Can a bacterium infect another bacterium?

Can a bacterium infect another bacterium?

We are searching data for your request:

Forums and discussions:
Manuals and reference books:
Data from registers:
Wait the end of the search in all databases.
Upon completion, a link will appear to access the found materials.

I researched about it by searching on Google and reading some bacteriological articles, but I did not get any answer. I also asked some of my teachers, and they were also a bit confused. Some said that it is possible and others said not. So the question remains:

Can a bacterium infect another bacterium? If so, how?

Bdellovibrio bacteriovorus (BV) “infects” other bacteria:

Similar to a virus, BV attacks bacteria such as Escherichia coli (E. coli) by attaching to and entering its prey, growing and replicating within the cell, and then suddenly bursting out, releasing its progeny into the surrounding environment. - How bacteria hunt other bacteria

Note that a lot of the answer to this question hinges on what you mean by "infect". Bdellovibrios (as Laurel has already established that this does happen) do something that does look a lot like infecting eukaryotic cells- but it is still spoken of as "hunting". Why? I am not sure.

There are lots of different ways that bacteria can have negative interactions with each other- though they often resemble "hunting" or "warfare" more than "infection".

Getting a bit more into the "how" of the question, a common mechanism for inter-bacterial negative interaction is the Type VI secretion system. This apparatus is often spoken of as a "weapon" that bacteria can use to kill each other, by adhering to the other cell and shooting toxins in through its membrane. They can use this to great ecological effect.

The type VI secretion system is also used in some contexts for infecting non-bacterial hosts, so by that logic you could argue that it resembles infection.

Update: for a short discussion of inter-bacterial killing (including Bdellovibrio + secretion systems) in the context of biotechnological applications, see here.

Bacteria and viruses infect our cells through sugars: Now researchers want to know how they do it

Sugar is not just something we eat. On the contrary. Sugar is one of the most naturally occurring molecules, and all cells in the body are covered by a thick layer of sugar that protects the cells from bacteria and virus attacks. In fact, close to 80 per cent of all viruses and bacteria bind to the sugars on the outside of our cells.

Sugar is such an important element that scientists refer to it as the third building block of life -- after DNA and protein. And last autumn, a group of researchers found that the spike protein in corona virus needs a particular sugar to bind to our cells efficiently.

Now the same group of researchers have completed a new study that further digs into the cell receptors to which sugars and thus bacteria and virus bind.

'We have established how the sugars bind to and activate the so-called Siglec receptors that regulate immunity. These receptors play a major role, as they tell the immune system to decrease or increase activities. This is an important mechanism in connection with autoimmune diseases', says the first author of the study, Postdoc Christian Büll from the Copenhagen Center for Glycomics (CCG) at the University of Copenhagen.

The unique sugar language

When the immune system receives wrong signals, it can lead to autoimmune diseases, which is when the immune system attacks itself. The Siglec receptors receive signals via the sialic acid sugar, a carbohydrate that typically closes the sugar chains on the surface of our cells. When Siglec receptors meet the right sugar chains, the immune system is told to dampen or activate.

'As part of the new study, we have created a cell library that can be used to study how various sugars bind to and interact with receptors. We have done this by creating tens of thousands of cells each containing a bit of the unique sugar language, which enables us to distinguish them from one another and to study their individual effect and process. This knowledge can help us develop better treatment options in the future', says Associate Professor Yoshiki Narimatsu from CCG, who also contributed to the study.

'The surface of the cells in the library is the same as the one found on cells in their natural environment. This means that we can study the sugars in an environment with the natural occurrence of e.g. proteins and other sugars, and we can thus study the cells in the form in which virus and bacteria find them', Yoshiki Narimatsu explains.

Important discovery for Alzheimer's

Working on the new study, the researchers identified the sugars that bind to the specific receptor that plays a main role in the development of Alzheimer's disease.

'Our main finding concerns the Siglec-3 receptor. Mutations in the Siglec-3 receptor is already known to play a role in connection with Alzheimer's, but we did not know what the receptor specifically binds to. Our method has now identified a potential natural sugar that binds specifically to the Siglec-3 receptor. This knowledge represents an important step forwards in understanding the genetic defects that cause a person to develop the disease', says Christian Büll.

The creation of the sugar libraries was funded by the Lundbeck Foundation and the Danish National Research Foundation.

Multidrug-Resistant Bacteria

Christopher Grace MD, FACP , in Critical Care Secrets (Fifth Edition) , 2013

7 How do bacteria become multiresistant?

Bacteria become resistant to antibiotics by DNA mutation at select points or by insertions or deletions that alter microbial enzymes or the antibiotic targets. Genetic material can be transferred between bacteria by plasmids (extrachromosomal double-stranded circular DNA) via direct cell-to-cell contact. Bacteria may also acquire new resistance genes by infection with bacteriophage viruses that carry resistance genes with them when they infect bacteria. Once bacteria develop or acquire new resistance genes they have a selective advantage when antibiotics are used. As more mutations or transferred genetic material accumulates, the more classes of antibiotics the bacteria become resistant to, inducing MDR.

Mystery molecule in bacteria is revealed to be a guard

Top row: E coli bacteria containing a retron break apart the membranes in the cell around 15 minutes after infection (center) Red reveals holes in membranes as cells die. (Right) 45 minutes post infection with a phage, many cells have died, but a few remain to restart growth. Bottom: bacteria lacking this retron look fine after 15 minutes, but 45 minutes later, the infected cells have died and the viral DNA has spilled out, on its way into the remaining few cells. Credit: Weizmann Institute of Science

Peculiar hybrid structures called retrons that are half RNA, half single-strand DNA are found in many species of bacteria. Since their discovery around 35 years ago, researchers have learned how to use retrons for producing single strands of DNA in the lab, but no one knew what their function was in the bacteria, despite much research into the matter. In a paper published today in Cell, a Weizmann Institute of Science team reports on solving the longstanding mystery: Retrons are immune system 'guards' that ensure the survival of the bacterial colony when it is infected by viruses. In addition to uncovering a new strategy used by bacteria to protect themselves against viral infection—one that is surprisingly similar to that employed by plant immune systems—the research revealed many new retrons that may, in the future, add to the genome-editing toolkit.

The study, conducted in the lab of Prof. Rotem Sorek of the Institute's Molecular Genetics Department, was led by Adi Millman, Dr. Aude Bernheim and Avigail Stokar-Avihail in his lab. Sorek and his team did not set out to solve the retron mystery they were seeking new elements of the bacterial immune system, specifically elements that help bacteria to fend off viral infection. Their search was made easier by their recent finding that bacteria's immune system genes tend to cluster together in the genome within so-called defense islands. When they uncovered the unique signature of retron within a bacterial defense island, the team decided to investigate further.

Their initial research showed that this retron was definitely involved in protecting bacteria against the viruses known as phages that specialize in infecting bacteria. As the researchers looked more closely at additional retrons located near known defense genes, they found that the retrons were always connected—physically and functionally—to one other gene. When either the accompanying gene or the retron was mutated, the bacteria were less successful in fighting off phage infection.

The researchers then set out to look for more such complexes in defense islands. Eventually, they identified some 5,000 retrons, many of them new, in different defense islands of numerous bacterial species.

To check if these retrons function, generally, as immune mechanisms, the researchers transplanted many retrons, one by one, into laboratory bacterial cells that were lacking retrons. As they suspected, in a great number of these cells they found retrons protecting the bacteria from phage infection.

How do retrons do this? Focusing back on one particular kind of retron and tracing its actions in the face of phage infection, the research team discovered that its function is to cause the infected cell to commit suicide. Cell suicide, once thought to belong solely to multicellular organisms, is a last-ditch means of aborting widespread infection—if the suicide mechanism works fast enough to kill the cell before the virus finishes making copies of itself and spreading out to other cells.

Further investigation showed that retrons do not sense the phage invasion itself, but rather keep watch on another part of the immune system known as RecBCD, which is one of the bacterium's first lines of defense. If it realizes that the phage has tampered with the cell's RecBCD, the retron activates its program through the second, linked genes to kill the infected cell and protect the rest of the colony.

"It's a clever strategy, and we found it works in a similar way to a guard mechanism employed in plant cells," says Sorek. "Just like viruses that infect plants, phages come equipped with a variety of inhibitors to block assorted parts of the cell immune response. The retron, like a guard mechanism known to exist in plants, does not need to be able to identify all possible inhibitors, just to have a handle on the functioning of one particular immune complex. Infected plant cells apply this 'abortive infection' method, killing off a small region of a leaf or root, in an effort to save the plant itself. Since most bacteria live in colonies, this same strategy can promote the survival of the group, even at the expense of individual members."

Retrons are so useful to biotechnology because they begin with a piece of RNA, which is the template for the synthesis of the DNA strand. This template in the retron sequence can be swapped out for any desired DNA sequence and used, sometimes in conjunction with another tool borrowed from the bacterial immune toolkit—CRISPR—to manipulate genes in various ways. Sorek and his team believe that within the diverse list of retrons they identified may be hiding more than a few that could provide better templates for specific gene editing needs.


Bacteria (also known as prokaryotes ) are Earth’s most ancient organisms. They are most famously known as scourges that cause deadly diseases. However, what has been discovered recently is that bacteria are also life-giving. Large communities of bacteria live in and on higher organisms (such as you) in assemblies called microbiomes . Microbiomes are crucial for human, animal, and plant health because microbiome bacteria supply their larger hosts with vital substances. Scientists now think that multicellular life on Earth co-evolved with bacteria and that the lives of humans and bacteria are intimately intertwined.

