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Yan Z, Ju X, Zhang Y, Wu Y, Sun Y, Xiong P, Li Y, Li R, Zhang R. Analysis of the transmission chain of carbapenem-resistant Enterobacter cloacae complex infections in clinical, intestinal and healthcare settings in Zhejiang province, China (2022-2023). Sci Total Environ 2024; 920:170635. [PMID: 38340846 DOI: 10.1016/j.scitotenv.2024.170635] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 01/12/2024] [Accepted: 01/31/2024] [Indexed: 02/12/2024]
Abstract
Considerable attention is given to intensive care unit-acquired infections; however, research on the transmission dynamics of multichain carbapenemase-resistant Enterobacter cloacae complex (CRECC) outbreaks remains elusive. A total of 118 non-duplicated CRECC strains were isolated from the clinical, intestinal, and hospital sewage samples collected from Zhejiang province of China during 2022-2023. A total of 64 CRECC strains were isolated from the hospital sewage samples, and their prevalence increased from 10.0 % (95 % confidence interval, CI = 0.52-45.8 %) in 2022 to 63.6 % (95 % CI = 31.6-87.6 %) in 2023. Species-specific identification revealed that Enterobacter hormaechei was the predominant CRECC species isolated in this study (53.4 %, 95 % CI = 44.0-62.6 %). The antimicrobial susceptibility profiles indicated that all 118 CRECC strains conferred high-level resistance to β-lactam antibiotics, ceftacillin/avibactam, and polymyxin. Furthermore, all CRECC strains exhibited resistance to β-lactams, quinolones, and fosfomycin, with a higher colistin resistance rate observed in the hospital sewage samples (67.2 %, 95 % CI = 54.2-78.1 %). Several antibiotic resistance genes were identified in CRECC strains, including Class A carbapenemases (blaKPC-2) and Class B carbapenemases (blaNDM-1/blaIMP), but not Class D carbapenemases. The WGS analysis showed that the majority of the CRECC strains carried carbapenemase-encoding genes, with blaNDM-1 being the most prevalent (86.9 %, 95 % CI = 77.4-92.9 %). Furthermore, sequence typing revealed that the isolated CRECC strains belonged to diverse sequence types (STs), among which ST418 was the most prevalent blaNDM-positive strain. The high risk of carbapenemase-producing ST418 E. hormaechei and the blaNDM-harboring IncFIB-type plasmid (81.4 %, 95 % CI = 72.9-87.7 %) were detected and emphasized in this study. This study provides valuable insights into the prevalence, antimicrobial resistance, genomic characteristics, and plasmid analysis of CRECC strains in diverse populations and environments. The clonal relatedness analysis showed sporadic clonal transmission of ST418 E. hormaechei strains, supporting inter-hospital transmission.
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Affiliation(s)
- Zelin Yan
- Department of Clinical Laboratory, Second Affiliated Hospital of Zhejiang University, School of Medicine, Hangzhou, China
| | - Xiaoyang Ju
- Department of Clinical Laboratory, Second Affiliated Hospital of Zhejiang University, School of Medicine, Hangzhou, China
| | - Yanyan Zhang
- Department of Clinical Laboratory, Second Affiliated Hospital of Zhejiang University, School of Medicine, Hangzhou, China
| | - Yuchen Wu
- Department of Clinical Laboratory, Second Affiliated Hospital of Zhejiang University, School of Medicine, Hangzhou, China
| | - Yi Sun
- Department of Clinical Laboratory, Second Affiliated Hospital of Zhejiang University, School of Medicine, Hangzhou, China
| | - Panfeng Xiong
- Joint Laboratory for Animal Health Big Data Analytics, College of Animal Science and Technology & College of Veterinary Medicine, Zhejiang A & F University, Hangzhou, China
| | - Yan Li
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou, 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, China
| | - Rong Zhang
- Department of Clinical Laboratory, Second Affiliated Hospital of Zhejiang University, School of Medicine, Hangzhou, China.
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Nasser-Ali M, Aja-Macaya P, Conde-Pérez K, Trigo-Tasende N, Rumbo-Feal S, Fernández-González A, Bou G, Poza M, Vallejo JA. Emergence of Carbapenemase Genes in Gram-Negative Bacteria Isolated from the Wastewater Treatment Plant in A Coruña, Spain. Antibiotics (Basel) 2024; 13:194. [PMID: 38391580 PMCID: PMC10886265 DOI: 10.3390/antibiotics13020194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 02/06/2024] [Accepted: 02/15/2024] [Indexed: 02/24/2024] Open
Abstract
Wastewater treatment plants (WWTPs) are recognized as important niches of antibiotic-resistant bacteria that can be easily spread to the environment. In this study, we collected wastewater samples from the WWTP of A Coruña (NW Spain) from April 2020 to February 2022 to evaluate the presence of Gram-negative bacteria harboring carbapenemase genes. Bacteria isolated from wastewater were classified and their antimicrobial profiles were determined. In total, 252 Gram-negative bacteria carrying various carbapenemase genes were described. Whole-genome sequencing was conducted on 55 selected carbapenemase producing isolates using Oxford Nanopore technology. This study revealed the presence of a significant population of bacteria carrying carbapenemase genes in WWTP, which constitutes a public health problem due to their risk of dissemination to the environment. This emphasizes the usefulness of WWTP monitoring for combating antibiotic resistance. Data revealed the presence of different types of sequences harboring carbapenemase genes, such as blaKPC-2, blaGES-5, blaGES-6, blaIMP-11, blaIMP-28, blaOXA-24, blaOXA-48, blaOXA-58, blaOXA-217, and blaVIM-2. Importantly, the presence of the blaKPC-2 gene in wastewater, several months before any clinical case was detected in University Hospital of A Coruña, suggests that wastewater-based epidemiology can be used as an early warning system for the surveillance of antibiotic-resistant bacteria.
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Affiliation(s)
- Mohammed Nasser-Ali
- Microbiology Research Group, Institute of Biomedical Research (INIBIC)-University Hospital of A Coruña (CHUAC)-Interdisciplinary Center for Chemistry and Biology (CICA)-University of A Coruña (UDC)-CIBER de Enfermedades Infecciosas (CIBERINFEC, ISCIII). Servicio de Microbiología, 3° planta, Edificio Sur, Hospital Universitario, As Xubias, 15006 A Coruna, Spain
| | - Pablo Aja-Macaya
- Microbiology Research Group, Institute of Biomedical Research (INIBIC)-University Hospital of A Coruña (CHUAC)-Interdisciplinary Center for Chemistry and Biology (CICA)-University of A Coruña (UDC)-CIBER de Enfermedades Infecciosas (CIBERINFEC, ISCIII). Servicio de Microbiología, 3° planta, Edificio Sur, Hospital Universitario, As Xubias, 15006 A Coruna, Spain
| | - Kelly Conde-Pérez
- Microbiology Research Group, Institute of Biomedical Research (INIBIC)-University Hospital of A Coruña (CHUAC)-Interdisciplinary Center for Chemistry and Biology (CICA)-University of A Coruña (UDC)-CIBER de Enfermedades Infecciosas (CIBERINFEC, ISCIII). Servicio de Microbiología, 3° planta, Edificio Sur, Hospital Universitario, As Xubias, 15006 A Coruna, Spain
| | - Noelia Trigo-Tasende
- Microbiology Research Group, Institute of Biomedical Research (INIBIC)-University Hospital of A Coruña (CHUAC)-Interdisciplinary Center for Chemistry and Biology (CICA)-University of A Coruña (UDC)-CIBER de Enfermedades Infecciosas (CIBERINFEC, ISCIII). Servicio de Microbiología, 3° planta, Edificio Sur, Hospital Universitario, As Xubias, 15006 A Coruna, Spain
| | - Soraya Rumbo-Feal
- Microbiology Research Group, Institute of Biomedical Research (INIBIC)-University Hospital of A Coruña (CHUAC)-Interdisciplinary Center for Chemistry and Biology (CICA)-University of A Coruña (UDC)-CIBER de Enfermedades Infecciosas (CIBERINFEC, ISCIII). Servicio de Microbiología, 3° planta, Edificio Sur, Hospital Universitario, As Xubias, 15006 A Coruna, Spain
| | - Ana Fernández-González
- Microbiology Research Group, Institute of Biomedical Research (INIBIC)-University Hospital of A Coruña (CHUAC)-Interdisciplinary Center for Chemistry and Biology (CICA)-University of A Coruña (UDC)-CIBER de Enfermedades Infecciosas (CIBERINFEC, ISCIII). Servicio de Microbiología, 3° planta, Edificio Sur, Hospital Universitario, As Xubias, 15006 A Coruna, Spain
| | - Germán Bou
- Microbiology Research Group, Institute of Biomedical Research (INIBIC)-University Hospital of A Coruña (CHUAC)-Interdisciplinary Center for Chemistry and Biology (CICA)-University of A Coruña (UDC)-CIBER de Enfermedades Infecciosas (CIBERINFEC, ISCIII). Servicio de Microbiología, 3° planta, Edificio Sur, Hospital Universitario, As Xubias, 15006 A Coruna, Spain
| | - Margarita Poza
- Microbiology Research Group, Institute of Biomedical Research (INIBIC)-University Hospital of A Coruña (CHUAC)-Interdisciplinary Center for Chemistry and Biology (CICA)-University of A Coruña (UDC)-CIBER de Enfermedades Infecciosas (CIBERINFEC, ISCIII). Servicio de Microbiología, 3° planta, Edificio Sur, Hospital Universitario, As Xubias, 15006 A Coruna, Spain
- Microbiome and Health Group, Faculty of Sciences, Campus da Zapateira, 15071 A Coruna, Spain
| | - Juan A Vallejo
- Microbiology Research Group, Institute of Biomedical Research (INIBIC)-University Hospital of A Coruña (CHUAC)-Interdisciplinary Center for Chemistry and Biology (CICA)-University of A Coruña (UDC)-CIBER de Enfermedades Infecciosas (CIBERINFEC, ISCIII). Servicio de Microbiología, 3° planta, Edificio Sur, Hospital Universitario, As Xubias, 15006 A Coruna, Spain
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Alioto TS, Gut M, Rodiño-Janeiro BK, Cruz F, Gómez-Garrido J, Vázquez-Ucha JC, Mata C, Antoni R, Briansó F, Dabad M, Casals E, Ingham M, Álvarez-Tejado M, Bou G, Gut IG. Development of a novel streamlined workflow (AACRE) and database (inCREDBle) for genomic analysis of carbapenem-resistant Enterobacterales. Microb Genom 2023; 9. [PMID: 38010338 DOI: 10.1099/mgen.0.001132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2023] Open
Abstract
In response to the threat of increasing antimicrobial resistance, we must increase the amount of available high-quality genomic data gathered on antibiotic-resistant bacteria. To this end, we developed an integrated pipeline for high-throughput long-read sequencing, assembly, annotation and analysis of bacterial isolates and used it to generate a large genomic data set of carbapenemase-producing Enterobacterales (CPE) isolates collected in Spain. The set of 461 isolates were sequenced with a combination of both Illumina and Oxford Nanopore Technologies (ONT) DNA sequencing technologies in order to provide genomic context for chromosomal loci and, most importantly, structural resolution of plasmids, important determinants for transmission of antimicrobial resistance. We developed an informatics pipeline called Assembly and Annotation of Carbapenem-Resistant Enterobacteriaceae (AACRE) for the full assembly and annotation of the bacterial genomes and their complement of plasmids. To explore the resulting genomic data set, we developed a new database called inCREDBle that not only stores the genomic data, but provides unique ways to filter and compare data, enabling comparative genomic analyses at the level of chromosomes, plasmids and individual genes. We identified a new sequence type, ST5000, and discovered a genomic locus unique to ST15 that may be linked to its increased spread in the population. In addition to our major objective of generating a large regional data set, we took the opportunity to compare the effects of sample quality and sequencing methods, including R9 versus R10 nanopore chemistry, on genome assembly and annotation quality. We conclude that converting short-read and hybrid microbial sequencing and assembly workflows to the latest nanopore chemistry will further reduce processing time and cost, truly enabling the routine monitoring of resistance transmission patterns at the resolution of complete chromosomes and plasmids.
