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Rodrigues DCS, Silveira MC, Pribul BR, Karam BRS, Picão RC, Kraychete GB, Pereira FM, de Lima RM, de Souza AKG, Leão RS, Marques EA, Rocha-de-Souza CM, Carvalho-Assef APD. Genomic study of Acinetobacter baumannii strains co-harboring bla OXA-58 and bla NDM-1 reveals a large multidrug-resistant plasmid encoding these carbapenemases in Brazil. Front Microbiol 2024; 15:1439373. [PMID: 39086650 PMCID: PMC11288812 DOI: 10.3389/fmicb.2024.1439373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2024] [Accepted: 07/01/2024] [Indexed: 08/02/2024] Open
Abstract
Introduction Acinetobacter baumannii contributes significantly to the global issue of multidrug-resistant (MDR) nosocomial infections. Often, these strains demonstrate resistance to carbapenems (MDR-CRAB), the first-line treatment for infections instigated by MDR A. baumannii. Our study focused on the antimicrobial susceptibility and genomic sequences related to plasmids from 12 clinical isolates of A. baumannii that carry both the blaOXA-58 and bla NDM-1 carbapenemase genes. Methods Whole-genome sequencing with long-read technology was employed for the characterization of an A. baumannii plasmid that harbors the bla OXA-58 and blaNDM-1 genes. The location of the bla OXA-58 and bla NDM-1 genes was confirmed through Southern blot hybridization assays. Antimicrobial susceptibility tests were conducted, and molecular characterization was performed using PCR and PFGE. Results Multilocus Sequence Typing analysis revealed considerable genetic diversity among bla OXA-58 and bla NDM-1 positive strains in Brazil. It was confirmed that these genes were located on a plasmid larger than 300 kb in isolates from the same hospital, which also carry other antimicrobial resistance genes. Different genetic contexts were observed for the co-occurrence of these carbapenemase-encoding genes in Brazilian strains. Discussion The propagation of bla OXA-58 and bla NDM-1 genes on the same plasmid, which also carries other resistance determinants, could potentially lead to the emergence of bacterial strains resistant to multiple classes of antimicrobials. Therefore, the characterization of these strains is of paramount importance for monitoring resistance evolution, curbing their rapid global dissemination, averting outbreaks, and optimizing therapy.
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Affiliation(s)
- Daiana Cristina Silva Rodrigues
- Laboratório de Bacteriologia Aplicada à Saúde Única e Resistência Antimicrobiana (LabSUR), Instituto Oswaldo Cruz (IOC), Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro, Brazil
| | - Melise Chaves Silveira
- Laboratório de Bacteriologia Aplicada à Saúde Única e Resistência Antimicrobiana (LabSUR), Instituto Oswaldo Cruz (IOC), Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro, Brazil
| | - Bruno Rocha Pribul
- Laboratório de Bacteriologia Aplicada à Saúde Única e Resistência Antimicrobiana (LabSUR), Instituto Oswaldo Cruz (IOC), Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro, Brazil
| | - Bruna Ribeiro Sued Karam
- Laboratório de Bacteriologia Aplicada à Saúde Única e Resistência Antimicrobiana (LabSUR), Instituto Oswaldo Cruz (IOC), Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro, Brazil
| | - Renata Cristina Picão
- Laboratório de Investigação em Microbiologia Médica (LIMM), Instituto de Microbiologia Paulo de Góes (IMPG), Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Gabriela Bergiante Kraychete
- Laboratório de Investigação em Microbiologia Médica (LIMM), Instituto de Microbiologia Paulo de Góes (IMPG), Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | | | - Rildo Mendes de Lima
- Laboratório Central de Saúde Pública da Fundação de Vigilância em Saúde do Amazonas (LACEN-AM/FVS-RCP), Amazonas, Brazil
| | | | - Robson Souza Leão
- Departamento de Microbiologia, Imunologia e Parasitologia (DMIP), Faculdade de Ciências Médicas (FCM), Universidade do Estado do Rio de Janeiro (UERJ), Rio de Janeiro, Brazil
| | - Elizabeth Andrade Marques
- Departamento de Microbiologia, Imunologia e Parasitologia (DMIP), Faculdade de Ciências Médicas (FCM), Universidade do Estado do Rio de Janeiro (UERJ), Rio de Janeiro, Brazil
| | - Cláudio Marcos Rocha-de-Souza
- Laboratório de Bacteriologia Aplicada à Saúde Única e Resistência Antimicrobiana (LabSUR), Instituto Oswaldo Cruz (IOC), Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro, Brazil
| | - Ana Paula D'Alincourt Carvalho-Assef
- Laboratório de Bacteriologia Aplicada à Saúde Única e Resistência Antimicrobiana (LabSUR), Instituto Oswaldo Cruz (IOC), Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro, Brazil
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Sotomayor N, Villacis JE, Burneo N, Reyes J, Zapata S, Bayas-Rea RDLÁ. Carbapenemase genes in clinical and environmental isolates of Acinetobacter spp. from Quito, Ecuador. PeerJ 2024; 12:e17199. [PMID: 38680892 PMCID: PMC11056107 DOI: 10.7717/peerj.17199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Accepted: 03/14/2024] [Indexed: 05/01/2024] Open
Abstract
