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Sources for contamination in breweries can occur as "primary" contaminations (yeast pitching, and brewhouse related contaminations), or as "secondary" contaminations (packaging and cellaring), as well as in tap systems. They are usually not sudden occurrences, but a result of the continued growth of microorganisms in a problem area. Historically, re-pitching yeast was often a source of contamination; however, more recently this has become less of a source for contaminations due to better education and techniques. Typical sources for contamination also include unclean equipment such as thermometers, manometers, valves, dead ends, gas pipes, leaks in any part of the system (especially at heat exchangers), wort aeration equipment, and even worn floor surfaces. More than half of the documented contaminations come from the packaging system. These are typically the sealer (35%), the filler (25%), the bottle inspector (10%), dripping water from the bottle washer (10%), and the environment close to the filler and sealer (10%). In regards to the environment as a source of contamination, this has been found to be from airborne contaminants near the filler and crowner in open bottles on their way from the bottle washer to the filler and from the filler to the capper. The higher the humidity and the more airflow, the more chances of airborne contamination <ref name="storgards_2000" /><ref name="Vaughan_2005" />. For example, ''Pectinatus'', while mostly found in lubrication oils, water systems, floors, water condensed on ceilings, etc., it can also survive on [https://en.wikipedia.org/wiki/Aerosol aerosols] in the air and is thought to possibly transferred to beer that is being packaged via the air <ref name="Suzuki_2012" />. In tap systems at taverns, 'one-way' valves that are attached to kegs have been found to be a source of contamination, as well as the dispensing line <ref name="storgards_2000" /><ref name="Vaughan_2005" />.
Thompson et al. (2024) divided the brewing environment into three "zones": areas that have direct contact with beer, such as the brewhouse, areas that are adjacent to beer production areas that have no physical barrier from the beer production area, and areas that have a physical barrier between the beer production areas, such as offices, tap rooms, etc. They took samples from all areas in three small microbreweries. The study found that racking arm valves were one of the worst offenders of housing contaminating microbes, although the results were skewed by one of the breweries having a higher load of contaminants in general between the three microbreweries. Proper cleaning, sanitation, and maintenance of racking arms is recommended to reduce biofilm formation. Other areas that harbored bacteria included the bottom valve, carb stone valve, spray ball valve, and the yeast pitch. All areas of the brewery that were swabbed show at least some bacterial growth, demonstrating that all areas of the brewery are potential sources of contamination. This study noticed that one brewery in particular had a higher occurrence of spoilage microbes; the study speculated that this might be due to cleaning and sanitation protocols during packaging, and heavy loads of contaminants were found in the packaging system <ref>[https://academicjournals.org/journal/JBD/article-full-text-pdf/705951B71856 Alex R. Thompson, Julie K. Northcutt and Paul Dawson. Bacterial contamination and surface hygiene in the microbrewery environment. Journal of Brewing and Distilling. Vol. 13(1), pp. 1-10, January-June 2024. DOI: 10.5897/JBD2024.0060.]</ref>.
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