Extended-spectrum β-lactamase (ESBL)-producing Klebsiella pneumoniae has been associated with a wide range of infections in humans and animals. The objective of this study was to determine the genomic characteristics of two multiple drug resistant, ESBLs-producing K. pneumoniae strains isolated from a swine in 2013 (KP2013Z28) and a hospitalized patient in 2014 (KP2014C46) in Malaysia. Genomic analyses of the two K. pneumoniae strains indicated the presence of various antimicrobial resistance genes associated with resistance to β-lactams, aminoglycosides, colistin, fluoroquinolones, phenicols, tetracycline, sulfonamides, and trimethoprim, corresponding to the antimicrobial susceptibility profiles of the strains. KP2013Z28 (ST25) and KP2014C46 (ST929) harbored 5 and 2 genomic plasmids, respectively. The phylogenomics of these two Malaysian K. pneumoniae, with other 19 strains around the world was determined based on SNPs analysis. Overall, the strains were resolved into five clusters that comprised of strains with different resistance determinants. This study provided a better understanding of the resistance mechanisms and phylogenetic relatedness of the Malaysian strains with 19 strains isolated worldwide. This study also highlighted the needs to monitor the usage of antibiotics in hospital settings, animal husbandry, and agricultural practices due to the increase of β-lactam, aminoglycosides, tetracycline, and colistin resistance among pathogenic bacteria for better infection control.
This is a preview of subscription content, access via your institution.
Buy single article
Instant access to the full article PDF.
Tax calculation will be finalised during checkout.
Ahmad N, Ali SM, Khan AU (2019) Molecular characterization of novel sequence type of carbapenem-resistant New Delhi metallo-β-lactamase-1-producing Klebsiella pneumoniae in the neonatal intensive care unit of an Indian hospital. Int J Antimicrob Agents 53(4):525–529
Ali T, Ali I, Khan NA, Han B, Gao J (2018) The growing genetic and functional diversity of extended spectrum beta-lactamases. Biomed Res Int 2018:9519718. https://doi.org/10.1155/2018/9519718
Al-Marzooq F, Mohd Yusof MY, Tay ST (2014) Molecular analysis of ciprofloxacin resistance mechanisms in Malaysian ESBL-producing Klebsiella pneumoniae isolates and development of mismatch amplification mutation assays (MAMA) for rapid detection of gyrA and parC mutations. Biomed Res Int 2014:1–10. https://doi.org/10.1155/2014/601630
Al-Marzooq F, Yusof MY, Tay ST (2015) Molecular analysis of antibiotic resistance determinants and plasmids in Malaysian isolates of multidrug resistant Klebsiella pneumoniae. PLoS One 10(7):e0133654
Amador P, Fernandes R, Prudêncio C, Duarte I (2019) Prevalence of antibiotic resistance genes in multidrug-resistant Enterobacteriaceae on Portuguese livestock manure. Antibiotics. 8(1):23
Antibiotic use and antibiotic resistance in food animals in Malaysia (2013): a threat to human and animal health, Health Action International Asia Pacific (HAIAP) Third World Network (TWN) Penang in association with Consumers’ Association of Penang.
Arabaghian H, Salloum T, Alousi S, Panossian B, Araj GF, Tokajian S (2019) Molecular characterization of carbapenem resistant Klebsiella pneumoniae and Klebsiella quasipneumoniae isolated from Lebanon. Sci Rep 9(1):1–2
Ben Hamouda T, Foulon T, Ben Cheikh Masmoudi A, Fendri C, Belhadj O, Ben Mahrez K (2003) Molecular epidemiology of an outbreak of multiresistant Klebsiella pneumoniae in a Tunisian neonatal ward. J Med Microbiol 52:427–433
Bialek-Davenet S, Criscuolo A, Ailloud F, Passet V, Jones L, Delannoy-Vieillard AS, Garin B, Le Hello S, Arlet G, Nicolas Chanoine MH, Decré D, Brisse S (2014) Genomic definition of hypervirulent and multidrug-resistant Klebsiella pneumoniae clonal groups. Emerg Infect Dis 20(11):1812–1820
Bidewell CA, Williamson SM, Rogers J, Tang Y, Ellis RJ, Petrovska L, AbuOun M (2018) Emergence of Klebsiella pneumoniae subspecies pneumoniae as a cause of septicaemia in pigs in England. PLoS One 13(2):e0191958
