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Cabrera R, Fernández-Barat L, Vázquez N, Alcaraz-Serrano V, Bueno-Freire L, Amaro R, López-Aladid R, Oscanoa P, Muñoz L, Vila J, Torres A. OUP accepted manuscript. J Antimicrob Chemother 2022; 77:1600-1610. [PMID: 35323912 PMCID: PMC9155640 DOI: 10.1093/jac/dkac084] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 02/14/2022] [Indexed: 11/25/2022] Open
Abstract
Background Non-cystic fibrosis bronchiectasis (BE) is a chronic structural lung condition that facilitates chronic colonization by different microorganisms and courses with recurrent respiratory infections and frequent exacerbations. One of the main pathogens involved in BE is Pseudomonas aeruginosa. Objectives To determine the molecular mechanisms of resistance and the molecular epidemiology of P. aeruginosa strains isolated from patients with BE. Methods A total of 43 strains of P. aeruginosa were isolated from the sputum of BE patients. Susceptibility to the following antimicrobials was analysed: ciprofloxacin, meropenem, imipenem, amikacin, tobramycin, aztreonam, piperacillin/tazobactam, ceftazidime, ceftazidime/avibactam, ceftolozane/tazobactam, cefepime and colistin. The resistance mechanisms present in each strain were assessed by PCR, sequencing and quantitative RT–PCR. Molecular epidemiology was determined by MLST. Phylogenetic analysis was carried out using the eBURST algorithm. Results High levels of resistance to ciprofloxacin (44.19%) were found. Mutations in the gyrA, gyrB, parC and parE genes were detected in ciprofloxacin-resistant P. aeruginosa strains. The number of mutated QRDR genes was related to increased MIC. Different β-lactamases were detected: blaOXA50, blaGES-2, blaIMI-2 and blaGIM-1. The aac(3)-Ia, aac(3)-Ic, aac(6″)-Ib and ant(2″)-Ia genes were associated with aminoglycoside-resistant strains. The gene expression analysis showed overproduction of the MexAB-OprM efflux system (46.5%) over the other efflux system. The most frequently detected clones were ST619, ST676, ST532 and ST109. Conclusions Resistance to first-line antimicrobials recommended in BE guidelines could threaten the treatment of BE and the eradication of P. aeruginosa, contributing to chronic infection.
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Affiliation(s)
- Roberto Cabrera
- Hospital Clínic, Cellex Laboratory, CIBERES (Center for net Biomedical Research Respiratory diseases, 06/06/0028) - Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), School of Medicine, University of Barcelona, Spain
- Respiratory Intensive Care Unit, Pneumology Department, Hospital Clínic, Barcelona, Spain
| | - Laia Fernández-Barat
- Hospital Clínic, Cellex Laboratory, CIBERES (Center for net Biomedical Research Respiratory diseases, 06/06/0028) - Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), School of Medicine, University of Barcelona, Spain
- Respiratory Intensive Care Unit, Pneumology Department, Hospital Clínic, Barcelona, Spain
- Corresponding author. E-mail:
| | - Nil Vázquez
- Hospital Clínic, Cellex Laboratory, CIBERES (Center for net Biomedical Research Respiratory diseases, 06/06/0028) - Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), School of Medicine, University of Barcelona, Spain
- Respiratory Intensive Care Unit, Pneumology Department, Hospital Clínic, Barcelona, Spain
| | - Victoria Alcaraz-Serrano
- Hospital Clínic, Cellex Laboratory, CIBERES (Center for net Biomedical Research Respiratory diseases, 06/06/0028) - Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), School of Medicine, University of Barcelona, Spain
- Respiratory Intensive Care Unit, Pneumology Department, Hospital Clínic, Barcelona, Spain
| | - Leticia Bueno-Freire
- Hospital Clínic, Cellex Laboratory, CIBERES (Center for net Biomedical Research Respiratory diseases, 06/06/0028) - Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), School of Medicine, University of Barcelona, Spain
- Respiratory Intensive Care Unit, Pneumology Department, Hospital Clínic, Barcelona, Spain
| | - Rosanel Amaro
- Hospital Clínic, Cellex Laboratory, CIBERES (Center for net Biomedical Research Respiratory diseases, 06/06/0028) - Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), School of Medicine, University of Barcelona, Spain
- Respiratory Intensive Care Unit, Pneumology Department, Hospital Clínic, Barcelona, Spain
| | - Rubén López-Aladid
- Hospital Clínic, Cellex Laboratory, CIBERES (Center for net Biomedical Research Respiratory diseases, 06/06/0028) - Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), School of Medicine, University of Barcelona, Spain
- Respiratory Intensive Care Unit, Pneumology Department, Hospital Clínic, Barcelona, Spain
| | - Patricia Oscanoa
- Hospital Clínic, Cellex Laboratory, CIBERES (Center for net Biomedical Research Respiratory diseases, 06/06/0028) - Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), School of Medicine, University of Barcelona, Spain
- Respiratory Intensive Care Unit, Pneumology Department, Hospital Clínic, Barcelona, Spain
| | - Laura Muñoz
- Barcelona Global Health Institute, Department of Clinical Microbiology, Hospital Clínic, University of Barcelona, Barcelona, Spain
| | - Jordi Vila
- Barcelona Global Health Institute, Department of Clinical Microbiology, Hospital Clínic, University of Barcelona, Barcelona, Spain
| | - Antoni Torres
- Hospital Clínic, Cellex Laboratory, CIBERES (Center for net Biomedical Research Respiratory diseases, 06/06/0028) - Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), School of Medicine, University of Barcelona, Spain
- Respiratory Intensive Care Unit, Pneumology Department, Hospital Clínic, Barcelona, Spain
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Tümmler B. What Makes Pseudomonas aeruginosa a Pathogen? ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1386:283-301. [DOI: 10.1007/978-3-031-08491-1_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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OUP accepted manuscript. J Antimicrob Chemother 2022; 77:1862-1872. [DOI: 10.1093/jac/dkac122] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 03/21/2022] [Indexed: 11/14/2022] Open
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Lebreton F, Snesrud E, Hall L, Mills E, Galac M, Stam J, Ong A, Maybank R, Kwak YI, Johnson S, Julius M, Ly M, Swierczewski B, Waterman PE, Hinkle M, Jones A, Lesho E, Bennett JW, McGann P. A panel of diverse Pseudomonas aeruginosa clinical isolates for research and development. JAC Antimicrob Resist 2021; 3:dlab179. [PMID: 34909689 DOI: 10.1093/jacamr/dlab179] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Accepted: 11/05/2021] [Indexed: 11/15/2022] Open
Abstract
Objectives Pseudomonas aeruginosa is a leading cause of community- and hospital-acquired infections. Successful treatment is hampered by its remarkable ability to rapidly develop resistance to antimicrobial agents, primarily through mutation. In response, WHO listed carbapenem-resistant P. aeruginosa as a Priority 1 (Critical) pathogen for research and development of new treatments. A key resource in developing effective countermeasures is access to diverse and clinically relevant strains for testing. Herein we describe a panel of 100 diverse P. aeruginosa strains to support this endeavour. Methods WGS was performed on 3785 P. aeruginosa isolates in our repository. Isolates were cultured from clinical samples collected from healthcare facilities around the world between 2003 and 2017. Core-genome MLST and high-resolution SNP-based phylogenetic analyses were used to select a panel of 100 strains that captured the genetic diversity of this collection. Antibiotic susceptibility testing was also performed using 14 clinically relevant antibiotics. Results This 100-strain diversity panel contained representative strains from 91 different STs, including genetically distinct strains from major epidemic clones ST-111, ST-235, ST-244 and ST-253. Seventy-one distinct antibiotic susceptibility profiles were identified ranging from pan-susceptible to pan-resistant. Known resistance alleles as well as the most prevalent mutations underlying the antibiotic susceptibilities were characterized for all isolates. Conclusions This panel provides a diverse and comprehensive set of P. aeruginosa strains for use in developing solutions to antibiotic resistance. The isolates and available metadata, including genome sequences, are available to industry, academia, federal and other laboratories at no additional cost.