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Affiliation(s)
- Tyler S Alioto
- Centro Nacional de Análisis Genómico, C/Baldiri Reixac 4, 08028 Barcelona, Spain
- Universitat de Barcelona (UB), Barcelona, Spain
| | - Marta Gut
- Centro Nacional de Análisis Genómico, C/Baldiri Reixac 4, 08028 Barcelona, Spain
- Universitat de Barcelona (UB), Barcelona, Spain
| | - Bruno Kotska Rodiño-Janeiro
- Microbiology Department, Complejo Hospitalario Universitario A Coruña-Instituto Investigación Biomédica A Coruña (INIBIC), A Coruña, Spain
| | - Fernando Cruz
- Centro Nacional de Análisis Genómico, C/Baldiri Reixac 4, 08028 Barcelona, Spain
- Universitat de Barcelona (UB), Barcelona, Spain
| | - Jèssica Gómez-Garrido
- Centro Nacional de Análisis Genómico, C/Baldiri Reixac 4, 08028 Barcelona, Spain
- Universitat de Barcelona (UB), Barcelona, Spain
| | - Juan Carlos Vázquez-Ucha
- Microbiology Department, Complejo Hospitalario Universitario A Coruña-Instituto Investigación Biomédica A Coruña (INIBIC), A Coruña, Spain
- CIBER de Enfermedades Infecciosas (CIBERINFEC), ISCIII, Madrid, Spain
| | - Caterina Mata
- Centro Nacional de Análisis Genómico, C/Baldiri Reixac 4, 08028 Barcelona, Spain
- Universitat de Barcelona (UB), Barcelona, Spain
| | - Regina Antoni
- Centro Nacional de Análisis Genómico, C/Baldiri Reixac 4, 08028 Barcelona, Spain
- Universitat de Barcelona (UB), Barcelona, Spain
| | - Ferran Briansó
- Department of Genetics, Microbiology and Statistics, Universitat de Barcelona (UB), Barcelona, Spain
- Roche Diagnostics, Sant Cugat del Vallès, Barcelona, Spain
| | - Marc Dabad
- Centro Nacional de Análisis Genómico, C/Baldiri Reixac 4, 08028 Barcelona, Spain
- Universitat de Barcelona (UB), Barcelona, Spain
| | - Eloi Casals
- Centro Nacional de Análisis Genómico, C/Baldiri Reixac 4, 08028 Barcelona, Spain
- Universitat de Barcelona (UB), Barcelona, Spain
| | - Matthew Ingham
- Centro Nacional de Análisis Genómico, C/Baldiri Reixac 4, 08028 Barcelona, Spain
- Universitat de Barcelona (UB), Barcelona, Spain
| | | | - Germán Bou
- Microbiology Department, Complejo Hospitalario Universitario A Coruña-Instituto Investigación Biomédica A Coruña (INIBIC), A Coruña, Spain
- CIBER de Enfermedades Infecciosas (CIBERINFEC), ISCIII, Madrid, Spain
| | - Ivo G Gut
- Centro Nacional de Análisis Genómico, C/Baldiri Reixac 4, 08028 Barcelona, Spain
- Universitat de Barcelona (UB), Barcelona, Spain
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Kozak S, Merda D, Duquesne F, Breuil MF, Mawhinney I, Petry S. Whole genome sequence analysis of the 2018 Persian onager isolate suggests sublineages within the Taylorella asinigenitalis species. Vet Microbiol 2023; 286:109884. [PMID: 37832214 DOI: 10.1016/j.vetmic.2023.109884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 09/26/2023] [Accepted: 10/01/2023] [Indexed: 10/15/2023]
Abstract
In 2018, a T. asinigenitalis strain (MCE663) was isolated in a Persian onager tested for contagious equine metritis (CEM) in a United Kingdom (UK) zoo. This bacterium had never been reported in the UK and Multilocus Sequence Typing described a new atypically divergent ST (ST60). Although the causative agent of CEM is the bacterium Taylorella equigenitalis, a first natural outbreak of endometritis caused by T. asinigenitalis ST70 was reported in 2019, putting its pathogenic potential into question. In this context, we aimed to further sequence the T. asinigenitalis MCE663 genome and characterize the strain using phenotypical and genetic approaches. Results showed that it gathered all identification characteristics of T. asinigenitalis with smaller colonies and it was susceptible to all tested antibiotics. Genome-level phylogeny showed that the genome MCE663 formed a distinct phylogroup, and only shared ≈ 96.1% of average nucleotide identity (ANI) with the three published T. asinigenitalis genomes, which together shared ≈ 98.3% ANI. According to current cut-offs consensus for species and subspecies delineation (95% and 98%, respectively), our results support the first insights of a sublineage delineation within the T. asinigenitalis species.
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Affiliation(s)
- Sofia Kozak
- ANSES, Laboratory for Animal Health, Physiopathology and Epidemiology of Equine Diseases Unit, Goustranville, France
| | - Déborah Merda
- ANSES, Paris Est University, SPAAD Unit, Maisons-Alfort, France
| | - Fabien Duquesne
- ANSES, Laboratory for Animal Health, Physiopathology and Epidemiology of Equine Diseases Unit, Goustranville, France
| | - Marie-France Breuil
- ANSES, Laboratory for Animal Health, Physiopathology and Epidemiology of Equine Diseases Unit, Goustranville, France
| | - Ian Mawhinney
- APHA Veterinary Investigation Centre, Rougham Hill, Bury St Edmunds, Suffolk, UK
| | - Sandrine Petry
- ANSES, Laboratory for Animal Health, Physiopathology and Epidemiology of Equine Diseases Unit, Goustranville, France.
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Morhart P, Gerlach RG, Kunz C, Held J, Valenza G, Wölfle J, Reutter H, Hanslik GJ, Fahlbusch FB. Application of Next-Generation Sequencing to Enterobacter Hormaechei Subspecies Analysis during a Neonatal Intensive Care Unit Outbreak. Children (Basel) 2023; 10:1696. [PMID: 37892359 PMCID: PMC10605273 DOI: 10.3390/children10101696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 10/04/2023] [Accepted: 10/13/2023] [Indexed: 10/29/2023]
Abstract
INTRODUCTION The Enterobacter cloacae complex (ECC) species are potential neonatal pathogens, and ECC strains are among the most commonly encountered Enterobacter spp. associated with nosocomial bloodstream infections. Outbreaks caused by ECC can lead to significant morbidity and mortality in susceptible neonates. At the molecular level, ECC exhibits genomic heterogeneity, with six closely related species and subspecies. Genetic variability poses a challenge in accurately identifying outbreaks by determining the clonality of ECC isolates. This difficulty is further compounded by the limitations of the commonly used molecular typing methods, such as pulsed field gel electrophoresis, which do not provide reliable accuracy in distinguishing between ECC strains and can lead to incorrect conclusions. Next-generation sequencing (NGS) offers superior resolution in determining strain relatedness. Therefore, we investigated the clinical pertinence of incorporating NGS into existing bundle measures to enhance patient management during an outbreak of ECC in a level-3 neonatal intensive care unit (NICU) in Germany. METHODS As the standard of care, all neonates on the NICU received weekly microbiological swabs (nasopharyngeal and rectal) and analysis of endotracheal secretion, where feasible. During the 2.5-month outbreak, colonisation with ECC was detected in n = 10 neonates. The phylogenetic relationship and potential antimicrobial resistance genes as well as mobile genetic elements were identified via bacterial whole-genome sequencing (WGS) using Illumina MiSeq followed by in silico data analysis. RESULTS Although all ECC isolates exhibited almost identical antimicrobial susceptibility patterns, the WGS data revealed the involvement of four different ECC clones. The isolates could be characterised as Enterobacter hormaechei subspecies steigerwaltii (n = 6, clonal), subsp. hoffmannii (n = 3, two clones) and subsp. oharae (n = 1). Despite the collection of environmental samples, no source of this diffuse outbreak could be identified. A new standardised operating procedure was implemented to enhance the management of neonates colonised with MRGN. This collaborative approach involved both parents and medical professionals and successfully prevented further transmission of ECC. CONCLUSIONS Initially, it was believed that the NICU outbreak was caused by a single ECC clone due to the similarity in antibiotic resistance. However, our findings show that antibiotic susceptibility patterns can be misleading in investigating outbreaks of multi-drug-resistant ECC. In contrast, bacterial WGS accurately identified ECC at the clonal level, which significantly helped to delineate the nature of the observed outbreak.
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Affiliation(s)
- Patrick Morhart
- Division of Neonatology and Paediatric Intensive Care Medicine, Department of Paediatrics and Adolescent Medicine, Friedrich-Alexander-University of Erlangen-Nürnberg, 91054 Erlangen, Germany; (P.M.); (H.R.); (G.J.H.)
| | - Roman G. Gerlach
- Institute of Microbiology—Clinical Microbiology, Immunology and Hygiene, Friedrich-Alexander-University of Erlangen-Nürnberg, 91054 Erlangen, Germany (C.K.); (J.H.); (G.V.)
| | - Caroline Kunz
- Institute of Microbiology—Clinical Microbiology, Immunology and Hygiene, Friedrich-Alexander-University of Erlangen-Nürnberg, 91054 Erlangen, Germany (C.K.); (J.H.); (G.V.)
| | - Jürgen Held
- Institute of Microbiology—Clinical Microbiology, Immunology and Hygiene, Friedrich-Alexander-University of Erlangen-Nürnberg, 91054 Erlangen, Germany (C.K.); (J.H.); (G.V.)
| | - Giuseppe Valenza
- Institute of Microbiology—Clinical Microbiology, Immunology and Hygiene, Friedrich-Alexander-University of Erlangen-Nürnberg, 91054 Erlangen, Germany (C.K.); (J.H.); (G.V.)
| | - Joachim Wölfle
- Department of Paediatrics and Adolescent Medicine, Friedrich-Alexander-University of Erlangen-Nürnberg, 91054 Erlangen, Germany;
| | - Heiko Reutter
- Division of Neonatology and Paediatric Intensive Care Medicine, Department of Paediatrics and Adolescent Medicine, Friedrich-Alexander-University of Erlangen-Nürnberg, 91054 Erlangen, Germany; (P.M.); (H.R.); (G.J.H.)
| | - Gregor J. Hanslik
- Division of Neonatology and Paediatric Intensive Care Medicine, Department of Paediatrics and Adolescent Medicine, Friedrich-Alexander-University of Erlangen-Nürnberg, 91054 Erlangen, Germany; (P.M.); (H.R.); (G.J.H.)
| | - Fabian B. Fahlbusch
- Neonatology and Pediatric Intensive Care, Faculty of Medicine, University of Augsburg, 86156 Augsburg, Germany
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Kang MG, Kwak MJ, Kim Y. Polystyrene microplastics biodegradation by gut bacterial Enterobacter hormaechei from mealworms under anaerobic conditions: Anaerobic oxidation and depolymerization. J Hazard Mater 2023; 459:132045. [PMID: 37480606 DOI: 10.1016/j.jhazmat.2023.132045] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 07/09/2023] [Accepted: 07/10/2023] [Indexed: 07/24/2023]
Abstract
Synthetic plastic is used throughout daily life and industry, threatening organisms with microplastic pollution. Polystyrene is a major plastic polymer and also widely found sources of plastic wastes and microplastics. Here, we report that Enterobacter hormaechei LG3 (CP118279.1), a facultative anaerobic bacterial strain isolated from the gut of Tenebrio molitor larvae (mealworms) can oxidize and depolymerize polystyrene under anaerobic conditions. LG3 performed biodegradation while forming a biofilm on the plastic surface. PS biodegradation was characterized by analyses of surface oxidation, change in morphology and molecular weights, and production of biodegraded derivative. The biodegradation performance by LG3 was compared with PS biodegradation by Bacillus amyloliquefaciens SCGB1 under both anaerobic and aerobic conditions. In addition, through nanopore sequencing technology, we identified degradative enzymes, including thiol peroxidase (tpx), alkyl hydroperoxide reductase C (ahpC) and bacterioferritin comigratory protein (bcp). Along with the upregulation of degradative enzymes for biodegradation, changes in lipid A and biofilm-associated proteins were also observed after the cells were incubated with polystyrene microplastics. Our results provide evidence for anaerobic biodegradation by polystyrene-degrading bacteria and show alterations in gene expression patterns after polystyrene microplastics treatment in the opportunistic pathogen Enterobacter hormaechei.
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Affiliation(s)
- Min-Geun Kang
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Science, Seoul National University, Seoul 08826, Republic of Korea
| | - Min-Jin Kwak
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Science, Seoul National University, Seoul 08826, Republic of Korea
| | - Younghoon Kim
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Science, Seoul National University, Seoul 08826, Republic of Korea.
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Huang Z, Liu S, Wang Y, Yao Z, Feng L, Lin Y, Ye J, Zhou T, Wang Z. Comparison of prevalence, resistance, biofilm-forming ability and virulence between carbapenem-non-susceptible and carbepenem-susceptible Enterobacter cloacae complex in clusters. J Hosp Infect 2023; 139:168-174. [PMID: 37348563 DOI: 10.1016/j.jhin.2023.06.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 05/30/2023] [Accepted: 06/07/2023] [Indexed: 06/24/2023]
Abstract
OBJECTIVES This study aimed to explore differences in prevalence, resistance, biofilm-forming ability and virulence between carbapenem-non-susceptible and carbapenem-susceptible Enterobacter cloacae complex (ECC) in different clusters. METHODS Ninety-one carbapenem-non-susceptible isolates and an equal number of carbapenem-susceptible isolates and their clinical information were collected from a university teaching hospital in China. The strains were divided into different clusters based on hsp60 analysis. The agar dilution method was used to determine the minimum inhibitory concentrations of common antibiotics. The crystal violet assay was used to measure biofilm-forming ability. The Galleria mellonella infection model and polymerase chain reaction of virulence genes were used to evaluate virulence. RESULTS The isolates were divided into 12 clusters based on hsp60 analysis. Cluster VIII accounted for a greater proportion of carbapenem-non-susceptible isolates than the other clusters. The same clusters exhibited different resistance rates in carbapenem-non-susceptible and carbapenem-susceptible isolates. Moreover, carbapenem-non-susceptible isolates carried fewer virulence genes than carbapenem-susceptible isolates, and carbapenem-non-susceptible isolates in cluster II in did not carry the detected virulence genes. Virulence of carbapenem-non-susceptible and carbapenem-susceptible isolates differed significantly in clusters I, III, VIII and IX, as evaluated using the G. mellonella infection model. Carbapenem-non-susceptible isolates in cluster VIII showed higher prevalence, resistance, biofilm-forming ability and pathogenicity compared with the other clusters. CONCLUSIONS The study findings indicate the need to identify subgroups of ECC, and provide better advice and guidance for the use of carbapenems.
