GenBank Database Research Articles

Molecular Characterization of Neem Rhizosphere Bacteria as A Nitrogen Fixer Isolated from The Dry Land of East Lombok

Bacteria have an important role in providing essential nutrients for plants in dry land through various beneficial working mechanisms. One of the main mechanisms is the involvement of bacteria in nutrient cycles, such as the nitrogen cycle. The aim of this research was to determine the type and ability of bacteria in the rhizosphere of neem (Azadirachta indica) to fix nitrogen. The method used in this research is an exploratory descriptive type. The results of the isolation carried out from the rhizosphere of neem (Azadirachta indica) taken from the East Lombok area of Jerowaru sub-district, 5 samples were obtained with the code LO, where 2 isolates had the ability to fix nitrogen, namely LO3 and LO4. This is proven by using NFB media where there is a change in the color of the media from green to blue, and quantitatively using a spectrophotometer with results of 1,112 ppm and 2,156 ppm, respectively. The results of the molecular identification of the potential bacteria, namely LO4, using the BLAST method at the GenBank data base (NCBI), show that LO4 is the closest relationship to the species Lysinibacillus fusiformis strain SMC303. The results above show that rhizobacteria isolated from neem have the potential to be developed as a biofertilizer that can be applied to future cultivated plants.

Isolation and Molecular Characterization of Brotowali (Tinospora crispa) Rhizosphere Bacteria Producing Siderophore from Dry Lands of Lombok Island

In the context of biopesticide development, siderophore-producing rhizosphere bacteria play an important role as potential biological control agents. Siderophores are complex organic compounds produced by microorganisms to bind and take up iron ions (Fe3+) from the surrounding environment. This compound is very important because iron is a nutrient necessary for life for many microorganisms and plants. The aim of this research was to determine the type and ability of bacteria in the rhizosphere of Brotowali (Tinospora crispa) to produce siderophores. The method used in this research is an exploratory descriptive type. The isolation results obtained from the North Lombok area obtained 5 samples with codes B4A1, B6A1, BT61, BT63 and BT83. The results of the bacterial isolate potency test with Media Kings showed that only isolate BT63 showed clear fluorescence when exposed to ultraviolet light. Meanwhile, the Arnow's Assay test showed that only BT63 colonies experienced a color change to pink. The results of the molecular identification of the potential bacteria, namely BT63, using the BLAST method using the GenBank data base at NCBI, show that it is closely related to the species Bacillus thuringiensis strain FDAARGOS 791. The results above show that the rhizobacteria isolated from Brotowali have the potential to be developed as a natural biopesticide that can be applied in the future.

The low level of plastome differentiation observed in some lineages of Poales hinders molecular species identification.

Chloroplast genomes are a source of information successfully used in various fields of plant genetics, including molecular species identification. However, recent studies indicate an extremely low level of interspecific variability in the plastomes of some taxonomic groups of plants, including the genus Stipa L., which is a representative of the grass family. In this study we aimed to analyze the level of chloroplast genome diversity within particular genera as well as the effectiveness of identifying plant species in the Poaceae family and the other representatives of Poales order. Analysis of complete plastid genome alignments created for 96 genera comprising 793 species and 1707 specimens obtained from the GenBank database allowed defining and categorizing molecular diagnostic characters distinguishing the analyzed species from the other representatives of the genus. The results also demonstrate which species do not have any species-specific mutations, thereby they cannot be identified on the basis of differences between the complete chloroplast genomes. Our research showed a huge diversity of the analyzed species in terms of the number of molecular diagnostic characters and indicated which genera pose a particular challenge in terms of molecular species identification. The results show that a very low level of genetic diversity between plastomes is not uncommon in Poales. This is the first extensive research on super-barcoding that tests this method on a large data set and illustrates its effectiveness against the background of phylogenetic relationships.