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Affiliation(s)
- Francois Lebreton
- Multidrug-Resistant Organism Repository and Surveillance Network (MRSN), Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Erik Snesrud
- Multidrug-Resistant Organism Repository and Surveillance Network (MRSN), Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Lindsey Hall
- Multidrug-Resistant Organism Repository and Surveillance Network (MRSN), Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Emma Mills
- Multidrug-Resistant Organism Repository and Surveillance Network (MRSN), Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Madeline Galac
- Multidrug-Resistant Organism Repository and Surveillance Network (MRSN), Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Jason Stam
- Multidrug-Resistant Organism Repository and Surveillance Network (MRSN), Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Ana Ong
- Multidrug-Resistant Organism Repository and Surveillance Network (MRSN), Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Rosslyn Maybank
- Multidrug-Resistant Organism Repository and Surveillance Network (MRSN), Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Yoon I Kwak
- Multidrug-Resistant Organism Repository and Surveillance Network (MRSN), Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Sheila Johnson
- Multidrug-Resistant Organism Repository and Surveillance Network (MRSN), Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Michael Julius
- Multidrug-Resistant Organism Repository and Surveillance Network (MRSN), Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Melissa Ly
- Multidrug-Resistant Organism Repository and Surveillance Network (MRSN), Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Brett Swierczewski
- Bacterial Disease Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | | | - Mary Hinkle
- Infectious Diseases Unit, Rochester General Hospital, Rochester, NY, USA
| | - Anthony Jones
- Department of Virology, Armed Forces Research Institute of Medical Sciences (AFRIMS), Bangkok, Thailand
| | - Emil Lesho
- Infectious Diseases Unit, Rochester General Hospital, Rochester, NY, USA
| | - Jason W Bennett
- Multidrug-Resistant Organism Repository and Surveillance Network (MRSN), Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Patrick McGann
- Multidrug-Resistant Organism Repository and Surveillance Network (MRSN), Walter Reed Army Institute of Research, Silver Spring, MD, USA
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Irum S, Naz K, Ullah N, Mustafa Z, Ali A, Arslan M, Khalid K, Andleeb S. Antimicrobial Resistance and Genomic Characterization of Six New Sequence Types in Multidrug-Resistant Pseudomonas aeruginosa Clinical Isolates from Pakistan. Antibiotics (Basel) 2021; 10:antibiotics10111386. [PMID: 34827324 PMCID: PMC8615273 DOI: 10.3390/antibiotics10111386] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 08/06/2021] [Accepted: 08/13/2021] [Indexed: 01/13/2023] Open
Abstract
Pseudomonas aeruginosa (P. aeruginosa) is a major bacterial pathogen associated with a variety of infections with high mortality rates. Most of the clinical P. aeruginosa isolates belong to a limited number of genetic subgroups characterized by multiple housekeeping genes’ sequences (usually 5–7) through the Multi-Locus Sequence Typing (MLST) scheme. The emergence and dissemination of novel multidrug-resistant (MDR) sequence types (ST) in P. aeruginosa pose serious clinical concerns. We performed whole-genome sequencing on a cohort (n = 160) of MDR P. aeruginosa isolates collected from a tertiary care hospital lab in Pakistan and found six isolates belonging to six unique MLST allelic profiles. The genomes were submitted to the PubMLST database and new ST numbers (ST3493, ST3494, ST3472, ST3489, ST3491, and ST3492) were assigned to the respective allele combinations. MLST and core-genome-based phylogenetic analysis confirmed the divergence of these isolates and positioned them in separate branches. Analysis of the resistome of the new STs isolates revealed the presence of genes blaOXA-50, blaPAO, blaPDC, blaVIM-2, aph(3′)-IIb, aac(6′)-II, aac(3)-Id, fosA, catB7, dfrB2, crpP, merP and a number of missense and frame-shift mutations in chromosomal genes conferring resistance to various antipseudomonal antibiotics. The exoS, exoT, pvdE, rhlI, rhlR, lasA, lasB, lasI, and lasR genes were the most prevalent virulence-related genes among the new ST isolates. The different genotypic features revealed the adaptation of these new clones to a variety of infections by various mutations in genes affecting antimicrobial resistance, quorum sensing and biofilm formation. Close monitoring of these antibiotic-resistant pathogens and surveillance mechanisms needs to be adopted to reduce their spread to the healthcare facilities of Pakistan. We believe that these strains can be used as reference strains for future comparative analysis of isolates belonging to the same STs.
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Affiliation(s)
- Sidra Irum
- Department of Industrial Biotechnology, Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences & Technology (NUST), Islamabad 44000, Pakistan; (S.I.); (K.N.); (N.U.); (Z.M.); (A.A.); (K.K.)
| | - Kanwal Naz
- Department of Industrial Biotechnology, Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences & Technology (NUST), Islamabad 44000, Pakistan; (S.I.); (K.N.); (N.U.); (Z.M.); (A.A.); (K.K.)
| | - Nimat Ullah
- Department of Industrial Biotechnology, Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences & Technology (NUST), Islamabad 44000, Pakistan; (S.I.); (K.N.); (N.U.); (Z.M.); (A.A.); (K.K.)
| | - Zeeshan Mustafa
- Department of Industrial Biotechnology, Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences & Technology (NUST), Islamabad 44000, Pakistan; (S.I.); (K.N.); (N.U.); (Z.M.); (A.A.); (K.K.)
| | - Amjad Ali
- Department of Industrial Biotechnology, Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences & Technology (NUST), Islamabad 44000, Pakistan; (S.I.); (K.N.); (N.U.); (Z.M.); (A.A.); (K.K.)
| | - Muhammad Arslan
- Pakistan Institute of Medical Sciences (PIMS), Islamabad 44000, Pakistan;
| | - Kashaf Khalid
- Department of Industrial Biotechnology, Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences & Technology (NUST), Islamabad 44000, Pakistan; (S.I.); (K.N.); (N.U.); (Z.M.); (A.A.); (K.K.)
| | - Saadia Andleeb
- Department of Industrial Biotechnology, Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences & Technology (NUST), Islamabad 44000, Pakistan; (S.I.); (K.N.); (N.U.); (Z.M.); (A.A.); (K.K.)
