Synanthropic Flies: Hidden Carriers of Disease and Their Role in Emerging Infections

For centuries, flies have been dismissed as nothing more than pests, buzzing around garbage or landing on food. Yet, these small insects hold a dark secret: they are among the most efficient carriers of disease in the natural world.

Recent research led by Dr. John G. Stoffolano Jr. reveals that synanthropic flies—species like houseflies (Musca domestica), blowflies (Calliphoridae), and flesh flies (Sarcophagidae) that thrive near humans—play a critical role in spreading pathogens between animals, humans, and the environment.

The Ancient Partnership Between Flies and Pathogens

Flies have existed for over 400 million years, long before humans walked the Earth. Their evolutionary journey has equipped them with unique tools to survive in diverse environments, including human settlements. One such tool is the diverticulated crop, a specialized organ in their digestive system.

The crop acts as a storage pouch, separate from the acidic midgut where digestion occurs. This separation allows pathogens ingested from feces, rotting meat, or open wounds to survive—and even multiply—for days.

For example, studies show that Bacillus anthracis, the bacterium causing anthrax (a deadly disease affecting both animals and humans), remains viable in the crop for up to four days. Similarly, the virus responsible for COVID-19, SARS-CoV-2, can cling to a housefly’s body long enough to infect new hosts.

Why the crop matters: Unlike the midgut, which breaks down food with enzymes, the crop’s neutral pH creates a safe haven for microbes. This organ essentially acts as a “biological backpack,” allowing flies to transport pathogens over distances.

For instance, when a blowfly feeds on an infected carcass, it stores harmful bacteria or spores in its crop and later regurgitates them onto plants, water, or food. This process, known as mechanical transmission, enables diseases to jump between species and environments.

This relationship between flies and pathogens is not new. Medieval records often linked fly swarms to plague outbreaks, though the science behind this connection was poorly understood. Today, advanced molecular tools confirm what ancient observers suspected: flies are far more than passive carriers. They actively shape disease dynamics by moving pathogens across ecosystems.

How Flies Spread Disease: A Closer Look

To understand why flies are such effective disease vectors, we must examine their feeding habits and biology. Flies lack teeth, so they liquefy food by regurgitating digestive enzymes onto it. This process, called “bubbling”, allows them to ingest nutrients but also leaves behind contaminated droplets. When a fly feeds on infected material—like animal feces or a decaying carcass—pathogens enter its crop. Later, these microbes are deposited onto human food, water, or wounds through regurgitation or defecation.

1. Regurgitation: Flies vomit small droplets of crop fluid to lighten their bodies before flight. These droplets often contain live pathogens.
2. Defecation: Undigested material from the midgut is expelled as feces, which can contaminate surfaces.
3. Surface contact: Pathogens stick to a fly’s legs, wings, or mouthparts and are transferred during feeding or grooming.

A striking example comes from Kruger National Park in South Africa. Blowflies feeding on anthrax-infected animal carcasses were found to regurgitate spores onto nearby plants. Grazing animals like kudus then consumed these plants, sparking outbreaks.

In Thailand, houseflies were linked to 33% of diarrheal cases in a rural village, spreading bacteria like Shigella (which causes dysentery) and Salmonella (a common foodborne pathogen) through contaminated food. Even more alarming, lab experiments confirm that houseflies can mechanically transmit SARS-CoV-2, raising concerns about their role in COVID-19 spread in crowded, unsanitary environments.

The problem is amplified by flies’ ability to travel long distances. While a single fly might only move a few meters after feeding, swarms can disperse pathogens across entire regions. For instance, during the 2011 anthrax outbreak in Zambia, flies feeding on a dead hippopotamus likely transferred spores to nearby vegetation, contributing to 511 human cases and five deaths.

The Crop: A Hidden Hub for Pathogen Evolution

The diverticulated crop is not just a storage unit—it’s a hotspot for microbial activity. Here, bacteria and viruses evade the fly’s immune defenses and interact with other microbes. This environment fosters 

horizontal gene transfer, a process where bacteria exchange genetic material, including antibiotic-resistant genes.

For example, studies show that houseflies can spread drug-resistant E. coli between livestock and humans, with resistance genes transferring at a rate of 10⁻² (transfers per day) in their crops.

Horizontal gene transfer explained: This process allows bacteria to share traits like antibiotic resistance, even between unrelated species. In the crop, resistant bacteria can pass genes to harmless microbes, creating “superbugs” that drugs cannot treat.

