Tuesday, 10 November 2026

When antibiotics cause harm: Peggy Lillis’ story puts a human face on the C. diff threat


Antibiotics are among medicine’s greatest achievements. They have turned once-lethal bacterial infections into treatable illnesses and made surgery, cancer therapy and much of modern medicine possible. Yet every antibiotic prescription also carries risk. Sometimes that risk can have devastating consequences.
 
By Tim Sandle 
 
Christian John Lillis knows this better than most. In 2010, his mother, Peggy Lillis, was a healthy 56-year-old kindergarten teacher when she underwent a root canal. According to her son’s account included in the new CDC Antimicrobial Resistance Threats Report, her dentist prescribed clindamycin. Four days later she developed diarrhoea. The family initially did not connect it with the antibiotic. Her condition deteriorated rapidly and, when she reached hospital, doctors diagnosed toxic megacolon caused by Clostridioides difficile, or C. diff, and septic shock. About a week after the dental procedure, she died. 
 
That experience ultimately led Christian John Lillis and his brother to establish the Peggy Lillis Foundation, an organisation dedicated to C. diff education and advocacy. A 2025 poll commissioned by the foundation found that 54% of 1,000 US respondents remained unfamiliar with C. diff, highlighting the continuing gap between the infection's public-health importance and public recognition. 
 
Now Christian John Lillis is bringing that patient and family perspective directly into the national conversation around antimicrobial resistance, participating in the CDC webinar Update to the Antimicrobial Resistance Threats Report: A Closer Look. His central message is deceptively simple: stewardship is not just about preserving antibiotics for the future. It is also about protecting the person receiving an antibiotic today.

What is C. diff?

Clostridioides difficile is a spore-forming bacterium capable of causing diarrhoea and inflammation of the colon. Severe disease can progress to complications including toxic megacolon, sepsis and death. Its hardy spores can also persist in the environment, facilitating transmission, particularly in healthcare settings. Its relationship with antibiotics is especially important.
 
The human intestine contains an extraordinarily complex microbial ecosystem. Collectively known as the gut microbiome, these microorganisms help occupy ecological niches and create what microbiologists call "colonisation resistance", making it harder for pathogens to proliferate.
 
Antibiotics can disturb that ecosystem. While killing the bacteria responsible for an infection, an antimicrobial can also eliminate susceptible members of the normal intestinal community. That ecological disruption can create an opportunity for C. diff to multiply and produce toxins that damage the intestinal lining.
 
The CDC therefore identifies recent antibiotic exposure as an important risk factor: the likelihood of developing C. diff is higher during antibiotic treatment and for up to three months afterwards. 
 
This does not mean that taking an antibiotic inevitably causes C. diff. Most courses do not. Risk depends on the drug, duration of treatment, individual susceptibility, healthcare exposure, age and other factors. But epidemiological evidence consistently establishes antibiotic exposure as a major modifiable risk factor for infection.
 
A large 2023 case-control study published in Open Forum Infectious Diseases, for example, compared the risks associated with different antibiotics and described antibiotic exposure as the greatest risk factor for community-associated C. diff. Importantly, risk varied substantially between antibiotic agents.

Why clindamycin matters

Peggy Lillis' treatment is particularly relevant because the antibiotic involved was clindamycin. Clindamycin has a long-recognised association with C. diff. The CDC's current guidance for dental prescribers explicitly advises avoiding clindamycin when alternatives are available because it can cause more frequent and severe adverse effects, including C. diff infection. 
 
This principle is also reflected in current American Dental Association antibiotic stewardship guidance. For odontogenic infections requiring systemic treatment, amoxicillin or penicillin V are listed as first-line options in appropriate patients, while clindamycin is reserved for circumstances in which alternatives such as azithromycin are unsuitable, specifically because of its high C. diff risk. 
 
The issue goes beyond one drug, however. Cephalosporins, fluoroquinolones, co-amoxiclav and other broad-spectrum agents have also been associated with C. diff. NICE notes that no antibiotic can be entirely excluded from the risk.
 
