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Kong H, Hu Z, Zhang L, Chen Q, Yang L, Li J, Tian B, Chai Y, Feng X. Clinical risk factors and outcomes of carbapenem-resistant Escherichia coli nosocomial infections in a Chinese teaching hospital: a retrospective study from 2013 to 2020. Microbiol Spectr 2024:e0422823. [PMID: 38814065 DOI: 10.1128/spectrum.04228-23] [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: 01/08/2024] [Accepted: 04/22/2024] [Indexed: 05/31/2024] Open
Abstract
The emergence of carbapenem-resistant Escherichia coli strains poses a considerable challenge to global public health, and little is known about carbapenemase-producing E. coli strains in Tianjin, China. This study aimed to investigate the risk factors for infections with carbapenem-resistant E. coli (CREC) strains. This retrospective case-control study was conducted at a tertiary teaching hospital. A total of 134 CREC clinical isolates were collected from the General Hospital of Tianjin Medical University between 2013 and 2020. The control group was selected at a ratio of 1:1 from patients with nosocomial carbapenem-susceptible E. coli infection. Risk factors for nosocomial CREC infection and clinical outcomes were analyzed using univariate and multivariate analyses. Multivariate analysis revealed that cephalosporin exposure (odd ratio OR = 2.01), carbapenem exposure (OR = 1.96), glucocorticoid exposure (OR = 32.45), and surgical history (OR = 3.26) were independent risk factors for CREC infection. The in-hospital mortality rate in the CREC group was 29.1%, and age >65 years (OR = 3.19), carbapenem exposure (OR = 3.54), and central venous catheter insertion (OR = 4.19) were independent risk factors for in-hospital mortality in patients with CREC infections. Several factors were identified in the development of nosocomial CREC infections. The CREC isolates were resistant to most antibiotics. Reducing CREC mortality requires a comprehensive consideration of appropriate antibiotic use, underlying diseases, and invasive procedures.IMPORTANCEEscherichia coli is an opportunistic pathogen that causes severe hospital-acquired infections. The spread of carbapenem-resistant E. coli is a global threat to public health, and only a few antibiotics are effective against these infections. Consequently, these infections are usually associated with poor prognosis and high mortality. Therefore, understanding the risk factors associated with the causes and outcomes of these infections is crucial to reduce their incidence and initiate appropriate therapies. In our study, several factors were found to be involved in nosocomial carbapenem-resistant E. coli (CREC) infections, and CREC isolates were resistant to most antibiotics. Reducing CREC mortality needs a comprehensive consideration of whether antibiotics are used appropriately, underlying diseases, and invasive interventions. These findings provide valuable evidence for the development of anti-infective therapy, infection prevention, and control of CREC-positive infections.
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Affiliation(s)
- Haifang Kong
- Department of Laboratory Medicine, Tianjin Medical University General Hospital, Tianjin, China
| | - Zhidong Hu
- Department of Laboratory Medicine, Tianjin Medical University General Hospital, Tianjin, China
| | - Longtao Zhang
- Tianjin Medical University General Hospital, Tianjin, China
| | - Qianqian Chen
- Department of Laboratory Medicine, Tianjin Medical University General Hospital, Tianjin, China
| | - Ling Yang
- Department of Laboratory Medicine, Tianjin Medical University General Hospital, Tianjin, China
| | - Jin Li
- Department of Laboratory Medicine, Tianjin Medical University General Hospital, Tianjin, China
| | - Bin Tian
- Department of Laboratory Medicine, Tianjin Medical University General Hospital, Tianjin, China
| | - Yamin Chai
- Department of Laboratory Medicine, Tianjin Medical University General Hospital, Tianjin, China
| | - Xuequan Feng
- Tianjin First Central Hospital of Nankai University, Tianjin, China
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Dahdouh E, Gómez-Marcos L, Cañada-García JE, de Arellano ER, Sánchez-García A, Sánchez-Romero I, López-Urrutia L, de la Iglesia P, Gonzalez-Praetorius A, Sotelo J, Valle-Millares D, Alonso-González I, Bautista V, Lara N, García-Cobos S, Cercenado E, Aracil B, Oteo-Iglesias J, Pérez-Vázquez M. Characterizing carbapenemase-producing Escherichia coli isolates from Spain: high genetic heterogeneity and wide geographical spread. Front Cell Infect Microbiol 2024; 14:1390966. [PMID: 38817448 PMCID: PMC11137265 DOI: 10.3389/fcimb.2024.1390966] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2024] [Accepted: 05/03/2024] [Indexed: 06/01/2024] Open
Abstract
Introduction Carbapenemase-Producing Escherichia coli (CP-Eco) isolates, though less prevalent than other CP-Enterobacterales, have the capacity to rapidly disseminate antibiotic resistance genes (ARGs) and cause serious difficult-to-treat infections. The aim of this study is phenotypically and genotypically characterizing CP-Eco isolates collected from Spain to better understand their resistance mechanisms and population structure. Methods Ninety representative isolates received from 2015 to 2020 from 25 provinces and 59 hospitals Spanish hospitals were included. Antibiotic susceptibility was determined according to EUCAST guidelines and whole-genome sequencing was performed. Antibiotic resistance and virulence-associated genes, phylogeny and population structure, and carbapenemase genes-carrying plasmids were analyzed. Results and discussion The 90 CP-Eco isolates were highly polyclonal, where the most prevalent was ST131, detected in 14 (15.6%) of the isolates. The carbapenemase genes detected were bla OXA-48 (45.6%), bla VIM-1 (23.3%), bla NDM-1 (7.8%), bla KPC-3 (6.7%), and bla NDM-5 (6.7%). Forty (44.4%) were resistant to 6 or more antibiotic groups and the most active antibiotics were colistin (98.9%), plazomicin (92.2%) and cefiderocol (92.2%). Four of the seven cefiderocol-resistant isolates belonged to ST167 and six harbored bla NDM. Five of the plazomicin-resistant isolates harbored rmt. IncL plasmids were the most frequent (45.7%) and eight of these harbored bla VIM-1. bla OXA-48 was found in IncF plasmids in eight isolates. Metallo-β-lactamases were more frequent in isolates with resistance to six or more antibiotic groups, with their genes often present on the same plasmid/integron. ST131 isolates were associated with sat and pap virulence genes. This study highlights the genetic versatility of CP-Eco and its potential to disseminate ARGs and cause community and nosocomial infections.
