Identification Of Subspecies Research Articles

Campylobacter fetus subspecies specific PCR assays inferred from comparative genomic analysis for accurate subspecies identification

Bovine Genital Campylobacteriosis (BGC) is caused by Campylobacter fetus subsp. venerealis and is a notifiable disease to the WOAH (World Organisation for Animal Health). For an effective BGC control program, the reliable differentiation of Campylobacter fetus subsp. venerealis (Cfv) from the closely related Campylobacter fetus subsp. fetus (Cff) is required. However, the available molecular C. fetus subspecies identification assays lack sensitivity and specificity to differentiate C. fetus isolates based on their phenotypic or genotypic differences. Furthermore, the current biochemical subspecies identification is not fully congruent with the genomic differentiation of C. fetus strains.In this study, the genome sequences of 41C. fetus strains with well identified subspecies, were analyzed with the large-scale BLAST score ratio (LS-BSR) pipeline to identify Cff and Cfv specific sequences. With this analysis, the asd gene encoding an aspartate-semialdehyde dehydrogenase was identified, which contained a 6-bp Cff-specific sequence, and this 6-bp sequence was absent in the asd gene of Cfv strains. This sequence was used for the development of PCR assays to differentiate Cff and Cfv strains. The C. fetus subspecies identification of the developed asd PCR assays was in full congruence with the genomic classification of strains and are recommended for molecular identification of C. fetus subspecies in BGC control programs.The asd PCR can be assessed on sequenced genomes using a web interface containing the Cfvcatch tool, which includes placement of the tested genome in a phylogenetic tree with reference C. fetus genomes to distinguish the two subspecies and to detect antimicrobial resistance genes.

TigerBase: A DNA registration system to enhance enforcement and compliance testing of captive tiger facilities

The illegal trade in tigers (Panthera tigris) and their derivatives, such as bones, teeth and pelts, is a major threat to the species’ long-term persistence. As wild tiger populations have dwindled, a large proportion of trafficked tiger products now derive from captive breeding facilities found throughout Asia. Moreover, wild tigers have been poached and laundered into captive facilities, then falsely designated as captive-bred. The establishment of a DNA registration system is recognized as a key tool to monitor compliance of captive facilities, support tiger trade investigations and improve prosecution outcomes. Here, we present a standardised wildlife forensic DNA profiling system for captive tigers called TigerBase. TigerBase has been developed in four South-East Asia countries with captive tiger facilities: Malaysia, Vietnam, Thailand and Lao PDR. TigerBase DNA profile data is based on 60 single nucleotide polymorphism (SNP) markers, genotyped using two different TaqMan®-based approaches: OpenArray® chip (capable of genotyping 60 SNPs for 48 samples in a single chip), and singleplex TaqMan® assays (capable of genotyping one SNP for one sample per reaction). Of the 60 SNPs, 53 are autosomal nuclear markers, suitable for individualisation and parentage applications, two are sex-linked markers, suitable for sexing, and five are mtDNA markers, suitable for maternal subspecies identification. We conducted a series of validation experiments to investigate the reliability and limitations of these SNP genotyping platforms. We found that the OpenArray® chip platform is more appropriate for generating reference data given its greater throughput, while the singleplex TaqMan® assays are more appropriate for genotyping lower quality casework samples, given their higher sensitivity and throughput flexibility. Only 19 autosomal nuclear markers were validated as singleplex TaqMan® assays, which generally provides ample power for individualisation analysis (probability of identity among siblings was <6.9 ×10−4), but may lack power for specific parentage questions, such as determining parentage of an offspring when one of the parent’s genotypes is missing. Further, we have developed pipelines to support standardised SNP calling and decrease the chance of genotyping errors through the use of analytical workflows and synthetic positive controls. We expect the implementation of TigerBase will enhance enforcement of tiger trafficking cases and encourage compliance among captive tiger facilities, together contributing to combatting the illegal tiger trade.