But how can bacteria, which are 500 times smaller than a human cell, kill us, or conversely, give us life? I have spent my life wondering how these tiny critters got the ability to control the fates of outrageously bigger organisms. What scientists found is that bacteria have power in numbers and that they have sophisticated communication abilities that, earlier, were thought impossible for such small, “primitive” organisms. In this Narrative, I will try to convince you that bacteria can “talk” to each other, that they are multilingual, that they act together in coordinated groups, and that these capabilities give bacteria their awesome power.

Bacteria communicate with one another—not with words but with chemicals. Bacteria release these chemical molecules (called autoinducers) into their environment and then they use the buildup of these signaling molecules to take a census of their cell numbers. When a critical number of cells is reached, the bacteria recognize that they are in a group and they behave as a coordinated team exhibiting new behaviors.

In the time-lapse movie shown here ( Video 1 ), a particular bacterial species (normally ocean-dwelling) is growing on a dish in a laboratory. When the bacterial cells reach a critical number, they start producing blue light, a process called “bioluminescence.” The release of chemical molecules called autoinducers (normally invisible but depicted in the cartoon) causes the bacteria to switch on light production. This process is called “quorum sensing.” In the Journey to Discovery , we will learn how scientists discovered quorum sensing and how they uncovered the autoinducers and their interacting “receptors” that underlie this phenomenon.

Video 1 Bacteria Cell Growth and Quorum Sensing. Time-lapse movie covers a period of 5 hours. The field of view is 0.2 millimeters. The animation depicts the production of autoinducer molecules that cause the bacteria to become bioluminescent at high density.

Quorum sensing allows bacteria to collectively accomplish tasks that would be unsuccessful if a single bacterium acted alone ( Figure 1 ). In addition to bioluminescence shown in the movie, quorum sensing controls the production of toxins that are crucial for bacteria to cause disease. Quorum sensing controls biofilm formation. Biofilms are communities of bacterial cells adhered to surfaces and a predominant form of bacterial life on Earth. Biofilms help many bacteria to act as pathogens and cause disease. Biofilms are also critical for beneficial bacterial behaviors such as symbiosis as well as in industrial applications, such as waste-water purification and bioremediation. Quorum sensing controls competence, which is the process that enables bacteria to acquire DNA from other cells. Competence allows bacteria to diversify their genomes and has been spectacularly exploited to get bacteria to harbor foreign genes in the biotechnology industry.

Figure 1 Quorum Sensing Controls Many Bacterial Behaviors at Low and High Cell Density.

Bacteria use multiple quorum-sensing autoinducers for communication in complex environments composed of many bacterial species, which is the normal situation in your intestine, mouth, skin, and other environments. They decode these chemical blends to distinguish self from other and, we think, in so doing, they discern friend from potential foe. This capability allows bacteria to form teams with the correct, helpful, team members, and avoid being duped by enemy bacteria in the neighborhood that might be trying to take advantage of them. Knowing self from other is crucial throughout all of biology.

In the Knowledge Overview , I will discuss how quorum sensing works through a process called signal transduction, which is triggered by autoinducer molecules binding to receptors (specific detector proteins), which subsequently leads to large numbers of genes being turned on or turned off. Only by first deeply understanding how bacteria communicate and the kinds of behaviors that are controlled by quorum sensing, can scientists think up cunning ways to tinker with the process, and in doing so, invent quorum-sensing-manipulation applications that will be successful. In the Frontiers section, I will provide some examples of the ways that scientists are using their understanding of quorum sensing to improve agriculture and fight disease.

I hope you will read on. My dream is that this text will make you feel as if you are looking over my shoulder, over the shoulders of three important scientists who came before me, and over the shoulders of the newest generation of scientists as we go on adventures. I hope you will understand and feel how we felt as we did our experiments, interpreted (and misinterpreted) our results, went down wrong paths, and also went down successful paths, as we made our discoveries showing that bacteria can “talk” to each other.

To Save Others, Bacteria Can Self-Destruct When Infected by a Virus

Scientists were studying viruses that infect and kill bacteria, called bacteriophages or phages as a therapeutic for bacterial infections over a hundred years ago. Antibiotics came along, however, and we no longer needed these viruses. Now that antibiotics are becoming less effective, researchers want to know more about phages, and how they can be used to treat bacterial infections that are antibiotic-resistant. Scientists have now identified an immune mechanism that shields bacteria from phages, and works by initiating a self-destruct mode in bacteria, thereby preventing the infection from spreading to other cells. The findings, which have implications for the use of phages as a treatment, have been reported in Molecular Cell.

"Abortive infection is an old concept, but it's still controversial -- a bacterial cell essentially takes one for the team, killing itself rather than being used to produce more phages," said the senior study author Kevin Corbett, Ph.D., associate professor of cellular and molecular medicine at the University of California San Diego School of Medicine.

"It's been debated whether or not it's logical, from an evolutionary standpoint, for single-celled organisms to do this. But if we think of bacteria as a cooperative community, a biofilm, rather than as individual cells, it makes sense."

Corbett's lab used to study a cell division process called meiosis. A protein family called HORMA became a focus of their research, and in 2015, bioinformatics data from the National Institutes of Health suggested that bacteria make these proteins.

"I'm a basic scientist, and I'm particularly interested in evolutionary connections between proteins and pathways that you would never expect to be related," said Corbett. "So I wondered, what could these proteins be doing in bacteria?"

This newly identified bacterial immune system, called CBASS, can be found in about ten percent of bacteria out of the roughly 75,000 with genomes that have been sequenced, said Corbett. His team engineered a lab strain of phage-sensitive Escherichia coli to carry CBASS. "We were thrilled to find that CBASS provided nearly absolute immunity to phages," Corbett noted.

The researchers also learned more about the molecular characteristics of the proteins that function in CBASS the HORMA proteins sense infection and trigger another protein to send a message. This message activates an enzyme that destroys the bacterial genome, which kills the cell and stops the phage from reproducing.

This work may help scientists create phage therapies that are impervious to CBASS, and more effective at stopping bacterial infections. The video above tells the story of a man that was saved by phages from a drug-resistant infection.

"On the other hand, if we can find a way to activate this system with a drug, we might be able to get CBASS-containing bacteria to kill themselves," he said. "Doing something like that really requires that we have a clear understanding of the detailed mechanisms at play.

"We've studied just one of more than 6,000 distinct CBASS systems, each of which encodes a different set of infection sensors, signaling proteins and effector proteins like the nuclease in our system. Understanding how these different sets of parts work together, and how bacteria have mixed and matched them as they've evolved, will give us a more complete picture of how it all works, and how we might best intervene."



Forget the stereotype of bacteria as simple life forms, swimming mindlessly in a water droplet or stuck on bathroom door handles, waiting for someone to pick them up. “Bacteria are not simple at all,” says Guillaume Lambert, Applied and Engineering Physics. “They are actually extremely sophisticated. They’ve been around for billions of years they have all kinds of tricks to survive.”

Lambert studies the tricks that help bacteria resist antibiotics. As the number of useful antibiotics continues to dwindle, this resistance is an increasing problem for humans, but it’s business as usual for bacteria. “Bacteria have been evolving resistance throughout their history—against fungi, against other bacteria,” he says. “There’s always been a war, but we humans have brought this to the forefront now.”

A New Technique for Studying Bacterial Cells in Real Time

A physicist by training, Lambert uses his physicist’s tool kit to pursue biological questions. His inquiry into the mechanisms of antibiotic resistance has led him to create a new technique for studying bacteria. Lambert’s technique relies on microfabrication and microfluidics to study individual cells in real time as they react to their environment.

“We focus on just a few individuals that are part of a larger population,” he explains. “In the case of antibiotic resistance, this means we can identify and observe how antibiotics impact cellular physiology. This is unlike the usual assays where you have a test tube of bacteria and you put in an antibiotic and all the cells die. You know you have a good antibiotic, but you don’t know what it actually does to the cells themselves.”

The Lambert lab uses a device called a mother machine, which allows the researchers to confine cells in microfluidic channels where flowing growth media is controlled at the micro level. As a mother cell grows and divides, its daughter cells migrate up the channel and eventually are washed away in the media, but the original mother cell always remains. With an imaging microscope, Lambert and his colleagues can record in real time the reactions of the cells to changes they induce in the environment, such as the addition of an antibiotic treatment.

A Persistent Survivor, a Dormant Bacterial Cell Called Persister

They are especially interested in a dormant bacterial cell type known as a persister cell. “A bacterium in the persister state can survive all kinds of environmental stressors that would normally kill it: antibiotics, PH changes, the bile salts we have in our guts, viruses called phages that infect the cells,” Lambert explains. “It’s a great survival strategy. If there’s an antibiotic treatment that kills 99.99 percent of bacteria, and you’re that .01 percent that went dormant, then when you wake up a few hours or a few days later, you’ve got the whole field to yourself.”

“Bacteria have been evolving resistance throughout their history—against fungi, against other bacteria. There’s always been a war, but we humans have brought this to the forefront now.”

By perturbing the bacteria, the researchers increase the odds of the formation of persister cells, making them easier to study. Then they treat the bacteria with rounds of an antibiotic that targets the machinery of cell division, giving the bacteria time to recover between each round. “With every treatment, there should be a 50 percent chance of any individual cell dying,” Lambert says. “But we are able to find a few cells that never die. The ancestry of these cells is distinct and special compared to the rest of the population. Because they survived, we know they did something right. By analyzing them, we can see what killed the rest by seeing what made the survivors fitter.”

