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000849.v2
10.1099/acmi.0.000849.v2
Research Article
Antimicrobial Resistance
Evolution
Genomic Sequencing
Molecular Epidemiology
Staphylococcus Aureus
Genomic epidemiology of mecC-carrying Staphylococcus aureus isolates from human clinical cases in New Zealand
http://orcid.org/0009-0009-5318-8151
Miller Hilary 1*hilary.miller@esr.cri.nz

http://orcid.org/0000-0003-1612-2136
Howard Julia 2Julia.Howard2@cdhb.health.nz

http://orcid.org/0009-0001-4482-6758
Elvy Juliet 13juliet.elvy@awanuilabs.co.nz

http://orcid.org/0000-0001-8031-9852
Campbell Patrick 4patrick.campbell@cdhb.health.nz

http://orcid.org/0000-0002-2454-4876
Anderson Trevor 2trevor.anderson@cdhb.health.nz

http://orcid.org/0000-0003-2700-2316
Bakker Sarah 1sarah.bakker@esr.cri.nz

http://orcid.org/0009-0002-6487-4017
Eustace Alexandra 1alexandra.eustace@esr.cri.nz

http://orcid.org/0000-0001-5519-5464
Perez Hermes 1hermes.perez@esr.cri.nz

http://orcid.org/0000-0002-6165-0029
Winter David 1david.winter@esr.cri.nz

http://orcid.org/0000-0003-2508-6843
Dyet Kristin 1kristin.dyet@esr.cri.nz

1 Institute of Environmental Science and Research, Wellington, New Zealand
2 Microbiology Department, Canterbury Health Laboratories, Christchurch, New Zealand
3 Department of Microbiology, Awanui Labs, Dunedin, New Zealand
4 Infection Management Service, Christchurch Hospital, Christchurch, New Zealand
The authors declare that there are no conflicts of interest.

HilaryMiller, hilary.miller@esr.cri.nz
Supplement: One supplementary figure and two supplementary tables are available with the online version of this article.

2024
05 9 2024
6 9 000849.v215 5 2024
17 7 2024
Copyright © 2024 The Authors
2024
https://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License. This article was made open access via a Publish and Read agreement between the Microbiology Society and the corresponding author’s institution.

Abstract

In 2011, a novel methicillin resistance gene, mecC, was described in human and bovine Staphylococcus aureus isolates. mecC-positive S. aureus is most commonly associated with livestock and wildlife populations across Europe and is particularly prevalent in hedgehogs, but only occasionally causes human infections. In this study, we characterize and investigate the origin of two human S. aureus isolates containing mecC genes from New Zealand. The two isolates were identified from patients with severe invasion infections as part of an S. aureus bacteraemia study. Whole-genome sequencing was used to characterize staphylococcal cassette chromosome mec (SCCmec) elements and perform phylogenetic comparisons with publicly available strains from mecC-associated clonal complexes, including isolates from hedgehogs from New Zealand and Europe/United Kingdom (UK), and livestock, wildlife and human isolates from Europe/UK. The two isolates from our study have almost identical SCCmec type XI elements containing a mecC gene. However, this gene contains a premature stop codon, consistent with the methicillin-susceptible phenotype observed for these isolates. Core genome SNP analyses showed that the two isolates are 234 SNPs apart and are most closely related to an isolate obtained from a New Zealand hedgehog. However, there are considerable differences in the mecC mobile element between the human and hedgehog isolates, indicating the presence of an as-yet-unknown reservoir of mecC S. aureus in the New Zealand environment.

antimicrobial resistance
mecC
MRSA
One Health
Staphylococcus aureus
whole-genome sequencing
Ministry of Health New Zealand Dyet Kristin
==== Body
pmcData Summary

Isolates sequenced in this study have been submitted to the National Center for Biotechnology Information under BioProject accession number PRJNA1029301. Accession numbers for other samples included in the study are given in Supplementary Material, available in the online version of this article.

