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Plasmid-encoded tet(X) genes that confer high-level tigecycline resistance in Escherichia coli

Nature Microbiology volume 4, pages 1457–1464 (2019)Cite this article

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Abstract

Tigecycline is one of the last-resort antibiotics to treat complicated infections caused by both multidrug-resistant Gram-negative and Gram-positive bacteria1. Tigecycline resistance has sporadically occurred in recent years, primarily due to chromosome-encoding mechanisms, such as overexpression of efflux pumps and ribosome protection2,3. Here, we report the emergence of the plasmid-mediated mobile tigecycline resistance mechanism Tet(X4) in Escherichia coli isolates from China, which is capable of degrading all tetracyclines, including tigecycline and the US FDA newly approved eravacycline. The tet(X4)-harbouring IncQ1 plasmid is highly transferable, and can be successfully mobilized and stabilized in recipient clinical and laboratory strains of Enterobacteriaceae bacteria. It is noteworthy that tet(X4)-positive E. coli strains, including isolates co-harbouring mcr-1, have been widely detected in pigs, chickens, soil and dust samples in China. In vivo murine models demonstrated that the presence of Tet(X4) led to tigecycline treatment failure. Consequently, the emergence of plasmid-mediated Tet(X4) challenges the clinical efficacy of the entire family of tetracycline antibiotics. Importantly, our study raises concern that the plasmid-mediated tigecycline resistance may further spread into various ecological niches and into clinical high-risk pathogens. Collective efforts are in urgent need to preserve the potency of these essential antibiotics.

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Fig. 1: Map of tet(X4) sampling areas in China.
Fig. 2: The activity of Tet(X4) on tetracyclines in vitro and in vivo.
Fig. 3: Characteristics of the IncQ1 tet(X4)-harbouring plasmid pLHM10-1-p6.
Fig. 4: PFGE-XbaI dendrogram and details about tet(X4)-positive E. coli isolates.

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Data availability

The whole-genome sequencing data of E. coli LHM10-1 and G3X16-2 strains have been submitted to the NCBI under the BioSample accession number SAMN11087649 and SAMN11180601, respectively. Extra data supporting the findings of this study are available from the corresponding authors on reasonable request.

References

  1. Seifert, H., Blondeau, J. & Dowzicky, M. J. In vitro activity of tigecycline and comparators (2014–2016) among key WHO ‘priority pathogens’ and longitudinal assessment (2004–2016) of antimicrobial resistance: a report from the T.E.S.T. study. Int. J. Antimicrob. Agents 52, 474–484 (2018).

    Article  CAS  Google Scholar 

  2. Gerson, S. et al. Diversity of mutations in regulatory genes of resistance-nodulation-cell division efflux pumps in association with tigecycline resistance in Acinetobacter baumannii. J. Antimicrob. Chemother. 73, 1501–1508 (2018).

    Article  CAS  Google Scholar 

  3. He, F. et al. Tigecycline resistance caused by rpsJ evolution in a 59-year-old male patient infected with KPC-producing Klebsiella pneumoniae during tigecycline treatment. Infect. Genet. Evol. 66, 188–191 (2018).

    Article  Google Scholar 

  4. Kumarasamy, K. K. et al. Emergence of a new antibiotic resistance mechanism in India, Pakistan, and the UK: a molecular, biological, and epidemiological study. Lancet Infect. Dis. 10, 597–602 (2010).

    Article  CAS  Google Scholar 

  5. Rodríguez-Baño, J., Gutiérrez-Gutiérrez, B., Machuca, I. & Pascual, A. Treatment of infections caused by extended-spectrum-beta-lactamase-, AmpC-, and carbapenemase-producing Enterobacteriaceae. Clin. Microbiol. Rev. 31, e00079-17 (2018).

    Article  Google Scholar 

  6. Liu, Y.-Y. et al. Emergence of plasmid-mediated colistin resistance mechanism MCR-1 in animals and human beings in China: a microbiological and molecular biological study. Lancet Infect. Dis. 16, 161–168 (2016).

    Article  Google Scholar 

  7. Zhang, R. et al. Evolution of tigecycline- and colistin-resistant CRKP (carbapenem-resistant Klebsiella pneumoniae) in vivo and its persistence in the GI tract. Emerg. Microbes Infect. 7, 127 (2018).

