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Shrimp aquaculture has been growing rapidly over the last three decades. However, high-density aquaculture together with environmental degradation has led to increased incidence of shrimp infections. Thus, devising and implementing effective strategies to predict, diagnose and control the spread of infections of shrimps are crucial, also to ensure biosecurity and sustainability of the food industry. With the recent advancements in biotechnology, more attention has been given to develop novel promising therapeutic tools with potential to prevent disease occurrence and better manage shrimp health. Furthermore, owing to the advent of the next-generation sequencing (NGS) platforms, it has become possible to analyze the genetic basis of susceptibility or resistance of different stocks of shrimps to infections and how sustainable aquaculture could be made free of shrimp diseases. [ABSTRACT FROM AUTHOR]

A decade since the availability of Mycobacterium tuberculosis (Mtb) genome sequence, no promising drug has seen the light of the day. This not only indicates the challenges in discovering new drugs but also suggests a gap in our current understanding of Mtb biology. We attempt to bridge this gap by carrying out extensive re-annotation and constructing a systems level protein interaction map of Mtb with an objective of finding novel drug target candidates. Towards this, we synergized crowd sourcing and social networking methods through an initiative 'Connect to Decode' (C2D) to generate the first and largest manually curated interactome of Mtb termed 'interactome pathway' (IPW), encompassing a total of 1434 proteins connected through 2575 functional relationships. Interactions leading to gene regulation, signal transduction, metabolism, structural complex formation have been catalogued. In the process, we have functionally annotated 87% of the Mtb genome in context of gene products. We further combine IPW with STRING based network to report central proteins, which may be assessed as potential drug targets for development of drugs with least possible side effects. The fact that five of the 17 predicted drug targets are already experimentally validated either genetically or biochemically lends credence to our unique approach.

Being able to link clinical outcomes to SARS‐CoV‐2 virus strains is a critical component of understanding COVID‐19. Here, we discuss how current processes hamper sustainable data collection to enable meaningful analysis and insights. Following the 'Fast Healthcare Interoperable Resource' (FHIR) implementation guide, we introduce an ontology‐based standard questionnaire to overcome these shortcomings and describe patient 'journeys' in coordination with the World Health Organization's recommendations. We identify steps in the clinical health data acquisition cycle and workflows that likely have the biggest impact in the data‐driven understanding of this virus. Specifically, we recommend detailed symptoms and medical history using the FHIR standards. We have taken the first steps towards this by making patient status mandatory in GISAID ('Global Initiative on Sharing All Influenza Data'), immediately resulting in a measurable increase in the fraction of cases with useful patient information. The main remaining limitation is the lack of controlled vocabulary or a medical ontology. [ABSTRACT FROM AUTHOR]

Exosomes are extracellular vesicles (EVs) of ~20–200 nm diameter that shuttle DNAs, RNAs, proteins and other biomolecules between cells. The large number of biomolecules present in exosomes demands the frequent use of high-throughput analysis. This, in turn, requires technical replicates (TRs), and biological replicates (BRs) to produce accurate results. As the number and abundance of identified biomolecules varies between replicates (Rs), establishing the replicate variability predicted for the event under study is essential in determining the number of Rs required. Although there have been few reports of replicate variability in high throughput biological data, none of them focused on exosomes. Herein, we determined the replicate variability in protein profiles found in exosomes released from 3 lung adenocarcinoma cell lines, H1993, A549 and H1975. Since exosome isolates are invariably contaminated by a small percentage of ~200–300 nm microvesicles, we refer to our samples as exosome-enriched EVs (EE-EVs). We generated BRs of EE-EVs from each cell line, and divided each group into 3 TRs. All Rs were analyzed by liquid chromatography/mass spectrometry (LC/MS/MS) and customized bioinformatics and biostatistical workflows (raw data available via ProteomeXchange: PXD012798). We found that the variability among TRs as well as BRs, was largely qualitative (protein present or absent) and higher among BRs. By contrast, the quantitative (protein abundance) variability was low, save for the H1975 cell line where the quantitative variability was significant. Importantly, our replicate strategy identified 90% of the most abundant proteins, thereby establishing the utility of our approach. [ABSTRACT FROM AUTHOR]

