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Batantou Mabandza D, Colletin E, Dagot C, Quétel I, Breurec S, Guyomard-Rabenirina S. Do Microorganisms in Bathing Water in Guadeloupe (French West Indies) Have Resistance Genes? Antibiotics (Basel) 2024; 13:87. [PMID: 38247646 PMCID: PMC10812525 DOI: 10.3390/antibiotics13010087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 01/05/2024] [Accepted: 01/11/2024] [Indexed: 01/23/2024] Open
Abstract
Waterborne faecal contamination is a major public health concern. The main objectives of this study were to investigate faecal contamination and Escherichia coli (E. coli) antibiotic resistance in recreational fresh water from Guadeloupe and to characterise the microbiome and resistome composition in biofilms from submerged rocks. Significant faecal contamination was observed at 14 freshwater sites. E. coli predominated (62%), followed by Enterobacter cloacae (11%) and Acinetobacter spp. (11%). Of 152 E. coli isolated, none produced extended-spectrum beta-lactamases (ESBLs), but 7% showed resistance to streptomycin and 4% to tetracycline. Biofilm resistome analysis revealed clinically significant antibiotic-resistance genes (ARGs), including those coding for resistance to sulfonamides (sul1), carbapenems (blaKPC), and third-generation cephalosporins (blaCTX-M). Mobile genetic elements (MGEs) (intI1, intI2, intI3) linked to resistance to aminoglycosides, beta-lactams, tetracycline, as well as heavy metal resistance determinants (copA, cusF, czcA, merA) conferring resistance to copper, silver, cadmium, and mercury were also detected. Diverse bacterial phyla were found in biofilm samples, of which Proteobacteria, Bacteroidetes, Planctonomycetes, and Cyanobacteria were predominant. Despite the frequent presence of E. coli exceeding regulatory standards, the low levels of antibiotic-resistant bacteria in freshwater and of ARGs and MGEs in associated biofilms suggest limited antibiotic resistance in Guadeloupean recreational waters.
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Affiliation(s)
- Degrâce Batantou Mabandza
- Transmission, Reservoir and Diversity of Pathogens Unit, Pasteur Institute of Guadeloupe, 97110 Pointe-à-Pitre, France
| | - Edlyne Colletin
- Transmission, Reservoir and Diversity of Pathogens Unit, Pasteur Institute of Guadeloupe, 97110 Pointe-à-Pitre, France
| | - Christophe Dagot
- University of Limoges, INSERM, CHU Limoges, RESINFIT, U1092, 87000 Limoges, France
| | - Isaure Quétel
- Transmission, Reservoir and Diversity of Pathogens Unit, Pasteur Institute of Guadeloupe, 97110 Pointe-à-Pitre, France
| | - Sébastien Breurec
- Transmission, Reservoir and Diversity of Pathogens Unit, Pasteur Institute of Guadeloupe, 97110 Pointe-à-Pitre, France
- Faculty of Medicine Hyacinthe Bastaraud, University of the Antilles, 97110 Pointe-à-Pitre, France
- INSERM, Centre for Clinical Investigation 1424, 97110 Pointe-à-Pitre, France
- Department of Pathogenesis and Control of Chronic and Emerging Infections, University of Montpellier, INSERM, 34394 Montpellier, France
- Laboratory of Clinical Microbiology, University Hospital Centre of Guadeloupe, 971110 Pointe-à-Pitre, France
| | - Stéphanie Guyomard-Rabenirina
- Transmission, Reservoir and Diversity of Pathogens Unit, Pasteur Institute of Guadeloupe, 97110 Pointe-à-Pitre, France
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Delumeau A, Quétel I, Harnais F, Sellin A, Gros O, Talarmin A, Marcelino I. Bacterial microbiota management in free-living amoebae (Heterolobosea lineage) isolated from water: The impact of amoebae identity, grazing conditions, and passage number. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 900:165816. [PMID: 37506913 DOI: 10.1016/j.scitotenv.2023.165816] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 07/24/2023] [Accepted: 07/24/2023] [Indexed: 07/30/2023]
Abstract
Free-living amoebae (FLA) are ubiquitous protozoa mainly found in aquatic environments. They are well-known reservoirs and vectors for the transmission of amoeba-resistant bacteria (ARB), most of which are pathogenic to humans. Yet, the natural bacterial microbiota associated with FLA remains largely unknown. Herein, we characterized the natural bacterial microbiota of different FLA species isolated from recreational waters in Guadeloupe. Monoxenic cultures of Naegleria australiensis, Naegleria sp. WTP3, Paravahlkampfia ustiana and Vahlkampfia sp. AK-2007 (Heterolobosea lineage) were cultivated under different grazing conditions, during successive passages. The whole bacterial microbiota of the waters and the amoebal cysts was characterized using 16S rRNA gene metabarcoding. The culturable subset of ARB was analyzed by mass spectrometry (MALDI-TOF MS), conventional 16S PCR, and disk diffusion method (to assess bacterial antibiotic resistance). Transmission electron microscopy was used to locate the ARB inside the amoebae. According to alpha and beta-diversity analyses, FLA bacterial microbiota were significantly different from the ones of their habitat. While Vogesella and Aquabacterium genera were detected in water, the most common ARB belonged to Pseudomonas, Bosea, and Escherichia/Shigella genera. The different FLA species showed both temporary and permanent associations with differentially bacterial taxa, suggesting host specificity. These associations depend on the number of passages and grazing conditions. Additionally, Naegleria, Vahlkampfia and Paravahlkampfia cysts were shown to naturally harbor viable bacteria of the Acinetobacter, Escherichia, Enterobacter, Pseudomonas and Microbacterium genera, all being pathogenic to humans. To our knowledge, this is the first time Paravahlkampfia and Vahlkampfia have been demonstrated as hosts of pathogenic ARB in water. Globally, the persistence of these ARB inside resistant cysts represents a potential health risk. To ensure the continued safety of recreational waters, it is crucial to (i) regularly control both the amoebae and their ARB and (ii) improve knowledge on amoebae-bacteria interactions to establish better water management protocols.