- Correspondence: or
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Laborda P, Sanz-García F, Hernando-Amado S, Martínez JL. Pseudomonas aeruginosa: an antibiotic resilient pathogen with environmental origin. Curr Opin Microbiol 2021; 64:125-132. [PMID: 34710741 DOI: 10.1016/j.mib.2021.09.010] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 08/31/2021] [Accepted: 09/23/2021] [Indexed: 12/24/2022]
Abstract
Pseudomonas aeruginosa, a bacterium characterized for its low antibiotics' susceptibility, is one of the most relevant opportunistic pathogens, causing infections at hospitals and in cystic fibrosis patients. Besides its relevance for human health, P. aeruginosa colonizes environmental ecosystems; therefore the elements driving its infectivity and antibiotic resistance must be analyzed from a One-Health perspective. Although some epidemic clones have been described, there are not specific lineages linked to infections, suggesting that P. aeruginosa virulence and antibiotic resistance determinants evolved in nature to play functions other than infecting the human host and avoiding antimicrobial treatment. Herein, we review current information on the population structure of P. aeruginosa and on the functional role that its resistance and virulence determinants have in non-clinical ecosystems.
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Affiliation(s)
- Pablo Laborda
- Centro Nacional de Biotecnología, CSIC, 28049, Madrid, Spain
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Recio R, Viedma E, González-Bodí S, Villa J, Orellana MÁ, Mancheño-Losa M, Lora-Tamayo J, Chaves F. Clinical and bacterial characteristics of Pseudomonas aeruginosa affecting the outcome of patients with bacteraemic pneumonia. Int J Antimicrob Agents 2021; 58:106450. [PMID: 34644604 DOI: 10.1016/j.ijantimicag.2021.106450] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2021] [Revised: 09/22/2021] [Accepted: 10/02/2021] [Indexed: 12/29/2022]
Abstract
Few studies have assessed the clinical and bacterial characteristics of Pseudomonas aeruginosa (PA) bacteraemic pneumonia (BP) episodes. This study analysed all non-duplicate PA-BP episodes from a tertiary hospital in 2013-2017. Epidemiology, clinical data, antimicrobial therapy and outcomes were recorded. Whole-genome sequencing was performed on PA blood isolates. The impact on early and late overall mortality of host, antimicrobial treatment and pathogen factors was assessed by multivariate logistic regression analysis. Of 55 PA-BP episodes, 32 (58.2%) were caused by extensively drug-resistant (XDR) PA. ST175 (32.7%) and ST235 (25.5%) were the most frequent high-risk clones. β-Lactamases/carbapenemases were detected in 29 isolates, including blaVIM-2 (27.2%) and blaGES type (25.5%) [blaGES-5 (20.0%), blaGES-1 (3.6%) and blaGES-20 (1.8%)]. The most prevalent O-antigen serotypes were O4 (34.5%) and O11 (30.9%). Overall, an extensive virulome was identified in all isolates. Early mortality (56.4%) was independently associated with severe neutropenia (aOR = 4.64, 95% CI 1.11-19.33; P = 0.035) and inappropriate empirical antimicrobial therapy (aOR = 5.71, 95% CI 1.41-22.98; P = 0.014). Additionally, late mortality (67.3%) was influenced by septic shock (aOR = 8.85, 95% CI 2.00-39.16; P = 0.004) and XDR phenotype (aOR = 5.46, 95% CI 1.25-23.85; P = 0.024). Moreover, specific genetic backgrounds [ST235, blaGES, gyrA (T83I), parC (S87L), exoU and O11 serotype] showed significant differences in patient outcomes. Our results confirm the high mortality associated with PA-BP. Besides relevant clinical characteristics and inappropriate empirical therapy, bacteria-specific genetics factors, such as XDR phenotype, adversely affect the outcome of PA-BP.
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Affiliation(s)
- Raúl Recio
- Department of Clinical Microbiology, Instituto de Investigación Hospital 12 de Octubre (imas12), Hospital Universitario 12 de Octubre, Madrid, Spain.
| | - Esther Viedma
- Department of Clinical Microbiology, Instituto de Investigación Hospital 12 de Octubre (imas12), Hospital Universitario 12 de Octubre, Madrid, Spain
| | - Sara González-Bodí
- Department of Clinical Microbiology, Instituto de Investigación Hospital 12 de Octubre (imas12), Hospital Universitario 12 de Octubre, Madrid, Spain
| | - Jennifer Villa
- Department of Clinical Microbiology, Instituto de Investigación Hospital 12 de Octubre (imas12), Hospital Universitario 12 de Octubre, Madrid, Spain
| | - María Ángeles Orellana
- Department of Clinical Microbiology, Instituto de Investigación Hospital 12 de Octubre (imas12), Hospital Universitario 12 de Octubre, Madrid, Spain
| | - Mikel Mancheño-Losa
- Department of Internal Medicine, Instituto de Investigación Hospital 12 de Octubre (imas12), Hospital Universitario 12 de Octubre, Madrid, Spain
| | - Jaime Lora-Tamayo
- Department of Internal Medicine, Instituto de Investigación Hospital 12 de Octubre (imas12), Hospital Universitario 12 de Octubre, Madrid, Spain
| | - Fernando Chaves
- Department of Clinical Microbiology, Instituto de Investigación Hospital 12 de Octubre (imas12), Hospital Universitario 12 de Octubre, Madrid, Spain
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Genomic surveillance of Pseudomonas aeruginosa in the Philippines, 2013-2014. Western Pac Surveill Response J 2021; 12:4-18. [PMID: 34540307 PMCID: PMC8421739 DOI: 10.5365/wpsar.2020.11.1.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Pseudomonas aeruginosa is an opportunistic pathogen that often causes nosocomial infections resistant to treatment. Rates of antimicrobial resistance (AMR) are increasing, as are rates of multidrug-resistant (MDR) and possible extensively drug-resistant (XDR) infections. Our objective was to characterize the molecular epidemiology and AMR mechanisms of this pathogen. We sequenced the whole genome for each of 176 P. aeruginosa isolates collected in the Philippines in 2013–2014; derived the multilocus sequence type (MLST), presence of AMR determinants and relatedness between isolates; and determined concordance between phenotypic and genotypic resistance. Carbapenem resistance was associated with loss of function of the OprD porin and acquisition of the metallo-β-lactamase (MBL) gene blaVIM. Concordance between phenotypic and genotypic resistance was 93.27% overall for six antibiotics in three classes, but varied among aminoglycosides. The population of P. aeruginosa was diverse, with clonal expansions of XDR genomes belonging to MLSTs ST235, ST244, ST309 and ST773. We found evidence of persistence or reintroduction of the predominant clone ST235 in one hospital, and of transfer between hospitals. Most of the ST235 genomes formed a distinct lineage from global genomes, thus raising the possibility that they may be unique to the Philippines. In addition, long-read sequencing of one representative XDR ST235 isolate identified an integron carrying multiple resistance genes (including blaVIM-2), with differences in gene composition and synteny from the P. aeruginosa class 1 integrons described previously. The survey bridges the gap in genomic data from the Western Pacific Region and will be useful for ongoing surveillance; it also highlights the importance of curtailing the spread of ST235 within the Philippines.
