Human microbiota drives hospital-associated antimicrobial resistance dissemination in the urban environment and mirrors patient case rates.

BACKGROUND: The microbial community composition of urban environments is primarily determined by human activity. The use of metagenomics to explore how microbial communities are shaped in a city provides a novel input that can improve decisions on public health measures, architectural design, and urban resilience. Of note, the sewage system in a city acts as a complex reservoir of bacteria, pharmaceuticals, and antimicrobial resistant (AMR) genes that can be an important source of epidemiological information. Hospital effluents are rich in patient-derived bacteria and can thus readily become a birthplace and hotspot reservoir for antibiotic resistant pathogens which are eventually incorporated into the environment. Yet, the scope to which nosocomial outbreaks impact the urban environment is still poorly understood. RESULTS: In this work, we extensively show that different urban waters from creeks, beaches, sewage spillways and collector pipes enclose discrete microbial communities that are characterized by a differential degree of contamination and admixture with human-derived bacteria. The abundance of human bacteria correlates with the abundance of AMR genes in the environment, with beta-lactamases being the top-contributing class to distinguish low vs. highly-impacted urban environments. Indeed, the abundance of beta-lactamase resistance and carbapenem resistance determinants in the urban environment significantly increased in a 1-year period. This was in line with a pronounced increase of nosocomial carbapenem-resistant infections reported during the same period that was mainly driven by an outbreak-causing, carbapenemase-producing Klebsiella pneumoniae (KPC) ST-11 strain. Genome-resolved metagenomics of urban waters before and after this outbreak, coupled with high-resolution whole-genome sequencing, confirmed the dissemination of the ST-11 strain and a novel KPC megaplasmid from the hospital to the urban environment. City-wide analysis showed that geospatial dissemination of the KPC megaplasmid in the urban environment inversely depended on the sewage system infrastructure. CONCLUSIONS: We show how urban metagenomics and outbreak genomic surveillance can be coupled to generate relevant information for infection control, antibiotic stewardship, and pathogen epidemiology. Our results highlight the need to better characterize and understand how human-derived bacteria and antimicrobial resistance disseminate in the urban environment to incorporate this information in the development of effluent treatment infrastructure and public health policies. Video Abstract.

Assessing the origin of a massive cyanobacterial bloom in the Río de la Plata (2019): Towards an early warning system.

The Río de la Plata estuary drains the second largest river basin of South America. The occurrence of frequent cyanobacterial blooms of the Microcystis and Dolichospermum complex in the Uruguayan coast are associated with high flows of Uruguay River due to rainy years. In summer 2019, a massive cyanobacterial bloom reached up to the Uruguayan Atlantic coast. This study seeks to unveil the origin and the environmental conditions that favored the occurrence of the last cyanobacterial bloom in the Río de la Plata, and to contribute with the development of an early warning system of cyanobacterial scum on Montevideo beaches. A complementary approach was applied with Sentinel-2 imagery, environmental data of monitoring programs of Salto Grande Reservoir and Montevideo beaches, hydro-meteorological information, and hydroelectric dam operation. Images were analyzed with the Normalized Difference Chlorophyll Index (NDCI), which allowed evaluating several water bodies within the same ranges. Positive anomalous rainfall increased river flows, particularly that of Uruguay and Negro rivers, which caused the opening of the dam spillways. NDCI maps showed that areas with high values (NDCI>0.06) in Salto Grande reservoir kept a similar surface area before and after the prolonged overflow period (8.7-7.8 km2, before and after). In the Río Negro reservoirs, however, NDCI>0.06 coverage remarkably changed (62.5 km2, Palmar reservoir), with a subsequent 56-fold reduction in the post-discharge of surface water. Twenty days after opening the spillways, Montevideo beaches were closed to swimming and the NDCI>0.06 surface reached 51.7 km2 in the Río de la Plata coast. The dynamics of NDCI areas, the downstream bloom discharge, and the predicted Río de la Plata residual currents, suggest that the cyanobacterial bloom originated in the Negro River (Palmar reservoir). This bloom event was one of the worst that occurred in the Río de la Plata in last 20 years, circulated along the Uruguayan sub-corridor to the Atlantic coast along 690 km from its origin, and lasted three months on Montevideo coast. This is the first study that addresses the impact of cyanobacterial blooms from the Negro River reservoirs on the Río de la Plata estuary. Therefore, the Negro River basin is where the main efforts should be directed to mitigate massive cyanobacterial blooms.