Pneumonia is a leading cause of hospitalization and death in the general population. Currently, the identification of bacterial pathogens and resistance rely mainly on microbiological cultures. PCR-assays are emerging as a rapid, complementary method of detecting both bacteria and resistance genes in lower respiratory tract infections.

This investigator-initiated, prospective, multicenter study explored the resistance patterns of bacteria detected in the brocho-alveolar lavage fluids (BALF).

BALF from 208 hospitalized patients with pneumonia was assessed for antimicrobial resistance (AMR) using conventional microbiological culture and multiplex bacterial PCR (Curetis, Holzgerlingen, Germany), which detects the following resistance genes: ermB, mecA, mecC, tem, shv, ctx-M, imp, kpc, ndm, oxa-23, oxa-24, oxa-48, oxa-58, vim, sul1, gzrA83 and gyrA87.

The patients? mean age was 66 ± 14 years (65% males; 56% immunocompromised). Among 48 PCR-positive BALFs six also detected a resistance gene (12.5%) and 3/6 detected multiple resistance genes. The most prevalent resistance gene was tem (determinant of resistance to penicillins and early cephalosporins). Thirty-nine cultures identified a pathogenic bacterial agent, of which 16/39 (41%) identified an antibiotic resistance. Only four samples showed a matching resistance pattern of PCR and culture-based antibiotic susceptibility testing (Kappa coefficient for agreement was 0.40), suggesting poor concordance between the two testing methods (McNemar?s test, p=0.014).

Molecular tests rarely detected resistance genes in a low resistance setting. The concordance with culture-based assays is low and requires further clinical validation.