Global monitoring of antimicrobial resistance based on metagenomics analyses of urban sewage

Antimicrobial resistance (AMR) is a serious threat to global public health, but obtaining representative data on AMR for healthy human populations is difficult. Here, we use meta-genomic analysis of untreated sewage to characterize the bacterial resistome from 79 sites in 60 countries. We find systematic differences in abundance and diversity of AMR genes between Europe/North-America/Oceania and Africa/Asia/South-America. Antimicrobial use data and bacterial taxonomy only explains a minor part of the AMR variation that we observe. We find no evidence for cross-selection between antimicrobial classes, or for effect of air travel between sites. However, AMR gene abundance strongly correlates with socio-economic, health and environmental factors, which we use to predict AMR gene abundances in all countries in the world. Our findings suggest that global AMR gene diversity and abundance vary by region, and that improving sanitation and health could potentially limit the global burden of AMR. We propose metagenomic analysis of sewage as an ethically acceptable and economically feasible approach for continuous global surveillance and prediction of AMR.Peer reviewe

Setting a baseline for global urban virome surveillance in sewage

The rapid development of megacities, and their growing connectedness across the world is becoming a distinct driver for emerging disease outbreaks. Early detection of unusual disease emergence and spread should therefore include such cities as part of risk-based surveillance. A catch-all metagenomic sequencing approach of urban sewage could potentially provide an unbiased insight into the dynamics of viral pathogens circulating in a community irrespective of access to care, a potential which already has been proven for the surveillance of poliovirus. Here, we present a detailed characterization of sewage viromes from a snapshot of 81 high density urban areas across the globe, including in-depth assessment of potential biases, as a proof of concept for catch-all viral pathogen surveillance. We show the ability to detect a wide range of viruses and geographical and seasonal differences for specific viral groups. Our findings offer a cross-sectional baseline for further research in viral surveillance from urban sewage samples and place previous studies in a global perspective

Cholera Incidence and Mortality in Sub-Saharan African Sites during Multi-country Surveillance

International audienc

Gender, age and season of occurrence of cholera suspect cases.

<p>N = 6280.</p

Suspect cases with culture done and Suspect cases with positive culture for <i>Vibrio cholera</i> (first part).

<p>Surveillance zone, Beira city, Mozambique (A); surveillance zone, Koumassi-Vridi-Port Boët district, Abidjan, Cote d’Ivoire (B); surveillance zone, Lake district, Togo (C); surveillance zone, Mbale-Manafwa-Butaleja districts, Uganda (D); surveillance zone, Lome-Golfe districts, Togo (E); surveillance zone, Conakry, Guinea (F); Dark blue bars show cases with culture test done, light blue bars show cases with culture test not done, green bars show cases with <i>Vibrio cholera</i> identified by culture, and yellow bars show cases having a culture negative for <i>Vibrio cholera</i>. The dashed line shows the first month of the enhanced Africhol surveillance. The dotted line shows the last month of the enhanced Africhol surveillance.</p

Case fatality ratio (CFR) among suspected and culture confirmed cholera cases.

<p>N = 5980.</p

Suspect cases with culture done and Suspect cases with positive culture for <i>Vibrio cholera</i> (second part).

<p>Surveillance zone, Goma-Karisimbi districts, DRC (G); outbreak site, Pemba city, Mozambique (H); outbreak site, Adiake prefecture, Cote d’Ivoire (I); outbreak site, Kasese district, Uganda (J); outbreak site, Maluku-Kingabwa-Massina districts, Kinshasa, DRC (K). Dark blue bars show cases with culture test done, light blue bars show cases with culture test not done, green bars show cases with <i>Vibrio cholera</i> identified by culture, and yellow bars show cases having a culture negative for <i>Vibrio cholera</i>. The dashed line shows the first month of the enhanced Africhol surveillance. The dotted line shows the last month of the enhanced Africhol surveillance.</p

Mean annual incidence rate of cholera suspect cases and culture confirmed cases (crude or corrected) in the Africhol sites.

<p>N = 13,377.</p

Suspect cases with stool sample collected, culture test done and culture positive result.

<p>N = 13,377.</p

Gender, age and season of occurrence of culture confirmed cholera cases.

<p>N = 1019.</p