Study results from Switzerland come as clinical laboratory scientists seek new ways to tackle the problem of antimicrobial resistance in hospitals
Microbiologists and clinical laboratory scientists engaged in the fight against antibiotic-resistant (aka, antimicrobial resistant) bacteria will be interested in a recent study conducted at the University of Basel and University Hospital Basel in Switzerland. The epidemiologists involved in the study discovered that some of these so-called “superbugs” can remain in the body for as long as nine years continuing to infect the host and others.
The researchers wanted to see how two species of drug-resistant bacteria—K. pneumoniae and E. coli—changed over time in the body, according to a press release from the university. They analyzed samples of the bacteria collected from patients who were admitted to the hospital over a 10-year period, focusing on older individuals with pre-existing conditions. They found that K. pneumoniae persisted for up to 4.5 years (1,704 days) and E. coli persisted for up to nine years (3,376 days).
“These patients not only repeatedly become ill themselves, but they also act as a source of infection for other people—a reservoir for these pathogens,” said Lisandra Aguilar-Bultet, PhD, the study’s lead author, in the press release.
“This is crucial information for choosing a treatment,” explained Sarah Tschudin Sutter, MD, Head of the Division of Infectious Diseases and Hospital Epidemiology, and of the Division of Hospital Epidemiology, who specializes in hospital-acquired infections and drug-resistant pathogens. Sutter led the Basel University study.
“The issue is that when patients have infections with these drug-resistant bacteria, they can still carry that organism in or on their bodies even after treatment,” said epidemiologist Maroya Spalding Walters, MD (above), who leads the Antimicrobial Resistance Team in the Division of Healthcare Quality Promotion at the federal Centers for Disease Control and Prevention (CDC). “They don’t show any signs or symptoms of illness, but they can get infections again, and they can also transmit the bacteria to other people.” Clinical laboratories working with microbiologists on antibiotic resistance will want to follow the research conducted into these deadly pathogens. (Photo copyright: Centers for Disease Control and Prevention.)
COVID-19 Pandemic Increased Antibiotic Resistance
The Basel researchers looked at 76 K. pneumoniae isolates recovered from 19 patients and 284 E. coli isolates taken from 61 patients, all between 2008 and 2018. The study was limited to patients in which the bacterial strains were detected from at least two consecutive screenings on admission to the hospital.
“DNA analysis indicates that the bacteria initially adapt quite quickly to the conditions in the colonized parts of the body, but undergo few genetic changes thereafter,” the Basel University press release states.
The researchers also discovered that some of the samples, including those from different species, had identical mechanisms of drug resistance, suggesting that the bacteria transmitted mobile genetic elements such as plasmids to each other.
One limitation of the study, the authors acknowledged, was that they could not assess the patients’ exposure to antibiotics.
Meanwhile, recent data from the World Health Organization (WHO) suggests that the COVID-19 pandemic might have exacerbated the challenges of antibiotic resistance. Even though COVID-19 is a viral infection, WHO scientists found that high percentages of patients hospitalized with the disease between 2020 and 2023 received antibiotics.
“While only 8% of hospitalized patients with COVID-19 had bacterial co-infections requiring antibiotics, three out of four or some 75% of patients have been treated with antibiotics ‘just in case’ they help,” the WHO stated in a press release.
WHO uses an antibiotic categorization system known as AWaRe (Access, Watch, Reserve) to classify antibiotics based on risk of resistance. The most frequently prescribed antibiotics were in the “Watch” group, indicating that they are “more prone to be a target of antibiotic resistance and thus prioritized as targets of stewardship programs and monitoring.”
“When a patient requires antibiotics, the benefits often outweigh the risks associated with side effects or antibiotic resistance,” said Silvia Bertagnolio, MD, Unit Head in the Antimicrobial resistance (AMR) Division at the WHO in the press release. “However, when they are unnecessary, they offer no benefit while posing risks, and their use contributes to the emergence and spread of antimicrobial resistance.”
