What can be lost? Genomic perspective on the lipid metabolism of Mucoromycota

Mucoromycota is a phylum of early diverging fungal (EDF) lineages, of mostly plant-associated terrestrial fungi. Some strains have been selected as promising biotechnological organisms due to their ability to produce polyunsaturated fatty acids and efficient conversion of nutrients into lipids. Others get their lipids from the host plant and are unable to produce even the essential ones on their own. Following the advancement in EDF genome sequencing, we carried out a systematic survey of lipid metabolism protein families across different EDF lineages. This enabled us to explore the genomic basis of the previously documented ability to produce several types of lipids within the fungal tree of life. The core lipid metabolism genes showed no significant diversity in distribution, however specialized lipid meta- bolic pathways differed in this regard among different fungal lineages. In total 165 out of 202 genes involved in lipid metabolism were present in all tested fungal lineages, while remaining 37 genes were found to be absent in some of fungal lineages. Duplications were observed for 69 genes. For the first time we demonstrate that ergosterol is not being produced by several independent groups of plant-associated fungi due to the losses of different ERG genes. Instead, they possess an ancestral pathway leading to the synthesis of cholesterol, which is absent in other fungal lineages. The lack of diacylglycerol kinase in both Mortierellomycotina and Blastocladiomycota opens the ques- tion on sterol equilibrium regulation in these organisms. Early diverging fungi retained most of beta oxidation com- ponents common with animals including Nudt7, Nudt12 and Nudt19 pointing at peroxisome divergence in Dikarya. Finally, Glomeromycotina and Mortierellomycotina representatives have a similar set of desaturases and elongases related to the synthesis of complex, polyunsaturated fatty acids pointing at an ancient expansion of fatty acid metab- olism currently being explored by biotechnological studies

Molecular Characterization of <em>Mycobacterium</em> spp. Isolated from Cattle and Wildlife in Poland

Although Poland is officially tuberculosis (TB) free, meaning that less than 0.1% of her cattle herd is TB-positive, the problem of bovine TB in Poland may be re-emerging: its presence has recently been confirmed in domestic and companion animals, wildlife such as the European bison, and even humans. The aim of this chapter was to review all reports of bovine TB in Poland described to date, with particular emphasis on molecular studies, and determine further research directions. These studies include a range of molecular methods for diagnosis, including genotyping, spoligotyping and MIRU- VNTR; such methods successfully identifies a tuberculosis-positive European bison as the source of wild boar infection in the Bieszczady Mountains based on its spoligotype. This chapter argues that identified trains should be better archived, as such records would allow detailed epidemiological investigations and shed greater light on the activity of Mycobacterium spp. The current epidemiological situation in Poland highlights the need for further studies to determine epidemiological links and confirm possible routes of transmission based on whole genome sequencing; this need is accentuated by the zoonotic potential of such infections and the endangered species at risk

Biopsy and tracheobronchial aspirates as additional tools for the diagnosis of bovine tuberculosis in living European bison (bison bonasus)

CITATION: Didkowska, Anna et al. 2020. Biopsy and tracheobronchial aspirates as additional tools for the diagnosis of bovine tuberculosis in living European bison (bison bonasus). Animals, 10(11):2017, doi:10.3390/ani10112017.The original publication is available at: https://www.mdpi.comENGLISH ABSTRACT: The diagnosis of bovine tuberculosis (BTB) in living wildlife remains a complex problem, and one of particular importance in endangered species like European bison (Bison bonasus). To identify infection and avoid the unnecessary culling of such valuable individuals, current best practice requires the collection and culture of material from living animals, as mycobacteria isolation remains the gold standard in BTB diagnosis. However, such isolation is challenging due to the need for the immobilization and collection of appropriate clinical material, and because of the sporadic shedding of mycobacteria. In the present study, we evaluated the potential of sampling for the detection of BTB in a group of seven living European bison suspected of being infected with Mycobacterium caprae. The specimens were collected both as swabs from the nasal and pharyngeal cavities, tracheobronchial aspirates (TBA), ultrasound-guided biopsies from lateral retropharyngeal lymph nodes, and post mortem, from mandibular, retropharyngeal and mediastinal lymph nodes. Clinical samples were tested for mycobacterial species via mycobacteriological culture and PCR. M. caprae was isolated from collected material in two out of four living infected individuals (TBA, biopsy) and mycobacterialDNAwas detected in three out of four (TBA, pharyngeal swab) bison. This is the first report of isolation of M. caprae in living European bison. Our findings demonstrate the value of diagnostic tests based on both molecular testing and culture in European bison and confirm the respiratory shedding of viable M. caprae in this host species.Publisher's versio

Two centrifugal flotation techniques for counting gastrointestinal parasite eggs and oocysts in alpaca faeces

The alpaca (Vicugna pacos) is a camelid native to South America, but the species has wide distribution outside its natural habitat and is found in various countries on other continents, Poland being one in Europe. Parasitic infections affect the productivity and health of alpacas. The aim of the study was to estimate the parasite loads in alpacas kept in Poland with the use of two direct centrifugal flotation methods