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Affiliation(s)
- Aurélie Delumeau
- Institut Pasteur de la Guadeloupe, Unité TReD-Path, Les Abymes, Guadeloupe, France
| | - Isaure Quétel
- Institut Pasteur de la Guadeloupe, Unité TReD-Path, Les Abymes, Guadeloupe, France
| | - Florian Harnais
- Institut Pasteur de la Guadeloupe, Unité TReD-Path, Les Abymes, Guadeloupe, France
| | - Arantxa Sellin
- Institut Pasteur de la Guadeloupe, Unité TReD-Path, Les Abymes, Guadeloupe, France
| | - Olivier Gros
- Institut de Systématique, Évolution, Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, Pointe-à-Pitre, Guadeloupe, France
| | - Antoine Talarmin
- Institut Pasteur de la Guadeloupe, Unité TReD-Path, Les Abymes, Guadeloupe, France
| | - Isabel Marcelino
- Institut Pasteur de la Guadeloupe, Unité TReD-Path, Les Abymes, Guadeloupe, France.
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Alghamdi M, Al-Judaibi E, Al-Rashede M, Al-Judaibi A. Comparative De Novo and Pan-Genome Analysis of MDR Nosocomial Bacteria Isolated from Hospitals in Jeddah, Saudi Arabia. Microorganisms 2023; 11:2432. [PMID: 37894090 PMCID: PMC10609288 DOI: 10.3390/microorganisms11102432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 09/14/2023] [Accepted: 09/26/2023] [Indexed: 10/29/2023] Open
Abstract
Multidrug-resistant (MDR) bacteria are one of the most serious threats to public health, and one of the most important types of MDR bacteria are those that are acquired in a hospital, known as nosocomial. This study aimed to isolate and identify MDR bacteria from selected hospitals in Jeddah and analyze their antibiotic-resistant genes. Bacteria were collected from different sources and wards of hospitals in Jeddah City. Phoenix BD was used to identify the strains and perform susceptibility testing. Identification of selected isolates showing MDR to more than three classes on antibiotics was based on 16S rRNA gene and whole genome sequencing. Genes conferring resistance were characterized using de novo and pan-genome analyses. In total, we isolated 108 bacterial strains, of which 75 (69.44%) were found to be MDR. Taxonomic identification revealed that 24 (32%) isolates were identified as Escherichia coli, 19 (25.3%) corresponded to Klebsiella pneumoniae, and 17 (22.67%) were methicillin-resistant Staphylococcus aureus (MRSA). Among the Gram-negative bacteria, K. pneumoniae isolates showed the highest resistance levels to most antibiotics. Of the Gram-positive bacteria, S. aureus (MRSA) strains were noticed to exhibit the uppermost degree of resistance to the tested antibiotics, which is higher than that observed for K. pneumoniae isolates. Taken together, our results illustrated that MDR Gram-negative bacteria are the most common cause of nosocomial infections, while MDR Gram-positive bacteria are characterized by a wider antibiotic resistance spectrum. Whole genome sequencing found the appearance of antibiotic resistance genes, including SHV, OXA, CTX-M, TEM-1, NDM-1, VIM-1, ere(A), ermA, ermB, ermC, msrA, qacA, qacB, and qacC.
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Affiliation(s)
- Molook Alghamdi
- Department of Biological Sciences, Microbiology Section, Faculty of Science, Jeddah University, Jeddah 21959, Saudi Arabia; (M.A.); (E.A.-J.)
| | - Effat Al-Judaibi
- Department of Biological Sciences, Microbiology Section, Faculty of Science, Jeddah University, Jeddah 21959, Saudi Arabia; (M.A.); (E.A.-J.)
| | | | - Awatif Al-Judaibi
- Department of Biological Sciences, Microbiology Section, Faculty of Science, Jeddah University, Jeddah 21959, Saudi Arabia; (M.A.); (E.A.-J.)
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Pot M, Ducat C, Reynaud Y, Couvin D, Ferdinand S, Breurec S, Talarmin A, Guyomard-Rabenirina S. Draft genome sequence of Enterobacter chengduensis ECC445, isolated from fresh water in the West Indies. BMC Genom Data 2023; 24:16. [PMID: 36906565 PMCID: PMC10007730 DOI: 10.1186/s12863-023-01116-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 02/21/2023] [Indexed: 03/13/2023] Open
Abstract
OBJECTIVES The Enterobacter cloacae complex is considered an important opportunistic pathogen. It comprises many members that remain difficult to delineate by phenotypic approaches. Despite its importance in human infection, there is a lack of information on associated members in other compartments. Here we report the first de novo assembled and annotated whole-genome sequence of a E. chengduensis strain isolated from the environment. DATA DESCRIPTION ECC445 specimen was isolated in 2018 from a drinking water catchment point in Guadeloupe. It was clearly related to E. chengduensis species according to hsp60 typing and genomic comparison. Its whole-genome sequence is 5,211,280-bp long divided into 68 contigs, and presents a G + C content of 55.78%. This genome and associated datasets provided here will serve as a useful resource for further analyses of this rarely reported Enterobacter species.
