Causes of Emerging Pathogens and Toxins

Across the globe, public health systems face an escalating challenge: the rise of emerging pathogens and toxins that threaten human health. From the zoonotic origins of COVID-19 to the expanding reach of drug-resistant bacteria, these microscopic threats are reshaping our understanding of disease emergence. The question is no longer if new pathogens will emerge, but when and where. Understanding what drives their appearance is crucial for protecting communities and preventing future outbreaks.

Zoonotic transmission: when animal diseases jump to humans 🔗

The majority of emerging infectious diseases don’t originate in humans at all. Approximately 60% of all known human infectious disease agents originate in animals, including bacteria, viruses, and parasites. This process, called zoonotic transmission, occurs when pathogens jump from their animal hosts to human populations.

Over 30 new human pathogens have been detected in the last three decades, with 75% originating in animals. Recent examples include SARS-CoV-2, Ebola virus, and MERS-CoV, all of which emerged from wildlife reservoirs. The transition from animal to human host requires specific conditions: close contact between species, a pathogen capable of infecting human cells, and often, environmental or behavioral changes that facilitate transmission.

Wildlife markets, bushmeat hunting, and agricultural expansion into natural habitats create these critical contact points. Activities such as agriculture near homes, raising livestock, mineral extraction near caves, and hunting or farming wildlife significantly increase the frequency and duration of contact between humans, livestock, and wildlife, providing opportunities for pathogens to make the cross-species leap.

Environmental changes and ecosystem disruption 🔗

Human modification of natural landscapes serves as a primary driver of pathogen emergence. Deforestation, urbanization, and agricultural development alter the delicate balance between pathogens, their animal hosts, and human populations. Land-use change and clearing of tropical and subtropical forests likely carries the highest risk for pathogen spillover.

When forests are cleared and ecosystems degraded, biodiversity declines while animals that thrive near human settlements-often those carrying zoonotic pathogens like bats and rodents-increase in number. This ecological disruption brings humans to the forest edge, increasing opportunities for contact with wildlife and subsequent pathogen transmission.

Climate change as a disease multiplier 🔗

Rising global temperatures and shifting weather patterns add another layer of complexity to pathogen emergence. Climate change affects disease transmission through multiple pathways: it alters the geographic distribution of disease vectors like mosquitoes and ticks, changes animal migration patterns, and creates new opportunities for pathogens to establish themselves in previously unsuitable regions.

Increasing water temperatures and salinity due to climate change affect the geographic range of pathogens like Vibrio vulnificus, a virulent human pathogen with high levels of antibiotic resistance. Warmer temperatures promote both the invasion of antimicrobial-resistant pathogens and the spread of vector-borne diseases into new territories.

Extreme weather events compound these risks. Flooding can compromise water safety and facilitate the proliferation of resistant bacteria, while droughts force animals and humans into closer contact around limited water sources, increasing transmission opportunities.

Genetic mutations and pathogen evolution 🔗

Pathogens don’t remain static-they evolve, and sometimes rapidly. Genetic mutations enable microorganisms to enhance their virulence, expand their host range, or develop resistance to treatments. Point mutations and gene acquisition through horizontal gene transfer are main driving forces for pathogen evolution.

Consider Shiga toxin-producing E. coli, which evolved through gene acquisition and deletions to become a significant foodborne pathogen. Similarly, new serotypes of Salmonella have emerged and spread globally, causing numerous outbreaks. These genetic changes can occur through various mechanisms: random mutations during replication, acquisition of genetic material from other microorganisms, or recombination of existing genetic sequences.

When pathogens successfully adapt to human hosts, they may gain the ability to transmit more efficiently between people, increasing their pandemic potential. The process is unpredictable, but environmental stress, antibiotic pressure, and repeated exposure to new hosts all accelerate evolutionary changes.

Globalization and international movement 🔗

Modern transportation systems have transformed the speed at which pathogens can spread. What once took months to travel between continents now takes hours. This interconnectedness, while beneficial for trade and cultural exchange, creates highways for pathogen dissemination.

