Emergence of methicillin resistance predates the clinical use of antibiotics

Abstract

The discovery of antibiotics more than 80 years ago has led to considerable improvements in human and animal health. Although antibiotic resistance in environmental bacteria is ancient, resistance in human pathogens is thought to be a modern phenomenon that is driven by the clinical use of antibiotics¹. Here we show that particular lineages of methicillin-resistant Staphylococcus aureus-a notorious human pathogen-appeared in European hedgehogs in the pre-antibiotic era. Subsequently, these lineages spread within the local hedgehog populations and between hedgehogs and secondary hosts, including livestock and humans. We also demonstrate that the hedgehog dermatophyte Trichophyton erinacei produces two β-lactam antibiotics that provide a natural selective environment in which methicillin-resistant S. aureus isolates have an advantage over susceptible isolates. Together, these results suggest that methicillin resistance emerged in the pre-antibiotic era as a co-evolutionary adaptation of S. aureus to the colonization of dermatophyte-infected hedgehogs. The evolution of clinically relevant antibiotic-resistance genes in wild animals and the connectivity of natural, agricultural and human ecosystems demonstrate that the use of a One Health approach is critical for our understanding and management of antibiotic resistance, which is one of the biggest threats to global health, food security and development.

Fig. 1. Distribution of mecC-MRSA clones in European and New Zealand hedgehog samples.

The analysis included 828 samples from the nasal area, skin and feet of 276 hedgehogs originating from 16 wildlife rescue centres in 10 European countries and 2 wildlife rescue centres in New Zealand. The red dots indicate the sampling locations. The pie charts are connected to the sampling locations by a red line. The area of the pie chart is proportional to the number of samples from that location. The introduction of European hedgehogs into New Zealand from the UK between 1869 and 1892 is shown. A detailed description of the results is provided in Extended Data Fig. 1. Maps were provided by Eurostat under a Creative Commons Attribution 4.0 International (CC BY 4.0) licence; the administrative boundaries are copyright of EuroGeographics. Source data

Fig. 2. Penicillin biosynthetic genes and antibiotic activity of T. erinacei IMI 101051.

a, Schematic of the key steps in the biosynthesis of penicillin G and cephalosporin C. The presence (green) or absence (red) of T. erinacei penicillin G and cephalosporin C biosynthetic genes is indicated. b, T. erinacei inhibition zones against a collection of S. aureus control strains (black) and two mecC-MRSA wild-type strains belonging to CC130 (green) and CC425 (blue) and their isogenic mutants. Two-tailed paired Student’s t-tests were used to compare inhibition zones of each mutant to the corresponding wild-type strain. Data are mean ± s.d.; n = 4 biologically independent fungal culture extracts. A detailed description of the results is provided in Extended Data Fig. 4. Source data

Fig. 3. Timeline of mecC-MRSA CC130, CC425 and CC1943 evolution in Europe.

Manual mapping of the tips on the type XI SCCmec phylogeny onto the CC130, CC425 and CC1943 phylogenies, and vice versa, enabled us to assign the mecC-MRSA isolates to 16 monophyletic lineages containing orthologous type XI SCCmec elements (A–G). The trees are redrawn from Supplementary Figs. 2–5 to illustrate the branching order of the different type XI SCCmec variants and mecC-MRSA lineages. Branch lengths are not drawn to scale. The presence and absence of hedgehog isolates in a given lineage are shown as black and white boxes, respectively. A detailed description of the geographical distribution and host range of major mecC-MRSA CC130, CC425 and CC1943 lineages is provided in Extended Data Fig. 7. The estimated date of the most recent common ancestor and 95% confidence interval of each mecC-MRSA lineage are illustrated by filled circles and horizontal lines, respectively. The introduction of penicillin G and methicillin as therapeutic options is indicated by red lines. Source data

Fig. 4. Population structures of Danish mecC-MRSA isolates from hedgehogs and humans.

