Unraveling novel mutation patterns and morphological variations in two dalbavancin-resistant MRSA strains in Austria using whole genome sequencing and transmission electron microscopy.
Humans
Methicillin-Resistant Staphylococcus aureus
/ genetics
Austria
/ epidemiology
Whole Genome Sequencing
Anti-Bacterial Agents
/ pharmacology
Teicoplanin
/ pharmacology
Microbial Sensitivity Tests
Staphylococcal Infections
/ microbiology
Microscopy, Electron, Transmission
Daptomycin
/ pharmacology
Mutation
Linezolid
/ pharmacology
Male
Mutation, Missense
Female
Antimicrobial resistance
Dalbavancin
Daptomycin
Linezolid
MRSA
Whole genome sequencing
Journal
BMC infectious diseases
ISSN: 1471-2334
Titre abrégé: BMC Infect Dis
Pays: England
ID NLM: 100968551
Informations de publication
Date de publication:
02 Sep 2024
02 Sep 2024
Historique:
received:
29
03
2024
accepted:
22
08
2024
medline:
3
9
2024
pubmed:
3
9
2024
entrez:
2
9
2024
Statut:
epublish
Résumé
The increasing prevalence of methicillin-resistant Staphylococcus aureus (MRSA) strains resistant to non-beta-lactam antimicrobials poses a significant challenge in treating severe MRSA bloodstream infections. This study explores resistance development and mechanisms in MRSA isolates, especially after the first dalbavancin-resistant MRSA strain in our hospital in 2016. This study investigated 55 MRSA bloodstream isolates (02/2015-02/2021) from the University Hospital of the Medical University of Vienna, Austria. The MICs of dalbavancin, linezolid, and daptomycin were assessed. Two isolates (16-33 and 19-362) resistant to dalbavancin were analyzed via whole-genome sequencing, with morphology evaluated using transmission electron microscopy (TEM). S.aureus BSI strain 19-362 had two novel missense mutations (p.I515M and p.A606D) in the pbp2 gene. Isolate 16-33 had a 534 bp deletion in the DHH domain of GdpP and a SNV in pbp2 (p.G146R). Both strains had mutations in the rpoB gene, but at different positions. TEM revealed significantly thicker cell walls in 16-33 (p < 0.05) compared to 19-362 and dalbavancin-susceptible strains. None of the MRSA isolates showed resistance to linezolid or daptomycin. In light of increasing vancomycin resistance reports, continuous surveillance is essential to comprehend the molecular mechanisms of resistance in alternative MRSA treatment options. In this work, two novel missense mutations (p.I515M and p.A606D) in the pbp2 gene were newly identified as possible causes of dalbavancin resistance.
Sections du résumé
BACKGROUND
BACKGROUND
The increasing prevalence of methicillin-resistant Staphylococcus aureus (MRSA) strains resistant to non-beta-lactam antimicrobials poses a significant challenge in treating severe MRSA bloodstream infections. This study explores resistance development and mechanisms in MRSA isolates, especially after the first dalbavancin-resistant MRSA strain in our hospital in 2016.
METHODS
METHODS
This study investigated 55 MRSA bloodstream isolates (02/2015-02/2021) from the University Hospital of the Medical University of Vienna, Austria. The MICs of dalbavancin, linezolid, and daptomycin were assessed. Two isolates (16-33 and 19-362) resistant to dalbavancin were analyzed via whole-genome sequencing, with morphology evaluated using transmission electron microscopy (TEM).
RESULTS
RESULTS
S.aureus BSI strain 19-362 had two novel missense mutations (p.I515M and p.A606D) in the pbp2 gene. Isolate 16-33 had a 534 bp deletion in the DHH domain of GdpP and a SNV in pbp2 (p.G146R). Both strains had mutations in the rpoB gene, but at different positions. TEM revealed significantly thicker cell walls in 16-33 (p < 0.05) compared to 19-362 and dalbavancin-susceptible strains. None of the MRSA isolates showed resistance to linezolid or daptomycin.
CONCLUSION
CONCLUSIONS
In light of increasing vancomycin resistance reports, continuous surveillance is essential to comprehend the molecular mechanisms of resistance in alternative MRSA treatment options. In this work, two novel missense mutations (p.I515M and p.A606D) in the pbp2 gene were newly identified as possible causes of dalbavancin resistance.
Identifiants
pubmed: 39223565
doi: 10.1186/s12879-024-09797-w
pii: 10.1186/s12879-024-09797-w
doi:
Substances chimiques
dalbavancin
808UI9MS5K
Anti-Bacterial Agents
0
Teicoplanin
61036-62-2
Daptomycin
NWQ5N31VKK
Linezolid
ISQ9I6J12J
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
899Informations de copyright
© 2024. The Author(s).