Citing research from the National Institutes of Health (NIH), NPR reported that in the US, hospital-acquired antibiotic-resistant infections increased 32% during the pandemic compared with data from just before the outbreak.
“While that number has dropped, it still hasn’t returned to pre-pandemic levels,” NPR noted.
The UPenn researchers have already developed an antimicrobial treatment derived from guava plants that has proved effective in mice, Vox reported. They’ve also trained an AI model to scan the proteomes of extinct organisms.
“The AI identified peptides from the woolly mammoth and the ancient sea cow, among other ancient animals, as promising candidates,” Vox noted. These, too, showed antimicrobial properties in tests on mice.
These findings can be used by clinical laboratories and microbiologists in their work with hospital infection control teams to better identify patients with antibiotic resistant strains of bacteria who, after discharge, may show up at the hospital months or years later.
Many clinical laboratory professionals are aware of the significant amount of waste going into landfills from spent COVID-19 rapid PCR tests that use biosensors to produce results. These biosensor systems “use printed circuit boards, or PCBs, the same materials used in computers. PCBs are difficult to recycle and slow to biodegrade, using large amounts of metal, plastic, and non-eco-friendly materials,” according to a Penn Engineering Today blog post.
UPenn’s new test does not use PCBs. Instead, its biosensor uses “bacterial cellulose (BC), an organic compound synthesized from several strains of bacteria,” the blog post noted.
“This new BC test is non-toxic, naturally biodegradable and both inexpensive and scalable to mass production, currently costing less than $4.00 per test to produce. Its cellulose fibers do not require the chemicals used to manufacture paper, and the test is almost entirely biodegradable,” the blog post continued.
“There is a need for biodegradable diagnostic testing,” said Cesar de la Fuente, PhD (above), Presidential Assistant Professor in the Psychiatry Department at the University of Pennsylvania’s Perelman School of Medicine. “We will be continuing to perfect this technology, which could hopefully help many people in the future, while also looking to expand it to other emerging pathogens in anticipation of future pandemics.” Clinical laboratories engaged in SARS-CoV-2 testing during the COVID-19 pandemic can attest to the massive amounts of waste generated by traditional PCR testing. (Photo copyright: University of Pennsylvania.)
Evolution of Improvement for SARS-CoV-2 Diagnostic Assays
Cesar de la Fuente, PhD, is Presidential Assistant Professor in the Psychiatry Department at the Perelman School of Medicine. His lab has been hard at work since the start of the pandemic to improve COVID-19 testing. The recent study was a collaboration between University of Pennsylvania’s de la Fuente Lab and William Reis de Araujo, Professor in Analytical Chemistry at the State University of Campinas (UNICAMP) in São Paulo, Brazil.
De Araujo leads the Portable Chemical Sensors Lab and has been pairing his electrochemistry expertise with de la Fuente’s lab for years, Penn Engineering Today noted.
The team wanted to combine the speed and cost-effectiveness of previous rapid tests with an eco-friendly biodegradable substrate material.
Bacterial cellulose (BC) was a great choice because it “naturally serves as a factory for the production of cellulose, a paper-like substance which can be used as the basis for biosensors,” Penn Engineering Today reported.
Additionally, BC has an excellent track record for a variety of uses, such as regenerative medicine, wound care, and point-of-care (POC) diagnostics, the blog post noted. UPenn’s test offers speed and accuracy without needing costly equipment making it desirable for clinical laboratories preparing to fight the next pandemic.
The test has shown to be capable of “correctly identifying multiple variants in under 10 minutes. This means that the tests won’t require ‘recalibration’ to accurately test for new variants,” Penn Engineering Today added.
Innovation Born from Inspiration
Though rapid tests are essential to help curb the spread of COVID-19, the negatives that come with these tests didn’t sit well with the UPenn team. This spurred them to strive for improvements.
PCR tests “are hampered by waste [metal, plastic, and the aforementioned PCBs]. They require significant time [results can take up to a day or more] as well as specialized equipment and labor, all of which increase costs,” Penn Engineering Today noted.
