Species-level Identification Research Articles

DNA barcoding of the leaf-miner flies (Diptera, Agromyzidae) of Mitaraka, French Guiana.

Species level identification of Agromyzidae based on morphology is often challenging due to their small size and morphological homogeneity. DNA barcoding has been used regularly to assist with the identification of economically important species of Agromyzidae, but rarely as a tool for species delineation or identification in biodiversity surveys. The main objective of this study was to investigate whether DNA barcoding and the BIN (Barcoding Index) system could assist with species identification, species delineation, male/ female association, and diversity assessment of Agromyzidae material previously determined to morphospecies from Mitaraka, French Guiana. Amplification success was low, with sequences over 400 bp recovered for only 24 (48%) of the selected specimens. Sequences assigned to 17 morphospecies formed 16 distinct branches or clusters separated by very high (minimum of 10%) sequence divergence. Following the reassessment and subsequent reassignment of one specimen, congruence between morphology and DNA barcodes was high with a single instance of two morphospecies sharing identical sequences. While DNA barcoding did not assist with identification (none of our sequences matched those of named taxa in BOLD or GenBank), it did provide support for most of our morphospecies concepts, including male/female associations. The BIN system also provided access to information about the distribution and habitat preferences of several taxa. We conclude that DNA barcoding was a useful approach to study the species diversity of our samples but that much work remains to be done before it can be used as an identification tool for the Agromyzidae fauna of Mitaraka and the rest of the Neotropical region.

Multicentre study on the reproducibility of MALDI-TOF MS for nontuberculous mycobacteria identification

The ability of MALDI-TOF for the identification of nontuberculous mycobacteria (NTM) has improved recently thanks to updated databases and optimized protein extraction procedures. Few multicentre studies on the reproducibility of MALDI-TOF have been performed so far, none on mycobacteria. The aim of this study was to evaluate the reproducibility of MALDI-TOF for the identification of NTM in 15 laboratories in 9 European countries. A total of 98 NTM clinical isolates were grown on Löwenstein-Jensen. Biomass was collected in tubes with water and ethanol, anonymized and sent out to the 15 participating laboratories. Isolates were identified using MALDI Biotyper (Bruker Daltonics). Up to 1330 MALDI-TOF identifications were collected in the study. A score ≥ 1.6 was obtained for 100% of isolates in 5 laboratories (68.2–98.6% in the other). Species-level identification provided by MALDI-TOF was 100% correct in 8 centres and 100% correct to complex-level in 12 laboratories. In most cases, the misidentifications obtained were associated with closely related species. The variability observed for a few isolates could be due to variations in the protein extraction procedure or to MALDI-TOF system status in each centre. In conclusion, MALDI-TOF showed to be a highly reproducible method and suitable for its implementation for NTM identification.

Paleoenvironmental conditions across the Santonian/Campanian boundary: Inferences by calcareous nannofossils from Kurdistan region, northeastern Iraq

The Santonian/Campanian boundary interval (calcareous nannofossil zones CC16 to CC18) sediments in the Kurdistan region (northeastern Iraq) is analyzed for paleoenvironmental analysis. Based on the stratigraphic distribution of calcareous nannofossil taxa, four intervals were quantitatively identified, two within the Zone CC16 and two corresponding to CC17 and CC18, respectively. The assemblages are dominated by Watznaueria barnesiae (that forms 58% of the total population) and yielded a statistically significant and negative relationship with species diversity (Shannon Index) suggesting digenetic overprinting of the primary ecological signal. However, the presence of dissolution-susceptible taxa of Eiffellithus, Lucianorhabdus, Tranolitus, Lithastrinus and Zeugrhabdotus (albeit in low relative abundances), the ease of species-level identifications, the relatively high species diversity index (up to 2.6) and species richness (up to 22) suggests that the primary ecological signal is still preserved and can be used to infer the broad paleoenvironment. The entire studied interval is marked by a warm and oligotrophic water mass that is punctuated by cooler waters in the middle of Zone CC16 (Interval 2), beginning of zones CC17 (Interval 3) and CC18 (Interval 4; at the Santonian/Campanian boundary). These brief intervals are marked by increased relative abundances of cooler water species (Micula decussata, Eiffellithus turriseiffelii and Broinsonia enormis) and are interpreted as brief upwelling events associated by higher species diversity and species richness. As in the present study, globally also, the Santonian/Campanian boundary is marked by cooler waters.