PSLBI-12 Screening and isolation of Fusobacterium necrophorum and Fusobacterium varium from seminal, and vagino-uterine microbiota of healthy cattle and sheep

Abstract Fusobacteria necrophorum is an important opportunistic bacterial pathogen associated with liver abscesses, foot rot, necrotic laryngitis and endometritis in both dairy and beef cattle. Recently, we identified F. necrophorum as one of the taxa in the uterine microbiota that are positively associated with pregnancy outcome in beef cows, and that Fusobacterium was identified as the most dominant genus in the bovine seminal microbiota. These findings indicate that Fusobacterium spp. may have a role in reproductive health and cattle fertility. Our objectives were to detect and isolate the F. necrophorum subsp necrophorum (FNN), F. necrophorum subsp. funduliforme (FNF) and F. varium (FV) in seminal, vaginal and uterine microbial ecosystems as well as fetal samples by culture and real-time PCR (qPCR) methods. The qPCR was performed on the DNA (n = 215) extracted from bull semen (n = 37), ram semen (n = 100), and vaginal (n = 25) and uterine swabs (n = 32), caruncles (n = 9), allantoic fluid (n = 6), and amniotic fluid (n = 6) from pregnant beef cows. The qPCR targeted the hgdA gene, and leukotoxin promoter regions (lktA-n and lktA-f) to detect and quantify FV, FNN and FNF, respectively. Cryopreserved samples (n = 174; 57 bull semen, 10 ram semen, 38 vaginal, and 47 uterine swabs) were cultured to detect and isolate FNN, FBF and FV by direct plating and after culturing in anaerobic peptone-yeast extract broth containing sodium lactate broth with josamycin, vancomycin and norfloxacin for selective enrichment of FN and FV. Also, 28 samples of 6-mo-old bovine fetuses caruncles, allantoic and amniotic fluids, and intestinal tissue) were screened for Fusobacterium species. By qPCR, FNF was detected in 75.7% of bull semen, and 8.0% of vaginal swabs as well as 33.3% of both allantoic fluid and caruncles, but was undetected in ram semen, uterine swabs, and amniotic fluids. Subspecies necrophorum was identified in 37.8% of bull semen, 3% of ram semen, 8.0% of vaginal and 15.6% of uterine 55.6 % of caruncles, 50% of allantoic fluid samples, but was not detected in amniotic fluid samples. Meanwhile FV was only detected in vaginal, uterine swabs and caruncles at 4%, 6.3%, and 11.1%, respectively. The culture method detected FNF in 63.2% of bull semen and 5.3% of vaginal samples, while FNN was identified in 1.8% of bull semen and 2.1% of uterine samples. F. varium was not isolated from any of the samples. Overall, FNF was the most prevalent subspecies present in the seminal microbiome of bulls. Identification of FNN subspecies and FV in seminal, vaginal, and uterine microbiota of healthy cattle, as well as in healthy calf fetus-associated samples suggests potential transfer from bulls to cows and then on to offspring, and potential involvement of the Fusobacterium spp. in cattle fertility.

Evaluation of the GenoType NTM-DR line probe assay for nontuberculous mycobacteria using whole genome sequences as reference standard

Pulmonary nontuberculous mycobacteria (NTM) disease is an emerging public health challenge that is especially problematic in people with cystic fibrosis (CF). Effective treatment depends on accurate species and subspecies identification and antimicrobial susceptibility status. We evaluated the GenoType NTM-DR VER 1.0 assay using biobanked NTM isolates with whole genome sequence (WGS) data and control isolates (total n=285). Species and subspecies detection sensitivity and specificity were 100 % for all species and subspecies except for two subspecies of M. intracellulare, that demonstrated a small degree of discrepant identification between M. intracellulare subspecies intracellulare and subspecies chimaera. All antimicrobial resistance markers were identified with 100 % sensitivity and specificity.We conclude that the GenoType NTM-DR assay offers a rapid and accurate option for identifying the most frequently encountered pathogenic NTM taxa and drug resistance markers.SUPPORT: Colorado CF Research Development Program and Colorado CF National Resource Centers funded by the Cystic Fibrosis Foundation, NJH Advanced Diagnostics Laboratories, Colorado Advanced Industries Accelerator Grant

Contribution of machine learning for subspecies identification from Mycobacterium abscessus with MALDI-TOF MS in solid and liquid media.

