Development of a multiplex PCR assay for rapid and simultaneous detection of four genera of fish pathogenic bacteria

Multiplex PCR assay for the accurate and rapid detection and differentiation of Lactococcus garvieae and L. petauri

Lactococcosis is a common bacterial fish disease caused by Lactococcus garvieae, L. petauri and L. formosensis. Although there are different PCR-based techniques to identify the etiological agent, none of these can differentiate these two bacteria without sequencing PCR-amplified fragments. In the present study, we developed a multiplex PCR assay for simultaneous detection and differentiation of L. garvieae and L. petauri. The specificity of the primers was validated against the bacterial DNA of the targeted and non-targeted bacteria. The sizes of the PCR amplicons were obtained as 204 bp for the DUF1430 domain-containing protein gene of L. garvieae, 465 bp for the Lichenan permease IIC component gene of L. petauri, and 302 bp for the teichoic acid biosynthesis protein F gene of both L. garvieae and L. petauri. The PCR amplicons were clearly separated by agarose gel electrophoresis. The multiplex PCR assay did not produce any amplification products with the DNA of the non-targeted bacteria. The multiplex PCR detection limits for L. garvieae and L. petauri were 5 and 4 CFU in pure culture and 50 and 40 CFU/g in spiked tissue samples, respectively. It takes less than 2 h from plate-cultured bacteria and 3 h from tissue samples to get results. In conclusion, the developed multiplex PCR assay is a rapid, specific, accurate, and cost-effective method for the detection and differentiation of L. garvieae and L. petauri and is suitable to be used for routine laboratory diagnosis of L. garvieae and L. petauri.

A Duplex PCR Assay for Rapid Detection of Klebsiella pneumoniae and Chryseobacterium in Large Yellow Croaker Fish

Both Klebsiella pneumoniae and Chryseobacterium cause an increasing number of diseases in fish, resulting in great economic losses in aquaculture. In addition, the disease infected with Klebsiella pneumoniae or Chryseobacterium exhibited the similar clinical symptoms in aquatic animals. However, there is no effective means for the simultaneous detection of co-infection and discrimination them for these two pathogens. Here, we developed a duplex polymerase chain reaction (PCR) method based on the outer membrane protein A (ompA) gene of Klebsiella pneumoniae and Chryseobacterium. The specificity and validity of the designed primers were confirmed experimentally using simplex PCR. The expected amplicons for Klebsiella pneumoniae and Chryseobacterium had a size of 663 and 1404 bp, respectively. The optimal condition for duplex PCR were determined to encompass a primer concentration of 0.5 μM and annealing temperature of 57°C. This method was analytical specific with no amplification being observed from the genomic DNA of Escherichia coli, Vibrio harveyi, Pseudomonas plecoglossicida, Aeromonas hydrophila and Acinetobacter johnsonii. The limit of detection was estimated to be 20 fg of genomic DNA for Chryseobacterium and 200 fg for Klebsiella pneumoniae, or 100 colony-forming units (CFU) of bacterial cells in both cases. The duplex PCR was capable of simultaneously amplifying target fragments from genomic DNA extracted from the bacteria and fish liver. For practical validation of the method, 20 diseased fish were collected from farms, among which 4 samples were PCR-positive for Klebsiella pneumoniae and Chryseobacterium. The duplex PCR method developed here is time-saving, specific, convenient, and may prove to be an invaluable tool for molecular detection and epidemiological investigation of Klebsiella pneumoniae and Chryseobacterium in the field of aquaculture.

