Sophie holds a PhD in molecular biology and postdoctoral experience in next-generation sequencing for infection control (SARS-CoV-2). She lives in the UK with her dog, Louie, and works as a freelance scientific content writer and producer for clients across the globe. You can view Sophie’s portfolio 

Sophie Prosolek, PhD

, has been used in the clinical assessment of human health and disease for centuries. In fact, it has been reported as perhaps the first analytical tool used in disease investigation, as described by Hippocrates in 400 

Its utility has been proven by numerous historic and modern-day scholars, including 20th-century Nobel Prize winner Linus Pauling, who was among the first to describe the cocktail mix of analytes that comprises this complex vapor matrix.

 Its ability to offer clinicians a snapshot of what is going on inside the body has provided game-changing 

 into human health and disease, particularly at times when more invasive methods held a greater risk.

Today, exhaled breath analysis (EBA) is used in clinical applications alongside histological tests (stool testing and blood culture) to explore pathogenic infections with accuracy, speed, and clear point-of-care outcomes.

 However, although the future of breath analysis appears promising, several challenges have limited its broader adoption as a modern diagnostic tool.

This article explores the growing role of exhaled breath in advancing infection control and highlights recent advances in the application of carbon-tracer
technology that may underpin the future of EBA in clinical settings.

What Do Exhaled Breath Samples Consist of?

Exhaled breath is so much more than just warm air; it's a variable mixture of water, soluble and insoluble compounds, and even some cellular materials originating from a variety of host and nonhost sources.

 Such is the complexity of exhaled breath that research has even shown its variability across various ventilatory conditions.

Although whole pathogens, including viruses and bacteria, may be present in the exhalant mixture (and may be of clinical note for risk management purposes), they are not generally considered EBA analytes themselves.

 Instead, most EBA methods rely on the detection of specific, pathogen-derived volatile organic compounds (VOCs).

 These VOCs are typically carbon-based molecules produced as a by-product of microbial metabolism.

They can be differentiated from one another and from other endogenous and exogenous volatiles using specific, detectable isotope tracers that cannot be broken down by mammalian cells.

 These tracers are typically administered orally shortly before sampling and are metabolized by the infecting pathogen into detectable waste products, such as carbon dioxide (CO

), which are exhaled during normal respiratory gas exchange.

Exhaled Breath in Infection Control, Today

A variety of infectious agents have been successfully detected using EBA methods; however, not all EBA tests are created equal.

 Some viral pathogens (such as SARS-CoV-2) hijack their host’s cellular metabolic machinery to complete their life cycle; this means that their diagnostic VOC profiles represent perturbations in host metabolic pathways (oxidative stress), not metabolic by-products from the virus itself.

 This can make EBA in viral illness a challenge due to a lack of specific detectable tracers that are not readily metabolized by the healthy cells of the body.

Bacteria, on the other hand, typically metabolize independently, allowing detection of their respiratory by-products under certain conditions.

 Moreover, bacterial infections of the upper gastrointestinal (GI) tract offer an opportunity for noninvasive EBA methods because orally administered carbon tracers can be used with minimal interference from commensal gut microbes.

 infection have been implemented at the point-of-care level.

 This test, known as the urea breath test (UBT), relies on the conversion of carbon 13 (

C) stable isotope–labeled urea into gaseous metabolites that, when excreted through the circulatory and ventilatory systems, are detectable by spectrometry methods and laboratory analytical teams 

Advancing Infection Detection: EBA Beyond the Gut

Increasingly, researchers are hopeful that new advancements will help them detect infections distal from the GI tract. However, the same stable isotope–labeled carbon tracers have pitfalls in this aspect. These isotopes, if administered orally, are broken down by the commensal gut microbiota, rendering breath testing impossible.

“Unless the microbe affects or changes a specific metabolic pathway, identifying VOCs for any specific infection still remains impossible. [However,] the 

C-urea breath test has already been extensively studied for the antibacterial eradication therapy for [

] infection [in the stomach],” said Anil Modak, PhD, associate director of medical products research and development at Owlstone Medical in Cambridge, England.