Références
Lowy FD. Staphylococcus aureus infections. N Engl J Med. 1998;339(8):520–32.
doi: 10.1056/NEJM199808203390806
pubmed: 9709046
Kourtis AP, Hatfield K, Baggs J, Mu Y, See I, Epson E, et al. Vital signs: Epidemiology and recent trends in Methicillin-resistant and in Methicillin-Susceptible Staphylococcus aureus Bloodstream Infections - United States. MMWR Morb Mortal Wkly Rep. 2019;68(9):214–9.
doi: 10.15585/mmwr.mm6809e1
pubmed: 30845118
pmcid: 6421967
Mermel LA, Allon M, Bouza E, Craven DE, Flynn P, O’Grady NP, et al. Clinical practice guidelines for the diagnosis and management of intravascular catheter-related infection: 2009 update by the Infectious Diseases Society of America. Clin Infect Dis. 2009;49(1):1–45.
doi: 10.1086/599376
pubmed: 19489710
The European Committee on Antimicrobial Susceptibility Testing. Breakpoint tables for interpretation of MICs and zone diameters. 2023;Version 13.1.
Dhand A, Sakoulas G. Reduced Vancomycin susceptibility among clinical Staphylococcus aureus isolates (‘the MIC Creep’): implications for therapy. F1000. Med Rep. 2012;4:4.
Périchon B, Courvalin P. VanA-type Vancomycin-resistant Staphylococcus aureus. Antimicrob Agents Chemother. 2009;53(11):4580–7.
doi: 10.1128/AAC.00346-09
pubmed: 19506057
pmcid: 2772335
Arthur M, Molinas C, Depardieu F, Courvalin P. Characterization of Tn1546, a Tn3-related transposon conferring glycopeptide resistance by synthesis of depsipeptide peptidoglycan precursors in Enterococcus faecium BM4147. J Bacteriol. 1993;175(1):117–27.
doi: 10.1128/jb.175.1.117-127.1993
pubmed: 8380148
pmcid: 196104
Andam CP, Fournier GP, Gogarten JP. Multilevel populations and the evolution of antibiotic resistance through horizontal gene transfer. FEMS Microbiol Rev. 2011;35(5):756–67.
doi: 10.1111/j.1574-6976.2011.00274.x
pubmed: 21521245
Watkins RR, Lemonovich TL, File TM. Jr. An evidence-based review of linezolid for the treatment of methicillin-resistant Staphylococcus aureus (MRSA): place in therapy. Core Evid. 2012;7:131–43.
doi: 10.2147/CE.S33430
pubmed: 23271985
pmcid: 3526863
Garnock-Jones KP, Single-Dose Dalbavancin. A review in Acute bacterial skin and skin structure infections. Drugs. 2017;77(1):75–83.
doi: 10.1007/s40265-016-0666-0
pubmed: 27988870
Werth BJ, Ashford NK, Penewit K, Waalkes A, Holmes EA, Ross DH, et al. Dalbavancin exposure in vitro selects for dalbavancin-non-susceptible and Vancomycin-intermediate strains of methicillin-resistant Staphylococcus aureus. Clin Microbiol Infect. 2021;27(6):910.e1-.e8.
doi: 10.1016/j.cmi.2020.08.025
Zhang R, Polenakovik H, Barreras Beltran IA, Waalkes A, Salipante SJ, Xu L, Werth BJ. Emergence of Dalbavancin, Vancomycin, and Daptomycin Nonsusceptible Staphylococcus aureus in a patient treated with dalbavancin: Case Report and isolate characterization. Clin Infect Dis. 2022;75(9):1641–4.
doi: 10.1093/cid/ciac341
pubmed: 35510938
pmcid: 10200325
Jones RN, Flamm RK, Sader HS. Surveillance of dalbavancin potency and spectrum in the United States (2012). Diagn Microbiol Infect Dis. 2013;76(1):122–3.
doi: 10.1016/j.diagmicrobio.2013.01.003
pubmed: 23433533
Zhanel GG, Calic D, Schweizer F, Zelenitsky S, Adam H, Lagacé-Wiens PR, et al. New lipoglycopeptides: a comparative review of dalbavancin, oritavancin and telavancin. Drugs. 2010;70(7):859–86.
doi: 10.2165/11534440-000000000-00000
pubmed: 20426497
Streit JM, Fritsche TR, Sader HS, Jones RN. Worldwide assessment of dalbavancin activity and spectrum against over 6,000 clinical isolates. Diagn Microbiol Infect Dis. 2004;48(2):137–43.
doi: 10.1016/j.diagmicrobio.2003.09.004
pubmed: 14972384
Guzek A, Rybicki Z, Tomaszewski D. In vitro analysis of the minimal inhibitory concentration values of different generations of anti-methicillin-resistant Staphylococcus aureus antibiotics. Indian J Med Microbiol. 2018;36(1):119–20.
doi: 10.4103/ijmm.IJMM_17_136
pubmed: 29735840
Koeth LM, DiFranco-Fisher JM, McCurdy S. A reference broth microdilution method for Dalbavancin in Vitro susceptibility testing of Bacteria that grow aerobically. J Vis Exp. 2015(103).