Impact Statement

Methicillin-resistant Staphylococcus aureus (MRSA) poses a significant public health threat worldwide. Methicillin resistance in humans is commonly mediated by the mecA gene. However, in 2011, a distinct methicillin resistance gene, mecC was identified. mecC-carrying S. aureus has now been found in diverse livestock and wildlife populations and represents an emerging source of MRSA cases in humans but is rarely reported outside of Europe. Our study is the first report of S. aureus isolates with a mecC-containing staphylococcal cassette chromosome mec type XI element from any species in New Zealand, thus expanding the geographic range where mecC S. aureus is known to occur. Through whole-genome sequencing and phylogenetic comparison with publicly available isolates, we show that these isolates form a clade with isolates from a New Zealand hedgehog but have considerable differences in their mecC mobile elements, indicating there may be another source of mecC in the New Zealand environment. Our study shows the need for further sampling of S. aureus from livestock, wildlife and humans in New Zealand to ascertain possible public health risks from mecC-carrying S. aureus.

Introduction

Methicillin-resistant Staphylococcus aureus (MRSA) is a major global healthcare issue. Methicillin resistance was originally associated with the acquisition of the mecA gene, which encodes an altered penicillin-binding protein 2a [1]. The mecA gene is located on a mobile genetic element, staphylococcal chromosomal cassette mec (SCCmec), which is incorporated into the S. aureus chromosome [2]. In 2011, a homologue of mecA, named mecC, was discovered in human and bovine S. aureus populations in the United Kingdom (UK) and Denmark [3]. The mecC gene was found to be on a novel SCCmec element, named type XI, which is most commonly found in clonal complexes 130, 425, 599 and 1943 [4].

Since 2011, mecC-positive S. aureus isolates have been found in humans, livestock, companion animals and wildlife throughout Europe and the UK [4, 57]. Reports from outside of Europe are less common, but it has also been detected in domestic cats in Australia [8] and dairy cattle in Malaysia [9] and Brazil [10]. Detections of mecC-MRSA are particularly common in hedgehog populations across Europe, with prevalence as high as 60% found in populations in Sweden, Denmark and the Netherlands [1113]. A recent study by Larsen et al. [14] found that mecC-MRSA in hedgehogs originated prior to the development of antibiotics and is likely related to colonization of hedgehogs with the penicillin-producing fungus Trichophyton erinacei rather than the widespread use of antibiotics in livestock farming.

Clinical infections of mecC-MRSA are uncommon in humans, but they can cause severe disease [15]. Surveillance of MRSA in Europe detected mecC in less than 1% of all MRSA [15], although slightly higher rates (around 2%) were reported in Denmark [16]. Although hedgehogs are a natural reservoir for S. aureus, and some mecC-MRSA strains from humans are closely related to those from hedgehogs [13], direct transmission between hedgehogs and humans has not yet been confirmed. However, potential transmission between humans and livestock animals has been detected in a small number of cases [717 18].

Here, we characterize the genomes of two isolates of S. aureus with non-functional mecC genes from human clinical cases where severe invasion infection was present. Prior to this study, mecC-carrying S. aureus had not previously been detected in human clinical isolates in New Zealand (NZ). However, mecC has been detected in a European hedgehog in NZ, with 1 out of 17 hedgehogs sampled by Larsen et al. (2022) testing positive for this strain. In this study, we aim to investigate the origin of the human clinical isolates by comparing them with mecC-positive S. aureus isolates from hedgehogs, humans and other livestock.

