Development of a sensor-based rapid microbial testing platform for the Irish meat industry

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dc.contributor.advisorPapkovsky, Dmitri B.
dc.contributor.advisorKerry, Joseph
dc.contributor.authorElisseeva, Sophiaen
dc.contributor.funderDepartment of Agriculture, Food and the Marine, Ireland
dc.contributor.funderDawn Meats
dc.date.accessioned2023-05-23T11:37:23Z
dc.date.available2023-05-23T11:37:23Z
dc.date.issued2023-01-05en
dc.date.submitted2023-01-05en
dc.description.abstractMicrobial spoilage and foodborne diseases cause significant productivity and economic losses for the food industry. There is a need for novel approaches to extend shelf life of products, improve quality and microbial safety, reduce spoilage and waste, and new assessment methods. Traditional methods are time consuming, labour intensive, centralised, have lengthy time to result, and some cannot analyse crude food homogenates. In this project, funded by the Irish Department of Agriculture, Food and the Marine and performed in partnership with a large Irish food company (Dawn Meats), several new optical oxygen sensor based systems were devised to increase efficiency and accuracy of testing. Chapter 1 (Literature review) describes the state of the art in the area, the range of existing approaches and analytical systems, and their capabilities. Experimental methods used in this study are summarised in Chapter 2 (Materials and Methods). The first experimental section (Chapter 3) describes the development of new multi-parametric toxicity testing platform based on the soluble oxygen probe, MitoXpress-Xtra, and 96 well plate format, which was used to investigate the antimicrobial effects of the compound Lauroyl Arginate Ethyl Ester (LAE) on pure cultures and whole meat microbiota. Through the measurement and analysis of the oxygen probe time profiles (phosphorescent lifetime) under different assay settings, we were able to assess and quantify the toxicity of LAE on different bacterial species, generating dose-response curves, and calculating EC50. The assay allowed for the simultaneous assessment of multiple variables and conditions such as bacterial species, temperature, growth media, sample type, and antimicrobial concentrations. The second experimental part (Chapter 4) describes the new portable and autonomous system(s) based on disposable vials integrated with solid state sensors, tailored for the analysis of meat samples, carcass swabs, and environmental swabs. Along with the disposable sensor vials, the system is composed of two additional parts; a handheld, autonomous sensor reader and a portable incubator/heater. Up to 20 samples were prepared using the standard methods (ISO 4833-1:2013; ISO 18593:2018) in sensor vials, incubated at 30C and measured hourly in a non-invasive, contactless manner. Such a simple system with manual measurements also revealed dissolved oxygen time profiles which were used to determine the threshold time of the sensor signal, which in turn, was used to calculate TVC values (CFU/ cm2 or CFU/g) using developed calibration equations. The method was validated using: i) meat samples and carcass swabs obtained from Dawn Meats, ii) brush swabs of artificially contaminated surfaces with E. coli, iii) swabs of surfaces contaminated with meat microbiota and iv) environmental swabs. No statistical difference was found between the sensor based method and reference method, providing the opportunity for the former to potentially replace the latter. Finally, in Chapter 5 the new respirometric sensor based system was applied to a shelf-life study with four different types of MAP mincemeat samples: beef, turkey, lamb and pork, together with the analysis of these samples by 16S rRNA sequencing. Respirometric profiles revealed unusual linear profiles for pork and lamb mince, the origins of which remain to be investigated. In addition to respirometric microbiological assessment, the whole microbiome of each mincemeat type was analysed using 16S rRNA sequencing, which revealed an overall decrease in alpha diversity with some taxa exhibiting statistically significant changes over shelf-life and after exposure to respirometry. Beta diversity was seen to be dictated by mincemeat type. Overall, the new optical oxygen respirometry systems are highly efficient and attractive for the food industry, with both developed systems improving existing methods in time to result, accuracy, user-friendliness, and on-site use. Furthermore, the portable sensor based system can be combined with cutting edge techniques such as next generation sequencing to provide more detailed information on the microbiota of food samples.en
dc.description.statusNot peer revieweden
dc.description.versionAccepted Versionen
dc.format.mimetypeapplication/pdfen
dc.identifier.citationElisseeva, S. 2023. Development of a sensor-based rapid microbial testing platform for the Irish meat industry. PhD Thesis, University College Cork.en
dc.identifier.endpage115en
dc.identifier.urihttps://hdl.handle.net/10468/14494
dc.language.isoenen
dc.publisherUniversity College Corken
dc.rights© 2023, Sophia Elisseeva.en
dc.rights.urihttps://creativecommons.org/licenses/by/4.0/
dc.subjectOxygen respirometryen
dc.subjectFood scienceen
dc.subjectOxygen sensorsen
dc.subjectFood safetyen
dc.subjectMeat microbiotaen
dc.subjectTotal viable countsen
dc.titleDevelopment of a sensor-based rapid microbial testing platform for the Irish meat industryen
dc.typeDoctoral thesisen
dc.type.qualificationlevelDoctoralen
dc.type.qualificationnamePhD - Doctor of Philosophyen
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