Skip to main content
Download PDF

Identification of beta-lactamase genes and molecular genotyping of multidrug-resistant clinical isolates of Klebsiella pneumoniae

BMC Microbiology volume 24, Article number: 549 (2024) Cite this article

Abstract

Background

Klebsiella pneumoniae is a clinically relevant pathogen that has raised considerable public health concerns. This study aims to determine the presence of beta-lactamase genes and perform molecular genotyping of multidrug-resistant (MDR) K. pneumoniae clinical isolates.

Methods

Clinical isolates of MDR K. pneumoniae were collected from educational hospitals affiliated with Babol University of Medical Sciences. The isolates of K. pneumoniae were identified through standard microbial and biochemical tests. Antibiotic resistance was assessed using disk diffusion, modified Hodge test (MHT), combined disk, and polymerase chain reaction (PCR) methods. Enterobacterial Repetitive Intergenic Consensus (ERIC)-PCR was performed for molecular typing.

Results

A total of 42 MDR K. pneumoniae isolates were obtained from various clinical specimens. The highest antibiotic resistance was observed for ampicillin (100%), while the lowest resistance was noted for amikacin (19.04%). The MHT indicated that 38.09% of K. pneumoniae isolates produced carbapenemase enzymes. Metallo-beta-lactamase (MBL) production was found in 54.76% of isolates. Molecular detection of beta-lactamase genes revealed the presence of blaNDM (21.42%), blaKPC (42.85%), blaTEM (76.19%), blaSHV (47.16%), and blaCTX−M (80.95%) genes. ERIC-PCR molecular typing identified seven distinct genetic patterns among the isolates.

Conclusions

This investigation demonstrates the high resistance levels of K. pneumoniae strains. The beta-lactamase genes with the highest and lowest frequencies correspond to blaCTX−M and blaNDM genes, respectively. ERIC-PCR dendrograms suggest a common origin for K. pneumoniae clinical isolates and the propagation of similar clones within hospital wards. These findings indicate that K. pneumoniae isolates are highly virulent, necessitating the development of more effective resistance-fighting techniques and gene transfer research.

Clinical trial number

Not applicable.

Peer Review reports

Introduction

Klebsiella pneumoniae is a clinically relevant pathogen that has raised considerable public health concerns [1]. This bacterium is responsible for numerous diseases, including pneumonia, urinary tract infections, bacteremia, meningitis, and liver abscesses [2]. The susceptibility to K. pneumoniae infection is influenced by various factors, including pathogen variables (such as virulence factors and antibiotic resistance), host internal variables (such as genetics, age, and immune status), and external variables (such as antibiotic consumption, environmental exposure, dietary habits, and alcoholism) [3].

Carbapenems were once regarded as the ultimate therapeutic option for treating multidrug-resistant (MDR) K. pneumoniae until 2001. However, the landscape changed with the first report of K. pneumoniae carbapenemase (KPC) production in isolates from North Carolina [4]. The escalating rate of drug resistance among K. pneumoniae isolates has since become a significant global concern. β-lactamases, the enzymes responsible for β-lactam antibiotic resistance, are categorized into classes A, B, C, and D based on the Ambler classification [5]. Class A β-lactamases, including KPC, can hydrolyze penicillins, cephalosporins, and carbapenems, and their activity can be inhibited by clavulanate or tazobactam [6]. On the other hand, Class B β-lactamases, with the genes blaIMP, blaNDM, and blaVIM being the most common, encode carbapenemase enzymes that act against all beta-lactams except aztreonam and are not susceptible to inhibition by clavulanate or tazobactam [7]. Class C encompasses cephalosporinases (but does not include carbapenemases), while Class D includes oxacillinases such as OXA− 48, OXA− 23, and OXA− 24 [8, 9].

In Iran, KPC-producing K. pneumoniae isolates have increasingly been reported, particularly in hospital settings, where they contribute significantly to MDR infections. Studies indicate that the prevalence of KPC in Iran varies across regions and hospitals, with some research showing rates as high as 30% among carbapenem-resistant K. pneumoniae isolates [10, 11]. Similarly, neighboring countries in the region, such as Iraq and Pakistan, have reported high rates of KPC [12, 13]. The spread of these resistant strains poses a substantial challenge to public health, necessitating enhanced surveillance, stringent infection control measures, and judicious use of antibiotics to curb the dissemination of these dangerous pathogens.