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Affiliation(s)
- Z Huang
- Department of Clinical Laboratory, First Affiliated Hospital of Wenzhou Medical University, Key Laboratory of Clinical Laboratory Diagnosis and Translational Research of Zhejiang Province, Wenzhou, Zhejiang Province, China
| | - S Liu
- Department of Clinical Laboratory, Children's Hospital of Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, China
| | - Y Wang
- Department of Clinical Laboratory, First Affiliated Hospital of Wenzhou Medical University, Key Laboratory of Clinical Laboratory Diagnosis and Translational Research of Zhejiang Province, Wenzhou, Zhejiang Province, China
| | - Z Yao
- School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, Zhejiang Province, China
| | - L Feng
- School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, Zhejiang Province, China
| | - Y Lin
- School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, Zhejiang Province, China
| | - J Ye
- Department of Clinical Laboratory, First Affiliated Hospital of Wenzhou Medical University, Key Laboratory of Clinical Laboratory Diagnosis and Translational Research of Zhejiang Province, Wenzhou, Zhejiang Province, China
| | - T Zhou
- Department of Clinical Laboratory, First Affiliated Hospital of Wenzhou Medical University, Key Laboratory of Clinical Laboratory Diagnosis and Translational Research of Zhejiang Province, Wenzhou, Zhejiang Province, China.
| | - Z Wang
- Department of Clinical Laboratory, First Affiliated Hospital of Wenzhou Medical University, Key Laboratory of Clinical Laboratory Diagnosis and Translational Research of Zhejiang Province, Wenzhou, Zhejiang Province, China.
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Fukuzawa S, Sato T, Aoki K, Yamamoto S, Ogasawara N, Nakajima C, Suzuki Y, Horiuchi M, Takahashi S, Yokota SI. High prevalence of colistin heteroresistance in specific species and lineages of Enterobacter cloacae complex derived from human clinical specimens. Ann Clin Microbiol Antimicrob 2023; 22:60. [PMID: 37454128 DOI: 10.1186/s12941-023-00610-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 07/05/2023] [Indexed: 07/18/2023] Open
Abstract
BACKGROUND Colistin (CST) is a last-line drug for multidrug-resistant Gram-negative bacterial infections. CST-heteroresistant Enterobacter cloacae complex (ECC) has been isolated. However, integrated analysis of epidemiology and resistance mechanisms based on the complete ECC species identification has not been performed. METHODS Clinical isolates identified as "E. cloacae complex" by MALDI-TOF MS Biotyper Compass in a university hospital in Japan were analyzed. Minimum inhibitory concentrations of CST were determined by the broth microdilution method. The population analysis profiling (PAP) was performed for detecting the heteroresistant phenotype. The heat shock protein 60 (hsp60) cluster was determined from its partial nucleotide sequence. From the data of whole-genome sequencing, average nucleotide identity (ANI) for determining ECC species, multilocus sequence type, core genome single-nucleotide-polymorphism-based phylogenetic analysis were performed. phoPQ-, eptA-, and arnT-deleted mutants were established to evaluate the mechanism underlying colistin heteroresistance. The arnT mRNA expression levels were determined by reverse transcription quantitative PCR. RESULTS Thirty-eight CST-resistant isolates, all of which exhibited the heteroresistant phenotype by PAP, were found from 138 ECC clinical isolates (27.5%). The prevalence of CST-resistant isolates did not significantly differ among the origin of specimens (29.0%, 27.8%, and 20.2% for respiratory, urine, and blood specimens, respectively). hsp60 clusters, core genome phylogeny, and ANI revealed that the CST-heteroresistant isolates were found in all or most of Enterobacter roggenkampii (hsp60 cluster IV), Enterobacter kobei (cluster II), Enterobacter chuandaensis (clusters III and IX), and Enterobacter cloacae subspecies (clusters XI and XII). No heteroresistant isolates were found in Enterobacter hormaechei subspecies (clusters VIII, VI, and III) and Enterobacter ludwigii (cluster V). CST-induced mRNA upregulation of arnT, which encodes 4-amino-4-deoxy-L-arabinose transferase, was observed in the CST-heteroresistant isolates, and it is mediated by phoPQ pathway. Isolates possessing mcr-9 and mcr-10 (3.6% and 5.6% of total ECC isolates, respectively) exhibited similar CST susceptibility and PAP compared with mcr-negative isolates. CONCLUSIONS Significant prevalence (approximately 28%) of CST heteroresistance is observed in ECC clinical isolates, and they are accumulated in specific species and lineages. Heteroresistance is occurred by upregulation of arnT mRNA induced by CST. Acquisition of mcr genes contributes less to CST resistance in ECC.
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Affiliation(s)
- Shota Fukuzawa
- Department of Microbiology, Sapporo Medical University School of Medicine, Sapporo, Japan
- Clinical Laboratory, National Hospital Organization Hokkaido Cancer Center, Sapporo, Japan
| | - Toyotaka Sato
- Department of Microbiology, Sapporo Medical University School of Medicine, Sapporo, Japan.
- Laboratory of Veterinary Hygiene, Faculty of Veterinary Medicine, Hokkaido University, Sapporo, Japan.
- Graduate School of Infectious Diseases, Hokkaido University, Sapporo, Japan.
- One Health Research Center, Hokkaido University, Sapporo, Japan.
| | - Kotaro Aoki
- Department of Microbiology and Infectious Diseases, Toho University School of Medicine, Tokyo, Japan
| | - Soh Yamamoto
- Department of Microbiology, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Noriko Ogasawara
- Department of Microbiology, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Chie Nakajima
- Division of Bioresources, Hokkaido University International Institute for Zoonosis Control, Sapporo, Japan
- International Collaboration Unit, Hokkaido University, International Institute for Zoonosis Control, Sapporo, Japan
- Institute for Vaccine Research and Development (HU-IVReD), Hokkaido University, Sapporo, Japan
| | - Yasuhiko Suzuki
- Division of Bioresources, Hokkaido University International Institute for Zoonosis Control, Sapporo, Japan
- International Collaboration Unit, Hokkaido University, International Institute for Zoonosis Control, Sapporo, Japan
- Institute for Vaccine Research and Development (HU-IVReD), Hokkaido University, Sapporo, Japan
| | - Motohiro Horiuchi
- Laboratory of Veterinary Hygiene, Faculty of Veterinary Medicine, Hokkaido University, Sapporo, Japan
- Graduate School of Infectious Diseases, Hokkaido University, Sapporo, Japan
- One Health Research Center, Hokkaido University, Sapporo, Japan
| | - Satoshi Takahashi
- Department of Infection Control and Laboratory Medicine, Sapporo Medical University School of Medicine, Sapporo, Japan
- Division of Laboratory Medicine, Sapporo Medical University Hospital, Sapporo, Japan
| | - Shin-Ichi Yokota
- Department of Microbiology, Sapporo Medical University School of Medicine, Sapporo, Japan
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Guérin F, Gravey F, Reissier S, Penven M, Michaux C, Le Hello S, Cattoir V. Temocillin Resistance in the Enterobacter cloacae Complex Is Conferred by a Single Point Mutation in BaeS, Leading to Overexpression of the AcrD Efflux Pump. Antimicrob Agents Chemother 2023; 67:e0035823. [PMID: 37195180 PMCID: PMC10269110 DOI: 10.1128/aac.00358-23] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 04/24/2023] [Indexed: 05/18/2023] Open
Abstract
The Enterobacter cloacae complex (ECC) has become a major opportunistic pathogen with antimicrobial resistance issues. Temocillin, an "old" carboxypenicillin that is remarkably stable toward β-lactamases, has been used as an alternative for the treatment of multidrug-resistant ECC infections. Here, we aimed at deciphering the never-investigated mechanisms of temocillin resistance acquisition in Enterobacterales. By comparative genomic analysis of two clonally related ECC clinical isolates, one susceptible (Temo_S [MIC of 4 mg/L]) and the other resistant (Temo_R [MIC of 32 mg/L]), we found that they differed by only 14 single-nucleotide polymorphisms, including one nonsynonymous mutation (Thr175Pro) in the two-component system (TCS) sensor histidine kinase BaeS. By site-directed mutagenesis in Escherichia coli CFT073, we demonstrated that this unique change in BaeS was responsible for a significant (16-fold) increase in temocillin MIC. Since the BaeSR TCS regulates the expression of two resistance-nodulation-cell division (RND)-type efflux pumps (namely, AcrD and MdtABCD) in E. coli and Salmonella, we demonstrated by quantitative reverse transcription-PCR that mdtB, baeS, and acrD genes were significantly overexpressed (15-, 11-, and 3-fold, respectively) in Temo_R. To confirm the role of each efflux pump in this mechanism, multicopy plasmids harboring mdtABCD or acrD were introduced into either Temo_S or the reference strain E. cloacae subsp. cloacae ATCC 13047. Interestingly, only the overexpression of acrD conferred a significant increase (from 8- to 16-fold) of the temocillin MIC. Altogether, we have shown that temocillin resistance in the ECC can result from a single BaeS alteration, likely resulting in the permanent phosphorylation of BaeR and leading to AcrD overexpression and temocillin resistance through enhanced active efflux.
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Affiliation(s)
- François Guérin
- Department of Clinical Microbiology, Rennes University Hospital, Rennes, France
- University of Rennes, INSERM UMR 1230 BRM, Rennes, France
| | - François Gravey
- Normandie Université, UNICAEN, UNIROUEN, INSERM UMR 1311 DYNAMICURE, Caen, France
- Microbiology Department, CHU Caen, Caen, France
| | - Sophie Reissier
- Department of Clinical Microbiology, Rennes University Hospital, Rennes, France
- University of Rennes, INSERM UMR 1230 BRM, Rennes, France
| | - Malo Penven
- Department of Clinical Microbiology, Rennes University Hospital, Rennes, France
- University of Rennes, INSERM UMR 1230 BRM, Rennes, France
| | | | - Simon Le Hello
- Normandie Université, UNICAEN, UNIROUEN, INSERM UMR 1311 DYNAMICURE, Caen, France
- Microbiology Department, CHU Caen, Caen, France
| | - Vincent Cattoir
- Department of Clinical Microbiology, Rennes University Hospital, Rennes, France
- University of Rennes, INSERM UMR 1230 BRM, Rennes, France
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Navarro-Carrera P, García-Clemente P, Gómez-Gil R, Cáceres-Sánchez R, Bloise I, Dahdouh E, Moreno-Ramos F, García-Rodríguez J, Mingorance J, Lázaro-Perona F. Resistance to meropenem-vaborbactam in clinical isolates of Enterobacter roggenkampii without previous exposure to vaborbactam. Clin Microbiol Infect 2022; 28:1662-4. [PMID: 36150673 DOI: 10.1016/j.cmi.2022.09.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 08/17/2022] [Accepted: 09/09/2022] [Indexed: 01/26/2023]
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Cañada-García JE, Grippo N, de Arellano ER, Bautista V, Lara N, Navarro AM, Cabezas T, Martínez-Ramírez NM, García-Cobos S, Calvo J, Cercenado E, Aracil B, Pérez-Vázquez M, Oteo-Iglesias J. Phenotypic and molecular characterization of IMP-producing Enterobacterales in Spain: Predominance of IMP-8 in Klebsiella pneumoniae and IMP-22 in Enterobacter roggenkampii. Front Microbiol 2022; 13:1000787. [PMID: 36246266 PMCID: PMC9554532 DOI: 10.3389/fmicb.2022.1000787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 09/08/2022] [Indexed: 11/13/2022] Open
Abstract
Objectives Little is known about IMP-producing Enterobacterales (IMP-Ent) in Europe. We analyzed at genomic and phenotypic level IMP-Ent isolates circulating in Spain in a 9-year period. Materials and methods IMP-Ent isolates submitted to our reference laboratory were included. Antibiotic susceptibility was performed using microdilution method (EUCAST), and IMP-carbapenemase activity was measured with carbapenemase inhibitors, the β-CARBA method, the modified Hodge test (MHT), and the modified carbapenemase inhibition method (mCIM). All isolates collected were sequenced for high-resolution single-nucleotide polymorphism (SNP) typing, core genome multilocus sequence typing (cgMLST), and resistome analysis. Results Fifty IMP-Ent isolates, collected from 19 hospitals in 13 Spanish provinces, were detected: Klebsiella pneumoniae (IMP-Kpn) (24; 48%), Enterobacter roggenkampii (13; 26%), Enterobacter hormaechei (8, 16%), Klebsiella oxytoca (two; 4%), Enterobacter asburiae (one, 2%), Serratia marcescens (one; 2%) and Escherichia coli (one; 2%). All isolates were positive by the MHT and β-CARBA tests; 48 (96%) were mCIM positive; 12 (24%) and 26 (52%) displayed positive inhibition with dipicolinic (meropenem) and EDTA (ertapenem), respectively. Five IMP-carbapenemase types were identified: IMP-8 (22; 44%), IMP-22 (17; 34%), IMP-13 (7; 14%), IMP-28 (two; 4%), and IMP-15 (two; 4%), predominating IMP-8 in K. pneumoniae and IMP-22 in E. roggenkampii. IMP-28 was exclusively identified in K. oxytoca and IMP-15 in E. hormaechei. Predominant STs were ST405 (29.2%), ST15 (25%) and ST464 (20.8%) in IMP-Kpn; ST96 (100%) in E. roggenkampii and ST182 (62.5%) in E. hormachei. Colistin and amikacin were the most active non-carbapenem antibiotics against IMP-Ent. Conclusion IMP-Ent isolates remain infrequent in Spain, although in recent years have been circulating causing nosocomial outbreaks, being IMP-8-producing K. pneumoniae and IMP-22-producing E. roggenkampii the most frequently detected in this study. Inhibition with EDTA or dipicolinic acid presented false negative results in some IMP-producing strains. Active microbiological and molecular surveillance is essential for a better comprehension and control of IMP-Ent dissemination.