Silver nanoparticles synthesized by probiotic bacteria and antibacterial role in resistant bacteria

Many dangerous bacteria have become highly resistant to traditional antibiotics, which is a huge public health concern. This study investigated the use of silver nanoparticles biosynthesized in a culture filtrate of Lactobacillus acidophilus as antimicrobials. UV–visual spectrophotometry, Fourier-transform-infrared spectroscopy, X-ray power diffraction, and scanning electron microscopy have all validated the findings. The biosynthesized nanoparticles ranged in size from 33 to 90 nm. The cytotoxicity of the nanosilver generated was then investigated using nine 200 g BW rats separated into three groups. When compared to the control group, the treated rats showed little signs of toxicity; parameters of physiological function, including alanine transaminase, aspartate aminotransferase, albumin, creatinine, and urea were significantly different in treated and non-treated animals. Moreover, the antibacterial role of the generated silver nanoparticles was examined in multi-drug resistant (MDR) pathogenic bacteria, Proteus vulgaris, Escherichia coli, Staphylococcus aureus, and Klebsiella pneumoniae, revealing high antibacterial activity against the examined bacteria. For more demonstration of the effect of the nanosilver on transcription and gene regulation of treated and non-treated bacteria differential display droplet digital-PCR was used, and the results revealed that several genes were up- and down-regulated. Some genes were selected for DNA sequencing and according to the sequence analysis, these genes were mecA, beta-lactam, and unidentified protein genes, and these have been deposited in the GenBank Database with the following accession numbers: Staphylococcus MZ748472 and Klebsiella MZ748473. We conclude that silver nanoparticles biosynthesized by L. acidophilus are environmentally friendly and have antibacterial activities against MDR pathogenic bacteria.

Molecular analysis and geographic distribution of the recent Indonesian rabies virus.

Some Indonesian islands, including Sumatra, Kalimantan, Sulawesi, Java, and East Nusa Tenggara, have endemic rabies. Rabies outbreaks in Bali began from 2008 to 2011 and continue to occur sporadically. This study aimed to study the molecular analysis and geographical distribution of Indonesian rabies virus (RABV) from 2016 to 2021 and compare to previous periods. Virus isolates from 2016 to 2021 were extracted from dog brains and sequenced at the nucleoprotein gene locus. They were compared with data sequences available in the GenBank database. Indonesian RABV from the previous three periods (before 1989, 1997-2003, and 2008-2010) was extracted from the GenBank database. The genetic diversity in this study was based on the N gene of Indonesian RABV. Asian RABV, which is genetically close to the Indonesian virus, is a virus from China (ASIA-3 cluster) and from the Southeast Asia region, namely, virus isolates from Sarawak and Malaysia and some Cambodian isolates. Rabies virus, which was isolated from the Bali islands, was the new cluster first detected and published in Bali, Indonesia, in 2008, while RABV from West Sumatra Province, which was isolated from 2016 to 2021, was also considered a new cluster that is genetically distant from other clusters in Indonesia. The RABV in Indonesia is divided into five clusters. The isolates from West Sumatra Province from 2016 to 2021 were a new cluster genetically distant from other Indonesian viruses.

RNA virus diversity in rodents.

Many zoonotic disease emergencies are associated with RNA viruses in rodents that substantially impact public health. With the widespread application of meta-genomics and meta-transcriptomics for virus discovery over the last decade, viral sequences deposited in public databases have expanded rapidly, and the number of novel viruses discovered in rodents has increased. As important reservoirs of zoonotic viruses, rodents have attracted increasing attention for the risk of potential spillover of rodent-borne viruses. However, knowledge of rodent viral diversity and the major factors contributing to the risk of zoonotic epidemic outbreaks remains limited. Therefore, this study analyzes the diversity and composition of rodent RNA viruses using virus records from the Database of Rodent-associated Viruses (DRodVir/ZOVER), which covers the published literatures and records in GenBank database, reviews the main rodent RNA virus-induced human infectious diseases, and discusses potential challenges in this field.

