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Commensal Escherichia coli are a reservoir for the transfer of XDR plasmids into epidemic fluoroquinolone-resistant Shigella sonnei

Nature Microbiology volume 5, pages 256–264 (2020)Cite this article

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Abstract

Despite the sporadic detection of fluoroquinolone-resistant Shigella in Asia in the early 2000s and the subsequent global spread of ciprofloxacin-resistant (cipR) Shigella sonnei from 2010, fluoroquinolones remain the recommended therapy for shigellosis1,2,3,4,5,6,7. The potential for cipR S. sonnei to develop resistance to alternative second-line drugs may further limit future treatment options8. Here, we aim to understand the evolution of novel antimicrobial resistant (AMR) S. sonnei variants after introduction into Vietnam. We found that cipR S. sonnei displaced the resident ciprofloxacin-susceptible (cipS) lineage while rapidly acquiring additional resistance to multiple alternative antimicrobial classes. We identified several independent acquisitions of extensively drug-resistant/multidrug-resistant-inducing plasmids, probably facilitated by horizontal transfer from commensals in the human gut. By characterizing commensal Escherichia coli from Shigella-infected and healthy children, we identified an extensive array of AMR genes and plasmids, including an identical multidrug-resistant plasmid isolated from both S. sonnei and E. coli in the gut of a single child. We additionally found that antimicrobial usage may impact plasmid transfer between commensal E. coli and S. sonnei. These results suggest that, in a setting with high antimicrobial use and a high prevalence of AMR commensals, cipR S. sonnei may be propelled towards pan-resistance by adherence to outdated international treatment guidelines.

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Fig. 1: The phylogenetic structure of S. sonnei in Vietnam, 2014–2016.
Fig. 2: The diversity of ESBL-encoding plasmids in ciprofloxacin-resistant S. sonnei.
Fig. 3: Antimicrobial resistance genes and plasmids in human commensal bacteria and S. sonnei.
Fig. 4: The conjugation efficiency of ESBL-encoding plasmids from human commensal E. coli to ciprofloxacin-resistant S. sonnei with and without supplementation with ciprofloxacin.

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Data availability

All raw genomic data that support the findings of this study have been deposited in the European Nucleotide Archive (ENA, project PRJEB30967) and can be accessed via this link. Details about the accession numbers of S. sonnei isolates are provided in Supplementary Table 1. The S. sonnei reference genome Ss046 chromosome (accession no. NC_007382), virulence plasmid pSs046 (accession no. NC_007385.1)<q> and three small plasmids commonly found in global lineage III S. sonnei—spA (accession no. NC_009345.1), spB (accession no. NC_009346.1) and spC (accession no. NC_009347.1)—were downloaded from GenBank. Raw MinION reads for plasmid p01_0123 are deposited in ENA (accession no. ERS3050922). Source data for the main figures (Figs. 2a, 3a and 4) and Extended Data Figs. 1 and 2 are provided with the paper. Additional data that support the findings of this study are available from the corresponding author upon request.

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Acknowledgements

This work was funded by a Senior Research Fellowship funded by the Wellcome Trust to S.B. (100087/Z/12/Z) and an Oak Leader Fellowship to D.P.T.

Author information

Author notes

  1. These authors contributed equally: Maia A. Rabaa and Stephen Baker.

Authors and Affiliations

  1. The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam

    Pham Thanh Duy, To Nguyen Thi Nguyen, Duong Vu Thuy, Hao Chung The, Felicity Alcock, Christine Boinett, Ho Ngoc Dan Thanh, Ha Thanh Tuyen, Guy E. Thwaites, Maia A. Rabaa & Stephen Baker

  2. Centre for Tropical Medicine, Oxford University, Oxford, UK

    Guy E. Thwaites & Maia A. Rabaa

  3. Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID) Department of Medicine, University of Cambridge, Cambridge, UK

    Stephen Baker

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Contributions

P.T.D., M.A.R. and S.B. designed the study. P.T.D. performed data analysis and interpreted the results under the scientific guidance of M.A.R. and S.B. P.T.D. drafted the paper, with M.A.R. and S.B. revising and structuring the paper. P.T.D. and H.N.D.T. performed whole genome sequencing. P.T.D. and T.N.T.N. performed plasmid isolation, digestion and sequencing. P.T.D., F.A. and T.N.T.N. performed the plasmid conjugation experiments. H.T.T. performed basic microbiology work. H.C.T. and C.B. assisted in the design of laboratory experiments. D.V.T. recruited patients and performed the clinical work required for the study. H.C.T., C.B. and G.E.T. contributed to the editing of the paper. All authors read and approved the final draft.

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Correspondence to Stephen Baker.

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Extended data

Extended Data Fig. 1 Plasmid profiling of Shigella sonnei in Vietnam, 2014–2016.

Dendrogram shows the difference in plasmid electrophoresis patterns between the resident S. sonnei clade and the cipR S. sonnei clade in Vietnam. Black lines separate lanes that were not contiguous in a gel. Data were obtained from a single experiment. Cluster analysis was performed with Bionumerics by using the Jaccard coefficient and the unweighted pair group mathematical average (UPGMA) clustering algorithm.

Source data

Extended Data Fig. 2 Distribution of antimicrobial resistance genes and plasmid groups in Shigella sonnei and human commensal bacteria.

The first column highlights the four different isolate types in different colors. Fecal/rectal swab cultures with ciprofloxacin-resistant and ESBL-producing isolates are highlighted in turquoise and red (second and third columns, respectively). The remaining columns show the distribution of all antimicrobial resistance genes and plasmid groups identified in commensal bacteria and S. sonnei. AMR genes are grouped together based on the class of antimicrobial agents to which they are resistant, with different variants of an AMR gene shown in different shades of blue.

Source data

Extended Data Fig. 3 Root-to-tip regression for the maximum likelihood tree of Shigella sonnei in Vietnam, 2014–2016.

Each point on the plot corresponds to a measurement of genetic distance from the inferred root to each tip in the tree (n = 81 biologically independent samples). The solid line is the regression line fitted using the ordinary least squares method. The slope of the line is a crude estimate of the evolutionary rate, the x-intercept corresponds to the inferred date of the most recent common ancestor, and the R2 value measures the degree of clock-like behavior.

Supplementary information

Reporting Summary

Supplementary Table 1

Shigella sonnei isolates and their corresponding metadata.

Source data

Source Data Fig. 2a

Raw unprocessed gels associated with Fig. 2a.

Source Data Fig. 3a

Source data of antimicrobial resistance genes and plasmids in Shigella sonnei and human commensal bacteria associated with Fig. 3a.

Source Data Fig. 4

Source data of the conjugation efficiency of ESBL-encoding plasmids from human commensal E. coli to ciprofloxacin-resistant Shigella sonnei with and without supplementation with ciprofloxacin associated with Fig. 4.

Source Data Extended Data Fig. 1

Raw unprocessed gels associated with Extended Data Fig.1.

Source Data Extended Data Fig. 2

Source data of distribution of antimicrobial resistance genes and plasmid groups in Shigella sonnei and human commensal bacteria associated with Extended Data Fig. 2.

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Thanh Duy, P., Thi Nguyen, T.N., Vu Thuy, D. et al. Commensal Escherichia coli are a reservoir for the transfer of XDR plasmids into epidemic fluoroquinolone-resistant Shigella sonnei. Nat Microbiol 5, 256–264 (2020). https://doi.org/10.1038/s41564-019-0645-9

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