1
|
Piazza A, Corbella M, Mattioni Marchetti V, Merla C, Mileto I, Kuka A, Petazzoni G, Gaiarsa S, Migliavacca R, Baldanti F, Cambieri P. Clinical isolates of ST131 blaOXA-244-positive Escherichia coli, Italy, December 2022 to July 2023. Euro Surveill 2024; 29:2400073. [PMID: 38390649 PMCID: PMC10899817 DOI: 10.2807/1560-7917.es.2024.29.8.2400073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Accepted: 02/22/2024] [Indexed: 02/24/2024] Open
Abstract
The dissemination of carbapenemase-producing Escherichia coli, although still at low level, should be continuously monitored. OXA-244 is emerging in Europe, mainly in E. coli. In Italy, this carbapenemase was reported from an environmental river sample in 2019. We report clinical isolates of OXA-244-producing ST131 E. coli in four patients admitted to an acute care hospital in Pavia, Italy. The association of this difficult-to-detect determinant with a globally circulating high-risk clone, ST131 E. coli, is of clinical relevance.
Collapse
Affiliation(s)
- Aurora Piazza
- IRCCS Fondazione Policlinico San Matteo, Pavia, Italy
- Department of Clinical, Surgical, Diagnostic and Paediatric Sciences, University of Pavia, Pavia, Italy
| | - Marta Corbella
- Microbiology and Virology Unit, IRCCS Fondazione Policlinico San Matteo, Pavia, Italy
| | - Vittoria Mattioni Marchetti
- Specialization School of Microbiology and Virology, University of Pavia, Italy
- Department of Clinical, Surgical, Diagnostic and Paediatric Sciences, University of Pavia, Pavia, Italy
| | - Cristina Merla
- Microbiology and Virology Unit, IRCCS Fondazione Policlinico San Matteo, Pavia, Italy
| | - Irene Mileto
- Specialization School of Microbiology and Virology, University of Pavia, Italy
- Microbiology and Virology Unit, IRCCS Fondazione Policlinico San Matteo, Pavia, Italy
| | - Angela Kuka
- Specialization School of Microbiology and Virology, University of Pavia, Italy
- Microbiology and Virology Unit, IRCCS Fondazione Policlinico San Matteo, Pavia, Italy
| | - Greta Petazzoni
- Microbiology and Virology Unit, IRCCS Fondazione Policlinico San Matteo, Pavia, Italy
- Department of Clinical, Surgical, Diagnostic and Paediatric Sciences, University of Pavia, Pavia, Italy
| | - Stefano Gaiarsa
- Microbiology and Virology Unit, IRCCS Fondazione Policlinico San Matteo, Pavia, Italy
| | - Roberta Migliavacca
- IRCCS Fondazione Policlinico San Matteo, Pavia, Italy
- Department of Clinical, Surgical, Diagnostic and Paediatric Sciences, University of Pavia, Pavia, Italy
| | - Fausto Baldanti
- Microbiology and Virology Unit, IRCCS Fondazione Policlinico San Matteo, Pavia, Italy
- IRCCS Fondazione Policlinico San Matteo, Pavia, Italy
- Department of Clinical, Surgical, Diagnostic and Paediatric Sciences, University of Pavia, Pavia, Italy
| | - Patrizia Cambieri
- Microbiology and Virology Unit, IRCCS Fondazione Policlinico San Matteo, Pavia, Italy
| |
Collapse
|
2
|
Wu T, Zhang Z, Li T, Dong X, Wu D, Zhu L, Xu K, Zhang Y. The type III secretion system facilitates systemic infections of Pseudomonas aeruginosa in the clinic. Microbiol Spectr 2024; 12:e0222423. [PMID: 38088541 PMCID: PMC10783026 DOI: 10.1128/spectrum.02224-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2023] [Accepted: 11/14/2023] [Indexed: 01/13/2024] Open
Abstract
IMPORTANCE The identification of decisive virulence-associated genes in highly pathogenic P. aeruginosa isolates in the clinic is essential for diagnosis and the start of appropriate treatment. Over the past decades, P. aeruginosa ST463 has spread rapidly in East China and is highly resistant to β-lactams. Given the poor clinical outcome caused by this phenotype, detailed information regarding its decisive virulence genes and factors affecting virulence expression needs to be deciphered. Here, we demonstrate that the T3SS effector ExoU has toxic effects on mammalian cells and is required for virulence in the murine bloodstream infection model. Moreover, a functional downstream SpcU is required for ExoU secretion and cytotoxicity. This work highlights the potential role of ExoU in the pathogenesis of disease and provides a new perspective for further research on the development of new antimicrobials with antivirulence ability.
Collapse
Affiliation(s)
- Tiantian Wu
- Department of Infectious Diseases, State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Zhenchuan Zhang
- Research Center for Healthcare Data Science, Zhejiang Lab, Hangzhou, China
| | - Tong Li
- Department of Infectious Diseases, State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Xu Dong
- Department of Infectious Diseases, State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Dan Wu
- Research and Service Center, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
- College of Food and Health, Zhejiang A&F University, Lin'an, Hangzhou, China
| | - Lixia Zhu
- Department of Hematology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Kaijin Xu
- Department of Infectious Diseases, State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Ying Zhang
- Department of Infectious Diseases, State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Jinan Microecological Biomedicine Shandong Laboratory, Jinan, China
| |
Collapse
|
3
|
Li Y, Fang L, Dong M, Cai H, Hua X, Jiang Y, Yu Y, Yang Q. bla KPC-2 overexpression and bla GES-5 carriage as major imipenem/relebactam resistance mechanisms in Pseudomonas aeruginosa high-risk clones ST463 and ST235, respectively, in China. Antimicrob Agents Chemother 2023; 67:e0067523. [PMID: 37819082 PMCID: PMC10649045 DOI: 10.1128/aac.00675-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2023] [Accepted: 08/03/2023] [Indexed: 10/13/2023] Open
Abstract
Pseudomonas aeruginosa high-risk clones pose severe threats to public health. Here, we characterize the imipenem/relebactam (IR) resistance mechanisms in P. aeruginosa high-risk clones sequence type 235 (ST235) and ST463 in China. Minimum inhibitory concentrations (MICs) were determined, and Illumina short-read sequencing was performed for 1,168 clinical carbapenem-resistant P. aeruginosa (CRPA) isolates. The gene copy number and expression level were analyzed by Illumina sequencing depth and reverse transcription-quantitative PCR, respectively. Resistance conferred by bla GES-5 was evaluated by cloning experiments. ST463 and ST235 accounted for 9.8% (115/1,168) and 4.5% (53/1,168) of total isolates, respectively, and showed high frequencies of extensively drug-resistant and difficult-to-treat resistant phenotypes. The overall IR-resistant rate in CRPA was 21.0% (245/1,168). However, the IR resistance rate was 81.7% (94/115) in ST463-PA and 52.8% (28/53) in ST235-PA. Of the ST463 isolates, 92.2% (106/115) were Klebsiella pneumoniae carbapenemase-producing P. aeruginosa (KPC-PA), and all 94 IR-resistant ST463-PA produced KPC-2. Compared to IR-susceptible ST463 KPC-2-PA, IR-resistant ST463 KPC-2-PA exhibited significantly higher bla KPC-2 copy numbers and expression levels. In ST463 KPC-2-PA, 16 mg/L relebactam resulted in additional fourfold reductions in imipenem MIC50/90 values compared to 4 mg/L relebactam. In ST235, 1.9% (1/53) carried bla IMP carbapenemase and 54.7% (29/53) carried bla GES carbapenemase. Other than the IMP producer, all 27 IR-resistant ST235-PA produced GES-5. Cloning experiments revealed that imipenem resistance in bla GES-5-carrying PAO1 transformants was generally unaffected by relebactam. In conclusion, IR-resistant CRPA isolates in China were mainly distributed in P. aeruginosa high-risk clones ST463 and ST235. The major underlying IR resistance mechanisms were bla KPC-2 overexpression and bla GES-5 carriage.
Collapse
Affiliation(s)
- Yue Li
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China
| | - Li Fang
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China
| | - Mengqian Dong
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China
| | - Heng Cai
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China
| | - Xiaoting Hua
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China
| | - Yan Jiang
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China
| | - Yunsong Yu
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China
| | - Qing Yang
- Department of Laboratory Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| |
Collapse
|
4
|
Pérez-Vázquez M, López-Causapé C, Corral-Lugo A, McConnell MJ, Oteo-Iglesias J, Oliver A, Martín-Galiano AJ. Mutation Analysis in Regulator DNA-Binding Regions for Antimicrobial Efflux Pumps in 17,000 Pseudomonas aeruginosa Genomes. Microorganisms 2023; 11:2486. [PMID: 37894144 PMCID: PMC10609311 DOI: 10.3390/microorganisms11102486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 09/26/2023] [Accepted: 09/27/2023] [Indexed: 10/29/2023] Open
Abstract
Mutations leading to upregulation of efflux pumps can produce multiple drug resistance in the pathogen Pseudomonas aeruginosa. Changes in their DNA binding regions, i.e., palindromic operators, can compromise pump depression and subsequently enhance resistance against several antibacterials and biocides. Here, we have identified (pseudo)palindromic repeats close to promoters of genes encoding 13 core drug-efflux pumps of P. aeruginosa. This framework was applied to detect mutations in these repeats in 17,292 genomes. Eighty-nine percent of isolates carried at least one mutation. Eight binary genetic properties potentially related to expression were calculated for mutations. These included palindromicity reduction, mutation type, positioning within the repeat and DNA-bending shift. High-risk ST298, ST308 and ST357 clones commonly carried four conserved mutations while ST175 and the cystic fibrosis-linked ST649 clones showed none. Remarkably, a T-to-C transition in the fourth position of the upstream repeat for mexEF-oprN was nearly exclusive of the high-risk ST111 clone. Other mutations were associated with high-risk sublineages using sample geotemporal metadata. Moreover, 1.5% of isolates carried five or more mutations suggesting they undergo an alternative program for regulation of their effluxome. Overall, P. aeruginosa shows a wide range of operator mutations with a potential effect on efflux pump expression and antibiotic resistance.
Collapse
Affiliation(s)
- María Pérez-Vázquez
- Reference and Research Laboratory for Antibiotic Resistance and Health Care Infections, National Centre for Microbiology, Instituto de Salud Carlos III (ISCIII), Majadahonda, 28029 Madrid, Spain; (M.P.-V.); (J.O.-I.)
- CIBER de Enfermedades Infecciosas (CIBERINFEC), 28029 Madrid, Spain; (C.L.-C.); (A.O.)
| | - Carla López-Causapé
- CIBER de Enfermedades Infecciosas (CIBERINFEC), 28029 Madrid, Spain; (C.L.-C.); (A.O.)
- Microbiology Department-Research Institute Biomedical Islas Baleares (IdISDBa), Hospital Son Espases, 07122 Palma de Mallorca, Spain
| | - Andrés Corral-Lugo
- Intrahospital Infections Unit, National Centre for Microbiology, ISCIII, Majadahonda, 28029 Madrid, Spain;
| | - Michael J. McConnell
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556, USA;
| | - Jesús Oteo-Iglesias
- Reference and Research Laboratory for Antibiotic Resistance and Health Care Infections, National Centre for Microbiology, Instituto de Salud Carlos III (ISCIII), Majadahonda, 28029 Madrid, Spain; (M.P.-V.); (J.O.-I.)
- CIBER de Enfermedades Infecciosas (CIBERINFEC), 28029 Madrid, Spain; (C.L.-C.); (A.O.)
| | - Antonio Oliver
- CIBER de Enfermedades Infecciosas (CIBERINFEC), 28029 Madrid, Spain; (C.L.-C.); (A.O.)