Grass pollen and phytoliths of the Falkland Islands

In the Falkland Islands, Poa flabellata (tussac grass) is regarded as a keystone species forming coastal breeding habitat for seabirds and pinnipeds. Tussac also produces high-resolution peat deposits that are useful paleoecological archives, but reconstructing its long-term dynamics in the pollen record requires species-level identifications. Grass pollen is notoriously difficult to differentiate to species, and is often identified to family or subfamily. Where pollen is unable to provide species-level taxonomic resolution, phytoliths can provide complementary information. We investigated morphological variations of pollen and siliceous phytoliths of native grasses to determine whether P. flabellata was distinctive at the species level. We found that while P. flabellata pollen cannot be distinguished from other native grasses, its phytoliths are distinctive. These findings reveal the potential for phytoliths to shed light on questions about the response of South Atlantic grasslands to environmental change using multi-proxy analyses.

Pragmatic Applications and Universality of DNA Barcoding for Substantial Organisms at Species Level: A Review to Explore a Way Forward.

DNA barcodes are regarded as hereditary succession codes that serve as a recognition marker to address several queries relating to the identification, classification, community ecology, and evolution of certain functional traits in organisms. The mitochondrial cytochrome c oxidase 1 (CO1) gene as a DNA barcode is highly efficient for discriminating vertebrate and invertebrate animal species. Similarly, different specific markers are used for other organisms, including ribulose bisphosphate carboxylase (rbcL), maturase kinase (matK), transfer RNA-H and photosystem II D1-ApbsArabidopsis thaliana (trnH-psbA), and internal transcribed spacer (ITS) for plant species; 16S ribosomal RNA (16S rRNA), elongation factor Tu gene (Tuf gene), and chaperonin for bacterial strains; and nuclear ITS for fungal strains. Nevertheless, the taxon coverage of reference sequences is far from complete for genus or species-level identification. Applying the next-generation sequencing approach to the parallel acquisition of DNA barcode sequences could greatly expand the potential for library preparation or accurate identification in biodiversity research. Overall, this review articulates on the DNA barcoding technology as applied to different organisms, its universality, applicability, and innovative approach to handling DNA-based species identification.

What's left in the tank? Identification of non-ascribed aquarium's coral collections with DNA barcodes as part of an integrated diagnostic approach.

The unprecedented threats to coral reef ecosystems from global climate change require an urgent response from the aquarium community, which is becoming an increasingly vital coral conservation resource. Unfortunately, many hermatypic corals in aquaria are not identified to species level, which hinders assessment of their conservation significance. Traditional methods of species identification using morphology can be challenging, especially to non-taxonomists. DNA barcoding is an option for species identification of Scleractinian corals, especially when used in concert with morphology-based assessment. This study uses DNA barcodes to try to identify aquarium specimens of the diverse reef-forming genus Acropora from 127 samples. We identified to our best current knowledge, to species name 44% of the analysed samples and provided provisional identification for 80% of them (101/127, in the form of a list of species names with associate confidence values). We highlighted a sampling bias in public nucleotide sequences repertories (e.g. GenBank) towards more charismatic and more studied species, even inside a well-studied genus like Acropora. In addition, we showed a potential “single observer” effect with over a quarter of the reference sequences used for these identifications coming from the same study. We propose the use of barcoding and query matching as an additional tool for taxonomic experts and general aquarists, as an additional tool to increase their chances of making high confidence species-level identifications. We produce a standardised and easily repeatable methodology to increase the capacity of aquariums and other facilities to assess non-ascribed species, emphasising the value of integrating this approach with morphological identification optimising usage of authoritative identification guides and expert opinion.Supplementary InformationThe online version contains supplementary material available at 10.1007/s12686-021-01250-3.

