Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Review Article
  • Published:

Mechanisms and clinical relevance of bacterial heteroresistance

Nature Reviews Microbiology volume 17, pages 479–496 (2019)Cite this article

Subjects

Abstract

Antibiotic heteroresistance is a phenotype in which a bacterial isolate contains subpopulations of cells that show a substantial reduction in antibiotic susceptibility compared with the main population. Recent work indicates that heteroresistance is very common for several different bacterial species and antibiotic classes. The resistance phenotype is often unstable, and in the absence of antibiotic pressure it rapidly reverts to susceptibility. A common mechanistic explanation for the instability is the occurrence of genetically unstable tandem amplifications of genes that cause resistance. Due to their instability, low frequency and transient character, it is challenging to detect and study these subpopulations, which often leads to difficulties in unambiguously classifying bacteria as susceptible or resistant. Finally, in vitro experiments, mathematical modelling, animal infection models and clinical studies show that the resistant subpopulations can be enriched during antibiotic exposure, and increasing evidence suggests that heteroresistance can lead to treatment failure.

This is a preview of subscription content, access via your institution

Access options

Buy this article

  • Purchase on Springer Link
  • Instant access to full article PDF
Buy now

Prices may be subject to local taxes which are calculated during checkout

Fig. 1: Factors to consider when defining heteroresistance.
Fig. 2: Population analysis profile (PAP) test to identify heteroresistance and clinical relevance of heteroresistance.
Fig. 3: Mechanisms of heteroresistance.
Fig. 4: Gene amplifications as a cause of unstable heteroresistance.

Similar content being viewed by others

References

  1. Hughes, D. & Andersson, D. I. Environmental and genetic modulation of the phenotypic expression of antibiotic resistance. FEMS Microbiol. Rev. 41, 374–391 (2017).

    CAS  PubMed  PubMed Central  Google Scholar 

  2. El-Halfawy, O. M. & Valvano, M. A. Antimicrobial heteroresistance: an emerging field in need of clarity. Clin. Microbiol. Rev. 28, 191–207 (2015). A comprehensive and clarifying review of heteroresistance in bacteria.

    CAS  PubMed  PubMed Central  Google Scholar 

  3. Alexander, H. E. & Leidy, G. Mode of action of streptomycin on type b Haemophilus influenzae: I. Origin of resistant organisms. J. Exp. Med. 85, 329–338 (1947).

    CAS  PubMed  PubMed Central  Google Scholar 

  4. Devi, Y., P. M., P., Thomas, S. & Veeraraghavan, B. Challenges in the laboratory diagnosis and clinical management of heteroresistant vancomycin Staphylococcus aureus (hVISA). Clin. Microbiol. 4, 214 (2015).

    Google Scholar 

  5. Zheng, C. et al. Mixed infections and rifampin heteroresistance among Mycobacterium tuberculosis clinical isolates. J. Clin. Microbiol. 53, 2138–2147 (2015).

    CAS  PubMed  PubMed Central  Google Scholar 

  6. Mascellino, M. T., Porowska, B., De Angelis, M. & Oliva, A. Antibiotic susceptibility, heteroresistance, and updated treatment strategies in Helicobacter pylori infection. Drug Des. Devel. Ther. 11, 2209–2220 (2017).

    CAS  PubMed  PubMed Central  Google Scholar 

  7. Canetti, G., Rist, N. & Grosset, J. Measurement of sensitivity of the tuberculous bacillus to antibacillary drugs by the method of proportions. Methodology, resistance criteria, results and interpretation [French]. Rev. Tuberc. Pneumol. 27, 217–272 (2015).

    Google Scholar 

  8. Barin, J., Martins, A. F., Heineck, B. L., Barth, A. L. & Zavascki, A. P. Hetero- and adaptive resistance to polymyxin B in OXA-23-producing carbapenem-resistant Acinetobacter baumannii isolates. Ann. Clin. Microbiol. Antimicrob. 12, 15 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  9. da Silva, A. E. B., Martins, A. F., Nodari, C. S., Magagnin, C. M. & Barth, A. L. Carbapenem-heteroresistance among isolates of the Enterobacter cloacae complex: is it a real concern? Eur. J. Clin. Microbiol. Infect. Dis. 37, 185–186 (2018).

    PubMed  Google Scholar 

  10. Oikonomou, O., Panopoulou, M. & Ikonomidis, A. Investigation of carbapenem heteroresistance among different sequence types of Pseudomonas aeruginosa clinical isolates reveals further diversity. J. Med. Microbiol. 60, 1556–1558 (2011).

    PubMed  Google Scholar 

  11. Hermes, D. M. et al. Evaluation of heteroresistance to polymyxin B among carbapenem-susceptible and -resistant Pseudomonas aeruginosa. J. Med. Microbiol. 62, 1184–1189 (2013).

    PubMed  Google Scholar 

  12. Pournaras, S. et al. Characteristics of meropenem heteroresistance in Klebsiella pneumoniae carbapenemase (KPC)-producing clinical Isolates of K. pneumoniae. J. Clin. Microbiol. 48, 2601–2604 (2010).

    CAS  PubMed  PubMed Central  Google Scholar 

  13. Nicoloff, H., Hjort, K., Levin, B. R. & Andersson, D. I. The high prevalence of antibiotic heteroresistance in pathogenic bacteria is mainly caused by gene amplification. Nat. Microbiol. 4, 504–514 (2019). A comprehensive analysis of heteroresistance in four Gram-negative species that demonstrates that more than one quarter of all species–antibiotic combinations show heteroresistance and that it is mainly caused by gene amplification.

