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Tobramycin was found to be less inhibitory to Flavobacterium columnare (formerly Flexibacter columnaris) than to other fish-associated bacteria. The selective capacity of Shieh medium, an isolation medium described for this species, was markedly enhanced by adding tobramycin at a concentration of 1 g/ml.

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Faeces from non-ruminating calves were found to contain several species of enterococci: Enterococcus avium, Ent. cecorum, Ent. durans, Ent. faecalis, Ent. faecium and Ent. hirae. Enterococcus faecalis was the most frequent. Few of these animals carried streptococci. Streptococcus bovis largely predominated in ruminating calves, young cattle and dairy cows. Other streptococci as well as enterococci were infrequent in dairy cows, but a variety of other streptococci and enterococci were found in the faeces of young ruminating animals.

In vitro studies of the interaction between pathogenic bacteria and the chicken intestinal epithelium are hampered by the lack of a host- and tissue-specific in vitro model. Therefore, a reproducible method for isolation and cultivation of chicken primary cecal epithelial cells was developed. Cecal crypts were isolated and cultured in vitro to form a semiconfluent layer of epithelial cells. Incubation of Salmonella enteritidis with these cells resulted in invasion. Pretreatment of the Salmonella bacteria with butyric acid resulted in a significant decrease of invasion of the bacteria in the chicken cecal epithelial cells, whereas pretreatment with acetic acid increased invasiveness. These interactions of S. enteritidis with primary chicken cecal epithelial cells were similar to the interactions with other epithelial cell types.

Background Implementation of Third-Generation Sequencing approaches for Whole Genome Sequencing (WGS) all-in-one diagnostics in human and veterinary medicine, requires the rapid and accurate generation of consensus genomes. Over the last years, Oxford Nanopore Technologies (ONT) released various new devices (e.g. the Flongle R9.4.1 flow cell) and bioinformatics tools (e.g. the in 2019-released Bonito basecaller), allowing cheap and user-friendly cost-efficient introduction in various NGS workflows. While single read, overall consensus accuracies, and completeness of genome sequences has been improved dramatically, further improvements are required when working with non-frequently sequenced organisms like Mycoplasma bovis. As an important primary respiratory pathogen in cattle, rapid M. bovis diagnostics is crucial to allow timely and targeted disease control and prevention. Current complete diagnostics (including identification, strain typing, and antimicrobial resistance (AMR) detection) require combined culture-based and molecular approaches, of which the first can take 1–2 weeks. At present, cheap and quick long read all-in-one WGS approaches can only be implemented if increased accuracies and genome completeness can be obtained. Results Here, a taxon-specific custom-trained Bonito v.0.1.3 basecalling model (custom-pg45) was implemented in various WGS assembly bioinformatics pipelines. Using MinION sequencing data, we showed improved consensus accuracies up to Q45.2 and Q46.7 for reference-based and Canu de novo assembled M. bovis genomes, respectively. Furthermore, the custom-pg45 model resulted in mean consensus accuracies of Q45.0 and genome completeness of 94.6% for nine M. bovis field strains. Improvements were also observed for the single-use Flongle sequencer (mean Q36.0 accuracies and 80.3% genome completeness). Conclusions These results implicate that taxon-specific basecalling of MinION and single-use Flongle Nanopore long reads are of great value to be implemented in rapid all-in-one WGS tools as evidenced for Mycoplasma bovis as an example.

Helicobacter pullorum is present in approximately one third of the chickens in Belgium.

Rapid identification of Mycoplasma bovis infections in cattle is a key factor to guide antimicrobial therapy and biosecurity measures. Recently, nanopore sequencing became an affordable diagnostic tool for both clinically relevant viruses and bacteria, but the diagnostic accuracy for M. bovis identification is undocumented. Therefore, in this study nanopore sequencing was compared to rapid identification of M. bovis with MALDI-TOF MS (RIMM), and triplex real-time PCR in a Bayesian latent class model (BLCM) for M. bovis in bronchoalveolar lavage fluid (BALf) obtained from calves. In practice, pooling of samples is often used to save money, but the influence on diagnostic accuracy has not been described for M. bovis . Therefore, a convenience sample of 17 pooled samples containing 5 individual BALf samples per farm was analyzed as well. The results of the pooled samples were compared to the individual samples, to determine sensitivity (Se) and specificity (Sp). The BLCM showed a good Se (77.3%; 95% Credible Interval: 57.8%-92.8%) and high Sp (97.4%; 91.5%-99.7%) for nanopore sequencing compared to RIMM (Se: 93.0%; 76.8%-99.5%, Sp: 91.3; 82.5%-97.0%) and real-time PCR (Se: 94.6%; 89.7%-97.7%, Sp: 86.0%; 76.1-93.6%). Se and Sp of pooled analysis for M. bovis were 85.7% (95% confidence interval: 59.8-111.6%) and 90.0% (71.4-108.6%%) for nanopore sequencing and 100% (100%-100%) and 88.9% (68.4-109.4%) for RIMM, respectively. In conclusion, nanopore sequencing is a rapid, reliable tool for the identification of M. bovis . To reduce costs and increase the chance of M. bovis identification, pooling of 5 samples for nanopore sequencing and RIMM is possible.