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Labecka L, Ķibilds J, Cīrulis A, Čeirāne ED, Zeltiņa I, Reinis A, Vilima B, Rudzīte D, Erts R, Mauliņa I, Bandere D, Krūmiņa A. Evaluation of Antimicrobial Resistancein Clinical Isolates of Enterococcus spp. Obtained from Hospital Patients in Latvia. MEDICINA (KAUNAS, LITHUANIA) 2024; 60:850. [PMID: 38929467 PMCID: PMC11206013 DOI: 10.3390/medicina60060850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Revised: 05/09/2024] [Accepted: 05/20/2024] [Indexed: 06/28/2024]
Abstract
Background and Objective: Enterococci are typically found in a healthy human gastrointestinal tract but can cause severe infections in immunocompromised patients. Such infections are treated with antibiotics. This study addresses the rising concern of antimicrobial resistance (AMR) in Enterococci, focusing on the prevalence of vancomycin-resistant enterococcus (VRE) strains. Materials and Methods: The pilot study involved 140 Enterococci isolates collected between 2021 and 2022 from two multidisciplinary hospitals (with and without local therapeutic drug monitoring protocol of vancomycin) in Latvia. Microbiological assays and whole genome sequencing were used. AMR gene prevalence with resistance profiles were determined and the genetic relationship and outbreak evaluation were made by applying core genome multi-locus sequence typing (cgMLST). Results: The acquired genes and mutations were responsible for resistance against 10 antimicrobial classes, including 25.0% of isolates expressing resistance to vancomycin, predominantly of the vanB type. Genetic diversity among E. faecalis and E. faecium isolates was observed and seven potential outbreak clusters were identified, three of them containing sequence types ST6, ST78 and ST80. The prevalence of vancomycin resistance was highest in the hospital without a therapeutic drug-monitoring protocol and in E. faecium. Notably, a case of linezolid resistance due to a mutation was documented. Conclusions: The study illustrates the concerning prevalence of multidrug-resistant Enterococci in Latvian hospitals, showcasing the rather widespread occurrence of vancomycin-resistant strains. This highlights the urgency of implementing efficient infection control mechanisms and the need for continuous VRE surveillance in Latvia to define the scope and pattern of the problem, influencing clinical decision making and planning further preventative measures.
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Affiliation(s)
- Linda Labecka
- Institute of Food Safety, Animal Health and Environment “BIOR”, Lejupes Street 3, LV-1076 Riga, Latvia (A.C.); (A.K.)
| | - Juris Ķibilds
- Institute of Food Safety, Animal Health and Environment “BIOR”, Lejupes Street 3, LV-1076 Riga, Latvia (A.C.); (A.K.)
| | - Aivars Cīrulis
- Institute of Food Safety, Animal Health and Environment “BIOR”, Lejupes Street 3, LV-1076 Riga, Latvia (A.C.); (A.K.)
- Faculty of Biology, University of Latvia, Jelgavas Street 1, LV-1004 Riga, Latvia
| | - Evelīna Diāna Čeirāne
- Faculty of Medicine, Riga Stradins University, Dzirciema Street 16, LV-1007 Riga, Latvia
| | - Indra Zeltiņa
- Department of Infectology, Riga Stradiņš University, Dzirciema Street 16, LV-1007 Riga, Latvia;
- Riga East Clinical University Hospital, Hipokrata Street 2, LV-1038 Riga, Latvia; (D.R.); (I.M.)
| | - Aigars Reinis
- Department of Biology and Microbiology, Riga Stradiņš University, Dzirciema Street 16, LV-1007 Riga, Latvia;
- Pauls Stradiņš Clinical University Hospital, Pilsoņu Street 13, LV-1002 Riga, Latvia
| | - Barba Vilima
- Vidzeme Hospital, Jumaras Street 195, LV-4201 Valmiera, Latvia;
| | - Dace Rudzīte
- Riga East Clinical University Hospital, Hipokrata Street 2, LV-1038 Riga, Latvia; (D.R.); (I.M.)
| | - Renārs Erts
- Faculty of Medicine, University of Latvia, Raiņa bulvāris 19, LV-1586 Riga, Latvia;
| | - Inga Mauliņa
- Riga East Clinical University Hospital, Hipokrata Street 2, LV-1038 Riga, Latvia; (D.R.); (I.M.)
- Vidzeme Hospital, Jumaras Street 195, LV-4201 Valmiera, Latvia;
- Department of Pharmaceutical Chemistry, Riga Stradiņš University, LV-1007 Riga, Latvia;
| | - Dace Bandere
- Department of Pharmaceutical Chemistry, Riga Stradiņš University, LV-1007 Riga, Latvia;
- Baltic Biomaterials Centre of Excellence, Headquarters at Riga Technical University, LV-1658 Riga, Latvia
| | - Angelika Krūmiņa
- Institute of Food Safety, Animal Health and Environment “BIOR”, Lejupes Street 3, LV-1076 Riga, Latvia (A.C.); (A.K.)
- Department of Infectology, Riga Stradiņš University, Dzirciema Street 16, LV-1007 Riga, Latvia;
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Meijers E, Verhees FB, Heemskerk D, Wessels E, Claas ECJ, Boers SA. Automating the Illumina DNA library preparation kit for whole genome sequencing applications on the flowbot ONE liquid handler robot. Sci Rep 2024; 14:8159. [PMID: 38589623 PMCID: PMC11001922 DOI: 10.1038/s41598-024-58963-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Accepted: 04/05/2024] [Indexed: 04/10/2024] Open
Abstract
Whole-genome sequencing (WGS) is currently making its transition from research tool into routine (clinical) diagnostic practice. The workflow for WGS includes the highly labor-intensive library preparations (LP), one of the most critical steps in the WGS procedure. Here, we describe the automation of the LP on the flowbot ONE robot to minimize the risk of human error and reduce hands-on time (HOT). For this, the robot was equipped, programmed, and optimized to perform the Illumina DNA Prep automatically. Results obtained from 16 LP that were performed both manually and automatically showed comparable library DNA yields (median of 1.5-fold difference), similar assembly quality values, and 100% concordance on the final core genome multilocus sequence typing results. In addition, reproducibility of results was confirmed by re-processing eight of the 16 LPs using the automated workflow. With the automated workflow, the HOT was reduced to 25 min compared to the 125 min needed when performing eight LPs using the manual workflow. The turn-around time was 170 and 200 min for the automated and manual workflow, respectively. In summary, the automated workflow on the flowbot ONE generates consistent results in terms of reliability and reproducibility, while significantly reducing HOT as compared to manual LP.
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Affiliation(s)
- Erin Meijers
- Department of Medical Microbiology, Leiden University Medical Center, Albinusdreef 2, 2333 ZA, Leiden, The Netherlands
| | - Fabienne B Verhees
- Department of Medical Microbiology, Leiden University Medical Center, Albinusdreef 2, 2333 ZA, Leiden, The Netherlands
| | - Dennis Heemskerk
- Department of Medical Microbiology, Leiden University Medical Center, Albinusdreef 2, 2333 ZA, Leiden, The Netherlands
| | - Els Wessels
- Department of Medical Microbiology, Leiden University Medical Center, Albinusdreef 2, 2333 ZA, Leiden, The Netherlands
| | - Eric C J Claas
- Department of Medical Microbiology, Leiden University Medical Center, Albinusdreef 2, 2333 ZA, Leiden, The Netherlands
| | - Stefan A Boers
- Department of Medical Microbiology, Leiden University Medical Center, Albinusdreef 2, 2333 ZA, Leiden, The Netherlands.
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Al Rubaye M, Janice J, Bjørnholt JV, Löhr IH, Sundsfjord A, Hegstad K. The first vanE-type vancomycin resistant Enterococcus faecalis isolates in Norway - phenotypic and molecular characteristics. J Glob Antimicrob Resist 2024; 36:193-199. [PMID: 38154751 DOI: 10.1016/j.jgar.2023.12.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 12/12/2023] [Accepted: 12/19/2023] [Indexed: 12/30/2023] Open
Abstract
OBJECTIVES We aimed to characterize the vanE cluster and its genetic support in the first Norwegian vanE-type isolates and assess genetic relatedness to other vanE isolates. METHODS Two vanE-type vancomycin resistant Enterococcus faecalis (vanE-VREfs) isolates (E1 and E2) recovered from the same patient 30 months apart were examined for antimicrobial susceptibility, genome sequence, vancomycin resistance induction, vanE transferability, genome mutation rate, and phylogenetic relationship to E. faecalis closed genomes and two vanE-VREfs from North America. RESULTS The ST34 E1 and E2 strains expressed low-level vancomycin resistance and susceptibility to teicoplanin. Their vanE gene clusters were part of a non-transferable Tn6202. The histidine kinase part of vanSE was expressed although a premature stop codon (E1) and insertion of a transposase (E2) truncated their vanSE gene. The vancomycin resistance phenotype in E1 was inducible while constitutive in E2. E1 showed a 125-fold higher mutation rate than E2. Variant calling showed 60 variants but nearly identical chromosomal gene content and synteny between the isolates. Their genomes also showed high similarity to another ST34 vanE-VREfs from Canada. CONCLUSION In-depth genomic analyses of the first two vanE-VREfs found in Europe identified a single chromosomal insertion site of two variants of vanE-conferring Tn6202. Single nucleotide polymorphism (SNP) and core genome multilocus sequence type (cgMLST) analyses show the genomes are different. This can be explained by the high mutation rate of E1 and acquisition of different mobile genetic elements; thus, we believe the two isolates from the same patient are genetically related. Genome similarities also suggest relatedness between the Canadian and Norwegian vanE-VREfs.
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Affiliation(s)
- Mushtaq Al Rubaye
- Research group for Host-Microbe Interactions, Department of Medical Biology, UiT The Arctic University of Norway, Tromsø, Norway
| | - Jessin Janice
- Research group for Host-Microbe Interactions, Department of Medical Biology, UiT The Arctic University of Norway, Tromsø, Norway; Norwegian National Advisory Unit on Detection of Antimicrobial Resistance, Department of Microbiology and Infection Control, University Hospital of North Norway, Tromsø, Norway
| | - Jørgen Vildershøj Bjørnholt
- Department of Clinical Microbiology, Oslo University Hospital, Oslo, Norway; Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Iren H Löhr
- Department of Medical Microbiology, Stavanger University Hospital, Stavanger, Norway; Department of Clinical Science, Faculty of Medicine, University of Bergen, Bergen, Norway
| | - Arnfinn Sundsfjord
- Research group for Host-Microbe Interactions, Department of Medical Biology, UiT The Arctic University of Norway, Tromsø, Norway; Norwegian National Advisory Unit on Detection of Antimicrobial Resistance, Department of Microbiology and Infection Control, University Hospital of North Norway, Tromsø, Norway
| | - Kristin Hegstad
- Research group for Host-Microbe Interactions, Department of Medical Biology, UiT The Arctic University of Norway, Tromsø, Norway; Norwegian National Advisory Unit on Detection of Antimicrobial Resistance, Department of Microbiology and Infection Control, University Hospital of North Norway, Tromsø, Norway.
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AL Rubaye M, Janice J, Bjørnholt JV, Kacelnik O, Haldorsen BC, Nygaard RM, Hegstad J, Sundsfjord A, Hegstad K. The population structure of vancomycin-resistant and -susceptible Enterococcus faecium in a low-prevalence antimicrobial resistance setting is highly influenced by circulating global hospital-associated clones. Microb Genom 2023; 9:001160. [PMID: 38112685 PMCID: PMC10763505 DOI: 10.1099/mgen.0.001160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 12/01/2023] [Indexed: 12/21/2023] Open
Abstract
Between 2010 and 2015 the incidence of vancomycin-resistant Enterococcus faecium (VREfm) in Norway increased dramatically. Hence, we selected (1) a random subset of vancomycin-resistant enterococci (VRE) from the Norwegian Surveillance System for Communicable Diseases (2010-15; n=239) and (2) Norwegian vancomycin-susceptible E. faecium (VSEfm) bacteraemia isolates from the national surveillance system for antimicrobial resistance in microbes (2008 and 2014; n=261) for further analysis. Whole-genome sequences were collected for population structure, van gene cluster, mobile genetic element and virulome analysis, as well as antimicrobial susceptibility testing. Comparative genomic and phylogeographical analyses were performed with complete genomes of global E. faecium strains from the National Center for Biotechnology Information (NCBI) (1946-2022; n=272). All Norwegian VREfm and most of the VSEfm clustered with global hospital-associated sequence types (STs) in the phylogenetic subclade A1. The vanB2 subtype carried by chromosomal Tn1549 integrative conjugative elements was the dominant van type. The major Norwegian VREfm cluster types (CTs) were in accordance with concurrent European CTs. The dominant vanB-type VREfm CTs, ST192-CT3/26 and ST117-CT24, were mostly linked to a single hospital in Norway where the clones spread after independent chromosomal acquisition of Tn1549. The less prevalent vanA VRE were associated with more diverse CTs and vanA carrying Inc18 or RepA_N plasmids with toxin-antitoxin systems. Only 5 % of the Norwegian VRE were Enterococcus faecalis, all of which contained vanB. The Norwegian VREfm and VSEfm isolates harboured CT-specific virulence factor (VF) profiles supporting biofilm formation and colonization. The dominant VREfm CTs in general hosted more virulence determinants than VSEfm. The phylogenetic clade B VSEfm isolates (n=21), recently classified as Enterococcus lactis, harboured fewer VFs than E. faecium in general, and particularly subclade A1 isolates. In conclusion, the population structure of Norwegian E. faecium isolates mirrors the globally prevalent clones and particularly concurrent European VREfm/VSEfm CTs. Novel chromosomal acquisition of vanB2 on Tn1549 from the gut microbiota, however, formed a single major hospital VREfm outbreak. Dominant VREfm CTs contained more VFs than VSEfm.