Mycobacterium abscessus (MABS) displays differential subspecies susceptibility to macrolides. Thus, identifying MABS's subspecies (M. abscessus, M. bolletii and M. massiliense) is a clinical necessity for guiding treatment decisions. We aimed to assess the potential of Machine Learning (ML)-based classifiers coupled to Matrix-Assisted Laser Desorption/Ionization Time-of-Flight (MALDI-TOF) MS to identify MABS subspecies. Two spectral databases were created by using 40 confirmed MABS strains. Spectra were obtained by using MALDI-TOF MS from strains cultivated on solid (Columbia Blood Agar, CBA) or liquid (MGIT®) media for 1 to 13 days. Each database was divided into a dataset for ML-based pipeline development and a dataset to assess the performance. An in-house programme was developed to identify discriminant peaks specific to each subspecies. The peak-based approach successfully distinguished M. massiliense from the other subspecies for strains grown on CBA. The ML approach achieved 100% accuracy for subspecies identification on CBA, falling to 77.5% on MGIT®. This study validates the usefulness of ML, in particular the Random Forest algorithm, to discriminate MABS subspecies by MALDI-TOF MS. However, identification in MGIT®, a medium largely used in mycobacteriology laboratories, is not yet reliable and should be a development priority.

Current expansion of the Barn Owl (&lt;i&gt;Tyto alba&lt;/i&gt;) (Tytonidae, Aves) in Northern Eurasia

In the north of Eurasia, until the mid-twentieth century, the Barn Owl (Tyto alba) was sporadically distributed only in the Baltic states, in the west of Belarus and Ukraine, and in Moldova. Once, in 1942, a vagrant bird was caught in Turkmenistan also. At the end of the 20th century, reports appeared of rare recordings of barn owls in Eastern Europe, and since the beginning of the 21st century, pronounced expansion of these birds has been noted, observed in the south of Ukraine, Crimea, Ciscaucasia, and Transcaucasia. Different subspecies living in Central and Southern Europe and the Middle East are simultaneously expanding their nesting areas, namely: a. guttata, T. a. alba, and T. a. erlangeri. However, visual identification of subspecies and clarification of the direction of their expansion are complicated by the similarity of various forms and their significant individual variability associated with age, sex, intergradation with neighboring subspecies and other factors. The appearance of sedentary barn owls in new places is usually preceded by their post-nesting dispersion, directed in all directions and in some cases reaching 1–2 thousand km from the place of birth. Owing to the expansion of its range, barn owl populations have increased many times in a number of regions over the past decades, but accurate estimates of their numbers there are missing due to the rarity and sporadical nature of new finds, the very secretive lifestyle of these birds and insufficient knowledge of their ecology and ethology in the north of Eurasia. The article examines the taxonomy of various barn owl populations in Northern Eurasia and main diagnostic characteristics of some subspecies living in the north of Eurasia, as well as analyzes features of their historical and current distribution and expansion in Eurasia. The author also discusses possible causes and mechanisms of the barn owl dispersion and touches on information on the dynamics of their numbers in few regions.

A rare family outbreak of Mycobacterium abscessus infection in immunocompetent fraternal triplets

BackgroundMycobacterium abscessus (M. abscessus) infection is rare in children who were previously healthy, particularly in infants. We present the first report of a family outbreak of M. abscessus infection among immunocompetent infant triplets. MethodsWe reviewed triplets’ demographic data, laboratory tests and imaging examinations to describe their clinical features. We performed whole-exome sequencing to rule out primary immunodeficiency disorders. We used DNA sequencing for M. abscessus subspecies identification. ResultsThe fraternal triplets (triples A, B and C) presented with a 10-day history of cough. Triple A also experienced a brief episode of fever, and triple B had tachypnea. Chest CT scans showed pulmonary masses and nodules in triples A and C, and cavities in triple B. Cultures of sputum and bronchoalveolar lavage fluid from all triplets yielded M. abscessus. Further subspecies identification showed that isolates from triples A and C were M. abscessus subsp. massiliense, and isolates from triple B were M. abscessus subsp. abscessus (MAA). After eight months of combination therapy, the pulmonary lesions of the triplets improved significantly. ConclusionOur study confirms that M. abscessus pulmonary disease can occur in immunocompetent infants. We hypothesize that the simultaneous infection of the triplets may be associated with their prematurity and extensive environmental exposure. This study highlights the importance to include M. abscessus infection in the differential diagnosis of pulmonary masses and/or cavities, regardless of the age of onset or the presence of underlying pathology or susceptible genes.

