1
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Cai M, Song K, Wang R, Wang S, Chen H, Wang H. Tracking intra-species and inter-genus transmission of KPC through global plasmids mining. Cell Rep 2024; 43:114351. [PMID: 38923465 DOI: 10.1016/j.celrep.2024.114351] [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: 03/21/2024] [Revised: 04/28/2024] [Accepted: 05/28/2024] [Indexed: 06/28/2024] Open
Abstract
Klebsiella pneumoniae carbapenemase (KPC) poses a major public health risk. Understanding its transmission dynamics requires examining the epidemiological features of related plasmids. Our study compiled 15,660 blaKPC-positive isolates globally over the past two decades. We found extensive diversity in the genetic background of KPC, with 23 Tn4401-related and 341 non-Tn4401 variants across 163 plasmid types in 14 genera. Intra-K. pneumoniae and cross-genus KPC transmission patterns varied across four distinct periods. In the initial periods, plasmids with narrow host ranges gradually established a survival advantage. In later periods, broad-host-range plasmids became crucial for cross-genera transmission. In total, 61 intra-K. pneumoniae and 66 cross-genus transmission units have been detected. Furthermore, phylogenetic reconstruction dated the origin of KPC transmission back to 1991 and revealed frequent exchanges across countries. Our research highlights the frequent and transient spread events of KPC mediated by plasmids across multiple genera and offers theoretical support for high-risk plasmid monitoring.
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Affiliation(s)
- Meng Cai
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing 100044, China
| | - Kaiwen Song
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing 100044, China; Institute of Medical Technology, Peking University Health Science Center, Beijing 100191, China
| | - Ruobing Wang
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing 100044, China
| | - Shuyi Wang
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing 100044, China
| | - Hongbin Chen
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing 100044, China.
| | - Hui Wang
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing 100044, China; Institute of Medical Technology, Peking University Health Science Center, Beijing 100191, China.
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2
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Robins K, O'Donnell G, Neumann A, Schmidt W, Hart A, Graham DW. Antimicrobial resistance in rural rivers: Comparative study of the Coquet (Northumberland) and Eden (Cumbria) River catchments. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 928:172348. [PMID: 38614353 DOI: 10.1016/j.scitotenv.2024.172348] [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: 12/20/2023] [Revised: 04/04/2024] [Accepted: 04/08/2024] [Indexed: 04/15/2024]
Abstract
Many studies have characterised resistomes in river microbial communities. However, few have compared resistomes in parallel rural catchments that have few point-source inputs of antimicrobial genes (ARGs) and organisms (i.e., AMR) - catchments where one can contrast more nebulous drivers of AMR in rural rivers. Here, we used quantitative microbial profiling (QMP) to compare resistomes and microbiomes in two rural river catchments in Northern England, the Coquet and Eden in Northumberland and Cumbria, respectively, with different hydrological and geographical conditions. The Eden has higher flow rates, higher annual surface runoff, and longer periods of soil saturation, whereas the Coquet is drier and has lower flowrates. QMP analysis showed the Eden contained significantly more abundant microbes associated with soil sources, animal faeces, and wastewater than the Coquet, which had microbiomes like less polluted rivers (Wilcoxon test, p < 0.01). The Eden also had greater ARG abundances and resistome diversity (Kruskal Wallis, p < 0.05), and higher levels of potentially clinically relevant ARGs. The Eden catchment had greater and flashier runoff and more extensive agricultural land use in its middle reach, which explains higher levels of AMR in the river. Hydrological and geographic factors drive AMR in rural rivers, which must be considered in environmental monitoring programmes.
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Affiliation(s)
- Katie Robins
- School of Engineering, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Greg O'Donnell
- School of Engineering, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Anke Neumann
- School of Engineering, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Wiebke Schmidt
- Chief Scientists Group, Environment Agency, Horizon House, Deanery Road, Bristol BS1 5AH, UK
| | - Alwyn Hart
- Chief Scientists Group, Environment Agency, Horizon House, Deanery Road, Bristol BS1 5AH, UK
| | - David W Graham
- School of Engineering, Newcastle University, Newcastle upon Tyne NE1 7RU, UK.
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3
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Hua S, Wang J, Zhao Z, Tian F, Zhao M, Wang Y, Zhang R, Han Z, Gao S, Lv X, Li H, Shen X, Ma X, Feng Z. A Multiplex Recombinase-Aided qPCR Assay for Highly Sensitive and Rapid Detection of khe, bla KPC -2, and bla NDM -1 Genes in Klebsiella pneumoniae. J Clin Lab Anal 2024; 38:e25038. [PMID: 38590133 PMCID: PMC11137842 DOI: 10.1002/jcla.25038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2023] [Revised: 03/08/2024] [Accepted: 03/26/2024] [Indexed: 04/10/2024] Open
Abstract
OBJECTIVE This study aimed to establish a highly sensitive and rapid single-tube, two-stage, multiplex recombinase-aided qPCR (mRAP) assay to specifically detect the khe, blaKPC-2, and blaNDM-1 genes in Klebsiella pneumoniae. METHODS mRAP was carried out in a qPCR instrument within 1 h. The analytical sensitivities of mRAP for khe, blaKPC-2, and blaNDM-1 genes were tested using recombinant plasmids and dilutions of reference strains. A total of 137 clinical isolates and 86 sputum samples were used to validate the clinical performance of mRAP. RESULTS mRAP achieved the sensitivities of 10, 8, and 14 copies/reaction for khe, blaKPC-2, and blaNDM-1 genes, respectively, superior to qPCR. The Kappa value of qPCR and mRAP for detecting khe, blaKPC-2, and blaNDM-1 genes was 1, 0.855, and 1, respectively (p < 0.05). CONCLUSION mRAP is a rapid and highly sensitive assay for potential clinical identification of khe, blaKPC-2, and blaNDM-1 genes in K. pneumoniae.
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Affiliation(s)
- Shao‐wei Hua
- Graduate SchoolHebei North UniversityZhangjiakouChina
- Department of Clinical LaboratoryHebei General HospitalShijiazhuangChina
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and PreventionChinese Center for Disease Control and PreventionBeijingChina
| | - Jie Wang
- Department of Clinical LaboratoryHebei General HospitalShijiazhuangChina
| | - Zi‐jin Zhao
- Graduate SchoolHebei North UniversityZhangjiakouChina
- Department of Clinical LaboratoryHebei General HospitalShijiazhuangChina
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and PreventionChinese Center for Disease Control and PreventionBeijingChina
| | - Feng‐yu Tian
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and PreventionChinese Center for Disease Control and PreventionBeijingChina
| | - Meng Zhao
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and PreventionChinese Center for Disease Control and PreventionBeijingChina
- Graduate SchoolHebei Medical UniversityShijiazhuangChina
| | - Yu‐xin Wang
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and PreventionChinese Center for Disease Control and PreventionBeijingChina
- Graduate SchoolHebei Medical UniversityShijiazhuangChina
| | - Rui‐qing Zhang
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and PreventionChinese Center for Disease Control and PreventionBeijingChina
| | - Zhi‐qiang Han
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and PreventionChinese Center for Disease Control and PreventionBeijingChina
- Graduate SchoolHebei Medical UniversityShijiazhuangChina
| | - Shi‐jue Gao
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and PreventionChinese Center for Disease Control and PreventionBeijingChina
| | - Xiao‐na Lv
- Graduate SchoolHebei North UniversityZhangjiakouChina
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and PreventionChinese Center for Disease Control and PreventionBeijingChina
| | - Hong‐yi Li
- Graduate SchoolHebei North UniversityZhangjiakouChina
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and PreventionChinese Center for Disease Control and PreventionBeijingChina
| | - Xin‐xin Shen
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and PreventionChinese Center for Disease Control and PreventionBeijingChina
| | - Xue‐jun Ma
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and PreventionChinese Center for Disease Control and PreventionBeijingChina
| | - Zhi‐shan Feng
- Department of Clinical LaboratoryHebei General HospitalShijiazhuangChina
- Hebei Key Laboratory of Molecular MedicineShijiazhuangChina
- Hebei Clinical Research Center for Laboratory MedicineShijiazhuangChina
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4
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Li X, Li C, Zhou L, Wang Q, Yao J, Zhang X, Yu Y, Li R, Zhou H, Tu Y. Global phylogeography and genomic characterization of bla KPC and bla NDM-positive clinical Klebsiella aerogenes isolates from China, 2016-2022. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 923:171560. [PMID: 38458455 DOI: 10.1016/j.scitotenv.2024.171560] [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: 12/20/2023] [Revised: 03/03/2024] [Accepted: 03/05/2024] [Indexed: 03/10/2024]
Abstract
Carbapenem-resistant Klebsiella aerogenes (CRKA), being one of the members of carbapenem-resistant Enterobacteriaceae (CRE), has caused great public health concern, but with fewer studies compared to other CRE members. Furthermore, studies on phylogenetic analysis based on whole genome Single-Nucleotide Polymorphism (SNP) of CRKA were limited. Here, 20 CRKA isolates (11 blaKPC-2-bearing and 9 blaNDM-1/5-harboring) were characterized by antimicrobial susceptibility testing, conjugation assay, whole genome sequencing (WGS) and bioinformatics analysis. Additionally, the phylogeographic relationships of K. aerogenes were further investigated from public databases. All isolates were multidrug-resistant (MDR) bacteria, and they demonstrated susceptibility to colistin. Most blaKPC-2 or blaNDM-1/5-carrying plasmids were found to be conjugative. Phylogenetic analysis revealed the clonal dissemination of K. aerogenes primarily occurred within clinical settings. Notably, some strains in this study showed the potential for clonal transmission, sharing few SNPs between K. aerogenes and KPC- and/or NDM-positive K. aerogenes isolated from various countries. The STs of K. aerogenes strains had significant diversity. WGS analysis showed that the IncFIIK plasmid was the most prevalent carrier of blaKPC-2, and, blaNDM-1/5 were detected on the IncX3 plasmids. The Tn6296 and Tn3000 transposons were most common vehicles for facilitating the transmission of blaKPC-2 and blaNDM-1/5, respectively. This study highlights the importance of continuous screening and surveillance by WGS for analysis of drug-resistant strains in hospital settings, and provide clinical information that supports epidemiological and public health research on human pathogens.
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Affiliation(s)
- Xi Li
- Laboratory Medicine Center, Department of Clinical Laboratory, Zhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical College, Hangzhou, Zhejiang 310014, China
| | - Changan Li
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Longjie Zhou
- Laboratory Medicine Center, Department of Clinical Laboratory, Zhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical College, Hangzhou, Zhejiang 310014, China
| | - Qiaojun Wang
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Jiayao Yao
- Laboratory Medicine Center, Department of Clinical Laboratory, Zhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical College, Hangzhou, Zhejiang 310014, China
| | - Xiaofan Zhang
- Laboratory Medicine Center, Department of Clinical Laboratory, Zhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical College, Hangzhou, Zhejiang 310014, China
| | - Yunsong Yu
- Center for General Practice Medicine, Department of Infectious Diseases, Zhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical College, Hangzhou, Zhejiang 310014, China
| | - Ruichao Li
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu 225009, China.
| | - Hua Zhou
- Department of Respiratory and Critical Care Medicine, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310003, China.
| | - Yuexing Tu
- Department of Critical Care Medicine, Tongde Hospital of Zhejiang Province, #234 Gucui Road, Hangzhou, Zhejiang 310012, China.
