Henrik Christensen

A new taxon, including 25 strains, obtained from the oral cavity of lions, tigers and a karakal in Danish zoos, was characterized phenotypically and genotypically. Colonies were typical of bacteria of taxa within Pasteurella cultured on Columbia blood agar or chocolate agar and demonstrated a variation in diameter of 1.5–2 mm after 24 h of incubation at 37 °C. Fourteen isolates were characterized by 16S rRNA gene sequencing and showed 98–100% identity with the highest similarity of 97–98% to the type strain of Pasteurella multocida . Partial rpoB gene sequences showed 97–100% identity among strains within the new taxon with the highest similarity of 90% to the type strain of Pasteurella stomatis , documenting a separate species status. Whole genomic sequences of ten strains showed the highest dDDH similarity of 25% to the genome of any Pasteurella species. The G+C content is 40.3 mol%. MALDI-TOF MS analysis clustered the isolates close together and clearly separated them from other Pasteurella species, making this the method of choice for identification. Based on monophyly and 97–98% 16S rRNA gene sequence identity to the type strain of P. multocida , as well as the presence of typical genotypic and phenotypic characteristics of Pasteurella sensu stricto like acid from (+)- d -galactose and (+)- d -mannose, the new species is classified in the genus Pasteurella as Pasteurella pantherarum . The type strain is RT1han1 ^T (=DSM 118579 ^T =CCUG 77951 ^T ), isolated from the oral cavity of a lion in a Danish zoo.

Opinion 133 addresses the unusual situation of two genus names that are homonyms and are also considered heterotypic synonyms. Furthermore, it clarifies the meaning of the term ‘homonym’ in the International Code of Nomenclature of Prokaryotes, as well as the implications of the absence of the term ‘isonym’ from that code. Isonyms are homotypic synonyms with the same spelling and as such are adequately regulated by the code. The Judicial Commission agrees that the names Methylacidiphilum caldifontis Awala et al . 2023, Methylacidiphilum Awala et al . 2023, Methylacidiphilaceae Awala et al . 2023 and Methylacidiphilales Awala et al . 2023 are illegitimate. The possible actions to resolve this illegitimacy are outlined. The request to conserve Methylacidiphilum Awala et al . 2023 over Methylacidiphilum Ratnadevi et al . 2023 is not granted. However, Methylacidiphilaceae Awala et al . 2023 and Methylacidiphilales Awala et al . 2023 are conserved with Methylacidiphilum Ratnadevi et al . 2023 as the type genus, thereby rendering them legitimate. Opinion 134 addresses two distinct enquiries arising from the same Request for an Opinion. The Judicial Commission confirms that the priority between Yokenella regensburgei Kosako et al . 1985 and its heterotypic synonym Koserella trabulsii Hickman-Brenner et al . 1985 may at present be unresolved. Considering previous statements by the Judicial Commission, the differences in the amount of usage between the two names and their medical relevance, the request is granted. The name Yokenella Kosako et al . 1985 is conserved over Koserella Hickman-Brenner et al . 1985, as is the epithet in Yokenella regensburgei Kosako et al . 1985 over the epithet in Koserella trabulsii Hickman-Brenner et al . 1985. The Judicial Commission also confirms that the epithet in Proteus inconstans (Ornstein 1920) Shaw and Clarke 1955 (Approved Lists 1980) has priority over the one in its homotypic synonym Providencia alcalifaciens (de Salles Gomes 1944) Ewing 1962 (Approved Lists 1980). However, it is doubtful whether this renders Providencia Ewing 1962 (Approved Lists 1980) illegitimate. There are other reasons to conserve the epithet in Providencia alcalifaciens (de Salles Gomes 1944) Ewing 1962 (Approved Lists 1980) over that in Proteus inconstans (Ornstein 1920) Shaw and Clarke 1955 (Approved Lists 1980), and this request is also granted.

Long-read sequencing technologies, particularly those developed by Oxford Nanopore Technologies (ONT), have transformed genome sequencing by enabling high-resolution analysis of complex microbial communities. Among ONT devices, the MinION remains affordable and scalable for low-resource settings. However, its limited onboard computing power constrains high-accuracy basecalling and limits its ability to address inherent sequencing errors effectively. To overcome these constraints, we assembled a streamlined in-house workflow that integrates at least five MinION devices with a GPU-powered workstation running Ubuntu 20 and MinKNOW. Rather than a new sequencing platform, this “home-made GridION” represents a practical integration of existing ONT devices with dedicated computing resources. At its core is a live basecalling pipeline capable of handling both FAST5 and POD5 file formats. The system supports high-throughput basecalling using Guppy on FAST5 files as well as Dorado on POD5 files, ensuring compatibility with both legacy and current ONT data standards. File monitoring is automated via inotifywait, enabling immediate detection of new files, real-time basecalling, and organized output of FASTQ batches. Beyond basecalling, we implemented an automated downstream pipeline for metagenomic analysis, enabling taxonomic profiling and detection of antimicrobial resistance genes (ARG). Tested on 10 hospital wastewater samples, the workflow generated at least 500,000 reads per sample within six hours, which were analysed for antimicrobial resistance gene abundance. This demonstrates its potential as an open, scalable hardware/software platform that extends the utility of MinION sequencing for microbial genomics in resource-limited environments. The setup can channel as many MinIONs as available USB ports, with a ratio of 1 MK1D for 1 TB of storage capacity on the associated computer.

