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Wranne MS, Karami N, Kk S, Jaén-Luchoro D, Yazdanshenas S, Lin YL, Kabbinale A, Flach CF, Westerlund F, Åhrén C. Comparison of CTX-M encoding plasmids present during the early phase of the ESBL pandemic in western Sweden. Sci Rep 2024; 14:11880. [PMID: 38789462 PMCID: PMC11126669 DOI: 10.1038/s41598-024-62663-2] [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: 02/09/2024] [Accepted: 05/20/2024] [Indexed: 05/26/2024] Open
Abstract
Plasmids encoding blaCTX-M genes have greatly shaped the evolution of E. coli producing extended-spectrum beta-lactamases (ESBL-E. coli) and adds to the global threat of multiresistant bacteria by promoting horizontal gene transfer (HGT). Here we screened the similarity of 47 blaCTX-M -encoding plasmids, from 45 epidemiologically unrelated and disperse ESBL-E. coli strains, isolated during the early phase (2009-2014) of the ESBL pandemic in western Sweden. Using optical DNA mapping (ODM), both similar and rare plasmids were identified. As many as 57% of the plasmids formed five ODM-plasmid groups of at least three similar plasmids per group. The most prevalent type (28%, IncIl, pMLST37) encoded blaCTX-M-15 (n = 10), blaCTX-M-3 (n = 2) or blaCTX-M-55 (n = 1). It was found in isolates of various sequence types (STs), including ST131. This could indicate ongoing local HGT as whole-genome sequencing only revealed similarities with a rarely reported, IncIl plasmid. The second most prevalent type (IncFII/FIA/FIB, F1:A2:B20) harboring blaCTX-M-27, was detected in ST131-C1-M27 isolates, and was similar to plasmids previously reported for this subclade. The results also highlight the need for local surveillance of plasmids and the importance of temporospatial epidemiological links so that detection of a prevalent plasmid is not overestimated as a potential plasmid transmission event in outbreak investigations.
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Affiliation(s)
- Moa S Wranne
- Department of Life Sciences, Chalmers University of Technology, Gothenburg, Sweden
- Centre for Antibiotic Resistance Research in Gothenburg (CARe), University of Gothenburg, Gothenburg, Sweden
| | - Nahid Karami
- Department of Infectious Diseases, Institute of Biomedicine, University of Gothenburg, Guldhedsgatan 10A, 413 46, Gothenburg, Sweden.
- Department of Clinical Microbiology, Sahlgrenska University Hospital, Region Västra Götaland, Gothenburg, Sweden.
- Centre for Antibiotic Resistance Research in Gothenburg (CARe), University of Gothenburg, Gothenburg, Sweden.
| | - Sriram Kk
- Department of Life Sciences, Chalmers University of Technology, Gothenburg, Sweden
| | - Daniel Jaén-Luchoro
- Department of Infectious Diseases, Institute of Biomedicine, University of Gothenburg, Guldhedsgatan 10A, 413 46, Gothenburg, Sweden
- Department of Clinical Microbiology, Sahlgrenska University Hospital, Region Västra Götaland, Gothenburg, Sweden
- Centre for Antibiotic Resistance Research in Gothenburg (CARe), University of Gothenburg, Gothenburg, Sweden
| | - Shora Yazdanshenas
- Department of Clinical Microbiology, Sahlgrenska University Hospital, Region Västra Götaland, Gothenburg, Sweden
| | - Yii-Lih Lin
- Department of Life Sciences, Chalmers University of Technology, Gothenburg, Sweden
- Centre for Antibiotic Resistance Research in Gothenburg (CARe), University of Gothenburg, Gothenburg, Sweden
| | - Arpitha Kabbinale
- Department of Life Sciences, Chalmers University of Technology, Gothenburg, Sweden
| | - Carl-Fredrik Flach
- Department of Infectious Diseases, Institute of Biomedicine, University of Gothenburg, Guldhedsgatan 10A, 413 46, Gothenburg, Sweden
- Centre for Antibiotic Resistance Research in Gothenburg (CARe), University of Gothenburg, Gothenburg, Sweden
| | - Fredrik Westerlund
- Department of Life Sciences, Chalmers University of Technology, Gothenburg, Sweden
- Centre for Antibiotic Resistance Research in Gothenburg (CARe), University of Gothenburg, Gothenburg, Sweden
| | - Christina Åhrén