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5
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Di Pilato V, Pollini S, Miriagou V, Rossolini GM, D'Andrea MM. Carbapenem-resistant Klebsiella pneumoniae: the role of plasmids in emergence, dissemination, and evolution of a major clinical challenge. Expert Rev Anti Infect Ther 2024; 22:25-43. [PMID: 38236906 DOI: 10.1080/14787210.2024.2305854] [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: 11/13/2023] [Accepted: 01/11/2024] [Indexed: 01/31/2024]
Abstract
INTRODUCTION Klebsiella pneumoniae is a major agent of healthcare-associated infections and a cause of some community-acquired infections, including severe bacteremic infections associated with metastatic abscesses in liver and other organs. Clinical relevance is compounded by its outstanding propensity to evolve antibiotic resistance. In particular, the emergence and dissemination of carbapenem resistance in K. pneumoniae has posed a major challenge due to the few residual treatment options, which have only recently been expanded by some new agents. The epidemiological success of carbapenem-resistant K. pneumoniae (CR-Kp) is mainly linked with clonal lineages that produce carbapenem-hydrolyzing enzymes (carbapenemases) encoded by plasmids. AREAS COVERED Here, we provide an updated overview on the mechanisms underlying the emergence and dissemination of CR-Kp, focusing on the role that plasmids have played in this phenomenon and in the co-evolution of resistance and virulence in K. pneumoniae. EXPERT OPINION CR-Kp have disseminated on a global scale, representing one of the most important contemporary public health issues. These strains are almost invariably associated with complex multi-drug resistance (MDR) phenotypes, which can also include recently approved antibiotics. The heterogeneity of the molecular bases responsible for these phenotypes poses significant hurdles for therapeutic and diagnostic purposes.
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Affiliation(s)
- Vincenzo Di Pilato
- Department of Surgical Sciences and Integrated Diagnostics (DISC), University of Genoa, Genoa, Italy
| | - Simona Pollini
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
- Microbiology and Virology Unit, Careggi University Hospital, Florence, Italy
| | - Vivi Miriagou
- Laboratory of Bacteriology, Hellenic Pasteur Institute, Athens, Greece
| | - Gian Maria Rossolini
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
- Microbiology and Virology Unit, Careggi University Hospital, Florence, Italy
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Mohamed HS, Galal L, Hayer J, Benavides JA, Bañuls AL, Dupont C, Conquet G, Carrière C, Dumont Y, Didelot MN, Michon AL, Jean-Pierre H, Aboubaker MH, Godreuil S. Genomic epidemiology of carbapenemase-producing Gram-negative bacteria at the human-animal-environment interface in Djibouti city, Djibouti. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 905:167160. [PMID: 37730061 DOI: 10.1016/j.scitotenv.2023.167160] [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: 06/16/2023] [Revised: 09/14/2023] [Accepted: 09/15/2023] [Indexed: 09/22/2023]
Abstract
The emergence of carbapenem resistance is a major public health threat in sub-Saharan Africa but remains poorly understood, particularly at the human-animal-environment interface. This study provides the first One Health-based study on the epidemiology of Carbapenemase-Producing Gram-Negative Bacteria (CP-GNB) in Djibouti City, Djibouti, East Africa. In total, 800 community urine samples and 500 hospital specimens from humans, 270 livestock fecal samples, 60 fish samples, and 20 water samples were collected and tested for carbapenem resistance. The overall estimated CP-GNB prevalence was 1.9 % (32/1650 samples) and specifically concerned 0.3 % of community urine samples, 2.8 % of clinical specimens, 2.6 % of livestock fecal samples, 11.7 % of fish samples, and 10 % of water samples. The 32 CP-GNB included 19 Escherichia coli, seven Acinetobacter baumannii, five Klebsiella pneumoniae, and one Proteus mirabilis isolate. Short-read (Illumina) and long-read (Nanopore) genome sequencing revealed that carbapenem resistance was mainly associated with chromosomal carriage of blaNDM-1, blaOXA-23, blaOXA-48, blaOXA-66, and blaOXA-69 in A. baumannii, and with plasmid carriage in Enterobacterales (blaNDM-1 and blaOXA-181 in E. coli, blaNDM-1, blaNDM-5 and blaOXA-48 in K. pneumoniae, and blaNDM-1 in P. mirabilis). Moreover, 17/32 CP-GNB isolates belonged to three epidemic clones: (1) A. baumannii sequence type (ST) 1697,2535 that showed a distribution pattern consistent with intra- and inter-hospital dissemination; (2) E. coli ST10 that circulated at the human-animal-environment interface; and (3) K. pneumoniae ST147 that circulated at the human-environment interface. Horizontal exchanges probably contributed to carbapenem resistance dissemination in the city, especially the blaOXA-181-carrying ColKP3-IncX3 hybrid plasmid that was found in E. coli isolates belonging to different STs. Our study highlights that despite a relatively low CP-GNB prevalence in Djibouti City, plasmids harboring carbapenem resistance circulate in humans, animals and environment. Our findings stress the need to implement preventive and control measures for reducing the circulation of this potentially emerging public health threat.
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Affiliation(s)
- Hasna Saïd Mohamed
- Laboratoire de Bactériologie, Centre Hospitalier Universitaire de Montpellier, Montpellier, France; UMR MIVEGEC, Université de Montpellier, IRD, CNRS, Montpellier, France; Hôpital Général Peltier de Djibouti, Djibouti ville, Djibouti; Laboratoire de Biologie Médicale de la Mer Rouge, Djibouti City, Djibouti
| | - Lokman Galal
- UMR MIVEGEC, Université de Montpellier, IRD, CNRS, Montpellier, France.
| | - Juliette Hayer
- UMR MIVEGEC, Université de Montpellier, IRD, CNRS, Montpellier, France
| | - Julio A Benavides
- UMR MIVEGEC, Université de Montpellier, IRD, CNRS, Montpellier, France; Doctorado en Medicina de la Conservación y Centro de Investigación para la Sustentabilidad, Facultad de Ciencias de la Vida, Universidad Andrés Bello, República 440, Santiago, Chile
| | - Anne-Laure Bañuls
- UMR MIVEGEC, Université de Montpellier, IRD, CNRS, Montpellier, France; LMI DRISA, Montpellier, France
| | - Chloé Dupont
- Laboratoire de Bactériologie, Centre Hospitalier Universitaire de Montpellier, Montpellier, France
| | - Guilhem Conquet
- Laboratoire de Bactériologie, Centre Hospitalier Universitaire de Montpellier, Montpellier, France; UMR MIVEGEC, Université de Montpellier, IRD, CNRS, Montpellier, France
| | - Christian Carrière
- Laboratoire de Bactériologie, Centre Hospitalier Universitaire de Montpellier, Montpellier, France; UMR MIVEGEC, Université de Montpellier, IRD, CNRS, Montpellier, France
| | - Yann Dumont
- Laboratoire de Bactériologie, Centre Hospitalier Universitaire de Montpellier, Montpellier, France; UMR MIVEGEC, Université de Montpellier, IRD, CNRS, Montpellier, France
| | - Marie-Noëlle Didelot
- Laboratoire de Bactériologie, Centre Hospitalier Universitaire de Montpellier, Montpellier, France; UMR MIVEGEC, Université de Montpellier, IRD, CNRS, Montpellier, France
| | - Anne-Laure Michon
- Laboratoire de Bactériologie, Centre Hospitalier Universitaire de Montpellier, Montpellier, France; UMR MIVEGEC, Université de Montpellier, IRD, CNRS, Montpellier, France
| | - Hélène Jean-Pierre
- Laboratoire de Bactériologie, Centre Hospitalier Universitaire de Montpellier, Montpellier, France; UMR MIVEGEC, Université de Montpellier, IRD, CNRS, Montpellier, France
| | - Mohamed Houmed Aboubaker
- Laboratoire de Biologie Médicale de la Mer Rouge, Djibouti City, Djibouti; Laboratoire de la Caisse Nationale de Sécurité Sociale, Djibouti City 696, Djibouti
| | - Sylvain Godreuil
- Laboratoire de Bactériologie, Centre Hospitalier Universitaire de Montpellier, Montpellier, France; UMR MIVEGEC, Université de Montpellier, IRD, CNRS, Montpellier, France; Jeune Equipe Associée à l'IRD (JEAI), FASORAM, Montpellier, France
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7
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Baker KS, Jauneikaite E, Hopkins KL, Lo SW, Sánchez-Busó L, Getino M, Howden BP, Holt KE, Musila LA, Hendriksen RS, Amoako DG, Aanensen DM, Okeke IN, Egyir B, Nunn JG, Midega JT, Feasey NA, Peacock SJ. Genomics for public health and international surveillance of antimicrobial resistance. THE LANCET. MICROBE 2023; 4:e1047-e1055. [PMID: 37977162 DOI: 10.1016/s2666-5247(23)00283-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 08/16/2023] [Accepted: 08/22/2023] [Indexed: 11/19/2023]
Abstract
Historically, epidemiological investigation and surveillance for bacterial antimicrobial resistance (AMR) has relied on low-resolution isolate-based phenotypic analyses undertaken at local and national reference laboratories. Genomic sequencing has the potential to provide a far more high-resolution picture of AMR evolution and transmission, and is already beginning to revolutionise how public health surveillance networks monitor and tackle bacterial AMR. However, the routine integration of genomics in surveillance pipelines still has considerable barriers to overcome. In 2022, a workshop series and online consultation brought together international experts in AMR and pathogen genomics to assess the status of genomic applications for AMR surveillance in a range of settings. Here we focus on discussions around the use of genomics for public health and international AMR surveillance, noting the potential advantages of, and barriers to, implementation, and proposing recommendations from the working group to help to drive the adoption of genomics in public health AMR surveillance. These recommendations include the need to build capacity for genome sequencing and analysis, harmonising and standardising surveillance systems, developing equitable data sharing and governance frameworks, and strengthening interactions and relationships among stakeholders at multiple levels.