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Affiliation(s)
- Mushtaq AL Rubaye
- Research group for Host–Microbe Interactions, Department of Medical Biology, UiT The Arctic University of Norway, Tromsø, Norway
| | - Jessin Janice
- Research group for Host–Microbe Interactions, Department of Medical Biology, UiT The Arctic University of Norway, Tromsø, Norway
- Norwegian National Advisory Unit on Detection of Antimicrobial Resistance, Department of Microbiology and Infection Control, University Hospital of North Norway, Tromsø, Norway
- Present address: Section for development, Department of Microbiology, Clinic for Laboratory Medicine, Oslo University Hospital, Oslo, Norway
| | - Jørgen Vildershøj Bjørnholt
- Department of Clinical Microbiology, Oslo University Hospital, Oslo, Norway
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Oliver Kacelnik
- Department of Antibiotic Resistance and Infection Prevention, Norwegian Institute of Public Health, Oslo, Norway
| | - Bjørg C. Haldorsen
- Norwegian National Advisory Unit on Detection of Antimicrobial Resistance, Department of Microbiology and Infection Control, University Hospital of North Norway, Tromsø, Norway
| | - Randi M. Nygaard
- Department of Microbiology, Haukeland University Hospital, Bergen, Norway
| | - Joachim Hegstad
- Department of Microbiology and Infection Control, University Hospital of North Norway, Tromsø, Norway
| | - Arnfinn Sundsfjord
- Research group for Host–Microbe Interactions, Department of Medical Biology, UiT The Arctic University of Norway, Tromsø, Norway
- Norwegian National Advisory Unit on Detection of Antimicrobial Resistance, Department of Microbiology and Infection Control, University Hospital of North Norway, Tromsø, Norway
| | - Kristin Hegstad
- Research group for Host–Microbe Interactions, Department of Medical Biology, UiT The Arctic University of Norway, Tromsø, Norway
- Norwegian National Advisory Unit on Detection of Antimicrobial Resistance, Department of Microbiology and Infection Control, University Hospital of North Norway, Tromsø, Norway
| | - the Norwegian VRE study group
- Research group for Host–Microbe Interactions, Department of Medical Biology, UiT The Arctic University of Norway, Tromsø, Norway
- Norwegian National Advisory Unit on Detection of Antimicrobial Resistance, Department of Microbiology and Infection Control, University Hospital of North Norway, Tromsø, Norway
- Department of Clinical Microbiology, Oslo University Hospital, Oslo, Norway
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Department of Antibiotic Resistance and Infection Prevention, Norwegian Institute of Public Health, Oslo, Norway
- Department of Microbiology, Haukeland University Hospital, Bergen, Norway
- Department of Microbiology and Infection Control, University Hospital of North Norway, Tromsø, Norway
- Present address: Section for development, Department of Microbiology, Clinic for Laboratory Medicine, Oslo University Hospital, Oslo, Norway
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Pereira AP, Antunes P, Bierge P, Willems RJL, Corander J, Coque TM, Pich OQ, Peixe L, Freitas AR, Novais C. Unraveling Enterococcus susceptibility to quaternary ammonium compounds: genes, phenotypes, and the impact of environmental conditions. Microbiol Spectr 2023; 11:e0232423. [PMID: 37737589 PMCID: PMC10581157 DOI: 10.1128/spectrum.02324-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2023] [Accepted: 07/24/2023] [Indexed: 09/23/2023] Open
Abstract
Quaternary ammonium compounds (QACs) have been extensively used in the community, healthcare facilities, and food chain, in concentrations between 20 and 30,000 mg/L. Enterococcus faecalis and Enterococcus faecium are ubiquitous in these settings and are recognized as nosocomial pathogens worldwide, but QACs' activity against strains from diverse epidemiological and genomic backgrounds remained largely unexplored. We evaluated the role of Enterococcus isolates from different sources, years, and clonal lineages as hosts of QACs tolerance genes and their susceptibility to QACs in optimal, single-stress and cross-stress growth conditions. Only 1% of the Enterococcus isolates included in this study and 0.5% of publicly available Enterococcus genomes carried qacA/B, qacC, qacG, qacJ, qacZ, qrg, bcrABC or oqxAB genes, shared with >60 species of Bacillota, Pseudomonadota, Actinomycetota, or Spirochaetota. These genes were generally found within close proximity of antibiotics and/or metals resistance genes. The minimum inhibitory concentrations (MIC) and minimum bactericidal concentrations (MBC) of benzalkonium chloride (BC) and didecyldimethylammonium chloride ranged between 0.5 and 4 mg/L (microdilution: 37°C/20 h/pH = 7/aerobiosis) for 210 E. faecalis and E. faecium isolates (two isolates carrying qacZ). Modified growth conditions (e.g., 22°C/pH = 5) increased MICBC/MBCBC (maximum of eightfold and MBCBC = 16 mg/L) and changed bacterial growth kinetics under BC toward later stationary phases in both species, including in isolates without QACs tolerance genes. In conclusion, Enterococcus are susceptible to in-use QACs concentrations and rarely carry QACs tolerance genes. However, their potential gene exchange with different microbiota, the decreased susceptibility to QACs under specific environmental conditions, and the presence of subinhibitory QACs concentrations in various settings may contribute to the selection of particular strains and, thus, require a One Health strategy to maintain QACs effectiveness. IMPORTANCE Despite the increasing use of quaternary ammonium compounds (QACs), the susceptibility of pathogens to these antimicrobials remains largely unknown. Enterococcus faecium and Enterococcus faecalis are susceptible to in-use QACs concentrations and are not main hosts of QACs tolerance genes but participate in gene transfer pathways with diverse bacterial taxa exposed to these biocides. Moreover, QACs tolerance genes often share the same genetic contexts with antibiotics and/or metals resistance genes, raising concerns about potential co-selection events. E. faecium and E. faecalis showed increased tolerance to benzalkonium chloride under specific environmental conditions (22°C, pH = 5), suggesting that strains might be selected in settings where they occur along with subinhibitory QACs concentrations. Transcriptomic studies investigating the cellular mechanisms of Enterococcus adaptation to QACs tolerance, along with longitudinal metadata analysis of tolerant populations dynamics under the influence of diverse environmental factors, are essential and should be prioritized within a One Health strategy.
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Affiliation(s)
- Ana P. Pereira
- UCIBIO-Applied Molecular Biosciences Unit, Laboratory of Microbiology, Faculty of Pharmacy, University of Porto, Porto, Portugal
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, Laboratory of Microbiology, Faculty of Pharmacy, University of Porto, Porto, Portugal
| | - Patrícia Antunes
- UCIBIO-Applied Molecular Biosciences Unit, Laboratory of Microbiology, Faculty of Pharmacy, University of Porto, Porto, Portugal
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, Laboratory of Microbiology, Faculty of Pharmacy, University of Porto, Porto, Portugal
- Faculty of Nutrition and Food Sciences, University of Porto, Porto, Portugal
| | - Paula Bierge
- Laboratori de Recerca en Microbiologia i Malalties Infeccioses, Parc Taulí Hospital Universitari, Institut d’Investigació i Innovació Parc Taulí (I3PT-CERCA), Universitat Autònoma de Barcelona, Sabadell, Spain
- Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Rob J. L. Willems
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Jukka Corander
- Department of Biostatistics, Faculty of Medicine, University of Oslo, Oslo, Norway
- Parasites and Microbes, Wellcome Sanger Institute, Cambridge, UK
- Department of Mathematics and Statistics, Helsinki Institute of Information Technology, University of Helsinki, Helsinki, Finland
| | - Teresa M. Coque
- Servicio de Microbiologia, Hospital Universitario Ramón y Cajal, Madrid, Spain
- Centro de Investigación Biomédica en Enfermedades Infecciosas (CIBERINFEC), Madrid, Spain
| | - Oscar Q. Pich
- Laboratori de Recerca en Microbiologia i Malalties Infeccioses, Parc Taulí Hospital Universitari, Institut d’Investigació i Innovació Parc Taulí (I3PT-CERCA), Universitat Autònoma de Barcelona, Sabadell, Spain
- Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Luisa Peixe
- UCIBIO-Applied Molecular Biosciences Unit, Laboratory of Microbiology, Faculty of Pharmacy, University of Porto, Porto, Portugal
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, Laboratory of Microbiology, Faculty of Pharmacy, University of Porto, Porto, Portugal
| | - Ana R. Freitas
- UCIBIO-Applied Molecular Biosciences Unit, Laboratory of Microbiology, Faculty of Pharmacy, University of Porto, Porto, Portugal
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, Laboratory of Microbiology, Faculty of Pharmacy, University of Porto, Porto, Portugal
- 1H-TOXRUN, One Health Toxicology Research Unit, University Institute of Health Sciences, CESPU, CRL., Gandra, Portugal
| | - Carla Novais
- UCIBIO-Applied Molecular Biosciences Unit, Laboratory of Microbiology, Faculty of Pharmacy, University of Porto, Porto, Portugal
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, Laboratory of Microbiology, Faculty of Pharmacy, University of Porto, Porto, Portugal
| | - from the ESCMID Study Group on Food- and Water-borne Infections (EFWISG)
- UCIBIO-Applied Molecular Biosciences Unit, Laboratory of Microbiology, Faculty of Pharmacy, University of Porto, Porto, Portugal
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, Laboratory of Microbiology, Faculty of Pharmacy, University of Porto, Porto, Portugal
- Faculty of Nutrition and Food Sciences, University of Porto, Porto, Portugal
- Laboratori de Recerca en Microbiologia i Malalties Infeccioses, Parc Taulí Hospital Universitari, Institut d’Investigació i Innovació Parc Taulí (I3PT-CERCA), Universitat Autònoma de Barcelona, Sabadell, Spain
- Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Bellaterra, Spain
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, the Netherlands
- Department of Biostatistics, Faculty of Medicine, University of Oslo, Oslo, Norway
- Parasites and Microbes, Wellcome Sanger Institute, Cambridge, UK
- Department of Mathematics and Statistics, Helsinki Institute of Information Technology, University of Helsinki, Helsinki, Finland
- Servicio de Microbiologia, Hospital Universitario Ramón y Cajal, Madrid, Spain
- Centro de Investigación Biomédica en Enfermedades Infecciosas (CIBERINFEC), Madrid, Spain
- 1H-TOXRUN, One Health Toxicology Research Unit, University Institute of Health Sciences, CESPU, CRL., Gandra, Portugal
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Monteiro Marques J, Coelho M, Santana AR, Pinto D, Semedo-Lemsaddek T. Dissemination of Enterococcal Genetic Lineages: A One Health Perspective. Antibiotics (Basel) 2023; 12:1140. [PMID: 37508236 PMCID: PMC10376465 DOI: 10.3390/antibiotics12071140] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 06/22/2023] [Accepted: 06/29/2023] [Indexed: 07/30/2023] Open
Abstract
Enterococcus spp. are commensals of the gastrointestinal tracts of humans and animals and colonize a variety of niches such as water, soil, and food. Over the last three decades, enterococci have evolved as opportunistic pathogens, being considered ESKAPE pathogens responsible for hospital-associated infections. Enterococci's ubiquitous nature, excellent adaptative capacity, and ability to acquire virulence and resistance genes make them excellent sentinel proxies for assessing the presence/spread of pathogenic and virulent clones and hazardous determinants across settings of the human-animal-environment triad, allowing for a more comprehensive analysis of the One Health continuum. This review provides an overview of enterococcal fitness and pathogenic traits; the most common clonal complexes identified in clinical, veterinary, food, and environmental sources; as well as the dissemination of pathogenic genomic traits (virulome, resistome, and mobilome) found in high-risk clones worldwide, across the One Health continuum.
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Affiliation(s)
- Joana Monteiro Marques
- Centre for Interdisciplinary Research in Animal Health (CIISA), Faculty of Veterinary Medicine, University of Lisbon, Av. da Universidade Técnica de Lisboa, 1300-477 Lisbon, Portugal
- Associate Laboratory for Animal and Veterinary Sciences (AL4AnimalS), 1300-477 Lisbon, Portugal
| | - Mariana Coelho
- Centre for Interdisciplinary Research in Animal Health (CIISA), Faculty of Veterinary Medicine, University of Lisbon, Av. da Universidade Técnica de Lisboa, 1300-477 Lisbon, Portugal
- Associate Laboratory for Animal and Veterinary Sciences (AL4AnimalS), 1300-477 Lisbon, Portugal
| | - Andressa Rodrigues Santana
- Centre for Interdisciplinary Research in Animal Health (CIISA), Faculty of Veterinary Medicine, University of Lisbon, Av. da Universidade Técnica de Lisboa, 1300-477 Lisbon, Portugal
- Associate Laboratory for Animal and Veterinary Sciences (AL4AnimalS), 1300-477 Lisbon, Portugal
| | - Daniel Pinto
- Centre for Interdisciplinary Research in Animal Health (CIISA), Faculty of Veterinary Medicine, University of Lisbon, Av. da Universidade Técnica de Lisboa, 1300-477 Lisbon, Portugal
- Associate Laboratory for Animal and Veterinary Sciences (AL4AnimalS), 1300-477 Lisbon, Portugal
| | - Teresa Semedo-Lemsaddek
- Centre for Interdisciplinary Research in Animal Health (CIISA), Faculty of Veterinary Medicine, University of Lisbon, Av. da Universidade Técnica de Lisboa, 1300-477 Lisbon, Portugal
- Associate Laboratory for Animal and Veterinary Sciences (AL4AnimalS), 1300-477 Lisbon, Portugal
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Web-based prediction of antimicrobial resistance in enterococcal clinical isolates by whole-genome sequencing. Eur J Clin Microbiol Infect Dis 2023; 42:67-76. [PMID: 36378364 DOI: 10.1007/s10096-022-04527-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 11/07/2022] [Indexed: 11/16/2022]
Abstract
Besides phenotypic antimicrobial susceptibility testing (AST), whole genome sequencing (WGS) is a promising alternative approach for detection of resistance phenotypes. The aim of this study was to investigate the concordance between WGS-based resistance prediction and phenotypic AST results for enterococcal clinical isolates using a user-friendly online tools and databases. A total of 172 clinical isolates (34 E. faecalis, 138 E. faecium) received at the French National Reference Center for enterococci from 2017 to 2020 were included. AST was performed by disc diffusion or MIC determination for 14 antibiotics according to CA-SFM/EUCAST guidelines. The genome of all strains was sequenced using the Illumina technology (MiSeq) with bioinformatic analysis from raw reads using online tools ResFinder 4.1 and LRE-finder 1.0. For both E. faecalis and E. faecium, performances of WGS-based genotype to predict resistant phenotypes were excellent (concordance > 90%), particularly for antibiotics commonly used for treatment of enterococcal infections such as ampicillin, gentamicin, vancomycin, teicoplanin, and linezolid. Note that 100% very major errors were found for quinupristin-dalfopristin, tigecycline, and rifampicin for which resistance mutations are not included in databases. Also, it was not possible to predict phenotype from genotype for daptomycin for the same reason. WGS combined with online tools could be easily used by non-expert clinical microbiologists as a rapid and reliable tool for prediction of phenotypic resistance to first-line antibiotics among enterococci. Nonetheless, some improvements should be made such as the implementation of resistance mutations in the database for some antibiotics.
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Tonkin-Hill G, Gladstone RA, Pöntinen AK, Arredondo-Alonso S, Bentley SD, Corander J. Robust analysis of prokaryotic pangenome gene gain and loss rates with Panstripe. Genome Res 2023; 33:129-140. [PMID: 36669850 PMCID: PMC9977150 DOI: 10.1101/gr.277340.122] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2022] [Accepted: 12/14/2022] [Indexed: 01/21/2023]
Abstract
Horizontal gene transfer (HGT) plays a critical role in the evolution and diversification of many microbial species. The resulting dynamics of gene gain and loss can have important implications for the development of antibiotic resistance and the design of vaccine and drug interventions. Methods for the analysis of gene presence/absence patterns typically do not account for errors introduced in the automated annotation and clustering of gene sequences. In particular, methods adapted from ecological studies, including the pangenome gene accumulation curve, can be misleading as they may reflect the underlying diversity in the temporal sampling of genomes rather than a difference in the dynamics of HGT. Here, we introduce Panstripe, a method based on generalized linear regression that is robust to population structure, sampling bias, and errors in the predicted presence/absence of genes. We show using simulations that Panstripe can effectively identify differences in the rate and number of genes involved in HGT events, and illustrate its capability by analyzing several diverse bacterial genome data sets representing major human pathogens.
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Affiliation(s)
- Gerry Tonkin-Hill
- Department of Biostatistics, University of Oslo, 0372 Blindern, Norway;,Parasites and Microbes, Wellcome Sanger Institute, Cambridge CB10 1RQ, United Kingdom
| | | | - Anna K. Pöntinen
- Department of Biostatistics, University of Oslo, 0372 Blindern, Norway
| | - Sergio Arredondo-Alonso
- Department of Biostatistics, University of Oslo, 0372 Blindern, Norway;,Parasites and Microbes, Wellcome Sanger Institute, Cambridge CB10 1RQ, United Kingdom
| | - Stephen D. Bentley
- Parasites and Microbes, Wellcome Sanger Institute, Cambridge CB10 1RQ, United Kingdom
| | - Jukka Corander
- Department of Biostatistics, University of Oslo, 0372 Blindern, Norway;,Parasites and Microbes, Wellcome Sanger Institute, Cambridge CB10 1RQ, United Kingdom;,Helsinki Institute for Information Technology HIIT, Department of Mathematics and Statistics, University of Helsinki, 00014 Helsinki, Finland
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9
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Rebelo A, Duarte B, Ferreira C, Mourão J, Ribeiro S, Freitas AR, Coque TM, Willems R, Corander J, Peixe L, Antunes P, Novais C. Enterococcus spp. from chicken meat collected 20 years apart overcome multiple stresses occurring in the poultry production chain: Antibiotics, copper and acids. Int J Food Microbiol 2023; 384:109981. [DOI: 10.1016/j.ijfoodmicro.2022.109981] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 10/03/2022] [Accepted: 10/11/2022] [Indexed: 11/06/2022]
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10
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Wang Z, Gu C, Sun L, Zhao F, Fu Y, Di L, Zhang J, Zhuang H, Jiang S, Wang H, Zhu F, Chen Y, Chen M, Ling X, Chen Y, Yu Y. Development of a novel core genome MLST scheme for tracing multidrug resistant Staphylococcus capitis. Nat Commun 2022; 13:4254. [PMID: 35869070 PMCID: PMC9307846 DOI: 10.1038/s41467-022-31908-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 07/08/2022] [Indexed: 11/09/2022] Open
Abstract
Staphylococcus capitis, which causes bloodstream infections in neonatal intensive care units, is a common cause of healthcare-associated infections. Thus, a standardized high-resolution typing method to document the transmission and dissemination of multidrug-resistant S. capitis isolates is required. We aimed to establish a core genome multilocus sequence typing (cgMLST) scheme to surveil S. capitis. The cgMLST scheme was defined based on primary and validation genome sets and tested with outbreaks of linezolid-resistant isolates and a validation set. Phylogenetic analysis was performed to investigate the population structure and compare it with the result of cgMLST analysis. The S. capitis population consists of 1 dominant, NRCS-A, and 4 less common clones. In this work, a multidrug-resistant clone (L clone) with linezolid resistance is identified. With the features of type III SCCmec and multiple copies of mutations of G2576T and C2104T in the 23S rRNA, the L clone has been spreading silently across China. Staphylococcus capitis is a common causative agent of bloodstream infections in neonatal intensive care units, with multidrug resistant isolates complicating treatment. Authors aimed to establish a core genome multilocus sequence typing (cgMLST) scheme to document the transmission and dissemination of multidrug-resistant S. capitis isolates.
