Short Communication

Emergence of hypermucoviscous colistin-resistant high-risk convergent Klebsiella pneumoniae ST-2096 clone from Pakistan

Department of Microbiology, Faculty of Biological Sciences, Quaid-i-Azam University Islamabad, 45320, Pakistan

Search for more papers by this author

Mehreen Shoukat

Department of Microbiology, Faculty of Biological Sciences, Quaid-i-Azam University Islamabad, 45320, Pakistan

Search for more papers by this author

Muhammad Imran

Department of Microbiology, Faculty of Biological Sciences, Quaid-i-Azam University Islamabad, 45320, Pakistan

Search for more papers by this author

Muhammad Ansar

Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University Islamabad, 45320, Pakistan

Search for more papers by this author

Rani Faryal

*Author for correspondence: Tel.: +92 519 064 3008;

E-mail Address: ranifaryal@qau.edu.pk

https://orcid.org/0000-0003-3018-0404

Department of Microbiology, Faculty of Biological Sciences, Quaid-i-Azam University Islamabad, 45320, Pakistan

Search for more papers by this author

Published Online:21 Jul 2022https://doi.org/10.2217/fmb-2021-0292

View article

Abstract

Klebsiella pneumoniae convergent clones are considered a threat to healthcare settings. Here we report a comprehensive genomic profiling of an emerging colistin-resistant K. pneumoniae ST-2096 convergent clone from Pakistan. Methods: Whole-genome sequencing was performed and raw reads were assembled antimicrobial resistance and virulence genes were predicted using various online tools. Results & conclusion: The phenotypically multidrug-resistant (MDR) and hypermucoviscous (hv) colistin-resistant K. pneumoniae (hvCRKP-10718), which, intriguingly, possessed a wide range of antimicrobial resistance (bla_TEM-1A, bla_OXA-1, bla_OXA-232, bla_CTX-M-15, bla_SHV-106, oqxA, oqxB, aac(6′)-Ib-cr, aadA2, aac(6′)-Ib-cr, armA, tetD, mphE, msrE, fosA, dfrA1, dfrA12, dfrA14, catB3, sul1) and virulence determinants (RmpA/RmpA2, yersiniabactin [ybt], aerobactin [iuc/iut], enterobactin). Furthermore, the acquisition of various mobile genetic elements (MDR/virulent plasmids, type II integron gene cassette, insertional sequences, transposases) and associated hv capsular type made this MDR/hv isolate a convergent clone belonging to a high-risk lineage (ST-2096). Based on core-genome multilocus sequence typing and single-nucleotide polymorphism analysis, this isolate showed ≥99% nucleotide identity with MDR K. pneumoniae isolates from India, depicting its evolutionary background. This study provides a comprehensive genomic profiling of this high-risk convergent K. pneumoniae ST-2096 clone from Pakistan. Comparative genomics of MDR/hv colistin-resistant K. pneumoniae isolates with other MDR convergent strains from the Indian subcontinent indicated the emergence of this evolving superbug.

Keywords:

