Fosfomycin (FOS) has been recently reintroduced into clinical practice, but its effectiveness against multidrug-resistant (MDR) Enterobacterales is reduced due to the emergence of FOS resistance. The copresence of carbapenemases and FOS resistance could drastically limit antibiotic treatment. The aims of this study were (i) to investigate fosfomycin susceptibility profiles among carbapenem-resistant Enterobacterales (CRE) in the Czech Republic, (ii) to characterize the genetic environment of fosA genes among the collection, and (iii) to evaluate the presence of amino acid mutations in proteins involved in FOS resistance mechanisms. During the period from December 2018 to February 2022, 293 CRE isolates were collected from different hospitals in the Czech Republic. FOS MICs were assessed by the agar dilution method (ADM), FosA and FosC2 production was detected by the sodium phosphonoformate (PPF) test, and the presence of fosA-like genes was confirmed by PCR. Whole-genome sequencing was conducted with an Illumina NovaSeq 6000 system on selected strains, and the effect of point mutations in the FOS pathway was predicted using PROVEAN. Of these strains, 29% showed low susceptibility to fosfomycin (MIC, ≥16 μg/mL) by ADM. An NDM-producing Escherichia coli sequence type 648 (ST648) strain harbored a fosA10 gene on an IncK plasmid, while a VIM-producing Citrobacter freundii ST673 strain harbored a new fosA7 variant, designated fosA7.9. Analysis of mutations in the FOS pathway revealed several deleterious mutations occurring in GlpT, UhpT, UhpC, CyaA, and GlpR. Results regarding single substitutions in amino acid sequences highlighted a relationship between ST and specific mutations and an enhanced predisposition for certain STs to develop resistance. This study highlights the occurrence of several FOS resistance mechanisms in different clones spreading in the Czech Republic. IMPORTANCE Antimicrobial resistance (AMR) currently represents a concern for human health, and the reintroduction of antibiotics such as fosfomycin into clinical practice can provide further option in treatment of multidrug-resistant (MDR) bacterial infections. However, there is a global increase of fosfomycin-resistant bacteria, reducing its effectiveness. Considering this increase, it is crucial to monitor the spread of fosfomycin resistance in MDR bacteria in clinical settings and to investigate the resistance mechanism at the molecular level. Our study reports a large variety of fosfomycin resistance mechanisms among carbapenemase-producing Enterobacterales (CRE) in the Czech Republic. Our study summarizes the main achievements of our research on the use of molecular technologies, such as next-generation sequencing (NGS), to describe the heterogeneous mechanisms that reduce fosfomycin effectiveness in CRE. The results suggest that a program for widespread monitoring of fosfomycin resistance and epidemiology fosfomycin-resistant organisms can aide timely implementation of countermeasures to maintain the effectiveness of fosfomycin.

Biomedical Center Faculty of Medicine Charles University Pilsen Czech Republic

Department of Microbiology Faculty of Medicine University Hospital in Pilsen Charles University Pilsen Czech Republic

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Dijkmans AC, Zacarías NVO, Burggraaf J, Mouton JW, Wilms EB, van Nieuwkoop C, Touw DJ, Stevens J, Kamerling IMC. 2017. Fosfomycin: pharmacological, clinical and future perspectives. Antibiotics 6:24. doi:10.3390/antibiotics6040024. PubMed DOI PMC

Castañeda-García A, Blázquez J, Rodríguez-Rojas A. 2013. Molecular mechanisms and clinical impact of acquired and intrinsic fosfomycin resistance. Antibiotics (Basel) 2:217–236. doi:10.3390/antibiotics2020217. PubMed DOI PMC

Takahata S, Ida T, Hiraishi T, Sakakibara S, Maebashi K, Terada S, Muratani T, Matsumoto T, Nakahama C, Tomono K. 2010. Molecular mechanisms of fosfomycin resistance in clinical isolates of Escherichia coli. Int J Antimicrob Agents 35:333–337. doi:10.1016/j.ijantimicag.2009.11.011. PubMed DOI

