MDR tuberculosis and non-compliance with therapy

The emergence of multidrug-resistant (MDR) tuberculosis is a worldwide public health problem. We reported a case of pulmonary MDR tuberculosis in a 41-year-old man with diabetes from the West Bank, Palestine. 1 The bacteria belonged to the Beijing family, which is highly virulent and easily disseminated. 2 The patient withdrew from treatment after 2 years while still sputum-positive. Despite persistent efforts of the tuberculosis directly observed treatment programme, he disappeared and cannot be located. The patient might have fled to a neighbouring country, and there is a risk that he will pass on MDR tuberculosis to people with whom he has contact

Simultaneous detection of Mycobacterium bovis and M. tuberculosis in an apparentlyimmunocompetent patient

Mycobacterium tuberculosis remains the main cause of human tuberculosis (TB), with an unknown proportion of cases caused by M. bovis. Here we describe a case of pulmonary TB caused by mixed infection as studied from sequential sputum sampling and isolation of M. tuberculosis and M. bovis using a reverse dot blot (RDB) assay

Mitochondrial Phylogeography Illuminates the Origin of the Extinct Caspian Tiger and Its Relationship to the Amur Tiger

The Caspian tiger (Panthera tigris virgata) flourished in Central Asian riverine forest systems in a range disjunct from that of other tigers, but was driven to extinction in 1970 prior to a modern molecular evaluation. For over a century naturalists puzzled over the taxonomic validity, placement, and biogeographic origin of this enigmatic animal. Using ancient-DNA (aDNA) methodology, we generated composite mtDNA haplotypes from twenty wild Caspian tigers from throughout their historic range sampled from museum collections. We found that Caspian tigers carry a major mtDNA haplotype differing by only a single nucleotide from the monomorphic haplotype found across all contemporary Amur tigers (P. t. altaica). Phylogeographic analysis with extant tiger subspecies suggests that less than 10,000 years ago the Caspian/Amur tiger ancestor colonized Central Asia via the Gansu Corridor (Silk Road) from eastern China then subsequently traversed Siberia eastward to establish the Amur tiger in the Russian Far East. The conservation implications of these findings are far reaching, as the observed genetic depletion characteristic of modern Amur tigers likely reflects these founder migrations and therefore predates human influence. Also, due to their evolutionary propinquity, living Amur tigers offer an appropriate genetic source should reintroductions to the former range of the Caspian tiger be implemented

Evolutionary changes in the genome of Mycobacterium tuberculosis and the human genome from 9000 years BP until modern times

The demonstration of Mycobacterium tuberculosis DNA in ancient skeletons gives researchers an insight into its evolution. Findings of the last two decades sketched the biological relationships between the various species of tubercle bacilli, the time scale involved, their possible origin and dispersal. This paper includes the available evidence and on-going research. In the submerged Eastern Mediterranean Neolithic village of Atlit Yam (9000 BP), a human lineage of M. tuberculosis, defined by the TbD1 deletion in its genome, was demonstrated. An infected infant at the site provides an example of active tuberculosis in a human with a naïve immune system. Over 4000 years later tuberculosis was found in Jericho. Urbanization increases population density encouraging M. tuberculosis/human co-evolution. As susceptible humans die of tuberculosis, survivors develop genetic resistance to disease. Thus in 18th century Hungarian mummies from V ac, 65% were positive for tuberculosis yet a 95-year-old woman had clearly survived a childhood Ghon lesion. Whole genome studies are in progress, to detect changes over the millennia both in bacterial virulence and also host susceptibility/resistance genes that determine the NRAMP protein and Killer Cell Immunoglobulin-like Receptors (KIRs). This paper surveys present evidence and includes initial findings.The contribution made by our many collaborators, researchers and students is gratefully acknowledged. Special acknowledgement is due to Dr Angela Gernaey (deceased) who helped pioneer the early mycolic acid work on the bison bone

Detection and Molecular Characterization of 9000-Year-Old Mycobacterium tuberculosis from a Neolithic Settlement in the Eastern Mediterranean

Background: Mycobacterium tuberculosis is the principal etiologic agent of human tuberculosis. It has no environmental reservoir and is believed to have co-evolved with its host over millennia. This is supported by skeletal evidence of the disease in early humans, and inferred from M. tuberculosis genomic analysis. Direct examination of ancient human remains for M. tuberculosis biomarkers should aid our understanding of the nature of prehistoric tuberculosis and the host/pathogen relationship.Methodology/Principal Findings: We used conventional PCR to examine bone samples with typical tuberculosis lesions from a woman and infant, who were buried together in the now submerged site of Atlit-Yam in the Eastern Mediterranean, dating from 9250-8160 years ago. Rigorous precautions were taken to prevent contamination, and independent centers were used to confirm authenticity of findings. DNA from five M. tuberculosis genetic loci was detected and had characteristics consistent with extant genetic lineages. High performance liquid chromatography was used as an independent method of verification and it directly detected mycolic acid lipid biomarkers, specific for the M. tuberculosis complex.Conclusions/Significance: Human tuberculosis was confirmed by morphological and molecular methods in a population living in one of the first villages with evidence of agriculture and animal domestication. The widespread use of animals was not a source of infection but may have supported a denser human population that facilitated transmission of the tubercle bacillus. The similarity of the M. tuberculosis genetic signature with those of today gives support to the theory of a long-term co-existence of host and pathogen

