Next generation genetics technology developed to counter the rise of antibiotic resistance

UC San Diego biologists leverage gene drive advances to stop genes responsible for drug resistance

University of California - San Diego

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Drug resistance has accelerated in recent years with the emergence of deadly bacteria and “superbugs.” UC San Diego biologists have developed a new CRISPR-based technology capable of removing antibiotic-resistant elements from populations of bacteria. 

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Credit: Bier Lab, UC San Diego

Antibiotic resistance (AR) has steadily accelerated in recent years to become a global health crisis. As deadly bacteria evolve new ways to elude drug treatments for a variety of illnesses, a growing number of “superbugs” have emerged, ramping up estimates of more than 10 million worldwide deaths per year by 2050.

Scientists are looking to recently developed technologies to address the pressing threat of antibiotic-resistant bacteria, which are known to flourish in hospital settings, sewage treatment areas, animal husbandry locations and fish farms. University of California San Diego scientists have now applied cutting-edge genetics tools to counteract antibiotic resistance.

The laboratories of UC San Diego School of Biological Sciences Professors Ethan Bier and Justin Meyer have collaborated on a novel method of removing antibiotic-resistant elements from populations of bacteria. The researchers developed a new CRISPR-based technology similar to gene drives, which are being applied in insect populations to disrupt the spread of harmful properties, such as parasites that cause malaria. The new Pro-Active Genetics (Pro-AG) tool called pPro-MobV is a second-generation technology that uses a similar approach to disable drug resistance in populations of bacteria.

“With pPro-MobV we have brought gene-drive thinking from insects to bacteria as a population engineering tool,” said Bier, a faculty member in the Department of Cell and Developmental Biology. “With this new CRISPR-based technology we can take a few cells and let them go to neutralize AR in a large target population.”

In 2019 Bier’s lab collaborated with Professor Victor Nizet’s group (UC San Diego School of Medicine) to develop the initial Pro-AG concept, in which a genetic cassette is introduced and copied between the genomes of bacteria to inactivate their antibiotic-resistant components. The cassette launches itself into an AR gene carried on plasmids, circular types of DNA that replicate within cells, thereby restoring sensitivity of the bacteria to antibiotic treatments.

Building upon this idea, Bier and his colleagues developed a follow-on system that spreads the antibiotic CRISPR cassette components via conjugal transfer, which is similar to mating in bacteria. As they described in the Nature journal npj Antimicrobials and Resistance, the researchers showed that this next-generation pPro-MobV system can exploit a naturally created bacterial mating tunnel between cells to spread the key disabling elements. They demonstrated the process working within bacterial biofilms, which are communities of microorganisms that contaminate various surfaces and can be extremely difficult to remove under conventional cleaning methods. Biofilms also contribute to the spread of disease and are created in the majority of infections that lead to serious disease, in part because biofilms help combat antibiotics by creating a protective layer of cells that is difficult for antibiotics to diffuse through. The new technology therefore carries potential in health care settings, environmental remediation and microbiome engineering.

“The biofilm context for combatting antibiotic resistance is particularly important since this is one of the most challenging forms of bacterial growth to overcome in the clinic or in enclosed environments such as aquafarm ponds and sewage treatment plants,” said Bier. “If you could reduce the spread from animals to humans you could have a significant impact on the antibiotic resistance problem since roughly half of it is estimated to come from the environment.”

The researchers also found that components of the active genetic system could be carried and delivered by bacteriophage, or phage, which are viruses that are natural evolutionary competitors of bacteria. Phage are being specially engineered to combat antibiotic resistance by evading bacterial defenses and inserting disruptive factors inside cells. pPro-MobV elements, the researchers envision, would work in conjunction with such engineered phage viruses. This active genetic platform also can incorporate a highly efficient process known as homology-based deletion as a safety measure to remove the gene cassette if desired.

“This technology is one of the few ways that I’m aware of that can actively reverse the spread of antibiotic-resistant genes, rather than just slowing or coping with their spread,” said Meyer, a professor in the Department of Ecology, Behavior and Evolution, who studies the evolutionary adaptations of bacteria and viruses.

