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Distinct increase in antimicrobial resistance genes among Escherichia coli during 50 years of antimicrobial use in livestock production in China

Abstract

Antimicrobial use in livestock production is linked to the emergence and spread of antimicrobial resistance (AMR), but large-scale studies on AMR changes in livestock isolates remain scarce. Here we applied whole-genome sequence analysis to 982 animal-derived Escherichia coli samples collected in China from the 1970s to 2019, finding that the number of AMR genes (ARGs) per isolate doubled—including those conferring resistance to critically important agents for both veterinary (florfenicol and norfloxacin) and human medicine (colistin, cephalosporins and meropenem). Plasmids of incompatibility groups IncC, IncHI2, IncK, IncI and IncX increased distinctly in the past 50 years, acting as highly effective vehicles for ARG spread. Using antimicrobials of the same class, or even unrelated classes, may co-select for mobile genetic elements carrying multiple co-existing ARGs. Prohibiting or strictly curtailing antimicrobial use in livestock is therefore urgently needed to reduce the growing threat from AMR.

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Fig. 1: Origins of the 982 E. coli isolates from 26 Chinese provinces.
Fig. 2: Temporal changes in AMR.
Fig. 3: Temporal changes in ESBL and PMQR gene profiles among the full genome set (n = 982).
Fig. 4: The correlation of antimicrobial production and resistance gene content.
Fig. 5: Co-occurrence of ARGs and plasmid replicons.
Fig. 6: ARG co-occurrence networks of phenicol, fluoroquinolone and polymyxin resistance genes among isolates.

Data availability

All data analysed in this study are publicly available. The whole-genome sequencing data downloaded from previous projects are listed in Supplementary Table 6, including the accession numbers, collection times and sampling preferences. The genomes of the newly sequenced isolates have been deposited in NCBI as well (BioProject accession number: PRJNA718052). The phylogenetic tree of all 982 genomes along with all metadata is available on the interactive online platform Microreact (https://microreact.org/project/9ozGFW62hE7LmgkVZ9Uouh/449bbe4b). The map we used for generating Fig. 1 was from an open-source database and free for use. Source data are provided with this paper.

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Acknowledgements

This work was supported in part by grants from the Laboratory of Lingnan Modern Agriculture Project (no. NT2021006 to Y.W., Z.S. and J.S.), the National Natural Science Foundation of China (no. 81991535 to C.W.) and the UK Medical Research Council (project DETER-XDR-China-HUB, grant no. MR/S013768/1 to T.R.W.).

Author information

Authors and Affiliations

Authors

Contributions

The study was conceived and supervised by J.S., Z.S. and Y.W., and designed by L.Y., Y.S., B.S. and C.W. L.Y., J.J. and X.W. completed the wet lab experiments. L.Y. and D.S. analysed the data under the guidance of M.M.C.L. and K.E.H. L.Y. and Y.W. drafted the majority of the manuscript, and T.R.W., S.S. and Z.S. also contributed to the text. All authors contributed to the review of the manuscript before submission for publication and approved the final version.

Corresponding authors

Correspondence to Yang Wang or Zhangqi Shen.

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The authors declare no competing interests.

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Nature Food thanks David Skurnik, Yahong Liu and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.

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Extended data

Extended Data Fig. 1 Phylogenetic tree of E. coli isolates from food-animal in China.

a. Phylogenetic tree of 982 E. coli isolates from food-animal in China. The midpoint-rooted tree was constructed using n=50672 core-genome SNPs, and the tree along with all these metadata have been uploaded to microreact (https://microreact.org/project/9ozGFW62hE7LmgkVZ9Uouh/449bbe4b). b. Phylogenetic tree of the two clades C1 and C2 highlighted in Fig. 1a and annotated by host, time group and gene content. The tips are colored by the host. Columns are as follows: sampling time, and presence or absence of ARGs (blue) and plasmid replicons (red).