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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] [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.
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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
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Teo JQM, Tang CY, Lim JC, Lee SJY, Tan SH, Koh TH, Sim JHC, Tan TT, Kwa ALH, Ong RTH. Genomic characterization of carbapenem-non-susceptible Pseudomonas aeruginosa in Singapore. Emerg Microbes Infect 2021; 10:1706-1716. [PMID: 34384341 PMCID: PMC8409972 DOI: 10.1080/22221751.2021.1968318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Pseudomonas aeruginosa is a clinically important pathogen implicated in many hospital-acquired infections. Its propensity to acquire broad-spectrum resistance has earned the organism its status as a severe public health threat requiring urgent control measures. While whole-genome sequencing-based genomic surveillance provides a means to track antimicrobial resistance, its use in molecular epidemiological surveys of P. aeruginosa remains limited, especially in the Southeast Asian region. We sequenced the whole genomes of 222 carbapenem-non-susceptible P. aeruginosa (CNPA) isolates collected in 2006–2020 at the largest public acute care hospital in Singapore. Antimicrobial susceptibilities were determined using broth microdilution. Clonal relatedness, multi-locus sequence types, and antimicrobial resistance determinants (acquired and chromosomal) were determined. In this study, CNPA exhibited broad-spectrum resistance (87.8% multi-drug resistance), retaining susceptibility only to polymyxin B (95.0%) and amikacin (55.0%). Carbapenemases were detected in 51.4% of the isolates, where IMP and NDM metallo-β-lactamases were the most frequent. Carbapenem resistance was also likely associated with OprD alterations or efflux mechanisms (ArmZ/NalD mutations), which occurred in strains with or without carbapenemases. The population of CNPA in the hospital was diverse; the 222 isolates grouped into 68 sequence types (ST), which included various high-risk clones. We detected an emerging clone, the NDM-1-producing ST308, in addition to the global high-risk ST235 clone which was the predominant clone in our population. Our results thus provide a “snapshot” of the circulating lineages of CNPA locally and the prevailing genetic mechanisms contributing to carbapenem resistance. This database also serves as the baseline for future prospective surveillance studies.
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Affiliation(s)
- Jocelyn Qi-Min Teo
- Department of Pharmacy, Singapore General Hospital, Singapore, Singapore.,Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore, Singapore
| | - Cheng Yee Tang
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore, Singapore
| | - Jie Chong Lim
- Department of Pharmacy, National University of Singapore, Singapore, Singapore
| | | | - Si Hui Tan
- Department of Pharmacy, Singapore General Hospital, Singapore, Singapore
| | - Tse-Hsien Koh
- Department of Microbiology, Singapore General Hospital, Singapore, Singapore
| | | | - Thuan-Tong Tan
- Department of Infectious Diseases, Singapore General Hospital, Singapore, Singapore.,Singhealth Duke-NUS Medicine Academic Clinical Programme, Singapore, Singapore
| | - Andrea Lay-Hoon Kwa
- Department of Pharmacy, Singapore General Hospital, Singapore, Singapore.,Singhealth Duke-NUS Medicine Academic Clinical Programme, Singapore, Singapore.,Emerging Infectious Diseases, Duke-National University of Singapore Medical School, Singapore, Singapore
| | - Rick Twee-Hee Ong
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore, Singapore
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Urbanowicz P, Izdebski R, Baraniak A, Żabicka D, Hryniewicz W, Gniadkowski M. Molecular and genomic epidemiology of VIM/IMP-like metallo-β-lactamase-producing Pseudomonas aeruginosa genotypes in Poland. J Antimicrob Chemother 2021; 76:2273-2284. [PMID: 34179963 DOI: 10.1093/jac/dkab188] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 05/06/2021] [Indexed: 12/31/2022] Open
Abstract
OBJECTIVES To identify key factors of the expansion of metallo-β-lactamase (MBL)-producing Pseudomonas aeruginosa (MPPA) in Poland, focusing on the role of clonal epidemic(s). METHODS MPPA isolates were typed by PFGE, followed by MLST. blaVIM/IMP MBL genes were amplified and sequenced within class 1 integrons. Their location was assessed by S1 nuclease-hybridization assays. Short-read WGS was performed, and genomes were subjected to SNP-based phylogenetic and resistome analyses. RESULTS Of 1314 MPPA isolates collected in 2005-15 from 212 hospitals, 454 representatives were selected. The isolates belonged to 120 pulsotypes and 52 STs, of which ST235 (∼31%), ST111 (∼17%), ST273 (∼16%) and ST654 (∼9%) prevailed, followed by ST244, ST17, ST395, ST175 and ST1567. The isolates produced seven VIM variants (97.5%) and four IMPs encoded by 46 integrons, most of which were observed only or mainly in Poland. Around 60% of the isolates resulted from (inter)regional clonal outbreaks of 10 individual ST235, ST111, ST273 and ST654 genotypes. The phylogenetic analysis of 163 genomes revealed heterogeneity of ST235 and ST111 populations, arising from transnational circulation and on-site differentiation of several clades/branches. Contrarily, ST273 and ST654 formed relatively homogeneous and apparently Poland-specific lineages, and a unique ST273 genotype with integron In249 was the most expansive organism. CONCLUSIONS Together with a previous report on self-transmissible In461-carrying IncP-2-type plasmids, this study revealed the molecular/genomic background of the rapid MPPA increase in Poland in 2001-15, evidencing multi-clonal spread as its leading factor. Numerous novel/specific MPPA characteristics were identified.
