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Revista da Sociedade Brasileira de Medicina Tropical

Print version ISSN 0037-8682On-line version ISSN 1678-9849

Rev. Soc. Bras. Med. Trop. vol.50 no.3 Uberaba May/June 2017 

Major Articles

Molecular detection of β-lactamase and integron genes in clinical strains of Klebsiella pneumoniae by multiplex polymerase chain reaction

Mansour Sedighi1 

Masoumeh Halajzadeh 1  

Rashid Ramazanzadeh2  3 

Noor Amirmozafari1 

Mohsen Heidary1 

Serve Pirouzi4 

1Department of Microbiology, School of Medicine, Iran University of Medical Sciences, Tehran, Islamic Republic of Iran.

2Cellular & Molecular Research Center, Kurdistan University of Medical Sciences, Sanandaj, Islamic Republic of Iran.

3Department of Microbiology, Faculty of Medicine, Kurdistan University of Medical Sciences, Sanandaj, Islamic Republic of Iran.

4School of Hejab, Baneh management, Department of Kurdistan Education and Training, Department of Iran Education and Training, Baneh, Islamic Republic of Iran.



Infections caused by β-lactamase-producing gram-negative bacteria, such as Klebsiella pneumoniae, are increasing globally with high morbidity and mortality. The aim of the current study was to determine antimicrobial susceptibility patterns and the prevalence of antibiotic resistance genes (β-lactamase and integron genes) using multiplex PCR.


One-hundred K. pneumoniae isolates were collected from different clinical samples. Antibiotic susceptibility testing was performed with thirteen different antibiotics. Multiplex-PCR was used to detect β-lactamase (bla TEM, bla CTX-M, bla SHV , bla VEB, bla PER, bla GES, bla VIM, bla IMP, bla OXA, and bla KPC) and integron genes (int I, int II, and int III).


The highest and lowest rate of resistance was exhibited against amikacin (93%) and imipenem (8%), respectively. The frequency of β-lactamase-positive K. pneumoniae was 37%, and the prevalence of the bla TEM, bla CTX-M, bla SHV , bla VEB, bla PER, bla GES, bla VIM, bla IMP, bla OXA, and bla KPC genes was 38%, 24%, 19%, 12%, 6%, 11%, 33%, 0%, 28%, and 23%, respectively. Of the 100 isolates, eight (8%) were positive for class I integrons; however, class II and III integrons were not detected in any of the strains.


These results indicate co-carriage of a number of β-lactamase genes and antibiotic resistance integrons on the same plasmids harboring multi-drug resistance genes. It seems that these properties help to decrease treatment complications due to resistant bacterial infections by rapid detection, infection-control programs and prevention of transmission of drug resistance.

