A First Record on Microplastic Ingestion by Tropical Estuarine Copepods of Bangladesh.

Microplastics (MPs) pollution is a profound problem around the world yet it's study on the effect on zooplankton including copepods are very limited. The study was conducted between January 2021 and January 2022 in the Lower Meghna Estuary to investigate MPs ingestion in two different family of copepod: Calanoid and Cyclopoid. A method of acid digestion along with Scanning Electron Microscope (SEM) was used to identify MPs ingested by copepods from the conducted area. However, three types of MPs namely fiber, fragment and foam were extracted from this copepod biomass. Fibers represent highest (> 50%) of the ingested MPs from both group of copepod that exceed fragments and foams in all sampling stations. The overall ingestion rate of Calanoid was found higher (0.084 ± 0.002 particles/individual) compared to the Cyclopoid group (0.077 ± 0.001 particles/individual). The results of the study have effectively illustrated that copepod, obtained from multiple sampling sites within the Lower Meghna Estuary, display a propensity to ingest MPs and subsequently endangering the food security of seafood industry.

Frequent contiguous pattern mining over biological sequences of protein misfolded diseases.

BACKGROUND: Proteins are integral part of all living beings, which are building blocks of many amino acids. To be functionally active, amino acids chain folds up in a complex way to give each protein a unique 3D shape, where a minor error may cause misfolded structure. Genetic disorder diseases i.e. Alzheimer, Parkinson, etc. arise due to misfolding in protein sequences. Thus, identifying patterns of amino acids is important for inferring protein associated genetic diseases. Recent studies in predicting amino acids patterns focused on only simple protein misfolded disease i.e. Chromaffin Tumor, by association rule mining. However, more complex diseases are yet to be attempted. Moreover, association rules obtained by these studies were not verified by usefulness measuring tools. RESULTS: In this work, we analyzed protein sequences associated with complex protein misfolded diseases (i.e. Sickle Cell Anemia, Breast Cancer, Cystic Fibrosis, Nephrogenic Diabetes Insipidus, and Retinitis Pigmentosa 4) by association rule mining technique and objective interestingness measuring tools. Experimental results show the effectiveness of our method. CONCLUSION: Adopting quantitative experimental methods, this work can form more reliable, useful and strong association rules i. e. dominating patterns of amino acid of complex protein misfolded diseases. Thus, in addition to usual applications, the identified patterns can be more useful in discovering medicines for protein misfolded diseases and thereby may open up new opportunities in medical science to handle genetic disorder diseases.

Molecular identification of white spot syndrome virus (WSSV) and associated risk factors for white spot disease (WSD) prevalence in shrimp (Penaeus monodon) aquaculture in Bangladesh.

White spot disease has caused significant economic losses in the shrimp farming industry of Bangladesh over the last two decades. The responsible virus, WSSV, may show severe disease with significant mortality depending on farm management and environmental and seasonal changes. Data on farm management and environmental parameters were collected from the southwest region of Bangladesh in 2018, and WSSV infection was confirmed by the species-specific gene VP28 using conventional PCR, real-time PCR and sequencing. Through bivariate analysis, nine significant risk factors for WSD were identified, viz. farm age, presence of nursery pond, reservoir of PL, weed in farm area, control of weed, stocking density, stocking frequency, ammonia and oxygen concentration. This study detected 46 WSSV-infected shrimp farms by conventional PCR, whereas real-time PCR identified 47 WSSV-positive out of 49 farms. WSSV prevalence was highest in the Khulna region, with 100% positivity in all seasons. WSSV loads ranged from 5.62 × 109 to 2.01 × 1015 copies/g of shrimp tissue. The VP28 gene sequence confirmed that 15 representative samples were 100% identical to the 2018 WSSV strain of India. The relationships among risk factors, prevalence and severity of disease, and origin of WSSV strains could be impactful for WSD management.

Genomic and evolutionary features of two AHPND positive Vibrio parahaemolyticus strains isolated from shrimp (Penaeus monodon) of south-west Bangladesh.

