Two novel Bartonella (sub)species isolated from edible dormice (Glis glis): hints of cultivation stress-induced genomic changes.

Bartonelloses are neglected emerging infectious diseases caused by facultatively intracellular bacteria transmitted between vertebrate hosts by various arthropod vectors. The highest diversity of Bartonella species has been identified in rodents. Within this study we focused on the edible dormouse (Glis glis), a rodent with unique life-history traits that often enters households and whose possible role in the epidemiology of Bartonella infections had been previously unknown. We identified and cultivated two distinct Bartonella sub(species) significantly diverging from previously described species, which were characterized using growth characteristics, biochemical tests, and various molecular techniques including also proteomics. Two novel (sub)species were described: Bartonella grahamii subsp. shimonis subsp. nov. and Bartonella gliris sp. nov. We sequenced two individual strains per each described (sub)species. During exploratory genomic analyses comparing two genotypes ultimately belonging to the same species, both factually and most importantly even spatiotemporally, we noticed unexpectedly significant structural variation between them. We found that most of the detected structural variants could be explained either by prophage excision or integration. Based on a detailed study of one such event, we argue that prophage deletion represents the most probable explanation of the observed phenomena. Moreover, in one strain of Bartonella grahamii subsp. shimonis subsp. nov. we identified a deletion related to Bartonella Adhesin A, a major pathogenicity factor that modulates bacteria-host interactions. Altogether, our results suggest that even a limited number of passages induced sufficient selective pressure to promote significant changes at the level of the genome.

Easy, Robust, and Repeatable Online Acid Cleavage of Proteins in Mobile Phase for Fast Quantitative LC-MS Bottom-Up Protein Analysis─Application for Ricin Detection.

Sample preparation involving the cleavage of proteins into peptides is the first critical step for successful bottom-up proteomics and protein analyses. Time- and labor-intensiveness are among the bottlenecks of the commonly used methods for protein sample preparation. Here, we report a fast online method for postinjection acid cleavage of proteins directly in the mobile phase typically used for LC-MS analyses in proteomics. The chemical cleavage is achieved in 0.1% formic acid within 35 s in a capillary heated to 195 °C installed upstream of the analytical column, enabling the generated peptides to be separated. The peptides generated by the optimized method covered the entire sequence except for one amino acid of trastuzumab used for the method development. The qualitative results are extraordinarily stable, even over a long period of time. Moreover, the method is also suitable for accurate and repeatable quantification. The procedure requires only one manual step, significantly decreasing sample transfer losses. To demonstrate its practical utility, we tested the method for the fast detection of ricin. Ricin can be unambiguously identified from an injection of 10 ng, and the results can be obtained within 7-8 min after receiving a suspicious sample. Because no sophisticated accessories and no additional reagents are needed, the method can be seamlessly transferred to any laboratory for high-throughput proteomic workflows.

The first detection of relapsing fever spirochete Borrelia miyamotoi in Ixodes ricinus ticks from the northeast Czech Republic.

Borrelia miyamotoi, a relapsing fever spirochete, is considered a human pathogen. Knowledge of this borrelia is currently limited. Data about its potential impact on public health, circulation in nature, or its occurrence in natural environments are insufficient. For our study, a total of 505 questing Ixodes ricinus ticks (337 nymphs, 85 females and 83 males) from Hradec Králové Region in the Czech Republic were collected. Additionally, 160 winged Lipoptena deer keds from Hradec Králové Region, from Pardubice Region, Czech Republic, and from one location in western Slovakia were collected. The presence of B. miyamotoi in ticks and deer keds was determined using polymerase chain reaction (PCR) targeting a gene encoding glycerophosphodiester phosphodiesterase (glpQ), antigenic protein specific to the relapsing fever spirochetes. Borrelia miyamotoi was identified in six nymphs and four females of I. ricinus ticks. The overall prevalence was 2%. None of the examined Lipoptena specimens were found to be infected. Although no human case of infection with B. miyamotoi has been reported in the Czech Republic yet, this spirochete is widespread in ticks, and therefore the risk of human infection exists.

A Complex In Vitro Degradation Study on Polydioxanone Biliary Stents during a Clinically Relevant Period with the Focus on Raman Spectroscopy Validation.

Biodegradable biliary stents are promising treatments for biliary benign stenoses. One of the materials considered for their production is polydioxanone (PPDX), which could exhibit a suitable degradation time for use in biodegradable stents. Proper material degradation characteristics, such as sufficient stiffness and disintegration resistance maintained for a clinically relevant period, are necessary to ensure stent safety and efficacy. The hydrolytic degradation of commercially available polydioxanone biliary stents (ELLA-CS, Hradec Králové, Czech Republic) in phosphate-buffered saline (PBS) was studied. During 9 weeks of degradation, structural, physical, and surface changes were monitored using Raman spectroscopy, differential scanning calorimetry, scanning electron microscopy, and tensile and torsion tests. It was found that the changes in mechanical properties are related to the increase in the ratio of amorphous to crystalline phase, the so-called amorphicity. Monitoring the amorphicity using Raman spectroscopy has proven to be an appropriate method to assess polydioxanone biliary stent degradation. At the 1732 cm-1 Raman peak, the normalized shoulder area is less than 9 cm-1 which indicates stent disintegration. The stent disintegration started after 9 weeks of degradation in PBS, which agrees with previous in vitro studies on polydioxanone materials as well as with in vivo studies on polydioxanone biliary stents.

Quantitative Proteome Profiling of Coxiella burnetii Reveals Major Metabolic and Stress Differences Under Axenic and Cell Culture Cultivation.

Coxiella burnetii is the causative agent of the zoonotic disease Q fever. To date, the lipopolysaccharide (LPS) is the only defined and characterized virulence determinant of C. burnetii. In this study, proteome profiles of C. burnetii Nine Mile phase I (RSA 493, NMI) and its isogenic Nine Mile phase II (RSA 439 NMII) isolate with a deep rough LPS were compared on L-929 mouse fibroblasts and in complex (ACCM-2), and defined (ACCM-D) media. Whole proteome extracts were analyzed using a label-free quantification approach. Between 659 and 1,046 C. burnetii proteins of the 2,132 annotated coding sequences (CDS) were identified in any particular experiment. Proteome profiles clustered according to the cultivation conditions used, indicating different regulation patterns. NMI proteome profiles compared to NMII in ACCM-D indicate transition from an exponential to a stationary phase. The levels of regulatory proteins such as RpoS, CsrA2, UspA1, and UspA2 were increased. Comparison of the oxidative stress response of NMI and NMII indicated that ACCM-2 represents a high oxidative stress environment. Expression of peroxidases, superoxide dismutases, as well as thioredoxins was increased for NMI. In contrast, in ACCM-D, only osmoregulation seems to be necessary. Proteome profiles of NMII do not differ and indicate that both axenic media represent similar oxidative stress environments. Deep rough LPS causes changes of the outer membrane stability and fluidity. This might be one reason for the observed differences. Proteins associated with the T4SS and Sec translocon as well as several effector proteins were detectable under all three conditions. Interestingly, none of these putatively secreted proteins are upregulated in ACCM-2 compared to ACCM-D, and L-929 mouse fibroblasts. Curiously, a higher similarity of proteomic patterns (overlapping up- and downregulated proteins) of ACCM-D and bacteria grown in cell culture was observed. Particularly, the proteins involved in a better adaptation or homeostasis in response to the harsh environment of the parasitophorous vacuole were demonstrated for NMI. This semi-quantitative proteomic analysis of C. burnetii compared axenically grown bacteria to those propagated in cell culture.