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Journal

npj Antimicrobials and Resistance

DOI

10.1038/s44259-026-00181-z 

Method of Research

Experimental study

Subject of Research

Cells

Article Title

A conjugal gene drive-like system efficiently suppresses antibiotic resistance in a bacterial population

Article Publication Date

2-Feb-2026

COI Statement

Professor Ethan Bier is a co-founder of the start-up company Agragene.

 

Tooling up to diagnose ocean health

Field-deployable CRISPR-based biosensing platform could enable facile, real-time monitoring of marine barometer species and ecosystems

Wyss Institute for Biologically Inspired Engineering at Harvard

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By Benjamin Boettner

(BOSTON) — Oceanic ecosystems are increasingly threatened by global warming which causes coral bleaching, species migration and, through the loss of habitats and biodiversity, food web disruptions on major scales. Also, pollutants such as plastics and other marine debris, wastewater, as well as chemical runoffs, including oil spills, cause major ecosystem disruptions. Importantly, given the interconnectedness of all life on the planet, the deteriorating health of our oceans directly impacts human health and sustenance.

Monitoring so-called “barometer species” can provide critical insights into the pulse of ocean health, reveal both acute local and long-term global trends, and help drive effective climate change policy, remediation and stewardship solutions. However, current marine surveillance methods like, for example, satellite-based ocean imaging or automated robotic systems are limited by their demands for extensive resources and, in many cases, limited spatial and biological resolution. Virtually all ocean or land-based laboratory approaches require sophisticated instruments, trained personnel, and long analysis times to quantify critical barometer species in water samples, which prevents frequent and wide-spread on-site analysis.

Now, addressing the urgent need for advanced ocean health monitoring, a research team at the Wyss Institute at Harvard University and Massachusetts Institute of Technology (MIT), led by Wyss Founding Core Faculty member James Collins, Ph.D. and Wyss Senior Scientist Peter Nguyen, Ph.D. in his group, have developed an inexpensive, laboratory-free approach to be used by many to rapidly quantify marine species and their physiological states on-site. Housed in highly portable, easy-to-handle device, the CRISPR-based biosensing platform has potential to be advanced to enable the prediction of outbreaks in marine communities, and routine monitoring of critically threatened species. The findings are published in Nature Sustainability.

“We aimed to lay the groundwork for more sustainable marine stewardship by developing a CRISPR-based technology platform that has the potential to reduce barriers to routine monitoring of critical oceanic species and to building large, user-driven data collections that can function as early warning systems of ecosystem disruptions,” said Collins, who is also the Termeer Professor of Medical Engineering & Science at MIT. “While our focus on three very different barometer species highlights the diverse applicability of this platform, it can be easily adapted for the detection of other species and their physiological states.”

From human to ocean health care

Critical for the study’s advances were diagnostic capabilities that the Collins group had developed for human health care, as well as their introduction of “smart materials” that are able to sense certain stimuli. Deeply rooted in synthetic biology, the team merged work in different research disciplines for the design of new biological parts and devices that greatly facilitate the detection of infectious and other diseases in relevant home and hospital settings, as well as medically underserved regions of the world. Leveraging their expertise in biomedical diagnostics, the group has turned their attention to the development of “planetary diagnostics” for understanding the dysregulation of ecosystems caused by climate change. In their new study, they succeeded in bringing these accomplishments and technologies to bear on challenges of ocean health care.

“About 90% of the excess heat in the atmosphere caused by global warming has been absorbed by the oceans over the past five decades. This has been disrupting marine communities at an accelerated pace and impacted many natural species and entire ecosystems, the aquaculture industry and, as a consequence, also human health,” said Nguyen. “Being able to sense these changes early and in real time through easy-to-handle diagnostic assays that can be performed by almost anyone, and whose results become immediately accessible to a large community of engaged sentinels is a first step toward mitigating arising threats.”