Methods

Sample collection and culture

Blood cultures were obtained from two patients admitted to Christchurch Hospital (patient 1) and Dunedin Hospital (patient 2) with severe invasive infection/multifocal bacteraemia. Samples were incubated in a BD BACTECTM FX blood culture analyser at Canterbury Health Laboratory (patient 1) or Awanui Labs Dunedin (patient 2). Positive cultures were plated on to blood and chocolate agar (Fort Richard laboratories, NZ) and incubated at 35–37 °C, and the presence of S. aureus was confirmed by matrix-assisted laser desorption/ionization-time of flight (Bruker Daltonics, Germany). Direct disc diffusion susceptibilities and BD PhoenixTM (Beckton Dickinson) automated broth microdilution were performed with susceptibilities interpreted using European Committee on Antimicrobial Susceptibility Testing breakpoint tables version 11.0 (https://www.eucast.org/ast_of_bacteria/previous_versions_of_documents). Isolates were submitted from the respective laboratories to ESR on nutrient agar slopes.

Preparation of PCR DNA template

Boiled lysis cell suspensions were used as a source of DNA templates in all PCRs. Plate cultures were used to prepare cell suspensions, approximately equivalent to a 0.5 McFarland standard, in DNase/RNase-free water. Suspensions were heated at 99 °C for 20 min. The heated suspensions were centrifuged to pellet cellular debris and then stored at 4 °C. The neat supernatants were used as a source of DNA templates.

PCR and spa typing

A real-time PCR assay was used to determine the presence of mecA, mecC, the S. aureus species-specific thermostable nuclease gene nuc and one of the two genes encoding Panton–Valentine leukocidin [19]. The polymorphic X region of the staphylococcal protein A gene (spa) was amplified as previously described [20]. PCR products were submitted to the sequencing laboratory at ESR for Sanger sequencing using an ABI 3130XL Sequencer. The spa sequences were analysed using Ridom StaphType software version 2.2.1 (Ridom GmbH, Würzburg, Germany). Sequences were automatically assigned repeats and spa types using the software.

Whole-genome sequencing and assembly

Whole-genome sequencing (WGS) was performed using Oxford Nanopore and Illumina sequencing. DNA was extracted from culture using the DNeasy Blood and Tissue Kit (QIAGEN, Hilden, Germany) and prepared for Illumina sequencing using the Nextera XT Library Kit (isolate 1) (Illumina, San Diego, CA, USA) or the plexWell 384 Library Kit (isolate 2) (seqWell Beverly, MA, USA). Paired-end 150-bp sequencing was performed on the NextSeq 550 platform (Illumina, San Diego, CA, USA). Sequence quality checks, de novo assembly and species identification were performed using an in-house pipeline comprising fastp v. 0.20.1 [21], Centrifuge v. 1.0.4 [22], SKESA v. 2.3.0 [23] and QUAST v. 5.0.2 [24].

Nanopore sequencing was performed using the rapid barcoding kit (SQK-RBK004, Oxford, UK) run on a GridION flow cell FLO-MIN106 (R9.4.1). Reads were base called using Guppy v 6.1.1 (Oxford Nanopore Technologies 2023; https://nanoporetech.com) using the super-accurate base calling model (dna_r9.4.1_450bps_sup). Quality trimming was performed using Filtlong v. 0.2.1 (https://github.com/rrwick/Filtlong), removing reads less than 1000-bp and retaining 90% of the best reads. Nanopore reads were assembled using Flye v. 2.9 [25] using the default settings and then polished with Illumina data using Pilon v. 1.23.0 [26]. The genome was then circularized using Circlator v. 1.5.5 [27] and annotated using Bakta v. 1.5.0 [28].

MLST was performed by comparing Illumina-assembled genomes to the S. aureus PubMLST typing scheme [29] using MLST v 2.19.0 (https://github.com/tseemann/mlst). The whole genome average nucleotide identity was computed using FastANI v. 1.33 [30]. Antimicrobial resistance (AMR) and virulence genes were detected from the WGS data using AMRFinderPlus v. 3.11.4 with database version 2023-09-26.1 and default settings [31].

Characterization of the SCCmec cassette

The SCCmec cassette was identified from the Bakta-generated annotations and by using the Annotate from Database tool in Geneious Prime v. 2022.2 (https://www.geneious.com). The reference genome LGA251 (GenBank ID: FR821779 [3]) was used as the source for Annotate from Database. The mecC coding sequence was translated and aligned to the reference using the Geneious aligner. SCCmec typing was performed using SCCmecFinder v. 1.2 [32].