Bowring BG, Fahy VA, Morris A, Collins AM (2017) An unusual culprit: Klebsiella pneumoniae causing septicaemia outbreaks in neonatal pigs? Vet Microbiol 203:267–270
Brolund A, Sundqvist M, Kahlmeter G, Grape M (2010) Molecular characterisation of trimethoprim resistance in Escherichia coli and Klebsiella pneumoniae during a two year intervention on trimethoprim use. PLoS One 5(2):e9233
Chen CJ, Wu TL, Lu PL, Chen YT, Fung CP, Chuang YC, Lin JC, Siu LK (2014) Closely related NDM-1-encoding plasmids from Escherichia coli and Klebsiella pneumoniae in Taiwan. PLoS One 9(8):e104899
Crémet L, Caroff N, Dauvergne S, Reynaud A, Lepelletier D, Corvec S (2011) Prevalence of plasmid-mediated quinolone resistance determinants in ESBL Enterobacteriaceae clinical isolates over a 1-year period in a French hospital. Pathol Biol 59(3):151–156
Cui M, Zhang J, Gu Z, Li R, Chan EWC, Yan M, Chen S (2017) Prevalence and molecular characterization of mcr-1-positive Salmonella strains recovered from clinical specimens in China. Antimicrob Agents Chemother 61(5): e02471–16
Dashti AA, Paton R, Amyes SGB (2006) Linkage of ciprofloxacin resistance with a single genotypic cluster of Klebsiella pneumoniae. Int J Antimicrob Agents 27(1):73–76
De Oliveira GD, Doi Y, Szabo D, Adams Haduch JM, Vaz TM, Leite D, Padoveze MC, Freire MP, Silveira FP, Paterson DL (2008) Multiclonal outbreak of Klebsiella pneumoniae producing extended-spectrum β-lactamase CTX-M-2 and novel variant CTX-M-59 in a neonatal intensive care unit in Brazil. Antimicrob Agents Chemother 52:1790–1793
Di Pilato V, Arena F, Tascini C, Cannatelli A, De Angelis LH, Fortunato S, Giani T, Menichetti F, Rossolini GM (2016) mcr-1.2, a new mcr variant carried on a transferable plasmid from a colistin-resistant KPC carbapenemase-producing Klebsiella pneumoniae strain of sequence type 512. Antimicrob Agents Chemother 60(9):5612–5615
Dolejska M, Villa L, Dobiasova H, Fortini D, Feudi C, Carattoli A (2013) Plasmid content of a clinically relevant Klebsiella pneumoniae clone from the Czech Republic producing CTX-M-15 and QnrB1. Antimicrob Agents Chemother 57(2):1073–1076
Doumith M, Godbole G, Ashton P, Larkin L, Dallman T, Day M, Day M, Muller-Pebody B, Ellington MJ, de Pinna E, Johnson AP (2016) Detection of the plasmid-mediated mcr-1 gene conferring colistin resistance in human and food isolates of Salmonella enterica and Escherichia coli in England and Wales. J Antimicrob Chemother 71(8):2300–2305
Falgenhauer L, Waezsada SE, Yao Y, Imirzalioglu C, Käsbohrer A, Roesler U, Michael GB, Schwarz S, Werner G, Kreienbrock L (2016) Colistin resistance gene mcr-1 in extended-spectrum β-lactamase-producing and carbapenemase-producing Gram-negative bacteria in Germany. Lancet Infect Dis 16(3):282–283
Health Action International Asia Pacific (HAIAP) Third World Network (TWN) Penang in association with Consumers’ Association of Penang (2013) Antibiotic use and antibiotic resistance in food animals in Malaysia: A threat to human and animal health
Hasman H, Hammerum AM, Hansen F, Hendriksen RS, Olesen B, Agersø Y, Zankari E, Leekitcharoenphon P, Stegger M, Kaas RS (2015) Detection of mcr-1 encoding plasmid-mediated colistin-resistant Escherichia coli isolates from human bloodstream infection and imported chicken meat, Denmark. Euro Surveill 20(49):261–262
Hopkins KL, Davies RH, Threlfall EJ (2005) Mechanisms of quinolone resistance in Escherichia coli and Salmonella: recent developments. Int J Antimicrob Agents 25(5):358–373
Hu Y, Liu F, Lin IY, Gao GF, Zhu B (2016) Dissemination of the mcr-1 colistin resistance gene. Lancet Infect Dis 16(2):146–147
Huang Y, Ogutu JO, Gu J, Ding F, You Y, Huo Y, Zhao H, Li W, Zhang Z, Zhang W, Chen X (2015) Comparative analysis of quinolone resistance in clinical isolates of Klebsiella pneumoniae and Escherichia coli from Chinese children and adults. BioMed Int 2015:1–6. https://doi.org/10.1155/2015/168292
