Wednesday 31 August 2022

Genetic method for identifying disease agents


In the pursuit of accurate diagnoses for illnesses, doctors have traditionally used multiple methods -- including culturing patient samples on a wide variety of media, reviewing countless medical records and analyzing clinical data using complex mathematical algorithms -- to try to identify the bacterium, virus, fungus or other pathogen responsible for an infection. The hunt is often slow and laborious, and the processes used may not be broad enough in scope to find specific disease agents.


One solution may be next-generation sequencing (NGS). NGS enables clinicians to simultaneously sequence multiple strands of DNA found in patient samples and use that analysis to rapidly and accurately identify a single pathogen -- from among hundreds of suspects.


Researchers compared the pathogen detecting ability of an NGS system -- the Respiratory Pathogen Infectious Diseases/Antimicrobial Resistance Panel (RPIP) -- with a previously studied NGS system and standard of care (SOC) diagnostic methods for samples obtained with bronchoalveolar lavage. This is where a bronchoscope is passed through the mouth or nose into the lungs, followed by a fluid wash that is collected for examination.


The researchers believe their study is among the first to compare NGS and SOC diagnostics for respiratory pathogens.


In their study, researchers first evaluated the diagnostic ability of metagenomic NGS, a previously studied workflow process during which all DNA obtained from a bronchoalveolar lavage is sequenced -- including genetic material unique to the patient (the "host read" or "human read") and the sought-after pathogen (the "microbial read"). Removing the host DNA enable clinicians to concentrate their search on the remaining genetic material to hopefully find the microbial read and ultimately, identify the cause of the patient's illness.


In the second part of their experiment, the researchers assessed a different NGS approach using the RPIP system called targeted NGS. In this method, everything in the patient respiratory sample is sequenced as with metagenomic NGS, but capture probes -- tiny fragments of single-stranded DNA that correspond structurally to the DNA of specific pathogens -- are used to enhance the searching ability.


The researchers found that the effectiveness of both the metagenomic and targeted NGS varied with the type of organism sought. They report that both NGS methods successfully identified viruses, with herpes viruses the most readily detected. Results for bacteria and mycobacteria (which include the organism causing tuberculosis) approached the level of SOC diagnostics, but dropped off as the number of organisms decreased -- even with use of the capture probes in targeted NGS. Neither NGS method detected fungi well.


Overall, the researchers found that the RIPP targeted workflow agreed with traditional diagnostics 66 percent of the time.


Along with its potential to accurately identify more than 300 pathogenic organisms from a bronchoalveolar lavage, the researchers feel that targeted NGS also shows great promise for one day being able to reveal some 1,200 genetic markers in pathogens that indicate which organisms are most likely to resist antibiotics.




David C. Gaston, Heather B. Miller, John A. Fissel, Emily Jacobs, Ethan Gough, Jiajun Wu, Eili Y. Klein, Karen C. Carroll, Patricia J. Simner. Evaluation of Metagenomic and Targeted Next-Generation Sequencing Workflows for Detection of Respiratory Pathogens from Bronchoalveolar Lavage Fluid Specimens. Journal of Clinical Microbiology, 2022; 60 (7) DOI: 10.1128/jcm.00526-22


Posted by Dr. Tim Sandle, Pharmaceutical Microbiology Resources (

Tuesday 30 August 2022

How Healthcare Apps Can Improve the Mental Health of Patients and Professionals

                                                        Image from Unsplash

Telehealth and healthcare apps have rocketed in popularity since the pandemic. In 2019, just 11% of U.S. consumers used any form of telehealth. Now, around 46% of patients use some form of telehealth service to receive access to the healthcare they need.

By Indiana Lee

The widespread adoption of telehealth technology and apps should be celebrated in the medical community. Healthcare apps make it easier than ever to connect with patients and streamline processes that were inefficient and ineffective.


Healthcare apps can also improve the mental health of patients and professionals alike. Apps that collect data and store relevant information can help patients connect with their physicians to put their minds at ease. Effective apps can also reduce healthcare professionals’ stress levels, as functional apps make it easier for them to focus on more meaningful work.

Privacy and Comfort

Patients who use apps to receive care and connect with their providers may find that their healthcare experience is more comfortable and less stressful. That’s because healthcare apps are usually discreet and offer private alternatives for folks who don’t want to seek help publicly.


Healthcare apps that champion users’ privacy may also improve uptake and improve public health. For example, many women now use birth control apps to take control of their lives and avoid unwanted pregnancies. Healthcare apps like Natural Cycles aren’t for everyone, as fertility-awareness methods have a 24% failure rate. Nonetheless, they do a great job of giving women autonomy over their fertility cycle through discreet design and constant access to data.


Healthcare apps can also provide private consultations to folks who don’t want to visit a doctor's office. Immunocompromised groups and patients who live in rural areas stand to benefit the most from private, easy-to-access telehealth. Being able to sign on to an app and see a physician may reduce the chance of further illnesses developing and ensure that everyone can access their provider when they need to.

