OXA-48-like carbapenemases in Proteus mirabilis – novel genetic environments and a challenge for detection

References

• Nordmann P, Poirel L. The difficult-to-control spread of carbapenemase producers among Enterobacteriaceae worldwide. Clin Microbiol Infect. 2014;20:821–830. doi:10.1111/1469-0691.12719
   PubMed Web of Science ®Google Scholar
• Potron A, Poirel L, Rondinaud E, et al. Intercontinental spread of OXA-48 beta-lactamase-producing Enterobacteriaceae over a 11-year period, 2001 to 2011. Eurosurveillance. 2013;18:20549. doi:10.2807/1560-7917.ES2013.18.31.20549
   Web of Science ®Google Scholar
• Girlich D, Bonnin RA, Dortet L, et al. Genetics of Acquired Antibiotic Resistance Genes in Proteus spp. Front Microbiol. 2020;11:256. doi:10.3389/fmicb.2020.00256
   PubMed Web of Science ®Google Scholar
• Pedraza R, Kieffer N, Guzmán-Puche J, et al. Hidden dissemination of carbapenem-susceptible OXA-48-producing Proteus mirabilis. J Antimicrob Chemother. 2022;77:3009–3015. doi:10.1093/jac/dkac267
   PubMed Web of Science ®Google Scholar
• Hamprecht A, Sattler J, Noster J, et al. Proteus mirabilis – analysis of a concealed source of carbapenemases and development of a diagnostic algorithm for detection. Clin Microbiol Infect. 2023;29:1198.e1–1198.e6. doi:10.1016/j.cmi.2023.05.032
   PubMed Web of Science ®Google Scholar
• European Committee on Antimicrobial Susceptibility Testing. EUCAST guidelines for detection of resistance mechanisms and specific resistances of clinical and/or epidemiological importance. Version 2.0. July 2017. Available from: https://www.eucast.org/resistance_mechanisms
   Google Scholar
• Huang T-D, Poirel L, Bogaerts P, et al. Temocillin and piperacillin/tazobactam resistance by disc diffusion as antimicrobial surrogate markers for the detection of carbapenemase-producing Enterobacteriaceae in geographical areas with a high prevalence of OXA-48 producers. J Antimicrob Chemother. 2014;69:445–450. doi:10.1093/jac/dkt367
   PubMed Web of Science ®Google Scholar
• Wiskirchen DE, Nordmann P, Crandon JL, et al. Efficacy of humanized carbapenem and ceftazidime regimens against Enterobacteriaceae producing OXA-48 carbapenemase in a murine infection model. Antimicrob Agents Chemother. 2014;58:1678–1683. doi:10.1128/AAC.01947-13
   PubMed Web of Science ®Google Scholar
• Skalova A, Chudejova K, Rotova V, et al. Molecular characterization of OXA-48-like-producing Enterobacteriaceae in the Czech Republic and evidence for horizontal transfer of pOXA-48-like plasmids. Antimicrob Agents Chemother. 2017;61:e01889–16. doi:10.1128/AAC.01889-16
   PubMed Web of Science ®Google Scholar
• Carrër A, Poirel L, Eraksoy H, et al. Spread of OXA-48-positive carbapenem-resistant Klebsiella pneumoniae isolates in Istanbul, Turkey. Antimicrob Agents Chemother. 2008;52:2950–2954. doi:10.1128/AAC.01672-07
   PubMed Web of Science ®Google Scholar
• Sattler J, Tsvetkov T, Stelzer Y, et al. Emergence of Tn1999.7, a new transposon in blaOXA-48-harboring plasmids associated with increased plasmid stability. Antimicrob Agents Chemother. 2022;0:e00787–22.