- Microbiology Department-Research Institute Biomedical Islas Baleares (IdISDBa), Hospital Son Espases, 07122 Palma de Mallorca, Spain
| | | |
Collapse
|
5
|
Emeraud C, Mahamat A, Jousset AB, Bernabeu S, Goncalves T, Pommier C, Girlich D, Birer A, Rodriguez C, Pawlotsky JM, Naas T, Bonnin RA, Dortet L. Emergence and rapid dissemination of highly resistant NDM-14-producing Klebsiella pneumoniae ST147, France, 2022. Euro Surveill 2023; 28:2300095. [PMID: 37855905 PMCID: PMC10588306 DOI: 10.2807/1560-7917.es.2023.28.42.2300095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 06/26/2023] [Indexed: 10/20/2023] Open
Abstract
BackgroundSince 2021, an emergence of New Delhi metallo-β-lactamase (NDM)-14-producing Klebsiella pneumoniae has been identified in France. This variant with increased carbapenemase activity was not previously detected in Enterobacterales.AimWe investigated the rapid dissemination of NDM-14 producers among patients in hospitals in France.MethodsAll NDM-14-producing non-duplicate clinical isolates identified in France until June 2022 (n = 37) were analysed by whole genome sequencing. The phylogeny of NDM-14-producers among all K. pneumoniae sequence type (ST) 147 reported in France since 2014 (n = 431) was performed. Antimicrobial susceptibility testing, conjugation experiments, clonal relationship and molecular clock analysis were performed.ResultsThe 37 NDM-14 producers recovered in France until 2022 belonged to K. pneumoniae ST147. The dissemination of NDM-14-producing K. pneumoniae was linked to a single clone, likely imported from Morocco and responsible for several outbreaks in France. The gene bla NDM-14 was harboured on a 54 kilobase non-conjugative IncFIB plasmid that shared high homology with a known bla NDM-1-carrying plasmid. Using Bayesian analysis, we estimated that the NDM-14-producing K. pneumoniae ST147 clone appeared in 2020. The evolutionary rate of this clone was estimated to 5.61 single nucleotide polymorphisms per genome per year. The NDM-14 producers were highly resistant to all antimicrobials tested except to colistin, cefiderocol (minimum inhibitory concentration 2 mg/L) and the combination of aztreonam/avibactam.ConclusionHighly resistant NDM-14 producing K. pneumoniae can rapidly spread in healthcare settings. Surveillance and thorough investigations of hospital outbreaks are critical to evaluate and limit the dissemination of this clone.
Collapse
Affiliation(s)
- Cécile Emeraud
- Department of Bacteriology-Hygiene, Bicêtre Hospital, Assistance Publique - Hôpitaux de Paris, Le Kremlin-Bicêtre, France
- UMR-1184, INSERM, University Paris-Saclay, CEA, Faculty of Medicine, Le Kremlin-Bicêtre, France
- French National Reference Center for Antibiotic Resistance, Le Kremlin-Bicêtre, France
| | - Aba Mahamat
- Corsica Centre for Healthcare-Associated Infections Control and Prevention, Hôpital Eugénie, Ajaccio, France
| | - Agnès B Jousset
- Department of Bacteriology-Hygiene, Bicêtre Hospital, Assistance Publique - Hôpitaux de Paris, Le Kremlin-Bicêtre, France
- UMR-1184, INSERM, University Paris-Saclay, CEA, Faculty of Medicine, Le Kremlin-Bicêtre, France
- French National Reference Center for Antibiotic Resistance, Le Kremlin-Bicêtre, France
| | - Sandrine Bernabeu
- Department of Bacteriology-Hygiene, Bicêtre Hospital, Assistance Publique - Hôpitaux de Paris, Le Kremlin-Bicêtre, France
- UMR-1184, INSERM, University Paris-Saclay, CEA, Faculty of Medicine, Le Kremlin-Bicêtre, France
| | - Tania Goncalves
- Department of Bacteriology-Hygiene, Bicêtre Hospital, Assistance Publique - Hôpitaux de Paris, Le Kremlin-Bicêtre, France
| | - Camille Pommier
- Department of Bacteriology-Hygiene, Bicêtre Hospital, Assistance Publique - Hôpitaux de Paris, Le Kremlin-Bicêtre, France
| | - Delphine Girlich
- UMR-1184, INSERM, University Paris-Saclay, CEA, Faculty of Medicine, Le Kremlin-Bicêtre, France
| | - Aurélien Birer
- Centre National de Référence de la Résistance aux antibiotiques, Service de Bactériologie, CHU Gabriel-Montpied, Clermont-Ferrand, France
| | - Christophe Rodriguez
- Université Paris-Est-Créteil (UPEC), Créteil, France
- Department of Virology, Hôpitaux Universitaires Henri Mondor, Assistance Publique-Hôpitaux de Paris, Créteil, France
- INSERM U955, Team Viruses, Hepatology, Cancer, Créteil, France
| | - Jean-Michel Pawlotsky
- Université Paris-Est-Créteil (UPEC), Créteil, France
- Department of Virology, Hôpitaux Universitaires Henri Mondor, Assistance Publique-Hôpitaux de Paris, Créteil, France
- INSERM U955, Team Viruses, Hepatology, Cancer, Créteil, France
| | - Thierry Naas
- Department of Bacteriology-Hygiene, Bicêtre Hospital, Assistance Publique - Hôpitaux de Paris, Le Kremlin-Bicêtre, France
- UMR-1184, INSERM, University Paris-Saclay, CEA, Faculty of Medicine, Le Kremlin-Bicêtre, France
- French National Reference Center for Antibiotic Resistance, Le Kremlin-Bicêtre, France
| | - Rémy A Bonnin
- UMR-1184, INSERM, University Paris-Saclay, CEA, Faculty of Medicine, Le Kremlin-Bicêtre, France
- French National Reference Center for Antibiotic Resistance, Le Kremlin-Bicêtre, France
| | - Laurent Dortet
- Department of Bacteriology-Hygiene, Bicêtre Hospital, Assistance Publique - Hôpitaux de Paris, Le Kremlin-Bicêtre, France
- UMR-1184, INSERM, University Paris-Saclay, CEA, Faculty of Medicine, Le Kremlin-Bicêtre, France
- French National Reference Center for Antibiotic Resistance, Le Kremlin-Bicêtre, France
| |
Collapse
|
6
|
Arcari G, Polani R, Santilli S, Capitani V, Sacco F, Bruno F, Garcia-Fernandez A, Raponi G, Villa L, Gentile G, Carattoli A. Multiplicity of blaKPC Genes and pKpQIL Plasmid Plasticity in the Development of Ceftazidime-Avibactam and Meropenem Coresistance in Klebsiella pneumoniae Sequence Type 307. Antimicrob Agents Chemother 2023; 67:e0036823. [PMID: 37428086 PMCID: PMC10433805 DOI: 10.1128/aac.00368-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 06/14/2023] [Indexed: 07/11/2023] Open
Abstract
In 2021, Klebsiella pneumoniae sequence type 307 (ST307) strains causing pulmonary and bloodstream infections identified in a hospital in Rome, Italy, reached high levels of resistance to ceftazidime-avibactam (CZA). One of these strains reached high levels of resistance to both CZA and carbapenems and carried two copies of blaKPC-3 and one copy of blaKPC-31 located on plasmid pKpQIL. The genomes and plasmids of CZA-resistant ST307 strains were analyzed to identify the molecular mechanisms leading to the evolution of resistance and compared with ST307 genomes at local and global levels. A complex pattern of multiple plasmids in rearranged configurations, coresident within the CZA-carbapenem-resistant K. pneumoniae strain, was observed. Characterization of these plasmids revealed recombination and segregation events explaining why K. pneumoniae isolates from the same patient had different antibiotic resistance profiles. This study illustrates the intense genetic plasticity occurring in ST307, one of the most worldwide-diffused K. pneumoniae high-risk clones.
Collapse
Affiliation(s)
- Gabriele Arcari
- Department of Molecular Medicine, Sapienza University of Rome, Rome, Italy
| | - Riccardo Polani
- Department of Molecular Medicine, Sapienza University of Rome, Rome, Italy
| | - Stefania Santilli
- Complex Operating Unit of Microbiology and Virology, Policlinico Umberto I, Rome, Italy
| | - Valerio Capitani
- Department of Molecular Medicine, Sapienza University of Rome, Rome, Italy
| | - Federica Sacco
- Department of Molecular Medicine, Sapienza University of Rome, Rome, Italy
- Complex Operating Unit of Microbiology and Virology, Policlinico Umberto I, Rome, Italy
| | - Francesco Bruno
- Department of Molecular Medicine, Sapienza University of Rome, Rome, Italy
| | | | - Giammarco Raponi
- Complex Operating Unit of Microbiology and Virology, Policlinico Umberto I, Rome, Italy
- Department of Public Health, Sapienza University of Rome, Rome, Italy
| | - Laura Villa
- Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - Giuseppe Gentile
- Department of Translational and Precision Medicine, Sapienza University of Rome, Rome, Italy
| | | |
Collapse
|
7
|
Lindemann PC, Pedersen T, Oma DH, Janice J, Grøvan F, Chedid GM, Hafne LJ, Josefsen EH, Kacelnik O, Sundsfjord A, Samuelsen Ø. Intraregional hospital outbreak of OXA-244-producing Escherichia coli ST38 in Norway, 2020. Euro Surveill 2023; 28:2200773. [PMID: 37410380 PMCID: PMC10370041 DOI: 10.2807/1560-7917.es.2023.28.27.2200773] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 05/09/2023] [Indexed: 07/07/2023] Open
Abstract
Infections with OXA-244-carbapenemase-producing Escherichia coli with sequence type (ST)38 have recently increased in Europe. Due to its low-level activity against carbapenems, OXA-244 can be difficult to detect. Previous assessments have not revealed a clear source and route of transmission for OXA-244-producing E. coli, but there are indications of non-healthcare related sources and community spread. Here we report a hospital-associated outbreak of OXA-244-producing E. coli ST38 involving three hospitals in Western Norway in 2020. The outbreak occurred over a 5-month period and included 12 cases identified through clinical (n = 6) and screening (n = 6) samples. The transmission chain was unclear; cases were identified in several wards and there was no clear overlap of patient stay. However, all patients had been admitted to the same tertiary hospital in the region, where screening revealed an outbreak in one ward (one clinical case and five screening cases). Outbreak control measures were instigated including contact tracing, isolation, and screening; no further cases were identified in 2021. This outbreak adds another dimension to the spread of OXA-244-producing E. coli ST38, illustrating this clone's ability to establish itself in the healthcare setting. Awareness of challenges concerning OXA-244-producing E. coli diagnostic is important to prevent further spread.
