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Salem S, Abdelsalam NA, Shata AH, Mouftah SF, Cobo-Díaz JF, Osama D, Atteya R, Elhadidy M. Unveiling the microevolution of antimicrobial resistance in selected Pseudomonas aeruginosa isolates from Egyptian healthcare settings: A genomic approach. Sci Rep 2024; 14:15500. [PMID: 38969684 PMCID: PMC11226647 DOI: 10.1038/s41598-024-65178-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2024] [Accepted: 06/18/2024] [Indexed: 07/07/2024] Open
Abstract
The incidence of Pseudomonas aeruginosa infections in healthcare environments, particularly in low-and middle-income countries, is on the rise. The purpose of this study was to provide comprehensive genomic insights into thirteen P. aeruginosa isolates obtained from Egyptian healthcare settings. Phenotypic analysis of the antimicrobial resistance profile and biofilm formation were performed using minimum inhibitory concentration and microtiter plate assay, respectively. Whole genome sequencing was employed to identify sequence typing, resistome, virulome, and mobile genetic elements. Our findings indicate that 92.3% of the isolates were classified as extensively drug-resistant, with 53.85% of these demonstrating strong biofilm production capabilities. The predominant clone observed in the study was ST773, followed by ST235, both of which were associated with the O11 serotype. Core genome multi-locus sequence typing comparison of these clones with global isolates suggested their potential global expansion and adaptation. A significant portion of the isolates harbored Col plasmids and various MGEs, all of which were linked to antimicrobial resistance genes. Single nucleotide polymorphisms in different genes were associated with the development of antimicrobial resistance in these isolates. In conclusion, this pilot study underscores the prevalence of extensively drug-resistant P. aeruginosa isolates and emphasizes the role of horizontal gene transfer facilitated by a diverse array of mobile genetic elements within various clones. Furthermore, specific insertion sequences and mutations were found to be associated with antibiotic resistance.
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Affiliation(s)
- Salma Salem
- Center for Genomics, Helmy Institute for Medical Sciences, Zewail City of Science and Technology, Giza, Egypt
- Biomedical Sciences Program, University of Science and Technology, Zewail City of Science and Technology, Giza, Egypt
| | - Nehal Adel Abdelsalam
- Center for Genomics, Helmy Institute for Medical Sciences, Zewail City of Science and Technology, Giza, Egypt
- Biomedical Sciences Program, University of Science and Technology, Zewail City of Science and Technology, Giza, Egypt
- Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Cairo, Egypt
| | - Ahmed H Shata
- Center for Genomics, Helmy Institute for Medical Sciences, Zewail City of Science and Technology, Giza, Egypt
- Biomedical Sciences Program, University of Science and Technology, Zewail City of Science and Technology, Giza, Egypt
| | - Shaimaa F Mouftah
- Biomedical Sciences Program, University of Science and Technology, Zewail City of Science and Technology, Giza, Egypt
| | - José F Cobo-Díaz
- Department of Food Hygiene and Technology, Institute of Food Science and Technology, Universidad de León, León, Spain
| | - Dina Osama
- Department of Microbiology and Immunology, Faculty of Pharmacy, October University for Modern Sciences and Arts (MSA), Cairo, Egypt
| | - Reham Atteya
- Center for Genomics, Helmy Institute for Medical Sciences, Zewail City of Science and Technology, Giza, Egypt
| | - Mohamed Elhadidy
- Center for Genomics, Helmy Institute for Medical Sciences, Zewail City of Science and Technology, Giza, Egypt.
- Biomedical Sciences Program, University of Science and Technology, Zewail City of Science and Technology, Giza, Egypt.
- Department of Bacteriology, Mycology and Immunology, Faculty of Veterinary Medicine, Mansoura University, Mansoura, Egypt.
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Mohamed HS, Galal L, Hayer J, Benavides JA, Bañuls AL, Dupont C, Conquet G, Carrière C, Dumont Y, Didelot MN, Michon AL, Jean-Pierre H, Aboubaker MH, Godreuil S. Genomic epidemiology of carbapenemase-producing Gram-negative bacteria at the human-animal-environment interface in Djibouti city, Djibouti. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 905:167160. [PMID: 37730061 DOI: 10.1016/j.scitotenv.2023.167160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 09/14/2023] [Accepted: 09/15/2023] [Indexed: 09/22/2023]
Abstract
The emergence of carbapenem resistance is a major public health threat in sub-Saharan Africa but remains poorly understood, particularly at the human-animal-environment interface. This study provides the first One Health-based study on the epidemiology of Carbapenemase-Producing Gram-Negative Bacteria (CP-GNB) in Djibouti City, Djibouti, East Africa. In total, 800 community urine samples and 500 hospital specimens from humans, 270 livestock fecal samples, 60 fish samples, and 20 water samples were collected and tested for carbapenem resistance. The overall estimated CP-GNB prevalence was 1.9 % (32/1650 samples) and specifically concerned 0.3 % of community urine samples, 2.8 % of clinical specimens, 2.6 % of livestock fecal samples, 11.7 % of fish samples, and 10 % of water samples. The 32 CP-GNB included 19 Escherichia coli, seven Acinetobacter baumannii, five Klebsiella pneumoniae, and one Proteus mirabilis isolate. Short-read (Illumina) and long-read (Nanopore) genome sequencing revealed that carbapenem resistance was mainly associated with chromosomal carriage of blaNDM-1, blaOXA-23, blaOXA-48, blaOXA-66, and blaOXA-69 in A. baumannii, and with plasmid carriage in Enterobacterales (blaNDM-1 and blaOXA-181 in E. coli, blaNDM-1, blaNDM-5 and blaOXA-48 in K. pneumoniae, and blaNDM-1 in P. mirabilis). Moreover, 17/32 CP-GNB isolates belonged to three epidemic clones: (1) A. baumannii sequence type (ST) 1697,2535 that showed a distribution pattern consistent with intra- and inter-hospital dissemination; (2) E. coli ST10 that circulated at the human-animal-environment interface; and (3) K. pneumoniae ST147 that circulated at the human-environment interface. Horizontal exchanges probably contributed to carbapenem resistance dissemination in the city, especially the blaOXA-181-carrying ColKP3-IncX3 hybrid plasmid that was found in E. coli isolates belonging to different STs. Our study highlights that despite a relatively low CP-GNB prevalence in Djibouti City, plasmids harboring carbapenem resistance circulate in humans, animals and environment. Our findings stress the need to implement preventive and control measures for reducing the circulation of this potentially emerging public health threat.
