ORCID

Abstract

Effective cleaning and sanitation are essential in cheese manufacturing to control microbial contamination and prevent biofilm formation. A multi-step approach was undertaken to assess microbial persistence and cleaning-in-place (CIP) strategies at an industrial Cheddar cheese facility with a production capacity of ∼40,000 tonnes. Pre- and post-CIP environmental swabs were analysed using plate counts and high-throughput (16S rRNA amplicon and shotgun) sequencing to identify microbial hotspots. Traditional CIP was broadly effective, however residual contamination persisted in critical zones such as the Alfomatic weir, curd distribution tank (CDT), and block formers. Industrial-scale trials comparing caustic and acid-based CIP with an enzymatic alternative revealed complete microbial elimination post traditional CIP, while enzymatic CIP left DNA signatures at one site, culturable cells were not detected. Sequencing identified Pseudomonas fluorescens as the dominant non-starter bacterium, suggesting possible biofilm formation. Parallel laboratory-scale studies of P. fluorescens biofilm removal using a CDC Biofilm Reactor® coupled with Scanning Electron Microscopy (SEM) compared caustic and enzymatic CIP. Caustic treatment completely removed the biofilm matrix but left adherent cells, while enzymatic treatments degraded the matrix but showed residual matrix fragments and adherent cells. Plate counts confirmed significant differences in residual biofilm populations, with average reductions of 3.75 log, 2.56 log, and 1.87 log after caustic, enzyme cocktail, and protease treatments, respectively (p < 0.0001), underscoring the incomplete nature of these approaches. Caustic CIP improves microbial reduction, while enzymes disrupt biofilm matrices. However, neither alone achieves complete removal, supporting combined strategies to enhance cleaning efficacy and sustainability in dairy processing.

Keywords

Microbial hotspots, Shotgun sequencing, cheese manufacturing, dairy processing

Publication Date

2026-01-01

Publication Title

Food Control

Volume

190

ISSN

0956-7135

Deposit Date

2026-06-15

Funding

This research was funded by the Department of Agriculture, Food and the Marine (DAFM) under the Food Institutional Research Measure (FIRM) programme (Grant No. 2019R475). Karan Pant is a recipient of Teagasc Walsh Scholarship. The authors also acknowledge the use of facilities and resources at the National Food Imaging Centre (NFIC), Teagasc.

Creative Commons License

Creative Commons Attribution 4.0 International License
This work is licensed under a Creative Commons Attribution 4.0 International License.

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