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11
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Ramadan AA. Bacterial typing methods from past to present: A comprehensive overview. GENE REPORTS 2022. [DOI: 10.1016/j.genrep.2022.101675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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12
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Brangsch H, Singha H, Laroucau K, Elschner M. Sequence-based detection and typing procedures for Burkholderia mallei: Assessment and prospects. Front Vet Sci 2022; 9:1056996. [PMID: 36452150 PMCID: PMC9703372 DOI: 10.3389/fvets.2022.1056996] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 10/26/2022] [Indexed: 10/28/2023] Open
Abstract
Although glanders has been eradicated in most of the developed world, the disease still persists in various countries such as Brazil, India, Pakistan, Bangladesh, Nepal, Iran, Bahrain, UAE and Turkey. It is one of the notifiable diseases listed by the World Organization for Animal Health. Occurrence of glanders imposes restriction on equestrian events and restricts equine movement, thus causing economic losses to equine industry. The genetic diversity and global distribution of the causing agent, Burkholderia (B.) mallei, have not been assessed in detail and are complicated by the high clonality of this organism. Among the identification and typing methods, PCR-based methods for distinguishing B. mallei from its close relative B. pseudomallei as well as genotyping using tandem repeat regions (MLVA) are established. The advent and continuous advancement of the sequencing techniques and the reconstruction of closed genomes enable the development of genome guided epidemiological tools. For achieving a higher genomic resolution, genotyping methods based on whole genome sequencing data can be employed, like genome-wide single nucleotide polymorphisms. One of the limitations in obtaining complete genomic sequences for further molecular characterization of B. mallei is its high GC content. In this review, we aim to provide an overview of the widely used detection and typing methods for B. mallei and illustrate gaps that still require development. The genomic features of Burkholderia, their high homology and clonality will be first described from a comparative genomics perspective. Then, the commonly used molecular detection (PCR systems) and typing systems (e.g., multilocus sequence typing, variable number of tandem repeat analysis) will be presented and put in perspective with recently developed genomic methods. Also, the increasing availability of B. mallei genomic sequences and evolution of the sequencing methods offers exciting prospects for further refinement of B. mallei typing, that could overcome the difficulties presently encountered with this particular bacterium.
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Affiliation(s)
- Hanka Brangsch
- Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institut – Federal Research Institute for Animal Health, Jena, Germany
| | | | - Karine Laroucau
- Bacterial Zoonosis Unit, Animal Health Laboratory, French Food Agency (Anses), Maisons-Alfort, France
| | - Mandy Elschner
- Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institut – Federal Research Institute for Animal Health, Jena, Germany
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13
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Cabal A, Rab G, Daza-Prieto B, Stöger A, Peischl N, Chakeri A, Mo SS, Bock H, Fuchs K, Sucher J, Rathammer K, Hasenberger P, Stadtbauer S, Caniça M, Strauß P, Allerberger F, Wögerbauer M, Ruppitsch W. Characterizing Antimicrobial Resistance in Clinically Relevant Bacteria Isolated at the Human/Animal/Environment Interface Using Whole-Genome Sequencing in Austria. Int J Mol Sci 2022; 23:ijms231911276. [PMID: 36232576 PMCID: PMC9570485 DOI: 10.3390/ijms231911276] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 09/19/2022] [Accepted: 09/20/2022] [Indexed: 11/16/2022] Open
Abstract
Antimicrobial resistance (AMR) is a public health issue attributed to the misuse of antibiotics in human and veterinary medicine. Since AMR surveillance requires a One Health approach, we sampled nine interconnected compartments at a hydrological open-air lab (HOAL) in Austria to obtain six bacterial species included in the WHO priority list of antibiotic-resistant bacteria (ARB). Whole genome sequencing-based typing included core genome multilocus sequence typing (cgMLST). Genetic and phenotypic characterization of AMR was performed for all isolates. Eighty-nine clinically-relevant bacteria were obtained from eight compartments including 49 E. coli, 27 E. faecalis, 7 K. pneumoniae and 6 E. faecium. Clusters of isolates from the same species obtained in different sample collection dates were detected. Of the isolates, 29.2% were resistant to at least one antimicrobial. E. coli and E. faecalis isolates from different compartments had acquired antimicrobial resistance genes (ARGs) associated with veterinary drugs such as aminoglycosides and tetracyclines, some of which were carried in conjugative and mobilizable plasmids. Three multidrug resistant (MDR) E. coli isolates were found in samples from field drainage and wastewater. Early detection of ARGs and ARB in natural and farm-related environments can identify hotspots of AMR and help prevent its emergence and dissemination along the food/feed chain.
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Affiliation(s)
- Adriana Cabal
- Austrian Agency for Health and Food Safety, 1096 Vienna, Austria
- Correspondence:
| | - Gerhard Rab
- Institute of Hydraulic Engineering and Water Resources Management, Technical University of Vienna, 1040 Vienna, Austria
- Institute for Land and Water Management Research, Federal Agency for Water Management, 3252 Petzenkirchen, Austria
| | - Beatriz Daza-Prieto
- Austrian Agency for Health and Food Safety, 1096 Vienna, Austria
- Institute of Chemical, Environmental and Bioscience Engineering, 1060 Vienna, Austria
| | - Anna Stöger
- Austrian Agency for Health and Food Safety, 1096 Vienna, Austria
| | - Nadine Peischl
- Austrian Agency for Health and Food Safety, 1096 Vienna, Austria
| | - Ali Chakeri
- Austrian Agency for Health and Food Safety, 1096 Vienna, Austria
- Center for Public Health, Medical University Vienna, 1090 Vienna, Austria
| | - Solveig Sølverød Mo
- Section for Food Safety and Animal Health Research, Department of Animal Health, Welfare and Food Safety, Norwegian Veterinary Institute, 1433 Ås, Norway
| | - Harald Bock
- Austrian Agency for Health and Food Safety, 1096 Vienna, Austria
| | - Klemens Fuchs
- Austrian Agency for Health and Food Safety, 1096 Vienna, Austria
| | - Jasmin Sucher
- Austrian Agency for Health and Food Safety, 1096 Vienna, Austria
| | - Krista Rathammer
- Austrian Agency for Health and Food Safety, 1096 Vienna, Austria
| | | | - Silke Stadtbauer
- Austrian Agency for Health and Food Safety, 1096 Vienna, Austria
| | - Manuela Caniça
- National Reference Laboratory of Antibiotic Resistances and Healthcare Associated Infections, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge, 1600-609 Lisbon, Portugal
| | - Peter Strauß
- Institute for Land and Water Management Research, Federal Agency for Water Management, 3252 Petzenkirchen, Austria
| | | | | | - Werner Ruppitsch
- Austrian Agency for Health and Food Safety, 1096 Vienna, Austria
- Department of Biotechnology, University of Natural Resources and Life Sciences, 1180 Vienna, Austria
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14
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Danneels P, Hamel JF, Picard L, Rezig S, Martinet P, Lorleac’h A, Talarmin JP, Buzelé R, Guimard T, Le Moal G, Brochard-Libois J, Beaudron A, Letheulle J, Codde C, Chenouard R, Boutoille D, Lemaignen A, Bernard L, Cattoir V, Dubée V. Impact of Enterococcus faecalis Endocarditis Treatment on Risk of Relapse. Clin Infect Dis 2022; 76:281-290. [PMID: 36124844 PMCID: PMC9839190 DOI: 10.1093/cid/ciac777] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 09/12/2022] [Accepted: 09/16/2022] [Indexed: 01/19/2023] Open
Abstract
BACKGROUND Enterococcus faecalis infective endocarditis (EFIE) is characterized by a higher frequency of relapses than other infective endocarditis. The role of the treatment on its occurrence remains poorly understood. The aim of this study was to investigate whether the antibiotic regimen could impact the risk of relapse in EFIE. MATERIALS This was a multicenter retrospective study of patients diagnosed with definite EFIE between 2015 and 2019 in 14 French hospitals. The primary endpoint was the occurrence of relapses within the year following endocarditis diagnosis. As death was a competing risk for relapse, Fine and Gray models were used for studying risk factors and impact of treatment. RESULTS Of the 279 patients included, 83 (29.7%) received the amoxicillin-gentamicin (A-G) combination, 114 (40.9%) amoxicillin-ceftriaxone (A-C), 63 (22.6%) A-G and A-C (A-G/A-C) sequentially, 9 (3.2%) amoxicillin (A), and 10 received other treatments. One-year-relapse rate was 9.3% (26 patients). Relapse occurred after a median delay of 107 days from EFIE diagnosis; 6 occurred after 6 months, and 6 were diagnosed by blood cultures in asymptomatic patients. In multivariate analysis, surgery during treatment was a protective factor against one-year relapse and death.The cumulative incidence of relapse 1 year after endocarditis was 46.2% for patients treated with amoxicillin, 13.4% with A-G, 14.7% with A-C, and 4.3% with A-G/A-C (P≥.05 in multivariate analysis). CONCLUSIONS Relapses after treatment of EFIE are frequent, frequently asymptomatic, and may occur more than 6 months after the initial episode.
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Affiliation(s)
- Pierre Danneels
- Infectious Diseases and Tropical Medicine, Angers University Hospital, Angers, France,Groupe d’Epidémiologie et Recherche en Infectiologie Clinique du Centre et de l’Ouest (GERICCO), France
| | | | - Léa Picard
- Infectious Diseases and Intensive Care Unit, Pontchaillou University Hospital, Rennes, France,Groupe d’Epidémiologie et Recherche en Infectiologie Clinique du Centre et de l’Ouest (GERICCO), France
| | - Schéhérazade Rezig
- Infectious Diseases and Tropical Medicine, La Cavale Blanche University Hospital, Brest, France,Groupe d’Epidémiologie et Recherche en Infectiologie Clinique du Centre et de l’Ouest (GERICCO), France
| | - Pauline Martinet
- Infectious Diseases and Tropical Medicine, La Cavale Blanche University Hospital, Brest, France,Groupe d’Epidémiologie et Recherche en Infectiologie Clinique du Centre et de l’Ouest (GERICCO), France
| | - Aurélien Lorleac’h
- Infectious Diseases and Tropical Medicine, Groupe Hospitalier Bretagne Sud, Lorient, France,Groupe d’Epidémiologie et Recherche en Infectiologie Clinique du Centre et de l’Ouest (GERICCO), France
| | - Jean-Philippe Talarmin
- Infectious Diseases and Tropical Medicine, Cornouaille Hospital, Quimper, France,Groupe d’Epidémiologie et Recherche en Infectiologie Clinique du Centre et de l’Ouest (GERICCO), France
| | - Rodolphe Buzelé
- Infectious Diseases and Tropical Medicine, Saint-Brieuc General Hospital, Saint-Brieuc, France,Groupe d’Epidémiologie et Recherche en Infectiologie Clinique du Centre et de l’Ouest (GERICCO), France
| | - Thomas Guimard
- Infectious Diseases and Tropical Medicine, Vendée Departmental Hospital, La Roche Sur Yon, France,Groupe d’Epidémiologie et Recherche en Infectiologie Clinique du Centre et de l’Ouest (GERICCO), France
| | - Gwenaël Le Moal
- Infectious Diseases and Tropical Medicine, Poitiers University Hospital, Poitiers, France,Groupe d’Epidémiologie et Recherche en Infectiologie Clinique du Centre et de l’Ouest (GERICCO), France
| | - Julia Brochard-Libois
- Infectious Diseases and Tropical Medicine, Saint Nazaire General Hospital, St-Nazaire, France,Groupe d’Epidémiologie et Recherche en Infectiologie Clinique du Centre et de l’Ouest (GERICCO), France
| | - Aurélie Beaudron
- Department of Bacteriology, Le Mans General Hospital, Le Mans, France,Groupe d’Epidémiologie et Recherche en Infectiologie Clinique du Centre et de l’Ouest (GERICCO), France
| | - Julien Letheulle
- Service de médecine polyvalente, Centre Hospitalier de Laval, Laval, France,Groupe d’Epidémiologie et Recherche en Infectiologie Clinique du Centre et de l’Ouest (GERICCO), France
| | - Cyrielle Codde
- Infectious Diseases and Tropical Medicine, Limoges University Hospital, Limoges, France,Groupe d’Epidémiologie et Recherche en Infectiologie Clinique du Centre et de l’Ouest (GERICCO), France
| | - Rachel Chenouard
- Department of Bacteriology, Angers University Hospital, Angers, France,Groupe d’Epidémiologie et Recherche en Infectiologie Clinique du Centre et de l’Ouest (GERICCO), France
| | - David Boutoille
- Service des Maladies Infectieuses et Tropicales, Centre Hospitalier Universitaire, CIC-UIC 1413 INSERM, Centre Hospitalier Universitaire de Nantes, Nantes, France,Groupe d’Epidémiologie et Recherche en Infectiologie Clinique du Centre et de l’Ouest (GERICCO), France
| | - Adrien Lemaignen
- Infectious Diseases and Tropical Medicine, Tours University Hospital, Tours, France,Groupe d’Epidémiologie et Recherche en Infectiologie Clinique du Centre et de l’Ouest (GERICCO), France
| | - Louis Bernard
- Infectious Diseases and Tropical Medicine, Tours University Hospital, Tours, France,Groupe d’Epidémiologie et Recherche en Infectiologie Clinique du Centre et de l’Ouest (GERICCO), France
| | - Vincent Cattoir
- Department of Bacteriology, Pontchaillou University Hospital, Rennes, France,National Reference Center for Enterococci, Pontchaillou University Hospital, Rennes, France,INSERM unit U1230, University of Rennes 1, Rennes, France
| | - Vincent Dubée
- Correspondence: V. Dubée, Infectious Diseases and Tropical Medicine, University Hospital. 4, Rue Larrey, 49100 Angers, France ()
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15
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Pereira AP, Antunes P, Willems R, Corander J, Coque TM, Peixe L, Freitas AR, Novais C. Evolution of Chlorhexidine Susceptibility and of the EfrEF Operon among Enterococcus faecalis from Diverse Environments, Clones, and Time Spans. Microbiol Spectr 2022; 10:e0117622. [PMID: 35862993 PMCID: PMC9430118 DOI: 10.1128/spectrum.01176-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 06/17/2022] [Indexed: 11/20/2022] Open
Abstract
Chlorhexidine (CHX) is widely used to control the spread of pathogens (e.g., human/animal clinical settings, ambulatory care, food industry). Enterococcus faecalis, a major nosocomial pathogen, is broadly distributed in diverse hosts and environments facilitating its exposure to CHX over the years. Nevertheless, CHX activity against E. faecalis is understudied. Our goal was to assess CHX activity and the variability of ChlR-EfrEF proteins (associated with CHX tolerance) among 673 field isolates and 1,784 E. faecalis genomes from the PATRIC database from different sources, time spans, clonal lineages, and antibiotic-resistance profiles. The CHX MIC (MICCHX) and minimum bactericidal concentration (MBCCHX) against E. faecalis presented normal distributions (0.5 to 64 mg/L). However, more CHX-tolerant isolates were detected in the food chain and recent human infections, suggesting an adaptability of E. faecalis populations in settings where CHX is heavily used. Heterogeneity in ChlR-EfrEF sequences was identified, with isolates harboring incomplete ChlR-EfrEF proteins, particularly the EfrE identified in the ST40 clonal lineage, showing low MICCHX (≤1mg/L). Distinct ST40-E. faecalis subpopulations carrying truncated and nontruncated EfrE were detected, with the former being predominant in human isolates. This study provides a new insight about CHX susceptibility and ChlR-EfrEF variability within diverse E. faecalis populations. The MICCHX/MBCCHX of more tolerant E. faecalis (MICCHX = 8 mg/L; MBCCHX = 64 mg/L) remain lower than in-use concentrations of CHX (≥500 mg/L). However, increased CHX use, combined with concentration gradients occurring in diverse environments, potentially selecting multidrug-resistant strains with different CHX susceptibilities, signals the importance of monitoring the trends of E. faecalis CHX tolerance within a One Health approach. IMPORTANCE Chlorhexidine (CHX) is a disinfectant and antiseptic used since the 1950s and included in the World Health Organization's list of essential medicines. It has been widely applied in hospitals, the community, the food industry, animal husbandry and pets. CHX tolerance in Enterococcus faecalis, a ubiquitous bacterium and one of the leading causes of human hospital-acquired infections, remains underexplored. Our study provides novel and comprehensive insights about CHX susceptibility within the E. faecalis population structure context, revealing more CHX-tolerant subpopulations from the food chain and recent human infections. We further show a detailed analysis of the genetic diversity of the efrEF operon (previously associated with E. faecalis CHX tolerance) and its correlation with CHX phenotypes. The recent strains with a higher tolerance to CHX and the multiple sources where bacteria are exposed to this biocide alert us to the need for the continuous monitoring of E. faecalis adaptation toward CHX tolerance within a One Health approach.