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Affiliation(s)
- P Urbanowicz
- Department of Molecular Microbiology, National Medicines Institute, 00-725, Warsaw, Poland
| | - R Izdebski
- Department of Molecular Microbiology, National Medicines Institute, 00-725, Warsaw, Poland
| | - A Baraniak
- Department of Molecular Microbiology, National Medicines Institute, 00-725, Warsaw, Poland
| | - D Żabicka
- Department of Epidemiology and Clinical Microbiology, The National Reference Centre for Susceptibility Testing, National Medicines Institute, 00-725, Warsaw, Poland
| | - W Hryniewicz
- Department of Epidemiology and Clinical Microbiology, The National Reference Centre for Susceptibility Testing, National Medicines Institute, 00-725, Warsaw, Poland
| | - M Gniadkowski
- Department of Molecular Microbiology, National Medicines Institute, 00-725, Warsaw, Poland
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Takahashi T, Tada T, Shrestha S, Hishinuma T, Sherchan JB, Tohya M, Kirikae T, Sherchand JB. Molecular characterisation of carbapenem-resistant Pseudomonas aeruginosa clinical isolates in Nepal. J Glob Antimicrob Resist 2021; 26:279-284. [PMID: 34284125 DOI: 10.1016/j.jgar.2021.07.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2021] [Revised: 06/14/2021] [Accepted: 07/06/2021] [Indexed: 11/30/2022] Open
Abstract
OBJECTIVES The emergence of carbapenem-resistant Pseudomonas aeruginosa has become a serious worldwide medical problem. The aim of this study was to determine the genetic and epidemiological properties of carbapenem-resistant P. aeruginosa strains isolated from hospitals in Nepal. METHODS A total of 43 carbapenem-resistant P. aeruginosa isolates obtained from patients in two hospitals in Nepal between 2018 and 2020 were analysed. Their whole genomes were sequenced by next-generation sequencing. A phylogenetic tree was constructed from single nucleotide polymorphism (SNP) concatemers. Multilocus sequence typing (MLST) was performed and antimicrobial resistance genes were identified. RESULTS Of the 43 isolates, 17 harboured genes encoding carbapenemases, including IMP-1, IMP-26, KPC-2, NDM-1, VIM-2 and VIM-5, and 12 harboured genes encoding 16S rRNA methylases, including RmtB4 and RmtF2. The carbapenem-resistant P. aeruginosa isolated in Nepal belonged to various sequence types (STs), including ST235 (5 isolates), ST244 (7 isolates), ST274 (1 isolate), ST357 (10 isolates), ST654 (3 isolates), ST664 (1 isolate), ST773 (1 isolate), ST823 (3 isolates), ST1047 (8 isolates), ST1203 (2 isolates) and ST3453 (2 isolates). CONCLUSION To the best of our knowledge, this is the first molecular epidemiological analysis of carbapenem-resistant P. aeruginosa clinical isolates from Nepal. The findings strongly suggest that P. aeruginosa isolates producing carbapenemases and 16S rRNA methylases have spread throughout medical settings in Nepal.
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Affiliation(s)
- Toshihiro Takahashi
- Department of Microbiology, Juntendo University Graduate School of Medicine, 2-1-1 Hongo, Bunkyo-ku, Tokyo 113-8421, Japan
| | - Tatsuya Tada
- Department of Microbiology, Juntendo University Graduate School of Medicine, 2-1-1 Hongo, Bunkyo-ku, Tokyo 113-8421, Japan.
| | - Shovita Shrestha
- Department of Microbiology, Institute of Medicine, Tribhuvan University Teaching Hospital, Kathmandu, Nepal
| | - Tomomi Hishinuma
- Department of Microbiology, Juntendo University Graduate School of Medicine, 2-1-1 Hongo, Bunkyo-ku, Tokyo 113-8421, Japan
| | - Jatan B Sherchan
- Department of Medical Microbiology, Kathmandu University School of Medical Sciences, Dhulikhel, Nepal
| | - Mari Tohya
- Department of Microbiology, Juntendo University Graduate School of Medicine, 2-1-1 Hongo, Bunkyo-ku, Tokyo 113-8421, Japan
| | - Teruo Kirikae
- Department of Microbiology, Juntendo University Graduate School of Medicine, 2-1-1 Hongo, Bunkyo-ku, Tokyo 113-8421, Japan
| | - Jeevan B Sherchand
- Department of Microbiology, Institute of Medicine, Tribhuvan University Teaching Hospital, Kathmandu, Nepal
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Prevalence and Characteristics of Metallo-beta-Lactamase-positive and High-risk Clone ST235 Pseudomonas aeruginosa at Ardabil Hospitals. Jundishapur J Microbiol 2021. [DOI: 10.5812/jjm.115819] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Background: Carbapenems are the most commonly administered drugs for the treatment of multidrug-resistant Pseudomonas aeruginosa (MDR P. aeruginosa) infections. However, carbapenem-resistant P. aeruginosa is spreading rapidly and has led to a new threat to human health worldwide. Objectives: The current study aimed to determine the prevalence of imipenem-resistant P. aeruginosa, detect metallo-β-lactamase (MBL)-producer isolates, and evaluate their clonal relationships in strains isolated from patients referring to the hospitals of Ardabil city, Iran. Methods: The resistance rate to imipenem was evaluated using the disk diffusion method. Double-disk synergy test and PCR technique were used for phenotypic and genotypic screening of MBL-positive P. aeruginosa, respectively. Ultimately, enterobacterial repetitive intergenic consensus-polymerase chain reaction (ERIC-PCR) and multilocus sequence typing (MLST) methods were used for assessing clonal relatedness among the isolates. Results: The prevalence of imipenem-resistant P. aeruginosa strains was estimated at 57.1% (48 out of 84 isolates). In addition, 45 (93.7%) out of 48 imipenem-resistant P. aeruginosa isolates were phenotypically screened as MBL-positive, among which 16 (35.5%) and three (6.6%) isolates harbored blaIMP and blaVIM-1 genes, respectively. However, blaNDM, blaSIM-2, blaSPM, and blaGIM-1 genes were not detected in this study. MBL-producing P. aeruginosa strains were divided into 42 ERIC-PCR types. Based on the results of MLST, P. aeruginosa ST235 was the only identified sequence type. Conclusions: Our results revealed a high and alarming prevalence of imipenem-resistant and blaIMP-positive P. aeruginosa ST235 at Ardabil hospitals. Continuous monitoring is essential to control the further spread of this highly virulent and drug-resistant clone.
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Rosales-Reyes R, Esposito F, Fontana H, Lezana-Fernández JL, Lascurain R, De la Cruz MA, Fuga B, Lincopan N, Santos-Preciado JI. Emergence of GES-19-producing Pseudomonas aeruginosa exoU+ belonging to the global high-risk clone ST235 in cystic fibrosis infection. Diagn Microbiol Infect Dis 2021; 101:115454. [PMID: 34271235 DOI: 10.1016/j.diagmicrobio.2021.115454] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 06/08/2021] [Accepted: 06/09/2021] [Indexed: 11/16/2022]
Abstract
The emergence of high-risk clones of priority pathogens exhibiting convergence of antimicrobial resistance and virulence is a critical issue worldwide. In a previous study, an extensively drug-resistant Pseudomonas aeruginosa was isolated from a chronically colonized pediatric patient with cystic fibrosis (CF). In this study, we analyzed genomic data of this strain (CF023-Psa42), extracting clinically and epidemiologically relevant information (i.e., the antimicrobial resistome, virulome, and sequence type). In this regard, we report the emergence of GES-19 (extended-spectrum β-lactamase)-producing P. aeruginosa with genotype exoU+. The CF023-Psa42 strain exhibited a broad resistome, belonging to the international high-risk clone sequence type ST235. The blaGES-19 gene was located on a class 1 integron, along to aac(6')-33, aac(6')-Ib-cr, blaOXA-2, aadA1, sul1, and qacEΔ1 resistance genes. Relevant virulence genes such as lasA (proteolysis and elastolysis), toxA (exotoxin A), alg (alginate biosynthesis operon), and exoU (toxin of type III secretion systems) were predicted. Our findings reveal the convergence of broad resistome and virulome in P. aeruginosa ST235. Genomic surveillance is essential to monitor the emergence and dissemination of priority pathogens with epidemiological success.