Species discrimination of novel chloroplast DNA barcodes and their application for identification of Panax (Aralioideae, Araliaceae).

Certain species within the genus Panax L. (Araliaceae) contain pharmacological precious ginsenosides, also known as ginseng saponins. Species containing these compounds are of high commercial value and are thus of particular urgency for conservation. However, within this genus, identifying the particular species that contain these compounds by morphological means is challenging. DNA barcoding is one method that is considered promising for species level identification. However, in an evolutionarily complex genus such as Panax, commonly used DNA barcodes such as nrITS, matK, psbA-trnH, rbcL do not provide species-level resolution. A recent in silico study proposed a set of novel chloroplast markers, trnQ-rps16, trnS-trnG, petB, and trnE-trnT for species level identification within Panax. In the current study, the discriminatory efficiency of these molecular markers is assessed and validated using 91 reference barcoding sequences and 38 complete chloroplast genomes for seven species, one unidentified species and one sub-species of Panax, and two outgroup species of Aralia L. along with empirical data of Panax taxa present in Vietnam via both distance-based and tree-based methods. The obtained results show that trnQ-rps16 can classify with species level resolution every clade tested here, including the highly valuable Panaxvietnamensis Ha et Grushv. We thus propose that this molecular marker to be used for identification of the species within Panax to support both its conservation and commercial trade.

Molecular characterisation of virulence genes in Staphylococcus aureus associated with clinical bovine mastitis

Staphylococcus aureus is the most frequently isolated pathogen from bovine mastitis including subclinical, clinical, and chronic infections. Virulence factors possessed by S. aureus aid in causing infection and inflammation by producing toxins and proteins, which are responsible for the pathogenesis of the disease. In the current study out of 51 animals presented with clinical mastitis, S. aureus was isolated from the milk of 18 animals. S. aureus was confirmed by genus and species level identification using polymerase chain reaction. Molecular characterization of selected virulence genes including thermonuclease (nuc) and Panton Valentine Leucocidin (PVL) was performed in all the S. aureus isolates. Presence of nuc gene was observed in all the isolates (100 %) of S. aureus. No isolates were found to be positive for the presence of PVL gene. Profiling the virulence genes is an important tool for epidemiological studies of mastitis, which can be employed for the prevention and control of the disease.

Comparative Evaluation of Two Automated ID/AST Systems and Mikrolatest Kit in Assessing the In Vitro Colistin Susceptibility of Carbapenem-Resistant Enterobacteriaceae Isolates: A Single-Center Exploratory Study from North India.

Aims:To generate preliminary data about comparative evaluation of two automated ID/AST systems and Mikrolatest kit in determining in vitro colistin susceptibility of carbapenem-resistant Enterobacteriaceae spp.Materials and methods:Twenty-three carbapenem-resistant Escherichia coli and Klebsiella pneumoniae and two carbapenem-sensitive multidrug-resistant E. coli isolates obtained from various clinical samples of inpatients were included in the study. Species-level identification and antibiotic susceptibility testing (AST) of test isolates was performed using BD phoenix and MicroScan WalkAway 96 Plus automated systems. Identity was reconfirmed by matrix-assisted laser desorption ionization-time-of-flight mass spectrometry (MALDI-TOF MS). Additional colistin susceptibility testing was performed using Mikrolatest MIC colistin susceptibility testing kit (reference method).Results:Results showed that 16% isolates (27.3% [3/11] K. pneumoniae and 7.1% [1/14] E. coli) exhibited in vitro colistin resistance by the reference method. While the categorical agreement between BD Phoenix M50 ID/AST system and reference test w. r. t in vitro colistin susceptibility results was 100% and 92.9% for K. pneumoniae & E. coli, respectively, it was much lower between MicroScan WalkAway 96 plus ID/AST system and the latter. Almost perfect agreement (96%; kappa: 0.834) was observed between BD Phoenix M50 system and reference method.Conclusions:The results of this study are preliminary and cannot be generalized. Multicentric studies with large sample sizes should be conducted throughout the country to gain a deeper understanding of the subject under consideration.