Extended-spectrum beta-lactamases (ESBLs) are crucial antibiotic resistance determinants passed on through horizontal gene transfer within the Enterobacterales family. Among several ESBL gene variants, the most prevalent and clinically relevant are blaTEM, blaSHV (sulphydryl variable) and blaCTX−M (cefotaxime-hydrolyzing β-lactamase) [14].

An essential aspect of preventing the transmission of healthcare-associated diseases and enhancing infection management is the identification of genetic relatedness among pathogenic strains [15]. Enterobacterial Repeated Intergenic Consensus (ERIC) sequences are repeated elements in bacterial genomes that vary in pattern and quantity, aiding in the distinction of bacterial strains [16]. These variations enable Enterobacterales molecular typing using the ERIC-Polymerase Chain Reaction (ERIC-PCR) approach. This method is fast, accurate, and affordable for analyzing genetic diversity among strains. It is crucial in epidemiological investigations, where genetic diversity monitoring can track illness transmission and inform public health measures [17, 18].

Identifying beta-lactamase genes and molecular genotyping of clinical isolates are potent tools to shed light on MDR K. pneumoniae infections. We also used ERIC-PCR to evaluate correlations between each and the resistance profiles of K. pneumoniae isolates.

Materials and methods

Bacterial isolation and identification

Samples of Klebsiella pneumoniae were obtained from educational hospitals associated with Babol University of Medical Sciences, located in Babol, Iran. The isolates were validated using conventional biochemical testing methods, including SH2/indole/motility (SIM) medium, triple sugar iron (TSI) agar, urease production, growth on Simmons’ citrate agar medium, and methyl red/Voges-Proskauer (MR/VP) tests.

Antimicrobial susceptibility

The antibiotic susceptibility of the isolates was assessed using the Kirby-Bauer disk diffusion method. Several antibiotics (Padtan Teb Co, Iran) were tested, including ampicillin (10 µg), cefotaxime (30 µg), imipenem (10 µg), gentamicin (10 µg), amikacin (30 µg), ciprofloxacin (5 µg), trimethoprim-sulfamethoxazole (1.25/23.75 µg), and chloramphenicol (30 µg). The testing method followed the recommendations of the Clinical and Laboratory Standards Institute (CLSI 2023). K. pneumoniae isolates demonstrating resistance to three or more different classes of antimicrobials were classified as MDR K. pneumoniae [19].

Detection of carbapenemase production

The Modified Hodge Test (MHT) is a straightforward phenotypic test used to identify the presence of the carbapenemase enzyme in bacteria. A 0.5 McFarland solution of Escherichia coli ATCC 25,922 was diluted to a tenth of its original concentration for the MHT. This diluted suspension was then evenly spread over a Mueller-Hinton agar plate. A 10-µg imipenem disk was placed in the center of the plate. The presumed carbapenemase-producing K. pneumoniae strain was then streaked from the edge of the disk to the edge of the plate, creating a linear and dense inoculum, and incubated for 24 h. The presence of carbapenemase production by the test isolate was indicated by the proliferation of susceptible E. coli in the background towards the disk, resulting in a cloverleaf-like appearance, following CLSI guidelines. A negative carbapenemase-producing isolate is indicated when there is no distortion of the inhibition zone around the imipenem disk. A positive result is indicated when there is any distortion of the inhibition zone around the imipenem disk in the presence of E. coli ATCC 25922 (indicator strain) [20].

Detection of metallo-beta-lactamase (MBL) production

Isolates of K. pneumoniae that showed resistance to carbapenems, namely imipenem (10 µg) according to the disk diffusion test, were suspected of potentially producing MBL. The combined disk (CD) test was used to confirm the phenotypes of MBL producers. In this procedure, two imipenem disks (10 µg) were placed 20 mm apart, and 5 µL of a 0.5 M EDTA solution was applied to one of the disks. The inhibitory zones of the imipenem and imipenem-EDTA disks were evaluated after 16–18 h of incubation at 37 °C under aerobic conditions. MBL production was established when the zone of inhibition of the imipenem plus EDTA disk was more than or equal to 7 mm compared to the imipenem disk alone [21].

