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Can Long-Term Use of Chlorine Dioxide Lead to Increased Microbial Tolerance? How Can the Risk Be Reduced?

28 - Aug - 2026

When discussing hospital wastewater disinfection, disinfectants are inevitably part of the conversation. Disinfectants cover a broad range of products, and chlorine dioxide has been increasingly adopted in medical wastewater treatment projects because of its strong oxidizing capacity and broad-spectrum disinfection properties.

However, an important question follows:

Could long-term use of chlorine dioxide make microorganisms increasingly difficult to inactivate, similar to what may occur with prolonged use of certain antimicrobial drugs, and gradually increase the difficulty of disinfection?

First, one key concept must be clarified:

Disinfectant tolerance and antibiotic resistance are not the same thing.

Chlorine dioxide primarily inactivates microorganisms through multi-target oxidative action. This differs significantly from many antibiotics that act on specific biological targets. Therefore, chlorine dioxide disinfection should not be directly equated with mechanisms of antibiotic resistance.

Based on current understanding, the risk of properly used chlorine dioxide inducing typical, stable, heritable resistance appears relatively low. However, actual disinfection performance can still be affected by microorganism type, water quality, microbial load, biofilms, suspended solids, effective concentration, and contact time.

What Are the Disinfection Advantages of Chlorine Dioxide?

The disinfection capability of chlorine dioxide mainly comes from its strong oxidizing properties.

It can oxidize microbial membranes, proteins, and key enzyme systems, and can further affect important intracellular biomolecules, disrupting normal physiological functions.

Because chlorine dioxide acts through multiple oxidative targets, microorganisms are generally less likely to develop the type of stable, heritable resistance commonly associated with some single-target antimicrobial drugs.

However, this does not mean that all microorganisms are equally sensitive to chlorine dioxide.

Different microorganisms have different levels of natural tolerance. Spores, biofilms, and protective effects created by complex wastewater environments can all influence actual disinfection performance.

Therefore, the real question is not simply whether “chlorine dioxide will stop working,” but rather:

Under long-term disinfection pressure, could the microbial community structure change so that microorganisms with naturally higher tolerance or greater environmental protection make up a larger proportion of the surviving population?

Microbial Tolerance and Community Changes

Under continuous disinfection selection pressure, the microbial community in wastewater may undergo certain changes.

These changes can be understood from several perspectives, but this does not mean that every chlorine dioxide disinfection system will inevitably follow a fixed “three-stage evolution.”

Stage 1: Decline of Sensitive Microbial Populations

During the initial period of disinfection, microorganisms that are relatively sensitive to chlorine dioxide, such as most Escherichia coli and some enteric pathogens, can decline significantly under effective disinfection conditions.

This is an important basis for achieving microbiological control in hospital wastewater treatment.

Stage 2: Naturally More Tolerant Microorganisms Become More Noticeable

As sensitive microorganisms are substantially reduced, microorganisms that already possess greater environmental tolerance may represent a larger proportion of the remaining population after disinfection.

For example:

Spore-forming microorganisms in their spore state are generally more tolerant to disinfection than their vegetative cells.

Some Pseudomonas and Acinetobacter species can produce extracellular polymeric substances and form biofilms, providing a degree of physical and chemical protection.

Some mycobacteria have specialized cell-wall structures and can show relatively high tolerance to various environmental stresses and certain disinfectants.

It is important to emphasize that:

Many of these phenomena involve natural tolerance, biofilm protection, or phenotypic tolerance. They do not necessarily mean that the microorganism has developed stable, heritable “resistance.”

Stage 3: Community Restructuring and Potential Selection of More Tolerant Subpopulations

Long-term exposure to sublethal disinfection conditions may theoretically allow more tolerant microbial subpopulations to survive more readily, leading to changes in microbial community structure.

Some microorganisms may also improve survival under low-level oxidative stress through enhanced oxidative-stress defenses, cell aggregation, extracellular polymeric protection, or improved damage-repair mechanisms.

However, this should be interpreted cautiously:

Current evidence that long-term chlorine dioxide use can consistently induce widespread, stable, heritable resistance or cross-resistance remains limited. Therefore, this potential risk should not be presented as an inevitable outcome.

A more scientifically appropriate statement is:

Long-term low-dose or sublethal exposure may increase the opportunity for more tolerant microbial subpopulations to be selected.

Could This Turn Into a “Dosage Competition”?

Theoretically, if more tolerant microorganisms account for a greater proportion of the post-treatment microbial population, or if protective factors such as biofilms and particles become more important, the effective disinfection exposure required to achieve the same level of inactivation may need to be reassessed under otherwise similar conditions.

The CT concept is often used to help evaluate disinfection performance, where C represents the effective disinfectant concentration and T represents the contact time.

However, in practical engineering applications, this should not be simplified to:

“If the microorganisms become harder to kill, simply increase the chlorine dioxide dosage.”

Actual disinfection performance is also affected by:

  • Wastewater quality;
  • Organic load;
  • Suspended solids;
  • Mixing efficiency;
  • Contact-tank hydraulics;
  • Disinfectant decay.