Keynan Y, Rubinstein E (2007) The changing face of Klebsiella pneumoniae infections in the community. Int J Antimicrob Agents 30:385–389
Kieffer N, Aires-de-Sousa M, Nordmann P, Poirel L (2017) High rate of MCR-1–producing Escherichia coli and Klebsiella pneumoniae among pigs, Portugal. Emerg Infect Dis 23(12):2023–2029
Kumar V, Sun P, Vamathevan J, Li Y, Ingraham K, Palmer L, Huang J, Brown JR (2011) Comparative genomics of Klebsiella pneumoniae strains with different antibiotic resistance profiles. Antimicrob Agents Chemother 55(9):4267–4276
Li CR, Li Y, Zhang PA (2003) Dissemination and spread of CTX-M extended-spectrum β-lactamases among clinical isolates of Klebsiella pneumoniae in central China. Int J Antimicrob Agents 22(5):521–525
Li R, Xie M, Zhang J, Yang Z, Liu L, Liu X, Zheng Z, Chan EW, Chen S (2016) Genetic characterization of mcr-1-bearing plasmids to depict molecular mechanisms underlying dissemination of the colistin resistance determinant. J Antimicrob Chemother 72(2):393–401
Lim KT, Yeo CC, Yasin RM, Balan G, Thong KL (2009) Characterization of multidrug-resistant and extended-spectrum β-lactamase-producing Klebsiella pneumoniae strains from Malaysian hospitals. J Med Microbiol 58:1463–1469
Liu C, Shi J, Guo J (2018) High prevalence of hypervirulent Klebsiella pneumoniae infection in the genetic background of elderly patients in two teaching hospitals in China. Infect Drug Res J 11:1031–1041. https://doi.org/10.2147/IDR.S161075
Liu YY, Wang Y, Walsh TR, Yi LX, Zhang R, Spencer J, Doi Y, Tian G, Dong B, Huang X, Yu LF, Gu D, Ren H, Chen X, Lv L, He D, Zhou H, Liang Z, Liu JH, Shen J (2016) Emergence of plasmid-mediated colistin resistance mechanism MCR-1 in animals and human beings in China: a microbiological and molecular biological study. Lancet Infect Dis 16(2):161–8
Liu S, Li X, Guo Z, Liu H, Sun Y, Liu Y, Wang Q, Liao S, Zhang K (2020) A core genome multilocus sequence typing scheme for Streptococcus mutans. mSphere 5(4):e00348–e00320
Low YM, Yap PS, Jabar KA, Ponnampalavanar S, Karunakaran R, Velayuthan R, Chong CW, Bakar SA, Yusof MY, Teh CS (2017) The emergence of carbapenem resistant Klebsiella pneumoniae in Malaysia: correlation between microbiological trends with host characteristics and clinical factors. Antimicrob Resist Infect Control 6(1):5
Ma L, Lin CJ, Chen JH, Fung CP, Chang FY, Lai YK, Lin JC, Siu LK, Taiwan Surveillance of Antimicrobial Resistance Project (2009) Widespread dissemination of aminoglycoside resistance genes armA and rmtB in Klebsiella pneumoniae isolates in Taiwan producing CTX-M-type extended-spectrum beta-lactamases. Antimicrob Agents Chemother 53(1):104–111
Marchant M, Vinué L, Torres C, Moreno MA (2013) Change of integrons over time in Escherichia coli isolates recovered from healthy pigs and chickens. Vet Microbiol 163:124–132
Mobasseri G, Teh CS, Ooi PT, Thong KL (2019a) The emergence of colistin-resistant Klebsiella pneumoniae strains from swine in Malaysia. J Glob Antimicrob Res, ISSN 17:2213–7165. https://doi.org/10.1016/j.jgar.2018.12.015
Mobasseri G, Teh CS, Rajasekaram G, Thong KL (2019b) Molecular characterization of multidrug-resistant and extended-spectrum beta-lactamase-producing Klebsiella pneumoniae strains from a Malaysian hospital. Braz J Microbiol 51(1):189–195
Nitzan O, Kennes Y, Colodner R, Saliba W, EdelsteinI H, Raz R, Chazan B (2015) Chloramphenicol use and susceptibility patterns in Israel: a national survey. Isr Med Assoc J 17(1):27–31
Olaitan AO, Diene SM, Kempf M, Berrazeg M, Bakour S, Gupta SK, Thongmalayvong B, Akkhavong K, Somphavong S, Paboriboune P (2014) Worldwide emergence of colistin resistance in Klebsiella pneumoniae from healthy humans and patients in Lao PDR, Thailand, Israel, Nigeria and France owing to inactivation of the PhoP/PhoQ regulator mgrB: an epidemiological and molecular study. Int J Antimicrob Agents 44:500–507