BACKGROUND: Due to its rapid lethal effect in the early development stage of shrimp, acute hepatopancreatic necrosis disease (AHPND) has been causing great economic losses, since its first outbreak in southeast China in 2009. Vibrio parahaemolyticus, carrying the pirA and pirB toxin genes is known to cause AHPND in shrimp. The overall objective of this study was to sequence the whole genome of AHPND positive V. parahaemolyticus strains isolated from shrimp (Peneaus monodon) of the south-west region of Bangladesh in 2016 and 2017 and characterize the genomic features and emergence pattern of this marine pathogen. RESULTS: Two targeted AHPND positive V. parahaemolyticus strains were confirmed using PCR with 16S rRNA, ldh, AP3 and AP4 primers. The assembled genomes of strain MSR16 and MSR17 were comprised of a total of 5,393,740 bp and 5,241,592 bp, respectively. From annotation, several virulence genes involved in chemotaxis and motility, EPS type II secretion system, Type III secretion system-1 (T3SS-1) and its secreted effectors, thermolabile hemolysin were found in both strains. Importantly, the ~ 69 kb plasmid was identified in both MSR16 and MSR17 strains containing the two toxin genes pirA and pirB. Antibiotic resistance genes were predicted against ß-lactam, fluoroquinolone, tetracycline and macrolide groups in both MSR16 and MSR17 strains. CONCLUSIONS: The findings of this research may facilitate the tracking of pathogenic and/or antibiotic-resistant V. parahaemolyticus isolates between production sites, and the identification of candidate strains for the production of vaccines as an aid to control of this devastating disease. Also, the emergence pattern of this pathogen can be highlighted to determine the characteristic differences of other strains found all over the world.

Molecular Typing of Vibrio parahaemolyticus Strains Isolated from Mollusks in the North Adriatic Sea.

BACKGROUND: Vibrio parahaemolyticus is an emerging foodborne pathogen in the Mediterranean, usually associated with shellfish consumption. The increase in the number of outbreaks in Europe is primarily associated with the global warming of the ocean that has a great impact on the spread and genetic selection of waterborne pathogens. The primary role of Italy in Europe's mollusk production, together with the fact that cases of infections with V. parahaemolyticus are not always notified to the European community, highlighted the necessity of acquiring new information about the epidemiological involvement of shellfish products. OBJECTIVE: The aim of the study was to provide useful insights into the first steps of the Risk Assessment associated with V. parahaemolyticus through the molecular characterization of isolates from commercialized mollusks. MATERIALS AND METHODS: A total of 102 strains identified as V. parahaemolyticus were investigated as part of a larger sampling (1-year survey) from several shellfish species collected from the Venice lagoon and the North Adriatic sea. All strains were characterized by multilocus sequence typing and tested for the presence of virulence genes (trh and tdh). The study of sampling/environmental factors and epidemiological analyses was performed to describe the behaviors of the different genetic populations. RESULTS: The population structure analysis highlighted three genetic clusters that could be subject to temperature selection during cold (≤15°C) and warm (>16°C) seasons. Moreover, other factors, such as molluscan species (clams/mussels), probably played a role in the distribution of genetic clusters. Although few strains carried the virulence factors (n = 6 trh+), epidemiological links with clinical isolates and a local dissemination of some sequence types were underlined. CONCLUSION: This work provides a useful background on the genotype spread as a first step in the Hazard Identification in light of future climate changes.

Vibrio trends in the ecology of the Venice lagoon.

Vibrio is a very diverse genus that is responsible for different human and animal diseases. The accurate identification of Vibrio at the species level is important to assess the risks related to public health and diseases caused by aquatic organisms. The ecology of Vibrio spp., together with their genetic background, represents an important key for species discrimination and evolution. Thus, analyses of population structure and ecology association are necessary for reliable characterization of bacteria and to investigate whether bacterial species are going through adaptation processes. In this study, a population of Vibrionaceae was isolated from shellfish of the Venice lagoon and analyzed in depth to study its structure and distribution in the environment. A multilocus sequence analysis (MLSA) was developed on the basis of four housekeeping genes. Both molecular and biochemical approaches were used for species characterization, and the results were compared to assess the consistency of the two methods. In addition, strain ecology and the association between genetic information and environment were investigated through statistical models. The phylogenetic and population analyses achieved good species clustering, while biochemical identification was demonstrated to be imprecise. In addition, this study provided a fine-scale overview of the distribution of Vibrio spp. in the Venice lagoon, and the results highlighted a preferential association of the species toward specific ecological variables. These findings support the use of MLSA for taxonomic studies and demonstrate the need to consider environmental information to obtain broader and more accurate bacterial characterization.

Retrospective analysis of Vibrio spp. isolated from marketed crustaceans using multilocus sequence analysis.