Zeng J, Hong Y, Zhao N, Liu Q, Zhu W, Xiao L, Wang W, Chen M, Hong S, Wu L, Xue Y, Wang D, Niu J, Drlica K, Zhao X. 2022. A broadly applicable, stress-mediated bacterial death pathway regulated by the phosphotransferase system (PTS) and the cAMP-Crp cascade. Proc Natl Acad Sci USA 119:e2118566119. doi:10.1073/pnas.2118566119. PubMed DOI PMC

Kimata K, Takahashi H, Inada T, Postma P, Aiba H. 1997. cAMP receptor protein-cAMP plays a crucial role in glucose-lactose diauxie by activating the major glucose transporter gene in Escherichia coli. Proc Natl Acad Sci USA 94:12914–12919. doi:10.1073/pnas.94.24.12914. PubMed DOI PMC

Kurabayashi K, Tanimoto K, Tomita H, Hirakawa H. 2017. Cooperative actions of CRP-cAMP and FNR increase the fosfomycin susceptibility of enterohaemorrhagic Escherichia coli (EHEC) by elevating the expression of glpT and uhpT under anaerobic conditions. Front Microbiol 8:426. doi:10.3389/fmicb.2017.00426. PubMed DOI PMC

Seeto S, Notley-McRobb L, Ferenci T. 2004. The multifactorial influences of RpoS, Mlc and cAMP on ptsG expression under glucose-limited and anaerobic conditions. Res Microbiol 155:211–215. doi:10.1016/j.resmic.2003.11.011. PubMed DOI

Ohshima N, Yamashita S, Takahashi N, Kuroishi C, Shiro Y, Takio K. 2008. Escherichia coli cytosolic glycerophosphodiester phosphodiesterase (UgpQ) requires Mg2+, Co2+, or Mn2+ for its enzyme activity. J Bacteriol 190:1219–1223. doi:10.1128/JB.01223-07. PubMed DOI PMC

Sorlozano-Puerto A, Lopez-Machado I, Albertuz-Crespo M, Martinez-Gonzalez LJ, Gutierrez-Fernandez J. 2020. Characterization of fosfomycin and nitrofurantoin resistance mechanisms in Escherichia coli isolated in clinical urine samples. Antibiotics 9:534. doi:10.3390/antibiotics9090534. PubMed DOI PMC

Kadner RJ. 1973. Genetic control of the transport of hexose phosphates in Escherichia coli: mapping of the uhp locus. J Bacteriol 116:764–770. doi:10.1128/jb.116.2.764-770.1973. PubMed DOI PMC

Tsuruoka T, Yamada Y. 1975. Charactertization of spontaneous fosfomycin (phosphonomycin)-resistant cells of Escherichia coli B in vitro. J Antibiot (Tokyo) 28:906–911. doi:10.7164/antibiotics.28.906. PubMed DOI

Zurfluh K, Treier A, Schmitt K, Stephan R. 2020. Mobile fosfomycin resistance genes in Enterobacteriaceae—an increasing threat. Microbiologyopen 9:e1135. doi:10.1002/mbo3.1135. PubMed DOI PMC

Zou M, Ma PP, Liu WS, Liang X, Li XY, Li YZ, Liu BT. 2021. Prevalence and antibiotic resistance characteristics of extraintestinal pathogenic Escherichia coli among healthy chickens from farms and live poultry markets in China. Animals 11:1112. doi:10.3390/ani11041112. PubMed DOI PMC

Huang L, Cao M, Hu Y, Zhang R, Xiao Y, Chen G. 2021. Prevalence and mechanisms of fosfomycin resistance among KPC-producing Klebsiella pneumoniae clinical isolates in China. Int J Antimicrob Agents 57:106226. doi:10.1016/j.ijantimicag.2020.106226. PubMed DOI