Collapse
Affiliation(s)
| | - Torunn Pedersen
- Norwegian National Advisory Unit on Detection of Antimicrobial Resistance, Department of Microbiology and Infection Control, University Hospital of North Norway, Tromsø, Norway
| | - Dorthea Hagen Oma
- Division of Patient Safety, Haukeland University Hospital, Bergen, Norway
| | - Jessin Janice
- Norwegian National Advisory Unit on Detection of Antimicrobial Resistance, Department of Microbiology and Infection Control, University Hospital of North Norway, Tromsø, Norway
| | | | | | - Liv Jorunn Hafne
- Department of Microbiology, Haugesund Hospital, Haugesund, Norway
| | - Ellen H Josefsen
- Norwegian National Advisory Unit on Detection of Antimicrobial Resistance, Department of Microbiology and Infection Control, University Hospital of North Norway, Tromsø, Norway
| | - Oliver Kacelnik
- Department of Antibiotic Resistance and Infection Prevention, Norwegian Institute of Public Health, Oslo, Norway
| | - Arnfinn Sundsfjord
- Norwegian National Advisory Unit on Detection of Antimicrobial Resistance, Department of Microbiology and Infection Control, University Hospital of North Norway, Tromsø, Norway
- Department of Medical Biology, UiT The Arctic University of Norway, Tromsø, Norway
| | - Ørjan Samuelsen
- Norwegian National Advisory Unit on Detection of Antimicrobial Resistance, Department of Microbiology and Infection Control, University Hospital of North Norway, Tromsø, Norway
- Department of Pharmacy, UiT The Arctic University of Norway, Tromsø, Norway
| |
Collapse
|
8
|
Dey S, Gaur M, Sykes EME, Prusty M, Elangovan S, Dixit S, Pati S, Kumar A, Subudhi E. Unravelling the Evolutionary Dynamics of High-Risk Klebsiella pneumoniae ST147 Clones: Insights from Comparative Pangenome Analysis. Genes (Basel) 2023; 14:genes14051037. [PMID: 37239397 DOI: 10.3390/genes14051037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 04/20/2023] [Accepted: 04/25/2023] [Indexed: 05/28/2023] Open
Abstract
BACKGROUND The high prevalence and rapid emergence of antibiotic resistance in high-risk Klebsiella pneumoniae (KP) ST147 clones is a global health concern and warrants molecular surveillance. METHODS A pangenome analysis was performed using publicly available ST147 complete genomes. The characteristics and evolutionary relationships among ST147 members were investigated through a Bayesian phylogenetic analysis. RESULTS The large number of accessory genes in the pangenome indicates genome plasticity and openness. Seventy-two antibiotic resistance genes were found to be linked with antibiotic inactivation, efflux, and target alteration. The exclusive detection of the blaOXA-232 gene within the ColKp3 plasmid of KP_SDL79 suggests its acquisition through horizontal gene transfer. The association of seventy-six virulence genes with the acrAB efflux pump, T6SS system and type I secretion system describes its pathogenicity. The presence of Tn6170, a putative Tn7-like transposon in KP_SDL79 with an insertion at the flanking region of the tnsB gene, establishes its transmission ability. The Bayesian phylogenetic analysis estimates ST147's initial divergence in 1951 and the most recent common ancestor for the entire KP population in 1621. CONCLUSIONS Present study highlights the genetic diversity and evolutionary dynamics of high-risk clones of K. pneumoniae. Further inter-clonal diversity studies will help us understand its outbreak more precisely and pave the way for therapeutic interventions.
Collapse
Affiliation(s)
- Suchanda Dey
- Centre for Biotechnology, School of Pharmaceutical Sciences, Siksha 'O' Anusandhan (Deemed to be University), Bhubaneswar 751003, India
| | - Mahendra Gaur
- Centre for Biotechnology, School of Pharmaceutical Sciences, Siksha 'O' Anusandhan (Deemed to be University), Bhubaneswar 751003, India
| | - Ellen M E Sykes
- Department of Microbiology, University of Manitoba, Winnipeg, MB R3T2N2, Canada
| | - Monica Prusty
- School of Biotechnology, Kalinga Institute of Industrial Technology, Bhubaneswar 751024, India
| | - Selvakumar Elangovan
- School of Biotechnology, Kalinga Institute of Industrial Technology, Bhubaneswar 751024, India
| | - Sangita Dixit
- Centre for Biotechnology, School of Pharmaceutical Sciences, Siksha 'O' Anusandhan (Deemed to be University), Bhubaneswar 751003, India
| | | | - Ayush Kumar
- Department of Microbiology, University of Manitoba, Winnipeg, MB R3T2N2, Canada
| | - Enketeswara Subudhi
- Centre for Biotechnology, School of Pharmaceutical Sciences, Siksha 'O' Anusandhan (Deemed to be University), Bhubaneswar 751003, India
| |
Collapse
|
9
|
Benlabidi S, Raddaoui A, Lengliz S, Cheriet S, Hynds P, Achour W, Ghrairi T, Abbassi MS. Occurrence of High-Risk Clonal Lineages ST58, ST69, ST224, and ST410 among Extended-Spectrum β-Lactamase-Producing Escherichia coli Isolated from Healthy Free-Range Chickens ( Gallus gallus domesticus) in a Rural Region in Tunisia. Genes (Basel) 2023; 14:genes14040875. [PMID: 37107633 PMCID: PMC10138121 DOI: 10.3390/genes14040875] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 03/23/2023] [Accepted: 04/03/2023] [Indexed: 04/29/2023] Open
Abstract
Antimicrobial-resistant Escherichia coli isolates have emerged in various ecologic compartments and evolved to spread globally. We sought to (1.) investigate the occurrence of ESBL-producing E. coli (ESBL-Ec) in feces from free-range chickens in a rural region and (2.) characterize the genetic background of antimicrobial resistance and the genetic relatedness of collected isolates. Ninety-five feces swabs from free-range chickens associated with two households (House 1/House 2) in a rural region in northern Tunisia were collected. Samples were screened to recover ESBL-Ec, and collected isolates were characterized for phenotype/genotype of antimicrobial resistance, integrons, and molecular typing (pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing (MLST)). Overall, 47 ESBL-Ec were identified, with the following genes detected: 35 blaCTX-M-1, 5 blaCTX-M-55, 5 blaCTX-M-15, 1 blaSHV-2, and 1 blaSHV-12. Resistance to fluoroquinolones, tetracycline, sulfonamides, and colistin was encoded by aac(6')-Ib-cr (n = 21), qnrB (n = 1), and qnrS (n = 2); tetA (n = 17)/tetB (n = 26); sul1 (n = 29)/sul2 (n = 18); and mcr-2 (n = 2) genes, respectively. PFGE and MLST identified genetic homogeneity of isolates in House 1; however, isolates from House 2 were heterogeneous. Notably, among nine identified sequence types, ST58, ST69, ST224, and ST410 belong to pandemic high-risk clonal lineages associated with extrapathogenic E. coli. Minor clones belonging to ST410 and ST471 were shared by chickens from both households. The virulence genes fyuA, fimH, papGIII, and iutA were detected in 35, 47, 17, and 23 isolates, respectively. Findings indicate a high occurrence of ESBL-Ec in free-range chickens and highlight the occurrence of pandemic zoonotic clones.
Collapse
Affiliation(s)
- Saloua Benlabidi
- Institute of Veterinary Research of Tunisia, University of Tunis El Manar, Tunis 1006, Tunisia
- Laboratory of Neurophysiology Cellular Physiopathology and Biomolecule Valorisation LR18ES03, Faculty of Sciences of Tunis, University Tunis El Manar, Tunis 1068, Tunisia
| | - Anis Raddaoui
- Laboratory Ward, National Bone Marrow Transplant Center, Tunis 1006, Tunisia
| | - Sana Lengliz
- Institute of Veterinary Research of Tunisia, University of Tunis El Manar, Tunis 1006, Tunisia
- Laboratory of Materials, Molecules and Application LR11ES22, Preparatory Institute for Scientific and Technical Studies, University of Carthage, Tunis 1054, Tunisia
| | - Sarah Cheriet
- Institute of Veterinary Research of Tunisia, University of Tunis El Manar, Tunis 1006, Tunisia
- Laboratory of Neurophysiology Cellular Physiopathology and Biomolecule Valorisation LR18ES03, Faculty of Sciences of Tunis, University Tunis El Manar, Tunis 1068, Tunisia
| | - Paul Hynds
- Environmental Sustainability and Health Institute (ESHI), Technological University Dublin, D07 H6K8 Dublin, Ireland
| | - Wafa Achour
- Laboratory Ward, National Bone Marrow Transplant Center, Tunis 1006, Tunisia
| | - Taoufik Ghrairi
- Laboratory of Neurophysiology Cellular Physiopathology and Biomolecule Valorisation LR18ES03, Faculty of Sciences of Tunis, University Tunis El Manar, Tunis 1068, Tunisia
| | - Mohamed Salah Abbassi
- Institute of Veterinary Research of Tunisia, University of Tunis El Manar, Tunis 1006, Tunisia
- Research Laboratory 'Antimicrobial Resistance' LR18ES39, Faculty of Medicine of Tunis, University of Tunis El Manar, Tunis 1006, Tunisia
| |
Collapse
|
10
|
Mohajer HB, Salimizand H, Gharanizadeh D, Hossainpanahi A, Ramazanzadeh R. Investigation of NDM-1 and OXA-48 producing carbapenem resistant Klebsiella pneumoniae ST15 in Iran. Acta Microbiol Immunol Hung 2023; 70:38-46. [PMID: 36648758 DOI: 10.1556/030.2023.01945] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 01/10/2023] [Indexed: 01/18/2023]
Abstract
The aim of this study was to determine the frequency of carbapenem resistant Klebsiella pneumoniae (CRKP) sequence types (STs) in Iran. Samples were collected from three university hospitals in Sanandaj, Iran, from December 2016 to March 2018. Antibiotic susceptibility testing, phenotypic and genotypic detection of carbapenemases were performed. Common K. pneumoniae capsular types were sought for all isolates. The genetic relatedness of isolates was investigated by multilocus sequence typing (MLST). Plasmids were detected by PCR-based Replicon Typing (PBRT). During the study, 67 K. pneumoniae isolates were identified. Of which, 18 (26.9%) isolates were detected as carbapenem-resistant. The most effective antibacterial agent was tigecycline (97%, 65 isolates) followed by imipenem and ertapenem (73.13%, 49 isolates). PCR showed that 13 isolates (19.4%) had blaNDM-1 gene and 5 (7.5%) harbored blaOXA-48. Examination of common capsular types showed that 2 isolates had K2 and 2 others had K54. REP-PCR revealed 10 clones and 11 singleton strains. MLST analysis of CRKP found ST15 as the most common type (13 isolates, 72.2%), but other STs were also detected namely, ST19, ST117, ST1390, and ST1594. ColE1 and IncL/M plasmids were the carriers of blaNDM-1 and blaOXA-48, respectively. The results showed that CRKP spread in our health centers. Our results, therefore, indicate a worrying trend of resistance to carbapenems in K. pneumoniae.
Collapse
Affiliation(s)
| | - Himen Salimizand
- 2Cellular and Molecular Research Center, Research Institute for Health Development, Kurdistan University of Medical Sciences, Sanandaj, Iran.,3Department of Microbiology, Faculty of Medicine, Kurdistan University of Medical Sciences, Sanandaj, Iran
| | - Dahieh Gharanizadeh
- 1Student Research Committee, Kurdistan University of Medical Sciences, Sanandaj, Iran
| | - Afra Hossainpanahi
- 3Department of Microbiology, Faculty of Medicine, Kurdistan University of Medical Sciences, Sanandaj, Iran
| | - Rashid Ramazanzadeh
- 4Department of Microbiology, Faculty of Medicine, Ardabil University of Medical Sciences, Ardabil, Iran
| |
Collapse
|
11
|
Zhao Y, Chen D, Ji B, Zhang X, Anbo M, Jelsbak L. Whole-genome sequencing reveals high-risk clones of Pseudomonas aeruginosa in Guangdong, China. Front Microbiol 2023; 14:1117017. [PMID: 37125174 PMCID: PMC10140354 DOI: 10.3389/fmicb.2023.1117017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 03/27/2023] [Indexed: 05/02/2023] Open
Abstract
The ever-increasing prevalence of infections produced by multidrug-resistant or extensively drug-resistant Pseudomonas aeruginosa is commonly linked to a limited number of aptly-named epidemical 'high-risk clones' that are widespread among and within hospitals worldwide. The emergence of new potential high-risk clone strains in hospitals highlights the need to better and further understand the underlying genetic mechanisms for their emergence and success. P. aeruginosa related high-risk clones have been sporadically found in China, their genome sequences have rarely been described. Therefore, the large-scale sequencing of multidrug-resistance high-risk clone strains will help us to understand the emergence and transmission of antibiotic resistances in P. aeruginosa high-risk clones. In this study, 212 P. aeruginosa strains were isolated from 2 tertiary hospitals within 3 years (2018-2020) in Guangdong Province, China. Whole-genome sequencing, multi-locus sequence typing (MLST) and antimicrobial susceptibility testing were applied to analyze the genomic epidemiology of P. aeruginosa in this region. We found that up to 130 (61.32%) of the isolates were shown to be multidrug resistant, and 196 (92.45%) isolates were Carbapenem-Resistant Pseudomonas aeruginosa. MLST analysis demonstrated high diversity of sequence types, and 18 reported international high-risk clones were identified. Furthermore, we discovered the co-presence of exoU and exoS genes in 5 collected strains. This study enhances insight into the regional research of molecular epidemiology and antimicrobial resistance of P. aeruginosa in China. The high diversity of clone types and regional genome characteristics can serve as a theoretical reference for public health policies and help guide measures for the prevention and control of P. aeruginosa resistance.