- Department of Infectious Diseases, Institute of Biomedicine, University of Gothenburg, Guldhedsgatan 10A, 413 46, Gothenburg, Sweden
- Centre for Antibiotic Resistance Research in Gothenburg (CARe), University of Gothenburg, Gothenburg, Sweden
- Swedish Strategic Program Against Antimicrobial Resistance (Strama), Region Västra Götaland, Gothenburg, Sweden
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Patil S, Pai L, Chen X, Francisco NM, Chen H, Chen Y, Dong S, Liu S, Wen F. Genomic characterisation of multi-drug resistant Escherichia coli and Klebsiella pneumoniae co-harbouring mcr-1 and mcr-3 genes on a single plasmid from paediatric clinical cases. J Glob Antimicrob Resist 2023; 34:134-140. [PMID: 37481113 DOI: 10.1016/j.jgar.2023.07.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 06/30/2023] [Accepted: 07/19/2023] [Indexed: 07/24/2023] Open
Abstract
OBJECTIVES Emergence of the plasmid-born mobile colistin resistance (mcr) gene is a growing concern in healthcare. Therefore, this study aimed to genomically characterise multidrug-resistant Escherichia coli and Klebsiella pneumoniae co-harbouring the mcr-1 and mcr-3 genes in young children. METHODS E. coli (n = 3) and K. pneumoniae (n = 2) were collected from abdominal secretions and blood, respectively. The isolates were screened using tryptone soy broth with 4 µL/mL polymyxin-B. Growing bacteria were identified using the VITEK-2 system, matrix-assisted laser desorption/ionisation time-of-flight, and 16s RNA sequencing, followed by antibiotic susceptibility testing. Metallo-β-lactamase (MBL) and extended-spectrum β-lactamase (ESBL) production was also detected. Afterwards, strains were subjected to molecular screening targeting mcr variants and ESBL/MBL-encoding genes. Conjugation, pulsed-field gel electrophoresis, Southern hybridisation, multilocus sequence typing, and phylogenic group detection were performed, along with plasmid-genome sequencing and bioinformatics analysis. RESULTS E. coli isolates (EC-19-322, 323, and 331) and K. pneumoniae isolates (KP-19-225 and 226) harboured both mcr-1 and mcr-3 genes. These strains were also found to be resistant to more than three classes of antibiotics. The conjugation experiment revealed the presence of mcr-1 and mcr-3 on a single plasmid, and the transmission frequency was 10-2 to 10-3. Both strains were found to be able to produce ESBLs and MBL. E. coli EC-19-322 and 323 were identified as ST131(O25a:H41); SP-19-331, as ST1577 (O16:H30); and K. pneumoniae, as ST231 (K2). All E. coli strains belonged to phylogenetic group B2, and the results of pulsed-field gel electrophoresis supported the multilocus sequence typing findings. CONCLUSION This study reported the co-occurrence of mcr-1 and mcr-3 genes on a single plasmid in pathogenic ESBL/MBL-producing E. coli and K. pneumoniae isolated from young children.
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Affiliation(s)
- Sandip Patil
- Department of Haematology and Oncology, Shenzhen Children's Hospital, Shenzhen, China; Paediatric Research Institute, Shenzhen Children's Hospital, Shenzhen, China
| | - Liu Pai
- Department of Haematology and Oncology, Shenzhen Children's Hospital, Shenzhen, China
| | - Xiowen Chen
- Department of Haematology and Oncology, Shenzhen Children's Hospital, Shenzhen, China; Paediatric Research Institute, Shenzhen Children's Hospital, Shenzhen, China
| | - Ngiambudulu M Francisco
- Grupo de Investigação Microbiana e Imunológica, Instituto Nacional de Investigação em Saúde (National Institute for Health Research), Luanda, Angola
| | - Hongyu Chen
- Department of Laboratory Medicine, Shenzhen Children's Hospital, Shenzhen, China
| | - Yunsheng Chen
- Department of Laboratory Medicine, Shenzhen Children's Hospital, Shenzhen, China
| | - Shaowei Dong
- Paediatric Research Institute, Shenzhen Children's Hospital, Shenzhen, China
| | - Sixi Liu
- Department of Haematology and Oncology, Shenzhen Children's Hospital, Shenzhen, China.
| | - Feiqiu Wen
- Department of Haematology and Oncology, Shenzhen Children's Hospital, Shenzhen, China; Paediatric Research Institute, Shenzhen Children's Hospital, Shenzhen, China.