Loras C, González-Prieto A, Pérez-Vázquez M, Bautista V, Ávila A, Campoy PS, Oteo-Iglesias J, Alós JI. 2021. Prevalence, detection and characterisation of fosfomycin-resistant Escherichia coli strains carrying fosA genes in Community of Madrid, Spain. J Glob Antimicrob Resist 25:137–141. doi:10.1016/j.jgar.2021.02.032. PubMed DOI

Huang Y, Lin Q, Zhou Q, Lv L, Wan M, Gao X, Wang C, Liu JH. 2020. Identification of fosA10, a novel plasmid-mediated fosfomycin resistance gene of Klebsiella pneumoniae origin, in Escherichia coli. Infect Drug Resist 13:1273–1279. doi:10.2147/IDR.S251360. PubMed DOI PMC

Singkham-In U, Muhummudaree N, Chatsuwan T. 2020. fosA3 overexpression with transporter mutations mediates high-level of fosfomycin resistance and silence of fosA3 in fosfomycin-susceptible Klebsiella pneumoniae producing carbapenemase clinical isolates. PLoS One 15:e0237474. doi:10.1371/journal.pone.0237474. PubMed DOI PMC

Zhang LJ, Gu XX, Zhang J, Yang L, Lu YW, Fang LX, Jiang HX. 2020. Characterization of a fosA3 carrying IncC-IncN plasmid from a multidrug-resistant ST17 Salmonella Indiana isolate. Front Microbiol 11:1582. doi:10.3389/fmicb.2020.01582. PubMed DOI PMC

Wang H, Min C, Li J, Yu T, Hu Y, Dou Q, Zou M. 2021. Characterization of fosfomycin resistance and molecular epidemiology among carbapenem-resistant Klebsiella pneumoniae strains from two tertiary hospitals in China. BMC Microbiol 21:109. doi:10.1186/s12866-021-02165-7. PubMed DOI PMC

Rehman MA, Yin X, Persaud-Lachhman MG, Diarra MS. 2017. First detection of a fosfomycin resistance gene, fosA7, in Salmonella enterica serovar Heidelberg isolated from broiler chickens. Antimicrob Agents Chemother 61:e00410-17. doi:10.1128/AAC.00410-17. PubMed DOI PMC

Wang J, Wang Y, Wang ZY, Wu H, Mei CY, Shen PC, Pan ZM, Jiao X. 2021. Chromosomally located fosA7 in Salmonella isolates from China. Front Microbiol 12:781306. doi:10.3389/fmicb.2021.781306. PubMed DOI PMC

Sun Y, Chen W, Wang S, Cao X. 2021. Co-occurrence of fosA5, blaSHV-145 and blaOXA-48 among a Klebsiella pneumoniae high-risk ST16 from a tertiary hospital in China: focusing on the phylogeny of OXA-48 genes from global Klebsiella pneumoniae isolates. Braz J Microbiol 52:2559–2563. doi:10.1007/s42770-021-00572-6. PubMed DOI PMC

Gou JJ, Liu N, Guo LH, Xu H, Lv T, Yu X, Chen YB, Guo XB, Rao YT, Zheng BW. 2020. Carbapenem-resistant Enterobacter hormaechei ST1103 with IMP-26 carbapenemase and ESBL gene blaSHV-178. Infect Drug Resist 13:597–605. doi:10.2147/IDR.S232514. PubMed DOI PMC

Sajeev S, Hamza M, Sivaraman GK, Ghatak S, Ojha R, Mendem SK, Murugesan D, Raisen C, Shome BR, Holmes MA. 2022. Genomic insights of beta-lactamase producing Klebsiella quasipneumoniae subsp. similipneumoniae belonging to sequence type 1699 from retail market fish, India. Arch Microbiol 204:454. doi:10.1007/s00203-022-03071-w. PubMed DOI

