Draft Genome Sequences of Five Clinical Strains of Brucella melitensis Isolated from Patients Residing in Kuwait

Khan, Mohd Wasif; Habibi, Nazima; Shaheed, Faraz; Mustafa, Abu Salim

doi:10.1128/genomea.01144-16

Cited by 10 publications

(10 citation statements)

References 10 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Fragmented DNA was processed through the steps of A-tailing, index ligation, and the addition of Illumina adapters at both the 5′ and 3′ ends of the DNA segments. The libraries were purified using the AMPure XP beads (Agencourt, Beckman Coulter Genomics) and quantified through qPCR (Life Technologies, Carlsbad, CA, USA) [ 39 ]. Post-normalization, the libraries were pooled and loaded at a 10.0 pM concentration on an Illumina NovaSeq 6000 platform (Illumina, San Diego) for 2 × 150 bp paired-end sequencing [ 36 ].…”

Section: Methodsmentioning

confidence: 99%

Metagenomes from Coastal Sediments of Kuwait: Insights into the Microbiome, Metabolic Functions and Resistome

et al. 2023

Self Cite

View full text Add to dashboard Cite

Coastal sediments in the proximity of wastewater and emergency outfalls are often sinks of pharmaceutical compounds and other organic and inorganic contaminants that are likely to affect the microbial community. The metabolites of these contaminants affect microbial diversity and their metabolic processes, resulting in undesirable effects on ecosystem functioning, thus necessitating the need to understand their composition and functions. In the present investigation, we studied the metagenomes of 12 coastal surface sediments through whole genome shot-gun sequencing. Taxonomic binning of the genes predicted about 86% as bacteria, 1% as archaea, >0.001% as viruses and Eukaryota, and 12% as other communities. The dominant bacterial, archaeal, and fungal genera were Woeseia, Nitrosopumilus, and Rhizophagus, respectively. The most prevalent viral families were Myoviridae and Siphoviridae, and the T4 virus was the most dominant bacteriophage. The unigenes further aligned to 26 clusters of orthologous genes (COGs) and five carbohydrate-active enzymes (CAZy) classes. Glycoside hydrolases (GH) and glycoside transferase (GT) were the highest-recorded CAzymes. The Kyoto Encyclopedia of Genes and Genomes (KEGG) level 3 functions were subjugated by purine metabolism > ABC transporters > oxidative phosphorylation > two-component system > pyrimidine metabolism > pyruvate metabolism > quorum sensing > carbon fixation pathways > ribosomes > and glyoxalate and dicarboxylate metabolism. Sequences allying with plasmids, integrons, insertion sequences and antibiotic-resistance genes were also observed. Both the taxonomies and functional abundances exhibited variation in relative abundances, with limited spatial variability (ANOVA p > 0.05; ANOSIM-0.05, p > 0.05). This study underlines the dominant microbial communities and functional genes in the marine sediments of Kuwait as a baseline for future biomonitoring programs.

show abstract

Section: Methodsmentioning

confidence: 99%

Metagenomes from Coastal Sediments of Kuwait: Insights into the Microbiome, Metabolic Functions and Resistome

et al. 2023

Self Cite

View full text Add to dashboard Cite

show abstract

“…Briefly, 1000 ng of qualified DNA was sonicated to produce 350 bp fragments. These short DNA segments were then end-repaired, A-tailed, and subjected to index PCR [38]. Amplified libraries were purified through Agencourt AMPure XP magnetic beads (Beckman Coulter Genomics, Brea, CA, USA) and quantified through qPCR [39].…”

