16S rRNA metagenomics data on the bacterial communities in integrated poultry-fish farm ponds.

In an integrated poultry-fish (IPF) farming system, fish and bird are reared simultaneously. It is a common practice in Sub-Saharan Africa countries like Nigeria, Cameroon, Madagascar, and Benin, offering economic benefits to farmers and minimizing farm running costs. It seems like another way for farmers to manage poultry waste as it is a common practice in IPF farm settings to feed reared fishes with wastes emanating from the poultry. This work provides dataset on the bacterial taxonomic profile and abundance in IPF farm pond water samples using the 16S rRNA sequencing approach. Using ZymoBIOMICS®-96 MagBead DNA Kit, total DNA was extracted from pond water samples collected from IPF farm located at Ila-Orangun, Osun State, Southwest Nigeria (Long: 8° 1' N; Lat: 4° 54' E) during two sampling visits. The V3-V4 region of the rRNA gene was amplified and sequenced on the Miseq Illumina sequencing platform. Raw reads obtained after demultiplexing were analyzed using DADA2 pipeline to obtain distinctive or unique amplicon sequence variants which were grouped into Operational Taxonomic Units (OTUs) based on similarities. Taxonomy assignment was performed using UCLUST and Bayesian classifier from QIIME v.1.9.1 with the Zymo Research Database as reference. The phyla Proteobacteria (26.7%), Actinobacteria (26.0%), Firmicutes (13.1%), and Cyanobacteria (10.1%) dominated the 35 phyla obtained from the OTUs. Interestingly, the abundance of bacterial pathogens commonly associated with human infections was low. The sequence and sample data have been deposited in NCBI database under Sequence Read Archive (SRA) with Bioproject identification number PRJNA760919 (Accession number: SRX12020336 - SRX12020346). The dataset obtained can bridge the gap of limited information on the impact of IPF farming on pond bacterial diversity, a critical factor for considerations as regards food safety, fish, and public health.

Microenvironments in tuberculous granulomas are delineated by distinct populations of macrophage subsets and expression of nitric oxide synthase and arginase isoforms.

Macrophages in granulomas are both antimycobacterial effector and host cell for Mycobacterium tuberculosis, yet basic aspects of macrophage diversity and function within the complex structures of granulomas remain poorly understood. To address this, we examined myeloid cell phenotypes and expression of enzymes correlated with host defense in macaque and human granulomas. Macaque granulomas had upregulated inducible and endothelial NO synthase (iNOS and eNOS) and arginase (Arg1 and Arg2) expression and enzyme activity compared with nongranulomatous tissue. Immunohistochemical analysis indicated macrophages adjacent to uninvolved normal tissue were more likely to express CD163, whereas epithelioid macrophages in regions where bacteria reside strongly expressed CD11c, CD68, and HAM56. Calprotectin-positive neutrophils were abundant in regions adjacent to caseum. iNOS, eNOS, Arg1, and Arg2 proteins were identified in macrophages and localized similarly in granulomas across species, with greater eNOS expression and ratio of iNOS/Arg1 expression in epithelioid macrophages as compared with cells in the lymphocyte cuff. iNOS, Arg1, and Arg2 expression in neutrophils was also identified. The combination of phenotypic and functional markers support that macrophages with anti-inflammatory phenotypes localized to outer regions of granulomas, whereas the inner regions were more likely to contain macrophages with proinflammatory, presumably bactericidal, phenotypes. Together, these data support the concept that granulomas have organized microenvironments that balance antimicrobial anti-inflammatory responses to limit pathology in the lungs.

Molecular epidemiology of Mycobacterium tuberculosis clinical isolates in Southwest Ireland.

Tuberculosis has had significant effects on Ireland over the past two centuries, causing persistently higher morbidity and mortality than in neighbouring countries until the last decade. This study describes the results of genotyping and drug susceptibility testing of 171 strains of Mycobacterium tuberculosis complex isolated between January 2004 and December 2006 in a region of Ireland centred on the city of Cork. Spoligotype comparisons were made with the SpolDB4 database and clustered 130 strains in 23 groups, forty-one strains showed unique Spoligotyping patterns. The commonest spoligotypes detected were ST0137 (X2) (16.9%), and ST0351 (15.8%) ('U' clade). The major spoligotype clades were X (26.2%), U (19.3%), T (15.2%), Beijing (5.9%), Haarlem (4.7%), LAM (4.1%), BOVIS (1.75%), with 12.9% unassigned strains. A 24-locus VNTR genotyping produced 15 clusters containing 49 isolates, with high discrimination index (HGDI>0.99). A combination of Spoligotyping and VNTR reduced the number of clustered isolates to 47 in 15 clusters (27.5%). This study identified ST351 as common among Irish nationals, and found a low rate of drug resistance with little evidence of transmission of drug resistant strains. Strain clustering was significantly associated with age under 55 years and Irish nationality. Only strains of Euro-American lineage formed clusters. Molecular typing did not completely coincide with the results of contact investigations.