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Denissen J, Havenga B, Reyneke B, Khan S, Khan W. Comparing antibiotic resistance and virulence profiles of Enterococcus faecium, Klebsiella pneumoniae, and Pseudomonas aeruginosa from environmental and clinical settings. Heliyon 2024; 10:e30215. [PMID: 38720709 PMCID: PMC11076977 DOI: 10.1016/j.heliyon.2024.e30215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 04/19/2024] [Accepted: 04/22/2024] [Indexed: 05/12/2024] Open
Abstract
Antibiotic resistance and virulence profiles of Enterococcus faecium, Klebsiella pneumoniae, and Pseudomonas aeruginosa, isolated from water sources collected in informal settlements, were compared to clinical counterparts. Cluster analysis using repetitive extragenic palindromic sequence-based polymerase chain reaction (REP-PCR) indicated that, for each respective species, low genetic relatedness was observed between most of the clinical and environmental isolates, with only one clinical P. aeruginosa (PAO1) and one clinical K. pneumoniae (P2) exhibiting high genetic similarity to the environmental strains. Based on the antibiograms, the clinical E. faecium Ef CD1 was extensively drug resistant (XDR); all K. pneumoniae isolates (n = 12) (except K. pneumoniae ATCC 13883) were multidrug resistant (MDR), while the P. aeruginosa (n = 16) isolates exhibited higher susceptibility profiles. The tetM gene (tetracycline resistance) was identified in 47.4 % (n = 6 environmental; n = 3 clinical) of the E. faecium isolates, while the blaKPC gene (carbapenem resistance) was detected in 52.6 % (n = 7 environmental; n = 3 clinical) and 15.4 % (n = 2 environmental) of the E. faecium and K. pneumoniae isolates, respectively. The E. faecium isolates were predominantly poor biofilm formers, the K. pneumoniae isolates were moderate biofilm formers, while the P. aeruginosa isolates were strong biofilm formers. All E. faecium and K. pneumoniae isolates were gamma (γ)-haemolytic, non-gelatinase producing (E. faecium only), and non-hypermucoviscous (K. pneumoniae only), while the P. aeruginosa isolates exhibited beta (β)-haemolysis and produced gelatinase. The fimH (type 1 fimbriae adhesion) and ugE (uridine diphosphate galacturonate 4-epimerase synthesis) virulence genes were detected in the K. pneumoniae isolates, while the P. aeruginosa isolates possessed the phzM (phenazine production) and algD (alginate biosynthesis) genes. Similarities in antibiotic resistance and virulence profiles of environmental and clinical E. faecium, K. pneumoniae, and P. aeruginosa, thus highlights the potential health risks posed by using environmental water sources for daily water needs in low-and-middle-income countries.
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Affiliation(s)
- Julia Denissen
- Department of Microbiology, Faculty of Science, Stellenbosch University, Private Bag X1, Stellenbosch, 7602, South Africa
| | - Benjamin Havenga
- Department of Microbiology, Faculty of Science, Stellenbosch University, Private Bag X1, Stellenbosch, 7602, South Africa
| | - Brandon Reyneke
- Faculty of Health Sciences, University of Johannesburg, PO Box 17011, Doornfontein, 2028, South Africa
| | - Sehaam Khan
- Faculty of Health Sciences, University of Johannesburg, PO Box 17011, Doornfontein, 2028, South Africa
| | - Wesaal Khan
- Department of Microbiology, Faculty of Science, Stellenbosch University, Private Bag X1, Stellenbosch, 7602, South Africa
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Hourigan D, Stefanovic E, Hill C, Ross RP. Promiscuous, persistent and problematic: insights into current enterococcal genomics to guide therapeutic strategy. BMC Microbiol 2024; 24:103. [PMID: 38539119 PMCID: PMC10976773 DOI: 10.1186/s12866-024-03243-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 02/28/2024] [Indexed: 04/19/2024] Open
Abstract
Vancomycin-resistant enterococci (VRE) are major opportunistic pathogens and the causative agents of serious diseases, such as urinary tract infections and endocarditis. VRE strains mainly include species of Enterococcus faecium and E. faecalis which can colonise the gastrointestinal tract (GIT) of patients and, following growth and persistence in the gut, can transfer to blood resulting in systemic dissemination in the body. Advancements in genomics have revealed that hospital-associated VRE strains are characterised by increased numbers of mobile genetic elements, higher numbers of antibiotic resistance genes and often lack active CRISPR-Cas systems. Additionally, comparative genomics have increased our understanding of dissemination routes among patients and healthcare workers. Since the efficiency of currently available antibiotics is rapidly declining, new measures to control infection and dissemination of these persistent pathogens are urgently needed. These approaches include combinatory administration of antibiotics, strengthening colonisation resistance of the gut microbiota to reduce VRE proliferation through commensals or probiotic bacteria, or switching to non-antibiotic bacterial killers, such as bacteriophages or bacteriocins. In this review, we discuss the current knowledge of the genomics of VRE isolates and state-of-the-art therapeutic advances against VRE infections.
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Affiliation(s)
- David Hourigan
- APC Microbiome Ireland, Biosciences Institute, Biosciences Research Institute, College Rd, University College, Cork, Ireland
- School of Microbiology, University College Cork, College Rd, University College, Cork, Ireland
| | - Ewelina Stefanovic
- APC Microbiome Ireland, Biosciences Institute, Biosciences Research Institute, College Rd, University College, Cork, Ireland
- Teagasc Food Research Centre, Moorepark, Moorepark West, Fermoy, Co. Cork, Ireland
| | - Colin Hill
- APC Microbiome Ireland, Biosciences Institute, Biosciences Research Institute, College Rd, University College, Cork, Ireland
- School of Microbiology, University College Cork, College Rd, University College, Cork, Ireland
| | - R Paul Ross
- APC Microbiome Ireland, Biosciences Institute, Biosciences Research Institute, College Rd, University College, Cork, Ireland.
- School of Microbiology, University College Cork, College Rd, University College, Cork, Ireland.
- Teagasc Food Research Centre, Moorepark, Moorepark West, Fermoy, Co. Cork, Ireland.
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3
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McHugh MP, Pettigrew KA, Taori S, Evans TJ, Leanord A, Gillespie SH, Templeton KE, Holden MTG. Consideration of within-patient diversity highlights transmission pathways and antimicrobial resistance gene variability in vancomycin-resistant Enterococcus faecium. J Antimicrob Chemother 2024; 79:656-668. [PMID: 38323373 PMCID: PMC11090465 DOI: 10.1093/jac/dkae023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 01/02/2024] [Indexed: 02/08/2024] Open
Abstract
BACKGROUND WGS is increasingly being applied to healthcare-associated vancomycin-resistant Enterococcus faecium (VREfm) outbreaks. Within-patient diversity could complicate transmission resolution if single colonies are sequenced from identified cases. OBJECTIVES Determine the impact of within-patient diversity on transmission resolution of VREfm. MATERIALS AND METHODS Fourteen colonies were collected from VREfm positive rectal screens, single colonies were collected from clinical samples and Illumina WGS was performed. Two isolates were selected for Oxford Nanopore sequencing and hybrid genome assembly to generate lineage-specific reference genomes. Mapping to closely related references was used to identify genetic variations and closely related genomes. A transmission network was inferred for the entire genome set using Phyloscanner. RESULTS AND DISCUSSION In total, 229 isolates from 11 patients were sequenced. Carriage of two or three sequence types was detected in 27% of patients. Presence of antimicrobial resistance genes and plasmids was variable within genomes from the same patient and sequence type. We identified two dominant sequence types (ST80 and ST1424), with two putative transmission clusters of two patients within ST80, and a single cluster of six patients within ST1424. We found transmission resolution was impaired using fewer than 14 colonies. CONCLUSIONS Patients can carry multiple sequence types of VREfm, and even within related lineages the presence of mobile genetic elements and antimicrobial resistance genes can vary. VREfm within-patient diversity could be considered in future to aid accurate resolution of transmission networks.
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Affiliation(s)
- Martin P McHugh
- School of Medicine, University of St Andrews, St Andrews, UK
- Medical Microbiology, Department of Laboratory Medicine, Royal Infirmary of Edinburgh, Edinburgh, UK
| | | | - Surabhi Taori
- Medical Microbiology, Department of Laboratory Medicine, Royal Infirmary of Edinburgh, Edinburgh, UK
| | - Thomas J Evans
- School of Infection and Immunity, University of Glasgow, Glasgow, UK
| | - Alistair Leanord
- School of Infection and Immunity, University of Glasgow, Glasgow, UK
- Scottish Microbiology Reference Laboratories, Glasgow Royal Infirmary, Glasgow, UK
| | | | - Kate E Templeton
- Medical Microbiology, Department of Laboratory Medicine, Royal Infirmary of Edinburgh, Edinburgh, UK
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4
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Bezdicek M, Hanslikova J, Nykrynova M, Dufkova K, Kocmanova I, Kubackova P, Mayer J, Lengerova M. New Multilocus Sequence Typing Scheme for Enterococcus faecium Based on Whole Genome Sequencing Data. Microbiol Spectr 2023; 11:e0510722. [PMID: 37306567 PMCID: PMC10434285 DOI: 10.1128/spectrum.05107-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 05/24/2023] [Indexed: 06/13/2023] Open
Abstract
The MLST scheme currently used for Enterococcus faecium typing was designed in 2002 and is based on putative gene functions and Enterococcus faecalis gene sequences available at that time. As a result, the original MLST scheme does not correspond to the real genetic relatedness of E. faecium strains and often clusters genetically distant strains to the same sequence types (ST). Nevertheless, typing has a significant impact on the subsequent epidemiological conclusions and introduction of appropriate epidemiological measures, thus it is crucial to use a more accurate MLST scheme. Based on the genome analysis of 1,843 E. faecium isolates, a new scheme, consisting of 8 highly discriminative loci, was created in this study. These strains were divided into 421 STs using the new MLST scheme, as opposed to 223 STs assigned by the original MLST scheme. The proposed MLST has a discriminatory power of D = 0.983 (CI95% 0.981 to 0.984), compared to the original scheme's D = 0.919 (CI95% 0.911 to 0.927). Moreover, we identified new clonal complexes with our newly designed MLST scheme. The scheme proposed here is available within the PubMLST database. Although whole genome sequencing availability has increased rapidly, MLST remains an integral part of clinical epidemiology, mainly due to its high standardization and excellent robustness. In this study, we proposed and validated a new MLST scheme for E. faecium, which is based on genome-wide data and thus reflects the tested isolates' more accurate genetic similarity. IMPORTANCE Enterococcus faecium is one of the most important pathogens causing health care associated infections. One of the main reasons for its clinical importance is a rapidly spreading resistance to vancomycin and linezolid, which significantly complicates antibiotic treatment of infections caused by such resistant strains. Monitoring the spread and relationships between resistant strains causing severe conditions represents an important tool for implementing appropriate preventive measures. Therefore, there is an urgent need to establish a robust method enabling strain monitoring and comparison at the local, national, and global level. Unfortunately, the current, extensively used MLST scheme does not reflect the real genetic relatedness between individual strains and thus does not provide sufficient discriminatory power. This can lead directly to incorrect epidemiological measures due to insufficient accuracy and biased results.
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Affiliation(s)
- Matej Bezdicek
- Department of Internal Medicine - Haematology and Oncology, University Hospital Brno, Brno, Czech Republic
- Department of Internal Medicine - Haematology and Oncology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Jana Hanslikova
- Department of Internal Medicine - Haematology and Oncology, University Hospital Brno, Brno, Czech Republic
| | - Marketa Nykrynova
- Department of Internal Medicine - Haematology and Oncology, University Hospital Brno, Brno, Czech Republic
- Department of Biomedical Engineering, Brno University of Technology, Brno, Czech Republic
| | - Kristyna Dufkova
- Department of Internal Medicine - Haematology and Oncology, University Hospital Brno, Brno, Czech Republic
- Department of Internal Medicine - Haematology and Oncology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Iva Kocmanova
- Department of Clinical Microbiology and Immunology, University Hospital Brno, Brno, Czech Republic
| | - Petra Kubackova
- Department of Clinical Microbiology and Immunology, University Hospital Brno, Brno, Czech Republic
| | - Jiri Mayer
- Department of Internal Medicine - Haematology and Oncology, University Hospital Brno, Brno, Czech Republic
- Department of Internal Medicine - Haematology and Oncology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Martina Lengerova
- Department of Internal Medicine - Haematology and Oncology, University Hospital Brno, Brno, Czech Republic
- Department of Internal Medicine - Haematology and Oncology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
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5
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Vancomycin-Resistant Enterococcus faecium and the emergence of new Sequence Types associated with Hospital Infection. Res Microbiol 2023; 174:104046. [PMID: 36858192 DOI: 10.1016/j.resmic.2023.104046] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 02/16/2023] [Accepted: 02/20/2023] [Indexed: 03/02/2023]
Abstract
Enterococcus faecium is a major cause of vancomycin-resistant enterococcal (VRE) infection. New variants of the pathogen have emerged and become dominant in healthcare settings. Two such examples, vanB ST796 and vanA ST1421 sequence types, originally arose in Australia and proceeded to cause VRE outbreaks in other countries. Of concern is the detection of a vancomycin variable enterococcal (VVE) variant of ST1421 in Europe that exhibits a vancomycin-susceptible phenotype but which can revert to resistant in the presence of vancomycin. The recent application of genome sequencing for increasing our understanding of the evolution and spread of VRE is also explored here.
