Genetic Distance Research Articles

Sequencing the Parasitic Nematode Contracaecum spp. in Edible Fish (Planiliza Abu)

Contracaecum rudolphii Hartwich,1 964 (Nematoda: Ascaridoidea, Anisakidae) is a typical anisakid recorded globally. Consumption of undercooked seafood, raw or infected, contains the nematode larvae that cause human anisakidosis . Fish (Planiliza abu) specimens were obtained from a local market in Karbala, Iraq. This type of fish came from the Razzaza Lake. The prevalence of Contracaecum spp. parasites was done over eight months from June 2022 until January 2023, using ITS1, morphological and molecular analysis of the nematodes Contracaecum spp from fish. Out of 395 fish, 124(31.3%) had visceral infections caused by Contracaecum spp. larval type (L3). The morphological and genetic identification of Contracaecum spp. was validated in the parasitology laboratory of the veterinary medicine college at Kerbala University. The result showed the infection rate in January 2023 was (46.6%) and it dropped in 2022, September with a percentage of (20%). With the use of ITS1 gene, the molecular analysis for Contracaecum spp. was to investigate Contracaecum spp. and to confirm it. However, the nematode count, number of infected fish, and length were all substantially different at the P≤0.05. This study detected the isolate=(a1) at the locus=OP787071 and sequencing the parasites. The isolates were confirmed as Contracaecum rudolphii, isolate a1 internal transcribed spacer 1, partial sequence. In conclusion, molecular genotyping might be a useful technique for identifying the Contracaecum L3 larval species., life-cycle biology, transmission methods, and types of intermediate hosts.

A novel LAMP-based assay for the identification of Streptococcus pneumoniae and Streptococcus pseudopneumoniae in clinical isolates.

The Gram-positive bacteria Streptococcus pneumoniae is part of the Streptococcus mitis group (SMG) and causes life-threatening infections, such as pneumonia, sepsis, and meningitis. The closely related Streptococcus pseudopneumoniae has recently been shown to cause respiratory tract infections, as well as invasive infections, especially in patients with comorbidities. Due to the genetic and phenotypic similarities of species belonging to the SMG, the identification of S. pneumoniae and S. pseudopneumoniae is difficult and unreliable using phenotypic tests, as well as matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) and 16S rRNA sequencing. In this study, a loop-mediated isothermal amplification (LAMP)-based assay was developed using molecular markers specific for S. pneumoniae (SPN0001) and S. pseudopneumoniae (SPPN_RS10375). The LAMP assay was evaluated using a collection of SMG clinical isolates, concluding that the method provides a correct, reliable, and fast identification of both S. pneumoniae and S. pseudopneumoniae clinical isolates.

Antimicrobial resistance, virulence factors and phylogenetic profiles of Vibrio parahaemolyticus in the eastern coast of Shenzhen

Vibrio parahaemolyticus (V. parahaemolyticus) is a major food-borne pathogen which causes human gastroenteritis. Since the characteristics of V. parahaemolyticus remain unknown, 220 isolates selected from clinical and environmental samples in Dapeng of Shenzhen were tested for the presence of two hemolysin-expressing genes tdh and trh. Among 27 clinical isolates, 26 carrired the tdh gene, and the other one carried both tdh and trh genes, however neither genes were detected in environmental isolates. Meanwhile, antimicrobial susceptibility profiles revealed the isolates with high frequency of resistance to ampicillin (77.73%) and colistin (71.82%) and medium to streptomycin (57.27%). Genetically, by whole genome sequencing (WGS), comparative genomics studies was performed on isolates from various districts and GenBank. Data analysis showed that antimicrobial resistance genes (ARGs) blaCARB, tet(34) and tet(35) were harbored in all genomes and other ARGs was absent in the genomes of 27 clinical isolates. Besides, little regional difference was observed. As for virulence factors, MAM7, T3SS1, T3SS1 secret effector, T3SS2, T3SS2 secret effector, and VpadF were carried by most isolates. Two isolates from other districts were tdh gene positive which clustered with clinical isolates from Dapeng in the same clade, indicating close genetic distance. This study revealed the widely distribution of V. parahaemolyticus in Shenzhen and the diverse ARGs and virulence genes it carried. Furthermore, pathways that pathogen disseminated through were discussed.