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Affiliation(s)
- 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
| | - Natalin Grippo
- 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 Educación Médica e Investigaciones Clínicas “Norberto Quirno”, Buenos Aires, Argentina
| | - 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
| | - 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
| | - Ana María Navarro
- 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
| | - Teresa Cabezas
- Servicio de Microbiología, Hospital de Poniente, Almería, 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
| | - Jorge Calvo
- CIBER de Enfermedades Infecciosas (CIBERINFEC), Spanish Network for Research in Infectious Diseases (REIPI), Instituto de Salud Carlos III, Madrid, Spain
- Servicio de Microbiología, Hospital Universitario Marqués de Valdecilla, Santander, Spain
| | - Emilia Cercenado
- Servicio de Microbiología, Hospital Universitario Gregorio Marañón, Madrid, Spain
- 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
- CIBER de Enfermedades Infecciosas (CIBERINFEC), Spanish Network for Research in Infectious Diseases (REIPI), 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
- CIBER de Enfermedades Infecciosas (CIBERINFEC), Spanish Network for Research in Infectious Diseases (REIPI), Instituto de Salud Carlos III, Madrid, Spain
- *Correspondence: María Pérez-Vázquez,
| | - 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
- CIBER de Enfermedades Infecciosas (CIBERINFEC), Spanish Network for Research in Infectious Diseases (REIPI), Instituto de Salud Carlos III, Madrid, Spain
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Kemp M, Jespersen MG, Toft A, Holm A. Free online genome analyses reveal multiple strains in the beginning of a hospital outbreak of Enterobacter hormaechei carrying bla OXA-436 carbapenemase gene. J Infect Prev 2022; 23:243-247. [PMID: 36003132 PMCID: PMC9393603 DOI: 10.1177/17571774221107293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 05/03/2022] [Indexed: 09/03/2023] Open
Abstract
Free online tools for bacterial genome analyses are available for local infection surveillance at hospitals. The tools do not require bioinformatic expertise and provide rapid actionable results. Within half a year carbapenemase producing Enterobacter cloacae was reported in clinical samples from three patients who had been hospitalized at the same ward. The aim of this outbreak investigation was to characterize and compare genomes of the isolated bacteria in order to determine molecular evidence of hospital transmission. The three isolates and two isolates reported as susceptible to carbapenems were locally analyzed by whole genome sequencing (WGS). Draft genome assembly, species identification, phylogenetic analyses, typing, resistance gene determination, and plasmid analyses were carried out using free online tools from the Center for Genomic Epidemiology (CGE). Genome analyses identified all three suspected outbreak isolates as E. hormaechei carrying bla OXA-436 gene. Two of the suspected outbreak isolates were closely related, while one was substantially different from them. Horizontal transfer of plasmid may have taken place in the ward. Detailed knowledge on the genomic composition of bacteria in suspected hospital outbreaks can be obtained by free online tools and may reveal transfer of resistance genes between different strains in addition to dissemination of specific clones.
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Affiliation(s)
- Michael Kemp
- Department Clinical Microbiology, Odense University Hospital, Odense, Denmark
- Clinical Department, University of Southern Denmark, Odense, Denmark
| | | | - Annette Toft
- Department Clinical Microbiology, Odense University Hospital, Odense, Denmark
| | - Anette Holm
- Department Clinical Microbiology, Odense University Hospital, Odense, Denmark
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Yao Y, Doijad S, Falgenhauer J, Schmiedel J, Imirzalioglu C, Chakraborty T. Co-occurrence of dual carbapenemases KPC-2 and OXA-48 with the mobile colistin resistance gene mcr-9.1 in Enterobacter xiangfangensis. Front Cell Infect Microbiol 2022; 12:960892. [PMID: 36061873 PMCID: PMC9428693 DOI: 10.3389/fcimb.2022.960892] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 07/25/2022] [Indexed: 11/30/2022] Open
Abstract
Bacterial infections with the genus Enterobacter are notoriously difficult to treat and often associated with resistance to penicillin, aminoglycosides, fluoroquinolones, and third-generation cephalosporins. Also, Enterobacter species have emerged as the third most common hosts for carbapenemases worldwide, forcing the use of colistin as a “last-resort” antibiotic for the treatment. Studies on the population structure of the genus Enterobacter repeatedly detect E. xiangfangensis as a common clinical species present worldwide. Here, we report on the characteristics of an extreme drug-resistant E. xiangfangensis isolate va18651 (ST88), obtained from a cervical swab of an expectant mother. The isolate was resistant to almost all the classes of antibiotics tested, including β-lactams (viz., penicillins, carbapenems, cephalosporin, monobactams, and their combinations), quinolone, aminoglycosides, and sulfonamide/dihydrofolate reductase inhibitor, and exhibited heteroresistance towards colistin. Analysis of its complete genome sequence revealed 37 antibiotic resistance genes (ARGs), including mcr-9.1, blaKPC-2, and blaOXA-48, encoded on three of the four different plasmids (cumulative plasmidome size 604,632 bp). An unusually high number of plasmid-based heavy metal resistance gene (HRG) clusters towards silver, arsenate, cadmium, copper, mercury, and tellurite were also detected. Virulence genes (VGs) for the lipopolysaccharide and capsular polysaccharide structures, iron acquisition (iroBCDEN, ent/fep/fes, sitABCD, iut, and fur), and a type VI secretion system, together with motility genes and Type IV pili, were encoded chromosomally. Thus, a unique combination of chromosomally encoded VGs, together with plasmid-encoded ARGs and HRGs, converged to result in an extreme drug-resistant, pathogenic isolate with survival potential in environmental settings. The use of a disinfectant, octenidine, led to its eradication; however, the existence of a highly antibiotic-resistant isolate with significant virulence potential is a matter of concern in public health settings and warrants further surveillance for extreme drug-resistant Enterobacter isolates.
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Affiliation(s)
- Yancheng Yao
- Institute of Medical Microbiology, Justus Liebig University Giessen, Giessen, Germany
- German Center for Infection Research (DZIF), Partner Site Giessen-Marburg-Langen, Justus-Liebig University Giessen, Giessen, Germany
| | - Swapnil Doijad
- Institute of Medical Microbiology, Justus Liebig University Giessen, Giessen, Germany
- German Center for Infection Research (DZIF), Partner Site Giessen-Marburg-Langen, Justus-Liebig University Giessen, Giessen, Germany
| | - Jane Falgenhauer
- Institute of Medical Microbiology, Justus Liebig University Giessen, Giessen, Germany
- German Center for Infection Research (DZIF), Partner Site Giessen-Marburg-Langen, Justus-Liebig University Giessen, Giessen, Germany
| | - Judith Schmiedel
- Institute of Medical Microbiology, University Hospital Giessen, Giessen, Germany
| | - Can Imirzalioglu
- Institute of Medical Microbiology, Justus Liebig University Giessen, Giessen, Germany
- German Center for Infection Research (DZIF), Partner Site Giessen-Marburg-Langen, Justus-Liebig University Giessen, Giessen, Germany
- Institute of Medical Microbiology, University Hospital Giessen, Giessen, Germany
| | - Trinad Chakraborty
- Institute of Medical Microbiology, Justus Liebig University Giessen, Giessen, Germany
- German Center for Infection Research (DZIF), Partner Site Giessen-Marburg-Langen, Justus-Liebig University Giessen, Giessen, Germany
- Institute of Medical Microbiology, University Hospital Giessen, Giessen, Germany
- *Correspondence: Trinad Chakraborty,
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Xie L, Xu R, Zhu D, Sun J. Emerging resistance to ceftriaxone treatment owing to different ampD mutations in Enterobacter roggenkampii. Infect Genet Evol 2022; 102:105301. [PMID: 35568334 DOI: 10.1016/j.meegid.2022.105301] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 05/08/2022] [Accepted: 05/09/2022] [Indexed: 06/15/2023]
Abstract
OBJECTIVES The Enterobacter cloacae complex is responsible for a variety of infections in hospitalized patients and is resistant to β-lactam antibiotics owing to the expression of AmpC β-lactamase. We report emerging resistance in Enterobacter roggenkampii exposed to ceftriaxone and explore the mechanism underlying mutations responsible for this resistance. METHODS Three strains were derived from different samples from one patient (blood and liver abscess fluid). Antimicrobial susceptibility was evaluated by standard broth microdilution, while ampC expression was determined via RT-PCR. Genetic relatedness was evaluated via pulsed-field gel electrophoresis (PFGE). Species identification and comparative genome analysis were performed via genome sequencing. Mutation rate testing and selection of AmpC-derepressed mutants were conducted to explore the mutation mechanism. RESULTS E. roggenkampii F1247 was susceptible to third-generation cephalosporins (3GCs); F95 and F1057, found in blood sample on day 11 and liver abscess drainage fluid on day 25, were resistant. ampC expression was 341- and 642-fold higher in F95 and F1057, respectively, than in F1247. Three isolates were the same PFGE and sequence types (ST1778) and were highly homologous (2 and 4 core genome single nucleotide polymorphism differences). Compared to F1247, F95 possessed a 575 bp deletion, including 537 bp of ampD, whereas F1057 harbored only one amino acid mutation (Leu140Pro in ampD). The mutation rates from F1247 exposure to cefotaxime, ceftazidime, ceftriaxone, piperacillin-tazobactam, and cefepime were (1.90 ± 0.21) × 10-8, (3.18 ± 0.43) × 10-8, (2.00 ± 0.20) × 10-8, (2.92 ± 0.29) × 10-9, and zero, respectively. In vitro-selected mutations responsible for resistance were identified in ampD, ampR, and dacB. CONCLUSIONS E. roggenkampii may develop resistance in vivo and in vitro upon exposure to 3GCs and to a lesser extent to piperacillin-tazobactam. 3GCs should not be used as a monotherapy for E. roggenkampii infections. Therapy using cefepime or carbapenems may be preferred to piperacillin-tazobactam in the treatment of E. roggenkampii, especially if source control is difficult.
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Affiliation(s)
- Lianyan Xie
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China; Department of Clinical Microbiology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Rong Xu
- Department of Clinical Microbiology, Shanghai Center for Clinical Laboratory, Shanghai, China
| | - Dongan Zhu
- Department of Clinical Laboratory, Shanghai Pudong Hospital, Fudan University Pudong Medical Center, Shanghai, China.
| | - Jingyong Sun
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China; Department of Clinical Microbiology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
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Yeh TK, Lin HJ, Liu PY, Wang JH, Hsueh PR. Antibiotic resistance in Enterobacter hormaechei. Int J Antimicrob Agents 2022; 60:106650. [DOI: 10.1016/j.ijantimicag.2022.106650] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 07/25/2022] [Accepted: 07/31/2022] [Indexed: 11/28/2022]
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Xu T, Xue CX, Chen Y, Huang J, Wu W, Lu Y, Huang Q, Chen D, Zhou K. Frequent convergence of mcr-9 and carbapenemase genes in Enterobacter cloacae complex driven by epidemic plasmids and host incompatibility. Emerg Microbes Infect 2022; 11:1959-1972. [PMID: 35848148 PMCID: PMC9359198 DOI: 10.1080/22221751.2022.2103456] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Convergence of mcr and carbapenemase genes has been sporadically detected in Enterobacter cloacae complex (ECC) with an upward trend. However, the state of the epidemic and underlying mechanism of such convergence has been poorly understood. In this study, the co-occurrence of MCR and carbapenemases was systematically analyzed in 230 clinical ECC isolates collected between 2000 and 2018 together with a global dataset consisting of 3,559 ECC genomes compiled from GenBank. We identified 48 mcr-9/mcr-10-positive isolates (MCR-ECC) (20.9%) in our collection, and a comparable ratio of MCR-ECC (720/3559, 20.2%) was detected in the global dataset. A high prevalence of carbapenemase-producing MCR-ECC (MCR-CREC) was further identified in the MCR-ECC of both datasets (16/48, 33.3%; 388/720, 53.9%), demonstrating a frequent convergence of mcr-9/10 and carbapenemase genes in ECC worldwide. An epidemic IncHI2/2A plasmid with a highly conserved backbone was identified and largely contributed to the dissemination of mcr-9 in ECC worldwide. A highly conserved IncX3-type NDM-1-carrying plasmid and IncN-type IMP-4-carrying plasmid were additionally detected in MCR-CREC isolated in China. Our surveillance data showed that MCR-CREC emerged (in 2013) much later than MCR-ECC (in 2000), indicating that MCR-CREC could be derived from MCR-ECC by additional captures of carbapenemase-encoding plasmids. Tests of plasmid stability and incompatibility showed that the mcr-9/mcr-10-encoding plasmids with the NDM-1-encoding plasmids stably remained in ECC but incompatible in Escherichia coli, suggesting that the convergence was host-dependent. The findings extend our concern on the convergence of resistance to the last resort antibiotics and highlight the necessity of continued surveillance in the future.
