Unravelling the genomic origins of lumpy skin disease virus in recent outbreaks.

Lumpy skin disease virus (LSDV) belongs to the genus Capripoxvirus and family Poxviridae. LSDV was endemic in most of Africa, the Middle East and Turkey, but since 2015, several outbreaks have been reported in other countries. In this study, we used whole genome sequencing approach to investigate the origin of the outbreak and understand the genomic landscape of the virus. Our study showed that the LSDV strain of 2022 outbreak exhibited many genetic variations compared to the Reference Neethling strain sequence and the previous field strains. A total of 1819 variations were found in 22 genome sequences, which includes 399 extragenic mutations, 153 insertion frameshift mutations, 234 deletion frameshift mutations, 271 Single nucleotide polymorphisms (SNPs) and 762 silent SNPs. Thirty-eight genes have more than 2 variations per gene, and these genes belong to viral-core proteins, viral binding proteins, replication, and RNA polymerase proteins. We highlight the importance of several SNPs in various genes, which may play an essential role in the pathogenesis of LSDV. Phylogenetic analysis performed on all whole genome sequences of LSDV showed two types of variants in India. One group of the variant with fewer mutations was found to lie closer to the LSDV 2019 strain from Ranchi while the other group clustered with previous Russian outbreaks from 2015. Our study highlights the importance of genomic characterization of viral outbreaks to not only monitor the frequency of mutations but also address its role in pathogenesis of LSDV as the outbreak continues.

Exploring genetic landscape of low-density polyethylene degradation for sustainable troubleshooting of plastic pollution at landfills.

Plastic pollution increases globally due to the high volume of its production and inadequate mismanagement, leading to dumps in landfills affecting terrestrial and aquatic ecosystems. Landfills, as sink for plastics, leach various toxic chemicals and microplastics into the environment. We scrutinized the genetic expression for low-density polyethylene (LDPE) degradation via microorganisms to investigate cell viability and metabolic activities for biodegradation and genetic profiling. Samples were collected from the Pirana waste landfill at Ahmedabad, Gujarat, which is one of the largest and oldest municipal solid waste (MSW) dump sites in Asia. Results analyzed that isolated bacterial culture PN(A)1 (Bacillus cereus) is metabolically active on LDPE as carbon source during starvation conditions when incubated for up to 60 days, which was confirmed via 2,3,5-triphenyl-tetrazolium chloride (TTC) reduction test, reported cell viability and LDPE degradation. Abrasions, surface erosions, and cavity formations were analyzed via scanning electron microscopy (SEM), whereas the breakdown of high molecular polymers converted to low molecules, i.e., depolymerization, was also observed via Fourier-transform infrared (FTIR) spectroscopy over 90 days, along with changes in functional groups of carboxylic acids and aldehyde as well as the formation of polysulfide, aliphatic compounds, aromatic ethers, alcohols, and ether linkages. Further, transcriptomic analysis was performed via DESeq2 analysis to understand key gene expression patterns and pathways involved in LDPE degradation. During the initial phase of LDPE degradation, genes related to biological processes, like membrane transportation, ABC transporters, carbon and lipid metabolism, fatty acid degradation/oxidation, and TCA cycle, are likely to indicate pathways for stress response and molecular functions, like oxidoreductase, catalytic, lyase, transferase, and hydrolase activities were expressed. Interlinking between metabolic pathways indicates biodegradation process that mineralizes LDPE during subsequent incubation days. These pathways can be targeted for increasing the efficiency of LDPE degradation using microbes in future studies. Thus, considering microbial-mediated biodegradation as practical, eco-friendly, and low-cost alternatives, healthy biomes can degrade polymers in natural environments explored by understanding the genetic and enzymatic expression, connecting their role in the process to the likely metabolic pathways involved, thereby increasing the rate of their biodegradation.

Resistome profiling reveals transmission dynamics of antimicrobial resistance genes from poultry litter to soil and plant.

Poultry farming is a major livelihood in South and Southeast Asian economies where it is undergoing rapid intensification to meet the growing human demand for dietary protein. Intensification of poultry production systems is commonly supported by increased antimicrobial drug use, risking greater selection and dissemination of antimicrobial resistance genes (ARGs). Transmission of ARGs through food chains is an emerging threat. Here, we investigated transmission of ARGs from chicken (broiler and layer) litter to soil and Sorghum bicolor (L.) Moench plants based on field and pot experiments. The results demonstrate ARGs transmission from poultry litter to plant systems under field as well as experimental pot conditions. The most common ARGs could be tracked for transmission from litter to soil to plants were identified as detected were cmx, ErmX, ErmF, lnuB, TEM-98 and TEM-99, while common microorganisms included Escherichia coli, Staphylococcus aureus, Enterococcus faecium, Pseudomonas aeruginosa, and Vibrio cholerae. Using next generation sequencing and digital PCR assays we detected ARGs transmitted from poultry litter in both the roots and stems of S. bicolor (L.) Moench plants. Poultry litter is frequently used as a fertiliser because of its high nitrogen content; our studies show that ARGs can transmit from litter to plants and illustrates the risks posed to the environment by antimicrobial treatment of poultry. This knowledge is useful for formulating intervention strategies that can reduce or prevent ARGs transmission from one value chain to another, improving understanding of impacts on human and environmental health. The research outcome will help in further understanding the transmission and risks posed by ARGs from poultry to environmental and human/animal health.