The Klebsiella group, found in humans, livestock, plants, soil, water and wild animals, is genetically and ecologically diverse. Many species are opportunistic pathogens and can harbour diverse classes of antimicrobial resistance genes. Healthcare-associated Klebsiella pneumoniae clones that are non-susceptible to carbapenems can spread rapidly, representing a high public health burden. Here we report an analysis of 3,482 genome sequences representing 15 Klebsiella species sampled over a 17-month period from a wide range of clinical, community, animal and environmental settings in and around the Italian city of Pavia. Northern Italy is a hotspot for hospital-acquired carbapenem non-susceptible Klebsiella and thus a pertinent setting to examine the overlap between isolates in clinical and non-clinical settings. We found no genotypic or phenotypic evidence for non-susceptibility to carbapenems outside the clinical environment. Although we noted occasional transmission between clinical and non-clinical settings, our data point to a limited role of animal and environmental reservoirs in the human acquisition of Klebsiella spp. We also provide a detailed genus-wide view of genomic diversity and population structure, including the identification of new groups.

The Klebsiella group is highly diverse both genetically and ecologically, being commonly recovered from humans, livestock, plants, soil, water, and wild animals. Many species are opportunistic pathogens, and can harbour diverse classes of antimicrobial resistance (AMR) genes. K. pneumoniae is responsible for a high public-health burden, due in part to the rapid spread of health-care associated clones that are non-susceptible to carbapenems. Klebsiella thus represents a highly pertinent taxon for assessing the risk to public health posed by animal and environmental reservoirs. Here we report an analysis of 6548 samples and 3,482 genome sequences representing 15 Klebsiella species sampled over a 15-month period from a wide range of clinical, community, animal and environmental settings in and around the city of Pavia, in the northern Italian region of Lombardy. Despite carbapenem-resistant clones circulating at a high frequency in the hospitals, we find no genotypic or phenotypic evidence for non-susceptibility to carbapenems outside of the clinical environment. The non-random distribution of species and strains across sources point to ecological barriers that are likely to limit AMR transmission. Although we find evidence for occasional transmission between settings, hierarchical modelling and intervention analysis suggests that direct transmission from the multiple non-human (animal and environmental) sources included in our sample accounts for less than 1% of hospital disease, with the vast majority of clinical cases originating from other humans.

Knowledge gaps in spatiotemporal changes in mangrove diversity and composition have obstructed mangrove conservation programs across the tropics, but particularly in the Sundarbans (10,017 km 2 ), the world's largest remaining natural mangrove ecosystem. Using mangrove tree data collected from Earth's largest permanent sample plot network at four historical time points (1986, 1994, 1999 and 2014), this study establishes spatially explicit baseline biodiversity information for the Sundarbans. We determined the spatial and temporal differences in alpha, beta, and gamma diversity in three ecological zones (hypo-, meso-, and hypersaline) and also uncovered changes in the mangroves' overall geographic range and abundances therein. Spatially, the hyposaline mangrove communities were the most diverse and heterogeneous in species composition while the hypersaline communities were the least diverse and most homogeneous at all historical time points. Since 1986, we detect an increasing trend of compositional homogeneity (between-site similarity in species composition) and a significant spatial contraction of distinct and diverse areas over the entire ecosystem. Temporally, the western and southern hypersaline communities have undergone radical shifts in species composition due to population increase and range expansion of the native invasive species Ceriops decandra and local extinction or range contraction of specialists including the globally endangered Heritiera fomes . The surviving biodiversity hotspots are distributed outside the legislated protected area network. In addition to suggesting the immediate coverage of these hotspots under protected area management, our novel biodiversity insights and spatial maps can form the basis for spatial conservation planning, biodiversity monitoring and protection initiatives for the Sundarbans.