Objective:To identify and trace the origin of the Francisella tularensis subsp. novicida strain SJCS-979 isolated from the blood of a patient, so as to provide a reference for the traceability investigation of such infection events. Methods:Hot spring water samples that the patient had recently bathed in were collected to culture the causative agent, combined with the pathogenic characteristics and the patient′s activity before the bloodstream infection. The water samples were concentrated, acid-treated, and then the isolation of the causative agent was performed, following the method for Legionella detection in circulating cooling water. Suspected strains detected from the hot spring water were subjected to classical phenotypic identification, API ZYM and API NH strips tests, drug sensitivity testing, and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) identification, and the obtained data were compared with those of strain SJCS-979 isolated from the patient′s blood. A phylogenetic tree was constructed based on genomic analysis to determine the taxonomic status of strain SJCS-979 and related strains. Epidemiological data of Francisella tularensis subsp. novicida were collected and analyzed by integrating the global genetic and genomic data on GenBank database. Core single nucleotide polymorphism(SNP) comparisons were obtained using Snippy 3.2 software, and then an evolutionary tree was built to determine its population structure based on BAPS analysis. Results:Strain CC-2, isolated from the hot spring water, shared the same biochemical and drug sensitivity phenotype, and had a nearly consistent mass spectrometric profile with strain SJCS-979 isolated from the blood of a patient. Genomic phylogenetic tree analysis based on 120 core protein sequences showed that strains SJCS-979 and CC-2 fell on the same branch with known Francisella tularensis subsp. novicida strains. Bayesian genotyping showed that the global Francisella tularensis subsp. novicida strains with genomic data could be divided into six different sequence clusters. Strains SJCS-979 and CC-2 were located in the same taxonomic group with only 4 SNP differences, indicating that they might be the same clone. Conclusions:This study reports a case of bacteremia caused by Francisella tularensis subsp. novicida, and natural hot spring water may be the environmental source of this infection event.

Objective:To identify and trace the origin of the Francisella tularensis subsp. novicida strain SJCS-979 isolated from the blood of a patient, so as to provide a reference for the traceability investigation of such infection events. Methods:Hot spring water samples that the patient had recently bathed in were collected to culture the causative agent, combined with the pathogenic characteristics and the patient′s activity before the bloodstream infection. The water samples were concentrated, acid-treated, and then the isolation of the causative agent was performed, following the method for Legionella detection in circulating cooling water. Suspected strains detected from the hot spring water were subjected to classical phenotypic identification, API ZYM and API NH strips tests, drug sensitivity testing, and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) identification, and the obtained data were compared with those of strain SJCS-979 isolated from the patient′s blood. A phylogenetic tree was constructed based on genomic analysis to determine the taxonomic status of strain SJCS-979 and related strains. Epidemiological data of Francisella tularensis subsp. novicida were collected and analyzed by integrating the global genetic and genomic data on GenBank database. Core single nucleotide polymorphism(SNP) comparisons were obtained using Snippy 3.2 software, and then an evolutionary tree was built to determine its population structure based on BAPS analysis. Results:Strain CC-2, isolated from the hot spring water, shared the same biochemical and drug sensitivity phenotype, and had a nearly consistent mass spectrometric profile with strain SJCS-979 isolated from the blood of a patient. Genomic phylogenetic tree analysis based on 120 core protein sequences showed that strains SJCS-979 and CC-2 fell on the same branch with known Francisella tularensis subsp. novicida strains. Bayesian genotyping showed that the global Francisella tularensis subsp. novicida strains with genomic data could be divided into six different sequence clusters. Strains SJCS-979 and CC-2 were located in the same taxonomic group with only 4 SNP differences, indicating that they might be the same clone. Conclusions:This study reports a case of bacteremia caused by Francisella tularensis subsp. novicida, and natural hot spring water may be the environmental source of this infection event.

Objective:To analyze the biological characteristics, phylogeny and the taxonomic status of strain 7712 (=CGMCC 1.17031=NBRC 113783=KCTC 15766) isolated from a clinical blood sample.Methods:Strain 7712 was identified by the cultural properties, cellular and colonial morphology, physiological and biochemical reactions, matrix-assisted laser desorption ionization time-of-flight mass spectrometry system, and genome correlation index analysis. The genomic phylogenetic tree was construct to analyze the taxonomic position. The virulence factors and resistance genes of strain 7712 and related strains were then compared by the online virulence factor database and online comprehensive antibiotic research database respectively.Results:Strain 7712 was urease negative, gram-negative nonfermenters, which was identified as Ochrobactrum anthropi by VITEK GN card. The 16S rRNA gene analysis showed that the strain was closely related to the members of genera Ochrobactrum and Brucella. The phylogenetic tree showed that strain 7712 was clustered together with Ochrobactrum teleogrylli LCB8 T and Ochrobactrum haematophilum CCUG 38531 T, along with genus Brucella and other Ochrobactrum species. The genome relatedness indexes analysis showed that the average nucleotide identity between strain 7712 and Ochrobactrum teleogrylli LCB8 T was 98.16%, which was higher than the threshold for prokaryotic species. Genetic prediction showed that strain 7712 carried several virulence-related genes and resistance-related genes, of which the existence of OCH gene might be responsible to the resistance to cephalosporin. Conclusions:A case of human infection caused by Ochrobactrum teleogrylli is identified, which would help promote the understanding of biodiversity of genus Ochrobactrum.