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Affiliation(s)
- Ana P. Pereira
- UCIBIO-Applied Molecular Biosciences Unit, Laboratory of Microbiology, Department of Biological Sciences, REQUIMTE Faculty of Pharmacy, University of Porto, Porto, Portugal
- Associate Laboratory i4HB, Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, Porto, Portugal
| | - Patrícia Antunes
- UCIBIO-Applied Molecular Biosciences Unit, Laboratory of Microbiology, Department of Biological Sciences, REQUIMTE Faculty of Pharmacy, University of Porto, Porto, Portugal
- Associate Laboratory i4HB, Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, Porto, Portugal
- Faculty of Nutrition and Food Sciences, University of Porto, Porto, Portugal
| | - Rob Willems
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Jukka Corander
- Department of Biostatistics, Faculty of Medicine, University of Oslo, Oslo, Norway
- Parasites and Microbes, Wellcome Sanger Institute, Cambridge, United Kingdom
- Helsinki Institute of Information Technology, Department of Mathematics and Statistics, University of Helsinki, Helsinki, Finland
| | - Teresa M. Coque
- Servicio de Microbiologia, Hospital Universitario Ramón y Cajal, Madrid, Spain
- Centro de Investigación Biomédica en Enfermedades Infecciosas (CIBER-EII), Madrid, Spain
| | - Luísa Peixe
- UCIBIO-Applied Molecular Biosciences Unit, Laboratory of Microbiology, Department of Biological Sciences, REQUIMTE Faculty of Pharmacy, University of Porto, Porto, Portugal
- Associate Laboratory i4HB, Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, Porto, Portugal
| | - Ana R. Freitas
- UCIBIO-Applied Molecular Biosciences Unit, Laboratory of Microbiology, Department of Biological Sciences, REQUIMTE Faculty of Pharmacy, University of Porto, Porto, Portugal
- Associate Laboratory i4HB, Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, Porto, Portugal
- TOXRUN, Toxicology Research Unit, University Institute of Health Sciences, CESPU, CRL, Gandra, Portugal
| | - Carla Novais
- UCIBIO-Applied Molecular Biosciences Unit, Laboratory of Microbiology, Department of Biological Sciences, REQUIMTE Faculty of Pharmacy, University of Porto, Porto, Portugal
- Associate Laboratory i4HB, Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, Porto, Portugal
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16
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Delineating Mycobacterium abscessus population structure and transmission employing high-resolution core genome multilocus sequence typing. Nat Commun 2022; 13:4936. [PMID: 35999208 PMCID: PMC9399081 DOI: 10.1038/s41467-022-32122-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 07/19/2022] [Indexed: 11/08/2022] Open
Abstract
Mycobacterium abscessus is an emerging multidrug-resistant non-tuberculous mycobacterium that causes a wide spectrum of infections and has caused several local outbreaks worldwide. To facilitate standardized prospective molecular surveillance, we established a novel core genome multilocus sequence typing (cgMLST) scheme. Whole genome sequencing data of 1991 isolates were employed to validate the scheme, re-analyze global population structure and set genetic distance thresholds for cluster detection and taxonomic identification. We confirmed and amended the nomenclature of the main dominant circulating clones and found that these also correlate well with traditional 7-loci MLST. Dominant circulating clones could be linked to a corresponding reference genome with less than 250 alleles while 99% of pairwise comparisons between epidemiologically linked isolates were below 25 alleles and 90% below 10 alleles. These thresholds can be used to guide further epidemiological investigations. Overall, the scheme will help to unravel the apparent global spread of certain clonal complexes and as yet undiscovered transmission routes.
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17
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Appelt S, Rohleder AM, Jacob D, von Buttlar H, Georgi E, Mueller K, Wernery U, Kinne J, Joseph M, Jose SV, Scholz HC. Genetic diversity and spatial distribution of Burkholderia mallei by core genome-based multilocus sequence typing analysis. PLoS One 2022; 17:e0270499. [PMID: 35793321 PMCID: PMC9258848 DOI: 10.1371/journal.pone.0270499] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 06/10/2022] [Indexed: 11/18/2022] Open
Abstract
Burkholderia mallei is the etiological agent of glanders, a highly contagious and often fatal disease in equids. Due to the high genetic clonality of B. mallei, high-resolution typing assays are necessary to differentiate between individual strains. Here we report on the development and validation of a robust and reproducible core genome-based Multi Locus Sequence Typing Assay (cgMLST) for B. mallei, which is based on 3328 gene targets and enables high-resolution typing at the strain level. The assay was validated using a set of 120 B. mallei genomes from public databases and 23 newly sequenced outbreak strains from in-house strain collections. In this cgMLST analysis, strains from different geographic regions were clearly distinguished by at least 70 allele differences, allowing spatial clustering while closely related and epidemiologically related strains were separated by only zero to three alleles. Neither the different sequencing technologies nor the assembly strategies had an influence on the cgMLST results. The developed cgMLST is highly robust, reproducible and can be used for outbreak investigations, source tracking and molecular characterization of new B. mallei isolates.
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Affiliation(s)
- Sandra Appelt
- Centre for Biological Threats and Special Pathogens (ZBS 2), Robert Koch Institute, Berlin, Germany
| | - Anna-Maria Rohleder
- Centre for Biological Threats and Special Pathogens (ZBS 2), Robert Koch Institute, Berlin, Germany
| | - Daniela Jacob
- Centre for Biological Threats and Special Pathogens (ZBS 2), Robert Koch Institute, Berlin, Germany
| | - Heiner von Buttlar
- Bundeswehr Institute of Microbiology, Department Bacteriology and Toxinology, Munich, Germany
| | - Enrico Georgi
- Bundeswehr Institute of Microbiology, Department Bacteriology and Toxinology, Munich, Germany
| | - Katharina Mueller
- Bundeswehr Institute of Microbiology, Department Bacteriology and Toxinology, Munich, Germany
| | - Ulrich Wernery
- Central Veterinary Research Laboratory, Dubai, United Arab Emirates
| | - Joerg Kinne
- Central Veterinary Research Laboratory, Dubai, United Arab Emirates
| | - Marina Joseph
- Central Veterinary Research Laboratory, Dubai, United Arab Emirates
| | | | - Holger C. Scholz
- Centre for Biological Threats and Special Pathogens (ZBS 2), Robert Koch Institute, Berlin, Germany
- Bundeswehr Institute of Microbiology, Department Bacteriology and Toxinology, Munich, Germany
- * E-mail:
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18
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Enterococcus Virulence and Resistant Traits Associated with Its Permanence in the Hospital Environment. Antibiotics (Basel) 2022; 11:antibiotics11070857. [PMID: 35884110 PMCID: PMC9311936 DOI: 10.3390/antibiotics11070857] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 06/23/2022] [Accepted: 06/24/2022] [Indexed: 11/17/2022] Open
Abstract
Enterococcus are opportunistic pathogens that have been gaining importance in the clinical setting, especially in terms of hospital-acquired infections. This problem has mainly been associated with the fact that these bacteria are able to present intrinsic and extrinsic resistance to different classes of antibiotics, with a great deal of importance being attributed to vancomycin-resistant enterococci. However, other aspects, such as the expression of different virulence factors including biofilm-forming ability, and its capacity of trading genetic information, makes this bacterial genus more capable of surviving harsh environmental conditions. All these characteristics, associated with some reports of decreased susceptibility to some biocides, all described in this literary review, allow enterococci to present a longer survival ability in the hospital environment, consequently giving them more opportunities to disseminate in these settings and be responsible for difficult-to-treat infections.
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19
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Ren Y, Yu G, Shi C, Liu L, Guo Q, Han C, Zhang D, Zhang L, Liu B, Gao H, Zeng J, Zhou Y, Qiu Y, Wei J, Luo Y, Zhu F, Li X, Wu Q, Li B, Fu W, Tong Y, Meng J, Fang Y, Dong J, Feng Y, Xie S, Yang Q, Yang H, Wang Y, Zhang J, Gu H, Xuan H, Zou G, Luo C, Huang L, Yang B, Dong Y, Zhao J, Han J, Zhang X, Huang H. Majorbio Cloud: A one-stop, comprehensive bioinformatic platform for multiomics analyses. IMETA 2022; 1:e12. [PMID: 38868573 PMCID: PMC10989754 DOI: 10.1002/imt2.12] [Citation(s) in RCA: 212] [Impact Index Per Article: 106.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 01/24/2022] [Accepted: 01/24/2022] [Indexed: 06/14/2024]
Abstract
The platform consists of three modules, which are pre-configured bioinformatic pipelines, cloud toolsets, and online omics' courses. The pre-configured bioinformatic pipelines not only combine analytic tools for metagenomics, genomes, transcriptome, proteomics and metabolomics, but also provide users with powerful and convenient interactive analysis reports, which allow them to analyze and mine data independently. As a useful supplement to the bioinformatics pipelines, a wide range of cloud toolsets can further meet the needs of users for daily biological data processing, statistics, and visualization. The rich online courses of multi-omics also provide a state-of-art platform to researchers in interactive communication and knowledge sharing.
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Affiliation(s)
- Yi Ren
- Shanghai Majorbio Bio‐pharm Technology Co., Ltd.ShanghaiChina
| | - Guo Yu
- Shanghai Majorbio Bio‐pharm Technology Co., Ltd.ShanghaiChina
| | - Caiping Shi
- Shanghai Majorbio Bio‐pharm Technology Co., Ltd.ShanghaiChina
| | - Linmeng Liu
- Shanghai Majorbio Bio‐pharm Technology Co., Ltd.ShanghaiChina
| | - Quan Guo
- Shanghai Majorbio Bio‐pharm Technology Co., Ltd.ShanghaiChina
| | - Chang Han
- Shanghai Majorbio Bio‐pharm Technology Co., Ltd.ShanghaiChina
| | - Dan Zhang
- Shanghai Majorbio Bio‐pharm Technology Co., Ltd.ShanghaiChina
| | - Lei Zhang
- Shanghai Majorbio Bio‐pharm Technology Co., Ltd.ShanghaiChina
| | - Binxu Liu
- Shanghai Majorbio Bio‐pharm Technology Co., Ltd.ShanghaiChina
| | - Hao Gao
- Shanghai Majorbio Bio‐pharm Technology Co., Ltd.ShanghaiChina
| | - Jing Zeng
- Shanghai Majorbio Bio‐pharm Technology Co., Ltd.ShanghaiChina
| | - Yong Zhou
- Shanghai Majorbio Bio‐pharm Technology Co., Ltd.ShanghaiChina
| | - Yuhan Qiu
- Shanghai Majorbio Bio‐pharm Technology Co., Ltd.ShanghaiChina
| | - Jian Wei
- Shanghai Majorbio Bio‐pharm Technology Co., Ltd.ShanghaiChina
| | - Yanchun Luo
- Shanghai Majorbio Bio‐pharm Technology Co., Ltd.ShanghaiChina
| | - Fengjuan Zhu
- Shanghai Majorbio Bio‐pharm Technology Co., Ltd.ShanghaiChina
| | - Xiaojie Li
- Shanghai Majorbio Bio‐pharm Technology Co., Ltd.ShanghaiChina
| | - Qin Wu
- Shanghai Majorbio Bio‐pharm Technology Co., Ltd.ShanghaiChina
| | - Bing Li
- Shanghai Majorbio Bio‐pharm Technology Co., Ltd.ShanghaiChina
| | - Wenyao Fu
- Shanghai Majorbio Bio‐pharm Technology Co., Ltd.ShanghaiChina
| | - Yanli Tong
- Shanghai Majorbio Bio‐pharm Technology Co., Ltd.ShanghaiChina
| | - Jie Meng
- Shanghai Majorbio Bio‐pharm Technology Co., Ltd.ShanghaiChina
| | - Yahong Fang
- Shanghai Majorbio Bio‐pharm Technology Co., Ltd.ShanghaiChina
| | - Jie Dong
- Shanghai Majorbio Bio‐pharm Technology Co., Ltd.ShanghaiChina
| | - Yitong Feng
- Shanghai Majorbio Bio‐pharm Technology Co., Ltd.ShanghaiChina
| | - Shichang Xie
- Shanghai Majorbio Bio‐pharm Technology Co., Ltd.ShanghaiChina
| | - Qianqian Yang
- Shanghai Majorbio Bio‐pharm Technology Co., Ltd.ShanghaiChina
| | - Hui Yang
- Shanghai Majorbio Bio‐pharm Technology Co., Ltd.ShanghaiChina
| | - Yan Wang
- Shanghai Majorbio Bio‐pharm Technology Co., Ltd.ShanghaiChina
| | - Junbiao Zhang
- Shanghai Majorbio Bio‐pharm Technology Co., Ltd.ShanghaiChina
| | - Haidong Gu
- Shanghai Majorbio Bio‐pharm Technology Co., Ltd.ShanghaiChina
| | - Hongdong Xuan
- Shanghai Majorbio Bio‐pharm Technology Co., Ltd.ShanghaiChina
| | - Guanqing Zou
- Shanghai Majorbio Bio‐pharm Technology Co., Ltd.ShanghaiChina
| | - Chun Luo
- Shanghai Majorbio Bio‐pharm Technology Co., Ltd.ShanghaiChina
| | - Long Huang
- Shanghai Majorbio Bio‐pharm Technology Co., Ltd.ShanghaiChina
| | - Bing Yang
- Shanghai Majorbio Bio‐pharm Technology Co., Ltd.ShanghaiChina
| | - Yachen Dong
- Shanghai Majorbio Bio‐pharm Technology Co., Ltd.ShanghaiChina
| | - Jianhua Zhao
- Shanghai Majorbio Bio‐pharm Technology Co., Ltd.ShanghaiChina
| | - Jichen Han
- Shanghai Majorbio Bio‐pharm Technology Co., Ltd.ShanghaiChina
| | - Xianglin Zhang
- Shanghai Majorbio Bio‐pharm Technology Co., Ltd.ShanghaiChina
| | - Huasheng Huang
- Shanghai Majorbio Bio‐pharm Technology Co., Ltd.ShanghaiChina
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20
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Annotated Whole-Genome Multilocus Sequence Typing Schema for Scalable High-Resolution Typing of Streptococcus pyogenes. J Clin Microbiol 2022; 60:e0031522. [DOI: 10.1128/jcm.00315-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Streptococcus pyogenes
is a major human pathogen with high genetic diversity, largely created by recombination and horizontal gene transfer, making it difficult to use single nucleotide polymorphism (SNP)-based genome-wide analyses for surveillance. Using a gene-by-gene approach on 208 complete genomes of
S. pyogenes
, a novel whole-genome multilocus sequence typing (wgMLST) schema was developed, comprising 3,044 target loci.