Access to Mental Health Services

The pandemic caused a mental health crisis across the globe. The World Health Organization (WHO) recently reported a 25% rise in anxiety and depression globally as people incurred great stress and faced gaps in healthcare equity.


Healthcare apps that offer mental health services may be able to close the care gap and provide users with the support they need. Mental health apps like TalkSpace and BetterHealth give users a chance to connect with licensed therapists at times that suit them. This could improve the uptake of therapy and help folks overcome the challenges they face in the post-pandemic world.


Mental health apps are particularly well positioned to help young people and vulnerable populations. Health care apps that platform therapists are usually low-cost and offer interactive sessions with a therapist. After a consultation ends, patients can continue to use the app to track their well-being and record changes in their condition.

Greater Autonomy

Healthcare apps give users the ability to make appointments, assess their progress, interact with health data and receive remote care. This gives users greater control over their healthcare and may help patients overcome medical anxiety.


Medical anxiety is commonly caused by a fear of hospitals and doctor’s offices. Some people associate healthcare with invasive treatments and a loss of bodily autonomy. One of the best ways to alleviate these fears is to give patients greater autonomy over the care they receive.


When using a healthcare app, users can progress at their own pace and avoid in-person interactions that may cause undue stress. Over time, using healthcare apps may even alleviate phobias like Iatrophobia. Iatrophobia — fear of doctors — usually occurs when patients have a bad experience with a healthcare professional. Using an app as an intermediary may help patients maintain their boundaries while ensuring they get the healthcare they need.

IoMT and Patient Care

Healthcare apps are great for patients who suffer from medical anxiety or live busy lifestyles. This makes it easier for physicians to gather patient data and connect with their patients on time. In turn, this reduces the stress that healthcare professionals face, as their jobs are made easier by healthcare apps that utilize the Internet of Medical Things (IoMT).


The IoMT was particularly important for healthcare professionals during the height of the pandemic. Healthcare apps that effectively leveraged the IoMT protected healthcare employees by encouraging remote patient monitoring and tracking outbreaks. This reduced transmission rates in hospitals and gave healthcare professionals the ability to request resources like PPE in real time.


As we exit the pandemic, the IoMT continues to promote professionals' mental health by reducing burnout and improving engagement and satisfaction. Healthcare workers who use IoMT-integrated apps can provide a better patient experience and manage existing patients more effectively. This allows medical professionals to focus more of their attention on providing high-quality care, as they don’t have to work through complicated, poorly designed electronic healthcare records.


Healthcare apps have grown in popularity since the start of the pandemic. These apps are more than just gimmicks and can make a meaningful difference to patients and healthcare professionals alike. Mental health apps help people get the help they need, and apps that leverage the IoMT give providers and patients access to important data in real time.


Pharmaceutical Microbiology Resources (

Monday 29 August 2022

Fungal infection risks: How antibiotics affect the gut microbiota


A new finding from the University of Birmingham (U.K.) demonstrates how antibiotics can lead to fungal infection because of the disruption of the drugs to the gut's immune system, altering the microbial balance. The research relates to the hospital setting, with a focus on invasive candidiasis.


When patients are given antibiotics to prevent sepsis and other bacterial infections that spread quickly around hospitals (such as Clostiroides difficile), the effect of the antibiotics does not only affect the target organism leading to alterations to the normal microbiota of the gut.  Consequently this creates opportunities for fungal to occur.


In other words, a reduction in the number of gut bacteria as a result of antibiotic therapy reduces competition for space and leaves more room for fungi to multiply. The problem for medics is that the underlying factors causing these infections are not well understood.


It was also of concern that where antibiotics disrupt the immune system, then fungal infections become poorly controlled and where such fungal infections develop, gut bacteria, including the target pathogens of the antibiotics, are also less prone to the effects of the antibiotic; hence, the risk of bacterial infection also increases.


To demonstrate this, the scientists used mice treated with a broad-spectrum antibiotic cocktail. The rodents were next infected with Candida albicans. It was found that while infected mice had increased mortality, this was caused by infection in the intestine, rather than in the kidneys or other organs.


Following this, the researchers pinpointed what parts of the immune system were missing from the gut after antibiotic treatment. These components were next added back into the mice using immune-boosting drugs. This approach helped reduce the severity of the fungal infection.


A follow-up assessment of hospital records suggested that similar co-infections probably occur in humans.


The research adds to our understanding of how antibiotics can have additional effects on our bodies. This further underscores the importance of careful stewardship of available antibiotics.


The counter the risk of fungal infections, the researchers speculate that the use of immune-boosting drugs at the same time that antibiotics are administered could reduce the health risks from e complex fungal infections.


The findings appear in the journal Cell Host & Microbe, titled “Long-term antibiotic exposure promotes mortality after systemic fungal infection by driving lymphocyte dysfunction and systemic escape of commensal bacteria.”


Posted by Dr. Tim Sandle, Pharmaceutical Microbiology Resources (

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