(Image credit: owlstonemedical.com. Used with permission.)

New research from St Jude Children’s Research Hospital and the University of California, San Francisco (UCSF) has highlighted the potential for new carbon-tracer applications to advance EBA for infection control.

 The study, led by David M. Wilson, MD, PhD, explored the application of injectable carbon tracers similar to, but distinct from, those applied in the UBT. These tracers were inspired by similar radiolabeled technology developed for PET applications and were designed to target bacterial metabolism in the same manner as their PET counterparts.

The study demonstrated that injectable, stable isotope–labeled metabolites—specifically, uniformly labeled (U)–

 by a number of clinically relevant infecting bacteria. In addition, the study confirmed that such methods could be used to measure bacterial burden, allowing the researchers to track infection responses to antibiotics over time.

While representing major advances in EBA research, the new St Jude’s study has some limitations. Firstly, although mouse infection models validate the method’s success in multiorgan, mammalian systems, they also represent a very early stage in diagnostic development. EBA samples were captured using metabolic chambers, a far cry from the handheld diagnostic devices that point-of-care clinicians might need. In addition, although stable isotope–labeled tracers are used in clinical applications today, specific ethical, regulatory, and current Good Manufacturing Practice approvals would be required to ensure their suitability and safety in this case.

“The main barrier to breath test rollout in clinics globally is the regulatory approval, the unmet clinical utility, the cost, and insurance coverage,” said Modak. “[Additionally], breath collection and analysis can be dangerous in certain circumstances, such as a respiratory disease pandemic (like COVID-19)—that is, if precautions are not taken to use new breath collection devices like mouthpieces or not using masks during the collection and analysis of samples.”

Furthermore, the St Jude/UCSF study only addresses part of a broader problem. The study successfully confirmed the presence of bacteria and identified the bacterial burden, but the tracers used were not strain- or species-specific and cannot confirm a diagnosis alone.

 Furthermore, EBA has historically been hailed as a less invasive diagnostic method, but injectable tracers may not offer the same benefit for patients or primary care physicians. In sum, such methods are not likely to replace other methods any time soon, but they may one day be used alongside other diagnostic approaches.

Exhaled Breath and Precision Monitoring in the Age of Antimicrobial Resistance

Perhaps the most compelling takeaway from the St Jude/UCSF study was not just the detection of infecting bacteria, but also the ability to monitor antibiotic treatment efficacy and the decrease in bacterial burden over time.

 In a clinical setting, confirming the presence of an infection is only half the battle; the rise of multidrug-resistant strains increases the risk of treatment failure, underscoring the need for accurate, real-time monitoring to support rapid clinical decision-making. Although the St Jude/UCSF approach cannot yet differentiate between sensitive and resistant strains,

 this method could serve as a rapid-response indicator. If a patient is prescribed an antibiotic and their breath does not indicate a drop in bacterial load, this provides an immediate objective signal of potential drug resistance and could support a faster pivot to alternative therapies or changes in medication regimes. Over time and with further development, this could offer a quicker, more portable, and more affordable alternative to other infection-monitoring tools (such as PET scanning).

Breath testing has come a long way since the time of Hippocrates, and even since the time of Pauling, but challenges remain for true, coordinated infection control. Not least, amid emerging global challenges (such as antimicrobial resistance and pandemic risks), novel breath analysis approaches could change the game on the clinical level. That said, although the latest research does hold promise for future clinical applications, development still has a long way to go. Breath testing may never entirely replace traditional blood cultures or PET scanning. Still, it may one day play a more diverse role in modern clinics, alongside the tools and technologies that have inspired its advancement. 

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Emerging breath analysis technologies could provide faster, less invasive detection of bacterial infections and help clinicians monitor antibiotic response, though significant research and regulatory hurdles remain before widespread clinical adoption.

Sophie Prosolek, PhD

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