Section: Metagenomic Sequencingmentioning

confidence: 99%

Antibiotic Resistance Genes Associated with Marine Surface Sediments: A Baseline from the Shores of Kuwait

et al. 2022

Self Cite

View full text Add to dashboard Cite

Marine sediments are a sink for antibiotic resistance genes (ARGs) and antibiotic-resistant microbes (ARMs). Wastewater discharge into the aquatic environment is the dominant pathway for pharmaceuticals reaching aquatic organisms. Hence, the characterization of ARGs is a priority research area. This baseline study reports the presence of ARGs in 12 coastal sediment samples covering the urban coastline of Kuwait through whole-genome metagenomic sequencing. The presence of 402 antibiotic resistance genes (ARGs) were recorded in these samples; the most prevalent were patA, adeF, ErmE, ErmF, TaeA, tetX, mphD, bcrC, srmB, mtrD, baeS, Erm30, vanTE, VIM-7, AcrF, ANT4-1a, tet33, adeB, efmA, and rpsL, which showed resistance against 34 drug classes. Maximum resistance was detected against the beta-lactams (cephalosporins and penam), and 46% of genes originated from the phylum Proteobacteria. Low abundances of ESKAPEE pathogens (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumonia, Acinetobacter baumanii, Pseudomonas aeruginosa, Enterobacter sps., and Escherichia coli) were also recorded. Approximately 42% of ARGs exhibited multiple drug resistance. All the ARGs exhibited spatial variations. The major mode of action was antibiotic efflux, followed by antibiotic inactivation, antibiotic target alteration, antibiotic target protection, and antibiotic target replacement. Our findings supported the occurrence of ARGs in coastal marine sediments and the possibility of their dissemination to surrounding ecosystems.

show abstract

“…Post-quality checks at BGI, the DNA was tagmented and subjected to library preparation. DNA fragments were end repaired, 3’A tailed and ligated with Illumina adapters ( Khan et al., 2016 ). Thereafter the libraries were purified through Agencourt AMPure XP magnetic beads (Beckman Coulter Genomics, Brea, CA, USA) ( Habibi et al., 2021 ).…”

Section: Methodsmentioning

confidence: 99%

Genome survey and genetic characterization of Acacia pachyceras O. Schwartz

Habibi

Salameen

Vyas³

et al. 2023

Front. Plant Sci.

Self Cite

View full text Add to dashboard Cite

Acacia pachyceras O. Schwartz (Leguminoseae), a woody tree growing in Kuwait is critically endangered. High throughput genomic research is immediately needed to formulate effective conservation strategies for its rehabilitation. We therefore, performed a genome survey analysis of the species. Whole genome sequencing generated ~97 Gb of raw reads (92x coverage) with a per base quality score above Q30. The k-mer analysis (17 mer) revealed its genome to be 720Mb in size with an average guanine-cytosine (GC) ratio of 35%. The assembled genome was analyzed for repeat regions (45.4%-interspersed repeats; 9%-retroelements; 2%-DNA transposons). BUSCO assessment of completeness of genome identified 93% of assembly to be complete. Gene alignments in BRAKER2 yielded 34,374 transcripts corresponding to 33,650 genes. Average length of coding sequences and protein sequences were recorded as 1,027nts and 342aa, respectively. GMATA software filtered a total of 901,755 simple sequence repeats (SSRs) regions against which 11,181 unique primers were designed. A subset of 110 SSR primers were PCR validated and demonstrated for its application in genetic diversity analysis of Acacia. The SSR primers successfully amplified A. gerrardii seedlings DNA depicting cross transferability among species. The principal coordinate analysis and the split decomposition tree (bootstrapping runs of 1000 replicates) distributed the Acacia genotypes into two clusters. The flow cytometry analysis revealed the A. pachyceras genome to be polyploid (6x). The DNA content was predicted as 2.46 pg, 1.23 pg, and 0.41 pg corresponding to 2C DNA, 1C DNA and 1Cx DNA, respectively. The results provide a base for further high throughput genomic studies and molecular breeding for its conservation.

show abstract

Draft Genome Sequences of Five Clinical Strains of Brucella melitensis Isolated from Patients Residing in Kuwait

Cited by 10 publications

References 10 publications

Metagenomes from Coastal Sediments of Kuwait: Insights into the Microbiome, Metabolic Functions and Resistome

Metagenomes from Coastal Sediments of Kuwait: Insights into the Microbiome, Metabolic Functions and Resistome

Antibiotic Resistance Genes Associated with Marine Surface Sediments: A Baseline from the Shores of Kuwait

Genome survey and genetic characterization of Acacia pachyceras O. Schwartz

Contact Info

Product

Resources

About