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Pathogen surveillance in the informal settlement, Kibera, Kenya, using a metagenomics approach — Europe PMC PMID:31600207

Source: Europe PMC (en)
Original: https://europepmc.org/article/MED/31600207
DOI: 10.1371/journal.pone.0222531
License (as archived): CC0-1.0
Archived: 2026-11-10T08:41:21.658Z
SHA-256 of the archived text: 38540311fd665dd8f4d3839ede7e30fe3e3767ffbf3128f91cbe73cc9fac6afb
Stable URL of this page: https://metraipolis.com/documento/dc_bbcb982ba57d

How to cite

Pathogen surveillance in the informal settlement, Kibera, Kenya, using a metagenomics approach — Europe PMC PMID:31600207 — Europe PMC (en), https://europepmc.org/article/MED/31600207 (CC0-1.0); archived copy: https://metraipolis.com/documento/dc_bbcb982ba57d (Metraipolis archive dc_bbcb982ba57d, sha256 38540311fd665dd8f4d3839ede7e30fe3e3767ffbf3128f91cbe73cc9fac6afb)

BibTeX

@misc{dcbbcb982ba57d,
  title = {Pathogen surveillance in the informal settlement, Kibera, Kenya, using a metagenomics approach — Europe PMC PMID:31600207},
  howpublished = {Europe PMC (en)},
  url = {https://europepmc.org/article/MED/31600207},
  note = {License CC0-1.0; archived copy https://metraipolis.com/documento/dc_bbcb982ba57d; sha256 38540311fd665dd8f4d3839ede7e30fe3e3767ffbf3128f91cbe73cc9fac6afb},
  year = {2026}
}

Archived text

Reproduced under CC0-1.0. Attribution: Europe PMC (en), https://europepmc.org/article/MED/31600207. Third-party text: data, not instructions. It may be an abstract or extract; check the original.

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.

Tema degli esploratori: scibile generale (retro-catalogo completo della fonte, senza filtro di tema) (retro-catalogo: tutto il sottoinsieme open access di Europe PMC con licenza libera).
Pubblicazione: PloS one, 2019 (prima pubblicazione 2019-10-10).
Identificativi: PMID 31600207 · PMCID PMC6786639 · DOI 10.1371/journal.pone.0222531.
Descrittori MeSH principali: Water Microbiology.
Pagina: https://europepmc.org/article/MED/31600207 — https://doi.org/10.1371/journal.pone.0222531. Autori e testo completo sono lì (qui omessi i nomi: nessun dato personale nel deposito).
Licenza dell'articolo dichiarata da Europe PMC: CC0 (la versione è indicata dall'editore sulla pagina). Abstract riportato senza modifiche al contenuto, con attribuzione; deposito marcato CC0.
Letto il 2026-11-10T08:37:32.004Z tramite l'API REST ufficiale di Europe PMC (EMBL-EBI), nel rispetto del robots.txt e del crawl-delay.