Carbapenem-resistant Acinetobacter spp. is associated with nosocomial infections in intensive care unit patients, resulting in high mortality. Although Acinetobacter spp. represent a serious public health problem worldwide, there are a few studies related to the presence of carbapenemases in health care facilities and other environmental settings in Ecuador. The main aim of this study was to characterize the carbapenem-resistant Acinetobacter spp. isolates obtained from four hospitals (52) and from five rivers (27) close to Quito. We used the disc diffusion and EDTA sinergy tests to determine the antimicrobial susceptibility and the production of metallo β-lactamases, respectively. We carried out a multiplex PCR of gyrB gene and the sequencing of partial rpoB gene to bacterial species identification. We performed molecular screening of nine carbapenem-resistant genes (blaSPM, blaSIM, blaGIM, blaGES, blaOXA-23, blaOXA-24, blaOXA-51, blaOXA-58, and blaOXA-143) by multiplex PCR, followed by identification using sequencing of blaOXA genes. Our findings showed that carbapenem-resistant A. baumannii were the main species found in health care facilities and rivers. Most of the clinical isolates came from respiratory tract samples and harbored blaOXA-23, blaOXA-366, blaOXA-72, blaOXA-65, blaOXA-70, and blaOXA-143-like genes. The river isolates harbored only the blaOXA-51 and probably blaOXA-259 genes. We concluded that the most predominant type of carbapenem genes among isolates were both blaOXA-23 and blaOXA-65 among A. baumannii clinical isolates.
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Affiliation(s)
- Nicole Sotomayor
- Escuela de Ciencias Biológicas, Pontificia Universidad Católica del Ecuador, Quito, Ecuador
| | - José Eduardo Villacis
- Centro de Referencia Nacional de Resistencia a los Antimicrobianos, Instituto Nacional de Investigación en Salud Pública-INSPI Dr. Leopoldo Izquieta Pérez, Quito, Ecuador
- Centro de Investigación para la Salud en América Latina (CISeAL), Pontificia Universidad Católica del Ecuador, Quito, Ecuador
| | - Noela Burneo
- Escuela de Ciencias Biológicas, Pontificia Universidad Católica del Ecuador, Quito, Ecuador
| | - Jorge Reyes
- Facultad de Ciencias Químicas, Universidad Central del Ecuador, Quito, Ecuador
| | - Sonia Zapata
- Instituto de Microbiología, Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito, Quito, Ecuador
| | - Rosa de los Ángeles Bayas-Rea
- Escuela de Ciencias Biológicas, Pontificia Universidad Católica del Ecuador, Quito, Ecuador
- Instituto de Microbiología, Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito, Quito, Ecuador
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Manyahi J, Moyo SJ, Kibwana U, Goodman RN, Allman E, Hubbard ATM, Blomberg B, Langeland N, Roberts AP. First identification of bla
NDM-5 producing Escherichia coli from neonates and a HIV infected adult in Tanzania. J Med Microbiol 2022; 71. [PMID: 35225760 PMCID: PMC8941953 DOI: 10.1099/jmm.0.001513] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Introduction. Carbapenem-resistant members of the family Enterobacteriaceae are emerging as a global public-health threat and cause substantial challenges in clinical practice. Gap Statement. There is a need for increased and continued genomic surveillance of antimicrobial resistance genes globally in order to detect outbreaks and dissemination of clinically important resistance genes and their associated mobile genetic elements in human pathogens. Aim. To describe the resistance mechanisms of carbapenem-resistant Escherichia coli. Methods. Rectal swabs from neonates and newly diagnosed human immunodeficiency virus (HIV) infected adults were collected between April 2017 and May 2018 and screened for faecal carriage of carbapenamases and OXA-48 producing members of the family Enterobacteriaceae. Bacterial isolates were identified using matrix assisted laser desorption ionization time of flight mass spectrometry. Antimicrobial susceptibility testing was performed by E-test. Whole genomes of carbapenem-resistant E. coli were investigated using a hybrid assembly of Illumina and Oxford Nanopore Technologies sequencing reads. Results. Three carbapenem-resistant E. coli were detected, two from neonates and one from an HIV infected adult. All three isolates carried blaNDM-5. Two E. coli from neonates belonged to ST167 and blaNDM-5 co-existed with blaCTX-M-15 and blaOXA-01, and all were carried on IncFIA type plasmids. The E. coli from the HIV infected adult belonged to ST2083, and carried blaNDM-5 on an IncX3 type plasmid and blaCMY-42 on an IncI type plasmid. All blaNDM-5 carrying plasmids contained conjugation related genes. In addition, E. coli from the HIV infected adult carried three more plasmid types; IncFIA, IncFIB and Col(BS512). One E. coli from a neonate also carried one extra plasmid Col(BS512). All three E. coli harboured resistance genes to fluoroquinolone, aminoglycosides, sulfamethoxazole, trimethoprim, macrolides and tetracycline, carried on the IncFIA type plasmid. Furthermore, E. coli from the neonates carried a chloramphenicol resistance gene (catB3), also on the IncFIA plasmid. All three isolates were susceptible to colistin. Conclusion. This is the first report, to our knowledge, from Tanzania detecting blaNDM-5 producing E. coli. The carbapenemase gene was carried on an IncFIA and IncX3 type plasmids. Our findings highlight the urgent need for a robust antimicrobial resistance (AMR) surveillance system to monitor and rapidly report on the incidence and spread of emerging resistant bacteria in Tanzania.