Biggel M, Zurfluh K, Treier A, Nüesch-Inderbinen M, Stephan R. 2021. Characteristics of fosA-carrying plasmids in E. coli and Klebsiella spp. isolates originating from food and environmental samples. J Antimicrob Chemother 76:2004–2011. doi:10.1093/jac/dkab119. PubMed DOI

Milner KA, Bay DC, Alexander D, Walkty A, Karlowsky JA, Mulvey MR, Sharma MK, Zhanel GG. 2020. Identification and characterization of a novel FosA7 member from fosfomycin-resistant Escherichia coli clinical isolates from Canadian hospitals. Antimicrob Agents Chemother 65:e00865-20. doi:10.1128/AAC.00865-20. PubMed DOI PMC

ten Doesschate T, Abbott IJ, Willems RJL, Top J, Rogers MRC, Bonten MM, Paganelli FL. 2019. In vivo acquisition of fosfomycin resistance in Escherichia coli by fosA transmission from commensal flora. J Antimicrob Chemother 74:3630–3632. doi:10.1093/jac/dkz380. PubMed DOI PMC

Hao Y, Zhao X, Zhang C, Bai Y, Song Z, Lu X, Chen R, Zhu Y, Wang Y. 2021. Clonal dissemination of clinical carbapenem-resistant Klebsiella pneumoniae isolates carrying fosA3 and blaKPC-2 coharboring plasmids in Shandong, China. Front Microbiol 12:771170. doi:10.3389/fmicb.2021.771170. PubMed DOI PMC

Zhou Y, Ai W, Cao Y, Guo Y, Wu X, Wang B, Rao L, Xu Y, Zhao H, Wang X, Yu F. 2021. The co-occurrence of NDM-5, MCR-1, and FosA3-encoding plasmids contributed to the generation of extensively drug-resistant Klebsiella pneumoniae. Front Microbiol 12:811263. doi:10.3389/fmicb.2021.811263. PubMed DOI PMC

Xiang D-R, Li J-J, Sheng Z-K, Yu H-Y, Deng M, Bi S, Hu F-S, Chen W, Xue X-W, Zhou Z-B, Doi Y, Sheng J-F, Li L-J. 2016. Complete sequence of a novel IncR-F33:A-:B- plasmid, pKP1034, harboring fosA3, blaKPC-2, blaCTX-M-65, blaSHV-12, and rmtB from an epidemic Klebsiella pneumoniae sequence type 11 strain in China. Antimicrob Agents Chemother 60:1343–1348. doi:10.1128/AAC.01488-15. PubMed DOI PMC

Wang Q, Zhang P, Zhao D, Jiang Y, Zhao F, Wang Y, Li X, Du X, Yu Y. 2018. Emergence of tigecycline resistance in Escherichia coli co-producing MCR-1 and NDM-5 during tigecycline salvage treatment. Infect Drug Resist 11:2241–2248. doi:10.2147/IDR.S179618. PubMed DOI PMC

Peng Z, Li X, Hu Z, Li Z, Lv Y, Lei M, Wu B, Chen H, Wang X. 2019. Characteristics of carbapenem-resistant and colistin-resistant Escherichia coli co-producing NDM-1 and MCR-1 from pig farms in China. Microorganisms 7:482. doi:10.3390/microorganisms7110482. PubMed DOI PMC

Tian X, Zheng X, Sun Y, Fang R, Zhang S, Zhang X, Lin J, Cao J, Zhou T. 2020. Molecular mechanisms and epidemiology of carbapenem-resistant Escherichia coli isolated from Chinese patients during 2002–2017. Infect Drug Resist 13:501–512. doi:10.2147/IDR.S232010. PubMed DOI PMC

Feng J, Qiu Y, Yin Z, Chen W, Yang H, Yang W, Wang J, Gao Y, Zhou D. 2015. Coexistence of a novel KPC-2-encoding MDR plasmid and an NDM-1-encoding pNDM-HN380-like plasmid in a clinical isolate of Citrobacter freundii. J Antimicrob Chemother 70:2987–2991. doi:10.1093/jac/dkv232. PubMed DOI

