Metagenomic Insights into Chicken Gut Antibiotic Resistomes and Microbiomes

Yang, Jingwen; Tong, Cuihong; Xiao, Danyu; Xie, Longfei; Zhao, Ruonan; Huo, Zhipeng; Tang, Zhonglin; Hao, Jie; Zeng, Zhenling; Xiong, Wenguang

doi:10.1128/spectrum.01907-21

Cited by 17 publications

(13 citation statements)

References 69 publications

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“…Again, without controls, the causes and directionality of these similarities cannot be ruled out, but it is suggestive of an interconnectedness of these environments (humans and chickens), which could, for example, be due to a common source. Some papers have described a high correlation between MGE presence and ARG presence [ 90 , 91 ], which may suggest, as discussed by others [ 1 ], that when investigating AMR, that focussing on individual ARGs and MGEs, may be more relevant than bacterial lineages.…”

Section: Discussionmentioning

confidence: 99%

Dissecting microbial communities and resistomes for interconnected humans, soil, and livestock

Maciel-Guerra

Baker

et al. 2022

The ISME Journal

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A debate is currently ongoing as to whether intensive livestock farms may constitute reservoirs of clinically relevant antimicrobial resistance (AMR), thus posing a threat to surrounding communities. Here, combining shotgun metagenome sequencing, machine learning (ML), and culture-based methods, we focused on a poultry farm and connected slaughterhouse in China, investigating the gut microbiome of livestock, workers and their households, and microbial communities in carcasses and soil. For both the microbiome and resistomes in this study, differences are observed across environments and hosts. However, at a finer scale, several similar clinically relevant antimicrobial resistance genes (ARGs) and similar associated mobile genetic elements were found in both human and broiler chicken samples. Next, we focused on Escherichia coli, an important indicator for the surveillance of AMR on the farm. Strains of E. coli were found intermixed between humans and chickens. We observed that several ARGs present in the chicken faecal resistome showed correlation to resistance/susceptibility profiles of E. coli isolates cultured from the same samples. Finally, by using environmental sensing these ARGs were found to be correlated to variations in environmental temperature and humidity. Our results show the importance of adopting a multi-domain and multi-scale approach when studying microbial communities and AMR in complex, interconnected environments.

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Section: Discussionmentioning

confidence: 99%

Dissecting microbial communities and resistomes for interconnected humans, soil, and livestock

Maciel-Guerra

Baker

et al. 2022

The ISME Journal

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“…In recent decades, tetracyclines have been widely incorporated into animal feed to reduce the incidence of diseases and increase growth rates. Although China banned the use of antibiotics as growth promoters in 2020, ARGs have already been deposited in microbial genomes ( Yang et al, 2022 ). All yellow feather broilers also did not receive any antibiotic treatment in our experiment, and the observation that the broiler gut microbiome has a broad-ranging resistome is not surprising.…”

Section: Discussionmentioning

confidence: 99%

Metagenomic analysis reveals the microbiome and antibiotic resistance genes in indigenous Chinese yellow-feathered chickens

Huang

Guo

et al. 2022

Front. Microbiol.

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Yellow-feathered chickens have great nutritional value and are widely and traditionally used in China, on an industrial scale as broilers. The presence of intestinal microbes has been shown to correlate with poultry performance and serves as an essential reservoir of antibiotic resistance genes (ARGs). Antibiotic resistance is a major public health concern. Here, we investigated functional characteristics of the gut microbiome of indigenous Chinese yellow-feathered chickens (the Huiyang Bearded, Xinghua, Huaixiang, Zhongshan Shanlan, Qingyuan Partridge, and Yangshan chickens) through metagenomic sequencing and reconstructed 409 draft genomes, including 60 novel species and 6 novel genera. Furthermore, we assessed the functions of the intestinal microbial communities and examined the ARGs within them. The results showed that the microbial populations of yellow-feathered broilers were primarily dominated by Bacteroidetes and Firmicutes at the phylum level and Bacteroides at the genus level. Furthermore, the Qingyuan Partridge chicken showed a significantly higher abundance of Prevotella than the other five breeds of chicken. Principal coordinates analysis indicated significant differences in the structures of microbial communities and ARGs, based on the binary Jaccard distance, among the six chicken breeds. Moreover, 989 ARGs conferring tetracycline, multidrug, and aminoglycoside resistance were identified, which represented more than 80% of the faecal resistomes; the most abundant gene in the yellow-feathered chickens was tet(Q). In addition, we found the greatest abundance of resistance genes in Xinghua chickens, indicating that Xinghua chickens are highly resistant to antibiotics. Overall, our findings revealed differences in the gut microbial community structure of indigenous Chinese yellow-feathered broiler breeds and the composition and characteristics of ARGs and antibiotic resistance that enabled us to reconstruct the yellow-feathered chicken gut microbial community genomes. The current data significantly improves our knowledge of the gut microbiome and antibiotic resistance of popular broiler breeds in China.