Additionally, “Sophistication of PCR tests makes them harder to tweak and therefore slower to respond to new variants,” the blog post concluded.
“There’s a tension between these two worlds of innovation and conservation,” de la Fuente told Penn Engineering Today. “When we create new technology, we have a responsibility to think through the consequences for the planet and to find ways to mitigate the environmental impact.”
Need for Biodegradable Diagnostic Tests
“COVID-19 has led to over 6.8 million deaths worldwide and continues to affect millions of people, primarily in low-income countries and communities with low vaccination coverage,” the Cell Reports Physical Science paper noted.
“There is a need for biodegradable diagnostic testing,” de la Fuentes told Penn Engineering Today. “We will be continuing to perfect this technology, which could hopefully help many people in the future, while also looking to expand it to other emerging pathogens in anticipation of future pandemics.”
While UPenn’s test will require clinical trials and FDA approval before it can become available to clinical laboratories and for point-of-care testing, it promises a bright, eco-friendly future for rapid viral testing.
The rapid diagnostic test costs less than $5 per unit and can be adapted for other diseases, the developers say, which opens a slew of possibilities for clinical laboratories
Just as the SARS-CoV-2 coronavirus spurred deployment of new vaccine technology based on messenger RNA (mRNA), the COVID-19 pandemic also could prove to be a watershed for in vitro diagnostics (IVD) innovation in ways that benefit clinical laboratories.
A Penn Medicine news release noted that “The RAPID technology … transforms the binding event between the SARS-CoV-2 viral spike protein and its receptor in the human body, the protein ACE2 (which provides the entry point for the coronavirus to hook into and infect human cells), into an electrical signal that clinicians and technicians can detect. That signal allows the test to discriminate between infected and healthy human samples. The signal can be read through a desktop instrument or a smartphone.”
Though still in its early stages, the technique potentially offers dramatically lower costs and faster results than traditional RT-PCR (reverse transcription polymerase chain reaction) molecular tests. Moreover, the RAPID technology might be useful for identifying other types of biomarkers and could be the basis for diagnostic tests that help reduce the cost-per-test in medical laboratory testing while providing comparable sensitivity and specificity to existing methodologies.
Clinical trials began on January 5, 2021, and the Penn Medicine researchers say the IVD test technology can be applied to other infectious diseases, which, if proven accurate, would be a boon to clinical laboratory testing.
Diagnostic Test Results in Four Minutes for Less than $5/Test
According to the news release, the RAPID 1.0 (Real-time Accurate Portable Impedimetric Detection prototype 1.0) biosensor test costs less than $5 and can deliver results in four minutes. The researchers reported overall accuracy of 87.1% on (139) nasal swab samples and 90% on (50) saliva samples.
The technology uses electrodes that can be mass-produced at low cost on commercially-available screen printers, the researchers said. Results can be read on electronic devices connected to a PC or smartphone.
RAPID 1.0 (above) is a low-cost COVID-19 diagnostic test developed at the César de la Fuente clinical laboratory at the Perelman School of Medicine University of Pennsylvania in Philadelphia. At less than $5/test, plus the ability to be adapted to other diseases, clinical laboratories performing disease screenings in rural or remote locations may have a new tool in the fight against infections. (Photo copyright: University of Pennsylvania.)
Does Penn Medicine’s RAPID 1.0 Test Replace Traditional RT-PCR Testing?
In their published study, the Penn Medicine researchers cited the need for “fast, reliable, inexpensive, and scalable point-of-care diagnostics.”
RT-PCR tests, they said, “are limited by their requirement of a large laboratory space, high reagent costs, multistep sample preparation, and the potential for cross-contamination. Moreover, results usually take hours to days to become available.”
Researchers who have studied the SARS-CoV-2 coronavirus know that it uses a spike-like protein to bind to angiotensin-converting enzyme 2 (ACE2) receptors on the surfaces of human cells.