 

To do this, the team harnessed the programmability of CRISPR technology to detect DNA and RNA nucleic acid molecules from key barometer species with high sensitivity and specificity, and integrated the assays into an automated workflow that can be fast and easily performed in a simple, yet sophisticated device.

An ocean of opportunities

“To demonstrate its broad applicability and programmability of our platform, we built biosensors for three climate-linked barometer species that inform about very diverse oceanic threats,” said the study’s first author Nayoung Kim, Ph.D., who spearheaded the study as a Wyss Technology Development Fellow in Collins’ group. In their first application, the team targeted a virulence-factor gene from pathogenic Vibrio spp.bacteria whose populations frequently explode in warming seawater. Vibrio outbreaks can devastate oyster beds and contribute to disease in adult shellfish and coral reefs. Contact with contaminated seawater or consumption of contaminated seafood can also cause vibriosis, a bacterial infection that can cause several illness, particularly in people with liver disease, diabetes and weakened immune systems. As a second target, they selected the microscopic, single-celled Pseudo-nitzschia spp. algae. During the blooming events, these diatoms produce large quantities of a potent neurotoxin which causes the death of shellfish, fish, marine mammals, and seabirds. Humans consuming seafood with this accumulated toxin can develop potentially lethal amnesiac shellfish poisoning (ASP). Finally, to diagnose the physiological state of coral communities under heat stress in warming seawater, the team adapted their biosensors to detect biomarker RNA transcripts produced by the easy-to-sample Caribbean Porites astreoides coral when it experiences thermal stress.

In designing their CRISPR-based biosensing assays, the team employed the CRISPR–Cas12a enzyme that can be guided to target DNA by complementary guide RNA (gRNA) molecules – in this case genes or reverse-transcribed transcripts from barometer species. Upon recognition of the target, Cas12a unleashes an indiscriminate “collateral” cleavage activity toward nearby single-stranded DNA (ssDNA) molecules. By offering the activated Cas12a enzyme ssDNA reporter molecules labeled with two binding moieties compatible with lateral-flow strips, the researchers implemented a colorimetric, lateral-flow assay (LFA)-based CRISPR biosensing platform. This approach is analogous to LFAs commonly used in infectious disease diagnostics and pregnancy tests. The appearance of a target-specific colored band on a paper strip enables simple, intuitive, instrument-free readout, making LFAs particularly much more suitable for field-deployable devices.

“In establishing accurate biosurveillance for these three barometer species, we had to pay close attention to both sensitivity and specificity,” said Kim. “It is essential to detect low levels of target nucleic acids that may signal early population disruption, while also discriminating among highly similar nucleic acid sequences from related species that have lower, different or no impact on ocean health – especially in the case of Vibrioand Pseudo-nitzschia species. For heat-stressed corals, it is also critical to capture early physiological changes through sensitive and specific detection of biomarker RNA transcripts associated with stress.” By systematically screening multiple sensor component designs, including gRNAs, the team developed CRISPR biosensors that are capable of selectively detecting miniscule amounts of target DNA or RNA molecules within about 40 min. “We demonstrated robust performance of our biosensors at ambient temperatures and in the presence of seawater, supporting their use in field settings,” said Kim. “The programmability of CRISPR allows this approach to be readily adapted for detecting a wide range of other marine species.”

However, while highly effective biosensors are a prerequisite for the detection of potentially harmful or harmed marine species, only their instrumentation in a practical device could provide a field-ready marine biosurveillance platform. “An important problem we had to solve for on-site marine monitoring was preparing samples and performing assays without laboratory instruments,” said Kim. “We drew inspiration from conventional ocean microbial sampling approaches, which involve passing liters of seawater through membranes to collect and concentrate organisms on filters. Rather than transporting these filters to centralized laboratories, we engineered low-cost, portable, 3D-printed devices that enable instrument-free sample processing and detection directly on site.”

