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Rodents may transmit fungal respiratory infections to humans – US study

Of all emerging diseases afflicting people around the globe, 75% are zoonotic (from animals), with a recent study from the US confirming that rats – an increasingly common presence in South Africa – carry fungal pathogens in their lungs that can cause diseases in humans.

The discovery was made during research led by the University of New Mexico, which entailed searching for fungi in the lung tissues of small mammals.

“This suggests these rodents can serve as reservoirs, agents of dispersal, and incubators of emerging fungal pathogens,” said the scientists, who have published their findings in Frontiers in Fungal Biology.

Fungal diseases in the human population are on the rise so it is important for health authorities to understand where these pathogens come from.

“Our analysis, which specifically focused on lung pathogens that cause disease in humans, detected a wide range of fungi in the lung tissues of small mammals,” said principal researcher Paris Salazar-Hamm.

Over the past four decades there has been an increase in reports of novel human pathogens.

In the same way as the virus that causes COVID-19, these pathogens are able to evolve and diversify as they change hosts.

In some cases, this could increase their virulence and thus effect on humans.
Prof Wanda Markotter, who leads the Centre for Viral Zoonoses at the University of Pretoria, told TimesLIVE: “If you don’t address these problems collectively, you are going to see more and more spillover of disease from animals to humans.”

She said the health of humans, animals and ecosystems is interlinked, and a “complete shift in mindset” is needed to prevent a frequent emergence of zoonotic diseases.

For that mindshift to be underscored by data, scientists worldwide are trying to find the link between different pathogens, the environment, animals and the human body. These data are urgent because, of all emerging diseases today, 75% result from animal to human spillover

“We wanted to understand if the fungal spores of respiratory pathogens reside in soils because they feed on dead and decaying plant matter, or if they are instead living within small animals and their spores are released into the soil after the rodents die,” said Salazar-Hamm.

In SA, though no study has been done, anecdotal evidence has suggested that rat infestations have increased with the reopening of restaurants in the wake of COVID-19 lockdowns.

Recently, Cape Town’s environmental health services ramped up their efforts to increase baiting points across the metropole, focusing on public spaces and informal residential areas.

“Rodents are likely to be found in areas with dense human settlements, a steady food supply in the form of food waste, good places for harbourage such as storm water drainage systems and an absence of predators,” said a spokesperson.

From July 2021 to February 2022, the department received 1 605 complaints relating to rats, and during the same period staff completed more than 41 000 services at baiting points across the metropole.

“Rodents are a phenomenon in most urban areas around the world … but we encourage residents to avoid using toxic and often illegal substances to manage pests in their homes,” said the spokesperson.

Researchers at the Institute for Communities and Wildlife in Africa at the University of Cape Town have also warned about the dangers of urban rat poisons, which are “spilling over into Cape Town’s natural environment, threatening species such as caracal, mongoose, otter and owl”.

Study details

Breathing can be dangerous: Opportunistic fungal pathogens and the diverse community of the small mammal lung mycobiome

Paris S. Salazar-Hamm, Kyana N. Montoya, Liliam Montoya, Kel Cook, Schuyler Liphardt, John W. Taylor, Joseph A. Cook, and Donald O. Natvig.

Published in Frontiers in Fungal Biology on 26 September 2022

Human lung mycobiome studies typically sample bronchoalveolar lavage or sputum, potentially overlooking fungi embedded in tissues. Employing ultra-frozen lung tissues from biorepositories, we obtained fungal ribosomal RNA ITS2 sequences from 199 small mammals across 39 species. We documented diverse fungi, including common environmental fungi such as Penicillium and Aspergillus, associates of the human mycobiome such as Malassezia and Candida, and others specifically adapted for lungs (Coccidioides, Blastomyces, and Pneumocystis). Pneumocystis sequences were detected in 83% of the samples and generally exhibited phylogenetic congruence with hosts. Among sequences from diverse opportunistic pathogens in the Onygenales, species of Coccidioides occurred in 12% of samples and species of Blastomyces in 85% of samples. Coccidioides sequences occurred in 14 mammalian species. The presence of neither Coccidioides nor Aspergillus fumigatus correlated with substantial shifts in the overall mycobiome, although there was some indication that fungal communities might be influenced by high levels of A. fumigatus.
Although members of the Onygenales were common in lung samples (92%), they are not common in environmental surveys. Our results indicate that Pneumocystis and certain Onygenales are common commensal members of the lung mycobiome. These results provide new insights into the biology of lung-inhabiting fungi and flag small mammals as potential reservoirs for emerging fungal pathogens.


Frontiers in Fungal Biology – Breathing can be dangerous: Opportunistic fungal pathogens and the diverse community of the small mammal lung mycobiome (Open access)


TimesLIVE article – Oh rats! Small mammals are passing fungal lung pathogens our way (Restricted access)


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