    PubMed  Google Scholar 

  14. Hernan, R. C. et al. Selection of colistin-resistant Acinetobacter baumannii isolates in postneurosurgical meningitis in an intensive care unit with high presence of heteroresistance to colistin. Diagn. Microbiol. Infect. Dis. 65, 188–191 (2009).

    PubMed  Google Scholar 

  15. Mei, S., Gao, Y., Zhu, C., Dong, C. & Chen, Y. Research of the heteroresistance of Pseudomonas aeruginosa to imipenem. Int. J. Clin. Exp. Med. 8, 6129–6132 (2015).

    CAS  PubMed  PubMed Central  Google Scholar 

  16. Wong, S. S. Y., Ho, P. L., Woo, P. C. Y. & Yuen, K. Y. Bacteremia caused by Staphylococci with inducible vancomycin heteroresistance. Clin. Infect. Dis. 29, 760–767 (1999).

    CAS  PubMed  Google Scholar 

  17. Bardet, L. et al. Deciphering heteroresistance to colistin in a Klebsiella pneumoniae isolate from Marseille, France. Antimicrob. Agents Chemother. 61, e00356-17 (2017).

    PubMed  PubMed Central  Google Scholar 

  18. Lucas, A. E. et al. Frequency and mechanisms of spontaneous fosfomycin nonsusceptibility observed upon disk diffusion testing of Escherichia coli. J. Clin. Microbiol. 56, e01368-17 (2018).

    CAS  PubMed  Google Scholar 

  19. Plipat, N., Livni, G., Bertram, H. & Thomson, R. B. Unstable vancomycin heteroresistance is common among clinical isolates of methiciliin-resistant Staphylococcus aureus. J. Clin. Microbiol. 43, 2494–2496 (2005).

    CAS  PubMed  PubMed Central  Google Scholar 

  20. Anderson, S. E., Sherman, E. X., Weiss, D. S. & Rather, P. N. Aminoglycoside heteroresistance in Acinetobacter baumannii AB5075. mSphere 3, e00271-18 (2018). A study that demonstrates the importance of gene amplification in heteroresistance.

    CAS  PubMed  PubMed Central  Google Scholar 

  21. Trauner, A. et al. The within-host population dynamics of Mycobacterium tuberculosis vary with treatment efficacy. Genome Biol. 18, 71 (2017).

    PubMed  PubMed Central  Google Scholar 

  22. Lieberman, T. D. et al. Genomic diversity in autopsy samples reveals within-host dissemination of HIV-associated Mycobacterium tuberculosis. Nat. Med. 22, 1470–1474 (2016).

    CAS  PubMed  PubMed Central  Google Scholar 

  23. Drlica, K., Shopsin, B. & Zhao, X. in Antimicrobial Resistance in the 21st Century (eds Fong, I. W., Shlaes, D. & Drlica, K.) 269–296 (Springer, 2018).

  24. Sun, L. et al. Droplet Digital PCR detection of Helicobacter pylori clarithromycin resistance reveals frequent heteroresistance. J. Clin. Microbiol. 56, e00019-18 (2018).

    CAS  PubMed  PubMed Central  Google Scholar 

  25. Colman, R. E. et al. Detection of low-level mixed-population drug resistance in Mycobacterium tuberculosis using high fidelity amplicon sequencing. PLOS ONE 10, e0126626 (2015).

    PubMed  PubMed Central  Google Scholar 

  26. Sanchez-Romero, M. A. & Casadesus, J. Contribution of phenotypic heterogeneity to adaptive antibiotic resistance. Proc. Natl Acad. Sci. USA 111, 355–360 (2014).

    PubMed  Google Scholar 

  27. Balaban, N. Persistence: mechanisms for triggering and enhancing phenotypic variability. Curr. Opin. Genet. Dev. 21, 768–775 (2011).

    CAS  PubMed  Google Scholar 

  28. Brauner, A., Fridman, O., Gefen, O. & Balaban, N. Q. Distinguishing between resistance, tolerance and persistence to antibiotic treatment. Nat. Rev. Microbiol. 14, 320–330 (2016).

    CAS  PubMed  Google Scholar 

  29. Cannatelli, A. et al. MgrB inactivation is a common mechanism of colistin resistance in KPC carbapenemase-producing Klebsiella pneumoniae of clinical origin. Antimicrob. Agents Chemother. 58, 5696–5703 (2014).

    PubMed  PubMed Central  Google Scholar 

  30. Machado, D. et al. Contribution of efflux to colistin heteroresistance in a multidrug resistant Acinetobacter baumannii clinical isolate. J. Med. Microbiol. 67, 740–749 (2018).

    PubMed  Google Scholar 

  31. He, J. et al. Heteroresistance to carbapenems in invasive Pseudomonas aeruginosa infections. Int. J. Antimicrob. Agents 51, 413–421 (2018).

    CAS  PubMed  Google Scholar 

  32. Ikonomidis, A. et al. Efflux system overexpression and decreased OprD contribute to the carbapenem heterogeneity in Pseudomonas aeruginosa. FEMS Microbiol. Lett. 279, 36–39 (2008).

    CAS  PubMed  Google Scholar 

  33. Lee, H.-Y. et al. Imipenem heteroresistance induced by imipenem in multidrug-resistant Acinetobacter baumannii: mechanism and clinical implications. Int. J. Antimicrob. Agents 37, 302–308 (2011).