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21
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Grujović MŽ, Mladenović KG, Semedo-Lemsaddek T, Laranjo M, Stefanović OD, Kocić-Tanackov SD. Advantages and disadvantages of non-starter lactic acid bacteria from traditional fermented foods: Potential use as starters or probiotics. Compr Rev Food Sci Food Saf 2022; 21:1537-1567. [PMID: 35029033 DOI: 10.1111/1541-4337.12897] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 11/30/2021] [Accepted: 12/02/2021] [Indexed: 12/12/2022]
Abstract
Traditional fermented foods are a significant source of starter and/or non-starter lactic acid bacteria (nsLAB). Moreover, these microorganisms are also known for their role as probiotics. The potential of nsLAB is huge; however, there are still challenges to be overcome with respect to characterization and application. In the present review, the most important steps that autochthonous lactic acid bacteria isolated from fermented foods need to overcome, to qualify as novel starter cultures, or as probiotics, in food technology and biotechnology, are considered. These different characterization steps include precise identification, detection of health-promoting properties, and safety evaluation. Each of these features is strain specific and needs to be accurately determined. This review highlights the advantages and disadvantages of nsLAB, isolated from traditional fermented foods, discussing safety aspects and sensory impact.
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Affiliation(s)
- Mirjana Ž Grujović
- Department of Science, Institute for Information Technologies, University of Kragujevac, Kragujevac, Republic of Serbia.,Department of Biology and Ecology, Faculty of Science, University of Kragujevac, Kragujevac, Republic of Serbia
| | - Katarina G Mladenović
- Department of Science, Institute for Information Technologies, University of Kragujevac, Kragujevac, Republic of Serbia.,Department of Biology and Ecology, Faculty of Science, University of Kragujevac, Kragujevac, Republic of Serbia
| | - Teresa Semedo-Lemsaddek
- CIISA-Centro de Investigação Interdisciplinar em Sanidade Animal, Faculdade de Medicina Veterinária, Universidade de Lisboa, Avenida da Universidade Técnica, Lisboa, Portugal
| | - Marta Laranjo
- MED-Mediterranean Institute for Agriculture, Environment and Development, Instituto de Investigação e Formação Avançada, Universidade de Évora, Évora, Portugal
| | - Olgica D Stefanović
- Department of Biology and Ecology, Faculty of Science, University of Kragujevac, Kragujevac, Republic of Serbia
| | - Sunčica D Kocić-Tanackov
- Department of Food Preservation Engineering, Faculty of Technology, University of Novi Sad, Novi Sad, Republic of Serbia
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22
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Lange I, Edel B, Dawczynski K, Proquitté H, Pletz MW, Kipp F, Stein C. Influence of the Incubator as Direct Patient Environment on Bacterial Colonization of Neonates. Microorganisms 2021; 9:microorganisms9122533. [PMID: 34946134 PMCID: PMC8709377 DOI: 10.3390/microorganisms9122533] [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: 09/29/2021] [Revised: 11/24/2021] [Accepted: 11/29/2021] [Indexed: 11/20/2022] Open
Abstract
Background: Preventing healthcare-associated infections (HAI) in neonatal intensive care units is a challenge of highest priority. For further insight into the incubator as direct patient environment and potential source for contamination, we present data correlating microbiological samples of very low birthweight infants in the form of colonization results of surveillance screenings with samples of their associated incubator in this study. Methods: Samples were taken via rectal and throat swabs of neonates as well as Polywipe® sponges for the incubator. If the same bacterial species was found in corresponding neonate and incubator samples, whole genome sequencing via Illumina technology was performed. Results: 52 microbiological species matches were found, and 30 matches were sequenced where we found 26 clonal pairs (12 E. faecalis, 10 S. aureus, 2 E. coli, 1 E. cloacae, and 1 E. faecium). Conclusion: The combinations of measurements of weekly screenings swabs, probing of surfaces with Polywipes®, and whole genome sequencing showed transmissions of microorganism and risk for potential non-physiological colonization of neonatal infants.
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Affiliation(s)
- Isabel Lange
- Institute for Infectious Diseases and Infection Control, Jena University Hospital, Am Klinikum 1, 07747 Jena, Germany; (M.W.P.); (F.K.); (C.S.)
- Correspondence: ; Tel.: +49-3641-9-324743
| | - Birgit Edel
- Institute of Medical Microbiology, Jena University Hospital, Am Klinikum 1, 07747 Jena, Germany;
| | - Kristin Dawczynski
- Department of Pediatrics Weimar, Sophien-und Hufeland Klinikum, Henry-van-de-Velde-Str. 1, 99425 Weimar, Germany;
| | - Hans Proquitté
- Unit of Neonatology, Department of Paediatrics, Jena University Hospital, Friedrich Schiller University Jena, 07747 Jena, Germany;
| | - Mathias W. Pletz
- Institute for Infectious Diseases and Infection Control, Jena University Hospital, Am Klinikum 1, 07747 Jena, Germany; (M.W.P.); (F.K.); (C.S.)
| | - Frank Kipp
- Institute for Infectious Diseases and Infection Control, Jena University Hospital, Am Klinikum 1, 07747 Jena, Germany; (M.W.P.); (F.K.); (C.S.)
| | - Claudia Stein
- Institute for Infectious Diseases and Infection Control, Jena University Hospital, Am Klinikum 1, 07747 Jena, Germany; (M.W.P.); (F.K.); (C.S.)
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23
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Cattoir V. The multifaceted lifestyle of enterococci: genetic diversity, ecology and risks for public health. Curr Opin Microbiol 2021; 65:73-80. [PMID: 34768106 DOI: 10.1016/j.mib.2021.10.013] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 08/29/2021] [Accepted: 10/21/2021] [Indexed: 12/26/2022]
Abstract
Enterococci are long-standing members of the gastrointestinal tract of humans and many animals and they are also ubiquitously distributed in natural environments. Classically as harmless bacteria, two main species (namely Enterococcus faecalis and Enterococcus faecium) have become a leading cause of human infections, especially in hospital settings, with the worldwide spread of multidrug-resistant isolates, especially vancomycin-resistant enterococci. In this review, it will be summarized what is known about genetic diversity and ecology of enterococci with a focus on E. faecalis and E. faecium from human and non-human habitats and related risks for public health.
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Affiliation(s)
- Vincent Cattoir
- Service de Bactériologie-Hygiène Hospitalière, CHU de Rennes, Rennes, France; CNR de la Résistance aux Antibiotiques (Laboratoire Associé 'Entérocoques'), Rennes, France; Unité Inserm U1230, Université de Rennes 1, Rennes, France.
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24
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Di Pasquale A, Radomski N, Mangone I, Calistri P, Lorusso A, Cammà C. SARS-CoV-2 surveillance in Italy through phylogenomic inferences based on Hamming distances derived from pan-SNPs, -MNPs and -InDels. BMC Genomics 2021; 22:782. [PMID: 34717546 PMCID: PMC8556844 DOI: 10.1186/s12864-021-08112-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 10/20/2021] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Faced with the ongoing global pandemic of coronavirus disease, the 'National Reference Centre for Whole Genome Sequencing of microbial pathogens: database and bioinformatic analysis' (GENPAT) formally established at the 'Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise' (IZSAM) in Teramo (Italy) is in charge of the SARS-CoV-2 surveillance at the genomic scale. In a context of SARS-CoV-2 surveillance requiring correct and fast assessment of epidemiological clusters from substantial amount of samples, the present study proposes an analytical workflow for identifying accurately the PANGO lineages of SARS-CoV-2 samples and building of discriminant minimum spanning trees (MST) bypassing the usual time consuming phylogenomic inferences based on multiple sequence alignment (MSA) and substitution model. RESULTS GENPAT constituted two collections of SARS-CoV-2 samples. The first collection consisted of SARS-CoV-2 positive swabs collected by IZSAM from the Abruzzo region (Italy), then sequenced by next generation sequencing (NGS) and analyzed in GENPAT (n = 1592), while the second collection included samples from several Italian provinces and retrieved from the reference Global Initiative on Sharing All Influenza Data (GISAID) (n = 17,201). The main results of the present work showed that (i) GENPAT and GISAID detected the same PANGO lineages, (ii) the PANGO lineages B.1.177 (i.e. historical in Italy) and B.1.1.7 (i.e. 'UK variant') are major concerns today in several Italian provinces, and the new MST-based method (iii) clusters most of the PANGO lineages together, (iv) with a higher dicriminatory power than PANGO lineages, (v) and faster that the usual phylogenomic methods based on MSA and substitution model. CONCLUSIONS The genome sequencing efforts of Italian provinces, combined with a structured national system of NGS data management, provided support for surveillance SARS-CoV-2 in Italy. We propose to build phylogenomic trees of SARS-CoV-2 variants through an accurate, discriminant and fast MST-based method avoiding the typical time consuming steps related to MSA and substitution model-based phylogenomic inference.
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Affiliation(s)
- Adriano Di Pasquale
- National Reference Centre (NRC) for Whole Genome Sequencing of microbial pathogens: data-base and bioinformatics analysis (GENPAT), Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise “Giuseppe Caporale” (IZSAM), via Campo Boario, 64100 Teramo, TE Italy
| | - Nicolas Radomski
- National Reference Centre (NRC) for Whole Genome Sequencing of microbial pathogens: data-base and bioinformatics analysis (GENPAT), Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise “Giuseppe Caporale” (IZSAM), via Campo Boario, 64100 Teramo, TE Italy
| | - Iolanda Mangone
- National Reference Centre (NRC) for Whole Genome Sequencing of microbial pathogens: data-base and bioinformatics analysis (GENPAT), Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise “Giuseppe Caporale” (IZSAM), via Campo Boario, 64100 Teramo, TE Italy
| | - Paolo Calistri
- National Reference Centre (NRC) for Whole Genome Sequencing of microbial pathogens: data-base and bioinformatics analysis (GENPAT), Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise “Giuseppe Caporale” (IZSAM), via Campo Boario, 64100 Teramo, TE Italy
| | - Alessio Lorusso
- National Reference Centre (NRC) for Whole Genome Sequencing of microbial pathogens: data-base and bioinformatics analysis (GENPAT), Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise “Giuseppe Caporale” (IZSAM), via Campo Boario, 64100 Teramo, TE Italy
| | - Cesare Cammà
- National Reference Centre (NRC) for Whole Genome Sequencing of microbial pathogens: data-base and bioinformatics analysis (GENPAT), Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise “Giuseppe Caporale” (IZSAM), via Campo Boario, 64100 Teramo, TE Italy
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25
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Timmermans M, Bogaerts B, Vanneste K, De Keersmaecker SCJ, Roosens NHC, Kowalewicz C, Simon G, Argudín MA, Deplano A, Hallin M, Wattiau P, Fretin D, Denis O, Boland C. Large diversity of linezolid-resistant isolates discovered in food-producing animals through linezolid selective monitoring in Belgium in 2019. J Antimicrob Chemother 2021; 77:49-57. [PMID: 34673924 PMCID: PMC8730767 DOI: 10.1093/jac/dkab376] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 09/20/2021] [Indexed: 11/14/2022] Open
Abstract
Background Linezolid is a critically important antibiotic used to treat human infections caused by MRSA and VRE. While linezolid is not licensed for food-producing animals, linezolid-resistant (LR) isolates have been reported in European countries, including Belgium. Objectives To: (i) assess LR occurrence in staphylococci and enterococci isolated from different Belgian food-producing animals in 2019 through selective monitoring; and (ii) investigate the genomes and relatedness of these isolates. Methods Faecal samples (n = 1325) and nasal swab samples (n = 148) were analysed with a protocol designed to select LR bacteria, including a 44–48 h incubation period. The presence of LR chromosomal mutations, transferable LR genes and their genetic organizations and other resistance genes, as well as LR isolate relatedness (from this study and the NCBI database) were assessed through WGS. Results The LR rate differed widely between animal host species, with the highest rates occurring in nasal samples from pigs and sows (25.7% and 20.5%, respectively) and faecal samples from veal calves (16.4%). WGS results showed that LR determinants are present in a large diversity of isolates circulating in the agricultural sector, with some isolates closely related to human isolates, posing a human health risk. Conclusions LR dedicated monitoring with WGS analysis could help to better understand the spread of LR. Cross-selection of LR transferable genes through other antibiotic use should be considered in future action plans aimed at combatting antimicrobial resistance and in future objectives for the rational use of antibiotics in a One Health perspective.
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Affiliation(s)
- Michaël Timmermans
- Veterinary Bacteriology, Sciensano, Ixelles, Belgium.,Faculté de Médecine, Université Libre de Bruxelles, Brussels, Belgium
| | - Bert Bogaerts
- Transversal Activities in Applied Genomics, Sciensano, Ixelles, Belgium
| | - Kevin Vanneste
- Transversal Activities in Applied Genomics, Sciensano, Ixelles, Belgium
| | | | - Nancy H C Roosens
- Transversal Activities in Applied Genomics, Sciensano, Ixelles, Belgium
| | | | | | - Maria A Argudín
- National Reference Centre-Staphylococcus aureus, Department of Microbiology, Hôpital Erasme, Université Libre de Bruxelles, Brussels, Belgium
| | - Ariane Deplano
- National Reference Centre-Staphylococcus aureus, Department of Microbiology, Hôpital Erasme, Université Libre de Bruxelles, Brussels, Belgium.,Department of Microbiology, LHUB-ULB, Université Libre de Bruxelles, Brussels, Belgium
| | - Marie Hallin
- National Reference Centre-Staphylococcus aureus, Department of Microbiology, Hôpital Erasme, Université Libre de Bruxelles, Brussels, Belgium.,Department of Microbiology, LHUB-ULB, Université Libre de Bruxelles, Brussels, Belgium.,Ecole de Santé Publique, Université Libre de Bruxelles, Brussels, Belgium
| | | | - David Fretin
- Veterinary Bacteriology, Sciensano, Ixelles, Belgium
| | - Olivier Denis
- Ecole de Santé Publique, Université Libre de Bruxelles, Brussels, Belgium.,Laboratory of Clinical Microbiology, National Reference Center for Monitoring Antimicrobial Resistance in Gram-Negative Bacteria, CHU UCL Namur, Yvoir, Belgium
| | - Cécile Boland
- Veterinary Bacteriology, Sciensano, Ixelles, Belgium
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26
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Scott P, Zhang J, Anderson T, Priest PC, Chambers S, Smith H, Murdoch DR, French N, Biggs PJ. Whole-genome sequencing and ad hoc shared genome analysis of Staphylococcus aureus isolates from a New Zealand primary school. Sci Rep 2021; 11:20328. [PMID: 34645857 PMCID: PMC8514452 DOI: 10.1038/s41598-021-99080-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 09/09/2021] [Indexed: 11/09/2022] Open
Abstract
Epidemiological studies of communicable diseases increasingly use large whole-genome sequencing (WGS) datasets to explore the transmission of pathogens. It is important to obtain an initial overview of datasets and identify closely related isolates, but this can be challenging with large numbers of isolates and imperfect sequencing. We used an ad hoc whole-genome multi locus sequence typing method to summarise data from a longitudinal study of Staphylococcus aureus in a primary school in New Zealand. Each pair of isolates was compared and the number of genes where alleles differed between isolates was tallied to produce a matrix of "allelic differences". We plotted histograms of the number of allelic differences between isolates for: all isolate pairs; pairs of isolates from different individuals; and pairs of isolates from the same individual. 340 sequenced isolates were included, and the ad hoc shared genome contained 445 genes. There were between 0 and 420 allelic differences between isolate pairs and the majority of pairs had more than 260 allelic differences. We found many genetically closely related S. aureus isolates from single individuals and a smaller number of closely-related isolates from separate individuals. Multiple S. aureus isolates from the same individual were usually very closely related or identical over the ad hoc shared genome. Siblings carried genetically similar, but not identical isolates. An ad hoc shared genome approach to WGS analysis can accommodate imperfect sequencing of the included isolates, and can provide insights into relationships between isolates in epidemiological studies with large WGS datasets containing diverse isolates.