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Affiliation(s)
- Tingting Xu
- Shenzhen Institute of Respiratory Diseases, Second Clinical Medical College (Shenzhen People's Hospital), Jinan University; the First Affiliated Hospital (Shenzhen People's Hospital), Southern University of Science and Technology, Shenzhen, China
| | - Chun-Xu Xue
- Shenzhen Institute of Respiratory Diseases, Second Clinical Medical College (Shenzhen People's Hospital), Jinan University; the First Affiliated Hospital (Shenzhen People's Hospital), Southern University of Science and Technology, Shenzhen, China
| | - Yuxin Chen
- Department of Laboratory Medicine, Nanjing Drum Tower Hospital Clinical College of Jiangsu University, Nanjing, Jiangsu, China
| | - Junxi Huang
- Shenzhen Institute of Respiratory Diseases, Second Clinical Medical College (Shenzhen People's Hospital), Jinan University; the First Affiliated Hospital (Shenzhen People's Hospital), Southern University of Science and Technology, Shenzhen, China
| | - Weiyuan Wu
- Clinical Laboratory, Second Clinical Medical College (Shenzhen People's Hospital), Jinan University; the First Affiliated Hospital (Shenzhen People's Hospital), Southern University of Science and Technology, Shenzhen, China
| | - Yuemei Lu
- Clinical Laboratory, Second Clinical Medical College (Shenzhen People's Hospital), Jinan University; the First Affiliated Hospital (Shenzhen People's Hospital), Southern University of Science and Technology, Shenzhen, China
| | - Qiuhui Huang
- Shenzhen Institute of Respiratory Diseases, Second Clinical Medical College (Shenzhen People's Hospital), Jinan University; the First Affiliated Hospital (Shenzhen People's Hospital), Southern University of Science and Technology, Shenzhen, China
| | - Dandan Chen
- Shenzhen Institute of Respiratory Diseases, Second Clinical Medical College (Shenzhen People's Hospital), Jinan University; the First Affiliated Hospital (Shenzhen People's Hospital), Southern University of Science and Technology, Shenzhen, China
| | - Kai Zhou
- Shenzhen Institute of Respiratory Diseases, Second Clinical Medical College (Shenzhen People's Hospital), Jinan University; the First Affiliated Hospital (Shenzhen People's Hospital), Southern University of Science and Technology, Shenzhen, China
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Duré FM, Silveira MC, Rocha-de-Souza CM, Leão RS, de Oliveira Santos IC, Albano RM, Marques EA, D’Alincourt Carvalho-Assef AP, da Silva FAB. CABGen: A Web Application for the Bioinformatic Analysis of Bacterial Genomes. Front Microbiol 2022; 13:893474. [PMID: 35711759 PMCID: PMC9196194 DOI: 10.3389/fmicb.2022.893474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 05/02/2022] [Indexed: 11/22/2022] Open
Abstract
Due to recent developments in NGS technologies, genome sequencing is generating large volumes of new data containing a wealth of biological information. Understanding sequenced genomes in a biologically meaningful way and delineating their functional and metabolic landscapes is a first-level challenge. Considering the global antimicrobial resistance (AMR) problem, investments to expand surveillance and improve existing genome analysis technologies are pressing. In addition, the speed at which new genomic data is generated surpasses our capacity to analyze it with available bioinformatics methods, thus creating a need to develop new, user-friendly and comprehensive analytical tools. To this end, we propose a new web application, CABGen,1 developed with open-source software. CABGen allows storing, organizing, analyzing, and interpreting bioinformatics data in a friendly, scalable, easy-to-use environment and can process data from bacterial isolates of different species and origins. CABGen has three modules: Upload Sequences, Analyze Sequences, and Verify Results. Functionalities include coverage estimation, species identification, de novo genome assembly, and assembly quality, genome annotation, MLST mapping, searches for genes related to AMR, virulence, and plasmids, and detection of point mutations in specific AMR genes. Visualization tools are also available, greatly facilitating the handling of biological data. The reports include those results that are clinically relevant. To illustrate the use of CABGen, whole-genome shotgun data from 181 bacterial isolates of different species collected in 5 Brazilian regions between 2018 and 2020 were uploaded and submitted to the platform’s modules.
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Affiliation(s)
- Felicita Mabel Duré
- Central Public Health Laboratory (LCSP), Ministry of Public Health and Social Welfare MSPyBS, Asunción, Paraguay
| | - Melise Chaves Silveira
- Hospital Infection Research Laboratory (LAPIH), Oswaldo Cruz Institute–Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro, Brazil
| | - Cláudio Marcos Rocha-de-Souza
- Hospital Infection Research Laboratory (LAPIH), Oswaldo Cruz Institute–Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro, Brazil
| | - Robson Souza Leão
- Department of Biochemistry, Roberto de Alcântara Gomes Biology Institute, State University of Rio de Janeiro – UERJ, Rio de Janeiro, Brazil
- Department of Microbiology, Immunology and Parasitology - Medical Sciences College - State University of Rio de Janeiro – UERJ, Rio de Janeiro, Brazil
| | | | - Rodolpho Mattos Albano
- Department of Biochemistry, Roberto de Alcântara Gomes Biology Institute, State University of Rio de Janeiro – UERJ, Rio de Janeiro, Brazil
| | - Elizabeth Andrade Marques
- Department of Biochemistry, Roberto de Alcântara Gomes Biology Institute, State University of Rio de Janeiro – UERJ, Rio de Janeiro, Brazil
- Department of Microbiology, Immunology and Parasitology - Medical Sciences College - State University of Rio de Janeiro – UERJ, Rio de Janeiro, Brazil
| | - Ana Paula D’Alincourt Carvalho-Assef
- Hospital Infection Research Laboratory (LAPIH), Oswaldo Cruz Institute–Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro, Brazil
- *Correspondence: Ana Paula D’Alincourt Carvalho-Assef,
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18
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Emeraud C, Petit C, Gauthier L, Bonnin RA, Naas T, Dortet L. Emergence of VIM-producing Enterobacter cloacae complex in France between 2015 and 2018. J Antimicrob Chemother 2022; 77:944-951. [PMID: 35045171 DOI: 10.1093/jac/dkab471] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 11/26/2021] [Indexed: 12/18/2022] Open
Abstract
OBJECTIVES To genetically characterize VIM-producing Enterobacter cloacae complex (ECC) isolates recovered in France from 2015 to 2018. METHODS WGS, species determination, MLST, clonal relationship and genetic characterization were performed on 149 VIM-producing ECC isolates. RESULTS Among VIM-producing Enterobacterales, the prevalence of ECC increased drastically from 6% in 2012 to 52% in 2018. The most prevalent species were Enterobacter hormaechei subsp. hoffmannii (40.9%), E. hormaechei subsp. steigerwaltii (21.5%), E. hormaechei subsp. xiangfangensis (14.8%) and ECC clade S (17.4%). Major STs were ST-873 (17.5%), ST-66 (12.1%), ST-78 (9.4%), ST-419 (8.1%), ST-145 (4.7%), ST-50 (4.0%), ST-118 (4.0%) and ST-168 (4.0%). Finally, six different integrons were identified, with some being specific to a given blaVIM variant (In916 with blaVIM-1-aacA4'-aphA15-aadA1-catB2 and In416 with blaVIM-4-aacA7-dfrA1b-aadA1b-smr2 genes). CONCLUSIONS This study demonstrated the genetic diversity among VIM-producing ECC isolates, indicating that their spread is not linked to a single clone.
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Affiliation(s)
- Cécile Emeraud
- Department of Bacteriology-Hygiene, Bicêtre Hospital, Assistance Publique-Hôpitaux de Paris, Le Kremlin-Bicêtre, France.,Team "Resist", UMR1184, Immunology of Viral, Auto-immune, Hematological and Bacterial diseases (IMVA-HB), INSERM, Paris-Saclay University, Faculty of Medicine, Le Kremlin-Bicêtre, France.,Associated French National Reference Center for Antibiotic Resistance: Carbapenemase-producing Enterobacteriaceae, Le Kremlin-Bicêtre, France
| | - Caroline Petit
- Department of Bacteriology-Hygiene, Bicêtre Hospital, Assistance Publique-Hôpitaux de Paris, Le Kremlin-Bicêtre, France
| | - Lauraine Gauthier
- Department of Bacteriology-Hygiene, Bicêtre Hospital, Assistance Publique-Hôpitaux de Paris, Le Kremlin-Bicêtre, France.,Team "Resist", UMR1184, Immunology of Viral, Auto-immune, Hematological and Bacterial diseases (IMVA-HB), INSERM, Paris-Saclay University, Faculty of Medicine, Le Kremlin-Bicêtre, France.,Associated French National Reference Center for Antibiotic Resistance: Carbapenemase-producing Enterobacteriaceae, Le Kremlin-Bicêtre, France
| | - Rémy A Bonnin
- Department of Bacteriology-Hygiene, Bicêtre Hospital, Assistance Publique-Hôpitaux de Paris, Le Kremlin-Bicêtre, France.,Team "Resist", UMR1184, Immunology of Viral, Auto-immune, Hematological and Bacterial diseases (IMVA-HB), INSERM, Paris-Saclay University, Faculty of Medicine, Le Kremlin-Bicêtre, France.,Associated French National Reference Center for Antibiotic Resistance: Carbapenemase-producing Enterobacteriaceae, Le Kremlin-Bicêtre, France
| | - Thierry Naas
- Department of Bacteriology-Hygiene, Bicêtre Hospital, Assistance Publique-Hôpitaux de Paris, Le Kremlin-Bicêtre, France.,Team "Resist", UMR1184, Immunology of Viral, Auto-immune, Hematological and Bacterial diseases (IMVA-HB), INSERM, Paris-Saclay University, Faculty of Medicine, Le Kremlin-Bicêtre, France.,Associated French National Reference Center for Antibiotic Resistance: Carbapenemase-producing Enterobacteriaceae, Le Kremlin-Bicêtre, France
| | - Laurent Dortet
- Department of Bacteriology-Hygiene, Bicêtre Hospital, Assistance Publique-Hôpitaux de Paris, Le Kremlin-Bicêtre, France.,Team "Resist", UMR1184, Immunology of Viral, Auto-immune, Hematological and Bacterial diseases (IMVA-HB), INSERM, Paris-Saclay University, Faculty of Medicine, Le Kremlin-Bicêtre, France.,Associated French National Reference Center for Antibiotic Resistance: Carbapenemase-producing Enterobacteriaceae, Le Kremlin-Bicêtre, France
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Long Z, Duan N, Xue Y, Wang M, Li J, Su Z, Liu Q, Mao D, Wei T. Characterization of a Novel Lutein Cleavage Dioxygenase, EhLCD, from Enterobacter hormaechei YT-3 for the Enzymatic Synthesis of 3-Hydroxy-β-ionone from Lutein. Catalysts 2021; 11:1257. [DOI: 10.3390/catal11111257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
3-Hydroxy-β-ionone, a flavor and fragrance compound with fruity violet-like characteristics, is widely applied in foodstuff and beverages, and is currently produced using synthetic chemistry. In this study, a novel lutein cleavage enzyme (EhLCD) was purified and characterized from Enterobacter hormaechei YT-3 to convert lutein to 3-hydroxy-β-ionone. Enzyme EhLCD was purified to homogeneity by ammonium sulfate precipitation, Q-Sepharose, phenyl-Sepharose, and Superdex 200 chromatography. The molecular mass of purified EhLCD, obtained by SDS-PAGE, was approximately 50 kDa. The enzyme exhibited the highest activity toward lutein, followed by zeaxanthin, β-cryptoxanthin, and β-carotene, suggesting that EhLCD exhibited higher catalytic efficiency for carotenoid substrates bearing 3-hydroxy-ionone rings. Isotope-labeling experiments showed that EhLCD incorporated oxygen from O2 into 3-hydroxy-β-ionone and followed a dioxygenase reaction mechanism for different carotenoid substrates. These results indicated that EhLCD is the first characterized bacterial lutein cleavage dioxygenase. Active EhLCD was also confirmed to be a Fe2+-dependent protein with 1 molar equivalent of non-haem Fe2+. The purified enzyme displayed optimal activity at 45 °C and pH 8.0. The optimum concentrations of the substrate, enzyme, and Tween 40 for 3-hydroxy-β-ionone production were 60 μM lutein/L, 1.5 U/mL, and 2% (w/v), respectively. Under optimum conditions, EhLCD produced 3-hydroxy-β-ionone (637.2 mg/L) in 60 min with a conversion of 87.0% (w/w), indicating that this enzyme is a potential candidate for the enzymatic synthesis of 3-hydroxy-β-ionone in biotechnological applications.
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20
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Maguvu TE, Bezuidenhout CC. Whole Genome Sequencing Based Taxonomic Classification, and Comparative Genomic Analysis of Potentially Human Pathogenic Enterobacter spp. Isolated from Chlorinated Wastewater in the North West Province, South Africa. Microorganisms 2021; 9:1928. [PMID: 34576823 DOI: 10.3390/microorganisms9091928] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 09/04/2021] [Accepted: 09/05/2021] [Indexed: 11/17/2022] Open
Abstract
Comparative genomics, in particular, pan-genome analysis, provides an in-depth understanding of the genetic variability and dynamics of a bacterial species. Coupled with whole-genome-based taxonomic analysis, these approaches can help to provide comprehensive, detailed insights into a bacterial species. Here, we report whole-genome-based taxonomic classification and comparative genomic analysis of potential human pathogenic Enterobacter hormaechei subsp. hoffmannii isolated from chlorinated wastewater. Genome Blast Distance Phylogeny (GBDP), digital DNA-DNA hybridization (dDDH), and average nucleotide identity (ANI) confirmed the identity of the isolates. The algorithm PathogenFinder predicted the isolates to be human pathogens with a probability of greater than 0.78. The potential pathogenic nature of the isolates was supported by the presence of biosynthetic gene clusters (BGCs), aerobactin, and aryl polyenes (APEs), which are known to be associated with pathogenic/virulent strains. Moreover, analysis of the genome sequences of the isolates reflected the presence of an arsenal of virulence factors and antibiotic resistance genes that augment the predictions of the algorithm PathogenFinder. The study comprehensively elucidated the genomic features of pathogenic Enterobacter isolates from wastewaters, highlighting the role of wastewaters in the dissemination of pathogenic microbes, and the need for monitoring the effectiveness of the wastewater treatment process.
