Molecular characterization of multidrug-resistant Escherichia coli isolated from human urine infections with their antibiogram profile

ICLE Urinary tract infection (UTI) is the leading cause of hospitalization due to bacterial infection, and the frequency of multidrug-resistant Escherichia coli isolates from these infections is increasing worldwide. The current study aims to isolate and characterize antibiotic-resistant Escherichia coli and their antibiogram typing from urine samples of humans. From April to December 2019, a total of 60 human urine samples were collected aseptically and treated to primary isolation by propagation in nutrient broth followed by culture on various agar media. Gram’s staining, string techniques, biochemical characterization, PCR, and Sanger sequencing were performed to confirm E. coli. The Kirby-Bauer disk diffusion technique was used to test the susceptibility of all bacterial strains to thirteen typically prescribed antibiotics. The overall prevalence of E. coli in UTI was 66.67%. Three variations were noted in E. coli, all of which were single substitutions (A>T, C>T, and T>A). Phylogenetic analysis of the 16S rRNA revealed that the E. coli discovered in this study belonged to the genus Escherichia but was distinct from those identified in other countries. The antibiograms revealed that all the isolates (100%) were resistant to penicillin, ampicillin, and amoxicillin; 94.87% to doxycycline; 79.16% to gentamycin; 75.48% to ciprofloxacin; 73.07% to erythromycin; 71.66% to levofloxacin; 47.36% to ceftriaxone; and 46.66% to tetracycline. In contrast, all E. coli strains were sensitive to amikacin (95%), vancomycin (92.50%), and azithromycin (92.50%). People with a UTI often have multidrug-resistant E. coli in their urine samples, which calls for a one-health strategy to deal with this rapidly changing condition

Complete Mitochondrial Genome Sequence of a Seabird, Wedge-Tailed Shearwater (Ardenna pacifica)

Here, we report the complete mitochondrial genome sequence of a seabird, wedge-tailed shearwater (Ardenna pacifica). The circular genome has a size of 16,434 bp and contains 13 protein-coding genes, 22 tRNA genes, and 2 rRNA genes. The study provides a reference mitochondrial genome of wedge-tailed shearwater for further molecular studies

Sustainable Antibiotic-Free Broiler Meat Production: Current Trends, Challenges, and Possibilities in a Developing Country Perspective

Antibiotic-free broiler meat production is becoming increasingly popular worldwide due to consumer perception that it is superior to conventional broiler meat. Globally, broiler farming impacts the income generation of low-income households, helping to alleviate poverty and secure food in the countryside and in semi-municipal societies. For decades, antibiotics have been utilized in the poultry industry to prevent and treat diseases and promote growth. This practice contributes to the development of drug-resistant bacteria in livestock, including poultry, and humans through the food chain, posing a global public health threat. Additionally, consumer demand for antibiotic-free broiler meat is increasing. However, there are many challenges that need to be overcome by adopting suitable strategies to produce antibiotic-free broiler meat with regards to food safety and chicken welfare issues. Herein, we focus on the importance and current scenario of antibiotic use, prospects, and challenges in the production of sustainable antibiotic-free broiler meat, emphasizing broiler farming in the context of Bangladesh. Moreover, we also discuss the need for and challenges of antibiotic alternatives and provide a future outlook for antibiotic-free broiler meat production

Coronavirus disease 2019 and future pandemics: Impacts on livestock health and production and possible mitigation measures

The World Health Organization declared coronavirus disease 2019 (COVID-19) a pandemic on March 11, 2020. COVID-19, the current global health emergency, is wreaking havoc on human health systems and, to a lesser degree, on animals globally. The outbreak has continued since the first report of COVID-19 in China in December 2019, and the second and third waves of the outbreak have already begun in several countries. COVID-19 is expected to have adverse effects on crop production, food security, integrated pest control, tourism, the car industry, and other sectors of the global economy. COVID-19 induces a range of effects in livestock that is reflected economically since human health and livelihood are intertwined with animal health. We summarize the potentially harmful effects of COVID-19 on livestock and possible mitigation steps in response to this global outbreak. Mitigation of the negative effects of COVID-19 and future pandemics on livestock requires the implementation of current guidelines

Characterization of a Complete Genome Sequence of Molluscum Contagiosum Virus from an Adult Woman in Australia

The complete genome sequence of molluscum contagiosum virus 1 (MOCV1) isolate NT2017 was sequenced from a tissue sample from an Australian woman. The genome consisted of 185,655 bp encoding 169 predicted open reading frames. Phylogenetically, isolate NT2017 was most closely related to an MOCV1 strain from Slovenia

Detection of regional DNA methylation using DNA-graphene affinity interactions

We report a new multiplexed strategy for the electrochemical detection of regional DNA methylation across multiple regions. Using the sequence dependent affinity of bisulfite treated DNA towards gold surfaces, the method integrates the high sensitivity of a micro-fabricated multiplex device comprising a microarray of gold electrodes, with the powerful multiplexing capability of multiplex-PCR. The synergy of this combination enables the monitoring of the methylation changes across several genomic regions simultaneously from as low as 500 pg μl(-1) of DNA with no sequencing requirement

The first genomic insight into Chlamydia psittaci sequence type (ST)24 from a healthy captive psittacine host in Australia demonstrates evolutionary proximity with strains from psittacine, human, and equine hosts

