Nicoletella

Nicoletella is a monotypic genus in the family Pasteurellaceae as determined by a polyphasic approach using 19 strains. They are Gram‐negative, nonmotile pleomorphic rods. Isolates do not grow on MacConkey agar and do not require hemin or β‐NAD. They reduce nitrate to nitrite and are catalase‐, oxidase‐, and urease‐positive. DNA–DNA hybridization data and multilocus phylogenetic analysis, including 16S rRNA gene, rpoB, and infB sequencing, clearly placed Nicoletella as a discrete genus in the family Pasteurellaceae. Otherwise, the only currently known species of the genus N. semolina is biochemically inert. Growth is fastidious, and the isolates have a distinctive colony morphology, with the colonies being dry and waxy and looking like a semolina particle that can be moved around on an agar plate without losing their shape. DNA G + C content (mol%): 39.4 (genome sequence). Type species: Nicoletella semolina Kuhnert et al. 2004, VL102

Prediction of whole-genome DNA-DNA similarity, determination of G+C content and phylogenetic analysis within the family Pasteurellaceae by multilocus sequence analysis (MLSA)

Genome predictions based on selected genes would be a very welcome approach for taxonomic studies, including DNA-DNA similarity, G+C content and representative phylogeny of bacteria. At present, DNA-DNA hybridizations are still considered the gold standard in species descriptions. However, this method is time-consuming and troublesome, and datasets can vary significantly between experiments as well as between laboratories. For the same reasons, full matrix hybridizations are rarely performed, weakening the significance of the results obtained. The authors established a universal sequencing approach for the three genes recN, rpoA and thdF for the Pasteurellaceae, and determined if the sequences could be used for predicting DNA-DNA relatedness within the family. The sequence-based similarity values calculated using a previously published formula proved most useful for species and genus separation, indicating that this method provides better resolution and no experimental variation compared to hybridization. By this method, cross-comparisons within the family over species and genus borders easily become possible. The three genes also serve as an indicator of the genome G+C content of a species. A mean divergence of around 1 % was observed from the classical method, which in itself has poor reproducibility. Finally, the three genes can be used alone or in combination with already-established 16S rRNA, rpoB and infB gene-sequencing strategies in a multisequence-based phylogeny for the family Pasteurellaceae. It is proposed to use the three sequences as a taxonomic tool, replacing DNA-DNA hybridization

Mycoplasma mycoides subsp. capri and Mycoplasma mycoides subsp. mycoides LC can be grouped into a single subspecies

Mycoplasma mycoides subsp. capri and Mycoplasma mycoides subsp. mycoides LC can be combined into one taxon on the basis of several contributions on both DNA sequence and protein analyses reported in the literature. Moreover, for the differentiation and identification of mycoplasmas of the "mycoides cluster", we investigated the rpoB gene, encoding the beta-subunit of the RNA polymerase. A segment of 527 bp of the rpoB gene was amplified from 31 strains of ruminant mycoplasmas by PCR. The nucleotide sequences were determined and aligned, and accurate genetic relationships were calculated. Cluster analysis of rpoB DNA allowed species differentiation within the "mycoides cluster" and confirmed that M. mycoides subsp. capri and M. mycoides subsp. mycoides LC cannot be distinguished from each other. "Mycoplasma mycoides subsp. capri" is proposed as a common name for both subspecies

Frederiksenia

The description of Frederiksenia is based on the characterization of 24 strains from five European countries and were mainly isolated from dogs and human dog‐bite wounds. The strains were previously classified as Bisgaard taxon 16 and formed a phenotypically and genetically homogenous group within the family Pasteurellaceae. The genus is phenotypically similar to Pasteurella, but phylogenetically forms a clearly separated monophyletic branch based on 16S rRNA, rpoB, infB, and recN gene sequences. Frederiksenia showed closest genetic relationship with Bibersteinia trehalosi. Predicted genome similarity values based on the recN gene sequences between taxon 16 isolates and the type strains of type species of known genera of Pasteurellaceae were below the genus level. Furthermore, MALDI‐TOF clearly separated it from all other genera of Pasteurellaceae, showing a characteristic peak combination. The genus is currently formed by a single species Frederiksenia canicola. Major whole‐cell fatty acids for the type strain of this species are C14:0, C16:0, C18:0, and C16:1 ω7c/C15:0 iso 2OH. Major respiratory quinones are menaquinone‐8, ubiquinone‐8, and demethylmenaquinone‐8. DNA G + C content (mol%): 42.6 by genome analysis of the type strain DSM 25797T. Type species: Frederiksenia canicola Korczak et al. 2014, VL158