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Affiliation(s)
- Kate S Baker
- Department for Clinical Infection, Microbiology, and Immunology, University of Liverpool, Liverpool, UK; Department of Genetics, University of Cambridge, Cambridge, UK.
| | - Elita Jauneikaite
- Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, UK; NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Department of Infectious Disease, Imperial College London, Hammersmith Hospital, London, UK
| | - Katie L Hopkins
- HCAI, Fungal, AMR, AMU & Sepsis Division, UK Health Security Agency, London, UK; Antimicrobial Resistance and Healthcare Associated Infections Reference Unit, UK Health Security Agency, London, UK
| | - Stephanie W Lo
- Parasites and Microbes, Wellcome Sanger Institute, Hinxton, UK
| | - Leonor Sánchez-Busó
- Genomics and Health Area, Foundation for the Promotion of Health and Biomedical Research in the Valencian Community (FISABIO-Public Health), Valencia, Spain; CIBERESP, ISCIII, Madrid, Spain
| | - Maria Getino
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Department of Infectious Disease, Imperial College London, Hammersmith Hospital, London, UK
| | - Benjamin P Howden
- The Centre for Pathogen Genomics, Doherty Institute, The University of Melbourne, Melbourne, VIC, Australia
| | - Kathryn E Holt
- Department of Infection Biology, London School of Hygiene & Tropical Medicine, London, UK; Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, VIC, Australia
| | - Lillian A Musila
- Department of Emerging Infectious Diseases, United States Army Medical Research Directorate - Africa, Nairobi, Kenya; Kenya Medical Research Institute, Nairobi, Kenya
| | - Rene S Hendriksen
- National Food Institute, Technical University of Denmark, Lyngby, Denmark
| | - Daniel G Amoako
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, Johannesburg, South Africa; School of Health Sciences, University of KwaZulu-Natal, Durban, South Africa; Department of Pathobiology, University of Guelph, Guelph, ON, Canada
| | - David M Aanensen
- Centre for Genomic Pathogen Surveillance, Nuffield Department of Medicine, University of Oxford, Big Data Institute, Oxford, UK
| | - Iruka N Okeke
- Department of Pharmaceutical Microbiology, Faculty of Pharmacy, University of Ibadan, Ibadan, Oyo State, Nigeria
| | - Beverly Egyir
- Department of Bacteriology, Noguchi Memorial Institute for Medical Research, University of Ghana, Legon-Accra, Ghana, West Africa
| | - Jamie G Nunn
- Infectious Disease Challenge Area, Wellcome Trust, London, UK
| | | | - Nicholas A Feasey
- Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, UK; Malawi Liverpool Wellcome Research Programme, Malawi
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8
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Macesic N, Hawkey J, Vezina B, Wisniewski JA, Cottingham H, Blakeway LV, Harshegyi T, Pragastis K, Badoordeen GZ, Dennison A, Spelman DW, Jenney AWJ, Peleg AY. Genomic dissection of endemic carbapenem resistance reveals metallo-beta-lactamase dissemination through clonal, plasmid and integron transfer. Nat Commun 2023; 14:4764. [PMID: 37553339 PMCID: PMC10409761 DOI: 10.1038/s41467-023-39915-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 07/03/2023] [Indexed: 08/10/2023] Open
Abstract
Infections caused by metallo-beta-lactamase-producing organisms (MBLs) are a global health threat. Our understanding of transmission dynamics and how MBLs establish endemicity remains limited. We analysed two decades of blaIMP-4 evolution in a hospital using sequence data from 270 clinical and environmental isolates (including 169 completed genomes) and identified the blaIMP-4 gene across 7 Gram-negative genera, 68 bacterial strains and 7 distinct plasmid types. We showed how an initial multi-species outbreak of conserved IncC plasmids (95 genomes across 37 strains) allowed endemicity to be established through the ability of blaIMP-4 to disseminate in successful strain-genetic setting pairs we termed propagators, in particular Serratia marcescens and Enterobacter hormaechei. From this reservoir, blaIMP-4 persisted through diversification of genetic settings that resulted from transfer of blaIMP-4 plasmids between bacterial hosts and of the integron carrying blaIMP-4 between plasmids. Our findings provide a framework for understanding endemicity and spread of MBLs and may have broader applicability to other carbapenemase-producing organisms.
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Affiliation(s)
- Nenad Macesic
- Department of Infectious Diseases, The Alfred Hospital and Central Clinical School, Monash University, Melbourne, Australia
- Centre to Impact AMR, Monash University, Clayton, Australia
| | - Jane Hawkey
- Department of Infectious Diseases, The Alfred Hospital and Central Clinical School, Monash University, Melbourne, Australia
| | - Ben Vezina
- Department of Infectious Diseases, The Alfred Hospital and Central Clinical School, Monash University, Melbourne, Australia
| | - Jessica A Wisniewski
- Department of Infectious Diseases, The Alfred Hospital and Central Clinical School, Monash University, Melbourne, Australia
| | - Hugh Cottingham
- Department of Infectious Diseases, The Alfred Hospital and Central Clinical School, Monash University, Melbourne, Australia
| | - Luke V Blakeway
- Department of Infectious Diseases, The Alfred Hospital and Central Clinical School, Monash University, Melbourne, Australia
| | - Taylor Harshegyi
- Department of Infectious Diseases, The Alfred Hospital and Central Clinical School, Monash University, Melbourne, Australia
| | - Katherine Pragastis
- Department of Infectious Diseases, The Alfred Hospital and Central Clinical School, Monash University, Melbourne, Australia
| | - Gnei Zweena Badoordeen
- Department of Infectious Diseases, The Alfred Hospital and Central Clinical School, Monash University, Melbourne, Australia
| | | | - Denis W Spelman
- Department of Infectious Diseases, The Alfred Hospital and Central Clinical School, Monash University, Melbourne, Australia
- Microbiology Unit, Alfred Hospital, Melbourne, Australia
| | - Adam W J Jenney
- Department of Infectious Diseases, The Alfred Hospital and Central Clinical School, Monash University, Melbourne, Australia
- Microbiology Unit, Alfred Hospital, Melbourne, Australia
| | - Anton Y Peleg
- Department of Infectious Diseases, The Alfred Hospital and Central Clinical School, Monash University, Melbourne, Australia.
- Centre to Impact AMR, Monash University, Clayton, Australia.
- Infection Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, Australia.
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9
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Simner PJ, Bergman Y, Fan Y, Jacobs EB, Ramakrishnan S, Lu J, Lewis S, Hanlon A, Tamma PD, Schatz MC, Timp W, Carroll KC. Multicentre genetic diversity study of carbapenem-resistant Enterobacterales: predominance of untypeable pUVA-like blaKPC bearing plasmids. JAC Antimicrob Resist 2023; 5:dlad061. [PMID: 37251303 PMCID: PMC10214462 DOI: 10.1093/jacamr/dlad061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 04/27/2023] [Indexed: 05/31/2023] Open
Abstract
Objectives Carbapenem-resistant Enterobacterales (CRE) are an urgent public health threat. A better understanding of the molecular epidemiology and transmission dynamics of CRE is necessary to limit their dissemination within healthcare settings. We sought to investigate the mechanisms of resistance and spread of CRE within multiple hospitals in Maryland. Methods From 2016 to 2018, all CRE were collected from any specimen source from The Johns Hopkins Medical Institutions. The isolates were further characterized using both phenotypic and genotypic approaches, including short- and/or long-read WGS. Results From 2016 to 2018, 302 of 40 908 (0.7%) unique Enterobacterales isolates were identified as CRE. Of CRE, 142 (47%) were carbapenemase-producing CRE with KPC (80.3%) predominating among various genera. Significant genetic diversity was identified among all CRE with high-risk clones serving as major drivers of clonal clusters. Further, we found the predominance of pUVA-like plasmids, with a subset harbouring resistance genes to environmental cleaning agents, involved in intergenus dissemination of blaKPC genes. Conclusions Our findings provide valuable data to understand the transmission dynamics of all CRE within the greater Maryland region. These data can help guide targeted interventions to limit CRE transmission in healthcare facilities.
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Affiliation(s)
| | - Yehudit Bergman
- Department of Pathology, Division of Medical Microbiology, Johns Hopkins University School of Medicine, 600 N Wolfe Street, Meyer B1-125, Baltimore, MD, USA
| | - Yunfan Fan
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Emily B Jacobs
- Department of Pathology, Division of Medical Microbiology, Johns Hopkins University School of Medicine, 600 N Wolfe Street, Meyer B1-125, Baltimore, MD, USA
| | | | - Jennifer Lu
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
- Center for Computations Biology, Whiting School of Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Shawna Lewis
- Department of Pathology, Division of Medical Microbiology, Johns Hopkins University School of Medicine, 600 N Wolfe Street, Meyer B1-125, Baltimore, MD, USA
| | - Ann Hanlon
- Department of Pathology, Division of Medical Microbiology, Johns Hopkins University School of Medicine, 600 N Wolfe Street, Meyer B1-125, Baltimore, MD, USA
| | - Pranita D Tamma
- Department of Pediatrics, Division of Pediatric Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Michael C Schatz
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
- Department of Biology, Johns Hopkins University, Baltimore, MD, USA
| | - Winston Timp
- Department of Medicine, Division of Infectious Disease, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
- Center for Computations Biology, Whiting School of Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Karen C Carroll
- Department of Pathology, Division of Medical Microbiology, Johns Hopkins University School of Medicine, 600 N Wolfe Street, Meyer B1-125, Baltimore, MD, USA
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10
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Werner G, Abu Sin M, Bahrs C, Brogden S, Feßler AT, Hagel S, Kaspar H, Köck R, Kreienbrock L, Krüger-Haker H, Maechler F, Noll I, Pletz MW, Tenhagen BA, Schwarz S, Walther B, Mielke M. [Therapy-relevant antibiotic resistances in a One Health context]. Bundesgesundheitsblatt Gesundheitsforschung Gesundheitsschutz 2023:10.1007/s00103-023-03713-4. [PMID: 37184673 DOI: 10.1007/s00103-023-03713-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 04/28/2023] [Indexed: 05/16/2023]
Abstract
One Health refers to a concept that links human, animal, and environmental health. In Germany, there is extensive data on antibiotic resistance (AMR) and multidrug-resistant (micro)organisms (MDRO) in human and veterinary medicine, as well as from studies in various environmental compartments (soil, water, wastewater). All these activities are conducted according to different specifications and standards, which makes it difficult to compare data. A focus on AMR and MDRO of human therapeutic importance is helpful to provide some guidance. Most data are available across sectors on methicillin-resistant Staphylococcus aureus (MRSA) and multiresistant Enterobacterales such as Escherichia coli and Klebsiella pneumoniae. Here, the trends of resistance are heterogeneous. Antibiotic use leads to MRE selection, which is well documented. Success in minimizing antibiotic use has also been demonstrated in recent years in several sectors and could be correlated with success in containing AMR and MDRO (e.g., decrease in MRSA in human medicine). Sector-specific measures to reduce the burden of MDRO and AMR are also necessary, as not all resistance problems are linked to other sectors. Carbapenem resistance is still rare, but most apparent in human pathogens. Colistin resistance occurs in different sectors but shows different mechanisms in each. Resistance to antibiotics of last resort such as linezolid is rare in Germany, but shows a specific One Health correlation. Efforts to harmonize methods, for example in the field of antimicrobial susceptibility testing and genome-based pathogen and AMR surveillance, are an important first step towards a better comparability of the different data collections.
