Determination of mycobacterial phylogeny on the basis of immunological relatedness of superoxide dismutases

Phylogenomics of the Phylum Proteobacteria: Resolving the Complex Relationships

Proteobacteria is one of the largest and phenotypically most diverse divisions within the domain bacteria. Due to the economic importance, this phylum demands an urgent need for a clear and scientifically sound classification system to streamline their characterization. The goal of our study was to carefully reevaluate the current system of classification and suggest changes wherein necessary. Phylogenetic trees of 84 Proteobacteria were constructed using single gene-based phylogeny involving 16S rRNA genes and protein sequences of 85 conserved genes, whole genome-based phylogenetic tree using CVtree3.0, amino acid Identity matrix tree, and concatenated tree with aforementioned conserved genes. The results of our study confirm the polyphyletic relationship between Desulfurella acetivorans, a Deltaproteobacteria with Epsilonproteobacteria. The group Syntrophobacterales was found to be polyphyletic with respect to Desulfarculus baarsii and the group Thiotrichales was found to be splitting in different phylogenetic trees. Placement of phylogenetic groups belonging to Rhodocyclales, Oceonospirilalles, and Chromatiales is controversial and requires further study and revisions. Based on our analysis, we strongly support reclassification of Magnetococcales as a separate class Etaproteobacteria. From our results, we conclude that concatenated trees of conserved proteins are a more accurate method for phylogenetic analysis, as compared to other methods used.

Seroprevalence and pathological studies of Salmonella infection in commercial white layer birds

The present study was conducted to determine the seroprevalence and pathology of Salmonella infection in white commercial layer birds of District Faisalabad during June 2018 and June 2020. The current study aimed to determine the isolation, identification of Salmonella gallinarum (S. gallinarum), its cultural prevalence, antimicrobial resistance, molecular characterization, and pathological lesions produced in different organs of commercial layer birds. Initial screening of poultry flocks was done through serum plate agglutination test followed by culturing in different media, motility test, molecular confirmation, and histopathology. Based on the serum plate agglutination test, seroprevalence in the commercial white layer in dead and live flocks was 40.09%. The cultural prevalence of Salmonella in the seropositive group was 75.36% and in the seronegative was 31.84%. Cultural prevalence in the liver of dead birds was 62.06%, in spleen 58.62%, and in cloacal swabs was 67.24%. A total of 178 isolates were characterized through cultural characteristic and motility tests, among them 63.48% isolates were S. gallinarum, and 36.51% isolates were S. pullorum. The antibiogram study revealed that all the tested isolates were resistant to amoxicillin, gentamycin, kanamycin, doxycyclin, and tetracyclin. While tested isolates were sensitive to ciprofloxacin against S. gallinarum. Pathologically liver was friable, showing bonze discoloration with focal necrosis, enteritis of various grades, mottled white spleen, and enlarged kidneys were found. Microscopically, leukocytic infiltration with focal necrosis and degeneration, in mucosa and submucosa of intestinal inflammatory cells were observed. In conclusion, the seroprevalence, antibiogram, and molecular characterization of Salmonella help to control the disease in a better way through bacterin production of local isolates.

Recent advances in the diagnosis of Mycobacterium tuberculosis

Molecular technologies offer the greatest potential for laboratories in resource-rich countries because they have the highest sensitivity and specificity. Continued use of new technologies will be crucial in elucidating the true epidemiology and pathogenesis of a disease, including the less well studied diseases. Continued development of affordable, sensitive, and specific diagnostic tools will be required for use in resource-poor settings, where the incidence of disease is highest.

Pathogeny of archaic mycobacteria at the emergence of urban life in Egypt (3400 BC)

In a previous study, we extracted, amplified and sequenced a DNA fragment from bone lesions similar to those of bone tuberculosis in a predynastic skeleton (Egypt, around 3400 BC). This 65 kDa gene fragment encodes the surface of the mycobacterium responsible for the lesions. In the present study, we reconstructed the phylogenetic tree of the Mycobacterium family using this fragment and 51 sequences of pathogens and environmental mycobacteria. This reconstruction enabled us to polarise the phylogenic tree and to confirm the originality of the sequence and its ancestral character. According to a recent evolutionary scenario for the Mycobacterium tuberculosis complex, these data suggest the pathogenicity of an archaic mycobacterium at the emergence of urban life. This result could lead to a better understanding of present day evolutionary processes, especially the emergence or re-emergence of non-tuberculosis mycobacteria infection and disease.

