Dataset Information

Molecular Characterization of Newcastle Disease Virus from Backyard Poultry Farms and Live Bird Markets in Kenya.

ABSTRACT: Newcastle disease (ND) is a serious disease of poultry that causes significant economic losses. Despite rampant ND outbreaks that occur annually in Kenya, the information about the NDV circulating in Kenya is still scarce. We report the first countrywide study of NDV in Kenya. Our study is aimed at evaluating the genetic characteristics of Newcastle disease viruses obtained from backyard poultry in farms and live bird markets in different regions of Kenya. We sequenced and analyzed fusion (F) protein gene, including the cleavage site, of the obtained viruses. We aligned and compared study sequences with representative NDV of different genotypes from GenBank. The fusion protein cleavage site of all the study sequences had the motif 112RRQKRFV118 indicating their velogenic nature. Phylogenetic analysis revealed that the NDV from various sites in Kenya was highly similar genetically and that it clustered together with NDV of genotype V. The study samples were 96% similar to previous Ugandan and Kenyan viruses grouped in subgenotype Vd This study points to possible circulation of NDV of similar genetic characteristics between backyard poultry farms and live bird markets in Kenya. The study also suggests the possible spread of velogenic NDV between Kenya and Uganda possibly through cross-border live bird trade. Our study provides baseline information on the genetic characteristics of NDV circulating in the Kenyan poultry population. This highlights the need for the ND control programmes to place more stringent measures on cross-border trade of live bird markets and poultry products to prevent the introduction of new strains of NDV that would otherwise be more difficult to control.

SUBMITTER: Ogali IN

PROVIDER: S-EPMC6098844 | biostudies-literature | 2018

REPOSITORIES: biostudies-literature

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Molecular Characterization of Newcastle Disease Virus from Backyard Poultry Farms and Live Bird Markets in Kenya.

Ogali Irene N IN Wamuyu Lucy W LW Lichoti Jacqueline K JK Mungube Erick O EO Agwanda Bernard B Ommeh Sheila C SC

International journal of microbiology 20180805

Newcastle disease (ND) is a serious disease of poultry that causes significant economic losses. Despite rampant ND outbreaks that occur annually in Kenya, the information about the NDV circulating in Kenya is still scarce. We report the first countrywide study of NDV in Kenya. Our study is aimed at evaluating the genetic characteristics of Newcastle disease viruses obtained from backyard poultry in farms and live bird markets in different regions of Kenya. We sequenced and analyzed fusion (F) pr ...[more]

PMID: 30154854

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Project description:Kenyan poultry consists of ~80% free-range indigenous chickens kept in small flocks (~30 birds) on backyard poultry farms (BPFs) and they are traded via live bird markets (LBMs). Newcastle disease virus (NDV) was detected in samples collected from chickens, wild farm birds, and other domestic poultry species during a 2017-2018 survey conducted at 66 BPFs and 21 LBMs in nine Kenyan counties. NDV nucleic acids were detected by rRT-PCR L-test in 39.5% (641/1621) of 1621 analyzed samples, of which 9.67% (62/641) were NDV-positive by both the L-test and a fusion-test designed to identify the virulent virus, with a majority being at LBMs (64.5%; 40/62) compared to BPFs (25.5%; 22/62). Virus isolation and next-generation sequencing (NGS) on a subset of samples resulted in 32 complete NDV genome sequences with 95.8-100% nucleotide identities amongst themselves and 95.7-98.2% identity with other east African isolates from 2010-2016. These isolates were classified as a new sub-genotype, V.3, and shared 86.5-88.9% and 88.5-91.8% nucleotide identities with subgenotypes V.1 and V.2 viruses, respectively. The putative fusion protein cleavage site (113R-Q-K-R↓F 117) in all 32 isolates, and a 1.86 ICPI score of an isolate from a BPF chicken that had clinical signs consistent with Newcastle disease, confirmed the high virulence of the NDVs. Compared to genotypes V and VI viruses, the attachment (HN) protein of 18 of the 32 vNDVs had amino acid substitutions in the antigenic sites. A time-scaled phylogeographic analysis suggests a west-to-east dispersal of the NDVs via the live chicken trade, but the virus origins remain unconfirmed due to scarcity of continuous and systematic surveillance data. This study reveals the widespread prevalence of vNDVs in Kenyan backyard poultry, the central role of LBMs in the dispersal and possibly generation of new virus variants, and the need for robust molecular epidemiological surveillance in poultry and non-poultry avian species.

Project description:Newcastle disease (ND) causes significant economic losses in the poultry industry in developing countries. In Kenya, despite rampant annual ND outbreaks, implementation of control strategies is hampered by a lack of adequate knowledge on the circulating and outbreak causing-NDV strains. This study reports the first complete genome sequences of NDV from backyard chicken in Kenya. The results showed that all three isolates are virulent, as assessed by the mean death time (MDT) and intracerebral pathogenicity index (ICPI) in specific antibody negative (SAN) embryonated eggs and 10-day-old chickens, respectively. Also, the polybasic amino acid sequence at the fusion-protein cleavage site had the motif 112RRQKRFV118. Histopathological findings in four-week-old SPF chicken challenged with the NDV isolates KE001, KE0811, and KE0698 showed multiple organ involvement at five days after infection with severe effects seen in lymphoid tissues and blood vessels. Analysis of genome sequences obtained from the three isolates showed that they were 15192 base pair (bp) in length and had genomic features consistent with other NDV strains, the functional sites within the coding sequence being highly conserved in the sequence of the three isolates. Amino acid residues and substitutions in the structural proteins of the three isolates were similar to the newly isolated Tanzanian NDV strain (Mbeya/MT15). A similarity matrix showed a high similarity of the isolates to NDV strains of class II genotype V (89-90%) and subgenotype Vd (95-97%). Phylogenetic analysis confirmed that the three isolates are closely related to NDV genotype V strains but form a distinct cluster together with NDV strains from the East African countries of Uganda and Tanzania to form the newly characterized subgenotype Vd. Our study provides the first description of the genomic and pathological characteristics of NDV of subgenotype Vd and lays a baseline in understanding the evolutionary dynamics of NDV and, in particular, Genotype V. This information will be useful in the development of specific markers for detection of viruses of genotype V and generation of genotype matched vaccines.