MIRU-VNTR Typing of Atypical Mycobacteria Isolated from the Lymph Nodes of Slaughtered Pigs from Poland

No regulations currently require the excision of lymph nodes from pig carcasses or the thermal processing of pork before consumption. Therefore, the presence of anatomopathological lesions with signs of coagulation necrosis in lymph nodes from pigs during post-mortem inspection is concerning, as is the increasing incidence of mycobacteriosis in humans. Therefore, the aim of the present study is to verify whether mycobacteria can be isolated from tuberculous-like lesions in mandibular lymph nodes in slaughtered pigs, and whether further molecular analysis based on MIRU-VNRT, used to identify mycobacteria from the Mycobacterium avium complex, can indicate zoonotic potential. Forty of the fifty isolates from the lymph nodes with signs of coagulation necrosis were classified as Mycobacterium avium complex. MIRU-VNTR analysis allowed for the isolation of six strains, one of which was classified as M. avium subsp. paratuberculosis (MAP). Our findings confirm the presence of atypical mycobacteria in the lymph nodes of slaughtered pigs. While the isolated strains (other than MAP) do not pose a significant or direct health risk to consumers, further research and monitoring are necessary. Atypical mycobacteria can cause a wide range of diseases in children and compromised adults, and often show resistance to many classes of antibiotics, including those used to treat tuberculosis

Legal Obstacles in the Eradication of Bovine Tuberculosis in European bison (Bison bonasus)&mdash;A Threat to an Effective Reintroduction Strategy

In Poland, bovine tuberculosis (BTB) is most often detected in cattle, although some cases have also been reported in pigs and in other non-domestic species. BTB is believed to be mainly present in the Bieszczady region, in the south-eastern part of the country. The present study analyses the practical applications of the law regarding the eradication of tuberculosis among European bison in Poland, as well as the influence of legal rules in species conservation effects. Its aim is to present and evaluate the effectiveness of legal provisions in selected cases of BTB detected in European bison. The analysis highlights key &ldquo;critical points&rdquo; in the management of cases of BTB in European bison, which resulted from the problematic interpretation and application of the existing legal provisions. Findings indicate that before the Animal Health Law, the eradication of BTB in European bison in Poland was not regulated clearly enough by the applicable laws in force prior to 2021. This posed a threat to an effective reintroduction strategy for bison based on creating larger metapopulations and maintaining small, isolated reservoir herds (breading centers) for fallback in the case of infectious disease. It should be emphasized that in the current legal system, there is no doubt that a District Veterinary Officer has the competence to prevent and control tuberculosis in European bison

Intra-Palpebral Tuberculin Skin Test and Interferon Gamma Release Assay in Diagnosing Tuberculosis Due to <i>Mycobacterium caprae</i> in European Bison (<i>Bison bonasus</i>)

Despite the threat posed by tuberculosis (TB) to the protected European bison (Bison bonasus), no validated TB tests exist for this species. This pilot study evaluates two tests based on detecting cellular immunity for this purpose: interferon gamma release assay (IGRA) and tuberculin skin test (TST). Ten animals were subjected to ante-mortem and post-mortem examinations. IGRA was performed using a commercial test, and the comparative TST was performed in the eyelids. The lesions were assessed post-mortem and material was collected for mycobacterial culture. The isolated strains were subjected to genotyping. At post-mortem examination, five out of ten individuals demonstrated both tuberculous lesions and positive culture results (Mycobacterium caprae). Compared to the palpebral TST, the findings of the IGRA are easier to interpret when diagnosing tuberculosis in European bison

Mycobacterial Interspersed Repeat Unit–Variable Number Tandem Repeat Typing of <i>Mycobacterium avium</i> Strains Isolated from the Lymph Nodes of Free-Living Carnivorous Animals in Poland

Non-tuberculous mycobacteria (NTM) are ubiquitous organisms, of which some, especially those of the Mycobacterium avium complex (MAC), may be opportunistic animal and human pathogens. Infection with NTM can interfere with tuberculosis (TB) diagnosis and induce zoonoses, especially in immunocompromised individuals. Diseases caused by NTM have become more readily recognized; however, they are likely still underestimated. In this study, we identified and genotyped Mycobacterium avium strains that were isolated during TB monitoring among free-living carnivorous animals from southeastern Poland. In 2011–2020, lymph node samples from 192 such animals were tested for mycobacteria. A total of 41 isolates of M. avium strains were detected with the use of IS901, IS900, IS1245, and mycobacterial interspersed repeat unit–variable number tandem repeat (MIRU-VNTR) identification. Thirty-three were identified as M. avium subsp. avium. These strains were derived from 1 beech marten (Martes foina), 1 common buzzard (Buteo buteo), 2 European badgers (Meles meles), 3 wolves (Canis lupus), and 26 red foxes (Vulpes vulpes). One strain isolated from a wolf was identified as M. avium subsp. hominissuis. The results show the widespread occurrence of MAC bacilli in the studied environment and additionally comprise new data on the molecular characteristics of M. avium subspecies carried by free-living southeastern Polish carnivores