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Affiliation(s)
- Roberto Rosales-Reyes
- Unidad de Investigación en Medicina Experimental, Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City, Mexico.
| | - Fernanda Esposito
- Departamento de Análises Clínicas, Faculdade de Ciências Farmacêuticas, Universidade de São Paulo, São Paulo, Brazil
| | - Herrison Fontana
- Departamento de Análises Clínicas, Faculdade de Ciências Farmacêuticas, Universidade de São Paulo, São Paulo, Brazil
| | - José Luis Lezana-Fernández
- Laboratorio de Fisiología Pulmonar, Clínica de Fibrosis Quistica, Hospital Infantil de México Federico Gómez, Mexico City, Mexico
| | - Ricardo Lascurain
- Departamento de Bioquímica, Facultad de Medicina, Universidad Nacional Autónoma de Mexico, Mexico City, Mexico
| | - Miguel A De la Cruz
- Unidad de Investigación Médica en Enfermedades Infecciosas y Parasitarias, Centro Médico Nacional Siglo XXI, Hospital de Pediatría, Instituto Mexicano del Seguro Social, Mexico City, Mexico
| | - Bruna Fuga
- Departamento de Análises Clínicas, Faculdade de Ciências Farmacêuticas, Universidade de São Paulo, São Paulo, Brazil; Departamento de Microbiologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, Brazil
| | - Nilton Lincopan
- Departamento de Análises Clínicas, Faculdade de Ciências Farmacêuticas, Universidade de São Paulo, São Paulo, Brazil; Departamento de Microbiologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, Brazil
| | - José Ignacio Santos-Preciado
- Unidad de Investigación en Medicina Experimental, Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City, Mexico
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Emergence and Expansion of a Carbapenem-Resistant Pseudomonas aeruginosa Clone Are Associated with Plasmid-Borne bla KPC-2 and Virulence-Related Genes. mSystems 2021; 6:6/3/e00154-21. [PMID: 34006625 PMCID: PMC8269210 DOI: 10.1128/msystems.00154-21] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Pseudomonas aeruginosa is a major opportunistic pathogen and one of the leading bacterial species causing health care-associated infections. Carbapenems are the most effective antimicrobial agents for the treatment of severe infections caused by P. aeruginosa However, our recent surveillance demonstrated that the prevalence of carbapenem-resistant P. aeruginosa (CRPA) reached 38.67% in Zhejiang, China. By analyzing CRPA isolates collected from patients from 2006 to 2018, we found that 33% of CRPA isolates carried the gene bla KPC-2, which conferred high-level resistance to carbapenems and other β-lactams. In particular, a CRPA clone, ST463 (sequence type 463), emerged and has become the predominant CRPA clone among the population. Genome sequencing demonstrated that ST463 expansion was associated with plasmid-borne bla KPC-2 The mobile element flanking bla KPC-2, the type IV secretion system, and the successful expansion of clone ST463 might have further favored bla KPC-2 spread in P. aeruginosa Molecular clock analysis dated the emergence of clone ST463 to around 2007. Genome-wide association analysis showed that 567 genes were associated with clone ST463, including several known virulence genes related to the biosynthesis of lipooligosaccharide (LOS) O-antigens and exotoxin. These findings indicate that ST463 is expanding with plasmid-borne bla KPC-2 and virulence-related genes in nosocomial infections, and close surveillance should be undertaken in the future.IMPORTANCE Health care-associated infections, also known as nosocomial infections, are the most frequent adverse events in health care delivery worldwide, causing high rates of morbidity and mortality and high health care costs. Pseudomonas aeruginosa is one of the leading bacterial species causing health care-associated infections. Carbapenems are the most effective antimicrobial agents for the treatment of its severe infections. However, the prevalence of carbapenem-resistant P. aeruginosa (CRPA) has been increasing rapidly in recent years, and our surveillance demonstrated that the prevalence of CRPA reached 38.67% in Zhejiang, China. Genome sequencing of CRPA isolates over a decade showed that a CRPA clone (ST463) emerged recently. The clone is highly resistant to β-lactams, including carbapenems, and fluoroquinolones. Genome-wide association analysis showed that the clone expanded with virulence-related genes and the plasmid-borne carbapenem-resistant gene bla KPC-2 These findings are of significant public health importance, as the information will facilitate the control and minimization of CRPA nosocomial infections.
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Pelegrin AC, Palmieri M, Mirande C, Oliver A, Moons P, Goossens H, van Belkum A. Pseudomonas aeruginosa: a clinical and genomics update. FEMS Microbiol Rev 2021; 45:6273131. [PMID: 33970247 DOI: 10.1093/femsre/fuab026] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2020] [Accepted: 05/07/2021] [Indexed: 12/13/2022] Open
Abstract
Antimicrobial resistance (AMR) has become a global medical priority that needs urgent resolution. Pseudomonas aeruginosa is a versatile, adaptable bacterial species with widespread environmental occurrence, strong medical relevance, a diverse set of virulence genes and a multitude of intrinsic and possibly acquired antibiotic resistance traits. P. aeruginosa causes a wide variety of infections and has an epidemic-clonal population structure. Several of its dominant global clones have collected a wide variety of resistance genes rendering them multi-drug resistant (MDR) and particularly threatening groups of vulnerable individuals including surgical patients, immunocompromised patients, Caucasians suffering from cystic fibrosis (CF) and more. AMR and MDR especially are particularly problematic in P. aeruginosa significantly complicating successful antibiotic treatment. In addition, antimicrobial susceptibility testing (AST) of P. aeruginosa can be cumbersome due to its slow growth or the massive production of exopolysaccharides and other extracellular compounds. For that reason, phenotypic AST is progressively challenged by genotypic methods using whole genome sequences (WGS) and large-scale phenotype databases as a framework of reference. We here summarize the state of affairs and the quality level of WGS-based AST for P. aeruginosa mostly from clinical origin.