Filters containing microbial or shed animal cells are loaded into the disposable, 3D-printed processor, where cells are lysed and target DNA or RNA is amplified directly on the filter in a single 30-minute step. Processed samples are then recovered by simple hand squeezing and detected using optimized CRISPR biosensors with LFA readouts. Reaction activity and lysis efficiency are supported by the inexpensive, insulated 3D-printed incubator warmed with an off-the-shelf, battery-powered hand warmer. “All temperature-sensitive reagents are provided in lyophilized form for shelf-stable deployment, and fluid volumes are optimized for dropper-based handling, allowing simple, in-field operation through squeezing and applying droplets,” said Kim. “Using this platform, we successfully demonstrated a fully field-deployable pipeline with live Vibriopathogens spiked into unfiltered natural seawater collected from three distinct ocean sites, using minimal contamination controls.”

The researchers think that their field-deployable system could provide a low-cost, portable solution for marine ecosystem monitoring in the hands of a wide range of users, including ecologists, marine biologists, citizen scientists, conservationists, coastal communities, aquaculture farmers, park rangers, and biosecurity officers. In some of these applications, individual measurements could be uploaded via smartphone apps into large data bases that with the help of analysts and AI could be used to synthesize more global trends and ring early alarms at critical moments.

“This truly empowering environmental diagnostic technology embodies how the Wyss Institute is leveraging its diverse engineering strengths, as well as internal collaborations between its Sustainable Futures and Diagnostics for Human and Planetary Health efforts, to pave the way towards protecting our oceans, our planet, and the health of humans world-wide,” said Wyss Founding Director Donald Ingber, M.D., Ph.D., who is also the Judah Folkman Professor of Vascular Biology at Harvard Medical School and Boston Children’s Hospital, and the Hansjörg Wyss Professor of Biologically Inspired Engineering at Harvard John A. Paulson School of Engineering and Applied Sciences.

 

Other authors on the study are Daniel Collins, Nina Gonghia, Benjamin Miller, Hani Sallum, Silvi Lybbert, Elena Perini, and James Niemi. The study was funded by the Wyss Institute at Harvard University.

PRESS CONTACT

Wyss Institute for Biologically Inspired Engineering at Harvard University
Benjamin Boettner, benjamin.boettner@wyss.harvard.edu

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The Wyss Institute for Biologically Inspired Engineering at Harvard University (www.wyss.harvard.edu) is a research and development engine for disruptive innovation powered by biologically-inspired engineering with visionary people at its heart. Our mission is to transform healthcare and the environment by developing ground-breaking technologies that emulate the way Nature builds and accelerate their translation into commercial products through formation of startups and corporate partnerships to bring about positive near-term impact in the world. We accomplish this by breaking down the traditional silos of academia and barriers with industry, enabling our world-leading faculty to collaborate creatively across our focus areas of diagnostics, therapeutics, medtech, and sustainability. Our consortium partners encompass the leading academic institutions and hospitals in the Boston area and throughout the world, including Harvard’s Schools of Medicine, Engineering, Arts & Sciences and Design, Beth Israel Deaconess Medical Center, Brigham and Women’s Hospital, Boston Children’s Hospital, Dana–Farber Cancer Institute, Massachusetts General Hospital, the University of Massachusetts Medical School, Spaulding Rehabilitation Hospital, Boston University, Tufts University, Charité – Universitätsmedizin Berlin, University of Zürich, and Massachusetts Institute of Technology.

 

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Journal

Nature Sustainability

Method of Research

Experimental study

Subject of Research

Not applicable

Article Title

A field deployable CRISPR-based biosensing platform for monitoring marine ecosystems

US lawmakers introduce bill to screen sales of potentially dangerous synthetic DNA

Reuters
Wed, February 4, 2026 



U.S. Senator Amy Klobuchar declares her candidacy for the 2020 Democratic presidential nomination in Minneapolis, Minnesota, U.S., February 10, 2019. REUTERS/Eric Miller


SAN FRANCISCO, Feb 4 (Reuters) - Two U.S. senators this week introduced a bill that would create new rules around the sale of synthetic gene sequences ​that could be used to create bioweapons.

Synthetic genes are sequences of nucleic acids - the ‌building blocks of biological life found in DNA - created in labs for use in medical research, gene therapies and ‌crop development, among other uses.