First record and phylogenetic relationship of the endangered species Betta foerschi (Vierke, 1979) (Anabantiformes : Osphronemidae) from Belitung Island, Indonesia

Betta foerschi (Vierke, 1979) is a betta fish group from the Osphronemidae family which is only known from Central and West Borneo Island, Indonesia. This species is classified as an Endangered (EN) by the IUCN Red List, where the population has recently been moderately decreased. The new distribution of B. foerschi fish has been found on Belitung Island based on morphological similarities. In this research, we report the first record and phylogenetic relationship of B. foerschi based on the DNA Barcoding method using the Cytochrome C Oxidase Subunit I (COI) gene from Belitung Island Indonesia. Additionally, the DNA barcoding for B. foerschi not only represents the first DNA record for Belitung Island, but also the first sequence reported in the Genbank database. The result showed that B. foerschi forms the same clade within the Osphronemidae family and Betta genus solidifying its position in this taxonomic group with the closest genetic distance that occurs between B. foerschi and B. persephone of 0.15 using the Maximum Composite Likelihood model analysis.

Prevalence and Molecular Identification of Cryptosporidium Species among Human Population in Zakho District, Duhok Province, Kurdistan Region, Iraq

This cross-sectional study was carried out to determine the prevalence and molecular identifications of Cryptosporidium species among the human population in Zakho district, Duhok Province, Kurdistan Region, Iraq. The study was performed during the period from August 2021 to March 2022 and involved 700 fecal specimens of both genders and different ages collected from Zakho General Hospital and pri¬mary schools located in the suburban area of Zakho City. The data were analyzed using statistical soft¬ware version SPSS (25). Cryptosporidium species oocyst was found in 87.57% (613/700) of the examined specimens using the Modified Ziehl Neelsen technique. Males showed a slightly higher infection rate than females (88.4% vs 85.5%) with a non-significant difference (P> 0.05). The highest infection rate (91.7%) was present in individuals between the ages of >30 to 40 years, with a statistically significant difference (P<0.05). Molecular identification of Cryptosporidium species was estimated using 18S-rRNA gene for Cryptosporidium genus using Nested PCR technique and genus-specific primers (Cry18 AS1 and Cry18 S2) that yielded 347 bps product indicating Cryptosporidium genus, then species-specific (Cry18 AS1 and Cry18 S1) were used for the detection of Cryptosporidium parvum and Cryptosporidium hominis. 45/50 samples were positive and revealed 240 bps. The acquired sequences were deposited into the GeneBank database under the accession numbers OP107010 for C. hominis, OP104444, OP153870, OP163188, OP163414, and OP164631 for C. parvum.

Molecular identification of Pelawan Merah (Tristaniopsis merguensis Griff.) as an endemic plant from Bangka Belitung Island using chloroplast DNA rbcL gene

The DNA barcoding from this molecular identification will be submitted to the NCBI Genbank database to become a standard in the identification of Tristaniopsis merguensis Griff based on the rbcL gene analysis. This research will be used as a crucial information to identify the endemic species of Tristaniopsis merguensis Griff. which has no conservation status yet on IUCN Red List & Threated species. The stages of this research were collecting samples of Pelawan Merah leaves from Hutan Pelawan Namang, Central Bangka Regency. Molecular analysis was carried out to obtain the marker gene of Tristaniopsis merguensis Griff. The DNA barcoding of Tristaniopsis merguensis Griff yielded a 516 base-pair long sequence of rbcL gene. This is the first report of Tristaniopsis merguensis Griff DNA barcoding in Indonesia and the barcode has registered in the GenBank. This DNA barcoding also aims to register the plant biodiversity in supporting of the Barcode of Life (CBOL). Based on the results of BLAST DNA analysis, Pelawan Merah from Bangka Island has similarity up to 100% with Tristaniopsis sp. found in Australia. Furthermore, the phylogenetic tree analysis reveals that the Tristaniopsis merguensis Griff. in this study was very closely related to other species of genus Tristaniopsis. This suggested that the rbcL gene analysis could identify Tristaniopsis at the genetic level or higher and other DNA barcoding region analysis as Internal Transcribed Spacer gene was necessary to complete the Pelawan Merah identification.