Towards a COST MOBILISE Guideline for Long Term Preservation and Archiving of Data Constructs from Scientific Collections Facilities

COST (European Cooperation in Science and Technology) is a funding organisation for research and innovation networks. One of the objectives of the COSTAction called “Mobilising Data, Policies and Experts in Scientific Collections“ (MOBILISE) is to work on documents for expert training with broad involvement of professionals from the participating European countries. The guideline presented here in its general concept will address principles, strategies and standards for long term preservation and archiving of data constructs (data packages, data products) as addressed by and under control of the scientific collections community. The document is being developed as part of the MOBILISE Action targeted towards primarily scientific staff at natural scientific collection facilities, as well as management bodies of collections like museums, herbaria and information technology personnel less familiar with data archiving principles and routines.The challenges of big data storage and (distributed, cloud-based) storage solutions as well as that of data mirroring, backing up, synchronisation and publication in productive data environments are well addressed by documents, guidelines and online platforms, e.g., in the DISSCo knowledge base (see Hardisty et al. (2020)) and as part of concepts of the European Open Science Cloud (EOSC). Archival processes and the resulting data constructs, however, are often left outside of the considerations. This is a large gap because archival issues are not only simple technical ones as addressed by the term “bit preservation” but also envisage a number of logical, functional, normative, administrative and semantic issues as addressed by the term “functional long-term archiving”.The main target digital object types addressed by this COST MOBILISE Guideline are data constructs called Digital or Digital Extended Specimens and data products with the persistent identifier assignment lying under the authority of scientific collections facilities. Such digital objects are specified according to the Digital Object Architecture (DOA , see Wittenburg et al. 2018) and similar abstract models introduced by Harjes et al. (2020) and Lannom et al. (2020). The scientific collection-specific types are defined following evolving concepts in the context of the Consortium of European Taxonomic Facilities (CETAF), the research infrastructure DiSSCo (Distributed System of Scientific Collections), and the Biodiversity Information Standards (TDWG). Archival processes are described following the OAIS (Open Archival Information System) reference model. The archived objects should be reusable in the sense of the FAIR (Findable, Accessible, Interoperable, and Reusable) guiding principles. Organisations like national (digital) archives, computing or professional (domain-specific) data centers as well as libraries might offer specific archiving services and act as partner organisations of scientific collections facilities.The guideline consists of key messages that have been defined. They address the collection community, especially the staff and leadership of taxonomic facilities. Aspects of several groups of stakeholders are discussed as well as cost models. The guideline does not recommend specific solutions for archiving software and workflows. Supplementary information is delivered via a wiki-based platform for the COST MOBILISE Archiving Working Group WG4. 

Fecal microbiota of the synanthropic golden jackal (Canis aureus)

Abstract The golden jackal (Canis aureus), is a medium canid carnivore widespread throughout the Mediterranean region and expanding into Europe. This species thrives near human settlements and is implicated in zoonoses such as rabies. This study explores for the first time, the golden jackal fecal microbiota. We analyzed 111 fecal samples of wild golden jackals using 16S rRNA amplicon sequencing the connection of the microbiome to animal characteristics, burden of pathogens and geographic and climate characteristics. We further compared the fecal microbiota of the golden jackal to the black-backed jackal and domestic dog. We found that the golden jackal fecal microbiota is dominated by the phyla Bacteroidota, Fusobacteriota and Firmicutes. The golden jackal fecal microbiota was associated with different variables, including geographic region, age-class, exposure to rabies oral vaccine, fecal parasites and toxoplasmosis. A remarkable variation in the relative abundance of different taxa was also found associated with different variables, such as age-class. Linear discriminant analysis effect size (LEfSe) analysis found abundance of specific taxons in each region, Megasphaera genus in group 1, Megamonas genus in group 2 and Bacteroides coprocola species in group 3. We also found a different composition between the fecal microbiota of the golden jackal, blacked-backed jackal and the domestic dog. Furthermore, LEfSe analysis found abundance of Fusobacterium and Bacteroides genera in the golden jackal, Clostridia class in blacked-backed jackal and Megamonas genus in domestic dog. The golden jackal fecal microbiota is influenced by multiple factors including host traits and pathogen burden. The characterization of the microbiota of this thriving species may aid in mapping its spread and proximity to human settlements. Moreover, understanding the jackal microbiota could inform the study of potential animal and human health risks and inform control measures

Detection of a Tumor Suppressor Gene Variant Predisposing to Colorectal Cancer in an 18th Century Hungarian Mummy.

Mutations of the Adenomatous polyposis coli (APC) gene are common and strongly associated with the development of colorectal adenomas and carcinomas. While extensively studied in modern populations, reports on visceral tumors in ancient populations are scarce. To the best of our knowledge, genetic characterization of mutations associated with colorectal cancer in ancient specimens has not yet been described. In this study we have sequenced hotspots for mutations in the APC gene isolated from 18th century naturally preserved human Hungarian mummies. While wild type APC sequences were found in two mummies, we discovered the E1317Q missense mutation, known to be a colorectal cancer predisposing mutation, in a large intestine tissue of an 18th century mummy. Our data suggests that this genetic predisposition to cancer already existed in the pre-industrialization era. This study calls for similar investigations of ancient specimens from different periods and geographical locations to be conducted and shared for the purpose of obtaining a larger scale analysis that will shed light on past cancer epidemiology and on cancer evolution