DNA extraction

Genomic DNA was extracted using the boiling method. To isolate DNA from agar plate colonies, resuspend the bacteria in 300 µL of Tris-EDTA buffer in an Eppendorf tube. Heat the mixture at 100 °C for 15 min, then freeze it at -20 °C for 20 min. Centrifuge the mixture at 8000 xg for 5 min, and transfer the resulting supernatant to a fresh Eppendorf tube. Store the tube at -20 °C until further use [22].

Detection of beta-lactamase genes by PCR

PCR was conducted using specific primers to identify genes encoding beta-lactamases (blaNDM, blaKPC, blaTEM, blaSHV, and blaCTX−M) as previously described (Table 1). The PCR products were resolved by electrophoresis in a 1% agarose gel using 1× TBE (Tris/borate/EDTA) buffer. The gel was stained with safe stain load dye (SinaClon, Iran) and visualized under UV light.

Table 1 Sequences of primers used in the study
Full size table

Molecular genotyping

In our study, ERIC-PCR reactions were performed in 15 µL volumes. ERIC-PCR reactions were performed in 15 µL volumes. The reaction mixture included 0.5 µL of each primer (ERIC 1: 5′-ATGTAAGCTCCTGGGGATTCAC-3′, ERIC 2: 5′-AAGTAAGTGACTGGGGTGAGCG-3′), 8 µL of the master mix (provided by SinaClon, Iran), 1 µL of DNA template, and 5 µL of deionized water. The ERIC-PCR reaction scheme included initial denaturation at 94 °C for 5 min, followed by 35 cycles of denaturation for 3 min, annealing for 40 s at 48 °C, extension at 72 °C for 2 min, and final extension for 5 min at 72 °C. After 40 min of 1.5% agarose gel (SinaClon, Iran) electrophoresis at 95 V, ERIC-PCR products were detected under UV light in a gel documentation system. The ERIC patterns were assessed using GelJ software, v.2.0, as previously described [11]. Isolates with an 80% or above similarity coefficient were categorized as the same genotypes.

Statistical analysis

The statistical analyses were conducted using SPSS, version 27.0. Fisher’s exact test was used to evaluate the data. A p-value less than 0.05 was considered statistically significant.

Results

Distribution and identification of isolates

From March to October 2023, conventional bacteriological methods were used to obtain 42 isolates of MDR K. pneumoniae from various clinical specimens and hospital wards. The specimens included urine (12 isolates, 28.57% of the total), blood (9 isolates, 21.42%), sputum (6 isolates, 14.28%), stool (5 isolates, 11.9%), wound swabs (4 isolates, 9.52%), bronchoalveolar lavage (BAL) samples (3 isolates, 7.14%), biopsies (2 isolates, 4.76%), and pus (1 isolate, 2.38%). The isolates were collected from various hospital wards, including the intensive care unit (ICU) (21 isolates, 50% of the total), internal medicine ward (10 isolates, 23.8%), infectious diseases ward (8 isolates, 19.04%), urology ward (6 isolates, 14.28%), and emergency ward (4 isolates, 9.52%).

Antibiotic susceptibility profile

The results of the antibiotic susceptibility tests demonstrated pronounced resistance to ampicillin, with 100% of the samples showing resistance. Conversely, amikacin exhibited the least resistance, with only 19.04% of the samples resistant (Fig. 1).

Fig. 1
figure 1

Number of K. pneumoniae isolates resistant to antimicrobials: AMP, ampicillin; CTX, cefotaxime; IPM, imipenem; GEN, gentamicin; AMK, amikacin; CIP, ciprofloxacin; SXT, trimethoprim-sulfamethoxazole

Full size image

Carbapenemase and MBL-producing isolates

The results of the MHT test revealed that, out of 42 isolates, 16 (38.09%) MDR K. pneumoniae isolates were positive for carbapenemase production. On the other hand, 23 out of 42 isolates (54.76%) were found to produce MBL. These two tests showed a statistically significant difference in their ability to detect carbapenemase resistance in MDR K. pneumoniae (p < 0.05).