Emended description of Actinobacillus capsulatus Arseculeratne 1962, 38AL

The taxonomic position of Actinobacillus capsulatus, a member of the family Pasteurellaceae found in rabbits, hares and hamsters, has been challenged. 16S rRNA gene (rrs) sequence data show the species to be heterogeneous. Using a polyphasic approach, 23 strains that were identified previously as belonging, or closely related, to A. capsulatus were analysed. Eighty characters were included in the phenotypic analysis. Phylogenetic analysis was done based on rrs, rpoB, infB and recN sequences. In addition, the recN sequence similarities were used to calculate the whole-genome sequence relatedness of all strains investigated as well as that with other members of the family Pasteurellaceae. The phenotypic analysis allowed identification of five groups. The major group of 17 strains could be classified as A. capsulatus. Two hamster isolates were closely related to A. capsulatus but differed in a few characters. Single isolates from a rabbit and snowshoe-hare were phenotypically related to Actinobacillus suis. One rabbit isolate was related to the genus Mannheimia, while another isolate could not be classified phenotypically with known taxa. The phylogenetic analysis confirmed the phenotypic grouping. In contrast to the rrs-based tree, the A. capsulatus strains clustered unambiguously with the type species and related species of the genus Actinobacillus in the rpoB-, infB- and recN-based trees. Genome similarity comparison using recN finally confirmed the high genomic relationship of the A. capsulatus strains with the type species and related species of the genus Actinobacillus and allowed a clear assignment of the other unrelated strains to the phenotypic and phylogenetic clusters outlined. The present findings allow the description of A. capsulatus to be emended and separate it more clearly from other species, both phenotypically and genotypically. The type strain of A. capsulatus is CCUG 12396(T) (=Frederiksen 243(T)=ATCC 51571(T)=NCTC 11408(T)=CIP 103283(T))

Multilocus sequence typing (MLST) of Mycoplasma hyopneumoniae: a diverse pathogen with limited clonality

A multilocus sequence typing (MLST) scheme was established and evaluated for Mycoplasma hyopneumoniae, the etiologic agent of enzootic pneumonia in swine with the aim of defining strains. Putative target genes were selected by genome sequence comparisons. Out of 12 housekeeping genes chosen and experimentally validated, the 7 genes efp, metG, pgiB, recA, adk, rpoB, and tpiA were finally used to establish the MLST scheme. Their usefulness was assessed individually and in combination using a set of well-defined field samples and strains of M. hyopneumoniae. A reduction to the three targets showing highest variation (adk, rpoB, and tpiA) was possible resulting in the same number of sequence types as using the seven targets. The established MLST approach was compared with the recently described typing method using the serine-rich repeat motif-encoding region of the p146 gene. There was coherence between the two methods, but MLST resulted in a slightly higher resolution. Farms recognized to be affected by enzootic pneumonia were always associated with a single M. hyopneumoniae clone, which in most cases differed from farm to farm. However, farms in close geographic or operational contact showed identical clones as defined by MLST typing. Population analysis showed that recombination in M. hyopneumoniae occurs and that strains are very diverse with only limited clonality observed. Elaborate classical MLST schemes using multiple targets for M. hyopneumoniae might therefore be of limited value. In contrast, MLST typing of M. hyopneumoniae using the three genes adk, rpoB, and tpiA seems to be sufficient for epidemiological investigations by direct amplification of target genes from lysate of clinical material without prior cultivation

Comparison of genotypes and antibiotic resistances of Campylobacter jejuni and Campylobacter coli on chicken retail meat and at slaughter

Multilocus sequence typing (MLST) and antibiotic resistance patterns of Campylobacter jejuni and Campylobacter coli from retail chicken meat showed high overlap with isolates collected at slaughterhouses, indicating little selection along the production chain. They also showed significant common sequence types with human clinical isolates, revealing chicken meat as a likely source for human infection

Phylogeny and prediction of genetic similarity of Cronobacter and related taxa by multilocus sequence analysis (MLSA)

Multilocus sequence analysis (MLSA) based on recN, rpoA and thdF genes was done on more than 30 species of the family Enterobacteriaceae with a focus on Cronobacter and the related genus Enterobacter. The sequences provide valuable data for phylogenetic, taxonomic and diagnostic purposes. Phylogenetic analysis showed that the genus Cronobacter forms a homogenous cluster related to recently described species of Enterobacter, but distant to other species of this genus. Combining sequence information on all three genes is highly representative for the species' %GC-content used as taxonomic marker. Sequence similarity of the three genes and even of recN alone can be used to extrapolate genetic similarities between species of Enterobacteriaceae. Finally, the rpoA gene sequence, which is the easiest one to determine, provides a powerful diagnostic tool to identify and differentiate species of this family. The comparative analysis gives important insights into the phylogeny and genetic relatedness of the family Enterobacteriaceae and will serve as a basis for further studies and clarifications on the taxonomy of this large and heterogeneous family