1
|
Wang Y, Dagan T. The evolution of antibiotic resistance islands occurs within the framework of plasmid lineages. Nat Commun 2024; 15:4555. [PMID: 38811529 PMCID: PMC11137137 DOI: 10.1038/s41467-024-48352-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Accepted: 04/25/2024] [Indexed: 05/31/2024] Open
Abstract
Bacterial pathogens carrying multidrug resistance (MDR) plasmids are a major threat to human health. The acquisition of antibiotic resistance genes (ARGs) in plasmids is often facilitated by mobile genetic elements that copy or translocate ARGs between DNA molecules. The agglomeration of mobile elements in plasmids generates resistance islands comprising multiple ARGs. However, whether the emergence of resistance islands is restricted to specific MDR plasmid lineages remains understudied. Here we show that the agglomeration of ARGs in resistance islands is biased towards specific large plasmid lineages. Analyzing 6784 plasmids in 2441 Escherichia, Salmonella, and Klebsiella isolates, we quantify that 84% of the ARGs in MDR plasmids are found in resistance islands. We furthermore observe rapid evolution of ARG combinations in resistance islands. Most regions identified as resistance islands are shared among closely related plasmids but rarely among distantly related plasmids. Our results suggest the presence of barriers for the dissemination of ARGs between plasmid lineages, which are related to plasmid genetic properties, host range and the plasmid evolutionary history. The agglomeration of ARGs in plasmids is attributed to the workings of mobile genetic elements that operate within the framework of existing plasmid lineages.
Collapse
Affiliation(s)
- Yiqing Wang
- Institute of General Microbiology, Kiel University, Kiel, Germany
| | - Tal Dagan
- Institute of General Microbiology, Kiel University, Kiel, Germany.
| |
Collapse
|
2
|
Aranzamendi M, Xanthopoulou K, Sánchez-Urtaza S, Burgwinkel T, Arazo del Pino R, Lucaßen K, Pérez-Vázquez M, Oteo-Iglesias J, Sota M, Marimón JM, Seifert H, Higgins PG, Gallego L. Genomic Surveillance Uncovers a 10-Year Persistence of an OXA-24/40 Acinetobacter baumannii Clone in a Tertiary Hospital in Northern Spain. Int J Mol Sci 2024; 25:2333. [PMID: 38397011 PMCID: PMC10889530 DOI: 10.3390/ijms25042333] [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: 01/03/2024] [Revised: 02/09/2024] [Accepted: 02/13/2024] [Indexed: 02/25/2024] Open
Abstract
Infections caused by carbapenem-resistant Acinetobacter baumannii are a global threat causing a high number of fatal infections. This microorganism can also easily acquire antibiotic resistance determinants, making the treatment of infections a big challenge, and has the ability to persist in the hospital environment under a wide range of conditions. The objective of this work was to study the molecular epidemiology and genetic characteristics of two blaOXA24/40Acinetobacter baumannii outbreaks (2009 and 2020-21) at a tertiary hospital in Northern Spain. Thirty-six isolates were investigated and genotypically screened by Whole Genome Sequencing to analyse the resistome and virulome. Isolates were resistant to carbapenems, aminoglycosides and fluoroquinolones. Multi-Locus Sequence Typing analysis identified that Outbreak 1 was mainly produced by isolates belonging to ST3Pas/ST106Oxf (IC3) containing blaOXA24/40, blaOXA71 and blaADC119. Outbreak 2 isolates were exclusively ST2Pas/ST801Oxf (IC2) blaOXA24/40, blaOXA66 and blaADC30, the same genotype seen in two isolates from 2009. Virulome analysis showed that IC2 isolates contained genes for capsular polysaccharide KL32 and lipooligosacharide OCL5. A 8.9 Kb plasmid encoding the blaOXA24/40 gene was common in all isolates. The persistance over time of a virulent IC2 clone highlights the need of active surveillance to control its spread.
Collapse
Affiliation(s)
- Maitane Aranzamendi
- Respiratory Infection and Antimicrobial Resistance Group, Microbiology Department, Infectious Diseases Area, Biogipuzkoa Health Research Institute, Osakidetza Basque Health Service, Donostialdea Integrated Health Organization, 20014 San Sebastián, Spain; (M.A.); (J.M.M.)
