Efficient outbreak management with bacterial strain typing

Animal diseases are migrating into previously unaffected ​​areas with potential wide-reaching consequences not only for animal health but also for global food security, human health and biodiversity.¹ In the farming community, around 20% of livestock are lost to disease each year, while many companion animals and wildlife also suffer the effects of illness.² The need for fast and accurate animal disease outbreak management has therefore never been more important.

In an outbreak situation, simply identifying the presence of a bacterium does not always provide sufficient information to initiate an effective containment and treatment strategy. Veterinary scientists are implementing a new bacterial strain typing method based on Fourier-transform infrared (FT-IR) spectroscopy which can help to differentiate between specific bacterial strains, support efficient outbreak management and ultimately protect animal and human health.

The case for bacterial strain typing

Traditional biochemical identification techniques and molecular tests such as polymerase chain reaction (PCR) are typically used for microorganism identification. Results obtained using these methods, however, can often come too late to respond to time-sensitive outbreak situations. Furthermore, although these techniques can confirm the presence of a bacterium, they cannot differentiate between specific strains.

For outbreak management, differentiating between specific bacterial strains is becoming increasingly necessary. It can help scientists to establish epidemiological links and separate strains based on their serotype, virulence properties or resistance to certain therapeutic agents. With this level of information, it is possible to trace the source of outbreaks more accurately and therefore introduce effective containment and treatment plans – fast.

Bacterial strain differentiation with FT-IR spectroscopy

FT-IR spectroscopy is an emerging technique in veterinary diagnostics, where it is being applied to classify bacterial strains with high specificity and compare isolates in the event of outbreaks.

Veterinary scientists have introduced a workflow for bacterial strain differentiation using FT-IR technology, which generates FT-IR spectra for various strains belonging to the same bacterial species. Cluster analysis techniques are then used to accurately distinguish between specific strains and determine whether animal infections are caused by related strains or different strains each time.

With short analysis timelines, FT-IR spectroscopy generates results quickly, allowing clinicians to react efficiently to outbreak situations. In comparison with conventional methods, FT-IR spectroscopy is not only more cost efficient, but has the versatility required to perform routine strain typing for a wide range of microbial species. Results obtained are highly reproducible and can help to reliably confirm the source of a suspected outbreak.

FT-IR spectroscopy in action:bovine K. pneumoniae mastitis

Mastitis caused by Klebsiella pneumoniae (K. pneumoniae) presents a considerable challenge for many dairy farmers and has become more common in recent years. A report investigating K. pneumoniae in global milk samples from mastitis cases estimates that the prevalence of K. pneumoniae has increased threefold between 2007 and 2020.³ Treatment outcomes are often poor, and, in some cases, mastitis can prove fatal. Efficient mastitis outbreak detection is essential both to protect the health of the herd and ensure high milk yield and quality.

Random amplified polymorphic deoxyribonucleic acid-PCR (RAPD-PCR) or pulsed-field gel electrophoresis (PFGE) are typically used in mastitis outbreak investigations; however, RAPD-PCR testing requires costly species-specific primers and PFGE can take as long as a week, delaying treatment and containment.

In response to a recent bovine K. pneumoniae mastitis outbreak, veterinary scientists explored FT-IR spectroscopy as a potential alternative. The workflow compared K. pneumoniae isolates from infected cows and other samples collected at the farm to determine whether the milking apparatus was the source or whether the infection stemmed from environmental conditions. Results confirmed the presence of multiple K. pneumoniae strains circulating in the farm and the subsequent implementation of a treatment and hygiene management plan contained the mastitis outbreak, with no further cases reported.

The future of FT-IR spectroscopy in veterinary diagnostics

Bacterial strain typing with FT-IR spectroscopy can help quickly contain an outbreak situation: rapid results confirm the source of a suspected outbreak and allow clinicians to respond fast. With incidence rates increasing, FT-IR spectroscopy could prove to be an invaluable tool for outbreak management. It is also showing promise in other applications, including the development of farm-specific autologous vaccines for bacterial species such asEscherichia coli (E. coli), and is set to have a transformative effect on veterinary diagnostics to help safeguard animal health globally.

1. Badara O. First Report on World’s Animal Health reveals changing spread of disease impacting food security, trade and ecosystems. World Organisation for Animal Health. June 24, 2025. Accessed February 27, 2026. https://www.woah.org/en/first-report-on-worlds-animal-health-reveals-changing-spread-of-disease-impacting-food-security-trade-and-ecosystems/.
2. Animal disease. HealthforAnimals global animal health association. Accessed February 26, 2026. https://healthforanimals.org/global-challenges/animal-disease/.
3. Payros D, Auvray F, Foucras G, Oswald E. Is klebsiella pneumoniae-associated bovine mastitis an emerging public health issue? A one health perspective. ASM Animal Microbiology. Published online February 12, 2026. https://journals.asm.org/doi/full/10.1128/asmam.00023-25.