A new species of the genus Scincella (Squamata: Scincidae) from Mount Fansipan, Hoang Lien Son Range, northwestern Vietnam

We describe a new species of the genus Scincella Mittleman, 1950 from northwestern Vietnam, based on a new collection of ground skinks from Mount Fansipan of the Hoang Lien Son Range in Lao Cai Province. Scincella fansipanensis sp. nov. is distinguished from other Scincella species in the Indochina region and southern China by body size (SVL), separation of prefrontals, number of midbody scale rows, paravertebral scale rows, nuchals and subdigital lamellae on toe IV, separation of toe from finger when limbs are adpressed along the body, and dorsal color pattern. The new species is further distinguished from its congeners by uncorrected genetic distances of 14.60–21.41% (COI gene). The new species is currently known only from high elevation areas of Mt. Fansipan in Vietnam.

Rhipicephalus simus ticks: new hosts for phleboviruses.

Ticks are widespread arthropods that transmit microorganisms of veterinary and medical significance to vertebrates, including humans. Rhipicephalus simus, an ixodid tick frequently infesting and feeding on humans, may play a crucial role in transmitting infectious agents across species. Despite the known association of many Rhipicephalus ticks with phleboviruses, information on R. simus is lacking. During a study in a riverine area in Lusaka Zambia, ten R. simus ticks were incidentally collected from the grass and bushes and subjected to metagenomic next generation sequencing (mNGS) in 2 pools of 5. Analysis detected a diverse microbial profile, including bacteria 82% (32/39), fungi 15.4% (6/39), and viruses 2.6% (1/39). Notably, viral sequence LSK-ZM-102022 exhibited similarity to tick phleboviruses, sharing 74.92% nucleotide identity in the RdRp gene and 72% in the NP gene with tick-borne phlebovirus (TBPV) from Greece and Romania, respectively. Its RNA-dependent RNA polymerase (RdRp) encoding region carried conserved RdRp and endonuclease domains characteristic of phenuiviridae viruses. Phylogenetic analysis positioned LSK-ZM-102022 in a distinct but lone lineage within tick phleboviruses basal to known species like brown dog tick phlebovirus and phlebovirus Antigone. Pair-wise genetic distance analysis revealed similar findings. This study emphasizes the urgency of further research on the ecology, transmission dynamics, and pathogenic potential of LSK-ZM-102022 and related TBPVs, crucial for local and global preparedness against emerging tick-borne diseases.

A Phylogenetic Assessment of HIV-1 Transmission Trends among People Who Inject Drugs from Coastal and Nairobi, Kenya

ABSTRACT Background Although recent modeling suggests needle-syringe programs have reduced parenteral HIV transmission among people who inject drugs (PWID) in Kenya, the prevalence in this population remains high (~14-20%, compared to ~4% in the larger population). Reducing transmission or acquisition requires understanding historic and modern transmission trends, but the relationship between the PWID HIV-1 sub-epidemic and the general epidemic in Kenya is not well understood. Methods We incorporated 303 new (2018-2021) HIV-1 pol sequences from PWID and their sexual and injecting partners with 2,666 previously published Kenyan HIV-1 sequences to quantify relative rates and direction of HIV-1 transmissions involving PWID from the coast and Nairobi regions of Kenya. We used genetic similarity cluster analysis (thresholds: patristic distance <0.045 & <0.015) and maximum likelihood and Bayesian ancestral state reconstruction to estimate transmission histories at the population group (female sex workers, men who have sex with men, PWID, or general population) and regional (coast or Nairobi) levels. Results Of 1,081 participants living with HIV-1, 274 (25%) were not virally suppressed and 303 (28%) had sequences available. Of new sequences from PWID, 58% were in phylogenetic clusters at distance threshold <0.045. Only 21% of clusters containing sequences from PWID included a second PWID sequence. Sequences from PWID were similarly likely to cluster with sequences from female sex workers, men who have sex with men, and the general population. Ancestral state reconstruction suggested transmission to PWID from other populations was more common than from PWID to other populations. Conclusion This study expands our understanding of the HIV-1 sub-epidemic among PWID in Kenya by incorporating 4-times more HIV-1 sequences from this population than prior studies. Despite recruiting many PWID from local sexual and injecting networks, we found low levels of linked transmission in this population. This may suggest lower relative levels of parenteral transmission in recent years and supports maintaining needle-syringe programs among PWID while also strengthening interventions to reduce HIV-1 sexual acquisition and transmission for this population.

