Biology subjects

Andleeb, S.

Publications and source records attributed to Andleeb, S..

4 recordsLinked to original sources

bioRxiv2024

Typhi Mykrobe: fast and accurate lineage identification and antimicrobial resistance genotyping directly from sequence reads for the typhoid fever agent Salmonella Typhi

BackgroundTyphoid fever results from systemic infection with Salmonella enterica serovar Typhi (Typhi) and causes 10 million illnesses annually. Disease control relies on prevention (water, sanitation, and hygiene interventions or vaccination) and effective antimicrobial treatment. Antimicrobial resistant (AMR) Typhi lineages have emerged and become established in many parts of the world. Knowledge of local pathogen populations informed by genomic surveillance, including of lineages (defined by the GenoTyphi scheme) and AMR determinants, is increasingly used to inform local treatment guidelines and to inform vaccination strategy. Current tools for genotyping Typhi require multiple read alignment or assembly steps and have not been validated for analysis of data generated with Oxford Nanopore Technologies (ONT) long-read sequencing devices. Here, we introduce Typhi Mykrobe, a command line software tool for rapid genotyping of Typhi lineages, AMR determinants, and plasmid replicons direct from sequencing reads. ResultsWe validated Typhi Mykrobe lineage genotyping by comparison with the current standard read mapping-based approach and demonstrated 99.8% concordance across nearly 13,000 genomes sequenced with Illumina platforms. For the few isolates with discordant calls, we show that Typhi Mykrobe results are better supported by the evidence from raw sequence read data than the results generated using the mapping-based approach. We also demonstrate 99.9% concordance for detection of AMR determinants compared with the current standard assembly-based approach, with similar results for plasmid marker detection. Typhi Mykrobe predicts clinical resistance categorisation (S/I/R) for eight drug classes, and we show strong agreement with phenotypic categorisations generated from reference laboratory minimum inhibitory concentration (MIC) data for n=1,572 Illumina-sequenced isolates (>99% agreement within one doubling dilution). We show strong concordance (>96% for genotype and >98% for AMR and plasmid) between calls made from ONT reads and those made from Illumina reads for isolates sequenced on both platforms (n =93 genomes). Typhi Mykrobe takes less than a minute per sample and is available at https://github.com/typhoidgenomics/genotyphi. ConclusionsTyphi Mykrobe provides rapid and sensitive genotyping of Typhi genomes direct from Illumina and ONT reads, although lower accuracy was observed for R9 ONT data. It demonstrated accurate assignment of GenoTyphi lineage, detection of AMR determinants and prediction of corresponding AMR phenotypes, and identification of plasmid replicons.

microbiology↗

bioRxiv2023

Indigenous probiotics Lactobacillus reuteri and Enterococcus faecium exhibit positive growth performance and disease prevention against extended-spectrum cephalosporin and fluoroquinolones resistant Salmonella enterica in broiler chicks.

ABSTRACTThe rapid increase in antibiotic resistance poses a global threat to public health, necessitating the development of effective antimicrobial alternatives. This study compared an indigenous probiotic mix containing Lactobacillus reuteri and two strains of Enterococcus faecium to a commercial probiotic blend ProtexinR on the growth performance, mortality rate, histomorphology, serum immunoglobulins, and intestinal microflora of broiler chickens challenged with two multi drug resistant Salmonella serovars, Typhimurium and Enteritidis. Two hundred and forty day-old broiler chicks were randomly assigned to six treatment groups for 4 weeks: the treatment groups were; birds continuously supplemented with only indigenous probiotic strains (108 CFU/mL) (IPRO-); birds challenged with Salmonella serovars 106 (CFU/mL) (PC+); birds continuously supplemented with indigenous probiotic strains and challenged with Salmonella serovars (IPRO+); birds supplemented with ProtexinR and challenged with Salmonella serovars (CM+); birds supplemented with only ProtexinR (CM-); and birds with no Salmonella challenge or probiotics (negative control; PC-). The results revealed that IPRO- diets significantly improved feed conversion ratio (FCR) and increased body weight (BW) (P [≤] 0.05). No effect of probiotic treatments was observed on IPRO- and CM- on relative organ weights as compared to the negative control (PC-). The Salmonella- challenged group PC+ had the highest (20%) mortality rate and lowest BW. The IPRO- had significantly lower FCR (1.55) compared to PC- (1.86) and PC+ (1.95). The broilers in the IPRO- group showed significantly increased serum concentrations of IgA and IgG relative to both control groups (P [≤] 0.05). Morphological analysis of the ileum revealed significant increases (P [≤] 0.05) in the villus height and villus height/crypt depth in birds fed IPRO- compared with the PC+. Cecal Lactobacillus and Enterococcus counts were the highest (P [≤] 0.05) and Salmonella counts were the lowest (P [≤] 0.05) in the IPRO- group compared to the Salmonella infected group PC+. These results indicated that indigenous probiotic strains Lactobacillus reuteri and Enterococcus faecium can be an effective and low-cost alternative compared to commercial probiotics in the Pakistan poultry industry.