    CAS  PubMed  Google Scholar 

  34. Fernández Cuenca, F. et al. Prevalence and analysis of microbiological factors associated with phenotypic heterogeneous resistance to carbapenems in Acinetobacter baumannii. Int. J. Antimicrob. Agents 39, 472–477 (2012).

    PubMed  Google Scholar 

  35. Hjort, K., Nicoloff, H. & Andersson, D. I. Unstable tandem gene amplification generates heteroresistance (variation in resistance within a population) to colistin in Salmonella enterica. Mol. Microbiol. 102, 274–289 (2016). The first demonstration that heteroresistance can be caused by unstable gene amplifications.

    CAS  PubMed  Google Scholar 

  36. Jayol, A., Nordmann, P., Brink, A. & Poirel, L. Heteroresistance to colistin in Klebsiella pneumoniae associated with alterations in the PhoPQ regulatory system. Antimicrob. Agents Chemother. 59, 2780–2784 (2015).

    CAS  PubMed  PubMed Central  Google Scholar 

  37. Halaby, T. et al. Genomic characterization of colistin heteroresistance in Klebsiella pneumoniae during a nosocomial outbreak. Antimicrob. Agents Chemother. 60, 6837–6843 (2016).

    CAS  PubMed  PubMed Central  Google Scholar 

  38. Landman, D., Salamera, J. & Quale, J. Irreproducible and uninterpretable polymyxin B MICs for Enterobacter cloacae and Enterobacter aerogenes. J. Clin. Microbiol. 51, 4106–4111 (2013).

    PubMed  PubMed Central  Google Scholar 

  39. Engel, H. et al. Heteroresistance to fosfomycin is predominant in Streptococcus pneumoniae and depends on the murA1 gene. Antimicrob. Agents Chemother. 57, 2801–2808 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  40. Higgins, P. G., Schneiders, T., Hamprecht, A. & Seifert, H. In vivo selection of a missense mutation in adeR and conversion of the novel blaOXA-164 gene into blaOXA-58 in carbapenem-resistant Acinetobacter baumannii isolates from a hospitalized patient. Antimicrob. Agents Chemother. 54, 5021–5027 (2010).

    CAS  PubMed  PubMed Central  Google Scholar 

  41. 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 

  42. Zheng, J. et al. Overexpression of OqxAB and MacAB efflux pumps contributes to eravacycline resistance and heteroresistance in clinical isolates of Klebsiella pneumoniae. Emerg. Microbes Infect. 7, 139 (2018).

    PubMed  PubMed Central  Google Scholar 

  43. Thulin, E., Sundqvist, M. & Andersson, D. I. Amdinocillin (mecillinam) resistance mutations in clinical isolates and laboratory-selected mutants of Escherichia coli. Antimicrob. Agents Chemother. 59, 1718–1727 (2015).

    PubMed  PubMed Central  Google Scholar 

  44. Reams, A. B., Kofoid, E., Savageau, M. & Roth, J. R. Duplication frequency in a population of Salmonella enterica rapidly approaches steady state with or without recombination. Genetics 184, 1077–1094 (2010).

    CAS  PubMed  PubMed Central  Google Scholar 

  45. Anderson, P. & Roth, J. Spontaneous tandem genetic duplications in Salmonella typhimurium arise by unequal recombination between rRNA (rrn) cistrons. Proc. Natl Acad. Sci. USA 78, 3113–3117 (1981).

    CAS  PubMed  Google Scholar 

  46. Pettersson, M. E., Sun, S., Andersson, D. I. & Berg, O. G. Evolution of new gene functions: simulation and analysis of the amplification model. Genetica 135, 309–324 (2009).

    CAS  PubMed  Google Scholar 

  47. Reams, A. B. & Roth, J. R. Mechanisms of gene duplication and amplification. Cold Spring Harb. Perspect. Biol. 7, a016592 (2015).

    PubMed  PubMed Central  Google Scholar 

  48. Sandegren, L. & Andersson, D. I. Bacterial gene amplification: implications for the evolution of antibiotic resistance. Nat. Rev. Microbiol. 7, 578–588 (2009).

    CAS  PubMed  Google Scholar 

  49. Adler, M., Anjum, M., Berg, O. G., Andersson, D. I. & Sandegren, L. High fitness costs and instability of gene duplications reduce rates of evolution of new genes by duplication-divergence mechanisms. Mol. Biol. Evol. 31, 1526–1535 (2014).

    CAS  PubMed  Google Scholar 

  50. Schechter, L. M. et al. Extensive gene amplification as a mechanism for piperacillin-tazobactam resistance in Escherichia coli. mBio 9, e00583-18 (2018).

    CAS  PubMed  PubMed Central  Google Scholar 

  51. Engel, H. et al. A low-affinity penicillin-binding protein 2x variant is required for heteroresistance in Streptococcus pneumoniae. Antimicrob. Agents Chemother. 58, 3934–3941 (2014).

    PubMed  PubMed Central  Google Scholar 

  52. Hooper, D. C. & Jacoby, G. A. Mechanisms of drug resistance: quinolone resistance. Ann. N. Y. Acad. Sci. 1354, 12–31 (2015).

    CAS  PubMed  PubMed Central  Google Scholar 

  53. Goldstein, B. P. Resistance to rifampicin: a review. J. Antibiot. 67, 625–630 (2014).

    CAS  PubMed  Google Scholar 

  54. Lo-Ten-Foe, J. R., de Smet, A. M. G. A., Diederen, B. M. W., Kluytmans, J. A. J. W. & van Keulen, P. H. J. Comparative evaluation of the VITEK 2, disk diffusion, etest, broth microdilution, and agar dilution susceptibility testing methods for colistin in clinical isolates, including heteroresistant Enterobacter cloacae and Acinetobacter baumannii. Antimicrob. Agents Chemother. 51, 3726–3730 (2007).