Background: Vibrio parahaemolyticus is a Gram-negative halophilic bacterium which is found largely in estuarine and coastal waters. The bacteria has been a main focus in gastro-intestinal infections caused primarily due to the consumption of contaminated seafood. It was shown to survive in magnesium concentrations as high as 300 mM which are toxic to various other micro-organisms. Several genes of V. parahaemolyticus were studied, among which gbpA (N-acetyl glucosamine binding protein) was reported in Vibrio cholerae. Methods: The current study investigates the V. parahaemolyticus gbpA gene expression at different concentrations of magnesium sulfate heptahydrate (MgSO4·7H2O, chosen as the magnesium environment), in the presence of the host's (prawn) carapace and the mimicked carapace [commercial chitin flakes (Sigma)]. The concentrations of MgSO4·7H2O utilized were approximately 0, 1, 75, 137, 225 and 300 mM. These were selected based upon the survival conditions required by prawn and bacteria, respectively. 0.05 gm/3 ml of carapace (by dry weight) and commercial chitin flakes were used in the experiments. Bacterial count was performed for the biological triplicates for the 3 experimental setups. The genome of Vibrio parahaemolyticus PCV08-7 (VPPCV08-7) was used as a reference, based on whose translated gbpA gene the probable protein-chemical interactions were determined on the STITCH database. Results: The GbpA protein was shown to interact with chitin on the STITCH database. In our experiments, the gbpA showed lower gene expression levels at different MgSO4·7H2O concentrations in the presence of chitin and carapace, than with the presence of only MgSO4•7H2O. In addition, the bacterial count for various concentrations of magnesium used, revealed a distinct decrease in bacterial count within and among each of the three experimental setups. Conclusion: In the presence of only magnesium, an increase in the gbpA expression with neither chitin nor carapace and vice versa supported by the results from the bacterial counts could help further studies to prove that the moulting phase of prawns may trigger increased expression of the V. parahaemolyticus gbpA gene. [ABSTRACT FROM AUTHOR]

Macro brachium rosenbergii is well-known as the giant freshwater prawn, and is a commercially significant source of seafood. Its production can be affected by various bacterial contaminations. Among which, the genus Vibrio shows a higher prevalence in aquatic organisms, especially M. rosenbergii, causing food-borne illnesses. Vibrio parahaemolyticus, a species of Vibrio is reported as the main causative of the early mortality syndrome. Vibrio parahaemolyticus infection in M. rosenbergii was studied previously in relation to the prawn's differentially expressed immune genes. In the current review, we will discuss the growth conditions for both V. parahaemolyticus and M. rosenbergii and highlight the role of magnesium in common, which need to be fully understood. Till date, there has not been much research on this aspect of magnesium. We postulate a model that screens a magnesium-dependent pathway which probably might take effect in connection with N-acetylglucosamine binding protein and chitin from V. parahaemolyticus and M. rosenbergii, respectively. Further studies on magnesium as an environment for V. parahaemolyticus and M. rosenbergii interaction studies will provide seafood industry with completely new strategies to employ and to avoid seafood related contaminations. [ABSTRACT FROM AUTHOR]

