Exploring antibiotic resistance genes, mobile gene elements, and virulence gene factors in an urban freshwater samples using metagenomic analysis

Noman, Sohail M.; Shafiq, Muhammad; Bibi, Shabana; Mittal, Bharti; Yuan, Yumeng; Zeng, Mi; Li, Xin; Olawale, Oluwaseyi Abraham; Jiao, Xiaoyang; Irshad, Muhammad

doi:10.1007/s11356-022-22197-4

Cited by 12 publications

(6 citation statements)

References 53 publications

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“…Supplementation with plant extracts can modulate broiler gut microbiota, which leads to the alteration of the ARG-harboring bacterial host composition (Huang et al, 2018;Koorakula et al, 2022). Changes in microbial community structure are associated with microbial VFG composition (Noman et al, 2022). In addition, ARGs are positively associated with certain VFGs in both commensal and pathogenic bacteria in the gut of broilers (Szmolka et al, 2012;Lee et al, 2021).…”

Section: Sfp and Lfp Supplementation Inhibited Clpc Abundance In Bact...mentioning

confidence: 99%

Differential Effects of Bacillus Species-Fermented Products on Antibiotic Resistome and Virulence Factor Gene Composition in the Cecal Digesta of Broilers

Hsiao,

Cheng,

Chen

et al. 2024

Annals of Animal Science

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This study investigated the differential effects of Bacillus subtilis – and Bacillus licheniformis – fermented products (defined as SFP and LFPs, respectively) on microbial antibiotic resistance gene (ARG) and virulence factor gene (VFG) composition in the cecal digesta of 35-day-old broilers by using metagenomic sequencing. First, 160 1-day-old unsexed Arbor Acres broiler chicks were randomly allocated to four treatment groups: basal diet (CON group); basal diet + enramycin (10 mg/kg, ENM group); basal diet + SFPs (108 colony-forming units (CFU) of B. subtilis spores/kg, SFP group); and basal diet + LFPs (108 CFU of B. licheniformis spores/kg, LFP group). Principal coordinate analysis of ARG and VFG composition indicated distinct clustering among the cecal samples of the groups. At the antibiotic resistance class level, LFP treatment increased the expression of peptide resistance genes and decreased the expression of aminocoumarin resistance genes compared with the other groups. Compared with the other groups, LFP treatment promoted bcrA, ugd, and efrB expression but suppressed parY expression, whereas SFP treatment inhibited efrA expression. The abundance of the peptide resistance gene bcrA in Lachnoclostridium species was higher in the CON and LFP groups than in the ENM and SFP groups, whereas the abundance of the peptide resistance gene rpoB2 in Bacteroides species was lower in the ENM and LFP groups than in the SFP group. No specific VFGs were regulated only by SFPs or LFPs. SFP and LFP treatment inhibited clpC expression compared with the other groups. clpC abundance in Bacteroides species was lower in the LFP group than in the CON group, whereas its abundance in Faecalibacterium species was lower in the SFP group than in the CON and ENM groups. These results demonstrated that SFPs and LFPs differentially regulate microbial ARG and VFG composition in the cecal digesta of broilers. LFP supplementation modulated more antibiotic resistance classes and ARGs than did SFP supplementation.

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Section: Sfp and Lfp Supplementation Inhibited Clpc Abundance In Bact...mentioning

confidence: 99%

Differential Effects of Bacillus Species-Fermented Products on Antibiotic Resistome and Virulence Factor Gene Composition in the Cecal Digesta of Broilers

Hsiao,

Cheng,

Chen

et al. 2024

Annals of Animal Science

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“…AMR studies from all over the world have reported widespread presence of resistance genes in water, soil as well as in food items. [143][144][145] This 'One health' approach of study underlines the importance of tracking resistance across abiotic environments alongside the clinics. 30 We thus looked for studies that reported whole-genome sequences of priority pathogens isolated from environments or food items.…”

Section: Indiamentioning

confidence: 99%

Genomic sequencing should extend to diverse priority pathogens for effective study and surveillance of antimicrobial resistance: a systematic review of whole-genome sequencing studies from India

