Metagenomic characterization of bacterial community and antibiotic resistance genes found in the mass transit system in Seoul, South Korea.

Mass transit systems, including subways and buses, are useful environments for studying the urban microbiome, as the vast majority of populations in urban areas use public transportation. Microbial communities in urban environments include both human- and environment-associated bacteria that play roles in health and pathogen transmission. In this study, we used shotgun metagenomic sequencing to profile microbial communities sampled from various surfaces found in subway stations and bus stops within the Seoul mass transit system. The metagenomic approach and network analysis were used to investigate broad-spectrum antibiotic resistance genes (ARGs) and their co-occurrence patterns. We uncovered 598 bacterial species in 76 samples collected from various surfaces within the Seoul mass transit system. All samples were dominated by the potential human pathogen Salmonella enterica (40 %) and the human skin bacterium Cutibacterium acnes (19 %). Significantly abundant biomarkers detected in subway station samples were associated with bacteria typically found in the human oral cavity and respiratory tract, whereas biomarkers detected in bus stop samples were associated with bacteria commonly found in soil, water, and plants. Temperature and location had significant effects on microbial community structure and diversity. In total, 41 unique ARG subtypes were identified, associated with single-drug or multidrug resistance to clinically important and extensively used antibiotics, including aminoglycosides, carbapenem, glycopeptide, and sulfonamides. We revealed that Seoul subway stations and bus stops possess unique microbiomes containing potential human pathogens and ARGs. These findings provide insights for refining location-specific responses to reduce exposure to potentially causative agents of infectious diseases, improving public health.

Ferrimonas sediminicola sp. nov. and Ferrimonas aestuarii sp. nov., Fe(III)-reducing bacteria isolated from marine environments.

Two Gram-stain-negative, Fe(III)-reducing, facultatively anaerobic, motile via a single polar flagellum, rod-shaped bacterial strains, designated IMCC35001T and IMCC35002T, were isolated from tidal flat sediment and seawater, respectively. Results of 16S rRNA gene sequence analysis showed that IMCC35001T and IMCC35002T shared 96.6 % sequence similarity and were most closely related to Ferrimonas futtsuensis FUT3661T (98.6 %) and Ferrimonas kyonanensis Asr22-7T (96.8 %), respectively. Draft genome sequences of IMCC35001T and IMCC35002T revealed 4.0 and 4.8 Mbp of genome size with 61.0 and 51.8 mol% of DNA G+C content, respectively. Average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between the two strains were 73.1 and 19.8 %, respectively, indicating that they are separate species. The two genomes showed ≤84.4 % ANI and ≤27.8 % dDDH to other species of the genus Ferrimonas, suggesting that the two strains each represent novel species. The two strains contained both menaquinone (MK-7) and ubiquinones (Q-7 and Q-8). Major fatty acids of strain IMCC35001T were iso-C15 : 0, C18 : 1 ω9c, C17 : 1 ω8c and C16 : 0 and those of strain IMCC35002 T were C18 : 1 ω9c, C16 : 0 and summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c). Major polar lipids in both strains were phosphatidylethanolamine, phosphatidylglycerol, unidentified phospholipid, unidentified aminophospholipid and unidentified lipids. The two strains reduced Fe(III) citrate, Fe(III) oxyhydroxide, Mn(IV) oxide and sodium selenate but did not reduce sodium sulfate. They were also differentiated by several phenotypic characteristics. Based on the polyphasic taxonomic data, IMCC35001T and IMCC35002T were considered to represent each novel species in the genus Ferrimonas, for which the names Ferrimonas sediminicola sp. nov. (IMCC35001T=KACC 21161T=NBRC 113699T) and Ferrimonas aestuarii (IMCC35002T=KACC 21162T=NBRC 113700T) sp. nov. are proposed.

Leeia aquatica sp. nov., isolated from freshwater.

