title: Whole genome sequencing uncovers a novel IND-16 metallo-β-lactamase from an extensively drug-resistantChryseobacterium indologenesstrain J31.
abstract: BACKGROUND
  Chryseobacterium indologenesis an emerging opportunistic pathogen in hospital-acquired infection, which is intrinsically resistant to most antimicrobial agents against gram-negative bacteria. In the purpose of extending our understanding of the resistance mechanism ofC. indologenes, we sequenced and analyzed the genome of an extensively antibiotic resistantC. indologenesstrain, isolated from a Chinese prostate cancer patient. We also investigated the presence of antibiotic resistance genes, particularly metallo-β-lactamase (MBL) genes, and performed a comparative genomic analysis with otherChryseobacteriumspecies.
  
  
  RESULTS
  16s rRNA sequencing indicated the isolate belongs toC. indologenes. We assembled a total of 1095M bp clean-filtered reads into 171 contigs by de novo assembly. The draft genome ofC. indologenesJ31 consisted of 5,830,795 bp with a GC content of 36.9 %. RAST analysis revealed the genome contained 5196 coding sequences (CDSs), 28 rRNAs, 81 tRNAs and 114 pseudogenes. We detected 90 antibiotic resistance genes from different drug classes in the whole genome. Notably, a novelblaINDalleleblaIND-16was identified, which shared 99 % identity withblaIND-8andblaIND-10. By comparing strain J31 genome to the closely four related neighbors in the genusChryseobacterium, we identified 2634 conserved genes, and 1449 unique genes.
  
  
  CONCLUSIONS
  In this study, we described the whole genome sequence ofC. indologenesstrain J31. Numerous resistance determinants were detected in the genome and might be responsible for the extensively antibiotic resistance of this strain. Comparative genomic analysis revealed the presence of considerable strain-specific genes which would contribute to the distinctive characteristics of strain J31. Our study provides the insight of the multidrug resistance mechanism in genusChryseobacterium.
authors: State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310003 China.|MOE Key Laboratory of Bioinformatics and Bioinformatics Division, TNLIST/Department of Automation, Center for Synthetic and Systems Biology, Tsinghua University, Beijing, 100084 China.
authors: Tingting
authors: T
authors: Wang
authors: College of Basic Medical Sciences, Zhejiang Chinese Medical University, Hangzhou, 310053 China.
authors: Xiawei
authors: X
authors: Jiang
authors: Institute of Animal Quarantine, Chinese Academy of Inspection and Quarantine, Beijing, 100029 China.
authors: Chunyan
authors: C
authors: Feng
authors: State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310003 China.
authors: Ang
authors: A
authors: Li
authors: State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310003 China.
authors: Huihui
authors: H
authors: Dong
authors: Institute of Animal Quarantine, Chinese Academy of Inspection and Quarantine, Beijing, 100029 China.
authors: Shaoqiang
authors: S
authors: Wu
authors: State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310003 China.
authors: Beiwen
authors: B
authors: Zheng
keywords: Chryseobacterium indologenes; Comparative genomic analysis; Extensively antibiotic resistant; IND-16; Whole genome sequencing