Frozen in time: bacterial strain trapped in ice for 5000 years emerges with multidrug resistance

The genome of a bacterial strain trapped in cave ice for 5000 years has been sequenced for the first time, providing an insight into antimicrobial resistance.

Researchers from the Institute of Biology Bucharest of the Romanian Academy, the University of Bucharest (both Romania) and the Universidad de Antofagasta (Chile) have reported the first whole-genome sequencing and functional characterization of Psychrobacter SC65A.3, a bacterial strain isolated from 5000-year-old cave ice. The preserved pathogen is impervious to ten modern antibiotics and hosts a suite of resistance genes, yet it also demonstrates promising antimicrobial activity that could inhibit multidrug-resistant superbugs.

Bacteria have evolved to colonize even the coldest reaches of our planet. These frosty domains, therefore, represent an often-overlooked reservoir of microorganisms and a source of genetic diversity that has not yet been studied in great detail. Icy cave habitats, in particular, have been poorly investigated, especially in comparison to the substantial literature on permafrost.

That said, Scarisoara Ice Cave in Romania, is one of the most extensively studied ice caves worldwide. Within this cave system, researchers discovered Psychrobacter SC65A.3, a bacterial strain belonging to the genus Psychrobacter, which thrives in cold environments. This group of microbes has biotechnological potential; however, their antibiotic resistance profiles are largely unknown.

“Studying microbes such as Psychrobacter SC65A.3 retrieved from millennia-old cave ice deposits reveals how antibiotic resistance evolved naturally in the environment, long before modern antibiotics were ever used,” author Cristina Purcarea (Institute of Biology Bucharest of the Romanian Academy) explained of the study’s rationale.

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After drilling down 25 meters into the 5000-year-old ice layer at Scarisoara Ice Cave, Purcarea and colleagues recovered numerous bacterial strains. Genomic DNA was isolated using a DNeasy Blood&Tissue Kit from Qiagen (MD, USA), and strain identification was performed by 16S rRNA gene sequencing.

Then, whole-genome sequencing was conducted using PacBio’s (CA, USA) RSII library construction and RSII SMRT cell sequencing, as well as Illumina’s (CA, USA) DNA PCR-free library preparation and NovaSeq. Alongside phenotypic characterization for extremotolerance, antibiotic susceptibility and biochemical profile, this was used to identify and functionally characterize Psychrobacter SC65A.3.

Antimicrobial susceptibility testing was carried out by the Kirby-Bauer standard method against 28 antibiotics belonging to 17 classes. Of these, Psychrobacter SC65A.3 was found to be resistant to ten antibiotics across eight classes, including drugs widely used in clinical practice, like rifampicin, vancomycin and ciprofloxacin.

Meanwhile, whole-genome analysis identified over 100 resistance-associated genes, including clinically relevant determinants, as well as multiple heavy-metal resistance and multidrug efflux genes. In addition, 45 stress-response genes related to cold/heat tolerance were detected.

However, it wasn’t all doom and gloom; the findings also revealed that Psychrobacter SC65A.3 inhibited 14 ESKAPE-group pathogens, including MRSA, Pseudomonas aeruginosa and Klebsiella pneumoniae.

Summing up the threat and promise this dual profile of multidrug resistance and antimicrobial activity poses, Purcarea commented: “If melting ice releases these microbes, these genes could spread to modern bacteria, adding to the global challenge of antibiotic resistance. On the other hand, they produce unique enzymes and antimicrobial compounds that could inspire new antibiotics, industrial enzymes and other biotechnological innovations.”