Sequencing the genomes of persister cells that survive, the researchers discovered that they are identical genetically to the other cells. “Through some network rearrangements we’re beginning to understand, they can enter this dormant state,” Lambert says. “They don’t have a mutation they just have a different phenotype.” He and his colleagues also found that cell death rate is dependent on age.

“If a cell is older, it’s more likely to divide, and if it divides with the antibiotic present, the cell wall will rupture,” Lambert explains. “But cells that are younger or have just divided will not divide for a while, and so they are protected for a time from the antibiotic effects.”

Creating Synthetic Bacteria for Alerting the Body of Trouble

In another line of research, the Lambert lab also investigates synthetic biology, the engineering of organisms for a specific purpose. “The long-term vision is to take bacteria and give them a brain,” Lambert says. “They can swim like bacteria and sense like bacteria and divide like bacteria, but they can also alert us, for example, when there’s a pathogen present in a patient’s body or a toxic compound in the environment.”

To create the synthetic organisms, the researchers insert into a bacterium pieces of DNA from other organisms such as fungi, phages, or other bacteria. To do this, they use CRISPR-Cas12, a process that employs the CRISPR (clustered regularly interspaced short palindromic repeats) DNA sequence and the nuclease Cas12 from bacteria to edit genes in living models. All the new components together create something like a circuit. “At the basic level, all this looks a lot like physics or electronics,” Lambert says. “The interaction between the different components are similar to the logic gates you have in a computer.”

By combining components in novel ways, Lambert and his colleagues hope to create a new function in bacteria that can be useful to humans. “In the future, you could have probiotics that live in your gut and act as sentries,” Lambert explains. “They could detect imbalances in nutrients or the presence of pathogens and then respond in real time. For instance, they might glow red in the presence of a pathogen, and you would be alerted when you saw that in your stool.”

The synthetic molecules might also one day treat diseases, Lambert suggests. For example, they might produce an antimicrobial compound if they detected infection. They could be used also to monitor the environment, such as lakes, where they might attack algae blooms when they sense them.

Using Physics to Study Biology

Lambert started his university work as a pure physicist with no interest in biology. “As an undergrad, I knew about microfabrication and transistors,” he says. “But in graduate school, one of my professors used physics to study biology. I thought, ‘This is so cool. I want to do this. I want to apply my knowledge to biology.’”

Now, as a professor, he has less time to tinker in the lab, but the hands-on approach still calls to him. “Every once in a while, I go into the lab and do a few quick experiments just to keep me grounded,” he says. “When I go in there, I forget about all the other problems I might have. I don’t get bogged down, and I can have a broader vision.”

Virus and Bacteria

Virus – A virus is a capsule of protein that contains genetic material. A virus cannot reproduce on its own it must infect a living cell to grow.

Bacteria – Bacteria are one-celled organisms that live on their own. They can multiply and reproduce by subdivision

Bacteria and viruses cause many of the diseases we’re familiar with and may sound synonymous they are greatly different from each other.

For one thing, they differ greatly in size. The biggest viruses are only as large as the tiniest bacteria. Viruses are microscopic they range in size from about 20 to 400 nanometers in diameter (1 nanometer = 10 -9 meters). By contrast, the smallest bacteria are about 400 nanometres in size.

Another difference is their structure. Bacteria are complex compared to viruses. A typical bacterium has a rigid cell wall and a thin, rubbery cell membrane surrounding the fluid, or cytoplasm inside the cell. A bacterium contains all of the genetic information needed to make copies of itself—its DNA—in a structure called a chromosome. In addition, it may have extra loose bits of DNA called plasmids floating in the cytoplasm. Bacteria also have ribosomes, tools necessary for copying DNA so bacteria can reproduce. Some have threadlike structures called flagella that they use to move.

A virus may or may not have an outermost spiky layer called the envelope. All viruses have a protein coat and a core of genetic material, either DNA or RNA. And that’s it.

The main difference between viruses and bacteria is the way they reproduce. Bacteria, given the proper nutrients, can grow and reproduce on their own, but… Viruses cannot “live” or reproduce without getting inside some living cell, whether it’s a plant, animal, or bacteria.

Viral vs. Bacterial Reproduction

Bacteria contain the genetic blueprint (DNA) and all the tools (ribosomes, proteins, etc.) they need to reproduce themselves.

Viruses are moochers. They contain only a limited genetic blueprint and they don’t have the necessary building tools. They have to invade other cells and hijack their cellular machinery to reproduce. Viruses invade by attaching to a cell and injecting their genes or by being swallowed up by the cell. Here’s an example of viral infection.

These are T4 bacteriophages. They are a kind of virus that infects bacteria. Here they are landing on the surface of an E. coli bacterium. The bacteriophage cuts a hole in the E. coli’s cell wall. It then injects its genetic material into the bacterium. By taking over the E. coli’s genetic machinery, the viral genes tell the bacterium to begin making new virus parts. These parts come together to make whole new viruses inside the bacterium. Eventually so many new viruses are made that the E. coli bursts open and dies, releasing all those new viruses to infect more cells!

How are bacterial infections treated?

Most bacterial infections can be effectively treated with antibiotics. They either kill bacteria or stop them multiplying. This helps the body’s immune system to fight the bacteria.

Your doctor’s choice of antibiotic will depend on the bacteria that is causing the infection. Antibiotics that work against a wide range of bacteria are called broad-spectrum antibiotics.

Antibiotic resistance is a growing problem so antibiotics may be prescribed only for serious bacterial infections.


Hooi, J. K. et al. Global prevalence of Helicobacter pylori infection: systematic review and meta-analysis. Gastroenterology 153, 420–429 (2017).

Yamaoka, Y. How to eliminate gastric cancer-related death worldwide? Nat. Rev. Clin. Oncol. 15, 407–408 (2018).

Sugano, K. et al. Kyoto global consensus report on Helicobacter pylori gastritis. Gut 64, 1353–1367 (2015).

Shiotani, A., Lu, H., Dore, M. P. & Graham, D. Y. Treating Helicobacter pylori effectively while minimizing misuse of antibiotics. Cleve. Clin. J. Med. 84, 310 (2017).

Graham D. Y. in Helicobacter pylori (eds Hunt, R. H. & Tytgat, G. N. J.) 531-537 (Springer, 1994).

Malfertheiner, P. et al. Management of Helicobacter pylori infection — the Maastricht V/Florence consensus report. Gut 66, 6–30 (2017).

Thung, I. et al. Review article: the global emergence of Helicobacter pylori antibiotic resistance. Aliment. Pharmacol. Ther. 43, 514–533 (2016).

Kasahun, G. G., Demoz, G. T. & Desta, D. M. Primary resistance pattern of Helicobacter pylori to antibiotics in adult population: a systematic review. Infect. Drug. Resistance 13, 1567–1573 (2020).

De Francesco, V. et al. Worldwide H. pylori antibiotic resistance: a systematic review. J. Gastrointest. Liver Dis. 19, 409–414 (2010).

Savoldi, A., Carrara, E., Graham, D. Y., Conti, M. & Tacconelli, E. Prevalence of antibiotic resistance in Helicobacter pylori: a systematic review and meta-analysis in World Health Organization regions. Gastroenterology 155, 1372–1382.e17 (2018).

Li, B.-Z. et al. Comparative effectiveness and tolerance of treatments for Helicobacter pylori: systematic review and network meta-analysis. BMJ 351, h4052 (2015).

Hu, Y., Zhu, Y. & Lu, N.-H. Novel and effective therapeutic regimens for Helicobacter pylori in an era of increasing antibiotic resistance. Front. Cell. Infect. Microbiol. 7, 168 (2017).

Fallone, C. A., Moss, S. F. & Malfertheiner, P. Reconciliation of recent Helicobacter pylori treatment guidelines in a time of increasing resistance to antibiotics. Gastroenterology 157, 44–53 (2019).

Tacconelli, E. et al. Discovery, research, and development of new antibiotics: the WHO priority list of antibiotic-resistant bacteria and tuberculosis. Lancet Infect. Dis. 18, 318–327 (2018).

Tuan, V. P. et al. A next-generation sequencing-based approach to identify genetic determinants of antibiotic resistance in Cambodian Helicobacter pylori clinical isolates. J. Clin. Med. 8, 858 (2019).

Lauener, F. N. et al. Genetic determinants and prediction of antibiotic resistance phenotypes in Helicobacter pylori. J. Clin. Med. 8, 53 (2019).

Yonezawa, H., Osaki, T. & Kamiya, S. Biofilm formation by Helicobacter pylori and its involvement for antibiotic resistance. Biomed Res. Int. 2015, 914791 (2015).

Zhang, Z., Liu, Z.-Q., Zheng, P.-Y., Tang, F.-A. & Yang, P.-C. Influence of efflux pump inhibitors on the multidrug resistance of Helicobacter pylori. World J. Gastroenterol. 16, 1279 (2010).

Gong, Y. & Yuan, Y. Resistance mechanisms of Helicobacter pylori and its dual target precise therapy. Crit. Rev. Microbiol. 44, 371–392 (2018).

Tshibangu-Kabamba, E. et al. Next-generation sequencing of the whole bacterial genome for tracking molecular insight into the broad-spectrum antimicrobial resistance of Helicobacter pylori clinical isolates from the Democratic Republic of Congo. Microorganisms 8, 887 (2020).

Binh, T. T. et al. Discovery of novel mutations for clarithromycin resistance in Helicobacter pylori by using next-generation sequencing. J. Antimicrob. Chemother. 69, 1796–1803 (2014).