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Affiliation(s)
- Joel Manyahi
- Department of Microbiology and Immunology, Muhimbili University of Health and Allied Sciences, MUHAS, Dar es Salaam, Tanzania
- Department of Clinical Science, University of Bergen, Bergen, Norway
- Norwegian National Advisory Unit for Tropical Infectious Diseases, Haukeland University Hospital, Bergen, Norway
| | - Sabrina J. Moyo
- Department of Clinical Science, University of Bergen, Bergen, Norway
- Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Liverpool L3 5QA, UK
- Department of Microbiology and Immunology, Muhimbili University of Health and Allied Sciences, MUHAS, Dar es Salaam, Tanzania
| | - Upendo Kibwana
- Department of Microbiology and Immunology, Muhimbili University of Health and Allied Sciences, MUHAS, Dar es Salaam, Tanzania
| | - Richard N. Goodman
- Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Liverpool L3 5QA, UK
| | - Ellie Allman
- Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Liverpool L3 5QA, UK
| | - Alasdair T. M. Hubbard
- Department of Biosciences, School of Science and Technology, Nottingham Trent University, Nottingham NG11 8NS, UK
- Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Liverpool L3 5QA, UK
| | - Bjørn Blomberg
- Norwegian National Advisory Unit for Tropical Infectious Diseases, Haukeland University Hospital, Bergen, Norway
- Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Nina Langeland
- Norwegian National Advisory Unit for Tropical Infectious Diseases, Haukeland University Hospital, Bergen, Norway
- Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Adam P. Roberts
- Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Liverpool L3 5QA, UK
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Naing SY, Hordijk J, Duim B, Broens EM, van der Graaf-van Bloois L, Rossen JW, Robben JH, Leendertse M, Wagenaar JA, Zomer AL. Genomic Investigation of Two Acinetobacter baumannii Outbreaks in a Veterinary Intensive Care Unit in The Netherlands. Pathogens 2022; 11:pathogens11020123. [PMID: 35215067 PMCID: PMC8875366 DOI: 10.3390/pathogens11020123] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 01/17/2022] [Accepted: 01/19/2022] [Indexed: 01/27/2023] Open
Abstract
Acinetobacter baumannii is a nosocomial pathogen that frequently causes healthcare-acquired infections. The global spread of multidrug-resistant (MDR) strains with its ability to survive in the environment for extended periods imposes a pressing public health threat. Two MDR A. baumannii outbreaks occurred in 2012 and 2014 in a companion animal intensive care unit (caICU) in the Netherlands. Whole-genome sequencing (WGS) was performed on dog clinical isolates (n = 6), environmental isolates (n = 5), and human reference strains (n = 3) to investigate if the isolates of the two outbreaks were related. All clinical isolates shared identical resistance phenotypes displaying multidrug resistance. Multi-locus Sequence Typing (MLST) revealed that all clinical isolates belonged to sequence type ST2. The core genome MLST (cgMLST) results confirmed that the isolates of the two outbreaks were not related. Comparative genome analysis showed that the outbreak isolates contained different gene contents, including mobile genetic elements associated with antimicrobial resistance genes (ARGs). The time-measured phylogenetic reconstruction revealed that the outbreak isolates diverged approximately 30 years before 2014. Our study shows the importance of WGS analyses combined with molecular clock investigations to reduce transmission of MDR A. baumannii infections in companion animal clinics.
