The current gold standard for clinical pathogen identification relies on a combination of culture-based methods, target-specific molecular techniques, and antigen-detection assays1. Known limitations of the first method include the requirement for viable and culturable microorganisms, while the second approach is constrained to a limited number of predefined targets. These constraints reduce their diagnostic success, as not all pathogens are culturable, easily isolated from commensal microbiota, or represented in the selected detection panels. While culture-based methods are widely recognized for their limited sensitivity, updated quantifications of their actual performance in real-world clinical settings are scarce.

To address this gap, we conducted a retrospective survey of all lower respiratory tract (LRT) samples processed by either culture or target-based molecular methods over a five-year period at a Portuguese hospital centre, providing a quantitative assessment of current diagnostic performance.

The authors have declared no competing interest.

This study did not receive any funding

I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained.

Yes

The details of the IRB/oversight body that provided approval or exemption for the research described are given below:

The study was approved by the Health Ethics Committee of the Unidade Local de Saude Regiao de Aveiro (ULSRA) (N/Ref 42-032021, 11/05/2022). The requirement to obtain informed written consent from each individual was waived as the study was limited to the data obtained from ULSRA database, without the need to identify patients.

I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals.

Yes

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Yes

I have followed all appropriate research reporting guidelines, such as any relevant EQUATOR Network research reporting checklist(s) and other pertinent material, if applicable.

Yes

All data produced in the present study are available upon reasonable request to the authors