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Affiliation(s)
- Guido Werner
- Robert Koch Institut, Berlin, Deutschland.
- Abt. Infektionskrankheiten, Fachgebiet Nosokomiale Infektionserreger und Antibiotikaresistenzen, Robert Koch-Institut, Außenstelle Wernigerode, Burgstr. 37, 38855, Wernigerode, Deutschland.
| | - Muna Abu Sin
- Robert Koch Institut, Berlin, Deutschland
- WHO Collaborating Centre for Antimicrobial Resistance, Consumption and Healthcare-Associated Infections, Berlin, Deutschland
| | - Christina Bahrs
- Institut für Infektionsmedizin und Krankenhaushygiene, Universitätsklinikum Jena, Jena, Deutschland
| | - Sandra Brogden
- Institut für Biometrie, Epidemiologie und Informationsverarbeitung, Stiftung Tierärztliche Hochschule Hannover, Hannover, Deutschland
- WHO Collaborating Centre for Research and Training for Health at the Human-Animal-Environment Interface, Hannover, Deutschland
| | - Andrea T Feßler
- Institut für Mikrobiologie und Tierseuchen, Fachbereich Veterinärmedizin, Freie Universität Berlin, Berlin, Deutschland
- Tiermedizinisches Zentrum für Resistenzforschung (TZR), Fachbereich Veterinärmedizin, Freie Universität Berlin, Berlin, Deutschland
| | - Stefan Hagel
- Institut für Infektionsmedizin und Krankenhaushygiene, Universitätsklinikum Jena, Jena, Deutschland
| | - Heike Kaspar
- Bundesamt für Verbraucherschutz und Lebensmittelsicherheit, Berlin, Deutschland
| | - Robin Köck
- Bereich Hygiene und Umweltmedizin, Universitätsmedizin Essen, Essen, Deutschland
- Institut für Hygiene, Universitätsklinikum Münster, Münster, Deutschland
| | - Lothar Kreienbrock
- Institut für Biometrie, Epidemiologie und Informationsverarbeitung, Stiftung Tierärztliche Hochschule Hannover, Hannover, Deutschland
- WHO Collaborating Centre for Research and Training for Health at the Human-Animal-Environment Interface, Hannover, Deutschland
| | - Henrike Krüger-Haker
- Institut für Mikrobiologie und Tierseuchen, Fachbereich Veterinärmedizin, Freie Universität Berlin, Berlin, Deutschland
- Tiermedizinisches Zentrum für Resistenzforschung (TZR), Fachbereich Veterinärmedizin, Freie Universität Berlin, Berlin, Deutschland
| | - Frederike Maechler
- Institut für Hygiene und Umweltmedizin, Charité - Universitätsmedizin Berlin, Berlin, Deutschland
| | - Ines Noll
- Robert Koch Institut, Berlin, Deutschland
- WHO Collaborating Centre for Antimicrobial Resistance, Consumption and Healthcare-Associated Infections, Berlin, Deutschland
| | - Mathias W Pletz
- Institut für Infektionsmedizin und Krankenhaushygiene, Universitätsklinikum Jena, Jena, Deutschland
| | - Bernd-Alois Tenhagen
- Fachbereich Epidemiologie, Zoonosen und Antibiotikaresistenz, Abteilung Biologische Sicherheit, Bundesinstitut für Risikobewertung BfR, Berlin, Deutschland
| | - Stefan Schwarz
- Institut für Mikrobiologie und Tierseuchen, Fachbereich Veterinärmedizin, Freie Universität Berlin, Berlin, Deutschland
- Tiermedizinisches Zentrum für Resistenzforschung (TZR), Fachbereich Veterinärmedizin, Freie Universität Berlin, Berlin, Deutschland
| | - Birgit Walther
- Robert Koch Institut, Berlin, Deutschland
- Fachgebiet Mikrobiologische Risiken, Abteilung Umwelthygiene, Umweltbundesamt, Berlin, Deutschland
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11
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Kessler C, Hou J, Neo O, Buckner MMC. In situ, in vivo, and in vitro approaches for studying AMR plasmid conjugation in the gut microbiome. FEMS Microbiol Rev 2022; 47:6807411. [PMID: 36341518 PMCID: PMC9841969 DOI: 10.1093/femsre/fuac044] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 09/23/2022] [Accepted: 11/03/2022] [Indexed: 11/09/2022] Open
Abstract
Antimicrobial resistance (AMR) is a global threat, with evolution and spread of resistance to frontline antibiotics outpacing the development of novel treatments. The spread of AMR is perpetuated by transfer of antimicrobial resistance genes (ARGs) between bacteria, notably those encoded by conjugative plasmids. The human gut microbiome is a known 'melting pot' for plasmid conjugation, with ARG transfer in this environment widely documented. There is a need to better understand the factors affecting the incidence of these transfer events, and to investigate methods of potentially counteracting the spread of ARGs. This review describes the use and potential of three approaches to studying conjugation in the human gut: observation of in situ events in hospitalized patients, modelling of the microbiome in vivo predominantly in rodent models, and the use of in vitro models of various complexities. Each has brought unique insights to our understanding of conjugation in the gut. The use and development of these systems, and combinations thereof, will be pivotal in better understanding the significance, prevalence, and manipulability of horizontal gene transfer in the gut microbiome.
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Affiliation(s)
- Celia Kessler
- Institute of Microbiology and Infection College of Medical and Dental Sciences Biosciences Building University Road West University of Birmingham, B15 2TT, United Kingdom
| | - Jingping Hou
- Institute of Microbiology and Infection College of Medical and Dental Sciences Biosciences Building University Road West University of Birmingham, B15 2TT, United Kingdom
| | - Onalenna Neo
- Institute of Microbiology and Infection College of Medical and Dental Sciences Biosciences Building University Road West University of Birmingham, B15 2TT, United Kingdom
| | - Michelle M C Buckner
- Corresponding author: Biosciences Building, University Road West, University of Birmingham, Birmingham B15 2TT, United Kingdom. Tel: +44 (0)121 415 8758; E-mail:
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12
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Jiang J, Chen L, Chen X, Li P, Xu X, Fowler VG, van Duin D, Wang M. Carbapenemase-Encoding Gene Copy Number Estimator (CCNE): a Tool for Carbapenemase Gene Copy Number Estimation. Microbiol Spectr 2022; 10:e0100022. [PMID: 35863018 PMCID: PMC9431437 DOI: 10.1128/spectrum.01000-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 06/14/2022] [Indexed: 11/20/2022] Open
Abstract
Carbapenemase production is one of the leading mechanisms of carbapenem resistance in Gram-negative bacteria. An increase in carbapenemase gene (blaCarb) copies is an important mechanism of carbapenem resistance. No currently available bioinformatics tools allow for reliable detection and reporting of carbapenemase gene copy numbers. Here, we describe the carbapenemase-encoding gene copy number estimator (CCNE), a ready-to-use bioinformatics tool that was developed to estimate blaCarb copy numbers from whole-genome sequencing data. Its performance on Klebsiella pneumoniae carbapenemase gene (blaKPC) copy number estimation was evaluated by simulation and quantitative PCR (qPCR), and the results were compared with available algorithms. CCNE has two components, CCNE-acc and CCNE-fast. CCNE-acc detects blaCarb copy number in a comprehensive and high-accuracy way, while CCNE-fast rapidly screens blaCarb copy numbers. CCNE-acc achieved the best accuracy (100%) and the lowest root mean squared error (RMSE; 0.07) in simulated noise data sets, compared to the assembly-based method (23.4% accuracy, 1.697 RMSE) and the OrthologsBased method (78.9% accuracy, 0.395 RMSE). In the qPCR validation, a high consistency was observed between the blaKPC copy number determined by qPCR and that determined with CCNE. Reverse transcription-qPCR transcriptional analysis of 40 isolates showed that blaKPC expression was positively correlated with the blaKPC copy numbers detected by CCNE (P < 0.001). An association study of 357 KPC-producing K. pneumoniae isolates and their antimicrobial susceptibility identified a significant association between the estimated blaKPC copy number and MICs of imipenem (P < 0.001) and ceftazidime-avibactam (P < 0.001). Overall, CCNE is a useful genomic tool for the analysis of antimicrobial resistance genes copy number; it is available at https://github.com/biojiang/ccne. IMPORTANCE Globally disseminated carbapenem-resistant Enterobacterales is an urgent threat to public health. The most common carbapenem resistance mechanism is the production of carbapenemases. Carbapenemase-producing isolates often exhibit a wide range of carbapenem MICs. Higher carbapenem MICs have been associated with treatment failure. The increase of carbapenemase gene (blaCarb) copy numbers contributes to increased carbapenem MICs. However, blaCarb gene copy number detection is not routinely conducted during a genomic analysis, in part due to the lack of optimal bioinformatics tools. In this study, we describe a ready-to-use tool we developed and designated the carbapenemase-encoding gene copy number estimator (CCNE) that can be used to estimate the blaCarb copy number directly from whole-genome sequencing data, and we extended the data to support the analysis of all known blaCarb genes and some other antimicrobial resistance genes. Furthermore, CCNE can be used to interrogate the correlations between genotypes and susceptibility phenotypes and to improve our understanding of antimicrobial resistance mechanisms.
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Affiliation(s)
- Jianping Jiang
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, China
| | - Liang Chen
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, New Jersey, USA
- Department of Medical Sciences, Hackensack Meridian School of Medicine, Nutley, New Jersey, USA
| | - Xin Chen
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, China
| | - Pei Li
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, China
| | - Xiaogang Xu
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, China
| | - Vance G. Fowler
- Division of Infectious Diseases, University of North Carolina, Chapel Hill, North Carolina, USA
| | - David van Duin
- Duke Clinical Research Institute, Duke University Medical Center, Durham, North Carolina, USA
| | - Minggui Wang
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, China
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13
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Bottery MJ. Ecological dynamics of plasmid transfer and persistence in microbial communities. Curr Opin Microbiol 2022; 68:102152. [PMID: 35504055 PMCID: PMC9586876 DOI: 10.1016/j.mib.2022.102152] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 03/18/2022] [Accepted: 04/01/2022] [Indexed: 11/28/2022]
Abstract
Plasmids are a major driver of horizontal gene transfer in prokaryotes, allowing the sharing of ecologically important accessory traits between distantly related bacterial taxa. Within microbial communities, interspecies transfer of conjugative plasmids can rapidly drive the generation genomic innovation and diversification. Recent studies are starting to shed light on how the microbial community context, that is, the bacterial diversity together with interspecies interactions that occur within a community, can alter the dynamics of conjugative plasmid transfer and persistence. Here, I summarise the latest research exploring how community ecology can both facilitate and impose barriers to the spread of conjugative plasmids within complex microbial communities. Ultimately, the fate of plasmids within communities is unlikely to be determined by any one individual host, rather it will depend on the interacting factors imposed by the community in which it is embedded.