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Affiliation(s)
- Matthieu Pot
- Transmission, Reservoir and Diversity of Pathogens Unit, Pasteur Institute of Guadeloupe, Pointe-À-Pitre, France
| | - Célia Ducat
- Transmission, Reservoir and Diversity of Pathogens Unit, Pasteur Institute of Guadeloupe, Pointe-À-Pitre, France
| | - Yann Reynaud
- Transmission, Reservoir and Diversity of Pathogens Unit, Pasteur Institute of Guadeloupe, Pointe-À-Pitre, France
| | - David Couvin
- Transmission, Reservoir and Diversity of Pathogens Unit, Pasteur Institute of Guadeloupe, Pointe-À-Pitre, France
| | - Séverine Ferdinand
- Transmission, Reservoir and Diversity of Pathogens Unit, Pasteur Institute of Guadeloupe, Pointe-À-Pitre, France
| | - Sébastien Breurec
- Transmission, Reservoir and Diversity of Pathogens Unit, Pasteur Institute of Guadeloupe, Pointe-À-Pitre, France
- Faculty of Medicine Hyacinthe Bastaraud, University of the Antilles, Pointe-À-Pitre, France
- grid.7429.80000000121866389Centre for Clinical Investigation 1424, INSERM, Pointe-À-Pitre/Les Abymes, France
- Laboratory of Clinical Microbiology, University Hospital Centre of Guadeloupe, Pointe-À-Pitre/Les Abymes, France
| | - Antoine Talarmin
- Transmission, Reservoir and Diversity of Pathogens Unit, Pasteur Institute of Guadeloupe, Pointe-À-Pitre, France
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Dereeper A, Gruel G, Pot M, Couvin D, Barbier E, Bastian S, Bambou JC, Gelu-Simeon M, Ferdinand S, Guyomard-Rabenirina S, Passet V, Martino F, Piveteau P, Reynaud Y, Rodrigues C, Roger PM, Roy X, Talarmin A, Tressieres B, Valette M, Brisse S, Breurec S. Limited Transmission of Klebsiella pneumoniae among Humans, Animals, and the Environment in a Caribbean Island, Guadeloupe (French West Indies). Microbiol Spectr 2022; 10:e0124222. [PMID: 36094181 PMCID: PMC9603589 DOI: 10.1128/spectrum.01242-22] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2022] [Accepted: 08/08/2022] [Indexed: 12/30/2022] Open
Abstract
Guadeloupe (French West Indies), a Caribbean island, is an ideal place to study the reservoirs of the Klebsiella pneumoniae species complex (KpSC) and identify the routes of transmission between human and nonhuman sources due to its insularity, small population size, and small area. Here, we report an analysis of 590 biological samples, 546 KpSC isolates, and 331 genome sequences collected between January 2018 and May 2019. The KpSC appears to be common whatever the source. Extended-spectrum-β-lactamase (ESBL)-producing isolates (21.4%) belonged to K. pneumoniae sensu stricto (phylogroup Kp1), and all but one were recovered from the hospital setting. The distribution of species and phylogroups across the different niches was clearly nonrandom, with a distinct separation of Kp1 and Klebsiella variicola (Kp3). The most frequent sequence types (STs) (≥5 isolates) were previously recognized as high-risk multidrug-resistant (MDR) clones, namely, ST17, ST307, ST11, ST147, ST152, and ST45. Only 8 out of the 63 STs (12.7%) associated with human isolates were also found in nonhuman sources. A total of 22 KpSC isolates were defined as hypervirulent: 15 associated with human infections (9.8% of all human isolates), 4 (8.9%) associated with dogs, and 3 (15%) associated with pigs. Most of the human isolates (33.3%) belonged to the globally successful sublineage CG23-I. ST86 was the only clone shared by a human and a nonhuman (dog) source. Our work shows the limited transmission of KpSC isolates between human and nonhuman sources and points to the hospital setting as a cornerstone of the spread of MDR clones and antibiotic resistance genes. IMPORTANCE In this study, we characterized the presence and genomic features of isolates of the Klebsiella pneumoniae species complex (KpSC) from human and nonhuman sources in Guadeloupe (French West Indies) in order to identify the reservoirs and routes of transmission. This is the first study in an island environment, an ideal setting that limits the contribution of external imports. Our data showed the limited transmission of KpSC isolates between the different compartments. In contrast, we identified the hospital setting as the epicenter of antibiotic resistance due to the nosocomial spread of successful multidrug-resistant (MDR) K. pneumoniae clones and antibiotic resistance genes. Ecological barriers and/or limited exposure may restrict spread from the hospital setting to other reservoirs and vice versa. These results highlight the need for control strategies focused on health care centers, using genomic surveillance to limit the spread, particularly of high-risk clones, of this important group of MDR pathogens.
