Discovery of bacteria's defence against viruses becomes a piece of the puzzle against resistance
Antibiotic resistance is a global health challenge that could overtake cancer mortality within a few decades. In a new study, researchers at Umeå University, Sweden, show that the emergence of resistance can be understood in the mechanism of how bacteria build up defences against being infected by viruses. It is about genes in the bacterium that interfere with the attacking virus's ability to multiply.
"A key to antibiotic resistance might be the use of viruses to kill bacteria, however, the systems that bacteria employ to defence themselves against viruses are unknown. Understanding these systems opens up for research into how we can break down the defence so that serious infection disease can be treated in the future," says Ignacio Mir-Sanchis, Assistant Professor at Umeå University and the study's lead author.
The Umeå researchers have studied the bacterium Staphylococcus aureus, which is a common but potentially fatal bacterium in cases such as septic shock and pneumonia. A subgroup of S. aureus has become multi-resistant to antibiotic treatment and thus poses a major danger to public health. In some countries, a quarter of S. aureus is now multi-resistant, in Sweden only one percent.
However, the bacteria themselves are vulnerable to infection by a type of virus called bacteriophages, or just phages. Throughout evolution, bacteria and phages have undergone an arms race in which phages infect bacteria, which in turn develop mechanisms to resist the attacks. Much of this defence is encoded in the part of the bacteria's genome that can easily be transferred between bacteria, the so-called mobilome. Such a transfer can mean that otherwise harmless bacteria can turn into lethal. This is because the mobilome often carries genes that are responsible for the production of toxins, i.e. toxic substances, and for resistance to antibiotics.
The research group has been able to identify a specific set of genes in S. aureus mobilome that confer immunity against infection with phages. This finding was possible thanks to Umeå University's cryoelectron microscope. These genes interfere with the ability of phages to spread and multiply. This happens because a key protein expressed by one of the genes forms a structure around an important protein encoded by the phage's genome, thereby blocking the phage's ability to copy its DNA and thus unable to infect more bacteria.
"The discovery of this mechanism could be a door opener to understand several aspects of bacterial pathogenesis. On the one hand, we now understand better how resistant bacteria defend themselves against viruses. On the other hand, because these set of genes also encode for toxins and antibiotic resistance genes, it may therefore turn out that this is an important piece of the puzzle in the fight against antibiotic resistance," says Ignacio Mir-Sanchis.
Journal
Nature Communications
Method of Research
Imaging analysis
Subject of Research
Cells
Article Title
Phage parasites targeting phage homologous recombinases provide antiviral immunity
LA REVUE GAUCHE - Left Comment: Search results for bacteriophage
Antibiotic resistance among key bacterial species plateaus over time
Use of antibiotics was weakly associated with resistance, indicating additional factors may be at play
Antibiotic resistance tends to stabilize over time, according to a study published April 3, 2025 in the open-access journal PLOS Pathogens by Sonja Lehtinen from the University of Lausanne, Switzerland, and colleagues.
Antibiotic resistance is a major public health concern, contributing to an estimated 5 million deaths per year. Understanding long-term resistance patterns could help public health researchers to monitor and characterize drug resistance as well as inform the impact of interventions on resistance.
In this study, researchers analyzed drug resistance in more than 3 million bacterial samples collected across 30 countries in Europe from 1998 to 2019. Samples encompassed eight bacteria species important to public health, including Streptococcus pneumoniae, Staphylococcus aureus, Escherichia coli, and Klebsiella pneumoniae.
They found that while antibiotic resistance initially rises in response to antibiotic use, it does not rise indefinitely. Instead, resistance rates reached an equilibrium over the 20-year period in most species. Antibiotic use contributed to how quickly resistance levels stabilized as well as variability in resistance rates across different countries. But the association between changes in drug resistance and antibiotic use was weak, suggesting that additional, yet unknown, factors are at play.
The study highlights that continued increase in antibiotic resistance is not inevitable and provides new insights to help researchers monitor drug resistance.