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Affiliation(s)
- Michael J Bottery
- Division of Evolution Infection and Genomics, School of Biological Sciences, University of Manchester, Manchester M13 9PL, UK.
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14
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Migliorini LB, Leaden L, de Sales RO, Correa NP, Marins MM, Koga PCM, Toniolo ADR, de Menezes FG, Martino MDV, Mingorance J, Severino P. The Gastrointestinal Load of Carbapenem-Resistant Enterobacteriacea Is Associated With the Transition From Colonization to Infection by Klebsiella pneumoniae Isolates Harboring the blaKPC Gene. Front Cell Infect Microbiol 2022; 12:928578. [PMID: 35865821 PMCID: PMC9294314 DOI: 10.3389/fcimb.2022.928578] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 05/26/2022] [Indexed: 01/15/2023] Open
Abstract
Background Healthcare-associated infections by carbapenem-resistant Klebsiella pneumoniae are difficult to control. Virulence and antibiotic resistance genes contribute to infection, but the mechanisms associated with the transition from colonization to infection remain unclear. Objective We investigated the transition from carriage to infection by K. pneumoniae isolates carrying the K. pneumoniae carbapenemase–encoding gene blaKPC (KpKPC). Methods KpKPC isolates detected within a 10-year period in a single tertiary-care hospital were characterized by pulsed-field gel electrophoresis (PFGE), multilocus sequencing typing, capsular lipopolysaccharide and polysaccharide typing, antimicrobial susceptibility profiles, and the presence of virulence genes. The gastrointestinal load of carbapenem-resistant Enterobacteriaceae and of blaKPC-carrying bacteria was estimated by relative quantification in rectal swabs. Results were evaluated as contributors to the progression from carriage to infection. Results No PGFE type; ST-, K-, or O-serotypes; antimicrobial susceptibility profiles; or the presence of virulence markers, such yersiniabactin and colibactin, were associated with carriage or infection, with ST437 and ST11 being the most prevalent clones. Admission to intensive and semi-intensive care units was a risk factor for the development of infections (OR 2.79, 95% CI 1.375 to 5.687, P=0.005), but higher intestinal loads of carbapenem-resistant Enterobacteriaceae or of blaKPC-carrying bacteria were the only factors associated with the transition from colonization to infection in this cohort (OR 8.601, 95% CI 2.44 to 30.352, P<0.001). Conclusion The presence of resistance and virulence mechanisms were not associated with progression from colonization to infection, while intestinal colonization by carbapenem-resistant Enterobacteriacea and, more specifically, the load of gastrointestinal carriage emerged as an important determinant of infection.
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Affiliation(s)
- Letícia Busato Migliorini
- Albert Einstein Research and Education Institute, Hospital Israelita Albert Einstein, Sao Paulo, Brazil
| | - Laura Leaden
- Albert Einstein Research and Education Institute, Hospital Israelita Albert Einstein, Sao Paulo, Brazil
| | - Romário Oliveira de Sales
- Albert Einstein Research and Education Institute, Hospital Israelita Albert Einstein, Sao Paulo, Brazil
| | | | - Maryana Mara Marins
- Albert Einstein Research and Education Institute, Hospital Israelita Albert Einstein, Sao Paulo, Brazil
| | | | | | | | | | - Jesús Mingorance
- Servicio de Microbiología, Hospital Universitario La Paz, IdiPAZ, Madrid, Spain
| | - Patricia Severino
- Albert Einstein Research and Education Institute, Hospital Israelita Albert Einstein, Sao Paulo, Brazil
- *Correspondence: Patricia Severino,
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15
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Xu C, Liu C, Chen K, Zeng P, Chan EWC, Chen S. Otilonium bromide boosts antimicrobial activities of colistin against Gram-negative pathogens and their persisters. Commun Biol 2022; 5:613. [PMID: 35729200 PMCID: PMC9213495 DOI: 10.1038/s42003-022-03561-z] [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: 11/29/2021] [Accepted: 06/02/2022] [Indexed: 11/09/2022] Open
Abstract
Colistin is the last-line antibiotic against Gram-negative pathogens. Here we identify an FDA-approved drug, Otilonium bromide (Ob), which restores the activity of colistin against colistin-resistant Gram-negative bacteria in vitro and in a mouse infection model. Ob also reduces the colistin dosage required for effective treatment of infections caused by colistin-susceptible bacteria, thereby reducing the toxicity of the drug regimen. Furthermore, Ob acts synergistically with colistin in eradicating multidrug-tolerant persisters of Gram-negative bacteria in vitro. Functional studies and microscopy assays confirm that the synergistic antimicrobial effect exhibited by the Ob and colistin involves permeabilizing the bacterial cell membrane, dissipating proton motive force and suppressing efflux pumps, resulting in membrane damages, cytosol leakage and eventually bacterial cell death. Our findings suggest that Ob is a colistin adjuvant which can restore the clinical value of colistin in combating life-threatening, multidrug resistant Gram-negative pathogens. The drug otilonium bromide restores the activity of colistin against colistinresistant Gram-negative bacteria in vitro and in a mouse infection model, suggesting that this combination may restore the value of colistin in treatment of antibiotic resistant disease.
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Affiliation(s)
- Chen Xu
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon, Hong Kong
| | - Chenyu Liu
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon, Hong Kong
| | - Kaichao Chen
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon, Hong Kong
| | - Ping Zeng
- State Key Lab of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong
| | - Edward Wai Chi Chan
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon, Hong Kong.,State Key Lab of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong
| | - Sheng Chen
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon, Hong Kong.
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16
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Salamzade R, Manson AL, Walker BJ, Brennan-Krohn T, Worby CJ, Ma P, He LL, Shea TP, Qu J, Chapman SB, Howe W, Young SK, Wurster JI, Delaney ML, Kanjilal S, Onderdonk AB, Bittencourt CE, Gussin GM, Kim D, Peterson EM, Ferraro MJ, Hooper DC, Shenoy ES, Cuomo CA, Cosimi LA, Huang SS, Kirby JE, Pierce VM, Bhattacharyya RP, Earl AM. Inter-species geographic signatures for tracing horizontal gene transfer and long-term persistence of carbapenem resistance. Genome Med 2022; 14:37. [PMID: 35379360 PMCID: PMC8981930 DOI: 10.1186/s13073-022-01040-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 03/22/2022] [Indexed: 01/21/2023] Open
Abstract
BACKGROUND Carbapenem-resistant Enterobacterales (CRE) are an urgent global health threat. Inferring the dynamics of local CRE dissemination is currently limited by our inability to confidently trace the spread of resistance determinants to unrelated bacterial hosts. Whole-genome sequence comparison is useful for identifying CRE clonal transmission and outbreaks, but high-frequency horizontal gene transfer (HGT) of carbapenem resistance genes and subsequent genome rearrangement complicate tracing the local persistence and mobilization of these genes across organisms. METHODS To overcome this limitation, we developed a new approach to identify recent HGT of large, near-identical plasmid segments across species boundaries, which also allowed us to overcome technical challenges with genome assembly. We applied this to complete and near-complete genome assemblies to examine the local spread of CRE in a systematic, prospective collection of all CRE, as well as time- and species-matched carbapenem-susceptible Enterobacterales, isolated from patients from four US hospitals over nearly 5 years. RESULTS Our CRE collection comprised a diverse range of species, lineages, and carbapenem resistance mechanisms, many of which were encoded on a variety of promiscuous plasmid types. We found and quantified rearrangement, persistence, and repeated transfer of plasmid segments, including those harboring carbapenemases, between organisms over multiple years. Some plasmid segments were found to be strongly associated with specific locales, thus representing geographic signatures that make it possible to trace recent and localized HGT events. Functional analysis of these signatures revealed genes commonly found in plasmids of nosocomial pathogens, such as functions required for plasmid retention and spread, as well survival against a variety of antibiotic and antiseptics common to the hospital environment. CONCLUSIONS Collectively, the framework we developed provides a clearer, high-resolution picture of the epidemiology of antibiotic resistance importation, spread, and persistence in patients and healthcare networks.
