Extremely thermophilic methanogens in the Methanococci and heterotrophs in the Thermococci are common in deep-sea hydrothermal vents. All Methanococci use H2 as an electron donor, and a few species can also use formate. Most Methanococci have a coenzyme F420-reducing formate dehydrogenase. All Thermococci reduce S0 but have hydrogenases and produce H2 in the absence of S0. Some Thermococci have formate hydrogenlyase (Fhl) that reversibly converts H2 and CO2 to formate or an NAD(P)+-reducing formate dehydrogenase (Nfd). Questions remain if Methanococci or Thermococci use or produce formate in nature, why only certain species can grow on or produce formate, and what the physiological role of formate is? Formate forms abiotically in hydrothermal fluids through chemical equilibrium with primarily H2, CO2, and CO and is strongly dependent upon H2 concentration, pH, and temperature. Formate concentrations are highest in hydrothermal fluids where H2 concentrations are also high, such as in ultramafic systems where serpentinization reactions occur. In nature, Methanococci are likely to use formate as an electron donor when H2 is limiting. Thermococci with Fhl likely convert H2 and CO2 to formate when H2 concentrations become inhibitory for growth. They are unlikely to grow on formate in nature unless formate is more abundant than H2 in the environment. Nearly all Methanococci and Thermococci have a gene for at least one formate dehydrogenase catalytic subunit, which may be used to provide free formate for de novo purine biosynthesis. However, only species with a membrane-bound formate transporter can grow on or secrete formate. Interspecies H2 transfer occurs between Thermococci and Methanococci. This and putative interspecies formate transfer may support Methanococci in low H2 environments, which in turn may prevent growth inhibition of Thermococci by its own H2. Future research directions include understanding when, where, and how formate is used and produced by these organisms in nature, and how transcription of Thermococci genes encoding formate-related enzymes are regulated.

Molecular characterization was performed for 46 vancomycin-resistant E. faecium (VREfm) isolates and one vancomycin-sensitive comparator obtained during routine fecal surveillance of high-risk patients from a Dallas, Texas area hospital system. Hybrid assemblies of long (Oxford Nanopore Technology) and short (Illumina) sequence reads enabled the generation of 31 complete and 16 draft high quality genome sequences. The VREfm isolates possessed up to 12 plasmids each. A total of 251 closed plasmid sequences, assigned to 12 previously described and 9 newly defined rep family types, were obtained. Phylogenetic analysis clustered the Dallas isolates into genomic Clade A1, including 10 different sequence types (STs), the most prevalent ones being ST17 and ST18. VREfm isolates with the novel sequence type ST1703 were also identified. All but three of the VREfm isolates encoded vanA-type vancomycin resistance within Tn1546-like elements on a pRUM-like plasmid backbone. New variants of the Tn1546 were described that harbored a combination of 7 insertion sequences (IS) including 3 novel IS elements reported in this study (ISEfa16, ISEfa17 and ISEfa18). The pRUM-like plasmids carrying the Tn1546 were grouped into 4 sub-groups based on the replication and stability modules of the plasmid backbone. Overall, we conclude that the VREfm isolates analyzed in our collection are representative of other global VanA-type VREfm in that they belong to the Clade A1 lineage, but they possess novel arrangements of the Tn1546-like elements and the vanA operon, which have evolved independently of the pRUM-like backbone.

Vancomycin is an antibiotic used to treat infections caused by multidrug-resistant Gram-positive bacteria. Vancomycin resistance is common in clinical isolates of the Gram-positive pathogen Enterococcus faecium .