Comparison of genotypic and phenotypic antimicrobial profile in carbapenemases producing Klebsiella pneumoniae The adoption of rapid antimicrobial susceptibility testing to improve patient’s outcomes

Main Article Content

Arcadia Del Rio
Mariangela Puci
Narcisa Muresu
Illari Sechi
Laura Saderi
Luigi Cugia
Giovanni Sotgiu
Andrea Piana


carbapenemases-encoding gene, rapid AST, Klebsiella pneumoniae, antimicrobial susceptibility testing


Background and aim: Prompt administration of appropriate antibiotic therapy is crucial in improving outcomes, particularly in cases sustained by multi-drug resistant strains. Although phenotypic antimicrobial susceptibility testing (AST) represents the gold standard to address antibiotics treatment, the long time required to obtained affordable results could negatively affect the prognosis. In contrast, rapid genotypic AST provide essential information for treatment and surveillance program. In order to evaluate the potential adoption of rapid AST in clinical routine, we compared the genotypic and phenotypic antimicrobial profiles of different K.pneumoniae strains, characterized by different expression of carbapenemases-encoding genes. Methods: A set of 109 strains of Cr-Kp were tested for the antimicrobial drugs by the automatized Vitek II system and, in parallel, to the new combination of β-lactams/β-lactamases inhibitors (BL/BLI) by Etest. An antimicrobial resistance index (ARI) was calculated for each strain, assigning each 1 or 0 points based on observed resistance/susceptibility, and dividing the total by the number of antibiotics tested. Kruskal-Wallis test, followed by Dunn's post hoc test (Bonferroni correction), were used to compare quantitative variables among resistance gene subgroups. Results: We observed a higher ARI score in KPC/OXA-48 strains, similar profile in KPC alone and KPC/CTX-M groups and a significant lower resistance in no-carbapenemases-producing group. Same trend was observed in AST for BL/BLI. Conclusions: These preliminary results showed a close link between genotypic and phenotypic AST, supporting the adoption of rapid AST in cases of severe infections, ensuring to saving time and providing, the surveillance of MDR strains and improving stewardship programs.


