Genomic insights into the evolution, pathogenicity, and extensively drug-resistance of emerging pathogens and .

INTRODUCTION

is a Gram-negative, flagellated, motile bacillus within the . The case reports of clinical infections shed light on the importance of this organism as an emerging opportunistic pathogen. The genus , which often be misidentified with , is also an important clinically relevant member of the . However, the identification of and is problematic, and their phylogenetic relationship remains unclear.

METHODS

Here, 81 strains of and 16 strains of were collected. A series of comparative genomics approaches were applied to the phylogenetic relationship reconstruction, virulence related genes profiles description, and antibiotic resistance genes prediction.

RESULTS

Using average nucleotide identity (ANI) and DNA-DNA hybridization (DDH), we offered reliable species designations of 97 strains, in which 40 (41.24%) strains were incorrectly labeled. A new genomospecies-1 were defined. and show great genome plasticity and inclusiveness, which may be related to their diverse ecological niches. An intergenomic distances threshold of 0.15875 was used for taxonomy reassignments at the phylogenomic-group level. Further principal coordinates analysis (PCoA) revealed 11 core genes of () that could be served as potential identification targets. Meanwhile, the specific virulence genes , were found to differentiate from . We concluded that the evolution rate of was 5.25E-6, approximately three times higher than that of . Additionally, the co-existence of ESBLs and carbapenem resistance genes were present in approximately 40% strains, suggesting the potential development of extensively drug-resistant or even fully drug-resistant strains.

DISCUSSION

This work provided a better understanding of the differences between closely related species and . Their genomes exhibited great genome plasticity and inclusiveness. They not only possess a potential pathogenicity threat, but also a risk of multi-drug resistance. The emerging pathogens and warrant close attention.