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6
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Messele YE, Hasoon MF, Trott DJ, Veltman T, McMeniman JP, Kidd SP, Low WY, Petrovski KR. Longitudinal Analysis of Antimicrobial Resistance among Enterococcus Species Isolated from Australian Beef Cattle Faeces at Feedlot Entry and Exit. Animals (Basel) 2022; 12:2690. [PMID: 36230431 PMCID: PMC9559632 DOI: 10.3390/ani12192690] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 10/02/2022] [Accepted: 10/05/2022] [Indexed: 11/16/2022] Open
Abstract
Enterococcus faecium are commensal bacteria inhabiting the gastrointestinal tract of animals and humans and an important cause of drug-resistant nosocomial infections. This longitudinal study aimed to determine whether changes in the antimicrobial resistance (AMR) phenotype and genotype occurred among Enterococcus spp. isolated from cattle rectal samples obtained at the entry to and exit from an Australian feedlot. The samples obtained at the feedlot induction yielded enterococci (104/150; 69.3%), speciated as E. hirae (90/104; 86.5%), E. faecium (9/104; 8.7%), E. mundtii (3/104; 2.9%), E. durans, and E. casseliflavus (1/104; 1.0% each). AMR was observed to lincomycin (63/104; 60.6%), daptomycin (26/104; 25.0%), nitrofurantoin (9/104; 8.7%), ciprofloxacin (7/104; 6.7%), tetracycline (5/104; 4.8%), tigecycline (4/104; 3.9%), and quinupristin/dalfopristin (3/104; 2.9%). From the rectal swab samples collected at the abattoir from the same animals (i.e., the feedlot exit), the enterococci recovery was significantly higher (144/150; 96.0%), with a marked shift in species distribution dominated by E. faecium (117/144; 81.3%). However, the prevalence of AMR to individual antimicrobials remained largely static between the entry and exit except for the increased resistance to nitrofurantoin (77/144; 53.5%) and quinupristin/dalfopristin (26/144; 18.1%). Overall, 13 AMR genes were observed among the 62 E. faecium isolates. These included aac(6')Ii, aac(6')-Iid, and ant(6)-Ia (aminoglycosides); eatAv, lnu(G), vat(E), msr(C), and erm(B) (macrolides, lincosamides, and streptogramins); efmA (fluoroquinolones); and tet(45), tet(L), tet(M), and tet(S) (tetracyclines). The results confirm the presence of fluoroquinolone- and streptogramin-resistant enterococci in cattle faeces at the feedlot entry in the absence of antimicrobial selection pressure. E. faecium, exhibiting increased nitrofurantoin resistance, became the dominant Enterococcus spp. during the feeding period.
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Affiliation(s)
- Yohannes E. Messele
- The Davies Livestock Research Centre, School of Animal and Veterinary Sciences, University of Adelaide, Adelaide, SA 5005, Australia
| | - Mauida F. Hasoon
- The Australian Centre for Antimicrobial Resistance Ecology, University of Adelaide, Adelaide, SA 5005, Australia
| | - Darren J. Trott
- The Australian Centre for Antimicrobial Resistance Ecology, University of Adelaide, Adelaide, SA 5005, Australia
| | - Tania Veltman
- The Australian Centre for Antimicrobial Resistance Ecology, University of Adelaide, Adelaide, SA 5005, Australia
| | - Joe P. McMeniman
- Meat & Livestock Australia, Level 1, 40 Mount Street, North Sydney, NSW 2060, Australia
| | - Stephen P. Kidd
- The Australian Centre for Antimicrobial Resistance Ecology, University of Adelaide, Adelaide, SA 5005, Australia
- Research Centre for Infectious Disease, School of Biological Sciences, University of Adelaide, Adelaide, SA 5005, Australia
| | - Wai Y. Low
- The Davies Livestock Research Centre, School of Animal and Veterinary Sciences, University of Adelaide, Adelaide, SA 5005, Australia
| | - Kiro R. Petrovski
- The Davies Livestock Research Centre, School of Animal and Veterinary Sciences, University of Adelaide, Adelaide, SA 5005, Australia
- The Australian Centre for Antimicrobial Resistance Ecology, University of Adelaide, Adelaide, SA 5005, Australia
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7
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Udaondo Z, Abram KZ, Kothari A, Jun SR. Insertion sequences and other mobile elements associated with antibiotic resistance genes in Enterococcus isolates from an inpatient with prolonged bacteraemia. Microb Genom 2022; 8. [PMID: 35921144 PMCID: PMC9484755 DOI: 10.1099/mgen.0.000855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Insertion sequences (ISs) and other transposable elements are associated with the mobilization of antibiotic resistance determinants and the modulation of pathogenic characteristics. In this work, we aimed to investigate the association between ISs and antibiotic resistance genes, and their role in the dissemination and modification of the antibiotic-resistant phenotype. To that end, we leveraged fully resolved Enterococcus faecium and Enterococcus faecalis genomes of isolates collected over 5 days from an inpatient with prolonged bacteraemia. Isolates from both species harboured similar IS family content but showed significant species-dependent differences in copy number and arrangements of ISs throughout their replicons. Here, we describe two inter-specific IS-mediated recombination events and IS-mediated excision events in plasmids of E. faecium isolates. We also characterize a novel arrangement of the ISs in a Tn1546-like transposon in E. faecalis isolates likely implicated in a vancomycin genotype–phenotype discrepancy. Furthermore, an extended analysis revealed a novel association between daptomycin resistance mutations in liaSR genes and a putative composite transposon in E. faecium, offering a new paradigm for the study of daptomycin resistance and novel insights into its dissemination. In conclusion, our study highlights the role ISs and other transposable elements play in the rapid adaptation and response to clinically relevant stresses such as aggressive antibiotic treatment in enterococci.
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Affiliation(s)
- Zulema Udaondo
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
| | - Kaleb Z Abram
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
| | - Atul Kothari
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA.,Arkansas Dept of Health, Healthcare Associated Infections and Outbreak Response Sections, Little Rock, AR 72205, USA
| | - Se-Ran Jun
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
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8
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Boumasmoud M, Dengler Haunreiter V, Schweizer TA, Meyer L, Chakrakodi B, Schreiber PW, Seidl K, Kühnert D, Kouyos RD, Zinkernagel AS. Genomic Surveillance of Vancomycin-Resistant Enterococcus faecium Reveals Spread of a Linear Plasmid Conferring a Nutrient Utilization Advantage. mBio 2022; 13:e0377121. [PMID: 35343787 PMCID: PMC9040824 DOI: 10.1128/mbio.03771-21] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 02/25/2022] [Indexed: 12/12/2022] Open
Abstract
Healthcare-associated outbreaks of vancomycin-resistant Enterococcus faecium (VREfm) are a worldwide problem with increasing prevalence. The genomic plasticity of this hospital-adapted pathogen contributes to its efficient spread despite infection control measures. Here, we aimed to identify the genomic and phenotypic determinants of health care-associated transmission of VREfm. We assessed the VREfm transmission networks at the tertiary-care University Hospital of Zurich (USZ) between October 2014 and February 2018 and investigated microevolutionary dynamics of this pathogen. We performed whole-genome sequencing for the 69 VREfm isolates collected during this time frame and assessed the population structure and variability of the vancomycin resistance transposon. Phylogenomic analysis allowed us to reconstruct transmission networks and to unveil external or wider transmission networks undetectable by routine surveillance. Notably, it unveiled a persistent clone, sampled 31 times over a 29-month period. Exploring the evolutionary dynamics of this clone and characterizing the phenotypic consequences revealed the spread of a variant with decreased daptomycin susceptibility and the acquired ability to utilize N-acetyl-galactosamine (GalNAc), one of the primary constituents of the human gut mucins. This nutrient utilization advantage was conferred by a novel plasmid, termed pELF_USZ, which exhibited a linear topology. This plasmid, which was harbored by two distinct clones, was transferable by conjugation. Overall, this work highlights the potential of combining epidemiological, functional genomic, and evolutionary perspectives to unveil adaptation strategies of VREfm. IMPORTANCE Sequencing microbial pathogens causing outbreaks has become a common practice to characterize transmission networks. In addition to the signal provided by vertical evolution, bacterial genomes harbor mobile genetic elements shared horizontally between clones. While macroevolutionary studies have revealed an important role of plasmids and genes encoding carbohydrate utilization systems in the adaptation of Enterococcus faecium to the hospital environment, mechanisms of dissemination and the specific function of many of these genetic determinants remain to be elucidated. Here, we characterize a plasmid providing a nutrient utilization advantage and show evidence for its clonal and horizontal spread at a local scale. Further studies integrating epidemiological, functional genomics, and evolutionary perspectives will be critical to identify changes shaping the success of this pathogen.
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Affiliation(s)
- Mathilde Boumasmoud
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Vanina Dengler Haunreiter
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Tiziano A. Schweizer
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Lilly Meyer
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Bhavya Chakrakodi
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Peter W. Schreiber
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Kati Seidl
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Denise Kühnert
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Roger D. Kouyos
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Annelies S. Zinkernagel
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
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9
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Peng Z, Yan L, Yang S, Yang D. Antimicrobial-Resistant Evolution and Global Spread of Enterococcus faecium Clonal Complex (CC) 17: Progressive Change from Gut Colonization to Hospital-Adapted Pathogen. China CDC Wkly 2022; 4:17-21. [PMID: 35586520 PMCID: PMC8796730 DOI: 10.46234/ccdcw2021.277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 12/21/2021] [Indexed: 11/22/2022] Open
Abstract
For a long time, Enterococcus faecium (E. faecium) was thought to be a commensal strain in human and animal digestive tracts. However, over the past three decades, some unique E. faecium clones rapidly acquired multiple antimicrobial resistance (AMR), which led these clones to survive hospital environments and become a hospital-adapted E. faecium clonal complex (CC) 17. Since the adaptation of these clones to changes in habitat, vancomycin-resistant E. faecium CC17 has emerged as the leading cause of hospital-acquired infections worldwide. This epidemic hospital-adapted lineage has diverged from other populations approximately 75 years ago. The CC17 lineage originated from animal strains, but not human commensal lines. We reviewed the evolutionary progress and the molecular mechanisms of E. faecium CC17 from a gut commensal to a multi-antimicrobial resistant nosocomial pathogen.
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Affiliation(s)
- Zixin Peng
- NHC Key Laboratory of Food Safety Risk Assessment, Chinese Academy of Medical Science Research Unit (2019RU014), China National Center for Food Safety Risk Assessment, Beijing, China
| | - Lin Yan
- NHC Key Laboratory of Food Safety Risk Assessment, Chinese Academy of Medical Science Research Unit (2019RU014), China National Center for Food Safety Risk Assessment, Beijing, China
| | - Shuran Yang
- NHC Key Laboratory of Food Safety Risk Assessment, Chinese Academy of Medical Science Research Unit (2019RU014), China National Center for Food Safety Risk Assessment, Beijing, China
| | - Dajin Yang
- NHC Key Laboratory of Food Safety Risk Assessment, Chinese Academy of Medical Science Research Unit (2019RU014), China National Center for Food Safety Risk Assessment, Beijing, China
- Dajin Yang,
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10
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Lisotto P, Couto N, Rosema S, Lokate M, Zhou X, Bathoorn E, Harmsen HJM, Friedrich AW, Rossen JWA, Chlebowicz-Fliss MA. Molecular Characterisation of Vancomycin-Resistant Enterococcus faecium Isolates Belonging to the Lineage ST117/CT24 Causing Hospital Outbreaks. Front Microbiol 2021; 12:728356. [PMID: 34646248 PMCID: PMC8503688 DOI: 10.3389/fmicb.2021.728356] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 08/27/2021] [Indexed: 12/02/2022] Open
Abstract
Background: Vancomycin-resistant Enterococcus faecium (VREfm) is a successful nosocomial pathogen. The current molecular method recommended in the Netherlands for VREfm typing is based on core genome Multilocus sequence typing (cgMLST), however, the rapid emergence of specific VREfm lineages challenges distinguishing outbreak isolates solely based on their core genome. Here, we explored if a detailed molecular characterisation of mobile genetic elements (MGEs) and accessory genes could support and expand the current molecular typing of VREfm isolates sharing the same genetic background, enhancing the discriminatory power of the analysis. Materials/Methods: The genomes of 39 VREfm and three vancomycin-susceptible E. faecium (VSEfm) isolates belonging to ST117/CT24, as assessed by cgMLST, were retrospectively analysed. The isolates were collected from patients and environmental samples from 2011 to 2017, and their genomes were analysed using short-read sequencing. Pangenome analysis was performed on de novo assemblies, which were also screened for known predicted virulence factors, antimicrobial resistance genes, bacteriocins, and prophages. Two representative isolates were also sequenced using long-read sequencing, which allowed a detailed analysis of their plasmid content. Results: The cgMLST analysis showed that the isolates were closely related, with a minimal allelic difference of 10 between each cluster’s closest related isolates. The vanB-carrying transposon Tn1549 was present in all VREfm isolates. However, in our data, we observed independent acquisitions of this transposon. The pangenome analysis revealed differences in the accessory genes related to prophages and bacteriocins content, whilst a similar profile was observed for known predicted virulence and resistance genes. Conclusion: In the case of closely related isolates sharing a similar genetic background, a detailed analysis of MGEs and the integration point of the vanB-carrying transposon allow to increase the discriminatory power compared to the use of cgMLST alone. Thus, enabling the identification of epidemiological links amongst hospitalised patients.