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Patil S, Chen X, Dong S, Mai H, Lopes BS, Liu S, Wen F. Resistance genomics and molecular epidemiology of high-risk clones of ESBL-producing Pseudomonas aeruginosa in young children. Front Cell Infect Microbiol 2023; 13:1168096. [PMID: 37293207 PMCID: PMC10244630 DOI: 10.3389/fcimb.2023.1168096] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 04/24/2023] [Indexed: 06/10/2023] Open
Abstract
Introduction The emergence of multidrug-resistant Pseudomonas aeruginosa poses a global threat, but the distribution and resistance profiling are unclear, especially in young children. Infections due to P. aeruginosa are common, associated with high mortality, and increasingly β-lactam drug resistant. Methods We studied the molecular epidemiology and antibiotic resistance mechanisms in 294 clinicalisolates of P. aeruginosa from a pediatric hospital in China. Non-duplicate isolates were recovered from clinical cases and were identified using an API-20 kit followed by antimicrobial susceptibility testing using the VITEK®2 compact system (BioMerieux, France) and also by broth dilution method. In addition, a double-disc synergy test for the ESBL/E-test for MBL was performed. The presence of beta-lactamases, plasmid types, and sequence types was determined by PCR and sequencing. Results Fifty-six percent (n = 164) of the isolates were resistant to piperacillin-tazobactam, followed by cefepime (40%; n = 117), ceftazidime (39%; n = 115), imipenem (36%; n = 106), meropenem (33%; n = 97), and ciprofloxacin (32%; n = 94). Forty-two percent (n = 126) of the isolates were positive for ESBL according to the double-disc synergy test. The blaCTX-M-15 cephalosporinase was observed in 32% (n = 40/126), while 26% (n = 33/126) werepositive for blaNDM-1 carbapenemase. Aminoglycoside resistance gene aac(3)IIIawas observed in 16% (n = 20/126), and glycylcyclines resistance gene tet(A) was observed in 12% (n = 15/126) of the isolates. A total of 23 sequence types were detected, including ST1963 (12%; n = 16), followed by ST381 (11%; n = 14), ST234 (10%; n = 13), ST145 (58%; n = 10), ST304 (57%; n = 9), ST663 (5%; n = 7), and a novel strain. In ESBL-producing P. aeruginosa, 12 different Incompatibility groups (Inc) were observed, the most common being IncFI, IncFIS, and IncA/C. The MOBP was the most common plasmid type, followed by MOBH, MOBF, and MOBQ. Discussion Our data suggest that the spread of antibiotic resistance is likely due toclonal spread and dissemination of different clinical strains of P. aeruginosa harbouring different plasmids. This is a growing threat in hospitals particularly in young children which needs robust prevention strategies.
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Affiliation(s)
- Sandip Patil
- Department of Haematology and Oncology, Shenzhen Children’s Hospital, Shenzhen, China
- Paediatric Research Institute, Shenzhen Children’s Hospital, Shenzhen, China
| | - Xiaowen Chen
- Paediatric Research Institute, Shenzhen Children’s Hospital, Shenzhen, China
| | - Shaowei Dong
- Paediatric Research Institute, Shenzhen Children’s Hospital, Shenzhen, China
| | - Huirong Mai
- Department of Haematology and Oncology, Shenzhen Children’s Hospital, Shenzhen, China
| | - Bruno Silvester Lopes
- School of Health and Life Sciences, Teesside University, Middlesbrough, United Kingdom
- National Horizons Centre, Teesside University, Darlington, United Kingdom
| | - Sixi Liu
- Department of Haematology and Oncology, Shenzhen Children’s Hospital, Shenzhen, China
| | - Feiqiu Wen
- Department of Haematology and Oncology, Shenzhen Children’s Hospital, Shenzhen, China
- Paediatric Research Institute, Shenzhen Children’s Hospital, Shenzhen, China
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Coque TM, Cantón R, Pérez-Cobas AE, Fernández-de-Bobadilla MD, Baquero F. Antimicrobial Resistance in the Global Health Network: Known Unknowns and Challenges for Efficient Responses in the 21st Century. Microorganisms 2023; 11:1050. [PMID: 37110473 PMCID: PMC10144039 DOI: 10.3390/microorganisms11041050] [Citation(s) in RCA: 32] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 03/28/2023] [Accepted: 03/31/2023] [Indexed: 04/29/2023] Open
Abstract
Antimicrobial resistance (AMR) is one of the Global Health challenges of the 21st century. The inclusion of AMR on the global map parallels the scientific, technological, and organizational progress of the healthcare system and the socioeconomic changes of the last 100 years. Available knowledge about AMR has mostly come from large healthcare institutions in high-income countries and is scattered in studies across various fields, focused on patient safety (infectious diseases), transmission pathways and pathogen reservoirs (molecular epidemiology), the extent of the problem at a population level (public health), their management and cost (health economics), cultural issues (community psychology), and events associated with historical periods (history of science). However, there is little dialogue between the aspects that facilitate the development, spread, and evolution of AMR and various stakeholders (patients, clinicians, public health professionals, scientists, economic sectors, and funding agencies). This study consists of four complementary sections. The first reviews the socioeconomic factors that have contributed to building the current Global Healthcare system, the scientific framework in which AMR has traditionally been approached in such a system, and the novel scientific and organizational challenges of approaching AMR in the fourth globalization scenario. The second discusses the need to reframe AMR in the current public health and global health contexts. Given that the implementation of policies and guidelines are greatly influenced by AMR information from surveillance systems, in the third section, we review the unit of analysis ("the what" and "the who") and the indicators (the "operational units of surveillance") used in AMR and discuss the factors that affect the validity, reliability, and comparability of the information to be applied in various healthcare (primary, secondary, and tertiary), demographic, and economic contexts (local, regional, global, and inter-sectorial levels). Finally, we discuss the disparities and similarities between distinct stakeholders' objectives and the gaps and challenges of combatting AMR at various levels. In summary, this is a comprehensive but not exhaustive revision of the known unknowns about how to analyze the heterogeneities of hosts, microbes, and hospital patches, the role of surrounding ecosystems, and the challenges they represent for surveillance, antimicrobial stewardship, and infection control programs, which are the traditional cornerstones for controlling AMR in human health.
