Sains Malaysiana 54(7)(2025): 1751-1762
http://doi.org/10.17576/jsm-2025-5407-09
The Molecular Characteristics of
Extended-Spectrum β-Lactamases (ESBL), Carbapenem-Resistant
Enterobacterales (CRE) and Susceptible Isolates of Klebsiella pneumoniae and Escherichia coli in Hospital Pakar Universiti Sains Malaysia
(HPUSM), Kelantan, Malaysia
(Pencirian Molekul Spektrum Lanjutan
β-Lactamases (ESBL), Carbapenem-Rintang Enterobacterales (CRE) serta Pencilan
Kerentanan Klebsiella pneumoniae dan Escherichia coli di Hospital
Pakar Universiti Sains Malaysia (HPUSM), Kelantan, Malaysia)
NUR HUSNA SHAHIMI1,
ZETI NORFIDIYATI SALMUNA2, MAWADDAH MOHD AZLAN1, HASLIZAI
HASSAN1 & NIK YUSNORAINI YUSOF1,*
1Institute for Research in Molecular
Medicine (INFORMM), Health Campus, Universiti Sains Malaysia, 16150 Kubang
Kerian, Kelantan, Malaysia
2Department of Medical Microbiology and
Parasitology, School of Medical Sciences, Health Campus, Universiti Sains
Malaysia, 16150 Kubang Kerian, Kelantan, Malaysia
Diserahkan:
29 Ogos 2024/Diterima: 14 Mei 2025
Abstract
Multidrug-resistance Klebsiella
pneumoniae (MDR-KP) has become a major challenge to clinicians as it caused significant morbidity and mortality among hospitalized patients. This
study aims to determine the antibiotic susceptibility profiles of 17 K.
pneumoniae strains isolated to different antimicrobial agents and to
characterize the genes encoding extended-spectrum β-lactamase (ESBL), AmpC
and (Carbapenem Resistance Enterobacteriacae (CRE) phenotypes by using VITEK
AST (Antimicrobial Susceptibility Test), phenotypic
disk confirmatory test (PDCT) and polymerase chain reaction (PCR). Out of 17 K.
pneumoniae isolates tested, seven (41.2%) were confirmed to be ESBL
producers, carrying blaTEM (1; 14.3%), blaSHV(1;
14.3%), blaCTXM-1 (4; 57.14%), blaCTXM-14 (2;
28.6%) and co-existence of both blaTEM and blaCTXM-1 (1;
14.3%) genes, while four K. pneumoniae (23.5%) isolates were CRE
strains, carrying co-existence of blaTEMand blaCTXM-1 genes, as well as blaNDM-1 (4; 100%). blaTEM and blaCTXMgenes were the most predominant genes
detected in both K. pneumoniae ESBL and CRE isolates and blaNDM-1 genes was detected in K. pneumoniae CRE isolates which were in line with
other findings worldwide. Understanding this link highlights the need for strategic
antibiotic usage in healthcare settings by providing a deeper understanding of
antibiotic resistance trends in multidrug resistant (MDR) organisms.
Keywords: Antibiotic resistant; CRE; ESBL; Klebsiella
pneumoniae
Abstrak
Klebsiella pneumoniae rintang pelbagai ubat (MDR-KP) telah
menjadi cabaran utama bagi pakar klinikal kerana ia menyebabkan morbiditi dan
kematian yang signifikan dalam kalangan pesakit yang telah dirawat di hospital.
Penyelidikan ini bertujuan untuk menentukan profil kerentanan antibiotik bagi
17 strain K. pneumoniae yang dipencilkan kepada agen antimikrob yang
berbeza dan untuk mencirikan gen beta-laktamase spektrum lanjutan (ESBL), AmpC
dan Enterobcacteriacae perintang karbapenem (CRE) menggunakan VITEK AST
(Ujian Kecenderungan Antimikrob), ujian pengesahan cakera fenotipik (PDCT) dan
reaksi rantaian polimerase (PCR). Daripada 17 pencilan K. pneumoniae yang diuji, tujuh pencilan (41.2%) telah disahkan sebagai pengeluar ESBL,
membawa gen blaTEM (1; 14.3%), blaSHV(1;
14.3%), blaCTXM-1 (4; 57.14%), blaCTXM-14 (2;
28.6%) serta kewujudan bersama blaTEM dan blaCTXM-1 (1;
14,5%), manakala empat pencilan CRE (23.5%) membawa kewujudan bersama gen blaTEM, blaCTXM-1 serta blaNDM-1 (4, 100%). Gen blaTEM dan blaCTXM adalah gen yang paling dominan yang dikesan
dalam kedua-dua pencilan K. pneumoniae ESBL dan CRE serta blaNDM-1 telah ditemui dalam K. pneumoniae CRE dan keputusan ini adalah sejajar
dengan penemuan lain di seluruh dunia. Memahami hubungan antara kedua-dua ini
menyerlahkan kepentingan penggunaan antibiotik secara strategik dalam penjagaan
kesihatan dengan menyediakan pemahaman yang lebih mendalam mengenai kerintangan
antibiotik dalam organisma yang rintang pelbagai ubat (MDR).