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Affiliation(s)
- Paola Lisotto
- Department of Medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Natacha Couto
- Department of Medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, Groningen, Netherlands.,The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom
| | - Sigrid Rosema
- Department of Medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Mariëtte Lokate
- Department of Medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Xuewei Zhou
- Department of Medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Erik Bathoorn
- Department of Medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Hermie J M Harmsen
- Department of Medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Alexander W Friedrich
- Department of Medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - John W A Rossen
- Department of Medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, Groningen, Netherlands.,Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT, United States.,IDbyDNA Inc., Salt Lake City, UT, United States
| | - Monika A Chlebowicz-Fliss
- Department of Medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
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11
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Wyres KL, Hawkey J, Mirčeta M, Judd LM, Wick RR, Gorrie CL, Pratt NF, Garlick JS, Watson KM, Pilcher DV, McGloughlin SA, Abbott IJ, Macesic N, Spelman DW, Jenney AWJ, Holt KE. Genomic surveillance of antimicrobial resistant bacterial colonisation and infection in intensive care patients. BMC Infect Dis 2021; 21:683. [PMID: 34261450 PMCID: PMC8278603 DOI: 10.1186/s12879-021-06386-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 06/21/2021] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Third-generation cephalosporin-resistant Gram-negatives (3GCR-GN) and vancomycin-resistant enterococci (VRE) are common causes of multi-drug resistant healthcare-associated infections, for which gut colonisation is considered a prerequisite. However, there remains a key knowledge gap about colonisation and infection dynamics in high-risk settings such as the intensive care unit (ICU), thus hampering infection prevention efforts. METHODS We performed a three-month prospective genomic survey of infecting and gut-colonising 3GCR-GN and VRE among patients admitted to an Australian ICU. Bacteria were isolated from rectal swabs (n = 287 and n = 103 patients ≤2 and > 2 days from admission, respectively) and diagnostic clinical specimens between Dec 2013 and March 2014. Isolates were subjected to Illumina whole-genome sequencing (n = 127 3GCR-GN, n = 41 VRE). Multi-locus sequence types (STs) and antimicrobial resistance determinants were identified from de novo assemblies. Twenty-three isolates were selected for sequencing on the Oxford Nanopore MinION device to generate completed reference genomes (one for each ST isolated from ≥2 patients). Single nucleotide variants (SNVs) were identified by read mapping and variant calling against these references. RESULTS Among 287 patients screened on admission, 17.4 and 8.4% were colonised by 3GCR-GN and VRE, respectively. Escherichia coli was the most common species (n = 36 episodes, 58.1%) and the most common cause of 3GCR-GN infection. Only two VRE infections were identified. The rate of infection among patients colonised with E. coli was low, but higher than those who were not colonised on admission (n = 2/33, 6% vs n = 4/254, 2%, respectively, p = 0.3). While few patients were colonised with 3GCR- Klebsiella pneumoniae or Pseudomonas aeruginosa on admission (n = 4), all such patients developed infections with the colonising strain. Genomic analyses revealed 10 putative nosocomial transmission clusters (≤20 SNVs for 3GCR-GN, ≤3 SNVs for VRE): four VRE, six 3GCR-GN, with epidemiologically linked clusters accounting for 21 and 6% of episodes, respectively (OR 4.3, p = 0.02). CONCLUSIONS 3GCR-E. coli and VRE were the most common gut colonisers. E. coli was the most common cause of 3GCR-GN infection, but other 3GCR-GN species showed greater risk for infection in colonised patients. Larger studies are warranted to elucidate the relative risks of different colonisers and guide the use of screening in ICU infection control.
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Affiliation(s)
- Kelly L Wyres
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Victoria, Australia.
| | - Jane Hawkey
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Victoria, Australia
| | - Mirianne Mirčeta
- Microbiology Unit, Alfred Health, Melbourne, Victoria, Australia
| | - Louise M Judd
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Victoria, Australia
| | - Ryan R Wick
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Victoria, Australia
| | - Claire L Gorrie
- Department of Microbiology and Immunology, University of Melbourne, Melbourne, Victoria, Australia
| | - Nigel F Pratt
- Infectious Diseases Clinical Research Unit, The Alfred Hospital, Melbourne, Victoria, Australia
| | - Jill S Garlick
- Infectious Diseases Clinical Research Unit, The Alfred Hospital, Melbourne, Victoria, Australia
| | - Kerrie M Watson
- Infectious Diseases Clinical Research Unit, The Alfred Hospital, Melbourne, Victoria, Australia
| | - David V Pilcher
- Intensive Care Unit, The Alfred Hospital, Melbourne, Victoria, Australia
- Australian and New Zealand Intensive Care - Research Centre, School of Public Health and Preventive Medicine, Monash University, Melbourne, Victoria, Australia
| | - Steve A McGloughlin
- Intensive Care Unit, The Alfred Hospital, Melbourne, Victoria, Australia
- Australian and New Zealand Intensive Care - Research Centre, School of Public Health and Preventive Medicine, Monash University, Melbourne, Victoria, Australia
| | - Iain J Abbott
- Department of Infectious Diseases, The Alfred Hospital, Melbourne, Victoria, Australia
| | - Nenad Macesic
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Victoria, Australia
- Department of Infectious Diseases, The Alfred Hospital, Melbourne, Victoria, Australia
| | - Denis W Spelman
- Department of Infectious Diseases, The Alfred Hospital, Melbourne, Victoria, Australia
| | - Adam W J Jenney
- Microbiology Unit, Alfred Health, Melbourne, Victoria, Australia.
- Department of Infectious Diseases, The Alfred Hospital, Melbourne, Victoria, Australia.
| | - Kathryn E Holt
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Victoria, Australia
- London School of Hygiene and Tropical Medicine, London, UK
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12
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Mlaga KD, Garcia V, Colson P, Ruimy R, Rolain JM, Diene SM. Extensive Comparative Genomic Analysis of Enterococcus faecalis and Enterococcus faecium Reveals a Direct Association between the Absence of CRISPR-Cas Systems, the Presence of Anti-Endonuclease (ardA) and the Acquisition of Vancomycin Resistance in E. faecium. Microorganisms 2021; 9:1118. [PMID: 34064241 PMCID: PMC8224324 DOI: 10.3390/microorganisms9061118] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 05/19/2021] [Accepted: 05/19/2021] [Indexed: 11/17/2022] Open
Abstract
Here, we performed a comparative genomic analysis of all available genomes of E. faecalis (n = 1591) and E. faecium (n = 1981) and investigated the association between the presence or absence of CRISPR-Cas systems, endonuclease/anti-endonuclease systems and the acquisition of antimicrobial resistance, especially vancomycin resistance genes. Most of the analysed Enterococci were isolated from humans and less than 14% of them were from foods and animals. We analysed and detected CRISPR-Cas systems in 75.36% of E. faecalis genomes and only 4.89% of E. faecium genomes with a significant difference (p-value < 10-5). We found a negative correlation between the number of CRISPR-Cas systems and genome size (r = -0.397, p-value < 10-5) and a positive correlation between the genome %GC content and the number of CRISPR-Cas systems (r = 0.215, p-value < 10-5). Our findings showed that the presence of the anti-endonuclease ardA gene may explain the decrease in the number of CRISPR-Cas systems in E. faecium, known to deactivate the endonucleases' protective activities and enable the E. faecium genome to be versatile in acquiring mobile genetic elements, including carriers of antimicrobial resistance genes, especially vanB. Most importantly, we observed that there was a direct association between the absence of CRISPR-Cas, the presence of the anti-CRISPR ardA gene and the acquisition of vancomycin resistance genes.
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Affiliation(s)
- Kodjovi D. Mlaga
- Aix Marseille University, IRD, APHM, MEPHI, IHU-Mediterranee Infection, 13005 Marseille, France; (K.D.M.); (V.G.); (P.C.); (J.-M.R.)
| | - Vincent Garcia
- Aix Marseille University, IRD, APHM, MEPHI, IHU-Mediterranee Infection, 13005 Marseille, France; (K.D.M.); (V.G.); (P.C.); (J.-M.R.)
| | - Philippe Colson
- Aix Marseille University, IRD, APHM, MEPHI, IHU-Mediterranee Infection, 13005 Marseille, France; (K.D.M.); (V.G.); (P.C.); (J.-M.R.)
- IHU-Mediterranee Infection, Aix-Marseille University, 13005 Marseille, France
| | - Raymond Ruimy
- Department of Bacteriology at Nice Academic Hospital, Nice Medical University, 06003 Nice, France;
| | - Jean-Marc Rolain
- Aix Marseille University, IRD, APHM, MEPHI, IHU-Mediterranee Infection, 13005 Marseille, France; (K.D.M.); (V.G.); (P.C.); (J.-M.R.)
- IHU-Mediterranee Infection, Aix-Marseille University, 13005 Marseille, France
| | - Seydina M. Diene
- Aix Marseille University, IRD, APHM, MEPHI, IHU-Mediterranee Infection, 13005 Marseille, France; (K.D.M.); (V.G.); (P.C.); (J.-M.R.)
- IHU-Mediterranee Infection, Aix-Marseille University, 13005 Marseille, France
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13
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van Hal SJ, Willems RJL, Gouliouris T, Ballard SA, Coque TM, Hammerum AM, Hegstad K, Westh HT, Howden BP, Malhotra-Kumar S, Werner G, Yanagihara K, Earl AM, Raven KE, Corander J, Bowden R. The global dissemination of hospital clones of Enterococcus faecium. Genome Med 2021; 13:52. [PMID: 33785076 PMCID: PMC8008517 DOI: 10.1186/s13073-021-00868-0] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Accepted: 03/15/2021] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND The hospital-adapted A1 group of Enterococcus faecium remains an organism of significant concern in the context of drug-resistant hospital-associated infections. How this pathogen evolves and disseminates remains poorly understood. METHODS A large, globally representative collection of short-read genomic data from the hospital-associated A1 group of Enterococcus faecium was assembled (n = 973). We analysed, using a novel analysis approach, global diversity in terms of both the dynamics of the accessory genome and homologous recombination among conserved genes. RESULTS Two main modes of genomic evolution continue to shape E. faecium: the acquisition and loss of genes, including antimicrobial resistance genes, through mobile genetic elements including plasmids, and homologous recombination of the core genome. These events lead to new clones emerging at the local level, followed by the erosion of signals of clonality through recombination, and in some identifiable cases producing new clonal clusters. These patterns lead to new, emerging lineages which are able to spread globally over relatively short timeframes. CONCLUSIONS The ability of A1 E. faecium to continually present new combinations of genes for potential selection suggests that controlling this pathogen will remain challenging but establishing a framework for understanding genomic evolution is likely to aid in tracking the threats posed by newly emerging lineages.
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Affiliation(s)
- Sebastiaan J. van Hal
- Department of Infectious Disesase and Microbiology, Royal Prince Alfred Hospital, Sydney, NSW Australia
- University of Sydney, Sydney, NSW Australia
| | - Rob J. L. Willems
- Department of Medical Microbiology, University Medical Center Utrech, Utrecht, The Netherlands
| | | | - Susan A. Ballard
- Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria Australia
| | - Teresa M. Coque
- Department of Microbiology, Ramón y Cajal University Hospital and Ramón y Cajal Health Research Institute (IRYCIS), Madrid, Spain
- Network Research Centre for Epidemiology and Public Health (CIBERESP), Madrid, Spain
| | | | - Kristin Hegstad
- Department of Microbiology and Infection Control, Norwegian National Advisory Unit on Detection of Antimicrobial Resistance, University Hospital of North-Norway, Tromsø, Norway
- Research Group for Host-Microbe Interactions, UiT – the Arctic University of Norway, Tromsø, Norway
| | - Hendrik T. Westh
- MRSA Knowledge Center, Department of Clinical Microbiology, Hvidovre Hospital, Hvidovre, Denmark
| | - Benjamin P. Howden
- Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria Australia
| | - Surbhi Malhotra-Kumar
- Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, Universiteit Antwerpen, Wilrijk, Belgium
| | - Guido Werner
- National Reference Centre for Staphylococci and Enterococci, Division of Nosocomial Pathogens and Antibiotic Resistances, Department of Infectious Diseases, Robert Koch Institute, Wernigerode Branch, Wernigerode, Germany
| | - Katsunori Yanagihara
- Department of Laboratory Medicine, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Ashlee M. Earl
- Infectious Disease & Microbiome Program, Broad Institute, Cambridge, MA USA
| | | | - Jukka Corander
- Department of Biostatistics, University of Oslo, Oslo, Norway
- Parasites and Microbes, Wellcome Sanger Institute, Hinxton, Cambridge, UK
| | - Rory Bowden
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052 Australia
- Department of Medical Biology, University of Melbourne, 1G Royal Parade, Melbourne, Victoria Australia
- Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, OX3 7BN UK
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14
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Chaturvedi P, Shukla P, Giri BS, Chowdhary P, Chandra R, Gupta P, Pandey A. Prevalence and hazardous impact of pharmaceutical and personal care products and antibiotics in environment: A review on emerging contaminants. ENVIRONMENTAL RESEARCH 2021; 194:110664. [PMID: 33400949 DOI: 10.1016/j.envres.2020.110664] [Citation(s) in RCA: 207] [Impact Index Per Article: 69.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 12/02/2020] [Accepted: 12/20/2020] [Indexed: 05/24/2023]
Abstract
Antibiotic resistance is a global health emergency linked to unrestrained use of pharmaceutical and personal care products (PPCPs) as prophylactic agent and therapeutic purposes across various industries. Occurrence of pharmaceuticals are identified in ground water, surface water, soils, and wastewater treatment plants (WWTPs) in ng/L to μg/L concentration range. The prevalence of organic compounds including antimicrobial agents, hormones, antibiotics, preservatives, disinfectants, synthetic musks etc. in environment have posed serious health concerns. The aim of this review is to elucidate the major sources accountable for emergence of antibiotic resistance. For this purpose, variety of introductory sources and fate of PPCPs in aquatic environment including human and veterinary wastes, aquaculture and agriculture related wastes, and other anthropogenic activities have been discussed. Furthermore, genetic and enzymatic factors responsible for transfer and appearance of antibiotic resistance genes are presented. Ecotoxicity of PPCPs has been studied in environment in order to present risk imposed to human and ecological health. As per published literature reports, the removal of antibiotics and related traces being difficult, couples the possibility of emergence of antibiotic resistance and hence sustainability in global water resources. Therefore, research on environmental behavior and control strategies should be conducted along with assessing their chronic toxicity to identify potential human and ecological risks.