Genetic identification, morphology and distribution of Natrixhelvetica subspecies in southern and western Switzerland (Reptilia, Squamata, Serpentes).

Most of Switzerland is inhabited by the nominotypical subspecies of the barred grass snake (Natrixhelveticahelvetica), which is characterized by mitochondrial DNA lineage E. Only in the northeast of the country, the common grass snake (N.natrix) occurs and hybridizes with N.h.helvetica in a narrow contact zone. However, we discovered that in southern and western Switzerland barred grass snakes representing another mtDNA lineage (lineage C) are widely distributed. Lineage C is typical for Alpine populations of the southern subspecies N.h.sicula. Our microsatellite analyses of the Swiss samples revealed differences between the two subspecies and also a substructure with two clusters in each subspecies. Furthermore, we discovered a contact and hybrid zone of N.h.helvetica and N.h.sicula along the northern shore of Lake Geneva and also confirm that interbreeding with alien common grass snakes (N.n.moreotica, mtDNA lineage 7) occurs there. This finding is of concern for nature conservation and measures should be taken to prevent further genetic pollution. Using morphometrics, we found no differences between the two subspecies of N.helvetica, while N.natrix was slightly distinct from N.helvetica.

Applications and advances in molecular diagnostics: revolutionizing non-tuberculous mycobacteria species and subspecies identification.

Non-tuberculous mycobacteria (NTM) infections pose a significant public health challenge worldwide, affecting individuals across a wide spectrum of immune statuses. Recent epidemiological studies indicate rising incidence rates in both immunocompromised and immunocompetent populations, underscoring the need for enhanced diagnostic and therapeutic approaches. NTM infections often present with symptoms similar to those of tuberculosis, yet with less specificity, increasing the risk of misdiagnosis and potentially adverse outcomes for patients. Consequently, rapid and accurate identification of the pathogen is crucial for precise diagnosis and treatment. Traditional detection methods, notably microbiological culture, are hampered by lengthy incubation periods and a limited capacity to differentiate closely related NTM subtypes, thereby delaying diagnosis and the initiation of targeted therapies. Emerging diagnostic technologies offer new possibilities for the swift detection and accurate identification of NTM infections, playing a critical role in early diagnosis and providing more accurate and comprehensive information. This review delineates the current molecular methodologies for NTM species and subspecies identification. We critically assess the limitations and challenges inherent in these technologies for diagnosing NTM and explore potential future directions for their advancement. It aims to provide valuable insights into advancing the application of molecular diagnostic techniques in NTM infection identification.

Ancient DNA study of Cervus canadensis unearthed from the Royal Sacrificial Site of the Northern Wei Dynasty in Inner Mongolia Autonomous Region, China

The practice of animal sacrifice was widespread in ancient societies, and the study of sacrificial animals holds significant importance. In this study, three samples excavated from the Royal Sacrificial Site of the Northern Wei Dynasty in Inner Mongolia Autonomous Region, China were initially identified as Cervinae subfamily animal based on their morphology. Through alignment analysis and principal component analysis, these samples were identified as belonging to the species Cervus canadensis. Meanwhile, through phylogenetic analyses and genetic distance calculations, it was determined that all three samples were of the Cervus canadensis alashanicus subspecies, proving the utility of ancient DNA technology in accurate subspecies identification. The analysis of the mitochondrial D-loop region revealed that the ancient Cervus canadensis alashanicus dated to 3800 BP and 5100 BP differed significantly from the modern ones in opposition to 1500 BP samples which were similar to them. The low genetic diversity of modern Cervus canadensis alashanicus was formed at least 1500 years ago and have lasted till today. In addition, as suggested by historical documents and archaeological studies, it is evident that the reverence for deer within the Tuoba Xianbei population had become a significant element of their culture and belief system. The identification of Cervus canadensis species in this study serves as evidence of the Northern Wei Emperor’s utilization of totem animals as sacrificial offerings to heaven.