Phylogenetic analyses

Core genome SNP analyses were performed using Snippy v. 4.6.0 (https://github.com/tseemann/snippy). Phylogenetic trees were built from the core genome SNP alignments with IQtree [33] using the built-in model selection and 1000 bootstrap replicates.

Comparison of SCCmec regions and mecC genes

The isolates used in the phylogenetic analyses which contained an SCCmec cassette were de novo assembled using Skesa v. 2.3.0 [23] using the default settings. The Geneious Prime ‘Annotate from Database’ operation was then used to annotate the SCCmec element in these isolates, using the SCCmec element from S. aureus LGA251 (GenBank ID: FR821779) as the source database. SCCmec elements were then extracted from the de novo assembly, aligned with MAFFT, and a phylogeny was built using RAxML v.8.2.11 [34], using the ‘rapid bootstrapping and search for best-scoring ML tree’ option with the GTR + GAMMA model and 500 bootstrap replicates.

For genomes from the NZ hedgehog isolates, where SCCmec was not identified using Geneious, a search for components of the SCCmec element was undertaken using a local blast search for the LGA251 SCCmec element. A blast search of the National Center for Biotechnology Information nucleotide database was also performed on the mecC gene from both the human clinical and hedgehog isolates from NZ.

Results

Two isolates submitted to ESR as part of the national S. aureus bacteraemia surveillance programme were mecC-positive by PCR. Isolate 1 was submitted to ESR in January 2022, and Isolate 2 was submitted in December 2022. Both isolates were reported to be methicillin-susceptible by standard antimicrobial susceptibility testing performed at the referring laboratories using cefoxitin disc testing and oxacillin MIC according to the European Committee on Antimicrobial Susceptibility Testing clinical breakpoints (https://www.eucast.org/ast_of_bacteria/). The presence of a truncated mecC gene was subsequently confirmed by WGS, as described below. Isolate 1 was spa type t208 and isolate 2 was spa type t14284. These spa types differ by one repeat insertion.

A complete genome sequence for isolate 1 was obtained by the assembly of nanopore reads, followed by polishing with Illumina reads. The chromosome is 2 780 834 bp long and has a GC content of 32.9%. No plasmids were present in the assembly. Annotation by Bakta identified 2541 coding sequences, 61 tRNAs, 19 rRNAs and 85 non-coding RNAs (ncRNAs). The MLST was unique, so the genome was submitted to PubMLST and assigned to ST-7767.

Because isolate 1 was a unique ST and was not closely related to any other isolates in the ESR surveillance dataset at the time it was sequenced early in 2022 (unpublished data), we compared it with 75 isolates from clonal complexes commonly associated with mecC (CC49, CC130, CC425, CC599, CC1943 and CC2616) published by Larsen et al. in 2022. These isolates were chosen to represent the breadth of CC, ST and SCCmec variant types from that study (see Supplementary Material). The core genome alignment for these isolates included 41 661 variable sites, with the S. aureus LGA251 (GenBank ID: FR821779) genome used as the reference, and the model selection procedure identified TVMe + ASC + G4 as the best-fitting model of nucleotide substitution. The phylogenetic tree built from the alignment of core genome SNPs shows that isolate 1 is within the CC49 clade and is most closely related to two isolates sampled from the NZ hedgehog, ERR5417136 and ERR5417137 (Fig. 1).

Fig. 1. Comparison of isolate 1 with strains from clonal complexes previously associated with mecC (CC1943, CC599, CC2616, CC130 and CC425). The maximum likelihood tree is built from a core genome SNP alignment of 41 661 SNPs and is midpoint-rooted. Isolate 1 and the isolates from the NZ hedgehog are labelled.