Martin M. Cutadapt removes adapter sequences from high-throughput sequencing reads. 2011. 2011;17(1):3.
Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2. Nat Methods. 2012;9(4):357–9.
doi: 10.1038/nmeth.1923
pubmed: 22388286
pmcid: 3322381
Koboldt DC, Zhang Q, Larson DE, Shen D, McLellan MD, Lin L, et al. VarScan 2: somatic mutation and copy number alteration discovery in cancer by exome sequencing. Genome Res. 2012;22(3):568–76.
doi: 10.1101/gr.129684.111
pubmed: 22300766
pmcid: 3290792
Prjibelski A, Antipov D, Meleshko D, Lapidus A, Korobeynikov A. Using SPAdes De Novo Assembler. Curr Protocols Bioinf. 2020;70(1):e102.
doi: 10.1002/cpbi.102
Alcock BP, Raphenya AR, Lau TTY, Tsang KK, Bouchard M, Edalatmand A, et al. CARD 2020: antibiotic resistome surveillance with the comprehensive antibiotic resistance database. Nucleic Acids Res. 2020;48(D1):D517–25.
pubmed: 31665441
Joensen KG, Scheutz F, Lund O, Hasman H, Kaas RS, Nielsen EM, Aarestrup FM. Real-time whole-genome sequencing for routine typing, surveillance, and outbreak detection of verotoxigenic Escherichia coli. J Clin Microbiol. 2014;52(5):1501–10.
doi: 10.1128/JCM.03617-13
pubmed: 24574290
pmcid: 3993690
Kussmann M, Karer M, Obermueller M, Schmidt K, Barousch W, Moser D, et al. Emergence of a dalbavancin induced glycopeptide/lipoglycopeptide non-susceptible Staphylococcus aureus during treatment of a cardiac device-related endocarditis. Emerg Microbes Infect. 2018;7(1):202.
doi: 10.1038/s41426-018-0205-z
pubmed: 30514923
pmcid: 6279813
Kuipers J, Giepmans BNG. Neodymium as an alternative contrast for uranium in electron microscopy. Histochem Cell Biol. 2020;153(4):271–7.
doi: 10.1007/s00418-020-01846-0
pubmed: 32008069
pmcid: 7160090
Jones RN, Sader HS, Flamm RK. Update of dalbavancin spectrum and potency in the USA: report from the SENTRY Antimicrobial Surveillance Program (2011). Diagn Microbiol Infect Dis. 2013;75(3):304–7.
doi: 10.1016/j.diagmicrobio.2012.11.024
pubmed: 23357293
Zhanel GG, Trapp S, Gin AS, DeCorby M, Lagacé-Wiens PR, Rubinstein E, et al. Dalbavancin and telavancin: novel lipoglycopeptides for the treatment of Gram-positive infections. Expert Rev Anti Infect Ther. 2008;6(1):67–81.
doi: 10.1586/14787210.6.1.67
pubmed: 18251665
Ortwine JK, Werth BJ, Sakoulas G, Rybak MJ. Reduced glycopeptide and lipopeptide susceptibility in Staphylococcus aureus and the seesaw effect: taking advantage of the back door left open? Drug Resist Updat. 2013;16(3–5):73–9.
doi: 10.1016/j.drup.2013.10.002
pubmed: 24268586
Werth BJ, Jain R, Hahn A, Cummings L, Weaver T, Waalkes A, et al. Emergence of dalbavancin non-susceptible, Vancomycin-intermediate Staphylococcus aureus (VISA) after treatment of MRSA central line-associated bloodstream infection with a dalbavancin- and Vancomycin-containing regimen. Clin Microbiol Infect. 2018;24(4):429.e1-.e5.
doi: 10.1016/j.cmi.2017.07.028
Njenga J, Nyasinga J, Munshi Z, Muraya A, Omuse G, Ngugi C, Revathi G. Genomic characterization of two community-acquired methicillin-resistant Staphylococcus aureus with novel sequence types in Kenya. Front Med (Lausanne). 2022;9:966283.
doi: 10.3389/fmed.2022.966283
pubmed: 36226152
Howden BP, McEvoy CR, Allen DL, Chua K, Gao W, Harrison PF, et al. Evolution of multidrug resistance during Staphylococcus aureus infection involves mutation of the essential two component regulator WalKR. PLoS Pathog. 2011;7(11):e1002359.
