The changing landscape of vancomycin-resistant Enterococcus faecium in Australia: a population-level genomic study

Lee, Robyn S; Silva, Anders Gonçalves da; Baines, Sarah L.; Strachan, Janet; Ballard, Susan A; Carter, Glen P.; Kwong, Jason C; Schultz, Mark B.; Bulach, Dieter; Seemann, Torsten; Stinear, Timothy P.; Howden, Benjamin P

doi:10.1093/jac/dky331

Cited by 30 publications

(47 citation statements)

References 48 publications

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“…In Australia, a study was conducted to obtain insights into the general VRE population of different hospitals. The researchers observed ST796 as the dominating lineage of the investigated region [60]. Hospital screening settings from Denmark observed the spread of several clones, including ST117, ST80, ST78, and ST192, and could further deduce VRE transmissions between patients, wards, and even hospitals.…”

Section: Molecular Analyses and Bioinformaticsmentioning

confidence: 92%

“…While cgMLST uses a defined core genome reference, the MCG approach calculates an ad hoc core genome of the included sequence collection, also including accessory elements such as the FFP method. Other studies relied on SNP-based analyses only by using a proper and highly related reference genome to enhance the power of discrimination by this approach [60]. While these analyses provide results in high resolution, they are lacking comparability and transferability to other settings [41].…”

Section: Molecular Analyses and Bioinformaticsmentioning

confidence: 99%

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Comprehensive integrated NGS-based surveillance and contact-network modeling unravels transmission dynamics of vancomycin-resistant enterococci in a high-risk population within a tertiary care hospital

et al. 2020

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Vancomycin-resistant E. faecium (VRE) are an important cause of nosocomial infections, which are rapidly transmitted in hospitals. To identify possible transmission routes, we applied combined genomics and contact-network modeling to retrospectively evaluate routine VRE screening data generated by the infection control program of a hemato-oncology unit. Over 1 year, a total of 111 VRE isolates from 111 patients were collected by anal swabs in a tertiary care hospital in Southern Germany. All isolated VRE were whole-genome sequenced, followed by different in-depth bioinformatics analyses including genotyping and determination of phylogenetic relations, aiming to evaluate a standardized workflow. Patient movement data were used to overlay sequencing data to infer transmission events and strain dynamics over time. A predominant clone harboring vanB and exhibiting genotype ST117/CT469 (n = 67) was identified. Our comprehensive combined analyses suggested intra-hospital spread, especially of clone ST117/CT469, despite of extensive screening, single room placement, and contact isolation. A new interactive tool to visualize these complex data was designed. Furthermore, a patient-contact network-modeling approach was developed, which indicates both the periodic import of the clone into the hospital and its spread within the hospital due to patient movements. The analyzed spread of VRE was most likely due to placement of patients in the same room prior to positivity of screening. We successfully demonstrated the added value for this combined strategy to extract well-founded knowledge from interdisciplinary data sources. The combination of patient-contact modeling and high-resolution typing unraveled the transmission dynamics within the hospital department and, additionally, a constant VRE influx over time.

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Section: Molecular Analyses and Bioinformaticsmentioning

confidence: 92%

Section: Molecular Analyses and Bioinformaticsmentioning

confidence: 99%

Comprehensive integrated NGS-based surveillance and contact-network modeling unravels transmission dynamics of vancomycin-resistant enterococci in a high-risk population within a tertiary care hospital

et al. 2020

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“…CP027500). 7 The structure of the present Tn1546-like element was similar to that strain but seems to be more complex (Figure 2). We also found a Tn1546-like element carrying IS1216 and IS1542 elements in similar position to that previously reported in E. gallinarum.…”

Section: Discussionmentioning

confidence: 60%

“…6 A total of eight acquired glycopeptide resistance determinants have been reported in enterococci (VanA, VanB, VanD, VanE, VanG, VanL, VanM and VanN), of which VanA is the most frequently encountered worldwide. 7 The vanA gene is traditionally associated with a plastic antimicrobial resistance transposon, Tn1546, which also contains the additional genes responsible for vancomycin resistance (vanR, vanS, vanH, vanX, vanYand vanZ). Tn1546 is able to easily transpose into diverse conjugative plasmids, and the horizontal transfer of Tn1546-like elements also plays an important role in the dissemination of vanA-type VRE.…”

Section: Introductionmentioning

confidence: 99%

Emergence of vanA-Type Vancomycin-Resistant Enterococcus faecium ST 78 Strain with a rep2-Type Plasmid Carrying a Tn1546-Like Element Isolated from a Urinary Tract Infection in China