    CAS  PubMed  PubMed Central  Google Scholar 

  55. van Hal, S. J. et al. Performance of various testing methodologies for detection of heteroresistant vancomycin-intermediate Staphylococcus aureus in bloodstream isolates. J. Clin. Microbiol. 49, 1489–1494 (2011).

    PubMed  PubMed Central  Google Scholar 

  56. Udekwu, K. I., Parrish, N., Ankomah, P., Baquero, F. & Levin, B. R. Functional relationship between bacterial cell density and the efficacy of antibiotics. J. Antimicrob. Chemother. 63, 745–757 (2009).

    CAS  PubMed  PubMed Central  Google Scholar 

  57. Sautrey, G., Duval, R. E., Chevalley, A., Fontanay, S. & Clarot, I. Capillary electrophoresis for fast detection of heterogeneous population in colistin-resistant Gram-negative bacteria. Electrophoresis 36, 2630–2633 (2015).

    CAS  PubMed  Google Scholar 

  58. Jayol, A. et al. Evaluation of the rapid polymyxin NP test and its industrial version for the detection of polymyxin-resistant Enterobacteriaceae. Diagn. Microbiol. Infect. Dis. 92, 90–94 (2018).

    CAS  PubMed  Google Scholar 

  59. Asakura, K. et al. Rapid and easy detection of low-level resistance to vancomycin in methicillin-resistant Staphylococcus aureus by matrix-assisted laser desorption ionization time-of-flight mass spectrometry. PLOS ONE 13, e0194212 (2018).

    PubMed  PubMed Central  Google Scholar 

  60. Price, C. S., Kon, S. E. & Metzger, S. Rapid antibiotic susceptibility phenotypic characterization of Staphylococcus aureus using automated microscopy of small numbers of cells. J. Microbiol. Methods 98, 50–58 (2014).

    CAS  PubMed  Google Scholar 

  61. Entenza, J. M. et al. Rapid detection of Staphylococcus aureus strains with reduced susceptibility to vancomycin by isothermal microcalorimetry. J. Clin. Microbiol. 52, 180–186 (2014).

    CAS  PubMed  PubMed Central  Google Scholar 

  62. Bradley, P. et al. Rapid antibiotic-resistance predictions from genome sequence data for Staphylococcus aureus and Mycobacterium tuberculosis. Nat. Commun. 6, 10063 (2015).

    CAS  PubMed  PubMed Central  Google Scholar 

  63. Pankhurst, L. J. et al. Rapid, comprehensive, and affordable mycobacterial diagnosis with whole-genome sequencing: a prospective study. Lancet Respir. Med. 4, 49–58 (2016).

    CAS  PubMed  PubMed Central  Google Scholar 

  64. Operario, D. J. et al. Prevalence and extent of heteroresistance by next generation sequencing of multidrug-resistant tuberculosis. PLOS ONE 12, e0176522 (2017).

    PubMed  PubMed Central  Google Scholar 

  65. Nunes, A. P. F. et al. Heterogeneous resistance to vancomycin and teicoplanin among Staphylococcus spp. isolated from bacteremia. Braz. J. Infect. Dis. 11, 345–350 (2007).

    CAS  PubMed  Google Scholar 

  66. Juhász, E., Iván, M., Pintér, E., Pongrácz, J. & Kristóf, K. Colistin resistance among blood culture isolates at a tertiary care centre in Hungary. J. Glob. Antimicrob. Resist. 11, 167–170 (2017).

    PubMed  Google Scholar 

  67. Zhang, S., Sun, X., Chang, W., Dai, Y. & Ma, X. Systematic review and meta-analysis of the epidemiology of vancomycin-intermediate and heterogeneous vancomycin-intermediate Staphylococcus aureus isolates. PLOS ONE 10, e0136082 (2015).

    PubMed  PubMed Central  Google Scholar 

  68. Park, Y. J. et al. Screening method for detecting staphylococci with reduced susceptibility to teicoplanin. J. Microbiol. Methods 40, 193–198 (2000).

    CAS  PubMed  Google Scholar 

  69. Tevell, S., Claesson, C., Hellmark, B., Söderquist, B. & Nilsdotter-Augustinsson, Å. Heterogeneous glycopeptide intermediate Staphylococcus epidermidis isolated from prosthetic joint infections. Eur. J. Clin. Microbiol. Infect. Dis. 33, 911–917 (2014).

    CAS  PubMed  Google Scholar 

  70. Chung, M. et al. Heterogeneous oxacillin-resistant phenotypes and production of PBP2A by oxacillin-susceptible/mecA-positive MRSA strains from Africa. J. Antimicrob. Chemother. 71, 2804–2809 (2016).

    CAS  PubMed  PubMed Central  Google Scholar 

  71. Frebourg, N. B., Nouet, D., Lemée, L., Martin, E. & Lemeland, J. F. Comparison of ATB staph, rapid ATB staph, Vitek, and E-test methods for detection of oxacillin heteroresistance in staphylococci possessing mecA. J. Clin. Microbiol. 36, 52–57 (1998).

    CAS  PubMed  PubMed Central  Google Scholar 

  72. Okado, J. B., Avaca-Crusca, J. S., Oliveira, A. L., Dabul, A. N. G. & Camargo, I. L. B. Daptomycin and vancomycin heteroresistance revealed among CC5-SCCmecII MRSA clone and in vitro evaluation of treatment alternatives. J. Glob. Antimicrob. Resist. 14, 209–216 (2018).

