Affiliation:
1. State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine , Hangzhou, China
2. Department of Laboratory Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine , Hangzhou, China
Abstract
ABSTRACT
Providencia rettgeri
is a clinically significant opportunistic pathogen that is involved in urinary tract infections. Due to the resolution limitations of identification, distinguishing
P. rettgeri
from closely related species is challenging by commercial biochemical test systems. Here, we first reported a novel species,
Providencia hangzhouensis
, which had been misidentified as
P. rettgeri
. Exhibiting ≤91.97% average nucleotide identity (ANI) and ≤46.10% in silico DNA-DNA hybridization values with all known
Providencia
species,
P. hangzhouensis
falls well beneath the established species-defining thresholds. We conducted a population genomics analysis of
P. hangzhouensis
isolates worldwide. Our study revealed that
P. hangzhouensis
has emerged in many countries and has formed several transmission clusters. We found that
P. hangzhouensis
shared the highest ANI values (91.54% and 91.97%) with
P. rettgeri
and
P. huaxiensis
, respectively. The pan-genome analysis revealed that these three species possessed a similar component of pan-genomes. Two genes associated with metabolism,
folE2
and
ccmM
, were identified to be specific to
P. hangzhouensis
. Furthermore, we also observed that carbapenem-resistance genes frequently occur in
P. hangzhouensis
with the
bla
IMP-27
being the most prevalent (46.15%; 36/78). The emergence of
P. hangzhouensis
is often accompanied by extended-spectrum β-lactamase and carbapenem-resistance genes, and calls for tailored surveillance of this species as a clinically relevant species in the future.
IMPORTANCE
Our study has identified and characterized a novel species,
Providencia hangzhouensis
, which is associated with urinary tract infections and was previously misidentified as
Providencia rettgeri
. Through this study, we have identified specific genes unique to
P. hangzhouensis
, which could serve as marker genes for rapid PCR identification. Additionally, our findings suggest that the emergence of
P. hangzhouensis
is often accompanied by extended-spectrum β-lactamase and carbapenem-resistance genes, emphasizing the need for attention to clinical management and the importance of accurate species identification and proper drug use.
Funder
National Infectious Disease Medical Center startup fund
Jinan Microecological Biomedicine Shandong Laboratory project
Leading Innovative and Entrepreneur Team Introduction Program of Zhejiang
Publisher
American Society for Microbiology
Subject
Infectious Diseases,Cell Biology,Microbiology (medical),Genetics,General Immunology and Microbiology,Ecology,Physiology