sequences of bacteria
Bacterial strainsFrom February 15 to March 13, 2024, the Neonatal Department of the Second Affiliated Hospital of Nanjing Medical University has admitted five newborn patients. A total of seven clinical samples were collected from these five newborn patients: blood samples from two infants , a sputum sample from one infantand environmental samples (incubator and T-piece resuscitator) from two infants . Strain identificationStrains were passaged overnight on blood agar plates and chocolate agar plates (Comag, Shanghai, China) at 37C under 5% CO.Species identification was performed using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) and Smart MS 5020 (Deer Biotech, Zhuhai, China). Antimicrobial susceptibility testingSusceptibility Testing MICs of 15 antibiotics were determined using the agar dilution method, following CLSI-M100s guidelinessulbactam/cefoperazone, tigecycline, and polymyxin, which were interpreted according to European Committee on Antimicrobial Susceptibility Testing (EUCAST) standards. WGS and Genome assembly and annotationGenomic DNA sample(s) was isolated from the cell pellets with a Bacteria DNA Kit (OMEGA) according to the manufacturers instructions. High qualified DNA sample was utilized to construct fragment library.Sequencing was performed by Shanghai Biozeron Biothchnology Co., Ltd. (Shanghai, China.) .For the prokaryotic organism, we used ab initio prediction method to get gene models for strain Klebsiella Pneumoniae. Gene models were identified using GeneMark 4.17. Then all gene models were blastp against non-redundant (NR in NCBI) database, CARD, VFDB to do functional annotation by blastp module. For the prokaryotic organism, we used ab initio prediction method to get gene models for strains. Gene models were identified using GeneMark 4.17 Multi-locus sequence typing and Core Genome SNP Phylogenetic TreeBased on the genome sequence assembled from WGS sequencing, the assembled genome was annotated using KLEBORATE. By utilizing the Pasteur Institute database at http://bigsdb.pasteur.fr/klebsiella/klebsiella.html/ to determine the number of alleles for seven housekeeping genes (gltA, gyrB, gdhB, recA, cpn60, gpi, and rpoD), to assign sequence types (STs). A core SNP-based phylogenetic tree was constructed using parsnp (v 1.3). The tree results were visualized and annotated using the iTOL online analysis platform: https://itol.embl.de/lost_password.cgi.