    PubMed  PubMed Central  Google Scholar 

  8. Li, X. et al. Rapid emergence of high-level tigecycline resistance in Escherichia coli strains harbouring bla NDM-5 in vivo. Int. J. Antimicrob. Agents 47, 324–327 (2016).

    Article  Google Scholar 

  9. Zhong, X. et al. First emergence of acrAB and oqxAB mediated tigecycline resistance in clinical isolates of Klebsiella pneumoniae pre-dating the use of tigecycline in a Chinese hospital. PLoS ONE 9, e115185 (2014).

    Article  Google Scholar 

  10. Chen, Y. et al. Efflux pump overexpression contributes to tigecycline heteroresistance in Salmonella enterica serovar Typhimurium. Front. Cell. Infect. Microbiol. 7, 37 (2017).

    PubMed  PubMed Central  Google Scholar 

  11. Ruzin, A., Keeney, D. & Bradford, P. A. AdeABC multidrug efflux pump is associated with decreased susceptibility to tigecycline in Acinetobacter calcoaceticus–Acinetobacter baumannii complex. J. Antimicrob. Chemother. 59, 1001–1004 (2007).

    Article  CAS  Google Scholar 

  12. Li, X. et al. Tigecycline resistance in Acinetobacter baumannii mediated by frameshift mutation in plsC, encoding 1-acyl-sn-glycerol-3-phosphate acyltransferase. Eur. J. Clin. Microbiol. Infect. Dis. 34, 625–631 (2015).

    Article  CAS  Google Scholar 

  13. Beabout, K. et al. The ribosomal S10 protein is a general target for decreased tigecycline susceptibility. Antimicrob. Agents Chemother. 59, 5561–5566 (2015).

    Article  CAS  Google Scholar 

  14. Chen, Q. et al. Decreased susceptibility to tigecycline in Acinetobacter baumannii mediated by a mutation in trm encoding SAM-dependent methyltransferase. J. Antimicrob. Chemother. 69, 72–76 (2014).

    Article  CAS  Google Scholar 

  15. Linkevicius, M., Sandegren, L. & Andersson, D. I. Potential of tetracycline resistance proteins to evolve tigecycline resistance. Antimicrob. Agents Chemother. 60, 789–796 (2016).

    Article  CAS  Google Scholar 

  16. Yao, H., Qin, S., Chen, S., Shen, J. & Du, X. D. Emergence of carbapenem-resistant hypervirulent Klebsiella pneumoniae. Lancet Infect. Dis. 18, 25 (2018).

    Article  Google Scholar 

  17. Forsberg, K. J., Patel, S., Wencewicz, T. A. & Dantas, G. The tetracycline destructases: a novel family of tetracycline-inactivating enzymes. Chem. Biol. 22, 888–897 (2015).

    Article  CAS  Google Scholar 

  18. Park, J. et al. Plasticity, dynamics, and inhibition of emerging tetracycline resistance enzymes. Nat. Chem. Biol. 13, 730–736 (2017).

    Article  CAS  Google Scholar 

  19. Moore, I. F., Hughes, D. W. & Wright, G. D. Tigecycline is modified by the flavin-dependent monooxygenase TetX. Biochemistry 44, 11829–11835 (2005).

    Article  CAS  Google Scholar 

  20. Leski, T. A. et al. Multidrug-resistant tet(X)-containing hospital isolates in Sierra Leone. Int. J. Antimicrob. Agents 42, 83–86 (2013).

    Article  CAS  Google Scholar 

  21. Deng, M. et al. Molecular epidemiology and mechanisms of tigecycline resistance in clinical isolates of Acinetobacter baumannii from a Chinese university hospital. Antimicrob. Agents Chemother. 58, 297–303 (2014).

    Article  Google Scholar 

  22. Abdallah, M. et al. Activity of eravacycline against Enterobacteriaceae and Acinetobacter baumannii, including multidrug-resistant isolates, from New York City. Antimicrob. Agents Chemother. 59, 1802–1805 (2015).

    Article  Google Scholar 

  23. Loftie-Eaton, W. & Rawlings, D. E. Diversity, biology and evolution of IncQ-family plasmids. Plasmid 67, 15–34 (2012).