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Affiliation(s)
- Rauf Salamzade
- grid.66859.340000 0004 0546 1623Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142 USA ,grid.14003.360000 0001 2167 3675Present Address: Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, WI 53706 USA
| | - Abigail L. Manson
- grid.66859.340000 0004 0546 1623Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142 USA
| | - Bruce J. Walker
- grid.66859.340000 0004 0546 1623Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142 USA ,Applied Invention, Cambridge, MA 02139 USA
| | - Thea Brennan-Krohn
- grid.239395.70000 0000 9011 8547Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215 USA
| | - Colin J. Worby
- grid.66859.340000 0004 0546 1623Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142 USA
| | - Peijun Ma
- grid.66859.340000 0004 0546 1623Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142 USA
| | - Lorrie L. He
- grid.66859.340000 0004 0546 1623Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142 USA
| | - Terrance P. Shea
- grid.66859.340000 0004 0546 1623Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142 USA
| | - James Qu
- grid.66859.340000 0004 0546 1623Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142 USA
| | - Sinéad B. Chapman
- grid.66859.340000 0004 0546 1623Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142 USA
| | - Whitney Howe
- grid.66859.340000 0004 0546 1623Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142 USA
| | - Sarah K. Young
- grid.66859.340000 0004 0546 1623Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142 USA
| | - Jenna I. Wurster
- grid.38142.3c000000041936754XDepartment of Ophthalmology, Department of Microbiology, Harvard Medical School and Massachusetts Eye and Ear Infirmary, 240 Charles St., Boston, MA 02114 USA
| | - Mary L. Delaney
- grid.38142.3c000000041936754XDivision of Infectious Disease, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115 USA
| | - Sanjat Kanjilal
- grid.38142.3c000000041936754XDivision of Infectious Disease, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115 USA ,grid.38142.3c000000041936754XDepartment of Population Medicine, Harvard Medical School and Harvard Pilgrim Healthcare Institute, Boston, MA 02215 USA
| | - Andrew B. Onderdonk
- grid.38142.3c000000041936754XDivision of Infectious Disease, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115 USA
| | - Cassiana E. Bittencourt
- grid.266093.80000 0001 0668 7243Department of Pathology and Laboratory Medicine, University of California Irvine School of Medicine, Orange, CA 92868 USA
| | - Gabrielle M. Gussin
- grid.266093.80000 0001 0668 7243Division of Infectious Diseases, University of California Irvine School of Medicine, Irvine, CA 92617 USA
| | - Diane Kim
- grid.266093.80000 0001 0668 7243Division of Infectious Diseases, University of California Irvine School of Medicine, Irvine, CA 92617 USA
| | - Ellena M. Peterson
- grid.266093.80000 0001 0668 7243Department of Pathology and Laboratory Medicine, University of California Irvine School of Medicine, Orange, CA 92868 USA
| | - Mary Jane Ferraro
- grid.32224.350000 0004 0386 9924Massachusetts General Hospital, Boston, MA 02114 USA
| | - David C. Hooper
- grid.32224.350000 0004 0386 9924Massachusetts General Hospital, Boston, MA 02114 USA
| | - Erica S. Shenoy
- grid.32224.350000 0004 0386 9924Massachusetts General Hospital, Boston, MA 02114 USA
| | - Christina A. Cuomo
- grid.66859.340000 0004 0546 1623Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142 USA
| | - Lisa A. Cosimi
- grid.66859.340000 0004 0546 1623Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142 USA ,grid.38142.3c000000041936754XDivision of Infectious Disease, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115 USA
| | - Susan S. Huang
- grid.266093.80000 0001 0668 7243Division of Infectious Diseases, University of California Irvine School of Medicine, Irvine, CA 92617 USA
| | - James E. Kirby
- grid.239395.70000 0000 9011 8547Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215 USA
| | - Virginia M. Pierce
- grid.32224.350000 0004 0386 9924Massachusetts General Hospital, Boston, MA 02114 USA
| | - Roby P. Bhattacharyya
- grid.66859.340000 0004 0546 1623Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142 USA ,grid.32224.350000 0004 0386 9924Massachusetts General Hospital, Boston, MA 02114 USA
| | - Ashlee M. Earl
- grid.66859.340000 0004 0546 1623Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142 USA
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17
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Vlachaki I, Zinzi D, Falla E, Mantopoulos T, Guy H, Jandu J, Dodgson A. Cost-effectiveness analysis of vaborem for the treatment of carbapenem-resistant Enterobacteriaceae-Klebsiella pneumoniae carbapenemase (CRE-KPC) infections in the UK. THE EUROPEAN JOURNAL OF HEALTH ECONOMICS : HEPAC : HEALTH ECONOMICS IN PREVENTION AND CARE 2022; 23:537-549. [PMID: 34546484 PMCID: PMC8453464 DOI: 10.1007/s10198-021-01375-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 08/24/2021] [Indexed: 06/13/2023]
Abstract
OBJECTIVE The study objective of this analysis was to determine the cost-effectiveness of vaborem (meropenem-vaborbactam) compared to the best available therapy (BAT) in adult patients with carbapenem-resistant Enterobacteriaceae-Klebsiella pneumoniae carbapenemase (CRE-KPC) infections from the perspective of the UK National Health Service (NHS) and Personal Social Services (PSS). METHODS A decision tree model was developed to conduct a cost-effectiveness analysis for Vaborem compared to BAT in CRE-KPC patients over a 5 year time horizon. The model structure for Vaborem simulated the clinical pathway of patients with a confirmed CRE-KPC infection. Model inputs for clinical effectiveness were sourced from the TANGO II trial, and published literature. Costs, resource use and utility values associated with CRE-KPC infections in the UK were sourced from the British National Formulary, NHS reference costs and published sources. RESULTS Over a 5 year time horizon, Vaborem use increased total costs by £5165 and increased quality-adjusted life years (QALYs) by 0.366, resulting in an incremental cost-effectiveness ratio (ICER) of £14,113 per QALY gained. The ICER was most sensitive to the probability of discharge to long-term care (LTC), the annual cost of LTC and the utility of discharge to home. At thresholds of £20,000/QALY and £30,000/QALY, the probability of Vaborem being cost-effective compared to BAT was 79.85% and 94.93%, respectively. CONCLUSION Due to a limited cost impact and increase in patient quality of life, vaborem can be considered as a cost-effective treatment option compared to BAT for adult patients with CRE-KPC infections in the UK.
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Affiliation(s)
| | | | - Edel Falla
- Real World Solutions, IQVIA Ltd, 37 North Wharf Road, London, W21AF, UK.
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18
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Li C, Jiang X, Yang T, Ju Y, Yin Z, Yue L, Ma G, Wang X, Jing Y, Luo X, Li S, Yang X, Chen F, Zhou D. Genomic epidemiology of carbapenemase-producing Klebsiella pneumoniae in china. GENOMICS, PROTEOMICS & BIOINFORMATICS 2022; 20:1154-1167. [PMID: 35307590 DOI: 10.1016/j.gpb.2022.02.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 02/14/2022] [Accepted: 02/25/2022] [Indexed: 11/26/2022]
Abstract
The rapid spread of carbapenemase-producing Klebsiella pneumoniae (cpKP) poses serious threats to public health, however, the underlying genetic basis for its dissemination is still unknown. We conducted a comprehensive genomic epidemiology analysis on 420 cpKP isolates collected from 70 hospitals in 24 provinces of China during 2009-2017 by short-/long-read sequencing. The results showed that most cpKP isolates were categorized into clonal group 258 (CG258), in which ST11 was the dominant clone. Phylogenetic analysis revealed three major clades including the top one of Clade 3 for CG258 cpKP isolates. Additionally, carbapenemase gene analysis indicated that blaKPC was dominant in the cpKP isolates, and most blaKPC genes were located in five major incompatibility (Inc) groups of blaKPC-harboring plasmids. Importantly, three advantageous combinations of host-blaKPC-carrying plasmids (Clade 3.1 + 3.2-IncFIIpHN7A8, Clade 3.1 + 3.2-IncFIIpHN7A8:IncR, and Clade 3.3-IncFIIpHN7A8:IncpA1763-KPC) were identified to confer cpKP isolates the advantages in both genotypes (strong correlation/co-evolution) and phenotypes (resistance/growth/competition) to facilitate the nationwide spread of ST11/CG258 cpKP. Intriguingly, Bayesian skyline analysis illustrated that the three advantageous combinations might be directly associated with the strong population expansion during 2007-2008 and subsequent maintenance of the population of ST11/CG258 cpKP after 2008. We then examined drug resistance profiles of these cpKP isolates and proposed combination treatment regimens for CG258/non-CG258 cpKP infections. Thus, the findings of our systematical analysis shed light on the molecular epidemiology and genetic basis for the dissemination of ST11/CG258 cpKP in China, and much emphasis should be given to the close monitoring of advantageous cpKP-plasmid combinations.
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Affiliation(s)
- Cuidan Li
- CAS Key Laboratory of Genome Sciences & Information, Beijing Institute of Genomics, Chinese Academy of Sciences, China National Center for Bioinformation, Beijing 100101, China
| | - Xiaoyuan Jiang
- CAS Key Laboratory of Genome Sciences & Information, Beijing Institute of Genomics, Chinese Academy of Sciences, China National Center for Bioinformation, Beijing 100101, China; State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China
| | - Tingting Yang
- CAS Key Laboratory of Genome Sciences & Information, Beijing Institute of Genomics, Chinese Academy of Sciences, China National Center for Bioinformation, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yingjiao Ju
- CAS Key Laboratory of Genome Sciences & Information, Beijing Institute of Genomics, Chinese Academy of Sciences, China National Center for Bioinformation, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhe Yin
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China
| | - Liya Yue
- CAS Key Laboratory of Genome Sciences & Information, Beijing Institute of Genomics, Chinese Academy of Sciences, China National Center for Bioinformation, Beijing 100101, China
| | - Guannan Ma
- CAS Key Laboratory of Genome Sciences & Information, Beijing Institute of Genomics, Chinese Academy of Sciences, China National Center for Bioinformation, Beijing 100101, China
| | - Xuebing Wang
- CAS Key Laboratory of Genome Sciences & Information, Beijing Institute of Genomics, Chinese Academy of Sciences, China National Center for Bioinformation, Beijing 100101, China
| | - Ying Jing
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China
| | - Xinhua Luo
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China
| | - Shuangshuang Li
- CAS Key Laboratory of Genome Sciences & Information, Beijing Institute of Genomics, Chinese Academy of Sciences, China National Center for Bioinformation, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xue Yang
- CAS Key Laboratory of Genome Sciences & Information, Beijing Institute of Genomics, Chinese Academy of Sciences, China National Center for Bioinformation, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Fei Chen
- CAS Key Laboratory of Genome Sciences & Information, Beijing Institute of Genomics, Chinese Academy of Sciences, China National Center for Bioinformation, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; State Key Laboratory of Pathogenesis, Prevention and Treatment of High Incidence Diseases in Central Asia, Urumqi 830011, China; Beijing Key Laboratory of Genome and Precision Medicine Technologies, Beijing 100101, China.
| | - Dongsheng Zhou
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China.
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19
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Turumtay H, Allam M, Sandalli A, Turumtay EA, Genç H, Sandalli C. Characteristics in the whole-genome sequence of Klebsiella pneumoniae ST147 from Turkey. Acta Microbiol Immunol Hung 2022. [PMID: 35195536 DOI: 10.1556/030.2022.01690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Accepted: 02/12/2022] [Indexed: 11/19/2022]
Abstract
The study aimed to analyze antibiotic resistance determinants in a carbapenem-resistant Klebsiella pneumoniae by whole-genome sequencing (WGS). K. pneumoniae was isolated from a urine sample and it was characterized by 16S rDNA sequencing in Turkey. This strain was named as Kpn Rize-53-TR. Antimicrobial susceptibility testing was performed for seventeen antibiotics by VITEK-2 and the result was confirmed by MIC. The whole genome of isolate was sequenced by Illumina and was analysed by bioinformatic tools for MLST, replicon types, and antimicrobial resistance genes. The whole genome data was submitted to NCBI. The isolate was found to be resistant to all tested β-lactam antibiotics and the highest MIC values were found for piperacillin, piperacillin/tazobactam (≥128). No resistance to colistin and moderate susceptibility to amikacin and tetracycline was observed. The isolate carried 12 resistance genes belonging to 10 resistance classes; ere(A), fosA, oqxB, cmlA1, aac(a)-IIa, bla KPC-2, bla TEM-1A, bla SHV-67, bla CTX-M-15, bla OXA-1-2-9. Mutations were detected in gyrA (83Y) and parC (80I) genes. Clonal subtype of the isolate was ST147, and it had wzi420 and wzc38 alleles. Its serotype was O3/O3a. The bla KPC-2 was firstly found in both ST147 clonal group in Turkey and in serotype O3/O3a in the world. By plasmid replicon typing, five plasmids IncFII(K), Col(BS512), IncR, IncFIA(HI1) and IncFIB(pQil) were determined in Kpn Rize-53-TR and bla KPC-2 was located on IncFII(K) plasmid. The presence of bla KPC-2 on the plasmid with other resistance genes accelerates its own spread together with other resistance genes.