Gerrits, M. et al. Alterations in penicillin-binding protein 1A confer resistance to β-lactam antibiotics in Helicobacter pylori. Antimicrob. Agents Chemother. 46, 2229–2233 (2002).

Nakamura, M. et al. Gastric juice, gastric tissue and blood antibiotic concentrations following omeprazole, amoxicillin and clarithromycin triple therapy. Helicobacter 8, 294–299 (2003).

Fallone, C. A. et al. The Toronto consensus for the treatment of Helicobacter pylori infection in adults. Gastroenterology 151, 51–69.e14 (2016).

Grayson, M., Eliopoulos, G., Ferraro, M. & Moellering, R. Effect of varying pH on the susceptibility of Campylobacter pylori to antimicrobial agents. Eur. J. Clin. Microbiol. Infect. Dis. 8, 888–889 (1989).

Zullo, A. The current role of dual therapy for treatment of Helicobacter pylori: back to the future? Eur. J. Gastroenterol. Hepatol. 32, 555–556 (2020).

Suarez, C. & Gudiol, F. Beta-lactam antibiotics [Spanish]. Enferm. Infecc. Microbiol. Clin. 27, 116–129 (2009).

Livermore, D. M. beta-Lactamases in laboratory and clinical resistance. Clin. Microbiol. Rev. 8, 557–584 (1995).

Gerrits, M. M. et al. Multiple mutations in or adjacent to the conserved penicillin-binding protein motifs of the penicillin-binding protein 1A confer amoxicillin resistance to Helicobacter pylori. Helicobacter 11, 181–187 (2006).

Okamoto, T. et al. A change in PBP1 is involved in amoxicillin resistance of clinical isolates of Helicobacter pylori. J. Antimicrob. Chemother. 50, 849–856 (2002).

Rimbara, E., Noguchi, N., Kawai, T. & Sasatsu, M. Mutations in penicillin-binding proteins 1, 2 and 3 are responsible for amoxicillin resistance in Helicobacter pylori. J. Antimicrob. Chemother. 61, 995–998 (2008).

Hu, Y., Zhang, M., Lu, B. & Dai, J. Helicobacter pylori and antibiotic resistance, a continuing and intractable problem. Helicobacter 21, 349–363 (2016).

Kwon, D. H. et al. High-level β-lactam resistance associated with acquired multidrug resistance in Helicobacter pylori. Antimicrob. Agents Chemother. 47, 2169–2178 (2003).

DeLoney, C. R. & Schiller, N. L. Characterization of an in vitro-selected amoxicillin-resistant strain of Helicobacter pylori. Antimicrob. Agents Chemother. 44, 3368–3373 (2000).

Dore, M. P. et al. Amoxycillin tolerance in Helicobacter pylori. J. Antimicrob. Chemother. 43, 47–54 (1999).

Drusano, G. et al. Pharmacokinetics and pharmacodynamics of fluoroquinolones. Clin. Microbiol. Infect. 4, 2S27–2S41 (1998).

Correia, S., Poeta, P., Hébraud, M., Capelo, J. L. & Igrejas, G. Mechanisms of quinolone action and resistance: where do we stand? J. Med. Microbiol. 66, 551–559 (2017).

Aldred, K. J., Kerns, R. J. & Osheroff, N. Mechanism of quinolone action and resistance. Biochemistry 53, 1565–1574 (2014).

Moore, R. A., Beckthold, B., Wong, S., Kureishi, A. & Bryan, L. E. Nucleotide sequence of the gyrA gene and characterization of ciprofloxacin-resistant mutants of Helicobacter pylori. Antimicrob. Agents Chemother. 39, 107–111 (1995).

Mori, H., Suzuki, H., Matsuzaki, J., Masaoka, T. & Kanai, T. Acquisition of double mutation in gyrA caused high resistance to sitafloxacin in Helicobacter pylori after unsuccessful eradication with sitafloxacin-containing regimens. United European Gastroenterol. J. 6, 391–397 (2018).

Miyachi, H. et al. Primary levofloxacin resistance and gyrA/B mutations among Helicobacter pylori Japan. Helicobacter 11, 243–249 (2006).

Rodvold, K. A. Clinical pharmacokinetics of clarithromycin. Clin. pharmacokinet. 37, 385–398 (1999).

Erah, P., Goddard, A., Barrett, D., Shaw, P. & Spiller, R. The stability of amoxycillin, clarithromycin and metronidazole in gastric juice: relevance to the treatment of Helicobacter pylori infection. J. Antimicrob. Chemother. 39, 5–12 (1997).

Gaynor, M. & Mankin, A. S. Macrolide antibiotics: binding site, mechanism of action, resistance. Curr. Top. Med. Chem. 3, 949–960 (2003).

Versalovic, J. et al. Mutations in 23S rRNA are associated with clarithromycin resistance in Helicobacter pylori. Antimicrob. Agents Chemother. 40, 477–480 (1996).

Hao, Q., Li, Y., Zhang, Z.-J., Liu, Y. & Gao, H. New mutation points in 23S rRNA gene associated with Helicobacter pylori resistance to clarithromycin in northeast China. World J. Gastroenterol. 10, 1075 (2004).

Debets-Ossenkopp, Y., Namavar, F. & MacLaren, D. Effect of an acidic environment on the susceptibility of Helicobacter pylori to trospectomycin and other antimicrobial agents. Eur. J. Clin. Microbiol. Infect. Dis. 14, 353–355 (1995).

Dingsdag, S. A. & Hunter, N. Metronidazole: an update on metabolism, structure–cytotoxicity and resistance mechanisms. J. Antimicrob. Chemother. 73, 265–279 (2018).

Hoffman, P. S., Goodwin, A., Johnsen, J., Magee, K. & van Zanten, S. V. Metabolic activities of metronidazole-sensitive and -resistant strains of Helicobacter pylori: repression of pyruvate oxidoreductase and expression of isocitrate lyase activity correlate with resistance. J. Bacteriol. 178, 4822–4829 (1996).

Kwon, D.-H. et al. Analysis of RdxA and involvement of additional genes encoding NAD(P)H flavin oxidoreductase (FrxA) and ferredoxin-like protein (FdxB) in metronidazole resistance of Helicobacter pylori. Antimicrob. Agents Chemother. 44, 2133–2142 (2000).

Kwon, D. H., Kato, M., El-Zaatari, F. A., Osato, M. S. & Graham, D. Y. Frame-shift mutations in NAD(P)H flavin oxidoreductase encoding gene (FrxA) from metronidazole resistant Helicobacter pylori ATCC43504 and its involvement in metronidazole resistance. FEMS Microbiol. Lett. 188, 197–202 (2000).

Martínez-Júlvez, M. et al. Structure of RdxA–an oxygen-insensitive nitroreductase essential for metronidazole activation in Helicobacter pylori. FEBS J. 279, 4306–4317 (2012).

Goodwin, A. et al. Metronidazole resistance in Helicobacter pylori is due to null mutations in a gene (RdxA) that encodes an oxygen-insensitive NADPH nitroreductase. Mol. Microbiol. 28, 383–393 (1998).

Sisson, G. et al. Metronidazole activation is mutagenic and causes DNA fragmentation in Helicobacter pylori and in Escherichia coli containing a cloned H. pylori RdxA + (nitroreductase) gene. J. Bacteriol. 182, 5091–5096 (2000).

Jeong, J.-Y. et al. Sequential inactivation of RdxA (HP0954) and FrxA (HP0642) nitroreductase genes causes moderate and high-level metronidazole resistance in Helicobacter pylori. J. Bacteriol. 182, 5082–5090 (2000).

Albert, T. J. et al. Mutation discovery in bacterial genomes: metronidazole resistance in Helicobacter pylori. Nat. Methods 2, 951–953 (2005).

Smith, M. A. & Edwards, D. I. Oxygen scavenging, NADH oxidase and metronidazole resistance in Helicobacter pylori. J. Antimicrob. Chemother. 39, 347–353 (1997).

Choi, S. S., Chivers, P. T. & Berg, D. E. Point mutations in Helicobacter pylori’s fur regulatory gene that alter resistance to metronidazole, a prodrug activated by chemical reduction. PLoS ONE 6, e18236 (2011).

Chang, K.-C., Ho, S.-W., Yang, J.-C. & Wang, J.-T. Isolation of a genetic locus associated with metronidazole resistance in Helicobacter pylori. Biochem. Biophys. Res. Commun. 236, 785–788 (1997).

Thompson, S. A. & Blaser, M. J. Isolation of the Helicobacter pylori recA gene and involvement of the recA region in resistance to low pH. Infect. Immun. 63, 2185–2193 (1995).

Tsugawa, H. et al. Enhanced bacterial efflux system is the first step to the development of metronidazole resistance in Helicobacter pylori. Biochem. biophys. Res. Commun. 404, 656–660 (2011).

Tsugawa, H. et al. Two amino acids mutation of ferric uptake regulator determines Helicobacter pylori resistance to metronidazole. Antioxid. Redox Signal. 14, 15–23 (2011).

Tsugawa, H., Suzuki, H., Matsuzaki, J., Hirata, K. & Hibi, T. FecA1, a bacterial iron transporter, determines the survival of Helicobacter pylori in the stomach. Free Radic. Biol. Med. 52, 1003–1010 (2012).

Lacey, S., Moss, S. & Taylor, G. Metronidazole uptake by sensitive and resistant isolates of Helicobacter pylori. J. Antimicrob. Chemother. 32, 393–400 (1993).

Moore, R. A., Beckthold, B. & Bryan, L. Metronidazole uptake in Helicobacter pylori. Can. J. Microbiol. 41, 746–749 (1995).

