Unveiling the Secrets of a Stealthy Superbug: Pseudomonas juntendi's Role in Carbapenem Resistance
The Emerging Threat: Pseudomonas juntendi, a recently discovered species, is emerging as a significant player in healthcare-associated infections, particularly among vulnerable patients. But here's where it gets controversial—this bacterium's ability to cause opportunistic infections and its association with multidrug resistance (MDR) is raising alarms.
The Clinical Challenge: Originally identified in sputum samples from Japan and Myanmar in 2019, P. juntendi has since been linked to various MDR infections, including ventilator-associated pneumonia and catheter-related bacteremia, with alarming mortality rates. Its clinical relevance is further heightened by its genomic plasticity, allowing it to acquire resistance genes horizontally.
The Resistance Enigma: Of particular concern is the blaVIM-2 gene, which confers resistance to carbapenems, a last-resort antibiotic class. This gene has been detected in P. juntendi isolates from both clinical and environmental sources, but its transmission dynamics and genetic context remain elusive.
Unraveling the Mystery: This study delves into the genomic characterization of two MDR P. juntendi strains isolated from human fecal specimens. By employing hybrid whole-genome sequencing, we aimed to explore their resistomes, plasmid profiles, and evolutionary links to aquatic reservoirs.
Methodological Approach: Bacterial isolation and phenotyping were performed on two strains, L2353hy and L2891hy, from male patients with diarrhea. Species identification was confirmed using ANI analysis against global P. juntendi genomes. Antimicrobial susceptibility was assessed using broth microdilution and disk diffusion methods.
Genomic Insights: Hybrid Nanopore Minion and Illumina NovaSeq sequencing revealed high-quality genomes with >100× coverage. Genome annotation identified resistance determinants, plasmid types, and virulence-associated genes. Notably, both strains harbored chromosomally encoded virulence factors, suggesting a robust capacity for host colonization and immune evasion.
Resistance and Plasmid Analysis: ResFinder analysis identified 13 resistance genes, including blaVIM-2, in both strains. Interestingly, all resistance genes were chromosomally encoded, indicating genomic integration. PlasmidFinder confirmed the absence of plasmid replicons, further emphasizing the role of the chromosome in resistance gene carriage.
Genetic Environment Exploration: Gene environment analysis revealed a conserved gene cluster surrounding blaVIM-2, including antibiotic resistance genes, heavy metal resistance genes, and mobile genetic elements (MGEs). The predominant MGEs were Tn3 and IS 91.
Phylogenetic Connections: Phylogenetic analysis revealed a distinct clade comprising the study strains and three closely related P. juntendi strains from human and animal sources. This clustering suggests a potential zoonotic transmission pathway, with aquatic reservoirs as a possible source of clinically relevant strains.
The Carbapenem Resistance Puzzle: The identification of P. juntendi as a carbapenem resistance reservoir is crucial. The close relationship between human and animal strains implies bidirectional gene flow at the human-animal interface. By analyzing the genetic environment of blaVIM-2, we uncovered a highly conserved gene cluster, reinforcing P. juntendi's genetic arsenal for colonization and immune evasion.
Implications and Future Directions: These findings advocate for a One Health approach to surveillance, considering the interconnectedness of human and animal health. The high-quality genomes generated in this study provide valuable resources for future research and surveillance of carbapenemase-producing pathogens.
Data and Ethical Transparency: Whole-genome sequencing data were deposited in the NCBI BioSample database, ensuring data accessibility. The study was ethically approved, utilizing residual clinical samples with waived informed consent due to the retrospective and anonymized nature of the analysis.
