Aeromonas hydrophila is a potential zoonotic pathogen and primary fish pathogen. With overlapping characteristics, multiple isolates are often mislabelled and misclassified. Moreover, the potential pathogenic factors among the publicly available genomes in A. hydrophila strains of different origins have not yet been investigated. To identify the valid strains of A. hydrophila and their pathogenic factors, we performed a pan-genomic study. It revealed that there were 13 mislabelled strains and 49 valid strains that were further verified by Average nucleotide identity (ANI), digital DNA-DNA hybridization (dDDH) and in silico multiple locus strain typing (MLST). Multiple numbers of phages were detected among the strains and among them Aeromonas phi 018 was frequently present. The diversity in type III secretion system (T3SS) and conservation of type II and type VI secretion systems (T2SS and T6SS, respectively) among all the strains are important to study for designing future strategies. The most prevalent antibiotic resistances were found to be beta-lactamase, polymyxin and colistin resistances. The comparative analyses of sequence type (ST) 251 and other ST groups revealed that there were higher numbers of virulence factors in ST-251 than in other STs group. Publicly available genomes have 13 mislabelled organisms, and there are only 49 valid A. hydrophila strains. This valid pan-genome identifies multiple prophages that can be further utilized. Different A. hydrophila strains harbour multiple virulence factors and antibiotic resistance genes. Identification of such factors is important for designing future treatment regimes.

Recently, there have been numerous reports showing that phthalates have negative human health impacts and may cause several diseases such as asthma, breast cancer, obesity, type II diabetes, and male infertility. Animals are also exposed to phthalates through the environment and can cause adverse health effects on them. Several studies have been found on the cytogenetic effects of dibutyl phthalate (DBP) on different organisms but no documented evidence has been found on the cytotoxic and genotoxic effects of dibutyl phthalate (DBP) on bovine cultured lymphocytes. MTT assay was performed on different series of DBP concentrations (10 μM, 20 μM, 30 μM, 50 μM, 70 μM, 100 μM). A concentration‐dependent decrease in cell viability was observed by the DBP. The LD50, LD50/2, and 2∗LD50 were found to be 50 μM, 30 μM, and 80 μM on bovine lymphocytes, respectively. Then, these concentrations of DBP were utilized to perform comet, micronucleus assays, and oxidative stress. A concentration‐dependent increase in DNA damage, oxidative stress, and micronuclei formation was observed in lymphocytes by the DBP as compared to the control group. Highest genotoxic effects were observed at a concentration of 2∗LD50. Similarly, total oxidative stress was found higher, and antioxidative stress was lower in concentration‐dependent manner by the DBP. The current study revealed a significant cytotoxic, genotoxic, and oxidative stress of DBP on cultured bovine lymphocytes.

Anthropogenic activities in the environment affect the ecosystem and can play an important role in selecting and spreading antibiotic‐resistant bacteria (ARB) and genes (ARGs). The dairy farm environment may serve as a hotspot and reservoir for exchanging and spreading ARGs, but studies are scarce. Here, we investigated and characterized the extended‐spectrum β‐lactamase producing Escherichia coli strains recovered from the dairy farm environment co‐harboring bla_OXA−1, catB3, and arr-3 genes. The isolates were identified and characterized by PCR, antimicrobial susceptibility testing, conjugation assay, whole genome sequencing (WGS), and multiple bioinformatics tools. Seven E. coli strains co‐harboring bla_OXA−1, catB3, and arr-3 genes were identified which belonged to distinct sequence types (STs) and carried diverse plasmid replicon types. The conjugation assay revealed a successful transfer of bla_OXA−1, catB3, and arr-3 genes into the recipient E. coli J53 with a co‐conjugation frequency ranging from (2.25 ± 0.3) × 10⁻⁴ to (3.85 ± 0.3) × 10⁻³. Bioinformatics analysis of WGS revealed the diversity of acquired ARGs, conferring resistance to aminoglycosides, beta‐lactams, quinolones, tetracyclines, macrolides, trimethoprim–sulfamethoxazole, phosphonic, phenicol, and rifamycin. The genetic environment analysis showed that aac(6^′)‐Ib-cr-bla_OXA−1‐catB3-arr-3-qacE1-sul1 was the common genetic backbone among the seven E. coli strains. Among the mobile genetic elements, insertion sequences were the predominant elements as compared to transposons. The phylogenetic analysis demonstrated a close relationship between the E. coli of this study and other strains of human–animal‐environment origin retrieved from the NCBI database. This study presented the whole genome‐based characterization of E. coli strains carrying the bla_OXA−1‐catB3-arr-3 genes. It provided evidence that the dairy environment may harbor a variety of ARGs and act as a potential reservoir for their spread in the ecosystem. The results recommend the routine surveillance of ARGs carrying bacteria in dairy environments and the need for additional studies to understand the dissemination mechanism within One Health perspective to prevent their further spread.

Hepatitis C virus (HCV) is highly infectious pathogen which is responsible for causing Hepatitis around 200 million individuals worldwide. In Pakistan, 4.7% of HCV prevalence has been reported and HCV genotype 3a has been found to be the major source of infection in Pakistan but still there is lack of information on distribution of HCV genotypes and viral load in various geographical regions of Pakistan. Therefore, current study was designed to determine distribution of HCV genotypes as well viral load in different areas of Punjab province of Pakistan.

The present study involves the chemical and bacteriological analysis of water from different sources i.e., bore, wells, bottle, and tap, from Peshawar, Mardan, Swat and Kohat districts of Khyber Pakhtunkhwa (KP) province, Pakistan. From each district, 50 water samples (10 samples from each source), regardless of urban and rural status, were collected from these sources and analysed for sulphates, nitrates, nitrites, chlorides, total soluble solids and coliforms (E. coli). Results indicated that majority of the water sources had unacceptable E. coli count i.e.> 34 CFU/100mL. E. coli positive samples were high in Mardan District, followed by Kohat, Swat and Peshawar district. Besides this, the some water sources were also chemically contaminated by different inorganic fertilizers (nitrates/nitrites of sodium, potassium) but under safe levels whereas agricultural and industrial wastes (chloride and sulphate compounds) were in unsafe range. Among all districts, the water quality was found comparatively more deteriorated in Kohat and Mardan districts than Peshawar and Swat districts. Such chemically and bacteriologically unfit water sources for drinking and can cause human health problems.

The main aim of this study was to develop a set of functions that can analyze the genomic data with less time consumption and memory. Epi‐gene is presented as a solution to large sequence file handling and computational time problems. It uses less time and less programming skills in order to work with a large number of genomes. In the current study, some features of the Epi‐gene R‐package were described and illustrated by using a dataset of the 14 Aeromonas hydrophila genomes. The joining, relabeling, and conversion functions were also included in this package to handle the FASTA formatted sequences. To calculate the subsets of core genes, accessory genes, and unique genes, various Epi‐gene functions have been used. Heat maps and phylogenetic genome trees were also constructed. This whole procedure was completed in less than 30 minutes. This package can only work on Windows operating systems. Different functions from other packages such as dplyr and ggtree were also used that were available in R computing environment.