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21
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Pot M, Reynaud Y, Couvin D, Ducat C, Ferdinand S, Gravey F, Gruel G, Guérin F, Malpote E, Breurec S, Talarmin A, Guyomard-Rabenirina S. Wide Distribution and Specific Resistance Pattern to Third-Generation Cephalosporins of Enterobacter cloacae Complex Members in Humans and in the Environment in Guadeloupe (French West Indies). Front Microbiol 2021; 12:628058. [PMID: 34248862 PMCID: PMC8268024 DOI: 10.3389/fmicb.2021.628058] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 05/31/2021] [Indexed: 11/25/2022] Open
Abstract
Species belonging to Enterobacter cloacae complex have been isolated in numerous environments and samples of various origins. They are also involved in opportunistic infections in plants, animals, and humans. Previous prospection in Guadeloupe (French West Indies) indicated a high frequency of E. cloacae complex strains resistant to third-generation cephalosporins (3GCs) in a local lizard population (Anolis marmoratus), but knowledge of the distribution and resistance of these strains in humans and the environment is limited. The aim of this study was to compare the distribution and antibiotic susceptibility pattern of E. cloacae complex members from different sources in a “one health” approach and to find possible explanations for the high level of resistance in non-human samples. E. cloacae complex strains were collected between January 2017 and the end of 2018 from anoles, farm animals, local fresh produce, water, and clinical human samples. Isolates were characterized by the heat-shock protein 60 gene-fragment typing method, and whole-genome sequencing was conducted on the most frequent clusters (i.e., C-VI and C-VIII). The prevalence of resistance to 3GCs was relatively high (56/346, 16.2%) in non-human samples. The associated resistance mechanism was related to an AmpC overproduction; however, in human samples, most of the resistant strains (40/62) produced an extended-spectrum beta-lactamase. No relation was found between resistance in isolates from wild anoles (35/168) and human activities. Specific core-genome phylogenetic analysis highlighted an important diversity in this bacterial population and no wide circulation among the different compartments. In our setting, the mutations responsible for resistance to 3GCs, especially in ampD, were diverse and not compartment specific. In conclusion, high levels of resistance in non-human E. cloacae complex isolates are probably due to environmental factors that favor the selection of these resistant strains, and this will be explored further.
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Affiliation(s)
- Matthieu Pot
- Transmission, Reservoir and Diversity of Pathogens Unit, Pasteur Institute of Guadeloupe, Les Abymes, France
| | - Yann Reynaud
- Transmission, Reservoir and Diversity of Pathogens Unit, Pasteur Institute of Guadeloupe, Les Abymes, France
| | - David Couvin
- Transmission, Reservoir and Diversity of Pathogens Unit, Pasteur Institute of Guadeloupe, Les Abymes, France
| | - Célia Ducat
- Transmission, Reservoir and Diversity of Pathogens Unit, Pasteur Institute of Guadeloupe, Les Abymes, France
| | - Séverine Ferdinand
- Transmission, Reservoir and Diversity of Pathogens Unit, Pasteur Institute of Guadeloupe, Les Abymes, France
| | - François Gravey
- GRAM 2.0, Normandie University, UNICAEN, UNIROUEN, Caen, France
| | - Gaëlle Gruel
- Transmission, Reservoir and Diversity of Pathogens Unit, Pasteur Institute of Guadeloupe, Les Abymes, France
| | - François Guérin
- GRAM 2.0, Normandie University, UNICAEN, UNIROUEN, Caen, France.,Department of Clinical Microbiology, Caen University Hospital, Caen, France
| | - Edith Malpote
- Laboratory of Clinical Microbiology, University Hospital of Guadeloupe, Pointe-à-Pitre/Les Abymes, France
| | - Sébastien Breurec
- Transmission, Reservoir and Diversity of Pathogens Unit, Pasteur Institute of Guadeloupe, Les Abymes, France.,Faculty of Medicine Hyacinthe Bastaraud, University of the Antilles, Pointe-à-Pitre, France.,Centre for Clinical Investigation 1424, INSERM, Pointe-à-Pitre/Les Abymes, France
| | - Antoine Talarmin
- Transmission, Reservoir and Diversity of Pathogens Unit, Pasteur Institute of Guadeloupe, Les Abymes, France
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Ji Y, Wang P, Xu T, Zhou Y, Chen R, Zhu H, Zhou K. Development of a One-Step Multiplex PCR Assay for Differential Detection of Four species ( Enterobacter cloacae, Enterobacter hormaechei, Enterobacter roggenkampii, and Enterobacter kobei) Belonging to Enterobacter cloacae Complex With Clinical Significance. Front Cell Infect Microbiol 2021; 11:677089. [PMID: 34095000 PMCID: PMC8169972 DOI: 10.3389/fcimb.2021.677089] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 04/06/2021] [Indexed: 11/13/2022] Open
Abstract
Enterobacter cloacae complex (ECC) is composed of multiple species and the taxonomic status is consecutively updated. In last decades ECC is frequently associated with multidrug resistance and become an important nosocomial pathogen. Currently, rapid and accurate identification of ECC to the species level remains a technical challenge, thus impedes our understanding of the population at the species level. Here, we aimed to develop a simple, reliable, and economical method to distinguish four epidemiologically prevalent species of ECC with clinical significance, i.e., E. cloacae, E. hormaechei, E. roggenkampii, and E. kobei. A total of 977 ECC genomes were retrieved from the GenBank, and unique gene for each species was obtained by core-genome comparisons. Four pairs of species-specific primers were designed based on the unique genes. A total of 231 ECC clinical strains were typed both by hsp60 typing and by species-specific PCRs. The specificity and sensitivity of the four species-specific PCRs ranged between 96.56% and 100% and between 76.47% and 100%, respectively. The PCR for E. cloacae showed the highest specificity and sensitivity. A one-step multiplex PCR was subsequently established by combining the species-specific primers. Additional 53 hsp60-typed ECC and 20 non-ECC isolates belonging to six species obtained from samples of patients, sewage water and feces of feeding animals were tested by the multiplex PCR. The identification results of both techniques were concordant. The multiplex PCR established in this study provides an accurate, expeditious, and cost-effective way for routine diagnosis and molecular surveillance of ECC strains at species level.
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Affiliation(s)
- Yang Ji
- Shenzhen Institute of Respiratory Diseases, Second Clinical Medical College, Jinan University (Shenzhen People's Hospital); The First Affiliated Hospital, Southern University of Science and Technology (Shenzhen People's Hospital), Shenzhen, China
| | - Peihong Wang
- State Key Laboratory for Turbulence and Complex Systems and Department of Biomedical Engineering, College of Engineering, Peking University, Beijing, China.,Center for Quantitative Biology, Peking University, Beijing, China
| | - Tingting Xu
- Shenzhen Institute of Respiratory Diseases, Second Clinical Medical College, Jinan University (Shenzhen People's Hospital); The First Affiliated Hospital, Southern University of Science and Technology (Shenzhen People's Hospital), Shenzhen, China
| | - Yanzi Zhou
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Rongchang Chen
- Shenzhen Institute of Respiratory Diseases, Second Clinical Medical College, Jinan University (Shenzhen People's Hospital); The First Affiliated Hospital, Southern University of Science and Technology (Shenzhen People's Hospital), Shenzhen, China
| | - Huaiqiu Zhu
- State Key Laboratory for Turbulence and Complex Systems and Department of Biomedical Engineering, College of Engineering, Peking University, Beijing, China.,Center for Quantitative Biology, Peking University, Beijing, China
| | - Kai Zhou
- Shenzhen Institute of Respiratory Diseases, Second Clinical Medical College, Jinan University (Shenzhen People's Hospital); The First Affiliated Hospital, Southern University of Science and Technology (Shenzhen People's Hospital), Shenzhen, China
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23
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Makhlouf J, Merhi G, Salloum T, Abboud E, Tokajian S. Molecular characterization of a carbapenem-resistant Enterobacter hormaechei ssp. xiangfangensis co-harbouring bla NDM-1 and a chromosomally encoded phage-linked bla CTX-M-15 genes. Infect Genet Evol 2021; 93:104924. [PMID: 34004359 DOI: 10.1016/j.meegid.2021.104924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 03/22/2021] [Accepted: 05/13/2021] [Indexed: 10/21/2022]
Abstract
Enterobacter cloacae complex (ECC) members are rapidly emerging as successful nosocomial pathogens, especially, with the emergence of carbapenem-resistant clones. In this study, we performed a comprehensive molecular characterization of a carbapenem-resistant E. hormaechei ssp. xiangfangensis LAU_ENC1. hsp60 and average nucleotide identity (ANI) were used for its identification. The repertoire of resistance genes and phage content were analyzed. Plasmid sequences were extracted and compared to closest references. The isolate LAU_ENC1 was identified as an E. hormaechei ssp. xiangfangensis and belonged to ST-114A sub-cluster. blaNDM-1, blaCTX-M-15, blaOXA-1, and blaACT-16 genes were detected as β-lactam resistance determinants. A chromosomal hybrid intact phage, Enterobacter phage LAU1, with blaCTX-M-15 integrated in its direct vicinity within an ISEcp1 - blaCTX-M-15 - wbuC - ∆Tn2 rare cassette was detected. blaNDM-1 was integrated within a novel IncFII conjugative plasmid, pLAU_ENC1, through an IS3000- ΔISAba125-blaNDM-1-bleMBL-//-Tn5403 cassette. To our knowledge, this is the first report of a multi-drug resistant (MDR) E. hormaechei ssp. xiangfangensis carrying a blaCTX-M-15 integrated within the proximity of a provirus chromosomal region. Treatment options for MDR ECC members are becoming scarce, thus warranting an increased monitoring of the dissemination of these pathogens in clinical settings.
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Affiliation(s)
- Jana Makhlouf
- Department of Natural Sciences, Lebanese American University, Lebanon
| | - Georgi Merhi
- Department of Natural Sciences, Lebanese American University, Lebanon
| | - Tamara Salloum
- Department of Natural Sciences, Lebanese American University, Lebanon
| | - Edmond Abboud
- Laboratory Department, Middle East Institute of Health University Hospital, Lebanon
| | - Sima Tokajian
- Department of Natural Sciences, Lebanese American University, Lebanon.
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24
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Solcova M, Demnerova K, Purkrtova S. Application of Nanopore Sequencing (MinION) for the Analysis of Bacteriome and Resistome of Bean Sprouts. Microorganisms 2021; 9:microorganisms9050937. [PMID: 33925711 PMCID: PMC8146283 DOI: 10.3390/microorganisms9050937] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 04/22/2021] [Accepted: 04/25/2021] [Indexed: 01/11/2023] Open
Abstract
The aspiration these days is to apply rapid methods for parallel analysis of bacteriome and resistome of food samples to increase food safety and prevent antibiotic resistance genes (ARGs) spreading. In this work, we used nanopore sequencing (NS) to determine the diversity and dynamics of the microbiome and resistome in two types of bean sprouts. We proved that NS provided an easy, quick, and reliable way to identify the microbiome and resistome of a food sample also. The species diversity obtained by NS and by cultivation methods with MALDI-TOF MS identification was comparable. In both samples, before and after cultivation (30 °C, 48 h), the dominant part of bacteriome formed Gammaproteobacteria (Enterobacteriaceae, Erwiniaceae, Pseudomonadaceae, Moraxellaceae) and then Firmicutes (Streptococcaceae). The diversity and abundance of single ARGs groups were comparable for both samples despite bacteriome differences. More than 50% of the detected ARGs alignments were mutations conferring resistance to aminoglycosides (16S rRNA), resistance to fluoroquinolones (gyrA, gyrB, parC, parD) and elfamycin (EF-Tu). ARGs encoding efflux pumps formed more than 30% of the detected alignments. Beta-lactamases were represented by many variants, but were less abundant.
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Affiliation(s)
- Milada Solcova
- Correspondence: (M.S.); (S.P.); Tel.: +420-220-44-5196 (M.S. & S.P.)
| | | | - Sabina Purkrtova
- Correspondence: (M.S.); (S.P.); Tel.: +420-220-44-5196 (M.S. & S.P.)
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Xu T, Ji Y, Song J, Huang J, Chen R, Qiu C, Zhou K. A novel host of MCR-5 belonging to Enterobacter spp. isolated from hospital sewage water. Environ Microbiol Rep 2021; 13:234-237. [PMID: 33599072 DOI: 10.1111/1758-2229.12937] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 01/22/2021] [Accepted: 02/04/2021] [Indexed: 06/12/2023]
Affiliation(s)
- Tingting Xu
- Shenzhen Institute of Respiratory Diseases, Second Clinical Medical College (Shenzhen People's Hospital), Jinan University, the First Affiliated Hospital (Shenzhen People's Hospital), Southern University of Science and Technology, Shenzhen, China
| | - Yang Ji
- Shenzhen Institute of Respiratory Diseases, Second Clinical Medical College (Shenzhen People's Hospital), Jinan University, the First Affiliated Hospital (Shenzhen People's Hospital), Southern University of Science and Technology, Shenzhen, China
| | - Jingjie Song
- Shenzhen Institute of Respiratory Diseases, Second Clinical Medical College (Shenzhen People's Hospital), Jinan University, the First Affiliated Hospital (Shenzhen People's Hospital), Southern University of Science and Technology, Shenzhen, China
| | - Junxi Huang
- College of Biotechnology, Guilin Medical University, Guilin, China
| | - Rongchang Chen
- Shenzhen Institute of Respiratory Diseases, Second Clinical Medical College (Shenzhen People's Hospital), Jinan University, the First Affiliated Hospital (Shenzhen People's Hospital), Southern University of Science and Technology, Shenzhen, China
| | - Chen Qiu
- Shenzhen Institute of Respiratory Diseases, Second Clinical Medical College (Shenzhen People's Hospital), Jinan University, the First Affiliated Hospital (Shenzhen People's Hospital), Southern University of Science and Technology, Shenzhen, China
| | - Kai Zhou
- Shenzhen Institute of Respiratory Diseases, Second Clinical Medical College (Shenzhen People's Hospital), Jinan University, the First Affiliated Hospital (Shenzhen People's Hospital), Southern University of Science and Technology, Shenzhen, China
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Umeda K, Nakamura H, Fukuda A, Matsumoto Y, Motooka D, Nakamura S, Yasui Y, Yoshida H, Kawahara R. Genomic characterization of clinical Enterobacter roggenkampii co-harbouring bla IMP-1- and bla GES-5-encoding IncP6 and mcr-9-encoding IncHI2 plasmids isolated in Japan. J Glob Antimicrob Resist 2021; 24:220-227. [PMID: 33385587 DOI: 10.1016/j.jgar.2020.11.028] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 11/29/2020] [Indexed: 12/31/2022] Open
Abstract
OBJECTIVES The spread of carbapenemase-producing Enterobacterales (CPE) with colistin resistance is a critical public health issue. We genetically characterized the clinical isolate Enterobacter roggenkampii OIPH-N260, which harboured carbapenemase genes blaIMP-1 and blaGES-5 with multiple resistance genes, including mcr-9 and blaCTX-M-9. METHODS This isolate was characterized by whole-genome sequencing, comparative analysis of resistance plasmids, susceptibility tests, bacterial conjugation, S1-nuclease digested pulsed-field-gel electrophoresis, and Southern blot hybridization. RESULTS The OIPH-N260 isolate exhibited resistance to most β-lactams and colistin. It co-harboured two resistance plasmids, the blaIMP-1- and blaGES-5-encoding IncP6 plasmid pN260-3 and mcr-9- and blaCTX-M-9-encoding IncHI2 plasmid pN260-1. The comparative analysis of pN260-3 indicated that a unique blaIMP-1-surrounding region was inserted into the blaGES-5-encoding plasmid with the mobile element IS26, which plays an important role in the spread of resistance genes. pN260-1 did not possess the mcr-9 expression regulative gene qseBC. Both plasmids were transferable into other bacterial species via conjugation. CONCLUSIONS This is the first study to report not only a blaIMP-1 and blaGES-5 co-encoding plasmid, but also the co-harbouring of another plasmid carrying mcr-9 and blaCTX-M-9 in Enterobacter cloacae complex. The development of advanced resistance via IS26-mediated insertion and the co-harbouring of resistance plasmids highlights the need to monitor for resistance genes in CPE.
