Table 3.

Methods for the detection of pathogenic bacteria in clinical settings along with respective main advantages and drawbacks.

Method	Advantages	Drawbacks
Conventional culturing methods	High reliability when thoroughly performed Simplicity of protocols Can indicated the contamination level in samples Some instruments are now largely automated (but therefore are no longer low-cost)	Time consuming (up to 7 days) Requires one to work in aseptic conditions: high risk of environmental contamination Needs trained staff Impossible to detect emerging and non-culturable pathogens
Polymerase Chain Reaction (PCR)	Rapid turnaround Can be multiplexed to target different genes Reliable in cases of high levels of contamination	Most tests do not distinguish live and dead bacteria Protocols need a high level of expertise for the handling Possible presence of PCR inhibitors in some matrices Only pathogens with known sequence data can be detected Contamination can lead to confusing results Instruments and consumables can be expensive
Mass Spectrometry	Rapid turnaround High throughput Low cost for single analyses (but expensive device)	Difficult to directly use raw samples (enrichment or extraction of bacteria is often needed) Only pathogens with known fingerprints can be reliably identified
Optical biosensors	Able to detect low bacterial concentrations in a rapid fashion Information is both quantitative and qualitative Protocols are simple and samples do not require laborious preparative steps	A lot of handling is required thus needing trained staff Low throughput
Label-free biosensors	High sensitivity Tunability of the specificity by tailoring ligands Easily automated and interpreted Some systems can assess the viability of bacteria Easily miniaturized: integrable in pre-existing routines and devices	Requires to develop adequate ligands Throughput depends on the system Scalability towards commercial systems still not assessed Varying cost depending on the technology