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Affiliation(s)
- Teresa M. Coque
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), 28034 Madrid, Spain
- CIBER en Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Rafael Cantón
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), 28034 Madrid, Spain
- CIBER en Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Ana Elena Pérez-Cobas
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), 28034 Madrid, Spain
- CIBER en Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Miguel D. Fernández-de-Bobadilla
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), 28034 Madrid, Spain
| | - Fernando Baquero
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), 28034 Madrid, Spain
- CIBER en Epidemiología y Salud Pública (CIBERESP), Instituto de Salud Carlos III, 28029 Madrid, Spain
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Atypical integrative element with strand-biased circularization activity assists interspecies antimicrobial resistance gene transfer from Vibrio alfacsensis. PLoS One 2022; 17:e0271627. [PMID: 35917316 PMCID: PMC9345347 DOI: 10.1371/journal.pone.0271627] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2021] [Accepted: 07/06/2022] [Indexed: 11/19/2022] Open
Abstract
The exchange of antimicrobial resistance (AMR) genes between aquaculture and terrestrial microbial populations has emerged as a serious public health concern. However, the nature of the mobile genetic elements in marine bacteria is poorly documented. To gain insight into the genetic mechanisms underlying AMR gene transfer from marine bacteria, we mated a multidrug-resistant Vibrio alfacsensis strain with an Escherichia coli strain, and then determined the complete genome sequences of the donor and the transconjugant strains. Sequence analysis revealed a conjugative multidrug resistance plasmid in the donor strain, which was integrated into the chromosome of the recipient. The plasmid backbone in the transconjugant chromosome was flanked by two copies of a 7.1 kb unclassifiable integrative element harboring a β-lactamase gene. The 7.1 kb element and the previously reported element Tn6283 share four coding sequences, two of which encode the catalytic R-H-R-Y motif of tyrosine recombinases. Polymerase chain reaction and sequencing experiments revealed that these elements generate a circular copy of one specific strand without leaving an empty site on the donor molecule, in contrast to the movement of integron gene cassettes or ICE/IMEs discovered to date. These elements are termed SEs (strand-biased circularizing integrative elements): SE-6945 (the 7.1 kb element) and SE-6283 (Tn6283). The copy number and location of SE-6945 in the chromosome affected the antibiotic resistance levels of the transconjugants. SEs were identified in the genomes of other Vibrio species. Overall, these results suggest that SEs are involved in the spread of AMR genes among marine bacteria.
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Avershina E, Frye SA, Ali J, Taxt AM, Ahmad R. Ultrafast and Cost-Effective Pathogen Identification and Resistance Gene Detection in a Clinical Setting Using Nanopore Flongle Sequencing. Front Microbiol 2022; 13:822402. [PMID: 35369431 PMCID: PMC8970966 DOI: 10.3389/fmicb.2022.822402] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 01/27/2022] [Indexed: 02/04/2023] Open
Abstract
Rapid bacterial identification and antimicrobial resistance gene (ARG) detection are crucial for fast optimization of antibiotic treatment, especially for septic patients where each hour of delayed antibiotic prescription might have lethal consequences. This work investigates whether the Oxford Nanopore Technology’s (ONT) Flongle sequencing platform is suitable for real-time sequencing directly from blood cultures to identify bacteria and detect resistance-encoding genes. For the analysis, we used pure bacterial cultures of four clinical isolates of Escherichia coli and Klebsiella pneumoniae and two blood samples spiked with either E. coli or K. pneumoniae that had been cultured overnight. We sequenced both the whole genome and plasmids isolated from these bacteria using two different sequencing kits. Generally, Flongle data allow rapid bacterial ID and resistome detection based on the first 1,000–3,000 generated sequences (10 min to 3 h from the sequencing start), albeit ARG variant identification did not always correspond to ONT MinION and Illumina sequencing-based data. Flongle data are sufficient for 99.9% genome coverage within at most 20,000 (clinical isolates) or 50,000 (positive blood cultures) sequences generated. The SQK-LSK110 Ligation kit resulted in higher genome coverage and more accurate bacterial identification than the SQK-RBK004 Rapid Barcode kit.
