The phylogenetic relationships of glycopeptide resistance proteins were investigated. The amino acid sequences of vanA, vanB, vanR and vanS were used as queries to search against bacterial genomes in the NCBI RefSeq database. Hits with >60% amino acid identity and >90% query coverage were aligned, and phylogenetic trees were reconstructed. The ligase gene phylogenies were highly similar for both queries, revealing two major clusters. One contained [[vanA:vanM][vanB:vanD]vanF] and related proteins, with proteins from different Bacillaceae, mostly from Paenibacillus spp., in basal positions to all, except vanB. Ligases from streptomycetes formed the other cluster. The relative positions of vanH and vanX differed from those of the associated ligases, but the basal position of the Paenibacillus spp. and the separation of proteins of Streptomyces origin were similar. The accessory genes vanW, vanY and vanZ were associated with vanB, vanA/vanM and vanA, respectively; the basal branches were always proteins from different Bacillaceae but never from streptomycetes. Multiple homologs of the regulatory genes vanR and vanS were found in the genomes; those associated with the different ligases were unique to the ligases. Similarly to the accessory genes, vanRS from Bacillales and Clostridia, but never from streptomycetes, was found in the basal positions. In conclusion, the core genes vanA/B/D/F/M, vanH and vanX originate most probably from glycopeptide-producing streptomycetes, with Paenibacillus spp. (or other Bacillaceae) mediating the transfer, while the accessory genes and the regulatory apparatus probably originate from these Bacillaceae.

Oxazolidinone resistance, especially transmissible resistance, is a major public health concern, and the origin of this resistance mechanism is not yet resolved. This study aims to delve into the phylogenetic origin of the transmissible oxazolidinone resistance mechanisms conferring cross-resistance to other drugs of human and veterinary importance. The amino acid sequences of the five cfr ribosomal methylases and optrA and poxtA were used as queries in searches against 219,549 bacterial proteomes in the NCBI RefSeq database. Hits with >40% amino acid identity and >80% query coverage were aligned, and phylogenetic trees were reconstructed. All five cfr genes yielded highly similar trees, with rlmN housekeeping ribosomal methylases located basal to the sister groups of S-adenosyl-methionine-dependent methyltransferases from various Deltaproteobacteria and Actinomycetia, including antibiotic-producing Streptomyces species, and the monophyletic group of cfr genes. The basal branches of the latter contained paenibacilli and other soil bacteria; they then could be split into the clades [cfr(C):cfr(E)] and [[cfr:cfr(B)]:cfr(D)], always with different Bacillaceae in their stems. Lachnospiraceae were encountered in the basal branches of both optrA and poxtA trees. The ultimate origin of the cfr genes is the rlmN housekeeping ribosomal methylases, which evolved into a suicide-avoiding methylase in antibiotic producers; a soil organism (Lachnospiraceae, Paenibacilli) probably acted as a transfer organism into pathogenic bacteria. In the case of optrA, the porcine pathogenic Streptococcus suis was present in all branches, while the proteins closest to poxtA originated from Clostridia.

Background: Carbapenem-resistant Escherichia coli (CREC) producing OXA-48-like carbapenemase was first detected in Hungary in 2022. The aim of the present study was to characterize such strains isolated in 2022–2025 in Baranya County, Hungary. Methods: Antibiotic susceptibility and the whole-genome sequence (WGS) of E. coli isolates, identified as OXA-48-like carbapenemase producers using the CARBA-5 NG test, were established. The transferability of bla_OXA-48-like plasmids was tested by conjugation. Results: Of the 6722 non-repeat E. coli isolates, 6 produced an OXA-48-like carbapenemase. They exhibited variable resistance to ertapenem and were susceptible to imipenem and meropenem. WGS revealed that all OXA-48-like producer E. coli belonged to high-risk clones: two clonally related OXA-181-producer E. coli ST405 were isolated in Hospital A, three OXA-244-producing E. coli ST38 (two identical via cgMLST from Hospital B), and an OXA-48-producing E. coli ST69. The bla_OXA-48 and bla_OXA-244 genes were chromosomally located, while bla_OXA-181 was on a non-conjugative IncFIB-IncFIC plasmid. So far, the bla_OXA-181-bearing plasmid of this incompatibility type has only been described in Ghana, but all bla_OXA-48-like gene-carrying transposons in this study have already been identified in Europe and other continents. The E. coli ST38 isolates, showing close association based on core genome SNP distances to European and Qatari strains, belonged to Cluster A and harbored bla_CTX-M-27. All but the E. coli ST69 isolate had cephalosporinase gene(s). Conclusions: This study describes small-scale intra-hospital transfers of OXA-48-like carbapenemase-producer E. coli. Interestingly, E. coli ST405 of Hungary carried bla_OXA-181 on an IncFIB-IncFIC plasmid, which has only been reported from Africa so far.