Draft genome sequence data of a clinical Enterococcus faecalis isolate SHH039 from a patient with cholecystitis from a tertiary care hospital in Sabah, Malaysia.

An Enterococcus faecalis strain SHH039 was isolated from a 68 year old man who was hospitalised with cholecystitis. The genomic sequence of this isolate which had a size of 2,990,081 bp and 2,663 proteins with functional assignments is presented here. Analysis of the genome revealed Enterococcus faecalis with multiple antibiotic resistance genes which may be associated with acute cholecystitis. It may be not clear if the infection symptoms are the consequence of enterococci manifestation. However, this opportunistic organism may play a minor role in the disease.

Whole genome sequence data of Chromobacterium violaceum WCH4, a human pathogenic strain from Sabah, Malaysia.

Chromobacterium violaceum is a gram-negative, facultative anaerobic bacillus which is commonly found in soil. It can cause mild diarrhoea upon infection but can progress, although rarely, to fatal multi-organ failure and death. Here we report the whole genome sequence data of Chromobacterium violaceum WCH4 strain, a pathogenic strain that was obtained from a 78 year old male patient suffering from an eye infection. This is a rare case of human infection of the bacteria. Blood culture report as well as 16S rRNA confirmed the presence of C. violaceum WCH4. DNA sequencing using the Illumina HiSeq 4000 system revealed a genome size of 4,637,406 bp with a GC-content of 64.89%. We identified 4,572 protein coding sequences (CDS), 78 transfer RNA (tRNA) genes, and 3 ribosomal RNA (rRNA) genes. The CDS included 1,261 hypothetical proteins and 3,311 proteins with functional assignments. We also identified seven putative genes involved in efflux pump and conferring multidrug antibiotic resistance. The genome data has been deposited at NCBI under the accession number JAFBBB000000000 and consist of full annotated genome and raw sequence data. Our data resource will assist in further downstream analysis and understanding of the mechanism of rare human infection caused by Chromobacterium violaceum WCH4 strain.

Shared Signature of Recent Positive Selection on the TSBP1-BTNL2-HLA-DRA Genes in Five Native Populations from North Borneo.

North Borneo (NB) is home to more than 40 native populations. These natives are believed to have undergone local adaptation in response to environmental challenges such as the mosquito-abundant tropical rainforest. We attempted to trace the footprints of natural selection from the genomic data of NB native populations using a panel of ∼2.2 million genome-wide single nucleotide polymorphisms. As a result, an ∼13-kb haplotype in the Major Histocompatibility Complex Class II region encompassing candidate genes TSBP1-BTNL2-HLA-DRA was identified to be undergoing natural selection. This putative signature of positive selection is shared among the five NB populations and is estimated to have arisen ∼5.5 thousand years (∼220 generations) ago, which coincides with the period of Austronesian expansion. Owing to the long history of endemic malaria in NB, the putative signature of positive selection is postulated to be driven by Plasmodium parasite infection. The findings of this study imply that despite high levels of genetic differentiation, the NB populations might have experienced similar local genetic adaptation resulting from stresses of the shared environment.

Whole genome sequencing data of a clinical Enterococcus gallinarum strain EGR748 from Sabah, Malaysia.

Enterococcus gallinarum is a gram positive facultatively anaerobic bacteria that is typically found in mammalian intestinal tracts. It is generally not considered pathogenic to humans and is rarely reported. Here, we present the draft genome sequence data of Enterococcus gallinarum strain EGR748 isolated from a human clinical sample, and sequenced using the Illumina HiSeq 4000 system. The estimated whole genome size of the strain was 3,730,000 bp with a G + C content of 40.43%. The de novo assembly of the genome generated 55 contigs with an N50 of 208,509 bp. In addition, the Maximum Likelihood phylogenetic analysis based on the 16S rRNA sequence data accurately clustered EGR748 with other E. gallinarum strains. The data may be useful to demonstrate the capacity of this enterococcal species becoming the causal agents of nosocomial blood-stream infections. The genome dataset has been deposited at DDBJ/ENA/GenBank under the accession number JAABOR000000000.

An analysis of the development assistance for health (DAH) allocations for STD control in Africa.