Genetic Diversity and Genome-Wide Association Study of Pleurotus pulmonarius Germplasm

Pleurotus pulmonarius is prized by consumers for its distinct flavor, strong aroma, and dense, crispy texture. Although China has extensive germplasm resources for P. pulmonarius, only a limited number of cultivars are commercially available. A comprehensive evaluation and detailed analysis of P. pulmonarius germplasm, alongside the exploration of superior germplasm resources, are essential for developing new varieties. In this study, we resequenced the genomes of 47 P. pulmonarius strains collected nationwide, identifying a total of 4,430,948 single nucleotide polymorphism (SNP) loci. After filtering based on minor allele frequency and data integrity, 181,731 high-quality SNP markers were retained. Phylogenetic analysis grouped the strains into six clusters, with strains from similar geographical regions clustering together. Most CBS strains formed a single cluster; cultivated varieties exhibited higher genetic similarity, whereas wild strains displayed greater diversity. Principal component analysis (PCA) and population structure analyses, using the same SNP markers, corroborated the phylogenetic findings. DNA fingerprinting, derived from 369 core SNPs, further underscored the genetic diversity among strains. Significant morphological variation was observed, with strains in groups ZP, CBS, and WHLJ exhibiting notably higher yields and cap widths compared to other groups. Correlation analysis revealed associations among various phenotypes, while genome-wide association study (GWAS) identified multiple SNP markers within candidate genes linked to agronomic traits, most of which were controlled by multiple genes. This research offers a molecular-level characterization and evaluation of P. pulmonarius germplasm resources, providing a scientific basis for enriching available germplasm and advancing breeding materials.

DurdusTools—An Online Genetic Distance Calculation Tool for Efficient Variety Testing in Durum Wheat (Triticum turgidum L. subsp. durum (Desf.) Husn.)

The management of variety collections can be supported by integrating molecular data into Distinctness, Uniformity, and Stability (DUS) testing. DurdusTools is a genetic distance (GD) calculation tool that supports planning field trials in durum wheat. A commercially available single-nucleotide polymorphism (SNP) wheat microarray is used to profile varieties and candidate varieties. Their molecular profiles are stored in a database. SNP markers selected based on quality parameters are used to calculate the pairwise genetic distance (GD) between the varieties. Combining molecular and variety information creates a downloadable, user-friendly Excel-based output. The file shows the pairwise GD of the varieties most similar to the candidate variety of interest and selected variety information. After the first year of field trials, the DUS experts use the phenotypic assessment data together with the GD information to select genotypes to be grown in the field for side-by-side comparisons. The principles of DurdusTools allow for an easy integration of molecular data into DUS testing. Using the tool requires neither specific infrastructure nor molecular expert knowledge and was developed by its users for DUS testing purposes. This makes DurdusTools an easily accessible and user-friendly tool that supports variety selection for DUS field trials through an improved data basis.

Hidden diversity in anthropophilic sand flies of the Monticola Series (Diptera, Psychodidae)

The Monticola series comprises two anthropophilic and widely distributed species in Brazil: Pintomyia (Pifanomyia) monticola (Costa Lima, 1932) and Pintomyia (Pifanomyia) misionensis (Castro, 1959). They mainly occur in the Atlantic Rainforest, and it is known that Pi. monticola comprises at least two well-structured genetic lineages regarding a fragment of the cytochrome c oxidase subunit I (COI) gene. Here, we aim to elucidate the taxonomic status of this group using integrative taxonomy tools. Collections were performed in nine localities of four Brazilian states, and COI fragments were sequenced and merged with publicly available data. Several single-locus species delimitation algorithms, genetic distance metrics, phylogenetic trees, and haplotype networks were used to uncover cryptic diversity and population structure within Pi. monticola and Pi. misionensis. The resulting genetic clusters were then tested for morphological differences through linear and geometric morphometry of several characters. We analyzed 152 COI sequences, comprising 48 haplotypes. The maximum intraspecific p distances were 8.21% (mean 4.17%) and 9.12% (mean 4.4%) for Pi. monticola and Pi. misionensis, respectively, while interspecific ones ranged from 10.94 to 14.09% (mean 12.33%). Phylogenetic gene trees showed well-supported clades for both species, with clear structuring patterns within them. Species-delimitation algorithms split our dataset into at least three putative species for each taxon. Moreover, population structure analysis showed a strong correlation between Atlantic Forest areas of endemism as sources of molecular variation in Pi. monticola. Morphometric analyses were significant for wing shape variation and some linear measurements (mainly of the head) when comparing specimens of different genetic clusters for both taxa. These results indicate strong genetic structuring of Monticola series species, confirmed by morphometry, indicating two possible cryptic species complexes.