Beta-lactamase genes and antibiotic resistant profile

Table 2 presents the beta-lactamase genes and antibiotic resistance profiles of MDR K. pneumoniae isolates. Molecular detection of Beta-Lactamase genes was performed on all 42 MDR K. pneumoniae isolates. The presence of blaNDM (n = 9), blaKPC (n = 18), blaTEM (n = 32), blaSHV (n = 20), and blaCTX−M (n = 34) was detected. Seven isolates did not have any beta-lactamase genes.

Table 2 Molecular-genetic characteristics of K. pneumonia isolates
Full size table

ERIC-PCR typing

Based on an 80% genetic similarity threshold, ERIC-PCR analysis identified six clusters (A, B, C, D, E, F, and G) among 42 MDR K. pneumoniae clinical isolates, with varying numbers of isolates in each cluster: A (7), B (6), C (3), D (4), E (5), F (6), and G (9). Two isolates (KP 1 and KP 8) were also classified as singletons (Fig. 2).

Fig. 2
figure 2

Dendogram of MDR K. pneumoniae clinical isolates clustering based on ERIC patterns, created using GelJ software, v.2.0

Full size image

Discussion

This research examined the antibiotic resistance and molecular genotyping of MDR K. pneumoniae clinical isolates obtained from patients admitted to the educational hospitals affiliated with Babol University of Medical Sciences. The findings indicated that most isolates were resistant to multiple antibiotics, particularly ampicillin and cefotaxime. ERIC-PCR for molecular typing identified seven distinct genetic patterns within the isolates, showing significant genetic diversity.

The findings of our study indicate that 38.09% of MDR K. pneumoniae isolates tested positive for carbapenemase production using the MHT test. This percentage is comparable to the results reported by Naeem et al. in Pakistan (30.9% positive isolates) [23]. However, our findings differ from those of other studies, such as the one conducted by Pourgholi et al. in Iran (8.82% positive isolates) and the study conducted by Patil et al. in India (84.3% positive isolates) [24, 25]. It is essential to recognize that while the MHT provides a practical and efficient means for detecting carbapenemase-producing bacteria, with notable benefits such as simplicity, rapid results, and cost-effectiveness, it has limitations. The test’s reduced specificity and the potential for false-positive or false-negative interpretations necessitate careful consideration when incorporating MHT into routine diagnostic protocols. Ensuring accurate interpretation and complementing MHT with more specific confirmatory tests can help mitigate these challenges and improve diagnostic reliability [26, 27].

Of all the K. pneumoniae isolates in our investigation, 54.76% were identified as MBL producers by CD assay. Our findings differ from the study done by Alizadeh et al. in Iran, which found that 30.8% of K. pneumoniae were MBL producers [25]. Research conducted in 2021 revealed that 22% of K. pneumoniae isolates could be MBL producers [23]. A study conducted by Aminul et al. in Bangladesh revealed that 24% of K. pneumoniae isolates were identified as MBL producers [28].

In our study, we found that among 42 MDR K. pneumoniae isolates, the genes blaNDM, blaKPC, blaTEM, blaSHV, and blaCTX−M were detected in 21.42%, 42.85%, 76.19%, 47.61%, and 80.95% of them, respectively, using PCR. Ahmadi et al. reported that out of 84 K. pneumoniae isolates, the frequencies of blaNDM, blaKPC, blaTEM, blaSHV, and blaCTX−M genes were 60%, 71%, 91%, 94%, and 96%, respectively [11]. In another study conducted by Farhadi et al., the rates of K. pneumoniae isolates positive for blaNDM, blaKPC, blaTEM, blaSHV, and blaCTX−M genes were 6.9%, 29.3%, 82.7%, 91.4%, and 79.3%, respectively [29]. The findings underscore a troubling prevalence of blaCTX−M, which consistently appears across most studies as the most commonly detected gene associated with antibiotic resistance in K. pneumoniae. The blaCTX−M gene is commonly associated with plasmids that facilitate the horizontal transfer of resistance genes and confer resistance to other antibiotics, including aminoglycosides and fluoroquinolones [30].