The Sustainable Development Goals set by the United Nations recognize the importance of making progress in the eradication and treatment of sexually transmitted deceases (STD). STD are among the most widespread diseases in the world and have the highest prevalence in Sub-Saharan Africa. The current study explored the associations between the allocation of the development assistance for health (DAH) in 54 African countries and key development indicators - STD incidence, Gross Domestic Product per capita, health expenditure, and life expectancy at birth. It employed descriptive statistical methods, the matrix scatter plot analysis and the Pearson correlation test for this purpose. The findings indicated that there was a considerable increase in the volume of the DAH given to control and prevent STD in Africa over the period of 2002-2011. A statistically significant positive association was detected between the STD incidence and the health aid allocations. At the same time, the imbalance in the distribution of the health aid between the major and minor aid recipients in the continent increased. The study concludes by discussing policy implications that can be drawn from these findings.

Analysis of five deep-sequenced trio-genomes of the Peninsular Malaysia Orang Asli and North Borneo populations.

BACKGROUND: Recent advances in genomic technologies have facilitated genome-wide investigation of human genetic variations. However, most efforts have focused on the major populations, yet trio genomes of indigenous populations from Southeast Asia have been under-investigated. RESULTS: We analyzed the whole-genome deep sequencing data (~ 30×) of five native trios from Peninsular Malaysia and North Borneo, and characterized the genomic variants, including single nucleotide variants (SNVs), small insertions and deletions (indels) and copy number variants (CNVs). We discovered approximately 6.9 million SNVs, 1.2 million indels, and 9000 CNVs in the 15 samples, of which 2.7% SNVs, 2.3% indels and 22% CNVs were novel, implying the insufficient coverage of population diversity in existing databases. We identified a higher proportion of novel variants in the Orang Asli (OA) samples, i.e., the indigenous people from Peninsular Malaysia, than that of the North Bornean (NB) samples, likely due to more complex demographic history and long-time isolation of the OA groups. We used the pedigree information to identify de novo variants and estimated the autosomal mutation rates to be 0.81 × 10- 8 - 1.33 × 10- 8, 1.0 × 10- 9 - 2.9 × 10- 9, and ~ 0.001 per site per generation for SNVs, indels, and CNVs, respectively. The trio-genomes also allowed for haplotype phasing with high accuracy, which serves as references to the future genomic studies of OA and NB populations. In addition, high-frequency inherited CNVs specific to OA or NB were identified. One example is a 50-kb duplication in DEFA1B detected only in the Negrito trios, implying plausible effects on host defense against the exposure of diverse microbial in tropical rainforest environment of these hunter-gatherers. The CNVs shared between OA and NB groups were much fewer than those specific to each group. Nevertheless, we identified a 142-kb duplication in AMY1A in all the 15 samples, and this gene is associated with the high-starch diet. Moreover, novel insertions shared with archaic hominids were identified in our samples. CONCLUSION: Our study presents a full catalogue of the genome variants of the native Malaysian populations, which is a complement of the genome diversity in Southeast Asians. It implies specific population history of the native inhabitants, and demonstrated the necessity of more genome sequencing efforts on the multi-ethnic native groups of Malaysia and Southeast Asia.

Concurrent juvenile myelomonocytic leukemia with thalassemia in a case with Plasmodium knowlesi infection from Sabah, Malaysian Borneo.

A 3-year-old male child was presented with worsening abdominal pain, abdominal distension, lethargy, pallor and hepatosplenomegaly. The patient had multiple outpatient visits in the past and was treated with oral antibiotics, oral anthelmintic agents, albeit with minimal benefit. The patient also had non-neutropenic pyrexia spikes and oral ulcers. The patient was an adopted child; hence details about his biological parents' previous history were unclear. Differential diagnosis of Chronic Myelomonocytic Leukemia (CMML), Juvenile Myelomonocytic Leukemia (JMML), Gaucher's disease, Thalassemia and discrete pancreatic pathology was considered. Hemoglobin electrophoresis was indicative of thalassemia. Also, molecular detection method by polymerase chain reaction confirms a concurrent infection with Plasmodium knowlesi malaria. The BCR-ABL fusion gene was found to be negative. Correlating with peripheral monocytosis, bone marrow aspiration and trephine biopsy with blasts only 3-4% and hepatosplenomegaly, a diagnosis of JMML was established. We present a rare phenomenon with an overlap of signs and symptoms between JMML, underlying thalassemia, and Plasmodium knowlesi, posing a diagnostic challenge to physicians.