Combining biometrics and genetics to distinguish two subspecies of the Great Cormorant Phalacrocorax carbo carbo and P. c. sinensis at an inland lake in southeast Norway

Cover photo: Adult Great Cormorant of the subspecies Phalacrocorax carbo sinensis in breeding plumage. Photo: Frode Falkenberg. Great Cormorants Phalacrocorax carbo are now regularly seen in inland watercourses in southeast Norway, after the P. c. sinensis subspecies first established breeding colonies in coastal south Norway in 1996. Although both the sinensis and carbo subspecies occur, the ratio between them is unknown. We tested the accuracy of subspecific identification based on biometrics and genetic analyses in 75 Great Cormorants that drowned in fishing nets in a lake in southeast Norway during the period 2009-2020. Primarily based on the gular pouch angle (GPA), we classified 40 individuals to the carbo subspecies and 35 individuals to the sinensis subspecies. Eight of the carbo individuals and 14 of the sinensis individuals were within the overlapping range of GPA and were therefore classified to subspecies by supplementary measurements (bill depth minimum and bill length). Genetic analyses were based on seven polymorphic microsatellite markers. Assuming one panmictic population, we performed Structure analyses to separate the genotypes into two assumed genetic clusters. The two clusters, carbo and sinensis, could only be separated when adding information about morphological subspecies identities for the carbo, sinensis and carbo/sinensis groups. The sinensis and the carbo/sinensis groups belonged almost entirely to one genetic cluster, whereas the carbo group consisted of individuals with varying proportions of mixed ancestry. Furthermore, we found significant genetic differentiation between the carbo and sinensis groups, and between the carbo and the carbo/sinensis groups, but no significant differentiation between the sinensis and the carbo/sinensis groups. Our results suggest that gene flow is more common from sinensis into carbo than vice-versa, and that the use of GPA &lt; 73° has limitations for the identification of Great Cormorant subspecies in areas where both forms occur. We conclude that the numbers of carbo vs. sinensis individuals in our sample were 32 and 43, respectively.

Combined Mutual Learning Net for Raman Spectral Microbial Strain Identification.

Infectious diseases pose a significant threat to global health, yet traditional microbiological identification methods suffer from drawbacks, such as high costs and long processing times. Raman spectroscopy, a label-free and noninvasive technique, provides rich chemical information and has tremendous potential in fast microbial diagnoses. Here, we propose a novel Combined Mutual Learning Net that precisely identifies microbial subspecies. It demonstrated an average identification accuracy of 87.96% in an open-access data set with thirty microbial strains, representing a 5.76% improvement. 50% of the microbial subspecies accuracies were elevated by 1% to 46%, especially for E. coli 2 improved from 31% to 77%. Furthermore, it achieved a remarkable subspecies accuracy of 92.4% in the custom-built fiber-optical tweezers Raman spectroscopy system, which collects Raman spectra at a single-cell level. This advancement demonstrates the effectiveness of this method in microbial subspecies identification, offering a promising solution for microbiology diagnosis.

Golden Eagle Populations, Movements, and Landscape Barriers: Insights from Scotland

GPS satellite tracking allows novel investigations of how golden eagles Aquila chrysaetos use the landscape at several scales and at different life history stages, including research on geographical barriers which may prevent or limit range expansion or create population/sub-population isolation. If there are significant barriers to golden eagle movements, there could be demographic and genetic consequences. Genetic studies have led investigations on the identification of sub-species, populations, and sub-populations but should be conjoined with demographic studies and dispersal movements to understand fully such designations and their geographic delimitation. Scottish eagles are genetically differentiated from continental European birds, with thousands of years of separation creating a distinct population, though without sub-species assignation. They present unique research opportunities to examine barriers to movements illustrated by satellite tracking under Scotland’s highly variable geography. We primarily examined two features, using more than seven million dispersal records from satellite tags fitted to 152 nestlings. The first was the presence of unsuitable terrestrial habitat. We found few movements across a region of largely unsuitable lowland habitat between upland regions substantially generated by geological features over 70 km apart (Highland Boundary Fault and Southern Uplands Fault). This was expected from the Golden Eagle Topography model, and presumed isolation was the premise for an ongoing reinforcement project in the south of Scotland, translocating eagles from the north (South Scotland Golden Eagle Project: SSGEP). Second was that larger expanses of water can be a barrier. We found that, for a northwestern archipelago (Outer Hebrides), isolated by ≥24 km of sea (and with prior assignation of genetical and historical separation), there were no tagged bird movements with the Inner Hebrides and/or the Highlands mainland (the main sub-population), confirming their characterisation as a second sub-population. Results on the willingness of eagles to cross open sea or sea lochs (fjords) elsewhere in Scotland were consistent on distance. While apparently weaker than the Outer Hebrides in terms of separation, the designation of a third sub-population in the south of Scotland seems appropriate. Our results validate the SSGEP, as we also observed no movement of birds across closer sea crossings from abundant Highland sources to the Southern Uplands. Based on telemetric results, we also identified where any re-colonisation of England, due to the SSGEP, is most likely to occur. We emphasise, nevertheless, that our study’s records during dispersal will be greater than the natal dispersal distances (NDDs), when birds settle to breed after dispersal, and NDDs are the better shorter arbiter for connectivity.

