Plazomicin was tested against 697 recently acquired carbapenem-resistant Klebsiella pneumoniae isolates from the Great Lakes region of the United States. Plazomicin MIC50 and MIC90 values were 0.25 and 1 mg/liter, respectively; 680 isolates (97.6%) were susceptible (MICs of ≤2 mg/liter), 9 (1.3%) intermediate (MICs of 4 mg/liter), and 8 (1.1%) resistant (MICs of >32 mg/liter). Resistance was associated with rmtF-, rmtB-, or armA-encoded 16S rRNA methyltransferases in all except 1 isolate.
KEYWORDS: Klebsiella, antibiotic resistance, carbapenemase, plazomicin
ABSTRACT
Plazomicin was tested against 697 recently acquired carbapenem-resistant Klebsiella pneumoniae isolates from the Great Lakes region of the United States. Plazomicin MIC50 and MIC90 values were 0.25 and 1 mg/liter, respectively; 680 isolates (97.6%) were susceptible (MICs of ≤2 mg/liter), 9 (1.3%) intermediate (MICs of 4 mg/liter), and 8 (1.1%) resistant (MICs of >32 mg/liter). Resistance was associated with rmtF-, rmtB-, or armA-encoded 16S rRNA methyltransferases in all except 1 isolate.
INTRODUCTION
Antimicrobial resistance is recognized as a major challenge by the World Health Organization and the U.S. Centers for Disease Control and Prevention, with carbapenem resistance in multidrug-resistant Gram-negative pathogens being of particular concern (1, 2). The most recent U.S. report notes that the burden of resistance is greater than initially estimated, documenting that there are now more than 2.8 million antibiotic-resistant infections in the United States each year, with over 35,000 fatalities (3).
A new aminoglycoside, plazomicin, was recently approved by the Food and Drug Administration (FDA) for the management of complicated urinary tract infections and pyelonephritis (4). Plazomicin is active against most aminoglycoside-resistant Enterobacteriaceae strains but is not uniformly active against Pseudomonas aeruginosa or Acinetobacter baumannii (5). The Consortium on Resistance Against Carbapenems in Klebsiella and Other Enterobacteriaceae (CRACKLE), part of the Antibacterial Resistance Leadership Group (ARLG), is a federally funded, prospective multicenter consortium that tracks carbapenem-resistant Enterobacteriaceae (CRE) strains. This analysis is the second in a series of ARLG Reference Group for the Testing of Novel Therapeutics (ARGONAUT) studies, in which the in vitro activities of plazomicin and comparators were evaluated against a CRACKLE collection of carbapenemase-producing Klebsiella pneumoniae clinical isolates collected from the Great Lakes region between 2012 and 2016 (6).
Plazomicin MICs against a collection of 697 carbapenem-resistant K. pneumoniae isolates with defined carbapenem resistance mechanisms (6) were determined by broth microdilution assays, according to current Clinical and Laboratory Standards Institute (CLSI) guidelines (7). Testing was performed using custom frozen panels (Thermo Fisher) containing plazomicin and comparator agents. MICs were interpreted according to FDA and CLSI breakpoints, with plazomicin MICs being interpreted as follows: susceptible, ≤2 mg/liter; intermediate, 4 mg/liter; resistant, ≥8 mg/liter. Resistance mechanisms of plazomicin-intermediate and resistant isolates were characterized by whole-genome sequencing (WGS; BioProject accession numbers PRJNA433394 and PRJNA339843) (6). Briefly, WGS was performed using paired-end Nextera XT libraries on an Illumina NextSeq (2 × 150 bp) to 100-fold coverage. Reads were assembled using SPAdes, annotated with the NCBI Prokaryotic Genome Annotation Pipeline, and used to determine resistome, plasmid types, and multilocus sequence type through ResFinder 3.2, PlasmidFinder 2.1, and MLST 2.0, respectively, from the Center for Genomic Epidemiology (http://www.genomicepidemiology.org/index.html).