Palasubramaniam S, Subramaniam G, Muniandy S, Parasakthi N (2005) SHV-5 extended-spectrum beta-lactamase from Klebsiella pneumoniae associated with a nosocomial outbreak in a paediatric oncology unit in Malaysia. Int J Infect Dis 9:170–172
Paterson DL, Bonomo RA (2005) Extended-spectrum β-lactamases: a clinical update. Clin Microbiol Rev 18(4):657–686
Ramirez MS, Tolmasky ME (2010) Aminoglycoside modifying enzymes. Drug Resist Updat 13(6):151–171
Robicsek A, Jacoby GA, Hooper DC (2006) The worldwide emergence of plasmid-mediated quinolone resistance. Lancet Infect Dis 6(10):629–640
Rodrigues C, Machado E, Ramos H, Peixe L, Novais Â (2014) Expansion of ESBL-producing Klebsiella pneumoniae in hospitalized patients: a successful story of international clones (ST15, ST147, ST336) and epidemic plasmids (IncR, IncFII K). Int J Med Microbiol 304:1100–1108
Romero EDV, Padilla TP, Hernández AH, Grande RP, Vázquez MF, García IG, García-Rodríguez JA, Muñoz Bellido JL (2007) Prevalence of clinical isolates of Escherichia coli and Klebsiella spp. producing multiple extended-spectrum β-lactamases. Diagn Microbiol Infect Dis 59:433–437
Shin SY, Kwon KC, Park JW et al (2009) Characteristics of aac(6′)-Ib-cr gene in extended-spectrum β-lactamase-producing Escherichia coli and Klebsiella pneumoniae isolated from Chungnam area. Korean J Lab Med 29(6):541–550
Sompolinsky D, Nitzan Y, Tetry S, Wolk M, Vulikh I, Kerrn MB, Sandvang D, Hershkovits G, Katcoff DJ (2005) Integron-mediated ESBL resistance in rare serotypes of Escherichia coli causing infections in an elderly population of Israel. J Antimicrob Chemother 55(1):119–122
Sood S (2016) Chloramphenicol - a potent armament against multi-drug resistant (MDR) gram negative bacilli. J Clin Diagn Res 10(2):DC01–DDC3
Villa L, García-Fernández A, Fortini D, Carattoli A (2010) Replicon sequence typing of IncF plasmids carrying virulence and resistance determinants. J Antimicrob Chemother 65(12):2518–2529. https://doi.org/10.1093/jac/dkq347
Xavier BB, Lammens C, Ruhal R, Kumar-Singh S, Butaye P, Goossens H, Malhotra Kumar S (2016) Identification of a novel plasmid-mediated colistin-resistance gene, mcr-2, in Escherichia coli, Belgium, June 2016. Euro Surveill Mon 21(27):30280
Yan J, Wang M, Zheng P, Tsai L, Wu J (2015) Associations of the major international high-risk resistant clones and virulent clones with specific ompK36 allele groups in Klebsiella pneumoniae in Taiwan. New Microbes New Infect 5:1–4
Yang H, Chen H, Yang Q, Chen M, Wang H (2008) High prevalence of plasmid-mediated quinolone resistance genes qnr and aac (6′)-Ibcr in clinical isolates of Enterobacteriaceae from nine teaching hospitals in China. Antimicrob Agents Chemother 52(12):4268–4273
Ye H, Li Y, Li Z, Gao R, Zhang H, Wen R, Gao GF, Hu Q, Feng Y (2016) Diversified mcr-1-harboring plasmid reservoirs confer resistance to colistin in human gut microbiota. M Bio 7(2):e00177–e00116
Zhang H, Miao M, Yan J, Wang M, Tang YW, Kreiswirth BN, Zhang X, Chen L, Du H (2017) Expression characteristics of the plasmid-borne mcr-1 colistin resistance gene. Oncotarget 8(64):107596
Zhou K, Lokate M, Deurenberg RH, Arends J, Foe LT, Grundmann H, Rossen JW, Friedrich AW (2015) Characterization of a CTX-M-15 producing Klebsiella pneumoniae outbreak strain assigned to a novel sequence type (1427). Front Microbiol 6:1250
We thank University of Malaya for financial support and facilities.
This work was supported by University of Malaya Postgraduate Research Grant (PG072-2014B) and High Impact Research (HIR) Grant (UM.C/625/1/HIR/MOHE/CHAN/11/02) to KL Thong.
Conflict of interest
The authors declare that they have no conflict of interest.
Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
About this article
Cite this article
Mobasseri, G., Thong, K. & Teh, C.S.J. Genomic analysis revealing the resistance mechanisms of extended-spectrum β-lactamase-producing Klebsiella pneumoniae isolated from pig and humans in Malaysia. Int Microbiol (2021). https://doi.org/10.1007/s10123-021-00161-5
- Klebsiella pneumoniae
- Whole genome sequencing
- Resistance genes