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Affiliation(s)
- Ekaterina Avershina
- Department of Biotechnology, Inland Norway University of Applied Sciences, Hamar, Norway
| | - Stephan A Frye
- Division of Laboratory Medicine, Department of Microbiology, Oslo University Hospital, Oslo, Norway
| | - Jawad Ali
- Department of Biotechnology, Inland Norway University of Applied Sciences, Hamar, Norway
| | - Arne M Taxt
- Division of Laboratory Medicine, Department of Microbiology, Oslo University Hospital, Oslo, Norway
| | - Rafi Ahmad
- Department of Biotechnology, Inland Norway University of Applied Sciences, Hamar, Norway.,Faculty of Health Sciences, Institute of Clinical Medicine, UiT - The Arctic University of Norway, Tromsø, Norway
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Carbapenem-resistant IMP-1-producing Pseudocitrobacter vendiensis emerging in a hemodialysis unit. Braz J Microbiol 2022; 53:251-254. [PMID: 35032310 PMCID: PMC8882528 DOI: 10.1007/s42770-021-00638-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 10/21/2021] [Indexed: 01/17/2023] Open
Abstract
Hemodialysis patients are at high risk for bloodstream infections associated with highest morbidity and mortality rates. Bacterial species not commonly related to such infections has been hardly identified by traditional methods. Pseudocitrobacter is a novel genus of the order Enterobacterales that is associated with carbapenemase genes and nosocomial infection. In this context, we have investigated nine cases of bloodstream infections by carbapenem-resistant Gram-negative bacilli in patients assisted at a hemodialysis unit in Brazil. The infections were caused by a metallo-β-lactamase (IMP-1)-producing clone (> 90% XbaI-PFGE similarity) of Pseudocitrobacter vendiensis, displaying a multidrug-resistant profile to broad-spectrum cephalosporins, carbapenems, chloramphenicol, and trimethoprim-sulfamethoxazole. S1-PFGE and Southern blot hybridization revealed that blaIMP-1 was carried by a 200-kb IncC/ST3 plasmid. Patients were successfully treated with amikacin, and strict disinfection procedures and hand washing protocols were reinforced. We report the emergence of P. vendiensis, a recently described species of the genus, in bloodstream infections of patients undergoing hemodialysis. Considering the epidemic potential of carbapenemase-producing Enterobacterales in hospital settings, surveillance of this emerging pathogen is of utmost importance.
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Baquero F, Martínez JL, F. Lanza V, Rodríguez-Beltrán J, Galán JC, San Millán A, Cantón R, Coque TM. Evolutionary Pathways and Trajectories in Antibiotic Resistance. Clin Microbiol Rev 2021; 34:e0005019. [PMID: 34190572 PMCID: PMC8404696 DOI: 10.1128/cmr.00050-19] [Citation(s) in RCA: 66] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Evolution is the hallmark of life. Descriptions of the evolution of microorganisms have provided a wealth of information, but knowledge regarding "what happened" has precluded a deeper understanding of "how" evolution has proceeded, as in the case of antimicrobial resistance. The difficulty in answering the "how" question lies in the multihierarchical dimensions of evolutionary processes, nested in complex networks, encompassing all units of selection, from genes to communities and ecosystems. At the simplest ontological level (as resistance genes), evolution proceeds by random (mutation and drift) and directional (natural selection) processes; however, sequential pathways of adaptive variation can occasionally be observed, and under fixed circumstances (particular fitness landscapes), evolution is predictable. At the highest level (such as that of plasmids, clones, species, microbiotas), the systems' degrees of freedom increase dramatically, related to the variable dispersal, fragmentation, relatedness, or coalescence of bacterial populations, depending on heterogeneous and changing niches and selective gradients in complex environments. Evolutionary trajectories of antibiotic resistance find their way in these changing landscapes subjected to random variations, becoming highly entropic and therefore unpredictable. However, experimental, phylogenetic, and ecogenetic analyses reveal preferential frequented paths (highways) where antibiotic resistance flows and propagates, allowing some understanding of evolutionary dynamics, modeling and designing interventions. Studies on antibiotic resistance have an applied aspect in improving individual health, One Health, and Global Health, as well as an academic value for understanding evolution. Most importantly, they have a heuristic significance as a model to reduce the negative influence of anthropogenic effects on the environment.