Morphological, ecological and genetic characteristics of the sandy sculpin (<i>Leocottus kesslerii</i>, Cottidae) from the lakes Baikal, Arakhlei and Gusinoe, Transbaikalia

Studies on local forms of the Sandy sculpin, Leocottus kesslerii, in the lakes Baikal, Arakhlei and Gusinoye show that the differences between lake forms in terms of external morphology lie in the head length to width ratio. In the Baikal form, the head is wider than long, vs the opposite in both Apakhlei and Gusinoe forms. In the Baikal and Gusinoe forms, there is a gap between the dorsal fins, a gap being absent from the Arakhlei form and the dorsal fins are in touch with each other. In the Arakhlei form, the anal fin is long (37.4–43%, on average 39.3% SL). In the Baikal form, the length of the A base reaches 32.9% SL (29.0–34.5%). In the Baikal and Arakhlei forms, small and sparse bone prickles are present on the body, these being large and dense in the Gusinoe form. The differences identified show a low level of morphological isolation of the forms. More significant differences are established in ecological features: growth rate, food spectrum, reproductive characteristics, and fecundity values. The differences in ecological features are due to the adaptation of the Sandy sculpin forms to specific conditions of the lakes they inhabit. Studies on genetic differentiation were carried out using the control region (CR) of mtDNA. The study forms of the Sandy sculpin revealed weak genetic isolation. The p-distances between the L. kesslerii forms averaged from 0.33 ± 0.12 to 0.51 ± 0.24%. Such low values of genetic distances clearly lie within the limits of intraspecific variability. The data obtained on the morphological, ecological and genetic differentiation of lake forms of the Sandy sculpin show that fish from the lakes Baikal, Arakhlei and Gusinoe belong to the same nominative subspecies, Leocottus kesslerii kesslerii.

Characterization of a new barley greenbug resistance gene Rsg4 in the Chinese landrace CI 2458.

Barley (Hordeum vulgare) is a climate-resilient crop widely cultivated in both highly productive and suboptimal agricultural systems, and its ability to adapt to multiple biotic and abiotic stresses has contributed significantly to food security. Greenbug is a destructive insect pest for global barley production, and new greenbug resistance genes are needed to overcome the challenges posed by diverse greenbug biotypes in fields. CI 2458 is a Chinese landrace exhibiting a unique resistance profile to a set of 14 greenbug biotypes, which suggests the presence of a new greenbug resistance gene in CI 2458. A recombinant inbred line population from the cross Weskan × CI 2458 was developed, evaluated for responses to greenbug biotype F, and genotyped using single nucleotide polymorphism (SNP) markers generated by genotyping-by-sequencing. Linkage analysis revealed a single gene, designated Rsg4, conditioning greenbug resistance in CI 2458. Rsg4 was delimited to a 1.14 Mb interval between SNP markers S3H_666512114 and S3H_667651446 in the terminal region of chromosome arm 3HL, with genetic distances of 1.2 cM proximal to S3H_667651446 and 1.1 cM distal to S3H_666512114. Allelism tests confirmed that Rsg4 is a new greenbug resistance gene independent of Rsg1 and Rsg3, which reside in the same chromosome arm. Rsg4 differs from Rsg1 alleles and Rsg3 in its resistance to greenbug biotype TX1, one of the most widely virulent biotypes. The introgression of Rsg4 into locally adapted barley cultivars is of agronomic importance, and kompetitive allele-specific polymerase chain reaction (KASP) markers flanking Rsg4, KASP-Rsg336-1 and KASP-Rsg336-2, enable rapid pyramiding of Rsg4 with other resistance genes to develop durable greenbug-resistant cultivars.

Estimation of Jacquard's genetic identity coefficients with bi-allelic variants by constrained least-squares.

