Genome-Based Analysis of Extended-Spectrum ß-Lactamase-Producing Escherichia coli in the Aquatic Environment and Nile Perch (Lates niloticus) of Lake Victoria, Tanzania.

Extended-spectrum ß-lactamase (ESBL)-producing bacteria constitute an emerging global health issue with food products being vehicles of transmission and the aquatic environments serving as potential reservoirs. This study aimed to characterize ESBL-producing Escherichia coli in Nile perch and water from Lake Victoria in Tanzania. A total of 180 samples of Nile perch and 60 water samples were screened for ESBL-producing E. coli on MacConkey agar supplemented with 2 µg/ml of cefotaxime and confirmed by bla CTX-M and bla TEM PCR. Antimicrobial resistance was determined by the disk diffusion method, and the ESBL-producing isolates were whole genome sequencing (WGS). ESBL-producing E. coli were detected in eight of the 180 analyzed Nile perch samples, and only one water sample was positive (1.7%, n = 60). Isolates were resistant to sulfamethoxazole-trimethoprim (100%), ampicillin/cloxacillin (100%), erythromycin 72.7% (8/11), tetracycline 90.9% (10/11), and nalidixic acid 63.6% (7/11). This mostly corroborates the resistance genes that they carried for sulfonamides (sul1 and sul2), trimethoprim (dfrA and dfrB), aminoglycosides [aac(3)-IId, strA, and strB], tetracycline [tet(B) and tet(D)], and fluoroquinolones (qepA4). They harbored plasmid replicon types IncF, IncX, IncQ, and Col and carried bla CTX-M- 15 and bla TEM- 1 B genes generally found on the same contigs as the IncF plasmid replicon. Although epidemiologically unrelated, the strains formed three separate sequence type-phylogroup-serotype-specific clusters: C1, C2, and C3. Cluster C1 included five strains (3 to 13 SNPs) belonging to ST167, phylogroup A, and serotype O9:H21; the two C2 strains (11 SNPs) belong to ST156, phylogroup B1, and serotype ONT:H28; and C3 was made up of four strains (SNPs ranged from 4 to 17) of ST636, phylogroup B2, and serotype O45:H7. The common virulence gene gad was reported in all strains. In addition, strains in C2 and C3 possessed iss, lpfA, and nfaE virulence genes, and the vat gene was found only in C3. The present study reports the occurrence of multidrug-resistant ESBL-producing E. coli carrying plasmid-mediated ESBL genes in offshore water and Nile perch in Lake Victoria. Strains formed three clonal clusters of unknown origin. This study reveals that the Lake may serve as reservoir for ESBL-producing bacteria that can be transmitted by fish as a food chain hazard of One-Health concern.

Characterization of Salmonella spp. from wastewater used for food production in Morogoro, Tanzania.

Wastewater use for crop irrigation and aquaculture is commonly practiced by communities situated close to wastewater treatment ponds. The objective of this study was to characterize Salmonella spp. and their antimicrobial susceptibility patterns among isolates from wastewater and Tilapia fish. A total of 123 Salmonella spp. isolates were isolated from 52 water and 21 fish intestinal samples. Genotyping of Salmonella spp. isolates was done by Pulsed-field Gel Electrophoresis (PFGE). Antimicrobial susceptibility testing was done by the minimal inhibitory concentration (MIC) technique. A total of 123 Salmonella spp. isolates represented 13 different serovars and 22 PFGE groups. Salmonella serovars showed resistance to 8 out of 14 antimicrobials; sulfamethaxazole (94%), streptomycin (61%), tetracycline (22%), ciprofloxacin and nalidixic acid (17%), trimethoprim (11%); gentamycin and chloramphenicol (6%). Salmonella Kentucky, S. Chandans, S. Durban and S. Kiambu showed multiple antimicrobial resistance to 7, 6 and 3 antimicrobials, respectively. This study has demonstrated that wastewater at the study sites is contaminated with Salmonella spp. which are resistant to common antimicrobials used for treatment of diseases in humans. Wastewater may, therefore, contaminate pristine surface water bodies and foodstuffs including fish and irrigated crops as well as food handlers.

Determination of Genetic Structure and Signatures of Selection in Three Strains of Tanzania Shorthorn Zebu, Boran and Friesian Cattle by Genome-Wide SNP Analyses.