microbiology↗

bioRxiv2022

Wound healing and anti-inflammatory potential of Ajuga bracteosa-conjugated silver nanoparticles in Balb/c mice

BackgroundWound therapy is complicated, uncomfortable for the patient, and costly for the health-care system. Silver nanoparticles (AgNP) have antibacterial characteristics that can prevent bacterial infection in wounds and speed up wound healing ObjectiveThe aim of current research was to investigate the wound healing and anti-inflammatory potential of biogenic synthesized silver nanoparticles (ABAgNP) using Ajuga bracteosa (ABaqu) in Swiss albino mice. MethodsIn vivo wound healing and anti-inflammatory activities were carried out using Bala/c mice. For in vivo screening of 200 mg/kg and 400 mg/kg of both ABAgNPs and ABaqu were used. Liver and kidney functional markers, hematology, and histopathological studies were carried out after 14 days of administration. ResultsThe obtained biogenic nanoparticles were characterized, dermal toxicity, wound excision repairing, and formalin-induced paw edema assays were performed in Swiss albino mice. Dermal toxicity showed that tested concentrations of ABaqu and ABAgNPs were safe. No adverse effects, changes, and alteration in the skin of treatment groups as well as the control vehicle group (petroleum jelly) were recorded. Results revealed that the enhanced wound contraction was observed in ABaqu, ABAgNP, and the Nitrofuranose treated groups from 7th to 11thdays. The anti-inflammatory activity in formalin-induced paw edema model illustrated the potential use of silver nanoparticles ABAgNPs and ABaqu as a reducing or inflammation inhibiting agents due to the release of acute inflammatory mediators. ConclusionTherefore, it was concluded that both silver nanoparticles (ABAgNP) and Ajuga bracteosa (ABaqu) extracts could be used as a wound healing and anti-inflammatory agents.

zoology↗

bioRxiv2022

In-silico design and assessment of OprD-based multi-epitope vaccine against Acinetobacter baumannii

Gram-negative, opportunist pathogen Acinetobacter baumannii is notorious for causing a plethora of nosocomial infections predominantly respiratory diseases and blood-stream infections. Due to resistance development towards last-resort antibiotics, its treatment is becoming increasingly difficult. Despite numerous therapeutic developments, no vaccine is available against this ubiquitous pathogen. It is therefore apropos to formulate a rational vaccine plan to get rid of the super-bug. Considering the importance of Outer Membrane Porin D (OprD) as a potential vaccine candidate, we methodically combined the most persistent epitopes present in the A. baumannii strains with the help of different immunoinformatic approaches to envisage a systematic multi-epitope vaccine. The proposed vaccine contains highly immunogenic stretches of linear B-cells, cytotoxic T lymphocyte epitopes, and helper T lymphocyte epitopes of outer membrane porin OprD. The finalized epitopes proved to be significant as they are conserved in A. baumannii strains. The final 3D structure of the construct was projected, refined, and verified by employing several in silico approaches. Apt binding of the protein and adjuvant with the TLR4 suggested significantly high immunogenic potential of our designed vaccine. MD simulations showed highly stable composition of the protein. Immune simulations disclosed a prominent increase in the levels of the immune response. The proposed vaccine model is proposed to be thermostable, immunogenic, water-soluble, and non-allergenic. However, this study is purely computational and needs to be validated by follow-up wet laboratory studies to confirm the safety and immunogenicity of our multi-epitope vaccine.

bioinformatics↗