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Affiliation(s)
- Hasna Saïd Mohamed
- Laboratoire de Bactériologie, Centre Hospitalier Universitaire de Montpellier, Montpellier, France; UMR MIVEGEC, Université de Montpellier, IRD, CNRS, Montpellier, France; Hôpital Général Peltier de Djibouti, Djibouti ville, Djibouti; Laboratoire de Biologie Médicale de la Mer Rouge, Djibouti City, Djibouti
| | - Lokman Galal
- UMR MIVEGEC, Université de Montpellier, IRD, CNRS, Montpellier, France.
| | - Juliette Hayer
- UMR MIVEGEC, Université de Montpellier, IRD, CNRS, Montpellier, France
| | - Julio A Benavides
- UMR MIVEGEC, Université de Montpellier, IRD, CNRS, Montpellier, France; Doctorado en Medicina de la Conservación y Centro de Investigación para la Sustentabilidad, Facultad de Ciencias de la Vida, Universidad Andrés Bello, República 440, Santiago, Chile
| | - Anne-Laure Bañuls
- UMR MIVEGEC, Université de Montpellier, IRD, CNRS, Montpellier, France; LMI DRISA, Montpellier, France
| | - Chloé Dupont
- Laboratoire de Bactériologie, Centre Hospitalier Universitaire de Montpellier, Montpellier, France
| | - Guilhem Conquet
- Laboratoire de Bactériologie, Centre Hospitalier Universitaire de Montpellier, Montpellier, France; UMR MIVEGEC, Université de Montpellier, IRD, CNRS, Montpellier, France
| | - Christian Carrière
- Laboratoire de Bactériologie, Centre Hospitalier Universitaire de Montpellier, Montpellier, France; UMR MIVEGEC, Université de Montpellier, IRD, CNRS, Montpellier, France
| | - Yann Dumont
- Laboratoire de Bactériologie, Centre Hospitalier Universitaire de Montpellier, Montpellier, France; UMR MIVEGEC, Université de Montpellier, IRD, CNRS, Montpellier, France
| | - Marie-Noëlle Didelot
- Laboratoire de Bactériologie, Centre Hospitalier Universitaire de Montpellier, Montpellier, France; UMR MIVEGEC, Université de Montpellier, IRD, CNRS, Montpellier, France
| | - Anne-Laure Michon
- Laboratoire de Bactériologie, Centre Hospitalier Universitaire de Montpellier, Montpellier, France; UMR MIVEGEC, Université de Montpellier, IRD, CNRS, Montpellier, France
| | - Hélène Jean-Pierre
- Laboratoire de Bactériologie, Centre Hospitalier Universitaire de Montpellier, Montpellier, France; UMR MIVEGEC, Université de Montpellier, IRD, CNRS, Montpellier, France
| | - Mohamed Houmed Aboubaker
- Laboratoire de Biologie Médicale de la Mer Rouge, Djibouti City, Djibouti; Laboratoire de la Caisse Nationale de Sécurité Sociale, Djibouti City 696, Djibouti
| | - Sylvain Godreuil
- Laboratoire de Bactériologie, Centre Hospitalier Universitaire de Montpellier, Montpellier, France; UMR MIVEGEC, Université de Montpellier, IRD, CNRS, Montpellier, France; Jeune Equipe Associée à l'IRD (JEAI), FASORAM, Montpellier, France
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Turton JF, Pike R, Perry C, Jenkins C, Turton JA, Meunier D, Hopkins KL. Wide distribution of Escherichia coli carrying IncF plasmids containing bla NDM-5 and rmtB resistance genes from hospitalized patients in England. J Med Microbiol 2022; 71. [PMID: 35925786 DOI: 10.1099/jmm.0.001569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Introduction. The New Delhi metallo-β-lactamase (NDM) variant NDM-5 was first described in 2011 in an isolate of Escherichia coli. We noted that a high proportion of isolates of E. coli positive for bla NDM carbapenemase genes submitted to the UK Health Security Agency (formerly Public Health England) between 2019 and mid-2021 carried the bla NDM-5 allele, with many co-harbouring rmtB, rendering them highly resistant to aminoglycosides as well as to most β-lactams.Hypothesis/Gap Statement. This observation suggested that a common plasmid may be circulating.Aim. To compare these isolates and describe the plasmids carrying these resistance elements.Methodology. All isolates were sequenced on an Illumina platform, with five also subjected to long-read nanopore sequencing to provide complete assemblies. The locations of bla NDM-5, rmtB and other associated genetic elements were identified. Susceptibility testing to a wide range of antibiotics was carried out on representative isolates.Results. The 34 isolates co-harbouring bla NDM-5 and rmtB were from 14 hospital groups and six different regions across England and consisted of 11 distinct sequence types. All carried IncF plasmids. Assembly of the NDM plasmids in five isolates revealed that they carried rmtB and bla NDM-5 in an IncF conjugative plasmid ranging in size from 85.5 to 161 kb. All carried a highly conserved region, previously described in E. coli plasmid pHC105-NDM, that included bla TEM-1B and rmtB followed by sequence bounded by two IS26 elements containing ΔISAba125, bla NDM-5, ble, trpF and tat followed by ISCR1 and an integron with sul1, aadA2 and dfrA12 cassettes. This arrangement has been described in isolates from other countries and continents, suggesting that such plasmids are widely distributed, at least in E. coli, with similar plasmids also found in Klebsiella pneumoniae. Tested isolates were resistant to most antibiotics except colistin, fosfomycin and tigecycline.Conclusion. These observations suggest that conjugative plasmids carrying a highly conserved resistance gene segment have become widespread in England and elsewhere. This study highlights the value of routine whole-genome sequencing in identifying genetic elements responsible for resistance dissemination.
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Affiliation(s)
- Jane F Turton
- Healthcare Associated Infections, Fungal, Antimicrobial Resistance, Antimicrobial Usage and Sepsis Division, UK Health Security Agency, London, UK
| | - Rachel Pike
- Reference Services Division, UK Health Security Agency, 61 Colindale Avenue, London NW9 5HT, UK
| | - Claire Perry
- Reference Services Division, UK Health Security Agency, 61 Colindale Avenue, London NW9 5HT, UK
| | - Claire Jenkins
- Reference Services Division, UK Health Security Agency, 61 Colindale Avenue, London NW9 5HT, UK
| | | | - Danièle Meunier
- Healthcare Associated Infections, Fungal, Antimicrobial Resistance, Antimicrobial Usage and Sepsis Division, UK Health Security Agency, London, UK
| | - Katie L Hopkins
- Healthcare Associated Infections, Fungal, Antimicrobial Resistance, Antimicrobial Usage and Sepsis Division, UK Health Security Agency, London, UK
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Plasmid-mediated ciprofloxacin, carbapenem and colistin resistance of a foodborne Escherichia coli isolate. Food Control 2022. [DOI: 10.1016/j.foodcont.2022.108937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Dewi DAR, Thomas T, Ahmad Mokhtar AM, Mat Nanyan NS, Zulfigar SB, Salikin NH. Carbapenem Resistance among Marine Bacteria-An Emerging Threat to the Global Health Sector. Microorganisms 2021; 9:microorganisms9102147. [PMID: 34683467 PMCID: PMC8537846 DOI: 10.3390/microorganisms9102147] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 10/08/2021] [Accepted: 10/10/2021] [Indexed: 01/24/2023] Open
Abstract
The emergence of antibiotic resistance among pathogenic microorganisms is a major issue for global public health, as it results in acute or chronic infections, debilitating diseases, and mortality. Of particular concern is the rapid and common spread of carbapenem resistance in healthcare settings. Carbapenems are a class of critical antibiotics reserved for treatment against multidrug-resistant microorganisms, and resistance to this antibiotic may result in limited treatment against infections. In addition to in clinical facilities, carbapenem resistance has also been identified in aquatic niches, including marine environments. Various carbapenem-resistant genes (CRGs) have been detected in different marine settings, with the majority of the genes incorporated in mobile genetic elements, i.e., transposons or plasmids, which may contribute to efficient genetic transfer. This review highlights the potential of the marine environment as a reservoir for carbapenem resistance and provides a general overview of CRG transmission among marine microbes.