- Acinetobacter baumannii Research Group, Department of Immunology, Microbiology and Parasitology, Faculty of Medicine and Nursing, University of the Basque Country UPV/EHU, 48940 Leioa, Spain;
| | - Kyriaki Xanthopoulou
- Institute for Medical Microbiology, Immunology and Hygiene, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50935 Cologne, Germany; (K.X.); (T.B.); (R.A.d.P.); (K.L.); (H.S.)
- German Center for Infection Research (DZIF), Partner Site Bonn-Cologne, 50935 Cologne, Germany
| | - Sandra Sánchez-Urtaza
- Acinetobacter baumannii Research Group, Department of Immunology, Microbiology and Parasitology, Faculty of Medicine and Nursing, University of the Basque Country UPV/EHU, 48940 Leioa, Spain;
| | - Tessa Burgwinkel
- Institute for Medical Microbiology, Immunology and Hygiene, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50935 Cologne, Germany; (K.X.); (T.B.); (R.A.d.P.); (K.L.); (H.S.)
- German Center for Infection Research (DZIF), Partner Site Bonn-Cologne, 50935 Cologne, Germany
| | - Rocío Arazo del Pino
- Institute for Medical Microbiology, Immunology and Hygiene, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50935 Cologne, Germany; (K.X.); (T.B.); (R.A.d.P.); (K.L.); (H.S.)
- German Center for Infection Research (DZIF), Partner Site Bonn-Cologne, 50935 Cologne, Germany
| | - Kai Lucaßen
- Institute for Medical Microbiology, Immunology and Hygiene, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50935 Cologne, Germany; (K.X.); (T.B.); (R.A.d.P.); (K.L.); (H.S.)
- German Center for Infection Research (DZIF), Partner Site Bonn-Cologne, 50935 Cologne, Germany
| | - M. Pérez-Vázquez
- National Center of Microbiology, Reference and Research Laboratory for Antibiotic Resistance, ISCIII, Centro de Investigación Biomédica en Red, Enfermedades Infecciosas (CIBERINFEC), 28220 Madrid, Spain; (M.P.-V.); (J.O.-I.)
| | - Jesús Oteo-Iglesias
- National Center of Microbiology, Reference and Research Laboratory for Antibiotic Resistance, ISCIII, Centro de Investigación Biomédica en Red, Enfermedades Infecciosas (CIBERINFEC), 28220 Madrid, Spain; (M.P.-V.); (J.O.-I.)
| | - Mercedes Sota
- Clinical Laboratory Management Department, IIS Biodonostia Health Research Institute, University Hospital Donostia, 20014 Donostia, Spain;
| | - Jose María Marimón
- Respiratory Infection and Antimicrobial Resistance Group, Microbiology Department, Infectious Diseases Area, Biogipuzkoa Health Research Institute, Osakidetza Basque Health Service, Donostialdea Integrated Health Organization, 20014 San Sebastián, Spain; (M.A.); (J.M.M.)
| | - Harald Seifert
- Institute for Medical Microbiology, Immunology and Hygiene, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50935 Cologne, Germany; (K.X.); (T.B.); (R.A.d.P.); (K.L.); (H.S.)
- German Center for Infection Research (DZIF), Partner Site Bonn-Cologne, 50935 Cologne, Germany
- Institute of Translational Research, CECAD Cluster of Excellence, University of Cologne, 50935, Cologne, Germany
| | - Paul G. Higgins
- Institute for Medical Microbiology, Immunology and Hygiene, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50935 Cologne, Germany; (K.X.); (T.B.); (R.A.d.P.); (K.L.); (H.S.)