DNA Barcoding of Locusta migratoria manilensis (Orthoptera: Acrididae) Reveals Insights into the Species and Subspecies Differentiation

Abstract Accurate identification and classification of insect species, especially those with significant economic and ecological implications, have historically presented challenges. Migratory locusts, Locusta migratoria manilensis (Meyen) (Orthoptera: Acrididae), are notorious for their destructive impact on crops. Traditional morphological methods often face limitations in distinguishing closely related species and require taxonomic expertise. However, the emergence of DNA barcoding as a powerful tool for species identification has revolutionized the field of entomology. DNA barcoding utilizes a standardized DNA sequence, a molecular barcode, which serves as a distinct genetic signature for rapid and accurate species identification. In this study, DNA barcoding techniques were employed to identify and differentiate the migratory locust subspecies manilensis, in both its solitary and gregarious forms, as well as to determine its phylogenetic relationship with other related species within the Acrididae family. GenBank reference sequences were used to identify the locusts at the molecular subspecies level. Although the COI marker did not exhibit significant differences between the solitary and migratory forms, it was valuable in resolving the identification of L. migratoria subspecies. This lack of significant differences may be attributed to limited genetic variation of COI at the subspecies level and substantial genetic similarities between the solitary and migratory forms, likely stemming from a recent common ancestor. Nonetheless, using COI remains beneficial for subspecies identification in migratory locusts.

Fatty Acid Methyl Ester Profiling of Californian Xylella fastidiosa Strains

Xylella fastidiosa ssp. fastidiosa ( Xff) is the causal agent of Pierce's disease of grapevine, a management-intensive and potentially deadly disease. However, different stains and other subspecies, such as Xylella fastidiosa ssp. multiplex ( Xfm), exist in the same regions and vary in capacity to cause disease. All strains differ in the fatty acids that comprise cell membranes, as these allow adaptations to specific host microenvironments. Therefore, studies were initiated to observe the fatty acid profiles of different Californian Xf isolates via fatty acid methyl ester (FAME) analysis. Observations revealed that the four Xff strains had similar FAME profiles that were distinct from those of the three Xfm strains, even in isolates that originated from the same host plant species. These data show consistent differences between Xff and Xfm strains and demonstrate the potential that FAME profiling has for Xylella subspecies identification of novel isolates. [Formula: see text] The author(s) have dedicated the work to the public domain under the Creative Commons CC0 “No Rights Reserved” license by waiving all of his or her rights to the work worldwide under copyright law, including all related and neighboring rights, to the extent allowed by law, 2024.

