Original Article

pKpQIL-like plasmid contributes to the dissemination of blaNDM-1 and plasmid mediated quinolone resistance determinants among multi drug resistant Klebsiella pneumoniae in Assiut university hospital, Egypt

Abstract

Background and Objectives: Concomitant carriage of blaNDM-1 and plasmid mediated quinolone resistance determinants (PMQRs) by multi drug resistant (MDR) Klebsiella pneumoniae (K. pneumoniae) has increased globally, often related to their presence on transmissible plasmids. In this study, we hypothesized the presence of blaNDM-1 and PMQRs on a single conjugative plasmid that circulates among K. pneumoniae strains isolated from Assiut University Hospital.
Materials and Methods: Twenty-two clinical MDR K. pneumoniae strains harboring both blaNDM-1 and PMQRs were genotyped using pulsed field gel electrophoresis. Horizontal transfer of blaNDM-1 and PMQRs was evaluated by conjugation and trans-conjugants were screened for the presence of both genes and integron by PCR. Trans-conjugant’s plasmid DNA bands were purified using agarose gel electrophoresis and different DNA bands were screened for blaNDM-1 and PMQRs. Plasmids carrying blaNDM-1 and PMQRs were typed by PCR based replicon typing.
Results: All MDR K. pneumoniae contained class 1 integron and belonged to 15 pulsotypes. BlaNDM-1 and PMQRs were co-transferred in each conjugation process. Multiple replicons (5-9 types) were detected in each trans-conjugant; with IncFIIK and IncFIB-KQ replicons being common among all trans-conjugants. Both blaNDM-1 and PMQRs were detected on a pKpQIL-like multi-replicon plasmid that was present in all K. pneumoniae strains.
Conclusion: In view of these results, the presence of blaNDM-1 and PMQRs on pKpQIL-like plasmid that existed in multiple unrelated K. pneumoniae isolates is highly suggestive of the circulation of pKpQIL-like MDR plasmids in our hospitals. Moreover, carriage of integrons by the-circulating MDR plasmids increases the risk of dissemination of antimicrobial resistance among pathogens.

1. Gorrie CL, Mirčeta M, Wick RR, Judd LM, Lam MMC, Gomi R, et al. Genomic dissection of Klebsiella pneumoniae infections in hospital patients reveals insights into an opportunistic pathogen. Nat Commun 2022; 13: 3017.
2. Hawkey PM, Warren RE, Livermore DM, McNulty CAM, Enoch DA, Otter JA, et al. Treatment of infections caused by multidrug-resistant Gram-negative bacteria: report of the British Society for Antimicrobial Chemotherapy/Healthcare Infection Society/British Infection Association Joint Working Party. J Antimicrob Chemother 2018; 73(suppl_3): iii2-iii78.
3. Effah CY, Sun T, Liu S, Wu Y. Klebsiella pneumoniae: an increasing threat to public health. Ann Clin Microbiol Antimicrob 2020; 19: 1.
4. Partridge SR, Kwong SM, Firth N, Jensen SO. Mobile genetic elements associated with antimicrobial resistance. Clin Microbiol Rev 2018; 31(4): e00088-17.
5. Fonseca ÉL, Vicente AC. Integron functionality, genome innovation: an update on the subtle and smart strategy of integrase and gene cassette expression regulation. Microorganisms 2022; 10: 224.
6. Cury J, Jove T, Touchon M, Neron B, Rocha EP. Identification and analysis of integrons and cassette arrays in bacterial genomes. Nucleic Acids Res 2016; 44: 4539-4550.
7. Ferreira RL, da Silva B, 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.
8. Zhan Q, Xu Y, Wang B, Yu J, Shen X, Liu L, et al. Distribution of fluoroquinolone resistance determinants in Carbapenem-resistant Klebsiella pneumoniae clinical isolates associated with bloodstream infections in China. BMC Microbiol 2021; 21: 164.
9. Mitra S, Mukherjee S, Naha S, Chattopadhyay P, Dutta S, Basu S. Evaluation of co-transfer of plasmid-mediated fluoroquinolone resistance genes and blaNDM gene in Enterobacteriaceae causing neonatal septicaemia. Antimicrob Resist Infect Control 2019; 8: 46.