Collapse
Affiliation(s)
- Yonggang Zhao
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Dingqiang Chen
- Department of Laboratory Medicine, Microbiome Medicine Center, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Boyang Ji
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | | | - Mikkel Anbo
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Lars Jelsbak
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
- *Correspondence: Lars Jelsbak,
| |
Collapse
|
12
|
de Sales RO, Leaden L, Migliorini LB, Severino P. A Comprehensive Genomic Analysis of the Emergent Klebsiella pneumoniae ST16 Lineage: Virulence, Antimicrobial Resistance and a Comparison with the Clinically Relevant ST11 Strain. Pathogens 2022; 11. [PMID: 36558729 DOI: 10.3390/pathogens11121394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 11/04/2022] [Accepted: 11/10/2022] [Indexed: 11/24/2022] Open
Abstract
Klebsiella pneumoniae is considered an opportunistic pathogen frequently involved with healthcare-associated infections. The genome of K. pneumoniae is versatile, harbors diverse virulence factors and easily acquires and exchanges resistance plasmids, facilitating the emergence of new threatening clones. In the last years, ST16 has been described as an emergent, clinically relevant strain, increasingly associated with outbreaks, and carrying virulence factors (such as ICEKp, iuc, rmpADC/2) and a diversity of resistance genes. However, a far-reaching phylogenetic study of ST16, including geographically, clinically and temporally distributed isolates is not available. In this work, we analyzed all publicly available ST16 K. pneumoniae genomes in terms of virulence factors, including capsular lipopolysaccharide and polysaccharide diversity, plasmids and antimicrobial resistance genes. A core genome SNP analysis shows that less than 1% of studied sites were variant sites, with a median pairwise single nucleotide polymorphism difference of 87 SNPs. The number and diversity of antimicrobial resistance genes, but not of virulence-related genes, increased consistently in ST16 strains during the studied period. A genomic comparison between ST16 and the high-risk clone ST11 K. pneumoniae, showed great similarities in their capacity to acquire resistance and virulence markers, differing mostly in the great diversity of capsular lipopolysaccharide and polysaccharide types in ST11, in comparison with ST16. While virulence and antimicrobial resistance scores indicated that ST11 might still constitute a more difficult-to-manage strain, results presented here demonstrate the great potential of the ST16 clone becoming critical in public health.
Collapse
|
13
|
Opazo-Capurro A, Morales-León F, Jerez C, Olivares-Pacheco J, Alcalde-Rico M, González-Muñoz P, Bello-Toledo H, Cardenas-Arias A, Esposito F, Lincopán N, Illesca V, González-Rocha G. Isolation of an Extensively Drug-Resistant Pseudomonas aeruginosa exoS(+)/O4 Strain Belonging to the "High-Risk" Clone ST654 and Coproducer of NDM-1 and the Novel VIM-80. Microbiol Spectr 2022; 10:e0143922. [PMID: 36214677 DOI: 10.1128/spectrum.01439-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
The aim of this study was to investigate the genomic features of an extensively drug-resistant (XDR) Pseudomonas aeruginosa isolate (P-469) emerging in Chile. Antibiotic susceptibility was determined by disk diffusion and "colistin agar" test. Whole-genome sequencing (WGS) was performed by the Illumina NextSeq 2000 platform, and epidemiologically and clinically relevant data (i.e., sequence-type, serotype, mobile genetic elements, virulome, resistome, plasmidome, prophages, and CRISPR-Cas systems) were retrieved using multiple bioinformatic tools. The P-469 strain displayed an XDR profile, remaining susceptible to colistin. Genomic analysis revealed that this isolate belonged to the "high-risk" clone ST654 (CC654), serotype O4, and genotype exoS+. Strikingly, two CRISPR-Cas systems, five intact prophages sequences, and a broad resistome that included blaNDM-1 and the novel blaVIM-80 carbapenemase genes were predicted. Our results revealed the genomic characteristics of P. aeruginosa belonging to the high-risk clone ST654/O4 coproducing NDM-1 and VIM-80 in Chile, supporting that genomic surveillance is necessary to track the emergence and spread of epidemiologically successful WHO's critical priority pathogens in order to prevent their rapid dissemination.
Collapse
|
14
|
Abstract
The rapid emergence of multidrug-resistant Klebsiella pneumoniae is being driven largely by the spread of specific clonal groups (CGs). Of these, CG147 includes 7-gene multilocus sequence typing (MLST) sequence types (STs) ST147, ST273 and ST392. CG147 has caused nosocomial outbreaks across the world, but its global population dynamics remain unknown. Here, we report a pandrug-resistant ST147 clinical isolate from India (strain DJ) and define the evolution and global emergence of CG147. Antimicrobial-susceptibility testing following European Committee on Antimicrobial Susceptibility Testing (EUCAST) guidelines and genome sequencing (Illumina and Oxford Nanopore Technologies, Unicycler assembly) were performed on strain DJ. Additionally, we collated 217 publicly available CG147 genomes [National Center for Biotechnology Information (NCBI), May 2019]. CG147 evolution was inferred within a temporal phylogenetic framework (beast) based on a recombination-free sequence alignment (Roary/Gubbins). Comparative genomic analyses focused on resistance and virulence genes and other genetic elements (BIGSdb, Kleborate, PlasmidFinder, phaster, ICEfinder and CRISPRCasFinder). Strain DJ had a pandrug-resistance phenotype. Its genome comprised the chromosome, seven plasmids and one linear phage-plasmid. Four carbapenemase genes were detected: blaNDM-5 and two copies of blaOXA-181 in the chromosome, and a second copy of blaNDM-5 on an 84 kb IncFII plasmid. CG147 genomes carried a mean of 13 acquired resistance genes or mutations; 63 % carried a carbapenemase gene and 83 % harboured blaCTX-M. All CG147 genomes presented GyrA and ParC mutations and a common subtype I-E CRISPR-Cas system. ST392 and ST273 emerged in 2005 and 1995, respectively. ST147, the most represented phylogenetic branch, was itself divided into two main clades with distinct capsular loci: KL64 (74 %, DJ included, emerged in 1994 and disseminated worldwide, with carbapenemases varying among world regions) and KL10 (20 %, emerged in 2002, predominantly found in Asian countries, associated with carbapenemases NDM and OXA-48-like). Furthermore, subclades within ST147-KL64 differed at the yersiniabactin locus, OmpK35/K36 mutations, plasmid replicons and prophages. The absence of IncF plasmids in some subclades was associated with a possible activity of a CRISPR-Cas system. K. pneumoniae CG147 comprises pandrug-resistant or extensively resistant isolates, and carries multiple and diverse resistance genes and mobile genetic elements, including chromosomal blaNDM-5. Its emergence is being driven by the spread of several phylogenetic clades marked by their own genomic features and specific temporo–spatial dynamics. These findings highlight the need for precision surveillance strategies to limit the spread of particularly concerning CG147 subsets.
Collapse
Affiliation(s)
- Carla Rodrigues
- Biodiversity and Epidemiology of Bacterial Pathogens, Institut Pasteur, Université de Paris, Paris, France
| | - Siddhi Desai
- Department of Microbiology and Biotechnology Centre, Faculty of Science, The Maharaja Sayajirao University of Baroda, Vadodara, Gujarat, India
| | - Virginie Passet
- Biodiversity and Epidemiology of Bacterial Pathogens, Institut Pasteur, Université de Paris, Paris, France
| | - Devarshi Gajjar
- Department of Microbiology and Biotechnology Centre, Faculty of Science, The Maharaja Sayajirao University of Baroda, Vadodara, Gujarat, India
| | - Sylvain Brisse
- Biodiversity and Epidemiology of Bacterial Pathogens, Institut Pasteur, Université de Paris, Paris, France
| |
Collapse
|
15
|
Marí-Almirall M, Ferrando N, Fernández MJ, Cosgaya C, Viñes J, Rubio E, Cuscó A, Muñoz L, Pellice M, Vergara A, Campo I, Rodríguez-Serna L, Santana G, Del Río A, Francino O, Ciruela P, Ballester F, Marco F, Martínez JA, Soriano Á, Pitart C, Vila J, Roca I. Clonal Spread and Intra- and Inter-Species Plasmid Dissemination Associated With Klebsiella pneumoniae Carbapenemase-Producing Enterobacterales During a Hospital Outbreak in Barcelona, Spain. Front Microbiol 2021; 12:781127. [PMID: 34867923 PMCID: PMC8637019 DOI: 10.3389/fmicb.2021.781127] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 10/25/2021] [Indexed: 02/03/2023] Open
Abstract
Objectives: The study aimed to characterize the clonal spread of resistant bacteria and dissemination of resistance plasmids among carbapenem-resistant Enterobacterales at a tertiary hospital in Catalonia, Spain. Methods: Isolates were recovered from surveillance rectal swabs and diagnostic samples. Species identification was by matrix-assisted laser desorption ionization-time time of flight mass spectrometry (MALDI-TOF MS). Molecular typing was performed by pulsed-field gel electrophoresis (PFGE) and multi-locus sequence typing (MLST). Antimicrobial susceptibility was assessed by gradient-diffusion and carriage of bla genes was detected by PCR. Plasmid typing, conjugation assays, S1-PFGE studies and long-read sequencing were used to characterize resistance plasmids. Results: From July 2018 to February 2019, 125 Klebsiella pneumoniae carbapenemase (KPC)-producing Enterobacterales were recovered from 101 inpatients from surveillance (74.4%) or clinical samples (25.6%), in a tertiary hospital in Barcelona. Clonality studies identified a major clone of Klebsiella pneumoniae belonging to sequence type ST15 and additional isolates of K. pneumoniae, Escherichia coli and Enterobacter sp. from different STs. All isolates but one carried the bla KPC-2 allelic variant. The bla KPC-2 gene was located in an IncFIIk plasmid of circa 106 Kb in a non-classical Tn4401 element designated NTEKPC-pMC-2-1. Whole-genome sequencing revealed different rearrangements of the 106 Kb plasmid while the NTEKPC-pMC-2-1 module was highly conserved. Conclusion: We report a hospital outbreak caused by the clonal dissemination of KPC-producing ST15 K. pneumoniae but also the intra- and inter-species transmission of the bla KPC-2 gene associated with plasmid conjugation and/or transposon dissemination. To our knowledge, this is the first report of an outbreak caused by KPC-producing Enterobacterales isolated from human patients in Catalonia and highlights the relevance of surveillance studies in the early detection and control of antibiotic resistant high-risk clones.