Keywords: K. Pneumoniae; β-lactamase; Integrons; Drug resistance; Multiplex PCR


Klebsiella pneumoniae is an important causative agent of both hospital-acquired and community-acquired infections such as pneumonia, urinary tract infections, meningitis, and septicemia1. Multi-drug resistant (MDR) strains can be quite problematic, especially for elderly or immunocompromised patients and infants with an immature physiology2. Release of β-lactamases is a significant resistance mechanism against antimicrobial agents3. β-lactamase-producing K. pneumonia can degrade a wide range of β-lactam antibiotics such as penicillins, carbapenems, cephalosporins, and cephamycins2,4. These enzymes can be divided into four classes (A, B, C, and D) based on the Ambler classification. The temoneira (TEM), cefotaximase (CTX-M), sulfhydryl variable (SHV), Vietnam extended-spectrum β-lactamase (VEB), Pseudomonas extended-resistant (PER), and Guiana extended-spectrum (GES) enzymes belong to class A; the Verona integron-encoded metallo-β-lactamase (VIM), imipenem (IMP), and K. pneumoniae carbapenemase (KPC) enzymes belong to class B; and oxacillin hydrolyzing enzyme (OXA) is classified as class D according to the Ambler classification5-7. Researchers have reported that the incidence of β-lactamase-producing K. pneumonia ranges from 6 to 88% at different health care locations8. Bla SHV β-lactamases are related to high level ceftazidime resistance, but not to cefazolin or cefotaxime resistance, while bla CTX-M β-lactamases are more effective against cefotaxime. In contrast, TEM β-lactamases confer resistance against oxyimino-β-lactams groups such as ceftazidime, cefotaxime, and aztreonam. In addition to β-lactamase encoding plasmids, transportable genetic elements such as integrons can also contribute to the evolution and distribution of MDR genes ( blaTEM , blaCTX-M , blaSHV, bla VEB, bla PER, bla GES, bla VIM, bla IMP, bla OXA, and bla KPC) in K. pneumoniae by vertical or horizontal transmission9,10. Five classes of integrons have been proposed based on the amino acid sequences of Int I proteins. Three classes of antibiotic resistance integrons (ARIs; I, II, and III), identified based on particular integrase genes11, are usually associated with MDR phenotypes. The transportable class I integron is related to transposon Tn21 and is commonly observed in β-lactamase-producing clinical isolates of K. pneumonia12. Class II integrons are detected less frequently in bla KPC-producing bacteria, such as K. pneumoniae and Escherichia coli, and class III integrons are detected quite infrequently in β-lactamase-producing K. pneumoniae13. Previous reports have demonstrated the production of various β-lactamases, such as bla-ESBL, and resistance to several antibiotics groups via ARI gene carriage in clinical isolates of K. pneumonia14. Unfortunately, the incidence of β-lactamase-producing K. pneumoniae is on the rise15. The detection of different β-lactamase genes in resistant bacteria and characterization of their antimicrobial susceptibility profiles could provide important data regarding high risk factors and infection epidemiology16-18. To date, only a few studies have investigated the types of β-lactamase-producing Enterobacteriaceae and strains possessing integrons present in Iranian hospitals19,20. Thus, the aim of the present study was to determine the prevalence of bla TEM, bla CTX-M, bla SHV , bla VEB, bla PER, bla GES, bla VIM, bla IMP, bla OXA, and bla KPC, as well as int genes (I, II and III) in clinical K. pneumonia strains isolated from two large urban university general hospitals in Tehran, Iran using multiplex-polymerase chain reaction (M-PCR).


This cross-sectional study was conducted from April 2014 to March 2015, at two teaching hospitals in Tehran, Iran. One hundred non-repetitive K. pneumonia isolates were obtained from different clinical specimens including blood, skin lesions, broncho-alveolar lavage (BAL), urine, sputum, cerebrospinal fluid (CSF), pus, pleural effusion, ascites, and catheter specimens. Each sample was cultured on MacConkey agar (Merck, Darmstadt, Germany) and incubated at 37°C for 24h. Resulting colonies were identified as K. pneumonia using standard biochemical and microbiological tests, including urease, oxidase, motility, citrate utilization, Triple sugar iron agar (TSI), Methyl Red-Voges Proskauer (MR-VP), and Sulfide Indole Motility (SIM), and were further confirmed with the API 20E system (Analytab, Inc., New York).

Antibiotic susceptibilities were determined using the disc diffusion method on Mueller-Hinton Agar (Merck Co., Germany) plates in accordance with the Clinical and Laboratory Standards Institute (CLSI) guidelines for the following antibiotics (Mast, Merseyside, UK): amoxicillin/clavulanate (AUG; 20/10μg), ciprofloxacin (CIP; 5μg), amikacin (AK; 30μg), trimethoprim-sulfamethoxazole (TS; 2.5μg), cefotaxime (CTX;30μg), Ampicillin (AMP; 10μg), aztreonam (AZT; 30μg), imipenem (IPM; 10μg), gentamicin (GEN; 10μg), ceftazidime (CAZ;30μg), cefepime (FEP; 30μg), ceftriaxone (CRO; 30μg), imipenem (IMP; 10μg), and levofloxacin (LEV; 5μg). Briefly, a bacterial suspension was obtained from fresh cultures. The turbidity of each bacterial suspension was adjusted to a value equivalent to the no. 0.5 McFarland turbidity standard and then cultured on Mueller-Hinton agar (Oxoid, UK). The zone of inhibition diameter was measured following incubation at 37°C for 18-24 hours; the results were reported as susceptible, intermediate, and resistant. K. pneumoniae ATCC1029 was used as the quality control14.