10. Datta S, Mitra S, Chattopadhyay P, Som T, Mukherjee S, Basu S. Spread and exchange of blaNDM-1 in hospitalized neonates: role of mobilizable genetic elements. Eur J Clin Microbiol Infect Dis 2017; 36: 255-265.
11. Kk S, Ekedahl E, Hoang NTB, Sewunet T, Berglund B, Lundberg L, et al. High diversity of blaNDM-1-encoding plasmids in Klebsiella pneumoniae isolated from neonates in a Vietnamese hospital. Int J Antimicrob Agents 2022; 59: 106496.
12. Di Pilato V, Henrici De Angelis L, Aiezza N, Baccani I, Niccolai C, Parisio EM, et al. Resistome and virulome accretion in an NDM-1-producing ST147 sub lineage of Klebsiella pneumoniae associated with an outbreak in Tuscany, Italy: a genotypic and phenotypic characterization. Lancet Microbe 2022; 3(3): e224-e234.
13. Leavitt A, Navon-Venezia S, Chmelnitsky I, Schwaber MJ, Carmeli Y. Emergence of KPC-2 and KPC-3 in carbapenem-resistant Klebsiella pneumoniae strains in an Israeli hospital. Antimicrob Agents Chemother 2007; 51: 3026-3029.
14. Leavitt A, Chmelnitsky I, Carmeli Y, Navon-Venezia S. Complete nucleotide sequence of KPC-3-encoding plasmid pKpQIL in the epidemic Klebsiella pneumoniae sequence Type 258. Antimicrob Agents Chemother 2010; 54: 4493-4496.
15. García-Fernández A, Villa L, Carta C, Venditti C, Giordano A, Venditti M, et al. Klebsiella pneumoniae ST258 producing KPC-3 identified in italy carries novel plasmids and OmpK36/OmpK35 porin variants. Antimicrob Agents Chemother 2012; 56: 2143-2145.
16. Doumith M, Findlay J, Hirani H, Hopkins KL, Livermore DM, Dodgson A, et al. Major role of pKpQIL-like plasmids in the early dissemination of KPC-type carbapenemases in the UK. J Antimicrob Chemother 2017; 72: 2241-2248.
17. Khalil MAF, Elgaml A, El-Mowafy M. Emergence of multidrug-resistant New Delhi metallo-β-lactamase-1-producing Klebsiella pneumoniae in Egypt. Microb Drug Resist 2017; 23: 480-487.
18. Abdel-Rahim MH, El-Badawy O, Hadiya S, Daef EA, Suh S-J, Boothe DM, et al. Patterns of fluoroquinolone resistance in enterobacteriaceae isolated from the Assiut University Hospitals, Egypt: A comparative study. Microb Drug Resist 2019; 25: 509-519.
19. Yao H, Liu J, Jiang X, Chen F, Lu X, Zhang J. Analysis of the clinical effect of combined drug susceptibility to guide medication for carbapenem-resistant Klebsiella pneumoniae patients based on the Kirby-Bauer disk diffusion method. Infect Drug Resist 2021; 14: 79-87.
20. CLSI (2019). Performance standards for antimicrobial susceptibility testing, 29th informational supplement (M100- S29). Clinical and Laboratory Standards Institute, Wayne, PA, USA.
21. Centers for Disease Control and Prevention (CDC) (2017). Standard operating procedure for PulseNet PFGE of Escherichia coli O157: H7, Escherichia coli non-O157 (STEC), Salmonella serotypes, Shigella sonnei and Shigella flexneri. http://www.cdc.gov/pulsenet/PDF/ecoli-shigella-salmonella-pfge-protocol-508c.pdf
22. Toledano-Tableros JE, Gayosso-Vázquez C, Jarillo-Quijada MD, Fernández-Vázquez JL, Morfin-Otero R, Rodríguez-Noriega E, et al. Dissemination of blaNDM-1 Gene among several Klebsiella pneumoniae sequence types in Mexico associated with horizontal transfer mediated by IncF-like plasmids. Front Microbiol 2021; 12: 611274.