The phylogenetic tree was constructed using the UPGMA method. The genetic relatedness among the isolates was determined, resulting in their classification into six clusters, labeled A-G, based on an 80% similarity threshold. Additionally, out of the strains analyzed, the highest count, 9, belonged to the G cluster. A study by Ahmadi et al. showed that ERIC-PCR successfully categorized 84 K. pneumoniae isolates into four clusters with a 70% similarity [11]. Sedighi et al. researched 72 K. pneumoniae isolates, identifying 25 different ERIC types, 14 common and 11 unique [31]. Attia et al.‘s work used ERIC-PCR profiles to categorize 46 K. pneumoniae isolates into three main clusters and 30 distinct ERIC genotypes [32]. Ferreira et al. used ERIC-PCR in their investigation, and the dendrogram showed a genetic connection between the 25 K. pneumoniae isolates they investigated. This concluded that there was a substantial genetic similarity among K. pneumoniae in the bloodstream despite the bacteria having been isolated from distinct patients [33]. These studies underscore the utility of ERIC-PCR as a robust tool for genetic characterization, providing insights into the genetic diversity and relatedness of K. pneumoniae isolates. Understanding these genetic relationships is critical for epidemiological surveillance and devising targeted interventions to control the spread of this pathogen [34].

This study is limited by the absence of ertapenem testing, which may have led to an underestimation of carbapenemase prevalence. Additionally, the molecular analysis did not include the OXA− 48 gene, and minimum inhibitory concentration (MIC) testing was not performed, which restricts the precision of the resistance assessment. Future studies should incorporate a broader range of carbapenem agents, additional resistance genes, and MIC testing for more comprehensive results.

Conclusions

The results of the present study demonstrated the high prevalence of resistant strains of K. pneumoniae. The highest resistance was found to be against ampicillin, while the lowest was observed against amikacin. The highest and lowest frequencies among beta-lactamase genes were also linked to blaCTX−M and blaNDM genes, respectively. Additionally, ERIC-PCR dendrograms showed a restricted genetic resemblance among the isolates analyzed, with just two of them forming singleton types. This discovery suggests a shared origin for K. pneumoniae clinical isolates and the spread of identical K. pneumoniae clones throughout hospital wards. These findings indicate a high pathogenic capacity of K. pneumoniae isolates, necessitating further strategies for combating resistance and in-depth studies of the resistance genes and their transfer.

Data availability

The datasets used and/or analysed during the current study are available from the corresponding author on reasonable request.

References

  1. Effah CY, Sun T, Liu S, Wu Y. Klebsiella pneumoniae: an increasing threat to public health. Ann Clin Microbiol Antimicrob. 2020;19:1–9.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  2. Guerra MES, Destro G, Vieira B, Lima AS, Ferraz LFC, Hakansson AP, et al. Klebsiella pneumoniae biofilms and their role in disease pathogenesis. Front Cell Infect Microbiol. 2022;12:877995.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  3. Chang D, Sharma L, Dela Cruz CS, Zhang D. Clinical epidemiology, risk factors, and control strategies of Klebsiella pneumoniae infection. Front Microbiol. 2021;12:750662.

    Article  PubMed  PubMed Central  Google Scholar 

  4. Yigit H, Queenan AM, Anderson GJ, Domenech-Sanchez A, Biddle JW, Steward CD, et al. Novel carbapenem-hydrolyzing β-lactamase, KPC-1, from a carbapenem-resistant strain of Klebsiella pneumoniae. Antimicrob Agents Chemother. 2001;45(4):1151–61.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  5. Bush K. Classification for β-lactamases: historical perspectives. Expert Rev Anti-infective Therapy. 2023;21(5):513–22.

    Article  CAS  PubMed  Google Scholar 

  6. Tooke CL, Hinchliffe P, Bragginton EC, Colenso CK, Hirvonen VH, Takebayashi Y, Spencer J. β-Lactamases and β-Lactamase inhibitors in the 21st Century. J Mol Biol. 2019;431(18):3472–500.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  7. Bush K, Bradford PA. Epidemiology of β-lactamase-producing pathogens. Clin Microbiol Rev. 2020;33(2). https://doi.org/10.1128/cmr. 00047 – 19.