Deciphering the genetic basis of resistome and virulome diversity among multidrug-resistant Mycoplasma hominis

Mycoplasma hominis, a commensal bacterium that commonly inhabits the genital tract, leading to infections in both the genitourinary and extragenital regions. However, the antimicrobial resistance and pathogenic mechanisms of M. hominis isolated from extra-urogenital cystic abscess is largely unknown. This study reports the genomic epidemiological characteristics of a M. hominis isolate recovered from a pelvic abscess sample in China. Genomic DNA was extracted and sequenced using Illumina HiSeq X Ten platform. De novo assembly was performed and in silico analysis was accomplished by multiple bioinformatics tools. For phylogenomic analysis, publicly available M. hominis genomes were retrieved from NCBI GenBank database. Whole genome sequencing data showed that the genome size of M. hominis MH4246 was calculated as 679,746 bp, with 558 protein-coding sequences and a G + C content of 26.9%. M. hominis MH4246 is resistant to fluoroquinolones and macrolides, harboring mutations in the quinolone resistance-determining regions (QRDRs) (GyrA S153L, ParC S91I and ParE V417I) and 23S rRNA gene (G280A, C1500T, T1548C and T2218C). Multiple virulence determinants, such as tuf, hlyA, vaa, oppA, MHO_0730 and alr genes, were identified. Phylogenetic analysis showed that the closest relative of M. hominis MH4246 was the strain MH-1 recovered from China, which differed by 3490 SNPs. Overall, this study contributes to the comprehension of genomic characteristics, antimicrobial resistance patterns, and the mechanisms underlying the pathogenicity of this pathogen.

Molecular analysis of adenovirus strains responsible for gastroenteritis in children, under five, in Tunisia

Purpose of workEnteric Adenovirus (EAdV) is recognized as one of the most commonly identified agents responsible for severe acute gastroenteritis (AGEs) in the stools of infants.We sought to determine the rate of human adenovirus (HAdV) infections, and the genotypic characterization of circulating strains of HAdV in children under 5 years of age with AGEs in university and regional hospitals, located in the Center-East of Tunisia, from January 2014 to December 2016. MethodsA classic PCR was performed on 582 stool samples taken within 5 days of the onset of symptoms. Chosen positive samples were sequenced, and some of the results were confirmed by the Next Generation Sequencing technique (NGS). Partial nucleotide sequences of the Hexon gene obtained in this study were compared with the NCBI GenBank database using BLAST. Multiple sequence alignment and phylogenetic analysis were conducted using MEGA6 software. The phylogenetic tree was generated using the maximum-likelihood method and bootstrap analysis was performed with 1000 replications. ResultsOut of 582 samples, 52 (8.93 %) cases were positive for HAdV, with a male predominance (57.4 %). Phylogenetic analyses showed that Tunisian HAdV strains clustered into five HAdV lineages corresponding to serotypes F41 (14/28), C2 (9/28), C5 (3/28), E4 (1/28), and A18 (1/28). HAdV was more frequent in children aged up to 12 months, as compared to the other age groups. The HAdV activity was noted in almost all the months of the year with a peak in autumn, in 2014 and 2015, and in winter in 2016. ConclusionThis study showed that infections with HAdV species were frequent in children suffering from AGE with the predominance of HAdV F41 and C2. This result underlines the importance of regular monitoring of circulating genotypes, and it could be useful for future epidemiological research.

