Emergence of carbapenem-resistant Phytobacter diazotrophicus in hospital effluent in Brazil

Background Phytobacter spp. have recently emerged as opportunistic pathogens in vulnerable patients and are increasingly recognized as carriers of clinically relevant carbapenemase genes, particularly bla KPC-2 . Phytobacter diazotrophicus is the most frequently recovered species from clinical specimens in cases of infections. Despite this growing clinical importance, little is known about the presence, genomic characteristics, and environmental dissemination of Phytobacter spp. outside clinical settings. Hospital effluent is recognized as an important environmental pollutant and source of antimicrobial-resistant bacteria carrying resistance genes. However, the occurrence and genomic context of carbapenemase-producing P. diazotrophicus in hospital wastewater remain largely unexplored, particularly in Brazil, where bla KPC-2 is endemic. Therefore, this study aimed to isolate and characterize carbapenem-resistant P. diazotrophicus from the effluent of a pediatric hospital in Brazil. Methods Wastewater samples were collected at Pequeno Príncipe Hospital, Curitiba Brazil. Phytobacter diazotrophicus isolates were isolated and identified using matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS). Whole-genome-based analysis was performed to confirm the identity of P. diazotrophicus isolates, and their antimicrobial susceptibility was tested using antimicrobial assays. Expression of the bla KPC gene was confirmed via polymerase chain reaction. Results MALDI-TOF MS revealed 345 microorganisms, and whole-genome comparisons supported the assignment of five strains to P. diazotrophicus . The resistance phenotypes determined via antimicrobial assays were consistent with the genomic antimicrobial resistance profiles, and two isolates (PHY1 and PHY5) exhibited resistance to carbapenems. Genomic analysis revealed the presence of bla KPC-2 in these two isolates. Conclusion To the best of our knowledge, this study provides the first evidence of bla KPC-2 harboring P. diazotrophicus in hospital effluent in Brazil. The detection of carbapenemase-producing bacteria in hospital wastewater underscores the importance of effluent surveillance as a strategy to monitor and mitigate the environmental dissemination of antimicrobial resistance.