Background: The Malaysian giant freshwater prawn, Macrobrachium rosenbergii, is an economically important crustacean worldwide. However, production of this prawn is facing a serious threat from Vibriosis disease caused by Vibrio species such as Vibrio parahaemolyticus. Unfortunately, the mechanisms involved in the immune response of this species to bacterial infection are not fully understood. We therefore used a high-throughput deep sequencing technology to investigate the transcriptome and comparative expression profiles of the hepatopancreas from this freshwater prawn infected with V. parahaemolyticus to gain an increased understanding of the molecular mechanisms underlying the species' immune response to this pathogenic bacteria. Result: A total of 59,122,940 raw reads were obtained from the control group, and 58,385,094 reads from the Vibrio-infected group. Via de novo assembly by Trinity assembler, 59,050 control unigenes and 73,946 Vibrio-infected group unigenes were obtained. By clustering unigenes from both libraries, a total of 64,411 standard unigenes were produced. The standard unigenes were annotated against the NCBI non-redundant, Swiss-Prot, Kyoto Encyclopaedia of Genes and Genome pathway (KEGG) and Orthologous Groups of Proteins (COG) databases, with 19,799 (30.73%), 16,832 (26.13%), 14,706 (22.83%) and 7,856 (12.19%) hits respectively, giving a final total of 22,455 significant hits (34.86% of all unigenes). A Gene Ontology (GO) analysis search using the Blast2GO program resulted in 6,007 unigenes (9.32%) being categorized into 55 functional groups. A differential gene expression analysis produced a total of 14,569 unigenes aberrantly expressed, with 11,446 unigenes significantly up-regulated and 3,103 unigenes significantly down-regulated. The differentially expressed immune genes fall under various processes of the animal immune system. Conclusion: This study provided an insight into the antibacterial mechanism in M. rosenbergii and the role of differentially expressed immune genes in response to V. parahaemolyticus infection. Furthermore, this study has generated an abundant list of transcript from M.rosenbergii which will provide a fundamental basis for future genomics research in this field. [ABSTRACT FROM AUTHOR]

Vibrio parahaemolyticus, an important human pathogen, is associated with gastroenteritis and transmitted through partially cooked seafood. It has become a major concern in the production and trade of marine food products. The prevalence of potentially virulent and pathogenic V. parahaemolyticus in raw seafood is of public health significance. Here we describe the genome sequence of a V. parahaemolyticus isolate of crustacean origin which was cultured from prawns in 2008 in Selangor, Malaysia (isolate PCV08-7). The next generation sequencing and analysis revealed that the genome of isolate PCV08-7 has closest similarity to that of V. parahaemolyticus RIMD2210633. However, there are certain unique features of the PCV08-7 genome such as the absence of TDH-related hemolysin (TRH), and the presence of HU-alpha insertion. The genome of isolate PCV08-7 encodes a thermostable direct hemolysin (TDH), an important virulence factor that classifies PCV08-7 isolate to be a serovariant of O3:K6 strain. Apart from these, we observed that there is certain pattern of genetic rearrangements that makes V. parahaemolyticus PCV08-7 a non-pandemic clone. We present detailed genome statistics and important genetic features of this bacterium and discuss how its survival, adaptation and virulence in marine and terrestrial hosts can be understood through the genomic blueprint and that the availability of genome sequence entailing this important Malaysian isolate would likely enhance our understanding of the epidemiology, evolution and transmission of foodborne Vibrios in Malaysia and elsewhere. [ABSTRACT FROM AUTHOR]

Uropathogenic Escherichia coli (UPEC) causes serious infections in people at risk and has a significant environmental prevalence due to contamination by human and animal excreta. In developing countries, UPEC assumes importance in certain dwellings because of poor community/personal hygiene and exposure to contaminated water or soil. We report the complete genome sequence of E. coli strain NA114 from India, a UPEC strain with a multidrug resistance phenotype and the capacity to produce extended-spectrum beta-lactamase. The genome sequence and comparative genomics emanating from it will be significant in understanding the genetic makeup of diverse UPEC strains and in boosting the development of new diagnostics/vaccines. [ABSTRACT FROM AUTHOR]