doi: 10.1371/journal.ppat.1002359
pubmed: 22102812
pmcid: 3213104
Watanabe Y, Cui L, Katayama Y, Kozue K, Hiramatsu K. Impact of rpoB mutations on reduced Vancomycin susceptibility in Staphylococcus aureus. J Clin Microbiol. 2011;49(7):2680–4.
doi: 10.1128/JCM.02144-10
pubmed: 21525224
pmcid: 3147882
Wichelhaus TA, Böddinghaus B, Besier S, Schäfer V, Brade V, Ludwig A. Biological cost of rifampin resistance from the perspective of Staphylococcus aureus. Antimicrob Agents Chemother. 2002;46(11):3381–5.
doi: 10.1128/AAC.46.11.3381-3385.2002
pubmed: 12384339
pmcid: 128759
Wang Y, Li X, Jiang L, Han W, Xie X, Jin Y, et al. Novel Mutation sites in the development of Vancomycin- Intermediate Resistance in Staphylococcus aureus. Front Microbiol. 2016;7:2163.
pubmed: 28119680
Tanaka M, Onodera Y, Uchida Y, Sato K. Quinolone resistance mutations in the GrlB protein of Staphylococcus aureus. Antimicrob Agents Chemother. 1998;42(11):3044–6.
doi: 10.1128/AAC.42.11.3044
pubmed: 9797253
pmcid: 105993
Conceição T, de Lencastre H, Aires-de-Sousa M. Prevalence of biocide resistance genes and chlorhexidine and mupirocin non-susceptibility in Portuguese hospitals during a 31-year period (1985–2016). J Glob Antimicrob Resist. 2021;24:169–74.
doi: 10.1016/j.jgar.2020.12.010
pubmed: 33373736
Bakthavatchalam YD, Babu P, Munusamy E, Dwarakanathan HT, Rupali P, Zervos M, et al. Genomic insights on heterogeneous resistance to Vancomycin and teicoplanin in Methicillin-resistant Staphylococcus aureus: a first report from South India. PLoS ONE. 2019;14(12):e0227009.
doi: 10.1371/journal.pone.0227009
pubmed: 31887179
pmcid: 6936811
Howden BP, Davies JK, Johnson PD, Stinear TP, Grayson ML. Reduced Vancomycin susceptibility in Staphylococcus aureus, including Vancomycin-intermediate and heterogeneous Vancomycin-intermediate strains: resistance mechanisms, laboratory detection, and clinical implications. Clin Microbiol Rev. 2010;23(1):99–139.
doi: 10.1128/CMR.00042-09
pubmed: 20065327
pmcid: 2806658
Fowler PW, Cole K, Gordon NC, Kearns AM, Llewelyn MJ, Peto TEA, et al. Robust prediction of resistance to Trimethoprim in Staphylococcus aureus. Cell Chem Biol. 2018;25(3):339–e494.
doi: 10.1016/j.chembiol.2017.12.009
pubmed: 29307840
Wang T, Tanaka M, Sato K. Detection of grlA and gyrA mutations in 344 Staphylococcus aureus strains. Antimicrob Agents Chemother. 1998;42(2):236–40.
doi: 10.1128/AAC.42.2.236
pubmed: 9527766
pmcid: 105394
Jian Y, Lv H, Liu J, Huang Q, Liu Y, Liu Q, Li M. Dynamic changes of Staphylococcus aureus susceptibility to Vancomycin, Teicoplanin, and Linezolid in a Central Teaching Hospital in Shanghai, China, 2008–2018. Front Microbiol. 2020;11:908.
doi: 10.3389/fmicb.2020.00908
pubmed: 32528428
pmcid: 7247803
Shariati A, Dadashi M, Chegini Z, van Belkum A, Mirzaii M, Khoramrooz SS, Darban-Sarokhalil D. The global prevalence of Daptomycin, Tigecycline, Quinupristin/Dalfopristin, and linezolid-resistant Staphylococcus aureus and coagulase-negative staphylococci strains: a systematic review and meta-analysis. Antimicrob Resist Infect Control. 2020;9(1):56.
doi: 10.1186/s13756-020-00714-9
pubmed: 32321574
pmcid: 7178749
Chen YH, Liu CY, Ko WC, Liao CH, Lu PL, Huang CH, et al. Trends in the susceptibility of methicillin-resistant Staphylococcus aureus to nine antimicrobial agents, including ceftobiprole, nemonoxacin, and tyrothricin: results from the Tigecycline in Vitro Surveillance in Taiwan (TIST) study, 2006–2010. Eur J Clin Microbiol Infect Dis. 2014;33(2):233–9.
doi: 10.1007/s10096-013-1949-y
pubmed: 23955154