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Affiliation(s)
- Alexis Dereeper
- Transmission, Reservoir and Diversity of Pathogens Unit, Pasteur Institute of Guadeloupe, Pointe-à-Pitre, France
| | - Gaëlle Gruel
- Transmission, Reservoir and Diversity of Pathogens Unit, Pasteur Institute of Guadeloupe, Pointe-à-Pitre, France
| | - Matthieu Pot
- Transmission, Reservoir and Diversity of Pathogens Unit, Pasteur Institute of Guadeloupe, Pointe-à-Pitre, France
| | - David Couvin
- Transmission, Reservoir and Diversity of Pathogens Unit, Pasteur Institute of Guadeloupe, Pointe-à-Pitre, France
| | - Elodie Barbier
- UMR AgroEcologie, INRAE, Bourgogne Franche-Comté University, Dijon, France
| | - Sylvaine Bastian
- Laboratory of Clinical Microbiology, University Hospital Center of Guadeloupe, Pointe-à-Pitre/Les Abymes, France
| | | | - Moana Gelu-Simeon
- Hepato-Gastroenterology Department, University Hospital Center of Guadeloupe, Pointe-à-Pitre/Les Abymes, France
| | - Séverine Ferdinand
- Transmission, Reservoir and Diversity of Pathogens Unit, Pasteur Institute of Guadeloupe, Pointe-à-Pitre, France
| | | | - Virginie Passet
- Institut Pasteur, University Paris Cité, Biodiversity and Epidemiology of Bacterial Pathogens, Paris, France
| | - Frederic Martino
- Intensive Care Department, University Hospital Center of Guadeloupe, Pointe-à-Pitre/Les Abymes, France
| | | | - Yann Reynaud
- Transmission, Reservoir and Diversity of Pathogens Unit, Pasteur Institute of Guadeloupe, Pointe-à-Pitre, France
| | - Carla Rodrigues
- Institut Pasteur, University Paris Cité, Biodiversity and Epidemiology of Bacterial Pathogens, Paris, France
| | - Pierre-Marie Roger
- Infectious Disease Department, University Hospital Center of Guadeloupe, Pointe-à-Pitre/Les Abymes, France
- Faculty of Medecine Hyacinthe Bastaraud, University of the Antilles, Pointe-à-Pitre, France
| | - Xavier Roy
- Veterinary Clinic, Baie-Mahault, Guadeloupe
| | - Antoine Talarmin
- Transmission, Reservoir and Diversity of Pathogens Unit, Pasteur Institute of Guadeloupe, Pointe-à-Pitre, France
| | - Benoit Tressieres
- INSERM Center for Clinical Investigation 1424, Pointe-à-Pitre/Les Abymes, France
| | - Marc Valette
- Intensive Care Department, University Hospital Center of Guadeloupe, Pointe-à-Pitre/Les Abymes, France
| | - Sylvain Brisse
- Institut Pasteur, University Paris Cité, Biodiversity and Epidemiology of Bacterial Pathogens, Paris, France
| | - Sébastien Breurec
- Transmission, Reservoir and Diversity of Pathogens Unit, Pasteur Institute of Guadeloupe, Pointe-à-Pitre, France
- Laboratory of Clinical Microbiology, University Hospital Center of Guadeloupe, Pointe-à-Pitre/Les Abymes, France
- Faculty of Medecine Hyacinthe Bastaraud, University of the Antilles, Pointe-à-Pitre, France
- INSERM Center for Clinical Investigation 1424, Pointe-à-Pitre/Les Abymes, France
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Pot M, Reynaud Y, Couvin D, Dereeper A, Ferdinand S, Bastian S, Foucan T, Pommier JD, Valette M, Talarmin A, Guyomard-Rabenirina S, Breurec S. Emergence of a Novel Lineage and Wide Spread of a blaCTX-M-15/IncHI2/ST1 Plasmid among Nosocomial Enterobacter in Guadeloupe. Antibiotics (Basel) 2022; 11:1443. [PMID: 36290101 PMCID: PMC9598596 DOI: 10.3390/antibiotics11101443] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 10/10/2022] [Accepted: 10/17/2022] [Indexed: 04/04/2024] Open
Abstract
Between April 2018 and August 2019, a total of 135 strains of Enterobacter cloacae complex (ECC) were randomly collected at the University Hospital Center of Guadeloupe to investigate the structure and diversity of the local bacterial population. These nosocomial isolates were initially identified genetically by the hsp60 typing method, which revealed the clinical relevance of E. xiangfangensis (n = 69). Overall, 57/94 of the third cephalosporin-resistant strains were characterized as extended-spectrum-β-lactamase (ESBL) producers, and their whole-genome was sequenced using Illumina technology to determine the clonal relatedness and diffusion of resistance genes. We found limited genetic diversity among sequence types (STs). ST114 (n = 13), ST1503 (n = 9), ST53 (n = 5) and ST113 (n = 4), which belong to three different Enterobacter species, were the most prevalent among the 57 ESBL producers. The blaCTXM-15 gene was the most prevalent ESBL determinant (56/57) and was in most cases associated with IncHI2/ST1 plasmid replicon carriage (36/57). To fully characterize this predominant blaCTXM-15/IncHI2/ST1 plasmid, four isolates from different lineages were also sequenced using Oxford Nanopore sequencing technology to generate long-reads. Hybrid sequence analyses confirmed the circulation of a well-conserved plasmid among ECC members. In addition, the novel ST1503 and its associated species (ECC taxon 4) were analyzed, in view of its high prevalence in nosocomial infections. These genetic observations confirmed the overall incidence of nosocomial ESBL Enterobacteriaceae infections acquired in this hospital during the study period, which was clearly higher in Guadeloupe (1.59/1000 hospitalization days) than in mainland France (0.52/1,000 hospitalization days). This project revealed issues and future challenges for the management and surveillance of nosocomial and multidrug-resistant Enterobacter in the Caribbean.