Graham, D. Y. Antibiotic resistance in Helicobacter pylori: implications for therapy. Gastroenterology 115, 1272–1277 (1998).

Chopra, I. & Roberts, M. Tetracycline antibiotics: mode of action, applications, molecular biology, and epidemiology of bacterial resistance. Microbiol. Mol. Biol. Rev. 65, 232–260 (2001).

Ross, J. I., Eady, E. A., Cove, J. H. & Cunliffe, W. J. 16S rRNA mutation associated with tetracycline resistance in a gram-positive bacterium. Antimicrob. Agents Chemother. 42, 1702–1705 (1998).

Dailidiene, D. et al. Emergence of tetracycline resistance in Helicobacter pylori: multiple mutational changes in 16S ribosomal DNA and other genetic loci. Antimicrob. Agents Chemother. 46, 3940–3946 (2002).

Gerrits, M. M., de Zoete, M. R., Arents, N. L., Kuipers, E. J. & Kusters, J. G. 16S rRNA mutation-mediated tetracycline resistance in Helicobacter pylori. Antimicrob. Agents Chemother. 46, 2996–3000 (2002).

Wu, J. Y. et al. Tetracycline-resistant clinical Helicobacter pylori isolates with and without mutations in 16S rRNA-encoding genes. Antimicrob. Agents Chemother. 49, 578–583 (2005).

Aristoff, P. A., Garcia, G. A., Kirchhoff, P. D. & Showalter, H. H. Rifamycins–obstacles and opportunities. Tuberculosis 90, 94–118 (2010).

Finch, C. K., Chrisman, C. R., Baciewicz, A. M. & Self, T. H. Rifampin and rifabutin drug interactions: an update. Arch. Intern. Med. 162, 985–992 (2002).

Mori, H. et al. Rifabutin-based 10-day and 14-day triple therapy as a third-line and fourth-line regimen for Helicobacter pylori eradication: a pilot study. United European Gastroenterol. J. 4, 380–387 (2016).

Gisbert, J. P. & Pajares, J. M. Helicobacter pylori “rescue” therapy after failure of two eradication treatments. Helicobacter 10, 363–372 (2005).

Nishizawa, T. et al. Helicobacter pylori resistance to rifabutin in the last 7 years. Antimicrob. Agents Chemother. 55, 5374–5375 (2011).

Kunin, C. M. Antimicrobial activity of rifabutin. Clin. Infect. Dis. 22, S3–S14 (1996).

Heep, M., Beck, D., Bayerdörffer, E. & Lehn, N. Rifampin and rifabutin resistance mechanism in Helicobacter pylori. Antimicrob. Agents Chemother. 43, 1497–1499 (1999).

Heep, M., Rieger, U., Beck, D. & Lehn, N. Mutations in the beginning of the rpoBGene can induce resistance to rifamycins in both Helicobacter pylori and Mycobacterium tuberculosis. Antimicrob. Agents Chemother. 44, 1075–1077 (2000).

Mori, H., Suzuki, H., Matsuzaki, J., Masaoka, T. & Kanai, T. 10-Year trends in Helicobacter pylori eradication rates by sitafloxacin-based third-line rescue therapy. Digestion 101, 644–650 (2019).

Siavoshi, F., Saniee, P. & Malekzadeh, R. Effective antimicrobial activity of rifabutin against multidrug-resistant Helicobacter pylori. Helicobacter 23, e12531 (2018).

Chey, W. D., Leontiadis, G. I., Howden, C. W. & Moss, S. F. ACG Clinical Guideline: treatment of Helicobacter pylori infection. Am. J. Gastroenterol. 112, 212–239 (2017).

Sisson, G. et al. Enzymes associated with reductive activation and action of nitazoxanide, nitrofurans, and metronidazole in Helicobacter pylori. Antimicrobial agents chemotherapy 46, 2116–2123 (2002).

Su, Z. et al. Mutations in Helicobacter pylori porD and oorD genes may contribute to furazolidone resistance. Croatian Med. J. 47, 410–415 (2006).

Buzás, G. M. & Józan, J. Nitrofuran-based regimens for the eradication of Helicobacter pylori infection. J. Gastroenterol. Hepatol. 22, 1571–1581 (2007).

Shao, Y. et al. Antibiotic resistance of Helicobacter pylori to 16 antibiotics in clinical patients. J. Clin. Lab. Anal. 32, e22339 (2018).

Moghaddam, A. B. et al. Sensitivity to nitazoxanide among metronidazole resistant Helicobacter pylori strains in patients with gastritis. Med. J. Islamic Repub. Iran. 30, 405 (2016).

Lee, S., Sneed, G. T. & Brown, J. N. Treatment of Helicobacter pylori with nitazoxanide-containing regimens: a systematic review. Infect. Dis. 52, 381–390 (2020).

Ji, C.-R. et al. Safety of furazolidone-containing regimen in Helicobacter pylori infection: a systematic review and meta-analysis. BMJ open. 10, e037375 (2020).

Zhuge, L. et al. Furazolidone treatment for Helicobacter pylori infection: a systematic review and meta-analysis. Helicobacter 23, e12468 (2018).

Graham, D. Y. & Lu, H. Furazolidone in Helicobacter pylori therapy: misunderstood and often unfairly maligned drug told in a story of French bread. Saudi J. Gastroenterol. 18, 1–2 (2012).

EFSA Panel on Contaminants in the Food Chain (CONTAM). Scientific opinion on nitrofurans and their metabolites in food. EFSA J. 13, 4140 (2015).

International Agency for Research on Cancer (IARC). IARC monographs on the identification of carcinogenic hazards to humans. (World Health Organization, 2019).

Zullo, A., Ierardi, E., Hassan, C. & De Francesco, V. Furazolidone-based therapies for Helicobacter pylori infection: a pooled-data analysis. Saudi J. Gastroenterol. 18, 11–17 (2012).

Boyanova, L., Hadzhiyski, P., Kandilarov, N., Markovska, R. & Mitov, I. Multidrug resistance in Helicobacter pylori: current state and future directions. Expert Rev. Clin. Pharmacol. 12, 909–915 (2019).

Hirata, K. et al. Contribution of efflux pumps to clarithromycin resistance in Helicobacter pylori. J. Gastroenterol. Hepatol. 25, S75–S79 (2010).

Ge, X. et al. Bifunctional enzyme SpoT is involved in biofilm formation of Helicobacter pylori with multidrug resistance by upregulating efflux pump Hp1174 (gluP). Antimicrob. Agents Chemother. 62, e00957-18 (2018).

Bos, M. P., Tefsen, B., Geurtsen, J. & Tommassen, J. Identification of an outer membrane protein required for the transport of lipopolysaccharide to the bacterial cell surface. Proc. Natl Acad. Sci. 101, 9417–9422 (2004).

Stark, R. et al. Biofilm formation by Helicobacter pylori. Lett. Appl. Microbiol. 28, 121–126 (1999).

Cole, S. P., Harwood, J., Lee, R., She, R. & Guiney, D. G. Characterization of monospecies biofilm formation by Helicobacter pylori. J. Bacteriol. 186, 3124–3132 (2004).

Carron, M. A., Tran, V. R., Sugawa, C. & Coticchia, J. M. Identification of Helicobacter pylori biofilms in human gastric mucosa. J. Gastrointest. Surg. 10, 712–717 (2006).

Yonezawa, H. et al. Assessment of in vitro biofilm formation by Helicobacter pylori. J. Gastroenterol. Hepatol. 25, S90–S94 (2010).

Cellini, L. et al. Dynamic colonization of Helicobacter pylori in human gastric mucosa. Scand. J. Gastroenterol. 43, 178–185 (2008).

Greene, C., Vadlamudi, G., Newton, D., Foxman, B. & Xi, C. The influence of biofilm formation and multidrug resistance on environmental survival of clinical and environmental isolates of Acinetobacter baumannii. Am. J. Infect. Control. 44, e65–e71 (2016).

Madsen, J. S., Burmølle, M., Hansen, L. H. & Sørensen, S. J. The interconnection between biofilm formation and horizontal gene transfer. FEMS Immunol. Med. Microbiol. 65, 183–195 (2012).

Burmølle, M. et al. Enhanced biofilm formation and increased resistance to antimicrobial agents and bacterial invasion are caused by synergistic interactions in multispecies biofilms. Appl. Environ. Microbiol. 72, 3916–3923 (2006).

Huang, J. Y., Goers Sweeney, E., Guillemin, K. & Amieva, M. R. Multiple acid sensors control Helicobacter pylori colonization of the stomach. PLoS Pathog. 13, e1006118 (2017).

Mackay, W., Gribbon, L., Barer, M. & Reid, D. Biofilms in drinking water systems: a possible reservoir for Helicobacter pylori. J. Appl. Microbiol. 85, 52S–59S (1998).

Berry, V., Jennings, K. & Woodnutt, G. Bactericidal and morphological effects of amoxicillin on Helicobacter pylori. Antimicrob. Agents Chemother. 39, 1859–1861 (1995).

Bode, G., Mauch, F. & Malfertheiner, P. The coccoid forms of Helicobacter pylori. Criteria for their viability. Epidemiol. Infect. 111, 483–490 (1993).

Sarem, M. & Corti, R. Role of Helicobacter pylori coccoid forms in infection and recrudescence. Gastroenterol. Hepatol. 39, 28–35 (2016).

Kadkhodaei, S., Siavoshi, F. & Akbari Noghabi, K. Mucoid and coccoid Helicobacter pylori with fast growth and antibiotic resistance. Helicobacter 25, e12678 (2020).

