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Updated: Oct 14, 2021

Editorial | Open Access | Published 30th September 2021

GUEST EDITORIAL by Tim Sandle - Disinfectant resistance: The next threat to pharmaceutical contamination control?

Throughout the 1980s and 1990s the idea of bacterial resistance to disinfectants, along the lines of bacteria becoming resistant to antibiotics (and other antimicrobials), was considered unlikely. It was during this period (in 1996) that EU GMP Annex 1 introduced the requirement to rotate between two biocides (and although not explicitly stated, this came to represent two biocides with different chemical formulations and ideally different modes of activity). This addition was not, as it was sometimes confusingly interpreted, to prevent the development of resistance but rather to broaden the spectrum of antimicrobial action.¹ Unfortunately, clarifying this has led to the assumption, especially within the pharmaceutical manufacturing world, that bacteria cannot become resistant to disinfectants. It is now time to reassess this assumption and not to consider disinfection as a panacea for weak contamination control measures.

Since the early 2000s there has been a number of research papers looking into the subject of disinfectant resistance across different genera of bacteria.² While earlier papers were speculative; later reviews were based on laboratory studies. The disinfectants against which bacterial resistance has been characterised include iodophors, quaternary ammonium compounds (QAC), peroxides, phenols, chlorine, and glutaraldehyde (to which potential resistance against alcohols has more recently emerged).³ This ground has shifted further within the past couple of years with empirical data reported that indicates that some bacteria can develop resistance to many types of disinfectants (and, according to some studies, this phenomenon is progressing at a rapid rate).⁴,⁵ The pace at which disinfectant resistance is spreading is probably a consequence of the over-use of biocides (as is the case with antibiotics).⁶ As this evolutionary pressure continues, this could create new pressures and concern for sectors that rely upon the use of disinfectants for hygiene control: hospitals, biosecurity, food, pharmaceuticals and so on.

In terms of how bacteria may develop resistance to disinfectants there are various factors being explored. These include the role of biofilm communities, where the mechanisms of layered protection ensure some community members are only exposed to sublethal concentrations of a disinfectant and this can lead to survivors passing on resistance to even some potent biocides like sodium hypochlorite.⁷ It has also been reported that oxidative stress (a detoxification mechanism within the cell) has made Pseudomonads within some environments resistant to chlorine.⁸ Another area that is being examined by researchers is the role of preservatives, as added to some non-sterile pharmaceutical formulations (as well as many foods), since the resistant mechanisms to preservatives appear similar to those required for resistance to disinfectants. Such resistant mechanisms are similar to the way bacteria develop antibiotic resistance: selective pressures leading to vertical and horizontal gene transfer (‘mobile genetic elements’) passed from low numbers of resistant bacteria to bacteria without the resistance mechanism, with the effect of generating larger resistant populations.⁹ It is theorised that QAC resistance genes are located on transmissible plasmids (double-stranded DNA molecules containing genes that provide bacteria with genetic advantages, including antibiotic resistance) and within conserved regions of integrons (genetic mechanisms that allow bacteria to adapt and evolve), that are capable of carrying multiple resistance genes.¹⁰

It follows that the commonly studied genes are qac genes, which impart resistance to QAC disinfectants. Our understanding of resistant genes has been advanced through genome engineering such as the CRISPR-Cas system.¹¹ This new(ish) technology has identified specific disinfectant resistance genes. These genes encode efflux pumps to act against QACs.¹² Efflux pumps are membrane proteins that can export harmful molecules (or ‘pumping out’ toxins from the bacterial cell as a stress response, to put it more crudely). Other disinfectant resistance mechanism indicated from research studies are cell membrane modification and the production of degradable enzymes.¹³

Scientists have postulated that mechanisms of cross-resistance can occur, such as isothiazolone (a preservative) resistant bacteria becoming cross-resistant to disinfectants like QACs.¹⁴ Additionally, benzalkonium chloride disinfectants have been found to promote antibiotic resistance through co-selection.¹⁵ This has an additional importance since empirical evidence suggests antibiotic resistant bacteria are more difficult to kill using disinfectants compared with other bacteria.¹⁶ As information about disinfectant resistance emerges there remains knowledge gaps, such as with the frequency at which resistance develops and the role that environmental factors play upon resistance development.