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Affiliation(s)
- Dewa A.P. Rasmika Dewi
- School of Medicine, International University of Health and Welfare, Narita 286-8686, Japan;
- Faculty of Medicine and Health Sciences, Udayana University, Bali 80232, Indonesia
| | - Torsten Thomas
- Centre for Marine Science and Innovation, School of Biological, Earth and Environmental Sciences, The University of New South Wales, Sydney 2052, Australia;
| | - Ana Masara Ahmad Mokhtar
- School of Industrial Technology, Universiti Sains Malaysia, Gelugor 11800, Penang, Malaysia; (A.M.A.M.); (N.S.M.N.); (S.B.Z.)
| | - Noreen Suliani Mat Nanyan
- School of Industrial Technology, Universiti Sains Malaysia, Gelugor 11800, Penang, Malaysia; (A.M.A.M.); (N.S.M.N.); (S.B.Z.)
| | - Siti Balqis Zulfigar
- School of Industrial Technology, Universiti Sains Malaysia, Gelugor 11800, Penang, Malaysia; (A.M.A.M.); (N.S.M.N.); (S.B.Z.)
| | - Nor Hawani Salikin
- School of Industrial Technology, Universiti Sains Malaysia, Gelugor 11800, Penang, Malaysia; (A.M.A.M.); (N.S.M.N.); (S.B.Z.)
- Correspondence: ; Tel.: +60-4-653-2241
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Lee H, Ko KS. Effect of multiple, compatible plasmids on the fitness of the bacterial host by inducing transcriptional changes. J Antimicrob Chemother 2021; 76:2528-2537. [PMID: 34279638 DOI: 10.1093/jac/dkab240] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 06/21/2021] [Indexed: 11/13/2022] Open
Abstract
OBJECTIVES Bacteria that acquire plasmids incur a biological cost. Despite this fact, clinical Enterobacteriaceae isolates commonly contain multiple co-existing plasmids harbouring carbapenemase genes. METHODS Six different plasmids carrying blaNDM-1, blaNDM-5, blaCTX-M-15, blaKPC-2, blaOXA-181 and blaOXA-232 genes were obtained from Klebsiella pneumoniae and Escherichia coli clinical isolates. Using the E. coli DH5α strain as recipient, 14 transconjugants with diverse plasmid combinations (single or double plasmids) were generated. For each of these, the effects of plasmid carriage on the bacterial host were investigated using in vitro and in vivo competition assays; additionally, the effects were investigated in the context of biofilm formation, serum resistance and survival inside macrophages. Transcriptomic changes in single- and double-plasmid recipients were also investigated. RESULTS Increased in vitro and in vivo competitiveness was observed when two plasmids carrying blaNDM-1 and blaOXA-232 were co-introduced into the host bacteria. However, DH5α::pNDM5 + pOXA232 and other double-plasmid recipients did not show such competitiveness. DH5α::pNDM5 + pOXA181 did not show any fitness cost compared with a plasmid-free host and single-plasmid transconjugants, while both the double-plasmid recipients with pCTXM15 or pKPC2 exhibited a fitness burden. The double-plasmid recipient DH5α::pNDM1 + pOXA232 also exhibited increased biofilm formation, serum resistance and survival inside macrophages. Transcriptomic analysis revealed that the genes of DH5α::pNDM1 + pOXA232 involved in metabolic pathways, transport and stress response were up-regulated, while those involved in translation were down-regulated. CONCLUSIONS Our study suggests that bacterial strains can gain fitness through the acquisition of multiple plasmids harbouring antibiotic resistance genes, which may be mediated by transcriptomic changes in the chromosomal genes of the bacterial host.
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Affiliation(s)
- Haejeong Lee
- Department of Microbiology, Sungkyunkwan University School of Medicine, Suwon 16419, Republic of Korea
| | - Kwan Soo Ko
- Department of Microbiology, Sungkyunkwan University School of Medicine, Suwon 16419, Republic of Korea
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Sugawara Y, Akeda Y, Hagiya H, Zin KN, Aye MM, Takeuchi D, Matsumoto Y, Motooka D, Nishi I, Tomono K, Hamada S. Characterization of bla NDM-5-harbouring Klebsiella pneumoniae sequence type 11 international high-risk clones isolated from clinical samples in Yangon General Hospital, a tertiary-care hospital in Myanmar. J Med Microbiol 2021; 70. [PMID: 34038339 DOI: 10.1099/jmm.0.001348] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Fifteen Klebsiella pneumoniae isolates harbouring bla NDM genes were identified from blood and sputum specimens of patients at a tertiary-care facility (Yangon General Hospital, Yangon, Myanmar) in 2018. Two of the isolates belonged to sequence type (ST) 11, an international high-risk clone. Whole-genome sequencing and phylogenetic analyses revealed that these two isolates were clustered together with other ST11 isolates originating from other countries. The isolates harboured the bla NDM-5 gene on an IncFII-type plasmid that is prevalent among carbapenemase-producing Enterobacteriaceae in Yangon but has rarely been found in other ST11 isolates. Our data suggests the regional presence of the ST11 international high-risk clone and its acquisition of an endemic bla NDM-5-carrying plasmid.
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Affiliation(s)
- Yo Sugawara
- Japan-Thailand Research Collaboration Center on Emerging and Re-emerging Infections, Research Institute for Microbial Diseases, Osaka University, Suita, Japan
| | - Yukihiro Akeda
- Department of Infection Control and Prevention, Graduate School of Medicine, Osaka University, Suita, Japan.,Japan-Thailand Research Collaboration Center on Emerging and Re-emerging Infections, Research Institute for Microbial Diseases, Osaka University, Suita, Japan
| | - Hideharu Hagiya
- Department of Infection Control and Prevention, Graduate School of Medicine, Osaka University, Suita, Japan
| | - Khwar Nyo Zin
- Clinical Laboratory Department, Yangon General Hospital, Yangon, Myanmar
| | - Mya Mya Aye
- Bacteriology Research Division, Department of Medical Research, Yangon, Myanmar
| | - Dan Takeuchi
- Japan-Thailand Research Collaboration Center on Emerging and Re-emerging Infections, Research Institute for Microbial Diseases, Osaka University, Suita, Japan
| | - Yuki Matsumoto
- Department of Infection Metagenomics, Research Institute for Microbial Diseases, Osaka University, Suita, Japan
| | - Daisuke Motooka
- Department of Infection Metagenomics, Research Institute for Microbial Diseases, Osaka University, Suita, Japan
| | - Isao Nishi
- Laboratory for Clinical Investigation, Osaka University Hospital, Suita, Japan
| | - Kazunori Tomono
- Department of Infection Control and Prevention, Graduate School of Medicine, Osaka University, Suita, Japan
| | - Shigeyuki Hamada
- Japan-Thailand Research Collaboration Center on Emerging and Re-emerging Infections, Research Institute for Microbial Diseases, Osaka University, Suita, Japan
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Diversity and Genetic Basis for Carbapenem Resistance in a Coastal Marine Environment. Appl Environ Microbiol 2020; 86:AEM.02939-19. [PMID: 32198174 DOI: 10.1128/aem.02939-19] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 03/07/2020] [Indexed: 11/20/2022] Open
Abstract
Resistance to the "last-resort" antibiotics, such as carbapenems, has led to very few antibiotics being left to treat infections by multidrug-resistant bacteria. Spread of carbapenem resistance (CR) has been well characterized for the clinical environment. However, there is a lack of information about its environmental distribution. Our study reveals that CR is present in a wide range of Gram-negative bacteria in the coastal seawater environment, including four phyla, eight classes, and 30 genera. These bacteria were likely introduced into seawater via stormwater flows. Some CR isolates found here, such as Acinetobacter junii, Acinetobacter johnsonii, Brevundimonas vesicularis, Enterococcus durans, Pseudomonas monteilii, Pseudomonas fulva, and Stenotrophomonas maltophilia, are further relevant to human health. We also describe a novel metallo-β-lactamase (MBL) for marine Rheinheimera isolates with CR, which has likely been horizontally transferred to Citrobacter freundii or Enterobacter cloacae In contrast, another MBL of the New Delhi type was likely acquired by environmental Variovorax isolates from Escherichia coli, Klebsiella pneumoniae, or Acinetobacter baumannii utilizing a plasmid. Our findings add to the growing body of evidence that the aquatic environment is both a reservoir and a vector for novel CR genes.IMPORTANCE Resistance against the "last-resort" antibiotics of the carbapenem family is often based on the production of carbapenemases, and this has been frequently observed in clinical samples. However, the dissemination of carbapenem resistance (CR) in the environment has been less well explored. Our study shows that CR is commonly found in a range of bacterial taxa in the coastal aquatic environment and can involve the exchange of novel metallo-β-lactamases from typical environmental bacteria to potential human pathogens or vice versa. The outcomes of this study contribute to a better understanding of how aquatic and marine bacteria can act as reservoirs and vectors for CR outside the clinical setting.
