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Permana B, Harris PNA, Runnegar N, Lindsay M, Henderson BC, Playford EG, Paterson DL, Beatson SA, Forde BM. Using Genomics To Investigate an Outbreak of Vancomycin-Resistant Enterococcus faecium ST78 at a Large Tertiary Hospital in Queensland. Microbiol Spectr 2023; 11:e0420422. [PMID: 37191518 PMCID: PMC10269735 DOI: 10.1128/spectrum.04204-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2022] [Accepted: 04/16/2023] [Indexed: 05/17/2023] Open
Abstract
To investigate an outbreak of vancomycin-resistant Enterococcus faecium (VREfm) sequence type 78 (ST78) in a large tertiary Australian hospital. A collection of 63 VREfm ST78 isolates, identified during a routine genomic surveillance program, were subjected to genomic epidemiological analysis based on whole-genome sequencing (WGS) data. The population structure was reconstructed using phylogenetic analysis, and a collection of publicly available VREfm ST78 genomes were used to provide global context. Core genome single nucleotide polymorphism (SNP) distances and available clinical metadata were used to characterize outbreak clusters and reconstruct transmission events. In silico genotyping confirmed that all study isolates were vanB-type VREfm carrying virulence characteristics of the hospital-associated E. faecium. Phylogenetic analysis identified two distinct phylogenetic clades, only one of which was responsible for a hospital outbreak. Four outbreak subtypes could be defined with examples of recent transmissions. Inference on transmission trees suggested complex transmission routes with unknown environmental reservoirs mediating the outbreak. WGS-based cluster analysis with publicly available genomes identified closely related Australian ST78 and ST203 isolates, highlighting the capacity for WGS to resolve complex clonal relationships between the VREfm lineages. Whole genome-based analysis has provided a high-resolution description of an outbreak of vanB-type VREfm ST78 in a Queensland hospital. Combined routine genomic surveillance and epidemiological analysis have facilitated better understanding of the local epidemiology of this endemic strain, providing valuable insight for better targeted control of VREfm. IMPORTANCE Vancomycin-resistant Enterococcus faecium (VREfm) is a leading cause of health care-associated infections (HAIs) globally. In Australia, the spread of hospital-adapted VREfm is largely driven by a single clonal group (clonal complex [CC]), CC17, to which the lineage ST78 belongs. While implementing a genomic surveillance program in Queensland, we observed increased incidence of ST78 colonizations and infections among patients. Here, we demonstrate the use of real-time genomic surveillance as a tool to support and enhance infection control (IC) practices. Our results show that real-time whole-genome sequencing (WGS) can efficiently disrupt outbreaks by identifying transmission routes that in turn can be targeted using resource-limited interventions. Additionally, we demonstrate that by placing local outbreaks in a global context, high-risk clones can be identified and targeted prior to them becoming established within clinical environments. Finally, the persistence of these organism within the hospital highlights the need for routine genomic surveillance as a management tool to control VRE transmission.
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Affiliation(s)
- Budi Permana
- School of Chemistry and Molecular Biosciences, Faculty of Science, The University of Queensland, Brisbane, Australia
- Australian Centre for Ecogenomics, The University of Queensland, Brisbane, Australia
- Herston Infectious Diseases Institute, Metro North Health, Brisbane, Australia
| | - Patrick N. A. Harris
- Australian Infectious Disease Research Centre, Faculty of Science, The University of Queensland, Brisbane, Australia
- University of Queensland Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Brisbane, Australia
- Pathology Queensland, Central Laboratory, Brisbane, Australia
| | - Naomi Runnegar
- Princess Alexandra–Southside Clinical School, Faculty of Medicine, The University of Queensland, Brisbane, Australia
- Infection Management Services, Princess Alexandra Hospital, Brisbane, Australia
| | - Margaret Lindsay
- Infection Management Services, Princess Alexandra Hospital, Brisbane, Australia
| | | | - E. G. Playford
- Infection Management Services, Princess Alexandra Hospital, Brisbane, Australia
| | - David L. Paterson
- University of Queensland Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Brisbane, Australia
| | - Scott A. Beatson
- School of Chemistry and Molecular Biosciences, Faculty of Science, The University of Queensland, Brisbane, Australia
- Australian Centre for Ecogenomics, The University of Queensland, Brisbane, Australia
- Australian Infectious Disease Research Centre, Faculty of Science, The University of Queensland, Brisbane, Australia
| | - Brian M. Forde
- Australian Infectious Disease Research Centre, Faculty of Science, The University of Queensland, Brisbane, Australia
- University of Queensland Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Brisbane, Australia