   Google Scholar
• Chen L, Laham A, Chavda N, et al. First report of an OXA-48-producing multidrug-resistant Proteus mirabilis strain from Gaza, Palestine. Antimicrob Agents Chemother; 2015; 59:4305–4307. doi:10.1128/AAC.00565-15
   PubMed Web of Science ®Google Scholar
• Greissl C, Saleh A, Hamprecht A. Rapid detection of OXA-48-like, KPC, NDM, and VIM carbapenemases in Enterobacterales by a new multiplex immunochromatographic test. Eur J Clin Microbiol Infect Dis. 2019;38:331–335. doi:10.1007/s10096-018-3432-2
   PubMed Web of Science ®Google Scholar
• Baeza LL, Pfennigwerth N, Greissl C, et al. Comparison of five methods for detection of carbapenemases in Enterobacterales with proposal of a new algorithm. Clin Microbiol Infect. 2019;25:1286.e9–1286.e15. doi:10.1016/j.cmi.2019.03.003
   PubMed Web of Science ®Google Scholar
• Wick RR, Judd LM, Cerdeira LT, et al. Trycycler: consensus long-read assemblies for bacterial genomes. Genome Biol. 2021;22:266. doi:10.1186/s13059-021-02483-z
   PubMed Web of Science ®Google Scholar
• Wright C, Wykes M. nanoporetech/medaka [Internet]. Oxford Nanopore Technologies; 2024 [cited 2024 Mar 8]. Available from: https://github.com/nanoporetech/medaka
   Google Scholar
• Wick RR, Holt KE. Polypolish: Short-read polishing of long-read bacterial genome assemblies. PLOS Comput Biol. 2022;18:e1009802. doi:10.1371/journal.pcbi.1009802
   PubMed Web of Science ®Google Scholar
• Zankari E, Hasman H, Cosentino S, et al. Identification of acquired antimicrobial resistance genes. J Antimicrob Chemother. 2012;67:2640–2644. doi:10.1093/jac/dks261
   PubMed Web of Science ®Google Scholar
• Carattoli A, Zankari E, García-Fernández A, et al. In silico detection and typing of plasmids using PlasmidFinder and plasmid multilocus sequence typing. Antimicrob Agents Chemother. 2014;58:3895–3903. doi:10.1128/AAC.02412-14
   PubMed Web of Science ®Google Scholar
• Garcillán-Barcia MP, Redondo-Salvo S, Vielva L, et al. Mobscan: automated annotation of MOB Relaxases. Methods Mol Biol Clifton NJ. 2020;2075:295–308. doi:10.1007/978-1-4939-9877-7_21
   PubMedGoogle Scholar
• Robertson J, Nash JHE. MOB-suite: software tools for clustering, reconstruction and typing of plasmids from draft assemblies. Microb Genomics. 2018;4:e000206.
   PubMed Web of Science ®Google Scholar
• Tatusova T, DiCuccio M, Badretdin A, et al. NCBI prokaryotic genome annotation pipeline. Nucleic Acids Res. 2016;44:6614–6624. doi:10.1093/nar/gkw569
   PubMed Web of Science ®Google Scholar
• Silva M, Machado MP, Silva DN, et al. chewBBACA: a complete suite for gene-by-gene schema creation and strain identification. Microb Genomics. 2018;4:e000166. doi:10.1099/mgen.0.000166
   PubMed Web of Science ®Google Scholar
• Zhou Z, Alikhan N-F, Sergeant MJ, et al. GrapeTree: visualization of core genomic relationships among 100,000 bacterial pathogens. Genome Res. 2018;28:1395–1404. doi:10.1101/gr.232397.117
   PubMed Web of Science ®Google Scholar
• Kaas RS, Leekitcharoenphon P, Aarestrup FM, et al. Solving the problem of comparing whole bacterial genomes across cifferent sequencing platforms. PLoS One. 2014;9:e104984. doi:10.1371/journal.pone.0104984
   PubMed Web of Science ®Google Scholar
• Alikhan N-F, Petty NK, Ben Zakour NL, et al. BLAST Ring Image Generator (BRIG): simple prokaryote genome comparisons. BMC Genomics. 2011;12:402. doi:10.1186/1471-2164-12-402
   PubMed Web of Science ®Google Scholar