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Affiliation(s)
- F. Baquero
- Department of Microbiology, Ramón y Cajal University Hospital, Ramón y Cajal Institute for Health Research (IRYCIS), Network Center for Research in Epidemiology and Public Health (CIBERESP), Madrid, Spain
| | - J. L. Martínez
- National Center for Biotechnology (CNB-CSIC), Madrid, Spain
| | - V. F. Lanza
- Department of Microbiology, Ramón y Cajal University Hospital, Ramón y Cajal Institute for Health Research (IRYCIS), Network Center for Research in Epidemiology and Public Health (CIBERESP), Madrid, Spain
- Central Bioinformatics Unit, Ramón y Cajal Institute for Health Research (IRYCIS), Madrid, Spain
| | - J. Rodríguez-Beltrán
- Department of Microbiology, Ramón y Cajal University Hospital, Ramón y Cajal Institute for Health Research (IRYCIS), Network Center for Research in Epidemiology and Public Health (CIBERESP), Madrid, Spain
| | - J. C. Galán
- Department of Microbiology, Ramón y Cajal University Hospital, Ramón y Cajal Institute for Health Research (IRYCIS), Network Center for Research in Epidemiology and Public Health (CIBERESP), Madrid, Spain
| | - A. San Millán
- National Center for Biotechnology (CNB-CSIC), Madrid, Spain
| | - R. Cantón
- Department of Microbiology, Ramón y Cajal University Hospital, Ramón y Cajal Institute for Health Research (IRYCIS), Network Center for Research in Epidemiology and Public Health (CIBERESP), Madrid, Spain
| | - T. M. Coque
- Department of Microbiology, Ramón y Cajal University Hospital, Ramón y Cajal Institute for Health Research (IRYCIS), Network Center for Research in Epidemiology and Public Health (CIBERESP), Madrid, Spain
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PLASmid TAXonomic PCR (PlasTax-PCR), a Multiplex Relaxase MOB Typing to Assort Plasmids into Taxonomic Units. Methods Mol Biol 2021. [PMID: 34773620 DOI: 10.1007/978-1-0716-1799-1_10] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/24/2024]
Abstract
Plasmids transmissible by conjugation are responsible for disseminating antibiotic-resistance genes, making plasmid detection relevant for pathogen tracking. We describe the use of a multiplex PCR method for the experimental identification of specific plasmid taxonomic units (PTUs) of transmissible plasmids. The PCR primers were designed to target conserved segments of the relaxase MOB gene of PTUs encoding adaptive traits for enterobacteria (antimicrobial resistance, virulence, and metabolism). In this way, PlasTax-PCR detects the presence of these plasmids and allows their direct assignation to a PTU.
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Abstract
A putative type II toxin-antitoxin (TA) module almost exclusively associated with conjugative IncC plasmids is homologous to the higBA family of TA systems found in chromosomes and plasmids of several species of bacteria. Despite the clinical significance and strong association with high-profile antimicrobial resistance (AMR) genes, the TA system of IncC plasmids remains largely uncharacterized. In this study, we present evidence that IncC plasmids encode a bona fide HigB-like toxin that strongly inhibits bacterial growth and results in cell elongation in Escherichia coli. IncC HigB toxin acts as a ribosome-dependent endoribonuclease that significantly reduces the transcript abundance of a subset of adenine-rich mRNA transcripts. A glycine residue at amino acid position 64 is highly conserved in HigB toxins from different bacterial species, and its replacement with valine (G64V) abolishes the toxicity and the mRNA cleavage activity of the IncC HigB toxin. The IncC plasmid higBA TA system functions as an effective addiction module that maintains plasmid stability in an antibiotic-free environment. This higBA addiction module is the only TA system that we identified in the IncC backbone and appears essential for the stable maintenance of IncC plasmids. We also observed that exposure to subinhibitory concentrations of ciprofloxacin, a DNA-damaging fluoroquinolone antibiotic, results in elevated higBA expression, which raises interesting questions about its regulatory mechanisms. A better understanding of this higBA-type TA module potentially allows for its subversion as part of an AMR eradication strategy. IMPORTANCE Toxin-antitoxin (TA) systems play vital roles in maintaining plasmids in bacteria. Plasmids with incompatibility group C are large plasmids that disseminate via conjugation and carry high-profile antibiotic resistance genes. We present experimental evidence that IncC plasmids carry a TA system that functions as an effective addiction module and maintains plasmid stability in an antibiotic-free environment. The toxin of IncC plasmids acts as an endoribonuclease that targets a subset of mRNA transcripts. Overexpressing the IncC toxin gene strongly inhibits bacterial growth and results in cell elongation in Escherichia coli hosts. We also identify a conserved amino acid residue in the toxin protein that is essential for its toxicity and show that the expression of this TA system is activated by a DNA-damaging antibiotic, ciprofloxacin. This mobile TA system may contribute to managing bacterial stress associated with DNA-damaging antibiotics.
