New Algorithm Detects and Identifies Novel Bacterial Organisms

Hospitals frequently encounter unknown germs, and identifying these pathogens is crucial for efficient bacterial infection treatment. Typically, medical laboratory analysis can identify these pathogens, but standard methods sometimes fall short, especially when dealing with unclassified bacterial species or those difficult to cultivate. Since 2014, a dedicated research team has been collecting and analyzing patient samples containing such elusive germs, leading to the discovery of over 30 new bacteria species, some linked to significant clinical infections.

The team at the University of Basel (Basel, Switzerland) examined a total of 61 unidentified bacterial pathogens from various patient blood and tissue samples. These pathogens had previously eluded identification by conventional lab techniques like mass spectroscopy or partial bacterial genome sequencing. The researchers then employed a more recent method to sequence the complete genetic material of these bacteria. By comparing the genomes with known strains using an online tool, they identified 35 previously unknown bacteria out of the 61 samples. The remaining 26 strains were classified as difficult to identify. These strains either had their genome sequences recently added to databases or had only recently received accurate taxonomic descriptions. Upon reviewing patient data, they found that seven of the 35 new strains had clinical relevance, indicating their potential to cause bacterial infections in humans. Most of these newly identified species belong to the Corynebacterium and Schaalia genera, gram-positive bacilli typically part of the natural human skin microbiome and mucosa. Although often overlooked and understudied, these species can lead to infections when they enter the bloodstream, such as through a tumor.

One particularly challenging pathogen and potentially clinically significant was identified in a patient's inflamed thumb following a dog bite. This finding led the Basel team to consider it an emerging pathogen requiring close monitoring. Similarly, a Canadian research group isolated this bacterium from wounds inflicted by dog or cat bites, naming it Vandammella animalimorsus in 2022. The Basel team is also planning to name their new species, with two already named: Pseudoclavibacter triregionum, referring to Basel's location near Switzerland, France, and Germany's borders. The project is ongoing, with the team at the University Hospital Basel continuing to collect and sequence unknown pathogens from patient samples. They have already identified over 20 additional new species. This ongoing research is crucial for the future of medical diagnostics, as it will enable more accurate diagnoses and effective treatment of infections caused by rare pathogens right from the start.

“Such direct links between newly identified species of bacteria and their clinical relevance have rarely been published in the past,” said microbiologist Dr. Daniel Goldenberger who led the team. “We have noticed a major dynamic here: thanks to technological advances in bacteriology, much more is being published about newly discovered species of bacteria.”

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University of Basel

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