Sun

Wang

et al. 2020

IDR

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The emergence of vancomycin-resistant enterococci (VRE) dramatically narrows therapeutic options. Although the prevalence of VRE in China has maintained a low level, VRE outbreaks have been reported in some tertiary hospitals in the developed areas of China. The clonal background of vanA-positive Enterococcus faecium strains has not been well characterized in China. Here, we report the whole-genome sequence of a vanA-type vancomycin-resistant E. faecium belonging to sequence type (ST) 78 isolated from a urinary tract infection in China. Patients and Methods: A vancomycin-resistant E. faecium was isolated from a 66-year-old male patient diagnosed with brainstem hemorrhage. Antibiotic susceptibility assays were performed according to the guidelines of the Clinical and Laboratory Standards Institute (CLSI). Complete genome sequencing was performed using both the HiSeq TM 4000 platform and the MinION platform. Plasmid, genomic and phylogenetic relationship analysis were further performed. Results: E. faecium VRE1 was resistant to all antimicrobials tested except for tetracyclines and oxazolidinones. The whole genome of E. faecium VRE1 was composed of one chromosomal DNA and four plasmids. Two virulence genes and five antimicrobial resistance genes were identified. In silico multilocus sequence typing (MLST) showed that it belonged to ST78 (clonal complex CC17), a well-known epidemic clone that is widespread in Europe and the United States. Three antimicrobial resistance genes, including aminoglycoside resistance genes ant(6)-Ia and aph(3ʹ)-III ; and glycopeptide resistance gene vanA, were located on a rep2-type plasmid carrying a Tn1546like element that has not been reported. The most closely related strain harboring a similar plasmid backbone was recovered from fodder sample in China that differed by 178 cgMLST loci. Conclusion: Our study characterizes the genomic feature of a vancomycin-resistant E. faecium ST78 strain harboring a vanA-carrying plasmid in China. The ST78 clonal group possessed the potential to emerge as a successful vanA-carrying epidemic lineage in China.

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“…Non-typeable VREfm strains have recently emerged and have been shown to be very rare in the UK: in a study encompassing whole genome sequencing of nearly 500 E. faecium healthcare-associated isolates from 2001-2011 in the UK and Ireland, there were only 5 cases of pstS -null VRE strains, all of which were isolated from a single English hospital, between 2004 and 2005 [7]. The emergence of such strains was even more recent in Australia: the first two strains were isolated in 2013, but numbers increased rapidly to a total of 89 cases, by the end of 2015 [8,29,30] and to about 300 cases, by the end of 2016 [25,30,31].…”

Section: Discussionmentioning

confidence: 99%

Emergence of an Australian-like pstS-null vancomycin resistant Enterococcus faecium clone in Scotland

Lemonidis

Salih

Dancer

et al. 2017

Preprint

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Multi-locus sequencing typing (MLST) is widely used to monitor the phylogeny of microbial outbreaks. However, several strains of vancomycin-resistant Enterococcus faecium (VREfm) with a missing MLST locus (pstS) have recently emerged in Australia, with a few cases also reported in England. Here, we identified similarly distinct strains circulating in two closely located hospitals in Scotland. Whole genome sequencing of five VREfm strains isolated from these hospitals identified four pstS-null strains across both hospitals, while the fifth was of a multi-locus sequence type (ST) 262, which is the first documented in the UK. All five Scottish isolates had an insertion in the tetM gene, which is associated with increased susceptibility to tetracyclines, providing no other tetracycline-resistant gene is present. Such an insertion, which encompasses a dfrG gene and two currently uncharacterised genes, was additionally identified in all tested VanA-type pstS-null VREfm strains (5 English and 18 Australian). Phylogenetic comparison with other VREfm genomes indicates that the four pstS-null Scottish isolates sequenced in this study are more closely related to pstS-null strains from Australia rather than the English pstS-null isolates. Given how rapidly such pstS-null strains have expanded in Australia, the emergence of this clone in Scotland raises concerns for a potential outbreak.

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The changing landscape of vancomycin-resistant Enterococcus faecium in Australia: a population-level genomic study

Abstract: Emerging vanA-VREfm in Australia is polyclonal, indicating repeat introductions of vanA-VREfm into hospitals and subsequent dissemination. The close relationship to global strains reinforces the need for ongoing screening and control of VREfm in Australia and abroad.

Cited by 30 publications

References 48 publications

Comprehensive integrated NGS-based surveillance and contact-network modeling unravels transmission dynamics of vancomycin-resistant enterococci in a high-risk population within a tertiary care hospital

Comprehensive integrated NGS-based surveillance and contact-network modeling unravels transmission dynamics of vancomycin-resistant enterococci in a high-risk population within a tertiary care hospital

<p>Emergence of <em>vanA</em>-Type Vancomycin-Resistant <em>Enterococcus faecium</em> ST 78 Strain with a rep2-Type Plasmid Carrying a Tn1546-Like Element Isolated from a Urinary Tract Infection in China</p>

Emergence of an Australian-like pstS-null vancomycin resistant Enterococcus faecium clone in Scotland

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