A 2026 real-world analysis of 201,911 patients with C. diff further illustrates this point. Among the study population, 33.9% had recorded antibiotic exposure, with extended-spectrum penicillins, third-generation cephalosporins and aminopenicillins among the most frequently used classes shortly before diagnosis. The authors argue that stewardship therefore needs to extend across antibiotic classes rather than simply targeting historically notorious agents such as clindamycin.

A major public-health burden

C. diff is sometimes viewed primarily as a hospital infection. That picture is now incomplete. In its 2026 Antimicrobial Resistance Threats Report, the CDC estimates that there were 412,504 C. diff cases in the United States in 2023, including 223,568 classified as community-associated and 188,936 as healthcare-associated. The agency estimates 11,339 deaths among hospitalised cases and more than $6.4 billion in attributable healthcare costs. 
 
Older adults remain particularly vulnerable. In 2023, the reported infection rate among those aged 65 and over was 351 cases per 100,000 people, compared with 75.5 per 100,000 among people under 65. 
 
There has nevertheless been progress. The CDC previously classified C. diff as an "urgent" antimicrobial-resistance threat. Following reductions in infections since 2011, it is now classified as a serious threat. Yet the agency cautions against complacency, particularly because community-associated infections have increased slightly since the pandemic-era decline. 
 
There is an apparent paradox here. C. diff is not primarily included in the report because it is intrinsically an antibiotic-resistant pathogen. Instead, it belongs in the antimicrobial-resistance conversation because antibiotic use and microbial transmission are forces driving both C. diff disease and antimicrobial resistance. 
 
Reducing unnecessary antibiotic exposure can therefore produce two benefits: lowering selection pressure for resistant organisms and reducing the immediate possibility of antibiotic-associated complications such as C. diff.

Dentistry and the stewardship opportunity

Peggy Lillis' case also raises questions about antibiotic use in dentistry. Modern stewardship guidance stresses that antibiotics should not substitute for definitive dental treatment. The CDC advises dentists to prioritise procedures such as drainage, extraction, pulpotomy or root-canal treatment for most appropriate dental conditions and generally not to add an antibiotic when definitive treatment is available. Systemic antibiotics become appropriate when findings indicate spreading or systemic infection, such as fever or malaise with intraoral swelling.
 
The American Dental Association similarly recommends against antibiotics for most pulpal and periapical dental pain and localised swelling in immunocompetent adults when definitive dental treatment can be provided. This is what antimicrobial stewardship looks like at the individual level: first determining whether an antibiotic is actually required, then selecting an appropriate drug, dose and duration.
 
Crucially, stewardship is not an anti-antibiotic philosophy. The Infectious Diseases Society of America and Society for Healthcare Epidemiology of America define it as coordinated interventions to improve and measure appropriate antibiotic use, including optimisation of drug selection, dose, duration and route. Among the demonstrated benefits are reductions in adverse events, including C. diff infection. Withholding an antibiotic when one is genuinely required can itself be dangerous. The objective is therefore not simply fewer antibiotics, but better antibiotic use.

Putting patients back into antimicrobial resistance

This distinction explains why the patient voice belongs alongside microbiologists, epidemiologists and infectious-disease specialists in discussions about antimicrobial resistance. Resistance is frequently communicated through abstract measures: susceptibility percentages, resistant isolates, surveillance graphs and national estimates. These are indispensable for understanding the problem, but they can obscure what antimicrobial exposure means at the level of an individual patient and family.
 
Christian John Lillis's perspective provides the missing human element. The lesson from his mother's death is not that antibiotics themselves should be feared. Indeed, he has described them as "miracle drugs" underpinning modern medicine. Rather, his argument is that society must recognise their potential harms alongside their benefits if these drugs are to be used safely and remain effective. That is the deeper connection between C. diff prevention and antimicrobial resistance.
 
Every unnecessary prescription represents an avoidable biological intervention in a patient's microbial ecosystem. Every appropriately avoided prescription reduces an individual's exposure to potential adverse effects while also reducing antibiotic selection pressure at population level.
 
Peggy Lillis' death occurred in 2010, but the science that followed has made its lesson increasingly difficult to ignore. Antibiotic stewardship is not simply a strategy for conserving medicines for some hypothetical future patient. It is a patient-safety intervention for the person sitting in the dental chair, clinic or hospital today.

