New insights into antimicrobial tolerance

Antimicrobial tolerance is

the ability of a normally susceptible, often dormant, bacterial population to survive, rather than die, during extended exposure to bactericidal drugs without changing their minimum inhibitory concentration (MIC). Unlike resistance, which allows growth despite drugs, tolerant bacteria temporarily endure treatment, leading to chronic, relapsing infections and potential evolution into resistant strains.

 

The following video provides some insights, looking at recent research: 

 

 

 

Key Aspects of Antimicrobial Tolerance:

• Mechanism: Often involves low metabolic states (dormancy) or specialized stress responses (e.g., SOS DNA damage repair, cell envelope stress systems).
• Persistence vs. Tolerance: Tolerance typically describes the survival of the entire population, whereas persistence describes a small subpopulation ("persister cells") that survives high drug concentrations.
• Clinical Impact: Contributes to treatment failure in infections like tuberculosis, as bacteria "reawaken" once the antibiotic is removed.
• Distinction from Resistance: Tolerant cells do not grow in the presence of the drug, unlike resistant cells.
• Evolutionary Role: Tolerance can serve as a stepping stone for the development of full resistance.

Common Tolerance Mechanisms:

• Metabolic Slowdown: Reduced metabolic rate makes cells less susceptible to metabolic-dependent antibiotics.
• Biofilm Formation: Bacteria in biofilms often exhibit higher tolerance due to nutrient limitation and stress responses.
• Stress Responses: Activation of pathways (e.g., SOS response) that repair damage caused by antibiotics.

Posted by Dr. Tim Sandle, Pharmaceutical Microbiology Resources (http://www.pharmamicroresources.com/)

5,000 year old ice cave bacterium resists modern antibiotics

 Cave. Image by Tim Sandle

Bacteria are remarkably adaptable, thriving in some of the harshest places on Earth, from boiling hot springs to deep freezes far below zero. Ice caves are one such extreme habitat, home to diverse microorganisms that scientists are only beginning to understand. These frozen environments may contain vast stores of genetic material that have gone largely unexplored. 

Deep inside a Romanian ice cave, locked away in a 5,000-year-old layer of ice, scientists have uncovered a bacterium with a startling secret: it’s resistant to many modern antibiotics. Despite predating the antibiotic era, this cold-loving microbe carries more than 100 resistance-related genes and can survive drugs used today to treat serious infections like tuberculosis and UTIs.

Psychrobacter 

The Psychrobacter SC65A.3 bacterial strain isolated from Scarisoara Ice Cave, despite its ancient origin, shows resistance to multiple modern antibiotics and carries over 100 resistance-related genes.

The bacterium can also inhibit the growth of several major antibiotic-resistant 'superbugs' and shows important enzymatic activities with important biotechnological potential.

Psychrobacter SC65A.3 belongs to a group of cold-adapted bacteria known as Psychrobacter. While some members of this genus can cause infections in people or animals, they are also considered promising for biotechnology applications. Until now, however, little was known about how these bacteria respond to antibiotics. 

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.

How the organism was isolated 

To retrieve the organism, the team drilled a 25-meter ice core from a section of the cave called the Great Hall, capturing a frozen record spanning 13,000 years. To prevent contamination, ice samples were sealed in sterile bags and transported in frozen conditions back to the laboratory. There, scientists isolated bacterial strains and sequenced their genomes to identify genes responsible for surviving extreme cold, as well as genes linked to antimicrobial resistance and activity.

The researchers then tested SC65A.3 against 28 antibiotics across 10 different classes. These drugs are commonly prescribed or reserved for serious bacterial infections. Some had already been associated with known resistance genes or mutations, allowing the team to compare predicted resistance mechanisms with actual laboratory results. "The 10 antibiotics we found resistance to are widely used in oral and injectable therapies used to treat a range of serious bacterial infections in clinical practice," Purcarea noted. Among them were rifampicin, vancomycin, and ciprofloxacin, medications used to treat conditions such as tuberculosis, colitis, and UTIs.

SC65A.3 is the first Psychrobacter strain found to resist certain antibiotics, including trimethoprim, clindamycin, and metronidazole. These drugs are typically used to treat UTIs and infections affecting the lungs, skin, bloodstream, and reproductive system. The strain's resistance profile suggests that bacteria adapted to cold environments could serve as reservoirs of resistance genes, which are segments of DNA that enable survival when exposed to antibiotics.

Significance of the discovery 

Genetic analysis of Psychrobacter SC65A.3 revealed nearly 600 genes with unknown functions, pointing to a largely untapped resource for uncovering new biological processes. The team also identified 11 genes that may have the ability to kill or inhibit bacteria, fungi, and even viruses.

As antibiotic resistance continues to rise worldwide, insights from ancient microbes are becoming increasingly valuable. Studying genomes preserved in ice helps scientists trace how resistance emerged and spread long before modern medicine existed.