References

1. Podschun R, Ullmann U. Klebsiella spp. as nosocomial pathogens: epidemiology, taxonomy, typing methods, and pathogenicity factors. Clin. Microbiol. Rev. 11(4), 589–603 (1998).
Medline CASGoogle Scholar
2. WHO. Global action plan on antimicrobial resistance. Microbe Mag. 10(9), 354–355 (2015).
Google Scholar
3. Wyres KL, Lam MMC, Holt KE. Population genomics of Klebsiella pneumoniae. Nat. Rev. Microbiol. 18(6), 344–359 (2020).
Medline CASGoogle Scholar
4. Araújo BF, Ferreira ML, de Campos PA et al. Hypervirulence and biofilm production in KPC-2-producing Klebsiella pneumoniae CG258 isolated in Brazil. J. Med. Microbiol. 67(4), 523–528 (2018).
Medline CASGoogle Scholar
5. Cerdeira L, Nakamura-Silva R, Oliveira-Silva M et al. Draft genome sequences of PDR and XDR Klebsiella pneumoniae belonging to high-risk CG258 isolated from a Brazilian tertiary hospital. Infect. Genet. Evol. 87, 104643 (2021).
Medline CASGoogle Scholar
6. Lam MMC, Wick RR, Watts SC, Cerdeira LT, Wyres KL, Holt KE. A genomic surveillance framework and genotyping tool for Klebsiella pneumoniae and its related species complex. Nat. Commun. 12(1), 4188 (2021).
Medline CASGoogle Scholar
7. Russo TA, Olson R, Fang CT et al. Identification of biomarkers for differentiation of hypervirulent Klebsiella pneumoniae from classical K. pneumoniae. J. Clin. Microbiol. 56(9), 776–794 (2018).
Medline CASGoogle Scholar
8. Lan P, Jiang Y, Zhou J, Yu Y. A global perspective on the convergence of hypervirulence and carbapenem resistance in Klebsiella pneumoniae. J. Glob. Antimicrob. Resist. 25, 26–34 (2021).
Medline CASGoogle Scholar
9. Cejas D, Canigia LF, Cruz GR et al. First isolate of KPC-2-producing Klebsiella pneumoniae sequence type 23 from the Americas. J. Clin. Microbiol. 52(9), 3483–3485 (2014).
MedlineGoogle Scholar
10. Turton J, Davies F, Turton J, Perry C, Payne Z, Pike R. Hybrid resistance and virulence plasmids in ‘high-risk’ clones of Klebsiella pneumoniae, including those carrying bla_NDM-5. Microorganisms 7(9), 326 (2019).
CASGoogle Scholar
11. Scaltriti E, Piccinelli G, Corbellini S, Caruso A, Latronico N, De Francesco MA. Detection of a hypermucoviscous Klebsiella pneumoniae co-producing NDM-5 and OXA-48 carbapenemases with sequence type 383, Brescia, Italy. Int. J. Antimicrob. Agents 56(4), 106130 (2020).
Medline CASGoogle Scholar
12. Mataseje LF, Boyd DA, Mulvey MR, Longtin Y. Two hypervirulent Klebsiella pneumoniae isolates producing a bla_KPC-2 carbapenemase from a canadian patient. Antimicrob. Agents Chemother. 63(7), PMC6591601 (2019).
Google Scholar
13. Lev AI, Astashkin EI, Kislichkina AA et al. Comparative analysis of Klebsiella pneumoniae strains isolated in 2012–2016 that differ by antibiotic resistance genes and virulence genes profiles. Pathog. Glob. Health. 112(3), 142–151 (2018).
Medline CASGoogle Scholar
14. Becker L, Kaase M, Pfeifer Y et al. Genome-based analysis of carbapenemase-producing Klebsiella pneumoniae isolates from German hospital patients, 2008-2014. Antimicrob. Resist. Infect. Control. 7(1), doi:10.1186/s13756-018-0352-y (2018).
MedlineGoogle Scholar
15. Harada S, Aoki K, Ishii Y et al. Emergence of IMP-producing hypervirulent Klebsiella pneumoniae carrying a pLVPK-like virulence plasmid. Int. J. Antimicrob. Agents 53(6), 873–875 (2019).
Medline CASGoogle Scholar
16. Octavia S, Kalisvar M, Venkatachalam I et al. Klebsiella pneumoniae and Klebsiella quasipneumoniae define the population structure of bla_KPC-2 Klebsiella: a 5 year retrospective genomic study in Singapore. J. Antimicrob. Chemother. 74(11), 3205–3210 (2019).
Medline CASGoogle Scholar
17. Mohammad Ali Tabrizi A, Badmasti F, Shahcheraghi F, Azizi O. Outbreak of hypervirulent Klebsiella pneumoniae harbouring bla_VIM-2 among mechanically-ventilated drug-poisoning patients with high mortality rate in Iran. J. Glob. Antimicrob. Resist. 15, 93–98 (2018).
MedlineGoogle Scholar
18. Mukherjee S, Naha S, Bhadury P et al. Emergence of OXA-232-producing hypervirulent Klebsiella pneumoniae ST23 causing neonatal sepsis. J. Antimicrob. Chemother. 75(7), 2004–2006 (2020).
Medline CASGoogle Scholar
19. Imtiaz W, Dasti JI, Andrews SC. Draft genome sequence of a carbapenemase-producing (NDM-1) and multidrug-resistant, hypervirulent Klebsiella pneumoniae ST11 isolate from Pakistan, with a non-hypermucoviscous phenotype associated with rmpA2 mutation. J. Glob. Antimicrob. Resist. 25, 359–362 (2021).
Medline CASGoogle Scholar
20. Shankar C, Vasudevan K, Jacob JJ et al. Mosaic antimicrobial resistance/virulence plasmid in hypervirulent ST2096 Klebsiella pneumoniae in India: the rise of a new superbug? doi: https://doi.org/10.1101/2020.12.11.422261 (2020) (Epub ahead of print).
Google Scholar
21. Shankar C, Jacob JJ, Vasudevan K et al. Emergence of multidrug resistant hypervirulent ST23 Klebsiella pneumoniae: multidrug resistant plasmid acquisition drives evolution. Front. Cell. Infect. Microbiol. 10(1), 35–44 (2020).
MedlineGoogle Scholar
22. Wyres KL, Nguyen TNT, Lam MMC et al. Genomic surveillance for hypervirulence and multi-drug resistance in invasive Klebsiella pneumoniae from South and Southeast Asia. Genome Med. 12(1), https://doi.org/10.1186/s13073-019-0706-y (2020).