Analysis of Genetic Variation of MatK Gene Sequences in Ammothamnus lehmannii NCBI Popset 2440747918 Using In Silico RFLP

Genetic diversity or genetic variation is variation that occurs in an organism due to differences in the sequence of nucleotide bases (adenine, thymine, guanine and cytosine) that form DNA in cells. Variation genetics can be studied in silico using available gene sequences in the NCBI genbank database. This study used the MatK (Maturase-K) gene sequence with the identity number Popset 2440747918 which was downloaded in fasta format from NCBI . Then screening of restriction enzyme candidates was carried out to determine the restriction enzymes prior to in silico RFLP. The restriction enzyme selected from the screening was the restriction enzyme HindIII which has the recognition site A'AGC_T. The results obtained from 79 samples of DNA sequences, 76 samples were cut and 3 samples were not. And found three allele variations with the percentage of the presence of fragments A1 (86.07%), A2 (10.12%) and A3 (3.79%). The percentage values and frequencies of these A1, A2 and A3 alleles indicate a low level of genetic variation.

Identification of Previously Unrecorded Bacills, Serratia, and Mucor Strains Isolated from Yogurt

(1) Background: Foodborne illnesses are recognized as a significant threat to public health and the economy in both developed and developing nations. The safety of foods containing microorganisms has consequently become a major worldwide concern. One of the most frequent causes of food deterioration in the world is microbial contamination. (2) Methods: Yogurt containers that were bought commercially in Riyadh, Saudi Arabia during their validity period contained four different species of bacteria and one type of fungus. Using nutritional agar and Czapek-Dox agar medium, the bacteria and fungi were isolated. The isolates of the fungi and bacteria were identified using a scanning microscope. The isolates were further identified and classified for molecular evolutionary analyses using the 16S rRNA and ITS sequences from the bacteria and fungi, respectively, in conjunction with the universal primers 27F, 1492R, ITS1F, and ITS4R. (3) Results: A total of 131 separate strains were identified from 12 yogurt samples based on their phenotypic characteristics. In total, 79 isolates (60.3%) consisted of Serratia marcescens, Bacillus subtilis, and Mucor circinelloides, with 52 isolates (39.7%) being Bacillus cereus. While the cells of Bacillus and Serratia are shaped like rods, the sporangia of Mucor are large, round, and black. Each strain was identified by its accession number, which were as follows: MK590996.1: B. cereus; MK591144.1: B. subtilis; MK591002.1 and MK591014.1: S. marcescens; and MK559692.1: M. circinelloides. The maximum identification was found to be between 98.64 and 100% when BLAST was used to compare the sequences to the NCBI GeneBank database. (4) Conclusions: Genus and species identification was performed using the similarity score values. Yogurt products containing high concentrations (39.7%) of Bacillus cereus isolates carry a significant risk of health hazards due to the potential for spreading pathogenic bacteria to humans.

Role of DLA-DRB1 amino acids outside the shared epitope in dachshund susceptibility to immune-mediated polyarthritis

Canine immune-mediated polyarthritis (IMPA) is an idiopathic disorder encompassing both erosive and non-erosive forms of rheumatoid arthritis (RA), with a clinical picture similar to human RA. Resemblance in major histocompatibility complex (MHC)-associated risk between the two was first noted within the specific amino acid motif known as the shared epitope (SE) on human leukocyte antigen DRB1. Following further identification of amino acids conferring risk for human RA outside the SE, this study was designed to examine amino acids both within and outside the classic SE in dachshunds, a breed with reported susceptibility to IMPA in Japan. Genome-wide association studies have linked positions 11, 13 and 71 with strong risk for human RA and important roles in antigen presentation to T cells. Sequence based genotyping of 16 case and 64 control dachshunds revealed strong associations comparable to human RA between IMPA risk and valine at position 11 (Val-11), phenylalanine at 13 (Phe-13), and arginine at 71 (Arg-71) on the dog leukocyte antigen (DLA)-DRB1 molecule (OR 2.89, 95%CI 1.3–6.4, p = 0.009), while association with the classic SE was significant only regarding homozygote frequency of the QRRAA haplotype—also carrying Val 11 and Phe 13 outside the SE (p = 0.04). Moreover, limited range in possible combinations of amino acids at positions 11, 13 and 71 starting with Val-11 among all DLA-DRB1 alleles registered with the GenBank and IPD-MHC canine databases, suggested potential of further single-breed analyses in dachshunds to clarify the disorder in terms of diagnosis, treatment, and epigenetic control, while clinical and immunopathogenetic similarities between human and dachshund RA also suggested the possibility of gaining insight into RA per se through study of canine IMPA as a spontaneous model of human RA.