Collapse
Affiliation(s)
- Marta Marí-Almirall
- Laboratory of Antimicrobial Resistance, ISGlobal, Hospital Clínic–Universitat de Barcelona, Barcelona, Spain
| | - Núria Ferrando
- Laboratory of Antimicrobial Resistance, ISGlobal, Hospital Clínic–Universitat de Barcelona, Barcelona, Spain
| | - Mariana José Fernández
- Department of Clinical Microbiology, Hospital Clínic–Universitat de Barcelona, Barcelona, Spain
| | - Clara Cosgaya
- Laboratory of Antimicrobial Resistance, ISGlobal, Hospital Clínic–Universitat de Barcelona, Barcelona, Spain
| | - Joaquim Viñes
- Molecular Genetics Veterinary Service, Universitat Autònoma de Barcelona, Barcelona, Spain
- Vetgenomics, PRUAB, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Elisa Rubio
- Department of Clinical Microbiology, Hospital Clínic–Universitat de Barcelona, Barcelona, Spain
| | - Anna Cuscó
- Vetgenomics, PRUAB, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Laura Muñoz
- Laboratory of Antimicrobial Resistance, ISGlobal, Hospital Clínic–Universitat de Barcelona, Barcelona, Spain
| | - Martina Pellice
- Department of Infectious Diseases, Hospital Clínic–Institut d’Investigacions Biomèdiques August Pi i Sunyer, Universitat de Barcelona, Barcelona, Spain
| | - Andrea Vergara
- Department of Clinical Microbiology, Hospital Clínic–Universitat de Barcelona, Barcelona, Spain
| | - Irene Campo
- Department of Clinical Microbiology, Hospital Clínic–Universitat de Barcelona, Barcelona, Spain
| | - Laura Rodríguez-Serna
- Department of Preventive Medicine and Epidemiology, Hospital Clínic–Universitat de Barcelona, Barcelona, Spain
| | - Gemina Santana
- Department of Preventive Medicine and Epidemiology, Hospital Clínic–Universitat de Barcelona, Barcelona, Spain
| | - Ana Del Río
- Department of Infectious Diseases, Hospital Clínic–Institut d’Investigacions Biomèdiques August Pi i Sunyer, Universitat de Barcelona, Barcelona, Spain
| | - Olga Francino
- Molecular Genetics Veterinary Service, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Pilar Ciruela
- Public Health Agency of Catalonia (ASPCAT), Generalitat de Catalunya, Barcelona, Spain
- CIBER de Epidemiología y Salud Pública, Instituto de Salud Carlos III, Madrid, Spain
| | - Frederic Ballester
- Hospital Universitari Sant Joan de Reus-Laboratori de Referència del Camp de Tarragona i de les Terres de l’Ebre, Reus, Spain
| | - Francesc Marco
- Laboratory of Antimicrobial Resistance, ISGlobal, Hospital Clínic–Universitat de Barcelona, Barcelona, Spain
- Department of Clinical Microbiology, Hospital Clínic–Universitat de Barcelona, Barcelona, Spain
| | - José Antonio Martínez
- Department of Infectious Diseases, Hospital Clínic–Institut d’Investigacions Biomèdiques August Pi i Sunyer, Universitat de Barcelona, Barcelona, Spain
| | - Álex Soriano
- Department of Infectious Diseases, Hospital Clínic–Institut d’Investigacions Biomèdiques August Pi i Sunyer, Universitat de Barcelona, Barcelona, Spain
| | - Cristina Pitart
- Laboratory of Antimicrobial Resistance, ISGlobal, Hospital Clínic–Universitat de Barcelona, Barcelona, Spain
- Department of Clinical Microbiology, Hospital Clínic–Universitat de Barcelona, Barcelona, Spain
| | - Jordi Vila
- Laboratory of Antimicrobial Resistance, ISGlobal, Hospital Clínic–Universitat de Barcelona, Barcelona, Spain
- Department of Clinical Microbiology, Hospital Clínic–Universitat de Barcelona, Barcelona, Spain
| | - Ignasi Roca
- Laboratory of Antimicrobial Resistance, ISGlobal, Hospital Clínic–Universitat de Barcelona, Barcelona, Spain
| |
Collapse
|
16
|
Cheng YH, Chou SH, Huang PH, Yang TC, Juan YF, Kreiswirth BN, Lin YT, Chen L. Characterization of a mcr-1 and CRISPR-Cas System Co-harboring Plasmid in a Carbapenemase-Producing High-Risk ST11 Klebsiella pneumoniae Strain. Front Microbiol 2021; 12:762947. [PMID: 34777318 PMCID: PMC8579119 DOI: 10.3389/fmicb.2021.762947] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 10/07/2021] [Indexed: 11/21/2022] Open
Abstract
We set out to study the prevalence of the mcr-1 gene in carbapenemase-producing Klebsiella pneumoniae (CPKP) strains, and to determine whether its presence is associated with a fitness cost. A total of 234 clinical CPKP isolates were collected from a tertiary medical center in Taiwan from January 2018 to January 2019. The mcr-1 and carbapenemase genes were detected by polymerase chain reaction (PCR) followed by Sanger sequencing. The mcr-1-positive carbapenemase-producing strain was characterized by whole genome sequencing, a plasmid stability test and a conjugation assay. In vitro growth rate and an in vivo virulence test were compared between the parental mcr-1-positive strain and its mcr-1 plasmid-cured strain. We identified only one mcr-1 positive strain (KP2509), co-harboring blaKPC–2 and blaOXA–48, among 234 (1/234, 0.43%) CPKP strains. KP2509 and its Escherichia coli mcr-1 transconjugant showed moderate colistin resistance (MIC = 8 mg/L). The mcr-1 is located on a large conjugative plasmid (317 kb), pKP2509-MCR, with three replicons, IncHI, IncFIB, and IncN. Interestingly, a complete Type IV-A3 CRISPR-Cas system was identified in pKP2509-MCR. Plasmid pKP2509-MCR was highly stable in KP2509 after 270 generation of passage, and the pKP2509-MCR cured strain PC-KP2509 showed similar growth rate and in vivo virulence in comparison to KP2509. The prevalence of mcr-1 in CPKP strains remains low in our center. Notably, we identified a large plasmid with multiple replicons containing both the mcr-1 and the Type IV-3A CRISPR-Cas genes. The further spread of this highly stable plasmid raises concern that it may promote the increase of mcr-1 prevalence in CPKP.
Collapse
Affiliation(s)
- Yi-Hsiang Cheng
- Division of Infectious Diseases, Department of Medicine, Taipei Veterans General Hospital, Taipei, Taiwan.,Institute of Emergency and Critical Care Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Sheng-Hua Chou
- Institute of Emergency and Critical Care Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Po-Han Huang
- Division of Infectious Diseases, Department of Medicine, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Tsuey-Ching Yang
- Department of Biotechnology and Laboratory Science in Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Yu-Fan Juan
- Division of Microbiology, Department of Pathology and Laboratory Medicine, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Barry N Kreiswirth
- Hackensack Meridian Health Center for Discovery and Innovation, Nutley, NJ, United States
| | - Yi-Tsung Lin
- Division of Infectious Diseases, Department of Medicine, Taipei Veterans General Hospital, Taipei, Taiwan.,Institute of Emergency and Critical Care Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Liang Chen
- Hackensack Meridian Health Center for Discovery and Innovation, Nutley, NJ, United States.,Department of Medical Sciences, Hackensack Meridian School of Medicine, Nutley, NJ, United States
| |
Collapse
|
17
|
Petitjean M, Juarez P, Meunier A, Daguindau E, Puja H, Bertrand X, Valot B, Hocquet D. The rise and the fall of a Pseudomonas aeruginosa endemic lineage in a hospital. Microb Genom 2021; 7. [PMID: 34473016 PMCID: PMC8715434 DOI: 10.1099/mgen.0.000629] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The biological features that allow a pathogen to survive in the hospital environment are mostly unknown. The extinction of bacterial epidemics in hospitals is mostly attributed to changes in medical practice, including infection control, but the role of bacterial adaptation has never been documented. We analysed a collection of Pseudomonas aeruginosa isolates belonging to the Besançon Epidemic Strain (BES), responsible for a 12year nosocomial outbreak, using a genotype-to-phenotype approach. Bayesian analysis estimated the emergence of the clone in the hospital 5 years before its opening, during the creation of its water distribution network made of copper. BES survived better than the reference strains PAO1 and PA14 in a copper solution due to a genomic island containing 13 metal-resistance genes and was specifically able to proliferate in the ubiquitous amoeba Vermamoeba vermiformis. Mutations affecting amino-acid metabolism, antibiotic resistance, lipopolysaccharide biosynthesis, and regulation were enriched during the spread of BES. Seven distinct regulatory mutations attenuated the overexpression of the genes encoding the efflux pump MexAB-OprM over time. The fitness of BES decreased over time in correlation with its genome size. Overall, the resistance to inhibitors and predators presumably aided the proliferation and propagation of BES in the plumbing system of the hospital. The pathogen further spread among patients via multiple routes of contamination. The decreased prevalence of patients infected by BES mirrored the parallel and convergent genomic evolution and reduction that affected bacterial fitness. Along with infection control measures, this may have participated in the extinction of BES in the hospital setting.
Collapse
Affiliation(s)
- Marie Petitjean
- Hygiène Hospitalière, Centre Hospitalier Universitaire, 25030 Besançon, France.,UMR CNRS 6249, Université de Bourgogne Franche-Comté, 25030 Besançon, France
| | - Paulo Juarez
- UMR CNRS 6249, Université de Bourgogne Franche-Comté, 25030 Besançon, France
| | - Alexandre Meunier
- Hygiène Hospitalière, Centre Hospitalier Universitaire, 25030 Besançon, France
| | - Etienne Daguindau
- UMR INSERM 1098, Université de Bourgogne Franche-Comté, 25030 Besançon, France
| | - Hélène Puja
- UMR CNRS 6249, Université de Bourgogne Franche-Comté, 25030 Besançon, France
| | - Xavier Bertrand
- Hygiène Hospitalière, Centre Hospitalier Universitaire, 25030 Besançon, France.,UMR CNRS 6249, Université de Bourgogne Franche-Comté, 25030 Besançon, France
| | - Benoit Valot
- UMR CNRS 6249, Université de Bourgogne Franche-Comté, 25030 Besançon, France.,Bioinformatique et Big Data au Service de la Santé, UFR Science de la Santé, Université de Bourgogne Franche-Comté, 25030 Besançon, France
| | - Didier Hocquet
- Hygiène Hospitalière, Centre Hospitalier Universitaire, 25030 Besançon, France.,UMR CNRS 6249, Université de Bourgogne Franche-Comté, 25030 Besançon, France.,Bioinformatique et Big Data au Service de la Santé, UFR Science de la Santé, Université de Bourgogne Franche-Comté, 25030 Besançon, France.,Centre de Ressources Biologiques - Filière Microbiologique de Besançon, Centre Hospitalier Universitaire, 25030 Besançon, France
| |
Collapse
|
18
|
Gu JN, Chen L, Weng XB, Yang XY, Pan DM. Clinical and Microbiological Characteristics of a Community-Acquired Carbapenem-Resistant Escherichia coli ST410 Isolate Harbouring blaNDM-5-Encoding IncX3-Type Plasmid From Blood. Front Med (Lausanne) 2021; 8:658058. [PMID: 34179042 PMCID: PMC8226244 DOI: 10.3389/fmed.2021.658058] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 05/13/2021] [Indexed: 11/20/2022] Open
Abstract
Objectives: The aim of this research was to investigate the clinical and microbiological characteristics of a case of community-acquired carbapenem-resistant Escherichia coli isolated from a patient with a bloodstream infection in China. Methods:Escherichia coli Huamei202001 was recovered from the first blood culture from a patient hospitalised in China. An antimicrobial susceptibility test was performed, and the genome was sequenced on an Illumina HiSeq X 10 platform with a 150-bp paired-end approach. The generated sequence reads were assembled using Unicycler, and the whole genome sequence data were analysed using bioinformatics tools. Moreover, the patient and her main family members obtained a faecal sample screening test for CRE, the positive strain was further isolated and the identification and antimicrobial susceptibility testing was performed. Results:Escherichia coli Huamei202001 belonged to sequence type 410. In addition, a blaNDM-5-encoding IncX3-type plasmid was responsible for the spreading of carbapenem resistance. Only the patient was detected as having a positive faecal sample screening test for CRE. Strain Fec01 was identified as E. coli, and the antibiotic susceptibility profile was the same as that of E. coli Huamei202001. Conclusions:Escherichia coli Huamei202001 is defined as community-acquired carbapenem-resistant Enterobacteriaceae. The clone ST410 that harbours the blaNDM-5-encoding IncX3-type plasmid is causing new high-risk clones globally. Thus, infection control measures should be strengthened to curb the dissemination of IncX3.