Download data is not yet available.
Abstract 174 | PDF Downloads 132


1. Pandey RP, Mukherjee R, Chang CM. Antimicrobial resistance surveillance system mapping in different countries. Drug Target Insights. 2022; 16:36-48. doi:10.33393/dti.2022.2482
2. Cassini A, Högberg LD, Plachouras D, et al. Attributable deaths and disability-adjusted life-years caused by infections with antibiotic-resistant bacteria in the EU and the European Economic Area in 2015: a population-level modelling analysis. Lancet Infect Dis. 2019; 19(1):56-66. doi:10.1016/S1473-3099(18)30605-4
3. Antimicrobial Resistance Collaborators. Global burden of bacterial antimicrobial resistance in 2019: a systematic analysis [published correction appears in Lancet. 2022 Oct 1;400(10358):1102]. Lancet. 2022;399(10325):629-655. doi:10.1016/S0140-6736(21)02724-0
4. European Centre for Disease Prevention and Control. Antimicrobial resistance in the EU/EEA (EARS-Net) - Annual Epidemiological Report 2021. Stockholm: ECDC; 2022, Available at: (Last access on 1st February 2023).
5. Theuretzbacher U, Carrara E, Conti M, Tacconelli E. Role of new antibiotics for KPC-producing Klebsiella pneumoniae. J Antimicrob Chemother. 2021;76(Suppl 1):i47-i54. doi:10.1093/jac/dkaa497
6. Munoz-Price LS, Poirel L, Bonomo RA, et al. Clinical epidemiology of the global expansion of Klebsiella pneumoniae carbapenemases. Lancet Infect Dis. 2013;13(9):785-796. doi:10.1016/S1473-3099(13)70190-7
7. Bush K, Jacoby GA, Medeiros AA. A functional classification scheme for beta-lactamases and its correlation with molecular structure. Antimicrob Agents Chemother. 1995;39(6):1211-1233. doi:10.1128/AAC.39.6.1211
8. Bonnin RA, Jousset AB, Emeraud C, Oueslati S, Dortet L, Naas T. Genetic Diversity, Biochemical Properties, and Detection Methods of Minor Carbapenemases in Enterobacterales. Front Med (Lausanne). 2021;7:616490. doi:10.3389/fmed.2020.616490
9. European Centre for Disease Prevention and Control. Antimicrobial resistance in the EU/EEA (EARS-Net)-Annual Epidemiological Report 2019. Stockholm: ECDC; 2020. Available online at: (Last access on 1st February 2023).
10. Meletis G. Carbapenem resistance: overview of the problem and future perspectives. Ther Adv Infect Dis. 2016;3(1):15-21. doi:10.1177/2049936115621709
11. Bassetti M, Peghin M, Vena A, Giacobbe DR. Treatment of Infections Due to MDR Gram-Negative Bacteria. Front Med (Lausanne). 2019;6:74. doi:10.3389/fmed.2019.00074
12. Castanheira M, Doyle TB, Deshpande LM, Mendes RE, Sader HS. Activity of ceftazidime/avibactam, meropenem/vaborbactam and imipenem/relebactam against carbapenemase-negative carbapenem-resistant Enterobacterales isolates from US hospitals. Int J Antimicrob Agents. 2021;58(5):106439. doi:10.1016/j.ijantimicag.2021.106439
13. Muresu N, Del Rio A, Fox V, et al. Genomic Characterization of KPC-31 and OXA-181 Klebsiella pneumoniae Resistant to New Generation of β-Lactam/β-Lactamase Inhibitor Combinations. Antibiotics (Basel). 2022;12(1):10. doi:10.3390/antibiotics12010010
14. Bovo F, Lombardo D, Lazzarotto T, Ambretti S, Gaibani P. Epidemiology and In Vitro Activity of Ceftazidime/Avibactam, Meropenem/Vaborbactam and Imipenem/Relebactam against KPC-Producing K. pneumoniae Collected from Bacteremic Patients, 2018 to 2020. Antibiotics (Basel). 2022;11(11):1621. doi:10.3390/antibiotics11111621
15. Doern CD. The Slow March toward Rapid Phenotypic Antimicrobial Susceptibility Testing: Are We There Yet?. J Clin Microbiol. 2018;56(4):e01999-17. doi:10.1128/JCM.01999-17
16. Smith KP, Kirby JE. Rapid Susceptibility Testing Methods. Clin Lab Med. 2019;39(3):333-344. doi:10.1016/j.cll.2019.04.001
17. Bonomo RA, Burd EM, Conly J, et al. Carbapenemase-Producing Organisms: A Global Scourge. Clin Infect Dis. 2018;66(8):1290-1297. doi:10.1093/cid/cix893
18. Sotgiu G, Are BM, Pesapane L, et al. Nosocomial transmission of carbapenem-resistant Klebsiella pneumoniae in an Italian university hospital: a molecular epidemiological study. J Hosp Infect. 2018;99(4):413-418. doi:10.1016/j.jhin.2018.03.033