Key sources

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

Saturday, 7 November 2026

History of the contact plate


 

A microbiological history: Agar contact plates are simple yet scientifically refined tools for pharmaceutical environmental monitoring. Developed as alternatives to surface swabbing, their performance depends on plate design, agar properties and sampling technique. What next? Automation may now reduce operator variability and improve microbial recovery consistency: 

READ MORE: https://www.linkedin.com/pulse/form-function-evolution-agar-contact-plate-professor-tim-djvke/

 

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

Tuesday, 3 November 2026

When Cockroaches Pollute the Air: Endotoxin, Allergens and the Hidden Health Risk in Household Dust


Cockroaches are usually regarded as an unpleasant sign of poor housing conditions. Yet their significance may extend beyond hygiene and the allergens traditionally associated with asthma. New research indicates that an infestation can substantially alter the microbial character of the indoor environment by adding large quantities of bacterial endotoxin to household dust and air.
 
Tim Sandle looks at some emerging research. 
 
A study led by researchers at North Carolina State University provides particularly persuasive evidence because the investigators did more than compare infested and uninfested homes. They followed what happened when cockroaches were eliminated. As pest control succeeded, concentrations of both cockroach allergen and endotoxin fell significantly. 
 
The findings matter because endotoxin is biologically active. Exposure can inflame the respiratory tract and has been associated with asthma and other respiratory disease. Yet its relationship with human health is surprisingly complicated. In some circumstances, particularly early-life exposures, endotoxin has even been associated with lower subsequent asthma risk. 
 
The important question, therefore, is not simply whether endotoxin is present, but where it comes from, how much people encounter, and in what biological context exposure occurs.

What exactly is endotoxin?

Despite its name, endotoxin is not a toxin actively secreted by living bacteria. The term generally refers to lipopolysaccharide (LPS), or closely related lipooligosaccharides, associated with the outer membrane of Gram-negative bacteria. These molecules act as microbial signals recognised by the innate immune system and can initiate inflammation.  That inflammatory property explains why endotoxin attracts considerable attention in occupational and environmental health.
 
High occupational exposures have been documented in agriculture, livestock facilities, grain handling, wastewater treatment, cotton processing and industrial composting. At sufficiently high exposures, endotoxin is associated with adverse respiratory effects including airway irritation, chronic bronchitis, non-allergic asthma and asthma-like syndromes.
 
The home represents a quite different exposure setting. Endotoxin can accumulate in settled dust, becoming part of the complex mixture of biological material to which occupants are exposed.
Cockroaches now appear capable of making a surprisingly large contribution to that mixture.

A microbial factory hiding in the kitchen

German cockroaches are omnivores with a diverse intestinal microbiome that includes abundant Gram-negative bacteria. The North Carolina State University investigators therefore asked whether cockroach intestines and faeces could explain the high endotoxin concentrations previously observed in infested housing.
 
Their laboratory measurements were striking. Female cockroaches excreted around 2,900 endotoxin units (EU) per milligram of faeces, compared with approximately 1,400 EU/mg in males. The researchers attributed the difference partly to females eating more food. 
 
Subsequent research strengthens the biological explanation. A 2026 study in the Journal of Medical Entomology found high levels of faecal endotoxin across cockroach life stages. Adult females produced roughly 2.5 to three times more endotoxin than males, while cockroaches whose intestines had been rendered essentially microbiota-free produced only trace amounts. The study also found that endotoxin in faecal residues remained stable for at least 30 days under ambient laboratory conditions. 
 
Together, those observations identify the cockroach gut microbiota as an important source rather than merely showing that endotoxin happens to coexist with infestations.

The experiment moves beyond correlation

This distinction is important. Previous surveys could show that homes reporting cockroaches contained more endotoxin, but that does not prove the insects produced it. Poor-quality housing could simultaneously encourage cockroach infestation and increase other microbial exposures. The new research gets closer to resolving that problem.
 
The investigators studied multi-unit apartments in Raleigh, North Carolina, measuring cockroach populations alongside the principal cockroach allergen Bla g 2 and endotoxin in household dust and HVAC filters. They compared infested homes subjected to an environmental intervention with untreated infested homes and residences without cockroaches. Measurements continued for six months following intervention. 
 