Kata
kunci: CRE; ESBL; Klebsiella pneumoniae; rintang antibiotik
RUJUKAN
Ang, S.H., Periyasamy, P., Shah, S.A., Ramli, R., Kori,
N. & Lau, C.L. 2022. Risk factors for complications and survival outcomes
of Klebsiella pneumoniae bacteraemia in Hospital Canselor Tuanku Muhriz
Universiti Kebangsaan Malaysia. Medical Journal of Malaysia 77(4): 440-445.
Ashurst, J.V. & Dawson, A. 2022. Klebsiella pneumonia. In
StatPearls. StatPearls Publishing. https://pubmed.ncbi.nlm.nih.gov/30085546/
Azimi, L., Rastegar-Lari, A., Talebi, M., Ebrahimzadeh-Namvar, A. &
Soleymanzadeh-Moghadam, S. 2013. Evaluation of phenotypic methods for detection
of Klebsiella pneumoniae carbapenemase-producing K. pneumoniae in
Tehran. Journal of Medical Bacteriology 2(3-4): 26-31. https://jmb.tums.ac.ir/index.php/jmb/article/view/48
Candan, E.D. & Aksöz, N. 2015. Klebsiella pneumoniae:
Characteristics of carbapenem resistance and virulence factors. Acta
Biochimica Polonica 62(4): 867-874. https://doi.org/10.18388/abp.2015_1148
Caneiras, C., Lito, L., Melo-Cristino, J. & Duarte, A. 2019.
Community-and hospital-acquired Klebsiella pneumoniae urinary tract
infections in Portugal: Virulence and antibiotic resistance. Microorganisms 7(5): 138. https://doi.org/10.3390/microorganisms7050138
Carvalho, I., Chenouf, N.S., Carvalho, J.A., Castro,
A.P., Silva, V., Capita, R., Alonso-Calleja, C., de Lurdes Nunes Enes
Dapkevicius, M., Igrejas, G., Torres, C. & Poeta, P. 2021.
Multidrug-resistant Klebsiella pneumoniae harboring extended spectrum
β-lactamase encoding genes isolated from human septicemias. PLoS ONE 16(5): e0250525. https://doi.org/10.1371/journal.pone.0250525
Centers for Disease Control and Prevention (CDC).
2019. Antibiotic Resistance Threats in the United States. Atlanta, GA:
US Department of Health and Human Services.
Centers for Disease Control and Prevention (CDC).
2019. Healthcare-Associated Infections (HAIs). https://www.cdc.gov/hai/organisms/cre/cre-patients.html (Accessed on 26 December 2023).
Chia, J.H., Chu, C., Su, L.H., Chiu, C.H., Kuo, A.J., Sun, C.F. & Wu,
T.L. 2005. Development of a multiplex PCR and SHV
melting-curve mutation detection system for detection of some SHV and CTX-M β-lactamases of Escherichia coli, Klebsiella pneumoniae, and Enterobacter
cloacae in Taiwan. Journal of Clinical Microbiology 43(9): 4486-4491. https://doi.org/10.1128/JCM.43.9.4486-4491.2005
Clinical &
Laboratory Standards Institute (CLSI). 2023. Performance Standards for
Antimicrobial Susceptibility Testing. 33rd ed. CLSI supplement
M100. Clinical and Laboratory Standard Institute, USA.
Copur Cicek, A., Saral, A., Ozad Duzgun, A., Yasar, E.,
Cizmeci, Z., Ozlem Balci, P., Sari, F., Firat, M., Altintop, Y.A., Ak, S.,
Caliskan, A., Yildiz, N., Sancaktar, M., Esra Budak, E., Erturk, A., Birol
Ozgumus, O. & Sandalli, C. 2013. Nationwide study of Escherichia coli producing extended-spectrum β-lactamases TEM, SHV and CTX-M in Turkey. Journal
of Antibiotics 66(11): 647-650. https://doi.org/10.1038/ja.2013.72
Dallenne, C., da Costa, A., Decré, D., Favier, C. &
Arlet, G. 2010. Development of a set of multiplex PCR assays for the detection
of genes encoding important β-lactamases in Enterobacteriaceae. Journal
of Antimicrobial Chemotherapy 65(3): 490-495.