If disinfectant resistance continues at pace, this could see the decreased efficacy of commonly used biocides and with it a growing preference for the use of oxidising agents (the ‘sporicides’). There will also be efforts to develop new disinfectants, although there are limitations with the types of available chemicals and with chemicals that do not endanger human safety or pose environmental issues. The area of disinfectant innovation that has recently shown the greatest level of innovation has been with QACs, which are now at the seventh generation stage.¹⁷

For pharmaceutical and healthcare products, what should be the response? The extended use of sporicides is an option, but this brings with it the hazards of corrosion to materials (principally stainless steel) and the need to equip operators with special protective clothing, such as respirators. The most important response is the subject of control. Disinfectants are used within cleanrooms and controlled environment to guard against control breakdown: how materials enter the facility, how operators behave, the effectiveness of air filtration systems, using validated sterilisation technology, and whether barrier technology is in place to separate the human from product. Continuing to strengthen and enforce controls helps with ensuring microorganisms are less likely to be present in locales where they are unwanted and the opportunities for cross-contamination are minimised. Hence, as disinfectant research continues, we need to ensure we are not regarding disinfection as the remediation for weak controls; instead, we need to ensure our controls are sufficiently strong in the first place.



01. Sandle, T. (2019) Disinfectants and Biocides. In Moldenhauer, J. (Ed.) Disinfection and Decontamination A Practical Handbook, CRC Press, Boca Raton, pp7-34


02. Chapman, J. (2003) Disinfectant resistance mechanisms, cross-resistance, and co-resistance, International Biodeterioration & Biodegradation, 51 (4): 271-276


03. Hassan, M., Al-Khafaji, N. (2021). Genotypic Detection of Disinfectant Resistant Genes among Bacterial Isolate of Surgical Site Infections. Annals of the Romanian Society for Cell Biology, 371–380


04. Bragg, R., Jansen, A., Coetzee, M., van der Westhuizen. W. (2014) Bacterial resistance to quaternary ammonium compounds (QAC) disinfectants, Adv. Exp. Med. Biol., 808: 1-13


05. Wassenaar, T., Ussery, D., Nielsen, L., Ingmer, H. (2015) Review and phylogenetic analysis of qac genes that reduce susceptibility to quaternary ammonium compounds in Staphylococcus species, Eur. J. Microbiol. Immunol., 5: 44-61


06. Roca, I., Kova, M., Baquero, F. et al. (2015) The global threat of antimicrobial resistance: science for intervention, New Microbes New Infect., 6: 22-29


07. Hu, W., Woo, D., Kang, Y., and. Koo, O. (2021) Biofilm and Spore Formation of Clostridium perfringens and Its Resistance to Disinfectant and Oxidative Stress, Antibiotics 10 (4): 396


08. Tong, C., Hu, H., Chen, G. et al. (2021) Chlorine disinfectants promote microbial resistance in Pseudomonas sp., Environmental Research, 199: 111296.


09. Partridge, S., Kwong, S., N. Firth, N., Jensen, S. (2018) Mobile genetic elements associated with antimicrobial resistance, Clin. Microbiol. Rev., 31: 1-61


10. Vijayakumar, R., Al-Aboody, M. S., AlFonaisan, M. K., Sandle, T. (2016) In vitro susceptibility of multidrug resistant Pseudomonas aeruginosa clinical isolates to common biocides, International Journal of Research in Pharmaceutical Sciences, 7 (1): 110-116


11. McCarlie, S., Boucher, C., Bragg, R. (2020) Molecular basis of bacterial disinfectant resistance, Drug Resistance Updates, 48: 100672


12. Wassenaar, T., Ussery, D., Nielsen, L., Ingmer, H. (2015) Review and phylogenetic analysis of qac genes that reduce susceptibility to quaternary ammonium compounds in Staphylococcus species, Eur. J. Microbiol. Immunol., 5: 44-61


13. Chen, B. and Han, J. and Dai, H. and Jia, P.(2020) Disinfectant- and Antibiotic-Resistance in Community Environments and Risk of Direct Transfers to Humans: Unintended Consequences of Community-Wide Surface Disinfecting during COVID-19?, SSRN:


14. Khan, S., Beattie, T., C. Knapp, C. (2016) Relationship between antibiotic- and disinfectant-resistance profiles in bacteria harvested from tap water, Chemosphere, 152: 132-141


15. Kim, M., Weigand, M., Oh, S. (2018) Widely used benzalkonium chloride disinfectants can promote antibiotic resistance, Appl. Environ. Microbiol., 84: 7-19


16. Vijayakumar, R. and Sandle, T. (2019) A review on biocide reduced susceptibility due to plasmid‐borne antiseptic‐resistant genes—special notes on pharmaceutical environmental isolates, Journal of Applied Microbiology, 126 (4): 1011-1022


17. Bazina L, Maravić A, Krce L. et al. (2019) Discovery of novel quaternary ammonium compounds based on quinuclidine-3-ol as new potential antimicrobial candidates. Eur J Med Chem. 163:626-35

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