Complete Genome Sequence of Vibrio campbellii LMB 29 Isolated from Red Drum with Four Native Megaplasmids

Abstract

Vibrio spp. are the most common pathogens for animals reared in aquaculture. Vibrio campbellii, which is often involved in shrimp, fish and mollusks diseases, is widely distributed in the marine environment worldwide, but our knowledge about its pathogenesis and antimicrobial resistance is very limited. The existence of this knowledge gap is at least partially because that V. campbellii was originally classified as Vibrio harveyi, and the detailed information of its comparative genome analysis to other Vibrio spp. is currently lacking. In this study, the complete genome of a V. campbellii predominant strain, LMB29, was determined by MiSeq in conjunction with PacBio SMRT sequencing. This genome consists of two circular DNA chromosomes and four megaplasmids. Comparative genome analysis indicates that LMB29 shares a 96.66% similarity (average nucleotide identity) with the V. campbellii ATCC strain BAA-1116 based on a 75% AF (average fraction) calculations, and its functional profile is very similar to V. campbellii E1 and V. campbellii CAIM115. Both type III secretion system (T3SS) and type VI secretion system (T6SS), along with the tlh gene which encodes a thermolabile hemolysin, are present in LMB29 which may contribute to the bacterial pathogenesis. The virulence of this strain was experimental confirmed by performing a LDH assay on a fish cell infection model, and cell death was observed as early as within 3 h post infection. Thirty-seven antimicrobial resistance genes (>45% identity) were predicted in LMB29 which includes a novel rifampicin ADP ribosyltransferase, arr-9, in plasmid pLMB157. The gene arr-9 was predicted on a genomic island with horizontal transferable potentials which may facilitate the rifampicin resistance dissemination. Future researches are needed to explore the pathogenesis of V. campbellii LMB29, but the availability of this genome sequence will certainly aid as a basis for further analysis.

Type III Secretion 1 Effector Gene Diversity Among Vibrio Isolates From Coastal Areas in China

“…In addition to V. parahaemolyticus, the T3SS1 and T3SS2 gene clusters were also found to be present in many other Vibrio species. Of these, the T3SS1 gene cluster was mainly present in several species of the harveyi clade, such as V. alginolyticus, V. harveyi, and V. campbellii (Henke and Bassler, 2004;Park et al, 2004;Zhao et al, 2010;Liu et al, 2017). This conclusion was well-supported by our data showing that all tested strains of V. parahaemolyticus, V. alginolyticus, V. harveyi, and V. campbellii in our collections possessed the T3SS1 gene cluster.…”

“…In addition, T3SS gene clusters (T3SS1 or T3SS2) were also found in some other Vibrio species, such as V. alginolyticus, V. harveyi, V. campbellii, Vibrio tubiashii, Vibrio mimicus, and non-O1/O139 V. cholerae (Henke and Bassler, 2004;Park et al, 2004;Dziejman et al, 2005;Okada et al, 2010;Zhao et al, 2010;Liu et al, 2017). Comparative analyses have revealed that most of these clusters are more similar to the T3SS1 of V. parahaemolyticus in gene synteny and homology and harbor identical T3SS1 backbones, including all the genes annotated to encode the basal body, the needle-like structure, and the translocator; however, the hypothetical regions (the so-called effector coding regions) located between vscL and vscU genes of T3SS1, which are supposed to encode the effectors, exhibit many differences in gene content and order among those species (Ono et al, 2006;Zhao et al, 2011;Liu et al, 2017). For example, VopR, an effector encoded by vp1683 in the V. parahaemolyticus strain RIMD2210633, which is involved in the T3SS1-mediated cytotoxicity toward HeLa cells, did not have an ortholog in the T3SS gene cluster of the V. alginolyticus strain ZJ51 (Zhao et al, 2010).…”

“…T3SS1 directly mediates cytotoxicity in host cells during the infection of cultured cells and is present in almost all clinical and environmental isolates of V. parahaemolyticus, whereas T3SS2 is typically associated with enterotoxicity during infection in animal models and found to be unique for Kanagawa phenomenon-positive V. parahaemolyticus (Park et al, 2004;Hiyoshi et al, 2010). In addition, T3SS gene clusters (T3SS1 or T3SS2) were also found in some other Vibrio species, such as V. alginolyticus, V. harveyi, V. campbellii, Vibrio tubiashii, Vibrio mimicus, and non-O1/O139 V. cholerae (Henke and Bassler, 2004;Park et al, 2004;Dziejman et al, 2005;Okada et al, 2010;Zhao et al, 2010;Liu et al, 2017). Comparative analyses have revealed that most of these clusters are more similar to the T3SS1 of V. parahaemolyticus in gene synteny and homology and harbor identical T3SS1 backbones, including all the genes annotated to encode the basal body, the needle-like structure, and the translocator; however, the hypothetical regions (the so-called effector coding regions) located between vscL and vscU genes of T3SS1, which are supposed to encode the effectors, exhibit many differences in gene content and order among those species (Ono et al, 2006;Zhao et al, 2011;Liu et al, 2017).…”

Genome-Wide Identification and Functional Characterization of β-Agarases in Vibrio astriarenae Strain HN897

“…Genomic DNA was extracted from the strain HN897 using the CTAB method with minor modification ( Liu et al, 2017 ). The concentration, quality and integrity of the DNA samples were evaluated using a NanoDrop 2000 Spectrophotometer (Thermo Scientific, United States) and a Bioanalyzer 2100 (Agilent Technologies, United States), respectively.…”

Biological characteristics and genome-wide sequence analysis of endophytic nitrogen-fixing bacteria Klebsiella variicola GN02

“…Finally, the results were corrected through pilon V1.22 software, and the final sequence was spliced to obtain the complete sequence [19,20]. The functional sequence analysis, sub-system analysis, subcellular localization analysis and functional annotation of the protein-encoding genes were performed based on the obtained complete sequence according to the previously reported method [21].…”