  8. Correa-León YP, Pérez-Hernández JM, Martinez-Guerra BA, Rodríguez-Noriega E, Mena-Ramírez JP, López-Gutiérrez E, et al. Evaluation of the BD Phoenix carbapenemase-producing organism panels for the detection of Carbapenemase Producers in Escherichia coli, Klebsiella pneumoniae and Pseudomonas aeruginosa. Diagnostics. 2023;13(22):3417.

    Article  PubMed  PubMed Central  Google Scholar 

  9. Khan F, Chaudhary B, Khan AU. Class D type Beta-lactamases. Beta-Lactam Resistance in Gram-negative Bacteria: threats and challenges. Springer; 2022. pp. 125–38.

  10. Pourakbari B, Mamishi S, Poormohammadi S, Hosseinpour Sadeghi R, Mahmoudi S. High prevalence of carbapenem resistance and clonal expansion of Bla NDM gene in Klebsiella pneumoniae isolates in an Iranian referral pediatric hospital. Gut Pathogens. 2024;16(1):17.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. Ahmadi M, Ranjbar R, Behzadi P, Mohammadian T. Virulence factors, antibiotic resistance patterns, and molecular types of clinical isolates of Klebsiella Pneumoniae. Expert Rev Anti-infective Therapy. 2022;20(3):463–72.

    Article  CAS  PubMed  Google Scholar 

  12. Hussein NH, Mohammed Kareem S, Hussein AL, Taha BM. The predominance of Klebsiella pneumoniae carbapenemase (KPC-type) gene among high-level carbapenem-resistant Klebsiella pneumoniae isolates in Baghdad, Iraq. Mol Biol Rep. 2022;49(6):4653–8.

    Article  CAS  PubMed  Google Scholar 

  13. Imtiaz W, Syed Z, Rafaque Z, Andrews SC, Dasti JI. Analysis of antibiotic resistance and virulence traits (genetic and phenotypic) in Klebsiella pneumoniae clinical isolates from Pakistan: identification of significant levels of carbapenem and colistin resistance. Infection and drug resistance. 2021:227 – 36.

  14. Ramatla T, Mafokwane T, Lekota K, Monyama M, Khasapane G, Serage N, et al. One Health perspective on prevalence of co-existing extended-spectrum β-lactamase (ESBL)-producing Escherichia coli and Klebsiella pneumoniae: a comprehensive systematic review and meta-analysis. Ann Clin Microbiol Antimicrob. 2023;22(1):88.

    Article  PubMed  PubMed Central  Google Scholar 

  15. Pavez M, Troncoso C, Osses I, Salazar R, Illesca V, Reydet P, et al. High prevalence of CTX-M-1 group in ESBL-producing enterobacteriaceae infection in intensive care units in southern Chile. Brazilian J Infect Dis. 2019;23:102–10.

    Article  Google Scholar 

  16. Ramadan AA. Bacterial typing methods from past to present: a comprehensive overview. Gene Rep. 2022;29:101675.

    Article  CAS  Google Scholar 

  17. Wilson LA, Sharp PM. Enterobacterial repetitive intergenic consensus (ERIC) sequences in Escherichia coli: evolution and implications for ERIC-PCR. Mol Biol Evol. 2006;23(6):1156–68.

    Article  CAS  PubMed  Google Scholar 

  18. Alsultan A, Elhadi N. Evaluation of ERIC-PCR method for determining genetic diversity among Escherichia coli isolated from human and retail imported frozen shrimp and beef. Int J Food Contam. 2022;9(1):12.

    Article  Google Scholar 

  19. Taşkın Kafa AH, Aslan R, Durna Daştan S, Çeli̇k C, Hasbek M, Emi̇noğlu A. Molecular diversity of Klebsiella pneumoniae clinical isolates: antimicrobial resistance, virulence, and biofilm formation. Nucleosides Nucleotides Nucleic Acids. 2024:1–17.