Gheewalla,

Jagannadham,

Kutum

et al. 2023

Preprint

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BackgroundAntimicrobial resistance (AMR) is a public health emergency in many low and middle-income countries, including India. To effectively tackle AMR, we need rapid diagnostics, effective surveillance and new antimicrobial drugs. Whole-genome sequencing of pathogens is the first definite step towards achieving these goals.MethodsIn this work, we review all the studies published till date that report whole-genome sequences of select priority AMR pathogens from India. We searched PubMed and Web of Science databases for the studies that involved whole-genome sequencing of AMR priority pathogens from India. For the top two highly sequenced pathogens,S. typhiandK. pneumoniae, we performed phylogenetic analyses to understand the geo-climatic distribution of genetically diverse strains.ResultsOur search reveals 94 studies that report 2547 unique whole-genome sequences. We find that most sequences are limited to select priority pathogens isolated from a couple of geo-climatic zones of India. Our phylogenetic analyses show that available data does not indicate systematic differences between the genomes of isolates from different geo-climatic zones. Our search also reveals complete absence of travel-related studies tracking possible movement of AMR pathogens within country. Lastly, we find very few studies that sequence AMR pathogens isolated from food, soil or other environments.ConclusionTogether, these observations suggest that lndia should prioritize sequencing of diverse AMR pathogens from clinics as well as from environments and travellers rather than extending the geo-climatic range of already-sequenced pathogens. Our recommendations can be potentially valuable for other low and middle-income countries with limited resources, high prevalence of AMR and diverse geo-climatic conditions.

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“…For instance, the WHO priority pathogen list calls for new antibacterials to treat infections caused by Pseudomonas aeruginosa and carbapenem-resistant bacteria (CRE) [6]. Tere are currently 32 antibiotics in clinical development that target WHO priority pathogens, but only six of them can be considered truly innovative [7].…”

Section: Introductionmentioning

confidence: 99%

Machine Learning Techniques for Antimicrobial Resistance Prediction of Pseudomonas Aeruginosa from Whole Genome Sequence Data

Noman

Zeeshan

Arshad

et al. 2023

Computational Intelligence and Neuroscience

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Aim. Due to the growing availability of genomic datasets, machine learning models have shown impressive diagnostic potential in identifying emerging and reemerging pathogens. This study aims to use machine learning techniques to develop and compare a model for predicting bacterial resistance to a panel of 12 classes of antibiotics using whole genome sequence (WGS) data of Pseudomonas aeruginosa. Method. A machine learning technique called Random Forest (RF) and BioWeka was used for classification accuracy assessment and logistic regression (LR) for statistical analysis. Results. Our results show 44.66% of isolates were resistant to twelve antimicrobial agents and 55.33% were sensitive. The mean classification accuracy was obtained ≥98% for BioWeka and ≥96 for RF on these families of antimicrobials. Where ampicillin was 99.31% and 94.00%, amoxicillin was 99.02% and 95.21%, meropenem was 98.27% and 96.63%, cefepime was 99.73% and 98.34%, fosfomycin was 96.44% and 99.23%, ceftazidime was 98.63% and 94.31%, chloramphenicol was 98.71% and 96.00%, erythromycin was 95.76% and 97.63%, tetracycline was 99.27% and 98.25%, gentamycin was 98.00% and 97.30%, butirosin was 99.57% and 98.03%, and ciprofloxacin was 96.17% and 98.97% with 10-fold-cross validation. In addition, out of twelve, eight drugs have found no false-positive and false-negative bacterial strains. Conclusion. The ability to accurately detect antibiotic resistance could help clinicians make educated decisions about empiric therapy based on the local antibiotic resistance pattern. Moreover, infection prevention may have major consequences if such prescribing practices become widespread for human health.

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Exploring antibiotic resistance genes, mobile gene elements, and virulence gene factors in an urban freshwater samples using metagenomic analysis

Cited by 12 publications

References 53 publications

Differential Effects of Bacillus Species-Fermented Products on Antibiotic Resistome and Virulence Factor Gene Composition in the Cecal Digesta of Broilers

Differential Effects of Bacillus Species-Fermented Products on Antibiotic Resistome and Virulence Factor Gene Composition in the Cecal Digesta of Broilers

Genomic sequencing should extend to diverse priority pathogens for effective study and surveillance of antimicrobial resistance: a systematic review of whole-genome sequencing studies from India

Machine Learning Techniques for Antimicrobial Resistance Prediction of Pseudomonas Aeruginosa from Whole Genome Sequence Data

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