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the exclusion of possible bacterial infection and thus avoids unnecessary use of antimicrobials .
The pathogen identification can help consolidate diagnosis ( e . g ., S . aureus isolated from skin and soft tissue infection ). This targeted approach can lead to improved patient outcomes through reducing unnecessary broad empiric antimicrobial prescribing and their associated increased risks of antimicrobial resistance and C . difficile selective pressure . Further confirmation or exclusion of common resistance mechanisms can be used to tailor empiric antimicrobial prescribing ( Figure 2 ).
Phenotypic vs genotypic diagnostic testing Phenotypic bacterial susceptibility testing using direct examination of microbes and culture-based susceptibility testing in vitro is utilised to identify resistance mechanisms and predict in vivo activity of antimicrobials . Microscopy , culture and susceptibility ( MC & S ) diagnostic testing within the microbiology laboratory has underpinned management of antimicrobials since their introduction into healthcare practice . The major limitation is their delayed results , with 36 – 72 hours lag for the full susceptibility results of the most common bacterial pathogens . Further delays are expected for slow-growing bacteria and culturing of certain species may be challenging due to the strict physiological requirements of these pathogens ( e . g ., strict anaerobes may be denatured when exposed to room air ).
For acutely ill patients , this wait might result in sub-optimal or delayed treatment . In settings with low resource or limited access to a central laboratory , MC & S is not always available , and all prescribing is completed empirically . 4
Developments in genotypic resistance testing , initially in research capacity but now in clinical settings , is transforming the capabilities of diagnostic testing . Molecular testing enables the detection of minute amounts of nucleic acids ( DNA or RNA ) in a diagnostic specimen . Nucleic acid amplification testing ( NAAT ), typically via polymerase chain reaction ( PCR ; or reverse transcriptase-PCR in the case of RNA viruses ), enables rapid identification of the microbe and any genetic resistance mechanisms present . Molecular testing can produce results within hours rather than days , thereby offering clear benefits over traditional MC & S diagnostic tests . Molecular testing is versatile and can be introduced in smaller labs for rapid turnover . NAAT testing has replaced MC & S in the genitourinary medicine clinics , where rapid identification of gonococcal infections and chlamydia can be completed in real-time , confirming , or excluding , the presence of an infective aetiology . This streamlines triage pathways in the sexual health clinics , allowing for rapid treatment plans , contact screening and prompt eradication therapy to be completed . 5
The access to molecular diagnostics tests in the microbiology lab is expected to improve as overhead costs for testing reduce . Advances in technologies following the COVID-19 pandemic will also see further availability of these tests and introduction of multiplex syndromic panels to aid diagnosis . 6 This allows for a single test to simultaneously target multiple pathogens with overlapping signs and symptoms for an infectious disease . For conditions such as respiratory illness , syndromic testing can detect common bacterial and viral pathogens associated with pneumonia and replace the current battery of testing recommended ( urinary antigen for Legionella pneumophila and Streptococcus pneumoniae , respiratory viral panel including influenza and SARS-CoV-2 , atypical bacterial serology and direct culture of sputum or deep respiratory samples ). Streamlining this diagnostic pathway will benefit patients ( shorter turnaround time to optimised treatment ) and healthcare professionals ( easier ordering process , faster answers ).
Advances in the molecular testing of common genotypic resistance mechanisms are improving the sensitivity for identifying potential multi-drug resistant pathogens . Combinations of multiple resistance mechanisms ( for example , OXA-1 plus CTX-M-15 ESBL colocation in Enterobacterales resulting in sub-optimal activity of piperacillin / tazobactam in vivo ) can be identified through these new diagnostic testing algorithms . Once identified , appropriate targeted antimicrobial therapies can be initiated and expected patient outcomes improved . Conversely , this will provide clinicians with more assurance in using narrower spectrum therapies , confident in the absence of potential resistance mechanisms . It is expected that there will be a continued role for direct culture and susceptibility testing alongside molecular testing as part of the laboratory service to help identify novel phenotypic mechanisms . >