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Affiliation(s)
- Elias Dahdouh
- Laboratorio de Referencia e Investigación en Resistencia a Antibióticos e Infecciones relacionadas con la Asistencia Sanitaria, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
- Centro de Investigacíon Biomédica en En Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
| | - Laro Gómez-Marcos
- Laboratorio de Referencia e Investigación en Resistencia a Antibióticos e Infecciones relacionadas con la Asistencia Sanitaria, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
| | - Javier E. Cañada-García
- Laboratorio de Referencia e Investigación en Resistencia a Antibióticos e Infecciones relacionadas con la Asistencia Sanitaria, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
- Centro de Investigacíon Biomédica en En Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
| | - Eva Ramírez de Arellano
- Laboratorio de Referencia e Investigación en Resistencia a Antibióticos e Infecciones relacionadas con la Asistencia Sanitaria, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
- Centro de Investigacíon Biomédica en En Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
| | - Aida Sánchez-García
- Servicio de Microbiología, URSalud UTE, Hospital Infanta Sofía, San Sebastián de los Reyes, Madrid, Spain
| | | | | | | | | | - Jared Sotelo
- Laboratorio de Referencia e Investigación en Resistencia a Antibióticos e Infecciones relacionadas con la Asistencia Sanitaria, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
- Centro de Investigacíon Biomédica en En Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
| | - Daniel Valle-Millares
- Centro de Investigacíon Biomédica en En Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
| | - Isabela Alonso-González
- Laboratorio de Referencia e Investigación en Resistencia a Antibióticos e Infecciones relacionadas con la Asistencia Sanitaria, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
- Centro de Investigacíon Biomédica en En Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
| | - Verónica Bautista
- Laboratorio de Referencia e Investigación en Resistencia a Antibióticos e Infecciones relacionadas con la Asistencia Sanitaria, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
| | - Noelia Lara
- Laboratorio de Referencia e Investigación en Resistencia a Antibióticos e Infecciones relacionadas con la Asistencia Sanitaria, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
| | - Silvia García-Cobos
- Laboratorio de Referencia e Investigación en Resistencia a Antibióticos e Infecciones relacionadas con la Asistencia Sanitaria, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
- Centro de Investigacíon Biomédica en En Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
| | - Emilia Cercenado
- Servicio de Microbiología, Hospital Universitario Gregorio Marañón, Madrid, Spain
- Centro de Investigacíon Biomédica en En Red (CIBER) de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, Spain
| | - Belén Aracil
- Laboratorio de Referencia e Investigación en Resistencia a Antibióticos e Infecciones relacionadas con la Asistencia Sanitaria, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
- Centro de Investigacíon Biomédica en En Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
| | - Jesús Oteo-Iglesias
- Laboratorio de Referencia e Investigación en Resistencia a Antibióticos e Infecciones relacionadas con la Asistencia Sanitaria, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
- Centro de Investigacíon Biomédica en En Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
| | - María Pérez-Vázquez
- Laboratorio de Referencia e Investigación en Resistencia a Antibióticos e Infecciones relacionadas con la Asistencia Sanitaria, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
- Centro de Investigacíon Biomédica en En Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
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Solis MN, Loaiza K, Torres-Elizalde L, Mina I, Šefcová MA, Larrea-Álvarez M. Detecting Class 1 Integrons and Their Variable Regions in Escherichia coli Whole-Genome Sequences Reported from Andean Community Countries. Antibiotics (Basel) 2024; 13:394. [PMID: 38786123 PMCID: PMC11117327 DOI: 10.3390/antibiotics13050394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Revised: 04/24/2024] [Accepted: 04/25/2024] [Indexed: 05/25/2024] Open
Abstract
Various genetic elements, including integrons, are known to contribute to the development of antimicrobial resistance. Class 1 integrons have been identified in E. coli isolates and are associated with multidrug resistance in countries of the Andean Community. However, detailed information on the gene cassettes located on the variable regions of integrons is lacking. Here, we investigated the presence and diversity of class 1 integrons, using an in silico approach, in 2533 whole-genome sequences obtained from EnteroBase. IntFinder v1.0 revealed that almost one-third of isolates contained these platforms. Integron-bearing isolates were associated with environmental, food, human, and animal origins reported from all countries under scrutiny. Moreover, they were identified in clones known for their pathogenicity or multidrug resistance. Integrons carried cassettes associated with aminoglycoside (aadA), trimethoprim (dfrA), cephalosporin (blaOXA; blaDHA), and fluoroquinolone (aac(6')-Ib-cr; qnrB) resistance. These platforms showed higher diversity and larger numbers than previously reported. Moreover, integrons carrying more than three cassettes in their variable regions were determined. Monitoring the prevalence and diversity of genetic elements is necessary for recognizing emergent patterns of resistance in pathogenic bacteria, especially in countries where various factors are recognized to favor the selection of resistant microorganisms.
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Affiliation(s)
- María Nicole Solis
- Facultad de Ciencias Médicas Enrique Ortega Moreira, Carrera de Medicina, Universidad Espíritu Santo, Samborondón 092301, Ecuador
| | - Karen Loaiza
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, 2300 Copenhagen, Denmark
| | - Lilibeth Torres-Elizalde
- Graduate School Life Sciences and Health (GS LSH), Université Paris-Saclay, 91198 Gif-sur-Yvette, France
| | - Ivan Mina
- School of Biological Science and Engineering, Yachay-Tech University, Urcuquí 100650, Ecuador
| | - Miroslava Anna Šefcová
- Facultad de Ciencias Médicas Enrique Ortega Moreira, Carrera de Medicina, Universidad Espíritu Santo, Samborondón 092301, Ecuador
| | - Marco Larrea-Álvarez
- Facultad de Ciencias Médicas Enrique Ortega Moreira, Carrera de Medicina, Universidad Espíritu Santo, Samborondón 092301, Ecuador
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4
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Das BJ, Singha KM, Wangkheimayum J, Dhar Chanda D, Bhattacharjee A. Incidence of carbapenem-resistant Escherichia coli ST2437 of clinical origin harbouring blaOXA-144 gene: a report from India. J Appl Microbiol 2024; 135:lxae087. [PMID: 38553965 DOI: 10.1093/jambio/lxae087] [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: 02/05/2024] [Revised: 03/20/2024] [Accepted: 03/27/2024] [Indexed: 04/13/2024]
Abstract
AIMS Carbapenem-resistant Escherichia coli has been categorized as a pathogen of critical priority by the World Health Organization as it is highly infectious with high mortality and morbidity rates and widespread transmission potential. Carbapenem resistance is primarily mediated by carbapenemase-encoding genes and, additionally, through intrinsic factors. In India, over the years, carbapenemase-encoding genes have been reported from diverse clinically significant pathogens. The present study identifies E. coli of clinical origin that harbours blaOXA-144. METHODS AND RESULTS The study isolate was obtained from a tertiary referral hospital in northeast India. Carbapenemase production was investigated through culture on chromogenic agar and Rapidec Carba NP test as per manufacturer's instructions. Susceptibility of the isolate was performed by the Kirby-Bauer disc diffusion method and agar dilution method following CLSI guidelines. PCR targeting carbapenemase-encoding genes was performed, followed by transformation and conjugation experiments. Whole-genome sequencing of the isolate was done through the Illumina sequencing platform and the data were analysed using the Centre for Genomic Epidemiology database. BJD_EC180 is 6 919 180 bp in length and consists of six rRNA operons, 111 tRNA, and 6849 predicted protein-coding sequences. BJD_EC180 belonged to ST2437 and harboured the carbapenemase-encoding gene blaOXA-144 with ISAba1 upstream, along with multiple antibiotic resistance genes conferring clinical resistance towards beta-lactams, aminoglycosides, amphenicols, sulphonamides, tetracyclines, trimethoprim, and rifampin. CONCLUSIONS Carbapenem-resistant E. coli harbouring blaOXA-144 associated with insertion sequence pose a serious health threat as their mobilization into carbapenem non-susceptible strains that will contribute to the resistance burden and therefore, needs urgent monitoring.