    PubMed  Google Scholar 

  73. Sakoulas, G., Alder, J., Thauvin-Eliopoulos, C., Moellering, R. C. & Eliopoulos, G. M. Induction of daptomycin heterogeneous susceptibility in Staphylococcus aureus by exposure to vancomycin. Antimicrob. Agents Chemother. 50, 1581–1585 (2006).

    CAS  PubMed  PubMed Central  Google Scholar 

  74. Saravolatz, S. N., Martin, H., Pawlak, J., Johnson, L. B. & Saravolatz, L. D. Ceftaroline-heteroresistant Staphylococcus aureus. Antimicrob. Agents Chemother. 58, 3133–3136 (2014).

    PubMed  PubMed Central  Google Scholar 

  75. Coelho, C., de Lencastre, H. & Aires-de-Sousa, M. Frequent occurrence of trimethoprim-sulfamethoxazole hetero-resistant Staphylococcus aureus isolates in different African countries. Eur. J. Clin. Microbiol. Infect. Dis. 36, 1243–1252 (2017).

    CAS  PubMed  Google Scholar 

  76. Poudyal, A. et al. In vitro pharmacodynamics of colistin against multidrug-resistant Klebsiella pneumoniae. J. Antimicrob. Chemother. 62, 1311–1318 (2008).

    CAS  PubMed  Google Scholar 

  77. Meletis, G., Tzampaz, E., Sianou, E., Tzavaras, I. & Sofianou, D. Colistin heteroresistance in carbapenemase-producing Klebsiella pneumoniae. J. Antimicrob. Chemother. 66, 946–947 (2011).

    CAS  PubMed  Google Scholar 

  78. Yau, W. et al. Colistin hetero-resistance in multidrug-resistant Acinetobacter baumannii clinical isolates from the Western Pacific region in the SENTRY antimicrobial surveillance programme. J. Infect. 58, 138–144 (2009).

    PubMed  Google Scholar 

  79. Guérin, F. et al. Cluster-dependent colistin hetero-resistance in Enterobacter cloacae complex. J. Antimicrob. Chemother. 71, 3058–3061 (2016).

    PubMed  Google Scholar 

  80. Cai, Y., Chai, D., Wang, R., Liang, B. & Bai, N. Colistin resistance of Acinetobacter baumannii: clinical reports, mechanisms and antimicrobial strategies. J. Antimicrob. Chemother. 67, 1607–1615 (2012).

    CAS  PubMed  Google Scholar 

  81. Walsh, C. C., McIntosh, M. P., Peleg, A. Y., Kirkpatrick, C. M. & Bergen, P. J. In vitro pharmacodynamics of fosfomycin against clinical isolates of Pseudomonas aeruginosa. J. Antimicrob. Chemother. 70, 3042–3050 (2015).

    CAS  PubMed  Google Scholar 

  82. Kaase, M., Szabados, F., Anders, A. & Gatermann, S. G. Fosfomycin susceptibility in carbapenem-resistant Enterobacteriaceae from Germany. J. Clin. Microbiol. 52, 1893–1897 (2014).

    CAS  PubMed  PubMed Central  Google Scholar 

  83. Ma, W., Sun, J., Yang, S. & Zhang, L. Epidemiological and clinical features for cefepime heteroresistant Escherichia coli infections in Southwest China. Eur. J. Clin. Microbiol. Infect. Dis. 35, 571–578 (2016).

    CAS  PubMed  Google Scholar 

  84. Savini, V. et al. Misidentification of ampicillin-sulbactam heteroresistance in Acinetobacter baumannii strains from ICU patients. J. Infect. 58, 316–317 (2009).

    PubMed  Google Scholar 

  85. Pelaez, T. et al. Metronidazole resistance in Clostridium difficile is heterogeneous. J. Clin. Microbiol. 46, 3028–3032 (2008).

    CAS  PubMed  PubMed Central  Google Scholar 

  86. Huang, H. et al. Antimicrobial susceptibility and heteroresistance in Chinese Clostridium difficile strains. Anaerobe 16, 633–635 (2010).

    CAS  PubMed  Google Scholar 

  87. Álvarez-Pérez, S., Blanco, J. L., Harmanus, C., Kuijper, E. & García, M. E. Subtyping and antimicrobial susceptibility of Clostridium difficile PCR ribotype 078/126 isolates of human and animal origin. Vet. Microbiol. 199, 15–22 (2017).

    PubMed  Google Scholar 

  88. Sun, J. D. et al. Impact of carbapenem heteroresistance among clinical isolates of invasive Escherichia coli in Chongqing, southwestern China. Clin. Microbiol. Infect. 21, 469.e1–469.e10 (2015).

    CAS  Google Scholar 

  89. Kang, C. K. et al. agr functionality affects clinical outcomes in patients with persistent methicillin-resistant Staphylococcus aureus bacteraemia. Eur. J. Clin. Microbiol. Infect. Dis. 36, 2187–2191 (2017).

    CAS  PubMed  Google Scholar 

  90. Park, K. H. et al. Comparison of the clinical features, bacterial genotypes and outcomes of patients with bacteraemia due to heteroresistant vancomycin-intermediate Staphylococcus aureus and vancomycin-susceptible S. aureus. J. Antimicrob. Chemother. 67, 1843–1849 (2012).