- German Center for Infection Research (DZIF), Partner Site Bonn-Cologne, 50935 Cologne, Germany
| | - Lucía Gallego
- Acinetobacter baumannii Research Group, Department of Immunology, Microbiology and Parasitology, Faculty of Medicine and Nursing, University of the Basque Country UPV/EHU, 48940 Leioa, Spain;
| |
Collapse
|
3
|
Wiradiputra MRD, Thirapanmethee K, Khuntayaporn P, Wanapaisan P, Chomnawang MT. Comparative genotypic characterization related to antibiotic resistance phenotypes of clinical carbapenem-resistant Acinetobacter baumannii MTC1106 (ST2) and MTC0619 (ST25). BMC Genomics 2023; 24:689. [PMID: 37978344 PMCID: PMC10655397 DOI: 10.1186/s12864-023-09734-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 10/11/2023] [Indexed: 11/19/2023] Open
Abstract
BACKGROUND The prevalence of Acinetobacter baumannii in nosocomial infections and its remarkable ability to develop antimicrobial resistance have been a critical issue in hospital settings. Here, we examined the genomic features related to resistance phenotype displayed by carbapenem-resistant A. baumannii (CRAB) MTC1106 (ST2) and MTC0619 (ST25). RESULTS Resistome analysis of both strains revealed that MTC1106 possessed higher numbers of antimicrobial resistance genes compared to MTC0619. Some of those genetic determinants were present in accordance with the susceptibility profile of the isolates. The predicted ISAba1 region upstream of blaOXA-23 gene was related to carbapenem resistance since this IS element was well-characterized to mediate overexpression of carbapenemase genes and eventually provided capability to confer resistance. Unlike MTC0619 strain, which only carried class B and D β-lactamase genes, MTC1106 strain also possessed blaTEM-1D, a class A β-lactamase. Regarding to aminoglycosides resistance, MTC0619 contained 5 related genes in which all of them belonged to three groups of aminoglycosides modifying enzyme (AME), namely, N-acetyltransferase (AAC), O-nucleotidyltransferase (ANT), and O-phosphotransferase (APH). On the other hand, MTC1106 lacked only the AAC of which found in MTC0619, yet it also carried an armA gene encoding for 16S rRNA methyltransferase. Two macrolides resistance genes, mph(E) and msr(E), were identified next to the armA gene of MTC1106 isolate in which they encoded for macrolide 2'-phosphotransferase and ABC-type efflux pump, respectively. Besides acquired resistance genes, some chromosomal genes and SNPs associated with resistance to fluoroquinolones (i.e. gyrA and parC) and colistin (i.e. pmrCAB, eptA, and emrAB) were observed. However, gene expression analysis suggested that the genetic determinants significantly contributing to low-level colistin resistance remained unclear. In addition, similar number of efflux pumps genes were identified in both lineages with only the absence of adeC, a part of adeABC RND-type multidrug efflux pump in MTC0619 strain. CONCLUSIONS We found that MTC1106 strain harbored more antimicrobial resistance genes and showed higher resistance to antibiotics than MTC0619 strain. Regarding genomic characterization, this study was likely the first genome comparative analysis of CARB that specifically included isolates belonging to ST2 and ST25 which were widely spread in Thailand. Taken altogether, this study suggests the importance to monitor the resistance status of circulating A. baumannii clones and identify genes that may contribute to shifting the resistance trend among isolates.
Collapse
Affiliation(s)
- Made Rai Dwitya Wiradiputra
- Antimicrobial Resistance Interdisciplinary Group (AmRIG), Faculty of Pharmacy, Mahidol University, Bangkok, Thailand
- Biopharmaceutical Sciences Program, Faculty of Pharmacy, Mahidol University, Bangkok, Thailand
| | - Krit Thirapanmethee
- Antimicrobial Resistance Interdisciplinary Group (AmRIG), Faculty of Pharmacy, Mahidol University, Bangkok, Thailand
- Department of Microbiology, Faculty of Pharmacy, Mahidol University, Bangkok, Thailand
| | - Piyatip Khuntayaporn
- Antimicrobial Resistance Interdisciplinary Group (AmRIG), Faculty of Pharmacy, Mahidol University, Bangkok, Thailand
- Department of Microbiology, Faculty of Pharmacy, Mahidol University, Bangkok, Thailand
| | - Pagakrong Wanapaisan
- Antimicrobial Resistance Interdisciplinary Group (AmRIG), Faculty of Pharmacy, Mahidol University, Bangkok, Thailand
- Department of Microbiology, Faculty of Pharmacy, Mahidol University, Bangkok, Thailand
| | - Mullika Traidej Chomnawang
- Antimicrobial Resistance Interdisciplinary Group (AmRIG), Faculty of Pharmacy, Mahidol University, Bangkok, Thailand.