Molecular Phylogeny of Myllocerus viridanus (Fabricius) by mitochondrial Cytochrome B gene Sequencing

In order to create accurate control techniques against insect pests, correct taxonomic identification is critical. This paper describes the molecular phylogeny of Grey weevil, Myllocerus viridanus (Fabricius) by the sequencing of their mitochondrial cytochrome B gene. The development of a simple and most elegant tools of DNA barcoding has made taxonomy and phylogeny studies a much facile process. M. viridanus is among the important polyphagous pests of plants of agricultural and horticultural importance. The sequencing of Cyt B gene yielded a 273 bp nucleotide product. Phylogentic analysis was carried out in Mega 11 software. Gen Bank deposition indicated the novel and first time records of cytochromeb gene barcode of M. viridanus and first time deposit of a species from the genus Myllocerus. The deposit was provided with an accession number OM223090. Further analysis showed that the partial sequence of mitochondrial cytochrome B of M.viridanus has 88.89% similarity with that of Romualdius bifoveolatus (KX087356) .The identity of M.viridanus(OM223090)ranged from 88.17 to 83.68% when nucleotide BLAST was carried out with nearest 21 species of curculionids (NCBI). The result indicated that cytochrome b gene barcoding can be successfully used to resolve species level identification of the members of the family Curculionidae and the genus Myllocerus of the order Coleoptera. Thus mitochondrial Cytochrome b gene like mitochondrial COX 1 gene, can be used as an efficient tool for the species level identification of the members of Coleopterans. Further interpretation on phylogeny was done by constructing neighbor joining tree using Kimura -2 Parameter. This approach was very informative and it helped in the better understanding of genetic variation among closely related species of Curculionids.

Evaluation of the mycobiome of ballast water and implications for fungal pathogen distribution

Marine transport has the potential to alter the geographic range of microorganisms through ballast water movement. Recent culture-independent studies investigated the bacteriome of ballast water, but no prior studies have examined the mycobiome. Here were examined 60 ballast and harbor samples from 4 major ports and 5 ocean samples using culture-independent techniques to determine (1) the composition of harbor and ballast water mycobiomes; (2) if ballast contained human and environmentally relevant fungal pathogens; and (3) the potential risk of introduction to coastal ecosystems. Results indicate that ballast water and harbor water contain a diverse mycobiome and that ballast water may contain fungal taxa that are relevant human and marine fish pathogens. Fungal genera were identified that contain known coral and coastal plant pathogen species; however, species-level identification of these potential pathogens could not be conclusively resolved. Ballast and harbor mycobiomes contained similar taxa, suggesting that environmental filtering may not inhibit the spread of fungal taxa between these ecosystems. This study highlights the potential risks of ballast movement and suggests further research of the ballast mycobiome is needed.

Genetic diversity of nontuberculous mycobacteria among symptomatic tuberculosis negative patients in Kenya.

