Identification of Vibrio alginolyticus virulent strain-specific DNA regions by suppression subtractive hybridization and PCR

Mobile genetic elements associated with utilization of dichloromethane and methanol as energy sources in Cupriavidus metallidurans

Cupriavidus metallidurans strain PD11 isolated from laboratory waste drainage can use C1 compounds, such as dichloromethane (DCM) and methanol, as a sole carbon and energy source. However, strain CH34 (a type-strain) cannot grow in the medium supplemented with DCM. In the present study, we aimed to unravel the genetic elements underlying the utilization of C1 compounds by strain PD11. The genome subtraction approach indicated that only strain PD11 had several genes highly homologous to those of Herminiimonas arsenicoxydans strain ULPAs1. Moreover, a series of polymerase chain reaction (PCR) to detect the orthologs of H. arsenicoxydans genes and the comparative study of the genomes of three strains revealed that the 87.9 kb DNA fragment corresponding to HEAR1959 to HEAR2054 might be horizontally transferred to strain PD11. The 87.9 kb DNA fragment identified was found to contain three genes whose products were putatively involved in the metabolism of formaldehyde, a common intermediate of DCM and methanol. In addition, reverse transcription PCR analysis showed that all three genes were significantly expressed when strain PD11 was cultivated in the presence of DCM or methanol. These findings suggest that strain PD11 can effectively utilize the C1 compounds because of transfer of the mobile genetic elements from other bacterial species, for instance, from H. arsenicoxydans.

Transcriptome analysis of the hepatopancreas from the Litopenaeus vannamei infected with different flagellum types of Vibrio alginolyticus strains

Vibrio alginolyticus, one of the prevalently harmful Vibrio species found in the ocean, causes significant economic damage in the shrimp farming industry. Its flagellum serves as a crucial virulence factor in the invasion of host organisms. However, the processes of bacteria flagella recognition and activation of the downstream immune system in shrimp remain unclear. To enhance comprehension of this, a ΔflhG strain was created by in-frame deletion of the flhG gene in V. alginolyticus strain HN08155. Then we utilized the transcriptome analysis to examine the different immune responses in Litopenaeus vannamei hepatopancreas after being infected with the wild type and the mutant strains. The results showed that the ΔflhG strain, unlike the wild type, lost its ability to regulate flagella numbers negatively and displayed multiple flagella. When infected with the hyperflagella-type strain, the RNA-seq revealed the upregulation of several immune-related genes in the shrimp hepatopancreas. Notably, two C-type lectins (CTLs), namely galactose-specific lectin nattectin and macrophage mannose receptor 1, and the TNF receptor-associated factor (TRAF) 6 gene were upregulated significantly. These findings suggested that C-type lectins were potentially involved in flagella recognition in shrimp and the immune system was activated through the TRAF6 pathway after flagella detection by CTLs.

Bioinformatic and functional characterization of cyclic-di-GMP metabolic proteins in Vibrio alginolyticus unveils key diguanylate cyclases controlling multiple biofilm-associated phenotypes

The biofilm lifestyle is critical for bacterial survival and proliferation in the fluctuating marine environment. Cyclic diguanylate (c-di-GMP) is a key second messenger during bacterial adaptation to various environmental signals, which has been identified as a master regulator of biofilm formation. However, little is known about whether and how c-di-GMP signaling regulates biofilm formation in Vibrio alginolyticus, a globally dominant marine pathogen. Here, a large set of 63 proteins were predicted to participate in c-di-GMP metabolism (biosynthesis or degradation) in a pathogenic V. alginolyticus strain HN08155. Guided by protein homology, conserved domains and gene context information, a representative subset of 22 c-di-GMP metabolic proteins were selected to determine which ones affect biofilm-associated phenotypes. By comparing phenotypic differences between the wild-type and mutants or overexpression strains, we found that 22 c-di-GMP metabolic proteins can separately regulate different phenotypic outputs in V. alginolyticus. The results indicated that overexpression of four c-di-GMP metabolic proteins, including VA0356, VA1591 (CdgM), VA4033 (DgcB) and VA0088, strongly enhanced rugose colony morphotypes and strengthened Congo Red (CR) binding capacity, both of which are indicators of biofilm matrix overproduction. Furthermore, rugose enhanced colonies were accompanied by increased transcript levels of extracellular polysaccharide (EPS) biosynthesis genes and decreased expression of flagellar synthesis genes compared to smooth colonies (WTpBAD control), as demonstrated by overexpression strains WTp4033 and ∆VA4033p4033. Overall, the high abundance of c-di-GMP metabolic proteins in V. alginolyticus suggests that c-di-GMP signaling and regulatory system could play a key role in its response and adaptation to the ever-changing marine environment. This work provides a robust foundation for the study of the molecular mechanisms of c-di-GMP in the biofilm formation of V. alginolyticus.

Application of MALDI-TOF MS Profiling Coupled With Functionalized Magnetic Enrichment for Rapid Identification of Pathogens in a Patient With Open Fracture

Posttraumatic infections can occur in orthopedic trauma patients, especially in open fractures. Rapid and accurate identification of pathogens in orthopedic trauma is important for clinical diagnosis and antimicrobial treatment. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) has been successfully used for first-line identification of pathogens grown on culture plates. However, for direct analysis of liquid clinical specimens, pre-purification of the sample is necessary. Herein, we investigated the feasibility of coupling Fc-MBL@Fe₃O₄ enrichment with MALDI-TOF MS profiling in the identification of pathogens in liquid-cultured samples. This method is successfully used for the identification of pathogens in a patient with an open-leg fracture obtained at sea. Pathogens were enriched by Fc-MBL@Fe₃O₄ from briefly pre-cultured liquid media and identified by MALDI-TOF MS. We identified an opportunistic pathogen, Vibrio alginolyticus, which is uncommon in clinical orthopedic trauma infection but exists widely in the sea. Therefore, combining Fc-MBL@Fe₃O₄ enrichment and MALDI-TOF MS profiling has great potential for direct identification of microbes in clinical samples.