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Kim SY, Seo J, Shin J, Chung YJ, Jeon IY, Yun SJ, Kim YS, Ko KS. Clonal spreading of NDM-5 carbapenemase-producing Escherichia coli isolates in a hospital in South Korea. Diagn Microbiol Infect Dis 2020; 97:115027. [PMID: 32273166 DOI: 10.1016/j.diagmicrobio.2020.115027] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Revised: 02/05/2020] [Accepted: 02/19/2020] [Indexed: 01/04/2023]
Affiliation(s)
- So Yeon Kim
- Division of Bacterial Disease Research, Korea National Institute of Health, Centers for Disease Control and Prevention, Cheongju, Republic of Korea
| | - Jungyu Seo
- Department of Molecular Cell Microbiology, Sungkyunkwan University School of Medicine, Suwon 16419, Republic of Korea
| | - Juyoun Shin
- Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul 06591, Republic of Korea
| | - Yeun-Jun Chung
- Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul 06591, Republic of Korea; Precision Medicine Research Center, Integrated Research Center for Genome Polymorphism, College of Medicine, The Catholic University of Korea, Seoul 06591, Republic of Korea
| | - In Young Jeon
- Department of Infection Control, Chungnam National University Hospital, Chungnam National University School of Medicine, Daejeon 35015, Republic of Korea
| | - Seon Jin Yun
- Department of Infection Control, Chungnam National University Hospital, Chungnam National University School of Medicine, Daejeon 35015, Republic of Korea
| | - Yeon-Sook Kim
- Division of Infectious Diseases, Chungnam National University Hospital, Chungnam National University School of Medicine, Daejeon 35015, Republic of Korea.
| | - Kwan Soo Ko
- Department of Molecular Cell Microbiology, Sungkyunkwan University School of Medicine, Suwon 16419, Republic of Korea.
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Simultaneous Infection with Enterobacteriaceae and Pseudomonas aeruginosa Harboring Multiple Carbapenemases in a Returning Traveler Colonized with Candida auris. Antimicrob Agents Chemother 2020; 64:AAC.01466-19. [PMID: 31658962 DOI: 10.1128/aac.01466-19] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2019] [Accepted: 10/15/2019] [Indexed: 02/05/2023] Open
Abstract
We report our clinical experience treating a critically ill patient with polymicrobial infections due to multidrug-resistant Escherichia coli, Klebsiella pneumoniae, and Pseudomonas aeruginosa in a 56-year-old woman who received health care in India and was also colonized by Candida auris A precision medicine approach using whole-genome sequencing revealed a multiplicity of mobile elements associated with NDM-1, NDM-5, and OXA-181 and, supplemented with susceptibility testing, guided the selection of rational antimicrobial therapy.
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11
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Kong Z, Cai R, Cheng C, Zhang C, Kang H, Ma P, Gu B. First Reported Nosocomial Outbreak Of NDM-5-Producing Klebsiella pneumoniae In A Neonatal Unit In China. Infect Drug Resist 2019; 12:3557-3566. [PMID: 31814744 PMCID: PMC6863125 DOI: 10.2147/idr.s218945] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Accepted: 09/20/2019] [Indexed: 12/20/2022] Open
Abstract
Purpose Carbapenem-resistant Klebsiella pneumoniae (CRKP) have emerged worldwide and also being a major threat to children and neonate. In this study, we describe a nosocomial outbreak of NDM-5-producing Klebsiella pneumoniae in neonatal unit of a teaching hospital in China from September 2015 to September 2016. Patients and methods We collected 12 carbapenem-resistant K. pneumoniae outbreak strains from 12 newborns and characterized these isolates for their antimicrobial susceptibility, clone relationships, and multi-locus sequence types using vitek-2 compact system, pulsed-field gel electrophoresis (PFGE) and multi-locus sequence typing (MLST). Resistant genes were detected by using PCR and sequencing. Plasmid conjugation experiment was carried out to determine the transferability of carbapenem resistance. PCR-based replicon typing (PBRT), S1 nuclease-PFGE, and southern blotting were conducted for plasmid profiling. Results All 12 K. pneumoniae isolates were resistant to carbapenems and carried blaNDM-5, blaTEM-1 and blaSHV-11. Furthermore, PFGE analysis showed that NDM-5-producing K. pneumoniae were clonally related and MLST assigned them to sequence type 337. Conjugative assays showed that plasmids harboring blaNDM-5 gene were self-transmissible. Plasmid analysis suggested that all blaNDM-5 gene located on a ~45 kb IncX3 type plasmid. Conclusion To the best of our knowledge, this is the first report of a clone outbreak of blaNDM-5-carrying K. pneumoniae isolates from neonates. There is an urgent need for effective infection control measures to prevent blaNDM-5 variants from becoming epidemic in the neonates in the future.
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Affiliation(s)
- Ziyan Kong
- Medical Technology School, Xuzhou Medical University, Xuzhou, Jiangsu Province, People's Republic of China
| | - Rui Cai
- Medical Technology School, Xuzhou Medical University, Xuzhou, Jiangsu Province, People's Republic of China
| | - Chen Cheng
- Medical Technology School, Xuzhou Medical University, Xuzhou, Jiangsu Province, People's Republic of China
| | - Chuanling Zhang
- Department of Laboratory Medicine, XuZhou Children's Hospital, Xuzhou, Jiangsu Province, People's Republic of China
| | - Haiquan Kang
- Department of Laboratory Medicine, Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu Province, People's Republic of China
| | - Ping Ma
- Department of Laboratory Medicine, Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu Province, People's Republic of China
| | - Bing Gu
- Medical Technology School, Xuzhou Medical University, Xuzhou, Jiangsu Province, People's Republic of China.,Department of Laboratory Medicine, Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu Province, People's Republic of China
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12
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Plasmid analysis of Escherichia coli isolates from South Korea co-producing NDM-5 and OXA-181 carbapenemases. Plasmid 2019; 104:102417. [PMID: 31150689 DOI: 10.1016/j.plasmid.2019.102417] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Revised: 05/02/2019] [Accepted: 05/27/2019] [Indexed: 11/23/2022]
Abstract
Recently, Escherichia coli isolates co-producing New Delhi metallo-β-lactamase (NDM)-5 and oxacillinase (OXA)-181 were identified in a tertiary-care hospital of South Korea. Isolate CC1702-1 was collected from urine in January 2017 and isolate CC1706-1 was recovered from a transtracheal aspirate of a hospitalized patient in May 2017. Carbapenemase genes were identified by multiplex PCR and sequencing, and whole genome sequencing was performed subsequently using the PacBio RSII system. Both E. coli isolates belonged to the same clone (ST410) and were resistant to all β-lactams including carbapenems. We obtained whole plasmid sequences of the isolates: pCC1702-NDM-5 from CC1702-1 and pCC1706-NDM-5 and pCC1706-OXA-181 from CC1706-1. The two E. coli isolates belonged to the same clone (ST410) and they were completely resistant to all β-lactams, as well as carbapenems. Two blaNDM-5-harboring plasmids belonged to the same incompatibility group, IncFIA/B, and consisted of 79,613 bp and 111,890 bp with 87 and 130 coding sequences, respectively. The genetic structures of the two blaNDM-5-bearing plasmids, which were distinct from the blaNDM-5-bearing plasmids from the Klebsiella pneumoniae isolates previously transmitted from the United Arab Emirates (UAE) to South Korea, differed from each other. While pCC1702-NDM-5 showed high degree of identity with the plasmid from a multidrug-resistant isolate of Citrobacter fruendii P5571 found in China, pCC1706-NDM-5 was very similar to the plasmid from a multidrug-resistant isolate of E. coli AMA1176 found in Denmark. pCC1706-OXA-181, which was a 51 kb, self-transmissible IncX3 plasmid, was identical to the E. coli plasmids pAMA1167-OXA-181 from Denmark and pOXA-181-WCHEC14828 from China. Plasmids harboring blaNDM-5 in E. coli isolates might not be transferred from K. pneumoniae isolates co-producing NDM-5 and OXA-181. They probably originated from multiple sources.