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Affiliation(s)
- Preeti Chaturvedi
- Aquatic Toxicology Laboratory, Environmental Toxicology Group, Council of Scientific and Industrial Research-Indian Institute of Toxicology Research (CSIR-IITR), Vishvigyan Bhawan, 31, M.G. Marg, Lucknow, 226001, Uttar Pradesh, India; Department of Biotechnology, National Institute of Technology-Raipur, G.E. Road, Raipur, 492010, Chhattisgarh, India.
| | - Parul Shukla
- Aquatic Toxicology Laboratory, Environmental Toxicology Group, Council of Scientific and Industrial Research-Indian Institute of Toxicology Research (CSIR-IITR), Vishvigyan Bhawan, 31, M.G. Marg, Lucknow, 226001, Uttar Pradesh, India
| | - Balendu Shekher Giri
- Aquatic Toxicology Laboratory, Environmental Toxicology Group, Council of Scientific and Industrial Research-Indian Institute of Toxicology Research (CSIR-IITR), Vishvigyan Bhawan, 31, M.G. Marg, Lucknow, 226001, Uttar Pradesh, India
| | - Pankaj Chowdhary
- Aquatic Toxicology Laboratory, Environmental Toxicology Group, Council of Scientific and Industrial Research-Indian Institute of Toxicology Research (CSIR-IITR), Vishvigyan Bhawan, 31, M.G. Marg, Lucknow, 226001, Uttar Pradesh, India
| | - Ram Chandra
- Department of Microbiology, Babasaheb Bhimrao Ambedkar University (A Central University), Vidya Vihar, Raebareli Road, Lucknow, Uttar Pradesh, 226 025, India
| | - Pratima Gupta
- Department of Biotechnology, National Institute of Technology-Raipur, G.E. Road, Raipur, 492010, Chhattisgarh, India.
| | - Ashok Pandey
- Centre for Innovation and Transnational Research, CSIR-Indian Institute of Toxicology Research, Lucknow, 226 001, Uttar Pradesh, India
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15
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Werner G, Neumann B, Weber RE, Kresken M, Wendt C, Bender JK. Thirty years of VRE in Germany - "expect the unexpected": The view from the National Reference Centre for Staphylococci and Enterococci. Drug Resist Updat 2020; 53:100732. [PMID: 33189998 DOI: 10.1016/j.drup.2020.100732] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 10/12/2020] [Accepted: 10/15/2020] [Indexed: 02/06/2023]
Abstract
Enterococci are commensals of the intestinal tract of many animals and humans. Of the various known and still unnamed new enterococcal species, only isolates of Enterococcus faecium and Enterococcus faecalis have received increased medical and public health attention. According to textbook knowledge, the majority of infections are caused by E. faecalis. In recent decades, the number of enterococcal infections has increased, with the increase being exclusively associated with a rising number of nosocomial E. faecium infections. This increase has been accompanied by the dissemination of certain hospital-acquired strain variants and an alarming progress in the development of antibiotic resistance namely vancomycin resistance. With this review we focus on a description of the specific situation of vancomycin resistance among clinical E. faecium isolates in Germany over the past 30 years. The present review describes three VRE episodes in Germany, each of which is framed by the beginning and end of the respective decade. The first episode is specified by the first appearance of VRE in 1990 and a country-wide spread of specific vanA-type VRE strains (ST117/CT24) until the late 1990s. The second decade was initially marked by regional clusters and VRE outbreaks in hospitals in South-Western Germany in 2004 and 2005, mainly caused by vanA-type VRE of ST203. Against the background of a certain "basic level" of VRE prevalence throughout Germany, an early shift from the vanA genotype to the vanB genotype in clinical isolates already occurred at the end of the 2000s without much notice. With the beginning of the third decade in 2010, VRE rates in Germany have permanently increased, first in some federal states and soon after country-wide. Besides an increase in VRE prevalence, this decade was marked by a sharp increase in vanB-type resistance and a dominance of a few, novel strain variants like ST192 and later on ST117 (CT71, CT469) and ST80 (CT1065). The largest VRE outbreak, which involved about 2,900 patients and lasted over three years, was caused by a novel and until that time, unknown strain type of ST80/CT1013 (vanB). Across all periods, VRE outbreaks were mainly oligoclonal and strain types varied over space (hospital wards) and time. The spread of VRE strains obviously respects political borders; for instance, both vancomycin-variable enterococci which were highly prevalent in Denmark and ST796 VRE which successfully disseminated in Australia and Switzerland, were still completely absent among German hospital patients, until to date.
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Affiliation(s)
- Guido Werner
- National Reference Centre for Staphylococci and Enterococci, Division Nosocomial Pathogens and Antibiotic Resistances, Department of Infectious Diseases, Robert Koch Institute, Wernigerode Branch, Germany.
| | - Bernd Neumann
- National Reference Centre for Staphylococci and Enterococci, Division Nosocomial Pathogens and Antibiotic Resistances, Department of Infectious Diseases, Robert Koch Institute, Wernigerode Branch, Germany
| | - Robert E Weber
- National Reference Centre for Staphylococci and Enterococci, Division Nosocomial Pathogens and Antibiotic Resistances, Department of Infectious Diseases, Robert Koch Institute, Wernigerode Branch, Germany
| | | | | | - Jennifer K Bender
- National Reference Centre for Staphylococci and Enterococci, Division Nosocomial Pathogens and Antibiotic Resistances, Department of Infectious Diseases, Robert Koch Institute, Wernigerode Branch, Germany
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16
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Quantifying acquisition and transmission of Enterococcus faecium using genomic surveillance. Nat Microbiol 2020; 6:103-111. [PMID: 33106672 PMCID: PMC7610418 DOI: 10.1038/s41564-020-00806-7] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Accepted: 09/30/2020] [Indexed: 12/15/2022]
Abstract
Nosocomial acquisition and transmission of vancomycin-resistant Enterococcus faecium (VREfm) is the driver for E. faecium carriage in hospitalized patients, which, in turn, is a risk factor for invasive infection in immunocompromised patients. In the present study, we provide a comprehensive picture of E. faecium transmission in an entire sampled patient population using a sequence-driven approach. We prospectively identified and followed 149 haematology patients admitted to a hospital in England for 6 months. Patient stools (n = 376) and environmental swabs (n = 922) were taken at intervals and cultured for E. faecium. We sequenced 1,560 isolates (1,001 stool, 559 environment) and focused our genomic analyses on 1,477 isolates (95%) in the hospital-adapted clade A1. Of 101 patients who provided two or more stool samples, 40 (40%) developed E. faecium carriage after admission based on culture, compared with 64 patients (63%) based on genomic analysis (73% VREfm). Half of 922 environmental swabs (447, 48%) were positive for VREfm. Network analysis showed that, of 111 patients positive for the A1 clade, 67 had strong epidemiological and genomic links with at least one other patient and/or their direct environment, supporting nosocomial transmission. Six patients (3.4%) developed an invasive E. faecium infection from their own gut-colonizing strain, which was preceded by nosocomial acquisition of the infecting isolate in half of these. Two informatics approaches (subtype categorization to define phylogenetic clusters and the development of an SNP cut-off for transmission) were central to our analyses, both of which will inform the future translation of E. faecium sequencing into routine outbreak detection and investigation. In conclusion, we showed that carriage and environmental contamination by the hospital-adapted E. faecium lineage were hyperendemic in our study population and that improved infection control measures will be needed to reduce hospital acquisition rates.
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17
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Zhou X, Willems RJL, Friedrich AW, Rossen JWA, Bathoorn E. Enterococcus faecium: from microbiological insights to practical recommendations for infection control and diagnostics. Antimicrob Resist Infect Control 2020; 9:130. [PMID: 32778149 PMCID: PMC7418317 DOI: 10.1186/s13756-020-00770-1] [Citation(s) in RCA: 87] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Accepted: 07/02/2020] [Indexed: 02/08/2023] Open
Abstract
Early in its evolution, Enterococcus faecium acquired traits that allowed it to become a successful nosocomial pathogen. E. faecium inherent tenacity to build resistance to antibiotics and environmental stressors that allows the species to thrive in hospital environments. The continual wide use of antibiotics in medicine has been an important driver in the evolution of E. faecium becoming a highly proficient hospital pathogen.For successful prevention and reduction of nosocomial infections with vancomycin resistant E. faecium (VREfm), it is essential to focus on reducing VREfm carriage and spread. The aim of this review is to incorporate microbiological insights of E. faecium into practical infection control recommendations, to reduce the spread of hospital-acquired VREfm (carriage and infections). The spread of VREfm can be controlled by intensified cleaning procedures, antibiotic stewardship, rapid screening of VREfm carriage focused on high-risk populations, and identification of transmission routes through accurate detection and typing methods in outbreak situations. Further, for successful management of E. faecium, continual innovation in the fields of diagnostics, treatment, and eradication is necessary.
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Affiliation(s)
- Xuewei Zhou
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.
| | - Rob J L Willems
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Alexander W Friedrich
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - John W A Rossen
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Erik Bathoorn
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
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18
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Rios R, Reyes J, Carvajal LP, Rincon S, Panesso D, Echeverri AM, Dinh A, Kolokotronis SO, Narechania A, Tran TT, Munita JM, Murray BE, Planet PJ, Arias CA, Diaz L. Genomic Epidemiology of Vancomycin-Resistant Enterococcus faecium (VREfm) in Latin America: Revisiting The Global VRE Population Structure. Sci Rep 2020; 10:5636. [PMID: 32221315 PMCID: PMC7101424 DOI: 10.1038/s41598-020-62371-7] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Accepted: 03/10/2020] [Indexed: 12/12/2022] Open
Abstract
Little is known about the population structure of vancomycin-resistant Enterococcus faecium (VREfm) in Latin America (LATAM). Here, we provide a complete genomic characterization of 55 representative Latin American VREfm recovered from 1998-2015 in 5 countries. The LATAM VREfm population is structured into two main clinical clades without geographical clustering. Using the LATAM genomes, we reconstructed the global population of VREfm by including 285 genomes from 36 countries spanning from 1946 to 2017. In contrast to previous studies, our results show an early branching of animal related isolates and a further split of clinical isolates into two sub-clades within clade A. The overall phylogenomic structure of clade A was highly dependent on recombination (54% of the genome) and the split between clades A and B was estimated to have occurred more than 2,765 years ago. Furthermore, our molecular clock calculations suggest the branching of animal isolates and clinical clades occurred ~502 years ago whereas the split within the clinical clade occurred ~302 years ago (previous studies showed a more recent split between clinical an animal branches around ~74 years ago). By including isolates from Latin America, we present novel insights into the population structure of VREfm and revisit the evolution of these pathogens.
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Affiliation(s)
- Rafael Rios
- Molecular Genetics and Antimicrobial Resistance Unit, International Center for Microbial Genomics, Universidad El Bosque, Bogotá, Colombia
| | - Jinnethe Reyes
- Molecular Genetics and Antimicrobial Resistance Unit, International Center for Microbial Genomics, Universidad El Bosque, Bogotá, Colombia.,Center for Antimicrobial Resistance and Microbial Genomics, McGovern Medical School, University of Texas Health Science Center, Houston, TX, USA
| | - Lina P Carvajal
- Molecular Genetics and Antimicrobial Resistance Unit, International Center for Microbial Genomics, Universidad El Bosque, Bogotá, Colombia
| | - Sandra Rincon
- Molecular Genetics and Antimicrobial Resistance Unit, International Center for Microbial Genomics, Universidad El Bosque, Bogotá, Colombia
| | - Diana Panesso
- Molecular Genetics and Antimicrobial Resistance Unit, International Center for Microbial Genomics, Universidad El Bosque, Bogotá, Colombia.,Center for Antimicrobial Resistance and Microbial Genomics, McGovern Medical School, University of Texas Health Science Center, Houston, TX, USA.,Division of Infectious Diseases, Department of Internal Medicine, McGovern Medical School, University of Texas Health Science Center, Houston, Texas, USA
| | - Aura M Echeverri
- Molecular Genetics and Antimicrobial Resistance Unit, International Center for Microbial Genomics, Universidad El Bosque, Bogotá, Colombia
| | - An Dinh
- Center for Antimicrobial Resistance and Microbial Genomics, McGovern Medical School, University of Texas Health Science Center, Houston, TX, USA.,Division of Infectious Diseases, Department of Internal Medicine, McGovern Medical School, University of Texas Health Science Center, Houston, Texas, USA
| | - Sergios-Orestis Kolokotronis
- Institute for Comparative Genomics, American Museum of Natural History, New York, NY, USA.,Department of Epidemiology and Biostatistics, School of Public Health, SUNY Downstate Health Sciences University, Brooklyn, NY, USA
| | - Apurva Narechania
- Institute for Comparative Genomics, American Museum of Natural History, New York, NY, USA
| | - Truc T Tran
- Center for Antimicrobial Resistance and Microbial Genomics, McGovern Medical School, University of Texas Health Science Center, Houston, TX, USA.,Division of Infectious Diseases, Department of Internal Medicine, McGovern Medical School, University of Texas Health Science Center, Houston, Texas, USA
| | - Jose M Munita
- Center for Antimicrobial Resistance and Microbial Genomics, McGovern Medical School, University of Texas Health Science Center, Houston, TX, USA.,Division of Infectious Diseases, Department of Internal Medicine, McGovern Medical School, University of Texas Health Science Center, Houston, Texas, USA.,Millennium Initiative for Collaborative Research On Bacterial Resistance (MICROB-R), Santiago, Chile.,Genomics and Resistant Microbes Group, Facultad de Medicina Clinica Alemana, Universidad del Desarrollo, Santiago, Chile
| | - Barbara E Murray
- Center for Antimicrobial Resistance and Microbial Genomics, McGovern Medical School, University of Texas Health Science Center, Houston, TX, USA.,Division of Infectious Diseases, Department of Internal Medicine, McGovern Medical School, University of Texas Health Science Center, Houston, Texas, USA.,Department of Microbiology and Molecular Genetics, McGovern Medical School, University of Texas Health Science Center, Houston, Texas, USA
| | - Paul J Planet
- Institute for Comparative Genomics, American Museum of Natural History, New York, NY, USA.,Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania & Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Cesar A Arias
- Molecular Genetics and Antimicrobial Resistance Unit, International Center for Microbial Genomics, Universidad El Bosque, Bogotá, Colombia.,Center for Antimicrobial Resistance and Microbial Genomics, McGovern Medical School, University of Texas Health Science Center, Houston, TX, USA.,Division of Infectious Diseases, Department of Internal Medicine, McGovern Medical School, University of Texas Health Science Center, Houston, Texas, USA.,Millennium Initiative for Collaborative Research On Bacterial Resistance (MICROB-R), Santiago, Chile.,Department of Microbiology and Molecular Genetics, McGovern Medical School, University of Texas Health Science Center, Houston, Texas, USA
| | - Lorena Diaz
- Molecular Genetics and Antimicrobial Resistance Unit, International Center for Microbial Genomics, Universidad El Bosque, Bogotá, Colombia. .,Center for Antimicrobial Resistance and Microbial Genomics, McGovern Medical School, University of Texas Health Science Center, Houston, TX, USA. .,Millennium Initiative for Collaborative Research On Bacterial Resistance (MICROB-R), Santiago, Chile.