Multiplex-PCRs were performed to detect β-lactamase genes ( blaTEM , blaCTX-M , blaSHV, bla VEB, bla PER, bla GES, bla VIM, bla IMP, bla OXA, and bla KPC) and int genes (I, II, and III) using a master cycler gradient (Eppendorf Co., Germany). Genomic deoxyribonucleic acid (DNA) was extracted from K. pneumoniae colonies grown overnight on blood agar (Merck Co., Germany) plates using the boiling method14. Briefly, a loopful of bacteria from a colony was suspended in 700µl sterile distilled water, boiled for 10 min, centrifuged at 7,000×g for 4 min at 4°C, cooled on ice for 10 min, and then centrifuged for 3 min at 8,000×g. The concentration and quality of the extracted cellular DNA were assessed using a Nanodrop spectrophotometer (ND-1,000; Thermo Scientific; Wilmington, DE, USA). The β-lactamase and integron genes were amplified by M-PCR using specific primers detailed in Table 1. M-PCR was carried using 1.5µl of extracted genomic DNA in a 25µl PCR reaction mixture consisting of 2.5µl 10× PCR buffer, 1.5µl MgCl2 (50mM), 0.5µl dNTPs (10mM), 1.5µl of each primer, 0.5µl of Taq DNA polymerase (5U/µl; Amplicon Co., Denmark), and 15.5µl sterile distilled water. M-PCR was performed under the following conditions: denaturation at 94°C for 1 min; 35 cycles of denaturation at 94°C for 30s, annealing at 59°C for 30s, and extension at 72°C for 1 min; and a final extension at 72°C for 6 min. For amplification of the int genes (I, II, and III), the reaction mixture was amplified using a thermal gradient cycler (Eppendorf Co., Germany) with the following PCR protocol: one cycle of 5 min at 95°C; 30 cycles of 1 min at 95°C, 1 min at 65°C, and 1 min at 72°C; and one cycle of 10 min at 72°C14.

TABLE 1 Nucleotide sequences of the primers used for M-PCR. 

Genes Oligonucleotide sequence (5ʹ→3ʹ) Size of amplicon (bp)

M-PCR: multiplex polymerase chain reaction; bla-TEM-1 : temoniera β-lactamase-1; bla-CTX-M : cefotaximase; bla-SHV : sulphydril variable β-lactamase; bla-PER : Pseudomonas extended resistance; bla-KPC : Klebsiella pneumoniae carbapenemase; bla-VEB : Vietnamese extended spectrum beta-lactamase; bla-GES : Guiana Extended Spectrumβ-Lactamases; bla-VIM : Verona imipenemase; bla-IMP : imipenemase; bla-OXA : oxacilinases ; Int I: class I integrons; Int II: class II integrons; Int III: class III integrons.


One-hundred K. pneumoniae isolates were obtained from 374 (26.7%) different clinical specimens. Specimens included blood (n=7, 7%), skin lesions (n=9, 9%), BAL (n=5, 5 %), urine (n= 62, 62%), sputum (n= 6, 6%), CSF (n=3, 3%), Pus/swap (n=2, 2 %), pleural effusion (n=1, 1%), ascites (n=2, 2%), and catheter (n= 3, 3%) samples. Distribution analysis of the K. pneumoniae strains showed that most (62%) isolates were obtained from urine and the lowest (1%) number was isolated from pleural effusion samples. The mean age of the population studied was 47±1.5 years, with a range of 10 to 76 years. The strains were isolated from patients belonging to various age groups: [(10-25 years; 29), (26-40 years; 38), (41-55 years; 43), (56-60 years; 11), and (60-76 years; 7)]. Sixty-seven (67%) patients were male and 33 (33%) were female.