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13
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Brinkac LM, White R, D'Souza R, Nguyen K, Obaro SK, Fouts DE. Emergence of New Delhi Metallo-β-Lactamase (NDM-5) in Klebsiella quasipneumoniae from Neonates in a Nigerian Hospital. mSphere 2019; 4:e00685-18. [PMID: 30867330 PMCID: PMC6416368 DOI: 10.1128/msphere.00685-18] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Accepted: 02/25/2019] [Indexed: 01/08/2023] Open
Abstract
Outbreaks of infection occur more often than they are reported in most developing countries, largely due to poor diagnostic services. A Klebsiella species bacteremia outbreak in a newborn unit with high mortality was recently encountered at a location being surveilled for childhood bacteremia. These surveillance efforts offered the opportunity to determine the cause of this neonatal outbreak. In this report, we present the whole-genome sequences of New Delhi metallo-β-lactamase (NDM-5)-containing Klebsiella quasipneumoniae subsp. similipneumoniae bloodstream isolates from a neonatal bacteremia outbreak at a tertiary hospital in Nigeria and as part of the largest collection of K. pneumoniae bloodstream isolates from children in Africa. Comparative analysis of the genetic environment surrounding the NDM-5 genes revealed nearly perfect sequence identity to blaNDM-5-bearing IncX3-type plasmids from other members of the EnterobacteriaceaeIMPORTANCE Carbapenem-resistant Klebsiella pneumoniae is of global health importance, yet there is a paucity of genome-based studies in Africa. Here we report fatal blood-borne NDM-5-producing K. quasipneumoniae subsp. similipneumoniae infections from Nigeria, Africa. New Delhi metallo-β-lactamase (NDM)-producing Klebsiella spp. are responsible for high mortality and morbidity, with the NDM-5 variant showing elevated carbapenem resistance. The prevalence of NDM-5 in Klebsiella has been limited primarily to K. pneumoniae, with only one isolate being collected from Africa. During an outbreak of sepsis in a teaching hospital in Nigeria, five NDM-5-producing K. quasipneumoniae subsp. similipneumoniae sequence type 476 isolates were identified. Given the increased resistance profile of these strains, this study highlights the emerging threat of blaNDM-5 dissemination in hospital environments. The observation of these NDM-5-producing isolates in Africa stresses the urgency to improve monitoring and clinical practices to reduce or prevent the further spread of resistance.
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Affiliation(s)
| | | | | | - Kevin Nguyen
- J. Craig Venter Institute, Rockville, Maryland, USA
| | - Stephen K Obaro
- University of Nebraska Medical Center, Omaha, Nebraska, USA
- Department of Pediatrics, University of Abuja Teaching Hospital, Abuja, Nigeria
- International Foundation against Infectious Diseases in Nigeria (IFAIN), Abuja, Nigeria
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14
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Xu L, Wang P, Cheng J, Qin S, Xie W. Characterization of a novel bla NDM-5-harboring IncFII plasmid and an mcr-1-bearing IncI2 plasmid in a single Escherichia coli ST167 clinical isolate. Infect Drug Resist 2019; 12:511-519. [PMID: 30881056 PMCID: PMC6402710 DOI: 10.2147/idr.s192998] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Background and purpose The spread of the plasmid-mediated, colistin-resistance gene mcr-1 into New Delhi metallo-β-lactamase (NDM)-producing bacterial isolates can cause untreatable infections. In this study, we conducted a molecular characterization of a novel, conjugative, blaNDM-5-positive IncFII plasmid (pNDM-EC16-50) together with an mcr-1-bearing IncI2 plasmid in a single Escherichia coli ST167 clinical isolate EC16-50. Methods and results EC16-50, which belongs to the E. coli strain ST167 and phylogroup A, was identified to co-produce NDM-5 and MCR-1. S1-PFGE and Southern blotting showed that blaNDM-5 and mcr-1 genes were located oñ95 kb and ~65 kb plasmids, respectively. A conjugation assay revealed that both blaNDM-5- and mcr-1-bearing plasmids were self-transmissible. Comparative plasmid analysis suggested that blaNDM-5-harboring F2:A-:B-plasmid might have evolved from the well-reported NDM-carrying pMC-NDM-like plasmid via recombination with a locally emerged pSJ_94 plasmid, whereas the mcr-1-carrying IncI2 plasmid was similar to previously reported mcr-1-bearing plasmids in China. Conclusion and impact This study represents the first report of the NDM-5 carrying Inc-FII- but not IncX3-type plasmid in an MCR-1-producing E. coli isolate. More striking was the dissemination of mcr-1 in a successful epidemic NDM-5-producing E. coli clone ST167, which could facilitate the spread of colistin resistance in carbapenemase-producing E. coli isolates.
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Affiliation(s)
- Lijuan Xu
- The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450001, China,
| | - Ping Wang
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, Henan 450001, China,
| | - Jing Cheng
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, Henan 450001, China,
| | - Shangshang Qin
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, Henan 450001, China, .,Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, Zhengzhou University, Zhengzhou, Henan 450001, China,
| | - Weihong Xie
- The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450001, China,
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15
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Ko KS. Antibiotic-resistant clones in Gram-negative pathogens: presence of global clones in Korea. J Microbiol 2018; 57:195-202. [PMID: 30552629 DOI: 10.1007/s12275-019-8491-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Revised: 10/01/2018] [Accepted: 10/02/2018] [Indexed: 12/26/2022]
Abstract
Antibiotic resistance is a global concern in public health. Antibiotic-resistant clones can spread nationally, internationally, and globally. This review considers representative antibiotic-resistant Gram-negative bacterial clones-CTX-M- 15-producing ST131 in Escherichia coli, extended-spectrum ß-lactamase-producing ST11 and KPC-producing ST258 in Klebsiella pneumoniae, IMP-6-producing, carbapenem-resistant ST235 in Pseudomonas aeruginosa, and OXA-23-producing global clone 2 in Acinetobacter baumannii-that have disseminated worldwide, including in Korea. The findings highlight the urgency for systematic monitoring and international cooperation to suppress the emergence and propagation of antibiotic resistance.
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Affiliation(s)
- Kwan Soo Ko
- Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine, Suwon, 16419, Republic of Korea.