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19
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Kim HM, Chung DR, Cho SY, Huh K, Kang CI, Peck KR. Emergence of vancomycin-resistant Enterococcus faecium ST1421 lacking the pstS gene in Korea. Eur J Clin Microbiol Infect Dis 2020; 39:1349-1356. [PMID: 32128641 DOI: 10.1007/s10096-020-03853-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2019] [Accepted: 02/16/2020] [Indexed: 12/12/2022]
Abstract
Although multilocus sequence typing (MLST) has been used to study molecular epidemiology and to explore the population structure of Enterococcus faecium, vancomycin-resistant E. faecium (VREF) strains lacking the pstS gene that were non-typable using conventional MLST methods were reported recently. We found nationwide emergence of VREF isolates lacking pstS in Korea and hereby report the molecular characteristics of these isolates. Forty-six VREF isolates lacking the pstS gene were identified among 300 VREF rectal isolates collected from hospitalized patients between 2014 and 2015. MLST was performed and clonal relatedness was determined by pulsed-field gel electrophoresis (PFGE). Four VREF ST1421 isolates were whole-genome sequenced. Among the VREF rectal isolates lacking pstS, 98% were classified as ST1421, which has identical allelic profiles to ST17 for all housekeeping genes except pstS. PFGE pattern analyses revealed 32 pulsotypes. All isolates harbored Tn1546 components with various transposase and insertion sequences. The whole-genome sequencing of four VREF ST1421 isolates showed that the pstS gene region was deleted at various locations with considerable inversion. The pstS gene was also depleted in 12.1% of 33 VREF clinical isolates in 2006-2007 and in 11.8% of 59 clinical isolates in 2012-2013. VREF ST1421 strains lacking the pstS gene have emerged in Korea. The emergence and spread of pstS-deleted VREF strains pose a serious challenge for epidemiological investigation. Alternative molecular typing methods to MLST will be increasingly necessary.
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Affiliation(s)
- Hye Mee Kim
- Division of Infectious Diseases, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, 81 Irwon-ro, Gangnam-gu, Seoul, 06351, South Korea.,Asia Pacific Foundation for Infectious Diseases (APFID), Seoul, South Korea
| | - Doo Ryeon Chung
- Division of Infectious Diseases, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, 81 Irwon-ro, Gangnam-gu, Seoul, 06351, South Korea. .,Asia Pacific Foundation for Infectious Diseases (APFID), Seoul, South Korea. .,Center for Infection Prevention and Control, Samsung Medical Center, Seoul, South Korea.
| | - Sun Young Cho
- Division of Infectious Diseases, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, 81 Irwon-ro, Gangnam-gu, Seoul, 06351, South Korea.,Center for Infection Prevention and Control, Samsung Medical Center, Seoul, South Korea
| | - Kyungmin Huh
- Division of Infectious Diseases, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, 81 Irwon-ro, Gangnam-gu, Seoul, 06351, South Korea
| | - Cheol-In Kang
- Division of Infectious Diseases, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, 81 Irwon-ro, Gangnam-gu, Seoul, 06351, South Korea
| | - Kyong Ran Peck
- Division of Infectious Diseases, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, 81 Irwon-ro, Gangnam-gu, Seoul, 06351, South Korea
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20
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Janes VA, Notermans DW, Spijkerman IJ, Visser CE, Jakobs ME, van Houdt R, Willems RJ, de Jong MD, Schultsz C, Matamoros S. Amplified fragment length polymorphism and whole genome sequencing: a comparison of methods in the investigation of a nosocomial outbreak with vancomycin resistant enterococci. Antimicrob Resist Infect Control 2019; 8:153. [PMID: 31572571 PMCID: PMC6757385 DOI: 10.1186/s13756-019-0604-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Accepted: 08/30/2019] [Indexed: 12/19/2022] Open
Abstract
Background Recognition of nosocomial outbreaks with antimicrobial resistant (AMR) pathogens and appropriate infection prevention measures are essential to limit the consequences of AMR pathogens to patients in hospitals. Because unrelated, but genetically similar AMR pathogens may circulate simultaneously, rapid high-resolution molecular typing methods are needed for outbreak management. We compared amplified fragment length polymorphism (AFLP) and whole genome sequencing (WGS) during a nosocomial outbreak of vancomycin-resistant Enterococcus faecium (VRE) that spanned 5 months. Methods Hierarchical clustering of AFLP profiles was performed using unweighted pair-grouping and similarity coefficients were calculated with Pearson correlation. For WGS-analysis, core single nucleotide polymorphisms (SNPs) were used to calculate the pairwise distance between isolates, construct a maximum likelihood phylogeny and establish a cut-off for relatedness of epidemiologically linked VRE isolates. SNP-variations in the vanB gene cluster were compared to increase the comparative resolution. Technical replicates of 2 isolates were sequenced to determine the number of core-SNPs derived from random sequencing errors. Results Of the 721 patients screened for VRE carriage, AFLP assigned isolates of 22 patients to the outbreak cluster. According to WGS, all 22 isolates belonged to ST117 but only 21 grouped in a tight phylogenetic cluster and carried vanB resistance gene clusters. Sequencing of technical replicates showed that 4-5 core-SNPs were derived by random sequencing errors. The cut-off for relatedness of epidemiologically linked VRE isolates was established at ≤7 core-SNPs. The discrepant isolate was separated from the index isolate by 61 core-SNPs and the vanB gene cluster was absent. In AFLP analysis this discrepant isolate was indistinguishable from the other outbreak isolates, forming a cluster with 92% similarity (cut-off for identical isolates ≥90%). The inclusion of the discrepant isolate in the outbreak resulted in the screening of 250 patients and quarantining of an entire ward. Conclusion AFLP was a rapid and affordable screening tool for characterising hospital VRE outbreaks. For in-depth understanding of the outbreak WGS was needed. Compared to AFLP, WGS provided higher resolution typing of VRE isolates with implications for outbreak management.
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Affiliation(s)
- Victoria A. Janes
- Amsterdam UMC, University of Amsterdam, Medical Microbiology, Amsterdam, The Netherlands
| | - Daan W. Notermans
- Amsterdam UMC, University of Amsterdam, Medical Microbiology, Amsterdam, The Netherlands
| | - Ingrid J.B. Spijkerman
- Amsterdam UMC, University of Amsterdam, Medical Microbiology, Amsterdam, The Netherlands
| | - Caroline E. Visser
- Amsterdam UMC, University of Amsterdam, Medical Microbiology, Amsterdam, The Netherlands
| | - Marja E. Jakobs
- Amsterdam UMC, University of Amsterdam, Clinical Genetics, Core Facility Genomics, Amsterdam, The Netherlands
| | - Robin van Houdt
- Amsterdam UMC, Vrije Universiteit, Medical Microbiology, Amsterdam, The Netherlands
| | - Rob J.L. Willems
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Menno D. de Jong
- Amsterdam UMC, University of Amsterdam, Medical Microbiology, Amsterdam, The Netherlands
| | - Constance Schultsz
- Amsterdam UMC, University of Amsterdam, Medical Microbiology, Amsterdam, The Netherlands
- Amsterdam UMC, University of Amsterdam, Global Health - Amsterdam Institute for Global Health and Development (AIGHD), Amsterdam, The Netherlands
| | - Sébastien Matamoros
- Amsterdam UMC, University of Amsterdam, Medical Microbiology, Amsterdam, The Netherlands
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21
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Abstract
Vancomycin-resistant Enterococcus faecium (VREfm) is a globally significant public health threat and was listed on the World Health Organization's 2017 list of high-priority pathogens for which new treatments are urgently needed. Treatment options for invasive VREfm infections are very limited, and outcomes are often poor. Whole-genome sequencing is providing important new insights into VREfm evolution, drug resistance and hospital adaptation, and is increasingly being used to track VREfm transmission within hospitals to detect outbreaks and inform infection control practices. This mini-review provides an overview of recent data on the use of genomics to understand and respond to the global problem of VREfm.
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Affiliation(s)
- Claire Gorrie
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Charlie Higgs
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Glen Carter
- Doherty Applied Microbial Genomics, Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia.,Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Timothy P Stinear
- Doherty Applied Microbial Genomics, Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia.,Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Benjamin Howden
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia.,Department of Infectious Diseases, Austin Health, Heidelberg, Australia.,Doherty Applied Microbial Genomics, Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
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22
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Lemonidis K, Salih TS, Dancer SJ, Hunter IS, Tucker NP. Emergence of an Australian-like pstS-null vancomycin resistant Enterococcus faecium clone in Scotland. PLoS One 2019; 14:e0218185. [PMID: 31194809 PMCID: PMC6563996 DOI: 10.1371/journal.pone.0218185] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Accepted: 05/28/2019] [Indexed: 12/18/2022] Open
Abstract
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 neighbouring hospitals in Scotland. Whole genome sequencing of five VREfm strains isolated from these hospitals identified four pstS-null strains in both hospitals, while the fifth was 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 68 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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Affiliation(s)
- Kimon Lemonidis
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, United Kingdom
- * E-mail:
| | - Talal S. Salih
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, United Kingdom
| | - Stephanie J. Dancer
- Department of Microbiology, Hairmyres Hospital, NHS Lanarkshire, United Kingdom
- School of Applied Sciences, Edinburgh Napier University, Edinburgh, United Kingdom
| | - Iain S. Hunter
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, United Kingdom
| | - Nicholas P. Tucker
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, United Kingdom
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23
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Abdelbary MHH, Senn L, Greub G, Chaillou G, Moulin E, Blanc DS. Whole-genome sequencing revealed independent emergence of vancomycin-resistant Enterococcus faecium causing sequential outbreaks over 3 years in a tertiary care hospital. Eur J Clin Microbiol Infect Dis 2019; 38:1163-1170. [PMID: 30888549 DOI: 10.1007/s10096-019-03524-z] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Accepted: 02/27/2019] [Indexed: 02/03/2023]
Abstract
Vancomycin-resistant Enterococcus faecium (VREfm) emerged as an important cause of nosocomial infections worldwide. Previous studies based on molecular typing revealed that VREfm outbreaks are mainly associated with a particular genetic lineage, namely clonal complex 17 (CC17), which harbours either vanA or vanB gene cluster. The University Hospital of Lausanne faced several VREfm episodes of transmissions between 2014 and 2017. In this study, we used whole-genome sequencing (WGS) to investigate the relatedness of 183 VREfm isolates collected from 156 patients. Sequence types (ST) 17, ST80 and ST117 were the most predominant clones. Based on epidemiological data, 10 outbreaks were identified, which were caused by at least 13 distinct genotypes. The majority of isolates involved in outbreaks (91%) differed by only 0 to 3 SNPs. Four outbreaks involved more than one genotype and half of the cases considered as sporadic were possibly linked to an outbreak. By sequencing all isolates, we were able to better understand our local epidemiology of VREfm. The polyclonal structure observed between the different outbreaks strains, the high level of recombination detected in isolates, the time elapsed between admission and the first VREfm detection and the negative screening at admission support the hypothesis of the emergence of new VREfm clones within the hospitalised population.
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Affiliation(s)
- Mohamed H H Abdelbary
- Service of hospital preventive medicine, Lausanne University Hospital, Rue du Bugnon 46, 1011, Lausanne, Switzerland.,Division of Oral Microbiology and Immunology, Department of Operative and Preventive Dentistry and Periodontology, RWTH Aachen University Hospital, Aachen, Germany
| | - Laurence Senn
- Service of hospital preventive medicine, Lausanne University Hospital, Rue du Bugnon 46, 1011, Lausanne, Switzerland
| | - Gilbert Greub
- Institute of Microbiology, Lausanne University Hospital, Lausanne, Switzerland
| | - Gregory Chaillou
- Service of hospital preventive medicine, Lausanne University Hospital, Rue du Bugnon 46, 1011, Lausanne, Switzerland
| | - Estelle Moulin
- Service of hospital preventive medicine, Lausanne University Hospital, Rue du Bugnon 46, 1011, Lausanne, Switzerland
| | - Dominique S Blanc
- Service of hospital preventive medicine, Lausanne University Hospital, Rue du Bugnon 46, 1011, Lausanne, Switzerland.
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24
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Aziz F, Khan MN, Ahmed S, Andrews SC. Draft genome sequence of Enterococcus faecium SP15, a potential probiotic strain isolated from spring water. BMC Res Notes 2019; 12:99. [PMID: 30795795 PMCID: PMC6387508 DOI: 10.1186/s13104-019-4136-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Accepted: 02/15/2019] [Indexed: 12/11/2022] Open
Abstract
Objectives Enterococci are Gram-positive lactic acid bacteria and common inhabitants of the gastrointestinal tract of mammals, including humans. They are also widely distributed in diverse environments such as soil, water, vegetables and food. Enterococcus faecium is able to produce antimicrobial compounds (enterocins) and thus can act as a probiotic. E. faecium SP15 is a newly identified enterocin-producing strain from spring water that has been subjected to genome sequence analysis to provide understanding of its antimicrobial and probiotic properties. Data description The draft genome of E. faecium SP15 comprises of 2,783,033 bp with a G+C content of 38.08%. Five genetic loci predicted to specify enterocin production were identified, but no virulence factors could be detected and only two potential antibiotic resistance genes were noted.