Carbapenemase genes present in the 697 study isolates included blaKPC-2 (n = 323), blaKPC-3 (n = 364), blaKPC-4 or blaKPC-4-like (n = 2), blaOXA-48-like (n = 7), and blaNDM-5 and blaOXA-48-like (n = 1). Antimicrobial susceptibility findings are shown in Table 1. Fewer than 1% of isolates were susceptible to ceftriaxone, ceftazidime, aztreonam, or piperacillin-tazobactam, while ≤5.4% were susceptible to imipenem, meropenem, or doripenem. Most isolates (95.9%) were also resistant to levofloxacin. Susceptibility to other agents was more varied, with 20.6% being susceptible to trimethoprim-sulfamethoxazole, 87.6% to tigecycline, 14.3% to tobramycin, 53.3% to gentamicin, and 64.1% to amikacin. Plazomicin MICs ranged from ≤0.12 to >32 mg/liter, with MIC50 and MIC90 values of 0.25 and 1 mg/liter, respectively. Overall, 680 isolates (97.6%) were susceptible (MICs of ≤2 mg/liter), while 9 (1.3%) were intermediate and 8 (1.1%) were resistant (MICs of >32 mg/liter) to plazomicin.
TABLE 1.
MIC ranges, MIC50 values, and MIC90 values, with percentages of isolates susceptible based on CLSI/FDA breakpoints
| Agent | MIC range (mg/liter) | MIC50 (mg/liter) | MIC90 (mg/liter) | % susceptible |
|---|---|---|---|---|
| Plazomicin | ≤0.12 to >32 | 0.25 | 1 | 97.6 |
| Gentamicin | ≤0.5 to >32 | 4 | >32 | 53.3 |
| Tobramycin | ≤0.25 to >32 | 32 | >32 | 14.3 |
| Amikacin | ≤1 to >64 | 16 | 32 | 64.1 |
| Ceftriaxone | ≤1 to >8 | >8 | >8 | 0.6 |
| Ceftazidime | ≤0.5 to >8 | >8 | >8 | 0.9 |
| Aztreonam | ≤1 to >16 | >16 | >16 | 0.9 |
| Imipenem | ≤0.25 to >8 | >8 | >8 | 3.3 |
| Meropenem | ≤0.12 to >8 | >8 | >8 | 4.6 |
| Doripenem | ≤0.12 to >8 | 8 | >8 | 5.4 |
| Piperacillin-tazobactam | 4/4 to >64/4 | >64/4 | >64/4 | 0.4 |
| Levofloxacin | ≤0.25 to >4 | >4 | >4 | 4.1 |
| Trimethoprim-sulfamethoxazole | ≤1/19 to >4/76 | >4/76 | >4/76 | 20.6 |
| Colistin | 0.5 to >8 | 0.5 | >8 | 85.3a |
| Tigecycline | 0.5 to >4 | 1 | 4 | 87.6 |
Percentage based on EUCAST breakpoint.
The 8 plazomicin-resistant isolates were also resistant to gentamicin, tobramycin, and amikacin; they were collected from hospitals in Ohio between 2014 and 2016. They were obtained from abscess (n = 3), urinary (n = 2), respiratory (n = 2), and wound (n = 1) cultures from 6 unique patients. These patients (4 male patients and 2 female patients) had a median age of 55 years (range, 25 to 69 years). Four patients were admitted from long-term-care facilities. One patient was admitted from home, and 1 was transferred from a hospital abroad. Five patients were admitted to the intensive care unit (ICU), with a median ICU stay of 6 days (range, 2 to 22 days). Five patients required mechanical ventilation and 3 patients underwent tracheostomy prior to the first positive CRE culture. Patients were treated with various antibiotics, sometimes in combination; 4 patients received tigecycline, 3 meropenem, 2 inhaled colistin, and 1 each ceftazidime-avibactam, gentamicin, amikacin, and trimethoprim-sulfamethoxazole. All patients survived their hospitalizations, with 4 being discharged to long-term-care facilities and 2 discharged home.
WGS of the 8 plazomicin-resistant isolates showed that the strains each carried several plasmids, had multiple antibiotic resistance determinants, and belonged to four multilocus sequence types (STs) (Table 2). The STs included ST16 (n = 1, associated with blaOXA-1), ST147 (n = 2, associated with blaOXA-181), ST395 (n = 2, associated with blaOXA-48), and ST231 (n = 3, associated with blaOXA-232). The isolates belonging to ST147, ST395, and ST231 harbored the same or very similar plasmids and resistance mechanisms associated with each ST (Table 2). Plazomicin resistance was associated with 16S rRNA methyltransferases (a known mechanism of resistance) in 7 of the 8 isolates (8). The 16S rRNA methyltransferase genes included rmtF in the ST16, ST147, and ST231 isolates (1 ST147 isolate also carried rmtB) and armA in 1 of the ST395 isolates. Known plazomicin resistance mechanisms could not be identified in the other ST395 isolate (ARLG-2882). Other studies have reported ST147 and ST231 as K. pneumoniae STs that carry rmt genes (9–12). Interestingly, 16S rRNA methyltransferase genes were not found by WGS in 8 of the 9 plazomicin-intermediate isolates (1 isolate was not sequenced).