    CAS  PubMed  Google Scholar 

  91. Maor, Y. et al. Clinical features of heteroresistant vancomycin-intermediate Staphylococcus aureus bacteremia versus those of methicillin-resistant S. aureus bacteremia. J. Infect. Dis. 199, 619–624 (2009).

    PubMed  Google Scholar 

  92. Charles, P. G., Ward, P. B., Johnson, P. D., Howden, B. P. & Grayson, M. L. Clinical features associated with bacteremia due to heterogeneous vancomycin-intermediate Staphylococcus aureus. Clin. Infect. Dis. 38, 448–451 (2004).

    PubMed  Google Scholar 

  93. Casapao, A. M. et al. Evaluation of vancomycin population susceptibility analysis profile as a predictor of outcomes for patients with infective endocarditis due to methicillin-resistant Staphylococcus aureus. Antimicrob. Agents Chemother. 58, 4636–4641 (2014).

    PubMed  PubMed Central  Google Scholar 

  94. Claeys, K. C. et al. Pneumonia caused by methicillin-resistant Staphylococcus aureus: Does vancomycin heteroresistance matter? Antimicrob. Agents Chemother. 60, 1708–1716 (2016).

    CAS  PubMed  PubMed Central  Google Scholar 

  95. van Hal, S. J., Jones, M., Gosbell, I. B. & Paterson, D. L. Vancomycin heteroresistance is associated with reduced mortality in ST239 methicillin-resistant Staphylococcus aureus blood stream infections. PLOS ONE 6, e21217 (2011).

    PubMed  PubMed Central  Google Scholar 

  96. Fernández-Cuenca, F. et al. Epidemiological and clinical features associated with colonisation/infection by Acinetobacter baumannii with phenotypic heterogeneous resistance to carbapenems. Int. J. Antimicrob. Agents 40, 235–238 (2012).

    PubMed  Google Scholar 

  97. Di Gregorio, S. et al. Clinical, microbiological, and genetic characteristics of heteroresistant vancomycin-intermediate Staphylococcus aureus bacteremia in a teaching hospital. Microb. Drug Resist. 21, 25–34 (2015).

    PubMed  PubMed Central  Google Scholar 

  98. Moosavian, M. et al. Post neurosurgical meningitis due to colistin heteroresistant Acinetobacter baumannii. Jundishapur J. Microbiol. 7, e12287 (2014).

    PubMed  PubMed Central  Google Scholar 

  99. Sieradzki, K., Roberts, R. B., Serur, D., Hargrave, J. & Tomasz, A. Heterogeneously vancomycin-resistant Staphylococcus epidermidis strain causing recurrent peritonitis in a dialysis patient during vancomycin therapy. J. Clin. Microbiol. 37, 39–44 (1999).

    CAS  PubMed  PubMed Central  Google Scholar 

  100. Rodríguez, C. H. et al. Impact of heteroresistance to colistin in meningitis caused by Acinetobacter baumannii. J. Infect. 64, 119–121 (2012).

    PubMed  Google Scholar 

  101. Srinivas, P. et al. Detection of colistin heteroresistance in Acinetobacter baumannii from blood and respiratory isolates. Diagn. Microbiol. Infect. Dis. 91, 194–198 (2018).

    CAS  PubMed  Google Scholar 

  102. Hiramatsu, K. et al. Dissemination in Japanese hospitals of strains of Staphylococcus aureus heterogeneously resistant to vancomycin. Lancet 350, 1670–1673 (1997).

    CAS  PubMed  Google Scholar 

  103. Wootton, M. et al. A modified population analysis profile (PAP) method to detect hetero-resistance to vancomycin in Staphylococcus aureus in a UK hospital. J. Antimicrob. Chemother. 47, 399–403 (2001).

    CAS  PubMed  Google Scholar 

  104. Band, V. I. et al. Antibiotic failure mediated by a resistant subpopulation in Enterobacter cloacae. Nat. Microbiol. 1, 16053 (2016). An important study demonstrating the ability of low-frequency bacterial subpopulations to contribute to clinically relevant colistin resistance.

    CAS  PubMed  PubMed Central  Google Scholar 

  105. Band, V. I. et al. Carbapenem-resistant Klebsiella pneumoniae exhibiting clinically undetected colistin heteroresistance leads to treatment failure in a murine model of infection. mBio 9, e02448-17 (2018). The first report of colistin-heteroresistant K. pneumoniae in the United States and a demonstration of how such isolates can lead to treatment failure in an in vivo model of infection.

    CAS  PubMed  PubMed Central  Google Scholar 

  106. Vaudaux, P., Francois, P., Berger-Bächi, B. & Lew, D. P. In vivo emergence of subpopulations expressing teicoplanin or vancomycin resistance phenotypes in a glycopeptide-susceptible, methicillin-resistant strain of Staphylococcus aureus. J. Antimicrob. Chemother. 47, 163–170 (2001).

    CAS  PubMed  Google Scholar 

  107. Napier, B. A. et al. Clinical use of colistin induces cross-resistance to host antimicrobials in Acinetobacter baumannii. mBio 4, e00021-13 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  108. Lippa, A. M. & Goulian, M. Feedback inhibition in the PhoQ/PhoP signaling system by a membrane peptide. PLOS Genet. 5, e1000788 (2009).