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16
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Spread of Plasmid-Encoded NDM-1 and GES-5 Carbapenemases among Extensively Drug-Resistant and Pandrug-Resistant Clinical Enterobacteriaceae in Durban, South Africa. Antimicrob Agents Chemother 2018; 62:AAC.02178-17. [PMID: 29507063 DOI: 10.1128/aac.02178-17] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Accepted: 02/23/2018] [Indexed: 01/09/2023] Open
Abstract
Whole-genome sequence analyses revealed the presence of blaNDM-1 (n = 31), blaGES-5 (n = 8), blaOXA-232 (n = 1), or blaNDM-5 (n = 1) in extensively drug-resistant and pandrug-resistant Enterobacteriaceae organisms isolated from in-patients in 10 private hospitals (2012 to 2013) in Durban, South Africa. Two novel NDM-1-encoding plasmids from Klebsiella pneumoniae were circularized by PacBio sequencing. In p19-10_01 [IncFIB(K); 223.434 bp], blaNDM-1 was part of a Tn1548-like structure (16.276 bp) delineated by IS26 The multireplicon plasmid p18-43_01 [IncR_1/IncFIB(pB171)/IncFII(Yp); 212.326 bp] shared an 80-kb region with p19-10_01, not including the blaNDM-1-containing region. The two plasmids were used as references for tracing NDM-1-encoding plasmids in the other genome assemblies. The p19-10_01 sequence was detected in K. pneumoniae (n = 7) only, whereas p18-43_01 was tracked to K. pneumoniae (n = 4), Klebsiella michiganensis (n = 1), Serratia marcescens (n = 11), Enterobacter spp. (n = 7), and Citrobacter freundii (n = 1), revealing horizontal spread of this blaNDM-1-bearing plasmid structure. Global phylogeny showed clustering of the K. pneumoniae (18/20) isolates together with closely related carbapenemase-negative ST101 isolates from other geographical origins. The South African isolates were divided into three phylogenetic subbranches, where each group had distinct resistance and replicon profiles, carrying either p19-10_01, p18-10_01, or pCHE-A1 (8,201 bp). The latter plasmid carried blaGES-5 and aacA4 within an integron mobilization unit. Our findings imply independent plasmid acquisition followed by local dissemination. Additionally, we detected blaOXA-232 carried by pPKPN4 in K. pneumoniae (ST14) and blaNDM-5 contained by a pNDM-MGR194-like genetic structure in Escherichia coli (ST167), adding even more complexity to the multilayer molecular mechanisms behind nosocomial spread of carbapenem-resistant Enterobacteriaceae in Durban, South Africa.
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17
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Potron A, Bernabeu S, Cuzon G, Pontiès V, Blanchard H, Seringe E, Naas T, Nordmann P, Dortet L. Analysis of OXA-204 carbapenemase-producing Enterobacteriaceae reveals possible endoscopy-associated transmission, France, 2012 to 2014. Euro Surveill 2017; 22:17-00048. [PMID: 29233256 PMCID: PMC5727592 DOI: 10.2807/1560-7917.es.2017.22.49.17-00048] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
OXA-48-like beta-lactamase producing bacteria are now endemic in several European and Mediterranean countries. Among this carbapenemase family, the OXA-48 and OXA-181 variants predominate, whereas other variants such as OXA-204 are rarely reported. Here, we report the molecular epidemiology of a collection of OXA-204-positive enterobacterial isolates (n = 29) recovered in France between October 2012 and May 2014. This study describes the first outbreak of OXA-204-producing Enterobacteriaceae in Europe, involving 12 isolates of an ST90 Escherichia coli clone and nine isolates of an ST147 Klebsiella pneumoniae clone. All isolates co-produced the cephalosporinase CMY-4, and 60% of them co-produced the extended-spectrum beta-lactamase CTX-M-15. The blaOXA-204 gene was located on a 150-kb IncA/C plasmid, isolated from various enterobacterial species in the same patient, indicating a high conjugative ability of this genetic vehicle.
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Affiliation(s)
- Anaïs Potron
- National Reference Centre for Antibiotic Resistance, (division of carbapenemase-producing Enterobacteriaceae), Le Kremlin-Bicêtre, France,Department of Bacteriology, University Hospital of Besançon, Université of Franche-Comté, Besançon, France
| | - Sandrine Bernabeu
- National Reference Centre for Antibiotic Resistance, (division of carbapenemase-producing Enterobacteriaceae), Le Kremlin-Bicêtre, France,Bacteriology-Hygiene Unit, Assistance Publique/Hôpitaux de Paris, Bicêtre Hospital, Le Kremlin-Bicêtre, France,EA7361 “Structure, Dynamic, Function and Expression of Broad Spectrum beta-Lactamases”, Paris-Sud University, LabEx Lermit, Faculty of Medicine, Le Kremlin-Bicêtre, France,Joint Research Unit EERA “Evolution and Ecology of Resistance to Antibiotics,” Institut Pasteur-APHP-Université Paris-Sud, Paris, France
| | - Gaëlle Cuzon
- National Reference Centre for Antibiotic Resistance, (division of carbapenemase-producing Enterobacteriaceae), Le Kremlin-Bicêtre, France,Bacteriology-Hygiene Unit, Assistance Publique/Hôpitaux de Paris, Bicêtre Hospital, Le Kremlin-Bicêtre, France,EA7361 “Structure, Dynamic, Function and Expression of Broad Spectrum beta-Lactamases”, Paris-Sud University, LabEx Lermit, Faculty of Medicine, Le Kremlin-Bicêtre, France,Joint Research Unit EERA “Evolution and Ecology of Resistance to Antibiotics,” Institut Pasteur-APHP-Université Paris-Sud, Paris, France
| | - Valérie Pontiès
- Santé Publique France, The French Public Health Agency, Saint-Maurice, France
| | - Hervé Blanchard
- Regional Coordinating Centre for Nosocomial Infection Control (C-CLIN Paris Nord), Paris, France
| | - Elise Seringe
- Regional Coordinating Centre for Nosocomial Infection Control (C-CLIN Paris Nord), Paris, France
| | - Thierry Naas
- National Reference Centre for Antibiotic Resistance, (division of carbapenemase-producing Enterobacteriaceae), Le Kremlin-Bicêtre, France,Bacteriology-Hygiene Unit, Assistance Publique/Hôpitaux de Paris, Bicêtre Hospital, Le Kremlin-Bicêtre, France,EA7361 “Structure, Dynamic, Function and Expression of Broad Spectrum beta-Lactamases”, Paris-Sud University, LabEx Lermit, Faculty of Medicine, Le Kremlin-Bicêtre, France,Joint Research Unit EERA “Evolution and Ecology of Resistance to Antibiotics,” Institut Pasteur-APHP-Université Paris-Sud, Paris, France
| | - Patrice Nordmann
- Emerging Antibiotic Resistance Unit, Medical and Molecular Microbiology, Department of Medicine, University of Fribourg, Fribourg, Switzerland,Institut National de la Santé et de la Recherche Médicale (INSERM) European Unit (LEA Paris, IAME, France), University of Fribourg, Switzerland,National Reference Centre for Emerging Antibiotic Resistance, Fribourg, Switzerland,Institute for Microbiology, University hospital and University of Lausanne, Lausanne, Switzerland
| | - Laurent Dortet
- National Reference Centre for Antibiotic Resistance, (division of carbapenemase-producing Enterobacteriaceae), Le Kremlin-Bicêtre, France,Bacteriology-Hygiene Unit, Assistance Publique/Hôpitaux de Paris, Bicêtre Hospital, Le Kremlin-Bicêtre, France,EA7361 “Structure, Dynamic, Function and Expression of Broad Spectrum beta-Lactamases”, Paris-Sud University, LabEx Lermit, Faculty of Medicine, Le Kremlin-Bicêtre, France,Joint Research Unit EERA “Evolution and Ecology of Resistance to Antibiotics,” Institut Pasteur-APHP-Université Paris-Sud, Paris, France
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18
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Genome Sequences of Two NDM-1 Metallo-β-Lactamase-Producing Multidrug-Resistant Strains of Klebsiella pneumoniae with a High Degree of Similarity, One of Which Contains Prophage. GENOME ANNOUNCEMENTS 2017; 5:5/42/e01173-17. [PMID: 29051261 PMCID: PMC5646414 DOI: 10.1128/genomea.01173-17] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
We report genome sequences of two NDM-1 metallo-β-lactamase-producing multidrug-resistant Klebsiella pneumoniae isolates of sequence type 147 (ST147) from one hospital. The genomes are highly similar and differ in prophage located in the chromosome of K. pneumoniae KPB-1470/16 and in the additional plasmid-carrying blaOXA-48 gene in K. pneumoniae KPB-417/16.
