Rare Bacteria Detection
Rare Bacteria Detection - Related Videos
14:06
Detection of Rare Genomic Variants from Pooled Sequencing Using SPLINTER
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Cited by 10 •
2012
Pooled DNA sequencing is a fast and cost-effective strategy to detect rare variants associated with complex phenotypes in large cohorts. Here we describe the computational analysis of pooled, next-generation sequencing of 32 cancer-related genes using the SPLINTER software package. This method is scalable, and applicable to any phenotype of interest.
13:20
Detection of Bacteria Using Fluorogenic DNAzymes
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Cited by 17 •
2012
We have recently reported a novel approach for generating fluorogenic DNAzyme probes that can be applied to set up a simple, "mix-and-read" fluorescent assay for bacterial detection. These special DNA probes catalyze the cleavage of a chromophore-modified DNA-RNA chimeric substrate in the presence of crude extracellular mixture (CEM) produced by a specific bacterium, thereby translating bacterial detection into fluorescence signal generation. In this report we will describe key experimental...
10:05
Colorimetric Detection of Bacteria Using Litmus Test
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Cited by 5 •
2016
We describe a protocol for colorimetric detection of E. coli using a modified litmus test that takes advantage of an RNA-cleaving DNAzyme, urease, and magnetic beads.
07:50
Chip-Based Digital PCR to Detect Rare Transcript Variants Using a Nanofluidic Chip
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2025
This video demonstrates chip-based digital PCR — a variation of the digital PCR technique that is useful in detecting rare transcript variants. The PCR reaction is partitioned into the chambers of a nanofluidic chip, each of which acts as an independent reaction. The detection of fluorescence signals from the chambers with amplified targets confirms the presence of rare transcript variants in the sample.
11:11
Detection of Rare Mutations in CtDNA Using Next Generation Sequencing
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Cited by 23 •
2017
This manuscript describes a technique for detecting mutations of low frequency in ctDNA, ER-Seq. This method is differentiated by its unique use of two-directional error correction, a special background filter, and efficient molecular acquirement.
FAQs
Selective enrichment increases the opportunity to observe an uncommon organism when more abundant microbes would otherwise dominate the sample. The process is used before downstream culture-based or microscopic examination, helping bring the low-abundance target into a form that can be assessed with biochemical tests or PCR. Its value is greatest when sample composition makes direct recognition difficult.
PCR targets species-specific DNA, allowing investigators to seek a defined bacterial genetic signature within a complex sample. This is particularly useful when culture is difficult or when the organism is present at low burden. Used alongside microscopy, biochemical testing, or culture, it adds a molecular line of evidence for identifying the organism under investigation.
Combining methods provides complementary information rather than relying on one signal. Microscopy can support direct examination after culture, biochemical testing can characterize the recovered organism, and PCR can target its species-specific DNA. This layered approach is useful when rare organisms are easily overlooked and when researchers need to connect detection with a particular bacterial identity.
A typical workflow begins with the sample and, when needed, selective enrichment or culture. Investigators then examine material by microscopy and apply biochemical testing, while nucleic acid amplification can target species-specific DNA. The sequence may be adapted to the sample and organism, but the central goal is to preserve sensitivity while generating evidence that supports identification.
In infection studies, a positive finding must be interpreted in relation to colonization and disease. Rare bacteria detection can help researchers ask whether an uncommon organism is associated with illness rather than merely present, and can support analysis of host immune responses to low-burden or difficult-to-culture infections. This makes detection relevant to both microbial identification and host-pathogen investigation.
The approach is useful when clinicians or researchers need information for antimicrobial decisions, surveillance of emerging pathogens, or investigation of environmental samples. Sensitive testing can reveal organisms that abundant microbes might conceal, supporting comparisons across clinical, environmental, and research settings. In surveillance, the same capability helps identify uncommon bacterial findings that may warrant closer attention.