In recent years, scientists have started using artificial intelligence to discover or design new sequences, which can then be synthesized on machines that can fit on a benchtop.

Senator Tom Cotton, an Arkansas Republican, and Senator Amy Klobuchar, a Minnesota Democrat, this week introduced ⁠a bill that directs the U.S. ‌Department of Commerce to require the labs that do gene synthesis work to screen their customers and orders to ensure that bad actors ‍are not ordering dangerous sequences.

The bill would require the Commerce Department, with the help of other federal agencies, to compile a list of potentially dangerous genetic sequences.

“While access to genetic material allows scientists to study ​diseases, develop lifesaving medicine, and improve crops, without safety standards it could be misused, ‌including to create bioweapons," Klobuchar, the No. 3 Democrat in the Senate, said in a statement.

The bill also takes the first steps toward pulling together current biosecurity regulations, which are scattered across the U.S. government, to both streamline the regulations, keep pace with fast-moving technology companies and address safety gaps.

“American innovations in biotechnology are too important to fall into the ⁠hands of bad actors or be hamstrung by ​outdated federal policies," Cotton, the No. 3 Republican in ​the Senate, said in a statement.

Gene synthesis has captured the attention of lawmakers before.

Last year, the U.S. House of Representatives committee on China sent a ‍letter to the directors ⁠of the FBI and national intelligence, renewing its concerns about GenScript Biotechnology's work with U.S. companies because of its ties to China.

A bipartisan group of lawmakers in both ⁠houses of the U.S. Congress also last year introduced a bill that would require U.S. firms to obtain ‌an export license before sending gene sequence data to China.

(Reporting by Stephen ‌Nellis in San Francisco; Editing by Michael Perry)


Senate Republican on suspected biolab found in Las Vegas: ‘Enormous problem’

Ashleigh Fields
Wed, February 4, 2026 

Sen. Ron Johnson (R-Wis.) on Tuesday said the suspected biological research lab found in Las Vegas poses an “enormous problem” to the public after investigators collected vials with “unknown liquids” at a private residence.

“This is a enormous problem. It’s under everybody’s, it’s under the radar. It’s very easy to obtain this kind of information, start doing this gain of function with CRISPR technology” Johnson said during an appearance on NewsNation’s “Katie Pavlich Tonight,” using the acronym for Clustered Regularly Interspaced Short Palindromic Repeats.

“This is a real threat to our national security,” he added.

Johnson referenced the possibility of individuals using CRISPR, which is a precise, efficient gene-editing technology derived from bacterial immune systems that acts as molecular scissors to modify, delete or correct DNA sequences, according to the Broad Institute, a non-profit biomedical research organization.

The technology also allows individuals to disable a gene or insert new genetic material.

Johnson told host Katie Pavlich that Congress has “no idea” how many illegal labs are operating across the country.

After an initial investigation, authorities believe the lab found in Las Vegas has possible ties to Jia Bei Zhu, who was arrested in 2023 for failing to obtain the proper permits to manufacture tests for COVID-19, pregnancy and HIV, and mislabeling some of the kits for a biolab in Reedley, Calif., according to The Associated Press.

Investigators also located “pathogen-labeled containers” with labels in English and Mandarin that read “dengue fever,” “HIV” and “malaria,” along with 1,000 mice, according to a federal report from the Select Committee on the Chinese Communist Party.

“He is not involved in any kind of a biolab being conducted in a home in Las Vegas,” his attorney, Anthony Capozzi, told the outlet.

“What went on in that residence we are unaware of,” he added.

However, his name is listed as the registered agent of the Las Vegas-based company that owns the property where SWAT officers executed a search warrant of the alleged biolab, according to KLAS. The LLC purchased the home in 2022.

In court documents, the man previously told a judge he no longer runs the companies, though he remained listed in Nevada business records, KLAS reported.

Copyright 2026 Nexstar Media, Inc. All rights reserved.