BACKGROUND: More than 90 percent of cattle in Tanzania belong to the indigenous Tanzania Short Horn Zebu (TSZ) population which has been classified into 12 strains based on historical evidence, morphological characteristics, and geographic distribution. However, specific genetic information of each TSZ population has been lacking and has caused difficulties in designing programs such as selection, crossbreeding, breed improvement or conservation. This study was designed to evaluate the genetic structure, assess genetic relationships, and to identify signatures of selection among cattle of Tanzania with the main goal of understanding genetic relationship, variation and uniqueness among them. METHODOLOGY/PRINCIPAL FINDINGS: The Illumina Bos indicus SNP 80K BeadChip was used to genotype genome wide SNPs in 168 DNA samples obtained from three strains of TSZ cattle namely Maasai, Tarime and Sukuma as well as two comparative breeds; Boran and Friesian. Population structure and signatures of selection were examined using principal component analysis (PCA), admixture analysis, pairwise distances (FST), integrated haplotype score (iHS), identical by state (IBS) and runs of homozygosity (ROH). There was a low level of inbreeding (F~0.01) in the TSZ population compared to the Boran and Friesian breeds. The analyses of FST, IBS and admixture identified no considerable differentiation between TSZ trains. Importantly, common ancestry in Boran and TSZ were revealed based on admixture and IBD, implying gene flow between two populations. In addition, Friesian ancestry was found in Boran. A few common significant iHS were detected, which may reflect influence of recent selection in each breed or strain. CONCLUSIONS: Population admixture and selection signatures could be applied to develop conservation plan of TSZ cattle as well as future breeding programs in East African cattle.

Preliminary investigation on presence of peste des petits ruminants in Dakawa, Mvomero district, Morogoro region, Tanzania.

Peste des petits ruminants (PPR) is an acute viral disease of small ruminants characterised by the sudden onset of depression, fever, oculonasal discharges, sores in the mouth, foul-smelling diarrhoea and death. For many years, in Africa, the disease was mainly confined to West and Central Africa but it has now spread southwards to previously PPR-free countries including Tanzania, Democratic Republic of Congo and Angola. The disease was first reported in Tanzania in 2008 when it was confined to the Northern Zone districts bordering Kenya. Presence of the disease has also been confirmed in southern Tanzania especially Mtwara region. Recently, a suspected outbreak of PPR in Dakawa area, Mvomero district, Morogoro region was reported. Clinical samples (lungs, intestines, lymph nodes, whole blood and sera) from suspected goats (n = 8) and sheep (n = 1) were submitted to Sokoine University of Agriculture for analysis. Molecular diagnosis by amplification of the nucleoprotein gene and the fusion gene of PPR virus (PPRV) using PPRV specific primers was done. Five goats and the sheep were positive for PPRV after performing RT-PCR. To our knowledge, this is the first report confirming the presence of PPR in the Mvomero district of the Morogoro region, Tanzania. Hence, more efforts should be put in place to prevent the spread of PPR in Tanzania.

Towards one health disease surveillance: the Southern African Centre for Infectious Disease Surveillance approach.

Africa has the highest burden of infectious diseases in the world and yet the least capacity for its risk management. It has therefore become increasingly important to search for 'fit-for- purpose' approaches to infectious disease surveillance and thereby targeted disease control. The fact that the majority of human infectious diseases are originally of animal origin means we have to consider One Health (OH) approaches which require inter-sectoral collaboration for custom-made infectious disease surveillance in the endemic settings of Africa. A baseline survey was conducted to assess the current status and performance of human and animal health surveillance systems and subsequently a strategy towards OH surveillance system was developed. The strategy focused on assessing the combination of participatory epidemiological approaches and the deployment of mobile technologies to enhance the effectiveness of disease alerts and surveillance at the point of occurrence, which often lies in remote areas. We selected three study sites, namely the Ngorongoro, Kagera River basin and Zambezi River basin ecosystems. We have piloted and introduced the next-generation Android mobile phones running the EpiCollect application developed by Imperial College to aid geo-spatial and clinical data capture and transmission of this data from the field to the remote Information Technology (IT) servers at the research hubs for storage, analysis, feedback and reporting. We expect that the combination of participatory epidemiology and technology will significantly improve OH disease surveillance in southern Africa.