About: Pathogen surveillance in the informal settlement, Kibera, Kenya, using a metagenomics approach

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About: Pathogen surveillance in the informal settlement, Kibera, Kenya, using a metagenomics approach Goto Sponge NotDistinct Permalink

An Entity of Type : schema:ScholarlyArticle, within Data Space : wasabi.inria.fr associated with source document(s)

Attributes	Values
type	Academic Article research paper schema:ScholarlyArticle
isDefinedBy	Covid-on-the-Web dataset
has title	Pathogen surveillance in the informal settlement, Kibera, Kenya, using a metagenomics approach
Creator	Bigogo, Godfrey Verani, Jennifer Montgomery, Joel Bergmark, Lasse Clayton, Onyango Fields, Barry Hald, Tine Karlsmose, Susanne Kiplangat, Samuel Lukjancenko, Oksana Oumar, Traoré Neatherlin, John Aarestrup, Frank Hjelmsø, Mathis Hendriksen Id, Rene Munk Id, Patrick Ng'eno, Eric Pamp, J Rö Der, Timo Sü,
Source	PMC
abstract	BACKGROUND: Worldwide, the number of emerging and re-emerging infectious diseases is increasing, highlighting the importance of global disease pathogen surveillance. Traditional population-based methods may fail to capture important events, particularly in settings with limited access to health care, such as urban informal settlements. In such environments, a mixture of surface water runoff and human feces containing pathogenic microorganisms could be used as a surveillance surrogate. METHOD: We conducted a temporal metagenomic analysis of urban sewage from Kibera, an urban informal settlement in Nairobi, Kenya, to detect and quantify bacterial and associated antimicrobial resistance (AMR) determinants, viral and parasitic pathogens. Data were examined in conjunction with data from ongoing clinical infectious disease surveillance. RESULTS: A large variation of read abundances related to bacteria, viruses, and parasites of medical importance, as well as bacterial associated antimicrobial resistance genes over time were detected. Significant increased abundances were observed for a number of bacterial pathogens coinciding with higher abundances of AMR genes. Vibrio cholerae as well as rotavirus A, among other virus peaked in several weeks during the study period whereas Cryptosporidium spp. and Giardia spp, varied more over time. CONCLUSION: The metagenomic surveillance approach for monitoring circulating pathogens in sewage was able to detect putative pathogen and resistance loads in an urban informal settlement. Thus, valuable if generated in real time to serve as a comprehensive infectious disease agent surveillance system with the potential to guide disease prevention and treatment. The approach may lead to a paradigm shift in conducting real-time global genomics-based surveillance in settings with limited access to health care.
has issue date	2019-10-10(xsd:dateTime)
bibo:doi	10.1371/journal.pone.0222531
bibo:pmid	31600207
has license	cc0
sha1sum (hex)	8538c23b7be59b19a8376c51d6ec269c00b34bec
schema:url	https://doi.org/10.1371/journal.pone.0222531
resource representing a document's title	Pathogen surveillance in the informal settlement, Kibera, Kenya, using a metagenomics approach
has PubMed Central identifier	PMC6786639
has PubMed identifier	31600207
schema:publication	PLoS One
resource representing a document's body	covid:8538c23b7be59b19a8376c51d6ec269c00b34bec#body_text
is schema:about of	named entity 'surveillance' named entity 'USED' named entity 'RUNOFF' named entity 'MIXTURE' named entity 'NUMBER OF' named entity 'SETTINGS' named entity 'CONTAINING' named entity 'ACCESS TO HEALTH CARE' named entity 'METHODS' named entity 'SURROGATE' named entity 'FECES' named entity 'URBAN' named entity 'CAPTURE' named entity 'IMPORTANT' named entity 'SURFACE WATER' named entity 'PATHOGEN SURVEILLANCE' named entity 'ENVIRONMENTS' named entity 'TRADITIONAL' named entity 'GLOBAL HEALTH' named entity 'DIVISION' named entity 'PROTECTION' named entity 'EMERGING INFECTIOUS DISEASES' named entity 'SURVEILLANCE' named entity 'FAIL' named entity 'HUMAN' named entity 'DISEASE' named entity 'WORLDWIDE' named entity 'COULD BE' named entity 'GLOBAL' named entity 'EVENTS' named entity 'PATHOGENIC' named entity 'INCREASING' named entity 'LIMITED' named entity 'MICROORGANISMS' named entity 'HIGHLIGHTING' covid:arg/8538c23b7be59b19a8376c51d6ec269c00b34bec named entity 'human feces' named entity 'pathogenic' named entity 'emerging infectious diseases' named entity 'pathogen' named entity 'human feces' named entity 'important events' named entity 'spp' named entity 'resistance genes' named entity 'fever' named entity 'fluoroquinolones' named entity 'genome' named entity 'diarrhea' named entity 'human parechovirus' named entity 'E. coli' named entity 'Shigella' named entity 'sewage' named entity 'pathogens' named entity 'Genbank' named entity 'diarrhea' named entity 'polioviruses' named entity 'viruses' named entity 'diarrhea' named entity 'bacteria' named entity 'public health' named entity 'E. coli' named entity 'standard deviation'

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