{"id":5107,"date":"2026-04-23T10:06:41","date_gmt":"2026-04-23T09:06:41","guid":{"rendered":"https:\/\/poulpharm.vermis.hu\/?p=5107"},"modified":"2026-04-28T14:23:53","modified_gmt":"2026-04-28T13:23:53","slug":"digital-pcr-as-a-robust-tool-for-low-level-pathogen-detection","status":"publish","type":"post","link":"https:\/\/poulpharm.vermis.hu\/?p=5107","title":{"rendered":"Digital PCR as a robust tool for low-level pathogen detection"},"content":{"rendered":"

Digital PCR as a robust tool for low-level pathogen detection<\/h1><\/h3><\/div>
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The Problem<\/strong><\/h4>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n
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Reliable and accurate quantification of pathogens is essential for determining (low) microbial levels in complex biological samples. However, the accuracy of culture\u2011based and molecular methods can differ, particularly at low target concentrations or in the presence of inhibitory substances from complex matrices such as feces or cloacal swabs. A direct comparison of these methods is therefore needed to identify which technique provides the most reliable and accurate results.<\/h3><\/div>

How We Investigated the Problem<\/strong><\/h4>\n<\/div>

A 1:10 dilution series was prepared from a\u00a0Salmonella<\/em>\u00a0vial with a known concentration (9.48 log10<\/sub>\u00a0CFU\/mL). This 1:10 dilution was used to compare four quantification methods: (1) classical bacterial enumeration, (2) Most Probable Number (MPN), (3) quantitative PCR (qPCR), and (4) digital PCR (dPCR). The same dilution was also used to spike fecal material and cloacal swabs, enabling evaluation of potential matrix effects for each method.<\/p>\n<\/div>

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Results<\/h4>\n<\/div>

Quantification of the vaccine dilution series<\/strong><\/p>\n

When comparing the four different methods, both molecular methods matched the expected concentrations in the higher dilution range (log9\u2013log6). At lower concentrations (log5\u2013log2), qPCR showed a slight loss in quantification, whereas dPCR continued to produce the expected values. The two bacterial methods showed a consistent pattern across all dilutions, measuring approximately one log lower than expected.<\/p>\n<\/div>

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Quantification of the vaccine spiked in complex matrices<\/h2>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/section>\n
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In both feces and cloacal swabs, the bacterial methods showed a two-log reduction relative to the expected concentration. The molecular methods showed a one log reduction in feces, while in cloacal swabs both qPCR and dPCR aligned with the expected concentration.<\/p>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/section>\n<\/div>

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Conclusions<\/h2>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/section>\n
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This study demonstrates that molecular techniques outperform culture\u2011based methods, with dPCR providing the highest accuracy and robustness. Its resistance to matrix inhibition highlights dPCR as a reliable tool for quantifying pathogens in complex biological samples at low levels. In addition, dPCR enables simultaneous quantification and detection of bacterial, viral, and parasitic genetic material and straightforward multiplexing without interference.<\/p>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/section>\n

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Do you want to discuss enumeration of Salmonella in different matrices?<\/h3>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/section>\n<\/div>

Do not hesitate to ask your questions, Poulpharm’s experts team are here to solve your problems!<\/h4>\n<\/div>
<\/i>Contact Us!<\/span><\/a><\/div><\/div><\/div><\/div><\/div>\n","protected":false},"excerpt":{"rendered":"","protected":false},"author":3,"featured_media":5045,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"_acf_changed":false,"footnotes":""},"categories":[4,3],"tags":[],"class_list":["post-5107","post","type-post","status-publish","format-standard","has-post-thumbnail","hentry","category-poulpharm","category-poultry"],"acf":[],"yoast_head":"\nDigital PCR as a robust tool for low-level pathogen detection - Poulpharm<\/title>\n<meta name=\"description\" content=\"Digital PCR as a robust tool for low-level pathogen detection.\" \/>\n<meta name=\"robots\" content=\"index, follow, max-snippet:-1, max-image-preview:large, max-video-preview:-1\" \/>\n<link rel=\"canonical\" href=\"https:\/\/poulpharm.vermis.hu\/?p=5107\" \/>\n<meta property=\"og:locale\" content=\"hu_HU\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Digital PCR as a robust tool for low-level pathogen detection - 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