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Affiliation(s)
- Matthieu Pot
- Transmission, Reservoir and Diversity of Pathogens Unit, Pasteur Institute of Guadeloupe, 97139 Les Abymes, France
| | - Yann Reynaud
- Transmission, Reservoir and Diversity of Pathogens Unit, Pasteur Institute of Guadeloupe, 97139 Les Abymes, France
| | - David Couvin
- Transmission, Reservoir and Diversity of Pathogens Unit, Pasteur Institute of Guadeloupe, 97139 Les Abymes, France
| | - Alexis Dereeper
- Transmission, Reservoir and Diversity of Pathogens Unit, Pasteur Institute of Guadeloupe, 97139 Les Abymes, France
| | - Séverine Ferdinand
- Transmission, Reservoir and Diversity of Pathogens Unit, Pasteur Institute of Guadeloupe, 97139 Les Abymes, France
| | - Sylvaine Bastian
- Laboratory of Clinical Microbiology, University Hospital Center of Guadeloupe, 97159 Pointe-à-Pitre, France
| | - Tania Foucan
- Operational Hygiene Team, University Hospital Center of Guadeloupe, 97159 Pointe-à-Pitre, France
| | - Jean-David Pommier
- Division of Intensive Care, University Hospital Center of Guadeloupe, 97159 Pointe-à-Pitre, France
| | - Marc Valette
- Division of Intensive Care, University Hospital Center of Guadeloupe, 97159 Pointe-à-Pitre, France
| | - Antoine Talarmin
- Transmission, Reservoir and Diversity of Pathogens Unit, Pasteur Institute of Guadeloupe, 97139 Les Abymes, France
| | | | - Sébastien Breurec
- Transmission, Reservoir and Diversity of Pathogens Unit, Pasteur Institute of Guadeloupe, 97139 Les Abymes, France
- Faculty of Medicine Hyacinthe Bastaraud, University of the Antilles, 97157 Pointe-à-Pitre, France
- INSERM, Center for Clinical Investigation 1424, 97139 Les Abymes, France
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Kashkouri N, Tabarsi P, Pourabdollah Toutkaboni M, Kazempour Dizaji M, Bahrami N, Narimani A, Mohamadnia A, Askari E. The Prevalence of Carbapenemase Genes in Carbapenem-resistant Gram-negative Bacilli, Masih Daneshvari Hospital, Tehran, Iran, 2019-2020. IRANIAN JOURNAL OF MEDICAL MICROBIOLOGY 2022. [DOI: 10.30699/ijmm.16.6.573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Chang CY, Huang PH, Lu PL. The Resistance Mechanisms and Clinical Impact of Resistance to the Third Generation Cephalosporins in Species of Enterobacter cloacae Complex in Taiwan. Antibiotics (Basel) 2022; 11:antibiotics11091153. [PMID: 36139933 PMCID: PMC9494969 DOI: 10.3390/antibiotics11091153] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Revised: 08/21/2022] [Accepted: 08/25/2022] [Indexed: 11/16/2022] Open
Abstract
Enterobacter cloacae complex (ECC) is ubiquitous in the environment and is an important pathogen causing nosocomial infections. Because routine methods used in clinical laboratories cannot identify species within ECC, the clinical significance of each species within ECC is less known. We applied hsp60 gene sequencing to identify the species/clusters of ECC and detected β-lactamase genes and class 1 integrons with PCR for 184 clinical ECC isolates in Taiwan from 2013 to 2014 to investigate the clinical impact of species within ECC. The four most common clusters were E. hormaechei subsp. steigerwaltii (cluster VIII) (29.9%), E. hormaechei subsp. oharae (cluster VI) (20.1%), E. cloacae subsp. cloacae (cluster XI) (12%), and E. kobei (cluster II) (10.3%). E. hormaechei, which consisted of four clusters (clusters III, VI, VII, and VIII), is the predominant species and accounted for 57.1% of the isolates. The ceftazidime resistance rate was 27.2%, and the ceftriaxone resistance rate was 29.3%. Resistance to third generation cephalosporin was associated with a higher 30-day mortality rate. In total, 5 (2.7%), 24 (13.0%), and 1 (0.5%) isolates carried ESBL, AmpC, and carbapenemase genes, respectively. Class 1 integrons were present in 24.5% of the isolates, and most of the cassettes pertain to antibiotic resistance. Resistance to third generation cephalosporins, multidrug resistance, and class 1 integrons were significantly more in E. hormaechei (clusters III, VI, VII, and VIII) than in the other species. The 30-day mortality rate and 100-day mortality did not differ significantly between patients with E. hormaechei and those with infections with the other species. In conclusion, the distribution of third generation cephalosporin resistance, multidrug resistance, and class 1 integrons were uneven among Enterobacter species. The resistance to third generation cephalosporins possessed significant impact on patient outcome.