Treatment of Mycobacterium abscessus complex pulmonary disease

Background: In South Korea, bacteria in the &lt;i&gt;Mycobacterium abscessus&lt;/i&gt; complex (MABC), a group of rapidly growing mycobacteria, are second to those in the &lt;i&gt;Mycobacterium avium&lt;/i&gt; complex as a cause of non-tuberculous mycobacterial pulmonary disease. The MABC includes several subspecies, including &lt;i&gt;M. abscessus&lt;/i&gt; subsp. &lt;i&gt;abscessus&lt;/i&gt; (&lt;i&gt;M. abscessus&lt;/i&gt;) and &lt;i&gt;M. abscessus&lt;/i&gt; subsp. &lt;i&gt;massiliense&lt;/i&gt; (&lt;i&gt;M. massiliense&lt;/i&gt;), the former of which is difficult to treat owing to its antibiotic resistance.Current Concepts: &lt;i&gt;M. abscessus&lt;/i&gt; encodes a functional erythromycin ribosomal methylase gene, &lt;i&gt;erm&lt;/i&gt;(41), that causes inducible macrolide resistance. Contrastingly, &lt;i&gt;M. massiliense&lt;/i&gt; lacks a functional &lt;i&gt;erm&lt;/i&gt;(41) gene owing to a partial deletion. Accordingly, culture conversion rates using currently recommended macrolide-based antibiotic treatments are considerably higher among patients with &lt;i&gt;M. massiliense&lt;/i&gt; infection than in those infected with &lt;i&gt;M. abscessus&lt;/i&gt;. Phase therapy (intensive and continuous) is recommended for MABC pulmonary disease and, depending on the subspecies and antimicrobial susceptibility test results, should include an initial treatment of ≥3 to 4 injectable and oral antibiotics, followed by inhaled or intravenous amikacin and ≥1 to 2 oral antibiotics. Recommended injectable antibiotics include amikacin, imipenem or cefoxitin, and tigecycline, and oral antibiotics include macrolides (azithromycin or clarithromycin), clofazimine, linezolid, and rifabutin. For some patients, surgery should be considered as an adjunctive treatment option.Discussion and Conclusion: Given that &lt;i&gt;M. abscessus&lt;/i&gt; expresses the inducible resistance gene &lt;i&gt;erm&lt;/i&gt;(41) associated with macrolide resistance, the identification of MABC subspecies is important for disease management. However, despite the combined application of several injectable/oral antibiotics, the treatment outcomes for &lt;i&gt;M. abscessus&lt;/i&gt; pulmonary disease remain unsatisfactory.

Clinical characteristics of 42 patients with different subspecies of Mycobacterium abscessus complex pulmonary disease

Objective: To compare clinical features and treatment outcomes of Mycobacterium abscessus (M.abscessus) and Mycobacterium massiliense (M.massiliense) pulmonary disease. Methods: A retrospective analysis was performed for 42 patients diagnosed with M.abscessus complex pulmonary disease for the first time in Guangzhou Chest Hospital from January to September 2021. The age of the 42 patients was 17-73 years, including 15 males and 27 females. According to the targeted next-generation sequencing, the patients were divided into M.abscessus group (28 patients, including 10 males and 18 females) and M. massiliense group (14 patients, including 5 males and 9 females). The clinical characteristics, radiological findings, drug sensitivity and clinical efficacy evaluation at 6 months of the two groups were compared. χ2 test and t-test were used for comparison between two groups. Results: The main symptoms in M. abscessus and M. massiliense groups were cough and sputum production. Radiological findings were significantly more frequent in the M. abscessus group than in the M. massiliense group, tree-in-bud sign [22/28 (78.5%) vs. 5/14], nodular bronchiectasis [27/28 (96.4%) vs. 11/14], and lesions involving more than three lung fields [23/28 (82.1%) vs. 7/14]. Both groups showed high levels of resistance to all antimicrobials. The sensitivity rate of the M. massiliense group to clarithromycin was higher than that of the M. abscessus[13/14 vs. 15/28 (53.5%)], and the success rate of treatment was significantly higher in patients with M. massiliense at the 6-month efficacy evaluation. Conclusions: The radiological findings, drug sensitivity and treatment outcomes differ between M. abscessus and M. massiliense pulmonary disease. Improving the identification of bacterial subspecies in clinical practice can effectively improve the diagnosis and treatment.

Creation of a Biobank of the Sperm of the Honey Bee Drones of Different Subspecies of Apis mellifera L.