TABLE 2.
Genes coding for resistance to antimicrobial agents, as detected by WGS of plazomicin-resistant isolates
| ST, plasmids, and resistance genes detected | ARLG-2713 | ARLG-2756a | ARLG-2757a | ARLG-2881b | ARLG-2882b | ARLG-3126 | ARLG-3135 | ARLG-3143 |
|---|---|---|---|---|---|---|---|---|
| ST | ST16 | ST147 | ST147 | ST395 | ST395 | ST231 | ST231 | ST231 |
| Plasmids | IncFIB(pQil), IncFII(K), IncFIB(K) | IncFII(Pkpx1), IncFII, ColpVC | IncFII(Pkpx1), IncFII, ColpVC | IncL/M(pOXA-48), IncFIB(Mar), IncR, IncHI1B | IncL/M(pOXA-48), IncFIB(Mar), IncR | IncFIB(pQil), IncFIA, Col4401, ColKP3, IncFII(K), IncFII(pAMA1167-NDM-5), Col(BS512) | IncFIB(pQil), IncFIA, Col4401, ColKP3, IncFII(K), IncFII(pAMA1167-NDM-5) | IncFIB(pQil), IncFIA, Col4401, ColKP3, IncFII(K), IncFII(pAMA1167-NDM-5), Col(BS512) |
| 16S rRNA methyltransferase genes | rmtF | rmtB, rmtF | rmtF | armA | None | rmtF | rmtF | rmtF |
| β-Lactamase genes | blaOXA-1, blaSHV-1, blaCTX-M-15c | blaOXA-181, blaSHV-11, blaTEM-1, blaCTX-M-15, blaNDM-5 | blaOXA-181, blaSHV-11, blaCTX-M-15 | blaOXA-48, blaSHV-11, blaTEM-1 | blaOXA-48, blaSHV-11, blaTEM-1 | blaOXA-232, blaSHV-1, blaTEM-1, blaCTX-M-15c | blaOXA-232, blaSHV-1, blaTEM-1, blaCTX-M-15 | blaOXA-232, blaSHV-1, blaTEM-1, blaCTX-M-15c |
| Genes for resistance to | ||||||||
| Aminoglycosides | aadA2 | aadA2, aac(6′)-Ib | aac(6′)-Ib | None | None | aac(6′)-Ib | aadA2, aac(6′)-Ib | aadA2, aac(6′)-Ib |
| Fluoroquinolones | gyrA D87N, parC E84K, parE S458T | parC S80I, qnrB1c | parC S80I, qnrB1c | parC S80I, qnrS1 | parC S80I, qnrS1 | parC S80I, qnrS1 | parC S80I, qnrS1 | parC S80I, qnrS1 |
| Macrolides, lincosamides, streptogramin B | mph(A), mrx | mph(A), mrx, erm(B) | None | msr(E), mph(E) | None | None | mph(A), erm(B) | mph(A), mrx, erm(B) |
| Chloramphenicol | catB4c | None | None | catA1 | catA1 | catA1 | catA1 | catA1 |
| Rifampin | arr-2 | arr-2 | arr-2 | None | None | arr-2 | arr-2 | arr-2 |
| Sulfonamides | sul1 | sul1 | None | sul1 | None | None | sul1 | sul1 |
| Tetracyclines | tet(A) | None | None | tet(A) | None | None | None | None |
| Trimethoprim | dfrA12 | dfrA12, dfrA14 | dfrA14 | dfrA1 | None | None | dfrA12 | dfrA12 |
ARLG-2756 and ARLG-2757 are isolates from the same patient (11).
ARLG-2881 and ARLG-2882 are isolates from the same patient.
Incomplete gene present.