International trade in animals and animal products poses particular risks. Changing demographics, unprecedented population movement, and increased global flow of people, goods, food animals, and domestic and wild animals all affect microbial traffic. Legal and illegal wildlife markets serve as mixing vessels where diverse species converge, facilitating pathogen exchange and amplification.

Air travel allows infected individuals to carry pathogens across borders before symptoms appear. Even agricultural products and contaminated materials can serve as vehicles for pathogen transport, introducing diseases to regions where they were previously unknown.

Agricultural practices and food production 🔗

Intensive farming and livestock production create conditions favorable for pathogen emergence and spread. Large concentrations of genetically similar animals in close quarters provide ideal environments for pathogens to circulate, mutate, and amplify. Intensified agricultural practices, combined with animal encroachment on wildlife habitats, contribute to cross-species pathogen transmission.

The use of antibiotics in agriculture adds another dimension to this problem. When antimicrobials are used for growth promotion or disease prevention in livestock, resistant bacteria can develop and transfer resistance genes to human pathogens. Runoff from farms introduces these resistant organisms into soil and water, creating environmental reservoirs of antimicrobial resistance.

The growing threat of antimicrobial resistance 🔗

Perhaps no challenge illustrates the intersection of multiple causes better than antimicrobial resistance. This phenomenon doesn’t just involve the emergence of new pathogens-it transforms existing ones into more dangerous forms. Temperature has been consistently positively correlated with resistance rates across bacterial species, with warmer conditions enhancing bacterial survival and transmission of resistant strains.

Antimicrobial resistance emerges through several pathways. Overuse and misuse of antibiotics in human healthcare and agriculture creates selection pressure that favors resistant strains. A 10°C increase in daily minimum temperature has been associated with small but significant increases in antibiotic resistance for common pathogens like E. coli, K. pneumoniae, and S. aureus.

Climate-driven changes in disease patterns compound the problem. As vector-borne diseases expand into new regions, increased antimicrobial use to treat these infections intensifies selective pressure on resistant pathogens. Extreme weather events that disrupt sanitation and healthcare systems create conditions where resistant bacteria can spread more easily.

Healthcare practices and nosocomial transmission 🔗

Healthcare facilities, paradoxically, can serve as hotspots for pathogen emergence and spread. Hospitals bring together vulnerable populations, concentrate pathogens, and provide environments where antimicrobial pressure is highest. Inadequate infection prevention measures can facilitate nosocomial outbreaks of emerging pathogens.

During outbreak investigations, many emerging zoonotic diseases have shown the ability to spread within healthcare settings through inadequate infection control practices. This amplification in clinical environments can transform a limited zoonotic spillover event into a larger outbreak affecting healthcare workers and other patients.

The path forward 🔗

Understanding these interconnected causes of pathogen emergence reveals a complex web of human activities and environmental changes. No single factor operates in isolation-climate change affects agricultural practices, which influence land use, which creates opportunities for zoonotic spillover, all while antimicrobial resistance develops in the background.

Addressing emerging pathogens requires integrated approaches that span sectors. Surveillance systems must monitor both animal and human populations. Land-use policies need to balance development with ecosystem preservation. Agricultural practices should minimize antimicrobial use and reduce wildlife contact. Climate adaptation strategies must incorporate disease prevention measures.

The challenge is substantial, but so is our capacity to respond. By recognizing the drivers of pathogen emergence, we can develop targeted interventions that reduce risks before outbreaks occur. Prevention remains far more effective-and less costly-than responding to established epidemics.

What do you think? How can communities balance economic development with the need to preserve natural barriers against disease emergence? What role should individuals play in preventing the conditions that allow new pathogens to threaten human health?

References

1. https://wwwnc.cdc.gov/eid/article/29/3/22-1079_article
2. https://www.emro.who.int/about-who/rc61/zoonotic-diseases.html
3. https://www.ncbi.nlm.nih.gov/books/NBK613994/
4. https://www.thelancet.com/journals/lanplh/article/PIIS2542-5196(24)00273-0/fulltext
5. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9415055/
6. https://www.ncbi.nlm.nih.gov/books/NBK215318/
7. https://link.springer.com/article/10.1186/s12879-025-11616-9
8. https://wellcome.org/news/climate-change-antimicrobial-resistance