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Karami N, KK S, Yazdanshenas S, Lin YL, Jaén-Luchoro D, Ekedahl E, Parameshwaran S, Lindblom A, Åhrén C, Westerlund F. Identity of blaCTX-M Carrying Plasmids in Sequential ESBL- E. coli Isolates from Patients with Recurrent Urinary Tract Infections. Microorganisms 2021; 9:microorganisms9061138. [PMID: 34070515 PMCID: PMC8226486 DOI: 10.3390/microorganisms9061138] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 05/10/2021] [Accepted: 05/20/2021] [Indexed: 11/16/2022] Open
Abstract
Plasmid-mediated multidrug resistance in E. coli is becoming increasingly prevalent. Considering this global threat to human health, it is important to understand how plasmid-mediated resistance spreads. From a cohort of 123 patients with recurrent urinary tract infections (RUTI) due to extended spectrum beta-lactamase (ESBL)-producing Escherichia coli (ESBL E. coli), only five events with a change of ESBL E. coli strain between RUTI episodes were identified. Their blaCTX-M encoding plasmids were compared within each pair of isolates using optical DNA mapping (ODM) and PCR-based replicon typing. Despite similar blaCTX-M genes and replicon types, ODM detected only one case with identical plasmids in the sequential ESBL E. coli strains, indicating that plasmid transfer could have occurred. For comparison, plasmids from seven patients with the same ESBL E. coli strain reoccurring in both episodes were analyzed. These plasmids (encoding blaCTX-M-3, blaCTX-M-14, and blaCTX-M-15) were unaltered for up to six months between recurrent infections. Thus, transmission of blaCTX-M plasmids appears to be a rare event during the course of RUTI. Despite the limited number (n = 23) of plasmids investigated, similar blaCTX-M-15 plasmids in unrelated isolates from different patients were detected, suggesting that some successful plasmids could be associated with specific strains, or are more easily transmitted.
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Affiliation(s)
- Nahid Karami
- Institute of Biomedicine, Department of Infectious Diseases and Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Guldhedsgatan 10 A, 413 46 Gothenburg, Sweden; (S.Y.); (D.J.-L.); (A.L.); (C.Å.)
- Västra Götaland Region, Sahlgrenska University Hospital, Department of Clinical Microbiology, Guldhedsgatan 10A, 413 46 Gothenburg, Sweden
- Correspondence: (N.K.); (F.W.); Tel.: +46-31-342-6173 (N.K.); +46-31-772-3049 (F.W.)
| | - Sriram KK
- Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivagen 10, 412 96 Gothenburg, Sweden; (S.K.); (Y.-L.L.); (E.E.); (S.P.)
| | - Shora Yazdanshenas
- Institute of Biomedicine, Department of Infectious Diseases and Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Guldhedsgatan 10 A, 413 46 Gothenburg, Sweden; (S.Y.); (D.J.-L.); (A.L.); (C.Å.)
- Västra Götaland Region, Sahlgrenska University Hospital, Department of Clinical Microbiology, Guldhedsgatan 10A, 413 46 Gothenburg, Sweden
| | - Yii-Lih Lin
- Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivagen 10, 412 96 Gothenburg, Sweden; (S.K.); (Y.-L.L.); (E.E.); (S.P.)
| | - Daniel Jaén-Luchoro
- Institute of Biomedicine, Department of Infectious Diseases and Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Guldhedsgatan 10 A, 413 46 Gothenburg, Sweden; (S.Y.); (D.J.-L.); (A.L.); (C.Å.)
| | - Elina Ekedahl
- Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivagen 10, 412 96 Gothenburg, Sweden; (S.K.); (Y.-L.L.); (E.E.); (S.P.)
| | - Sanjana Parameshwaran
- Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivagen 10, 412 96 Gothenburg, Sweden; (S.K.); (Y.-L.L.); (E.E.); (S.P.)
| | - Anna Lindblom
- Institute of Biomedicine, Department of Infectious Diseases and Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Guldhedsgatan 10 A, 413 46 Gothenburg, Sweden; (S.Y.); (D.J.-L.); (A.L.); (C.Å.)
- Västra Götaland Region, Sahlgrenska University Hospital, Department of Clinical Microbiology, Guldhedsgatan 10A, 413 46 Gothenburg, Sweden
| | - Christina Åhrén
- Institute of Biomedicine, Department of Infectious Diseases and Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Guldhedsgatan 10 A, 413 46 Gothenburg, Sweden; (S.Y.); (D.J.-L.); (A.L.); (C.Å.)
- Swedish Strategic Program against Antimicrobial Resistance (Strama), Västra Götaland Region, Regionens Hus, 405 44 Gothenburg, Sweden
| | - Fredrik Westerlund
- Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivagen 10, 412 96 Gothenburg, Sweden; (S.K.); (Y.-L.L.); (E.E.); (S.P.)
- Correspondence: (N.K.); (F.W.); Tel.: +46-31-342-6173 (N.K.); +46-31-772-3049 (F.W.)