Senior author Francois Blanquart notes: "When we looked into the dynamics of antibiotic resistance in many important bacterial pathogens all over Europe and in the last few decades, we often found that resistance frequency initially increases and then stabilises to an intermediate level. The consumption of the antibiotic in the country explained both the speed of initial increase and the level of stabilization."
Senior author Sonja Lehtinen summarizes: "In this study, we were interested in whether antibiotic resistance frequencies in Europe were systematically increasing over the long-term. Instead, we find a pattern where, after an initial increase, resistance frequencies tend to reach a stable plateau."
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In your coverage please use this URL to provide access to the freely available article in PLOS Pathogens: https://plos.io/42cePEV
Citation: Emons M, Blanquart F, Lehtinen S (2025) The evolution of antibiotic resistance in Europe, 1998–2019. PLoS Pathog 21(4): e1012945. https://doi.org/10.1371/journal.ppat.1012945
Author Countries: France, Switzerland
Funding: FB is funded by ERC StG 949208 EvoComBac. SL is funded by the Swiss National Science Foundation (PR00P3_201618). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Journal
PLOS Pathogens
Method of Research
Experimental study
Subject of Research
Not applicable
Article Publication Date
3-Apr-2025
Machine learning helps construct an evolutionary timeline of bacteria
University of Queensland
University of Queensland scientists have helped to construct a detailed timeline for bacterial evolution, suggesting some bacteria used oxygen long before evolving the ability to produce it through photosynthesis.
The multinational collaboration – led by researchers from the Okinawa Institute of Science and Technology, the University of Bristol, Queensland University of Technology and UQ – focused on how microorganisms responded to the Great Oxygenation Event (GOE) about 2.33 billion years ago, which changed Earth’s atmosphere from mostly devoid of oxygen to one that allows humans to breathe.
Professor Phil Hugenholtz from UQ’s School of Chemistry and Molecular Biosciences said establishing accurate timescales for how bacteria evolved before, during and after the GOE had been difficult until now, because of incomplete fossil evidence.
“Most microbial life leaves no direct fossil record, which means that fossils are missing from the majority of life’s history on Earth,” Professor Hugenholtz said.
“But we know ancient rocks hold chemical clues of how bacteria lived and fed, and we were able to address the gaps by concurrently analysing geological and genomic records.
“The key innovation was using the GOE as a time boundary, assuming that most aerobic branches of bacteria are unlikely to be older than this event unless fossil or genetic signals suggested otherwise.”
The team first estimated which genes were present in ancestral genomes. They then used machine learning to predict whether or not each ancestor used oxygen to live.
To best utilise fossil records, the researchers included genes from mitochondria (related to alphaproteobacteria) and chloroplasts (related to cyanobacteria), which allowed them to use data from early complex cells to better estimate when events happened.
“Results show that at least 3 aerobic lineages appeared before the GOE – by nearly 900 million years – suggesting that a capacity for using oxygen evolved well before its widespread accumulation in the atmosphere,” Professor Hugenholtz said.
“Evidence suggests that the earliest aerobic transition occurred around 3.2 billion years ago in the cyanobacterial ancestor, which points to the possibility that aerobic metabolism occurred before the evolution of oxygenic photosynthesis.”
Lead author Dr Adrián Arellano Davín said the combined approach of using genomic data, fossils and Earth’s geochemical history married together cutting-edge technologies to clarify evolutionary timelines.
“By using machine learning to predict cell function, we can not only predict the aerobic metabolisms of ancestral bacteria but also start to take incomplete genomes to try to predict other traits that could impact the world now, such as whether certain bacteria might be resistant to antibiotics,” Dr Davin said.
The research has been published in Science.
Journal
Science
Method of Research
Data/statistical analysis
Subject of Research
Not applicable
Article Title
A geological timescale for bacterial evolution and oxygen adaptation
Article Publication Date
3-Apr-2025
COI Statement
R.M. is currently affiliated with Dept Life Sciences, University of Nevada, Las Vegas. All other authors declare no other competing interests.