Phylodynamic characteristics of the LMP-1 gene of the Epstein–Barr virus isolated in the Nizhny Novgorod region

Introduction. Epstein–Barr virus (EBV) is one of the most common herpesviruses and has a pronounced genetic polymorphism. The study of the phylodynamic characteristics of the virus is an important aspect of the study of evolutionary changes in the LMP-1 gene and their consequences.
 The aim of the work was a philodynamic analysis of EBV isolates from Nizhny Novgorod region based on the C-terminal fragment of the LMP-1 gene.
 Materials and methods. The study included 158 EBV isolates obtained from blood leukocytes and saliva of children aged 1–17 years with a diagnosis of infectious mononucleosis caused by EBV (n = 68) and apparently healthy children of comparable sex and age (n = 29). LMP-1 genovariants were obtained using the Sanger sequencing method. Comparative analysis of amino acid sequences was performed using the MEGA X program. Philodynamic analysis of the obtained nucleotide sequences and isolates deposited in GenBank was carried out using the BEAST v. 1.10.4 software package. Recombination analysis was performed using the Simplot program.
 Results. 158 nucleotide sequences of the C-terminal fragment of the LMP-1 gene from Nizhny Novgorod region EBV isolates were obtained and deposited in the GenBank database. The circulation time of the nearest common ancestor for the modified B95-8 genovariants with G212S + E328Q + S366T and NC mutations with the D250N substitution has been established dating back to 1994 and 1923. The rate of evolution of these genovariants was the highest and amounted to 1.298 × 10–4 and 7.868 × 10–4 nucleotide substitutions/site/year. Recombinations were detected in the Nizhny Novgorod region sequences Med-, B95-8, China 1 with mutations G212S, G212S, E214Q, respectively.
 Conclusion. For the first time, a phylodynamic characterization of Nizhny Novgorod region isolates and LMP-1 EBV genovariants isolated in various regions of the world is given. The data obtained expand the existing understanding of the circulation of EBV LMP-1 genovariants in the territory of the European part of Russia.

Analysis of changes in the genome of Vibrio cholerae O1 El Tor genovariants during the current period of the cholera pandemic

Introduction. The genome variability of genetic variants of El Tor cholera agent has led to the emergence of strains carrying mutations in various genes associated with epidemically important pathogen properties. This situation requires an assessment of the trends in these changes in order to predict the pathogenic potential of previously unknown variants and promptly develop new tools for their diagnostics and prevention.
 The purpose of this work was to analyze the dynamic changes in pathogenicity and drug resistance genes of V. cholerae El Tor genetic variants from endemic countries and Russia.
 Materials and methods. We analyzed complete genome nucleotide sequences of 104 V. cholerae El Tor strains from the NCBI Gen Bank and European Nucleotide Archive databases, as well as those obtained by us. The nucleotide sequences were analyzed using the UGEN v. 45.1 software. The dendrogram was constructed using maximum parsimony algorithm in BioNumerics v.7.6 software package based on the multiple alignment generated using the Snippy 4.6.0 program.
 Results. Genomic sequences of 103 strain genovariants isolated on the territory of nine endemic countries of Asia and Africa, as well as in Russia in 1991-2022, have been compared. It is shown that the process of genovariant genome changing was multistage and occurred due to the continuous accumulation of point mutations in key (ctxB and tcpA) and additional (rtxA) genes of pathogenicity and core genes of antibiotic resistance (gyrA, parC and carR), as well as a deletion in SXT element. The most important was the change in the ctxB gene and the emergence of new genovariants with the ctxB7 allele, which replaced the previously prevalent strains. Analysis of altered genome regions of 83 strains from endemic regions has revealed eight genotypes, while the strains (21 isolates) imported to Russia belonged to only five of them including highly virulent strains with the ctxB7 allele and lost PolR biovar-specific feature due to carR gene mutation. The established close phylogenetic relatedness of genovariants from Russia with strains from endemic Asian countries confirms their importation from this region.
 Conclusion. The sequential occurrence and accumulation of mutations in the pathogenicity and drug resistance genes in the genome of genovariants in endemic regions have been shown, which leads to a change in their epidemically important features. The importation of new highly virulent genovariants into Russia has been established, which indicates the need for an ongoing assessment of changes in the genome of this pathogen for the timely development of adequate means of gene diagnostics and prevention.