23. Poirel L, Revathi G, Bernabeu S, Nordmann P. Detection of NDM-1-producing Klebsiella pneumoniae in Kenya. Antimicrob Agents Chemother 2011; 55: 934-936.
24. Gay K, Robicsek A, Strahilevitz J, Park CH, Jacoby G, Barrett TJ, et al. Plasmid-mediated quinolone resistance in non-Typhi serotypes of Salmonella enterica. Clin Infect Dis 2006; 43: 297-304.
25. Wu J-J, Ko W-C, Tsai S-H, Yan J-J. Prevalence of plasmid-mediated quinolone resistance determinants QnrA, QnrB, and QnrS among clinical isolates of Enterobacter cloacae in a Taiwanese hospital. Antimicrob Agents Chemother 2007; 51: 1223-1227.
26. Park CH, Robicsek A, Jacoby GA, Sahm D, Hooper DC. Prevalence in the United States of aac(6`)-Ib-cr encoding a ciprofloxacin modifying enzyme. Antimicrob Agents Chemother 2006; 50: 3953-3955.
27. Cocchi S, Grasselli E, Gutacker M, Benagli C, Convert M, Piffaretti J. Distribution and characterization of integrons in Escherichia coli strains of animal and human origin. FEMS Immunol Med Microbiol 2007; 50: 126-132.
28. Kaushik M, Khare N, Kumar S, Gulati P. High prevalence of antibiotic resistance and integrons in E. coli isolated from an urban river water, India. Microb Drug Resist 2019; 25: 359-370.
29. Magi G, Tontaerlli F, Caucci S, Sante LD, Brenciani A, Morroni G, et al. High prevalence of carbapenem-resistant Klebsiella pneumoniae ST307 recovered from fecal samples in an Italian hospital. Future Microbiol 2021; 16: 703-711.
30. Martin RM, Bachman MA. Colonization, infection, and the accessory genome of Klebsiella pneumoniae. Front Cell Infect Microbiol 2018; 8: 4.
31. Sugawara Y, Akeda Y, Hagiya H, Sakamoto N, Takeuchi D, Shanmugakani RK, et al. Spreading patterns of NDM-producing Enterobacteriaceae in clinical and environmental settings in Yangon, Myanmar. Antimicrob Agents Chemother 2019; 63(3): e01924-18.
32. Reygaert WC. An overview of the antimicrobial resistance mechanisms of bacteria. AIMS Microbiol 2018; 4: 482-501.
33. Mohamed ER, Aly SA, Halby HM, Ahmed SH, Zakaria AM, El-Asheer OM. Epidemiological typing of multidrug-resistant Klebsiella pneumoniae, which causes paediatric ventilator-associated pneumonia in Egypt. J Med Microbiol 2017; 66: 628-634.
34. Bassetti M, Righi E, Carnelutti A, Graziano E, Russo A. Multidrug-resistant Klebsiella pneumoniae: challenges for treatment, prevention and infection control. Expert Rev Anti Infect Ther 2018; 16: 749-761.
35. Huang X, Cheng X, Sun P, Tang C, Ni F, Liu G. Characteristics of NDM-1-producing Klebsiella pneumoniae ST234 and ST1412 isolates spread in a neonatal unit. BMC Microbiol 2018; 18: 186.
36. Xue G, Li J, Feng Y, Xu W, Li S, Yan C, et al. High prevalence of plasmid-mediated quinolone resistance determinants in Escherichia coli and Klebsiella pneumoniae isolates from pediatric patients in China. Microb Drug Resist 2017; 23: 107-114.
37. Tang M, Kong X, Hao J, Liu J. Epidemiological characteristics and formation mechanisms of multidrug-resistant hypervirulent Klebsiella pneumoniae. Front Microbiol 2020; 11: 581543.
38. Moghadam MT, Shariati A, Mirkalantari S, Karmostaji A. The complex genetic region conferring transferable antibiotic resistance in multidrug-resistant and extremely drug-resistant Klebsiella pneumoniae clinical isolates. New Microbes New Infect 2020; 36: 100693.