19. Del Rio A, Muresu N, Sotgiu G, et al. High-Risk Clone of Klebsiella pneumoniae Co-Harbouring Class A and D Carbapenemases in Italy. Int J Environ Res Public Health. 2022;19(5):2623. doi:10.3390/ijerph19052623
20. VITEK® 2 microbial ID/AST testing system. Available at:
21. Sreenivasan P, Sharma B, Kaur S, et al. In-vitro susceptibility testing methods for the combination of ceftazidime-avibactam with aztreonam in metallo beta-lactamase producing organisms: Role of combination drugs in antibiotic resistance era. J Antibiot (Tokyo). 2022;75(8):454-462. doi:10.1038/s41429-022-00537-3
22. Clinical breakpoints of EUCAST v.13.0. Available at: (Last access on 18 January 2023)
23. Allplex™ Entero-DR Assay - Arrow Diagnostics. Available online at: (Last access on 1st February 2023).
24. De Socio GV, Rubbioni P, Botta D, et al. Measurement and prediction of antimicrobial resistance in bloodstream infections by ESKAPE pathogens and Escherichia coli. J Glob Antimicrob Resist. 2019;19:154-160. doi:10.1016/j.jgar.2019.05.013
25. Bassetti M, Akova M, Tumbarello M. Treatment and mortality of Klebslella pneumoniae infections in critically ill patients: should we do and predict them better? [published correction appears in Intensive Care Med. 2018 Nov 9]. Intensive Care Med. 2018;44(11):1982-1984. doi:10.1007/s00134-018-5390-7
26. Magiorakos AP, Burns K, Rodríguez Baño J, et al. Infection prevention and control measures and tools for the prevention of entry of carbapenem-resistant Enterobacteriaceae into healthcare settings: guidance from the European Centre for Disease Prevention and Control. Antimicrob Resist Infect Control. 2017;6:113. doi:10.1186/s13756-017-0259-z
27. Magiorakos AP, Srinivasan A, Carey RB, et al. Multidrug-resistant, extensively drug-resistant and pandrug-resistant bacteria: an international expert proposal for interim standard definitions for acquired resistance. Clin Microbiol Infect. 2012;18(3):268-281. doi:10.1111/j.1469-0691.2011.03570.x
28. Mohd Asri NA, Ahmad S, Mohamud R, et al. Global Prevalence of Nosocomial Multidrug-Resistant Klebsiella pneumoniae: A Systematic Review and Meta-Analysis. Antibiotics (Basel). 2021;10(12):1508. doi:10.3390/antibiotics10121508
29. Armstrong T, Fenn SJ, Hardie KR. JMM Profile: Carbapenems: a broad-spectrum antibiotic. J Med Microbiol. 2021;70(12):001462. doi:10.1099/jmm.0.001462
30. Stewart A, Harris P, Henderson A, Paterson D. Treatment of Infections by OXA-48-Producing Enterobacteriaceae. Antimicrob Agents Chemother. 2018;62(11):e01195-18. doi:10.1128/AAC.01195-18
31. Jorgensen SCJ, Trinh TD, Zasowski EJ, et al. Real-World Experience With Ceftazidime-Avibactam for Multidrug-Resistant Gram-Negative Bacterial Infections. Open Forum Infect Dis. 2019;6(12):ofz522. doi:10.1093/ofid/ofz522
32. van Asten SAV, Boattini M, Kraakman MEM, et al. Ceftazidime-avibactam resistance and restoration of carbapenem susceptibility in KPC-producing Klebsiella pneumoniae infections: A case series. J Infect Chemother. 2021;27(5):778-780. doi:10.1016/j.jiac.2021.01.014
33. Shields RK, Nguyen MH, Press EG, Chen L, Kreiswirth BN, Clancy CJ. Emergence of Ceftazidime-Avibactam Resistance and Restoration of Carbapenem Susceptibility in Klebsiella pneumoniae Carbapenemase-Producing K pneumoniae: A Case Report and Review of Literature. Open Forum Infect Dis. 2017;4(3):ofx101. doi:10.1093/ofid/ofx101
34. Effah CY, Drokow EK, Agboyibor C, et al. Evaluation of the Therapeutic Outcomes of Antibiotic Regimen Against Carbapenemase-Producing Klebsiella pneumoniae: A Systematic Review and Meta-Analysis. Front Pharmacol. 2021;12:597907. doi:10.3389/fphar.2021.597907
35. Bassetti M, Kanj SS, Kiratisin P, et al. Early appropriate diagnostics and treatment of MDR Gram-negative infections. JAC Antimicrob Resist. 2022;4(5):dlac089. doi:10.1093/jacamr/dlac089