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Affiliation(s)
- Pippa Scott
- Department of Pathology and Biomedical Science, University of Otago, Christchurch, New Zealand.
| | - Ji Zhang
- School of Veterinary Science, Massey University, Palmerston North, New Zealand
| | - Trevor Anderson
- Canterbury Health Laboratories, Canterbury District Health Board, Christchurch, New Zealand
| | - Patricia C Priest
- Department of Preventive and Social Medicine, University of Otago, Dunedin, New Zealand
| | - Stephen Chambers
- Department of Pathology and Biomedical Science, University of Otago, Christchurch, New Zealand
| | - Helen Smith
- School of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| | - David R Murdoch
- Department of Pathology and Biomedical Science, University of Otago, Christchurch, New Zealand
| | - Nigel French
- School of Veterinary Science, Massey University, Palmerston North, New Zealand
| | - Patrick J Biggs
- School of Veterinary Science, Massey University, Palmerston North, New Zealand.,School of Fundamental Sciences, Massey University, Palmerston North, New Zealand
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27
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Liu S, Liu Y, Zhang R, Lu X, Hu H, Hu J, Zhang K, Sun Y. [Association of sepM gene mutation with mutacin Ⅳ production by Streptococcus mutans]. NAN FANG YI KE DA XUE XUE BAO = JOURNAL OF SOUTHERN MEDICAL UNIVERSITY 2021; 41:876-882. [PMID: 34238740 DOI: 10.12122/j.issn.1673-4254.2021.06.10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
OBJECTIVE To investigate the types of sepM gene mutations and their distribution in clinical isolates of Streptococcus mutans (S. mutans) and explore the association of sepM gene mutation with the capacity of mutacin Ⅳ production by S. mutans. OBJECTIVE We assessed the capacity of mutacin Ⅳ production in 80 clinical isolates of S. mutans using an inhibition zone assay. The minimum spanning tree and phylogenetic tree of these isolates were constructed using core genome multilocus sequence typing and maximum likelihood method, respectively. GeneMarkS software was used to predict the coding genes of these isolates, and the predicted genes were blasted against the sepM gene sequence of the reference genome UA159 to determine sepM gene mutations and their distribution characteristics in the clinical isolates. The mutation types affecting mutacin Ⅳ production were identified by analyzing the differentially distributed mutations between mutacin Ⅳ-producing isolates and mutacin Ⅳ-free isolates and by comparing the inhibition zones between isolates with sepM gene mutations and those without mutations. OBJECTIVE Among the 80 clinical isolates of S. mutans, 25 isolates were capable of mutacin Ⅳ production and 55 did not produce mutacin Ⅳ. The minimum spanning tree showed that the allelic differences were less among the mutacin Ⅳproducing isolates than among the mutacin Ⅳ-free isolates, and the origins of the mutacin Ⅳ-producing isolates were similar. We identified a total of 34 single base mutations in the 80 clinical isolates, and among them, C31T (P=0.001), G533A (P < 0.001), C756T (P=0.025), and C1036T (P=0.003) showed significant differential distributions between the mutacin Ⅳ-producing and mutacin Ⅳ-free isolates. These differentially distributed mutations were positively correlated with the capacity of mutacin Ⅳ production of the bacteria. OBJECTIVE sepM gene mutations that affect the capacity of mutacin Ⅳ production are present in the clinical strains of S. mutans.
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Affiliation(s)
- S Liu
- Department of Stomatology, First Affiliated Hospital of Bengbu Medical College, Bengbu 233004, China
| | - Y Liu
- Department of histology and Embryology, Bengbu Medical College, Bengbu 233030, China
| | - R Zhang
- Department of Stomatology, First Affiliated Hospital of Bengbu Medical College, Bengbu 233004, China
| | - X Lu
- Department of Stomatology, First Affiliated Hospital of Bengbu Medical College, Bengbu 233004, China
| | - H Hu
- Department of Stomatology, First Affiliated Hospital of Bengbu Medical College, Bengbu 233004, China
| | - J Hu
- Department of Stomatology, First Affiliated Hospital of Bengbu Medical College, Bengbu 233004, China
| | - K Zhang
- Department of Stomatology, First Affiliated Hospital of Bengbu Medical College, Bengbu 233004, China
| | - Y Sun
- Department of Health Inspection and Quarantine, Bengbu Medical College, Bengbu 233030, China
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Bortolaia V, Kaas RS, Ruppe E, Roberts MC, Schwarz S, Cattoir V, Philippon A, Allesoe RL, Rebelo AR, Florensa AF, Fagelhauer L, Chakraborty T, Neumann B, Werner G, Bender JK, Stingl K, Nguyen M, Coppens J, Xavier BB, Malhotra-Kumar S, Westh H, Pinholt M, Anjum MF, Duggett NA, Kempf I, Nykäsenoja S, Olkkola S, Wieczorek K, Amaro A, Clemente L, Mossong J, Losch S, Ragimbeau C, Lund O, Aarestrup FM. ResFinder 4.0 for predictions of phenotypes from genotypes. J Antimicrob Chemother 2021; 75:3491-3500. [PMID: 32780112 PMCID: PMC7662176 DOI: 10.1093/jac/dkaa345] [Citation(s) in RCA: 1414] [Impact Index Per Article: 471.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 06/30/2020] [Indexed: 12/16/2022] Open
Abstract
Objectives WGS-based antimicrobial susceptibility testing (AST) is as reliable as phenotypic AST for several antimicrobial/bacterial species combinations. However, routine use of WGS-based AST is hindered by the need for bioinformatics skills and knowledge of antimicrobial resistance (AMR) determinants to operate the vast majority of tools developed to date. By leveraging on ResFinder and PointFinder, two freely accessible tools that can also assist users without bioinformatics skills, we aimed at increasing their speed and providing an easily interpretable antibiogram as output. Methods The ResFinder code was re-written to process raw reads and use Kmer-based alignment. The existing ResFinder and PointFinder databases were revised and expanded. Additional databases were developed including a genotype-to-phenotype key associating each AMR determinant with a phenotype at the antimicrobial compound level, and species-specific panels for in silico antibiograms. ResFinder 4.0 was validated using Escherichia coli (n = 584), Salmonella spp. (n = 1081), Campylobacter jejuni (n = 239), Enterococcus faecium (n = 106), Enterococcus faecalis (n = 50) and Staphylococcus aureus (n = 163) exhibiting different AST profiles, and from different human and animal sources and geographical origins. Results Genotype–phenotype concordance was ≥95% for 46/51 and 25/32 of the antimicrobial/species combinations evaluated for Gram-negative and Gram-positive bacteria, respectively. When genotype–phenotype concordance was <95%, discrepancies were mainly linked to criteria for interpretation of phenotypic tests and suboptimal sequence quality, and not to ResFinder 4.0 performance. Conclusions WGS-based AST using ResFinder 4.0 provides in silico antibiograms as reliable as those obtained by phenotypic AST at least for the bacterial species/antimicrobial agents of major public health relevance considered.
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Affiliation(s)
- Valeria Bortolaia
- Technical University of Denmark, National Food Institute, European Union Reference Laboratory for Antimicrobial Resistance, WHO Collaborating Centre for Antimicrobial Resistance in Foodborne Pathogens and Genomics, FAO Reference Laboratory for Antimicrobial Resistance, Kgs. Lyngby, Denmark
| | - Rolf S Kaas
- Technical University of Denmark, National Food Institute, European Union Reference Laboratory for Antimicrobial Resistance, WHO Collaborating Centre for Antimicrobial Resistance in Foodborne Pathogens and Genomics, FAO Reference Laboratory for Antimicrobial Resistance, Kgs. Lyngby, Denmark
| | | | - Marilyn C Roberts
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, WA, USA
| | - Stefan Schwarz
- Institute of Microbiology and Epizootics, Centre for Infection Medicine, Department of Veterinary Medicine, Freie Universität Berlin, Berlin, Germany
| | - Vincent Cattoir
- Rennes University Hospital, Department of Clinical Microbiology, Rennes, France.,National Reference Center for Antimicrobial Resistance (lab Enterococci), Rennes, France.,University of Rennes 1, INSERM U1230, Rennes, France
| | - Alain Philippon
- Faculty of Medicine Paris Descartes, Bacteriology, Paris, France
| | - Rosa L Allesoe
- Technical University of Denmark, National Food Institute, European Union Reference Laboratory for Antimicrobial Resistance, WHO Collaborating Centre for Antimicrobial Resistance in Foodborne Pathogens and Genomics, FAO Reference Laboratory for Antimicrobial Resistance, Kgs. Lyngby, Denmark.,Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen N, Denmark
| | - Ana Rita Rebelo
- Technical University of Denmark, National Food Institute, European Union Reference Laboratory for Antimicrobial Resistance, WHO Collaborating Centre for Antimicrobial Resistance in Foodborne Pathogens and Genomics, FAO Reference Laboratory for Antimicrobial Resistance, Kgs. Lyngby, Denmark
| | - Alfred Ferrer Florensa
- Technical University of Denmark, National Food Institute, European Union Reference Laboratory for Antimicrobial Resistance, WHO Collaborating Centre for Antimicrobial Resistance in Foodborne Pathogens and Genomics, FAO Reference Laboratory for Antimicrobial Resistance, Kgs. Lyngby, Denmark
| | - Linda Fagelhauer
- Institute of Medical Microbiolgy, Justus Liebig University Giessen, Giessen, Germany.,German Center for Infection Research, site Giessen-Marburg-Langen, Justus Liebig University Giessen, Giessen, Germany.,Institute of Hygiene and Environmental Medicine, Justus Liebig University Giessen, Giessen, Germany
| | - Trinad Chakraborty
- Institute of Medical Microbiolgy, Justus Liebig University Giessen, Giessen, Germany.,German Center for Infection Research, site Giessen-Marburg-Langen, Justus Liebig University Giessen, Giessen, Germany
| | - Bernd Neumann
- Robert Koch Institute, Wernigerode Branch, Department of Infectious Diseases, Division of Nosocomial Pathogens and Antibiotic Resistances, Wernigerode, Germany
| | - Guido Werner
- Robert Koch Institute, Wernigerode Branch, Department of Infectious Diseases, Division of Nosocomial Pathogens and Antibiotic Resistances, Wernigerode, Germany
| | - Jennifer K Bender
- Robert Koch Institute, Wernigerode Branch, Department of Infectious Diseases, Division of Nosocomial Pathogens and Antibiotic Resistances, Wernigerode, Germany
| | - Kerstin Stingl
- German Federal Institute for Risk Assessment, Department of Biological Safety, National Reference Laboratory for Campylobacter, Berlin, Germany
| | - Minh Nguyen
- Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, University of Antwerp, Belgium
| | - Jasmine Coppens
- Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, University of Antwerp, Belgium
| | - Basil Britto Xavier
- Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, University of Antwerp, Belgium
| | - Surbhi Malhotra-Kumar
- Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, University of Antwerp, Belgium
| | - Henrik Westh
- Department of Clinical Microbiology, Hvidovre University Hospital, Hvidovre, Denmark.,Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Mette Pinholt
- Department of Clinical Microbiology, Hvidovre University Hospital, Hvidovre, Denmark
| | - Muna F Anjum
- Animal and Plant Health Agency, Addlestone, Surrey, UK
| | | | - Isabelle Kempf
- ANSES, Ploufragan-Plouzané-Niort Laboratory, Ploufragan, France
| | | | | | | | - Ana Amaro
- National Institute of Agrarian and Veterinary Research (INIAV), National Reference Laboratory for Animal Health, Oeiras, Portugal
| | - Lurdes Clemente
- National Institute of Agrarian and Veterinary Research (INIAV), National Reference Laboratory for Animal Health, Oeiras, Portugal
| | - Joël Mossong
- Laboratoire National de Santé, Epidemiology and Microbial Genomics, Dudelange, Luxembourg
| | - Serge Losch
- Laboratoire de Médecine Vétérinaire de l'Etat, Veterinary Services Administration, Dudelange, Luxembourg
| | - Catherine Ragimbeau
- Laboratoire National de Santé, Epidemiology and Microbial Genomics, Dudelange, Luxembourg
| | - Ole Lund
- Technical University of Denmark, National Food Institute, European Union Reference Laboratory for Antimicrobial Resistance, WHO Collaborating Centre for Antimicrobial Resistance in Foodborne Pathogens and Genomics, FAO Reference Laboratory for Antimicrobial Resistance, Kgs. Lyngby, Denmark
| | - Frank M Aarestrup
- Technical University of Denmark, National Food Institute, European Union Reference Laboratory for Antimicrobial Resistance, WHO Collaborating Centre for Antimicrobial Resistance in Foodborne Pathogens and Genomics, FAO Reference Laboratory for Antimicrobial Resistance, Kgs. Lyngby, Denmark
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29
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Pöntinen AK, Top J, Arredondo-Alonso S, Tonkin-Hill G, Freitas AR, Novais C, Gladstone RA, Pesonen M, Meneses R, Pesonen H, Lees JA, Jamrozy D, Bentley SD, Lanza VF, Torres C, Peixe L, Coque TM, Parkhill J, Schürch AC, Willems RJL, Corander J. Apparent nosocomial adaptation of Enterococcus faecalis predates the modern hospital era. Nat Commun 2021; 12:1523. [PMID: 33750782 PMCID: PMC7943827 DOI: 10.1038/s41467-021-21749-5] [Citation(s) in RCA: 58] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Accepted: 02/05/2021] [Indexed: 12/20/2022] Open
Abstract
Enterococcus faecalis is a commensal and nosocomial pathogen, which is also ubiquitous in animals and insects, representing a classical generalist microorganism. Here, we study E. faecalis isolates ranging from the pre-antibiotic era in 1936 up to 2018, covering a large set of host species including wild birds, mammals, healthy humans, and hospitalised patients. We sequence the bacterial genomes using short- and long-read techniques, and identify multiple extant hospital-associated lineages, with last common ancestors dating back as far as the 19th century. We find a population cohesively connected through homologous recombination, a metabolic flexibility despite a small genome size, and a stable large core genome. Our findings indicate that the apparent hospital adaptations found in hospital-associated E. faecalis lineages likely predate the "modern hospital" era, suggesting selection in another niche, and underlining the generalist nature of this nosocomial pathogen.
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Affiliation(s)
- Anna K Pöntinen
- Department of Biostatistics, Faculty of Medicine, University of Oslo, Oslo, Norway.
| | - Janetta Top
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Sergio Arredondo-Alonso
- Department of Biostatistics, Faculty of Medicine, University of Oslo, Oslo, Norway
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | | | - Ana R Freitas
- UCIBIO/REQUIMTE, Laboratory of Microbiology, Biological Sciences Department, Faculty of Pharmacy, University of Porto, Porto, Portugal
| | - Carla Novais
- UCIBIO/REQUIMTE, Laboratory of Microbiology, Biological Sciences Department, Faculty of Pharmacy, University of Porto, Porto, Portugal
| | - Rebecca A Gladstone
- Department of Biostatistics, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Maiju Pesonen
- Oslo Centre for Biostatistics and Epidemiology (OCBE), Oslo University Hospital Research Support Services, Oslo, Norway
| | - Rodrigo Meneses
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Henri Pesonen
- Department of Biostatistics, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - John A Lees
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Dorota Jamrozy
- Parasites and Microbes, Wellcome Sanger Institute, Cambridge, UK
| | | | | | - Carmen Torres
- Department of Food and Agriculture, Area of Biochemistry and Molecular Biology, University of La Rioja, Logroño, Spain
| | - Luisa Peixe
- UCIBIO/REQUIMTE, Laboratory of Microbiology, Biological Sciences Department, Faculty of Pharmacy, University of Porto, Porto, Portugal
| | - Teresa M Coque
- Department of Microbiology, Ramón y Cajal Institute for Health Research Ramón y Cajal University Hospital, Madrid, Spain
- CIBER in Epidemiology and Public Health (CIBERESP), Madrid, Spain
| | - Julian Parkhill
- Wellcome Sanger Institute, Cambridge, UK
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Anita C Schürch
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Rob J L Willems
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Jukka Corander
- Department of Biostatistics, Faculty of Medicine, University of Oslo, Oslo, Norway.
- Parasites and Microbes, Wellcome Sanger Institute, Cambridge, UK.
- Helsinki Institute of Information Technology, Department of Mathematics and Statistics, University of Helsinki, Helsinki, Finland.