Plazomicin resistance is frequently associated with strains harboring New Delhi metallo-β-lactamases (NDMs) in other countries (12–15). However, NDM is not commonly encountered in the United States (13), and only 1 of the 8 plazomicin-resistant strains in our study possessed NDM-mediated carbapenem resistance (Table 2).
Plazomicin is a recently approved next-generation aminoglycoside agent with activity against carbapenemase-producing Enterobacteriaceae strains, with potency comparable to that of ceftazidime-avibactam, meropenem-vaborbactam, and imipenem-relebactam (16). Our results compare favorably with a recently published study in which 94.9% of 117 blaKPC-positive isolates were susceptible to plazomicin, compared to 43.6%, 56.4%, and 5.1% susceptible to amikacin, gentamicin, and tobramycin, respectively (17). Although plazomicin resistance is infrequent in the United States, of concern is the occurrence of armA and rmtF 16S rRNA methyltransferase genes in 7 of our plazomicin-resistant isolates, a finding noted in other recent studies (8, 13–15, 18). Our study documents the in vitro activity of plazomicin against a large U.S. collection of carbapenemase-producing K. pneumoniae isolates, with 97.6% of isolates being susceptible to this agent.
ACKNOWLEDGMENTS
Research reported in this publication was supported by the National Institute of Allergy and Infectious Diseases of the National Institutes of Health (NIH) under grant UM1AI104681. Additional NIH support included grants R01AI100560, R01AI063517, and R01AI072219 to R.A.B. and grant R01AI090155 to B.N.K.; WGS of the isolates was funded in whole or in part with federal funds from the National Institute of Allergy and Infectious Diseases under grant U19AI110819. This study was also supported in part by funds and/or facilities provided by the Cleveland Department of Veterans Affairs, grant 1I01BX001974 to R.A.B. from the Biomedical Laboratory Research and Development Service of the VA Office of Research and Development, and the Geriatric Research Education and Clinical Center, VISN 10. Research support was also received from Achaogen. The content is solely the responsibility of the authors and does not necessarily represent the official views of the NIH or the Department of Veterans Affairs.
REFERENCES
- 1.World Health Organization. 2018. Global antimicrobial resistance surveillance system (GLASS) report: early implementation 2017–2018. World Health Organization, Geneva, Switzerland: https://www.who.int/docs/default-source/searo/amr/global-antimicrobial-resistance-surveillance-system---glass-report-early-implementation-2017-2018.pdf?sfvrsn=7e629fec_6. [Google Scholar]
- 2.Centers for Disease Control and Prevention. 2013. Antibiotic resistance threats in the United States, 2013. Centers for Disease Control and Prevention, Atlanta, GA: https://www.cdc.gov/drugresistance/pdf/ar-threats-2013-508.pdf. [Google Scholar]
- 3.Centers for Disease Control and Prevention. 2019. Antibiotic resistance threats in the United States, 2019. Centers for Disease Control and Prevention, Atlanta, GA: https://www.cdc.gov/drugresistance/pdf/threats-report/2019-ar-threats-report-508.pdf. [Google Scholar]
- 4.Saravolatz LD, Stein GE. 2020. Plazomicin: a new aminoglycoside. Clin Infect Dis 70:704–709. doi: 10.1093/cid/ciz640. [DOI] [PubMed] [Google Scholar]
- 5.Shaeer KM, Zmarlicka MT, Chahine EB, Piccicacco N, Cho JC. 2019. Plazomicin: a next-generation aminoglycoside. Pharmacotherapy 39:77–93. doi: 10.1002/phar.2203. [DOI] [PubMed] [Google Scholar]