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Affiliation(s)
- Bhaskar Jyoti Das
- Department of Microbiology, Assam University, Silchar, Cachar, Assam 788011, India
| | - K Melson Singha
- Department of Microbiology, Silchar Medical College and Hospital, Silchar, Cachar, Assam 788014, India
| | | | - Debadatta Dhar Chanda
- Department of Microbiology, Silchar Medical College and Hospital, Silchar, Cachar, Assam 788014, India
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Smit CCH, Lambert M, Rogers K, Djordjevic SP, Van Oijen AM, Keighley C, Taxis K, Robertson H, Pont LG. One Health Determinants of Escherichia coli Antimicrobial Resistance in Humans in the Community: An Umbrella Review. Int J Mol Sci 2023; 24:17204. [PMID: 38139033 PMCID: PMC10743193 DOI: 10.3390/ijms242417204] [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: 11/14/2023] [Revised: 11/29/2023] [Accepted: 12/01/2023] [Indexed: 12/24/2023] Open
Abstract
To date, the scientific literature on health variables for Escherichia coli antimicrobial resistance (AMR) has been investigated throughout several systematic reviews, often with a focus on only one aspect of the One Health variables: human, animal, or environment. The aim of this umbrella review is to conduct a systematic synthesis of existing evidence on Escherichia coli AMR in humans in the community from a One Health perspective. PubMed, EMBASE, and CINAHL were searched on "antibiotic resistance" and "systematic review" from inception until 25 March 2022 (PROSPERO: CRD42022316431). The methodological quality was assessed, and the importance of identified variables was tabulated across all included reviews. Twenty-three reviews were included in this study, covering 860 primary studies. All reviews were of (critically) low quality. Most reviews focused on humans (20), 3 on animals, and 1 on both human and environmental variables. Antibiotic use, urinary tract infections, diabetes, and international travel were identified as the most important human variables. Poultry farms and swimming in freshwater were identified as potential sources for AMR transmission from the animal and environmental perspectives. This umbrella review highlights a gap in high-quality literature investigating the time between variable exposure, AMR testing, and animal and environmental AMR variables.
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Affiliation(s)
- Chloé C. H. Smit
- Graduate School of Health, University of Technology Sydney, Sydney, NSW 2008, Australia; (C.C.H.S.); (K.R.)
| | - Maarten Lambert
- Department of PharmacoTherapy, -Epidemiology and -Economics, Faculty of Science and Engineering, University of Groningen, 9713 AV Groningen, The Netherlands; (M.L.); (K.T.)
| | - Kris Rogers
- Graduate School of Health, University of Technology Sydney, Sydney, NSW 2008, Australia; (C.C.H.S.); (K.R.)
| | - Steven P. Djordjevic
- The Australian Institute for Microbiology & Infection, University of Technology Sydney, Sydney, NSW 2007, Australia;
| | - Antoine M. Van Oijen
- Faculty of Medicine and Health, University of Sydney, Sydney, NSW 2050, Australia;
| | - Caitlin Keighley
- Southern.IML Pathology, Sonic Healthcare, 3 Bridge St, Wollongong, NSW 2500, Australia
- Graduate School of Medicine, University of Wollongong, Wollongong, NSW 2522, Australia
| | - Katja Taxis
- Department of PharmacoTherapy, -Epidemiology and -Economics, Faculty of Science and Engineering, University of Groningen, 9713 AV Groningen, The Netherlands; (M.L.); (K.T.)
| | - Hamish Robertson
- School of Public Health & Social Work, Queensland University of Technology, Brisbane, QLD 4059, Australia;
| | - Lisa G. Pont
- Graduate School of Health, University of Technology Sydney, Sydney, NSW 2008, Australia; (C.C.H.S.); (K.R.)
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Lutgring JD, Kent AG, Bowers JR, Jasso-Selles DE, Albrecht V, Stevens VA, Pfeiffer A, Barnes R, Engelthaler DM, Johnson JK, Gargis AS, Rasheed JK, Limbago BM, Elkins CA, Karlsson M, Halpin AL. Comparison of carbapenem-susceptible and carbapenem-resistant Enterobacterales at nine sites in the USA, 2013-2016: a resource for antimicrobial resistance investigators. Microb Genom 2023; 9. [PMID: 37987646 DOI: 10.1099/mgen.0.001119] [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] [Indexed: 11/22/2023] Open
Abstract
Carbapenem-resistant Enterobacterales (CRE) are an urgent public health threat. Genomic sequencing is an important tool for investigating CRE. Through the Division of Healthcare Quality Promotion Sentinel Surveillance system, we collected CRE and carbapenem-susceptible Enterobacterales (CSE) from nine clinical laboratories in the USA from 2013 to 2016 and analysed both phenotypic and genomic sequencing data for 680 isolates. We describe the molecular epidemiology and antimicrobial susceptibility testing (AST) data of this collection of isolates. We also performed a phenotype-genotype correlation for the carbapenems and evaluated the presence of virulence genes in Klebsiella pneumoniae complex isolates. These AST and genomic sequencing data can be used to compare and contrast CRE and CSE at these sites and serve as a resource for the antimicrobial resistance research community.