Aeromonas dhakensis: A Zoonotic Bacterium of Increasing Importance in Aquaculture

Aeromonas dhakensis is increasingly recognised to be an important pathogen responsible for disease losses in warm-water aquaculture and, similar to several other Aeromonas species, it can infect humans. Knowledge of A. dhakensis is accumulating, but this species remains relatively under-investigated compared to its close relative, Aeromonas hydrophila. The significance of A. dhakensis may have been overlooked in disease events of aquatic animals due to issues with reliable identification. Critical to appreciating the importance of this pathogen is the application of dependable molecular tools that enable accurate identification and discrimination from A. hydrophila and other motile aeromonads. This review aims to synthesise the key literature on A. dhakensis, particularly with relevance to aquaculture, including knowledge of the bacterium derived from disease case studies in aquatic hosts. Identification methods and strain phylogeny are discussed, with accurate detection important for prompt diagnosis and for distinguishing strains with heightened virulence. Increasing evidence suggests that A. dhakensis may be more virulent than A. hydrophila and correct identification is required to determine the zoonotic risks posed, which includes concerns for antibiotic-resistant strains. This review provides an impetus to improve species identification in the future and screen strain collections of presumptive Aeromonas spp. retrospectively to reveal the true prevalence and impact of A. dhakensis in aquaculture, the environment, and healthcare settings.

Physicochemical and Microbiological Water Quality Assessment of a Northwestern Algerian Dam: Detection of Ichtyopathogenic Bacteria

Freshwater fish are often exposed to threats from anthropogenic or natural origins, such as pathogenic or opportunistic microorganisms responsible for a broad range of severe infections. In this study, we aimed to assess this microbiological threat to fish in an Algerian northwestern dam Sekkak (Tlemcen) by evaluating the diversity of ichtyopathogenic bacteria. In order to determine the water quality, physicochemical analyses of the dam water were carried out in situ. Ichtyopathogenic bacteria were isolated on selective media and identified by API galleries and molecular techniques (PCR and sequencing of the 16S rRNA gene). Besides, the antibiograms were constructed for all the isolates. The physicochemical and bacteriological analyses allowed us to classify the dam water as moderately polluted to polluted. Furthermore, an important diversity of ichtyopathogenic bacterial species was observed as Aeromonas hydrophila, Providencia rettgeri, and Pseudomonas aeruginosa were retrieved. The antibiogram test revealed notable resistance. The antibiotic family for which most resistances were found was the β-lactam family, followed by aminoglycosides and macrolides. These results indicate that aquatic environments can shelter multidrug-resistant pathogenic bacteria representing a threat to the endemic fauna. Therefore, it is important to closely monitor these waters in order to improve the fish's living environment and ensure healthier production.

Genetic characterization and antimicrobial profiling of bacterial isolates collected from Nile tilapia (Oreochromis niloticus) affected by summer mortality syndrome

In recent years, Egyptian tilapia aquaculture has experienced mortality episodes during the summer months. The causative agents responsible for such mortalities have not been clearly identified. A total of 400 fish specimens were collected from affected tilapia farms within five Egyptian governorates. A total of 344 bacterial isolates were identified from the examined fish specimens. Bacterial isolates were grouped into seven genera based on API 20E results. The most prevalent pathogens were Aeromonas spp. (42%), Vibrio spp. (21%), and Streptococcus agalactiae (14.5%). Other emerging infections like, Plesiomonas shigelloides (10%), Staphyloccocus spp. (8%), Pseudomonas oryzihabitans, and Acinetobacter lwoffii (2.3%) were also detected. Sequence analysis of the 16S ribosomal RNA bacterial gene of some isolates, confirmed the phenotypic identification results. The analysis of antibiotic resistance genes revealed the presence of aac(6')-Ib-cr (35.7%), blaCTX gene (23.8%), qnrS (19%), ampC (16.7%), floR (14.3%), sul1, tetA, and van.C1 (2.4%) genes in some isolates. The antimicrobia resistance gene, qac was reported in 46% of screened isolates. Bacterial strains showed variable virulence genes profiles. Aeromonas spp. harboured (act, gcat, aerA, lip, fla, and ser) genes. All Vibrio spp. possessed the hlyA gene, while cylE, hylB, and lmb genes, were detected in S. agalactiae strains. Our findings point to the possible role of the identified bacterial pathogens in tilapia summer mortality syndrome and highlight the risk of the irresponsible use of antibiotics on antimicrobial resistance in aquaculture.