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Affiliation(s)
- Kaoru Umeda
- Division of Microbiology, Osaka Institute of Public Health, 8-34 Tojo-cho, Tennoji-ku, Osaka, Japan.
| | - Hiromi Nakamura
- Division of Microbiology, Osaka Institute of Public Health, 8-34 Tojo-cho, Tennoji-ku, Osaka, Japan
| | - Akira Fukuda
- Division of Microbiology, Osaka Institute of Public Health, 8-34 Tojo-cho, Tennoji-ku, Osaka, Japan; Department of Health and Environmental Sciences, School of Veterinary Medicine, Rakuno Gakuen University, 582 Bunkyodai Midorimachi, Ebetsu, Hokkaido, Japan
| | - Yuki Matsumoto
- Genome Information Research Center, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita, Osaka, Japan
| | - Daisuke Motooka
- Genome Information Research Center, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita, Osaka, Japan
| | - Shota Nakamura
- Genome Information Research Center, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita, Osaka, Japan
| | - Yoshinori Yasui
- Osaka Saiseikai Nakatsu Hospital, 2-10-39 Shibata, Kita-ku, Osaka, Japan
| | - Hideki Yoshida
- Osaka City Public Health Office, 1-2-7-1000 Asahi-cho, Abeno-ku, Osaka, Japan
| | - Ryuji Kawahara
- Division of Microbiology, Osaka Institute of Public Health, 8-34 Tojo-cho, Tennoji-ku, Osaka, Japan
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Akita H, Itoiri Y, Takeda N, Matsushika A, Kimura ZI. Paenibacillus glycanilyticus subsp. hiroshimensis subsp. nov., isolated from leaf soil collected in Japan. Arch Microbiol 2021; 203:1787-1793. [PMID: 33481072 DOI: 10.1007/s00203-020-02166-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Revised: 12/22/2020] [Accepted: 12/27/2020] [Indexed: 11/29/2022]
Abstract
Strain CCI5, an oligotrophic bacterium, was isolated from leaf soil collected in Japan. Strain CCI5 grew at temperatures between 25 °C and 43 °C (optimum temperature, 40 °C) and at pHs between 6.0 and 10.0 (optimum pH, 9.0). Its major fatty acids were anteiso-C15:0 and iso-C16:0, and menaquinone 7 was the only detected quinone system. In a phylogenetic analysis based on 16S rRNA gene sequences, strain CCI5 presented as a member of the genus Paenibacillus. Moreover, multilocus sequence analysis based on partial sequences of the atpD, dnaA, gmk, and infB genes showed that strain CCI5 tightly clustered with P. glycanilyticus DS-1T. The draft genome of strain CCI5 consisted of 6,864,972 bp with a G+C content of 50.7% and comprised 6,189 predicted coding sequences. The genome average nucleotide identity value (97.8%) between strain CCI5 and P. glycanilyticus DS-1T was below the cut-off value for prokaryotic subspecies delineation. Based on its phenotypic, chemotaxonomic, and phylogenetic features, strain CCI5 (= HUT-8145T = KCTC 43270T) can be considered as a novel subspecies within the genus Paenibacillus with the proposed name Paenibacillus glycanilyticus subsp. hiroshimensis subsp. nov.
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Affiliation(s)
- Hironaga Akita
- Research Institute for Sustainable Chemistry, National Institute of Advanced Industrial Science and Technology (AIST), 3-11-32 Kagamiyama, Higashi-Hiroshima, Hiroshima, 739-0046, Japan.
| | - Yuya Itoiri
- Department of Civil and Environmental Engineering, National Institute of Technology, Kure College, 2-2-11 Aga-minami, Kure, Hiroshima, 737-8506, Japan
| | - Noriyo Takeda
- Research Institute for Sustainable Chemistry, National Institute of Advanced Industrial Science and Technology (AIST), 3-11-32 Kagamiyama, Higashi-Hiroshima, Hiroshima, 739-0046, Japan
| | - Akinori Matsushika
- Research Institute for Sustainable Chemistry, National Institute of Advanced Industrial Science and Technology (AIST), 3-11-32 Kagamiyama, Higashi-Hiroshima, Hiroshima, 739-0046, Japan.,Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima, 739-8530, Japan
| | - Zen-Ichiro Kimura
- Department of Civil and Environmental Engineering, National Institute of Technology, Kure College, 2-2-11 Aga-minami, Kure, Hiroshima, 737-8506, Japan
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Zong Z, Feng Y, McNally A. Carbapenem and Colistin Resistance in Enterobacter: Determinants and Clones. Trends Microbiol 2021; 29:473-476. [PMID: 33431326 DOI: 10.1016/j.tim.2020.12.009] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 12/15/2020] [Accepted: 12/15/2020] [Indexed: 02/05/2023]
Abstract
Enterobacter is a globally important pathogen. Here we clarify its taxonomy and review recent developments in its resistance to carbapenem and colistin, illustrating that Enterobacter has a large arsenal of mechanisms to grow under antimicrobial pressure. Further studies are required to decipher colistin heteroresistance and understand why certain Enterobacter lineages have emerged clinically.
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Affiliation(s)
- Zhiyong Zong
- Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, China; Center for Pathogen Research, West China Hospital, Sichuan University, Chengdu, China; Department of Infection Control, West China Hospital, Sichuan University, Chengdu, China; Division of Infectious Diseases, State Key Laboratory of Biotherapy, Chengdu, China.
| | - Yu Feng
- Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, China; Center for Pathogen Research, West China Hospital, Sichuan University, Chengdu, China; Division of Infectious Diseases, State Key Laboratory of Biotherapy, Chengdu, China
| | - Alan McNally
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
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Xu T, Zhang C, Ji Y, Song J, Liu Y, Guo Y, Zhou K. Identification of mcr-10 carried by self-transmissible plasmids and chromosome in Enterobacter roggenkampii strains isolated from hospital sewage water. Environ Pollut 2021; 268:115706. [PMID: 33069047 DOI: 10.1016/j.envpol.2020.115706] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 09/09/2020] [Accepted: 09/21/2020] [Indexed: 06/11/2023]
Abstract
The recent emergence of plasmid-borne mobilized colistin resistance (mcr) genes largely challenges the clinical use of colistin. Monitoring the distribution of mcr genes in environment is important for aiding to develop effective control measures. In this study, we aimed to evaluate the occurrence of a recent reported mcr variant, mcr-10, in hospital sewage water. mcr-10 was identified in three Enterobacter roggenkampii strains with high-level colistin resistance (MIC ≥ 16 mg/L). The three strains were assigned to different sequence types suggesting a sporadic dissemination of mcr-10 in the sewage water. Pairwise comparisons of the predicted protein structures of ten mcr homologues revealed that MCR-10 shares a higher similarity with MCR-3, MCR-4, MCR-7, and MCR-9. Overexpression in Escherichia coli Top10 showed that the activity of mcr-10 against colistin is lower than that of mcr-9. mcr-10 expression can be specifically induced by colistin, and it was co-upregulated with phoPQ to mediate the high-level colistin resistance. The mcr-10 gene was detected on self-transmissible plasmids in two isolates and on the chromosome in the other one. Blasting in Genbank suggested that the two mcr-10-bearing plasmids (pECL981-1 and pECL983-1) were novel plasmids, and replicon typing showed that they belong to IncFIB-FII and IncFIB, respectively. Plasmid-curing assay evidence that pECL981-1 was lack of fitness cost for the host. Three novel types of the genetic context were found for the mcr-10 gene in the three isolates. The structure xerC-mcr10 was dominant in mcr-10-positive genomes (39/42) retrieved in Genbank, suggesting that xerC might be involved in the mobilization of mcr-10. To our knowledge, this is the first report of mcr-10-producing E. roggenkampii detected in hospital sewage water. Our study highlights that continuous monitoring of mcr genes in hospital sewage water is imperative for understanding and tackling the dissemination.
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Affiliation(s)
- Tingting Xu
- Shenzhen Institute of Respiratory Diseases, Second Clinical Medical College (Shenzhen People's Hospital), Jinan University, The First Affiliated Hospital (Shenzhen People's Hospital), Southern University of Science and Technology, Shenzhen, China
| | - Chuqiu Zhang
- Shenzhen Institute of Respiratory Diseases, Second Clinical Medical College (Shenzhen People's Hospital), Jinan University, The First Affiliated Hospital (Shenzhen People's Hospital), Southern University of Science and Technology, Shenzhen, China
| | - Yang Ji
- Shenzhen Institute of Respiratory Diseases, Second Clinical Medical College (Shenzhen People's Hospital), Jinan University, The First Affiliated Hospital (Shenzhen People's Hospital), Southern University of Science and Technology, Shenzhen, China
| | - Jingjie Song
- Shenzhen Institute of Respiratory Diseases, Second Clinical Medical College (Shenzhen People's Hospital), Jinan University, The First Affiliated Hospital (Shenzhen People's Hospital), Southern University of Science and Technology, Shenzhen, China
| | - Yang Liu
- Shenzhen Institute of Respiratory Diseases, Second Clinical Medical College (Shenzhen People's Hospital), Jinan University, The First Affiliated Hospital (Shenzhen People's Hospital), Southern University of Science and Technology, Shenzhen, China
| | - Yuqi Guo
- Shenzhen Institute of Respiratory Diseases, Second Clinical Medical College (Shenzhen People's Hospital), Jinan University, The First Affiliated Hospital (Shenzhen People's Hospital), Southern University of Science and Technology, Shenzhen, China
| | - Kai Zhou
- Shenzhen Institute of Respiratory Diseases, Second Clinical Medical College (Shenzhen People's Hospital), Jinan University, The First Affiliated Hospital (Shenzhen People's Hospital), Southern University of Science and Technology, Shenzhen, China.
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Wu W, Feng Y, Zong Z. Precise Species Identification for Enterobacter: a Genome Sequence-Based Study with Reporting of Two Novel Species, Enterobacter quasiroggenkampii sp. nov. and Enterobacter quasimori sp. nov. mSystems 2020; 5:e00527-20. [PMID: 32753511 DOI: 10.1128/mSystems.00527-20] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Enterobacter species are major human pathogens. Precise species identification lays a foundation for microbiology, but the taxonomy of Enterobacter is complicated and confusing. In this study, first, we significantly updated the taxonomy of Enterobacter by rigorous genome analyses and found that all subspecies assignments of Enterobacter were incorrect. Second, we characterized and reported two novel Enterobacter species with clinical significance. Third, we curated 1,997 Enterobacter genome sequences deposited in GenBank and found that the species identification of most Enterobacter strains needed to be corrected. Fourth, we found that the most common Enterobacter species seen in clinical samples is Enterobacter xiangfangensis rather than Enterobacter cloacae. Fifth, we identified 14 tentative novel Enterobacter and 18 tentative novel non-Enterobacter species. This study highlights that updated and curated taxonomic assignments are the premise of correct species identification. We recommend that future Enterobacter studies need to use the updated taxonomy to avoid misleading information. The genus Enterobacter comprises common pathogens and has a complicated taxonomy. Precise taxonomic assignation lays a foundation for microbiology. In this study, we updated the Enterobacter taxonomy based on robust genome analyses. We found that all Enterobacter subspecies assignments were incorrect. Enterobacter cloacae subsp. dissolvens and Enterobacter hormaechei subsp. hoffmannii are species (Enterobacter dissolvens and Enterobacter hoffmannii, respectively) rather than subspecies. Enterobacter xiangfangensis, Enterobacter hormaechei subsp. oharae, and Enterobacter hormaechei subsp. steigerwaltii are not Enterobacter hormaechei subspecies but belong to the same species (Enterobacter xiangfangensis). Enterobacter timonensis should be removed to Pseudenterobacter, a novel genus. We then reported two novel species, Enterobacter quasiroggenkampii and Enterobacter quasimori, by genome- and phenotype-based characterization. We also applied the updated taxonomy to curate 1,997 Enterobacter genomes in GenBank. Species identification was changed following our updated taxonomy for the majority of publicly available strains (1,542, 77.2%). The most common Enterobacter species was E. xiangfangensis. We identified 14 novel tentative Enterobacter genomospecies. This study highlights that updated and curated taxonomic assignments are the premise of correct identification. IMPORTANCEEnterobacter species are major human pathogens. Precise species identification lays a foundation for microbiology, but the taxonomy of Enterobacter is complicated and confusing. In this study, first, we significantly updated the taxonomy of Enterobacter by rigorous genome analyses and found that all subspecies assignments of Enterobacter were incorrect. Second, we characterized and reported two novel Enterobacter species with clinical significance. Third, we curated 1,997 Enterobacter genome sequences deposited in GenBank and found that the species identification of most Enterobacter strains needed to be corrected. Fourth, we found that the most common Enterobacter species seen in clinical samples is Enterobacter xiangfangensis rather than Enterobacter cloacae. Fifth, we identified 14 tentative novel Enterobacter and 18 tentative novel non-Enterobacter species. This study highlights that updated and curated taxonomic assignments are the premise of correct species identification. We recommend that future Enterobacter studies need to use the updated taxonomy to avoid misleading information.