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30
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Kaplan M, Özgür E, Ersoy O, Kehribar L, İdil N, Uzun L. Borate mineral loading into acrylic bone cements to gain cost-effectivity, enhanced antibacterial resistivity, and better cellular integration properties. JOURNAL OF BIOMATERIALS SCIENCE-POLYMER EDITION 2021; 32:980-993. [PMID: 33492195 DOI: 10.1080/09205063.2021.1880169] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Polymethyl methacrylate (PMMA), called as bone cement, has been used in implant surgery, initially in dental practices, then in arthroplasty surgery for decades. Bone cement is a highly preferred chemical in the field of orthopedics due to its bone-like hardness and mechanical strength. Meanwhile, antibiotic-loaded cements are used in joints and similar surgeries are generally due to the risk of infection. In this study, we aimed to demonstrate the effects of borate mineral loading into bone cement on enhancing the antibacterial resistivity and cell integration as well as retaining mechanical properties. Moreover, the incorporation of minerals into bone cements makes them much more cost-friendly biomaterials for surgical operations. Herein, antibacterial properties were evaluated by using vancomycin- and gentamycin-susceptible strains of Enterococcus faecalis and Staphylococcus aureus whereas cell viability tests were performed by osteoblast cell lines. Three sets of the bone cements, plain, calcium borate-, and sodium borate-loaded, were prepared through commercial procedures and subjected to mechanical, antibacterial and cell viability tests. Percentage deformation determined by compression tests under 0.100 MPa pressure was determined in the range of 12.58%-10.67% in respect to the amount of sodium borate mineral loaded whereas that was determined in the range of 12.54%-9.87% in respect to the amount of calcium borate mineral loaded. Micro-CT results also supported good mineral integration and structural features of the composite bone cements. Furthermore, mineral incorporation enhanced the cell viability, in other words, cellular integrity, up to 101.28% for sodium borate-loaded (NB75, 7.5 g mineral) and 72.04% for calcium borate-loaded (CB75, 7.5 g mineral) bone cement according to the negative control group, fresh culture medium. As a conclusion, both of these minerals could be classified as promising alternatives for developing bone cements with better antibacterial resistivity and cellular integration properties.
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Affiliation(s)
- Mesut Kaplan
- Institute of Science, Division of Bioengineering, Hacettepe University, Ankara, Turkey
| | - Erdoğan Özgür
- Advanced Technologies Application and Research Center, Hacettepe University, Ankara, Turkey
| | - Orkun Ersoy
- Faculty of Engineering, Department of Geological Engineering, Hacettepe University, Ankara, Turkey
| | | | - Neslihan İdil
- Faculty of Science, Department of Biology, Hacettepe University, Ankara, Turkey
| | - Lokman Uzun
- Institute of Science, Division of Bioengineering, Hacettepe University, Ankara, Turkey.,Faculty of Science, Department of Chemistry, Hacettepe University, Ankara, Turkey
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31
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Enterococcus phage Nonaheksakonda infecting clinical isolates of Enterococcus faecalis represents a new lineage in the family Siphoviridae. Arch Virol 2021; 166:593-599. [PMID: 33392817 DOI: 10.1007/s00705-020-04905-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Accepted: 10/15/2020] [Indexed: 01/11/2023]
Abstract
Enterococcus phage Nonaheksakonda was isolated from wastewater, using a vancomycin-resistant strain of the opportunistic pathogen Enterococcus faecalis (VRE) as a host. Nonaheksakonda is a lytic phage infecting E. faecalis V583 and clinical isolates with at least four different multi-locus sequence types (MLSTs). The genome is a 41.9-kb double-stranded DNA molecule (34.6% GC) with 74 coding sequences. Comparative analysis revealed only one close relative, Enterococcus phage heks. All other phages had low protein similarity and shared less than 54% nucleotide sequence identity with phage Nonaheksakonda. The most similar phages were all classified and unclassified efquatroviruses. We propose that the phages Nonaheksakonda and heks represent a novel genus within the family Siphoviridae, order Caudovirales, for which we propose the name "Nonaheksakondavirus".
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32
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Liang KYH, Orata FD, Islam MT, Nasreen T, Alam M, Tarr CL, Boucher YF. A Vibrio cholerae Core Genome Multilocus Sequence Typing Scheme To Facilitate the Epidemiological Study of Cholera. J Bacteriol 2020; 202:e00086-20. [PMID: 32540931 PMCID: PMC7685551 DOI: 10.1128/jb.00086-20] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Accepted: 06/07/2020] [Indexed: 12/11/2022] Open
Abstract
Core genome multilocus sequence typing (cgMLST) has gained popularity in recent years in epidemiological research and subspecies-level classification. cgMLST retains the intuitive nature of traditional MLST but offers much greater resolution by utilizing significantly larger portions of the genome. Here, we introduce a cgMLST scheme for Vibrio cholerae, a bacterium abundant in marine and freshwater environments and the etiologic agent of cholera. A set of 2,443 core genes ubiquitous in V. cholerae were used to analyze a comprehensive data set of 1,262 clinical and environmental strains collected from 52 countries, including 65 newly sequenced genomes in this study. We established a sublineage threshold based on 133 allelic differences that creates clusters nearly identical to traditional MLST types, providing backwards compatibility to new cgMLST classifications. We also defined an outbreak threshold based on seven allelic differences that is capable of identifying strains from the same outbreak and closely related isolates that could give clues on outbreak origin. Using cgMLST, we confirmed the South Asian origin of modern epidemics and identified clustering affinity among sublineages of environmental isolates from the same geographic origin. Advantages of this method are highlighted by direct comparison with existing classification methods, such as MLST and single-nucleotide polymorphism-based methods. cgMLST outperforms all existing methods in terms of resolution, standardization, and ease of use. We anticipate this scheme will serve as a basis for a universally applicable and standardized classification system for V. cholerae research and epidemiological surveillance in the future. This cgMLST scheme is publicly available on PubMLST (https://pubmlst.org/vcholerae/).IMPORTANCE Toxigenic Vibrio cholerae isolates of the O1 and O139 serogroups are the causative agents of cholera, an acute diarrheal disease that plagued the world for centuries, if not millennia. Here, we introduce a core genome multilocus sequence typing scheme for V. cholerae Using this scheme, we have standardized the definition for subspecies-level classification, facilitating global collaboration in the surveillance of V. cholerae In addition, this typing scheme allows for quick identification of outbreak-related isolates that can guide subsequent analyses, serving as an important first step in epidemiological research. This scheme is also easily scalable to analyze thousands of isolates at various levels of resolution, making it an invaluable tool for large-scale ecological and evolutionary analyses.
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Affiliation(s)
- Kevin Y H Liang
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Fabini D Orata
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | | | - Tania Nasreen
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Munirul Alam
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research, Dhaka, Bangladesh
| | - Cheryl L Tarr
- Enteric Diseases Laboratory Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Yann F Boucher
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore
- Singapore Center for Environmental Life Sciences Engineering, National University of Singapore, Singapore, Singapore
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33
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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: 45] [Impact Index Per Article: 11.3] [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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34
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Kerschner H, Rosel AC, Hartl R, Hyden P, Stoeger A, Ruppitsch W, Allerberger F, Apfalter P. Oxazolidinone Resistance Mediated by optrA in Clinical Enterococcus faecalis Isolates in Upper Austria: First Report and Characterization by Whole Genome Sequencing. Microb Drug Resist 2020; 27:685-690. [PMID: 33090061 DOI: 10.1089/mdr.2020.0098] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The genetic mechanisms associated with acquisition of linezolid (LZD) resistance are diverse, including point mutations in the V domain of the 23S rRNA and the 50S ribosomal proteins as well as cfr, optrA, and/or poxtA genes, which may be plasmid- or chromosomally encoded. The aim of this study was to investigate through Whole Genome Sequencing (WGS)-based typing the presence and location of genes and point mutations associated with LZD resistance in two Enterococcus faecalis isolates from Upper Austrian patients. The isolates were retrieved during screening by LZD disk diffusion test of a total of 911 clinical E. faecalis isolates in 2017. The two E. faecalis isolates had LZD minimum inhibitory concentrations of 8 and 32 mg/L and were optrA-positive (ST476 and ST585). Bioinformatic analysis revealed the presence of optrA located in the chromosome of both isolates. One isolate carried the optrA gene in the transposon 6674, previously reported as chromosomally encoded, and the second isolate in fragments originating from the integrative plasmid pEF10748. Additional mechanisms of LZD resistance on the 23S rRNA and the 50S ribosomal proteins were detected. None of the patients reported travels to geographical areas with high LZD resistance or previous LZD treatments. This is the first report of optrA carrying E. faecalis, including characterization by WGS from Austria. LZD resistance in a low-prevalence setting is of concern and should be further monitored.
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Affiliation(s)
- Heidrun Kerschner
- National Reference Center for Antimicrobial Resistance and Nosocomial Infections (NRZ), Institute for Hygiene, Microbiology and Tropical Medicine, Ordensklinikum Linz Elisabethinen, Linz, Austria
| | - Adriana Cabal Rosel
- AGES-Austrian Agency for Health and Food Safety, Institute of Medical Microbiology and Hygiene, Vienna, Austria
| | - Rainer Hartl
- National Reference Center for Antimicrobial Resistance and Nosocomial Infections (NRZ), Institute for Hygiene, Microbiology and Tropical Medicine, Ordensklinikum Linz Elisabethinen, Linz, Austria
| | - Patrick Hyden
- CUBE, Division of Computational Systems Biology, University of Vienna, Vienna, Austria
| | - Anna Stoeger
- AGES-Austrian Agency for Health and Food Safety, Institute of Medical Microbiology and Hygiene, Vienna, Austria
| | - Werner Ruppitsch
- AGES-Austrian Agency for Health and Food Safety, Institute of Medical Microbiology and Hygiene, Vienna, Austria
| | - Franz Allerberger
- AGES-Austrian Agency for Health and Food Safety, Institute of Medical Microbiology and Hygiene, Vienna, Austria
| | - Petra Apfalter
- National Reference Center for Antimicrobial Resistance and Nosocomial Infections (NRZ), Institute for Hygiene, Microbiology and Tropical Medicine, Ordensklinikum Linz Elisabethinen, Linz, Austria
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35
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Gu J, Xie XJ, Liu JX, Shui JR, Zhang HY, Feng GY, Liu XY, Li LC, Lan QW, Jin QH, Li R, Peng L, Lei CW, Zhang AY. Prevalence and transmission of antimicrobial-resistant Staphylococci and Enterococci from shared bicycles in Chengdu, China. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 738:139735. [PMID: 32531590 DOI: 10.1016/j.scitotenv.2020.139735] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 04/27/2020] [Accepted: 05/25/2020] [Indexed: 06/11/2023]
Abstract
Shared bicycles are prevailing in China but the extent to which they contribute to maintaining and transmitting pathogens and antibiotic-resistant bacteria remain largely unknown. To fill the knowledge gap, herein, swab samples (n = 963) were collected from handlebars of shared bicycles in areas of hospital, school, metro station (n = 887) and riders (n = 76) in Chengdu, China. Staphylococci (n = 241) and Enterococci (n = 69) were widely distributed across sampling locations at a frequency of 2.3%-12.9%, and 0.08%-5.5%, respectively. Bicycle or rider-borne Gram-positive bacteria were frequently resistant to clinically important antibiotics including linezolid, fosfomycin, and vancomycin, and a significant portion of these isolates (3.4%-16.6% for Staphylococci and 0.1%-13.8% for Enterococci) indicated multidrug resistance. Nineteen Staphylococcus aureus isolates were identified in this collection and 52.6% of which were considered as methicillin-resistant S. aureus. Whole genome sequencing further characterized 26 antimicrobial resistance genes (ARGs) including fosB, fusB, and lnu(G) in S. aureus and 21 ARGs including optrA in Enterococci. Leveraging a complementary approach with conventional MLST, whole genome SNP and MLST analyses, we present that genetically closely-related bacteria were found in bicycles and riders across geographical-distinct locations suggesting bacterial transmission. Further, five new ST types 5697-5701 were firstly characterized in S. aureus. ST 942 and ST 1640 are new ST types observed in E. faecalis, and E. faecium, respectively. Our results highlighted the risk of shared bicycle system in disseminating pathogens and antibiotic resistance which warrants effective disinfections.
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Affiliation(s)
- Ju Gu
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, Sichuan, PR China
| | - Xian-Jun Xie
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, Sichuan, PR China
| | - Jin-Xin Liu
- Department of Food Science and Technology, Robert Mondavi Institute for Wine and Food Science, University of California, Davis, One Shields Ave., Davis, CA 95616, United States of America
| | - Jun-Rui Shui
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, Sichuan, PR China
| | - Hao-Yu Zhang
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, Sichuan, PR China
| | - Gan-Yu Feng
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, Sichuan, PR China
| | - Xiao-Yu Liu
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, Sichuan, PR China
| | - Lin-Can Li
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, Sichuan, PR China
| | - Qi-Wei Lan
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, Sichuan, PR China
| | - Qi-Han Jin
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, Sichuan, PR China
| | - Rui Li
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, Sichuan, PR China
| | - Li Peng
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, Sichuan, PR China
| | - Chang-Wei Lei
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, Sichuan, PR China
| | - An-Yun Zhang
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, Sichuan, PR China.
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Huang CH, Chen CC, Chiu SH, Liou JS, Lin YC, Lin JS, Huang L, Watanabe K. Development of a High-Resolution Single-Nucleotide Polymorphism Strain-Typing Assay Using Whole Genome-Based Analyses for the Lactobacillus acidophilus Probiotic Strain. Microorganisms 2020; 8:E1445. [PMID: 32967209 PMCID: PMC7564606 DOI: 10.3390/microorganisms8091445] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 09/02/2020] [Accepted: 09/16/2020] [Indexed: 11/24/2022] Open
Abstract
Lactobacillus acidophilus is one of the most commonly used industrial products worldwide. Since its probiotic efficacy is strain-specific, the identification of probiotics at both the species and strain levels is necessary. However, neither phenotypic nor conventional genotypic methods have enabled the effective differentiation of L. acidophilus strains. In this study, a whole-genome sequence-based analysis was carried out to establish high-resolution strain typing of 41 L. acidophilus strains (including commercial isolates and reference strains) using the cano-wgMLST_BacCompare analytics platform; consequently, a strain-specific discrimination method for the probiotic strain LA1063 was developed. Using a core-genome multilocus sequence-typing (cgMLST) scheme based on 1390 highly conserved genes, 41 strains could be assigned to 34 sequence types. Subsequently, we screened a set of 92 loci with a discriminatory power equal to that of the 1390 loci cgMLST scheme. A strain-specific polymerase chain reaction combined with a multiplex minisequencing method was developed based on four (phoU, secY, tilS, and uvrA_1) out of 21 loci, which could be discriminated between LA1063 and other L. acidophilus strains using the cgMLST data. We confirmed that the strain-specific single-nucleotide polymorphisms method could be used to quickly and accurately identify the L. acidophilus probiotic strain LA1063 in commercial products.
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Affiliation(s)
- Chien-Hsun Huang
- Bioresource Collection and Research Center, Food Industry Research and Development Institute, 331 Shih-Pin Rd, Hsinchu 30062, Taiwan; (C.-H.H.); (S.-H.C.); (J.-S.L.); (L.H.)
| | - Chih-Chieh Chen
- Institute of Medical Science and Technology, National Sun Yat-sen University, Kaohsiung 80424, Taiwan;
- Rapid Screening Research Center for Toxicology and Biomedicine, National Sun Yat-sen University, Kaohsiung 80424, Taiwan
| | - Shih-Hau Chiu
- Bioresource Collection and Research Center, Food Industry Research and Development Institute, 331 Shih-Pin Rd, Hsinchu 30062, Taiwan; (C.-H.H.); (S.-H.C.); (J.-S.L.); (L.H.)
| | - Jong-Shian Liou
- Bioresource Collection and Research Center, Food Industry Research and Development Institute, 331 Shih-Pin Rd, Hsinchu 30062, Taiwan; (C.-H.H.); (S.-H.C.); (J.-S.L.); (L.H.)
| | - Yu-Chun Lin
- Livestock Research Institute, Council of Agriculture, Executive Yuan, Tainan 71246, Taiwan;
| | - Jin-Seng Lin
- Culture Collection & Research Institute, Synbio Tech Inc., Kaohsiung 82151, Taiwan;
| | - Lina Huang
- Bioresource Collection and Research Center, Food Industry Research and Development Institute, 331 Shih-Pin Rd, Hsinchu 30062, Taiwan; (C.-H.H.); (S.-H.C.); (J.-S.L.); (L.H.)
| | - Koichi Watanabe
- Bioresource Collection and Research Center, Food Industry Research and Development Institute, 331 Shih-Pin Rd, Hsinchu 30062, Taiwan; (C.-H.H.); (S.-H.C.); (J.-S.L.); (L.H.)