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Affiliation(s)
- Chung-Yu Chang
- School of Post-Baccalaureate Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
- Department of Microbiology and Immunology, School of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
- Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
| | - Po-Hao Huang
- Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
| | - Po-Liang Lu
- School of Post-Baccalaureate Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
- Division of Infectious Diseases, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
- Center for Liquid Biopsy and Cohort Research, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
- Department of Biological Science and Technology, College of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu 30068, Taiwan
- M.Sc. Program in Tropical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
- Correspondence: ; Tel.: +886-7-3121101 (ext. 5675)
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Wei X, Wang W, Lu N, Wu L, Dong Z, Li B, Zhou X, Cheng F, Zhou K, Cheng H, Shi H, Zhang J. Prevalence of Multidrug-Resistant CTX-M Extended Spectrum Beta-Lactamase-Producing Escherichia coli From Different Bovine Faeces in China. Front Vet Sci 2022; 9:738904. [PMID: 35978707 PMCID: PMC9376260 DOI: 10.3389/fvets.2022.738904] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 05/19/2022] [Indexed: 01/24/2023] Open
Abstract
CTX-M extended spectrum beta-lactamase-producing Escherichia coli cause severe health hazards in livestock breeding. To date, little is known about antibiotic resistance differences among bacterial isolates from yaks, cows, and beef cattle; therefore, the aims of this study were to analyse the prevalence of CTX-M-producing E. coli in yak, beef cattle, and dairy cattle feces from different provinces in China. A total of 790 fecal samples from yaks, beef cattle, and dairy cows were used. Among all the samples, 523 non duplicate E. coli isolates were identified, and 29.6% of samples harbored CTX-M producers. The results showed that these E. coli strains harbored 15 clusters of CTX-M genes: CTX-M-79, CTX-M-55, CTX-M-15, CTX-M-14, CTX-M-28, CTX-M-179, CTX-M-65, CTX-M-24, CTX-M-27, CTX-M-102, CTX-M-105, CTX-M-173, CTX-M-238, CTX-M-196, and CTX-M-10. The dominant resistance genes were CTX-M-15, CTX-M-14, and CTX-M-55. Moreover, the distribution of CTX-M genes was related to geographical region. Based on the above findings, we reasoned that bovines are potential reservoirs of antibiotic resistance, and this problem should be given adequate attention.
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Affiliation(s)
- Xiaojuan Wei
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Science (CAAS), Lanzhou, China,Key Laboratory of New Animal Drug Project of Gansu Province, Lanzhou, China,Key Laboratory of Veterinary Pharmaceutical Development, Ministry of Agriculture, Lanzhou, China
| | - Weiwei Wang
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Science (CAAS), Lanzhou, China,Key Laboratory of New Animal Drug Project of Gansu Province, Lanzhou, China,Key Laboratory of Veterinary Pharmaceutical Development, Ministry of Agriculture, Lanzhou, China
| | - Ningning Lu
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Science (CAAS), Lanzhou, China,Key Laboratory of New Animal Drug Project of Gansu Province, Lanzhou, China,Key Laboratory of Veterinary Pharmaceutical Development, Ministry of Agriculture, Lanzhou, China
| | - Lingyu Wu
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Science (CAAS), Lanzhou, China,Key Laboratory of New Animal Drug Project of Gansu Province, Lanzhou, China,Key Laboratory of Veterinary Pharmaceutical Development, Ministry of Agriculture, Lanzhou, China
| | - Zhen Dong
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Science (CAAS), Lanzhou, China,Key Laboratory of New Animal Drug Project of Gansu Province, Lanzhou, China,Key Laboratory of Veterinary Pharmaceutical Development, Ministry of Agriculture, Lanzhou, China
| | - Bing Li
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Science (CAAS), Lanzhou, China,Key Laboratory of New Animal Drug Project of Gansu Province, Lanzhou, China,Key Laboratory of Veterinary Pharmaceutical Development, Ministry of Agriculture, Lanzhou, China
| | - Xuzheng Zhou
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Science (CAAS), Lanzhou, China,Key Laboratory of New Animal Drug Project of Gansu Province, Lanzhou, China,Key Laboratory of Veterinary Pharmaceutical Development, Ministry of Agriculture, Lanzhou, China
| | - Fusheng Cheng
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Science (CAAS), Lanzhou, China,Key Laboratory of New Animal Drug Project of Gansu Province, Lanzhou, China,Key Laboratory of Veterinary Pharmaceutical Development, Ministry of Agriculture, Lanzhou, China
| | - Kairen Zhou
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Science (CAAS), Lanzhou, China,Key Laboratory of New Animal Drug Project of Gansu Province, Lanzhou, China,Key Laboratory of Veterinary Pharmaceutical Development, Ministry of Agriculture, Lanzhou, China
| | - Haijian Cheng
- Shandong Institute of Animal Science and Veterinary Medicine, Jinan, China
| | - Hongmei Shi
- Gannan Tibetan Autonomous Prefecture Institute of Animal Husbandry Science, Gannan, China
| | - Jiyu Zhang
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Science (CAAS), Lanzhou, China,Key Laboratory of New Animal Drug Project of Gansu Province, Lanzhou, China,Key Laboratory of Veterinary Pharmaceutical Development, Ministry of Agriculture, Lanzhou, China,*Correspondence: Jiyu Zhang