A draft genome for isolate 2 was obtained from Illumina sequencing. The assembly comprised 46 contigs with N50 of 129584 bp. Annotation by Bakta identified 2445 coding sequences, 58 tRNAs, 5 rRNAs and 73 ncRNAs. This isolate was assigned to ST49 (CC49) by MLST and differs from isolate 1 at only one MLST locus. The whole genome average nucleotide identity between isolates 1 and 2 was 99.95%.

To further investigate the origin of our human isolates, we compared them to 61 other CC49 isolates, including 20 hedgehog isolates from NZ, Denmark, Portugal, Spain and the Netherlands (Larsen et al. (2022) [13, 35]), 12 human isolates from Germany and the UK (https://pathogen.watch/, accessed 14 November 2023) and 29 isolates from other European wildlife and livestock species [3536] (https://pathogen.watch/, see Supplementary Material). This phylogeny is based on 4273 core genome SNPs, using the Tager 104 complete genome (GenBank ID: CP012409) as the reference and the TVMe + ASC model of nucleotide substitution. Tager 104 is an ancestral ST49 strain that was originally isolated in 1947 [3738]. This analysis confirms that the two isolates sequenced in this study are most closely related to the two isolates from a NZ hedgehog (Fig. 2). On this tree, the NZ isolates, both hedgehog and human, form a separate clade from all European/UK isolates, which broadly cluster by country and host species. In this core genome SNP comparison, isolates 1 and 2 are 234 SNPs apart and 233–234 SNPs distant from the NZ hedgehog isolates.

Fig. 2. Maximum likelihood phylogenetic tree of 63 S. aureus CC49 isolates, based on 4273 core genome SNPs. The tree is mid-point-rooted. The two genomes sequenced in this study and the isolates from NZ hedgehogs are shaded grey. The country of origin, host species and the presence or absence of mecA, mecC and a full typeXI(8E) SCCmec element are shown in the coloured bars.

The mecC gene was identified by PCR in both isolates, and analysis of the annotated genome assemblies showed a full SCCmec element was present. This was identified by SCCmecFinder as a type XI(8E) SCCmec element. Pairwise nucleotide identity between isolates 1 and 2 across this region is 99.99%. The mecC genes from the two isolates are identical and contain single base pair deletions at positions 831 and 1012, which introduce a premature stop codon and likely render the gene non-functional (Fig. 3). These deletions were also found in the Sanger sequencing data and are consistent with the methicillin-susceptible phenotype observed for these isolates. A blast search of the GenBank Nucleotide database did not find any other mecC genes containing similar deletions.

Fig. 3. Alignment of mecC genes from isolates 1 and 2 and the reference sequence NC_017349. Only the region containing the first frameshift mutation (highlighted in the red box) and the subsequent premature stop codon (denoted by the asterisk in the amino acid sequence) are shown.

The SCCmec elements from our isolates are most closely related to SCCmec elements from isolates in clonal complexes 130, 425 and 1943 (Fig. S1). SCCmec elements do not cluster by clonal complex, and only 7 out of 61 other CC49 isolates have a full SCCmec type XI element. The two NZ hedgehog isolates have a partial SCCmec element including a functional mecC gene. However, a blast search revealed the NZ hedgehog mecC gene has 100% identity with mecC allotype C2 from Mammaliicoccus sciuri (formerly Staphylococcus sciuri) and has only approximately 96% identity with mecC from the other isolates in our study, including the two human isolates we sequenced.

Analysis of AMR and virulence genes using AMRFinder found the beta-lactamase blaZ and the tetracycline resistance gene tet [37] in both isolates. The leukocidin-encoding lukE gene was detected in genomic data in both isolates. Neither isolate contained Panton–Valentine leucocidin genes (tested with both rtPCR and WGS) or the immune-evasion genes chp, sak and scn [39]. A full list of virulence genes identified is listed in Table S2 .