The Jacquard genetic identity coefficients are of fundamental importance in relatedness research. We address the estimation of these coefficients as well as other relationship parameters that derive from them such as kinship and inbreeding coefficients using a concise matrix framework. Estimation of the Jacquard coefficients via likelihood methods and the expectation-maximization algorithm is computationally very demanding for large numbers of polymorphisms. We propose a constrained least squares approach to estimate the Jacquard coefficients. A simulation study shows constrained least squares achieves root-mean-squared errors that are comparable with those of the maximum likelihood approach, in particular when founder allele frequencies are unknown, while obtaining enormous computational savings.

Least absolute shrinkage and selection operator regression used to select important features when predicting wheat yield from various genotype groups

Abstract Bread wheat and durum wheat genotypes were grown in field experiments at two locations in New South Wales, Australia across several years and using two sowing times (‘early’ v. ‘late’). Genotypes were grouped based on genetic similarity. Grain yield, grain size, soil characteristics and daily weather data were collected. The weather data were used to calculate water and heat stress indices for four key growth periods around flowering. Least absolute shrinkage and selection operator (LASSO) was used to predict grain yield and to identify the most influential features (a combination of index and growth period). A novel approach involving the crop water supply–demand ratio effectively summarized water relations during growth. LASSO predicted grain yield quite well (adjusted R2 from 0.57 to 0.98), especially in a set of durum genotypes. However, the addition of other important variables such as lodging score, disease incidence, weed incidence and insect damage could have improved modelling results. Growth period 2 (30 days pre-flowering up to flowering) was the most sensitive for yield loss from heat stress and water stress for most features. Although one group of bread wheat genotypes was more sensitive to water stress (drought) in period 3 (20 days pre-flowering to 10 days post-flowering). Evapotranspiration was a significant positive feature but only in the vegetative phase (pre-flowering, period 1). This study confirms the usefulness of LASSO modelling as a technique to make predictions that could be used to identify genotypes that are suitable candidates for further investigation by breeders for their stress-tolerance ability.

The genetics of fruit skin separation in date palm

The physical appearance of date palm (Phoenix dactylifera) fruit (dates) is important for its market value. Many date-producing countries experience significant financial losses due to the poor appearance of the fruit, skin separation or puffiness being a major reason. Previous research showed evidence linking the skin separation phenotype to environmental conditions. To investigate this further, a genome-wide association study was conducted using genome data from 199 samples collected from 14 countries. Here, we identified nine genetic loci associated with this phenotype and investigated genes in these regions that may contribute to the phenotype overall. Multiple genes in the associated regions have functional responses to growth regulators and are involved in cell wall development and modification. Analysis of gene expression data shows many are expressed during fruit development. We show that there are both environmental and genetic contributions to the fruit skin separation phenotype. Our results indicate that different date cultivars exhibit varying degrees of skin separation despite genetic similarities or differences. However, genetically different cultivars show extreme differences compared to the phenotype variation between genetically similar cultivars. We demonstrate that beyond environmental factors, genetics is a strong contributor to the most extreme skin separation in some cultivars. Identifying the genetic factors may help better understand the biology and pathways that lead to the environmental effects on skin separation and improve commercial date production. In conclusion, our key finding is that both environmental and genetic factors contribute to skin separation variation, and improvements in environmental factors alone cannot overcome the extreme level of variation observed in some cultivars.

First report on the diversity of domestic pigeons (Columba livia) using plumage coloration and patterning in Saravena, Arauca, Colombia

The domestic pigeon (Columba livia Gmelin, 1789), native to Africa and Eurasia, is extensively found across Europe, Western Asia, Africa, and the Americas. The pigeon (Columba livia) was domesticated several centuries ago and holds a privileged place as a symbol of peace, love, fidelity, and ornamentation in parks. In recent decades, an increase in the populations of these pigeons has been detected. The Spanish brought Columba livia to Colombia in the 15th century. The objective of this study was to evaluate the genetic diversity of the domestic pigeon using loci related to plumage coloration and patterning in Saravena. Random sampling was conducted in six colonies between March and April 2024. Through urban visits, direct observation, and photographic records, a phenotypic classification of each of the 580 pigeons from the different flocks studied was carried out. Autosomal markers associated with coloration and plumage were analysed: Grizzle, Spread, Checker, and the sex-linked locus Ash-Red. Genetic profiles were calculated using indices: allele frequency, genetic diversity, and population structure, estimated with the PopGene 1.31 program. Diversity was assessed using the FSTAT program. The dendrogram was constructed with the MEGA X program. The marker with the highest allele frequency was Grizzle (P=0.1834), while the Spread marker had the lowest values (P=0.0300). The highest HT value was 0.3002 for the Grizzle marker, GST showed figures of 0.0360, and gene flow was 20.6; the FIS and FIT statistics reported values of 0.2779 and 0.2848, and FIT was 0.0091. Moderate genetic diversity, a deficit of heterozygotes, and an excess of homozygotes were observed, along with low interpopulation genetic differentiation and high gene flow between subpopulations. Low genetic distance values were also found between the studied subpopulations. The populations are closely related genetically, which may be due to their geographical proximity, which has favoured genetic exchange.