Microchip coupled with MALDI-TOF MS for the investigation of bacterial contamination of fish muscle products

Bacterial contamination is a significant concern in food safety. Traditional methods, though being a gold standard for bacterial detection, are time-consuming. In this work, we managed to establish a simple and versatile magnetic-assisted microfluidic method for rapid bacterial detection of fish muscle products, by manipulating anti-human IgG functionalized magnetic beads in a zig-zag shaped microfluidic channel, increasing the probability for bacteria capture. The captured bacteria were characterized by matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS). This method is capable of isolating Escherichia coli, Staphylococcus aureus and Klebsiella pneumoniae from 5 μL of sablefish sarcoplasmic protein sample, and detecting Escherichia coli in the range of 6.0 to 6.0×10⁴ CFU/mL with a detection limit of 6 CFU/mL. Bacterial growth on salmon sashimi during its period of storage was successfully monitored. The current protocol holds great potential for pathogen detection and microbial control in the food industry.

Quantifying dominant bacterial genera detected in metagenomic data from fish eggs and larvae using genus‐specific primers

The goal of this study was to design genus‐specific primers for rapid evaluation of the most abundant bacterial genera identified using amplicon‐based sequencing of the 16S rRNA gene in fish‐related samples and surrounding water. Efficient genus‐specific primers were designed for 11 bacterial genera including Alkalimarinus, Colwellia, Enterovibrio, Marinomonas, Massilia, Oleispira, Phaeobacter, Photobacterium, Polarbacerium, Pseudomonas, and Psychrobium. The specificity of the primers was confirmed by the phylogeny of the sequenced polymerase chain reaction (PCR) amplicons that indicated primers were genus‐specific except in the case of Colwellia and Phaeobacter. Copy number of the 16S rRNA gene obtained by quantitative PCR using genus‐specific primers and the relative abundance obtained by 16S rRNA gene sequencing using universal primers were well correlated for the five analyzed abundant bacterial genera. Low correlations between quantitative PCR and 16S rRNA gene sequencing for Pseudomonas were explained by the higher coverage of known Pseudomonas species by the designed genus‐specific primers than the universal primers used in 16S rRNA gene sequencing. The designed genus‐specific primers are proposed as rapid and cost‐effective tools to evaluate the most abundant bacterial genera in fish‐related or potentially other metagenomics samples.

Nano-scale applications in aquaculture: Opportunities for improved production and disease control

Aquaculture is the fastest growing food-production sector and is vital to food security, habitat restoration and endangered species conservation. One of the continued challenges to the industry is our ability to manage aquatic disease agents that can rapidly decimate operations and are a constant threat to sustainability. Such threats also evolve as microbes acquire resistance and/or new pathogens emerge. The advent of nanotechnology has transformed our approach to fisheries disease management with advances in water disinfection, food conversion, fish health and management systems. In this review, several nano-enabled technology successes will be discussed as they relate to the challenges associated with disease management in the aquaculture sector, with a particular focus on fishes. Future perspectives on how nanotechnology can offer functional approaches for improving disinfection and innovating at the practical space of early warning systems will be discussed. Finally, the importance of "safety by design" approaches to the development of novel commercial nano-enabled products will be emphasized.

A novel multiplex PCR assay for rapid detection of virulent Aeromonas in cultured eels

AIMS

Under intensive and stressful aquaculture conditions, cultured eels are highly susceptible to virulent Aeromonas sp. infections. To rapidly and simultaneously confirm Aeromonas isolate and its virulence, a two-tube multiplex PCR (mPCR) assay incorporating gyrB gene for genus-specific recognition and seven major virulence genes for virulence assessment was developed.