- Department of Microbiology, Faculty of Pharmacy, Mahidol University, Bangkok, Thailand.
| |
Collapse
|
4
|
Gaillot S, Oueslati S, Vuillemenot JB, Bour M, Iorga BI, Triponney P, Plésiat P, Bonnin RA, Naas T, Jeannot K, Potron A. Genomic characterization of an NDM-9-producing Acinetobacter baumannii clinical isolate and role of Glu152Lys substitution in the enhanced cefiderocol hydrolysis of NDM-9. Front Microbiol 2023; 14:1253160. [PMID: 37700870 PMCID: PMC10493327 DOI: 10.3389/fmicb.2023.1253160] [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: 07/04/2023] [Accepted: 08/08/2023] [Indexed: 09/14/2023] Open
Abstract
Here, we characterized the first French NDM-9-producing Acinetobacter baumannii isolate. A. baumannii 13A297, which belonged to the STPas25 (international clone IC7), was highly resistant to β-lactams including cefiderocol (MIC >32 mg/L). Whole genome sequencing (WGS) using both Illumina and Oxford Nanopore technologies revealed a 166-kb non-conjugative plasmid harboring a blaNDM-9 gene embedded in a Tn125 composite transposon. Complementation of E. coli DH5α and A. baumannii CIP70.10 strains with the pABEC plasmid carrying the blaNDM-1 or blaNDM-9 gene, respectively, resulted in a significant increase in cefiderocol MIC values (16 to >256-fold), particularly in the NDM-9 transformants. Interestingly, steady-state kinetic parameters, measured using purified NDM-1 and NDM-9 (Glu152Lys) enzymes, revealed that the affinity for cefiderocol was 3-fold higher for NDM-9 (Km = 53 μM) than for NDM-1 (Km = 161 μM), leading to a 2-fold increase in catalytic efficiency for NDM-9 (0.13 and 0.069 μM-1.s-1, for NDM-9 and NDM-1, respectively). Finally, we showed by molecular docking experiments that the residue 152 of NDM-like enzymes plays a key role in cefiderocol binding and resistance, by allowing a strong ionic interaction between the Lys152 residue of NDM-9 with both the Asp223 residue of NDM-9 and the carboxylate group of the R1 substituent of cefiderocol.
Collapse
Affiliation(s)
- Susie Gaillot
- Université de Franche-Comté, UMR CNRS 6249 Chrono-Environnement, Besançon, France
| | - Saoussen Oueslati
- Université Paris-Saclay, Equipe INSERM ReSIST, Faculté de Médecine, Le Kremlin-Bicêtre, France
| | - Jean-Baptiste Vuillemenot
- Université de Franche-Comté, UMR CNRS 6249 Chrono-Environnement, Besançon, France
- Laboratoire Associé du Centre National de Référence de la Résistance aux Antibiotiques, Centre Hospitalier Universitaire de Besançon, Besançon, France
| | - Maxime Bour
- Laboratoire Associé du Centre National de Référence de la Résistance aux Antibiotiques, Centre Hospitalier Universitaire de Besançon, Besançon, France
| | - Bogdan I. Iorga
- Université Paris-Saclay, CNRS Institut de Chimie des Substances Naturelles, Gif-sur-Yvette, France
| | - Pauline Triponney
- Laboratoire Associé du Centre National de Référence de la Résistance aux Antibiotiques, Centre Hospitalier Universitaire de Besançon, Besançon, France
| | - Patrick Plésiat
- Université de Franche-Comté, UMR CNRS 6249 Chrono-Environnement, Besançon, France
- Laboratoire Associé du Centre National de Référence de la Résistance aux Antibiotiques, Centre Hospitalier Universitaire de Besançon, Besançon, France
| | - Rémy A. Bonnin
- Université Paris-Saclay, Equipe INSERM ReSIST, Faculté de Médecine, Le Kremlin-Bicêtre, France
- Laboratoire Associé du Centre National de Référence de la Résistance aux Antibiotiques: Entérobactéries Résistantes aux Carbapénèmes, Le Kremlin-Bicêtre, France
| | - Thierry Naas