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10
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Couvin D, Dereeper A, Meyer DF, Noroy C, Gaete S, Bhakkan B, Poullet N, Gaspard S, Bezault E, Marcelino I, Pruneau L, Segretier W, Stattner E, Cazenave D, Garnier M, Pot M, Tressières B, Deloumeaux J, Breurec S, Ferdinand S, Gonzalez-Rizzo S, Reynaud Y. KaruBioNet: a network and discussion group for a better collaboration and structuring of bioinformatics in Guadeloupe (French West Indies). BIOINFORMATICS ADVANCES 2022; 2:vbac010. [PMID: 36699379 PMCID: PMC9710593 DOI: 10.1093/bioadv/vbac010] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 01/24/2022] [Accepted: 02/09/2022] [Indexed: 01/28/2023]
Abstract
Summary Sequencing and other biological data are now more frequently available and at a lower price. Mutual tools and strategies are needed to analyze the huge amount of heterogeneous data generated by several research teams and devices. Bioinformatics represents a growing field in the scientific community globally. This multidisciplinary field provides a great amount of tools and methods that can be used to conduct scientific studies in a more strategic way. Coordinated actions and collaborations are needed to find more innovative and accurate methods for a better understanding of real-life data. A wide variety of organizations are contributing to KaruBioNet in Guadeloupe (French West Indies), a Caribbean archipelago. The purpose of this group is to foster collaboration and mutual aid among people from different disciplines using a 'one health' approach, for a better comprehension and surveillance of humans, plants or animals' health and diseases. The KaruBioNet network particularly aims to help researchers in their studies related to 'omics' data, but also more general aspects concerning biological data analysis. This transdisciplinary network is a platform for discussion, sharing, training and support between scientists interested in bioinformatics and related fields. Starting from a little archipelago in the Caribbean, we envision to facilitate exchange between other Caribbean partners in the future, knowing that the Caribbean is a region with non-negligible biodiversity which should be preserved and protected. Joining forces with other Caribbean countries or territories would strengthen scientific collaborative impact in the region. Information related to this network can be found at: http://www.pasteur-guadeloupe.fr/karubionet.html. Furthermore, a dedicated 'Galaxy KaruBioNet' platform is available at: http://calamar.univ-ag.fr/c3i/galaxy_karubionet.html. Availability and implementation Information about KaruBioNet is availabe at: http://www.pasteur-guadeloupe.fr/karubionet.html. Contact dcouvin@pasteur-guadeloupe.fr. Supplementary information Supplementary data are available at Bioinformatics Advances online.
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Affiliation(s)
- David Couvin
- Unité Transmission, Réservoir et Diversité des Pathogènes, Institut Pasteur de Guadeloupe, Les Abymes, Guadeloupe 97139, France,To whom correspondence should be addressed
| | - Alexis Dereeper
- Unité Transmission, Réservoir et Diversité des Pathogènes, Institut Pasteur de Guadeloupe, Les Abymes, Guadeloupe 97139, France
| | - Damien F Meyer
- CIRAD, UMR ASTRE, Petit-Bourg, Guadeloupe 97170, France,ASTRE, Univ Montpellier, CIRAD, INRAE, Montpellier 34000, France
| | - Christophe Noroy
- Développement, Analyse, Transfert et Application (DATA), Lamentin, Guadeloupe 97129, France
| | - Stanie Gaete
- Karubiotec Centre de Ressources Biologiques-UF 0216, CHU de la Guadeloupe, Pointe-à-Pitre 97110, France
| | - Bernard Bhakkan
- Registre des cancers de Guadeloupe, CHU de la Guadeloupe, Pointe-à-Pitre 97110, France
| | - Nausicaa Poullet
- URZ Recherches Zootechniques, INRAE, Petit-Bourg, Guadeloupe 97170, France
| | - Sarra Gaspard
- Laboratoire COVACHIMM2E EA3592, Université des Antilles, Pointe-à-Pitre, Guadeloupe 97110, France
| | - Etienne Bezault
- UMR BOREA (MNHN, CNRS-7208, IRD-207, Sorbonne Université, UCN, UA), Université des Antilles, Pointe-à-Pitre, Guadeloupe 97110, France
| | - Isabel Marcelino
- Unité Transmission, Réservoir et Diversité des Pathogènes, Institut Pasteur de Guadeloupe, Les Abymes, Guadeloupe 97139, France
| | - Ludovic Pruneau
- Équipe « Biologie de la mangrove » UMR7205 « ISYEB » MNHN-CNRS-Sorbonne Université-EPHE-UA, UFR SEN Département de Biologie, Université des Antilles, Pointe-à-Pitre, Guadeloupe 97110, France
| | - Wilfried Segretier
- Laboratoire de Mathématiques Informatique et Applications (LAMIA), Université des Antilles, Pointe-à-Pitre, Guadeloupe 97110, France
| | - Erick Stattner
- Laboratoire de Mathématiques Informatique et Applications (LAMIA), Université des Antilles, Pointe-à-Pitre, Guadeloupe 97110, France
| | - Damien Cazenave
- Unité Transmission, Réservoir et Diversité des Pathogènes, Institut Pasteur de Guadeloupe, Les Abymes, Guadeloupe 97139, France
| | - Maëlle Garnier
- Unité Transmission, Réservoir et Diversité des Pathogènes, Institut Pasteur de Guadeloupe, Les Abymes, Guadeloupe 97139, France
| | - Matthieu Pot
- Unité Transmission, Réservoir et Diversité des Pathogènes, Institut Pasteur de Guadeloupe, Les Abymes, Guadeloupe 97139, France
| | - Benoît Tressières
- Centre d’Investigation Clinique Antilles Guyane, Inserm CIC 1424, Les Abymes, Pointe-à-Pitre, Guadeloupe 97110, France
| | - Jacqueline Deloumeaux
- Karubiotec Centre de Ressources Biologiques-UF 0216, CHU de la Guadeloupe, Pointe-à-Pitre 97110, France,Registre des cancers de Guadeloupe, CHU de la Guadeloupe, Pointe-à-Pitre 97110, France