Draft genome sequence of the basidiomycetous fungus Tinctoporellus epimiltinus strain RS1.

Members of the genus Tinctoporellus, which belong to the wood-degrading basidiomycetes, possess the ability to synthesize an array of industrially potent enzymes and metabolites. Here, we present the draft genome sequence of the species Tinctoporellus epimiltinus strain RS1, which is the first to represent its genus. The genome was sequenced using Illumina's 2 × 150 bp paired-end Nextera protocol. The draft genome assembly was 46.2 Mb in size consisting of 13,791 protein coding genes. Identification of carbohydrate active enzymes and laccases from the data may be useful in order to harness the metabolic potentials of the fungi. The data can be accessed at ENA under the accession number FTLJ00000000.

Genomic structure of the native inhabitants of Peninsular Malaysia and North Borneo suggests complex human population history in Southeast Asia.

Southeast Asia (SEA) is enriched with a complex history of peopling. Malaysia, which is located at the crossroads of SEA, has been recognized as one of the hubs for early human migration. To unravel the genomic complexity of the native inhabitants of Malaysia, we sequenced 12 samples from 3 indigenous populations from Peninsular Malaysia and 4 native populations from North Borneo to a high coverage of 28-37×. We showed that the Negritos from Peninsular Malaysia shared a common ancestor with the East Asians, but exhibited some level of gene flow from South Asia, while the North Borneo populations exhibited closer genetic affinity towards East Asians than the Malays. The analysis of time of divergence suggested that ancestors of Negrito were the earliest settlers in the Malay Peninsula, whom first separated from the Papuans ~ 50-33 thousand years ago (kya), followed by East Asian (~ 40-15 kya), while the divergence time frame between North Borneo and East Asia populations predates the Austronesian expansion period implies a possible pre-Neolithic colonization. Substantial Neanderthal ancestry was confirmed in our genomes, as was observed in other East Asians. However, no significant difference was observed, in terms of the proportion of Denisovan gene flow into these native inhabitants from Malaysia. Judging from the similar amount of introgression in the Southeast Asians and East Asians, our findings suggest that the Denisovan gene flow may have occurred before the divergence of these populations and that the shared similarities are likely an ancestral component.

Determinants of antiretroviral therapy coverage in Sub-Saharan Africa.

Among 35 million people living with the human immunodeficiency virus (HIV) in 2013, only 37% had access to antiretroviral therapy (ART). Despite global concerted efforts to provide the universal access to the ART treatment, the ART coverage varies among countries and regions. At present, there is a lack of systematic empirical analyses on factors that determine the ART coverage. Therefore, the current study aimed to identify the determinants of the ART coverage in 41 countries in Sub-Saharan Africa. It employed statistical analyses for this purpose. Four elements, namely, the HIV prevalence, the level of national income, the level of medical expenditure and the number of nurses, were hypothesised to determine the ART coverage. The findings revealed that among the four proposed determinants only the HIV prevalence had a statistically significant impact on the ART coverage. In other words, the HIV prevalence was the sole determinant of the ART coverage in Sub-Saharan Africa.

Polycyclic aromatic hydrocarbons in Bangladeshi vegetables and fruits.

Polycyclic aromatic hydrocarbons (PAHs) occur as contaminants in different types of food predominantly from environmental pollution, food packaging and food processing and the levels found depend on the source of the contamination. PAHs emissions from automobile traffic and industry activities were shown to influence the PAHs levels and profiles in vegetables and fruits grown nearby. The present study was carried out to determine the levels of PAHs in samples of tomato, cabbage and apple, collected from six different places of urban and rural areas of plantation in Dhaka city. Eight PAHs listed in the priority pollutant of US Environment Protection Agency and regarded as carcinogens were analyzed in this study. The analytical method involved saponification with methanolic KOH, liquid-liquid extraction with cyclohexane, clean-up on silica gel column and determination by Gas chromatography and mass spectrometry. The mean levels of total PAHs were 9.50 µg/kg in tomato, 8.86 µg/kg in cabbage and 4.05 µg/kg in apple. Of the carcinogenic PAHs, benzo(a)anthracene was the most representative, being found in 89% of all samples analysed. Chrysene was not detected in any sample.