The cryopreservation of gametes and embryos is an important element of biodiversity conservation. One species in need of conservation is the honey bee Apis mellifera L. Changing environmental factors, especially the anthropogenic factor, have led to a reduction in the numbers of this insect species. In this study, we provide an example of the creation of a biobank of honey bee drone sperm. For sperm cryopreservation, drones of the most common subspecies of honey bees common in Russia were selected. These were the dark forest bee, Apis mellifera mellifera, from the Republic of Bashkortostan, with three subspecies (A. m. carnica, A. m. carpatica, and A. m. caucasica) from the southern regions of Russia, as well as two breeding stocks, the Far Eastern bee and Prioksky bee. For subspecies identification, morphometric and genetic methods were used. The subspecies of the studied samples were confirmed via the analysis of the tRNAleu-COII locus of mitochondrial DNA and nine microsatellite markers of nuclear DNA. It was shown that bees of the Prioksky breeding stock belong to the subspecies A. m. caucasica based on phylogenetic analysis, and the Far Eastern breeding stock is a stable hybrid, descending on the maternal line from the evolutionary lineage C or O. The results of the morphometric analysis are consistent with the results of the genetic analysis. For the cryopreservation of sperm, we used a cryoprotectant solution with honey. As a result, the viability of frozen–thawed sperm decreased by 20.3% compared to fresh sperm, and overall motility decreased 25-fold. The measurement of the sperm concentration in the spermatheca of artificially inseminated queens showed that it varied from 0.22 to 4.4 million/μL. Therefore, the use of honey in sperm cryopreservation has great potential.

Mycobacteriosis in slaughter pigs from South Africa from 1991 to 2002: Mycobacterium spp. diversity and Mycobacterium avium complex genotypes.

Mycobacterium avium complex (MAC) bacteria are the most prominent etiological agents of lymphadenitis in pigs. M. avium subspecies hominissuis (MAH) is a member of MAC and has been reported in many parts of the world to be the most prevalent non-tuberculous mycobacteria (NTM) to cause mycobacteriosis in humans, mainly in children. Thus, the economic and zoonotic impact of MAC species are increasingly being recognized. In South Africa, little is known about the distribution of NTM and the molecular epidemiology of M. avium in pigs. In this study, lymph nodes including mandibular, mesenteric, submandibular, and retropharyngeal, with tuberculosis-like lesions were collected during routine meat inspection of slaughter pigs with no disease symptoms (n = 132), between 1991 and 2002. These pigs were slaughtered at 44 abattoirs distributed across seven of the nine South African provinces. Mycobacterial culture, polymerase chain reaction (PCR), and sequencing of the Mycobacterium specific 577 bp 16S rRNA gene fragment were performed for species and subspecies identification. The majority of the isolates (each per sample); 114 (86.4%) were identified as MAH, 8 (6%) as MAA/M. avium subsp. silvaticum, 4 (3%) were Mycobacterium tuberculosis, 2 (1.5%) as Mycobacterium intracellulare, and 1 (0.75%) as Mycobacterium bovis. The other isolates were identified as Mycobacterium lentiflavum (0.75%), Mycobacterium novocastrense (0.75%), and a Micrococcus spp. (0.75%). Using an eight-marker MLVA typing tool, we deciphered at least nine MIRU VNTR INMV types of MAH and MAA. Identification of known zoonotic mycobacteria, including MAH, MAA, M. intracellulare, M. bovis, and M. tuberculosis, from slaughter pigs has a potential public health impact and also strengthens recognition of the potential economic impact of MAC. This study has also for the first time in South Africa, revealed MAC MIRU VNTR INMV genotypes which will aid in the future epidemiological investigation of MAC in South Africa.

Species identification and drug susceptibility testing of non-tuberculous mycobacteria by Line Probe Assay in Lambaréné, Gabon—a cross-sectional study

BackgroundNon-tuberculous mycobacteria (NTM) are a group of bacteria that cause rare lung infections and are increasingly recognized as causative agents of opportunistic and device-associated infections in humans. In Gabon, there is a lack of data on NTM species identification and drug susceptibility. The aim of this study was to identify the frequency of NTM species and their genotypic susceptibility pattern to commonly used antibiotics for NTM infections in Gabon.MethodsA cross-sectional study was conducted at the CERMEL TB laboratory from January 2020 to December 2022, NTM subspecies identification and drug susceptibility testing to macrolides and aminoglycosides were performed using the genotype NTM-DR kit.ResultsThe study found that out of 524 culture-positive specimens, 146 (28%) were NTM, with the predominant group being Mycobacterium avium complex (MAC) and Mycobacterium abscessus complex (MABC). All MAC isolates were fully susceptible to macrolides and aminoglycosides, while five MABC isolates carried mutations indicative of reduced susceptibility to macrolide and aminoglycoside drugs.ConclusionsThese findings suggest that clinicians may use macrolides and aminoglycosides to manage NTM infections caused by MAC, but further investigation is required to determine MABC drug susceptibility.