Collapse
Affiliation(s)
- Ji-Na Gu
- Department of Infectious Medicine, Hwa Mei Hospital, University of Chinese Academy of Sciences, Ningbo, China
| | - Lin Chen
- Department of Infectious Medicine, Hwa Mei Hospital, University of Chinese Academy of Sciences, Ningbo, China
| | - Xing-Bei Weng
- Department of Laboratory Medicine, Ningbo First Hospital, Ningbo, China
| | - Xiao-Yan Yang
- Department of Infectious Medicine, Hwa Mei Hospital, University of Chinese Academy of Sciences, Ningbo, China
| | - Dan-Mei Pan
- Department of Infectious Medicine, Hwa Mei Hospital, University of Chinese Academy of Sciences, Ningbo, China
| |
Collapse
|
19
|
Fischer S, Dethlefsen S, Klockgether J, Tümmler B. Phenotypic and Genomic Comparison of the Two Most Common ExoU-Positive Pseudomonas aeruginosa Clones, PA14 and ST235. mSystems 2020; 5:e01007-20. [PMID: 33293405 DOI: 10.1128/mSystems.01007-20] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Genotyping of 2,882 Pseudomonas aeruginosa isolates that had been collected during the last 40 years identified the ExoU-positive lineages PA14 (ST253) and ST235 as the second and third most frequent clones in the P. aeruginosa population. Both clones were approximately 2-fold more frequently detected in animate habitats than in soil or aquatic habitats. While ST253 clone isolates were causing mainly acute and chronic infections in humans, ST235 isolates had been preferentially collected from hospitalized patients with severe acute infections, particularly, keratitis, urinary tract infections, burn wounds, and ventilator-associated pneumonia. The two major exoU clones differed substantially in the composition and flexibility of the accessory genome and by more than 8,000 amino acid sequences. Pronounced sequence variation between orthologs was noted in genes encoding elements of secretion systems and secreted effector molecules, including the type III secretion system, indicating the modes of action of the different clones. When comparing representatives of the two clones in batch culture, the PA14 strain orchestrated the quorum sensing circuitry for the expression of pathogenic traits and stopped growing in batch culture when it entered the stationary phase, but the quorum sensing-deficient ST235 strain expressed high type III secretion activity and continued to grow and to divide. In summary, unrestricted growth, high constitutive type III secretion activity, and facilitated uptake of foreign DNA could be major features that have made ST235 a global high-risk clone associated with poor outcomes of acute nosocomial infections.IMPORTANCE The ubiquitous and metabolically versatile environmental bacterium Pseudomonas aeruginosa can cause infections in a wide variety of hosts, including insects, plants, animals, and humans. P. aeruginosa is one of the ESKAPE (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter species) pathogens that are the major cause of nosocomial infections in the United States and are a threat all over the world because of their capacity to become increasingly resistant to all available antibiotics. Most experimental work on P. aeruginosa has been performed with reference strains PAO1 and PA14, providing deep insight into key metabolic and regulatory pathways thought to be applicable to all P. aeruginosa strains. However, this comparative study on the two most common exoU-positive clones taught us that there are major lineages in the population such as the global high-risk clone ST235 that exhibit uncommon traits of lifestyle, genome mobility, and pathogenicity distinct from those in our knowledge gained from the studies with the reference strains.
Collapse
|
20
|
Gondal AJ, Saleem S, Jahan S, Choudhry N, Yasmin N. Novel Carbapenem-Resistant Klebsiella pneumoniae ST147 Coharboring bla NDM-1, bla OXA-48 and Extended-Spectrum β-Lactamases from Pakistan. Infect Drug Resist 2020; 13:2105-2115. [PMID: 32669863 PMCID: PMC7337428 DOI: 10.2147/idr.s251532] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 05/07/2020] [Indexed: 12/14/2022] Open
Abstract
Purpose The emergence of multidrug-resistant Klebsiella pneumoniae (K. pneumoniae) is associated with the acquisition of multiple carbapenemases. Their clonal spread is a worldwide concern due to their critical role in nosocomial infections. Therefore, the identification of high-risk clones with antibiotic resistance genes is very crucial for controlling its global spread. Materials and Methods A total of 227 K. pneumoniae strains collected during April 2018 to November 2019 were confirmed by PCR. Carbapenemases and extended-spectrum β-lactamases (ESBL) were detected phenotypically. Confirmation of carbapenemases was carried out by PCR and Sanger sequencing. The clonal lineages were assigned to selected isolates by multilocus sequence typing (MLST), and the plasmid analysis was done by PCR-based detection of the plasmid replicon typing. Results Of the total K. pneumoniae, 117 (51.5%) were carbapenem resistant (CRKP) and 140 (61.7%) were identified as ESBL producers. Intermediate to high resistance was detected in the tested β-lactam drugs while polymyxin-B and tigecycline were found to be susceptible. Among CRKP, 91 (77.8%) isolates were detected as carbapenemase producing, while 55 (47%) were positive for blaNDM-1 23.9% (n=28), blaOXA-48 22.2% (n=26) and blaVIM 0.85% (n=1) while 12.7% (n=7) carried both blaNDM-1 and blaOXA-48 genes. The CRKP coharboring blaNDM-1 and blaOXA-48 genes (n=7) were positive for blaCTX-MblaSHV (n=3), blaSHV (n=1) and blaCTX-M (n=3). The novel CRKP with the coexistence of blaNDM-1, blaOXA-48, blaCTX-M and blaSHV genes were associated with the high-risk clone ST147 (n=5) and ST11 (n=2). The assigned replicon types were IncL/M, IncFII, IncA/C and IncH1. Conclusion This is the first report of the coexistence of blaNDM-1, blaOXA-48, blaCTX-M and blaSHV genes on a high-risk lineage ST147 from Pakistan. This study highlights the successful dissemination of carbapenemase resistance genes in the high-risk clones that emphasizes the importance of monitoring and controlling the spread of these diverse clones globally.
Collapse
Affiliation(s)
- Aamir Jamal Gondal
- Department of Microbiology, University of Health Sciences, Lahore, Pakistan.,Department of Biomedical Sciences, King Edward Medical University, Lahore, Pakistan
| | - Sidrah Saleem
- Department of Microbiology, University of Health Sciences, Lahore, Pakistan
| | - Shah Jahan
- Department of Immunology, University of Health Sciences, Lahore, Pakistan
| | - Nakhshab Choudhry
- Department of Biochemistry, King Edward Medical University, Lahore, Pakistan
| | - Nighat Yasmin
- Department of Biomedical Sciences, King Edward Medical University, Lahore, Pakistan
| |
Collapse
|
21
|
Wang S, Zhao J, Liu N, Yang F, Zhong Y, Gu X, Jian Z, Yan Q, Liu Q, Li H, Li Y, Liu J, Li H, Chen L, Liu W. IMP-38-Producing High-Risk Sequence Type 307 Klebsiella pneumoniae Strains from a Neonatal Unit in China. mSphere 2020; 5:e00407-20. [PMID: 32611699 PMCID: PMC7333572 DOI: 10.1128/msphere.00407-20] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2020] [Accepted: 06/08/2020] [Indexed: 12/31/2022] Open
Abstract
An emerging multidrug-resistant Klebsiella pneumoniae high-risk clone of sequence type 307 (ST307) has been increasingly reported worldwide. Here, we described the genomic characteristics of an IMP-38-producing ST307 K. pneumoniae strain and investigated the prevalence of blaIMP-38 among carbapenem-resistant Klebsiella pneumoniae isolates from a tertiary care hospital in central China. A total of 14 IMP-38-producing ST307 K. pneumoniae strains were identified from 2013 to 2016, with 13 strains isolated from patients with neonatal sepsis in the neonatal ward. PacBio and Illumina whole-genome sequencing analysis performed on a representative IMP-38-producing K. pneumoniae strain, WCGKP294, showed that it contained a circular chromosome and two plasmids. Carbapenemase gene blaIMP-38 is colocated with blaCTX-M-3 in transposon Tn6382 on an IncHI5 plasmid (pWCGKP294-2). WCGKP294 harbors another IncFIB plasmid, pWCGKP294-1, carrying three copies of tandem-repeated IS26-blaSHV-2A-deoR-ygbJ-ygbK-fucA-IS26 composite transposon elements. Phylogenetic analysis placed WCGKP294 in the global ST307 cluster, distant from the U.S. (Texas) and South Africa clusters. Nevertheless, WCGKP294 does not contain the chromosomal fluoroquinolone resistance-associated mutations and IncFIIK/IncFIBK plasmid-associated blaCTX-M-15 gene that are frequently found in other global ST307 strains.IMPORTANCE We described the genome and resistome characterization of a carbapenem-resistant Klebsiella pneumoniae ST307 strain carrying blaIMP-38 in China. This report highlights that the high-risk ST307 clone continues to acquire different antimicrobial resistance genes, posing significant challenges to clinical practice, and should be closely monitored.
Collapse
Affiliation(s)
- Siyi Wang
- Department of Clinical Laboratory, Xiangya Hospital of Central South University, Changsha, China
| | - Juan Zhao
- Department of Clinical Laboratory, Xiangya Hospital of Central South University, Changsha, China
| | - Ning Liu
- Department of Clinical Laboratory, Xiangya Hospital of Central South University, Changsha, China
| | - Fang Yang
- Department of Clinical Laboratory, Xiangya Hospital of Central South University, Changsha, China
| | - Yiming Zhong
- Department of Clinical Laboratory, Xiangya Hospital of Central South University, Changsha, China
| | - Xiumei Gu
- Department of Clinical Laboratory, Xiangya Hospital of Central South University, Changsha, China
| | - Zijuan Jian
- Department of Clinical Laboratory, Xiangya Hospital of Central South University, Changsha, China
| | - Qun Yan
- Department of Clinical Laboratory, Xiangya Hospital of Central South University, Changsha, China
| | - Qingxia Liu
- Department of Clinical Laboratory, Xiangya Hospital of Central South University, Changsha, China
| | - Hongling Li
- Department of Clinical Laboratory, Xiangya Hospital of Central South University, Changsha, China
| | - Yanming Li
- Department of Clinical Laboratory, Xiangya Hospital of Central South University, Changsha, China
| | - Jing Liu
- Molecular Biology Research Center and Hunan Province Key Laboratory of Basic and Applied Hematology, School of Life Sciences, Central South University, Changsha, China
| | - Hui Li
- Molecular Biology Research Center and Hunan Province Key Laboratory of Basic and Applied Hematology, School of Life Sciences, Central South University, Changsha, China
| | - Liang Chen
- Center for Discovery and Innovation, Hackensack-Meridian Health, Nutley, New Jersey, USA
- Hackensack Meridian School of Medicine, Seton Hall University, Nutley, New Jersey, USA
| | - Wenen Liu
- Department of Clinical Laboratory, Xiangya Hospital of Central South University, Changsha, China
| |
Collapse
|
22
|
Álvarez VE, Quiroga MP, Galán AV, Vilacoba E, Quiroga C, Ramírez MS, Centrón D. Crucial Role of the Accessory Genome in the Evolutionary Trajectory of Acinetobacter baumannii Global Clone 1. Front Microbiol 2020; 11:342. [PMID: 32256462 PMCID: PMC7093585 DOI: 10.3389/fmicb.2020.00342] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Accepted: 02/17/2020] [Indexed: 01/08/2023] Open
Abstract
Acinetobacter baumannii is one of the most important nosocomial pathogens able to rapidly develop extensive drug resistance. Here, we study the role of accessory genome in the success of the globally disseminated clone 1 (GC1) with functional and genomic approaches. Comparative genomics was performed with available GC1 genomes (n = 106) against other A. baumannii high-risk and sporadic clones. Genetic traits related to accessory genome were found common and conserved along time as two novel regions of genome plasticity, and a CRISPR-Cas system acquired before clonal diversification located at the same loci as “sedentary” modules. Although identified within hotspot for recombination, other block of accessory genome was also “sedentary” in lineage 1 of GC1 with signs of microevolution as the AbaR0-type genomic island (GI) identified in A144 and in A155 strains which were maintained one month in independent experiments without antimicrobial pressure. The prophage YMC/09/02/B1251_ABA_BP was found to be “mobile” since, although it was shared by all GC1 genomes, it showed high intrinsic microevolution as well as mobility to different insertion sites. Interestingly, a wide variety of Insertion Sequences (IS), probably acquired by the flow of plasmids related to Rep_3 superfamily was found. These IS showed dissimilar genomic location amongst GC1 genomes presumably associated with promptly niche adaptation. On the other hand, a type VI secretion system and three efflux pumps were subjected to deep processes of genomic loss in A. baumannii but not in GC1. As a whole, these findings suggest that preservation of some genetic modules of accessory genome harbored by strains from different continents in combination with great plasticity of IS and varied flow of plasmids, may be central features of the genomic structure of GC1. Competition of A144 and A155 versus A118 (ST 404/ND) without antimicrobial pressure suggested a higher ability of GC1 to grow over a clone with sporadic behavior which explains, from an ecological perspective, the global achievement of this successful pandemic clone in the hospital habitat. Together, these data suggest an essential role of still unknown properties of “mobile” and “sedentary” accessory genome that is preserved over time under different antibiotic or stress conditions.
