Abstract
Chryseobacterium demonstrates a diverse environmental presence and a significant pathogenic potential across various ecosystems. This clinical case showcases a rare instance of bacterial infection in a 75-year-old male with untreated diabetes and recurrent urinary tract infections (UTIs). The patient presented symptoms of abdominal pain, burning urination, fever, and an elevated eosinophil count. A subsequent urine culture identified a Chryseobacterium-related bacterium as the causative agent, exhibiting sensitivity to piperacillin/tazobactam, trimethoprim/sulfamethoxazole, and nitrofurantoin, which led to successful treatment using oral nitrofurantoin. Analysis of the 16S rRNA gene sequence of APV-1T revealed a close relationship of 98.2% similarity to Chryseobacterium gambrini strain 5-1St1aT (AM232810). Furthermore, comparative genome analysis, incorporating Average Nucleotide Identity (ANI), Digital DNA–DNA Hybridization (dDDH) values, and comprehensive phylogenetic assessments utilizing 16S rRNA gene sequences, core genes, and amino acid sequences of core proteins, highlighted the unique phylogenetic positioning of APV-1T within the Chryseobacterium genus. Distinct carbon utilization and assimilation patterns, along with major fatty acid content, set APV-1T apart from C. gambrini strain 5-1St1aT. These findings, encompassing phenotypic, genotypic, and chemotaxonomic characteristics, strongly support the proposal of a novel species named Chryseobacterium urinae sp. nov., with APV-1T designated as the type strain (= MCC 50690 = JCM 36476). Despite its successful treatment, the strain displayed resistance to multiple antibiotics. Genomic analysis further unveiled core-conserved genes, strain-specific clusters, and genes associated with antibiotic resistance and virulence. This report underscores the vital importance of elucidating susceptibility patterns of rare pathogens like Chryseobacterium, particularly in immunocompromised individuals. It advocates for further analyses to understand the functional significance of identified genes and their implications in treatment and pathogenesis.
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Data availability
The GenBank/EMBL/DDBJ accession number for the reference 16S rRNA gene sequences of the strain APV-1T is OR210930. The accession number of the whole genome of strain APV-1T is JAULSJ000000000; the genome has been submitted under BioProject ID PRJNA989146 (SUB13582581).
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Acknowledgements
The authors express their gratitude to Prof. Aharon Oren for his invaluable etymology checks and nomenclature suggestions for the proposed species. Additionally, the authors extend their thanks to Dr. Amaraja Joshi, Mrs. Sonia Thite, and Ms. Prachi Karodi for their assistance in conducting BIOLOG and Polar Lipid assays.
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The authors acknowledge the funding by Department of Biotechnology (DBT), Government of India under Grant No. BT/COORD.II/01/03/2016 (NCMR).
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SP collected the sample and primary patient data; KP compiled patient data; RP and SM processed the sample, conducted susceptibility tests, and deposited the samples; AB and KK performed DNA-based identification, genome sequencing, genome analysis, phylogenetic analysis, and genome-based AMR profile; LT conducted MALDI-TOF-MS profiling; SK supervised the VITEK profiling, while AY supervised the MALDI-TOF-MS and DNA-based studies; SK and AB drafted the initial version of the manuscript; AY and KK revised and edited the initial draft; AY and SK conceptualized, revised, and finalized the manuscript. All authors have read and approved the final version of the manuscript.
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Bhatt, A., Pujari, S., Mantri, S. et al. A rare urinary tract infection of multidrug-resistant Chryseobacterium urinae sp. nov. isolated from a diabetic, non-catheterized patient. Arch Microbiol 206, 150 (2024). https://doi.org/10.1007/s00203-024-03881-0
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DOI: https://doi.org/10.1007/s00203-024-03881-0