Laboratory of Immunology and Animal Biotechnology, Department of Animal Production and Aquatic Ecology, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium.
Laboratory of Aquaculture & Artemia Reference Center, Department of Animal Production and Aquatic Ecology, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium.
BMC Genomics. 2024 Feb 14;25(1):178. doi: 10.1186/s12864-024-10093-9.
Acute Hepatopancreatic Necrosis Disease (AHPND) causes significant mortality in shrimp aquaculture. The infection is primarily instigated by Vibrio parahaemolyticus (Vp) strains carrying a plasmid encoding the binary toxin PirAB. Yet, comprehension of supplementary virulence factors associated with this relatively recent disease remains limited. Furthermore, the same holds for gastroenteritis in humans caused by other Vp genotypes. Additionally, given the prevalent use of antibiotics to combat bacterial infections, it becomes imperative to illuminate the presence of antimicrobial resistance genes within these bacteria.
A subsampled number of 1,036 Vp genomes was screened for the presence of antimicrobial resistance genes, revealing an average prevalence of 5 ± 2 (SD) genes. Additional phenotypic antimicrobial susceptibility testing of three Vp strains (M0904, TW01, and PV1) sequenced in this study demonstrated resistance to ampicillin by all tested strains. Additionally, Vp M0904 showed multidrug resistance (against ampicillin, tetracycline, and trimethoprim-sulfamethoxazole). With a focus on AHPND, a screening of all Vibrio spp. for the presence of pirA and/or pirB indicates an estimated prevalence of 0.6%, including four V. campbellii, four V. owensii, and a Vibrio sp. next to Vp. Their pirAB-encoding plasmids exhibited a highly conserved backbone, with variations primarily in the region of the Tn3 family transposase. Furthermore, an assessment of the subsampled Vp genomes for the presence of known virulence factors showed a correlation between the presence of the Type 3 Secretion System 2 and tdh, while the presence of the Type 6 Secretion System 1 was clade dependent. Furthermore, a genome-wide association study (GWAS) unveiled (new) genes associated with pirA, pirB, tdh, and trh genotypes. Notable associations with the pirAB genotype included outer membrane proteins, immunoglobulin-like domain containing proteins, and toxin-antitoxin systems. For the tdh + /trh + genotypes (containing tdh, trh, or both genes), associations were found with T3SS2 genes, urease-related genes and nickel-transport system genes, and genes involved in a 'minimal' type I-F CRISPR mechanism.
This study highlights the prevalence of antimicrobial resistance and virulence genes in Vp, identifying novel genetic markers associated with AHPND and tdh + /trh + genotypes. These findings contribute valuable insights into the genomic basis of these genotypes, with implications for shrimp aquaculture and food safety.
急性肝胰腺坏死病 (AHPND) 导致虾类养殖业大量死亡。感染主要由携带编码二聚毒素 PirAB 质粒的副溶血弧菌 (Vp) 菌株引发。然而，对于与这种相对较新疾病相关的其他毒力因子的理解仍然有限。此外，其他 Vp 基因型引起的人类肠胃炎也是如此。此外，鉴于抗生素被广泛用于治疗细菌感染，阐明这些细菌中存在的抗微生物药物耐药基因变得至关重要。
对 1036 个副溶血弧菌基因组进行了抗微生物药物耐药基因的筛选，发现平均存在 5±2（标准差）个基因。对本研究中测序的 3 株副溶血弧菌（M0904、TW01 和 PV1）进行的额外表型抗微生物药物敏感性测试表明，所有测试菌株均对氨苄西林产生耐药性。此外，Vp M0904 表现出多药耐药性（对氨苄西林、四环素和甲氧苄啶-磺胺甲恶唑耐药）。在关注 AHPND 的情况下，对所有 Vibrio spp. 进行 pirA 和/或 pirB 的存在情况筛查表明，其流行率估计为 0.6%，包括 4 株霍乱弧菌、4 株欧文氏弧菌和 1 株副溶血弧菌。它们编码 pirAB 的质粒显示出高度保守的骨架，主要在 Tn3 家族转座酶区域存在变异。此外，对副溶血弧菌基因组进行了已知毒力因子存在情况的评估，结果表明 3 型分泌系统 2 和 tdh 的存在与 tdh 之间存在相关性，而 6 型分泌系统 1 的存在与进化枝有关。此外，全基因组关联研究 (GWAS) 揭示了与 pirA、pirB、tdh 和 trh 基因型相关的（新）基因。与 pirAB 基因型的显著关联包括外膜蛋白、免疫球蛋白样结构域蛋白和毒素-抗毒素系统。对于 tdh+ / trh+基因型（包含 tdh、trh 或这两个基因），与 T3SS2 基因、脲酶相关基因和镍转运系统基因以及参与“最小”I-F CRISPR 机制的基因有关。
本研究强调了副溶血弧菌中抗微生物药物耐药性和毒力基因的流行情况，确定了与 AHPND 和 tdh+ / trh+基因型相关的新型遗传标记。这些发现为这些基因型的基因组基础提供了有价值的见解，对虾类养殖业和食品安全具有重要意义。