Research paper

Victoria Ioana Paun, Corina Itcus, Paris Lavin, Mariana Carmen Chifiriuc, Cristina Purcarea. First genome sequence and functional profiling of Psychrobacter SC65A.3 preserved in 5,000-year-old cave ice: insights into ancient resistome, antimicrobial potential, and enzymatic activities. Frontiers in Microbiology, 2026; 16 DOI: 10.3389/fmicb.2025.1713017 

 

Posted by Dr. Tim Sandle, Pharmaceutical Microbiology Resources (http://www.pharmamicroresources.com/)

Publications by Tim Sandle

 

Category	Number	Running total
Books*	41 (excluding new editions) 48 (with new additions)	41
Booklets and monographs	13	54
Book chapters**	120	174
Peer reviewed papers	236	410
White papers	17	425
Technical articles	637	1,047
University courses authored	15
Training packages	5
Commissioned reports and working papers	7
Written papers for conferences	14
Technical guides	15
Interviews (published)	35
Poster abstracts	1
Other published writing	21
Self-published industry aids	6

 

Posted by Dr. Tim Sandle, Pharmaceutical Microbiology Resources (http://www.pharmamicroresources.com/)

Engineering Clostridium sporogenes to fight cancer

Image: Clostridium sporogenes. Centers for Disease Control and Prevention's Public Health Image Library (PHIL), with identification number #15884 (public domain).
 

Researchers are engineering bacteria to invade tumors and consume them from the inside. Because tumor cores lack oxygen, they’re the perfect breeding ground for these microbes. The team added a genetic tweak that helps the bacteria survive longer near oxygen-exposed edges — but only once enough of them are present to trigger the change. It’s a carefully programmed biological attack that could one day offer a new way to destroy cancer.

The engineering of living cells and microbes is ushering in a new era of cancer therapy.

Scientists at the University of Waterloo (Canada) are working on a new cancer treatment that uses specially engineered bacteria to consume tumors from the inside. The strategy relies on microbes that naturally thrive in oxygen-free environments, which makes the interior of many solid tumors an ideal target.

Clostridium sporogenes is a species of Gram-positive bacteria that belongs to the genus Clostridium. Like other strains of Clostridium, it is an anaerobic, rod-shaped bacterium that produces oval, subterminal endospores and is commonly found in soil. The organism is being investigated for its cancer cell killing properties. 

Bacteria spores enter the tumor, finding an environment where there are lots of nutrients and no oxygen, which this organism prefers, and so it starts eating those nutrients and growing in size.

At the centre of this approach is Clostridium sporogenes, a bacterium commonly found in soil. It can survive only in places that contain absolutely no oxygen. The inner core of solid tumors is made up of dead cells and lacks oxygen, creating the perfect conditions for this microbe to multiply and spread.

Difficult challenge

There is a challenge, however. As the bacteria expand outward and reach areas of the tumor exposed to small amounts of oxygen, they begin to die off before fully eliminating the cancer.

To address this limitation, the team inserted a gene from a related bacterium that is more tolerant of oxygen. This modification allows the engineered microbes to survive longer near the tumor's outer regions.

The researchers also needed a way to control when that oxygen-tolerance feature turns on. Activating it too early could allow the bacteria to grow in oxygen-rich areas such as the bloodstream, which would be unsafe. To prevent that, they used a natural bacterial communication process called quorum sensing.

Quorum sensing relies on chemical signals released by bacteria. As their numbers increase, the signal grows stronger. Only after enough bacteria have accumulated inside a tumor does the signal reach a level that switches on the oxygen-resistant gene. This timing ensures the bacteria activate their survival mechanism only when it is needed.

Synthetic Biology and DNA Circuits

In an earlier study, the team showed that Clostridium sporogenes could be genetically altered to better withstand oxygen. In a follow-up experiment, they tested their quorum sensing design by programming bacteria to produce a green fluorescent protein, allowing them to confirm that the system activated at the intended moment.

The next step is to combine both the oxygen-tolerance gene and the quorum-sensing control system into a single bacterium and evaluate it against tumors in pre-clinical trials.

Research paper 

The research appears in the journal ACS Synthetic Biology, titled " Construction and Functional Characterization of a Heterologous Quorum Sensing Circuit in Clostridium sporogenes."

 

 

Posted by Dr. Tim Sandle, Pharmaceutical Microbiology Resources (http://www.pharmamicroresources.com/)

Shedding light on the dark proteome

New technology feature

 

Proteins drive biology and some of our most devastating diseases, but existing tools can barely measure 8% of them. Nautilus Biotechnology has unveiled Voyager to shed light on this dark proteome - for good. 

 

Voyager is designed to be a standard benchtop instrument that features Nautilus’ Iterative Mapping technology for rapidly and simultaneously measuring up to 10 billion intact proteins per experiment. Leading researchers are already field-testing it and finding: 

 

1. High accuracy, precision, and reproducibility in studies looking at proteins (the targets of 95% of all FDA-approved drugs)
2. Voyager is the only tech out there that can measure intact proteins at this scale. No breaking down proteins
3. Novel insights into biomarkers and proteoform biology, starting with neurodegenerative diseases (e.g. Alzheimer’s tau, Parkinson’s alpha-synuclein)

 

Posted by Dr. Tim Sandle, Pharmaceutical Microbiology Resources (http://www.pharmamicroresources.com/)