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Affiliation(s)
- Andreu Coello Pelegrin
- bioMérieux, Data Analytics Unit, 3 Route du Port Michaud, 38390 La Balme les Grottes, France
| | - Mattia Palmieri
- bioMérieux, Data Analytics Unit, 3 Route du Port Michaud, 38390 La Balme les Grottes, France
| | - Caroline Mirande
- bioMérieux, R&D Microbiology, Route du Port Michaud, 38390 La Balme-les-Grottes, France
| | - Antonio Oliver
- Servicio de Microbiología, Módulo J, segundo piso, Hospital Universitario Son Espases, Instituto de Investigación Sanitaria Illes Balears (IdISBa), Ctra. Valldemossa, 79, 07120 Palma de Mallorca, Spain
| | - Pieter Moons
- Laboratory of Medical Microbiology, University of Antwerp, Universiteitsplein 1, building S, 2610 Wilrijk, Antwerp, Belgium
| | - Herman Goossens
- Laboratory of Medical Microbiology, Vaccine and Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
| | - Alex van Belkum
- bioMérieux, Open Innovation and Partnerships, 3 Route du Port Michaud, 38390 La Balme Les Grottes, France
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Long-Term Exposure to Octenidine in a Simulated Sink Trap Environment Results in Selection of Pseudomonas aeruginosa, Citrobacter, and Enterobacter Isolates with Mutations in Efflux Pump Regulators. Appl Environ Microbiol 2021; 87:AEM.00210-21. [PMID: 33674437 DOI: 10.1128/aem.00210-21] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 02/25/2021] [Indexed: 12/14/2022] Open
Abstract
Octenidine-based disinfection products are becoming increasingly popular for infection control of multidrug-resistant (MDR) Gram-negative isolates. When a waste trap was removed from a hospital and allowed to acclimatize in a standard tap rig in our laboratory, it was shown that Klebsiella pneumoniae, Pseudomonas aeruginosa, and Citrobacter and Enterobacter spp. were readily isolated. This study aimed to understand the potential impact of prolonged exposure to low doses of a commercial product containing octenidine on these bacteria. Phenotypic and genotypic analyses showed that P. aeruginosa strains had increased tolerance to octenidine, which was characterized by mutations in the Tet repressor SmvR. Enterobacter species demonstrated increased tolerance to many other cationic biocides, although not octenidine, as well as the antibiotics ciprofloxacin, chloramphenicol, and ceftazidime, through mutations in another Tet repressor, RamR. Citrobacter species with mutations in RamR and MarR were identified following octenidine exposure, and this is linked to development of resistance to ampicillin, piperacillin, and chloramphenicol, as well as an increased MIC for ciprofloxacin. Isolates were able to retain fitness, as characterized by growth, biofilm formation, and virulence in Galleria mellonella, after prolonged contact with octenidine, although there were strain-to-strain differences. These results demonstrate that continued low-level octenidine exposure in a simulated sink trap environment selects for mutations that affect smvR It may also promote microbial adaptation to other cationic biocides and cross-resistance to antibiotics, while not incurring a fitness cost. This suggests that hospital sink traps may act as a reservoir for more biocide-tolerant organisms.IMPORTANCE Multidrug-resistant (MDR) strains of bacteria are a major clinical problem, and several reports have linked outbreaks of MDR bacteria with bacterial populations in hospital sinks. Biocides such as octenidine are used clinically in body washes and other products, such as wound dressings for infection control. Therefore, increased tolerance to these biocides would be detrimental to infection control processes. Here, we exposed bacterial populations originally from hospital sink traps to repeated dosing with an octenidine-containing product over several weeks and observed how particular species adapted. We found mutations in genes related to biocide and antibiotic susceptibility, which resulted in increased tolerance, although this was species dependent. Bacteria that became more tolerant to octenidine also showed no loss of fitness. This shows that prolonged octenidine exposure has the potential to promote microbial adaptation in the environment and that hospital sink traps may act as a reservoir for increased biocide- and antibiotic-tolerant organisms.
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Molecular Detection of Drug-Resistance Genes of blaOXA-23-blaOXA-51 and mcr-1 in Clinical Isolates of Pseudomonas aeruginosa. Microorganisms 2021; 9:microorganisms9040786. [PMID: 33918745 PMCID: PMC8069495 DOI: 10.3390/microorganisms9040786] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 04/01/2021] [Accepted: 04/05/2021] [Indexed: 02/06/2023] Open
Abstract
Pseudomonas aeruginosa has caused high rates of mortality due to the appearance of strains with multidrug resistance (MDR) profiles. This study aimed to characterize the molecular profile of virulence and resistance genes in 99 isolates of P. aeruginosa recovered from different clinical specimens. The isolates were identified by the automated method Vitek2, and the antibiotic susceptibility profile was determined using different classes of antimicrobials. The genomic DNA was extracted and amplified by multiplex polymerase chain reaction (mPCR) to detect different virulence and antimicrobial resistance genes. Molecular typing was performed using the enterobacterial repetitive intergenic consensus (ERIC-PCR) technique to determine the clonal relationship among P. aeruginosa isolates. The drug susceptibility profiles of P. aeruginosa for all strains showed high levels of drug resistance, particularly, 27 (27.3%) isolates that exhibited extensively drug-resistant (XDR) profiles, and the other isolates showed MDR profiles. We detected the polymyxin E (mcr-1) gene in one strain that showed resistance against colistin. The genes that confer resistance to oxacillin (blaOXA-23 and blaOXA-51) were present in three isolates. One of these isolates carried both genes. As far as we know from the literature, this is the first report of the presence of blaOXA-23 and blaOXA-51 genes in P. aeruginosa.
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Lee C, Klockgether J, Fischer S, Trcek J, Tümmler B, Römling U. Why? - Successful Pseudomonas aeruginosa clones with a focus on clone C. FEMS Microbiol Rev 2021; 44:740-762. [PMID: 32990729 PMCID: PMC7685784 DOI: 10.1093/femsre/fuaa029] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Accepted: 07/12/2020] [Indexed: 12/20/2022] Open
Abstract
The environmental species Pseudomonas aeruginosa thrives in a variety of habitats. Within the epidemic population structure of P. aeruginosa, occassionally highly successful clones that are equally capable to succeed in the environment and the human host arise. Framed by a highly conserved core genome, individual members of successful clones are characterized by a high variability in their accessory genome. The abundance of successful clones might be funded in specific features of the core genome or, although not mutually exclusive, in the variability of the accessory genome. In clone C, one of the most predominant clones, the plasmid pKLC102 and the PACGI-1 genomic island are two ubiquitous accessory genetic elements. The conserved transmissible locus of protein quality control (TLPQC) at the border of PACGI-1 is a unique horizontally transferred compository element, which codes predominantly for stress-related cargo gene products such as involved in protein homeostasis. As a hallmark, most TLPQC xenologues possess a core genome equivalent. With elevated temperature tolerance as a characteristic of clone C strains, the unique P. aeruginosa and clone C specific disaggregase ClpG is a major contributor to tolerance. As other successful clones, such as PA14, do not encode the TLPQC locus, ubiquitous denominators of success, if existing, need to be identified.
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Affiliation(s)
- Changhan Lee
- Department of Microbiology, Tumor and Cell Biology, Biomedicum C8, Karolinska Institutet, SE-171 77 Stockholm, Sweden
| | - Jens Klockgether
- Clinic for Paediatric Pneumology, Allergology and Neonatology, Clinical Research Group 'Pseudomonas Genomics', Hannover Medical School, D-30625 Hannover, Germany
| | - Sebastian Fischer
- Clinic for Paediatric Pneumology, Allergology and Neonatology, Clinical Research Group 'Pseudomonas Genomics', Hannover Medical School, D-30625 Hannover, Germany
| | - Janja Trcek
- Faculty of Natural Sciences and Mathematics, Department of Biology, University of Maribor, Maribor, 2000, Slovenia
| | - Burkhard Tümmler
- Clinic for Paediatric Pneumology, Allergology and Neonatology, Clinical Research Group 'Pseudomonas Genomics', Hannover Medical School, D-30625 Hannover, Germany
| | - Ute Römling
- Department of Microbiology, Tumor and Cell Biology, Biomedicum C8, Karolinska Institutet, SE-171 77 Stockholm, Sweden
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Yoon EJ, Jeong SH. Mobile Carbapenemase Genes in Pseudomonas aeruginosa. Front Microbiol 2021; 12:614058. [PMID: 33679638 PMCID: PMC7930500 DOI: 10.3389/fmicb.2021.614058] [Citation(s) in RCA: 82] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 01/04/2021] [Indexed: 02/06/2023] Open
Abstract
Carbapenem-resistant Pseudomonas aeruginosa is one of the major concerns in clinical settings impelling a great challenge to antimicrobial therapy for patients with infections caused by the pathogen. While membrane permeability, together with derepression of the intrinsic beta-lactamase gene, is the global prevailing mechanism of carbapenem resistance in P. aeruginosa, the acquired genes for carbapenemases need special attention because horizontal gene transfer through mobile genetic elements, such as integrons, transposons, plasmids, and integrative and conjugative elements, could accelerate the dissemination of the carbapenem-resistant P. aeruginosa. This review aimed to illustrate epidemiologically the carbapenem resistance in P. aeruginosa, including the resistance rates worldwide and the carbapenemase-encoding genes along with the mobile genetic elements responsible for the horizontal dissemination of the drug resistance determinants. Moreover, the modular mobile elements including the carbapenemase-encoding gene, also known as the P. aeruginosa resistance islands, are scrutinized mostly for their structures.