Nine isolates from the gingiva of cheetahs kept in captivity were subjected to genotypic and phenotypic characterization. Sequencing of the 16S rRNA gene documented the highest identity of three representative strains to the type strain of Pasteurella multocida subsp. septica with 95.82%. The highest digital DNA–DNA hybridization predicted from the whole-genome sequence of strain 22721-9-1 ^T was to Haemophilus felis with 25.0%. The highest average nucleotide identity of strain 22721-9-1 ^T was also to H. felis with 74.36%, confirming a separate taxonomic status at species level. The phylogenetic comparison of concatenated conserved protein sequences showed a unique position of the taxon investigated, which qualifies for the status of a new genus, since the highest identity was found to Lonepinella koalarum with 83%, well below the upper threshold among genera of 91%. A new genus with one species, Reella acinonychis , is proposed. Production of indole and acid from sucrose and dulcitol separate the genus from most of the other genera of the Pasteurellaceae . Matrix-assisted laser desorption/ionization-time of flight MS analysis of the isolates clustered them close together and clearly separated them from other Pasteurellaceae species, allowing clear discrimination and making this the method of choice for identification. The G+C content of the type strain 22721-9-1 ^T (=DSM 118580 ^T =CCUG 77953 ^T ) is 38.53 mol%, calculated from the whole genome.

Investigation of clonal development of dominant persistent clones of avian pathogenic Escherichia coli (APEC) is important to understand their evolution and to gain knowledge to improve their control in poultry production. Whole-genomic sequencing, including hybrid assembled genomes of short and long reads, was used to analyse clonal persistence and evolution of APEC. Two vertically transferred E. coli clones, represented by ten isolates from sequence type (ST) 95-PFGE type 65 and eight isolates from ST131-PFGE type 47, were selected to identify genomic variations. The isolates had been sampled in broiler production during a period of 9 months in a previous study. The main differences among strains within each clone were related to plasmids, transposases, incomplete phage elements and amino acid substitutions which by far exceeded the genetic variation related to core-genome SNPs (cgSNPs). Fourier-transform infrared spectroscopy was, for the most part, only able to trace clones within the same ST. The genome-wide mutation rate was equivalent to 1.48 mutations per genome per year for ST95-PFGE65 and 2.86 for ST131-PFGE47, respectively. The most recent common ancestors were estimated back to 2009 for ST95-PFGE65 and to 2011 for ST131-PFGE47, with further divergence occurring in years until sampling in 2014–2015. The methodology introduced is able to trace the temporal origin of APEC clones. The conventional threshold of ten or fewer cgSNPs to include strains in the same clone did not consider any gain or loss of plasmids for the strains compared. On average, one plasmid transfer event was predicted every second year. For strains expected to be vertically transferred during the long production periods of great-grandparents over grandparents and parents to broilers, one to two plasmid transfers are therefore predicted, and several cgSNPs may be introduced, whereas up to one cgSNP is expected to be manifested during a broiler production cycle and rarely involving plasmid transfer.

The Ad Hoc Committee on Mitigating Changes in Prokaryotic Nomenclature was recently established under the auspices of the International Committee on Systematics of Prokaryotes to address the impact of name changes of prokaryotic taxa in databases, scientific publications and other sources, particularly agencies responsible for establishing protocols and standards for infectious disease control. Here, we report on the activities of the committee and the actions taken to date. A first key task of the Committee was to emphasize to stakeholders that the vast majority of name changes are not mandatory under the International Code of Nomenclature of Prokaryotes (ICNP), and to provide guidance. The second key task was to compile a List of Recommended Names (LoRN) for bacteria of human or veterinary medical importance. This list has been incorporated into the List of Prokaryotic names with Standing in Nomenclature (LPSN) and is easily and freely available from LPSN. The principles for compiling and updating the list are described. Use of this list, rather than automatically treating the most recently proposed name of a taxon that has obtained standing under the ICNP as the name to be applied to the taxon, will greatly reduce the burden on practitioners who need to use prokaryotic names, e.g. in human and veterinary medical routines, and the risk associated with new, unfamiliar names. Other databases are encouraged to use LoRN.

Pseudomonas aeruginosa is an opportunistic pathogen commonly associated with infections in hospitalized and immunocompromised patients due to its virulence and antimicrobial resistance. In the poultry industry, it has been associated with hatchery mortality. This study aimed to characterize P. aeruginosa isolated from pipped eggs, one-day-old chicks, and broiler carcasses obtained from a slaughterhouse in São Paulo state, Brazil. Nineteen strains of P. aeruginosa were selected and their virulence genes were amplified via PCR. Clonality analysis was performed using BOX-PCR, and three strains were selected for whole-genome sequencing (WGS). All isolates carried aprA, plcH, plcN, lasA, lasB, lasI, lasR, rhlAB, and phzH. The exoA gene was detected in 73.7% of strains, while algD was present in 21.1%. The exoY and exoT genes were present in 94.7% of strains (18/19), whereas exoS was present in 47.4% (9/19). None of the isolates harbored the exoU gene. BOX-PCR and phylogenetic analyses revealed diverse clonal patterns. The sequenced strains were classified as O3 ST116, O2 ST1649, and O3 ST1744. The presence of virulence and antimicrobial resistance determinants in poultry-associated strains underscores the need for surveillance, as these isolates may represent a source for transmission of P. aeruginosa to humans. Our findings highlight the importance of monitoring P. aeruginosa within poultry production and emphasize the value of genomic approaches to understand its diversity, evolution, and public health risks.