Biological Characterization and Evaluation of the Therapeutic Value of Vibrio Phages 4141 and MJW Isolated from Clinical and Sewage Water Samples of Kolkata

The growing prevalence of antimicrobial resistance (AMR) necessitates the development of new treatment methods to combat diseases like cholera. Lytic bacteriophages are viruses that specifically target and lyse bacteria upon infection, making them a possible treatment option for multi-drug-resistant pathogens. The current study investigated the potential role of bacteriophages isolated from clinical stool and sewage water samples in treating multi-drug-resistant Vibrio cholerae infection, finding that over 95% of the strains were susceptible. Whole-genome sequencing (WGS) analysis revealed that both Vibrio phage 4141 (4141) and Vibrio phage MJW (MJW) contain double-stranded DNA genomes consisting of 38,498 bp (43% GC) and 49,880 bp (42.5% GC) with 46 and 64 open reading frames (ORFs), respectively. Transmission electron microscope (TEM) and WGS analysis of Vibrio phage 4141 and Vibrio phage MJW validated that they are classified under the family Autographiviridae and Zobellviridae, respectively. Furthermore, both the phages showed highly significant biofilm degradation properties. The characterization of the phages and their strict host range, high spectrum of lytic ability, high efficiency of biofilm degradation, and close genetic similarity to the therapeutic phages indicates that these phages may be useful for therapeutic purposes for treating MDR V. cholerae infection in the future.

Genetic diversity assessment of cucumber landraces using molecular signatures

Genetic profiling of the biodiversity in cultivated crop plants is necessary to preserve important genes and utilize them in a breeding program. Cucumber is used as a model plant to study various characteristics of Cucurbitaceae. Its adaptation to a wide range of climatic conditions suggested analyzing the landraces. The present study was conducted to evaluate the differences, at the genetic level, among landraces spanning five continents. DNA extracted from fifty-six landraces selected from USDA germplasm bank to cover a global representative sample of world cucumber landraces was used for polymerase chain reaction using twenty-eight polymorphic expressed sequence tags simple sequence repeat (EST-SSR) markers. Twenty-eight EST-SSR markers covering all seven chromosomes yielded 98 bands with an average of 3.42 bands per marker. Polymorphic information content ranged from 0.00 (EC35) to 0.74 (EC17) with an average of 0.34. Six clusters provided an appropriate summary of the variation among the landraces, with the two largest groups including 32 (Asiatic) and 17 (European and American) landraces, respectively. Four small groups, three with two members, and one with one member (PI 525155-Egypt) were dissimilar to the two main groups. Landraces from the same region were often clustered together. Genetic similarity of the landraces was revealed by marker banding patterns. The locations of genetic diversity for cucumber landraces can be identified from this study.

Pasteurella multocida from deep nasal swabs and tracheobronchial lavage in bovine calves from Sweden