Antibiotic susceptibility tests using the Kirby-Bauer method showed that the level of resistance to amoxicillin/clavulanate, ciprofloxacin, amikacin, trimethoprim-sulfamethoxazole, cefotaxime, ampicillin, aztreonam, imipenem, gentamicin, ceftazidime, cefepime, ceftriaxone, and levofloxacin was 37%, 37%, 93%, 84%, 52%, 87%, 59%, 8%, 24%, 67%,52%, 43%, and 26%, respectively (Table 2). The antibiotic susceptibility profiles of non-β-lactamase-producing and β-lactamase-producing K. pneumoniae strains are detailed in Table 3.

TABLE 2 Antibiotic resistance patterns in Klebsiella pneumoniae isolates. 

Antibiotic Resistant Intermediate Susceptible
No % no % no %
Amoxicillin/clavulanate (Aug) 37 37.0 0 0.0 63 63.0
Ciprofloxacin (CIP) 37 37.0 5 5.0 58 58.0
Amikacin (AK) 93 93.0 3 3.0 4 4.0
Trimethoprim-sulfamethoxazole (TS) 84 84.0 4 4.0 12 12.0
Cefotaxime (CTX) 52 52.0 1 1.0 47 47.0
Ampicillin (AMP) 87 87.0 2 2.0 11 11.0
Aztreonam(AZT) 59 59.0 1 1.0 40 40.0
Imipenem (IPM) 8 8.0 9 9.0 83 83.0
Gentamicin (GEN) 24 24.0 6 6.0 70 70.0
Ceftazidime (CAZ) 67 67.0 2 2.0 31 31.0
Cefepime (FEP) 52 52.0 0 0.0 48 48.0
Ceftriaxone (CRO) 43 43.0 1 1.0 56 56.0
Levofloxacin (LEV) 26 26.0 0 0.0 74 74.0

TABLE 3 Antibiotic resistance rates of non-β-lactamase-producing and β-lactamase-producing Klebsiella pneumoniae strains. 

Antibiotic Non-β-lactamase-producing β-lactamase-producing
Klebsiella pneumoniae strains (%) Klebsiella pneumoniae strains (%)
Amoxicillin/clavulanate (Aug) 37.0 63.0
Ciprofloxacin(CIP) 21.0 42.0
Amikacin (AK) 18.0 45.0
Trimethoprim-sulfamethoxazole (TS) 32.0 31.0
Cefotaxime (CTX) 14.0 49.0
Ampicillin (AMP) 35.0 28.0
Aztreonam(AZT) 12.0 51.0
Imipenem (IPM) 6.0 57.0
Gentamicin (GEN) 31.0 32.0
Ceftazidime (CAZ) 33.0 30.0
Cefepime (FEP) 24.0 39.0
Ceftriaxone (CRO) 15.0 48.0
Levofloxacin (LEV) 7.0 56.0

The β-lactamase gene amplification test (M-PCR) simultaneously amplified and identified the existence of the target genes and showed that the prevalence of the blaTEM , blaCTX-M , blaSHV, bla VEB, bla PER, bla GES, bla VIM, bla IMP, bla OXA, and bla KPC genes was 38%, 24%, 19%, 12%, 6%, 11%, 33%, 0%, 28%, and 23%, respectively (Figure 1). Molecular distribution analysis of the integron genes showed that only 11 (8.6%) of the 100 isolates contained class I integrons; however, class II and class III integrons were not detected in any of the isolates (Figure 2).

FIGURE 1 M-PCR amplification of β-lactamase genes in selected Klebsiella pneumoniae isolates. Lane 1: bla-TEM-1 (447bp), Lane 2: bla-CTX-M (593bp), Lane 3: bla-SHV gene (747bp), Lane 4: bla-PER (925bp), Lane 5: bla-KPC (538bp), Lane 6: bla-VEB (643bp), Lane 7: bla-GES (860bp), Lane 8: bla-VIM (390bp), Lane 9: bla-IMP (448bp), Lane 10: bla-OXA (919bp), Lane 11: negative control; Escherichia coli ATCC 25922, Ladder: 50bp DNA size ladder. M-PCR: multiplex polymerase chain reaction; bla-TEM-1 : temoniera β-lactamase-1; bla-CTX-M : Cefotaximase; bla-SHV : sulphydril variable β-lactamase; bla-PER : Pseudomonas extended resistance; bla-KPC : Klebsiella pneumoniae carbapenemase; bla-VEB : Vietnamese extended spectrum beta-lactamase ; bla-GES : Guiana Extended Spectrumβ-Lactamases; bla-VIM : Verona imipenemase; bla-IMP : Imipenemase; bla-OXA : oxacilinases ; DNA: deoxyribonucleic acid. 