THE NEW GREEN REVOLUTION

Grant to expand self-cloning crop technology for Indian farmers

Plant biologist receives grant to produce higher-yielding crops for sustainable agriculture

University of California - Davis

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Venkatesan Sundaresan, a Distinguished Professor of plant biology and plant sciences at the University of California, Davis, has been awarded a Gates Foundation grant to develop self-cloning crops for Indian farmers. The five-year, $4.9 million project is a collaboration with researchers Myeong-Je Cho at UC Berkeley’s Innovative Genomics Institute (IGI), Viswanathan Chinnusamy at the ICAR-Indian Agricultural Research Institute (ICAR-IARI), New Delhi and Ravi Maruthachalam at the Indian Institutes of Science Education and Research (IISER-Thiruvananthapuram). 

The project aims to sustainably improve agricultural productivity by producing high-yielding crops that clone themselves, allowing farmers to save their superior seeds from one season to the next. It’s based on a technology called “synthetic apomixis,” which Sundaresan’s lab previously developed in rice. 

With the new funding, the team will expand the technology into other staple crops, starting with pearl millet and Indian mustard, two crops that are regionally important in India but do not usually receive international research attention.

“It’s wonderful that the Gates Foundation has taken an interest in this technology,” said Sundaresan. “Their funding makes it possible for us to apply our method to specific crops in contexts where it can make a difference.”

Giving neglected crops the attention they deserve

Pearl millet and Indian mustard (also known as brown mustard) are widely cultivated in India, but are not traded much internationally. That means they receive less attention from funding agencies, seed developers and agricultural companies.

“Big seed companies generally want to work on huge worldwide crops like corn, soybeans and tomatoes,” said Sundaresan. “The technology we develop with this grant will directly benefit smallholder farmers in developing countries.”

Like many other crops, pearl millet and Indian mustard produce higher yields through hybrid breeding — when two genetically different varieties are crossbred. However, hybrid seeds are expensive to produce and must be purchased each year, because when hybrid plants self-fertilize, their optimal genetic combination gets scrambled, resulting in offspring with sub-par yields. 

To make hybrid crops’ high-yielding capacity stable from generation to generation, Sundaresan’s lab developed synthetic apomixis, which allows plants to clone themselves. Self-cloning hybrid varieties of pearl millet and Indian mustard will be more accessible to smallholder farmers.

Branching from grains to vegetable crops 

Sundaresan’s team originally developed synthetic apomixis in rice and has shown that the same approach can work in maize. An independent research team recently used their methods to produce self-cloning sorghum.

Extending synthetic apomixis to Indian mustard may present an additional hurdle, because it belongs to a very different branch of the plant evolutionary tree. Whereas rice, sorghum and pearl millet are all grass-like monocots, Indian mustard is a dicot in the same genus as cabbage, kale and broccoli. Because embryonic development is different in dicots, the researchers may need to significantly modify parts of their method in order to obtain self-cloning mustard. If they succeed, it will open up the possibility of using synthetic apomixis in a broad range of vegetable crops.

“It may be more complicated to move this technology into dicots, because the embryo initiation process is a little different, but I'm hoping that in five years, we'll have the technology working in Indian mustard,” said Sundaresan. “Our discoveries will also yield valuable information for other dicot crops.”

A tweak to remove transgenics 

In addition to extending synthetic apomixis to new crop species, the project aims to tweak the technology so that it no longer involves transgenics — the insertion of foreign DNA from one species into another. Instead, the researchers want to develop a version of synthetic apomixis that relies exclusively on gene editing, which involves mutating or editing an organism’s existing genes using methods such as CRISPR/Cas9.

Doing so will make synthetic apomixis more widely accessible, because gene-edited crops are usually subject to less stringent regulations than transgenic crops. India recently passed laws to deregulate gene-edited crops, which means that, if successful, any self-cloning varieties produced through this project will be treated in the same way as conventionally bred varieties.

“The time is right to develop these crops in India,” said Sundaresan. “If the technology is a success there, I think it will quickly become adopted by other countries around the developing world. I'm hoping that we have, so to speak, the seeds of a new agricultural revolution in place.”