    Article  CAS  Google Scholar 

  24. Hou, J. et al. Occurrence and distribution of sulfonamides, tetracyclines, quinolones, macrolides, and nitrofurans in livestock manure and amended soils of northern China. Environ. Sci. Pollut. Res. Int. 22, 4545–4554 (2015).

    Article  CAS  Google Scholar 

  25. Zhang, Q. Q., Ying, G. G., Pan, C. G., Liu, Y. S. & Zhao, J. L. Comprehensive evaluation of antibiotics emission and fate in the river basins of China: source analysis, multimedia modeling, and linkage to bacterial resistance. Environ. Sci. Technol. 49, 6772–6782 (2015).

    Article  CAS  Google Scholar 

  26. European Centre for Disease Prevention and Control (ECDC), European Food Safety Authority (EFSA) & European Medicines Agency (EMA) ECDC/EFSA/EMA second joint report on the integrated analysis of the consumption of antimicrobial agents and occurrence of antimicrobial resistance in bacteria from humans and food‐producing animals. EFSA J. 15, 4872 (2017).

  27. Wick, R. R., Judd, L. M., Gorrie, C. L. & Holt, K. E. Unicycler: resolving bacterial genome assemblies from short and long sequencing reads. PLoS Comput. Biol. 13, e1005595 (2017).

    Article  Google Scholar 

  28. Walker, B. J. et al. Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement. PLoS ONE 9, e112963 (2014).

    Article  Google Scholar 

  29. Aziz, R. K. et al. The RAST Server: rapid annotations using subsystems technology. BMC Genomics 9, 75 (2008).

    Article  Google Scholar 

  30. Carver, T., Thomson, N., Bleasby, A., Berriman, M. & Parkhill, J. DNAPlotter: circular and linear interactive genome visualization. Bioinformatics 25, 119–120 (2009).

    Article  CAS  Google Scholar 

  31. Balouiri, M., Sadiki, M. & Ibnsouda, S. K. Methods for in vitro evaluating antimicrobial activity: a review. J. Pharm. Anal. 6, 71–79 (2016).

    Article  Google Scholar 

  32. Jitkova, Y. et al. A novel formulation of tigecycline has enhanced stability and sustained antibacterial and antileukemic activity. PLoS ONE 9, e95281 (2014).

    Article  Google Scholar 

  33. Zhu, W., Clark, N. & Patel, J. B. pSK41-like plasmid is necessary for Inc18-like vanA plasmid transfer from Enterococcus faecalis to Staphylococcus aureus in vitro. Antimicrob. Agents Chemother. 57, 212–219 (2013).

    Article  CAS  Google Scholar 

  34. Sandegren, L., Linkevicius, M., Lytsy, B., Melhus, A. & Andersson, D. I. Transfer of an Escherichia coli ST131 multiresistance cassette has created a Klebsiella pneumoniae-specific plasmid associated with a major nosocomial outbreak. J. Antimicrob. Chemother. 67, 74–83 (2012).

    Article  CAS  Google Scholar 

  35. Carattoli, A. et al. Identification of plasmids by PCR-based replicon typing. J. Microbiol. Methods 63, 219–228 (2005).

    Article  CAS  Google Scholar 

  36. Johnson, T. J. et al. Expansion of the IncX plasmid family for improved identification and typing of novel plasmids in drug-resistant Enterobacteriaceae. Plasmid 68, 43–50 (2012).

    Article  CAS  Google Scholar 

  37. Lv, L. et al. Genetic characterization of IncI2 plasmids carrying bla CTX-M-55 spreading in both pets and food animals in China. Antimicrob. Agents Chemother. 57, 2824–2827 (2013).

    Article  CAS  Google Scholar 

  38. Crandon, J. L., Banevicius, M. A. & Nicolau, D. P. Pharmacodynamics of tigecycline against phenotypically diverse Staphylococcus aureus isolates in a murine thigh model. Antimicrob. Agents Chemother. 53, 1165–1169 (2009).

    Article  CAS  Google Scholar 

  39. Muralidharan, G., Micalizzi, M., Speth, J., Raible, D. & Troy, S. Pharmacokinetics of tigecycline after single and multiple doses in healthy subjects. Antimicrob. Agents Chemother. 49, 220–229 (2005).

