From Bottlenecks to Breakthroughs: Addressing Today’s Top Microbiology Challenges

One of the most pressing challenges in microbiology today is the growing shortage of qualified professionals in both public health and industrial labs.

A recent submission to the UK Parliament Committees from the Society for Applied Microbiology highlights that both medical and non-medical labs are facing critical technician shortages, exacerbated by the high demands during COVID-19 and compounded by funding constraints within institutions like the NHS.¹

In the United States it’s a similar story, with post-pandemic, increased demand for microbiologists, coupled with an aging workforce (1 in 10 microbiologists in the USA is aged 65 or older) and academic pipelines that haven’t kept pace with staffing requirements, placing burden on an already stretched segment.²

Other global factors, from politics to technological advancements, further exacerbate the issue through funding cuts, technology skill gaps, and other barriers to entry within the industry. 

The microbial world is changing - fast. As globalization, climate change, antibiotic overuse, and urbanization accelerate microbial evolution and spread, the job of today’s microbiologist is significantly more complex than it was even a decade ago.  

One major concern is the increasing threat of antimicrobial resistance (AMR): According to the WHO, AMR is one of the top 10 global health threats. In 2019 alone, it was directly responsible for an estimated 1.27 million deaths globally, with resistant infections tied to over 4.95 million deaths in total.³ Resistant strains like Carbapenem-resistant Enterobacteriaceae (CRE) or Colistin-resistant E. coli are particularly difficult to detect and treat using traditional workflows. 

Linking to this are the growing concerns around emerging pathogens. Pathogens like Candida auris and various zoonotic viruses (e.g., Nipah virus, novel coronaviruses) have made headlines in recent years. Many labs, especially those relying on outdated identification protocols, are poorly equipped to detect them promptly. For instance, a 2022 Microbiology study found that many routine lab techniques failed to differentiate pathogenic Klebsiella species from commensal strains without supplemental molecular testing⁴ — demonstrating how microbial diversity is outpacing classical diagnostics. 

Global interconnectedness also means that pathogens no longer respect geographic boundaries, as international travel, trade, and climate change contribute to the rapid transcontinental movement of microbes.   

Sustainability has moved from a “nice to have” to a non-negotiable priority. The shift has been driven by the considerable evolution in climate change science, which informed the conclusion of the 2018 Intergovernmental Panel on Climate Change: that we have until 2030 to reduce emissions or face irreversible damage that will destroy ecosystems and leave millions of people in poverty.⁵ 

Microbiology labs, which often rely on single-use plastics, energy-intensive equipment, and complex waste streams, are under increasing scrutiny to reduce their environmental impact. The statistics are telling: on average, labs use 10x more energy than offices, whilst also generating around 5.5 million metric tons of plastic waste annually.⁶ 

As we progress through this decade and beyond, balancing sterility and consumable requirements with a greener approach to lab practices will be key to securing the future of our planet. In clinical and pharmaceutical settings this can be particularly challenging due to throughput and anti-contamination needs. 

As microbiology adopts increasingly sophisticated tools - from digital plate readers to real-time PCR-the amount of data generated per sample has skyrocketed. While this data offers unprecedented insight into organisms and resistance mechanisms, many labs are overwhelmed rather than empowered by it. 

In a single day, even a medium-sized lab might generate thousands of data points, each needing to be validated, interpreted, and appropriately reported. Yet many labs still rely on spreadsheets or manual transcription to interpret and store this data, risking transcription errors and data loss.

There is also a regulatory angle to this issue, as standards such as ISO 17025 require labs to store raw and processed data securely, ensure traceability of all results and maintain audit trails for all test decisions.⁷ For microbiology data, this includes time-stamped colony images, digital AST curves, instrument logs, and sequence metadata. Without automated retention systems, labs are left trying to organize massive archives of inconsistent data formats—often with no guarantee of retrievability.

The issue that arguably underpins all others, however, concerns the fact that microbiology labs are continually being pushed to generate more results, faster, and with increasingly complex considerations to meet today’s high-demand testing landscape.  

In the fast-moving, high-volume, low-margin business of food, streamlining testing workflows is essential to boosting productivity and profitability (especially for perishable foods), without compromising on safety or accuracy. 

Pharmaceutical manufacturers are equally under pressure to produce sterile pharmaceuticals, vaccines and biotechnology products more rapidly, while meeting evolving regulatory and quality assurance standards.  

Meanwhile for clinical laboratories, time-to-result has a critical impact on patient outcomes, yet accuracy of result is equally imperative. This, coupled with the evolving challenges of antibiotic resistance, creates pressure from all angles for laboratories conducting this critical work.