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Affiliation(s)
- Joseph D Lutgring
- Division of Healthcare Quality Promotion, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Alyssa G Kent
- Division of Healthcare Quality Promotion, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
- Goldbelt C6, LLC, Chesapeake, Virginia, USA
| | - Jolene R Bowers
- Pathogen and Microbiome Division, Translational Genomics Research Institute North, Flagstaff, Arizona, USA
| | - Daniel E Jasso-Selles
- Pathogen and Microbiome Division, Translational Genomics Research Institute North, Flagstaff, Arizona, USA
| | - Valerie Albrecht
- Division of Healthcare Quality Promotion, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
- Present address: Office of the Director, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Valerie A Stevens
- Division of Healthcare Quality Promotion, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Ashlyn Pfeiffer
- Pathogen and Microbiome Division, Translational Genomics Research Institute North, Flagstaff, Arizona, USA
| | - Riley Barnes
- Pathogen and Microbiome Division, Translational Genomics Research Institute North, Flagstaff, Arizona, USA
| | - David M Engelthaler
- Pathogen and Microbiome Division, Translational Genomics Research Institute North, Flagstaff, Arizona, USA
| | - J Kristie Johnson
- Department of Pathology, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Amy S Gargis
- Division of Healthcare Quality Promotion, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - J Kamile Rasheed
- Division of Healthcare Quality Promotion, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Brandi M Limbago
- Division of Healthcare Quality Promotion, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
- Present address: Office of Science, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Christopher A Elkins
- Division of Healthcare Quality Promotion, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Maria Karlsson
- Division of Healthcare Quality Promotion, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
- Goldbelt C6, LLC, Chesapeake, Virginia, USA
| | - Alison L Halpin
- Division of Healthcare Quality Promotion, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
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Yang TY, Hung WC, Tsai TH, Lu PL, Wang SF, Wang LC, Lin YT, Tseng SP. Potentials of organic tellurium-containing compound AS101 to overcome carbapenemase-producing Escherichia coli. JOURNAL OF MICROBIOLOGY, IMMUNOLOGY, AND INFECTION = WEI MIAN YU GAN RAN ZA ZHI 2023; 56:1016-1025. [PMID: 37516546 DOI: 10.1016/j.jmii.2023.07.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 06/11/2023] [Accepted: 07/06/2023] [Indexed: 07/31/2023]
Abstract
BACKGROUND The issue of carbapenem-resistant Escherichia coli was aggravated yearly. The previous studies reported the varied but critical epidemiology of carbapenem-resistant E. coli among which the carbapenemase-producing strains were regarded as one of the most notorious issues. AS101, an organic tellurium-containing compound undergoing clinical trials, was revealed with antibacterial activities. However, little is known about the antibacterial effect of AS101 against carbapenemase-producing E. coli (CPEC). MATERIALS AND METHODS The minimum inhibitory concentration (MIC) of AS101 against the 15 isolates was examined using a broth microdilution method. The scanning electron microscopy, pharmaceutical manipulations, reactive oxygen species level, and DNA fragmentation assay were carried out to investigate the antibacterial mechanism. The sepsis mouse model was employed to assess the in vivo treatment effect. RESULTS The blaNDM (33.3%) was revealed as the dominant carbapenemase gene among the 15 CPEC isolates, followed by the blaKPC gene (26.7%). The MICs of AS101 against the 15 isolates ranged from 0.5 to 32 μg/ml, and 99.9% of bacterial eradication was observed at 8 h, 4 h, and 2 h for 1×, 2×, and 4 × MIC, respectively. The mechanistic investigations suggest that AS101 would enter the bacterial cell, and induce ROS generation, leading to DNA fragmentation. The in vivo study exhibited that AS101 possessed a steady treatment effect in a sepsis mouse model, with an up to 83.3% of survival rate. CONCLUSION The in vitro activities, mechanisms, and in vivo study of AS101 against CPEC were unveiled. Our finding provided further evidence for the antibiotic development of AS101.
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Affiliation(s)
- Tsung-Ying Yang
- Department of Medical Laboratory Science, I-Shou University, Kaohsiung, Taiwan; Research Organization for Nano and Life Innovation, Future Innovation Institute, Waseda University, Japan; Research Institute for Science and Engineering, Waseda University, Japan; School of Education, Waseda University, Japan
| | - Wei-Chun Hung
- Department of Microbiology and Immunology, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Tsung-Han Tsai
- Department of Medical Laboratory Science and Biotechnology, College of Health Sciences, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Po-Liang Lu
- Center for Liquid Biopsy and Cohort Research, Kaohsiung Medical University, Kaohsiung, Taiwan; Division of Infectious Diseases, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
| | - Sheng-Fan Wang
- Department of Medical Laboratory Science and Biotechnology, College of Health Sciences, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Liang-Chun Wang
- Department of Marine Biotechnology and Resources, National Sun Yat-sen University, Kaohsiung, Taiwan
| | - Yu-Tzu Lin
- Department of Medical Laboratory Science and Biotechnology, China Medical University, Taichung, Taiwan.
| | - Sung-Pin Tseng
- Department of Medical Laboratory Science and Biotechnology, College of Health Sciences, Kaohsiung Medical University, Kaohsiung, Taiwan; Department of Marine Biotechnology and Resources, National Sun Yat-sen University, Kaohsiung, Taiwan; Graduate Institute of Animal Vaccine Technology, College of Veterinary Medicine, National Pingtung University of Science and Technology, Pingtung, Taiwan; Center for Tropical Medicine and Infectious Disease Research, Kaohsiung Medical University, Kaohsiung, Taiwan.
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8
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Wang L, Ma X, Chen Y, Gao S, He H, Su L, Guo Y, Shan G, Hu Y, Zhou X, Liu D. Carbapenem is not always the best choice in the treatment of septic shock. Eur J Med Res 2023; 28:372. [PMID: 37749658 PMCID: PMC10518951 DOI: 10.1186/s40001-023-01341-x] [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: 06/21/2023] [Accepted: 09/04/2023] [Indexed: 09/27/2023] Open
Abstract
BACKGROUND Septic shock is a global public health burden. In addition to the improvement of the level of individual care, the improvement of the overall hospital quality control management is also an essential key aspect of the Surviving Sepsis Campaign (SSC). Using of antibiotics is a cornerstone in the treatment of septic shock, so we conducted this study to investigate the influence of antibiotics and pathogenic bacteria on the mortality of septic shock at the level of overall hospital in China. METHODS This was an observational database study in 2021 enrolled the data of 787 hospitals from 31 provinces/municipalities/autonomous regions of Mainland China collected in a survey from January 1, 2021 to December 31, 2021. RESULTS The proportion of ICU patients with septic shock was 3.55%, while the patient mortality of septic shock was 23.08%. While carbapenem was the most preferred antibiotic medication used in 459 of the 782 hospitals, the preference for carbapenem did not show significant effect on the patient mortality in the treatment of septic shock (p-value 0.59). Compared with patients with fermenting bacteria as the most common pathogenic bacteria causing septic shock, patients with non-fermenting bacteria had a higher mortality (p-value 0.01). CONCLUSIONS Whether using carbapenem as the preferred antibiotic or not, did not show effect on the patient mortality of septic shock. Compared with patients with fermenting bacteria as the most common pathogenic bacteria, patients of septic shock with non-fermenting bacteria had a higher mortality.