    PubMed  PubMed Central  Google Scholar 

  109. Cannatelli, A. et al. In vivo emergence of colistin resistance in Klebsiella pneumoniae producing KPC-type carbapenemases mediated by insertional inactivation of the PhoQ/PhoP mgrB regulator. Antimicrob. Agents Chemother. 57, 5521–5526 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  110. Moore, M. R., Perdreau-Remington, F. & Chambers, H. F. Vancomycin treatment failure associated with heterogeneous vancomycin-intermediate Staphylococcus aureus in a patient with endocarditis and in the rabbit model of endocarditis. Antimicrob. Agents Chemother. 47, 1262–1266 (2003).

    CAS  PubMed  PubMed Central  Google Scholar 

  111. Tan, C.-H., Li, J. & Nation, R. L. Activity of colistin against heteroresistant Acinetobacter baumannii and emergence of resistance in an in vitro pharmacokinetic/pharmacodynamic model. Antimicrob. Agents Chemother. 51, 3413–3415 (2007).

    CAS  PubMed  PubMed Central  Google Scholar 

  112. Baltekin, Ö., Boucharin, A., Tano, E., Andersson, D. I. & Elf, J. Antibiotic susceptibility testing in less than 30 min using direct single-cell imaging. Proc. Natl Acad. Sci. USA 114, 9170–9175 (2017).

    CAS  PubMed  Google Scholar 

  113. Creely, D. et al. International dissemination of Escherichia coli strains with discrepant behaviour in phenotypic antimicrobial susceptibility tests. Eur. J. Clin. Microbiol. Infect. Dis. 32, 997–1002 (2013).

    CAS  PubMed  Google Scholar 

  114. Shubert, C. et al. Population analysis of Escherichia coli isolates with discordant resistance levels by piperacillin-tazobactam broth microdilution and agar dilution testing. Antimicrob. Agents Chemother. 58, 1779–1781 (2014).

    PubMed  PubMed Central  Google Scholar 

  115. Ballestero-Téllez, M. et al. Role of inoculum and mutant frequency on fosfomycin MIC discrepancies by agar dilution and broth microdilution methods in Enterobacteriaceae. Clin. Microbiol. Infect. 23, 325–331 (2017).

    PubMed  Google Scholar 

  116. Tato, M. et al. Carbapenem heteroresistance in VIM-1-producing Klebsiella pneumoniae isolates belonging to the same clone: consequences for routine susceptibility testing. J. Clin. Microbiol. 48, 4089–4093 (2010).

    CAS  PubMed  PubMed Central  Google Scholar 

  117. Hung, K.-H., Wang, M.-C., Huang, A.-H., Yan, J.-J. & Wu, J.-J. Heteroresistance to cephalosporins and penicillins in Acinetobacter baumannii. J. Clin. Microbiol. 50, 721–726 (2012).

    CAS  PubMed  PubMed Central  Google Scholar 

  118. Sun, S., Berg, O. G., Roth, J. R. & Andersson, D. I. Contribution of gene amplification to evolution of increased antibiotic resistance in Salmonella typhimurium. Genetics 182, 1183–1195 (2009).

    CAS  PubMed  PubMed Central  Google Scholar 

  119. Li, J. et al. Heteroresistance to colistin in multidrug-resistant Acinetobacter baumannii. Antimicrob. Agents Chemother. 50, 2946–2950 (2006).

    CAS  PubMed  PubMed Central  Google Scholar 

  120. Hawley, J. S., Murray, C. K. & Jorgensen, J. H. Colistin heteroresistance in acinetobacter and its association with previous colistin therapy. Antimicrob. Agents Chemother. 52, 351–352 (2008).

    CAS  PubMed  Google Scholar 

  121. Cherkaoui, A. et al. Imipenem heteroresistance in nontypeable Haemophilus influenzae is linked to a combination of altered PBP3, slow drug influx and direct efflux regulation. Clin. Microbiol. Infect. 23, 118.e9–118.e19 (2017).

    CAS  Google Scholar 

  122. Pournaras, S. et al. Characterization of clinical isolates of Pseudomonas aeruginosa heterogeneously resistant to carbapenems. J. Med. Microbiol. 56, 66–70 (2007).

    CAS  PubMed  Google Scholar 

  123. Pfeltz, R. F., Schmidt, J. L. & Wilkinson, B. J. A microdilution plating method for population analysis of antibiotic-resistant Staphylococci. Microb. Drug Resist. 7, 289–295 (2001).

    CAS  PubMed  Google Scholar 

  124. Leonard, S. N., Rossi, K. L., Newton, K. L. & Rybak, M. J. Evaluation of the Etest GRD for the detection of Staphylococcus aureus with reduced susceptibility to glycopeptides. J. Antimicrob. Chemother. 63, 489–492 (2009).

    CAS  PubMed  Google Scholar 

  125. Satola, S. W., Farley, M. M., Anderson, K. F. & Patel, J. B. Comparison of detection methods for heteroresistant vancomycin-intermediate Staphylococcus aureus, with the population analysis profile method as the reference method. J. Clin. Microbiol. 49, 177–183 (2011).

    PubMed  Google Scholar 

  126. Silveira, A., Cunha, D., Caierão, G. R., Cordova, D. & Azevedo, C. Evaluation of the accuracy of phenotypic methods for the detection of heteroresistant vancomycin-intermediate Staphylococcus aureus (hVISA). JSM Microbiol. 4, 1031 (2016).

    Google Scholar 

  127. Gordon, N. C. & Wareham, D. W. Failure of the MicroScan WalkAway system to detect heteroresistance to carbapenems in a patient with Enterobacter aerogenes bacteremia. J. Clin. Microbiol. 47, 3024–3025 (2009).

