Table 2.

Application of detection methods for pathogens and their detection limits.

Detection Method	Water Pathogens	Detection Limit (LOD)	Matrix Sample	References
PCR	E. coli	1 cfu /100 mL	Contaminated tap water.	[34]
	Enterotoxigenic E. coli (ETEC)	4 cfu/mL	Water samples spiked by ETEC and nonpathogenic E. coli.	[35]
	Cryptosporidium and Giardia	1 to 10 oocyst and 5–50 cysts	Environmental water samples.	[36]
Multiplex PCR	EHEC, Shigella sp., Vibrio parahaemolyticus, P. aeruginosa and Salmonella sp.	101 cfu, 102 cfu, 102 cfu, 102 cfu and 101 cfu	Polluted water and natural water.	[37]
Quantitative PCR (qPCR)	Adenovirus (adenovirus fiber gene in AdV40 and AdV41)	5–8 copies of AdV40/41	Wastewater, drinking water, recreational waters, and rivers.	[38]
	L. monocytogenes, V. cholerae, V. parahaemolyticus, Pseudogulbenkiana sp., S. typhimurium, S. flexneri, C. perfringens and pathogenic E. coli (Microfluidic qPCR)	From 102 to 104 cells per ca. 200 mg fecal samples of pathogens 100 cells/L	Spiked environmental water samples (pond) and natural fresh water lake.	[39]
	Adenovirus, Aichi virus, astrovirus, enterovirus, human norovirus, rotavirus, sapovirus, and hepatitis A and E viruses (Microfluidic qPCR)	2 copies/μL of cDNA/DNA	River water contaminated with effluents from a wastewater treatment plant.	[40]
Real-time PCR	V. cholerae	1 cfu/100 mL	Ballast water.	[41]
	C. hominis, C. parvum, C. meleagridis, C. wrairi	1 oocyst	Sewage and river water.	[42,43]
	Astrovirus	5–7 GC logs /100 mL	Sewage.	[44]
	L. monocytogenes on biofilms	6 × 102 cfu/cm2	Artificial biofilms.	[45]
Microarrays	Bacillus anthracis, Brucella abortus, C. botulinum, Coxiella burnetii, Francisella tularensi, Rickettsia prowazekii, C. perfringens, S. aureus, V. cholerae, V. alginolyticus, Yersinia pestis Western equine encephalitis, Eastern equine encephalitis, Ebola, Venezuelan equine encephalitis virus, Alexandrium cantenella, Fusarium sporotrichioides	10 fg of B. anthracis DNA, 500 fg of F. tularensis DNA and Y. pestis DNA	Environmental water and ocean water spiked with pathogen.	[46]
	Y. enterocolitica, E. coli, S.enterica Typhimurium,	1 × 107 S. typhimurium cells (104 S. enterica genomes)	Wastewater.	[47]
	Cryptosporidium, Acanthamoeba spp., Blastocystis hominis, Entamoeba spp., Giardia intestinalis, Naegleria spp.	1 × 103 target genes, or 50 Cryptosporidium parvum oocysts, per assay	Municipal wastewater treatment plants.	[48]
Microarray	E. coli, A. hydrophila (DNA microarray and real-time qPCR techniques)	103 A. hydrophila cells per sample, 5 ng of E. coli and 10 ng of A. hydrophila	Municipal wastewater treatment plant in each stage of the disinfection process.	[49]
	C. parvum, C. hominis, E. faecium, B. anthracis, F. tularensis	100 ng of DNA, Microarray assay: 20 genomic copies without a PCR pre-amplification step	Tap water spiked with multiple organisms.	[50]
Pyrosequencing	Y. pestis	0.9 cfu/mL	Milk.	[51]
	B. anthracis (Immunomagnetic separation and pyrosequencing)	6 cfu/mL	Bottled water, milk and juice.	[52]
	Comamonadaceae, Proteobacteria, Bacteroidetes, Planctomycetes, and Elusimicrobia	1.3 ×105 cells/mL	Drinking water of the non-chlorinated distribution system.	[53]
Biosensors	C. parvum	105 oocysts/mL	Oocysts diluted in PBS.	[54]
	E. coli 0157:H7 (NASBA +LFA biosensor)	40 cells/mL	Drinking water.	[55]
	V. cholerae (Amperometric)	8 cfu/mL	Ground and sea water.	[56]
	Microcystis spp. (Optical fibre)	30 ng/L	Lake water.	[57,58]
Fluorescence in situ hybridization (FISH)	F. psychrophilum	7.3 × 105 cells/mL	Culture suspension.	[59]
	E. coli (catalyzed reporter deposition (CARD)-FISH)	8.9 ±1.5 16S rRNA molecules per cell	Mixed pure cultures and sludge.	[60]
	E. coli	1,400 ± 170 16S rRNA copies per E. coli	Activated sludge.	[60]
Immunology-based methods	E. coli O157:H7 and S. enterica typhimurium.	1.8 × 103 cfu/mL of E. coli and 9.2 × 103 cfu/mL of Salmonella	Contaminated food.	[61,62]

* GC logs are mean values of genome copy logs.