https://doi.org/10.1093/jac/dkp498
Ejaz, H., Younas, S., Abosalif, K.O.A., Junaid, K.,
Alzahrani, B., Alsrhani, A., Abdalla, A.E., Ullah, M.I., Qamar, M.U. &
Hamam, S.S.M. 2021. Molecular analysis of blaSHV, blaTEM, and blaCTX-M in
extended-spectrum β-lactamase producing enterobacteriaceae recovered from
fecal specimens of animals. PLoS ONE 16(1): 0245126.
https://doi.org/10.1371/journal.pone.0245126
Ellington, M.J., Kistler, J., Livermore, D.M. &
Woodford, N. 2007. Multiplex PCR for rapid detection of genes encoding acquired
metallo-β-lactamases. Journal of Antimicrobial Chemotherapy 59(2):
321-322. https://doi.org/10.1093/jac/dkl481
Esposito, E.P., Cervoni, M., Bernardo, M., Crivaro, V., Cuccurullo, S.,
Imperi, F. & Zarrilli, R. 2018. Molecular epidemiology and virulence
profiles of colistin-resistant Klebsiella pneumoniae blood isolates from
the hospital agency “Ospedale dei Colli,” Naples, Italy. Frontiers in
Microbiology 9: 1463. https://doi.org/10.3389/fmicb.2018.01463
Feizabadi, M.M., Mohammadi-Yeganeh, S., Mirsalehian, A.,
Azimi, P., Mirafshar, S.M., Mahboobi, M., Nili, F. & Yadegarinia, D. 2010.
Genetic characterization of ESBL-producing strains of Klebsiella pneumoniae from Tehran hospitals. Journal of Infection in Developing Countries 4(10): 609-615. https://doi.org/10.3855/jidc.1059
Fils, P.E.L., Cholley, P., Gbaguidi-Haore, H., Hocquet, D., Sauget, M.
& Bertrand, X. 2021. ESBL-producing Klebsiella pneumoniae in a
University Hospital: Molecular features, diffusion of epidemic clones and
evaluation of cross-transmission. PLoS ONE 16(3): e0247875.
https://doi.org/10.1371/journal.pone.0247875
González, I.A., Palavecino, A., Núñez, C., Dreyse, P.,
Melo-González, F., Bueno, S.M. & Palavecino, C.E. 2021. Effective treatment
against ESBL-producing Klebsiella pneumoniae through synergism of the
photodynamic activity of Re (I) compounds with beta-lactams. Pharmaceutics 13(11): 1889. https://doi.org/10.3390/pharmaceutics13111889
He, Y., Guo,
X., Xiang, S., Li, J., Li, X.,
Xiang, H., He, J., Chen, D. & Chen, J. 2016. Comparative analyses of
phenotypic methods and 16S rRNA, khe, rpoB genes sequencing for identification
of clinical isolates of Klebsiella pneumoniae. Antonie van
Leeuwenhoek 109(7): 1029-1040. https://doi.org/10.1007/s10482-016-0702-9
Islam, M.S., Sobur, M.A., Rahman, S., Ballah, F.M., Ievy,
S., Siddique, M.P., Rahman, M., Kafi, M.A. & Rahman, M.T. 2022. Detection
of blaTEM, blaCTX-M, blaCMY, and blaSHV genes among extended-spectrum
beta-lactamase-producing Escherichia coli isolated from migratory birds
travelling to Bangladesh. Microbial Ecology 83(4): 942-950.
https://doi.org/10.1007/s00248-021-01803-x
Jiang, W., Yang, W., Zhao, X., Wang, N. & Ren, H.
2020. Klebsiella pneumoniae presents antimicrobial drug resistance for
β‑lactam through the ESBL/PBP signaling pathway. Experimental and
Therapeutic Medicine 19(4): 2449-2456.
https://doi.org/10.3892/etm.2020.8498
Karaman, E., Çiçek, A.Ç., Şemen, V. &
Beriş, F.S. 2024.
Characterization of resistance genes and replicon typing in
Carbapenem-resistant Klebsiella pneumoniae strains. Annals of
Clinical Microbiology and Antimicrobials 23: 19.