FIGURE 2 M-PCR amplification of int genes in four selected Klebsiella pneumoniae isolates. M: 100bp DNA size marker; Lane +: quality control (K. pneumoniae ATCC 1029); Lane -: negative control (Escherichia coli ATCC 25922), Lane 1-4: M-PCR gene products. Int I: class I integrons; Int II: class II integrons; Int III: class III integrons; M-PCR: multiplex polymerase chain reaction; DNA: deoxyribonucleic acid. 


β-lactamase-producing K. pneumoniae was first identified in 198321. Most infections caused by K. pneumoniae are due to multi-drug resistant strains such as β-lactamase producing isolates22. Recent studies have shown that the incidence of β-lactamase-producing K. pneumoniae is increasing in several countries such as Iran22,23, India24,25, and Italy26. Resistance to various antibiotics is related to the existence of transmissible plasmids and integrons, which can be integrated into plasmids or the chromosome27. These transmissible elements often contain resistance factors that can be transferred to other microorganisms. In this study, we examined the susceptibility of 100 clinical K. pneumonia strains against thirteen antibiotics; high resistance was observed for AK (93%), TS (84%), AMP (87%), AZT (59%), GEN (67%), and FEP (52%). Amiri et al.28 reported that the resistance to ampicillin, ceftazidime, ceftriaxone, aztreonam, and cefotaxime was 92%, 67%, 65%, 64%, and 59%, respectively in K. pneumoniae isolates28, values similar to the rates reported in this study. Our results indicate that only eight β-lactamase-producing isolates were resistant to imipenem using the disk diffusion method. This high (83%) susceptibility to imipenem is in agreement with the reports of Mansury et al.29, Ahmad et al.30, Amiri et al.28, and Edelstein et al.31. Only three K. pneumoniae isolates were resistant to all antibiotics tested.

Multi-drug resistant (MDR) strains are defined as strains resistant to three classes of antimicrobial agents32; therefore, 31% of our isolates can be classified as MDR. This finding contrasts those reported by Mansury et al.29. A total of 52% and 67% of our isolates were resistant to the third generation cephalosporins ceftazidime and cefotaxime, respectively, which is similar to the rates reported by Ullah et al.33, Amiri et al.28, and Jalalpoor et al.34. Of the MDR isolates, 28 strains were β-lactamase-positive (28%). These results are in agreement with those of Shukla et al.35 and Sarojamma et al.36 who reported that 28% and 32% of their strains were β-lactamase producers, respectively35,36. The incidence of β-lactamase-producing Klebsiella spp. has been reported to vary from 42-44% (in the USA)37-39, 4.9% (in Canada)40, 20.8% (in Spain)41, 28.4% (in Taiwan)42, 78.6% (in Turkey)43, 20% (in Algeria)44, and 51% (in China)45. In this study, the highest percentage of β-lactamase-roducing strains was derived from urine samples (14%).

The aim of this study was to determine the prevalence of several β-lactamase and integrin genes (I, II, III) in clinical K. pneumoniae isolates. The M-PCR results for each resistance gene were as follows: bla TEM was detected in 37.8% (14.37), blaCTX in 24.3% (9.37), blaSHV in 18.9% (7.37), bla VEB in 10.8% (4.37), bla PER in 5.4% (2.37), bla GES in10.8% (4.37), bla VIM in 8.1% (3.37), bla IMP in 0% (0.37), bla OXA in 27% (10.37), and bla KPC in 24.3% (9.37) of the isolates. Bora et al.46 reported that of the three β-lactamase genotypes, blaTEM in detected most predominately in β-lactamase-producing K. pneumoniae (77.58%)46. Monstein et al.47 detected bla SHV in 8.1% (3.37); bla SHV and bla TEM in 2.7% (1.37); and bla TEM, bla SHV, and bla CTX-M in 8% (3.37) of their K. pneumonia isolates47. Hassan and Abdalhamid.48 reported a very high prevalence of blaCTX -M (97.4%) in comparison to the prevalence of blaSHV (23.1%) in K. pneumoniae strains48. However, in Europe, East Asia, and Latin America, as well as in the current study, blaTEM , blaCTX , and blaSHV appear to be the predominant β-lactamase genes in clinical K. pneumoniae isolates.