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Affiliation(s)
- Lu Wang
- Department of Critical Care Medicine, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Xudong Ma
- Department of Medical Administration, National Health Commission of the People's Republic of China, Beijing, 100044, China
| | - Yujie Chen
- Department of Critical Care Medicine, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Sifa Gao
- Department of Medical Administration, National Health Commission of the People's Republic of China, Beijing, 100044, China
| | - Huaiwu He
- Department of Critical Care Medicine, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Longxiang Su
- Department of Critical Care Medicine, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Yanhong Guo
- Department of Medical Administration, National Health Commission of the People's Republic of China, Beijing, 100044, China
| | - Guangliang Shan
- Department of Epidemiology and Biostatistics, Institute of Basic Medicine Sciences, Chinese Academy of Medical Sciences (CAMS) & School of Basic Medicine, Peking Union Medical College, Beijing, 100730, China
| | - Yaoda Hu
- Department of Epidemiology and Biostatistics, Institute of Basic Medicine Sciences, Chinese Academy of Medical Sciences (CAMS) & School of Basic Medicine, Peking Union Medical College, Beijing, 100730, China
| | - Xiang Zhou
- Department of Critical Care Medicine, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, 100730, China.
- Information Center Department/Department of Information Management, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, 100730, China.
| | - Dawei Liu
- Department of Critical Care Medicine, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, 100730, China.
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9
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Johnston BD, Clabots C, Bender T, Porter SB, van den Dobbelsteen G, Poolman J, Thuras P, Johnson JR. Colonization with Escherichia coli ST131- H30R ( H30R) Corresponds with Increased Serum Anti-O25 IgG Levels and Decreased TNFα and IL-10 Responsiveness to H30R. Pathogens 2023; 12:pathogens12040603. [PMID: 37111489 PMCID: PMC10142592 DOI: 10.3390/pathogens12040603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 04/04/2023] [Accepted: 04/11/2023] [Indexed: 04/29/2023] Open
Abstract
An exceptional gut-colonizing ability may underlie the dramatic epidemiological success of the multidrug-resistant H30R subclone of Escherichia coli sequence type 131 (O25b:K+:H4). In order to inform the development of colonization-preventing measures, we studied systemic immune correlates of H30R intestinal colonization. Human volunteers' fecal samples were screened for H30R by selective culture and PCR. Subjects were assessed by enzyme immunoassay for serum levels of anti-O25 IgG (representing H30R) and anti-O6 IgG (representing non-H30 E. coli generally), initially and for up to 14 months. Whole blood was tested for the antigen-stimulated release of IFNγ, TNFα, IL-4, IL-10, and IL-17 after incubation with E. coli strains JJ1886 (H30R; O25b:K+:H4) or CFT073 (non-H30; O6:K2:H1). Three main findings were obtained. First, H30R-colonized subjects had significantly higher anti-O25 IgG levels than controls, but similar anti-O6 IgG levels, suggesting an IgG response to H30R colonization. Second, anti-O25 and anti-O6 IgG levels were stable over time. Third, H30R-colonized subjects exhibited a lower TNFα and IL-10 release than controls in response to strain JJ1886 (H30R) relative to strain CFT073 (non-H30R), consistent with TNFα hypo-responsiveness to H30R possibly predisposing to H30R colonization. Thus, H30R-colonized hosts exhibit a sustained serum anti-O25 IgG response and an underlying deficit in TNFα responsiveness to H30R that could potentially be addressed for colonization prevention.
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Affiliation(s)
- Brian D Johnston
- Departments of Medicine and Psychiatry, University of Minnesota, Minneapolis 55455, MN, USA
| | - Connie Clabots
- Infectious Diseases (111F), Minneapolis VA Health Care System, Minneapolis 55417, MN, USA
| | - Tricia Bender
- Infectious Diseases (111F), Minneapolis VA Health Care System, Minneapolis 55417, MN, USA
| | - Stephen B Porter
- Infectious Diseases (111F), Minneapolis VA Health Care System, Minneapolis 55417, MN, USA
| | | | - Jan Poolman
- Janssen Vaccines & Prevention B.V., 2333 CN Leiden, The Netherlands
| | - Paul Thuras
- Departments of Medicine and Psychiatry, University of Minnesota, Minneapolis 55455, MN, USA
- Infectious Diseases (111F), Minneapolis VA Health Care System, Minneapolis 55417, MN, USA
| | - James R Johnson
- Departments of Medicine and Psychiatry, University of Minnesota, Minneapolis 55455, MN, USA
- Infectious Diseases (111F), Minneapolis VA Health Care System, Minneapolis 55417, MN, USA
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10
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Pitout JD, Peirano G, DeVinney R. The contributions of multidrug resistant clones to the success of pandemic extra-intestinal Pathogenic Escherichia coli. Expert Rev Anti Infect Ther 2023; 21:343-353. [PMID: 36822840 DOI: 10.1080/14787210.2023.2184348] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2023]
Abstract
INTRODUCTION High-risk multidrug (MDR) clones have played essential roles in the global emergence and spread of antimicrobial resistance (AMR), especially among Extra-intestinal Escherichia coli (ExPEC). AREAS COVERED Successful global ExPEC MDR clones are linked with the acquisition of fluoroquinolone resistance, CTX-M enzymes, and with carbapenemases. This article described the underlying mechanisms of fluoroquinolone resistance, the acquisition of CTX-M and carbapenemase genes among three global ExPEC high-risk MDR clones, namely i) ST1193 as being an example of a fluoroquinolone resistant clone. ii) ST131 as an example of a fluoroquinolone resistant and CTX-M clone. iii) ST410 as an example of a fluoroquinolone resistant, CTX-M and carbapenemase clone. This article also highlighted the contributions of these MDR determinants in the evolution of these high-risk MDR clones. EXPERT OPINION There is an enormous public health burden due to E. coli MDR high-risk clones such as ST1193, ST131 and ST410. These clones have played pivotal roles in the global spread of AMR. Sparse information is available on which specific features of these high-risk MDR clones have enabled them to become such successful global pathogens in relative short time periods.