Discussion

The mecC-PCR-positive S. aureus isolates reported in this study are, to our knowledge, the first human clinical cases of mecC S. aureus from NZ. National MRSA surveillance studies conducted by ESR have been screened for mecC by PCR since 2014. However, prior to the national S. aureus bacteraemia surveillance programme, which ran from January 2021 to December 2023, no systematic molecular surveillance of methicillin-susceptible S. aureus (MSSA) had been carried out in NZ. Therefore, the presence of non-functional mecC in clinical MSSA isolates from other sources and from prior to 2021 cannot be ruled out.

The genomes obtained from the two mecC-PCR-positive isolates are in the same clonal complex and contain almost identical SCCmec elements with the same mutations in the mecC locus. The level of pairwise identity between the two isolates (99.95% ANI and 234 core genome SNPs) rules out the direct transmission or a very recent common ancestor between the two cases but is consistent with membership in a circulating lineage. Both cases resided in the South Island of NZ but lived approximately 250 km apart, and no epidemiological links between them could be determined. This suggests there may be undetected cases, or a reservoir, of mecC-positive S. aureus in livestock or wildlife populations.

The isolates sequenced in this study fall within CC49 and are the first clinical isolates from CC49 identified in NZ. On the core SNP phylogenetic tree, these isolates cluster with two isolates obtained from a single hedgehog sampled in NZ. European hedgehogs (Erinaceus europaeus) were introduced to NZ from the UK in the late nineteenth century. They are now widespread throughout the country and are common in both urban and rural areas. A survey of 59 hedgehogs in NZ in the 1960s found that 85% were infected with S. aureus, and of these, 86% exhibited resistance to penicillin [40]. Both cases in this study lived in rural areas and spent time gardening and may have come into contact with hedgehogs either directly or indirectly. However, conclusions on transmission between hedgehogs and humans cannot be drawn from only a single hedgehog, and we cannot rule out transmission from livestock, other animals or an environmental source.

Internationally, CC49 is rare in humans [41] and typically animal-associated, having been detected in a range of wildlife in Europe including wild boar, squirrels, rodents, voles and cats, in addition to hedgehogs [3542]. CC49 has not been detected in studies of S. aureus in cattle in NZ to date [4344], and its prevalence in other livestock or introduced mammals in NZ is unknown. In our isolates, we did not detect the chp, sak, or scn virulence factors, which is consistent with an animal origin for this lineage. These wSa3 phage-encoded virulence factors are normally present in human strains of S. aureus, where they are thought to be involved in modulating the innate immune response in humans [39], but are commonly absent in animal-derived mecC-positive strains [13].

Despite the overall close genomic relationship between the human and NZ hedgehog isolates in this study, there are considerable differences in the SCCmec elements between these isolates. The hedgehog isolates do not contain a full SCCmec type XI(8E) element, and their mecC gene is a different allotype (mecC2) more commonly seen in non-aureus staphylococcal and mammaliicoccal species. However, we only have sequence data from a single hedgehog from NZ in this study for comparison, so the prevalence of the SCCmec elements and genomic variability of S. aureus in hedgehogs in NZ is unknown. Isolates from CC49 are more commonly MSSA, with only 7 of the 61 isolates in our comparison containing a SCCmec type XI element (including only one hedgehog isolate). Phylogenetic comparisons of the SCCmec element in our human isolates and the other isolates in this study show it is more closely related to those from clonal complexes 130, 425 and 1943 than CC49. SCCmec type XI(8E) has been identified across Europe in a diversity of host species, including livestock, companion animals and wildlife [45], but has not previously been detected in NZ in either humans or animals [4344]. Thus, it is unclear where the mecC cassette was acquired by our human isolates, and further sampling across livestock and wildlife populations will be required to determine its origin.