The diverse clinical outcomes of colonization by Helicobacter pylori reflect the need to understand the genomic rearrangements enabling the bacterium to adapt to host niches and exhibit varied colonization/virulence potential. We describe the genome sequences of the two serial isolates, H. pylori 2017 and 2018 (the chronological subclones of H. pylori 908), cultured in 2003 from the antrum and corpus, respectively, of an African patient who suffered from recrudescent duodenal ulcer disease. When compared with the genome of the parent strain, 908 (isolated from the antrum of the same patient in 1994), the genome sequences revealed genomic alterations relevant to virulence optimization or host-specific adaptation. [ABSTRACT FROM AUTHOR]

Many of the developing countries of the Southeast Asian region are significantly affected by endemic typhoid fever, possibly as a result of marginal living standards. It is an important public health problem in countries such as Papua New Guinea, which is geographically close to some of the foci of endemicity in Asia. The severity of the disease varies in different regions, and this may be attributable to genetic diversity among the native strains. Genome sequence data on strains from different countries are needed to clearly understand their genetic makeup and virulence potential. We describe the genomes of two Salmonella Typhi isolates from patients with fatal and nonfatal cases of typhoid fever in Papua New Guinea. We discuss in brief the underlying sequencing methodology, assembly, genome statistics, and important features of the two draft genomes, which form an essentia step in our functional molecular infection epidemiology program centering on typhoid fever. The comparative genomics of thes and other isolates would enable us to identify genetic rearrangements and mechanisms responsible for endemicity and the differential severity of pathogenic salmonellae in Papua New Guinea and elsewhere. [ABSTRACT FROM AUTHOR]

Helicobacter pylori is a genetically diverse and coevolved pathogen inhabiting human gastric niches and leading to a spectrum of gastric diseases in susceptible populations. We describe the genome sequence of H. pylori 908, which was originally isolated from an African patient living in France who suffered with recrudescent duodenal ulcer disease. The strain was found to be phylogenetically related to H. pylori J99, and its comparative analysis revealed several specific genome features and novel insertion-deletion and substitution events. The genome sequence revealed several strain-specific deletions and/or gain of genes exclusively present in HP908 compared with different sequenced genomes already available in the public domain. Comparative and functional genomics of HP908 and its subclones will be important in understanding genomic plasticity and the capacity to colonize and persist in a changing host environment. [ABSTRACT FROM AUTHOR]

Salmonella enterica serovar Typhi is a human pathogen that causes typhoid fever predominantly in developing countries. In this article, we describe the whole genome sequence of the S. Typhi strain CR0044 isolated from a typhoid fever carrier in Kelantan, Malaysia. These data will further enhance the understanding of its host persistence and adaptive mechanism. [ABSTRACT FROM AUTHOR]

The prevalence of different H. pylori genotypes in various geographical regions indicates region-specific adaptations during the course of evolution. Complete genomes of H. pylori from countries with high infection burdens, such as India, have not yet been described. Herein we present genome sequences of two H. pylori strains, NAB47 and NAD1, from India. In this report, we briefly mention the sequencing and finishing approaches, genome assembly with downstream statistics, and important features of the two draft genomes, including their phylogenetic status. We believe that these genome sequences and the comparative genomics emanating thereupon will help us to clearly understand the ancestry and biology of the Indian H. pylori genotypes, and this will be helpful in solving the so-called Indian enigma, by which high infection rates do not corroborate the minuscule number of serious outcomes observed, including gastric cancer. [ABSTRACT FROM AUTHOR]

Salmonella enterica serovar Typhi is the causative agent of typhoid fever, which causes nearly 21.7 million illnesses and 217,000 deaths globally. Herein, we describe the whole-genome sequence of the Salmonella Typhi strain ST0208, isolated from a sporadic case of typhoid fever in Kuala Lumpur, Malaysia. The whole-genome sequence and comparative genomics allow an in-depth understanding of the genetic diversity, and its link to pathogenicity and evolutionary dynamics, of this highly clonal pathogen that is endemic to Malaysia. [ABSTRACT FROM AUTHOR]