- Culture Collection & Research Institute, Synbio Tech Inc., Kaohsiung 82151, Taiwan;
- Department of Animal Science and Technology, College of Bioresources and Agriculture, National Taiwan University, No. 50, Ln. 155, Sec. 3, Keelung Rd., Taipei 10673, Taiwan
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Roer L, Hansen F, Hasman H, Hammerum AM, Cavaco LM. Characterisation of extended-spectrum β-lactamase/plasmid AmpC-β-lactamase-producing Escherichia coli isolates from long-term recurrent bloodstream infections. Int J Antimicrob Agents 2020; 56:106041. [PMID: 32479890 DOI: 10.1016/j.ijantimicag.2020.106041] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Revised: 04/24/2020] [Accepted: 05/21/2020] [Indexed: 11/29/2022]
Abstract
The aim of this study was to investigate recurrent infections in individual patients caused by extended-spectrum β-lactamase and plasmid AmpC β-lactamase-producing Escherichia coli (ESBL/pAmpC-Ec) isolates with >12-month interval. The Danish national collection of ESBL/pAmpC-Ec isolates collected from January 2014 through June 2017 was screened for patients with multiple isolates with >12 months between the episodes. Isolates underwent whole-genome sequencing and were analysed for antimicrobial resistance genes, virulence genes and multilocus sequence typing (MLST). Isolates were subtyped by core genome MLST (cgMLST) and CH typing. From a total of 970 patients, 15 unrelated patients experienced recurrent infections with ESBL/pAmpC-Ec. Of the 15 patients, 10 (67%) were found to be infected a second or third time with a genetically identical or similar strain. The resistance and virulence properties of the strains were similar in individual patients, however they were quite diverse when comparing between patients. Recurrent ESBL/pAmpC-Ec bloodstream infections of genetically related strains occurring with >12-month interval might be related to the previous episode and to a lesser extent be caused by re-infection. With >1000 days between the first and second episode of genetically similar strains (four allele differences), the recurrent infection is likely due to long-term host colonisation by ESBL/pAmpC-Ec. From this analysis, strains able to cause such recurrent infection were relatively diverse between patients. Knowledge about host and strain factors influencing such recurrent infections is needed to implement preventive measures.
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Affiliation(s)
- Louise Roer
- Department of Bacteria, Parasites & Fungi, Infectious Disease Preparedness, Statens Serum Institut, Artillerivej 5, 2300 Copenhagen S, Denmark.
| | - Frank Hansen
- Department of Bacteria, Parasites & Fungi, Infectious Disease Preparedness, Statens Serum Institut, Artillerivej 5, 2300 Copenhagen S, Denmark
| | - Henrik Hasman
- Department of Bacteria, Parasites & Fungi, Infectious Disease Preparedness, Statens Serum Institut, Artillerivej 5, 2300 Copenhagen S, Denmark
| | - Anette M Hammerum
- Department of Bacteria, Parasites & Fungi, Infectious Disease Preparedness, Statens Serum Institut, Artillerivej 5, 2300 Copenhagen S, Denmark
| | - Lina Maria Cavaco
- Department of Bacteria, Parasites & Fungi, Infectious Disease Preparedness, Statens Serum Institut, Artillerivej 5, 2300 Copenhagen S, Denmark; Department of Cellular and Molecular Medicine, Center for Peptide-Based Antibiotics, The Panum Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3, 2200 Copenhagen N, Denmark
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38
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Neumann B, Bender JK, Maier BF, Wittig A, Fuchs S, Brockmann D, Semmler T, Einsele H, Kraus S, Wieler LH, Vogel U, Werner G. Comprehensive integrated NGS-based surveillance and contact-network modeling unravels transmission dynamics of vancomycin-resistant enterococci in a high-risk population within a tertiary care hospital. PLoS One 2020; 15:e0235160. [PMID: 32579600 PMCID: PMC7314025 DOI: 10.1371/journal.pone.0235160] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Accepted: 06/09/2020] [Indexed: 02/07/2023] Open
Abstract
Vancomycin-resistant E. faecium (VRE) are an important cause of nosocomial infections, which are rapidly transmitted in hospitals. To identify possible transmission routes, we applied combined genomics and contact-network modeling to retrospectively evaluate routine VRE screening data generated by the infection control program of a hemato-oncology unit. Over 1 year, a total of 111 VRE isolates from 111 patients were collected by anal swabs in a tertiary care hospital in Southern Germany. All isolated VRE were whole-genome sequenced, followed by different in-depth bioinformatics analyses including genotyping and determination of phylogenetic relations, aiming to evaluate a standardized workflow. Patient movement data were used to overlay sequencing data to infer transmission events and strain dynamics over time. A predominant clone harboring vanB and exhibiting genotype ST117/CT469 (n = 67) was identified. Our comprehensive combined analyses suggested intra-hospital spread, especially of clone ST117/CT469, despite of extensive screening, single room placement, and contact isolation. A new interactive tool to visualize these complex data was designed. Furthermore, a patient-contact network-modeling approach was developed, which indicates both the periodic import of the clone into the hospital and its spread within the hospital due to patient movements. The analyzed spread of VRE was most likely due to placement of patients in the same room prior to positivity of screening. We successfully demonstrated the added value for this combined strategy to extract well-founded knowledge from interdisciplinary data sources. The combination of patient-contact modeling and high-resolution typing unraveled the transmission dynamics within the hospital department and, additionally, a constant VRE influx over time.
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Affiliation(s)
- Bernd Neumann
- Division of Nosocomial Pathogens and Antibiotic Resistance, Robert Koch Institute, Wernigerode, Germany
- * E-mail:
| | - Jennifer K. Bender
- Division of Nosocomial Pathogens and Antibiotic Resistance, Robert Koch Institute, Wernigerode, Germany
| | - Benjamin F. Maier
- Computational Epidemiology, Robert Koch Institute, Berlin, Germany
- Department of Physics, Humboldt University of Berlin, Berlin, Germany
| | - Alice Wittig
- Computational Epidemiology, Robert Koch Institute, Berlin, Germany
- Institute for Theoretical Biology, Humboldt University of Berlin, Berlin, Germany
| | - Stephan Fuchs
- Division of Nosocomial Pathogens and Antibiotic Resistance, Robert Koch Institute, Wernigerode, Germany
| | - Dirk Brockmann
- Computational Epidemiology, Robert Koch Institute, Berlin, Germany
- Institute for Theoretical Biology, Humboldt University of Berlin, Berlin, Germany
| | | | - Hermann Einsele
- Department of Internal Medicine II, University Hospital Würzburg, Wüzburg, Germany
| | - Sabrina Kraus
- Department of Internal Medicine II, University Hospital Würzburg, Wüzburg, Germany
| | | | - Ulrich Vogel
- Institute for Hygiene and Microbiology, Julius-Maximilians University Würzburg, Würzburg, Germany
| | - Guido Werner
- Division of Nosocomial Pathogens and Antibiotic Resistance, Robert Koch Institute, Wernigerode, Germany
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39
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de Sales RO, Migliorini LB, Puga R, Kocsis B, Severino P. A Core Genome Multilocus Sequence Typing Scheme for Pseudomonas aeruginosa. Front Microbiol 2020; 11:1049. [PMID: 32528447 PMCID: PMC7264379 DOI: 10.3389/fmicb.2020.01049] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Accepted: 04/28/2020] [Indexed: 12/15/2022] Open
Abstract
Pseudomonas aeruginosa is a ubiquitous microorganism and an important opportunistic pathogen responsible for a broad spectrum of infections mainly in immunosuppressed and critically ill patients. Molecular investigations traditionally rely on pulsed field gel electrophoresis (PFGE) and multilocus sequence typing (MLST). In this work we propose a core genome multilocus sequence typing (cgMLST) scheme for P. aeruginosa, a methodology that combines traditional MLST principles with whole genome sequencing data. All publicly available complete P. aeruginosa genomes, representing the diversity of this species, were used to establish a cgMLST scheme targeting 2,653 genes. The scheme was then tested using genomes available at contig, chromosome and scaffold levels. The proposed cgMLST scheme for P. aeruginosa typed over 99% (2,314/2,325) of the genomes available for this study considering at least 95% of the cgMLST target genes present. The absence of a certain number gene targets at the threshold considered for both the creation and validation steps due to low genome sequence quality is possibly the main reason for this result. The cgMLST scheme was compared with previously published whole genome single nucleotide polymorphism analysis for the characterization of the population structure of the epidemic clone ST235 and results were highly similar. In order to evaluate the typing resolution of the proposed scheme, collections of isolates belonging to two important STs associated with cystic fibrosis, ST146 and ST274, were typed using this scheme, and ST235 isolates associated with an outbreak were evaluated. Besides confirming the relatedness of all the isolates, earlier determined by MLST, the higher resolution of cgMLST denotes that it may be suitable for surveillance programs, overcoming possible shortcomings of classical MLST. The proposed scheme is publicly available at: https://github.com/BioinformaticsHIAEMolecularMicrobiology/cgMLST-Pseudomonas-aeruginosa.
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Affiliation(s)
- Romário Oliveira de Sales
- Hospital Israelita Albert Einstein, Albert Einstein Research and Education Institute, São Paulo, Brazil
| | - Letícia Busato Migliorini
- Hospital Israelita Albert Einstein, Albert Einstein Research and Education Institute, São Paulo, Brazil
| | - Renato Puga
- Hospital Israelita Albert Einstein, Albert Einstein Research and Education Institute, São Paulo, Brazil
| | - Bela Kocsis
- Institute of Medical Microbiology, Semmelweis University, Budapest, Hungary
| | - Patricia Severino
- Hospital Israelita Albert Einstein, Albert Einstein Research and Education Institute, São Paulo, Brazil
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40
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Fida M, Cunningham SA, Murphy MP, Bonomo RA, Hujer KM, Hujer AM, Kreiswirth BN, Chia N, Jeraldo PR, Nelson H, Zinsmaster NM, Toraskar N, Chang W, Patel R. Core genome MLST and resistome analysis of Klebsiella pneumoniae using a clinically amenable workflow. Diagn Microbiol Infect Dis 2020; 97:114996. [PMID: 32098688 DOI: 10.1016/j.diagmicrobio.2020.114996] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Revised: 01/13/2020] [Accepted: 01/16/2020] [Indexed: 12/19/2022]
Abstract
Whole genome sequencing (WGS) is replacing traditional microbiological typing methods for investigation of outbreaks in clinical settings. Here, we used a clinical microbiology laboratory core genome multilocus sequence typing (cgMLST) workflow to analyze 40 isolates of K. pneumoniae which are part of the Antimicrobial Resistance Leadership Group (ARLG) isolate collection, alongside 10 Mayo Clinic K. pneumoniae isolates, comparing results to those of pulsed-field gel electrophoresis (PFGE). Additionally, we used the WGS data to predict phenotypic antimicrobial susceptibility (AST). Thirty-one of 40 ARLG K. pneumoniae isolates belonged to the same PFGE type, all of which, alongside 3 isolates of different PFGE types, formed a large cluster by cgMLST. PFGE and cgMLST were completely concordant for the 10 Mayo Clinic K. pneumoniae isolates. For AST prediction, the overall agreement between phenotypic AST and genotypic prediction was 95.6%.
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Affiliation(s)
- Madiha Fida
- Division of Infectious Diseases, Department of Medicine, Mayo Clinic, Rochester, MN.
| | | | | | - Robert A Bonomo
- Louis Stokes Cleveland Department of Veteran Affairs Medical Center, Cleveland, OH; Department of Medicine, Case Western Reserve University, Cleveland, OH; Departments of Pharmacology, Biochemistry, Molecular Biology and Microbiology, and the Center for Proteomics and Bioinformatics, Case Western Reserve University, Cleveland, OH, and CWRU-Cleveland VAMC Center for Antimicrobial Resistance and Epidemiology (Case VA CARES), Cleveland, OH
| | - Kristine M Hujer
- Louis Stokes Cleveland Department of Veteran Affairs Medical Center, Cleveland, OH; Department of Medicine, Case Western Reserve University, Cleveland, OH
| | - Andrea M Hujer
- Louis Stokes Cleveland Department of Veteran Affairs Medical Center, Cleveland, OH; Department of Medicine, Case Western Reserve University, Cleveland, OH
| | | | - Nicholas Chia
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN; Department of Surgery, Mayo Clinic, Rochester, MN
| | - Patricio R Jeraldo
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN; Department of Surgery, Mayo Clinic, Rochester, MN
| | - Heidi Nelson
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN; Department of Surgery, Mayo Clinic, Rochester, MN
| | | | | | | | - Robin Patel
- Division of Infectious Diseases, Department of Medicine, Mayo Clinic, Rochester, MN; Division of Clinical Microbiology, Mayo Clinic, Rochester, MN
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41
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Kim B, Wang YC, Hespen CW, Espinosa J, Salje J, Rangan KJ, Oren DA, Kang JY, Pedicord VA, Hang HC. Enterococcus faecium secreted antigen A generates muropeptides to enhance host immunity and limit bacterial pathogenesis. eLife 2019; 8:e45343. [PMID: 30969170 PMCID: PMC6483599 DOI: 10.7554/elife.45343] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Accepted: 04/04/2019] [Indexed: 12/16/2022] Open
Abstract
We discovered that Enterococcus faecium (E. faecium), a ubiquitous commensal bacterium, and its secreted peptidoglycan hydrolase (SagA) were sufficient to enhance intestinal barrier function and pathogen tolerance, but the precise biochemical mechanism was unknown. Here we show E. faecium has unique peptidoglycan composition and remodeling activity through SagA, which generates smaller muropeptides that more effectively activates nucleotide-binding oligomerization domain-containing protein 2 (NOD2) in mammalian cells. Our structural and biochemical studies show that SagA is a NlpC/p60-endopeptidase that preferentially hydrolyzes crosslinked Lys-type peptidoglycan fragments. SagA secretion and NlpC/p60-endopeptidase activity was required for enhancing probiotic bacteria activity against Clostridium difficile pathogenesis in vivo. Our results demonstrate that the peptidoglycan composition and hydrolase activity of specific microbiota species can activate host immune pathways and enhance tolerance to pathogens.
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Affiliation(s)
- Byungchul Kim
- Laboratory of Chemical Biology and Microbial PathogenesisThe Rockefeller UniversityNew YorkUnited States
| | - Yen-Chih Wang
- Laboratory of Chemical Biology and Microbial PathogenesisThe Rockefeller UniversityNew YorkUnited States
| | - Charles W Hespen
- Laboratory of Chemical Biology and Microbial PathogenesisThe Rockefeller UniversityNew YorkUnited States
| | - Juliel Espinosa
- Laboratory of Chemical Biology and Microbial PathogenesisThe Rockefeller UniversityNew YorkUnited States
| | - Jeanne Salje
- Centre for Tropical Medicine and Global Health, Nuffield Department of MedicineUniversity of OxfordOxfordUnited Kingdom
| | - Kavita J Rangan
- Laboratory of Chemical Biology and Microbial PathogenesisThe Rockefeller UniversityNew YorkUnited States
| | - Deena A Oren
- Structural Biology Resource CenterThe Rockefeller UniversityNew YorkUnited States
| | - Jin Young Kang
- Laboratory of Molecular BiophysicsThe Rockefeller UniversityNew YorkUnited States
| | - Virginia A Pedicord
- Laboratory of Chemical Biology and Microbial PathogenesisThe Rockefeller UniversityNew YorkUnited States
- Cambridge Institute of Therapeutic Immunology & Infectious DiseaseUniversity of CambridgeCambridgeUnited Kingdom
| | - Howard C Hang
- Laboratory of Chemical Biology and Microbial PathogenesisThe Rockefeller UniversityNew YorkUnited States
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