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Berbers B, Ceyssens PJ, Bogaerts P, Vanneste K, Roosens NHC, Marchal K, De Keersmaecker SCJ. Development of an NGS-Based Workflow for Improved Monitoring of Circulating Plasmids in Support of Risk Assessment of Antimicrobial Resistance Gene Dissemination. Antibiotics (Basel) 2020; 9:E503. [PMID: 32796589 PMCID: PMC7460218 DOI: 10.3390/antibiotics9080503] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 08/07/2020] [Accepted: 08/08/2020] [Indexed: 11/29/2022] Open
Abstract
Antimicrobial resistance (AMR) is one of the most prominent public health threats. AMR genes localized on plasmids can be easily transferred between bacterial isolates by horizontal gene transfer, thereby contributing to the spread of AMR. Next-generation sequencing (NGS) technologies are ideal for the detection of AMR genes; however, reliable reconstruction of plasmids is still a challenge due to large repetitive regions. This study proposes a workflow to reconstruct plasmids with NGS data in view of AMR gene localization, i.e., chromosomal or on a plasmid. Whole-genome and plasmid DNA extraction methods were compared, as were assemblies consisting of short reads (Illumina MiSeq), long reads (Oxford Nanopore Technologies) and a combination of both (hybrid). Furthermore, the added value of conjugation of a plasmid to a known host was evaluated. As a case study, an isolate harboring a large, low-copy mcr-1-carrying plasmid (>200 kb) was used. Hybrid assemblies of NGS data obtained from whole-genome DNA extractions of the original isolates resulted in the most complete reconstruction of plasmids. The optimal workflow was successfully applied to multidrug-resistant Salmonella Kentucky isolates, where the transfer of an ESBL-gene-containing fragment from a plasmid to the chromosome was detected. This study highlights a strategy including wet and dry lab parameters that allows accurate plasmid reconstruction, which will contribute to an improved monitoring of circulating plasmids and the assessment of their risk of transfer.
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Affiliation(s)
- Bas Berbers
- Transversal Activities in Applied Genomics, Sciensano, 1050 Brussels, Belgium; (B.B.); (K.V.); (N.H.C.R.)
- Department of Information Technology, IDLab, Ghent University, IMEC, 9052 Ghent, Belgium;
| | | | - Pierre Bogaerts
- National Reference Center for Antimicrobial Resistance in Gram-Negative Bacteria, CHU UCL Namur, 5530 Yvoir, Belgium;
| | - Kevin Vanneste
- Transversal Activities in Applied Genomics, Sciensano, 1050 Brussels, Belgium; (B.B.); (K.V.); (N.H.C.R.)
| | - Nancy H. C. Roosens
- Transversal Activities in Applied Genomics, Sciensano, 1050 Brussels, Belgium; (B.B.); (K.V.); (N.H.C.R.)
| | - Kathleen Marchal
- Department of Information Technology, IDLab, Ghent University, IMEC, 9052 Ghent, Belgium;
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- Department of Genetics, University of Pretoria, Pretoria 0083, South Africa
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Kamruzzaman M, Iredell JR. CRISPR-Cas System in Antibiotic Resistance Plasmids in Klebsiella pneumoniae. Front Microbiol 2020; 10:2934. [PMID: 31998256 PMCID: PMC6965323 DOI: 10.3389/fmicb.2019.02934] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 12/06/2019] [Indexed: 12/26/2022] Open
Abstract
CRISPR-Cas (clustered regularly interspersed short palindromic repeats-CRISPR-associated protein) is a microbial adaptive immune system involved in defense against different types of mobile genetic elements. CRISPR-Cas systems are usually found in bacterial and archaeal chromosomes but have also been reported in bacteriophage genomes and in a few mega-plasmids. Klebsiella pneumoniae is an important member of the Enterobacteriaceae with which they share a huge pool of antibiotic resistance genes, mostly via plasmids. CRISPR-Cas systems have been identified in K. pneumoniae chromosomes, but relatively little is known of CRISPR-Cas in the plasmids resident in this species. In this study, we searched for CRISPR-Cas system in 699 complete plasmid sequences (>50-kb) and 217 complete chromosomal sequences of K. pneumoniae from GenBank and analyzed the CRISPR-Cas systems and CRISPR spacers found in plasmids and chromosomes. We found a putative CRISPR-Cas system in the 44 plasmids from Klebsiella species and GenBank search also identified the identical system in three plasmids from other Enterobacteriaceae, with CRISPR spacers targeting different plasmid and chromosome sequences. 45 of 47 plasmids with putative type IV CRISPR had IncFIB replicon and 36 of them had an additional IncHI1B replicon. All plasmids except two are very large (>200 kb) and half of them carried multiple antibiotic resistance genes including bla CTX-M , bla NDM , bla OXA . To our knowledge, this is the first report of multi drug resistance plasmids from Enterobacteriaceae with their own CRISPR-Cas system and it is possible that the plasmid type IV CRISPR may depend on the chromosomal type I-E CRISPRs for their competence. Both chromosomal and plasmid CRISPRs target a large variety of plasmids from this species, further suggesting key roles in the epidemiology of large plasmids.
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Affiliation(s)
- Muhammad Kamruzzaman
- Centre for Infectious Diseases and Microbiology, The Westmead Institute for Medical Research, The University of Sydney, Westmead, NSW, Australia
| | - Jonathan R Iredell
- Centre for Infectious Diseases and Microbiology, The Westmead Institute for Medical Research, The University of Sydney, Westmead, NSW, Australia.,Westmead Hospital, Westmead, NSW, Australia
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