MedlineGoogle Scholar
23. Hala S, Antony CP, Alshehri M et al. An emerging clone (ST2096) of Klebsiella pneumoniae clonal complex 14 with enhanced virulence causes an outbreak in Saudi Arabia. J. Infect. Public Health 13(2), 363–364 (2020).
Google Scholar
24. Rahmat Ullah S, Majid M, Andleeb S. Draft genome sequence of an extensively drug-resistant neonatal Klebsiella pneumoniae isolate harbouring multiple plasmids contributing to antibiotic resistance. J. Glob. Antimicrob. Resist. 23, 100–101 (2020).
MedlineGoogle Scholar
25. Shon AS, Bajwa RPS, Russo TA. Hypervirulent (hypermucoviscous) Klebsiella pneumoniae: a new and dangerous breed. Virulence 4(2), 107–118 (2013).
MedlineGoogle Scholar
26. Institute CALS. CLSI 2019.pdf (2019). https://clsi.org/
Google Scholar
27. Feng Y, Zou S, Chen H, Yu Y, Ruan Z. BacWGSTdb 2.0: a one-stop repository for bacterial whole-genome sequence typing and source tracking. Nucleic Acids Res. 49(D1), D644–D650 (2021).
Medline CASGoogle Scholar
28. Cury J, Jové T, Touchon M, Néron B, Rocha EP. Identification and analysis of integrons and cassette arrays in bacterial genomes. Nucleic Acids Res. 44(10), 4539–4550 (2016).
Medline CASGoogle Scholar
29. Tang M, Kong X, Hao J, Liu J. Epidemiological characteristics and formation mechanisms of multidrug-resistant hypervirulent Klebsiella pneumoniae. Front. Microbiol. 11, 581543 (2020).
MedlineGoogle Scholar
30. Lan P, Jiang Y, Zhou J, Yu Y. A global perspective on the convergence of hypervirulence and carbapenem resistance in Klebsiella pneumoniae. J. Glob. Antimicrob. Resist. 25, 26–34 (2021).
Medline CASGoogle Scholar
31. Sabbagh P, Rajabnia M, Maali A, Ferdosi-Shahandashti E. Integron and its role in antimicrobial resistance: a literature review on some bacterial pathogens. Iran. J. Basic Med. Sci. 24(2), 136–142 (2021).
MedlineGoogle Scholar
32. Yang X, Dong N, Chan EWC, Zhang R, Chen S. Carbapenem resistance-encoding and virulence-encoding conjugative plasmids in Klebsiella pneumoniae. Trends Microbiol. 29(1), 65–83 (2021).
Medline CASGoogle Scholar
33. Wyres KL, Nguyen TNT, Lam MMC et al. Genomic surveillance for hypervirulence and multi-drug resistance in invasive Klebsiella pneumoniae from South and Southeast Asia. Genome Med. 12(1), 1–16 (2020).
Google Scholar
34. Lam MMC, Wick RR, Wyres KL et al. Genetic diversity, mobilisation and spread of the yersiniabactin-encoding mobile element ICEKp in Klebsiella pneumoniae populations. Microb. Genomics. 4(9), e000196 (2018).
Google Scholar
35. Liu C, Guo J. Characteristics of ventilator-associated pneumonia due to hypervirulent Klebsiella pneumoniae genotype in genetic background for the elderly in two tertiary hospitals in China. Antimicrob. Resist. Infect. Control. 7(1), doi:10.1186/s13756-018-0371-8 (2018).
Google Scholar
36. Li J, Ren J, Wang W et al. Risk factors and clinical outcomes of hypervirulent Klebsiella pneumoniae induced bloodstream infections. Eur. J. Clin. Microbiol. Infect. Dis. 37(4), 679–689 (2018).
MedlineGoogle Scholar
37. de Campos TA, Gonçalves LF, Magalhães KG et al. A fatal bacteremia caused by hypermucousviscous KPC-2 producing extensively drug-resistant K64-ST11 Klebsiella pneumoniae in Brazil. Front. Med. 5, 265 (2018).
Google Scholar
38. Osei Sekyere J, Govinden U, Bester LA, Essack SY. Colistin and tigecycline resistance in carbapenemase-producing Gram-negative bacteria: emerging resistance mechanisms and detection methods. J. Appl. Microbiol. 121(3), 601–617 (2016).
MedlineGoogle Scholar
39. Hussein NH, Al-Kadmy IMS, Taha BM, Hussein JD. Mobilized colistin resistance (mcr) genes from 1 to 10: a comprehensive review. Mol. Biol. Rep. 48(3), 2897–2907 (2021).
Medline CASGoogle Scholar
40. Binsker U, Käsbohrer A, Hammerl JA. Global colistin use: a review of the emergence of resistant Enterobacterales and the impact on their genetic basis. FEMS Microbiol. Rev. 46(1), 1–37 (2022).
Google Scholar
41. Mathur P, Veeraraghavan B, Devanga Ragupathi NK et al. Multiple mutations in lipid-A modification pathway & novel fosA variants in colistin-resistant Klebsiella pneumoniae. Futur. Sci. OA 4(7), FSO319 (2018).
Medline CASGoogle Scholar
42. Pragasam AK, Shankar C, Veeraraghavan B et al. Molecular mechanisms of colistin resistance in Klebsiella pneumoniae causing bacteremia from India – a first report. Front. Microbiol. 7), 2135 (2017).
MedlineGoogle Scholar
43. Boszczowski I, Salomão MC, Moura ML et al. Multidrug-resistant Klebsiella pneumoniae: genetic diversity, mechanisms of resistance to polymyxins and clinical outcomes in a tertiary teaching hospital in Brazil. Rev. Inst. Med. Trop. Sao Paulo 61, 1–9 (2019).
Google Scholar
44. Silvester R, Madhavan A, Kokkat A et al. Global surveillance of antimicrobial resistance and hypervirulence in Klebsiella pneumoniae from LMICs: an in-silico approach. Sci. Total Environ. 802, 149859 (2022).
Medline CASGoogle Scholar
45. 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. Infect. Drug Resist. 14, 227–236 (2021).
MedlineGoogle Scholar