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Zhou K, Zhou Y, Zhang C, Song J, Cao X, Yu X, Shen P, Xiao Y. Dissemination of a 'rare' extended-spectrum β-lactamase gene bla SFO-1 mediated by epidemic clones of carbapenemase-producing Enterobacter hormaechei in China. Int J Antimicrob Agents 2020; 56:106079. [PMID: 32634604 DOI: 10.1016/j.ijantimicag.2020.106079] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Revised: 04/16/2020] [Accepted: 06/28/2020] [Indexed: 12/17/2022]
Abstract
An increasing trend of the coexistence of a rare extended-spectrum β-lactamase gene blaSFO-1 and carbapenemase genes in Enterobacteriaceae has recently been noted. This study aimed to determine the epidemiological and genetic characterisation of SFO-1-positive carbapenem-resistant Enterobacter cloacae complex (CREC) isolates. A total of 61 CREC clinical isolates were collected in the framework of a national surveillance for carbapenem-resistant Enterobacteriaceae during 2011-2015 in China. Seven SFO-1-positive CREC isolates (11.5%) were identified in four provinces, suggesting a wide dissemination of the blaSFO-1 gene among the CREC population in China. Five SFO-1-positive CREC isolates were further identified by screening 1625 genomes of E. cloacae complex strains retrieved from GenBank. The 12 SFO-1-positive CREC isolates were further identified as Enterobacter hormaechei, of which 10 belonged to epidemic clones (ST93, ST114 and ST418), indicating that these clones might largely contribute to the dissemination of blaSFO-1. Phylogenomics analysis further identified the occurrence of clonal dissemination in the community setting. The blaSFO-1-bearing plasmids were assigned to various incompatibility groups with highly diverse sizes (~104-370 kb), suggesting a wide vector range of blaSFO-1. Two types of genetic context, with and without insertion sequence IS26, were identified for the blaSFO-1 gene. The genetic context flanked by IS26 was more prevalent, thus largely facilitating the mobility of blaSFO-1. This study revealed that the blaSFO-1 gene is not as rare as previously found and that epidemic clones of CREC are responsible for its dissemination in China. These findings highlight the potential of wide dissemination of low-prevalence antimicrobial resistance genes.
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Teixeira P, Tacão M, Pureza L, Gonçalves J, Silva A, Cruz-Schneider MP, Henriques I. Occurrence of carbapenemase-producing Enterobacteriaceae in a Portuguese river: bla NDM, bla KPC and bla GES among the detected genes. Environ Pollut 2020; 260:113913. [PMID: 31972417 DOI: 10.1016/j.envpol.2020.113913] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Revised: 12/11/2019] [Accepted: 01/02/2020] [Indexed: 06/10/2023]
Abstract
Carbapenems are used as last-resort drugs to treat infections caused by multidrug-resistant bacteria. Despite the increasing number of reports of carbapenem-resistant Enterobacteriaceae (CRE), there is still limited information on their distribution or prevalence in the environment. Our aim was to assess the occurrence of CRE in the Lis river (Portugal) and to characterize the genetic platforms linked to carbapenemase genes. We collected six water samples from sites near a wastewater treatment plant (n = 4 samples) and livestock farms (n = 2). Twenty-four CRE were characterized by BOX element-polymerase chain reaction (BOX-PCR), and thirteen representative isolates were analysed by Pulsed-Field Gel Electrophoresis (PFGE) and by sequencing the 16S rRNA gene. Antimicrobial susceptibility testing, PCR screening for carbapenemase-encoding genes, conjugation experiments and plasmid analysis were performed. Four isolates were chosen for whole-genome sequencing. All water samples contained CRE (4.0 CFU/mL on average). Representative isolates were multidrug-resistant (resistant to ciprofloxacin, trimethoprim-sulfamethoxazole and to all β-lactams tested) and were identified as K. pneumoniae, Enterobacter and Citrobacter. Isolates carried plasmids and harboured carbapenemase-encoding genes: blaKPC-3 in K. pneumoniae (n = 9), blaNDM-1 in Enterobacter (n = 3) and blaGES-5 in Citrobacter (n = 1). Conjugation experiments were successful in two Klebsiella isolates. Enterobacter PFGE profiles grouped in one cluster while Klebsiella were divided in three clusters and a singleton. Whole-genome sequencing analysis revealed blaGES-5 within a novel class 3 integron (In3-16) located on an IncQ/pQ7-like plasmid in Citrobacter freundii CR16. blaKPC-3 was present on IncFIA-FII pBK30683-like plasmids, which were subsequently confirmed in all K. pneumoniae (n = 9). Furthermore, blaKPC-3 was part of a genomic island in K. pneumoniae CR12. In E. roggenkampii CR11, blaNDM-1 was on an IncA/C2 plasmid. The carbapenemase-encoding plasmids harboured other resistance determinants and mobile genetic elements. Our results demonstrate that Lis river is contaminated with CRE, highlighting the need for monitoring antibiotic resistance in aquatic environments, especially to last-resort drugs.
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Affiliation(s)
- Pedro Teixeira
- Biology Department, University of Aveiro, Aveiro, Portugal; CESAM (Centre for Marine and Environmental Studies), University of Aveiro, Aveiro, Portugal
| | - Marta Tacão
- Biology Department, University of Aveiro, Aveiro, Portugal; CESAM (Centre for Marine and Environmental Studies), University of Aveiro, Aveiro, Portugal.
| | - Leide Pureza
- Biology Department, University of Aveiro, Aveiro, Portugal; Laboratory of Genomics and Bioinformatics, Center of Genomics and Systems Biology, Institute of Biological Sciences, Federal University of Pará, Belém, Pará, Brazil
| | | | - Artur Silva
- Laboratory of Genomics and Bioinformatics, Center of Genomics and Systems Biology, Institute of Biological Sciences, Federal University of Pará, Belém, Pará, Brazil
| | - Maria Paula Cruz-Schneider
- Laboratory of Genomics and Bioinformatics, Center of Genomics and Systems Biology, Institute of Biological Sciences, Federal University of Pará, Belém, Pará, Brazil
| | - Isabel Henriques
- CESAM (Centre for Marine and Environmental Studies), University of Aveiro, Aveiro, Portugal; Department of Life Sciences, Faculty of Science and Technology, University of Coimbra, Coimbra, Portugal
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Abstract
Mobile colistin resistance (mcr) genes represent an emerging challenge. Here we describe a novel mcr gene, mcr-10, on an IncFIA plasmid of an Enterobacter roggenkampii clinical strain. mcr-10 has the highest nucleotide identity (79.69%) with mcr-9 and encodes MCR-10 with 82.93% amino acids identical to MCR-9. mcr-10 confers 4-fold increase in colistin MIC (from 1 to 4 mg/L) when cloned into a colistin-susceptible E. roggenkampii strain. By screening GenBank, mcr-10 was found in various Enterobacteriaceae species of countries in four continents, suggesting that this gene has widely spread. MCR-10 shows 79.04% to 83.67% amino acid identity and highly conserved predicted protein structures with chromosomally encoded MCR-like phosphoethanolamine transferases (designated MCR-B here) of various Buttiauxella species. MCR-10, MCR-9 and MCR-B proteins may, therefore, originate from a common ancestor. mcr-10 was adjacent to a site-specific recombinase-encoding gene and was bracketed by IS903 and may be mobilized by site-specific recombination or composite transposon. Our results indicate that mcr-10 is a novel plasmid-borne colistin resistance gene and warrants immediate monitoring and further studies.
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Affiliation(s)
- Chengcheng Wang
- Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, People's Republic of China.,Division of Infectious Diseases, State Key Laboratory of Biotherapy, Chengdu, People's Republic of China.,Center for Pathogen Research, West China Hospital, Sichuan University, Chengdu, People's Republic of China
| | - Yu Feng
- Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, People's Republic of China.,Division of Infectious Diseases, State Key Laboratory of Biotherapy, Chengdu, People's Republic of China.,Center for Pathogen Research, West China Hospital, Sichuan University, Chengdu, People's Republic of China
| | - Lina Liu
- Center for Pathogen Research, West China Hospital, Sichuan University, Chengdu, People's Republic of China
| | - Li Wei
- Department of Infection Control, West China Hospital, Sichuan University, Chengdu, People's Republic of China
| | - Mei Kang
- Laboratory of Clinical Microbiology, Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, People's Republic of China
| | - Zhiyong Zong
- Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, People's Republic of China.,Division of Infectious Diseases, State Key Laboratory of Biotherapy, Chengdu, People's Republic of China.,Center for Pathogen Research, West China Hospital, Sichuan University, Chengdu, People's Republic of China.,Department of Infection Control, West China Hospital, Sichuan University, Chengdu, People's Republic of China
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Martins ER, Bueno MFC, Francisco GR, Casella T, de Oliveira Garcia D, Cerdeira LT, Gerber AL, de Almeida LGP, Lincopan N, de Vasconcelos ATR, Nogueira MCL, Estofolete CF. Genome and plasmid context of two rmtG-carrying Enterobacter hormaechei isolated from urinary tract infections in Brazil. J Glob Antimicrob Resist 2020; 20:36-40. [DOI: 10.1016/j.jgar.2019.06.020] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Revised: 06/19/2019] [Accepted: 06/25/2019] [Indexed: 10/26/2022] Open
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Davin-Regli A, Lavigne JP, Pagès JM. Enterobacter spp.: Update on Taxonomy, Clinical Aspects, and Emerging Antimicrobial Resistance. Clin Microbiol Rev 2019; 32:e00002-19. [PMID: 31315895 DOI: 10.1128/CMR.00002-19] [Citation(s) in RCA: 218] [Impact Index Per Article: 43.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
The genus Enterobacter is a member of the ESKAPE group, which contains the major resistant bacterial pathogens. First described in 1960, this group member has proven to be more complex as a result of the exponential evolution of phenotypic and genotypic methods. Today, 22 species belong to the Enterobacter genus. These species are described in the environment and have been reported as opportunistic pathogens in plants, animals, and humans. The pathogenicity/virulence of this bacterium remains rather unclear due to the limited amount of work performed to date in this field. In contrast, its resistance against antibacterial agents has been extensively studied. In the face of antibiotic treatment, it is able to manage different mechanisms of resistance via various local and global regulator genes and the modulation of the expression of different proteins, including enzymes (β-lactamases, etc.) or membrane transporters, such as porins and efflux pumps. During various hospital outbreaks, the Enterobacter aerogenes and E. cloacae complex exhibited a multidrug-resistant phenotype, which has stimulated questions about the role of cascade regulation in the emergence of these well-adapted clones.
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Matteoli FP, Passarelli-Araujo H, Pedrosa-Silva F, Olivares FL, Venancio TM. Population structure and pangenome analysis of Enterobacter bugandensis uncover the presence of bla CTX-M-55, bla NDM-5 and bla IMI-1, along with sophisticated iron acquisition strategies. Genomics 2019; 112:1182-1191. [PMID: 31279858 DOI: 10.1016/j.ygeno.2019.07.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Revised: 07/02/2019] [Accepted: 07/03/2019] [Indexed: 01/22/2023]
Abstract
Enterobacter bugandensis is a recently described species that has been largely associated with nosocomial infections. We report the genome of a non-clinical E. bugandensis strain, which was integrated with publicly available genomes to study the pangenome and general population structure of E. bugandensis. Core- and whole-genome multilocus sequence typing allowed the detection of five E. bugandensis phylogroups (PG-A to E), which contain important antimicrobial resistance and virulence determinants. We uncovered several extended-spectrum β-lactamases, including blaCTX-M-55 and blaNDM-5, present in an IncX replicon type plasmid, described here for the first time in E. bugandensis. Genetic context analysis of blaNDM-5 revealed the resemblance of this plasmid with other IncX plasmids from other bacteria from the same country. Three distinctive siderophore producing operons were found in E. bugandensis: enterobactin (ent), aerobactin (iuc/iut), and salmochelin (iro). Our findings provide novel insights on the lifestyle, physiology, antimicrobial, and virulence profiles of E. bugandensis.
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Affiliation(s)
- Filipe P Matteoli
- Laboratório de Química e Função de Proteínas e Peptídeos, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Brazil
| | - Hemanoel Passarelli-Araujo
- Laboratório de Química e Função de Proteínas e Peptídeos, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Brazil; Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Francisnei Pedrosa-Silva
- Laboratório de Química e Função de Proteínas e Peptídeos, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Brazil
| | - Fabio L Olivares
- Núcleo de Desenvolvimento de Insumos Biológicos para a Agricultura (NUDIBA), UENF, Brazil; Laboratório de Biologia Celular e Tecidual, Centro de Biociências e Biotecnologia, UENF, Brazil
| | - Thiago M Venancio
- Laboratório de Química e Função de Proteínas e Peptídeos, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Brazil.
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