Objective:To identify and characterize one Spiroplasma strain (designated as DGKH1) isolated from the blood of a patient with sepsis. Methods:The traditional bacterial culture, staining, morphological observation, physiological and biochemical identification, 16S rRNA gene sequencing, phylogenetic analysis, genome sequencing, and the genome-related index analysis were performed to accurately determine the taxonomic status of the strain DGKH1. Antibiotic susceptibility testing was performed using a specific kit for culturing and testing Ureaplasma urealyticum/ Metamycoplasma hominis. Results:The strain DGKH1 could weakly grow on Columbia blood agar, chocolate agar, and Haemophilus chocolate 2 agar. However, it did not grow in liquid culture medium containing tetracycline (4 μg/ml), doxycycline (1 μg/ml), minocycline (1 μg/ml), josamycin (2 μg/ml), roxithromycin (1 μg/ml), clarithromycin (1 μg/ml), or telithromycin (1 μg/ml). DGKH1 resembling Metamycoplasma hominis formed "fried egg-like colonies" on Mycoplasma solid culture medium. DGKH1 could not be stained by Gram staining. When observed under transmission electron microscopy (TEM) using phosphate buffer as the matrix, the bacteria were spiral-shaped. Results of 16S rRNA gene sequence alignment showed that DGKH1 was highly similar (99.85%) to Spiroplasma eriocheiris CCTCC M 207170 T. However, the urea decomposition test was positive, which was different from all of the known Spiroplasma species. The phylogenetic analysis based on whole genome showed that DGKH1 was clustered in a small branch along with Spiroplasma eriocheiris CCTCC M 207170 T. However, the average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between the two strains were 94.14% and 56.00%, respectively, both below the threshold for prokaryotic species identification. Conclusions:DGKH1 represented a potential new species of genus Spiroplasma, closely related to Spiroplasma eriocheiris. Some microbiological characteristics of DGKH1 were similar to Mycoplasmas. However, the natural host and epidemiological data of DGKH1 need to be further studied.

Objective:To analyze the molecular epidemiological characteristics of Campylobacter fetus subsp. testudinum ( Cft). Methods:Fifteen strains of Cft collected in our laboratory from 2010 to 2022 were subjected to whole-genome sequencing. Their epidemiological characteristics were analyzed based on the global genome data of Cft on GenBank database. MLST-GrapeTree software was used to obtain the genetic structure of Cft strains. A phylogenetic tree was constructed using core-genome single nucleotide polymorphism (cgSNP) analysis, and the sequence clusters were identified using rhierBAPS. Virulence genes and drug resistance genes of Cft strains were annotated using CARD, ResFinder and VFDB database. Their susceptibility to antibiotics was tested using E-test method and the results were analyzed using the CLSI-M45 sensitivity standard for Campylobacter jejuni/ Campylobacter coli. Results:Based on average nucleotide identity (ANI) analysis, the genome data of 41 Cft strains including 24 isolated from human, 13 from animals and four of unknown sources were collected from GenBank database. Among the 24 human-derived strains, 20 were linked to Asian descent and only one was linked to Caucasian descent (spouse of Asian descent), showing statistically significant differences in human ethnicity. All of the 13 animal-derived strains were originated from reptilian sources, including six from turtles, four from snakes and three from lizards. MLST revealed that ST46 was the predominant ST in China, while ST15 was the major sequence type in the United States. Grapetree analysis also demonstrated that the genetic diversity in China was greater than that in the United States. The phylogenetic tree constructed based on cgSNP and BAPS identified six distinct sequence clusters. The Chinese isolates were scattered in diverse sequence clusters and closely related to animal-derived strains, while the American isolates mainly belonged to ST15. The genes encoding virulence factors such as flagella, glycosylation systems and adhesins were carried by all of the 41 Cft strains (100.00%). The invasion-related virulence genes, such as the genes encoding the IV type secretion system ( virB4, virB9, virD4) and the resistance-related tetO efflux pump gene were specifically identified in the emerging ST74 clones. In vitro drug susceptibility testing of 15 Chinese isolates revealed 46.67% of the Cft strains were resistant to ciprofloxacin and 100.00% were sensitive to erythromycin. Conclusions:The global sequence clusters of Cft isolates showed a great genetic diversity. Most of the people with Cft infection had basic immune diseases and might have eaten or had contact with reptiles. Notably, the Chinese domestic infection of ST46 and the emerging ST74 should arouse our more attention.

Objective:To study the molecular phylogeny and virulence gene profile of Francisella salimarina. Methods:Phylogenetic analysis of Francisella salimarina was performed based on the global genome data of related Francisella species on GenBank database. The consistency in phylogenetic analysis based on single marker genes (such as 16S rRNA gene, rpoB gene and mdh gene) and the core genome as compared. Virulence genes and antibiotic resistance genes were annotated using the virulence factor database (VFDB) and the Comprehensive Antibiotic Resistance Database (CARD), respectively. The virulence of Francisella salimarina was analyzed with a Galleria mellonella (greater wax moth) infection model using Francisella philomiragia ATCC 25015 T as reference strain. Results:The phylogenetic analysis revealed that Francisella salimarina was closely related to Francisella philomiragia. The phylogenetic tree based on mdh gene was highly similar to that based on the core genome. Francisella salimarina could be differentiated from other related species by 16S rRNA gene or mdh gene, with the latter being more accurate. Eight Francisella salimarina strains carried multiple virulence genes, mainly involved in secretion, adhesion, immune regulation, motility and stress survival. Moreover, beta-lactam resistance gene blaFPH was identified in all eight strains. Francisella salimarina showed high lethality in the Galleria mellonella infection model, which was similar to Francisella philomiragia ATCC 25015 T. Conclusions:Francisella salimarina was a rare pathogen with similar pathogenicity to Francisella philomiragia. The mdh gene could be used as a molecular target for rapid identification of Francisella salimarina.