| | - Sébastien Breurec
- Unité Transmission, Réservoir et Diversité des Pathogènes, Institut Pasteur de Guadeloupe, Les Abymes, Guadeloupe 97139, France,Centre d’Investigation Clinique Antilles Guyane, Inserm CIC 1424, Les Abymes, Pointe-à-Pitre, Guadeloupe 97110, France,Faculté de Médecine Hyacinthe Bastaraud, Université des Antilles, Pointe-à-Pitre, Guadeloupe 97110, France
| | - Séverine Ferdinand
- Unité Transmission, Réservoir et Diversité des Pathogènes, Institut Pasteur de Guadeloupe, Les Abymes, Guadeloupe 97139, France
| | - Silvina Gonzalez-Rizzo
- Équipe « Biologie de la mangrove » UMR7205 « ISYEB » MNHN-CNRS-Sorbonne Université-EPHE-UA, UFR SEN Département de Biologie, Université des Antilles, Pointe-à-Pitre, Guadeloupe 97110, France
| | - Yann Reynaud
- Unité Transmission, Réservoir et Diversité des Pathogènes, Institut Pasteur de Guadeloupe, Les Abymes, Guadeloupe 97139, France
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Liu S, Huang N, Zhou C, Lin Y, Zhang Y, Wang L, Zheng X, Zhou T, Wang Z. Molecular Mechanisms and Epidemiology of Carbapenem-Resistant Enterobacter cloacae Complex Isolated from Chinese Patients During 2004-2018. Infect Drug Resist 2021; 14:3647-3658. [PMID: 34522107 PMCID: PMC8434891 DOI: 10.2147/idr.s327595] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 09/02/2021] [Indexed: 12/17/2022] Open
Abstract
Background The emergence and spread of carbapenem-resistant Enterobacter cloacae complex (ECC) have posed a serious threat to human health worldwide. This study aimed to investigate the molecular mechanism of carbapenem resistance and its prevalence among ECC in China. Methods A total of 1314 ECC clinical isolates were collected from the First Affiliated Hospital of Wenzhou Medical University from 2004 to 2018. Sensitivity to antibiotics was determined using the agar dilution method. The production of carbapenemases and the prevalence of resistance-associated genes were investigated using PCR. The expression of outer membrane porin (OMP) genes (ompC/ompF) and cephalosporinase gene ampC was analyzed by quantitative real-time PCR. The effect of efflux pump mechanism on carbapenem resistance was tested. ECC was typed by multilocus sequence typing (MLST). Results In this study, 113 carbapenem-nonsusceptible ECC strains were identified. The prevalence rates of carbapenemase genes bla KPC-2 and bla NDM were 12.4% (14/113) and 17.7% (20/113), and that of the extended-spectrum β-lactamase (ESBL) genes bla CTX-M, bla TEM, and bla SHV were 28.3% (32/113), 27.4% (31/113), and 14.2% (16/113), respectively. Among 67 carbapenem-nonsusceptible ECC isolates producing non-carbapenemase, low expression of ompC/ompF and overexpression of ampC were found in 46 and 40 strains, respectively. In addition, the carbapenem resistance was related to the overexpression of the efflux pump in the study. Finally, the 113 carbapenem-nonsusceptible ECC strains were categorized into 39 different sequence types using MLST. Conclusion Carbapenem-nonsusceptible ECC strains producing non-carbapenemase were predominant. The low expression of OMP with the overexpression of cephalosporinase or production of ESBLs and overexpression of efflux pump might contribute to the resistance to carbapenem for carbapenem-nonsusceptible ECC strains producing non-carbapenemase. The bla NDM and bla KPC comprised the principal resistance mechanism of carbapenemase-producing ECC in the hospital, causing a threat to public health. Therefore, monitoring programs to prevent the emergence and further spread of antibiotic resistance are urgently needed.
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Affiliation(s)
- Shixing Liu
- Department of Clinical Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang Province, People's Republic of China
| | - Na Huang
- Department of Clinical Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang Province, People's Republic of China
| | - Cui Zhou
- Department of Clinical Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang Province, People's Republic of China
| | - Yishuai Lin
- School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, Zhejiang Province, People's Republic of China
| | - Ying Zhang
- School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, Zhejiang Province, People's Republic of China
| | - Lingbo Wang
- Department of Clinical Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang Province, People's Republic of China
| | - Xiangkuo Zheng
- Department of Clinical Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang Province, People's Republic of China
| | - Tieli Zhou
- Department of Clinical Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang Province, People's Republic of China
| | - Zhongyong Wang
- Department of Clinical Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang Province, People's Republic of China
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12
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Draft Genome Sequence of Enterobacter oligotrophicus, Isolated from the Microbiome of a Lizard in the Caribbean. Microbiol Resour Announc 2021; 10:e0060221. [PMID: 34472977 PMCID: PMC8411919 DOI: 10.1128/mra.00602-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Here, we describe the genome sequence of ECC486. This Enterobacter oligotrophicus strain was isolated from a wild specimen of Anolis marmoratus speciosus, a lizard endemic to the territory of Guadeloupe (French West Indies). Its draft genome sequence consists of 40 contigs and contains a total of 4,504,233 bp, with a G+C content of 54.1%.
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