Ahmed et al.49 reported that the prevalence of bla PER was 22.4%; however Nasehi et al.20, detected bla PER in only 7.5% of their isolates, which is similar to the results of this study. Borges-Cabral et al.50, reported that bla KPC was present in 41.7% of their isolates; however, Bina et al.51 did not observed bla KPC (0%) in any of their strains and the rate in the present study was 23%. Limbago et al.52 observed the bla IMP gene in all of their clinical K. pneumoniae isolates; however, we did not detect this gene in any of our isolates. Udomsantisuk et al.53 reported that the frequency of the bla VEB gene was 30% among β-lactamase-positive K. pneumoniae strains; however, in the current study, the frequncy of bla VEB gene was 12%. Iraz et al.54 reported that 86% of the carbapenem-resistant K. pneumoniae strains carried the bla OXA gene; however, Charrouf et al.55 found that only 6% of their isolates carried this gene. Our results did not match either of these studies; in our study, the prevalence of this gene was 28%. Psichogiou et al.56 found that the frequency of the bla VIM gene in clinical K. pneumoniae strains was 37.6%, which is consistent with our results (33%). This reflects a significant increase in the prevalence of blaTEM and bla VIM in Iran. In comparison, the major β-lactamase gene found in Arab countries appears to be bla CTX-M57-59.

In addition to β-lactamase genes, we also evaluated integron gene prevalence in the 100 K. pneumoniae isolates. Our results indicate that only eight isolates were positive for class I integrons, while class II and class III integrons were not detected in any of the isolates. This finding is comparable to those of Lima et al.60 and Ashayeri et al.61. Class III integrons have been reported only in very few studies14,62 63. Mobarak-Qamsari et al.64 identified 22 (44%) class I integron-carrying K. pneumoniae isolates, but only three (6%) of the isolates had class II integrons and none contained class III integrons64. These findings suggest that class I integron genes may play a critical role in the distribution of β-lactamase-encoding genes among clinical β-lactamase-producing K. pneumoniae isolates. The increase in multidrug resistance and the underlying mechanisms require further investigation

In conclusions, our study demonstrates that there is a high level of bla TEM, bla VIM, and class I integrons in the β-lactamase-producing K. pneumoniae strains circulating in hospitals in Tehran, Iran. This trend of MDR profiles associated with the presence of bla TEM, bla VIM, and class I integron genes is worrying. The high prevalence rate of these resistance genes highlights the necessity for establishing a national antibiotic susceptibility surveillance network for monitoring infections due to Enterobacteriaceae spp. in Iran. It seems that these properties help to decrease treatment complications and mortality rate due to resistant bacterial infections by rapid detection of β-lactamases genes, infection-control programs and prevention of transmission of drug resistant-strains. A combination therapy can be useful to prevent resistance during therapy resulting in complete remission of patient and resistant infections control. One of the limitations of the present study was that, other β-lactamases family genes and also other antibiotic resistance mechanisms were not assessed due to the financial constraints of molecular and gene tests. So, further investigations are needed to obtain more accurate and effective results.


The authors are greatly thankful to Serwa Pirouzi and Saadat Pirouzi for help with the English language version of this paper. Also, authors would like to thank the director and principal of Iran university of medical sciences for their constant encouragement and support for the current study.


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Received: February 04, 2017; Accepted: April 24, 2017

Corresponding author: Prof. Noor Amirmozafari.

Conflict of interest: The authors declare that there is no conflict of interest in the present study.

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