Project description:BACKGROUND:Understanding potential risks of multi-drug resistant (MDR) pathogens from the booming poultry sector is a crucial public health concern. Campylobacter spp. are among the most important zoonotic pathogens associated with MDR infections in poultry and human. This study systematically examined potential risks and associated socio-environmental factors of MDR Campylobacter spp. in poultry farms and live bird markets (LBMs) of Bangladesh. METHODS:Microbial culture and PCR-based methods were applied to examine the occurrence and MDR patterns of Campylobacter spp. in potential sources (n =?224) at 7 hatcheries, 9 broiler farms and 4 LBMs in three sub-districts. Antimicrobial residues in broiler meat and liver samples (n =?50) were detected by advanced chromatographic techniques. A questionnaire based cross-sectional survey was conducted on socio-environmental factors. RESULTS:Overall, 32% (71/ 224) samples were found contaminated with Campylobacter spp. In poultry farms, Campylobacter spp. was primarily found in cloacal swab (21/49, 43%), followed by drinking water (8/24, 33%), and meat (8/28, 29%) samples of broilers. Remarkably, at LBMs, Campylobacter spp. was detected in higher prevalence (p <?0.05) in broiler meat (14/26, 54%), which could be related (p <?0.01) to bacterial contamination of drinking water (11/21, 52%) and floor (9/21, 43%). Campylobacter isolates, one from each of 71 positive samples, were differentiated into Campylobacter jejuni (66%) and Campylobacter coli (34%). Alarmingly, 49 and 42% strains of C. jejuni and C. coli, respectively, were observed as MDR, i.e., resistant to three or more antimicrobials, including, tetracycline, amoxicillin, streptomycin, fluoroquinolones, and macrolides. Residual antimicrobials (oxytetracycline, ciprofloxacin and enrofloxacin) were detected in majority of broiler liver (79%) and meat (62%) samples, among which 33 and 19%, respectively, had concentration above acceptable limit. Inadequate personal and environmental hygiene, unscrupulously use of antimicrobials, improper waste disposal, and lack of health surveillance were distinguishable risk factors, with local diversity and compound influences on MDR pathogens. CONCLUSION:Potential contamination sources and anthropogenic factors associated with the alarming occurrence of MDR Campylobacter, noted in this study, would aid in developing interventions to minimize the increasing risks of poultry-associated MDR pathogens under 'One Health' banner that includes poultry, human and environment perspectives.

Project description:Background Campylobacter species (spp.) are one of the most important zoonotic bacteria possessing potential hazards for animal and human health worldwide. Migratory birds are implicated as significant carriers for microbes and a play very important role in the dissemination of Campylobacter to broiler chickens and their environment. The purpose of this investigation was to detect the prevalence, antibiotic resistant patterns, virulence and diversity of pathogenic Campylobacter spp. in 7 migratory bird species (Northern shoveler, Common pochard, Common teal, Northern pintail, Eared Grebe, Great Crested Grebe and Garganey) and broiler chickens that were collected from broiler poultry farms and live bird markets. Results The prevalence of Campylobacter was 12.5% (25/200), of which 15% (15/100) was recovered from 5 migratory bird species only and 10% (10/100) from broiler chickens. At the level of migratory birds, eight isolates (53.3%) were Campylobacter jejuni (C. jejuni) and 7 isolates (46.7%) were Campylobacter coli (C. coli) meanwhile, in broiler chickens C. jejuni and C. coli were 50% (5/10) for each. All isolated strains had phenotypic resistance to doxycycline, while all of the isolates were susceptible to amikacin. The multidrug resistance to three, four or five antimicrobial classes was found in 72% (18/25) of the isolated strains. The multiantibiotic resistance index between the examined isolates was 0.22–0.77, with 10 antibiotic resistance patterns. The virulence of isolated Campylobacter strains (from both migratory birds and broiler chicken birds) was detected by targeting the VirB11, ciaB and iam genes which were recorded at 16%, 52% and 100%, respectively. Additionally, 100% and 84% of the antibiotic resistance genes were identified as tetA and BlaOXA-61, respectively. Conclusions The results of this study revealed the diversity between all the isolated strains from migratory birds and their similarity to broiler chicken isolates. The findings of the present study highlight the impact of migratory birds visiting Egypt and other countries on pathogenic Campylobacter spp. carrying pathogenic virulence and resistance genes, necessitating the application of biosecurity measures to prevent migratory birds from entering farms during their migration period. Supplementary Information The online version contains supplementary material available at 10.1186/s12866-023-02794-0.

Dataset Information

Molecular Characterization of Newcastle Disease Virus from Backyard Poultry Farms and Live Bird Markets in Kenya.

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Molecular Characterization of Newcastle Disease Virus from Backyard Poultry Farms and Live Bird Markets in Kenya.

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