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Affiliation(s)
- Johann Dd Pitout
- University of Calgary, Calgary, Alberta, Canada.,Dynalife Laboratories, University of Calgary, Calgary, Alberta, Canada.,University of Pretoria, Pretoria, Gauteng, South Africa
| | - Gisele Peirano
- University of Calgary, Calgary, Alberta, Canada.,Dynalife Laboratories, University of Calgary, Calgary, Alberta, Canada
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11
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Piekar M, Álvarez VE, Knecht C, Leguina C, García Allende N, Carrera Páez L, Gambino AS, González Machuca A, Campos J, Fox B, Carpio E, Aguilar A, Alonso FM, Fernández Canigia L, Quiroga MP, Centrón D. Genomic data reveals the emergence of the co-occurrence of bla KPC-2 and bla CTX-M-15 in an Escherichia coli ST648 strain isolated from rectal swab within the framework of hospital surveillance. J Glob Antimicrob Resist 2023; 32:108-112. [PMID: 36708770 DOI: 10.1016/j.jgar.2022.12.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 12/06/2022] [Accepted: 12/31/2022] [Indexed: 01/26/2023] Open
Abstract
OBJECTIVES The worldwide dissemination of carbapenemase-producing Escherichia coli lineages belonging to high-risk clones poses a challenging public health menace. The aim of this work was to investigate genomic features of a colonizing multidrug-resistant strain of Klebsiella pneumoniae carbapenemase (KPC)-producing E. coli from our institution. METHODS Whole-genome sequencing was done by Illumina MiSeq-I, and de novo assembly was achieved using SPAdes. Resistome, mobilome, plasmids, virulome, and integrons were analysed using ResFinder, AMRFinder, ISFinder, PlasmidFinder, MOB-suite, VirulenceFinder, and IntegronFinder. Sequence types (STs) were identified with pubMLST and BIGSdb databases. Conjugation assays were also performed. RESULTS Escherichia coli HA25pEc was isolated from a rectal swab sample taken within the framework of the hospital epidemiological surveillance protocol for detection of carbapenemase-producing Enterobacterales. Escherichia coli HA25pEc corresponded to the first report of ST648 co-harbouring blaKPC-2 and blaCTX-M-15 in Latin America from a colonized patient. It had 19 antibiotic resistance genes (ARGs), including blaKPC-2, located on a Tn4401a isoform. Conjugation assays revealed that blaKPC-2 was not transferred by conjugation to E. coli J53 under our experimental conditions. CONCLUSION Escherichia coli ST648 has been detected previously in companion and farm animals as well as in hospital- and community-acquired infections worldwide. Although scarcely reported as KPC-producers, our finding in a culture surveillance with several acquired ARGs, including blaCTX-M-15, alerts the potential of this clone for worldwide unnoticed spreading of extreme drug resistance to β-lactams. These data reinforce the importance of carrying out molecular surveillance to identify reservoirs and warn about the dissemination of new international clones in carbapenemase-bearing patients.
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Affiliation(s)
- María Piekar
- Laboratorio de Investigaciones en Mecanismos de Resistencia a Antibióticos (LIMRA), Instituto de Investigaciones en Microbiología y Parasitología Médica, Universidad de Buenos Aires - Consejo Nacional de Investigaciones Científicas y Técnicas (IMPaM, UBA-CONICET), Ciudad Autónoma de Buenos Aires, Argentina
| | - Verónica E Álvarez
- Laboratorio de Investigaciones en Mecanismos de Resistencia a Antibióticos (LIMRA), Instituto de Investigaciones en Microbiología y Parasitología Médica, Universidad de Buenos Aires - Consejo Nacional de Investigaciones Científicas y Técnicas (IMPaM, UBA-CONICET), Ciudad Autónoma de Buenos Aires, Argentina.
| | - Camila Knecht
- Laboratorio de Investigaciones en Mecanismos de Resistencia a Antibióticos (LIMRA), Instituto de Investigaciones en Microbiología y Parasitología Médica, Universidad de Buenos Aires - Consejo Nacional de Investigaciones Científicas y Técnicas (IMPaM, UBA-CONICET), Ciudad Autónoma de Buenos Aires, Argentina
| | - Carolina Leguina
- Laboratorio de Investigaciones en Mecanismos de Resistencia a Antibióticos (LIMRA), Instituto de Investigaciones en Microbiología y Parasitología Médica, Universidad de Buenos Aires - Consejo Nacional de Investigaciones Científicas y Técnicas (IMPaM, UBA-CONICET), Ciudad Autónoma de Buenos Aires, Argentina
| | - Natalia García Allende
- Laboratorio de Investigaciones en Mecanismos de Resistencia a Antibióticos (LIMRA), Instituto de Investigaciones en Microbiología y Parasitología Médica, Universidad de Buenos Aires - Consejo Nacional de Investigaciones Científicas y Técnicas (IMPaM, UBA-CONICET), Ciudad Autónoma de Buenos Aires, Argentina; Hospital Alemán, Ciudad Autónoma de Buenos Aires, Argentina
| | - Laura Carrera Páez
- Laboratorio de Investigaciones en Mecanismos de Resistencia a Antibióticos (LIMRA), Instituto de Investigaciones en Microbiología y Parasitología Médica, Universidad de Buenos Aires - Consejo Nacional de Investigaciones Científicas y Técnicas (IMPaM, UBA-CONICET), Ciudad Autónoma de Buenos Aires, Argentina
| | - Anahí S Gambino
- Laboratorio de Investigaciones en Mecanismos de Resistencia a Antibióticos (LIMRA), Instituto de Investigaciones en Microbiología y Parasitología Médica, Universidad de Buenos Aires - Consejo Nacional de Investigaciones Científicas y Técnicas (IMPaM, UBA-CONICET), Ciudad Autónoma de Buenos Aires, Argentina
| | - Adrián González Machuca
- Laboratorio de Investigaciones en Mecanismos de Resistencia a Antibióticos (LIMRA), Instituto de Investigaciones en Microbiología y Parasitología Médica, Universidad de Buenos Aires - Consejo Nacional de Investigaciones Científicas y Técnicas (IMPaM, UBA-CONICET), Ciudad Autónoma de Buenos Aires, Argentina
| | - Josefina Campos
- Plataforma de Genómica y Bioinformática, INEI-ANLIS 'Dr. Carlos G. Malbrán', Buenos Aires, Argentina
| | - Barbara Fox
- Hospital Alemán, Ciudad Autónoma de Buenos Aires, Argentina
| | - Eduardo Carpio
- Laboratorio de Investigaciones en Mecanismos de Resistencia a Antibióticos (LIMRA), Instituto de Investigaciones en Microbiología y Parasitología Médica, Universidad de Buenos Aires - Consejo Nacional de Investigaciones Científicas y Técnicas (IMPaM, UBA-CONICET), Ciudad Autónoma de Buenos Aires, Argentina
| | - Andrea Aguilar
- Nodo Bioinformático IMPaM, Instituto de Investigaciones en Microbiología y Parasitología Médica, Facultad de Medicina, Universidad de Buenos Aires - Consejo Nacional de Investigaciones Científicas y Técnicas (IMPaM, UBA-CONICET), Ciudad Autónoma de Buenos Aires, Argentina
| | - Fernando M Alonso
- Laboratorio de Investigaciones en Mecanismos de Resistencia a Antibióticos (LIMRA), Instituto de Investigaciones en Microbiología y Parasitología Médica, Universidad de Buenos Aires - Consejo Nacional de Investigaciones Científicas y Técnicas (IMPaM, UBA-CONICET), Ciudad Autónoma de Buenos Aires, Argentina
| | | | - María Paula Quiroga
- Laboratorio de Investigaciones en Mecanismos de Resistencia a Antibióticos (LIMRA), Instituto de Investigaciones en Microbiología y Parasitología Médica, Universidad de Buenos Aires - Consejo Nacional de Investigaciones Científicas y Técnicas (IMPaM, UBA-CONICET), Ciudad Autónoma de Buenos Aires, Argentina; Nodo Bioinformático IMPaM, Instituto de Investigaciones en Microbiología y Parasitología Médica, Facultad de Medicina, Universidad de Buenos Aires - Consejo Nacional de Investigaciones Científicas y Técnicas (IMPaM, UBA-CONICET), Ciudad Autónoma de Buenos Aires, Argentina
| | - Daniela Centrón
- Laboratorio de Investigaciones en Mecanismos de Resistencia a Antibióticos (LIMRA), Instituto de Investigaciones en Microbiología y Parasitología Médica, Universidad de Buenos Aires - Consejo Nacional de Investigaciones Científicas y Técnicas (IMPaM, UBA-CONICET), Ciudad Autónoma de Buenos Aires, Argentina.