Bitar I, Caltagirone M, Villa L, Mattioni Marchetti V, Nucleo E, Sarti M, Migliavacca R, Carattoli A. 2019. Interplay among IncA and blaKPC-carrying plasmids in Citrobacter freundii. Antimicrob Agents Chemother 63:e02609-18. doi:10.1128/AAC.02609-18. PubMed DOI PMC

Kraftova L, Finianos M, Studentova V, Chudejova K, Jakubu V, Zemlickova H, Papagiannitsis CC, Bitar I, Hrabak J. 2021. Evidence of an epidemic spread of KPC-producing Enterobacterales in Czech hospitals. Sci Rep 11:15732. doi:10.1038/s41598-021-95285-z. PubMed DOI PMC

Chudejova K, Kraftova L, Mattioni Marchetti V, Hrabak J, Papagiannitsis CC, Bitar I. 2021. Genetic plurality of OXA/NDM-encoding features characterized from Enterobacterales recovered from Czech hospitals. Front Microbiol 12:641415. doi:10.3389/fmicb.2021.641415. PubMed DOI PMC

Li Z, Lin Y, Lu L, Wang K, Yang L, Li P, Li J, Jia L, Li P, Song H. 2020. Genetic characterisation of a complex class 1 integron in an NDM-1-producing Citrobacter freundii ST396 clinical strain isolated from a urine sample. J Glob Antimicrob Resist 23:64–66. doi:10.1016/j.jgar.2020.08.002. PubMed DOI

AbuOun M, Jones H, Stubberfield E, Gilson D, Shaw LP, Hubbard ATM, Chau KK, Sebra R, Peto TEA, Crook DW, Read DS, Gweon HS, Walker AS, Stoesser N, Smith RP, Anjum MF. The Rehab Consortium. 2021. A genomic epidemiological study shows that prevalence of antimicrobial resistance in Enterobacterales is associated with the livestock host, as well as antimicrobial usage. Microb Genom 7:e000630. doi:10.1099/mgen.0.000630. PubMed DOI PMC

Korotetskiy IS, Jumagaziyeva AB, Shilov SV, Kuznetsova TV, Iskakbayeva ZА, Myrzabayeva AN, Korotetskaya N, Ilin AI, Reva ON. 2020. Phenotypic and genotypic characterisation of clinical isolates of nosocomial infections. Eurasian J Appl Biotechnol doi:10.11134/btp.1.2020.5. DOI

Kahan FM, Kahan JS, Cassidy PJ, Kropp H. 1974. The mechanism of action of fosfomycin (phosphonomycin). Ann N Y Acad Sci 235:364–386. doi:10.1111/j.1749-6632.1974.tb43277.x. PubMed DOI

Hardisson C, Llaneza J. 1977. The action of fosfomycin on the growth of Pseudomonas aeruginosa. Chemotherapy 23:37–44. doi:10.1159/000222024. PubMed DOI

Lindgren V. 1978. Mapping of a genetic locus that affects glycerol 3-phosphate transport in Bacillus subtilis. J Bacteriol 133:667–670. doi:10.1128/jb.133.2.667-670.1978. PubMed DOI PMC

Nilsson AI, Berg OG, Aspevall O, Kahlmeter G, Andersson DI. 2003. Biological costs and mechanisms of fosfomycin resistance in Escherichia coli. Antimicrob Agents Chemother 47:2850–2858. doi:10.1128/AAC.47.9.2850-2858.2003. PubMed DOI PMC

Whitmer GR, Moorthy G, Arshad M. 2019. The pandemic Escherichia coli sequence type 131 strain is acquired even in the absence of antibiotic exposure. PLoS Pathog 15:e1008162. doi:10.1371/journal.ppat.1008162. PubMed DOI PMC