Non-Tuberculous Mycobacteria (NTM) transmission to humans occurs through inhalation of dust particles or vaporized water containing NTM leading to pulmonary manifestations. NTM infections are often misdiagnosed for tuberculosis (TB) due to their similar clinical and radiological manifestations. We, therefore, performed a species-level identification of NTM in symptomatic TB negative patients through sequencing of the hsp65 gene. We conducted a cross-sectional study at the National Tuberculosis Reference Laboratory in the period between January to November 2020. One hundred and sixty-six mycobacterial culture-positive samples that tested negative for TB using capilia underwent Polymerase Chain Reaction targeting the hsp65 gene. Isolates showing a band with gel electrophoresis at 441 bp position were sequenced using Sanger technology. Geneious software was used to analyze the obtained sequences, and the National Center for Biotechnology Information gene database identified NTM species for each isolate. A phylogenetic tree was constructed from the DNA sequences and evolutionary distances computed using the general time-reversible method. Pearson chi-square was used to determine the association between NTM infection and participants' characteristics. Our study identified 43 different NTM species. The dominant NTM belonged to Mycobacterium avium complex 37 (31%). Slow-growing NTM were the majority at 86 (71%) while rapid-growing NTM were 36 (29%). A significant association (P<0.05) was observed for regions and age, while patient type had a weak likelihood of NTM infection. Our study characterized the diversity of NTM in Kenya for the first time and showed that species belonging to M. Avium Complex are the most prevalent in the country.

Origin of marine invertebrate larvae on an Arctic inflow shelf

Many benthic invertebrate taxa possess planktonic early life stages which drift with water currents and contribute to dispersal of the species, sometimes reaching areas beyond the current ranges of the adults. Until recently, it had been difficult to identify planktonic larvae to species level due to lack of distinguishing features, preventing detection of expatriate species. Here, we used DNA metabarcoding of the COI gene to obtain species-level identification of early life stages of benthic invertebrates in zooplankton samples from the Barents Sea and around Svalbard, where, regionally, large volumes of warm Atlantic Water enter the Arctic from the south. We compared the larval community in the water column to the adult community on the seafloor to identify mismatches. In addition, we implemented particle tracking analysis to identify the possible areas of origin of larvae. Our results show that 30-45% of larval taxa—largely polychaetes and nudibranchs—were not local to the sampling area, though most were found nearby in the Barents Sea. In the particle tracking analysis, some larvae originating along the Norwegian coast were capable of reaching the northwest coast of Svalbard within 3 mo, but larvae found east of Svalbard had a more constrained possible area of origin which did not extend to the Norwegian coast. This study highlights largely regional-scale larval connectivity in the Barents Sea but demonstrates the potential for some long-lived larval taxa to travel to Svalbard and the Barents Sea from further south.

An unusual case of Candida parapsilosis causing infectious crystalline keratopathy in Steven–Johnson syndrome

A 41-year-old female, a known case of Steven–Johnson syndrome (SJS) with ocular involvement, had a pthisical right eye (RE) and a history of mucous membrane grafting (MMG) in the left eye. Two weeks post-MMG, the patient developed a pearly white crystalline anterior stromal infiltrate suggestive of infectious crystalline keratopathy (ICK). The Gram stain showed gram-positive, round-to-oval budding cells and the culture on sheep blood agar showed smooth white yeast colonies. VITEK 2 compact automated microbiology system-enabled species-level identification was Candida parapsilosis in addition to the antifungal sensitivity. Based on the sensitivity report, the patient responded well to oral fluconazole and topical voriconazole with corneal scar formation. Clinical and microbiological evaluations of ICK in an unusual setting like SJS is prudent for a successful outcome.

Update on dermatophytosis in Mashhad, Northeastern Iran, emergence of infection with Trichophyton persicum.