Hathroubi, S., Servetas, S. L., Windham, I., Merrell, D. S. & Ottemann, K. M. Helicobacter pylori biofilm formation and its potential role in pathogenesis. Microbiol. Mol. Biol. Rev. 82, e00001-18 (2018).

Andersson, D. I., Nicoloff, H. & Hjort, K. Mechanisms and clinical relevance of bacterial heteroresistance. Nat. Rev. Microbiol. 17, 479–496 (2019).

Falagas, M., Makris, G., Dimopoulos, G. & Matthaiou, D. Heteroresistance: a concern of increasing clinical significance? Clin. Microbiol. Infect. 14, 101–104 (2008).

Li, J. et al. Heteroresistance to colistin in multidrug-resistant Acinetobacter baumannii. Antimicrob. Agents Chemother. 50, 2946–2950 (2006).

Ailloud, F. et al. Within-host evolution of Helicobacter pylori shaped by niche-specific adaptation, intragastric migrations and selective sweeps. Nat. Commun. 10, 1–13 (2019).

Sun, L. et al. Droplet digital PCR-based detection of clarithromycin resistance in Helicobacter pylori isolates reveals frequent heteroresistance. J. Clin. Microbiol. 56, e00019-18 (2018).

Kocsmár, É. et al. Helicobacter pylori heteroresistance to clarithromycin in adults – New data by in situ detection and improved concept. Helicobacter 25, e12670 (2020).

Kao, C.-Y. et al. Heteroresistance of Helicobacter pylori from the same patient prior to antibiotic treatment. Infect. Genet. Evol. 23, 196–202 (2014).

Hamidi, S. et al. Antibiotic resistance and clonal relatedness of Helicobacter pylori strains isolated from stomach biopsy specimens in northeast of Iran. Helicobacter 25, e12684 (2020).

Rizvanov, A., Haertlé, T., Bogomolnaya, L. & Talebi Bezmin Abadi, A. Helicobacter pylori and its antibiotic heteroresistance: a neglected issue in published guidelines. Front. Microbiol. 10, 1796 (2019).

Arévalo-Jaimes, B. V. et al. Genotypic determination of resistance and heteroresistance to clarithromycin in Helicobacter pylori isolates from antrum and corpus of Colombian symptomatic patients. BMC Infect. Dis. 19, 546 (2019).

Matteo, M. J., Granados, G., Olmos, M., Wonaga, A. & Catalano, M. Helicobacter pylori amoxicillin heteroresistance due to point mutations in PBP-1A in isogenic isolates. J. Antimicrob. Chemother. 61, 474–477 (2008).

Alebouyeh, M. et al. Impacts of H. pylori mixed-infection and heteroresistance on clinical outcomes. Gastroenterol. Hepatol. Bed Bench 8, S1–S5 (2015).

Kim, J. J., Kim, J. G. & Kwon, D. H. Mixed-infection of antibiotic susceptible and resistant Helicobacter pylori isolates in a single patient and underestimation of antimicrobial susceptibility testing. Helicobacter 8, 202–206 (2003).

Farzi, N. et al. Characterization of clarithromycin heteroresistance among Helicobacter pylori strains isolated from the antrum and corpus of the stomach. Folia Microbiol. 64, 143–151 (2019).

Dore, M. P., Leandro, G., Realdi, G., Sepulveda, A. R. & Graham, D. Y. Effect of pretreatment antibiotic resistance to metronidazole and clarithromycin on outcome of Helicobacter pylori therapy. Dig. Dis. Sci. 45, 68–76 (2000).

Fischbach, L. & Evans, E. L. Meta-analysis: the effect of antibiotic resistance status on the efficacy of triple and quadruple first-line therapies for Helicobacter pylori. Aliment. Pharmacol. Ther. 26, 343–357 (2007).

Gisbert, J. P. & Calvet, X. Update on non-bismuth quadruple (concomitant) therapy for eradication of Helicobacter pylori. Clin. Exp. Gastroenterol. 5, 23 (2012).

Greenberg, E. R. et al. 14-day triple, 5-day concomitant, and 10-day sequential therapies for Helicobacter pylori infection in seven Latin American sites: a randomised trial. Lancet 378, 507–514 (2011).

Luther, J. et al. Empiric quadruple vs. triple therapy for primary treatment of Helicobacter pylori infection: systematic review and meta-analysis of efficacy and tolerability. Am. J. Gastroenterol. 105, 65–73 (2010).

Zou, Y. et al. The effect of antibiotic resistance on Helicobacter pylori eradication efficacy: a systematic review and meta-analysis. Helicobacter 25, e12714 (2020).

Malfertheiner, P. et al. Helicobacter pylori eradication with a capsule containing bismuth subcitrate potassium, metronidazole, and tetracycline given with omeprazole versus clarithromycin-based triple therapy: a randomised, open-label, non-inferiority, phase 3 trial. Lancet 377, 905–913 (2011).

Smith, S. M., O’Morain, C. & McNamara, D. Antimicrobial susceptibility testing for Helicobacter pylori in times of increasing antibiotic resistance. World J. Gastroenterol. 20, 9912 (2014).

Mégraud, F. & Lehours, P. Helicobacter pylori detection and antimicrobial susceptibility testing. Clin. Microbiol. Rev. 20, 280–322 (2007).

Debets-Ossenkopp, Y., Brinkman, A., Kuipers, E., Vandenbroucke-Grauls, C. & Kusters, J. Explaining the bias in the 23S rRNA gene mutations associated with clarithromycin resistance in clinical isolates of Helicobacter pylori. Antimicrob. Agents Chemother. 42, 2749–2751 (1998).

Dore, M. P. et al. Amoxycillin resistance is one reason for failure of amoxycillin-omeprazole treatment of Helicobacter pylori infection. Aliment. Pharmacol. ther. 12, 635–639 (1998).

Ecclissato, C. et al. Increased primary resistance to recommended antibiotics negatively affects Helicobacter pylori eradication. Helicobacter 7, 53–59 (2002).

Trieber, C. A. & Taylor, D. E. Mutations in the 16S rRNA genes of Helicobacter pylori mediate resistance to tetracycline. J. Bacteriol. 184, 2131–2140 (2002).

Realdi, G. et al. Pretreatment antibiotic resistance in Helicobacter pylori infection: results of three randomized controlled studies. Helicobacter 4, 106–112 (1999).

Nishizawa, T. et al. Enhancement of amoxicillin resistance after unsuccessful Helicobacter pylori eradication. Antimicrob. Agents Chemother. 55, 3012–3014 (2011).

Graham, D. Y., Lee, Y. C. & Wu, M. S. Rational Helicobacter pylori therapy: evidence-based medicine rather than medicine-based evidence. Clin. Gastroenterol. Hepatol. 12, 177–186.e3 (2014).

Noach, L., Rolf, T. & Tytgat, G. Electron microscopic study of association between Helicobacter pylori and gastric and duodenal mucosa. J. Clin. Pathol. 47, 699–704 (1994).

De Francesco, V. et al. Role of MIC levels of resistance to clarithromycin and metronidazole in Helicobacter pylori eradication. J. Antimicrob. Chemother. 74, 772–774 (2019).

Graham, D. Y. et al. Factors influencing the eradication of Helicobacter pylori with triple therapy. Gastroenterology 102, 493–496 (1992).

Buring, S. M., Winner, L. H., Hatton, R. C. & Doering, P. L. Discontinuation rates of Helicobacter pylori treatment regimens: a meta-analysis. Pharmacotherapy 19, 324–332 (1999).

Tang, H.-L., Li, Y., Hu, Y.-F., Xie, H.-G. & Zhai, S.-D. Effects of CYP2C19 loss-of-function variants on the eradication of H. pylori infection in patients treated with proton pump inhibitor-based triple therapy regimens: a meta-analysis of randomized clinical trials. PLoS ONE 8, e62162 (2013).

Horikawa, C. et al. High risk of failing eradication of Helicobacter pylori in patients with diabetes: a meta-analysis. Diabetes Res. Clin. Pract. 106, 81–87 (2014).

Kaneko, F. et al. High prevalence rate of Helicobacter pylori resistance to clarithromycin during long-term multiple antibiotic therapy for chronic respiratory disease cause by nontuberculous mycobacteria. Aliment. Pharmacol. Ther. 20 (Suppl. 1), 62–67 (2004).

Adamsson, I., Edlund, C. & Nord, C. Impact of treatment of Helicobacter pylori on the normal gastrointestinal microflora. Clin. Microbiol. Infect. 6, 175–177 (2000).

Jakobsson, H. et al. Macrolide resistance in the normal microbiota after Helicobacter pylori treatment. Scand. J. Infect. Dis. 39, 757–763 (2007).

Chen, L. et al. The impact of Helicobacter pylori infection, eradication therapy and probiotic supplementation on gut microenvironment homeostasis: an open-label, randomized clinical trial. EBioMedicine 35, 87–96 (2018).

Yang, L. et al. Helicobacter pylori infection aggravates dysbiosis of gut microbiome in children with gastritis. Front. Cell. Infect. Microbiol. 9, 375 (2019).

Wu, L. et al. Effects of anti-H. pylori triple therapy and a probiotic complex on intestinal microbiota in duodenal ulcer. Sci. Rep. 9, 12874 (2019).

Iino, C. et al. Infection of Helicobacter pylori and atrophic gastritis influence Lactobacillus in gut microbiota in a Japanese population. Front. Immunol. 9, 712 (2018).