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Forde BM, Bergh H, Cuddihy T, Hajkowicz K, Hurst T, Playford EG, Henderson BC, Runnegar N, Clark J, Jennison AV, Moss S, Hume A, Leroux H, Beatson SA, Paterson DL, Harris PNA. Clinical Implementation of Routine Whole-genome Sequencing for Hospital Infection Control of Multi-drug Resistant Pathogens. Clin Infect Dis 2023; 76:e1277-e1284. [PMID: 36056896 DOI: 10.1093/cid/ciac726] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 08/25/2022] [Accepted: 08/30/2022] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND Prospective whole-genome sequencing (WGS)-based surveillance may be the optimal approach to rapidly identify transmission of multi-drug resistant (MDR) bacteria in the healthcare setting. METHODS We prospectively collected methicillin-resistant Staphylococcus aureus (MRSA), vancomycin-resistant enterococci (VRE), carbapenem-resistant Acinetobacter baumannii (CRAB), extended-spectrum beta-lactamase (ESBL-E), and carbapenemase-producing Enterobacterales (CPE) isolated from blood cultures, sterile sites, or screening specimens across three large tertiary referral hospitals (2 adult, 1 paediatric) in Brisbane, Australia. WGS was used to determine in silico multi-locus sequence typing (MLST) and resistance gene profiling via a bespoke genomic analysis pipeline. Putative transmission events were identified by comparison of core genome single nucleotide polymorphisms (SNPs). Relevant clinical meta-data were combined with genomic analyses via customised automation, collated into hospital-specific reports regularly distributed to infection control teams. RESULTS Over 4 years (April 2017 to July 2021) 2660 isolates were sequenced. This included MDR gram-negative bacilli (n = 293 CPE, n = 1309 ESBL), MRSA (n = 620), and VRE (n = 433). A total of 379 clinical reports were issued. Core genome SNP data identified that 33% of isolates formed 76 distinct clusters. Of the 76 clusters, 43 were contained to the 3 target hospitals, suggesting ongoing transmission within the clinical environment. The remaining 33 clusters represented possible inter-hospital transmission events or strains circulating in the community. In 1 hospital, proven negligible transmission of non-multi-resistant MRSA enabled changes to infection control policy. CONCLUSIONS Implementation of routine WGS for MDR pathogens in clinical laboratories is feasible and can enable targeted infection prevention and control interventions.
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Affiliation(s)
- Brian M Forde
- Faculty of Medicine, UQ Centre for Clinical Research, University of Queensland, Brisbane, QLD, Australia
| | - Haakon Bergh
- Central Microbiology, Pathology Queensland, Royal Brisbane & Women's Hospital, Brisbane, QLD, Australia
| | - Thom Cuddihy
- Faculty of Medicine, UQ Centre for Clinical Research, University of Queensland, Brisbane, QLD, Australia
| | - Krispin Hajkowicz
- Infectious Diseases Unit, Royal Brisbane and Women's Hospital, Herston, QLD, Australia
| | - Trish Hurst
- Infectious Diseases Unit, Royal Brisbane and Women's Hospital, Herston, QLD, Australia
| | - E Geoffrey Playford
- Infection Management Services, Princess Alexandra Hospital, Metro South Hospital and Health Service, Brisbane, QLD, Australia
| | - Belinda C Henderson
- Infection Management Services, Princess Alexandra Hospital, Metro South Hospital and Health Service, Brisbane, QLD, Australia
| | - Naomi Runnegar
- Infection Management Services, Princess Alexandra Hospital, Metro South Hospital and Health Service, Brisbane, QLD, Australia.,Faculty of Medicine, PA-Southside Clinical School, University of Queensland, Brisbane, QLD, Australia
| | - Julia Clark
- Infection Management and Prevention Service, Queensland Children's Hospital, Brisbane, QLD, Australia.,Centre for Children's Health Research, Children's Health Queensland, Brisbane, Australia
| | - Amy V Jennison
- Public Health Microbiology, Forensic and Scientific Services, Queensland Health, Brisbane, QLD, Australia
| | - Susan Moss
- Public Health Microbiology, Forensic and Scientific Services, Queensland Health, Brisbane, QLD, Australia
| | - Anna Hume
- Central Microbiology, Pathology Queensland, Royal Brisbane & Women's Hospital, Brisbane, QLD, Australia.,Infectious Diseases Unit, Royal Brisbane and Women's Hospital, Herston, QLD, Australia
| | - Hugo Leroux
- Australian e-Health Research Centre, CSIRO, Brisbane, QLD, Australia
| | - Scott A Beatson
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, QLD, Australia
| | - David L Paterson
- Faculty of Medicine, UQ Centre for Clinical Research, University of Queensland, Brisbane, QLD, Australia.,Infectious Diseases Unit, Royal Brisbane and Women's Hospital, Herston, QLD, Australia
| | - Patrick N A Harris
- Faculty of Medicine, UQ Centre for Clinical Research, University of Queensland, Brisbane, QLD, Australia.,Central Microbiology, Pathology Queensland, Royal Brisbane & Women's Hospital, Brisbane, QLD, Australia