  20. Ojo AE, Adebajo SO, Fasina KA, Odejinmi B, Ojo OA, Ooladotun A, Ibeaha J. Phenotypic detection of carbapenem resistant Enterobacteriaceae and characterization of Klebsiella pneumoniae carbapenemase (KPC) producing Klebsiella pneumonia. Microbes Infect Dis. 2021;2(4):760–6.

    CAS  Google Scholar 

  21. Kuinkel S, Acharya J, Dhungel B, Adhikari S, Adhikari N, Shrestha UT, et al. Biofilm formation and phenotypic detection of ESBL, MBL, KPC and AmpC enzymes and their coexistence in Klebsiella spp. isolated at the National Reference Laboratory, Kathmandu, Nepal. Microbiol Res. 2021;12(3):49.

    Article  Google Scholar 

  22. Al-Kraety IAA, Alquraishi ZHO, Alsadawi AA. Molecular study of fimh gene in Klebisella pneumoniae isolated from urinary catheter patients. Indian J Forensic Med Toxicol. 2020;14(2).

  23. Naeem S, Bilal H, Muhammad H, Khan MA, Hameed F, Bahadur S, Rehman TU. Detection of blaNDM-1 gene in ESBL producing Escherichia coli and Klebsiella pneumoniae isolated from urine samples. J Infect Developing Ctries. 2021;15(04):516–22.

    Article  CAS  Google Scholar 

  24. Patil PS, Shah H, Singh BN. Phenotypic Detection of Carbapenem Resistance in Clinical Isolate of Klebsiella Pneumoniae in Tertiary Care Hospital. J Pharm Negat Results. 2022;13(08):3559–65.

  25. Pourgholi L, Farhadinia H, Hosseindokht M, Ziaee S, Nosrati R, Nosrati M, Boroumand M. Analysis of carbapenemases genes of carbapenem-resistant Klebsiella pneumoniae isolated from Tehran heart center. Iran J Microbiol. 2022;14(1):38.

    PubMed  PubMed Central  Google Scholar 

  26. Tsai Y-M, Wang S, Chiu H-C, Kao C-Y, Wen L-L. Combination of modified carbapenem inactivation method (mCIM) and EDTA-CIM (eCIM) for phenotypic detection of carbapenemase-producing Enterobacteriaceae. BMC Microbiol. 2020;20:1–7.

    Article  Google Scholar 

  27. Viau R, Frank KM, Jacobs MR, Wilson B, Kaye K, Donskey CJ, et al. Intestinal carriage of carbapenemase-producing organisms: current status of surveillance methods. Clin Microbiol Rev. 2016;29(1):1–27.

    Article  CAS  PubMed  Google Scholar 

  28. Aminul P, Anwar S, Molla MMA, Miah MRA. Evaluation of antibiotic resistance patterns in clinical isolates of Klebsiella pneumoniae in Bangladesh. Biosaf Health. 2021;3(06):301–6.

    Article  Google Scholar 

  29. Farhadi M, Ahanjan M, Goli HR, Haghshenas MR, Gholami M. High frequency of multidrug-resistant (MDR) Klebsiella pneumoniae harboring several β-lactamase and integron genes collected from several hospitals in the north of Iran. Ann Clin Microbiol Antimicrob. 2021;20:1–9.

    Article  Google Scholar 

  30. El Aila NA, Laham NAA, Ayesh BM, Naas T. Fecal carriage of extended-spectrum β-lactamase-producing enterobacterales from hospitals and community settings in Gaza Strip, Palestine. BMC Microbiol. 2023;23(1):376.

    Article  PubMed  PubMed Central  Google Scholar 

  31. Sedighi P, Zarei O, Karimi K, Taheri M, Karami P, Shokoohizadeh L. Molecular typing of Klebsiella pneumoniae clinical isolates by Enterobacterial repetitive intergenic consensus polymerase chain reaction. Int J Microbiol. 2020;2020(1):8894727.

    Google Scholar 

  32. Attia NM, El-Ghazzawi E, Elkhwsky F, Metwally DES, Ramadan A. Klebsiella pneumoniae isolated from an Egyptian pediatric hospital: prevalence, antibiotic resistance, biofilm formation, and genotyping. Microbes Infect Dis. 2023;4(3):871–83.

