in clinical departments (n = 162)
| Department | Strains (n) | Rate (%) |
|---|---|---|
| Intensive care unit | 37 | 22.8 |
| Hepatobiliary Surgery | 24 | 14.8 |
| Neurosurgery | 19 | 11.7 |
| Respiratory Department | 13 | 8.0 |
| Haematology Department | 13 | 8.0 |
| Tumour Department | 11 | 6.8 |
| Cardiothoracic Surgery | 10 | 6.2 |
| Neurology Department | 8 | 4.9 |
| Rehabilitation Department | 7 | 4.3 |
| Outpatient and Emergency | 7 | 4.3 |
| Others | 13 | 8.0 |
Antibiotics resistance in K. pneumoniae
Antimicrobial susceptibility and the comparison of antimicrobial-resistance between ESBLs-positive and ESBLs-negative K. pneumoniae are shown in Table 3. The results of confirmatory tests showed that the rate of ESBLs-producing K. pneumoniae was 47.5% (77/162). Antibiotic susceptibility tests showed that ESBLs-producing K. pneumoniae was most sensitive to imipenem with a rate of 98.7%, followed by 75.3% for amikacin, and 71.4% for piperacillin/tazobactam. The resistance rate of ESBLs-negative K. pneumoniae to ampicillin was 87.0%, but was below 25% for the other antibiotics. Except for imipenem and amikacin, resistance rates of ESBLs-producing strains were significantly higher than those of ESBLs-negative strains (P<0.05), which may have been caused by other resistance mechanisms in those ESBLs-producing K. pneumoniae isolates [1,14].
Table 3.
Comparison of antimicrobial-resistance between ESBLs-positive and ESBLs-negative K. pneumoniae
| Antibiotics | ESBLs (+) (n = 77) | ESBLs (-) (n = 85) | x2 | P | ||||
|---|---|---|---|---|---|---|---|---|
|
| ||||||||
| R (%) | I (%) | S (%) | R (%) | I (%) | S (%) | |||
| Ampicillin | 98.7 | 0.0 | 1.3 | 87.0 | 11.8 | 1.2 | 7.984 | 0.005 |
| Piperacillin | 97.4 | 0.0 | 2.6 | 24.7 | 15.3 | 60.0 | 88.438 | 0.000 |
| Ampicillin/sulbactam | 83.1 | 11.7 | 5.2 | 12.9 | 11.8 | 75.3 | 80.024 | 0.000 |
| Amoxycillin/clavulanic acid | 26.0 | 27.3 | 46.7 | 3.5 | 5.9 | 90.6 | 16.707 | 0.000 |
| Piperacillin/tazobactam | 23.4 | 5.2 | 71.4 | 1.2 | 1.2 | 97.6 | 19.233 | 0.000 |
| Ticarcillin/clavulanic acid | 31.2 | 32.5 | 36.4 | 3.5 | 2.4 | 94.1 | 22.222 | 0.000 |
| Cefazolin | 93.5 | 1.3 | 5.2 | 7.1 | 1.2 | 91.8 | 120.936 | 0.000 |
| Cefotaxime | 84.4 | 9.1 | 6.5 | 1.2 | 1.2 | 97.6 | 115.948 | 0.000 |
| Ceftazidime | 48.0 | 23.4 | 28.6 | 0.0 | 0.0 | 100.0 | 52.934 | 0.000 |
| Ceftriaxone | 85.7 | 5.2 | 9.1 | 1.2 | 1.2 | 97.6 | 119.050 | 0.000 |
| Cefepime | 72.7 | 15.6 | 11.7 | 1.2 | 0.0 | 98.8 | 90.696 | 0.000 |
| Cefoxitin | 35.1 | 5.2 | 59.7 | 5.9 | 1.2 | 92.9 | 21.706 | 0.000 |
| Aztreonam | 61.0 | 10.4 | 28.6 | 1.2 | 0.0 | 98.8 | 69.437 | 0.000 |
| Imipenem | 1.3 | 0.0 | 98.7 | 1.2 | 0.0 | 98.8 | 0.005 | 0.944 |
| Ciprofloxacin | 45.5 | 11.7 | 42.8 | 16.5 | 2.4 | 81.1 | 16.087 | 0.000 |
| Levofloxacin | 37.7 | 5.2 | 57.1 | 8.2 | 3.5 | 88.3 | 20.242 | 0.000 |
| Amikacin | 22.1 | 2.6 | 75.3 | 12.9 | 1.2 | 85.9 | 2.648 | 0.104 |
| Gentamycin | 59.7 | 2.6 | 37.7 | 17.6 | 1.2 | 81.2 | 28.631 | 0.000 |
| Tobramycin | 44.2 | 14.3 | 41.5 | 10.6 | 1.2 | 88.2 | 23.348 | 0.000 |
| Sulphamethoxazole/trimethoprim | 68.8 | 0.0 | 31.2 | 21.2 | 1.2 | 77.6 | 37.268 | 0.000 |
P = comparison of Klebsiella pneumoniae between ESBLs (+) and ESBLs (-).