Background:Dermatophytosis is a common global superficial mycosis caused by a group of keratinophilic moulds known as dermatophytes that invade the skin and keratinized tissues such as hair and nails of humans and animals. This study takes identification of a collection of clinical dermatophyte isolates by using partial sequencing of translation elongation factor-1α (Tef-1α) gene aiming both to update the epidemiological status of dermatophytosis in Mashhad, Northeastern Iran and to corroborate the efficacy of Tef-1α for species-level identification of dermatophytes.Method:The demographic data related to 87 culture-positive dermatophytes isolated from patients clinically suspected to have dermatophytosis were collected. The dermatophyte isolates were subjected to a partial polymerase chain reaction (PCR)-sequencing of Tef-1α gene by using specific pan-dermatophyte primers. The data were analysed by SeqMan software, the sequences were compared and aligned with the GenBank database and the isolates were identified.Results:Identification based on Tef-1α partial sequence was successful for all isolates. The identified dermatophyte isolates in decreasing order were as Trichophyton interdigitale 19 (22%), T. tonsurans 19 (22%), T. mentagrophytes 13 (15%), T. persicum 10 (11.5%), Epidermophyton floccosum 9 (10.3%), Microsporum canis 7 (8%), T. rubrum 5 (5.7%), T. violaceum 2 (2.2%), Nannizzia fulva 2 (2.2%) and N. persicolor 1 (1.1%). The isolates have been associated with clinical forms of tinea corporis (n = 38; 43.7%), tinea faciei (n = 13; 15%), tinea cruris (n = 12; 13.9%), tinea manuum (n = 7; 8%), tinea unguium (n = 7; 8%), tinea capitis (n = 7; 8%) and tinea pedis (n = 3; 3.4%).Conclusion:Dermatophytosis has yet remained a public health problem in Northeastern Iran, and infection with new and less frequent species, e.g., T. persicum, N. fulva and N. persicolor have emerged. The Tef-1α gene partial sequencing reconfirmed the resolution power of this locus for the determination of species boundaries in dermatophytes.

Antifungal Susceptibility Pattern of Candida albicans and Non Candida albicans Species Isolates at a Tertiary Care Hospital in India

Vulvovaginal candidiasis (VVC) is a widespread fungus that affects women of all ages. After bacterial vaginosis, vulvovaginal candidiasis is the second most prevalent cause of vaginitis, affecting 40% of women with vaginal discharge. Candida is a fungus that is one of the most common opportunistic fungi in humans. The samples were processed using standard Candida isolation techniques. Candida species were identified using germ tube tests and Candida agar media. On Mueller Hinton Agar (MHA) supplemented with 2 percent glucose and 0.5 g/ ml methylene blue dye, the disc diffusion method was employed to investigate antifungal sensitivity. Candida albicans was responsible for 42 (36.3%) of the 350 Candida isolates, followed by Candida glabrata (24.1%), Candida tropicalis (22.5%), Candida krusei (12.3%), and Candida parapsilosis (12.3%). (9.7 percent). With a sensitivity pattern of 106/116, amphotericin Bis is the most effective antifungal medication against Candida isolates (91.3 percent). The resistance to ketoconazole, on the other hand, was the highest (20.6 percent). In light of the rising tide of antimicrobial resistance to fungal medicines, the current study suggests that species-level identification of Candida isolates should be encouraged.

ĐỊNH DANH ĐẾN LOÀI MỘT SỐ CHỦNG MYCOBACTERIA BẰNG PHƯƠNG PHÁP GIẢI TRÌNH TỰ GEN

Objective: To discriminate and describe the prevalence between MTBC and NTM in the mycobacteria isolates at National Lung Hospital from the August of 2019 to the August of 2020, of which MPT64 cannot be detected by TBc ID. Methods: Identification mycobacteria isolates to the species level by analysis several target genes, including 16S rRNA, gyrB, rpoB, hsp65 and ITS. Results: Overall, there are 105 (100%) TBc ID negative strains, including 56 MTBC strains (53,3%) and 49 NTM strains (46,7%). Looking closely to species level identification, of all 56 MTBC strains, there are 55 M. tuberculosis strains (98,2%) and solely 1 M. bovis strains (1,8%). Within 49 NTM strains, the highest frequency is M. abscessus/ M. chelonae (27 strains- 55,1%), the second is MAC (8 strains- 16,3%) and other 13 NTM species take some small portions. Conclusion: Some strains of MTBC cannot be detected by TBc ID, including M. tuberculosis and M. bovis. The predominant NTM species related to pulmonary disease in Vietnam are M. abscessus/ M. chelonae and MAC. Keywords: Mycobacteria, MTBC, NTM, TBcID, sequencing

