Water Conditioning & Purification Magazine

Microbes and Emerging Chlorine Resistance

By Kelly A. Reynolds, MSPH, PhD

Chlorine disinfection is used by the majority of drinking water treatment municipalities to control microbial pathogens. Some microbes, however, are resistant to chlorine disinfectants and require additional or substitutive treatment methods for effective control. In addition to well-known hazards, recent research suggests there are new, emerging microbes that exhibit chlorine resistance.

History of drinking water disinfection
The use of disinfectants to treat drinking water supplies is considered one of the greatest advancements in public health and attributed to saving millions of lives worldwide. Chlorine disinfectants were among the earliest interventions in water treatment and provided a simple, low-cost method for dramatically improving water quality and reducing the spread of disease. The first US city to routinely disinfect community drinking water supplies was Jersey City, NJ, in 1908.

In 1900, diarrhea and enteritis were among the top three causes of death in the US, along with pneumonia and tuberculosis. Following the widespread use of chlorine to disinfect drinking water supplies, death rates from epidemics such as cholera and typhoid decreased dramatically, from 100 cases per 100,000 people to 33.8 approximately a decade later.

Despite past successes in improved sanitation, hygiene and disease reduction, infectious agents continued to emerge. New viruses, such as the human immunodeficiency virus (HIV) that causes AIDS, appeared in the 80s and multi-drug resistant strains of bacteria, such as Mycobacterium tuberculosis, proved that microbes would continue to adapt and elude human defenses.1 Advances in molecular genetics in the 90s provided new evidence on how quickly microbes change, by either trading bacterial resistance genes in the environment or repairing random viral replication errors that sometimes created more virulent strains of organisms that survived better in harsh environments or were not affected by current vaccines, medications or disinfectants.

Lessons learned
While chlorine disinfectants are generally effective against bacteria and viruses, protozoan pathogens like Cryptosporidium, are highly resistant. This lesson was hard-learned. In 1993, the largest documented waterborne disease outbreak in the US occurred in Milwaukee, WI due to a massive contamination of municipal water with Cryptosporidium. More than 25 percent, or 400,000 people were affected and at least 69 people died, the majority of whom were immunocompromised from HIV infections. Later, reports would indicate that the outbreak cost over $96 million dollars in healthcare costs and productivity losses.2 Combined evidence of widespread gastrointestinal illness reported from hospitals, emergency rooms and clinical test labs, along with anecdotal information of anti-diarrheal medication shortages from pharmacies and consumer reports of poor taste and odor characteristics of the tap water, eventually led to the discovery of the outbreak. Water quality monitoring data, however, from the previous month indicated an increase in water turbidity readings, but the values were still within regulatory limits.

It would be another two and a half days before the community’s drinking water system would be implicated and a boil-water notice issued. The Milwaukee outbreak changed drinking water treatment works dramatically and led to increased recognition for the importance of source-water protection, targeting treatment deficiencies, monitoring and regulatory compliance. Surface-water treatment works, in particular, began using filtration methods along with UV and ozone to target reductions in pathogenic protozoa.

There are still more lessons to be learned relative to microbes and their variable response and emergent changes over time. For example, there is a difference between intrinsic and acquired resistance which may be a function of the microbes’ adaptive ability relative to their environment, genetic predisposition and evolving traits. Additionally, the efficacy of chemical disinfectants may be a function of concentration and contact time required to reach targeted reductions in pathogen concentrations. Efficacies are known to vary across environmental conditions (i.e., temperature, pH, turbidity) and type and strain of microorganism.

Evolving resistance
The 1993 Cryptosporidium outbreak was the result of increased source-water contamination from nearby livestock following recent rainfall events. In addition, water turbidity increases resulted in decreased efficacy of chemical disinfectants in use. Another major driver was that Cryptosporidium was intrinsically resistant to chlorine. The organism had an innate ability to resist the oxidative effects of chlorine. After more than 100 years of using chlorine disinfectants on water supplies, a handful of innately resistant microbes have been identified, but evidence of acquired resistance has not been documented. The world of microbes, however, is constantly evolving and the environment is rapidly changing. For example, a recent study of the persistence of echovirus 11 under varying environmental conditions found that the pathogen evolved toward increased survival when suspended in warmer waters. Another factor in the warm-water-adapted virus was that it was also more resistant to chlorine disinfection.3

Echovirus derives its name from enteric cytopathic human orphan (ECHO) virus. Shed in the feces and other bodily fluids of infected individuals, echoviruses have been associated with waterborne outbreaks. Symptoms range from mild, flu-like illness to severe cases of meningitis and paralysis. Studies showing increased virus adaptation to warm environments warn that these organisms may be harder to eliminate with current disinfection strategies. Further, increased survival in environmental waters relates to increased exposure risks and adverse human health outcomes.3 Additional studies have found that chlorine disinfection efficacy varies widely across different virus strains, compared to ultraviolet (UV) light disinfectant applications. Even slight differences in viral genomes can lead to increased survival capabilities of viruses in the environment, as well as increased resistance to disinfectants.4

Inevitable change
Disinfectant applications are not a one-size-fits-all solution and chlorine chemistries can be very complex when used in changing environmental conditions. New genetic variants of microbes are continuously emerging. Some of these changes cause no measurable effects while others may produce a completely new hazard for which the general population has no immunity to or treatment for. Staying one step ahead of waterborne microbes will require constant monitoring, genetic sequencing analysis, multi-disciplinary approaches and multi-barrier treatments.


  1. National Center for Environmental Health; National Center for Health Statistics; National Center for Infectious Diseases C. Achievements in Public Health, 1900-1999: Control of Infectious Diseases. MMWR. Morbidity and mortality weekly report. https://www.cdc.gov/mmwr/preview/mmwrhtml/mm4829a1.htm#fig1. Published 1999. Accessed September 13, 2020.
  2. Gradus S. Milwaukee, 1993: The Largest Documented Waterborne Disease Outbreak in US History–Water Quality and Health Council. Water Quality and Health Council. https://waterandhealth.org/safe-drinking-water/drinking-water/milwaukee-1993-largest-documented-waterborne-disease-outbreak-history/. Published 2014. Accessed September 13, 2020.
  3. Carratalà A, Bachmann V, Julian TR, Kohn T. Adaptation of Human Enterovirus to Warm Environments Leads to Resistance against Chlorine Disinfection. Environ Sci Technol. September 2020:acs.est.0c03199. doi:10.1021/acs.est.0c03199.
  4. Sigstam T, Gannon G, Cascella M, Pecson BM, Wigginton KR, Kohn T. Subtle differences in virus composition affect disinfection kinetics and mechanisms. Appl Environ Microbiol. 2013;79(11):3455-3467. doi:10.1128/AEM.00663-13.

About the author
Dr. Kelly A. Reynolds is a University of Arizona Professor at the College of Public Health; Chair of Community, Environment and Policy; Program Director of Environmental Health Sciences and Director of Environment, Exposure Science and Risk Assessment Center (ESRAC). She holds a Master of Science Degree in public health (MSPH) from the University of South Florida and a doctorate in microbiology from the University of Arizona. Reynolds is WC&P’s Public Health Editor and a former member of the Technical Review Committee. She can be reached via email at reynolds@u.arizona.edu

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