    CAS  PubMed  PubMed Central  Google Scholar 

  128. Zhang, Z., Wang, Y., Pang, Y. & Liu, C. Comparison of different drug susceptibility test methods to detect rifampin heteroresistance in Mycobacterium tuberculosis. Antimicrob. Agents Chemother. 58, 5632–5635 (2014).

    PubMed  PubMed Central  Google Scholar 

  129. Zhang, Z., Lu, J., Wang, Y., Pang, Y. & Zhao, Y. Automated liquid culture system misses isoniazid heteroresistance in Mycobacterium tuberculosis isolates with mutations in the promoter region of the inhA gene. Eur. J. Clin. Microbiol. Infect. Dis. 34, 555–560 (2015).

    CAS  PubMed  Google Scholar 

  130. Nikolayevskyy, V. et al. Performance of the Genotype® MTBDRPlus assay in the diagnosis of tuberculosis and drug resistance in Samara, Russian Federation. BMC Clin. Pathol. 9, 2 (2009).

    PubMed  PubMed Central  Google Scholar 

  131. Rinder, H., Mieskes, K. T. & Löscher, T. Heteroresistance in Mycobacterium tuberculosis. Int. J. Tuberc. Lung Dis. 5, 339–345 (2001).

    CAS  PubMed  Google Scholar 

  132. Chakravorty, S. et al. The Nnew Xpert MTB/RIF Ultra: improving detection of Mycobacterium tuberculosis and resistance to rifampin in an assay suitable for point-of-care testing. mBio 8, e00812-17 (2017).

    PubMed  PubMed Central  Google Scholar 

  133. Driesen, M. et al. Evaluation of a novel line probe assay to detect resistance to pyrazinamide, a key drug used for tuberculosis treatment. Clin. Microbiol. Infect. 24, 60–64 (2018).

    CAS  PubMed  PubMed Central  Google Scholar 

  134. Hofmann-Thiel, S. et al. Mechanisms of heteroresistance to isoniazid and rifampin of Mycobacterium tuberculosis in Tashkent, Uzbekistan. Eur. Respir. J. 33, 368–374 (2008).

    PubMed  Google Scholar 

  135. Cambau, E. et al. Evaluation of a new test, GenoType HelicoDR, for molecular detection of antibiotic resistance in Helicobacter pylori. J. Clin. Microbiol. 47, 3600–3607 (2009).

    CAS  PubMed  PubMed Central  Google Scholar 

  136. Brennan, D. E. et al. Molecular detection of Helicobacter pylori antibiotic resistance in stool versus biopsy samples. World J. Gastroenterol. 22, 9214–9221 (2016).

    CAS  PubMed  PubMed Central  Google Scholar 

  137. Zetola, N. M. et al. Mixed Mycobacterium tuberculosis complex infections and false-negative results for rifampin resistance by GeneXpert MTB/RIF are associated with poor clinical outcomes. J. Clin. Microbiol. 52, 2422–2429 (2014).

    PubMed  PubMed Central  Google Scholar 

Download references

Acknowledgements

Work in the authors’ laboratory was supported by a grant from the Swedish Research Council (to D.I.A.).

Author information

Authors and Affiliations

  1. Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden

    Dan I. Andersson, Hervé Nicoloff & Karin Hjort

Authors
  1. Dan I. Andersson
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Hervé Nicoloff
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Karin Hjort
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

D.I.A., H.N. and K.H. researched data for the article, contributed substantially to the discussion of content, wrote the article and reviewed and edited the manuscript before submission.

Corresponding author

Correspondence to Dan I. Andersson.

Ethics declarations

Competing interests

The authors declare no competing interests.

Additional information

Publisher’s note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Peer review information

Nature Reviews Microbiology thanks W. van Schaik, M. Valvano and D. S. Weiss for their contribution to the peer review of this work.

Glossary

Minimal inhibitory concentration

(MIC). The lowest concentration of an antimicrobial drug that prevents growth of a bacterial population.

Antimicrobial susceptibility test

(AST). A method used to determine the minimal inhibitory concentration or clinical resistance level of a bacterial isolate.

Clinical breakpoint

The concentration of an antibiotic that defines whether infection with a bacterial species is treatable with the antibiotic (susceptible) or untreatable (resistant) with the antibiotic.

Persister cells

Bacteria that are sensitive to an antibiotic but that can survive in the presence of the antibiotic because their growth has temporarily stopped.

Compensatory mutations

Mutations that alleviate or suppress the phenotypic effect of a previous mutation.

Small colony variant

Naturally occurring bacterial mutants with defects in electron transport that result in slow growth and resistance to certain antibiotic classes.

Pseudorevertants

Mutants that carry a second mutation (see Compensatory mutations) that alleviates or reverses the phenotypic effects of an already existing mutation.

Inoculum effect

A phenomenon where the minimal inhibitory concentration of an antibiotic increases with the density of cells in the inoculum in the antimicrobial susceptibility test.

Major errors

Major errors are observed when one bacterial isolate is characterized as susceptible to an antibiotic when tested by one type of antimicrobial susceptibility test but is characterized as resistant to that antibiotic when tested by another antimicrobial susceptibility test.

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Andersson, D.I., Nicoloff, H. & Hjort, K. Mechanisms and clinical relevance of bacterial heteroresistance. Nat Rev Microbiol 17, 479–496 (2019). https://doi.org/10.1038/s41579-019-0218-1

Download citation

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/s41579-019-0218-1

This article is cited by

Search

Advanced search

Quick links

Nature Briefing Microbiology

Sign up for the Nature Briefing: Microbiology newsletter — what matters in microbiology research, free to your inbox weekly.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing: Microbiology