a, The map of Denmark shows the geographical ranges of two of the three hedgehog subpopulations in Jutland and on the major islands. b, The geographical distribution of major mecC-MRSA CC130, CC425 and CC1943 lineages in two broad collections of mecC-MRSA isolates recovered from hedgehogs (n = 141) and humans (n = 327) in Jutland and on the major islands. Hedgehog and human isolates from the remaining hedgehog subpopulation on the small island of Bornholm (not shown) were excluded from the analysis due to their small sample size (n = 9). A detailed map of the sampling locations is provided in Extended Data Fig. 8. Maps were provided by Eurostat under a Creative Commons Attribution 4.0 International (CC BY 4.0) licence; the administrative boundaries are copyright of EuroGeographics. Source data

Extended Data Fig. 1. Distribution of mecC-MRSA clones in European and New Zealand hedgehogs.

The analysis included 828 samples from the nasal area, skin and feet of 276 hedgehogs originating from 16 wildlife rescue centres in ten European countries and two wildlife rescue centres in New Zealand. a, Presence of mecC-MRSA in hedgehogs (n = 276). Presence and absence are shown as black and white boxes, respectively. b, Distribution of mecC-MRSA clones in hedgehog samples (n = 828). c, Distribution of MSSA clones in MRSA-negative hedgehog samples (n = 606). Source data

Extended Data Fig. 2. Detection of penicillin G in T. erinacei IMI 101051 culture broth.

a, Left and right panels show extracted ion chromatogram of a pure standard of penicillin G and in T. erinacei culture broth, respectively. b, Upper and lower panels show MS² spectra of penicillin G in a T. erinacei culture broth and a pure standard of penicillin G, respectively.

Extended Data Fig. 3. Detection of KPN in T. erinacei IMI 101051 culture broth.

a, Left and right panels show extracted ion chromatogram of a pure standard of penicillin G and KPN in T. erinacei culture broth, respectively. b, Upper and lower panels show MS² spectra of KPN in a T. erinacei culture broth and a pure standard of penicillin G, respectively.

Extended Data Fig. 4. Antibiotic activity of T. erinacei IMI 101051.

T. erinacei inhibition zones against a collection of S. aureus control strains and two mecC-MRSA wild-type strains belonging to CC130 (02.5099.D) and CC425 (LGA251) and their isogenic mutants. The numbers on the plates refer to each of four biologically independent fungal culture extracts. Source data

Extended Data Fig. 5. Root-to-tip linear regression analysis of the type XI SCCmec dataset.

The correlation between root-to-tip distances and isolation dates is very weak with a coefficient of determination R² = −0.05.

Extended Data Fig. 6. Number of mecC-MRSA CC1943 sublineages.

The bars show the number of sublineages of mecC-MRSA CC1943:C1, mecC-MRSA CC1943:C2 and mecC-MRSA CC1943:C3 at different time points. Source data

Extended Data Fig. 7. Geographical distribution and host range of major mecC-MRSA CC130, CC425 and CC1943 lineages.

The study collection included 991 mecC-MRSA CC130, CC425 and CC1943 isolates originating from 16 European countries. The countries of sampling and the eight largest (≥25 isolates) mecC-MRSA lineages are shown. Isolates belonging to the eight minor mecC-MRSA lineages are grouped together (others). The pie charts depict the proportion of mecC-MRSA isolates from hedgehogs (black), humans (grey) and other sources (white). The area of the pie chart is proportional to the number of mecC-MRSA isolates from that country. Source data

Extended Data Fig. 8. Sampling locations of Danish mecC-MRSA isolates from hedgehogs and humans.

The maps of Denmark relate to the map shown in Fig. 4. a, mecC-MRSA recovered from hedgehogs (n = 141). b, mecC-MRSA recovered from humans (n = 327). The location of each sample is given at the zip code area level. Maps were provided by Eurostat under a Creative Commons Attribution 4.0 International (CC BY 4.0) licence; the administrative boundaries are copyright of EuroGeographics.

Extended Data Fig. 9. Frequency of potential transmission events of mecC-MRSA CC130 isolates within wildlife rescue centres.

The bars show the proportion of isolates that belong to clusters defined at different pairwise SNP distance thresholds. Source data