39. Facciolà A, Pellicanò GF, Visalli G, Paolucci IA, Venanzi Rullo E, Ceccarelli M, et al. The role of the hospital environment in the healthcare-associated infections: a general review of the literature. Eur Rev Med Pharmacol Sci 2019; 23: 1266-1278.
40. Vrancianu CO, Popa LI, Bleotu C, Chifiriuc MC. Targeting plasmids to limit acquisition and transmission of antimicrobial resistance. Front Microbiol 2020; 11: 761.
41. Bi R, Kong Z, Qian H, Jiang F, Kang H, Gu B, et al. High prevalence of blaNDM variants among carbapenem-resistant Escherichia coli in Northern Jiangsu province, China. Front Microbiol 2018; 9: 2704.
42. Toledano-Tableros JE, Gayosso-Vázquez C, Jarillo-Quijada MD, Fernández-Vázquez JL, Morfin-Otero R, Rodríguez-Noriega E, et al. Dissemination of blaNDM-1 Gene among several Klebsiella pneumoniae sequence types in Mexico associated with horizontal transfer mediated by IncF-Like plasmids. Front Microbiol 2021; 12: 611274.
43. Chang C-Y, Lin H-J, Chang L-L, Ma L, Siu LK, Tung Y-C, et al. Characterization of extended-spectrum β-lactamase-carrying plasmids in clinical isolates of Klebsiella pneumoniae from Taiwan. Microb Drug Resist 2017; 23: 98-106.
44. Al-Marzooq F, Mohd Yusof MY, Tay ST. Molecular analysis of antibiotic resistance determinants and plasmids in Malaysian isolates of multidrug resistant Klebsiella pneumoniae. PLoS One 2015; 10(7): e0133654.
45. Zaman TU, Alrodayyan M, Albladi M, Aldrees M, Siddique MI, Aljohani S, et al. Clonal diversity and genetic profiling of antibiotic resistance among multidrug/carbapenem-resistant Klebsiella pneumoniae isolates from a tertiary care hospital in Saudi Arabia. BMC Infect Dis 2018; 18: 205.
46. Mohamed ER, Ali MY, Waly NGFM, Halby HM, El-Baky RMA. The Inc FII Plasmid and its Contribution in the Transmission of blaNDM1 and blaKPC2 in Klebsiella pneumoniae in Egypt. Antibiotics (Basel) 2019; 8: 266.
47. Chen L, Chavda KD, Melano RG, Jacobs MR, Koll B, Hong T, et al. Comparative genomic analysis of KPC-encoding pKpQIL-like plasmids and their distribution in New Jersey and New York Hospitals. Antimicrob Agents Chemother 2014; 58: 2871-2877.
48. Leavitt A, Chmelnitsky I, Ofek I, Carmeli Y, Navon-Venezia S. Plasmid pKpQIL encoding KPC-3 and TEM-1 confers carbapenem resistance in an extremely drug-resistant epidemic Klebsiella pneumoniae strain. J Antimicrob Chemother 2010; 65: 243-248.
49. Reyes J, Cárdenas P, Tamayo R, Villavicencio F, Aguilar A, Melano RG, et al. Characterization of
blaKPC-2-Harboring Klebsiella pneumoniae isolates and mobile genetic elements from outbreaks in a Hospital in Ecuador. Microb Drug Resist 2021; 27: 752-759.
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IssueVol 15 No 2 (2023) QRcode
SectionOriginal Article(s)
DOI https://doi.org/10.18502/ijm.v15i2.12471
Keywords
Klebsiella pneumoniae; Plasmids; New Delhi metalo beta-lactamase; Drug resistance; Polymerase chain reaction

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How to Cite
1.
Hammad H, Mohamed I, El-Badawy O, Zakaria A, Shabaan L, Aly S. pKpQIL-like plasmid contributes to the dissemination of blaNDM-1 and plasmid mediated quinolone resistance determinants among multi drug resistant Klebsiella pneumoniae in Assiut university hospital, Egypt. Iran J Microbiol. 2023;15(2):208-218.