Use of Bacteroidales Microbial Source Tracking To Monitor Fecal Contamination in Fresh Produce Production

DOI: 10.1128/AEM.02891-13

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FIG 1
Box and whisker plot depicting the concentration (in log₁₀ GEC/100 ml) of the AllBac marker on hands, in irrigation water (source and in-field), and on produce samples, sorted by produce type. The lower boundary of the box indicates the 25th percentile, the line within the box represents the median, and the boundary of the box farthest from zero indicates the 75th percentile. Whiskers above the box indicate the 90th percentiles. Points represent outliers. A statistically significant difference was detected in AllBac marker concentration by produce type (P < 0.0001) but not by sample type (P > 0.05).
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FIG 2
Box and whisker plot depicting the concentration (in log₁₀ GEC/100 ml) of the BFD marker on hands, in irrigation water, and on produce samples, sorted by produce type. The lower boundary of the box indicates the 25th percentile, the line within the box represents the median, and the boundary of the box farthest from zero indicates the 75th percentile. Whiskers above the box indicate the 90th percentiles. Points represent outliers. There was no statistically significant difference in the concentrations of the BFD marker between produce types or between sample types (P > 0.05).

TABLE 1

Primers and probes used in this study

Marker	Assay	Oligonucleotide name	5′→3′ sequence^{^a}	Reference or source
General fecal contamination	AllBac	AllBac296f	GAGAGGAAGGTCCCCCAC	25
	AllBac	AllBac412r	CGCTACTTGGCTGGTTCAG
	AllBac	AllBac375Bhqr	(FAM)-CCATTGACCAATATTCCTCACTGCTGCCT-(BHQ-1)
Bovine	BoBac	BoBac367f	GAAG(G/A)CTGAACCAGCCAAGTA	25
	BoBac	BoBac467r	GCTTATTCATACGGTACATACAAG
	BoBac	BoBac402Bhqr	(FAM)-TGAAGGATGAAGGTTCTATGGATTGTAAACTT-(BHQ-1)
Human	HF183	HF183	ATCATGAGTTCACATGTCCG	16
	HF183	BFDRev	CGTAGGAGTTTGGACCGTGT
	HF183	BFDFAM	(FAM)-CTGAGAGGAAGGTCCCCCACATTGGA-(BHQ-1)
	BFD	BFDFor	CGTTCCATTAGGCAGTTGGT	26
	BFD	BFDRev	CGTAGGAGTTTGGACCGTGT
	BFD	BFDFAM	(FAM)-CTGAGAGGAAGGTCCCCCACATTGGA-(BHQ-1)
	Bvulg	BVulgF1	CATCATGAGTCCRCATGTTCA	16
	Bvulg	BFDRev	CGTAGGAGTTTGGACCGTGT
	Bvulg	BFDFAM	(FAM)-CTGAGAGGAAGGTCCCCCACATTGGA-(BHQ-1)
IAC		IACProbe	(TET)-ATCTCAGTTCGGTGTAGGTCGTTCGCTCC-(BHQ-1)	This study

↵a FAM, 6-carboxyfluorescein; BHQ-1, black hole quencher 1; TET, 6-carboxy-2′,4,7,7′-tetrachlorofluorescein succinimidyl ester.

TABLE 2

Percent of samples positive, negative, and uninterpretable for the AllBac Bacteroidales marker

TABLE 3

Percent of AllBac-positive samples also positive for human-source marker (BFD, HF183, or BVulg)