A Gram-stain-negative, rod-shaped, obligately aerobic, motile by a single polar flagellum, chemoheterotrophic bacterium, designated strain IMCC25680T, was isolated from surface water in Chungju Lake, Republic of Korea. 16S rRNA gene sequence analysis revealed that strain IMCC25680T was most closely related to Leeia oryzae HW7T with 95.5% sequence similarity and formed a robust clade with L. oryzae HW7T. Whole genome sequencing showed that strain IMCC25680T had a genome 3.6 Mbp long with 60.7 mol% DNA G+C content. Average nucleotide identity and digital DNA-DNA hybridization values between strain IMCC25680T and L. oryzae HW7T were 72.4% and 18.5%, respectively, indicating that the novel strain represents a novel species of the genus Leeia. The major cellular fatty acids of strain IMCC25680T were iso-C16:0 and summed feature 3 (comprising C16:1 ω6c and/or C16:1 ω7c). The respiratory quinone detected in the strain was ubiquinone-8. The major polar lipids were found to be phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and two unidentified polar lipids. On the basis of the phylogenetic and phenotypic characterization, strain IMCC25680T was considered to represent a novel species within the genus Leeia, for which the name Leeia aquatica sp. nov. is proposed. The type strain is IMCC25680T (=KACC 19487T =NBRC 113132T).

Sphingobacterium chungjuense sp. nov., isolated from a freshwater lake.

A Gram-stain-negative, rod-shaped, aerobic, non-flagellated, chemoheterotrophic bacterium, designated strain IMCC25678T, was isolated from an artificial freshwater reservoir, Chungju Lake, in the Republic of Korea. The 16S rRNA gene sequence analysis indicated that strain IMCC25678T belongs to the genus Sphingobacterium with ≤98.7 % sequence similarities to Sphingobacterium species. Whole genome sequencing of strain IMCC25678T revealed a 3.9 Mbp genome size with a DNA G+C content of 42.2 mol%. The IMCC25678T genome shared ≤89.7 % average nucleotide identity and ≤21.4 % digital DNA-DNA hybridization values with closely related species of the genus Sphingobacterium, indicating that the strain represents a novel species. Summed feature 3 (C16 : 1 ω6c and/or C16 : 1 ω7c), iso-C15 : 0 and iso-C17 : 0 3-OH were found to be the predominant cellular fatty acid constituents in the strain. The major respiratory quinone was MK-7. The major polar lipids were phosphatidylethanolamine, one unidentified phosphoglycolipid, one unidentified sphingolipid and three unidentified polar lipids. Based on the phylogenetic and phenotypic characteristics, strain IMCC25678T was considered to represent a novel species within the genus Sphingobacterium, for which the name Sphingobacterium chungjuense sp. nov. is proposed. The type strain is IMCC25678T (=KACC 19485T=NBRC 113130T).

A sulfate-reducing bacterial genus, Desulfosediminicola gen. nov., comprising two novel species cultivated from tidal-flat sediments.

Tidal-flat sediments harbor a diverse array of sulfate-reducing bacteria. To isolate novel sulfate-reducing bacteria and determine their abundance, a tidal-flat sediment sample collected off Ganghwa Island (Korea) was investigated using cultivation-based and culture-independent approaches. Two Gram-stain-negative, strictly anaerobic, rod-shaped, sulfate-reducing bacteria, designated IMCC35004T and IMCC35005T, were isolated from the sample. The two strains reduced sulfate, sulfite, elemental sulfur, thiosulfate, Fe(III) citrate, and Mn(IV) oxide by utilizing several carbon sources, including acetate. The 16S rRNA gene amplicon sequencing revealed that the tidal-flat sediment contained diverse members of the phylum Desulfobacterota, and the phylotypes related to IMCC35004T and IMCC35005T were < 1%. The two strains shared 97.6% similarity in 16S rRNA gene sequence and were closely related to Desulfopila aestuarii DSM 18488T (96.1-96.5%). The average nucleotide identity, level of digital DNA-DNA hybridization, average amino acid identity, and percentages of conserved proteins determined analyzing the whole-genome sequences, as well as the chemotaxonomic data showed that the two strains belong to two novel species of a novel genus. Additionally, genes related to dissimilatory sulfate reduction were detected in the genomes of the two strains. Unlike the genera Desulfopila and Desulfotalea, IMCC35004T and IMCC35005T contained menaquinone-5 as the major respiratory quinone. Collectively, IMCC35004T and IMCC35005T were concluded to represent two novel species of a novel genus within the family Desulfocapsaceae, for which the names Desulfosediminicola ganghwensis gen. nov., sp. nov. (IMCC35004T = KCTC 15826T = NBRC 114003T) and Desulfosediminicola flagellatus sp. nov. (IMCC35005T = KCTC 15827T = NBRC 114004T) are proposed.