Leavitt, A., Chmelnitsky, I., Colodner, R., Ofek, I.,
Carmeli, Y. & Navon-Venezia, S. 2009. Ertapenem resistance among
extended-spectrum-β-lactamase-producing Klebsiella pneumoniae isolates. Journal of Clinical Microbiology 47(4): 969-974.
https://doi.org/10.1128/JCM.00651-08
Lee, Y.Q., Sri La Sri Ponnampalavanar, S., Chong, C.W.,
Karunakaran, R., Vellasamy, K.M., Abdul Jabar, K., Kong, Z.X., Lau, M.Y. &
Teh, C.S.J. 2022. Characterisation of non-carbapenemase-producing
carbapenem-resistant Klebsiella pneumoniae based on their clinical and
molecular profile in Malaysia. Antibiotics 11(11): 1670.
https://doi.org/10.3390/antibiotics11111670
Li, M., Liu, Y., Gong, Y., Yan, X., Wang, L., Zheng, W.,
Ai, H. & Zhao, Y. 2023. Recent advances in nanoantibiotics against
multidrug-resistant bacteria. Nanoscale Advances 5(23): 6278-6317. https://doi.org/10.1039/d3na00530e
Magill, S.S., Edwards, J.R., Bamberg, W., Beldavs, Z.G., Dumyati, G.,
Kainer, M.A., Lynfield, R., Maloney, M., McAllister-Hollod, L., Nadle, J., Ray,
S.M., Thompson, D.L., Wilson, L.E. & Fridkin, S.K. 2014. Multistate point-prevalence
survey of health care–associated infections. New England Journal of Medicine 370(13): 1198-1208. https://doi.org/10.1056/nejmoa1306801
Marimuthu, K., Venkatachalam, I., Khong, W.X., Koh, T.H.,
Cherng, B.P.Z., Van La, M., Pratim De, P., Krishnan, P.U., Tan, T.Y., Choon,
R.F.K., Pada, S.K., Lam, C.W., Ooi, S.T., Deepak, R.N., Smitasin, N., Tan,
E.L., Lee, J.J., Kurup, A., Young, B., Sim, T.W.N., Thoon, K.C., Fisher, D.,
Ling, M.L., Peng, A.S.B., Teo, Y., Hsu, L.Y., Lin, T.P.R., Ong, T.H.R., Teo,
J., Ng, O.T.; Carbapenemase-Producing
Enterobacteriaceae in Singapore (CaPES) Study Group. 2017. Clinical and molecular epidemiology of
carbapenem-resistant enterobacteriaceae among adult inpatients in Singapore. Clinical
Infectious Diseases 64(Suppl 2): S68-S75.
https://doi.org/10.1093/cid/cix113
Morrill, H.J., Pogue, J.M., Kaye, K.S. & LaPlante,
K.L. 2015. Treatment options for carbapenem-resistant enterobacteriaceae
infections. Open Forum Infectious Disease 2(2): ofv050.
https://doi.org/10.1093/o
Moya, C. & Maicas, S. 2020. Antimicrobial resistance
in Klebsiella pneumoniae strains: Mechanisms and outbreaks. Proceedings
of the 1st International Electronic Conference on Microbiology 66(1):
11. https://doi.org/10.3390/proceedings2020066011
Muzaheed, M., Sattar Shaikh, N., Sattar Shaikh, S.,
Acharya, S., Sarwar Moosa, S., Habeeb Shaikh, M., M. Alzahrani, F. &
Ibrahim Alomar, A. 2021. Characterization of CTX-M-15-Klebsiella pneumoniae from inpatients and outpatients of a teaching hospital. F1000 Research 10: 444. https://doi.org/10.12688/f1000research.53221.1
Nordmann, P., Dortet, L. & Poirel, L. 2012.
Carbapenem resistance in enterobacteriaceae: Here is the storm! Trends in
Molecular Medicine 18(5): 263-272.
https://doi.org/10.1016/j.molmed.2012.03.003
Paterson, D.L. & Bonomo, R.A. 2005. Extended spectrum
beta lactamases: A critical update. Clinical Microbiology Reviews 18(4):
657-686. https://doi.org/10.2174/978160805292911201010115
Peymani, A., Naserpour-Farivar, T., Zare, E. &
Azarhoosh, K. 2017. Distribution of blaTEM, blaSHV, and blaCTX-M genes among
ESBL-producing P. aeruginosa isolated from Qazvin and Tehran hospitals,
Iran. Journal of Preventive Medicine and Hygiene 58(2): E155-E160.
Pishtiwan, A.H. & Khadija, K.M. 2019. Prevalence of
blaTEM, blaSHV, and blaCTX-M genes among ESBL-producing Klebsiella
pneumoniae and Escherichia coli isolated from thalassemia patients
in Erbil, Iraq. Mediterranean Journal of Hematology and Infectious Diseases 11: e2019041. https://doi.org/10.4084/mjhid.2009.001
Pitout, J.D.D., Nordmann, P. & Poirel, L. 2015.