• Gilchrist CLM, Chooi Y-H. Clinker & clustermap.js: automatic generation of gene cluster comparison figures. Bioinformatics. 2021;37:2473–2475. doi:10.1093/bioinformatics/btab007
   PubMed Web of Science ®Google Scholar
• Lei C-W, Yao T-G, Yan J, et al. Identification of Proteus genomic island 2 variants in two clonal Proteus mirabilis isolates with coexistence of a novel genomic resistance island PmGRI1. J Antimicrob Chemother. 2020;75:2503–2507. doi:10.1093/jac/dkaa215
   PubMed Web of Science ®Google Scholar
• Hua X, Zhang L, Moran RA, et al. Cointegration as a mechanism for the evolution of a KPC-producing multidrug resistance plasmid in Proteus mirabilis. Emerg Microbes Infect. 2020;9:1206–1218. doi:10.1080/22221751.2020.1773322
   PubMed Web of Science ®Google Scholar
• Alvarez-Fraga L, Phan M-D, Goh KGK, et al. Differential Afa/Dr fimbriae expression in the multidrug-resistant Escherichia coli ST131 clone. mBio. 2022;13:e03519–21. doi:10.1128/mbio.03519-21
   PubMed Web of Science ®Google Scholar
• Liu Y, Feng Y, Wu W, et al. First report of OXA-181-producing Escherichia coli in China and characterization of the isolate using whole-genome sequencing. Antimicrob Agents Chemother. 2015;59:5022–5025. doi:10.1128/AAC.00442-15
   PubMed Web of Science ®Google Scholar
• Tansirichaiya S, MdA R, Roberts AP. The transposon registry. Mob DNA. 2019;10:40. doi:10.1186/s13100-019-0182-3
   PubMed Web of Science ®Google Scholar
• Hamprecht A, Sommer J, Willmann M, et al. Pathogenicity of clinical OXA-48 isolates and impact of the OXA-48 IncL plasmid on virulence and bacterial fitness. Front Microbiol. 2019;10:2509. doi:10.3389/fmicb.2019.02509
   PubMed Web of Science ®Google Scholar
• Fursova NK, Astashkin EI, Knyazeva AI, et al. The spread of blaOXA-48 and blaOXA-244 carbapenemase genes among Klebsiella pneumoniae, Proteus mirabilis and Enterobacter spp. isolated in Moscow, Russia. Ann Clin Microbiol Antimicrob. 2015;14:46. doi:10.1186/s12941-015-0108-y
   PubMed Web of Science ®Google Scholar
• Beyrouthy R, Robin F, Delmas J, et al. IS1R-mediated plasticity of IncL/M plasmids leads to the insertion of blaOXA-48 into the Escherichia coli chromosome. Antimicrob Agents Chemother. 2014;58:3785–3790. doi:10.1128/AAC.02669-14
   PubMed Web of Science ®Google Scholar
• Ahmed AM, Hussein AIA, Shimamoto T. Proteus mirabilis clinical isolate harbouring a new variant of Salmonella genomic island 1 containing the multiple antibiotic resistance region. J Antimicrob Chemother. 2007;59:184–190. doi:10.1093/jac/dkl471
   PubMed Web of Science ®Google Scholar
• Siebor E, Neuwirth C. Proteus genomic island 1 (PGI1), a new resistance genomic island from two Proteus mirabilis French clinical isolates. J Antimicrob Chemother. 2014;69:3216–3220. doi:10.1093/jac/dku314
   PubMed Web of Science ®Google Scholar
• Lei C-W, Chen Y-P, Kong L-H, et al. PGI2 is a novel SGI1-relative multidrug-resistant genomic island characterized in Proteus mirabilis. Antimicrob Agents Chemother. 2018;62. doi:10.1128/aac.00019-18
   Google Scholar
• Siebor E, de Curraize C, Neuwirth C. Genomic context of resistance genes within a French clinical MDR Proteus mirabilis: identification of the novel genomic resistance island GIPmi1. J Antimicrob Chemother. 2018;73:1808–1811. doi:10.1093/jac/dky126
   PubMed Web of Science ®Google Scholar
• Hamidian M, Hawkey J, Wick R, et al. Evolution of a clade of Acinetobacter baumannii global clone 1, lineage 1 via acquisition of carbapenem- and aminoglycoside-resistance genes and dispersion of ISAba1. Microb Genomics. 2019;5:e000242.