At baseline, infested homes contained significantly higher concentrations of both Bla g 2 and endotoxin than uninfested residences. Untreated infested homes remained high in both throughout the study. Where intervention successfully eliminated cockroaches, however, cockroach allergen and endotoxin concentrations declined significantly. This before-and-after intervention considerably strengthens the argument that cockroaches themselves were responsible for an important proportion of household endotoxin.
 
Location mattered too. More endotoxin was detected in kitchens than bedrooms, consistent with cockroaches congregating around readily available food. Crucially for respiratory exposure, the investigators also detected allergens and endotoxins in airborne material, not merely settled floor dust.

Why inhaled endotoxin matters

Once endotoxin becomes airborne, the issue changes from one of cleanliness to one of respiratory exposure. The immune system recognises bacterial components such as LPS as signs of microbial presence. That makes endotoxin a powerful initiator of innate inflammatory responses. Environmental endotoxin exposure has consequently been associated with respiratory disease across occupational, agricultural and domestic environments. 
 
For someone with asthma, the picture is especially relevant because a cockroach-infested home can create co-exposure. An occupant may inhale cockroach allergens capable of provoking allergic responses while simultaneously inhaling bacterial endotoxin capable of stimulating inflammatory pathways. Cockroach allergens themselves are established risk factors for allergic rhinitis and asthma, particularly among children living in low-income urban households. The authors of the new study therefore conclude that cockroaches represent a significant source of both potent allergens and endotoxin, potentially exposing susceptible children to both simultaneously. 
 
Whether the combination produces a greater clinical effect than either exposure independently remains an important unanswered question. The North Carolina State University researchers specifically identify interactions between cockroach allergen and endotoxin in experimental asthma models as a subject for further investigation.
 
The study demonstrated environmental exposure reduction, not improved asthma outcomes in the occupants.

The endotoxin paradox

There is another reason not to translate "more endotoxin" automatically into "more asthma". Epidemiological evidence reveals an apparent paradox. Indoor endotoxin can increase asthma symptoms and is associated with respiratory morbidity, yet some studies of early-life exposure, particularly in rural environments, have associated microbial or endotoxin-rich exposures with a reduced likelihood of developing asthma. 
 
An American Journal of Respiratory and Critical Care Medicine editorial described this as the "yin and yang" of endotoxin exposure. It noted evidence that early rural exposure can be protective against asthma development while endotoxin's pro-inflammatory effects can aggravate symptoms in other settings. This is not necessarily contradictory. Developing an allergic disease and triggering symptoms in somebody who already has susceptible airways are biologically different processes. Exposure timing, concentration, accompanying allergens and pollutants, underlying sensitisation and the composition of the wider microbial environment may all matter. Consequently, the new cockroach research should not be interpreted as demonstrating that every encounter with environmental endotoxin is intrinsically harmful.

A housing and environmental-health issue

The findings have an important social dimension. Cockroach allergens are particularly recognised as risk factors for asthma and allergic rhinitis among children in low-income urban households, and previous US surveys have reported a stronger association between cockroach evidence and household endotoxin in low-income housing than in single-family homes. 
 
That turns pest management into more than a matter of domestic aesthetics. Where substantial infestations occur, eliminating cockroaches can remove a biological source of both allergens and endotoxin.
The word eliminating is important. According to study co-author Coby Schal, small reductions in cockroach populations did not necessarily lower allergen concentrations because surviving insects continued depositing allergenic material. Homes in which cockroaches were successfully eliminated, by contrast, experienced significant decreases in endotoxin. The environmental endpoint is therefore meaningful: effective control changed measurable indoor contamination.
 
There is also a broader lesson here about microbial contamination. Microorganisms themselves need not remain alive for their biological components to matter. Endotoxin is a particularly clear example of why the absence of viable Gram-negative bacteria does not necessarily mean the absence of microbially derived inflammatory material.