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12
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Emergence and Dissemination of Extraintestinal Pathogenic High-Risk International Clones of Escherichia coli. LIFE (BASEL, SWITZERLAND) 2022; 12:life12122077. [PMID: 36556442 PMCID: PMC9780897 DOI: 10.3390/life12122077] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 12/06/2022] [Accepted: 12/08/2022] [Indexed: 12/14/2022]
Abstract
Multiresistant Escherichia coli has been disseminated worldwide, and it is one of the major causative agents of nosocomial infections. E. coli has a remarkable and complex genomic plasticity for taking up and accumulating genetic elements; thus, multiresistant high-risk clones can evolve. In this review, we summarise all available data about internationally disseminated extraintestinal pathogenic high-risk E. coli clones based on whole-genome sequence (WGS) data and confirmed outbreaks. Based on genetic markers, E. coli is clustered into eight phylogenetic groups. Nowadays, the E. coli ST131 clone from phylogenetic group B2 is the predominant high-risk clone worldwide. Currently, strains of the C1-M27 subclade within clade C of ST131 are circulating and becoming prominent in Canada, China, Germany, Hungary and Japan. The C1-M27 subclade is characterised by blaCTX-M-27. Recently, the ST1193 clone has been reported as an emerging high-risk clone from phylogenetic group B2. ST38 clone carrying blaOXA-244 (a blaOXA-48-like carbapenemase gene) caused several outbreaks in Germany and Switzerland. Further high-risk international E. coli clones include ST10, ST69, ST73, ST405, ST410, ST457. High-risk E. coli strains are present in different niches, in the human intestinal tract and in animals, and persist in environment. These strains can be transmitted easily within the community as well as in hospital settings. WGS analysis is a useful tool for tracking the dissemination of resistance determinants, the emergence of high-risk mulitresistant E. coli clones and to analyse changes in the E. coli population on a genomic level.
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13
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Downing T, Lee MJ, Archbold C, McDonnell A, Rahm A. Informing plasmid compatibility with bacterial hosts using protein-protein interaction data. Genomics 2022; 114:110509. [PMID: 36273742 DOI: 10.1016/j.ygeno.2022.110509] [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: 08/19/2022] [Revised: 09/23/2022] [Accepted: 10/19/2022] [Indexed: 01/15/2023]
Abstract
The compatibility of plasmids with new host cells is significant given their role in spreading antimicrobial resistance (AMR) and virulence factor genes. Evaluating this using in vitro screening is laborious and can be informed by computational analyses of plasmid-host compatibility through rates of protein-protein interactions (PPIs) between plasmid and host cell proteins. We identified large excesses of such PPIs in eight important plasmids, including pOXA-48, using most known bacteria (n = 4363). 23 species had high rates of interactions with four blaOXA-48-positive plasmids. We also identified 48 species with high interaction rates with plasmids common in Escherichia coli. We found a strong association between one plasmid and the fimbrial adhesin operon pil, which could enhance host cell adhesion in aqueous environments. An excess rate of PPIs could be a sign of host-plasmid compatibility, which is important for AMR control given that plasmids like pOXA-48 move between species with ease.
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Affiliation(s)
- Tim Downing
- School of Biotechnology, Dublin City University, Dublin, Ireland; The Pirbright Institute, UK.
| | - Min Jie Lee
- School of Biotechnology, Dublin City University, Dublin, Ireland
| | - Conor Archbold
- School of Biotechnology, Dublin City University, Dublin, Ireland
| | - Adam McDonnell
- School of Biotechnology, Dublin City University, Dublin, Ireland
| | - Alexander Rahm
- GAATI Lab, University of French Polynesia, Tahiti, French Polynesia
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14
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Peirano G, Chen L, Nobrega D, Finn TJ, Kreiswirth BN, DeVinney R, Pitout JDD. Genomic Epidemiology of Global Carbapenemase-Producing Escherichia coli, 2015-2017. Emerg Infect Dis 2022; 28. [PMID: 35451367 PMCID: PMC9045447 DOI: 10.3201/eid2805.212535] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
We describe the global molecular epidemiology of 229 carbapenemase-producing Escherichia coli in 36 countries during 2015-2017. Common carbapenemases were oxacillinase (OXA) 181 (23%), New Delhi metallo-β-lactamase (NDM) 5 (20%), OXA-48 (17%), Klebsiella pneumoniae carbapenemase 2 (15%), and NDM-1 (10%). We identified 5 dominant sequence types (STs); 4 were global (ST410, ST131, ST167, and ST405), and 1 (ST1284) was limited to Turkey. OXA-181 was frequent in Jordan (because of the ST410-B4/H24RxC subclade) and Turkey (because of ST1284). We found nearly identical IncX3-blaOXA-181 plasmids among 11 STs from 12 countries. NDM-5 was frequent in Egypt, Thailand (linked with ST410-B4/H24RxC and ST167-B subclades), and Vietnam (because of ST448). OXA-48 was common in Turkey (linked with ST11260). Global K. pneumoniae carbapenemases were linked with ST131 C1/H30 subclade and NDM-1 with various STs. The global carbapenemase E. coli population is dominated by diverse STs with different characteristics and varied geographic distributions, requiring ongoing genomic surveillance.