The genus Vibrio includes bacteria with different morphological and metabolic characteristics responsible for different human and animal diseases. An accurate identification is essential to assess the risks in regard to aquatic organisms and consequently to public health. The Multilocus Sequence Analysis (MLSA) scheme developed on the basis of 4 housekeeping genes (gyrB, pyrH, recA and atpA) was applied to identify 92 Vibrio strains isolated from crustaceans in 2011. Concatenated sequences were used for the phylogenetic and population analyses and the results were compared with those from biochemical identification tests. From the phylogenetic analysis, 10 clusters and 4 singletons emerged, whereas the population analysis highlighted 12 subpopulations that were well supported by phylogeny with few exceptions. The retrospective analysis allowed correct re-attribution of isolated species, indicating how, for some pathogens, there may be an overestimation of phenotypic identification (e.g. V. parahaemolyticus). Use of the PubMLST Vibrio database highlighted a possible genetic link between Sequence Type (ST) 529 and ST195 (V. alginolyticus) isolated from a human case in Norway during 2018. In addition to the identification of major risk groups of V. cholerae, V. vulnificus and V. parahaemolyticus, MLSA could be a valid support for species considered a minor risk, such as V. alginolyticus, V. mimicus and V. fluvialis. Due to the increased incidence of vibriosis in Europe, the application of different tools will also have to be considered to investigate the possible epidemiological links of the various species in the perspective of Open Science to protect the consumer.

Community Structure and Functional Annotations of the Skin Microbiome in Healthy and Diseased Catfish, Heteropneustes fossilis.

The skin mucosa of fish serves as a primary barrier against pathogens. In lesion sites in diseased fish, the mucosal barrier is expected to be compromised, with a substantial presence of potential pathogens. An understanding of the skin microbiome and its functional repertoire would provide important insights into host-microbe interactions, which has important implications for prophylactic measures in aquaculture. This study revealed the skin microbiomes and their functional annotations from healthy and diseased stinging catfish (Heteropneustes fossilis) based on 16S rRNA metagenomics. The OTUs consisted of four major phyla, Proteobacteria, Bacteroidota, Actinobacteriota and Firmicutes. Among members of the predominant phyla, Proteobacteria were rich in healthy fishes, but Bacteroidota and Firmicutes were significantly differentiated in healthy and diseased fish. The diversified microbiome was high in the skin of healthy fishes and did not significantly differ from that of the diseased groups. At the genus level, Pseudomonas showed the highest abundance in healthy fish but was nearly absent in diseased fish, whereas Flavobacterium showed the highest abundance in diseased fish. Linear discriminant analysis identified two phyla (Bacteroidota, Firmicutes) and two genera (Flavobacterium, Allorhizobium) that were consistently identified in diseased fishes. Functional prediction analysis specified that the genes related to physiological functions such as metabolism, immune and digestive systems and environmental adaptations could be highly expressed in diseased fishes. The present study indicates that the compositions, richness and functions of the bacterial community could influence the health status of cultured stinging catfish. Aquaculture-associated pathogenic bacteria may be identified, and preventive measures can be taken for the surveillance of fish health.

Molecular identification and antibiotic resistance patterns of diverse bacteria associated with shrimp PL nurseries of Bangladesh: suspecting Acinetobacter venetianus as future threat.

Shrimp aquaculture has been accomplished with breeding and nursing of shrimp in an artificial environment to fulfill the increasing demand of shrimp consumption worldwide. However, the microbial diseases appear as a serious problem in this industry. The study was designed to identify the diverse bacteria from shrimp PL (post-larvae) nurseries and to profile antibiotic resistance patterns. The rearing water (raw seawater, treated and outlet water) and shrimp PL were collected from eight nurseries of south-west Bangladesh. Using selective agar plates, thirty representative isolates were selected for 16S rRNA gene sequencing, antibiotic susceptibility test and MAR index calculation. Representative isolates were identified as Aeromonas caviae, Pseudomonas monteilii, Shewanella algae, Vibrio alginolyticus, V. brasiliensis, V. natriegens, V. parahaemolyticus, V. shilonii, V. xuii, Zobellella denitrificans which are Gram-negative, and Bacillus licheniformis and B. pumilus which are Gram-positive. Notably, six strains identified as Acinetobacter venetianus might be a concern of risk for shrimp industry. The antibiotic resistance pattern reveals that the strain YWO8-97 (identified as P. monteilii) was resistant to all twelve antibiotics. Ceftazidime was the most powerful antibiotic since most of the studied strains were sensitive against it. The six strains of A. venetianus showed multiple antibiotic resistance patterns. MAR index were ranged from 0.08 to 1.0, and values of 26 isolates were more than 0.2 which means prior high exposure to the antibiotics. From the present study, it can be concluded that shrimp PL nurseries in southern part of Bangladesh are getting contaminated with antibiotic resistant pathogenic bacteria.