From pest control to pollution control

Cockroaches have long occupied an uncomfortable intersection between housing quality, allergy and public health. The emerging evidence adds a further dimension: they can function as vectors of microbial material into the indoor environment, continuously depositing endotoxin-rich faeces alongside potent allergens. The strongest conclusion from the latest research is consequently quite specific. Cockroach infestation can be an important source of household endotoxin, and successfully eliminating that source significantly reduces environmental concentrations. 
 
What has not yet been demonstrated by this intervention is equally important. The research does not show how much eliminating cockroach-derived endotoxin reduces asthma attacks or other clinical outcomes, nor does it establish that endotoxin and cockroach allergens act synergistically in people. Those are questions for the next generation of studies.
 
Even so, the evidence changes how we might think about an infestation. The problem is not simply the cockroaches we can see. It is the invisible biological residue they continuously leave behind, some of which can enter the air we breathe.

Sources and further reading

 Pharmaceutical Microbiology Resources (http://www.pharmamicroresources.com/)

Sunday, 1 November 2026

Pharmig - 2026 annual conference


 

Pharmig - the only global professional body for pharmaceutical microbiologists - One day to go until Pharmig's annual conference - the 34th conference and Pharmig's 35th Birthday. It's not too late to drop in on 3rd and 4th November 2026 in the UK. Further details here: https://www.pharmig.org.uk/en/product/pharmigs-34th-annual-conference/  

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

Microbiology books

Tim Sandle's books, available via Amazon: https://amzn.to/4A9jM0A

 

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

Wednesday, 28 October 2026

CDC AMR report downgrades C. diff threat level in US


Image by ItsHong - Own work, CC BY-SA 4.0, https://commons.wikimedia.org/w/index.php?curid=144440730

 

A new report from the CDC has downgraded the threat of C. diff infections in the United States from ‘urgent’ to ‘serious’. The CDC has reported a decline in overall cases in the past 15 years, but data shows community-associated cases are on the rise.

 

The Antimicrobial Resistance Threats report provides a snapshot of the threat that bacterial and fungal pathogens pose to human health in the US. Antibiotics can disrupt the levels of helpful bacteria in the gut and create an environment for C. diff bacteria to thrive.

 

Clostridioides difficile, or C. diff, bacteria cause diarrhea and colitis (inflammation of the colon). C. diff can spread from person to person in fecal matter (poop) or by touching contaminated surfaces. These bacteria are common in health care and the natural environment. While rare, serious complications of C. diff infections can occur, including toxic megacolon (a severe intestinal condition), sepsis (the body's extreme response to an infection), and even death.

In 2023, Clostridioides difficile (C. diff) caused more than 400,000 estimated cases among hospitalized and non-hospitalized patients, more than 11,000 estimated deaths among hospitalized patients, and more than $6.4 billion in healthcare costs overall.

Previous Antimicrobial Resistance Threats Reports (AR Threats Report) only included hospitalized C. diff cases. This report expands that scope to include both hospitalized and non-hospitalized C. diff cases, offering a more comprehensive picture of C. diff's burden in the United States.

While C. diff was on CDC's urgent threats list in the 2013 and 2019 AR Threats Reports, CDC has measured declines in cases since 2011. Because of successful prevention actions, especially in healthcare settings, C. diff is now categorized as a serious threat. Still, C. diff causes substantial infections, deaths, and healthcare costs in the United States. C. diff remains one of the most common causes of healthcare-associated infections in hospitals, and there is an even greater number of community-associated cases. Continued infection control and appropriate antibiotic use remain important for sustaining progress in reducing C. diff infections. CDC will continue to monitor trends in C. diff burden and the potential for the development of resistance to treatments.

 

The story of Peggy Lillis is used in this year’s report as a reminder of the harm that antibiotic overuse can cause. The healthy 56-year-old was prescribed the antibiotic, clindamycin, following a root canal. She died from complications of C. diff about a week later.

 

“Antibiotics are miracle drugs. They underpin most modern medicine. To avoid unnecessary infections and prolong these drugs' effectiveness, we must first see both the potential harms, as well as benefits, of antibiotics,” said Peggy’s son, Christian.

 

Christian and his brother founded the Peggy Lillis Foundation in their mother’s honor to raise awareness of C. diff and educate the public about the growing threat of antimicrobial resistance. More of her story is shared in the new report, at the link below:

https://arpsp.cdc.gov/artr/cdiff#story

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

Tuesday, 27 October 2026

Robots as a Tool for Reducing Contamination in Pharmaceutical Facilities


 Image by Tim Sandle.

