Haruo Suzuki

RNA viruses represent an integral component of human-associated environments and human health. However, the ecology of environmental RNA viruses remains largely unexplored. Here, we analyzed 2922 metatranscriptomic samples collected from urban and surrounding environments—including human-dense settings (e.g., transit hubs, hospitals, banks), alongside peri-urban settings — across 102 cities in 31 countries and constructed the Urban & Peri-urban RNA Virus Atlas (UPVAtlas), comprising 54,945 RNA viruses, 77% of which had not been previously observed. Phylogenetic reconstruction based on RNA-dependent RNA polymerases from UPVAtlas greatly expanded the evolutionary diversity of RNA viruses, leading to the identification of two potential candidate phyla, one candidate class, and several unclassified clades. Host association analyses further revealed the ecological complexity of environmental RNA viruses, with the diversity of vertebrate-related and ESKAPE pathogen-related viruses underscoring the importance of continued monitoring of urban environments for tracking RNA viral prevalence and dynamics, with direct relevance to future public health.

Microbiome research encompasses “external microbiomes”—those residing outside the human body, particularly within urban and man-made environments (the built environment)

Objectives: The urban microbiome is a significantly underexplored ecosystem which contributes to the health and resilience of the human population and less is known about the microbiome of urban transportation systems that commuters interact with daily. Shotgun metagenomic sequencing data from swab samples were collected at a representative medium-scale urban commuter railway station in Tokyo, Japan, with daily passenger volumes on the order of tens of thousands, in October 2021. The dataset was generated as part of the nationwide “Urban Microbiomes in Japan” project and provides a resource for comparative analyses of urban microbial diversity and future public health surveillance studies in urban environments. Data description: Three surface swab samples were collected in October 2021 from concrete floor areas near ticket gates at a major railway station in Shinagawa, Tokyo. Samples were collected using Isohelix swabs with DNA/RNA Shield stabilization solution. Metagenomic DNA was extracted and subjected to shotgun sequencing, generating 2 × 150 bp paired-end reads.

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The environmental realm has been acknowledged as a pivotal arena for the emergence and propagation of antimicrobial resistance. To further explore insight into antimicrobial resistance dynamics beyond clinical and veterinary settings, we embarked on an environmental surveillance initiative targeting the prevalence of antibiotic-resistant bacteria within the bustling confines of an international airport in Japan. Our findings illuminate a high prevalence of methicillin-resistant staphylococci (46.3%) on frequently contacted surfaces in the public domain. Notably, Staphylococcus haemolyticus and S. epidermidis emerged as the preeminent carriers of the mecA gene. Intriguingly, we encountered a virulent strain of livestock-associated MRSA harboring a PVL-positive ST1232 clone, CC398 lineage. Further scrutiny unveiled a repertoire of resistance mechanisms, the methicillin-resistant isolates exhibited two or more resistance genes conferring resistance against different types of antibiotics, including beta-lactams, macrolides, lincosamides, aminoglycosides, chloramphenicol, and fosfomycin. Revealing multidrug-resistant CoNS and a LA-MRSA across various surfaces in urban public areas unearths a looming public health hazard. Thus, implementation of molecular surveillance is imperative, augmenting our capacity for early detection and mitigation of the insidious spread and potential transfer of antibiotic resistance genes and virulence factors amidst urban settings, notably within pivotal nodes such as airports.

SUMMARY: Plasmids are the most influential engines of bacterial evolution and horizontal gene transfer, fueling the global spread of traits such as antimicrobial resistance. Their deep evolutionary relationships, however, remain difficult to resolve because current classification schemes are constrained by host range and nucleotide similarity. Replication initiation proteins (RIPs), which govern plasmid persistence and diversification, also remain poorly annotated across public databases. Here we establish PInc, a curated and experimentally grounded replicon classification framework anchored in historically defined incompatibility groups of Pseudomonas plasmids. Homology searches beyond PInc revealed that most replication initiators analyzed here share a conserved winged-helix (WH) domain, defining a broad WH RIP superfamily. Using the conserved WH region, we reconstructed a large-scale phylogeny that linked WH RIPs to over 100,000 plasmids, representing approximately half of those analyzed across public databases. This phylogeny resolved eight major clades and the deep split between the single- and double-winged-helix superclades, while revealing clade-specific host and environmental distributions and substantial RIP diversity not captured by current typing tools or annotation schemes. Together, these results overcome the historical host bias of plasmid typing and provide a replication-centered view of plasmid diversification across bacterial lineages and environments.

We obtained shotgun metagenome sequences from swab samples obtained through 3-minute swabbing of different surfaces and the air within buildings at three university campuses in part of the Greater Tokyo Area in Japan. These data aid in understanding built environment microbial communities and elucidate various microbial profiles across different locations.

Objective: Metatranscriptomic analysis of RNA viromes on built-environment surfaces is hampered by low RNA yields and high abundance of rRNA. Therefore, we evaluated the quality of libraries, efficiency of rRNA depletion, and viral detection sensitivity using a mock community and a melamine-coated table surface RNA with levels below those required (< 5 ng) with a library preparation kit (NEBNext Ultra II Directional RNA Library Prep Kit). Results: Good-quality RNA libraries were obtained from 0.1 ng of mock community and table surface RNA by changing the adapter concentration and number of PCR cycles. Differences in the target species of the rRNA depletion method affected the community composition and sensitivity of virus detection. The percentage of viral occupancy in two replicates was 0.259 and 0.290% in both human and bacterial rRNA-depleted samples, a 3.4 and 3.8-fold increase compared with that for only bacterial rRNA-depleted samples. Comparison of SARS-CoV-2 spiked-in human rRNA and bacterial rRNA-depleted samples suggested that more SARS-CoV-2 reads were detected in bacterial rRNA-depleted samples. We demonstrated that metatranscriptome analysis of RNA viromes is possible from RNA isolated from an indoor surface (representing a built-environment surface) using a standard library preparation kit.