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Affiliation(s)
- Halbay Turumtay
- 1 Karadeniz Technical University, Department of Energy System Engineering, 61830, Trabzon, Turkey
- 2 Joint BioEnergy Institute, Feedstocks Division, Emeryville, CA 94608, USA
| | - Mushal Allam
- 3 Department of Genetics and Genomics, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Aytül Sandalli
- 4 Recep Tayyip Erdoğan University, Department of Biology, 53020, Rize, Turkey
| | | | - Hacer Genç
- 6 Rize Tea Research and Application Center (ÇAYMER), 53100, Rize, Turkey
| | - Cemal Sandalli
- 4 Recep Tayyip Erdoğan University, Department of Biology, 53020, Rize, Turkey
- 7 Firtina Research Group, Fener Mahallesi, VillaKent Konutları, 53020 Rize, Turkey
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20
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Waddington C, Carey ME, Boinett CJ, Higginson E, Veeraraghavan B, Baker S. Exploiting genomics to mitigate the public health impact of antimicrobial resistance. Genome Med 2022; 14:15. [PMID: 35172877 PMCID: PMC8849018 DOI: 10.1186/s13073-022-01020-2] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 02/04/2022] [Indexed: 12/13/2022] Open
Abstract
Antimicrobial resistance (AMR) is a major global public health threat, which has been largely driven by the excessive use of antimicrobials. Control measures are urgently needed to slow the trajectory of AMR but are hampered by an incomplete understanding of the interplay between pathogens, AMR encoding genes, and mobile genetic elements at a microbial level. These factors, combined with the human, animal, and environmental interactions that underlie AMR dissemination at a population level, make for a highly complex landscape. Whole-genome sequencing (WGS) and, more recently, metagenomic analyses have greatly enhanced our understanding of these processes, and these approaches are informing mitigation strategies for how we better understand and control AMR. This review explores how WGS techniques have advanced global, national, and local AMR surveillance, and how this improved understanding is being applied to inform solutions, such as novel diagnostic methods that allow antimicrobial use to be optimised and vaccination strategies for better controlling AMR. We highlight some future opportunities for AMR control informed by genomic sequencing, along with the remaining challenges that must be overcome to fully realise the potential of WGS approaches for international AMR control.
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Affiliation(s)
- Claire Waddington
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, CB2 0AW, UK.,Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, UK
| | - Megan E Carey
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, CB2 0AW, UK.,Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, UK
| | | | - Ellen Higginson
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, CB2 0AW, UK.,Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, UK
| | - Balaji Veeraraghavan
- Department of Microbiology, Christian Medical College, Vellore, Tamil Nadu, India
| | - Stephen Baker
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, CB2 0AW, UK. .,Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, UK.
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21
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Sugita K, Aoki K, Komori K, Nagasawa T, Ishii Y, Iwata S, Tateda K. Molecular Analysis of blaKPC-2-Harboring Plasmids: Tn 4401a Interplasmid Transposition and Tn 4401a-Carrying ColRNAI Plasmid Mobilization from Klebsiella pneumoniae to Citrobacter europaeus and Morganella morganii in a Single Patient. mSphere 2021; 6:e0085021. [PMID: 34730375 PMCID: PMC8565517 DOI: 10.1128/msphere.00850-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 10/21/2021] [Indexed: 11/20/2022] Open
Abstract
The spread of Klebsiella pneumoniae carbapenemase (KPC)-producing Enterobacterales is a public health concern. KPC-encoding blaKPC is predominantly spread by strains of a particular phylogenetic lineage, clonal group 258, but can also be spread by horizontal transfer of blaKPC-carrying plasmids. Here, we report the transfer of a blaKPC-2-harboring plasmid via mobilization from K. pneumoniae to Citrobacter freundii complex and Morganella morganii strains in a single patient. We performed draft whole-genome sequencing to analyze 20 carbapenemase-producing Enterobacterales strains (15 of K. pneumoniae, two of C. freundii complex, and three of M. morganii) and all K. pneumoniae strains using MiSeq and/or MinION isolated from a patient who was hospitalized in New York and Montreal before returning to Japan. All strains harbored blaKPC-2-containing Tn4401a. The 15 K. pneumoniae strains each belonged to sequence type 258 and harbored a Tn4401a-carrying multireplicon-type plasmid, IncN and IncR (IncN+R). Three of these K. pneumoniae strains also possessed a Tn4401a-carrying ColRNAI plasmid, suggesting that Tn4401a underwent interplasmid transposition. Of these three ColRNAI plasmids, two and one were identical to plasmids harbored by two Citrobacter europaeus and three M. morganii strains, respectively. The Tn4401a-carrying ColRNAI plasmids were each 23,753 bp long and incapable of conjugal transfer via their own genes alone, but they mobilized during the conjugal transfer of Tn4401a-carrying IncN+R plasmids in K. pneumoniae. Interplasmid transposition of Tn4401a from an IncN+R plasmid to a ColRNAI plasmid in K. pneumoniae and mobilization of Tn4401a-carrying ColRNAI plasmids contributed to the acquisition of blaKPC-2 in C. europaeus and M. morganii. IMPORTANCE Plasmid transfer plays an important role in the interspecies spread of carbapenemase genes, including the Klebsiella pneumoniae carbapenemase (KPC)-coding gene, blaKPC. We conducted whole-genome sequencing (WGS) analysis and transmission experiments to analyze blaKPC-2-carrying mobile genetic elements (MGEs) between the blaKPC-2-harboring K. pneumoniae, Citrobacter europaeus, and Morganella morganii strains isolated from a single patient. blaKPC-2 was contained within an MGE, Tn4401a. WGS of blaKPC-2-carrying K. pneumoniae, C. europaeus, and M. morganii strains isolated from one patient revealed that Tn4401a-carrying ColRNAI plasmids were generated by plasmid-to-plasmid transfer of Tn4401a from a multireplicon-type IncN and IncR (IncN+R) plasmid in K. pneumoniae strains. Tn4401a-carrying ColRNAI plasmids were incapable of conjugal transfer in C. europaeus and M. morganii but mobilized from K. pneumoniae to a recipient Escherichia coli strain during the conjugal transfer of Tn4401a-carrying IncN+R plasmid. Therefore, Tn4401a-carrying ColRNAI plasmids contributed to the acquisition of blaKPC-2 in C. europaeus and M. morganii.
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Affiliation(s)
- Kayoko Sugita
- Department of Microbiology and Infectious Diseases, Toho University Graduate School of Medicine, Tokyo, Japan
- Department of Microbiology and Immunology, Keio University School of Medicine, Tokyo, Japan
| | - Kotaro Aoki
- Department of Microbiology and Infectious Diseases, Toho University School of Medicine, Tokyo, Japan
| | - Kohji Komori
- Department of Microbiology and Infectious Diseases, Toho University Graduate School of Medicine, Tokyo, Japan
| | - Tatsuya Nagasawa
- Department of Microbiology and Infectious Diseases, Toho University Graduate School of Medicine, Tokyo, Japan
| | - Yoshikazu Ishii
- Department of Microbiology and Infectious Diseases, Toho University Graduate School of Medicine, Tokyo, Japan
- Department of Microbiology and Infectious Diseases, Toho University School of Medicine, Tokyo, Japan
| | - Satoshi Iwata
- Department of Infectious Diseases, Keio University School of Medicine, Tokyo, Japan
- Department of Infectious Diseases, National Cancer Center Hospital, Tokyo, Japan
| | - Kazuhiro Tateda
- Department of Microbiology and Infectious Diseases, Toho University Graduate School of Medicine, Tokyo, Japan
- Department of Microbiology and Infectious Diseases, Toho University School of Medicine, Tokyo, Japan
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22
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Viehweger A, Blumenscheit C, Lippmann N, Wyres KL, Brandt C, Hans JB, Hölzer M, Irber L, Gatermann S, Lübbert C, Pletz MW, Holt KE, König B. Context-aware genomic surveillance reveals hidden transmission of a carbapenemase-producing Klebsiella pneumoniae. Microb Genom 2021; 7:000741. [PMID: 34913861 PMCID: PMC8767333 DOI: 10.1099/mgen.0.000741] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Genomic surveillance can inform effective public health responses to pathogen outbreaks. However, integration of non-local data is rarely done. We investigate two large hospital outbreaks of a carbapenemase-carrying Klebsiella pneumoniae strain in Germany and show the value of contextual data. By screening about 10 000 genomes, over 400 000 metagenomes and two culture collections using in silico and in vitro methods, we identify a total of 415 closely related genomes reported in 28 studies. We identify the relationship between the two outbreaks through time-dated phylogeny, including their respective origin. One of the outbreaks presents extensive hidden transmission, with descendant isolates only identified in other studies. We then leverage the genome collection from this meta-analysis to identify genes under positive selection. We thereby identify an inner membrane transporter (ynjC) with a putative role in colistin resistance. Contextual data from other sources can thus enhance local genomic surveillance at multiple levels and should be integrated by default when available.
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Affiliation(s)
- Adrian Viehweger
- Institute of Medical Microbiology and Virology, University Hospital Leipzig, Leipzig, Germany
- *Correspondence: Adrian Viehweger,
| | | | - Norman Lippmann
- Institute of Medical Microbiology and Virology, University Hospital Leipzig, Leipzig, Germany
| | - Kelly L. Wyres
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Australia
| | - Christian Brandt
- Institute for Infectious Diseases and Infection Control, Jena University Hospital, Jena, Germany
| | - Jörg B. Hans
- National Reference Center for multidrug-resistant Gram-negative bacteria, Department for Medical Microbiology, Ruhr-University Bochum, Bochum, Germany
| | - Martin Hölzer
- Methodology and Research Infrastructure, MF1 Bioinformatics, Robert Koch Institute, Berlin, Germany
| | - Luiz Irber
- Department of Population Health and Reproduction, University of California, Davis, Davis, California, USA
| | - Sören Gatermann
- National Reference Center for multidrug-resistant Gram-negative bacteria, Department for Medical Microbiology, Ruhr-University Bochum, Bochum, Germany
| | - Christoph Lübbert
- Division of Infectious Diseases and Tropical Medicine, Department of Medicine II, University Hospital Leipzig, Leipzig, Germany
| | - Mathias W. Pletz
- Institute for Infectious Diseases and Infection Control, Jena University Hospital, Jena, Germany
| | - Kathryn E. Holt
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Australia
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, London, UK
| | - Brigitte König
- Institute of Medical Microbiology and Virology, University Hospital Leipzig, Leipzig, Germany
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23
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Distinguishing bla KPC Gene-Containing IncF Plasmids from Epidemiologically Related and Unrelated Enterobacteriaceae Based on Short- and Long-Read Sequence Data. Antimicrob Agents Chemother 2021; 65:AAC.00147-21. [PMID: 33820769 DOI: 10.1128/aac.00147-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 03/26/2021] [Indexed: 11/20/2022] Open
Abstract
Limited information is available on whether bla KPC-containing plasmids from isolates in a hospital outbreak can be differentiated from epidemiologically unrelated bla KPC-containing plasmids based on sequence data. This study aimed to evaluate the performance of three approaches to distinguish epidemiologically related from unrelated bla KPC-containing pKpQiL-like IncFII(k2)-IncFIB(pQiL) plasmids. Epidemiologically related isolates were subjected to short- and long-read whole-genome sequencing. A hybrid assembly was performed, and plasmid sequences were extracted from the assembly graph. Epidemiologically unrelated plasmid sequences were extracted from GenBank. Pairwise comparisons of epidemiologically related and unrelated plasmids based on SNPs using snippy and of phylogenetic distance using Roary and using a similarity index that penalizes size differences between plasmids (Stoesser index) were performed. The percentage of pairwise comparisons misclassified as genetically related or as clonally unrelated was determined using different genetic thresholds for genetic relatedness. The ranges of number of SNPs, Roary phylogenetic distance, and Stoesser index overlapped between the epidemiologically related and unrelated plasmids. When a genetic similarity threshold that classified 100% of epidemiologically related plasmid pairs as genetically related was used, the percentages of plasmids misclassified as epidemiologically related ranged from 6.7% (Roary) to 20.8% (Stoesser index). Although epidemiologically related plasmids can be distinguished from unrelated plasmids based on genetic differences, bla KPC-containing pKpQiL-like IncFII(k2)-IncFIB(pQiL) plasmids show a high degree of sequence similarity. The phylogenetic distance as determined using Roary showed the highest degree of discriminatory power between the epidemiologically related and unrelated plasmids.