Geographical Distribution and Multimethod Species Identification of Forensically Important Necrophagous Flies on Hainan Island.

Forensic entomology offers unique advantages for the minimum postmortem interval (PMImin) estimation of decomposed corpses in forensic investigations. Accurate species identification and up-to-date locality information are essential. Hainan Island has a tropical rainforest climate and a vast territory. In this study, the community structure of necrophagous flies on Hainan Island was investigated in detail according to geographical environment. The results showed that the dominant species included C. megacephala, S. peregrina, C. rufifacies, S. misera, H. ligurriens, S. sericea, S. cinerea, S. dux, C. pinguis, and M. domestica. Furthermore, C. rufifacies and C. villeneuvi were found only in the high-altitude areas of Wuzhi Mountain, while S. cinerea was distributed only in coastal areas; the latter is a representative species of Hainan Island and has not been reported before. Furthermore, a GenBank database of forensically important flies was established, whilst a high-resolution melt (HRM) curve analysis was applied to identify the common species of Hainan Island for the first time. This study enriches the database of forensically important flies in tropical rainforest regions.

Retrospective analysis of Marek's disease virus outbreak in 2013 on chicken farms in North Sumatra, Indonesia

<p class="MDPI17abstract"><strong>Objective:</strong> Marek's disease is lymphoma in chicken caused by Marek's disease virus serotype 1 (MDV-1), characterized by paralysis and tumour formation. The disease has caused enormous economic loss worldwide, including in Indonesia. Unfortunately, molecular data related to MDV-1 from Indonesia is limited. Therefore, this study aimed to identify genetic characteristics of MDV-1 causing outbreaks in commercial farms in North Sumatra, Indonesia, 2013.</p><p class="MDPI17abstract"><strong>Methods:</strong> The amplification of Meq, pp38, gC, and gE genes of the strain MDN2013 was carried out using the PCR protocol. Fragment gene sequencing was accomplished using the Sanger method. Subsequently, the bioinformatic analyses of BLASTN and phylogenetic tree were applied to analyze the molecular characteristics of these gene sequences.</p><p class="MDPI17abstract"><strong>Results:</strong> The Meq, pp38, gC, and gE genes of the strain MDN2013 were successfully sequenced and submitted to the NCBI GenBank database. The Meq genes share a high identity with Asian viruses, mainly those originating from Indonesia, India, and China. The pp38, gC, and gE genes share similarities with other viruses in more diverse regions in Asia, Africa, Europe, and America. The phylogenetic tree analysis of the Meq gene demonstrated specific patterns for pathotype biodiversity where the strain MDN2013 has been categorized as virulent up to very virulent virus.</p><p class="MDPI17abstract"><strong>Conclusion:</strong> In conclusion, the molecular approach is an effective tool for investigating the MDV-1 biodiversity in the field, especially the Meq gene sequence analysis.</p>

Retrospective analysis of Marek's disease virus outbreak in 2013 on chicken farms in North Sumatra, Indonesia