Isolation and characterization of polycyclic aromatic hydrocarbon-degrading Mycobacterium isolates from soil

Bioremediation of soils contaminated with wood preservatives containing polycyclic aromatic hydrocarbons (PAHs) is desired because of their toxic, mutagenic, and carcinogenic properties. Creosote wood preservative-contaminated soils at the Champion International Superfund Site in Libby, Montana currently undergo bioremediation in a prepared-bed land treatment unit (LTU) process. Microbes isolated from these LTU soils rapidly mineralized the (14)C-labeled PAH pyrene in the LTU soil. Gram staining, electron microscopy, and 16S rDNA-sequencing revealed that three of these bacteria, JLS, KMS, and MCS, were Mycobacterium strains. The phylogeny of the 16S rDNA showed that they were distinct from other Mycobacterium isolates with PAH-degrading activities. Catalase and superoxide dismutase (SOD) isozyme profiles confirmed that each isolate was distinct from each other and from the PAH-degrading mycobacterium, Mycobacterium vanbaalenii sp. nov, isolated from a petroleum-contaminated soil. We find that dioxygenase genes nidA and nidB are present in each of the Libby Mycobacterium isolates and are adjacent to each other in the sequence nidB-nidA, an order that is unique to the PAH-degrading mycobacteria.

Impact of genotypic studies on mycobacterial taxonomy: the new mycobacteria of the 1990s

The advancement of genetic techniques has greatly boosted taxonomic studies in recent years. Within the genus Mycobacterium, 42 new species have been detected since 1990, most of which were grown from clinical samples. Along with species for which relatively large numbers of strains have been reported, some of the new species of mycobacteria have been detected rarely or even only once. From the phenotypic point of view, among the new taxa, chromogens exceed nonchromogens while the numbers of slowly and rapidly growing species are equivalent. Whereas conventional identification tests were usually inconclusive, an important role was played by lipid analyses and in particular by high-performance liquid chromatography. Genotypic investigations based on sequencing of 16S rRNA gene have certainly made the most important contribution. The investigation of genetic relatedness led to the redistribution of the species previously included in the classically known categories of slow and rapid growers into new groupings. Within slow growers, the intermediate branch related to Mycobacterium simiae and the cluster of organisms related to Mycobacterium terrae have been differentiated; among rapid growers, the group of thermotolerant mycobacteria has emerged. The majority of species are resistant to isoniazid and, to a lesser extent, to rifampin. Many of the new species of mycobacteria are potentially pathogenic, and there are numerous reports of their involvement in diseases. Apart from disseminated and localized diseases in immunocompromised patients, the most frequent infections in immunocompetent people involve the lungs, skin, and, in children, cervical lymph nodes. The awareness of such new mycobacteria, far from being a merely speculative exercise, is therefore important for clinicians and microbiologists.

Histologic and genotypic characterization of a novel Mycobacterium species found in three cats

Three cases of feline atypical mycobacteriosis from different geographical regions in North America were characterized by large clusters of filamentous bacteria visible on hematoxylin-and-eosin-stained tissue sections. PCR amplification demonstrated the presence of Mycobacterium-specific nucleic acid in samples of skin lesions from these cases. PCR-assisted cloning and DNA sequence analysis of a 541-bp length of the Mycobacterium 16S rRNA gene generated DNA sequences which were >95% identical, suggesting that the three isolates were closely related. Two of the sequences were 99% identical and may represent the same species. Alignment with comparable 16S rRNA gene sequences from 66 Mycobacterium species and partially characterized isolates highlighted similarities (>94%) with Mycobacterium bohemicum, Mycobacterium haemophilum, Mycobacterium ulcerans, Mycobacterium avium subsp. avium, and isolate IWGMT 90242. Parsimony analysis of sequence data suggested relatedness to M. leprae. Significant molecular genetic and pathobiological differences between these three similar isolates and other known species of mycobacteria suggested that the organisms may not have been described previously and that these cases may represent a new form of mycobacterial disease in cats. We suggest the term "Mycobacterium visibilis" to describe the organism from which the two nearly identical sequences were obtained.

Differentiation of phylogenetically related slowly growing mycobacteria by their gyrB sequences

The conventional methods for identifying mycobacterial species are based on their phenotypic characterization. Since some problematic species are slow growers, their taxonomy takes several weeks or months to identify. The ribosomal DNA (rDNA) sequence-based identification strategy has been adopted to solve this problem. More recently, the gyrB sequences have been shown to be useful phylogenetic markers for the identification of species. We determined the gyrB sequences of 43 slowly growing strains belonging to 15 species in the genus Mycobacterium. The frequencies of base substitutions in the gyrB sequences were comparable to those in the 16S-23S rDNA internal transcribed spacer (ITS) sequences. The ITS sequences of four species belonging to the M. tuberculosis complex (M. tuberculosis, M. bovis, M. africanum, and M. microti) were 100% identical, while four synonymous substitutions were found in the gyrB sequences of these strains. Based on the differences found in the gyrB sequences, we developed PCR and PCR-restriction fragment length polymorphism methods to discriminate these species.