   PubMed Web of Science ®Google Scholar
• Hua X, Moran RA, Xu Q, et al. Acquisition of a genomic resistance island (AbGRI5) from global clone 2 through homologous recombination in a clinical Acinetobacter baumannii isolate. J Antimicrob Chemother. 2021;76:65–69. doi:10.1093/jac/dkaa389
   PubMed Web of Science ®Google Scholar
• Pilato D, Chiarelli V, Boinett A, et al. Complete genome sequence of the first KPC-type carbapenemase-positive Proteus mirabilis strain from a bloodstream infection. Genome Announc. 2016;4. doi:10.1128/genomeA.00607-16
   Google Scholar
• Li Y, Liu Q, Qiu Y, et al. Genomic characteristics of clinical multidrug-resistant Proteus isolates from a tertiary care hospital in southwest China. Front Microbiol. 2022;13:977356. doi:10.3389/fmicb.2022.977356
   PubMedGoogle Scholar
• He J, Lei C, Li C, et al. Identification of a novel genomic resistance island PmGRI1-STP3 and an SXT/R391 integrative conjugative element in Proteus mirabilis of swine origin in China. J Glob Antimicrob Resist. 2021;25:77–81. doi:10.1016/j.jgar.2021.02.018
   PubMed Web of Science ®Google Scholar
• Schultz E, Haenni M, Mereghetti L, et al. Survey of multidrug resistance integrative mobilizable elements SGI1 and PGI1 in Proteus mirabilis in humans and dogs in France, 2010–13. J Antimicrob Chemother. 2015;70:2543–2546. doi:10.1093/jac/dkv154
   PubMed Web of Science ®Google Scholar
• Potron A, Nordmann P, Lafeuille E, et al. Characterization of OXA-181, a carbapenem-hydrolyzing class D β-lactamase from Klebsiella pneumoniae. Antimicrob Agents Chemother. 2011;55:4896–4899. doi:10.1128/AAC.00481-11
   PubMed Web of Science ®Google Scholar
• Tsakris A, Poulou A, Bogaerts P, et al. Evaluation of a new phenotypic OXA-48 disk test for differentiation of OXA-48 carbapenemase-producing Enterobacteriaceae clinical isolates. J Clin Microbiol. 2015;53:1245–1251. doi:10.1128/JCM.03318-14
   PubMed Web of Science ®Google Scholar
• Neuwirth C, Siébor E, Duez J-M, et al. Imipenem resistance in clinical isolates of Proteus mirabilis associated with alterations in penicillin-binding proteins. J Antimicrob Chemother. 1995;36:335–342. doi:10.1093/jac/36.2.335
   PubMed Web of Science ®Google Scholar
• Tsai Y-L, Wang M-C, Hsueh P-R, et al. Overexpression of an outer membrane protein associated with decreased susceptibility to carbapenems in Proteus mirabilis. PLoS One. 2015;10:e0120395.
   PubMed Web of Science ®Google Scholar
• Sommer J, Gerbracht KM, Krause FF, et al. OXA-484, an OXA-48-type carbapenem-hydrolyzing class D β-lactamase from Escherichia coli. Front Microbiol. 2021;12:660094–660094. doi:10.3389/fmicb.2021.660094
   PubMed Web of Science ®Google Scholar
• Potron A, Poirel L, Nordmann P. Plasmid-mediated transfer of the blaNDM-1 gene in Gram-negative rods. FEMS Microbiol Lett. 2011;324:111–116. doi:10.1111/j.1574-6968.2011.02392.x
   PubMed Web of Science ®Google Scholar
• Potron A, Bernabeu S, Cuzon G, et al. Analysis of OXA-204 carbapenemase-producing Enterobacteriaceae reveals possible endoscopy-associated transmission, France, 2012 to 2014. Eurosurveillance. 2017;22:17. doi:10.2807/1560-7917.ES.2017.22.49.17-00048
   Web of Science ®Google Scholar