Collapse
Affiliation(s)
- Verónica Elizabeth Álvarez
- Laboratorio de Investigaciones en Mecanismos de Resistencia a Antibióticos, Instituto de Investigaciones en Microbiología y Parasitología Médica, Facultad de Medicina, Universidad de Buenos Aires - Consejo Nacional de Investigaciones Científicas y Tecnológicas (IMPaM, UBA-CONICET), Buenos Aires, Argentina
| | - María Paula Quiroga
- Laboratorio de Investigaciones en Mecanismos de Resistencia a Antibióticos, Instituto de Investigaciones en Microbiología y Parasitología Médica, Facultad de Medicina, Universidad de Buenos Aires - Consejo Nacional de Investigaciones Científicas y Tecnológicas (IMPaM, UBA-CONICET), Buenos Aires, Argentina
| | - Angélica Viviana Galán
- Laboratorio de Investigaciones en Mecanismos de Resistencia a Antibióticos, Instituto de Investigaciones en Microbiología y Parasitología Médica, Facultad de Medicina, Universidad de Buenos Aires - Consejo Nacional de Investigaciones Científicas y Tecnológicas (IMPaM, UBA-CONICET), Buenos Aires, Argentina
| | - Elisabet Vilacoba
- Laboratorio de Investigaciones en Mecanismos de Resistencia a Antibióticos, Instituto de Investigaciones en Microbiología y Parasitología Médica, Facultad de Medicina, Universidad de Buenos Aires - Consejo Nacional de Investigaciones Científicas y Tecnológicas (IMPaM, UBA-CONICET), Buenos Aires, Argentina
| | - Cecilia Quiroga
- Instituto de Investigaciones en Microbiología y Parasitología Médica, Facultad de Medicina, Universidad de Buenos Aires - Consejo Nacional de Investigaciones Científicas y Tecnológicas (IMPaM, UBA-CONICET), Buenos Aires, Argentina
| | - María Soledad Ramírez
- Center for Applied Biotechnology Studies, Department of Biological Science, California State University Fullerton, Fullerton, CA, United States
| | - Daniela Centrón
- Laboratorio de Investigaciones en Mecanismos de Resistencia a Antibióticos, Instituto de Investigaciones en Microbiología y Parasitología Médica, Facultad de Medicina, Universidad de Buenos Aires - Consejo Nacional de Investigaciones Científicas y Tecnológicas (IMPaM, UBA-CONICET), Buenos Aires, Argentina
| |
Collapse
|
23
|
Vatansever C, Menekse S, Dogan O, Gucer LS, Ozer B, Ergonul O, Can F. Co-existence of OXA-48 and NDM-1 in colistin resistant Pseudomonas aeruginosa ST235. Emerg Microbes Infect 2020; 9:152-154. [PMID: 31964275 PMCID: PMC7006663 DOI: 10.1080/22221751.2020.1713025] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Here, we presented 11 cases with colistin-resistant Pseudomonas aeruginosa infection and co-existence of OXA-48 and NDM-1 in the ST235 high-risk clone. The molecular analyses were performed by Sanger sequencing and RT-PCR. The eight patients (72.7%) had an invasive infection and three (27.3%) had colonization. The 30-day mortality rate was 87.5% (7/8). Three patients (37.5%, 3/8) received colistin therapy before isolation of P. aeruginosa. In the Multilocus sequence typing (MLST) analysis of 11 isolates, eight (72.7%) isolates belonged to P. aeruginosa ST235 clone. All isolates were NDM-1 positive, and nine isolates (81.8%) were found to be positive for both OXA-48 and NDM-1. Sequences of pmrAB and phoPQ revealed numerous insertions and deletions in all isolates. In 10 isolates pmrAB and phoPQ were found to be upregulated. In conclusion, the co-existence of OXA-48 and NDM-1 genes in colistin-resistant P. aeruginosa ST235 high-risk clone indicates the spread of carbapenemases in clinical isolates and highlights need of continuous surveillance for high-risk clones of P. aeruginosa.
Collapse
Affiliation(s)
- Cansel Vatansever
- Department of Infectious Diseases and Clinical Microbiology, Koc University School of Medicine, Istanbul, Turkey
| | - Sirin Menekse
- Department of Infectious Diseases and Clinical Microbiology, Kosuyolu State Hospital, Istanbul, Turkey
| | - Ozlem Dogan
- Department of Infectious Diseases and Clinical Microbiology, Koc University School of Medicine, Istanbul, Turkey
| | - Lal Sude Gucer
- Department of Infectious Diseases and Clinical Microbiology, Koc University School of Medicine, Istanbul, Turkey
| | - Berna Ozer
- Department of Infectious Diseases and Clinical Microbiology, Koc University School of Medicine, Istanbul, Turkey
| | - Onder Ergonul
- Department of Infectious Diseases and Clinical Microbiology, Koc University School of Medicine, Istanbul, Turkey
| | - Fusun Can
- Department of Infectious Diseases and Clinical Microbiology, Koc University School of Medicine, Istanbul, Turkey
| |
Collapse
|
24
|
Pincus NB, Bachta KER, Ozer EA, Allen JP, Pura ON, Qi C, Rhodes NJ, Marty FM, Pandit A, Mekalanos JJ, Oliver A, Hauser AR. Long-term Persistence of an Extensively Drug-Resistant Subclade of Globally Distributed Pseudomonas aeruginosa Clonal Complex 446 in an Academic Medical Center. Clin Infect Dis 2019; 71:1524-1531. [PMID: 31583403 PMCID: PMC7486844 DOI: 10.1093/cid/ciz973] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2019] [Accepted: 09/30/2019] [Indexed: 01/24/2023] Open
Abstract
BACKGROUND Antimicrobial resistance (AMR) is a major challenge in the treatment of infections caused by Pseudomonas aeruginosa. Highly drug-resistant infections are disproportionally caused by a small subset of globally distributed P. aeruginosa sequence types (STs), termed "high-risk clones." We noted that clonal complex (CC) 446 (which includes STs 298 and 446) isolates were repeatedly cultured at 1 medical center and asked whether this lineage might constitute an emerging high-risk clone. METHODS We searched P. aeruginosa genomes from collections available from several institutions and from a public database for the presence of CC446 isolates. We determined antibacterial susceptibility using microbroth dilution and examined genome sequences to characterize the population structure of CC446 and investigate the genetic basis of AMR. RESULTS CC446 was globally distributed over 5 continents. CC446 isolates demonstrated high rates of AMR, with 51.9% (28/54) being multidrug-resistant (MDR) and 53.6% of these (15/28) being extensively drug-resistant (XDR). Phylogenetic analysis revealed that most MDR/XDR isolates belonged to a subclade of ST298 (designated ST298*) of which 100% (21/21) were MDR and 61.9% (13/21) were XDR. XDR ST298* was identified repeatedly and consistently at a single academic medical center from 2001 through 2017. These isolates harbored a large plasmid that carries a novel antibiotic resistance integron. CONCLUSIONS CC446 isolates are globally distributed with multiple occurrences of high AMR. The subclade ST298* is responsible for a prolonged epidemic (≥16 years) of XDR infections at an academic medical center. These findings indicate that CC446 is an emerging high-risk clone deserving further surveillance.
Collapse
Affiliation(s)
- Nathan B Pincus
- Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Kelly E R Bachta
- Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA,Department of Medicine, Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Egon A Ozer
- Department of Medicine, Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Jonathan P Allen
- Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA,Present address: Department of Microbiology and Immunology, Loyola University, Chicago, CTRE 218, 2160 S. First Ave. Maywood, IL 60153
| | - Olivia N Pura
- Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Chao Qi
- Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Nathaniel J Rhodes
- Department of Pharmacy Practice, Chicago College of Pharmacy, Midwestern University, Downers Grove, Illinois, USA,Pharmacometrics Center of Excellence, Chicago College of Pharmacy, Midwestern University, Downers Grove, Illinois, USA,Department of Pharmacy, Northwestern Memorial Hospital, Chicago, Illinois, USA
| | - Francisco M Marty
- Division of Infectious Diseases, Brigham and Women’s Hospital, Boston, Massachusetts, USA
| | - Alisha Pandit
- Division of Infectious Diseases, Brigham and Women’s Hospital, Boston, Massachusetts, USA
| | - John J Mekalanos
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts, USA
| | - Antonio Oliver
- Servicio de Microbiología y Unidad de Investigación, Hospital Universitari Son Espases, Institut d’Investigació Sanitaria Illes Balears, Palma de Mallorca, Spain
| | - Alan R Hauser
- Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA,Department of Medicine, Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA,Correspondence: A. R. Hauser, 303 E. Chicago Ave., Ward 6–035, Chicago, IL 60611 ()
| |
Collapse
|
25
|
Turton J, Davies F, Turton J, Perry C, Payne Z, Pike R. Hybrid Resistance and Virulence Plasmids in "High-Risk" Clones of Klebsiella pneumoniae, Including Those Carrying blaNDM-5. Microorganisms 2019; 7:microorganisms7090326. [PMID: 31500105 PMCID: PMC6780558 DOI: 10.3390/microorganisms7090326] [Citation(s) in RCA: 72] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Revised: 09/02/2019] [Accepted: 09/03/2019] [Indexed: 01/12/2023] Open
Abstract
Virulence plasmids are associated with hypervirulent types of Klebsiella pneumoniae, which generally do not carry antibiotic resistance genes. In contrast, nosocomial isolates are often associated with resistance, but rarely with virulence plasmids. Here, we describe virulence plasmids in nosocomial isolates of "high-risk" clones of sequence types (STs) 15, 48, 101, 147 and 383 carrying carbapenemase genes. The whole genome sequences were determined by long-read nanopore sequencing. The 12 isolates all contained hybrid plasmids containing both resistance and virulence genes. All carried rmpA/rmpA2 and the aerobactin cluster, with the virulence plasmids of two of three representatives of ST383 carrying blaNDM-5 and seventeen other resistance genes. Representatives of ST48 and ST15 had virulence plasmid-associated genes distributed between two plasmids, both containing antibiotic resistance genes. Representatives of ST101 were remarkable in all sharing virulence plasmids in which iucC and terAWXYZ were missing and iucB and iucD truncated. The combination of resistance and virulence in plasmids of high-risk clones is extremely worrying. Virulence plasmids were often notably consistent within a lineage, even in the absence of epidemiological links, suggesting they are not moving between types. However, there was a common segment containing multiple resistance genes in virulence plasmids of representatives of both STs 48 and 383.