Vol. 17, No. 13

Supplemental Materials

Metrics

Downloaded 120 times

History

Received 3 December 2021

Accepted 14 June 2022

Published online 21 July 2022

Published in print September 2022

Information

Keywords

Supplementary data

To view the supplementary data that accompany this paper please visit the journal website at: www.futuremedicine.com/doi/suppl/10.2217/fmb-2021-0292

Author contributions

R Faryal and M Urooj conceived and designed the experiments and wrote the paper; M Urooj and M Shoukat performed the isolation, identification and antimicrobial susceptibility experiments; M Urooj, M Imran and M Ansar performed the sequencing and genomic analysis. All authors reviewed, edited and approved the final version of the manuscript.

Acknowledgments

The authors would like to acknowledge Z Rafaque for her continuous support in sequencing data analysis.

Financial & competing interests disclosure

This work was supported by Higher Education Commission (HEC) Pakistan under HEC indigenous PhD scholarships (HEC-PIN no. 158-81359-2BS5-012) which helped us to execute this study. HEC played no direct role in sample collection, data analysis, paper writeup or publication of this work. The authors have no other relevant affiliations or financial involvement with any organization or entity with a financial interest in or financial conflict with the subject matter or materials discussed in the manuscript apart from those disclosed.

No writing assistance was utilized in the production of this manuscript.

Ethical conduct of research

The author state that they have obtained ethical approval from the Ethics Review Board of the Shaheed Zulfikar Ali Bhutto Medical University, PIMS (approval no: F.1-1/2015/ERB/SZABMU/). In addition, for investigations involving human subjects, informed consent has been obtained from the participants involved.

Sequencing data accession number

This whole-genome shotgun project has been deposited at DDBJ/ENA/GenBank under the accession JAFIDU000000000. The version described in this paper is version JAFIDU01000000. The Bio Project PRJNA704247 can be accessed from https://ncbi.nlm.nih.gov/

PDF download