METHODS AND RESULTS

Eight pairs of primers were designed and divided into two groups-gyrB, ahpA, epr and aerA in tube 1 and alt, act, ast and hlyA in tube 2. The optimized mPCR conditions were the same except for their final concentrations. The specificity of the mPCR was validated by the extracted DNA of 10 Aeromonas and 8 non-Aeromonas species, or mixed DNA templates. Detection limits were determined to be 200 copies per μl in tube 1 and 20 copies per μl in tube 2. The mPCR reproducibility was tested by both artificial challenge and clinical samples.

CONCLUSIONS

The results showed this two-tube mPCR assay was rapid, specific, sensitive and reliable.

SIGNIFICANCE AND IMPACT OF THE STUDY

To our knowledge, this is the first report to distinguish virulent Aeromonas isolates from nonvirulent ones by seven popular and major virulence genes at the genus-specific level. And it will be useful for large-scale screening of virulent Aeromonas sp. in cultured eels.

Multiplex PCR for the rapid detection of insulin-like growth factor in the Pacific oyster, Crassostrea gigas: a useful indicator for growth assessment

Insulin-like growth factor (IGF) expression plays a critical role in the endocrine regulation of proliferation, differentiation, and growth in shellfish as well as in fish. The Pacific oyster, Crassostrea gigas, is a significant aquaculture species that comprises a large percentage of the Korean shellfish industry; moreover, its growth is economically important in aquaculture. However, when measuring the growth rate in shellfish, the soft tissue weight is difficult to determine because of the shell weight. In the present study, we describe an indirect method of measuring the growth rate using multiplex polymerase chain reaction (PCR) and analyzing levels of molluscan insulin-related peptide (MIP), the acid labile subunit of the IGF-binding protein complex (IGFBP ALS), and insulin-related peptide receptor (CIR) in Pacific oysters. The predicted sizes of amplicons were 776, 537, 380, and 198 bp, and the detection limit of the annealing temperatures was confirmed to be 65 °C. The annual expression of MIP and IGFBP ALS in tissues reached high levels in the winter following the condition index (CI). MIP and IGFBP ALS in male gonads and CIR in female gonads were related to the CI. This newly improved multiplex PCR provides an indirect measure of the growth rate; thus, it can be used to rapidly assess the growth rate. In addition, this method can supplement traditional growth data from oyster farms.

Antibody-free detection of infectious bacteria using quantum dots-based barcode assay

Staphylococcus aureus, methicillin-resistant Staphylococcus aureus and Klebsiella pneumoniae are the most representative bacteria causing infectious diseases. Due to the increased application of antibiotics, the bacterial resistance is growing causing severe complications. Therefore, a sensitive determination of these pathogens is crucial for effective treatment. The aim of this study was to design an effective method for multiplex detection of Staphylococcus aureus, methicillin-resistant Staphylococcus aureus and Klebsiella pneumoniae taking advantage from properties of magnetic particles as well as fluorescent nanoparticles (quantum dots). The method was able to detect as low concentrations of bacteria as 10² CFU/mL using the bacteria-specific genes (fnbA, mecA and wcaG).

Recent Major Advances of Biotechnology and Sustainable Aquaculture in China

Background:

Global aquaculture production has increased continuously over the last five decades, and particularly in China. Its aquaculture has become the fastest growing and most efficient agri-sector, with production accounting for more than 70% of the world’s aquaculture output. In the new century, with serious challenges regarding population, resources and the environment, China has been working to develop high-quality, effective, healthy, and sustainable blue agriculture through the application of modern biotechnology. Sound knowledge related to the biology and ecology of aquatic organisms has laid a solid foundation and provided the innovation and technology for rapid development of the aquaculture industry. Marine biotechnology, which is enabling solutions for ocean productivity and sustainability, has been promoted since the last decades of the 20th Century in China.

Objective:

In this article, priority areas of research, mainly genetic breeding, omics studies, novel production systems, biosecurity, bioprocesses and biorefinery, as well as the major progress of marine biotechnology R&D in China are reviewed.

Conclusion:

Current innovative achievements in China are not enough and the level and frequency of academic advancements must be improved. International cooperation and assistance remain crucial for the success of marine biotechnology.