    CAS  Google Scholar 

  33. Ferreira RL, Da Silva BC, Rezende GS, Nakamura-Silva R, Pitondo-Silva A, Campanini EB, et al. High prevalence of multidrug-resistant Klebsiella pneumoniae harboring several virulence and β-lactamase encoding genes in a Brazilian intensive care unit. Front Microbiol. 2019;9:3198.

    Article  PubMed  PubMed Central  Google Scholar 

  34. Parsaie Mehr V, Shokoohizadeh L, Mirzaee M, Savari M. Molecular typing of Klebsiella pneumoniae isolates by enterobacterial repetitive intergenic consensus (ERIC)–PCR. Infect Epidemiol Microbiol. 2017;3(4):112–6.

    Google Scholar 

Download references

Acknowledgements

The authors would like to express their gratitude to the Research and Technology Vice-Chancellor of Babol University of Medical Sciences as well as the Biomedical and Microbial Advanced Technologies Research Center (BMAT) at the Health Research Institute in Babol, Iran, for their support.

Funding

This research did not receive any specific grant from funding agencies in the public, commercial, or not-for-profit sectors.

Author information

Authors and Affiliations

  1. Department of Microbiology, Ayatollah Amoli Branch, Islamic Azad University, Amol, Iran

    Azadeh Ferdosi-Shahandashti & Fatemeh Zaboli

  2. Infectious Diseases and Tropical Medicine Research Center, Health Research Institute, Babol University of Medical Sciences, Babol, Iran

    Abazar Pournajaf

  3. Biomedical and Microbial Advanced Technologies Research Center, Health Research Institute, Babol University of Medical Sciences, Babol, Iran

    Elaheh Ferdosi-Shahandashti

  4. Department of Microbiology, Faculty of Medicine, Shahed University, Tehran, Iran

    Kasra Javadi

Authors
  1. Azadeh Ferdosi-Shahandashti
    View author publications

    Search author on:PubMed Google Scholar

  2. Abazar Pournajaf
    View author publications

    Search author on:PubMed Google Scholar

  3. Elaheh Ferdosi-Shahandashti
    View author publications

    Search author on:PubMed Google Scholar

  4. Fatemeh Zaboli
    View author publications

    Search author on:PubMed Google Scholar

  5. Kasra Javadi
    View author publications

    Search author on:PubMed Google Scholar

Contributions

A.FS. and E.FS. conceived and designed the experiments. K.J. wrote the main manuscript text. A.FS., E.FS., F.Z. and A.P. collected samples and performed the experiments. E.FS. analyzed the data, prepared the Figs. E.FS. and A.FS. reviewed and finalized the manuscript. All authors contributed to the article and approved the submitted version.

Corresponding author

Correspondence to Elaheh Ferdosi-Shahandashti.

Ethics declarations

Ethics approval and consent to participate

This study was performed in line with the principles of the Declaration of Helsinki. Approval was granted by the Ethics Committee of Islamic Azad University - Ayatollah Amoli Branch; Amol, Iran (2022-09-11/ IR.IAU.AMOL.REC.1401.087). Informed consent was obtained from all individual participants included in the study.

Consent for publication

Not applicable.

Competing interests

The authors declare no competing interests.

Additional information

Publisher’s note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Rights and permissions

Open Access This article is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License, which permits any non-commercial use, sharing, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if you modified the licensed material. You do not have permission under this licence to share adapted material derived from this article or parts of it. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by-nc-nd/4.0/.

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Ferdosi-Shahandashti, A., Pournajaf, A., Ferdosi-Shahandashti, E. et al. Identification of beta-lactamase genes and molecular genotyping of multidrug-resistant clinical isolates of Klebsiella pneumoniae. BMC Microbiol 24, 549 (2024). https://doi.org/10.1186/s12866-024-03679-6

Download citation

  • Received:

  • Accepted:

  • Published:

  • DOI: https://doi.org/10.1186/s12866-024-03679-6

Keywords

BMC Microbiology

ISSN: 1471-2180

Contact us