As described in Penn Medicine’s published study, the biosensor contains ACE2 and other biochemical agents anchored to an electrode. When the SARS-CoV-2 coronavirus attaches to the ACE2, the biosensor transforms the chemical reaction into an electrical signal that can be measured on a device known as a potentiostat.
The researchers tested their RAPID 1.0 technology with two commercially available potentiostat models:
The researchers initially developed the electrode as a printed circuit board, which is relatively expensive. To reduce costs, they constructed a version that uses filter paper as the main component. The researchers noted that one screen printer in a lab can produce 35,000 electrodes per day, including time needed to incorporate the chemical elements. “However, it must be noted that these steps can be fully automated into a production line for industrial purposes, drastically reducing time requirements,” they wrote.
The test can be performed at room temperature, they added, and total cost per unit is $4.67. Much of that—$4.50—is for functionalizing the ACE2 recognition agent. The cost for the bare electrode is just seven cents.
“The overall cost of RAPID may be further reduced through recombinant production of ACE2 and ACE2 variants,” the researchers said, adding that the RAPID 1.0 test can detect the SARS-CoV-2 coronavirus at low concentrations correlating to the earliest stages of the COVID-19 disease.
The Penn Medicine research team was led by César de la Fuente, PhD (above), an Assistant Professor in Psychiatry, Microbiology, Chemical and Biomolecular Engineering and Bioengineering at the Perelman School of Medicine. “Prior to the pandemic, our lab was working on diagnostics for bacterial infections,” he said in the Penn Medicine news release. “But then, COVID-19 hit. We felt a responsibility to use our expertise to help—and the diagnostic space was ripe for improvements.” (Photo copyright: University of Pennsylvania.)
Testing Penn Medicine’s RAPID 1.0 Test
The researchers evaluated the technology in blinded tests with clinical samples from the Hospital of the University of Pennsylvania. The evaluation included 139 nasal swab samples, of which 109 were determined to be COVID-19 positive by RT-PCR tests and clinical assessments. Among these, the RAPID test successfully detected the SARS-CoV-2 coronavirus in 91 samples, for a sensitivity rate of 83.5%. One sample was from a patient diagnosed with the highly contagious SARS-CoV-2 Alpha variant B.1.1.7, which the test correctly identified as positive.
Among the 30 samples determined to be COVID negative, the RAPID test scored a specificity rate of 100%, meaning no false positives. Overall accuracy, including sensitivity and specificity, was 87.1%.
The researchers also analyzed 50 saliva samples: 13 COVID-positive and 37 COVID-negative. The test correctly identified all 13 positive samples but produced five false-positives among the 37 negative samples, for a specificity rate of 86.5%. The researchers speculated that this could be due to interactions between ACE2 and other biomolecules in the saliva but suggested that performance “will improve when using fresh saliva samples at the point-of-care.”
Are There Other Applications for the RAPID Test?
The Penn Medicine news release said the RAPID technology can be adapted to detect other viruses, including those that cause Influenza and sexually-transmitted diseases.
Robert Michel, Editor-in-Chief of Dark Daily and its sister publication The Dark Report, said the test points to one silver lining in the COVID-19 pandemic. “Researchers around the world intensified their work to find ways to identify the SARS-CoV-2 virus that are faster, cheaper, and more accurate than the diagnostic technologies that existed at the time of the outbreak. In this regard, the COVID-19 pandemic may have accelerated the development and refinement of useful diagnostic technologies that will disrupt long-established methods of testing.”
Marcelo Der Torossian Torres, PhD, postdoctoral researcher at Penn Medicine and lead author of the study, said in the news release, “Quick and reliable tests like RAPID allow for high-frequency testing, which can help identify asymptomatic individuals who, once they learn they are infected, will stay home and decrease spread.
“We envision this type of test being able to be used at high-populated locations such as schools, airports, stadiums, companies—or even in one’s own home,” he added.
Clinical laboratory managers may want to stay current on the development and possible commercialization of the RAPID 1.0 (Real-time Accurate Portable Impedimetric Detection prototype 1.0) biosensor test by the research team at Penn Medicine.
