Table 4.

Rapid nucleic acid isolation systems for pathogen detection in urine.

Sample Type	Target Pathogen		Cell Lysis Method	Nucleic Acid Extraction Technique	Nucleic Acid Amplification Method	LOD/Extraction Efficiency	Total Sample-To-Answer/Sample Preparation Time	Reference
Urine	E. coli		On-chip hybrid chemical/mechanical cell lysis	SPE using silica impregnated polymer monolith	Benchtop real-time PCR	10 CFU/mL	40 min (sample preparation)	Kulinski et al. (2009)
Urine	Chlamydia trachomatis		Chemical lysis	Paper-based SPE into a micropipette tip	HDA	1000 cells/sample	~50 min (sample-to-answer)	Linnes et al. (2014)
Urine	Zika virus		Chemical lysis	Magnetic particles based SPE in a modified 3D printer	RT-RPA using prestored liquid reagents	5 PFU/mL	15 min (sample preparation) 25 min (sample to answer)	Chan et al. (2016b)
Urine	Zika virus		Wax printed paper microfluidic chip was used to filter target pathogens		Paper based RT-LAMP	1 copy/μL	15 min (sample to answer)	Kaarj et al. (2018)
Urine	E. coli, Klebsiella pneumoniae and S. aureus	Chemical lysis		Chitosan-modified glass filter paper embedded in capillaries captured nucleic acids	LAMP amplification using prestored LAMP primers	200 CFU per capillary	85 min (sample-to-answer)	Hui et al. (2018)
Urine	Zika Virus	Chemical lysis		Cellulose paper-based RNA extraction	RT-LAMP	3.5 PFU/mL	50 min (sample to answer)	Jiang et al. (2018)
Urine	Brucella ovis		Pathogen enrichment, chemical cell lysis and functionalized Teflon filter-based DNA extraction		Benchtop real-time PCR	1 CFU/mL	Less than 20 min (sample preparation)	Zhao et al. (2019)
Urine	M. tb	Chemical cell lysis		Magnetic bead-based DNA extraction into a transfer pipette	Benchtop real-time PCR	90% (extraction efficiency)	~20 min (sample preparation)	Pearlman et al. (2020)
Urine	Trichomonas vaginalis (TV)	Chemical lysis		Chitosan-modified Fusion 5 membrane captured DNA	HDA	7 genomic equivalents of TV DNA per mL	2 min (sample preparation)	Rosenbohm et al. (2020)