Prevalence of AMEs genes and 16S rRNA methylase genes
Molecular identification of the 162 isolates obtained from the hospital showed that the positive rates of AMEs genes, such as aac (3)-II, aac (6’)-Ib, ant (3”)-I and ant (2”)-I, were 30.2%, 19.8%, 13.6% and 4.3%, respectively. Also 16S rRNA methylase genes were also identified with positive rates of armA and rmtB of 11.1% and 6.2%, respectively. All sequences of the detected amplicons were aligned and it was shown that there was over 99% identity with the reported target genes accessed from NCBI.
The distribution of AMEs and 16S rRNA methylase gene in K. pneumoniae is shown in Table 4. Among them, 28 strains carried both AMEs and 16S rRNA methylase genes. A total of 62 strains carrying resistance genes included 16 strains with 1 genotype, 26 strains with 2 genotypes, 12 strains with 3 genotypes, 6 strains with 4 genotypes and 2 strains with 5 genotypes. The most common genotype was aac (3)-II+aac (6’)-Ib, and the positive rate was 12.9% (8/62); this was followed by aac (3)-II with the a positive rate of 11.3% (7/62). It was reported that 16S rRNA methylases first appeared in K. pneumoniae in 2003 [15]. RmtB was first identified in S. marcescens from Japan in 2004, and was subsequently found in K. pneumoniae and E. coli isolates from Taiwan, Korea and Belgium [1,8,16,17]. To date, the 16S rRNA methylase genes were prevalent globally [1]. In this study, AMEs genes of aac (3)-II, aac (6’)-Ib, ant (3”)-I and ant (2”)-I and 16S rRNA methylase genes of armA and rmtB were all prevalent in K. pneumoniae in China.
Table 4.
The distribution of AMEs and 16S rRNA methylase gene in K. pneumoniae (n = 162)
| Gene Types | Strains Num. | Rate (%) |
|---|---|---|
| aac (3)-II | 7 | 11.3 |
| aac (6’)-Ib | 5 | 8.1 |
| ant (3”)-I | 3 | 4.8 |
| ant (2”)-I | 1 | 1.6 |
| armA+aac (3)-II | 5 | 8.1 |
| armA+ant (3”)-I | 4 | 6.5 |
| rmtB+aac (3)-II | 5 | 8.1 |
| aac (3)-II+aac (6’)-Ib | 8 | 12.9 |
| aac (3)-II+ant (3”)-I | 4 | 6.5 |
| armA+aac (3)-II+aac (6’)-Ib | 3 | 4.8 |
| armA+aac (3)-II+ant (3”)-I | 1 | 1.6 |
| rmtB+aac (3)-II+aac (6’)-Ib | 4 | 6.5 |
| aac (3)-II+aac (6’)-Ib+ant (3”)-I | 2 | 3.2 |
| aac (3)-II+aac (6’)-Ib+ant (2”)-I | 2 | 3.2 |
| armA+aac (3)-II+aac (6’)-Ib+ant (3”＂)-I | 3 | 4.8 |
| rmtB+aac (3)-II+aac (6’)-Ib+ant (3”)-I | 1 | 1.6 |
| aac (3)-II+aac (6’)-Ib+ant (3”)-I+ant (2”)-I | 2 | 3.2 |
| armA+aac (3)-II+aac (6’)-Ib+ant (3”)-I+ant (2”)-I | 2 | 3.2 |
Conclusions
The present study reported the prevalence of the K. pneumoniae infection, the antimicrobial resistance and, the characterisation of ESBL, and underlined the importance of the prudent use of antimicrobials and routine monitoring of susceptibility patterns to minimise the spread of antibiotic resistance. Of note, these findings also showed that the emergence of armA, rmtB, aac (3)-II, aac (6’)-Ib, ant (3”)-I, and ant (2”)-I in K. pneumoniae in China, is related to aminoglycosides antimicrobial resistance. Moreover, the exact role and the spread mechanisms of these resistance genes in K. pneumoniae still await further studies.
Acknowledgements
This work was supported by grants from the Scientific Technologic Research Fund of Guangdong Province, China (NO. 2011B021800075).
Disclosure of conflict of interest
None.
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