Collapse
Affiliation(s)
- Jane Turton
- National Infection Service, Public Health England, 61, Colindale Avenue, London NW9 5EQ, UK.
| | - Frances Davies
- Imperial College Healthcare NHS Trust, North West London Pathology, Hammersmith Hospital, Du Cane Road, London W12 0HS, UK.
| | - Jack Turton
- Independent Informatician, NW9 0TA c/o National Infection Service, Public Health England, 61, Colindale Avenue, London NW9 5EQ, UK.
| | - Claire Perry
- National Infection Service, Public Health England, 61, Colindale Avenue, London NW9 5EQ, UK.
| | - Zoë Payne
- National Infection Service, Public Health England, 61, Colindale Avenue, London NW9 5EQ, UK.
| | - Rachel Pike
- National Infection Service, Public Health England, 61, Colindale Avenue, London NW9 5EQ, UK.
| |
Collapse
|
26
|
Hanczvikkel A, Füzi M, Ungvári E, Tóth Á. Transmissible silver resistance readily evolves in high-risk clone isolates of Klebsiella pneumoniae. Acta Microbiol Immunol Hung 2018; 65:387-403. [PMID: 30043621 DOI: 10.1556/030.65.2018.031] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Silver is used extensively in both hospitals and outpatient clinics as a disinfectant coating agent on various devices. Resistance to silver was recently reported as an emerging problem in Enterobacteriaceae. Multidrug-resistant high-risk clones of Klebsiella pneumoniae are common causes of serious healthcare-associated infections worldwide posing a serious threat to patients. In this study, we investigated the capacity of both high-risk (CG14/15 and CG258) and minor clone strains of K. pneumoniae to develop resistance to silver. Resistance was induced in vitro in silver-susceptible but otherwise multidrug-resistant clinical isolates. Genetic alterations in the silver-resistant derivative strains with regard to the silver-susceptible isolates were investigated by whole-genome sequencing. The transferability of high-level resistance to silver was also tested. We demonstrated that the high-level resistance to silver can quickly evolve as a consequence of a single-point mutation either in the cusS gene of the chromosomally encoded CusCFBARS efflux system and/or in the silS gene of the plasmid-encoded Copper Homeostasis and Silver Resistance Island (CHASRI) coding also for a metallic efflux. The minimal inhibitory concentrations (MICs) of the strains increased from 4 mg/L (23.5 μM) AgNO3 to >8,500 mg/L (>50,000 μM) AgNO3 during induction. Harboring the CHASRI proved an important selective asset for K. pneumoniae when exposed to silver. Successful conjugation experiments using Escherichia coli K12 J5-3Rif as recipient showed that high-level silver resistance can transmit between strains of high-risk clones of K. pneumoniae (ST15 and ST11) and isolates from additional species of Enterobacteriaceae. The lack of fitness cost associated with the carriage of the CHASRI in a silver-free environment and the presence of the RelEB toxin-antitoxin system on the conjugative plasmids could advance the dissemination of silver resistance. Our results show that multidrug-resistant high-risk clones of K. pneumoniae are capable of evolving and transmitting high-level resistance to silver. This observation should warrant a more judicious use of silver coated-devices to prevent the extensive dissemination of silver resistance.
Collapse
Affiliation(s)
- Adrienn Hanczvikkel
- 1 Doctoral School on Material Sciences and Technologies, Óbuda University, Budapest, Hungary
| | - Miklós Füzi
- 2 Institute of Medical Microbiology, Semmelweis University, Budapest, Hungary
| | - Erika Ungvári
- 3 Division of Bacteriology, Mycology, Parasitology and Typing, National Public Health Institute, Budapest, Hungary
| | - Ákos Tóth
- 3 Division of Bacteriology, Mycology, Parasitology and Typing, National Public Health Institute, Budapest, Hungary
| |
Collapse
|
27
|
Roer L, Overballe-Petersen S, Hansen F, Schønning K, Wang M, Røder BL, Hansen DS, Justesen US, Andersen LP, Fulgsang-Damgaard D, Hopkins KL, Woodford N, Falgenhauer L, Chakraborty T, Samuelsen Ø, Sjöström K, Johannesen TB, Ng K, Nielsen J, Ethelberg S, Stegger M, Hammerum AM, Hasman H. Escherichia coli Sequence Type 410 Is Causing New International High-Risk Clones. mSphere 2018; 3:e00337-18. [PMID: 30021879 DOI: 10.1128/mSphere.00337-18] [Citation(s) in RCA: 152] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Extraintestinal pathogenic Escherichia coli (ExPEC) is the main cause of urinary tract infections and septicemia. Significant attention has been given to the ExPEC sequence type ST131, which has been categorized as a “high-risk” clone. High-risk clones are globally distributed clones associated with various antimicrobial resistance determinants, ease of transmission, persistence in hosts, and effective transmission between hosts. The high-risk clones have enhanced pathogenicity and cause severe and/or recurrent infections. We show that clones of the E. coli ST410 lineage persist and/or cause recurrent infections in humans, including bloodstream infections. We found evidence of ST410 being a highly resistant globally distributed lineage, capable of patient-to-patient transmission causing hospital outbreaks. Our analysis suggests that the ST410 lineage should be classified with the potential to cause new high-risk clones. Thus, with the clonal expansion over the past decades and increased antimicrobial resistance to last-resort treatment options, ST410 needs to be monitored prospectively. Escherichia coli sequence type 410 (ST410) has been reported worldwide as an extraintestinal pathogen associated with resistance to fluoroquinolones, third-generation cephalosporins, and carbapenems. In the present study, we investigated national epidemiology of ST410 E. coli isolates from Danish patients. Furthermore, E. coli ST410 was investigated in a global context to provide further insight into the acquisition of the carbapenemase genes blaOXA-181 and blaNDM-5 of this successful lineage. From 127 whole-genome-sequenced isolates, we reconstructed an evolutionary framework of E. coli ST410 which portrays the antimicrobial-resistant clades B2/H24R, B3/H24Rx, and B4/H24RxC. The B2/H24R and B3/H24Rx clades emerged around 1987, concurrently with the C1/H30R and C2/H30Rx clades in E. coli ST131. B3/H24Rx appears to have evolved by the acquisition of the extended-spectrum β-lactamase (ESBL)-encoding gene blaCTX-M-15 and an IncFII plasmid, encoding IncFIA and IncFIB. Around 2003, the carbapenem-resistant clade B4/H24RxC emerged when ST410 acquired an IncX3 plasmid carrying a blaOXA-181 carbapenemase gene. Around 2014, the clade B4/H24RxC acquired a second carbapenemase gene, blaNDM-5, on a conserved IncFII plasmid. From an epidemiological investigation of 49 E. coli ST410 isolates from Danish patients, we identified five possible regional outbreaks, of which one outbreak involved nine patients with blaOXA-181- and blaNDM-5-carrying B4/H24RxC isolates. The accumulated multidrug resistance in E. coli ST410 over the past two decades, together with its proven potential of transmission between patients, poses a high risk in clinical settings, and thus, E. coli ST410 should be considered a lineage with emerging “high-risk” clones, which should be monitored closely in the future. IMPORTANCE Extraintestinal pathogenic Escherichia coli (ExPEC) is the main cause of urinary tract infections and septicemia. Significant attention has been given to the ExPEC sequence type ST131, which has been categorized as a “high-risk” clone. High-risk clones are globally distributed clones associated with various antimicrobial resistance determinants, ease of transmission, persistence in hosts, and effective transmission between hosts. The high-risk clones have enhanced pathogenicity and cause severe and/or recurrent infections. We show that clones of the E. coli ST410 lineage persist and/or cause recurrent infections in humans, including bloodstream infections. We found evidence of ST410 being a highly resistant globally distributed lineage, capable of patient-to-patient transmission causing hospital outbreaks. Our analysis suggests that the ST410 lineage should be classified with the potential to cause new high-risk clones. Thus, with the clonal expansion over the past decades and increased antimicrobial resistance to last-resort treatment options, ST410 needs to be monitored prospectively.
Collapse
|
28
|
Petitjean M, Martak D, Silvant A, Bertrand X, Valot B, Hocquet D. Genomic characterization of a local epidemic Pseudomonas aeruginosa reveals specific features of the widespread clone ST395. Microb Genom 2017; 3:e000129. [PMID: 29177088 PMCID: PMC5695207 DOI: 10.1099/mgen.0.000129] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Accepted: 07/23/2017] [Indexed: 12/21/2022] Open
Abstract
Pseudomonas aeruginosa is a ubiquitous opportunistic pathogen with several clones being frequently associated with outbreaks in hospital settings. ST395 is among these so-called ‘international’ clones. We aimed here to define the biological features that could have helped the implantation and spread of the clone ST395 in hospital settings. The complete genome of a multidrug resistant index isolate (DHS01) of a large hospital outbreak was analysed. We identified DHS01-specific genetic elements, among which were identified those shared with a panel of six independent ST395 isolates responsible for outbreaks in other hospitals. DHS01 has the fifth largest chromosome of the species (7.1 Mbp), with most of its 1555 accessory genes borne by either genomic islands (GIs, n=48) or integrative and conjugative elements (ICEs, n=5). DHS01 is multidrug resistant mostly due to chromosomal mutations. It displayed signatures of adaptation to chronic infection in part due to the loss of a 131 kbp chromosomal fragment. Four GIs were specific to the clone ST395 and contained genes involved in metabolism (GI-4), in virulence (GI-6) and in resistance to copper (GI-7). GI-7 harboured an array of six copper transporters and was shared with non-pathogenic Pseudomonas sp. retrieved from copper-contaminated environments. Copper resistance was confirmed phenotypically in all other ST395 isolates and possibly accounted for the spreading capability of the clone in hospital outbreaks, where water networks have been incriminated. This suggests that genes transferred from copper-polluted environments may have favoured the implantation and spread of the international clone P. aeruginosa ST395 in hospital settings.
Collapse
Affiliation(s)
- Marie Petitjean
- 1Hygiène Hospitalière, Centre Hospitalier Régional Universitaire de Besançon, Besançon, France.,2UMR CNRS 6249 Chrono-Environnement, Université de Bourgogne Franche-Comté, Besançon, France
| | - Daniel Martak
- 1Hygiène Hospitalière, Centre Hospitalier Régional Universitaire de Besançon, Besançon, France.,2UMR CNRS 6249 Chrono-Environnement, Université de Bourgogne Franche-Comté, Besançon, France
| | - Alicia Silvant
- 1Hygiène Hospitalière, Centre Hospitalier Régional Universitaire de Besançon, Besançon, France
| | - Xavier Bertrand
- 1Hygiène Hospitalière, Centre Hospitalier Régional Universitaire de Besançon, Besançon, France.,2UMR CNRS 6249 Chrono-Environnement, Université de Bourgogne Franche-Comté, Besançon, France
| | - Benoit Valot
- 2UMR CNRS 6249 Chrono-Environnement, Université de Bourgogne Franche-Comté, Besançon, France
| | - Didier Hocquet
- 2UMR CNRS 6249 Chrono-Environnement, Université de Bourgogne Franche-Comté, Besançon, France.,3Centre de Ressources Biologiques - Filière Microbiologique, Centre Hospitalier Universitaire de Besançon, 3 Boulevard Fleming, Besançon, France.,1Hygiène Hospitalière, Centre Hospitalier Régional Universitaire de Besançon, Besançon, France
| |
Collapse
|