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Affiliation(s)
- Fauzia Aziz
- Department of Zoology, The University of Azad Jammu and Kashmir, Muzaffarabad, Azad Kashmir, Pakistan. .,School of Biological Sciences, University of Reading, Reading, RG6 6AJ, UK. .,Department of Zoology, The University of Poonch, Rawalakot, Azad Kashmir, Pakistan.
| | - Muhammad Nasim Khan
- Department of Zoology, The University of Azad Jammu and Kashmir, Muzaffarabad, Azad Kashmir, Pakistan
| | - Safia Ahmed
- Department of Microbiology, Quaid-I-Azam University, Islamabad, 45230, Pakistan
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25
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Genomic Surveillance of Enterococcus faecium Reveals Limited Sharing of Strains and Resistance Genes between Livestock and Humans in the United Kingdom. mBio 2018; 9:mBio.01780-18. [PMID: 30401778 PMCID: PMC6222123 DOI: 10.1128/mbio.01780-18] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The rise in rates of human infection caused by vancomycin-resistant Enterococcus faecium (VREfm) strains between 1988 to the 2000s in Europe was suggested to be associated with acquisition from livestock. As a result, the European Union banned the use of the glycopeptide drug avoparcin as a growth promoter in livestock feed. While some studies reported a decrease in VREfm in livestock, others reported no reduction. Here, we report the first livestock VREfm prevalence survey in the UK since 2003 and the first large-scale study using whole-genome sequencing to investigate the relationship between E. faecium strains in livestock and humans. We found a low prevalence of VREfm in retail meat and limited evidence for recent sharing of strains between livestock and humans with bloodstream infection. There was evidence for limited sharing of genes encoding antibiotic resistance between these reservoirs, a finding which requires further research. Vancomycin-resistant Enterococcus faecium (VREfm) is a major cause of nosocomial infection and is categorized as high priority by the World Health Organization global priority list of antibiotic-resistant bacteria. In the past, livestock have been proposed as a putative reservoir for drug-resistant E. faecium strains that infect humans, and isolates of the same lineage have been found in both reservoirs. We undertook cross-sectional surveys to isolate E. faecium (including VREfm) from livestock farms, retail meat, and wastewater treatment plants in the United Kingdom. More than 600 isolates from these sources were sequenced, and their relatedness and antibiotic resistance genes were compared with genomes of almost 800 E. faecium isolates from patients with bloodstream infection in the United Kingdom and Ireland. E. faecium was isolated from 28/29 farms; none of these isolates were VREfm, suggesting a decrease in VREfm prevalence since the last UK livestock survey in 2003. However, VREfm was isolated from 1% to 2% of retail meat products and was ubiquitous in wastewater treatment plants. Phylogenetic comparison demonstrated that the majority of human and livestock-related isolates were genetically distinct, although pig isolates from three farms were more genetically related to human isolates from 2001 to 2004 (minimum of 50 single-nucleotide polymorphisms [SNPs]). Analysis of accessory (variable) genes added further evidence for distinct niche adaptation. An analysis of acquired antibiotic resistance genes and their variants revealed limited sharing between humans and livestock. Our findings indicate that the majority of E. faecium strains infecting patients are largely distinct from those from livestock in this setting, with limited sharing of strains and resistance genes.
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26
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Arredondo-Alonso S, Rogers MRC, Braat JC, Verschuuren TD, Top J, Corander J, Willems RJL, Schürch AC. mlplasmids: a user-friendly tool to predict plasmid- and chromosome-derived sequences for single species. Microb Genom 2018; 4. [PMID: 30383524 PMCID: PMC6321875 DOI: 10.1099/mgen.0.000224] [Citation(s) in RCA: 94] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Assembly of bacterial short-read whole-genome sequencing data frequently results in hundreds of contigs for which the origin, plasmid or chromosome, is unclear. Complete genomes resolved by long-read sequencing can be used to generate and label short-read contigs. These were used to train several popular machine learning methods to classify the origin of contigs from Enterococcus faecium, Klebsiella pneumoniae and Escherichia coli using pentamer frequencies. We selected support-vector machine (SVM) models as the best classifier for all three bacterial species (F1-score E. faecium=0.92, F1-score K. pneumoniae=0.90, F1-score E. coli=0.76), which outperformed other existing plasmid prediction tools using a benchmarking set of isolates. We demonstrated the scalability of our models by accurately predicting the plasmidome of a large collection of 1644 E. faecium isolates and illustrate its applicability by predicting the location of antibiotic-resistance genes in all three species. The SVM classifiers are publicly available as an R package and graphical-user interface called 'mlplasmids'. We anticipate that this tool may significantly facilitate research on the dissemination of plasmids encoding antibiotic resistance and/or contributing to host adaptation.
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Affiliation(s)
- Sergio Arredondo-Alonso
- 1Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Malbert R C Rogers
- 1Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Johanna C Braat
- 1Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Tess D Verschuuren
- 2Julius Centre for Health Sciences and Primary Care, University Medical Centre Utrecht, Utrecht, The Netherlands
| | - Janetta Top
- 1Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Jukka Corander
- 3Faculty of Medicine, Department of Biostatistics, University of Oslo, Oslo, Norway.,4Department of Mathematics and Statistics, University of Helsinki, Helsinki, Finland.,5Infection Genomics, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Rob J L Willems
- 1Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Anita C Schürch
- 1Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
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27
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Palma F, Manfreda G, Silva M, Parisi A, Barker DOR, Taboada EN, Pasquali F, Rossi M. Genome-wide identification of geographical segregated genetic markers in Salmonella enterica serovar Typhimurium variant 4,[5],12:i:. Sci Rep 2018; 8:15251. [PMID: 30323193 PMCID: PMC6189080 DOI: 10.1038/s41598-018-33266-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Accepted: 08/22/2018] [Indexed: 01/18/2023] Open
Abstract
Salmonella enterica ser. Typhimurium monophasic variant 4,[5],12:i:- has been associated with food-borne epidemics worldwide and swine appeared to be the main reservoir in most of the countries of isolation. However, the monomorphic nature of this serovar has, so far, hindered identification of the source due to expansion of clonal lineages in multiple hosts and food producing systems. Since geographically structured genetic signals can shape bacterial populations, identification of biogeographical markers in S. 1,4,[5],12:i:- genomes can contribute to improving source attribution. In this study, the phylogeographical structure of 148 geographically and temporally related Italian S. 1,4,[5],12:i:- has been investigated. The Italian isolates belong to a large population of clonal S. Typhimurium/1,4,[5],12:i:- isolates collected worldwide in two decades showing up to 2.5% of allele differences. Phylogenetic reconstruction revealed that isolates from the same geographical origin form highly supported monophyletic groups, suggesting discrete geographical segregation. These monophyletic groups are characterized by the gene content of a large sopE-containing prophage. Within this prophage, genome-wide comparison identified several genes overrepresented in strains of Italian origin. This suggests that certain lineages may be characterized by the acquisition of specific accessory genetic markers useful for improving identification of the source in ongoing epidemics.
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Affiliation(s)
- Federica Palma
- Department of Agricultural and Food Sciences, School of Agriculture and Veterinary Medicine, University of Bologna, Bologna, Italy.
| | - Gerardo Manfreda
- Department of Agricultural and Food Sciences, School of Agriculture and Veterinary Medicine, University of Bologna, Bologna, Italy
| | - Mickael Silva
- Instituto de Microbiologia, Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
| | - Antonio Parisi
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, Foggia, Italy
| | - Dillon O R Barker
- National Microbiology Laboratory at Lethbridge, Public Health Agency of Canada, Lethbridge, Canada
| | - Eduardo N Taboada
- National Microbiology Laboratory at Lethbridge, Public Health Agency of Canada, Lethbridge, Canada
| | - Frédérique Pasquali
- Department of Agricultural and Food Sciences, School of Agriculture and Veterinary Medicine, University of Bologna, Bologna, Italy
| | - Mirko Rossi
- Department of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
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28
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Sadowy E, Gawryszewska I, Kuch A, Żabicka D, Hryniewicz W. The changing epidemiology of VanB Enterococcus faecium in Poland. Eur J Clin Microbiol Infect Dis 2018; 37:927-936. [PMID: 29442195 PMCID: PMC5916999 DOI: 10.1007/s10096-018-3209-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Accepted: 02/01/2018] [Indexed: 01/02/2023]
Abstract
Increasing prevalence of VanB Enterococcus faecium in Polish hospitals reported to National Reference Centre for Susceptibility Testing (NRCST) prompted us to investigate the basis of this phenomenon. Two-hundred seventy-eight E. faecium isolates of VanB phenotype from the period 1999 to 2010 obtained by NRCST were investigated by multilocus sequence typing (MLST) and multilocus VNTR analysis (MLVA). Localization, transferability, and partial structure of the vanB-carrying Tn1549 transposon were studied by hybridization, PCR mapping, sequencing, and conjugation. VanB isolates almost exclusively represented hospital-associated E. faecium, with a significant shift from representatives of 17/18 lineage to 78 lineage after 2005. The vanB determinant, initially located mostly on transferable plasmids of the pRUM-, pLG1-, and pRE25-replicon types, later on was found almost exclusively on the host chromosome. Fifteen different plasmid and chromosomal insertion sites were identified, typically associated with single transposon coupling sequences, mostly not observed before. Our study demonstrates the significant change in the epidemiology of VanB-E. faecium in Poland, associated with the introduction and spread of the lineage 78 of the hospital-adapted E. faecium. These data point to the importance of the lineage 78 for the spread of vancomycin-resistance, determined by the vanB gene cluster, resulting in an increasing VRE prevalence in hospitals. This study also supports the scenario, in which representatives of the hospital-associated E. faecium independently acquire the vanB determinant de novo and spread within and among hospitals, concomitantly undergoing differentiation.
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Affiliation(s)
- Ewa Sadowy
- Department of Molecular Microbiology, National Medicines Institute, ul. Chełmska 30/34, 00-725, Warsaw, Poland.
| | - Iwona Gawryszewska
- Department of Molecular Microbiology, National Medicines Institute, ul. Chełmska 30/34, 00-725, Warsaw, Poland
| | - Alicja Kuch
- Department of Epidemiology and Clinical Microbiology, National Medicines Institute, Chełmska 30/34, 00-725, Warsaw, Poland
| | - Dorota Żabicka
- Department of Epidemiology and Clinical Microbiology, National Medicines Institute, Chełmska 30/34, 00-725, Warsaw, Poland
| | - Waleria Hryniewicz
- Department of Epidemiology and Clinical Microbiology, National Medicines Institute, Chełmska 30/34, 00-725, Warsaw, Poland
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29
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Mahony AA, Buultjens AH, Ballard SA, Grabsch EA, Xie S, Seemann T, Stuart RL, Kotsanas D, Cheng A, Heffernan H, Roberts SA, Coombs GW, Bak N, Ferguson JK, Carter GC, Howden BP, Stinear TP, Johnson PDR. Vancomycin-resistant Enterococcus faecium sequence type 796 - rapid international dissemination of a new epidemic clone. Antimicrob Resist Infect Control 2018; 7:44. [PMID: 29588851 PMCID: PMC5863837 DOI: 10.1186/s13756-018-0335-z] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Accepted: 03/14/2018] [Indexed: 02/07/2023] Open
Abstract
Background Vancomycin-resistant Enterococcus faecium (VRE) is a leading cause of hospital-acquired infections. New, presumably better-adapted strains of VRE appear unpredictably; it is uncertain how they spread despite improved infection control. We aimed to investigate the relatedness of a novel sequence type (ST) of vanB E. faecium - ST796 - very near its time of origin from hospitals in three Australian states and New Zealand. Methods Following near-simultaneous outbreaks of ST796 in multiple institutions, we gathered then tested colonization and bloodstream infection isolates’ antimicrobial resistance (AMR) phenotypes, and phylogenomic relationships using whole genome sequencing (WGS). Patient meta-data was explored to trace the spread of ST796. Results A novel clone of vanB E. faecium (ST796) was first detected at one Australian hospital in late 2011, then in two New Zealand hospitals linked by inter-hospital transfers from separate Melbourne hospitals. ST796 also appeared in hospitals in South Australia and New South Wales and was responsible for at least one major colonization outbreak in a Neonatal Intensive Care Unit without identifiable links between centers. No exceptional AMR was detected in the isolates. While WGS analysis showed very limited diversity at the core genome, consistent with recent emergence of the clone, clustering by institution was observed. Conclusions Evolution of new E. faecium clones, followed by recognized or unrecognized movement of colonized individuals then rapid intra-institutional cross-transmission best explain the multi-center, multistate and international outbreak we observed. Electronic supplementary material The online version of this article (10.1186/s13756-018-0335-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Andrew A Mahony
- 1Department of Infectious Diseases, Austin Health, 145 Studley Rd, Heidelberg, VIC 3084 Australia.,2Department of Medicine, The University of Melbourne, Heidelberg, VIC 3084 Australia
| | - Andrew H Buultjens
- 3Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000 Australia
| | - Susan A Ballard
- 1Department of Infectious Diseases, Austin Health, 145 Studley Rd, Heidelberg, VIC 3084 Australia.,4Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000 Australia
| | | | - Shirley Xie
- 5Department of Microbiology, Austin Health, Heidelberg, VIC 3084 Australia
| | - Torsten Seemann
- 6Melbourne Bioinformatics, The University of Melbourne, Parkville, VIC 3010 Australia
| | - Rhonda L Stuart
- 7Monash Infectious Diseases, Monash Health, Clayton, VIC 3168 Australia
| | - Despina Kotsanas
- 7Monash Infectious Diseases, Monash Health, Clayton, VIC 3168 Australia
| | - Allen Cheng
- 8Department of Infectious Diseases, Alfred Health, School of Public Health and Preventive Medicine, Monash University, Prahran, VIC 3181 Australia
| | - Helen Heffernan
- 9Antimicrobial Reference Laboratory, Institute of Environmental Science and Research (ESR), Wellington, 5022 New Zealand
| | - Sally A Roberts
- 10Department of Clinical Microbiology, Auckland District Health Board, Auckland, 1051 New Zealand
| | - Geoffrey W Coombs
- 11School of Veterinary and Life Sciences, Murdoch University, Murdoch, WA 6150 Australia.,12Microbiology Department, PathWest Laboratory Medicine - WA, Fiona Stanley Hospital, Murdoch, WA 6150 Australia
| | - Narin Bak
- 13Department of Infectious Diseases, Royal Adelaide Hospital, Adelaide, South Australia 5000 Australia
| | - John K Ferguson
- Division of Microbiology, Health Pathology, NSW Department of Immunology and Infectious Diseases, John Hunter Hospital, University of Newcastle, Newcastle, NSW 2305 Australia
| | - Glen C Carter
- 4Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000 Australia
| | - Benjamin P Howden
- 3Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000 Australia.,4Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000 Australia
| | - Timothy P Stinear
- 3Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000 Australia
| | - Paul D R Johnson
- 1Department of Infectious Diseases, Austin Health, 145 Studley Rd, Heidelberg, VIC 3084 Australia.,2Department of Medicine, The University of Melbourne, Heidelberg, VIC 3084 Australia.,3Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000 Australia
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30
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Rubio-Cosials A, Schulz EC, Lambertsen L, Smyshlyaev G, Rojas-Cordova C, Forslund K, Karaca E, Bebel A, Bork P, Barabas O. Transposase-DNA Complex Structures Reveal Mechanisms for Conjugative Transposition of Antibiotic Resistance. Cell 2018; 173:208-220.e20. [PMID: 29551265 PMCID: PMC5871717 DOI: 10.1016/j.cell.2018.02.032] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Revised: 01/08/2018] [Accepted: 02/12/2018] [Indexed: 12/28/2022]
Abstract
Conjugative transposition drives the emergence of multidrug resistance in diverse bacterial pathogens, yet the mechanisms are poorly characterized. The Tn1549 conjugative transposon propagates resistance to the antibiotic vancomycin used for severe drug-resistant infections. Here, we present four high-resolution structures of the conserved Y-transposase of Tn1549 complexed with circular transposon DNA intermediates. The structures reveal individual transposition steps and explain how specific DNA distortion and cleavage mechanisms enable DNA strand exchange with an absolute minimum homology requirement. This appears to uniquely allow Tn916-like conjugative transposons to bypass DNA homology and insert into diverse genomic sites, expanding gene transfer. We further uncover a structural regulatory mechanism that prevents premature cleavage of the transposon DNA before a suitable target DNA is found and generate a peptide antagonist that interferes with the transposase-DNA structure to block transposition. Our results reveal mechanistic principles of conjugative transposition that could help control the spread of antibiotic resistance genes. Antibiotic resistance-carrying conjugative transposon integrase structure revealed DNA distortion and special cleavage site allow insertion into diverse genomic sites Key structural features are conserved among numerous conjugative transposons Structures uncover auto-inhibition, allowing transposition antagonist design
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Affiliation(s)
- Anna Rubio-Cosials
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany
| | - Eike C Schulz
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany; Hamburg Outstation, European Molecular Biology Laboratory, 22603 Hamburg, Germany
| | - Lotte Lambertsen
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany
| | - Georgy Smyshlyaev
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany; European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Hinxton CB10 1SD, UK
| | - Carlos Rojas-Cordova
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany
| | - Kristoffer Forslund
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany
| | - Ezgi Karaca
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany; Izmir Biomedicine and Genome Center (IBG), 35340 Izmir, Turkey
| | - Aleksandra Bebel
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany
| | - Peer Bork
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany; Max Delbrück Center for Molecular Medicine, 13125 Berlin, Germany; Molecular Medicine Partnership Unit, 69120 Heidelberg, Germany; Department of Bioinformatics, Biocenter, University of Würzburg, 97074 Würzburg, Germany
| | - Orsolya Barabas
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany.