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Affiliation(s)
- Soe Yu Naing
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, 3584 CM Utrecht, The Netherlands; (S.Y.N.); (J.H.); (B.D.); (E.M.B.); (L.v.d.G.-v.B.); (M.L.); (J.A.W.)
| | - Joost Hordijk
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, 3584 CM Utrecht, The Netherlands; (S.Y.N.); (J.H.); (B.D.); (E.M.B.); (L.v.d.G.-v.B.); (M.L.); (J.A.W.)
| | - Birgitta Duim
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, 3584 CM Utrecht, The Netherlands; (S.Y.N.); (J.H.); (B.D.); (E.M.B.); (L.v.d.G.-v.B.); (M.L.); (J.A.W.)
| | - Els M. Broens
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, 3584 CM Utrecht, The Netherlands; (S.Y.N.); (J.H.); (B.D.); (E.M.B.); (L.v.d.G.-v.B.); (M.L.); (J.A.W.)
| | - Linda van der Graaf-van Bloois
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, 3584 CM Utrecht, The Netherlands; (S.Y.N.); (J.H.); (B.D.); (E.M.B.); (L.v.d.G.-v.B.); (M.L.); (J.A.W.)
| | - John W. Rossen
- Department of Medical Microbiology, University Medical Center, University of Groningen, 9700 AB Groningen, The Netherlands;
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Joris H. Robben
- Department of Clinical Sciences of Companion Animals, Faculty of Veterinary Medicine, Utrecht University, 3584 CM Utrecht, The Netherlands;
| | - Masja Leendertse
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, 3584 CM Utrecht, The Netherlands; (S.Y.N.); (J.H.); (B.D.); (E.M.B.); (L.v.d.G.-v.B.); (M.L.); (J.A.W.)
| | - Jaap A. Wagenaar
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, 3584 CM Utrecht, The Netherlands; (S.Y.N.); (J.H.); (B.D.); (E.M.B.); (L.v.d.G.-v.B.); (M.L.); (J.A.W.)
| | - Aldert L. Zomer
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, 3584 CM Utrecht, The Netherlands; (S.Y.N.); (J.H.); (B.D.); (E.M.B.); (L.v.d.G.-v.B.); (M.L.); (J.A.W.)
- Correspondence:
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Intracellular Transposition and Capture of Mobile Genetic Elements following Intercellular Conjugation of Multidrug Resistance Conjugative Plasmids from Clinical Enterobacteriaceae Isolates. Microbiol Spectr 2022; 10:e0214021. [PMID: 35044219 PMCID: PMC8768599 DOI: 10.1128/spectrum.02140-21] [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] [Indexed: 11/20/2022] Open
Abstract
Mobile genetic elements (MGEs) are often associated with antimicrobial resistance genes (ARGs). They are responsible for intracellular transposition between different replicons and intercellular conjugation and are therefore important agents of ARG dissemination. Detection and characterization of functional MGEs, especially in clinical isolates, would increase our understanding of the underlying pathways of transposition and recombination and allow us to determine interventional strategies to interrupt this process. Entrapment vectors can be used to capture active MGEs, as they contain a positive selection genetic system conferring a selectable phenotype upon the insertion of an MGE within certain regions of that system. Previously, we developed the pBACpAK entrapment vector that results in a tetracycline-resistant phenotype when MGEs translocate and disrupt the cI repressor gene. We have previously used pBACpAK to capture MGEs in clinical Escherichia coli isolates following transformation with pBACpAK. In this study, we aimed to extend the utilization of pBACpAK to other bacterial taxa. We utilized an MGE-free recipient E. coli strain containing pBACpAK to capture MGEs on conjugative, ARG-containing plasmids following conjugation from clinical Enterobacteriaceae donors. Following the conjugative transfer of multiple conjugative plasmids and screening for tetracycline resistance in these transconjugants, we captured several insertion sequence (IS) elements and novel transposons (Tn7350 and Tn7351) and detected the de novo formation of novel putative composite transposons where the pBACpAK-located tet(A) is flanked by ISKpn25 from the transferred conjugative plasmid, as well as the ISKpn14-mediated integration of an entire 119-kb, blaNDM-1-containing conjugative plasmid from Klebsiella pneumoniae. IMPORTANCE By analyzing transposition activity within our MGE-free recipient, we can gain insights into the interaction and evolution of multidrug resistance-conferring MGEs following conjugation, including the movement of multiple ISs, the formation of composite transposons, and cointegration and/or recombination between different replicons in the same cell. This combination of recipient and entrapment vector will allow fine-scale experimental studies of factors affecting intracellular transposition and MGE formation in and from ARG-encoding MGEs from multiple species of clinically relevant Enterobacteriaceae.
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