Genetic Diversity, Population Structure, and Intra-Host Variation of Mycobacterium avium subsp. hominissuis in Fattening Pigs

In the quiet corners of the natural world, microscopic bacteria live in the soil, water, and dust that surround us. Most of these organisms are harmless, but a few can cause trouble if they find their way into the bodies of animals or people. One such bacterium, known as Mycobacterium avium subspecies hominissuis, is an opportunistic pathogen. This means it usually waits for a chance to infect, thriving in environments where it can slip into pigs, humans, and occasionally other animals. In pigs, this infection often hides without causing obvious sickness until the animal is sent to a slaughterhouse, where inspectors look for telltale signs of disease in the lymph nodes. For farmers, finding these signs means losing money, as the meat must be discarded. For public health, understanding how this bacterium moves through the food supply is crucial, especially since it can jump between species. The big question for scientists has always been: where do these bacteria come from, and how do they spread through the complex network of pig farms?

A team of researchers at the University of Zurich decided to answer this by looking closely at the genetic makeup of the bacteria found in Swiss pigs. They collected tissue samples from 120 pigs that had been slaughtered between 2015 and 2022. These animals came from 64 different birth farms and 75 different fattening farms across 13 regions of Switzerland. The researchers were interested in pigs that showed granulomatous lesions, which are small, knot-like lumps in the tissue that often signal an infection. They took samples from various parts of the body, including the lymph nodes in the jaw and belly, as well as the liver, lungs, and even muscle tissue. Their goal was not just to confirm the presence of the bacteria, but to map out the genetic diversity of the strains they found, essentially creating a family tree to see how related the bacteria were to one another.

To do this, the scientists used a method called variable-number tandem repeat typing. Imagine the bacterial DNA as a long string of code. In certain spots along this string, the bacteria repeat a specific sequence of letters over and over again. The number of times these sequences repeat can vary from one bacterium to another, acting like a unique fingerprint. By counting these repeats at fifteen different locations and also reading a specific gene called hsp65, the researchers could distinguish between different strains with high precision. They found that out of 342 bacterial samples they successfully grew in the lab, there were 84 distinct genetic types. This revealed a population that was incredibly diverse, filled with many rare variants that appeared only once or twice, alongside a handful of dominant strains that showed up again and again.

The study uncovered a surprising level of complexity in how these infections spread. Nearly half of the pigs, 56 out of 117, were infected with two or more different strains of the bacteria at the same time. In some cases, a single animal carried up to six different strains. This suggests that pigs are not just catching one bug and keeping it; they are being exposed to a constant stream of different bacterial variants from their environment. The researchers found that these mixed infections were common not just across different animals, but even within the same animal's body. They discovered that the same strain could be found in multiple organs, indicating a widespread infection, but they also found different strains co-existing in the same tissue. This pattern points strongly toward the idea that pigs are repeatedly exposed to the bacteria from the soil, water, or bedding in their farms, rather than catching a single infection from another pig and spreading it like a chain reaction.

When the team looked at the geography of the outbreak, they found that the most common strains were not stuck in one specific region. Instead, the same dominant strains were found on farms scattered across different cantons and years. While farms that were closer together were slightly more likely to share the same strains, the difference was not significant enough to prove that distance was the main factor. The bacteria seemed to be everywhere, moving through the highly connected system of Swiss pig farming. The researchers also compared their findings with data from cattle and humans in other countries. They discovered that some of the exact same bacterial strains found in Swiss pigs were also present in cattle in Switzerland and in humans in the Netherlands and Japan. This shared genetic identity reinforces the concept of "One Health," which recognizes that the health of animals, people, and the environment are deeply linked.

One of the most striking findings was that the bacteria were not limited to the lymph nodes where disease is usually spotted. The researchers successfully grew the bacteria from five muscle samples that looked perfectly healthy to the naked eye. In every one of these cases, the bacteria were also found in other organs like the liver or lungs. This confirms that the infection can spread to edible muscle tissue, even when there are no visible signs of disease. While the study does not prove that eating this meat causes illness in humans, it highlights a potential pathway for exposure that meat inspectors might miss. The study also noted that while some other types of bacteria were found, the vast majority of the lesions were caused by this specific Mycobacterium strain, confirming its role as the primary culprit in these cases.

The researchers concluded that the population of this bacterium in Swiss pigs is driven by repeated exposure to the environment. The high genetic diversity, the presence of many rare strains, and the frequent mixing of different strains within a single animal all point to pigs picking up bacteria from their surroundings throughout their lives. The few dominant strains that appear everywhere suggest that some variants are particularly good at surviving and spreading through the farming system, but they are surrounded by a sea of unique, local variants. This study provides a clearer picture of how these bacteria move, showing that they are not just a simple chain of infection from one pig to another, but a complex web of environmental exposure that touches farms, animals, and potentially people across the globe. By understanding this diversity, scientists and farmers can better track these invisible threats and develop strategies to keep the food supply safe.