Repurposing Eltrombopag for Multidrug Resistant Staphylococcus aureus Infections.

The continuous rise of antimicrobial resistance urgently demands new therapeutic agents for human health. Drug repurposing is an attractive strategy that could significantly save time delivering new antibiotics to clinics. We screened 182 US Food and Drug Administration (FDA)-approved drugs to identify potential antibiotic candidates against Staphylococcus aureus, a major pathogenic bacterium. This screening revealed the significant antibacterial activity of three small molecule drugs against S. aureus: (1) LDK378 (Ceritinib), an anaplastic lymphoma kinase (ALK) inhibitor for the treatment of lung cancer, (2) dronedarone HCl, an antiarrhythmic drug for the treatment of atrial fibrillation, and (3) eltrombopag, a thrombopoietin receptor agonist for the treatment of thrombocytopenia. Among these, eltrombopag showed the highest potency against not only a drug-sensitive S. aureus strain but also 55 clinical isolates including 35 methicillin-resistant S. aureus (Minimum inhibitory concentration, MIC, to inhibit 50% growth [MIC50] = 1.4-3.2 mg/L). Furthermore, we showed that eltrombopag inhibited bacterial growth in a cell infection model and reduced bacterial loads in infected mice, demonstrating its potential as a new antibiotic agent against S. aureus that can overcome current antibiotic resistance.

Aequoribacter fuscus gen. nov., sp. nov., a new member of the family Halieaceae, isolated from coastal seawater.

A Gram-stain-negative, rod-shaped, obligately aerobic, nonflagellated, and chemoheterotrophic bacterium, designated IMCC3088T, was isolated from coastal seawater of the Yellow Sea. The 16S rRNA gene sequence analysis indicated that this strain belonged to the family Halieaceae which shared the highest sequence similarities with Luminiphilus syltensis NOR5-1BT (94.5%) and Halioglobus pacificus S1-72T (94.5%), followed by 92.3-94.3% sequence similarities with other species within the aforementioned family. Phylogenetic analyses demonstrated that strain IMCC3088T was robustly clustered with Luminiphilus syltensis NOR5-1BT within the family Halieaceae. However, average amino acid identity (AAI), percentages of conserved proteins (POCP), average nucleotide identity (ANI), and alignment fraction (AF) between strain IMCC3088T and Luminiphilus syltensis NOR5-1BT were 54.5%, 47.7%, 68.0%, and 16.5%, respectively, suggesting that they belonged to different genera. Whole-genome sequencing of strain IMCC3088T revealed a 3.1 Mbp genome size with a DNA G + C content of 51.7 mol%. The genome encoded diverse metabolic pathways including sulfur oxidation, phenol degradation, and proteorhodopsin phototrophy. Mono-unsaturated fatty acids were found to be the predominant cellular fatty acid components in the strain. Phosphatidylethanolamine, phosphatidylglycerol, and diphosphatidylglycerol were the primarily identified polar lipids, and ubiquinone-8 was identified as a major respiratory quinone. The taxonomic data collected herein suggested that strain IMCC3088T represented a novel genus and species of the family Halieaceae, for which the name Aequoribacter fuscus gen. nov., sp. nov. is proposed with the type strain (= KACC 15529T = NBRC 108213T).