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19
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Sugawara Y, Akeda Y, Sakamoto N, Takeuchi D, Motooka D, Nakamura S, Hagiya H, Yamamoto N, Nishi I, Yoshida H, Okada K, Zin KN, Aye MM, Tonomo K, Hamada S. Genetic characterization of blaNDM-harboring plasmids in carbapenem-resistant Escherichia coli from Myanmar. PLoS One 2017; 12:e0184720. [PMID: 28910381 PMCID: PMC5598989 DOI: 10.1371/journal.pone.0184720] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Accepted: 08/29/2017] [Indexed: 11/19/2022] Open
Abstract
The bacterial enzyme New Delhi metallo-β-lactamase hydrolyzes almost all β-lactam antibiotics, including carbapenems, which are drugs of last resort for severe bacterial infections. The spread of carbapenem-resistant Enterobacteriaceae that carry the New Delhi metallo-β-lactamase gene, blaNDM, poses a serious threat to public health. In this study, we genetically characterized eight carbapenem-resistant Escherichia coli isolates from a tertiary care hospital in Yangon, Myanmar. The eight isolates belonged to five multilocus-sequence types and harbored multiple antimicrobial-resistance genes, resulting in resistance against nearly all of the antimicrobial agents tested, except colistin and fosfomycin. Nine plasmids harboring blaNDM genes were identified from these isolates. Multiple blaNDM genes were found in the distinct Inc-replicon types of the following plasmids: an IncA/C2 plasmid harboring blaNDM-1 (n = 1), IncX3 plasmids harboring blaNDM-4 (n = 2) or blaNDM-7 (n = 1), IncFII plasmids harboring blaNDM-4 (n = 1) or blaNDM-5 (n = 3), and a multireplicon F plasmid harboring blaNDM-5 (n = 1). Comparative analysis highlighted the diversity of the blaNDM-harboring plasmids and their distinct characteristics, which depended on plasmid replicon types. The results indicate circulation of phylogenetically distinct strains of carbapenem-resistant E. coli with various plasmids harboring blaNDM genes in the hospital.
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Affiliation(s)
- Yo Sugawara
- Thailand–Japan Research Collaboration Center on Emerging and Re-emerging Infections, Research Institute for Microbial Diseases, Osaka University, Suita, Japan
- * E-mail: (YA); (YS)
| | - Yukihiro Akeda
- Thailand–Japan Research Collaboration Center on Emerging and Re-emerging Infections, Research Institute for Microbial Diseases, Osaka University, Suita, Japan
- Division of Infection Control and Prevention, Osaka University Hospital, Suita, Japan
- * E-mail: (YA); (YS)
| | - Noriko Sakamoto
- Thailand–Japan Research Collaboration Center on Emerging and Re-emerging Infections, Research Institute for Microbial Diseases, Osaka University, Suita, Japan
| | - Dan Takeuchi
- Thailand–Japan Research Collaboration Center on Emerging and Re-emerging Infections, Research Institute for Microbial Diseases, Osaka University, Suita, Japan
| | - Daisuke Motooka
- Department of Infection Metagenomics, Research Institute for Microbial Diseases, Osaka University, Suita, Japan
| | - Shota Nakamura
- Department of Infection Metagenomics, Research Institute for Microbial Diseases, Osaka University, Suita, Japan
| | - Hideharu Hagiya
- Division of Infection Control and Prevention, Osaka University Hospital, Suita, Japan
| | - Norihisa Yamamoto
- Division of Infection Control and Prevention, Osaka University Hospital, Suita, Japan
| | - Isao Nishi
- Laboratory for Clinical Investigation, Osaka University Hospital, Suita, Japan
| | - Hisao Yoshida
- Division of Infection Control and Prevention, Osaka University Hospital, Suita, Japan
| | - Kazuhisa Okada
- Thailand–Japan Research Collaboration Center on Emerging and Re-emerging Infections, Research Institute for Microbial Diseases, Osaka University, Suita, Japan
| | - Khwar Nyo Zin
- Clinical Laboratory Department, Yangon General Hospital, Yangon, Myanmar
| | - Mya Mya Aye
- Bacteriology Research Division, Department of Medical Research, Yangon, Myanmar
| | - Kazunori Tonomo
- Division of Infection Control and Prevention, Osaka University Hospital, Suita, Japan
| | - Shigeyuki Hamada
- Thailand–Japan Research Collaboration Center on Emerging and Re-emerging Infections, Research Institute for Microbial Diseases, Osaka University, Suita, Japan
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20
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Multihospital Occurrence of Pan-Resistant Klebsiella pneumoniae Sequence Type 147 with an IS Ecp1-Directed blaOXA-181 Insertion in the mgrB Gene in the United Arab Emirates. Antimicrob Agents Chemother 2017; 61:AAC.00418-17. [PMID: 28438945 DOI: 10.1128/aac.00418-17] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2017] [Accepted: 04/19/2017] [Indexed: 11/20/2022] Open
Abstract
The emergence of pan-resistant Klebsiella pneumoniae strains is an increasing concern. In the present study, we describe a cluster of 9 pan-resistant K. pneumoniae sequence type 147 (ST147) isolates encountered in 4 patients over nearly 1 year in 3 hospitals of the United Arab Emirates (UAE). The isolates exhibited highly similar genotypes. All produced chromosomally encoded OXA-181, and the majority also produced the NDM-5 carbapenemase. As with the previously described single isolate from the UAE, MS6671, the mgrB was disrupted by a functional, ISEcp1-driven blaOXA-181 insertion causing resistance to carbapenems. The mutation was successfully complemented with an intact mgrB gene, indicating that it was responsible for colistin resistance. blaNDM-5 was located within a resistance island of an approximately 100-kb IncFII plasmid carrying ermB, mph(A), blaTEM-1B, rmtB, blaNDM-5, sul1, aadA2, and dfrA12 resistance genes. Sequencing this plasmid (pABC143-NDM) revealed that its backbone was nearly identical to that of plasmid pMS6671E from which several resistance genes, including blaNDM-5, had been deleted. More extensive similarities of the backbone and the resistance island were found between pABC143C-NDM and the blaNDM-5-carrying IncFII plasmids of two K. pneumoniae ST147 isolates from South Korea, one of which was colistin resistant, and both also produced OXA-181. Notably, one of these strains was isolated from a patient transferred from the UAE. Our data show that this pan-resistant clone has an alarming capacity to maintain itself over an extended period of time and is even likely to be transmitted internationally.