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Forde BM, Henderson A, Playford EG, Looke D, Henderson BC, Watson C, Steen JA, Sidjabat HE, Laurie G, Muttaiyah S, Nimmo GR, Lampe G, Smith H, Jennison AV, McCall B, Carroll H, Cooper MA, Paterson DL, Beatson SA. Fatal respiratory diphtheria caused by β-lactam-resistant Corynebacterium diphtheriae. Clin Infect Dis 2020; 73:e4531-e4538. [PMID: 32772111 DOI: 10.1093/cid/ciaa1147] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Accepted: 08/03/2020] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND Diphtheria is a potentially fatal respiratory disease caused by toxigenic Corynebacterium diphtheriae. Although resistance to erythromycin has been recognised, β-lactam resistance in toxigenic diphtheria has not been described. Here, we report a case of fatal respiratory diphtheria caused by toxigenic C. diphtheriae resistant to penicillin and all other β-lactam antibiotics and describe a novel mechanism of inducible carbapenem resistance associated with the acquisition of a mobile resistance element. METHODS Long-read whole genome sequencing was performed using Pacific Biosciences SMRT sequencing to determine the genome sequence of C. diphtheriae BQ11 and mechanism of β-lactam resistance. To investigate phenotypic inducibility of meropenem resistance, short read sequencing was performed using an Illumina NextSeq500 sequencer on the strain with and without exposure to meropenem. RESULTS BQ11 demonstrated high-level resistance to penicillin (benzylpenicillin MIC ≥ 256 μg/ml), β-lactam/β-lactamase inhibitors and cephalosporins (amoxicillin/clavulanic acid MIC ≥ 256 μg/mL; ceftriaxone MIC ≥ 8 μg/L). Genomic analysis of BQ11 identified acquisition of a novel transposon carrying the penicillin binding protein Pbp2c, responsible for resistance to penicillin and cephalosporins. When strain BQ11 was exposed to meropenem, selective pressure drove amplification of the transposon in a tandem array and led to a corresponding change from a low level to high level meropenem resistant phenotype. CONCLUSIONS We have identified a novel mechanism of inducible antibiotic resistance whereby isolates that appear to be carbapenem susceptible on initial testing can develop in vivo resistance to carbapenems with repeated exposure. This phenomenon could have significant implications for treatment of C. diphtheriae infection and may lead to clinical failure.
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Affiliation(s)
- Brian M Forde
- School of Chemistry and Molecular Biosciences, University of Queensland, QLD, Australia.,Australian Infectious Diseases Research Centre, University of Queensland, QLD, Australia.,Australian Centre for Ecogenomics, University of Queensland, QLD, Australia
| | - Andrew Henderson
- University of Queensland Centre For Clinical Research, University of Queensland, QLD, Australia.,Infection Management Services, Princess Alexandra Hospital, QLD, Australia
| | - Elliott G Playford
- Infection Management Services, Princess Alexandra Hospital, QLD, Australia.,School of Medicine, University of Queensland, QLD, Australia
| | - David Looke
- Infection Management Services, Princess Alexandra Hospital, QLD, Australia.,School of Medicine, University of Queensland, QLD, Australia
| | | | - Catherine Watson
- Infection Management Services, Princess Alexandra Hospital, QLD, Australia
| | - Jason A Steen
- Institute for Molecular Biosciences, University of Queensland, QLD, Australia
| | - Hanna E Sidjabat
- Australian Infectious Diseases Research Centre, University of Queensland, QLD, Australia.,University of Queensland Centre For Clinical Research, University of Queensland, QLD, Australia
| | - Gordon Laurie
- Intensive Care Unit, Princess Alexandra Hospital, QLD, Australia
| | | | - Graeme R Nimmo
- Department of Microbiology, Pathology Queensland, QLD, Australia
| | - Guy Lampe
- Department of Anatomical Pathology, Pathology Queensland, QLD, Australia
| | - Helen Smith
- Public Health Microbiology, Forensic and Scientific Services, Queensland Health
| | - Amy V Jennison
- Public Health Microbiology, Forensic and Scientific Services, Queensland Health
| | - Brad McCall
- Metro South Public Health Unit, Metro South Health, Brisbane, QLD, Australia
| | - Heidi Carroll
- Communicable Diseases Branch, Prevention Division, Department of Health, Queensland Health, QLD, Australia
| | - Matthew A Cooper
- Institute for Molecular Biosciences, University of Queensland, QLD, Australia
| | - David L Paterson
- Australian Infectious Diseases Research Centre, University of Queensland, QLD, Australia.,University of Queensland Centre For Clinical Research, University of Queensland, QLD, Australia
| | - Scott A Beatson
- School of Chemistry and Molecular Biosciences, University of Queensland, QLD, Australia.,Australian Infectious Diseases Research Centre, University of Queensland, QLD, Australia.,Australian Centre for Ecogenomics, University of Queensland, QLD, Australia
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Henderson BC. Modification of slip-knot suture for Molteno shunt tube occlusion. Ophthalmic Surg 1991; 22:113. [PMID: 2038471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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Butrus SI, Sessums SO, Henderson BC, Ganley JP. Syndrome of inappropriate antidiuretic hormone secretion. Arch Ophthalmol 1985; 103:759, 762. [PMID: 4004609 DOI: 10.1001/archopht.1985.01050060017005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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