Doi Y, Park YS, Rivera JI, Adams-Haduch JM, Hingwe A, Sordillo EM, Lewis JS, Howard WJ, Johnson LE, Polsky B, Jorgensen JH, Richter SS, Shutt KA, Paterson DL. 2013. Community-associated extended-spectrum β-lactamase-producing Escherichia coli infection in the United States. Clin Infect Dis 56:641–648. doi:10.1093/cid/cis942. PubMed DOI PMC

Piazza A, Principe L, Comandatore F, Perini M, Meroni E, Mattioni Marchetti V, Migliavacca R, Luzzaro F. 2021. Whole-genome sequencing investigation of a large nosocomial outbreak caused by ST131 H30Rx KPC-producing Escherichia coli in Italy. Antibiotics 10:718. doi:10.3390/antibiotics10060718. PubMed DOI PMC

Peirano G, Chen L, Nobrega D, Finn TJ, Kreiswirth BN, DeVinney R, Pitout JDD. 2022. Genomic epidemiology of global carbapenemase-producing Escherichia coli, 2015–2017. Emerg Infect Dis 28:924–931. doi:10.3201/eid2805.212535. PubMed DOI PMC

Samuelsen Ø, Overballe-Petersen S, Bjørnholt JV, Brisse S, Doumith M, Woodford N, Hopkins KL, Aasnæs B, Haldorsen B, Sundsfjord A. Norwegian Study Group on CPE. 2017. Molecular and epidemiological characterization of carbapenemase-producing Enterobacteriaceae in Norway, 2007 to 2014. PLoS One 12:e0187832. doi:10.1371/journal.pone.0187832. PubMed DOI PMC

Schweizer C, Bischoff P, Bender J, Kola A, Gastmeier P, Hummel M, Klefisch FR, Schoenrath F, Frühauf A, Pfeifer Y. 2019. Plasmid-mediated transmission of KPC-2 carbapenemase in Enterobacteriaceae in critically ill patients. Front Microbiol 10:276. doi:10.3389/fmicb.2019.00276. PubMed DOI PMC

Fernandes MR, Sellera FP, Moura Q, Gaspar VC, Cerdeira L, Lincopan N. 2018. International high-risk clonal lineages of CTX-M-producing Escherichia coli F-ST648 in free-roaming cats, South America. Infect Genet Evol 66:48–51. doi:10.1016/j.meegid.2018.09.009. PubMed DOI

Sellera FP, Fernandes MR, Moura Q, Souza TA, Cerdeira L, Lincopan N. 2017. Draft genome sequence of Enterobacter cloacae ST520 harbouring blaKPC-2, blaCTX-M-15 and blaOXA-17 isolated from coastal waters of the South Atlantic Ocean. J Glob Antimicrob Resist 10:279–280. doi:10.1016/j.jgar.2017.07.017. PubMed DOI

Solgi H, Badmasti F, Aminzadeh Z, Giske CG, Pourahmad M, Vaziri F, Havaei SA, Shahcheraghi F. 2017. Molecular characterization of intestinal carriage of carbapenem-resistant Enterobacteriaceae among inpatients at two Iranian university hospitals: first report of co-production of bla NDM-7 and bla OXA-48. Eur J Clin Microbiol Infect Dis 36:2127–2135. doi:10.1007/s10096-017-3035-3. PubMed DOI

Qamar MU, Walsh TR, Toleman MA, Saleem S, Jahan S. 2018. First identification of clinical isolate of a novel “NDM-4” producing Escherichia coli ST405 from urine sample in Pakistan. Braz J Microbiol 49:949–950. doi:10.1016/j.bjm.2018.02.009. PubMed DOI PMC