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“…PCR ampli cation was with the bacterial LbLMA1-rev (5' -CTC AAA ACT AAA CAA AGT TTC -3') forward and R16-1 (5' -CTT GTA CAC ACC GCC CGT CA -3') reverse primer pair [23]. Genomic DNA (gDNA) extraction and puri cation was as described by Yang et al [24]. Reaction conditions (for PCR) consisted of an initial denaturation at 94˚C for 4min, 35 cycles at 94˚C for 30s, 55˚C for 30s and 70˚C for 30s.…”

Section: Identi Cation Of Isolates Using 16s Rrna Gene Sequencingmentioning

confidence: 99%

“…While AMR microbial infections (global annual mortality rates of > 700,000-1 million, and projected to reach 10 million by 2050) [9,10,11,12] have drawn considerable scienti c and medical attention, evidence has been growing of continuous gene exchange between pathogenic strains and ostensibly harmless or even bene cial commensal species. The implication is that the latter are now considered "reservoirs" of antibiotics resistance genes (ARGs), which, through multiple pathways, they may propagate and eventually share with pathogens or pathobionts [4,13,14,15]. In recent times, emergence has occurred of LAB strains, displaying single or multiple antibiotic resistance phenotypes, spurring concerns that these genes may, by genetic mechanisms like horizontal gene transfer through mobile elements like plasmids and transposons, be acquired by human and animal pathogens [16,17,18,19].…”

Section: Introductionmentioning

confidence: 99%

Antibiotic Resistance in Potential Probiotic Lactobacillary Strains of Fermented Foods and Human Origin From Nigeria

Duche

Singh

Wandhare

et al. 2022

Preprint

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Probiotic Lactobacillus strains are generally recognized as safe and are being used in several food and pharma formulations. Antimicrobial resistance is of growing concern globally. The presence of antibiotic resistance traits in bacterial strains of food origin and their possible transmission via functional foods is increasingly being emphasized. To be adequately suitable for use in foods/feed production for human and animal consumption, probiotic strains need to be free from transferable antibiotic resistance traits. This study screened potential probiotic Lactobacillus strains for their phenotypic and genotypic antibiotic resistance (AR) profiles. A wide spectrum of susceptibility and resistance was observed against different antibiotic classes. LAB isolates irrespective of origin displayed marked resistance against cephalosporins, aminoglycosides, quinolones, glycopeptides and methicillin among beta-lactams with few exceptions. In contrary, high sensitivity was recorded against macrolides, sulphonamides and carbapenems sub-group of beta-lactams with few variations. The parC gene, associated with resistance to ciprofloxacin was detected in 76.5% of the strains. Other prevalent resistant determinants observed were aac(6’)Ii (42.1%), ermB and ermC (29.4%), and tetM (20.5%). Six (≈ 17.6%) of isolates showed none of the resistance genes screened in this study. Study revealed the presence of AR genes among Lactobacillus species isolated from both fermented foods and human sources.

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Metagenomic Insights into Chicken Gut Antibiotic Resistomes and Microbiomes

Cited by 17 publications

References 69 publications

Dissecting microbial communities and resistomes for interconnected humans, soil, and livestock

Dissecting microbial communities and resistomes for interconnected humans, soil, and livestock

Metagenomic analysis reveals the microbiome and antibiotic resistance genes in indigenous Chinese yellow-feathered chickens

Antibiotic Resistance in Potential Probiotic Lactobacillary Strains of Fermented Foods and Human Origin From Nigeria

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