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31
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Genome-Based Analysis of Enterococcus faecium Bacteremia Associated with Recurrent and Mixed-Strain Infection. J Clin Microbiol 2018; 56:JCM.01520-17. [PMID: 29263205 PMCID: PMC5824064 DOI: 10.1128/jcm.01520-17] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Accepted: 12/12/2017] [Indexed: 11/20/2022] Open
Abstract
Vancomycin-resistant Enterococcus faecium (VREfm) bloodstream infections are associated with high recurrence rates. This study used genome sequencing to accurately distinguish the frequency of relapse and reinfection in patients with recurrent E. faecium bacteremia and to investigate strain relatedness in patients with apparent VREfm and vancomycin-susceptible E. faecium (VSEfm) mixed infection. A retrospective study was performed at the Cambridge University Hospitals NHS Foundation Trust (CUH) between November 2006 and December 2012. We analyzed the genomes of 44 E. faecium isolates from 21 patients (26 VREfm isolates from 12 patients with recurrent bacteremia and 18 isolates from 9 patients with putative VREfm/VSEfm mixed infection). Phenotypic antibiotic susceptibility was determined using a Vitek2 instrument. Genomes were compared with those of a further 263 E. faecium isolates associated with bacteremia in patients at CUH over the same time period. Pairwise comparison of core genomes indicated that 10 (71%) episodes of recurrent VREfm bacteremia were due to reinfection with a new strain, with reinfection being more likely with increasing time between the two positive cultures. The majority (78%) of patients with a mixed VREfm and VSEfm infection had unrelated strains. More than half (59%) of study isolates were closely related to another isolate associated with bacteremia from CUH. This included 60% of isolates associated with reinfection, indicating acquisition in the hospital. This study provides the first high-resolution insights into recurrence and mixed infection by E. faecium and demonstrates that reinfection with a new strain, often acquired from the hospital, is a driver of recurrence.
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32
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Moradigaravand D, Gouliouris T, Blane B, Naydenova P, Ludden C, Crawley C, Brown NM, Török ME, Parkhill J, Peacock SJ. Within-host evolution of Enterococcus faecium during longitudinal carriage and transition to bloodstream infection in immunocompromised patients. Genome Med 2017; 9:119. [PMID: 29282103 PMCID: PMC5744393 DOI: 10.1186/s13073-017-0507-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Accepted: 12/07/2017] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND Enterococcus faecium is a leading cause of hospital-acquired infection, particularly in the immunocompromised. Here, we use whole genome sequencing of E. faecium to study within-host evolution and the transition from gut carriage to invasive disease. METHODS We isolated and sequenced 180 E. faecium from four immunocompromised patients who developed bloodstream infection during longitudinal surveillance of E. faecium in stool and their immediate environment. RESULTS A phylogenetic tree based on single nucleotide polymorphisms (SNPs) in the core genome of the 180 isolates demonstrated several distinct clones. This was highly concordant with the population structure inferred by Bayesian methods, which contained four main BAPS (Bayesian Analysis of Population Structure) groups. The majority of isolates from each patient resided in a single group, but all four patients also carried minority populations in stool from multiple phylogenetic groups. Bloodstream isolates from each case belonged to a single BAPS group, which differed in all four patients. Analysis of 87 isolates (56 from blood) belonging to a single BAPS group that were cultured from the same patient over 54 days identified 30 SNPs in the core genome (nine intergenic, 13 non-synonymous, eight synonymous), and 250 accessory genes that were variably present. Comparison of these genetic variants in blood isolates versus those from stool or environment did not identify any variants associated with bloodstream infection. The substitution rate for these isolates was estimated to be 128 (95% confidence interval 79.82 181.77) mutations per genome per year, more than ten times higher than previous estimates for E. faecium. Within-patient variation in vancomycin resistance associated with vanA was common and could be explained by plasmid loss, or less often by transposon loss. CONCLUSIONS These findings demonstrate the diversity of E. faecium carriage by individual patients and significant within-host diversity of E. faecium, but do not provide evidence for adaptive genetic variation associated with invasion.
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Affiliation(s)
- Danesh Moradigaravand
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK.
| | - Theodore Gouliouris
- Department of Medicine, University of Cambridge, Box 157, Addenbrooke's Hospital, Hills Road, Cambridge, CB2 0QQ, UK.
- Cambridge University Hospitals NHS Foundation Trust, Addenbrooke's Hospital, Hills Road, Cambridge, CB2 0QQ, UK.
- Public Health England, Clinical Microbiology and Public Health Laboratory, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK.
| | - Beth Blane
- Department of Medicine, University of Cambridge, Box 157, Addenbrooke's Hospital, Hills Road, Cambridge, CB2 0QQ, UK
| | - Plamena Naydenova
- Department of Medicine, University of Cambridge, Box 157, Addenbrooke's Hospital, Hills Road, Cambridge, CB2 0QQ, UK
| | - Catherine Ludden
- London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK
| | - Charles Crawley
- Cambridge University Hospitals NHS Foundation Trust, Addenbrooke's Hospital, Hills Road, Cambridge, CB2 0QQ, UK
| | - Nicholas M Brown
- Cambridge University Hospitals NHS Foundation Trust, Addenbrooke's Hospital, Hills Road, Cambridge, CB2 0QQ, UK
- Public Health England, Clinical Microbiology and Public Health Laboratory, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - M Estée Török
- Department of Medicine, University of Cambridge, Box 157, Addenbrooke's Hospital, Hills Road, Cambridge, CB2 0QQ, UK
- Cambridge University Hospitals NHS Foundation Trust, Addenbrooke's Hospital, Hills Road, Cambridge, CB2 0QQ, UK
- Public Health England, Clinical Microbiology and Public Health Laboratory, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Julian Parkhill
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - Sharon J Peacock
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK
- Department of Medicine, University of Cambridge, Box 157, Addenbrooke's Hospital, Hills Road, Cambridge, CB2 0QQ, UK
- London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK
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33
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Genetic characteristics of VanA-type vancomycin-resistant Enterococcus faecalis and Enterococcus faecium in Cuba. New Microbes New Infect 2017; 21:125-127. [PMID: 29348921 PMCID: PMC5766742 DOI: 10.1016/j.nmni.2017.12.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Revised: 11/27/2017] [Accepted: 12/01/2017] [Indexed: 12/05/2022] Open
Abstract
VanA-type vancomycin-resistant enterococci isolates from bloodstream infections in Cuba were genetically characterized. Enterococcus faecalis isolates were assigned to sequence type (ST) 28, closely related to Eastern Europe, while Enterococcus faecium belonged to ST262, ST656 and ST1349, and showed different genetic profiles.
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34
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van Hal SJ, Espedido BA, Coombs GW, Howden BP, Korman TM, Nimmo GR, Gosbell IB, Jensen SO. Polyclonal emergence of vanA vancomycin-resistant Enterococcus faecium in Australia. J Antimicrob Chemother 2017; 72:998-1001. [PMID: 28031272 DOI: 10.1093/jac/dkw539] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2016] [Accepted: 11/21/2016] [Indexed: 02/06/2023] Open
Abstract
Objectives To investigate the genetic context associated with the emergence of vanA VRE in Australia. Methods The whole genomes of 18 randomly selected vanA -positive Enterococcus faecium patient isolates, collected between 2011 and 2013 from hospitals in four Australian capitals, were sequenced and analysed. Results In silico typing and transposon/plasmid assembly revealed that the sequenced isolates represented (in most cases) different hospital-adapted STs and were associated with a variety of different Tn 1546 variants and plasmid backbone structures. Conclusions The recent emergence of vanA VRE in Australia was polyclonal and not associated with the dissemination of a single 'dominant' ST or vanA -encoding plasmid. Interestingly, the factors contributing to this epidemiological change are not known and future studies may need to consider investigation of potential community sources.
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Affiliation(s)
- Sebastiaan J van Hal
- School of Medicine, Western Sydney University, Sydney, NSW, Australia.,Royal Prince Alfred Hospital, Sydney, NSW, Australia
| | - Björn A Espedido
- School of Medicine, Western Sydney University, Sydney, NSW, Australia.,Antimicrobial Resistance and Mobile Elements Group, Ingham Institute for Applied Medical Research, Sydney, NSW, Australia
| | - Geoffrey W Coombs
- School of Veterinary and Life Sciences, Murdoch University, Perth, WA, Australia.,PathWest Laboratory Medicine, Fiona Stanley Hospital, Perth, WA, Australia
| | - Benjamin P Howden
- Austin Health, Melbourne, Vic., Australia.,Department of Microbiology and Immunology, The University of Melbourne, Melbourne, Vic., Australia
| | | | | | - Iain B Gosbell
- School of Medicine, Western Sydney University, Sydney, NSW, Australia.,Antimicrobial Resistance and Mobile Elements Group, Ingham Institute for Applied Medical Research, Sydney, NSW, Australia.,Sydney South Western Pathology Service, NSW Pathology, Sydney, NSW, Australia
| | - Slade O Jensen
- School of Medicine, Western Sydney University, Sydney, NSW, Australia.,Antimicrobial Resistance and Mobile Elements Group, Ingham Institute for Applied Medical Research, Sydney, NSW, Australia
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35
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Rapid detection of high-risk Enterococcus faecium clones by matrix-assisted laser desorption ionization time-of-flight mass spectrometry. Diagn Microbiol Infect Dis 2017; 87:299-307. [DOI: 10.1016/j.diagmicrobio.2016.12.007] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Revised: 11/07/2016] [Accepted: 12/11/2016] [Indexed: 12/18/2022]
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36
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Raven KE, Gouliouris T, Brodrick H, Coll F, Brown NM, Reynolds R, Reuter S, Török ME, Parkhill J, Peacock SJ. Complex Routes of Nosocomial Vancomycin-Resistant Enterococcus faecium Transmission Revealed by Genome Sequencing. Clin Infect Dis 2017; 64:886-893. [PMID: 28362945 PMCID: PMC5439346 DOI: 10.1093/cid/ciw872] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Accepted: 01/04/2017] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Vancomycin-resistant Enterococcus faecium (VREfm) is a leading cause of nosocomial infection. Here, we describe the utility of whole-genome sequencing in defining nosocomial VREfm transmission. METHODS A retrospective study at a single hospital in the United Kingdom identified 342 patients with E. faecium bloodstream infection over 7 years. Of these, 293 patients had a stored isolate and formed the basis for the study. The first stored isolate from each case was sequenced (200 VREfm [197 vanA, 2 vanB, and 1 isolate containing both vanA and vanB], 93 vancomycin-susceptible E. faecium) and epidemiological data were collected. Genomes were also available for E. faecium associated with bloodstream infections in 15 patients in neighboring hospitals, and 456 patients across the United Kingdom and Ireland. RESULTS The majority of infections in the 293 patients were hospital-acquired (n = 249) or healthcare-associated (n = 42). Phylogenetic analysis showed that 291 of 293 isolates resided in a hospital-associated clade that contained numerous discrete clusters of closely related isolates, indicative of multiple introductions into the hospital followed by clonal expansion associated with transmission. Fine-scale analysis of 6 exemplar phylogenetic clusters containing isolates from 93 patients (32%) identified complex transmission routes that spanned numerous wards and years, extending beyond the detection of conventional infection control. These contained both vancomycin-resistant and -susceptible isolates. We also identified closely related isolates from patients at Cambridge University Hospitals NHS Foundation Trust and regional and national hospitals, suggesting interhospital transmission. CONCLUSIONS These findings provide important insights for infection control practice and signpost areas for interventions. We conclude that sequencing represents a powerful tool for the enhanced surveillance and control of nosocomial E. faecium transmission and infection.