Therefore, when disinfection performance declines, the first question should be:

Has microbial tolerance actually changed, or have the effective concentration, contact time, mixing conditions, or pretreatment performance deviated from the original design conditions?

Whether a hospital wastewater disinfection system enters a so-called “dosage competition” depends on multiple factors.

Disinfection intensity and effective contact: Proper dosing combined with sufficient effective contact can reduce sublethal exposure and the number of surviving microorganisms. From a risk-management perspective, this can reduce opportunities for continuously selecting more tolerant subpopulations.

Microbial sources and continuous input: Microorganisms in hospital wastewater are continuously introduced from patient excreta, domestic wastewater, and other sources. The microbial community therefore remains dynamic and should not be viewed as a closed culture system in which a single microbial population evolves continuously over a long period.

System complexity: Organic matter, Fe²⁺, Mn²⁺, sulfides, and other reducing substances in wastewater can create chlorine dioxide demand, reducing the actual effective concentration and potentially creating conditions for sublethal exposure.

How Should We Respond? Scientific Management Is the Key

There is no need for alarm, but appropriate risk awareness is necessary.

The real issue to avoid is not simply “using chlorine dioxide for many years,” but rather:

Long-term underdosing, inadequate mixing, insufficient contact time, poor pretreatment performance, and persistent biofilms.

The following measures can help optimize the system.

Optimize the Disinfection Process

The chlorine dioxide dosage and effective contact time should be reasonably determined according to wastewater quality, treatment flow, and microbiological control objectives, while avoiding prolonged operation under clearly insufficient sublethal conditions.

At the same time, effluent quality, actual chlorine dioxide performance, and microbiological indicators should be monitored regularly, and operating parameters should be dynamically optimized based on actual data.

CT can be an important tool for evaluating the disinfection process, but it should not be used independently of water quality, mixing conditions, and hydraulic performance.

Strengthen Pretreatment

Biological treatment, sedimentation, filtration, and other upstream processes should be optimized to reduce organic matter and suspended-solid loads as much as possible.

This can not only reduce non-target consumption of chlorine dioxide, but also reduce the protection provided to microorganisms by particles and biofilms.

From an engineering perspective:

Many cases in which microorganisms appear to be “increasingly difficult to kill” are not actually caused by heritable resistance. Instead, the disinfectant may simply not be reaching the target microorganisms at a sufficiently effective concentration.

Consider Combined Disinfection When Appropriate

If a chlorine dioxide-only process cannot consistently achieve the expected performance under certain water-quality conditions or against specific target microorganisms, combined treatment with ultraviolet disinfection, ozone, or other suitable technologies may be considered based on project evaluation.

Whether combined or rotational disinfection should be adopted should depend on:

  • Effluent requirements;
  • Microbiological risk;
  • Water-quality conditions;
  • Equipment capability;
  • Operating cost.

It should not be adopted solely for the purpose of “preventing tolerance.”

Strengthen Monitoring of Microbial Tolerance and Resistance Risks

During routine operation, microbiological indicators required by applicable regulations and project specifications should remain the primary monitoring targets.

Institutions with stronger research capabilities may also combine:

  • Microbial community analysis;
  • Disinfectant susceptibility testing of representative isolates;
  • Biofilm monitoring;
  • Where necessary, antibiotic resistance gene analysis;

to comprehensively evaluate environmental microbiological risks in hospital wastewater.

One point should be emphasized:

Antibiotic resistance genes cannot be directly equated with genes responsible for chlorine dioxide tolerance.

Therefore, test results should always be interpreted according to the specific purpose of the investigation.

Hospital wastewater disinfection is a continuously managed and dynamic process.

Long-term use of chlorine dioxide does not mean that so-called “disinfectant-resistant bacteria” will inevitably develop.

A more accurate understanding is:

Continuous disinfection selection pressure may alter the microbial community structure in wastewater, allowing naturally more tolerant microorganisms or those protected by biofilms and environmental conditions to represent a greater proportion of the surviving population.

However, this does not mean that:

Long-term chlorine dioxide use will inevitably induce stable, heritable resistant microorganisms.

From an engineering management perspective, the real concern is prolonged sublethal exposure.

Insufficient dosage, inadequate mixing, insufficient contact time, poor pretreatment, and persistent biofilms can all allow some microorganisms to survive continuously.

Therefore, through scientific dosage management, effective pretreatment, appropriate contact conditions, necessary combined treatment, and continuous monitoring, the risk of repeatedly selecting more tolerant microbial subpopulations can be reduced while improving the long-term stability of hospital wastewater disinfection.

For chlorine dioxide, the professional approach should not be:

“If it is used for many years, microorganisms will definitely become resistant.”

Nor should it be:

“Microorganisms can never develop any tolerance to chlorine dioxide.”

A more scientifically appropriate conclusion is:

The multi-target oxidative mechanism of chlorine dioxide makes typical stable, heritable resistance relatively difficult to develop. However, natural microbial tolerance, biofilm protection, and long-term sublethal exposure still deserve attention, and potential risks should therefore be reduced through standardized operation and continuous monitoring.