Harada S, Suzuki M, Sasaki T, Sakurai A, Inaba M, Takuya H, Wakuda M, Doi Y. 2021. Transmission of NDM-5-producing and OXA-48-producing Escherichia coli sequence type 648 by international visitors without previous medical exposure. Microbiol Spectr 9:e01827-21. doi:10.1128/spectrum.01827-21. PubMed DOI PMC

Yang RS, Feng Y, Lv XY, Duan JH, Chen J, Fang LX, Xia J, Liao XP, Sun J, Liu YH. 2016. Emergence of NDM-5- and MCR-1-producing Escherichia coli clones ST648 and ST156 from a single Muscovy duck (Cairina moschata). Antimicrob Agents Chemother 60:6899–6902. doi:10.1128/AAC.01365-16. PubMed DOI PMC

Queenan AM, Bush K. 2007. Carbapenemases: the versatile beta-lactamases. Clin Microbiol Rev 20:440–458. doi:10.1128/CMR.00001-07. PubMed DOI PMC

Edgell DR. 2009. Selfish DNA: homing endonucleases find a home. Curr Biol 19:R115–117. doi:10.1016/j.cub.2008.12.019. PubMed DOI

Li T, Chen H, Zhao J, Tao Z, Lan W, Zhao Y, Sun X. 2023. Characterization of phage vB_SalM_SPJ41 and the reduction of risk of antibiotic-resistant Salmonella enterica contamination in two ready-to-eat foods. Antibiotics (Basel) 12:364. doi:10.3390/antibiotics12020364. PubMed DOI PMC

Nakamura G, Wachino J, Sato N, Kimura K, Yamada K, Jin W, Shibayama K, Yagi T, Kawamura K, Arakawa Y. 2014. Practical agar-based disk potentiation test for detection of fosfomycin-nonsusceptible Escherichia coli clinical isolates producing glutathione S-transferases. J Clin Microbiol 52:3175–3179. doi:10.1128/JCM.01094-14. PubMed DOI PMC

Benzerara Y, Gallah S, Hommeril B, Genel N, Decré D, Rottman M, Arlet G. 2017. Emergence of plasmid-mediated fosfomycin-resistance genes among Escherichia coli isolates, France. Emerg Infect Dis 23:1564–1567. doi:10.3201/eid2309.170560. PubMed DOI PMC

Nurk S, Bankevich A, Antipov D, Gurevich AA, Korobeynikov A, Lapidus A, Prjibelski AD, Pyshkin A, Sirotkin A, Sirotkin Y, Stepanauskas R, Clingenpeel SR, Woyke T, McLean JS, Lasken R, Tesler G, Alekseyev MA, Pevzner PA. 2013. Assembling single-cell genomes and mini-metagenomes from chimeric MDA products. J Comput Biol 20:714–737. doi:10.1089/cmb.2013.0084. PubMed DOI PMC

Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA, Formsma K, Gerdes S, Glass EM, Kubal M, Meyer F, Olsen GJ, Olson R, Osterman AL, Overbeek RA, McNeil LK, Paarmann D, Paczian T, Parrello B, Pusch GD, Reich C, Stevens R, Vassieva O, Vonstein V, Wilke A, Zagnitko O. 2008. The RAST server: rapid annotations using subsystems technology. BMC Genomics 9:75. doi:10.1186/1471-2164-9-75. PubMed DOI PMC

Zankari E, Hasman H, Cosentino S, Vestergaard M, Rasmussen S, Lund O, Aarestrup FM, Larsen MV. 2012. Identification of acquired antimicrobial resistance genes. J Antimicrob Chemother 67:2640–2644. doi:10.1093/jac/dks261. PubMed DOI PMC