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Affiliation(s)
| | - Theodore Gouliouris
- Department of Medicine, University of Cambridge
- Public Health England, Clinical Microbiology and Public Health Laboratory, Addenbrooke's Hospital, and
- Cambridge University Hospitals NHS Foundation Trust, Cambridge
| | | | | | - Nicholas M Brown
- Public Health England, Clinical Microbiology and Public Health Laboratory, Addenbrooke's Hospital, and
- Cambridge University Hospitals NHS Foundation Trust, Cambridge
| | - Rosy Reynolds
- British Society for Antimicrobial Chemotherapy, Birmingham
- North Bristol NHS Trust, Southmead Hospital, Bristol; and
| | | | - M Estée Török
- Department of Medicine, University of Cambridge
- Public Health England, Clinical Microbiology and Public Health Laboratory, Addenbrooke's Hospital, and
- Cambridge University Hospitals NHS Foundation Trust, Cambridge
| | - Julian Parkhill
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, United Kingdom
| | - Sharon J Peacock
- Department of Medicine, University of Cambridge
- Cambridge University Hospitals NHS Foundation Trust, Cambridge
- London School of Hygiene and Tropical Medicine
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, United Kingdom
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37
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Guo Y, Yang X, Qi Y, Wen S, Liu Y, Tang S, Huang R, Tang L. Long-term use of ceftriaxone sodium induced changes in gut microbiota and immune system. Sci Rep 2017; 7:43035. [PMID: 28220870 PMCID: PMC5318879 DOI: 10.1038/srep43035] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Accepted: 01/18/2017] [Indexed: 02/07/2023] Open
Abstract
Antibiotic administration, while facilitating clearance of targeted infections, also perturbs commensal microbial communities. Previous studies have all focused on the effects of short term use of antibiotics. Here, we focus on the effects of long term use of antibiotic on gut microbiota and immunity. BALB/c mice received saline or different doses of ceftriaxone sodium (100, 200 and 400 mg/mL) via daily gavage for 150 days. Alterations of fecal microbiota, small intestine histopathology, body weight, spleen index, serum IgG, mucus SIgA, IFN-γ/IL-4 ratio, CD4/CD8 ratio and CD4+CD25+ cells were evaluated. Long term ceftriaxone sodium administration resulted in gut microbiota dysbiosis, intestine histological lesions, growth inhibition, spleen index reducing. The immune defense ability reduced as serum IgG and mucus SIgA decreased significantly. Not only the immune defense, long term ceftriaxone administration also affected immune regulation. The IFN-γ/IL-4 and CD4/CD8 ratios increased, the CD4+CD25+ cells reduced on days 30 and 60 after ceftriaxone administration. However, after 90 days of ceftriaxone administration, the IFN-γ/IL-4, CD4/CD8 ratios and CD4+CD25+ cells restored, which indicated a new balance of immune regulation had been formed. Overall, these findings contribute to our understanding of long term antibiotic administration influencing gut microbiota and immunity.
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Affiliation(s)
- Yanjie Guo
- Department of Microecology, School of Basic Medical Science, Dalian Medical University, Dalian, Liaoning, China
| | - Xuefei Yang
- Department of Microecology, School of Basic Medical Science, Dalian Medical University, Dalian, Liaoning, China
| | - Yane Qi
- Department of Microecology, School of Basic Medical Science, Dalian Medical University, Dalian, Liaoning, China
| | - Shu Wen
- Department of Microecology, School of Basic Medical Science, Dalian Medical University, Dalian, Liaoning, China
| | - Yinhui Liu
- Department of Microecology, School of Basic Medical Science, Dalian Medical University, Dalian, Liaoning, China
| | - Shaoying Tang
- The second clinical college, Dalian Medical University, Dalian, Liaoning, China
| | - Rongsheng Huang
- The second clinical college, Dalian Medical University, Dalian, Liaoning, China
| | - Li Tang
- Department of Microecology, School of Basic Medical Science, Dalian Medical University, Dalian, Liaoning, China
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38
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Raven KE, Reuter S, Reynolds R, Brodrick HJ, Russell JE, Török ME, Parkhill J, Peacock SJ. A decade of genomic history for healthcare-associated Enterococcus faecium in the United Kingdom and Ireland. Genome Res 2016; 26:1388-1396. [PMID: 27527616 PMCID: PMC5052055 DOI: 10.1101/gr.204024.116] [Citation(s) in RCA: 79] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Accepted: 08/15/2016] [Indexed: 01/07/2023]
Abstract
Vancomycin-resistant Enterococcus faecium (VREfm) is an important cause of healthcare-associated infections worldwide. We undertook whole-genome sequencing (WGS) of 495 E. faecium bloodstream isolates from 2001-2011 in the United Kingdom and Ireland (UK&I) and 11 E. faecium isolates from a reference collection. Comparison between WGS and multilocus sequence typing (MLST) identified major discrepancies for 17% of isolates, with multiple instances of the same sequence type (ST) being located in genetically distant positions in the WGS tree. This confirms that WGS is superior to MLST for evolutionary analyses and is more accurate than current typing methods used during outbreak investigations. E. faecium has been categorized as belonging to three clades (Clades A1, hospital-associated; A2, animal-associated; and B, community-associated). Phylogenetic analysis of our isolates replicated the distinction between Clade A (97% of isolates) and Clade B but did not support the subdivision of Clade A into Clade A1 and A2. Phylogeographic analyses revealed that Clade A had been introduced multiple times into each hospital referral network or country, indicating frequent movement of E. faecium between regions that rarely share hospital patients. Numerous genetic clusters contained highly related vanA-positive and -negative E. faecium, which implies that control of vancomycin-resistant enterococci (VRE) in hospitals also requires consideration of vancomycin-susceptible E. faecium Our findings reveal the evolution and dissemination of hospital-associated E. faecium in the UK&I and provide evidence for WGS as an instrument for infection control.
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Affiliation(s)
- Kathy E Raven
- University of Cambridge, Department of Medicine, Addenbrooke's Hospital, Cambridge CB2 0QQ, United Kingdom
| | - Sandra Reuter
- University of Cambridge, Department of Medicine, Addenbrooke's Hospital, Cambridge CB2 0QQ, United Kingdom; The Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, United Kingdom
| | - Rosy Reynolds
- British Society for Antimicrobial Chemotherapy, Birmingham B1 3NJ, United Kingdom; North Bristol NHS Trust, Southmead Hospital, Bristol, BS10 5NB, United Kingdom
| | - Hayley J Brodrick
- University of Cambridge, Department of Medicine, Addenbrooke's Hospital, Cambridge CB2 0QQ, United Kingdom
| | - Julie E Russell
- Culture Collections, Public Health England, Porton Down, Salisbury SP4 0JG, United Kingdom
| | - M Estée Török
- University of Cambridge, Department of Medicine, Addenbrooke's Hospital, Cambridge CB2 0QQ, United Kingdom; Public Health England, Clinical Microbiology and Public Health Laboratory, Addenbrooke's Hospital, Cambridge CB2 0QQ, United Kingdom; Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, United Kingdom
| | - Julian Parkhill
- The Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, United Kingdom
| | - Sharon J Peacock
- University of Cambridge, Department of Medicine, Addenbrooke's Hospital, Cambridge CB2 0QQ, United Kingdom; The Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, United Kingdom; Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, United Kingdom; London School of Hygiene and Tropical Medicine, London, WC1E 7HT, United Kingdom
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Guzman Prieto AM, van Schaik W, Rogers MRC, Coque TM, Baquero F, Corander J, Willems RJL. Global Emergence and Dissemination of Enterococci as Nosocomial Pathogens: Attack of the Clones? Front Microbiol 2016; 7:788. [PMID: 27303380 PMCID: PMC4880559 DOI: 10.3389/fmicb.2016.00788] [Citation(s) in RCA: 202] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Accepted: 05/09/2016] [Indexed: 12/13/2022] Open
Abstract
Enterococci are Gram-positive bacteria that are found in plants, soil and as commensals of the gastrointestinal tract of humans, mammals, and insects. Despite their commensal nature, they have also become globally important nosocomial pathogens. Within the genus Enterococcus, Enterococcus faecium, and Enterococcus faecalis are clinically most relevant. In this review, we will discuss how E. faecium and E. faecalis have evolved to become a globally disseminated nosocomial pathogen. E. faecium has a defined sub-population that is associated with hospitalized patients and is rarely encountered in community settings. These hospital-associated clones are characterized by the acquisition of adaptive genetic elements, including genes involved in metabolism, biofilm formation, and antibiotic resistance. In contrast to E. faecium, clones of E. faecalis isolated from hospitalized patients, including strains causing clinical infections, are not exclusively found in hospitals but are also present in healthy individuals and animals. This observation suggests that the division between commensals and hospital-adapted lineages is less clear for E. faecalis than for E. faecium. In addition, genes that are reported to be associated with virulence of E. faecalis are often not unique to clinical isolates, but are also found in strains that originate from commensal niches. As a reflection of more ancient association of E. faecalis with different hosts, these determinants Thus, they may not represent genuine virulence genes but may act as host-adaptive functions that are useful in a variety of intestinal environments. The scope of the review is to summarize recent trends in the emergence of antibiotic resistance and explore recent developments in the molecular epidemiology, population structure and mechanisms of adaptation of E. faecium and E. faecalis.
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Affiliation(s)
- Ana M Guzman Prieto
- Department of Medical Microbiology, University Medical Center Utrecht Utrecht, Netherlands
| | - Willem van Schaik
- Department of Medical Microbiology, University Medical Center Utrecht Utrecht, Netherlands
| | - Malbert R C Rogers
- Department of Medical Microbiology, University Medical Center Utrecht Utrecht, Netherlands
| | - Teresa M Coque
- Hospital Universitario Ramon y Cajal, Instituto Ramón y Cajal de Investigación SanitariaMadrid, Spain; CIBER Epidemiología y Salud PúblicaMadrid, Spain; Unidad de Resistencia a Antibióticos y Virulencia Bacteriana Asociada al Consejo Superior de Investigaciones CientíficasMadrid, Spain
| | - Fernando Baquero
- Hospital Universitario Ramon y Cajal, Instituto Ramón y Cajal de Investigación SanitariaMadrid, Spain; CIBER Epidemiología y Salud PúblicaMadrid, Spain; Unidad de Resistencia a Antibióticos y Virulencia Bacteriana Asociada al Consejo Superior de Investigaciones CientíficasMadrid, Spain
| | - Jukka Corander
- Department of Mathematics and Statistics, University of Helsinki Helsinki, Finland
| | - Rob J L Willems
- Department of Medical Microbiology, University Medical Center Utrecht Utrecht, Netherlands
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Schultz MB, Pham Thanh D, Tran Do Hoan N, Wick RR, Ingle DJ, Hawkey J, Edwards DJ, Kenyon JJ, Phu Huong Lan N, Campbell JI, Thwaites G, Thi Khanh Nhu N, Hall RM, Fournier-Level A, Baker S, Holt KE. Repeated local emergence of carbapenem-resistant Acinetobacter baumannii in a single hospital ward. Microb Genom 2016; 2:e000050. [PMID: 28348846 PMCID: PMC5320574 DOI: 10.1099/mgen.0.000050] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Accepted: 01/12/2016] [Indexed: 12/20/2022] Open
Abstract
We recently reported a dramatic increase in the prevalence of carbapenem-resistant Acinetobacter baumannii infections in the intensive care unit (ICU) of a Vietnamese hospital. This upsurge was associated with a specific oxa23-positive clone that was identified by multilocus VNTR analysis. Here, we used whole-genome sequence analysis to dissect the emergence of carbapenem-resistant A. baumannii causing ventilator-associated pneumonia (VAP) in the ICU during 2009–2012. To provide historical context and distinguish microevolution from strain introduction, we compared these genomes with those of A. baumannii asymptomatic carriage and VAP isolates from this same ICU collected during 2003–2007. We identified diverse lineages co-circulating over many years. Carbapenem resistance was associated with the presence of oxa23, oxa40, oxa58 and ndm1 genes in multiple lineages. The majority of resistant isolates were oxa23-positive global clone GC2; fine-scale phylogenomic analysis revealed five distinct GC2 sublineages within the ICU that had evolved locally via independent chromosomal insertions of oxa23 transposons. The increase in infections caused by carbapenem-resistant A. baumannii was associated with transposon-mediated transmission of a carbapenemase gene, rather than clonal expansion or spread of a carbapenemase-harbouring plasmid. Additionally, we found evidence of homologous recombination creating diversity within the local GC2 population, including several events resulting in replacement of the capsule locus. We identified likely donors of the imported capsule locus sequences amongst the A. baumannii isolated on the same ward, suggesting that diversification was largely facilitated via reassortment and sharing of genetic material within the localized A. baumannii population.
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Affiliation(s)
- Mark B Schultz
- 2Centre for Systems Genomics, University of Melbourne, Parkville, Victoria 3010, Australia.,1Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Duy Pham Thanh
- 3The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Nhu Tran Do Hoan
- 3The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Ryan R Wick
- 1Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3010, Australia.,2Centre for Systems Genomics, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Danielle J Ingle
- 1Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3010, Australia.,2Centre for Systems Genomics, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Jane Hawkey
- 1Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3010, Australia.,2Centre for Systems Genomics, University of Melbourne, Parkville, Victoria 3010, Australia
| | - David J Edwards
- 1Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3010, Australia.,2Centre for Systems Genomics, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Johanna J Kenyon
- 4School of Molecular Bioscience, University of Sydney, New South Wales, Australia.,5School of Biomedical Science, Queensland University of Technology, Queensland, Australia
| | - Nguyen Phu Huong Lan
- 3The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam.,6Centre for Tropical Medicine, Nuffield Department of Medicine, Oxford University, London, UK
| | - James I Campbell
- 3The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Guy Thwaites
- 3The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Nguyen Thi Khanh Nhu
- 3The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam.,6Centre for Tropical Medicine, Nuffield Department of Medicine, Oxford University, London, UK
| | - Ruth M Hall
- 4School of Molecular Bioscience, University of Sydney, New South Wales, Australia
| | | | - Stephen Baker
- 3The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam.,6Centre for Tropical Medicine, Nuffield Department of Medicine, Oxford University, London, UK
| | - Kathryn E Holt
- 1Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3010, Australia.,2Centre for Systems Genomics, University of Melbourne, Parkville, Victoria 3010, Australia
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