- Université Paris-Saclay, Equipe INSERM ReSIST, Faculté de Médecine, Le Kremlin-Bicêtre, France
- Laboratoire Associé du Centre National de Référence de la Résistance aux Antibiotiques: Entérobactéries Résistantes aux Carbapénèmes, Le Kremlin-Bicêtre, France
| | - Katy Jeannot
- Université de Franche-Comté, UMR CNRS 6249 Chrono-Environnement, Besançon, France
- Laboratoire Associé du Centre National de Référence de la Résistance aux Antibiotiques, Centre Hospitalier Universitaire de Besançon, Besançon, France
| | - Anaïs Potron
- Université de Franche-Comté, UMR CNRS 6249 Chrono-Environnement, Besançon, France
- Laboratoire Associé du Centre National de Référence de la Résistance aux Antibiotiques, Centre Hospitalier Universitaire de Besançon, Besançon, France
| |
Collapse
|
5
|
Prity FT, Tobin LA, Maharajan R, Paulsen IT, Cain AK, Hamidian M. The evolutionary tale of eight novel plasmids in a colistin-resistant environmental Acinetobacter baumannii isolate. Microb Genom 2023; 9. [PMID: 37171842 DOI: 10.1099/mgen.0.001010] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/13/2023] Open
Abstract
Acinetobacter baumannii is an important opportunistic pathogen known for its high levels of resistance to many antibiotics, particularly those considered last resorts such as colistin and carbapenems. Plasmids of this organism are increasingly associated with the spread of clinically important antibiotic resistance genes. Although A. baumannii is a ubiquitous organism, to date, most of the focus has been on studying strains recovered from clinical samples ignoring those isolated in the environment (soil, water, food, etc.). Here, we analysed the genetic structures of eight novel plasmids carried by an environmental colistin-resistant A. baumannii (strain E-072658) recovered in a recycled fibre pulp in a paper mill in Finland. It was shown that E-072658 carries a new variant of the mcr-4 colistin resistance gene (mcr-4.7) in a novel Tn3-family transposon (called Tn6926) carried by a novel plasmid p8E072658. E-072658 is also resistant to sulphonamide compounds; consistent with this, the sul2 sulphonamide resistance gene was found in a pdif module. E-072658 also carries six additional plasmids with no antibiotic resistance genes, but they contained several pdif modules shared with plasmids carried by clinical strains. Detailed analysis of the genetic structure of all eight plasmids carried by E-072658 showed a complex evolutionary history revealing genetic exchange events within the genus Acinetobacter beyond the clinical or environmental origin of the strains. This work provides evidence that environmental strains might act as a source for some of the clinically significant antibiotic resistance genes.
Collapse
Affiliation(s)
- Farzana T Prity
- ARC Centre of Excellence in Synthetic Biology, School of Natural Sciences, Macquarie University, Sydney, NSW, 2109, Australia
| | - Liam A Tobin
- Australian Institute for Microbiology & Infection, University of Technology Sydney, Ultimo, NSW, 2007, Australia
| | - Ram Maharajan
- ARC Centre of Excellence in Synthetic Biology, School of Natural Sciences, Macquarie University, Sydney, NSW, 2109, Australia
| | - Ian T Paulsen
- ARC Centre of Excellence in Synthetic Biology, School of Natural Sciences, Macquarie University, Sydney, NSW, 2109, Australia
| | - Amy K Cain
- ARC Centre of Excellence in Synthetic Biology, School of Natural Sciences, Macquarie University, Sydney, NSW, 2109, Australia
| | - Mehrad Hamidian
- Australian Institute for Microbiology & Infection, University of Technology Sydney, Ultimo, NSW, 2007, Australia
| |
Collapse
|