The mecC gene in our human isolates is truncated due to the presence of a deletion in the gene that introduces a premature stop codon. Consistent with this, both clinical cases in this study had an MSSA phenotype and were able to be treated successfully with beta-lactam antibiotics. We did not find any other instances in the literature or databases of mecC genes with similar deletions rendering them non-functional. However, it is possible that non-functional mec genes are not detected or reported in other studies where the presence or absence of methicillin resistance is only established by doing phenotypic susceptibility testing. In these cases, the MSSA phenotype may not be investigated further for the presence of mec genes. Reversion of mecA isolates from MRSA to MSSA phenotype has been occasionally observed in other studies where discrepancies between resistance phenotype and genotype are specifically investigated. Ledda et al. (2017) reported the re-emergence of an MSSA phenotype among ST36 mecA-positive S. aureus isolates [46]. For some of the isolates in their study, reversion to the MSSA phenotype was caused by the loss of the entire SCCmec cassette, but in one isolate, they observed a single bp deletion that caused a frameshift and premature stop codon in the mecA gene, similar to what we observed in the isolates in this study. In a study of 1470 strains of S. aureus, Kime et al. (2019) found that around 10% of the isolates had silenced resistance genes, including mecA, and in two isolates, antibiotic susceptibility was linked to frameshift mutations in the mecA gene [47]. Reversion from MRSA to MSSA may occur where there is little selection pressure to maintain the resistance phenotype, indicating that our isolates may have evolved in an environment where there is little or no antibiotic use. This lends weight to the hypothesis that the human infections were not the result of direct transmission from hedgehogs, as selection pressure from the Trichophyton fungus would be more likely to retain a functional mecC gene in S. aureus isolates from hedgehogs. However, as we do not know the origin of the SCCmec cassette in the CC49 strains reported here or at what point the cassette was acquired by these strains, we cannot determine at what point the mecC gene became non-functional.

In conclusion, our study characterizes two S. aureus isolates containing an SCCmec type XI element with a non-functional mecC gene in NZ, thus expanding the geographic range where mecC S. aureus is known to occur. These isolates are the first isolates from any species in NZ with a mecC-containing SCCmec type XI element and also the first human isolates from CC49 found in NZ. The presence of two cases with no epidemiological links indicates there may be a reservoir of mecC S. aureus in NZ. However, further sampling of livestock, wildlife and humans, particularly in the South Island, where the human cases were located, will be required to understand the prevalence of mecC S. aureus in NZ and ascertain the origin of the human infections.

supplementary material

10.1099/acmi.0.000849.v2 Supplementary Material 1.

10.1099/acmi.0.000849.v2 Supplementary Material 2.

Acknowledgements

The authors thank the diagnostic laboratories for referring isolates to ESR for surveillance and to the NGS laboratory at ESR for sequencing the isolates described in this study. The authors also thank Una Ren, Rhys White and Anjan Purkayastha for comments on the manuscript and to Rhys for assistance with finding and retrieving isolates from the National Centre for Biotechnology Information.

Abbreviations

AMR antimicrobial resistance

MRSA methicillin-resistant Staphylococcus aureus

MSSA methicillin-sensitive Staphylococcus aureus

ncRNA non-coding RNA

NZ New Zealand

SCCmec staphylococcal cassette chromosome mec

UK United Kingdom

WGS whole-genome sequencing

Funding: Surveillance work performed at ESR was funded by the New Zealand Ministry of Health.

Ethical statement: Consent for publication was obtained from the two clinical cases described in this paper. The Staphylococcus aureus isolates were submitted to the Institute of Environmental Science (ESR) as part of a national S. aureus bacteraemia surveillance programme funded by the New Zealand Ministry of Health, where clinical diagnostic laboratories (human health) were requested to send all S. aureus isolated from blood cultures to the ESR for further characterization.

Author contributions: H.M. performed bioinformatic analyses and drafted the manuscript; J.H., J.E., P.C. and T.A. collected samples and provided clinical information; S.B. and A.E. performed laboratory work; H.P. performed bioinformatics analysis; D.W. and K.D. conceived the research. All authors contributed to and agreed to the published version of the manuscript.
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