The Floodplain Forests of the Mamberamo Basin, Papua, Indonesia (Western New Guinea): Vegetation, Soils, and Local Use

New Guinea is the world’s largest, most speciose, and most culturally rich tropical island, and the little-studied Mamberamo Basin of Papua (Indonesian New Guinea) is recognised among the region’s most-important areas for biological diversity. Here, we examined the floodplain forests in the indigenous territory of Papasena, within the Mamberamo-Foja Wildlife Reserve in the Mamberamo Basin. As part of a training activity with local researchers, students, and civil servants, and with the permission and assistance of the local people, we employed various methods including the field surveys detailed here. We used variable-area tree plots, transects for non-trees and soil sampling, and local informants to document 17 plots: four in old-growth dryland forest, five in old-growth swamp forests (two seasonally flooded and three permanently wet including one dominated by sago, Metroxylon sagu Rottb.), five in secondary forest (fallows), and three in gardens (two in swamps and one on dryland). In total, we measured 475 trees over 10 cm in diameter at 1.3 m (dbh). The swamp forests had high local basal areas (highest value 45.1 m2 ha−1) but relatively low statures (20 m but with emergent trees over 40 m). In total, 422 morphospecies from 247 genera and 89 different families were distinguished. These included 138 tree species and 284 non-tree plant species. A quarter (105) of the morphospecies lacked species-level identifications. The woody families Rubiaceae, Araceae, Moraceae, and Euphorbiaceae were especially diverse, with 20 or more morphospecies each. Tree richness was highest in dryland forest (plot 7 having 28 species in 40 stems over 10 cm dbh) with more variation in the flooded forests. Non-tree vegetation showed similar patterns ranging from 65 species in one 40-by-5 m primary forest plot to just 5 in one seasonally flooded forest plot. The local people identified many plants as useful. Among trees, at least 59 species were useful for construction (the most common use), while, for non-trees, medicinal uses were most frequent. Inceptisols dominated (12 plots), followed by Ultisols and Entisols (3 and 2 plots, respectively). Drainage appeared poor and nutrient availability low, while land-suitability criteria implied little potential for crops aside from sago. We discuss the implication of local practises and more recent developments that may threaten the conservation of these floodplain systems. We underline the key role of local people in the oversight and protection of these ecosystems.

The dilemma of identifying Peptoniphilus species by using two MALDI-TOF MS systems

Two commercial MALDI-TOF MS systems were used to identify 18 isolates, belonging to the Peptoniphilus genus; also the 16S rRNA sequencing identity was compared against the MALDI-TOF MS system results. Bruker Biotyper system provided higher accuracy than Vitek MS system, however, adding spectra could allow a more reliable species level identification.

Detection of Nontuberculous Mycobacterial Species from Tissue Samples of Cattle and Buffaloes by PCR and PRA (PCR-RFLP)

Background: Nontuberculous mycobacteria are opportunistic pathogens and some of them may cause disease in humans and animals causing pulmonary infections, mastitis, lesions in respiratory tract and lymph nodes of cattle, due to which they are being recognized worldwide and also interfere with the diagnosis of bovine tuberculosis. Methods: The present study was conducted for detection of nontuberculous mycobacterial species (NTM) in tissue samples (with and without tubercle lesions) in cattle and buffaloes from postmortem hall GADVASU, Ludhiana. Polymerase Chain Reaction and PCR-RFLP which involved hsp65 gene amplification (439 bp) and restriction analysis of amplified product was performed on 30 tissue samples for detection of nontuberculous mycobacterial species. Result: Three out of 30 samples showed hsp65 gene amplification and 2 were identified as M. kansasii using restriction analysis technique and one could not be identified as the RFLP patterns was different from other known PCR-RFLP profiles. NTM such as M. kansasi may cause infection in animals and PRA (PCR-Restriction Fragment Length Polymorphism Analysis) technique was found to be a rapid tool for identification and differentiation of NTM upto species level.