Community-Acquired Hafnia paralvei Pneumonia in an Immunocompetent Adult: A Case Report, Genomic Characterization of Antimicrobial Resistance, and Literature Review

Background. Hafnia alvei is considered an uncommon pathogen in immunocompetent individuals. It has been isolated in several cases of nosocomial pneumonia, but it has rarely been associated with community-acquired pneumonia (CAP) in immunocompetent adults. In 2010 a genotypically distinct species of Hafnia was identified, for which the name Hafnia paralvei was proposed. Since then, very few cases of human infection by H. paralvei have been reported. We describe here a case of CAP sustained by H. paralvei in a man without major systemic comorbidities and the genomic characterization of antibiotic resistance, together with a review of the literature on this topic. Case presentation. A 54-year-old man was admitted to the Emergency Room (ER) with a 3-day history of fever, fatigue, nausea. In the ER a thoracic CT scan revealed an extensive area of consolidation in the left lower lobe. He was empirically treated with piperacillin/tazobactam + azithromycin. After an initial improvement, clinical conditions worsened and empirical therapy was changed to meropenem + linezolid. An aerosol-induced sputum for bacterial culture yielded Hafnia alvei 107 colony-forming-units/mL; the germ was resistant to piperacillin/tazobactam and was sensitive to ceftriaxone, cefepime, and meropenem. Therefore, linezolid was withdrawn and meropenem continued obtaining resolution of the pneumonia. During the revision process, in silico analysis of sequences using three independent genome-based methods was performed: all three approaches, each relying on a different taxonomic metric, consistently assigned the isolate to H. paralvei. Moreover, the study of resistance-associated genes showed that the isolate harbored blaACC-1a and blamcr-9.1. Conclusion. We have described a case of CAP due to H. paralvei in an immunocompetent man. Limitations in antibiotic choices and duration of treatment have been discussed, and genomic characterization of antibiotic resistance has been studied.