Alcock BP, Raphenya AR, Lau TTY, Tsang KK, Bouchard M, Edalatmand A, Huynh W, Nguyen AV, Cheng AA, Liu S, Min SY, Miroshnichenko A, Tran HK, Werfalli RE, Nasir JA, Oloni M, Speicher DJ, Florescu A, Singh B, Faltyn M, Hernandez-Koutoucheva A, Sharma AN, Bordeleau E, Pawlowski AC, Zubyk HL, Dooley D, Griffiths E, Maguire F, Winsor GL, Beiko RG, Brinkman FSL, Hsiao WWL, Domselaar GV, McArthur AG. 2020. CARD 2020: antibiotic resistome surveillance with the comprehensive antibiotic resistance database. Nucleic Acids Res 48:D517–D525. doi:10.1093/nar/gkz935. PubMed DOI PMC

Carattoli A, Zankari E, García-Fernández A, Voldby Larsen M, Lund O, Villa L, Møller Aarestrup F, Hasman H. 2014. In silico detection and typing of plasmids using PlasmidFinder and plasmid multilocus sequence typing. Antimicrob Agents Chemother 58:3895–3903. doi:10.1128/AAC.02412-14. PubMed DOI PMC

Siguier P, Perochon J, Lestrade L, Mahillon J, Chandler M. 2006. ISfinder: the reference centre for bacterial insertion sequences. Nucleic Acids Res 34:D32–D36. doi:10.1093/nar/gkj014. PubMed DOI PMC

Larsen MV, Cosentino S, Rasmussen S, Friis C, Hasman H, Marvig RL, Jelsbak L, Sicheritz-Pontén T, Ussery DW, Aarestrup FM, Lund O. 2012. Multilocus sequence typing of total-genome-sequenced bacteria. J Clin Microbiol 50:1355–1361. doi:10.1128/JCM.06094-11. PubMed DOI PMC

Sullivan MJ, Petty NK, Beatson SA. 2011. Easyfig: a genome comparison visualizer. Bioinformatics 27:1009–1010. doi:10.1093/bioinformatics/btr039. PubMed DOI PMC

Treangen TJ, Ondov BD, Koren S, Phillippy AM. 2014. The Harvest suite for rapid core-genome alignment and visualization of thousands of intraspecific microbial genomes. Genome Biol 15:524. doi:10.1186/s13059-014-0524-x. PubMed DOI PMC

Letunic I, Bork P. 2021. Interactive Tree Of Life (iTOL) v5: an online tool for phylogenetic tree display and annotation. Nucleic Acids Res 49:W293–W296. doi:10.1093/nar/gkab301. PubMed DOI PMC

Tamura K, Stecher G, Kumar S. 2021. MEGA11: Molecular Evolutionary Genetics Analysis version 11. Mol Biol Evol 38:3022–3027. doi:10.1093/molbev/msab120. PubMed DOI PMC

Jones DT, Taylor WR, Thornton JM. 1992. The rapid generation of mutation data matrices from protein sequences. Comput Appl Biosci 8:275–282. doi:10.1093/bioinformatics/8.3.275. PubMed DOI

Carattoli A, Bertini A, Villa L, Falbo V, Hopkins KL, Threlfall EJ. 2005. Identification of plasmids by PCR-based replicon typing. J Microbiol Methods 63:219–228. doi:10.1016/j.mimet.2005.03.018. PubMed DOI

Sambrook J, Russell DW. 2006. Preparation and transformation of competent E. coli using calcium chloride. Cold Spring Harb Protoc 2006:pdb.prot3932. doi:10.1101/pdb.prot3932. PubMed DOI

Choi Y, Chan AP. 2015. PROVEAN web server: a tool to predict the functional effect of amino acid substitutions and indels. Bioinformatics 31:2745–2747. doi:10.1093/bioinformatics/btv195. PubMed DOI PMC

Bitar I, Papagiannitsis CC, Kraftova L, Marchetti VM, Petinaki E, Finianos M, Chudejova K, Zemlickova H, Hrabak J. 2022. Implication of different replicons in the spread of the VIM-1-encoding integron, In110, in Enterobacterales from Czech hospitals. Front Microbiol 13:993240. doi:10.3389/fmicb.2022.993240. PubMed DOI PMC

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