Source data

Extended Data Fig. 2 Minimum spanning tree of the whole data set by multi-locus sequence typing.

The time group of all isolates is indicated by different colors.

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Extended Data Fig. 3 Prevalence of some specific STs with a rising (red) or declining (blue) trend over time and the ARG containing numbers in these STs.

The average numbers were noted by ‘x’, and discrete numbers were showed as dots. For some groups like ST46, most of the isolates (n = 17) contain same n umber of ARGs (n = 9, including colistin resistance gene mcr-1), which were overlapped on the ‘x’.

Source data

Extended Data Fig. 4 The distribution of the number of plasmid replicon genes and virulence genes per isolate in different time group.

The mean ARG count for each group is noted above. The ‘*’ on the right represent p-values. *: p < 0.05; **: p < 0.01; ***: p < 0.001.

Source data

Extended Data Fig. 5 The prevalence of plasmid replicon genes and P-values between different groups.

a. The prevalence of plasmid replicon genes grouped by time and host. b. The P-values of pairwise comparisons of prevalence of time-groups.

Source data

Extended Data Fig. 6 Comparison of AMR genotype and phenotype of different antimicrobial agents.

The bars labeled name of antimicrobial agents represent the resistance rate. And the label with ‘lab’, ‘NCBI’ and ‘overall’ represent the prevalence of corresponding resistant genes in lab-preserved strains (n=450), NCBI-downloaded strains (n=532) and the overall dataset (n=982), respectively.

Source data

Extended Data Fig. 7 The value of antimicrobial production with phenotype and genotype changes over the time.

a. The dark grey histogram shows the mean value of production of norfloxacin per year in different time groups. The light grey histogram shows the mean value of production of other quinolones used in animals (ciprofloxacin, ofloxacin, levofloxacin, lomefloxacin, pefloxacin and pipemidic acid) per year, and data were only available from 2000s. The black line represents the prevalence of norfloxacin resistance and the orange lines represent the prevalence of quinolone-resistant genes. b. The histogram shows the mean value of production of colistin in different time groups. The black line represents the prevalence of colistin resistance and the green line represent the prevalence of colistin-resistant gene mcr-1. Production data before 2000 were unavailable.

Source data

Extended Data Fig. 8 The correlation of mean counts of ARGs, plasmid replicons, and virulence genes detected from genomes.

a. The correlation between ARG and virulence genes counts. b. The correlation between plasmid replicon and ARG counts. c. The correlation between plasmid replicons and virulence gene counts.

Source data

Extended Data Fig. 9 The co-occurrence of ARGs and plasmid replicons in different time groups.

The first two of the groups (1970s-80s and 1990s) were merged as ‘before 2000’, due to the smaller quantities of isolates. We define the false discovery rate (FDR) threshold as 0.05 in this algorithm; significant pairwise values from 1 (blue) to -1 (red) (that is co-occurrence and mutual exclusivity) are shown. The blue box labelled ‘ARG-ARG’ shows the pairwise co-occurrence and mutual exclusivity of ARGs, and the red box labelled ‘plasmid-plasmid’ shows the pairwise co-occurrence and mutual exclusivity of plasmid replicons. The gold boxes labelled with numbers indicate the co-occurrence and mutual exclusivity between ARGs and plasmid replicons, and these are annotated on the bottom left.

Source data

Extended Data Fig. 10 Per Capita Consumption of food and population size in China.

a. Per Capita Consumption of pork and chicken in rural area, urban area and nationwide. b. Population size in China.

Source data

Supplementary information

Supplementary Information

Supplementary Figs. 1–5 and Tables 2 and 4–7.

Reporting Summary

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Supplementary Tables 1, 3 and 8.

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Yang, L., Shen, Y., Jiang, J. et al. Distinct increase in antimicrobial resistance genes among Escherichia coli during 50 years of antimicrobial use in livestock production in China. Nat Food 3, 197–205 (2022). https://doi.org/10.1038/s43016-022-00470-6

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