Q&A: Tackling antimicrobial resistance in resource-constrained laboratories

Chris Armstrong: What’s changed is the pace and complexity of the threat, combined with the operational realities labs are dealing with. We’re seeing more multidrug-resistant organisms, including emerging fungal pathogens like Candida auris, which bring both clinical and infection prevention challenges.¹ At the same time, laboratories are under real strain with fewer experienced staff, increasing workloads, and pressure to deliver faster results.

That combination means laboratories may need to move beyond traditional one-size-fits-all workflows that were designed for a different era. The question is no longer just “Can we detect this organism?” but “Can we detect it quickly, consistently, and with the resources we actually have?”

How do staffing shortages specifically impact a lab’s ability to respond to AMR?

Chris Armstrong: Staffing shortages affect both capacity and capability. Many labs are operating with fewer highly experienced microbiologists, while newer staff are being asked to take on more complex tasks earlier in their careers.²

That has two implications. First, processes that depend heavily on expert interpretation become harder to sustain. Second, variability can increase—between shifts, between individuals, and even between sites in larger networks.

So, addressing AMR today isn’t just about having the right tests. It’s about designing workflows that are more intuitive, more standardized, and less dependent on scarce expertise, while seeking to maintain accuracy.

Cost pressures are also significant. How should laboratories balance cost control with the need to improve AMR detection?

Chris Armstrong: Cost is often viewed narrowly, typically at the level of individual consumables or tests. But in practice, laboratories operate as systems. Decisions made at the front end of the workflow can have downstream consequences for labor, turnaround time, repeat testing, and even patient management.

For example, if a method requires additional confirmatory steps or increases interpretation time, that has a real cost in terms of staff effort and reporting delays. In contrast, methods that streamline decision-making or reduce ambiguity may help offset higher downstream costs.

The shift we’re seeing is toward evaluating total workflow impact rather than unit price alone. That’s especially important in the context of AMR, where delays or inconsistencies can have broader clinical and operational implications.

Emerging pathogens like Candida auris are a growing concern. What makes them particularly challenging for laboratories?

Chris Armstrong: C. auris is a good example of how AMR is evolving. It’s not just resistant; it’s also difficult to identify using some conventional methods, and it can spread within healthcare settings.^3,4

That creates a dual challenge: accurate detection and timely reporting. Laboratories need to be confident in their presumptive identification so that appropriate infection control measures can be initiated quickly, while also ensuring confirmatory methods are in place.

It also highlights the importance of surveillance. Detecting colonization and tracking spread, within validated laboratory protocols, are just as critical as diagnosing infection, and that can place additional demands on laboratory workflows.

What role do new workflow tools play in addressing these challenges?

Chris Armstrong: Clinical microbiological tools are often undervalued, but they’re critical. They shape how samples are processed, how results are interpreted, and how efficiently the lab operates overall.

In the context of AMR, innovative technologies, as well as optimally deployed existing methods, may support improved differentiation, reduce ambiguity, or support faster identification and — very relevant to AMR — antimicrobic susceptibility. This can then support efforts to inform outbreak management and clinical decision-making. New products may help prioritize samples, reduce follow-up workload in some settings, and contribute to more consistent processes.

Importantly, these tools don’t replace confirmatory methods like MALDI-TOF mass spectrometry or molecular assays. Instead, they complement them by improving the efficiency and effectiveness of the overall workflow.

How can laboratories ensure consistency in results despite variability in staffing and experience levels?

Chris Armstrong: Consistency comes from a combination of standardization and simplification. Standardized protocols, clear decision criteria, and methods that are easier to perform and interpret can all contribute to more reproducible results.

Automation also plays a role, particularly in larger laboratories, but it’s not the only answer. Even in less automated settings, choosing methods that reduce subjectivity can help ensure that results are consistent, regardless of who is performing the test.

Ultimately, the goal is to make high-quality microbiology more repeatable across shifts, across teams, and across different levels of experience.

What practical steps can laboratory leaders take to strengthen their AMR response today?

Chris Armstrong: There are a few key areas to focus on:

• Evaluate workflows holistically: Look beyond individual tests to understand where time, effort, and variability are introduced.
• Prioritize methods that reduce complexity: Especially in high-volume labs or when the stakes are high, like for multi-drug-resistant organisms.  Differentiate technologies and use the right one for the job, as opposed to complementing existing routines to fill gaps.
• Invest in training and standardization: Ensure staff are supported with clear protocols and ongoing education.
• Align analytical strategies with clinical needs: Consider how laboratory results feed into infection prevention and patient management decisions.

These steps don’t necessarily require large-scale transformation. Often, incremental changes as part of a validated diagnostic workflow design can have a significant impact.

Looking ahead, what will define successful laboratories in the fight against AMR?

Chris Armstrong: Laboratories that are able to adapt may be better positioned, both technically and operationally. They’ll combine robust detection capabilities with efficient, scalable workflows that reflect the realities of modern healthcare.

AMR is a growing healthcare challenge, and our response needs to evolve. Laboratories that take a proactive approach, continually evaluating and refining how they work, will be best positioned to meet the challenge.

Conclusion

As antimicrobial resistance continues to evolve, clinical laboratories must balance accuracy, speed, and efficiency in increasingly constrained environments. By focusing on workflow design, standardization, and practical front-end improvements, laboratories can strengthen their response to emerging threats while maintaining operational sustainability.

References

1. WHO fungal priority pathogens list to guide research, development and public health action. Who.int. October 25, 2022. Accessed April 2, 2026. https://www.who.int/publications/i/item/9789240060241.
2. Heggeness ML, Zambrana CE, Ginther DK. Workforce trends: The future of microbial sciences. Asm.org. May 30, 2023. Accessed April 2, 2026. https://asm.org/getmedia/9ec71b59-0c57-4f14-9e53-04c88717f0d8/workforce-report.pdf?ext=.pdf.
3. CDC. Clinical overview of candida auris. Candida auris (C. auris). February 26, 2026. Accessed April 2, 2026. https://www.cdc.gov/candida-auris/hcp/clinical-overview/index.html.
4. Rapid risk assessment: Candida auris in healthcare settings – Europe. European Centre for Disease Prevention and Control. April 23, 2018. Accessed April 2, 2026. https://www.ecdc.europa.eu/en/publications-data/rapid-risk-assessment-candida-auris-healthcare-settings-europe.