    Article  CAS  Google Scholar 

  40. Volkers, G., Palm, G. J., Weiss, M. S., Wright, G. D. & Hinrichs, W. Structural basis for a new tetracycline resistance mechanism relying on the TetX monooxygenase. FEBS Lett. 585, 1061–1066 (2011).

    Article  CAS  Google Scholar 

  41. Kelley, L. A., Mezulis, S., Yates, C. M., Wass, M. N. & Sternberg, M. J. The Phyre2 web portal for protein modeling, prediction and analysis. Nat. Protoc. 10, 845–858 (2015).

    Article  CAS  Google Scholar 

  42. Morris, G. M. et al. AutoDock4 and AutoDockTools4: automated docking with selective receptor flexibility. J. Comput. Chem. 30, 2785–2791 (2009).

    Article  CAS  Google Scholar 

  43. Sullivan, M. J., Petty, N. K. & Beatson, S. A. Easyfig: a genome comparison visualizer. Bioinformatics 27, 1009–1010 (2011).

    Article  CAS  Google Scholar 

Download references

Acknowledgements

This work was jointly supported by the National Key Research and Development Program of China (2016YFD0501300), the Program for Innovative Research Team in the University of Ministry of Education of China (IRT_17R39), and the Foundation for Innovation and Strengthening School Project of Guangdong, China (2016KCXTD010). L.C. and B.N.K. receive support from the US National Institutes of Health grants (R21AI117338, R01AI090155 and R21AI135250).

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  1. These authors contributed equally: Jian Sun, Chong Chen.

Authors and Affiliations

  1. National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, China

    Jian Sun, Chong Chen, Chao-Yue Cui, Yan Zhang, Xiao Liu, Ze-Hua Cui, Xiao-Yu Ma, Youjun Feng, Liang-Xing Fang, Xin-Lei Lian, Rong-Min Zhang, You-Zhi Tang, Xiao-Ping Liao & Ya-Hong Liu

  2. College of Veterinary Medicine, South China Agricultural University, Guangzhou, China

    Jian Sun, Chong Chen, Chao-Yue Cui, Yan Zhang, Xiao Liu, Ze-Hua Cui, Xiao-Yu Ma, Youjun Feng, Liang-Xing Fang, Xin-Lei Lian, Rong-Min Zhang, You-Zhi Tang, Xiao-Ping Liao & Ya-Hong Liu

  3. Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, China

    You-Zhi Tang & Ya-Hong Liu

  4. Intensive Care Unit, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China

    Kou-Xing Zhang & Zhi-Hui Zhuang

  5. Intensive Care Unit, Huizhou Municipal Central Hospital, Huizhou, China

    Han-Mian Liu & Shi-Dan Zhou

  6. Department of Clinical Laboratory, The Second Affiliated Hospital of Soochow University, Suzhou, China

    Jing-Nan Lv & Hong Du

  7. Department of Laboratory Medicine, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China

    Bin Huang

  8. Department of Clinical Laboratory, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, China

    Fang-You Yu

  9. Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY, USA

    Barun Mathema

  10. Hackensack-Meridian Health Center for Discovery and Innovation, Nutley, NJ, USA

    Barry N. Kreiswirth & Liang Chen

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Contributions

J.S. and C.C. contributed equally in this study. Y.-H.L., L.C., X.-P.L. and J.S. designed the study. C.C., C.-Y.C., Y.Z., X.L., Z.-H.C., X.-Y.M., K.-X.Z., H.-M.L., Z.-H.Z., S.-D.Z., J.-N.L., H.D., B.H. and F.-Y.Y. collected the data. J.S., C.C., Y.F., L.-X.F., X.-L.L., R.-M.Z. and Y.-Z.T. analysed and interpreted the data. Y.-H.L., B.M., B.N.K., L.C., J.S., X.-P.L. and C.C. wrote the draft of the manuscript. All authors reviewed, revised and approved the final report.

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Correspondence to Xiao-Ping Liao, Liang Chen or Ya-Hong Liu.

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Sun, J., Chen, C., Cui, CY. et al. Plasmid-encoded tet(X) genes that confer high-level tigecycline resistance in Escherichia coli. Nat Microbiol 4, 1457–1464 (2019). https://doi.org/10.1038/s41564-019-0496-4

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