Carbapenemase-producing Klebsiella pneumoniae, a key pathogen set for
global nosocomial dominance. Antimicrobial Agents and Chemotherapy 59(10): 5873-5884. https://doi.org/10.1128/AAC.01019-15
Queenan, A.M. & Bush, K. 2007. Carbapenemases: The
versatile β-lactamases. Clinical Microbiology Reviews 20(3): 440-458.
https://doi.org/10.1128/CMR.00001-07
Sarojamma, V. & Ramakrishna, V. 2011. Prevalence of
ESBL-producing Klebsiella pneumoniae isolates in tertiary care hospital. ISRN Microbiology 2011: 318348. https://doi.org/10.5402/2011/318348
Shalmashi, H., Farajnia, S., Sadeghi, M., Tanoumand, A.,
Veissi, K., Hamishekar, H. & Gotaslou, R. 2022. Detection of ESBLs types
blaCTX-M, blaSHV and blaTEM resistance genes among clinical isolates of Pseudomonas
aeruginosa. Gene Reports 28: 101637.
https://doi.org/10.1016/j.genrep.2022.101637
Vock, I. & Tschudin-Sutter, S. 2019. Carbapenem-resistant Klebsiella pneumoniae - impact of infection-prevention and control
interventions. Annals of Translational Medicine 7(S8): S344.
https://doi.org/10.21037/atm.2019.09.91
Walter, J., Haller, S., Quinten, C., Kärki, T., Zacher, B., Eckmanns, T.,
Abu Sin, M., Plachouras, D., Kinross, P., Suetens, C.; ECDC PPS study group.
2018. Healthcare-associated pneumonia in acute care hospitals in European
union/European economic area countries: an analysis of data from a point
prevalence survey, 2011 to 2012. Eurosurveillance 23(32): 1700843.
https://doi.org/10.2807/1560-7917.ES.2018.23.32.1700843
Wei, J., Wenjie, Y., Ping, L., Na, W., Haixia, R. &
Xuequn, Z. 2018. Antibiotic resistance of Klebsiella pneumoniae through
β-arrestin recruitment-induced β-lactamase signaling pathway. Experimental
and Therapeutic Medicine 15(3): 2247-2254.
https://doi.org/10.3892/etm.2018.5728
Woodford, N., Fagan, E.J. & Ellington, M.J. 2006.
Multiplex PCR for rapid detection of genes encoding CTX-M extended-spectrum
β-lactamases. Journal of Antimicrobial Chemotherapy 57(1): 154-155.
https://doi.org/10.1093/jac/dki412
Wu, A.Y.J., Chang, H., Wang, N.Y., Sun, F.J. & Liu,
C.P. 2022. Clinical and molecular characteristics and risk factors for patients
acquiring carbapenemase-producing and non-carbapenemase-producing carbapenem-nonsusceptible-enterobacterales
bacteremia. Journal of Microbiology, Immunology and Infection 55(6):
1229-1238. https://doi.org/10.1016/j.jmii.2021.10.008
Wu, J.J., Wang, L.R., Liu, Y.F., Chen, H.M. & Yan,
J.J. 2011. Prevalence and characteristics of ertapenem-resistant Klebsiella
pneumoniae isolates in a Taiwanese University Hospital. Microbial Drug
Resistance 17(2): 259-266. https://doi.org/10.1089/mdr.2010.0115
Zhang, J., Zhou, K., Zheng, B., Zhao, L., Shen, P., Ji,
J., Wei, Z., Li, L., Zhou, J. & Xiao, Y. 2016. High prevalence of
ESBL-producing Klebsiella pneumoniae causing community-onset infections
in China. Frontiers in Microbiology 7: 1830.
https://doi.org/10.3389/fmicb.2016.01830
Zhang, Y.L., Huang, F.Y., Gan, L.L., Yu, X., Cai, D.J.,
Fang, J., Zhong, Z.J., Guo, H.R. Xie, Y., Yi, J., Wang, Z.S. & Zuo, Z.C.
2021. High prevalence of bla CTX-M and bla SHV among ESBL producing E. coli isolates from beef cattle in China’s Sichuan-Chongqing circle. Scientific
Report 11(1): 13725. https://doi.org/10.1038/s41598-021-93201-z
Zhang, N., Wang, X., Li, Y., Lu, Y., Sheng, C., Sun, Y. & Jiao, Y.
2025. Mechanisms and therapeutic implications of gene expression regulation by
circRNA- protein interactions in cancer. Commun. Biol. 8(1): 77. https://doi.org/10.1038/s42003-024-07383-z
*Pengarang untuk surat-menyurat; email: nikyus@usm.my