Chlamydia psittaci is a zoonotic pathogen that infects birds, humans, and other mammals. Notably, recent studies suggested the human-to-human transmission of C. psittaci, and this pathogen also causes equine reproductive loss in Australia. Molecular studies in Australia to date have focused on and described clonal sequence type (ST)24 strains infecting horses, wild psittacine, and humans. In contrast, the genetic identity of C. psittaci strains from captive psittacine hosts is scarce. In 2022, C. psittaci was detected in the faeces of a healthy captive blue-fronted parrot (Amazona aestiva). Genomic DNA was extracted and underwent whole-genome sequencing. Here we report the 1,160,701 bp circular chromosome of C. psittaci strain BF_amazon_parrot13 and the 7,553 bp circular plasmid pCpsBF_amazon_parrot13. Initial in silico multi-locus sequence typing and ompA genotyping revealed that BF_amazon_parrot13 belongs to the clonal ST24 lineage and has an ompA genotype A. Further context involved the genomes of 31 published ST24 strains, utilising a single-nucleotide variant (SNV) based clustering approach. Despite temporal, host, and biogeographical separation, a core-genome SNV-based phylogeny revealed that BF_amazon_parrot13 clustered in a distinct subcluster with seven C. psittaci strains from equines in Australia (maximum pairwise distance of 13 SNVs). BF_amazon_parrot13 represents the first complete C. psittaci ST24 genome from a captive psittacine in Australia. Furthermore, by using whole-genome sequencing to coordinate surveillance, we can also learn more about the possible health risks and routes of chlamydia transmission among people, livestock, wild animals, and domesticated animals

Quantification of gene-specific DNA methylation in oesophageal cancer via electrochemistry

Development of simple and inexpensive method for the analysis of gene-specific DNA methylation is important for the diagnosis and prognosis of patients with cancer. Herein, we report a relatively simple and inexpensive electrochemical method for the sensitive and selective detection of gene-specific DNA methylation in oesophageal cancer. The underlying principle of the method relies on the affinity interaction between DNA bases and unmodified gold electrode. Since the affinity trend of DNA bases towards the gold surface follows as adenine (A) > cytosine (C) > guanine (G)> thymine (T), a relatively larger amount of bisulfite-treated adenine-enriched unmethylated DNA adsorbs on the screen-printed gold electrodes (SPE-Au) in comparison to the guanine-enriched methylated sample. The methylation levels were (i.e., different level of surface attached DNA molecules due to the base dependent differential adsorption pattern) quantified by measuring saturated amount of charge-compensating [Ru(NH ) ] molecules in the surface-attached DNAs by chronocoulometry as redox charge of the [Ru(NH ) ] molecules quantitatively reflects the amount of the adsorbed DNA confined at the electrode surface. The assay could successfully distinguish methylated and unmethylated DNA sequences at single CpG resolution and as low as 10% differences in DNA methylation. In addition, the assay showed fairly good reproducibility (% RSD

Colorimetric and electrochemical quantification of global DNA methylation using a methyl cytosine-specific antibody

We report a simple colorimetric (naked-eye) and electrochemical method for the rapid, sensitive and specific quantification of global methylation levels using only 25 ng of input DNA. Our approach utilises a three-step strategy; (i) initial adsorption of the extracted, purified and denatured bisulfite-treated DNA on a screen-printed gold electrode (SPE-Au), (ii) immuno-recognition of methylated DNA using a horseradish peroxidase (HRP)-conjugated methylcytosine (HRP-5mC) antibody and (iii) subsequent colorimetric detection by the enzymatic oxidation of 3,3′,5,5′-tetramethylbenzidin (TMB)/H2O2 which generated a blue-coloured product in the presence of methylated DNA and HRP-5mC immunocomplex. As TMB(ox) is electroactive, it also produces detectable amperometric current at +150 mV versus a Ag pseudo-reference electrode (electrochemical detection). The assay could successfully differentiate 5-aza-2′-deoxycytidine drug-treated and untreated Jurkat DNA samples. It showed good reproducibility (relative standard deviation (% RSD) = <5%, for n = 3) with fairly good sensitivity (as low as 5% difference in methylation levels) and specificity while analysing various levels of global DNA methylation in synthetic samples and cell lines. The method has also been tested for analysing the methylation level in fresh tissue samples collected from eight patients with oesophageal squamous cell carcinoma. We believe that this assay could be potentially useful as a low-cost alternative for genome-wide DNA methylation analysis in point-of-care applications.Office of the Snr Dep Vice Chancellor, Institute for GlycomicsNo Full Tex

Resolution of the phylogenetic relationship of the vulnerable flesh-footed shearwater (Ardenna carneipes) seabird using a complete mitochondrial genome

Flesh-footed shearwater (Ardenna carneipes) is recognized as vulnerable seabird species in Western Australia and New South Wales, Australia, and its genetic variability and a well-resolved phylogeny is imperative for the species’ conservation. Here, we report the first sequenced mitogenome of the Australian A. carneipes. The mitogenome of A. carneipes was 16,370 bp in total length and encompassed 13 protein-coding genes, two ribosomal RNAs, 22 transfer RNAs, and one non-coding region (D-loop). All of the genes were encoded on the H-strand with the exception of ND6 and eight tRNAs, which is a conserved pattern of the mitogenome for other vertebrates. The mitogenome of A. carneipes was dominated by higher AT (56.5%) than GC (43.5%) content. In the resulting phylogenetic tree using complete mitogenome sequences, flesh-footed shearwater and gray petrel (Procellaria cinerea) grouped together despite the high genetic distance (11.0%) between them, belonging to family Procellariidae. However, the phylogenetic tree was consistent with a previous study using partial nucleotide sequences of the cytochrome b gene. These results highlight that further mitogenome sequences will be required from the closely related species under the genus Ardenna to delineate well-resolved phylogenetic classification at the genus and or species level. The present study provides a reference mitochondrial genome of flesh-footed shearwater for further molecular studies