Guo, Y. et al. Effect of Helicobacter pylori on gastrointestinal microbiota: a population-based study in Linqu, a high-risk area of gastric cancer. Gut 69, 1598–1607 (2020).

Megraud, F. Resistance of Helicobacter pylori to antibiotics. Aliment. Pharmacol. Ther. 11, 43–53 (1997).

Hombach, M., Zbinden, R. & Böttger, E. C. Standardisation of disk diffusion results for antibiotic susceptibility testing using the sirscan automated zone reader. BMC Microbiol. 13, 225 (2013).

Smith, S., Fowora, M. & Pellicano, R. Infections with Helicobacter pylori and challenges encountered in Africa. World J. Gastroenterol. 25, 3183 (2019).

Şen, N., Yilmaz, Ö., Şımşek, İ., Küpelıoğlu, A. A. & Ellıdokuz, H. Detection of Helicobacter pylori DNA by a simple stool PCR method in adult dyspeptic patients. Helicobacter 10, 353–359 (2005).

Clayton, C., Kleanthous, H., Coates, P., Morgan, D. & Tabaqchali, S. Sensitive detection of Helicobacter pylori by using polymerase chain reaction. J. Clin. Microbiol. 30, 192–200 (1992).

van Doorn, L.-J. et al. Accurate prediction of macrolide resistance in Helicobacter pylori by a PCR line probe assay for detection of mutations in the 23S rRNA gene: multicenter validation study. Antimicrob. Agents Chemother. 45, 1500–1504 (2001).

Schabereiter-Gurtner, C. et al. Novel real-time PCR assay for detection of Helicobacter pylori infection and simultaneous clarithromycin susceptibility testing of stool and biopsy specimens. J. Clin. Microbiol. 42, 4512–4518 (2004).

Mitui, M., Patel, A., Leos, N. K., Doern, C. D. & Park, J. Y. Novel Helicobacter pylori sequencing test identifies high rate of clarithromycin resistance. J. Pediatric Gastroenterol. Nutr. 59, 6–9 (2014).

Rüssmann, H. et al. Rapid and accurate determination of genotypic clarithromycin resistance in cultured Helicobacter pylori by fluorescent in situ hybridization. J. Clin. Microbiol. 39, 4142–4144 (2001).

Nishizawa, T. & Suzuki, H. Mechanisms of Helicobacter pylori antibiotic resistance and molecular testing. Front. Mol. Biosci. 1, 19 (2014).

Nishizawa, T. et al. Rapid detection of point mutations conferring resistance to fluoroquinolone in gyrA of Helicobacter pylori by allele-specific PCR. J. Clin. Microbiol. 45, 303–305 (2007).

Patel, S. K., Pratap, C. B., Jain, A. K., Gulati, A. K. & Nath, G. Diagnosis of Helicobacter pylori: what should be the gold standard? World J. Gastroenterol. 20, 12847–12859 (2014).

Ciesielska, U., Jagoda, E. & Marciniak, Z. Value of PCR technique in detection of Helicobacter pylori in paraffin-embedded material. Folia Histochem. Cytobiol. 40, 129–130 (2002).

Maljkovic, I. B. et al. Next generation sequencing and bioinformatics methodologies for infectious disease research and public health: approaches, applications, and considerations for development of laboratory capacity. J. Infect. Dis. 221 (Suppl. 3), 292–307 (2020).

Hendriksen, R. S. et al. Using genomics to track global antimicrobial resistance. Front. Public Health 7, 242 (2019).

Su, M., Satola, S. W. & Read, T. D. Genome-based prediction of bacterial antibiotic resistance. J. Clin. Microbiol. 57, e01405-18 (2019).

Gardy, J. L. & Loman, N. J. Towards a genomics-informed, real-time, global pathogen surveillance system. Nat. Rev. Genet. 19, 9–20 (2018).

Goldberg, B., Sichtig, H., Geyer, C., Ledeboer, N. & Weinstock, G. M. Making the leap from research laboratory to clinic: challenges and opportunities for next-generation sequencing in infectious disease diagnostics. mBio 6, e01888-15e01888-15 (2015).

MacCannell, D. Next generation sequencing in clinical and public health microbiology. Clin. Microbiol. Newsl. 38, 169–176 (2016).

Moss, E. L., Maghini, D. G. & Bhatt, A. S. Complete, closed bacterial genomes from microbiomes using nanopore sequencing. Nat. Biotechnol. 38, 701–707 (2020).

D’Elios, M. M. & Czinn, S. J. Immunity, inflammation, and vaccines for Helicobacter pylori. Helicobacter 19, 19–26 (2014).

Zeng, M. et al. Efficacy, safety, and immunogenicity of an oral recombinant Helicobacter pylori vaccine in children in China: a randomised, double-blind, placebo-controlled, phase 3 trial. Lancet 386, 1457–1464 (2015).

Graham, D. Y. & Dore, M. P. Helicobacter pylori therapy: a paradigm shift. Expert Rev. Anti Infect. Ther. 14, 577–585 (2016).

Hori, Y. et al. 1-[5-(2-Fluorophenyl)-1-(pyridin-3-ylsulfonyl)-1H-pyrrol-3-yl]-N-methylmethanamine monofumarate (TAK-438), a novel and potent potassium-competitive acid blocker for the treatment of acid-related diseases. J. Pharmacol. Exp. Ther. 335, 231–238 (2010).

Murakami, K. et al. Vonoprazan, a novel potassium-competitive acid blocker, as a component of first-line and second-line triple therapy for Helicobacter pylori eradication: a phase III, randomised, double-blind study. Gut 65, 1439–1446 (2016).

Kiyotoki, S., Nishikawa, J. & Sakaida, I. Efficacy of vonoprazan for Helicobacter pylori eradication. Int. Med. 59, 153–161 (2020).

McFarland, L. V., Huang, Y., Wang, L. & Malfertheiner, P. Systematic review and meta-analysis: multi-strain probiotics as adjunct therapy for Helicobacter pylori eradication and prevention of adverse events. United European Gastroenterol. J. 4, 546–561 (2016).

Zhang, M.-M., Qian, W., Qin, Y.-Y., He, J. & Zhou, Y.-H. Probiotics in Helicobacter pylori eradication therapy: a systematic review and meta-analysis. World J. Gastroenterol. 21, 4345–4357 (2015).

Shi, X. et al. Efficacy and safety of probiotics in eradicating Helicobacter pylori: a network meta-analysis. Medicine 98, e15180 (2019).

Mégraud, F., Occhialini, A. & Rossignol, J. F. Nitazoxanide, a potential drug for eradication of Helicobacter pylori with no cross-resistance to metronidazole. Antimicrob. Agents Chemother. 42, 2836–2840 (1998).

Yamamoto, Y. et al. Nitazoxanide, a nitrothiazolide antiparasitic drug, is an anti-Helicobacter pylori agent with anti-vacuolating toxin activity. Chemotherapy 45, 303–312 (1999).

Mohammadi, M., Attaran, B., Malekzadeh, R. & Graham, D. Y. Furazolidone, an underutilized drug for H. pylori eradication: lessons from Iran. Dig. Dis. Sci. 62, 1890–1896 (2017).

Matsuzaki, J. et al. Efficacy of sitafloxacin-based rescue therapy for Helicobacter pylori after failures of first- and second-line therapies. Antimicrob. Agents Chemother. 56, 1643–1645 (2012).

Sugimoto, M. et al. High Helicobacter pylori cure rate with sitafloxacin-based triple therapy. Aliment. Pharmacol. Therapeut. 42, 477–483 (2015).

Nilius, A. M. et al. In vitro antibacterial potency and spectrum of ABT-492, a new fluoroquinolone. Antimicrob. Agents Chemother. 47, 3260–3269 (2003).

Van Bambeke, F. Delafloxacin, a non-zwitterionic fluoroquinolone in phase III of clinical development: evaluation of its pharmacology, pharmacokinetics, pharmacodynamics and clinical efficacy. Future microbiol. 10, 1111–1123 (2015).

Mori, H., Suzuki, H., Matsuzaki, J., Masaoka, T. & Kanai, T. Antibiotic resistance and gyrA mutation affect the efficacy of 10-day sitafloxacin-metronidazole-esomeprazole therapy for Helicobacter pylori in penicillin allergic patients. United European Gastroenterol. J. 5, 796–804 (2017).

Suzuki, H., Nishizawa, T., Muraoka, H. & Hibi, T. Sitafloxacin and garenoxacin may overcome the antibiotic resistance of Helicobacter pylori with gyrA mutation. Antimicrob. Agents Chemother. 53, 1720–1721 (2009).

Shah, S. C., Iyer, P. G. & Moss, S. F. AGA clinical practice update on the management of refractory Helicobacter pylori infection: expert review. Gastroenterology 160, 1831–1841 (2021).

Hong, J. et al. Antibiotic resistance and CYP2C19 polymorphisms affect the efficacy of concomitant therapies for Helicobacter pylori infection: an open-label, randomized, single-centre clinical trial. J. Antimicrob. Chemother. 71, 2280–2285 (2016).

Berthenet, E. et al. A GWAS on Helicobacter pylori strains points to genetic variants associated with gastric cancer risk. BMC Biol. 16, 84 (2018).

Windham, I. H. et al. Helicobacter pylori biofilm formation is differentially affected by common culture conditions, and proteins play a central role in the biofilm matrix. Appl. Environ. Microbiol. 84, e00391-18 (2018).