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24
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Harris HC, Buckley AM, Spittal W, Ewin D, Clark E, Altringham J, Bentley K, Moura IB, Wilcox MH, Woodford N, Davies K, Chilton CH. The effect of intestinal microbiota dysbiosis on growth and detection of carbapenemase-producing Enterobacterales within an in vitro gut model. J Hosp Infect 2021; 113:1-9. [PMID: 33932556 DOI: 10.1016/j.jhin.2021.04.014] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 03/18/2021] [Accepted: 04/14/2021] [Indexed: 01/07/2023]
Abstract
BACKGROUND Carbapenemase-producing Enterobacterales (CPE) can colonize the gut and are of major clinical concern. Identification of CPE colonization is problematic; there is no gold-standard detection method, and the effects of antibiotic exposure and microbiota dysbiosis on detection are unknown. AIM Based on a national survey we selected four CPE screening assays in common use. We used a clinically reflective in vitro model of human gut microbiota to investigate the performance of each test to detect three different CPE strains under different, clinically relevant antibiotic exposures. METHODS Twelve gut models were seeded with a pooled faecal slurry and exposed to CPE either before, after, concomitant with, or in the absence of piperacillin-tazobactam (358 mg/L, 3 × daily, seven days). Total Enterobacterales and CPE populations were enumerated daily. Regular screening for CPE was performed using Cepheid Xpert® Carba-R molecular test, and with Brilliance™ CRE, Colorex™ mSuperCARBA and CHROMID® CARBA SMART agars. FINDINGS Detection of CPE when the microbiota are intact is problematic. Antibiotic exposure disrupts microbiota populations and allows CPE proliferation, increasing detection. The performances of assays varied, particularly with respect to different CPE strains. The Cepheid assay performed better than the three agar methods for detecting a low level of CPE within an intact microbiota, although performance of all screening methods was comparable when CPE populations increased in a disrupted microbiota. CONCLUSION CPE strains differed in their dynamics of colonization in an in vitro gut model and in their subsequent response to antibiotic exposure. This affected detection by molecular and screening methods, which has implications for the sensitivity of CPE screening in healthcare settings.
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Affiliation(s)
- H C Harris
- Heath Care Associated Infection Research Group, Leeds Institute of Medical Research, Faculty of Medicine and Health, University of Leeds, Leeds, UK
| | - A M Buckley
- Heath Care Associated Infection Research Group, Leeds Institute of Medical Research, Faculty of Medicine and Health, University of Leeds, Leeds, UK
| | - W Spittal
- Heath Care Associated Infection Research Group, Leeds Institute of Medical Research, Faculty of Medicine and Health, University of Leeds, Leeds, UK
| | - D Ewin
- Heath Care Associated Infection Research Group, Leeds Institute of Medical Research, Faculty of Medicine and Health, University of Leeds, Leeds, UK
| | - E Clark
- Heath Care Associated Infection Research Group, Leeds Institute of Medical Research, Faculty of Medicine and Health, University of Leeds, Leeds, UK
| | - J Altringham
- Heath Care Associated Infection Research Group, Leeds Institute of Medical Research, Faculty of Medicine and Health, University of Leeds, Leeds, UK
| | - K Bentley
- Heath Care Associated Infection Research Group, Leeds Institute of Medical Research, Faculty of Medicine and Health, University of Leeds, Leeds, UK
| | - I B Moura
- Heath Care Associated Infection Research Group, Leeds Institute of Medical Research, Faculty of Medicine and Health, University of Leeds, Leeds, UK
| | - M H Wilcox
- Heath Care Associated Infection Research Group, Leeds Institute of Medical Research, Faculty of Medicine and Health, University of Leeds, Leeds, UK; Department of Microbiology, Leeds Teaching Hospitals NHS Trust, The General Infirmary, Leeds, UK
| | - N Woodford
- Antimicrobial Resistance and Healthcare Associated Infections (AMRHAI), Reference Unit, Microbiology Services - Colindale, Public Health England, UK
| | - K Davies
- Heath Care Associated Infection Research Group, Leeds Institute of Medical Research, Faculty of Medicine and Health, University of Leeds, Leeds, UK; Department of Microbiology, Leeds Teaching Hospitals NHS Trust, The General Infirmary, Leeds, UK
| | - C H Chilton
- Heath Care Associated Infection Research Group, Leeds Institute of Medical Research, Faculty of Medicine and Health, University of Leeds, Leeds, UK.
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Dynamics of bla KPC-2 Dissemination from Non-CG258 Klebsiella pneumoniae to Other Enterobacterales via IncN Plasmids in an Area of High Endemicity. Antimicrob Agents Chemother 2020; 64:AAC.01743-20. [PMID: 32958711 DOI: 10.1128/aac.01743-20] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Accepted: 09/15/2020] [Indexed: 02/06/2023] Open
Abstract
Carbapenem-resistant Enterobacterales (CRE) pose a significant threat to global public health. The most important mechanism for carbapenem resistance is the production of carbapenemases. Klebsiella pneumoniae carbapenemase (KPC) represents one of the main carbapenemases worldwide. Complex mechanisms of bla KPC dissemination have been reported in Colombia, a country with a high endemicity of carbapenem resistance. Here, we characterized the dynamics of dissemination of bla KPC gene among CRE infecting and colonizing patients in three hospitals localized in a highly endemic area of Colombia (2013 and 2015). We identified the genomic characteristics of KPC-producing Enterobacterales recovered from patients infected/colonized and reconstructed the dynamics of dissemination of bla KPC-2 using both short and long read sequencing. We found that spread of bla KPC-2 among Enterobacterales in the participating hospitals was due to intra- and interspecies horizontal gene transfer (HGT) mediated by promiscuous plasmids associated with transposable elements that was originated from a multispecies outbreak of KPC-producing Enterobacterales in a neonatal intensive care unit. The plasmids were detected in isolates recovered in other units within the same hospital and nearby hospitals. The gene "epidemic" was driven by IncN-pST15-type plasmids carrying a novel Tn4401b structure and non-Tn4401 elements (NTEKPC) in Klebsiella spp., Escherichia coli, Enterobacter spp., and Citrobacter spp. Of note, mcr-9 was found to coexist with bla KPC-2 in species of the Enterobacter cloacae complex. Our findings suggest that the main mechanism for dissemination of bla KPC-2 is HGT mediated by highly transferable plasmids among species of Enterobacterales in infected/colonized patients, presenting a major challenge for public health interventions in developing countries such as Colombia.
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Mabrouk SS, Abdellatif GR, El-Ansary MR, Aboshanab KM, Ragab YM. Carbapenemase Producers Among Extensive Drug-Resistant Gram-Negative Pathogens Recovered from Febrile Neutrophilic Patients in Egypt. Infect Drug Resist 2020; 13:3113-3124. [PMID: 32982326 PMCID: PMC7495499 DOI: 10.2147/idr.s269971] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 08/16/2020] [Indexed: 01/19/2023] Open
Abstract
Purpose This study aimed to detect the prevalence of carbapenemase producers (CPs) among extensive drug-resistant (XDR)-carbapenemase producing Gram-negative bacteria (GNB) recovered from various clinical specimens of hospitalized neutrophilic febrile patients in two major tertiary care hospitals in Egypt. Methods Standard methods were used to evaluate the antimicrobial susceptibility of clinical isolates according to the guidelines of the Clinical and Laboratory Standards Institute (CLSI). Phenotypic and genotypic analysis of CPs were carried out and statistically analyzed using standard methods. Results Three hundred and forty-two GNB were obtained from 342 clinical specimens during the period of the study, where 162 (47%) were enterobacterial isolates, including, 63 (18.4%) Escherichia coli, 87 (25.4%) Klebsiella spp., 5 (1.46%) Enterobacter cloacae, 5 (1.46%) Salmonella spp. and 2 (0.6%) Proteus and 180 (53%) were non-fermentative bacilli including, 129 (37.7%), Acinetobacter baumannii, and 51 (14.9%), Pseudomonas spp. Out of the 342 GNB, 188 (54.9%) isolates were multi-drug resistant (MDR). Of these, 52 (27.6%) were XDR as well as CPs as confirmed phenotypically. The MIC of imipenem against the XDR GNB against showed either low (11 isolates; 21.1%; MIC range =4–32 µg/mL) or high levels of resistance (41 isolates; 78.8%; MIC range = 64-≥1024). The most prevalent carbapenem resistance (CR) genes were blaKPC (63.5%) followed by blaOXA-48 (55.7%) and blaVIM (28.8%). No significant association could be observed between the MIC level and the presence of CR genes (P value >0.05). Conclusion High prevalence of MDR (54.9%) and XDR (27.6%) GNB pathogens associated with high levels of resistance to carbapenems were observed. All XDR GNB were CPs and tested positive for at least one of the CR genes. However, most of them (78.8%) showed a high level of CR (MIC range = 64-≥1024) with no significant association with the CR genes.
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Affiliation(s)
- Samar S Mabrouk
- Department of Microbiology, Faculty of Pharmacy, Ahram Canadian University (ACU), 6th of October, Giza, Egypt
| | - Ghada R Abdellatif
- Department of Microbiology, Faculty of Pharmacy, Ahram Canadian University (ACU), 6th of October, Giza, Egypt
| | - Mona R El-Ansary
- Department of Biochemistry, Modern University for Technology and Information (MTI), Cairo, Egypt
| | - Khaled M Aboshanab
- Department of Microbiology and Immunology, Faculty of Pharmacy, Ain Shams University (ASU), Cairo, Egypt
| | - Yasser M Ragab
- Department of Microbiology & Immunology, Faculty of Pharmacy, Cairo University (CU), Cairo, Egypt
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