Next-Generation Sequencing Based Gut Resistome Profiling of Broiler Chickens Infected with Multidrug-Resistant Escherichia coli

Afridi, Ome Kalsoom; Ali, Johar; Chang, Jeong Ho

doi:10.3390/ani10122350

Cited by 17 publications

(12 citation statements)

References 52 publications

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“…Arguably, a greater threat to human and animal health is posed by multidrug-resistant (MDR) bacteria, with an alarming increase being observed in the number of MDR strains isolated from the poultry meat production chain ( Afridi et al, 2020 ). Unusually high levels of MDR bacteria, especially those of the Enterobacteriaceae , have been isolated from poultry.…”

Section: The Use Of Antibiotics In the Poultry Industry And Its Effect On The Poultry Manure Resistomementioning

confidence: 99%

Antibiotics and Antibiotic Resistance Genes in Animal Manure – Consequences of Its Application in Agriculture

et al. 2021

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Antibiotic resistance genes (ARGs) are a relatively new type of pollutant. The rise in antibiotic resistance observed recently is closely correlated with the uncontrolled and widespread use of antibiotics in agriculture and the treatment of humans and animals. Resistant bacteria have been identified in soil, animal feces, animal housing (e.g., pens, barns, or pastures), the areas around farms, manure storage facilities, and the guts of farm animals. The selection pressure caused by the irrational use of antibiotics in animal production sectors not only promotes the survival of existing antibiotic-resistant bacteria but also the development of new resistant forms. One of the most critical hot-spots related to the development and dissemination of ARGs is livestock and poultry production. Manure is widely used as a fertilizer thanks to its rich nutrient and organic matter content. However, research indicates that its application may pose a severe threat to human and animal health by facilitating the dissemination of ARGs to arable soil and edible crops. This review examines the pathogens, potentially pathogenic microorganisms and ARGs which may be found in animal manure, and evaluates their effect on human health through their exposure to soil and plant resistomes. It takes a broader view than previous studies of this topic, discussing recent data on antibiotic use in farm animals and the effect of these practices on the composition of animal manure; it also examines how fertilization with animal manure may alter soil and crop microbiomes, and proposes the drivers of such changes and their consequences for human health.

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Section: The Use Of Antibiotics In the Poultry Industry And Its Effect On The Poultry Manure Resistomementioning

confidence: 99%

Antibiotics and Antibiotic Resistance Genes in Animal Manure – Consequences of Its Application in Agriculture

et al. 2021

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“…This change may be attributed to the detected significant increase in the transcript abundance of Escherichia ( Figure 7 ) after AGP + PFA administration at Day 35. In fact, in a previous study, the Escherichia genus was found to be the most common host for multidrug resistance ARGs ( Li B. et al, 2015 ; Xiong et al, 2018 ; Afridi et al, 2020 ). While interesting, we note that this may very well be also due to the fact that Escherichia coli is a popular model organism.…”

Section: Discussionmentioning

confidence: 95%

Metatranscriptomic Analysis of the Chicken Gut Resistome Response to In-Feed Antibiotics and Natural Feed Additives

Koorakula

Schiavinato

Ghanbari³

et al. 2022

Front. Microbiol.

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The emergence of resistance against common antibiotics in the gut microbiota is a major issue for both human and livestock health. This highlights the need for understanding the impact of such application on the reservoir of antibiotic resistance genes in poultry gut and devising means to circumvent the potential resistome expansion. Phytogenic feed additives (PFAs) are potential natural alternative to antibiotic to improve animal health and performance, supposedly via positively affecting the gut microbial ecosystem, but there is little systematic information available. In this time-course study, we applied a shotgun meta-transcriptomics approach to investigate the impact of a PFA product as well as the commonly used antibiotic, zinc bacitracin either at AGP concentration or therapeutic concentration on the gut microbiome and resistome of broiler chickens raised for 35 days. Over the course of the trial, PFA treatments increased the abundance of Firmicutes such as Lactobacillus and resulted in a lower abundance of Escherichia, while the latter group increased significantly in the feces of chickens that received either AGP or AB doses of bacitracin. Tetracycline resistance and aminoglycoside resistance were the predominant antibiotic resistance gene (ARG) classes found, regardless of the treatment. PFA application resulted in a decrease in abundance of ARGs compared to those in the control group and other antibiotic treatment groups. In summary, the findings from this study demonstrate the potential of phytogenic feed additives could be an alternative to antibiotics in poultry farming, with the added benefit of counteracting antimicrobial resistance development.

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“…In chickens, Proteobacteria (38.9%) were dominant, followed by Firmicutes (36.4%), Bacteroidetes (15.8%), and Tenericutes (8.9%) (38). The differences between the abovementioned studies may be due to specific factors, such as animal species, growth stage, sampling position, and dietary components used.…”

Section: Discussionmentioning

confidence: 97%

Dietary protein levels modulate the gut microbiome composition through fecal samples derived from lactating ewes

Liang,

Ali,

et al. 2023

Front. Endocrinol.

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In ruminants, the digestion and utilization of dietary proteins are closely linked to the bacterial populations that are present in the gastrointestinal tract. In the present study, 16S rDNA sequencing, together with a metagenomic strategy was used to characterize the fecal bacteria of ewes in the early lactation stage after feeding with three levels of dietary proteins 8.58%, 10.34%, and 13.93%, in three different groups (H_1), (H_m) and (H_h), respectively. A total of 376,278,516 clean data-points were obtained by metagenomic sequencing. Firmicutes and Bacteroidetes were the dominant phyla, regardless of the dietary protein levels. In the H_h group, the phyla Proteobacteria, Caldiserica, and Candidatus_Cryosericota were less abundant than those in the H_I group. In contrast, Lentisphaerae, Chlamydiae, and Planctomycetes were significantly more abundant in the H_h group. Some genera, such as Prevotella, Roseburia, and Firmicutes_unclassified, were less abundant in the H_h group than those in the H_I group. In contrast, Ruminococcus, Ruminococcaceae_noname, Anaerotruncus, Thermotalae, Lentisphaerae_noname, and Paraprevotella were enriched in the H_h group. The acquired microbial genes were mainly clustered into biological processes; molecular functions; cytosol; cellular components; cytoplasm; structural constituents of ribosomes; plasma membranes; translation; and catalytic activities. 205987 genes were significantly enriched in the H_h group. In contrast, 108129 genes were more abundant in the H_I group. Our findings reveal that dynamic changes in fecal bacteria and their genes are strongly influenced by the levels of dietary proteins. We discovered that differentially expressed genes mainly regulate metabolic activity and KEGG demonstrated the primary involvement of these genes in the metabolism of carbohydrates, amino acids, nucleotides, and vitamins. Additionally, genes responsible for metabolism were more abundant in the H_h group. Investigating fecal bacterial characteristics may help researchers develop a dietary formula for lactating ewes to optimize the growth and health of ewes and lambs.

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Next-Generation Sequencing Based Gut Resistome Profiling of Broiler Chickens Infected with Multidrug-Resistant Escherichia coli

Cited by 17 publications

References 52 publications

Antibiotics and Antibiotic Resistance Genes in Animal Manure – Consequences of Its Application in Agriculture

Antibiotics and Antibiotic Resistance Genes in Animal Manure – Consequences of Its Application in Agriculture

Metatranscriptomic Analysis of the Chicken Gut Resistome Response to In-Feed Antibiotics and Natural Feed Additives

Dietary protein levels modulate the gut microbiome composition through fecal samples derived from lactating ewes

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