Moreover, the crop’s neutral pH allows pathogens to thrive. For example, Chlamydia trachomatis, which causes eye infections, survives in the crop for 24 hours. When flies feed on eye secretions, they deposit the bacterium into new hosts.

Similarly, the orf virus, which causes painful sores in livestock, remains infectious in fly regurgitant for six hours. These findings underscore the crop’s role as a “bioreactor” where pathogens adapt and evolve.

Flies as Bridges Between Species

Flies do not discriminate between hosts. They feed on bats, birds, livestock, and humans, creating pathways for zoonotic diseases—those that jump from animals to humans. Bats, which harbor over 320,000 undiscovered viruses (Anthony et al., 2013), are a prime example.

Flies feeding on bat guano (feces) or half-eaten fruits can transfer viruses like Nipah (a deadly virus causing brain inflammation) to humans. In Uganda, flies were implicated in spreading Bacillus cereus Biovar anthracis from mangabey monkeys to humans, causing sylvatic anthrax—a form of the disease that circulates in wildlife.

Non-human primates (NHPs) are equally vulnerable. Flies follow chimpanzee troops for up to 1.3 kilometers, feeding on their feces and wounds. This behavior facilitates the spread of diseases like yaws, a debilitating infection caused by Treponema pallidum pertenue. DNA analysis confirmed the pathogen in fly crops, linking their feeding habits to outbreaks in wildlife and humans.

Why Female Flies Pose a Greater Threat

Female flies are disproportionately responsible for disease transmission. Their need for protein to develop eggs drives them to seek out nutrient-rich—and often pathogen-laden—sources like carcasses and feces. Gravid females (those carrying eggs) produce 6.5 times more defecation spots than males, increasing contamination risks.

Larger species, such as blowflies, pose an even greater threat due to their bigger crops, which can store 18 microliters of fluid—enough to hold millions of bacterial spores. In agricultural settings, female flies exacerbate foodborne illnesses. A study in the U.S. found that houseflies contaminated 65% of spinach samples with E. coli, highlighting their role in farm-to-table disease spread.

Climate Change and Urbanization: Fueling the Fly-Disease Cycle

As global temperatures rise, flies are thriving. A 1°C increase in temperature boosts fly activity by 10% in tropical regions, accelerating their breeding cycles. Urbanization compounds the problem. Slums and wet markets (where live animals are sold) create ideal habitats for flies.

In Malaysia, researchers collected 1,037 flies from garbage sites, kitchens, and cafeterias, with Muscidae (houseflies) being the most common. These environments are ticking time bombs for disease emergence.

Antibiotic resistance adds another layer of complexity. Flies frequent hospitals, farms, and waste sites, picking up drug-resistant bacteria. In Bangladesh, 75% of houseflies carried multidrug-resistant E. coli (strains immune to multiple antibiotics), posing a dire threat to public health.

Combating Fly-Borne Diseases: Strategies for the Future

Addressing fly-borne diseases requires a multifaceted approach. Improved sanitation is the first line of defense. Reducing organic waste disrupts fly breeding sites, while sealing food and managing landfills limits their access to pathogens. In rural Zambia, where bushmeat consumption triggered an anthrax outbreak, education campaigns could reduce risks by promoting safer food practices.

Technology also plays a role. DNA metabarcoding, a technique that identifies pathogens in fly populations using genetic markers, could revolutionize disease surveillance. By analyzing fly samples from outbreak zones, scientists can detect emerging threats before they spread.

Finally, global collaboration is essential. Flies know no borders, and neither do pathogens. International efforts to monitor fly populations in high-risk areas—like tropical forests and urban slums—could prevent the next pandemic.

Conclusion

Flies have been humanity’s unwelcome companions for millennia. Yet, their role in disease transmission has been underestimated, overshadowed by more visible threats like mosquitoes. Dr. Stoffolano’s research urges us to reconsider this oversight. From ancient plagues to modern pandemics, flies have shaped human history in ways we are only beginning to understand.

The key to mitigating their impact lies in recognizing their biology and behavior. By studying their crop, tracking their movements, and addressing the environmental factors that fuel their spread, we can disrupt the cycle of disease. In a world grappling with climate change and antibiotic resistance, this knowledge is not just academic—it’s a matter of survival.