- 6.Jacobs MR, Abdelhamed AM, Good CE, Rhoads DD, Hujer KM, Hujer AM, Domitrovic TN, Rudin SD, Richter SS, van Duin D, Kreiswirth BN, Greco C, Fouts DE, Bonomo RA. 2019. ARGONAUT-I: activity of cefiderocol (S-649266), a siderophore cephalosporin, against Gram-negative bacteria, including carbapenem-resistant nonfermenters and Enterobacteriaceae with defined extended-spectrum β-lactamases and carbapenemases. Antimicrob Agents Chemother 63:e01801-18. doi: 10.1128/AAC.01801-18. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 7.Clinical and Laboratory Standards Institute. 2018. Methods for dilution antimicrobial susceptibility tests for bacteria that grow aerobically, 11th ed M07 Clinical and Laboratory Standards Institute, Wayne, PA. [Google Scholar]
- 8.Doi Y, Wachino J-I, Arakawa Y. 2016. Aminoglycoside resistance: the emergence of acquired 16S ribosomal RNA methyltransferases. Infect Dis Clin North Am 30:523–537. doi: 10.1016/j.idc.2016.02.011. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 9.Gamal D, Fernández-Martínez M, Salem D, El-Defrawy I, Montes LÁ, Ocampo-Sosa AA, Martínez-Martínez L. 2016. Carbapenem-resistant Klebsiella pneumoniae isolates from Egypt containing blaNDM-1 on IncR plasmids and its association with rmtF. Int J Infect Dis 43:17–20. doi: 10.1016/j.ijid.2015.12.003. [DOI] [PubMed] [Google Scholar]
- 10.Mancini S, Poirel L, Tritten ML, Lienhard R, Bassi C, Nordmann P. 2018. Emergence of an MDR Klebsiella pneumoniae ST231 producing OXA-232 and RmtF in Switzerland. J Antimicrob Chemother 73:821–823. doi: 10.1093/jac/dkx428. [DOI] [PubMed] [Google Scholar]
- 11.Rojas LJ, Hujer AM, Rudin SD, Wright MS, Domitrovic TN, Marshall SH, Hujer KM, Richter SS, Cober E, Perez F, Adams MD, van Duin D, Bonomo RA. 2017. NDM-5 and OXA-181 beta-lactamases, a significant threat continues to spread in the Americas. Antimicrob Agents Chemother 61:e00454-17. doi: 10.1128/AAC.00454-17. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 12.Taylor E, Sriskandan S, Woodford N, Hopkins KL. 2018. High prevalence of 16S rRNA methyltransferases among carbapenemase-producing Enterobacteriaceae in the UK and Ireland. Int J Antimicrob Agents 52:278–282. doi: 10.1016/j.ijantimicag.2018.03.016. [DOI] [PubMed] [Google Scholar]
- 13.Castanheira M, Davis AP, Serio AW, Krause KM, Mendes RE. 2019. In vitro activity of plazomicin against Enterobacteriaceae isolates carrying genes encoding aminoglycoside-modifying enzymes most common in US Census divisions. Diagn Microbiol Infect Dis 94:73–77. doi: 10.1016/j.diagmicrobio.2018.10.023. [DOI] [PubMed] [Google Scholar]
- 14.Galani I, Nafplioti K, Adamou P, Karaiskos I, Giamarellou H, Souli M. 2019. Nationwide epidemiology of carbapenem resistant Klebsiella pneumoniae isolates from Greek hospitals, with regard to plazomicin and aminoglycoside resistance. BMC Infect Dis 19:167. doi: 10.1186/s12879-019-3801-1. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 15.Serio AW, Keepers T, Krause KM. 2019. Plazomicin is active against metallo-β-lactamase-producing Enterobacteriaceae. Open Forum Infect Dis 6:ofz123. doi: 10.1093/ofid/ofz123. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 16.Rodriguez-Bano J, Gutierrez-Gutierrez B, Machuca I, Pascual A. 2018. Treatment of infections caused by extended-spectrum-beta-lactamase-, AmpC-, and carbapenemase-producing Enterobacteriaceae. Clin Microbiol Rev 31:e00079-17. doi: 10.1128/CMR.00079-17. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 17.Fleischmann WA, Greenwood-Quaintance KE, Patel R. 2020. In vitro activity of plazomicin compared to amikacin, gentamicin, and tobramycin against multidrug resistant aerobic Gram-negative bacilli. Antimicrob Agents Chemother 64:e01711-19. doi: 10.1128/AAC.01711-19. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 18.Castanheira M, Deshpande LM, Woosley LN, Serio AW, Krause KM, Flamm RK. 2018. Activity of plazomicin compared with other aminoglycosides against isolates from European and adjacent countries, including Enterobacteriaceae molecularly characterized for aminoglycoside-modifying enzymes and other resistance mechanisms. J Antimicrob Chemother 73:3346–3354. doi: 10.1093/jac/dky344. [DOI] [PubMed] [Google Scholar]