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Some hand sanitizers contain triclosan to kill bacteria. Triclosan has been found to contribute to antibacterial resistance.

I'm trying to reduce my use of products that contribute to antibacterial resistance, but hand sanitizers are convenient when hand washing is unavailable. If I switch to a hand sanitizer with Isopropyl alcohol, will that still effectively kill germs without contributing to antibacterial resistance?

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The safest hand sanitizer from the perspective of reducing antibiotic resistance is the alcohol-based sanitizer. It's effective against a wide variety of microorganisms.

Remember, though, that hand sanitizers don't remove dirt and chemicals from your skin, and all of the ingredients in hand sanitizers are left to fully absorb into your skin. Alcohol makes the skin a bit more permeable to chemicals, so the current recommendation in hospital workers is to wash with soap and water after a few uses of hand sanitizer. (See the first reference for the rest of us.)

Hand sanitizers should primarily be used only as an optional follow-up to traditional hand washing with soap and water, except in situations where soap and water are not available. In those instances, use of an alcohol-based sanitizer is better than nothing at all. Alcohol-based hand sanitizer are about equal in their ability to remove or kill germs on hands, shown in many studies including one small one involving influenza:

Hand hygiene with soap and water or alcohol-based hand rub is highly effective in reducing influenza A virus on human hands, although soap and water is the most effective intervention.

Soap and water eliminated more virus than the three alcohol-based hand rubs, although the difference between these strategies was not great.

While in theory this remains possible, research so far has not found evidence that use of triclosan leads to bacterial resistance.

The [FDA] said there is no evidence to date suggesting that triclosan is hazardous to humans, but several studies have found that triclosan can contribute to the development of bacterial resistance (Aiello AE et al. Clin Infect Dis. 2007;45[suppl 2]:S137-S147). In addition, animal studies have found that the chemical can interfere with thyroid function (Paul KB et al. Toxicol Sci. 2010;113[2]:367-379).

Pediatricians are recommending that it be avoided in homes with children. It has become almost ubiquitous in the environment, so it should probably be avoided in hand-cleansers, as most of it ends up not on out hands, but in our water supply, etc.

The evidence is a only a bit clearer for quaternary ammonium compounds (such as benzalkonium chloride) because of a bacterial genetic element called an integron:

In recent decades, various genetic mechanisms involved in the spread of resistance genes among bacteria have been identified. Integrons – genetic elements that acquire, exchange, and express genes embedded within gene cassettes (GC) – are one of these mechanisms. ...Initially studied mainly in the clinical setting for their involvement in antibiotic resistance, their role in the environment is now an increasing focus of attention.

There is some evidence that QAC's may cause a selection pressure for bacteria carrying antibiotic resistance integrons:

Class 1 integrons are genetic elements that carry antibiotic and quaternary ammonium compound (QAC) resistance genes that confer resistance to detergents and biocides. ...We show that prevalence of class 1 integrons is higher in bacteria exposed to detergents and/or antibiotic residues...

Resistance toward QACs is widespread among a diverse range of microorganisms... Development of resistance in both pathogenic and nonpathogenic bacteria has been related to application in human medicine and the food industry. QACs in cosmetic products will inevitably come into intimate contact with the skin or mucosal linings in the mouth and thus are likely to add to the selection pressure toward more QAC-resistant microorganisms among the skin or mouth flora.

Hand Hygiene and Hand Sanitizers good overview
Integron Involvement in Environmental Spread of Antibiotic Resistance
Impacts of anthropogenic activity on the ecology of class 1 integrons and integron-associated genes in the environment
Efficacy of Soap and Water and Alcohol-Based Hand-Rub Preparations against Live H1N1 Influenza Virus on the Hands of Human Volunteers
Does the wide use of quaternary ammonium compounds enhance the selection and spread of antimicrobial resistance and thus threaten our health?

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