How antimicrobial-resistant microbes journey from environment to humans

From gut to gut: How antimicrobial-resistant microbes make their way from the environment to humans

There are numerous ways for antibiotic-resistant microbes to enter the human body. Credit: Biorender, author provided

From sore throats to fevers to life-threatening infections, most people have taken antibiotics on a regular basis. Recent reports show that the global COVID-19 pandemic has increased the use of antibiotics.

Some microbes can be naturally resistant to certain antimicrobials. In other cases, improper use of antimicrobials promotes the alteration of microbial genes (genes are units of DNA), making the microbes resistant to antimicrobials. The man behind the discovery of antibiotics, Alexander Fleming, warned of this issue in his 1945 Nobel Lecture:

“Mr. X. has a sore throat. He buys some penicillin and gives himself, not enough to kill the strep (bacteria known to cause sore throats and tonsils) but enough to get them to resist penicillin. Then he infects his wife. X gets pneumonia and is treated with penicillin. Because the streptococci are now resistant to penicillin, treatment fails. Mrs X dies. Who is primarily responsible for the death of Mrs. X?”

This situation is called antimicrobial resistance, and the genes that confer resistance are called antimicrobial resistance genes (ARGs).

Antimicrobial resistance genes

Health problems due to antibiotic resistance are increasing worldwide. One of the main reasons is the mobility of ARGs. The resistance genes can be passed from one generation of microbes to the next through reproduction and can also be transmitted through horizontal gene transfer (non-sexual transfer of genetic material between different microbes).

This implies that antimicrobial resistance genes, regardless of their origin from environmental sources, can be transferred to the human gut and vice versa.

As environmental engineers, our research at McGill University is focused on developing tools to monitor the movement of antimicrobial resistance genes in effluent and understanding the effects of ARG transfer on human gut microbes. Aside from the human-to-human transmission of resistant microbes described by Fleming, there are several other ways these microbes can enter the human body.

From gut to gut: How antimicrobial-resistant microbes make their way from the environment to humans

Different pathways of transmission of antimicrobial resistance genes from the environment to the human gut. Credit:, author provided


Wastewater is a sink for human activities and contains resistance genes from human faeces, farms, homes and hospitals. Treated effluents are often discharged into surface waters such as rivers used for recreational activities such as sports, fishing and swimming. A cross-sectional study found that the guts of surfers are three to four times more likely to be colonized by multidrug-resistant microbes than the guts of non-surfers.

In addition, drinking water is obtained from treated surface or ground water. Research has shown that drinking water biofilms (aggregates of microbes living on surfaces) can transfer antimicrobial resistance genes to the mouse gut, suggesting that they could be transferred to the human gut as well.


Antimicrobial agents are often used on farms to increase animal productivity, which can lead to the selection and development of resistance genes. The use of animal manure and sewage sludge (a by-product of wastewater treatment) in agriculture can mediate the transmission of antimicrobial resistance genes to food crops. Several ARGs have been found to travel from the soil to edible plant parts such as tomatoes, lettuce and field beans.


Inhalable antimicrobial resistance genes pose an increasingly growing silent health threat. Recent reports from hospital samples have revealed that daily human exposure to resistant bacteria contained in aerosols is ten times higher than that found in drinking water.

From gut to gut: How antimicrobial-resistant microbes make their way from the environment to humans

One health approach to combat antimicrobial resistance. Credit: Centers for Disease Control and Prevention

health Center

Healthcare facilities are one of the most prominent sites for multidrug-resistant infections due to the presence of opportunistic pathogens infecting immunocompromised patients. The presence of antimicrobials further assists in the development and selection of resistant microbes, which can then be transmitted from one patient to another through interpersonal contact or through shared surfaces such as door handles, bed rails, or lockers.


International travelers who have traveled to developing countries have been found to get multidrug-resistant bacteria. They may have acquired these microbes through contaminated food and water, poor hygiene practices, or different policies on antibiotic use across countries.

A One Health approach

It’s obvious that we’re surrounded by antibiotic-resistant microbes, and it’s normal to worry. But what’s even more important to recognize are the small steps we can all still take. This includes ensuring that patients are treated with the appropriate antibiotic at the right dose.

On a global scale, understanding how resistant microbes are transmitted is part of a One Health approach. The holistic concept of One Health recognizes that human health is linked to the health of animals and our environment. This allows pooling of resources and policies to monitor and combat antimicrobial resistance.

In fact, resistant microbes are running a marathon with antimicrobials, and we need to take steps to slow their pace. In the long term, this would ensure that antimicrobials would continue to support human survival.

Modeling antimicrobial use and resistance in Canadian turkey flocks

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