Robotics is becoming increasingly important in pharmaceutical contamination control, particularly where manufacturing or testing requires very low levels of microbial and particulate contamination. The central advantage is straightforward: robots can remove or reduce the human operator from critical activities. This is significant because personnel are one of the principal sources of microorganisms, particles and fibres within cleanrooms. Internal guidance on advanced robotics similarly identifies reduced human intervention in aseptic manufacture as an important means of lowering contamination risk.

This principle fits particularly well with modern Contamination Control Strategy (CCS) thinking. Rather than relying primarily upon environmental monitoring to detect contamination after it has occurred, facilities should seek to prevent contamination through appropriate engineering and process design. Isolators already contribute to this by providing a physical separation between the operator and critical processing environment. More advanced isolators go further, replacing glove-port manipulations with robotics.

Robotic environmental monitoring

One particularly useful application is the robotic handling of environmental monitoring media within an isolator. Conventionally, placing, exposing, retrieving and manipulating settle plates or other microbiological monitoring devices may require glove manipulations. Every such manipulation introduces some risk through glove contact, disturbance of airflow or accidental interference with critical surfaces.

A robotic system can instead manipulate Petri dishes in a predefined and repeatable manner. For example, a robot could position a settle plate at a defined monitoring location, remove or replace its lid as required by the validated monitoring procedure, and subsequently retrieve the plate for transfer from the isolator. The important contamination-control benefit is not that the robot is intrinsically sterile, but that the operation becomes repeatable and less dependent upon human intervention.

This is particularly attractive in gloveless isolators, where the objective is to eliminate operator intervention in the critical zone. Internal material on modern aseptic filling describes closed, automated isolators without human intervention and specifically identifies robotic systems as technologies that can increase protection from extraneous contamination sources.

Robotics can similarly be applied to vial and syringe handling, component transfer, filling, stoppering, sampling and inspection. The technology therefore supports an important principle of aseptic processing: where an intervention can reasonably be eliminated through engineering, elimination is preferable to attempting repeatedly to control the same manual intervention.

Robots beyond the isolator

Robotics can also help contamination control at room level. Autonomous mobile robots, for example, can undertake selected cleaning or disinfection activities. One technology considered internally is autonomous UV-C disinfection. The information describes robots capable of mapping their environment and performing repeatable UV-C cycles with electronic recording of parameters such as exposure time and distance.

Such systems can reduce the amount of routine manual activity within controlled environments. However, they should be viewed as part of the CCS rather than as replacements for fundamental controls such as appropriate facility design, validated cleaning and disinfection, air filtration, material transfer controls and environmental monitoring.

Qualification and contamination-control considerations

Introducing robots does not automatically remove contamination risk. It changes the nature of the risk. Robotic equipment itself requires suitable hygienic design, cleanroom-compatible materials and surfaces that can be effectively cleaned or decontaminated. Equipment movement must not disrupt critical airflow, generate unacceptable particles or create difficult-to-clean areas.

For aseptic applications, the robotic operation also needs appropriate qualification and validation. Particular attention should be given to:

  • reproducibility of movements and positioning;
  • impact on first-air protection and airflow patterns;
  • cleaning and biodecontamination compatibility;
  • particle generation and lubricant containment;
  • recovery from robot faults or dropped components;
  • interventions required following mechanical failure;
  • data integrity and software control; and
  • integration into APS/media-fill studies where applicable.

These considerations are especially important because an automated process may operate reliably hundreds of times but still require a human intervention when an abnormal event occurs. Such exceptional interventions should therefore be anticipated and designed into the contamination-control strategy, rather than regarded simply as equipment failures.

Ultimately, the greatest microbiological benefit of robotics is not speed or labour saving. It is the ability to design human intervention out of contamination-sensitive processes. A robot placing Petri dishes inside an isolator is a relatively simple example, but it illustrates a much broader direction for pharmaceutical manufacturing: moving from controlling operator-generated contamination towards removing the opportunity for that contamination to arise in the first place.

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

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