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15
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Sanz MB, De Belder D, de Mendieta JM, Faccone D, Poklepovich T, Lucero C, Rapoport M, Campos J, Tuduri E, Saavedra MO, Van der Ploeg C, Rogé A, Pasteran F, Corso A, Rosato AE, Gomez SA. Carbapenemase-Producing Extraintestinal Pathogenic Escherichia coli From Argentina: Clonal Diversity and Predominance of Hyperepidemic Clones CC10 and CC131. Front Microbiol 2022; 13:830209. [PMID: 35369469 PMCID: PMC8971848 DOI: 10.3389/fmicb.2022.830209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 01/31/2022] [Indexed: 11/13/2022] Open
Abstract
Extraintestinal pathogenic Escherichia coli (ExPEC) causes infections outside the intestine. Particular ExPEC clones, such as clonal complex (CC)/sequence type (ST)131, have been known to sequentially accumulate antimicrobial resistance that starts with chromosomal mutations against fluoroquinolones, followed with the acquisition of blaCTX–M–15 and, more recently, carbapenemases. Here we aimed to investigate the distribution of global epidemic clones of carbapenemase-producing ExPEC from Argentina in representative clinical isolates recovered between July 2008 and March 2017. Carbapenemase-producing ExPEC (n = 160) were referred to the Argentinean reference laboratory. Of these, 71 were selected for genome sequencing. Phenotypic and microbiological studies confirmed the presence of carbapenemases confirmed as KPC-2 (n = 52), NDM-1 (n = 16), IMP-8 (n = 2), and VIM-1 (n = 1) producers. The isolates had been recovered mainly from urine, blood, and abdominal fluids among others, and some were from screening samples. After analyzing the virulence gene content, 76% of the isolates were considered ExPEC, although non-ExPEC isolates were also obtained from extraintestinal sites. Pan-genome phylogeny and clonal analysis showed great clonal diversity, although the first phylogroup in abundance was phylogroup A, harboring CC10 isolates, followed by phylogroup B2 with CC/ST131, mostly H30Rx, the subclone co-producing CTX-M-15. Phylogroups D, B1, C, F, and E were also detected with fewer strains. CC10 and CC/ST131 were found throughout the country. In addition, CC10 nucleated most metalloenzymes, such as NDM-1. Other relevant international clones were identified, such as CC/ST38, CC155, CC14/ST1193, and CC23. Two isolates co-produced KPC-2 and OXA-163 or OXA-439, a point mutation variant of OXA-163, and three isolates co-produced MCR-1 among other resistance genes. To conclude, in this work, we described the molecular epidemiology of carbapenemase-producing ExPEC in Argentina. Further studies are necessary to determine the plasmid families disseminating carbapenemases in ExPEC in this region.
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Affiliation(s)
- María Belén Sanz
- Servicio Antimicrobianos, Laboratorio Nacional de Referencia en Resistencia a los Antimicrobianos (LNRRA), INEI-ANLIS "Dr. Carlos G. Malbrán", Buenos Aires, Argentina
| | - Denise De Belder
- Servicio Antimicrobianos, Laboratorio Nacional de Referencia en Resistencia a los Antimicrobianos (LNRRA), INEI-ANLIS "Dr. Carlos G. Malbrán", Buenos Aires, Argentina.,Plataforma Genómica y Bioinformática (PLABIO), INEI-ANLIS "Dr. Carlos G. Malbrán", Buenos Aires, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - J M de Mendieta
- Servicio Antimicrobianos, Laboratorio Nacional de Referencia en Resistencia a los Antimicrobianos (LNRRA), INEI-ANLIS "Dr. Carlos G. Malbrán", Buenos Aires, Argentina
| | - Diego Faccone
- Servicio Antimicrobianos, Laboratorio Nacional de Referencia en Resistencia a los Antimicrobianos (LNRRA), INEI-ANLIS "Dr. Carlos G. Malbrán", Buenos Aires, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Tomás Poklepovich
- Plataforma Genómica y Bioinformática (PLABIO), INEI-ANLIS "Dr. Carlos G. Malbrán", Buenos Aires, Argentina
| | - Celeste Lucero
- Servicio Antimicrobianos, Laboratorio Nacional de Referencia en Resistencia a los Antimicrobianos (LNRRA), INEI-ANLIS "Dr. Carlos G. Malbrán", Buenos Aires, Argentina
| | - Melina Rapoport
- Servicio Antimicrobianos, Laboratorio Nacional de Referencia en Resistencia a los Antimicrobianos (LNRRA), INEI-ANLIS "Dr. Carlos G. Malbrán", Buenos Aires, Argentina
| | - Josefina Campos
- Plataforma Genómica y Bioinformática (PLABIO), INEI-ANLIS "Dr. Carlos G. Malbrán", Buenos Aires, Argentina
| | - Ezequiel Tuduri
- Servicio Antimicrobianos, Laboratorio Nacional de Referencia en Resistencia a los Antimicrobianos (LNRRA), INEI-ANLIS "Dr. Carlos G. Malbrán", Buenos Aires, Argentina.,Plataforma Genómica y Bioinformática (PLABIO), INEI-ANLIS "Dr. Carlos G. Malbrán", Buenos Aires, Argentina
| | - Mathew O Saavedra
- Department of Pathology and Genomic Medicine, Center for Molecular and Translational Human Infectious Diseases Research, Houston Methodist Hospital, Houston Methodist Research Institute, Houston, TX, United States
| | - Claudia Van der Ploeg
- Servicio de Antígenos y Antisueros, INPB-ANLIS "Dr. Carlos G. Malbrán", Buenos Aires, Argentina
| | - Ariel Rogé
- Servicio de Antígenos y Antisueros, INPB-ANLIS "Dr. Carlos G. Malbrán", Buenos Aires, Argentina
| | | | - Fernando Pasteran
- Servicio Antimicrobianos, Laboratorio Nacional de Referencia en Resistencia a los Antimicrobianos (LNRRA), INEI-ANLIS "Dr. Carlos G. Malbrán", Buenos Aires, Argentina
| | - Alejandra Corso
- Servicio Antimicrobianos, Laboratorio Nacional de Referencia en Resistencia a los Antimicrobianos (LNRRA), INEI-ANLIS "Dr. Carlos G. Malbrán", Buenos Aires, Argentina
| | - Adriana E Rosato
- Department of Pathology and Molecular Microbiology Diagnostics-Research, Riverside University Health System, Moreno Valley, CA, United States.,School of Medicine, University of California, Riverside, Riverside, CA, United States
| | - Sonia A Gomez
- Servicio Antimicrobianos, Laboratorio Nacional de Referencia en Resistencia a los Antimicrobianos (LNRRA), INEI-ANLIS "Dr. Carlos G. Malbrán", Buenos Aires, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
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