BackgroundBovine respiratory disease (BRD) is common in intensively raised cattle and is often treated with antibiotics. For practitioners, knowledge of the bacteria involved in an outbreak and their antibiotic susceptibility is warranted. To this end, samples from the upper or lower respiratory tract of calves can be submitted for bacteriological culture and susceptibility testing of relevant isolates. However, it is debated whether isolates from the upper respiratory tract are representative of bacteria causing infections in the lower respiratory tract. In this study, we used MALDI-TOF MS, multilocus sequence typing (MLST) and core-genome multilocus sequence typing (cgMLST) to compare culture results of 219 paired samples (sample pairs) of deep nasal swabs (DNS) and tracheobronchial lavage (TBL). The sample pairs came from 171 calves in 30 calf groups across 25 farms with 48 calves sampled twice.ResultsThe predominant bacterial pathogen was Pasteurella multocida, which was isolated from 37.4% of DNS and 22.4% of TBL. There was no statistically significant difference in isolation frequency of P. multocida between calves considered healthy and those suspected for BRD for DNS (P = 0.778) or TBL (P = 0.410). Among the 49 sample pairs where P. multocida was isolated from TBL, the same species was isolated from DNS in 29 sample pairs (59.2%). Isolates from 28 of these sample pairs were evaluated by MLST, and in 24 pairs (86.0%) P. multocida from DNS and TBL were of the same sequence type (ST). Moreover, cgMLST showed that the genetic distance between isolates within 21 of the 28 sample pairs (75.0%), was less than two alleles, and DNS and TBL isolates were considered identical. In seven sample pairs (25%), the genetic distance was greater, and DNS and TBL isolates were considered nonidentical.ConclusionsPasteurella multocida was readily isolated from DNS and in calves where this species was isolated also from TBL, DNS and TBL isolates were identical in 75% of the sample pairs. This suggests that during an outbreak of BRD, submission of DNS samples from 4 to 6 calves could be a convenient approach for practitioners seeking guidance on P. multocida present in the lower respiratory tract and their antibiotic susceptibility.

Genomic DNA extraction methods and phylogenetic analysis of Beauveria bassiana from Central Java, Indonesia, and its toxicity against the fall armyworm, Spodoptera frugiperda J.E. Smith (Lepidoptera: Noctuidae)

BackgroundControl techniques using biological control agents such as Beauveria bassiana (Balsamo) Vuillemin have the advantage of not showing any negative impacts on environmental health and safety issues. This study used isolates from B. bassiana collection from Laboratory of Pest Monitoring belonging to Indonesian Ministry of Agriculture (LPHP) in Central Java which showed potential in controlling target pest. The problems that still occur are the lack of facilities and infrastructure and the lack of quality testing of collection isolates in LPHP, so that the isolate identification process is still carried out in simple method, and bioassay testing on the fall armyworm (FAW), Spodoptera frugiperda J.E. Smith (Lepidoptera: Noctuidae) as a target pest, is not commonly conducted. The results of bioassay testing can be used to determine the potential of a biological agent to control target pest.ResultThe two DNA extraction methods showed different results regarding DNA concentration and purity values, but both methods were good and could be used to amplify DNA using PCR. The DNA band was amplified at 500–600 bp using primers ITS 1 and ITS 4. The results of molecular analysis showed that the four isolates of B. bassiana from Central Java were found in the same clade as B. bassiana from South Sumatra, Dhaka, and Oromia, where these isolates showed similar similarities descended from a common ancestor. Genetically, B. bassiana isolates from Central Java show more genetic similarities to B. bassiana isolates from South Sumatra, Indonesia. Quality testing was carried out by calculating the density and germination ability values for LPHP isolates from Sukoharjo (Sukoharjo isolate), Temanggung (Purworejo isolate), and Banyumas (Banyumas and Cilacap isolate), which showed varying results. The bioassay test used three isolates, namely B. bassiana from Sukoharjo, Banyumas, and Cilacap, which were selected based on density values, germination ability, and molecular analysis. The ability to cause death of the three isolates against S. frugiperda showed different results where the isolate from Sukoharjo, Banyumas, and Cilacap caused mortality of 60, 40, and 60%, and the LC50 value of each isolate was 3.3 × 106, 1.3 × 107, and 3.5 × 107 conidia ml−1, respectively.ConclusionMorphological identification by macroscopic, microscopic, and molecular analysis showed that the isolate from the LPHP collection in Central Java, Indonesia, was B. bassiana. Genetically, the four isolates showed similar characteristics to isolates from South Sumatra, Indonesia. B. bassiana isolates from collections from Central Java showed potentials as a biological control agent against S. frugiperda.

Fine-scale genetic structure and rare variant frequencies.

In response to the current challenge in genetic studies to make new associations, we advocate for a shift toward leveraging population fine-scale structure. Our exploration brings to light distinct fine-structure within populations having undergone a founder effect such as the Ashkenazi Jews and the population of the Quebec' province. We leverage the fine-scale population structure to explore its impact on the frequency of rare variants. Notably, we observed an 8-fold increase in frequency for a variant associated with the Usher syndrome in one Quebec subpopulation. Our study underscores that smaller cohorts with greater genetic similarity demonstrate an important increase in rare variant frequencies, offering a promising avenue for new genetic variants' discovery.