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21
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Mei YF, Liu PP, Wan LG, Liu Y, Wang LH, Wei DD, Deng Q, Cao XW. Virulence and Genomic Feature of a Virulent Klebsiella pneumoniae Sequence Type 14 Strain of Serotype K2 Harboring blaNDM-5 in China. Front Microbiol 2017; 8:335. [PMID: 28386246 PMCID: PMC5362587 DOI: 10.3389/fmicb.2017.00335] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Accepted: 02/17/2017] [Indexed: 01/08/2023] Open
Abstract
The objective of this study was to reveal the molecular mechanism involved in carbapenem resistance and virulence of a K2 Klebsiella pneumoniae clinical isolate 24835. The virulence of the strain was determined by in vitro and in vivo methods. The de novo whole-genome sequencing technology and molecular biology methods were used to analyze the genomic features associated with the carbapenem resistance and virulence of K. pneumoniae 24835. Strain 24835 was highly resistant to carbapenems and belonged to ST14, exhibited hypermucoviscous and unique K2-aerobactin-kfu-rmpA positive phenotype. As the only carbapenemase gene in strain 24835, blaNDM–5 was located on a 46-kb IncX3 self-transmissible plasmid, which is a very close relation of pNDM-MGR194 from India. Genetic context of blaNDM–5 in strain 24835 was closely related to those on IncX3 plasmids in various Enterobacteriaceae species in China. The combination of multiple virulence genes may work together to confer the relative higher virulence in K. pneumoniae 24835. Significantly increased resistance to serum killing and mice mortality were found in the virulent New Delhi metallo-β-lactamase (NDM)-producing K. pneumoniae strain compared to the other NDM-producing K. pneumoniae strain. Our study provides basic information of phenotypic and genomic features of K. pneumoniae 24835, a strain displaying carbapenem resistance and relatively high level of virulence. These findings are concerning for the potential of NDM-like genes to disseminate among virulent K. pneumoniae isolates.
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Affiliation(s)
- Yan-Fang Mei
- Department of Clinical Microbiology, First Affiliated Hospital of Nanchang University, Nanchang University, Nanchang, China
| | - Pan-Pan Liu
- Department of Clinical Microbiology, First Affiliated Hospital of Nanchang University, Nanchang University, Nanchang, China
| | - La-Gen Wan
- Department of Clinical Microbiology, First Affiliated Hospital of Nanchang University, Nanchang University, Nanchang, China
| | - Yang Liu
- Department of Clinical Microbiology, First Affiliated Hospital of Nanchang University, Nanchang University, Nanchang, China
| | - Lian-Hui Wang
- Department of Clinical Microbiology, First Affiliated Hospital of Nanchang University, Nanchang University, Nanchang, China
| | - Dan-Dan Wei
- Department of Clinical Microbiology, First Affiliated Hospital of Nanchang University, Nanchang University, Nanchang, China
| | - Qiong Deng
- Department of Infection Control, First Affiliated Hospital of Nanchang University, Nanchang University, Nanchang, China
| | - Xian-Wei Cao
- Department of Infection Control, First Affiliated Hospital of Nanchang University, Nanchang University, Nanchang, China
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22
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Lahlaoui H, Bonnin RA, Moussa MB, Khelifa ABH, Naas T. First report of OXA-232-producing Klebsiella pneumoniae strains in Tunisia. Diagn Microbiol Infect Dis 2017; 88:195-197. [PMID: 28341097 DOI: 10.1016/j.diagmicrobio.2017.03.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Revised: 02/28/2017] [Accepted: 03/08/2017] [Indexed: 11/26/2022]
Abstract
Eleven carbapenem-resistant Klebsiella pneumoniae isolates were recovered from the military hospital of Tunis, Tunisia. Three of these isolates carried the carbapenemase blaOXA-232 gene recently identified in France. These isolates were clonally related and co-expressed the extended-spectrum ß-lactamase, CTX-M-15. This work identified the occurrence of OXA-232 producers in North-African countries.
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Affiliation(s)
- Hella Lahlaoui
- EA7361, Université Paris-Sud, Université Paris-Saclay, LabEx Lermit, Bacteriology-Hygiene unit, APHP, Hôpital Bicêtre, Le Kremlin-Bicêtre, France; Laboratory of Microbiology, Military Hospital of Tunis, Monfleury, Tunisia
| | - Rémy A Bonnin
- EA7361, Université Paris-Sud, Université Paris-Saclay, LabEx Lermit, Bacteriology-Hygiene unit, APHP, Hôpital Bicêtre, Le Kremlin-Bicêtre, France; Associated French National Reference Center for Antibiotic Resistance: Carbapenemase-producing Enterobacteriaceae, Le Kremlin-Bicêtre, France; Evolution and Ecology of Resistance to Antibiotics Unit, Institut Pasteur-APHP-Université Paris Sud, Paris, France.
| | - Mohamed Ben Moussa
- Laboratory of Microbiology, Military Hospital of Tunis, Monfleury, Tunisia
| | | | - Thierry Naas
- EA7361, Université Paris-Sud, Université Paris-Saclay, LabEx Lermit, Bacteriology-Hygiene unit, APHP, Hôpital Bicêtre, Le Kremlin-Bicêtre, France; Associated French National Reference Center for Antibiotic Resistance: Carbapenemase-producing Enterobacteriaceae, Le Kremlin-Bicêtre, France; Evolution and Ecology of Resistance to Antibiotics Unit, Institut Pasteur-APHP-Université Paris Sud, Paris, France
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23
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Potter RF, D'Souza AW, Dantas G. The rapid spread of carbapenem-resistant Enterobacteriaceae. Drug Resist Updat 2016; 29:30-46. [PMID: 27912842 DOI: 10.1016/j.drup.2016.09.002] [Citation(s) in RCA: 239] [Impact Index Per Article: 29.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Revised: 08/23/2016] [Accepted: 09/07/2016] [Indexed: 02/07/2023]
Abstract
Carbapenems, our one-time silver bullet for multidrug resistant bacterial infections, are now threatened by widespread dissemination of carbapenem-resistant Enterobacteriaceae (CRE). Successful expansion of Enterobacteriaceae clonal groups and frequent horizontal gene transfer of carbapenemase expressing plasmids are causing increasing carbapenem resistance. Recent advances in genetic and phenotypic detection facilitate global surveillance of CRE diversity and prevalence. In particular, whole genome sequencing enabled efficient tracking, annotation, and study of genetic elements colocalized with carbapenemase genes on chromosomes and on plasmids. Improved characterization helps detail the co-occurrence of other antibiotic resistance genes in CRE isolates and helps identify pan-drug resistance mechanisms. The novel β-lactamase inhibitor, avibactam, combined with ceftazidime or aztreonam, is a promising CRE treatment compared to current colistin or tigecycline regimens. To halt increasing CRE-associated morbidity and mortality, we must continue quality, cooperative monitoring and urgently investigate novel treatments.
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Affiliation(s)
- Robert F Potter
- Center for Genome Sciences and System Biology, Washington University School of Medicine, 4515 McKinley Avenue, Campus Box 8510, St. Louis, MO 63110, USA
| | - Alaric W D'Souza
- Center for Genome Sciences and System Biology, Washington University School of Medicine, 4515 McKinley Avenue, Campus Box 8510, St. Louis, MO 63110, USA
| | - Gautam Dantas
- Center for Genome Sciences and System Biology, Washington University School of Medicine, 4515 McKinley Avenue, Campus Box 8510, St. Louis, MO 63110, USA; Department of Pathology & Immunology, Washington University School of Medicine, 660 South Euclid Ave, St. Louis, MO 63110, USA; Department of Biomedical Engineering, Washington University in Saint Louis, 1 Brookings Drive, St. Louis, MO 63130, USA; Department of Molecular Microbiology, Washington University School of Medicine, 660 S. Euclid Ave, St. Louis, MO 63110, USA.
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