<p class="MDPI17abstract"><strong>Objective:</strong> Marek's disease is lymphoma in chicken caused by Marek's disease virus serotype 1 (MDV-1), characterized by paralysis and tumour formation. The disease has caused enormous economic loss worldwide, including in Indonesia. Unfortunately, molecular data related to MDV-1 from Indonesia is limited. Therefore, this study aimed to identify genetic characteristics of MDV-1 causing outbreaks in commercial farms in North Sumatra, Indonesia, 2013.</p><p class="MDPI17abstract"><strong>Methods:</strong> The amplification of Meq, pp38, gC, and gE genes of the strain MDN2013 was carried out using the PCR protocol. Fragment gene sequencing was accomplished using the Sanger method. Subsequently, the bioinformatic analyses of BLASTN and phylogenetic tree were applied to analyze the molecular characteristics of these gene sequences.</p><p class="MDPI17abstract"><strong>Results:</strong> The Meq, pp38, gC, and gE genes of the strain MDN2013 were successfully sequenced and submitted to the NCBI GenBank database. The Meq genes share a high identity with Asian viruses, mainly those originating from Indonesia, India, and China. The pp38, gC, and gE genes share similarities with other viruses in more diverse regions in Asia, Africa, Europe, and America. The phylogenetic tree analysis of the Meq gene demonstrated specific patterns for pathotype biodiversity where the strain MDN2013 has been categorized as virulent up to very virulent virus.</p><p class="MDPI17abstract"><strong>Conclusion:</strong> In conclusion, the molecular approach is an effective tool for investigating the MDV-1 biodiversity in the field, especially the Meq gene sequence analysis.</p>

Decoding the genetic structure of conjugative plasmids in international clones of Klebsiella pneumoniae: A deep dive into blaKPC, blaNDM, blaOXA-48, and blaGES genes

Carbapanem-resistant Klebsiella pneumoniae is a globally healthcare crisis. The distribution of plasmids carrying carbapenemase genes among K. pneumoniae poses a serious threat in clinical settings. Here, we characterized the genetic structure of plasmids harboring major carbapenemases (e.g. blaKPC, blaNDM, blaOXA-48-like, and blaGES) from K. pneumoniae using bioinformatics tools. The plasmids carrying at least one major carbapenemase gene were retrieved from the GenBank database. The DNA length, Inc type, and conjugal apparatus of these plasmids were detected. Additionally, allele types, co-existence, co-occurrence of carbapenemase genes, gene repetition, and sequence types of isolates, were characterized. There were 2254 plasmids harboring carbapenemase genes in the database. This study revealed that blaKPC-2, blaNDM-1, blaOXA-48, and blaGES-5 were the most prevalent allele types. Out of 1140 (50%) plasmids were potentially conjugative. IncFII, IncR, IncX3, and IncL replicon types were predominant. The co-existence analysis revealed that the most prevalent of other resistance genes were blaTEM-1 (related to blaKPC), blaOXA-232 (related to blaOXA-48), bleMBL (related to blaNDM), and aac (6′)-Ib4 (related to blaGES). The co-occurrence of carbapenemases was detected in 42 plasmids while 15 plasmids contained carbapenemase gene repetitions. Sequence alignments highlighted that plasmids carrying blaKPC and blaOXA-48-like were more homogeneous whereas the plasmids carrying blaNDM were divergent. It seems that K. pneumoniae utilizes diversity of genetic flexibility and recombination for resistance against carbapenems. The genetic structure of the plasmids showed that class I and III, Tn3 family, Tn5403 family derivatives, and Tn7-like elements were strongly associated with carbapenemases. The mobilizable plasmids carrying carbapenemases play an important role in the spread of these genes. In addition, gene repetition maybe is related to carbapenem heteroresistance. According to MST (minimum spanning tree) results, the majority of plasmids belonged to sequence type (ST) 11, ST14, and ST12. These international clones have a high capacity to acquire the carbapenemase-containing plasmids.