Study examines the spread of the Klebsiella superbug between humans and the environment

Study examines the spread of the Klebsiella superbug between humans and the environment

An international team of scientists studying the transmission of a deadly drug-resistant bacterium that competes with MRSA has found that while the bugs are found in livestock, pets and the wider environment, they are rarely transmitted to humans this way.

The researchers, led by Professor Ed Feil from the Milner Center for Evolution at the University of Bath, examined the spread of Klebsiella, a family of bacteria that lives harmlessly in the gut but can be dangerous if it spreads to other parts of the body.

Klebsiella pneumoniae is the best-known species in this family, which can cause pneumonia, meningitis, urinary tract infections, and bloodstream infections.

These bacteria are now highly resistant to antibiotics, with some strains even resistant to carbapenems, a class of so-called “last resort” antibiotics that are only used when no other antibiotic treatment works.

Klebsiella has overtaken MRSA as a health problem in the UK, with rates steadily rising. The WHO has recognized the bacterium as a pathogen of critical health priority.

In addition to being found in hospitals, the microbe has also been detected in the environment, including livestock and wastewater, but until now it was not clear whether the bacteria were passed between clinical and non-clinical settings.

In the largest study ever conducted, the team collected 6,548 samples over a 15-month period from various locations in and around the Italian city of Pavia, where this pathogen is a major problem in hospitals, and analyzed them using whole genome sequencing techniques to detect and identify any Klebsiella bacteria present.

The team swabbed patients in hospitals and healthy "carriers" in the community, took samples from farms, puddles, pets and even houseflies and other insects to determine where the bacteria were present.

They found 3,482 isolates, including 15 different species of Klebsiella, with half of the positive samples containing K. pneumoniae.

When the team genetically sequenced the bacteria to find out which strains were present, they found that there was very little overlap between the bugs found in the hospitals and those in the environment.

Professor Ed Feil, who led the study, said: "Klebsiella infections are becoming increasingly resistant to antibiotics. While previously most urinary tract infections could be easily treated, it is now more common for patients to get infections that recur and cause problems.

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"Klebsiella can also cause pneumonia, which kills around half of patients. This bacteria is a bigger problem in the UK than MRSA.

“Our researchers wanted to find out if resistant bacteria are now spreading in pets, farms, livestock, plants and water, and so we wanted to study where Klebsiella is found and monitor how it spreads to inform how best to prevent and control outbreaks.

“We found that it was present everywhere, but were surprised that the strains found in the hospital were different from those found in the environment, suggesting that there is very little transmission between the two habitats: people almost always get this from other people.

“This confirms that the best way to control infection for these bacteria remains strict hospital hygiene and that the likelihood of outbreaks caused by contact with animals or the environment is lower than previously feared, at least in a resource-rich country like Italy.”

The fear was that farmers could get these bacteria from their livestock or soil, that we could become infected from contaminated lettuce, or that we could get sick from swimming in infected lakes.

Our research found no evidence of this, but we did find resistant Klebsiella in pets such as cats and dogs. Veterinarians and owners should be aware of this as these animals could pose a risk for spreading the bacteria.”

Dr. Harry Thorpe,first author of the work,University of Oslo (Norway)

The project consortium, called SpARK, was led by Bath but included researchers from the UK (Wellcome Sanger Institute, Universities of Bristol and Glasgow), Norway, France, Finland and Italy. The work was funded by the Joint Programming Initiative on Antimicrobial Resistance (JPI-AMR) and the MRC and published in Nature Microbiology.

Professor Feil said: “This is the largest and most systematic study conducted simultaneously in a single geographical location.

“We have studied transmission of strains, but antibiotic resistance can be transmitted very easily to other strains when they exchange and take up circular pieces of DNA called plasmids.

“Next, we want to track how plasmids are transferred between strains using a technique called long-read sequencing.”

For this purpose, the team recently received network funding from JPIAMR, which builds on a GW4 research community and was supported by the GW4 AMR Alliance.

Source:

University of Bath

Reference:

Thorpe, H.A., et al. (2022) A large-scale genomic snapshot of Klebsiella spp. Isolates in northern Italy show limited transmission between clinical and non-clinical settings. Natural microbiology. doi.org/10.1038/s41564-022-01263-0.

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