Chen, X. et al. Rhamnolipid-involved antibiotics combinations improve the eradication of Helicobacter pylori biofilm in vitro: a comparison with conventional triple therapy. Microb. Pathog. 131, 112–119 (2019).

Tsugawa, H. et al. Alpha-ketoglutarate oxidoreductase, an essential salvage enzyme of energy metabolism, in coccoid form of Helicobacter pylori. Biochem. Biophys. Res. Commun. 376, 46–51 (2008).

Hindson, B. J. et al. High-throughput droplet digital PCR system for absolute quantitation of DNA copy number. Anal. Chem. 83, 8604–8610 (2011).

Talarico, S. et al. High prevalence of Helicobacter pylori clarithromycin resistance mutations among Seattle patients measured by droplet digital PCR. Helicobacter 23, e12472 (2018).

Sedlak, R. H., Kuypers, J. & Jerome, K. R. A multiplexed droplet digital PCR assay performs better than qPCR on inhibition prone samples. Diagn. Microbiol. Infect. Dis. 80, 285–286 (2014).

Lee, K. H. et al. Can aminoglycosides be used as a new treatment for Helicobacter pylori? In vitro activity of recently isolated Helicobacter pylori. Infect. Chemother. 51, 10–20 (2019).

Jeong, S. J. et al. Gentamicin-intercalated smectite as a new therapeutic option for Helicobacter pylori eradication. J. Antimicrob. Chemother. 73, 1324–1329 (2018).

Shi, J., Jiang, Y. & Zhao, Y. Promising in vitro and in vivo inhibition of multidrug-resistant Helicobacter pylori by linezolid and novel oxazolidinone analogues. J. Glob. Antimicrob. Resist. 7, 106–109 (2016).

Kiga, K. et al. Development of CRISPR-Cas13a-based antimicrobials capable of sequence-specific killing of target bacteria. Nat. Commun. 11, 2934 (2020).

Latham, S. R., Labigne, A. & Jenks, P. J. Production of the RdxA protein in metronidazole-susceptible and -resistant isolates of Helicobacter pylori cultured from treated mice. J. Antimicrob. Chemother. 49, 675–678 (2002).

Kim, S. Y. et al. Genetic analysis of Helicobacter pylori clinical isolates suggests resistance to metronidazole can occur without the loss of functional RdxA. J. Antibiot. 62, 43–50 (2009).

Binh, T. T., Suzuki, R., Trang, T. T. H., Kwon, D. H. & Yamaoka, Y. Search for novel candidate mutations for metronidazole resistance in Helicobacter pylori using next-generation sequencing. Antimicrob. Agents Chemother. 59, 2343–2348 (2015).

Suzuki, S. et al. Past rifampicin dosing determines rifabutin resistance of Helicobacter pylori. Digestion 79, 1–4 (2009).

Den Dunnen, J. & Antonarakis, S. Nomenclature for the description of human sequence variations. Hum. Genet. 109, 121–124 (2001).

Ogino, S. et al. Standard mutation nomenclature in molecular diagnostics: practical and educational challenges. J. Mol. Diag. 9, 1–6 (2007).

Clinical and Laboratory Standards Institute. Performance standards for antimicrobial susceptibility testing. (Clinical and Laboratory Standards Institute, 2016).

Kahlmeter, G. et al. European Committee on Antimicrobial Susceptibility Testing (EUCAST) technical notes on antimicrobial susceptibility testing. Clin. Microbiol. Infect. 12, 501–503 (2006).

Gao, C. et al. Eradication treatment of Helicobacter pylori infection based on molecular pathologic antibiotic resistance. Infect. Drug. Resist. 13, 69–79 (2020).

Luo, X.-F. et al. Establishment of a nested-ASP-PCR method to determine the clarithromycin resistance of Helicobacter pylori. World J. Gastroenterol. 22, 5822–5830 (2016).

Ménard, A., Santos, A., Mégraud, F. & Oleastro, M. PCR-restriction fragment length polymorphism can also detect point mutation A2142C in the 23S rRNA gene, associated with Helicobacter pylori resistance to clarithromycin. Antimicrob. Agents Chemother. 46, 1156–1157 (2002).

Occhialini, A. et al. Macrolide resistance in Helicobacter pylori: rapid detection of point mutations and assays of macrolide binding to ribosomes. Antimicrob. Agents Chemother. 41, 2724–2728 (1997).

Szczebara, F., Dhaenens, L., Vincent, P. & Husson, M. Evaluation of rapid molecular methods for detection of clarithromycin resistance in Helicobacter pylori. Eur. J. Clin. Microbiol. Infect. Dis. 16, 162–164 (1997).

Versalovic, J. et al. Point mutations in the 23S rRNA gene of Helicobacter pylori associated with different levels of clarithromycin resistance. J. Antimicrob. Chemother. 40, 283–286 (1997).

Ribeiro, M. L. et al. Detection of high-level tetracycline resistance in clinical isolates of Helicobacter pylori using PCR-RFLP. FEMS Immunol. Med. Microbiol. 40, 57–61 (2004).

Stone, G. G. et al. A PCR-oligonucleotide ligation assay to determine the prevalence of 23S rRNA gene mutations in clarithromycin-resistant Helicobacter pylori. Antimicrob. Agents Chemother. 41, 712–714 (1997).

Nahm, J. H., Kim, W. K., Kwon, Y. & Kim, H. Detection of Helicobacter pylori with clarithromycin resistance-associated mutations using peptide nucleic acid probe-based melting point analysis. Helicobacter 24, e12634 (2019).

Lehours, P., Siffré, E. & Mégraud, F. DPO multiplex PCR as an alternative to culture and susceptibility testing to detect Helicobacter pylori and its resistance to clarithromycin. BMC Gastroenterol. 11, 112 (2011).

Pina, M., Occhialini, A., Monteiro, L., Doermann, H.-P. & Mégraud, F. Detection of point mutations associated with resistance of Helicobacter pylori to clarithromycin by hybridization in liquid phase. J. Clin. Microbiol. 36, 3285–3290 (1998).

Van Doorn, L. J. et al. Rapid detection, by PCR and reverse hybridization, of mutations in the Helicobacter pylori 23S rRNA gene, associated with macrolide resistance. Antimicrob. Agents Chemother. 43, 1779–1782 (1999).

Maeda, S. et al. Detection of clarithromycin-resistant Helicobacter pylori strains by a preferential homoduplex formation assay. J. Clin. Microbiol. 38, 210–214 (2000).

Alarcón, T., Domingo, D., Prieto, N. & Lopez-Brea, M. Clarithromycin resistance stability in Helicobacter pylori: influence of the MIC and type of mutation in the 23S rRNA. J. Antimicrob. Chemother. 46, 613–616 (2000).

Chisholm, S. A., Owen, R. J., Teare, E. L. & Saverymuttu, S. PCR-based diagnosis of Helicobacter pylori infection and real-time determination of clarithromycin resistance directly from human gastric biopsy samples. J. Clin. Microbiol. 39, 1217–1220 (2001).

Gibson, J., Saunders, N., Burke, B. & Owen, R. Novel method for rapid determination of clarithromycin sensitivity in Helicobacter pylori. J. Clin. Microbiol. 37, 3746–3748 (1999).

Matsumura, M. et al. Rapid detection of mutations in the 23S rRNA gene of Helicobacter pylori that confers resistance to clarithromycin treatment to the bacterium. J. Clin. Microbiol. 39, 691–695 (2001).

Oleastro, M. et al. Real-time PCR assay for rapid and accurate detection of point mutations conferring resistance to clarithromycin in Helicobacter pylori. J. Clin. Microbiol. 41, 397–402 (2003).

Glocker, E., Berning, M., Gerrits, M., Kusters, J. & Kist, M. Real-time PCR screening for 16S rRNA mutations associated with resistance to tetracycline in Helicobacter pylori. Antimicrob. Agents Chemother. 49, 3166–3170 (2005).

Glocker, E. & Kist, M. Rapid detection of point mutations in the gyrA gene of Helicobacter pylori conferring resistance to ciprofloxacin by a fluorescence resonance energy transfer-based real-time PCR approach. J. Clin. Microbiol. 42, 2241–2246 (2004).

Da Hyun Jung, J.-H. K. et al. Peptide nucleic acid probe-based analysis as a new detection method for clarithromycin resistance in Helicobacter pylori. Gut Liver 12, 641–647 (2018).

Yilmaz, Ö. & Demiray, E. Clinical role and importance of fluorescence in situ hybridization method in diagnosis of H pylori infection and determination of clarithromycin resistance in H pylori eradication therapy. World J. Gastroenterol. 13, 671–675 (2007).

Trebesius, K. et al. Rapid and specific detection of Helicobacter pylori macrolide resistance in gastric tissue by fluorescent in situ hybridisation. Gut 46, 608–614 (2000).

Cerqueira, L. et al. PNA-FISH as a new diagnostic method for the determination of clarithromycin resistance of Helicobacter pylori. BMC Microbiol. 11, 101 (2011).

Latham, S. R., Owen, R. J., Elviss, N. C., Labigne, A. & Jenks, P. J. Differentiation of metronidazole-sensitive and -resistant clinical isolates of Helicobacter pylori by immunoblotting with antisera to the RdxA protein. J. Clin. Microbiol. 39, 3052–3055 (2001).

Fauzia, K. A. et al. Biofilm formation and antibiotic resistance phenotype of Helicobacter pylori clinical isolates. Toxins 12, 473 (2020).

Slatko, B. E., Gardner, A. F. & Ausubel, F. M. Overview of next-generation sequencing technologies. Curr. Protoc. Mol. Biol. 122, e59 (2018).