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Affiliation(s)
- Eun-Jeong Yoon
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Seoul, South Korea
| | - Seok Hoon Jeong
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Seoul, South Korea
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Diversity and Distribution of Resistance Markers in Pseudomonas aeruginosa International High-Risk Clones. Microorganisms 2021; 9:microorganisms9020359. [PMID: 33673029 PMCID: PMC7918723 DOI: 10.3390/microorganisms9020359] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Revised: 02/08/2021] [Accepted: 02/08/2021] [Indexed: 12/12/2022] Open
Abstract
Pseudomonas aeruginosa high-risk clones are disseminated worldwide and they are common causative agents of hospital-acquired infections. In this review, we will summarize available data of high-risk P. aeruginosa clones from confirmed outbreaks and based on whole-genome sequence data. Common feature of high-risk clones is the production of beta-lactamases and among metallo-beta-lactamases NDM, VIM and IMP types are widely disseminated in different sequence types (STs), by contrast FIM type has been reported in ST235 in Italy, whereas GIM type in ST111 in Germany. In the case of ST277, it is most frequently detected in Brazil and it carries a resistome linked to blaSPM. Colistin resistance develops among P. aeruginosa clones in a lesser extent compared to other resistance mechanisms, as ST235 strains remain mainly susceptible to colistin however, some reports described mcr positive P. aeurigonsa ST235. Transferable quinolone resistance determinants are detected in P. aeruginosa high-risk clones and aac(6′)-Ib-cr variant is the most frequently reported as this determinant is incorporated in integrons. Additionally, qnrVC1 was recently detected in ST773 in Hungary and in ST175 in Spain. Continuous monitoring and surveillance programs are mandatory to track high-risk clones and to analyze emergence of novel clones as well as novel resistance determinants.
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Behzadi P, Baráth Z, Gajdács M. It's Not Easy Being Green: A Narrative Review on the Microbiology, Virulence and Therapeutic Prospects of Multidrug-Resistant Pseudomonas aeruginosa. Antibiotics (Basel) 2021; 10:42. [PMID: 33406652 PMCID: PMC7823828 DOI: 10.3390/antibiotics10010042] [Citation(s) in RCA: 109] [Impact Index Per Article: 36.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 12/29/2020] [Accepted: 12/31/2020] [Indexed: 12/11/2022] Open
Abstract
Pseudomonas aeruginosa is the most frequent cause of infection among non-fermenting Gram-negative bacteria, predominantly affecting immunocompromised patients, but its pathogenic role should not be disregarded in immunocompetent patients. These pathogens present a concerning therapeutic challenge to clinicians, both in community and in hospital settings, due to their increasing prevalence of resistance, and this may lead to prolonged therapy, sequelae, and excess mortality in the affected patient population. The resistance mechanisms of P. aeruginosa may be classified into intrinsic and acquired resistance mechanisms. These mechanisms lead to occurrence of resistant strains against important antibiotics-relevant in the treatment of P. aeruginosa infections-such as β-lactams, quinolones, aminoglycosides, and colistin. The occurrence of a specific resistotype of P. aeruginosa, namely the emergence of carbapenem-resistant but cephalosporin-susceptible (Car-R/Ceph-S) strains, has received substantial attention from clinical microbiologists and infection control specialists; nevertheless, the available literature on this topic is still scarce. The aim of this present review paper is to provide a concise summary on the adaptability, virulence, and antibiotic resistance of P. aeruginosa to a readership of basic scientists and clinicians.
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Affiliation(s)
- Payam Behzadi
- Department of Microbiology, College of Basic Sciences, Shahr-e-Qods Branch, Islamic Azad University, Tehran 37541-374, Iran;
| | - Zoltán Baráth
- Department of Prosthodontics, Faculty of Dentistry, University of Szeged, Tisza Lajos körút 62-64, 6720 Szeged, Hungary;
| | - Márió Gajdács
- Institute of Medical Microbiology, Faculty of Medicine, Semmelweis University, 1089 Budapest, Hungary
- Department of Pharmacodynamics and Biopharmacy, Faculty of Pharmacy, University of Szeged, 6720 Szeged, Hungary
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73
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Tsang KK, Maguire F, Zubyk HL, Chou S, Edalatmand A, Wright GD, Beiko RG, McArthur AG. Identifying novel β-lactamase substrate activity through in silico prediction of antimicrobial resistance. Microb Genom 2021; 7:mgen000500. [PMID: 33416461 PMCID: PMC8115898 DOI: 10.1099/mgen.0.000500] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Accepted: 12/08/2020] [Indexed: 11/25/2022] Open
Abstract
Diagnosing antimicrobial resistance (AMR) in the clinic is based on empirical evidence and current gold standard laboratory phenotypic methods. Genotypic methods have the potential advantages of being faster and cheaper, and having improved mechanistic resolution over phenotypic methods. We generated and applied rule-based and logistic regression models to predict the AMR phenotype from Escherichia coli and Pseudomonas aeruginosa multidrug-resistant clinical isolate genomes. By inspecting and evaluating these models, we identified previously unknown β-lactamase substrate activities. In total, 22 unknown β-lactamase substrate activities were experimentally validated using targeted gene expression studies. Our results demonstrate that generating and analysing predictive models can help guide researchers to the mechanisms driving resistance and improve annotation of AMR genes and phenotypic prediction, and suggest that we cannot solely rely on curated knowledge to predict resistance phenotypes.
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Affiliation(s)
- Kara K. Tsang
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada
- M.G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Finlay Maguire
- Faculty of Computer Science, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Haley L. Zubyk
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada
- M.G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Sommer Chou
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada
- M.G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Arman Edalatmand
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada
- M.G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Gerard D. Wright
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada
- M.G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Robert G. Beiko
- Faculty of Computer Science, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Andrew G. McArthur
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada
- M.G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
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74
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Nageeb W, Amin DH, Mohammedsaleh ZM, Makharita RR. Novel Molecular Markers Linked to Pseudomonas aeruginosa Epidemic High-Risk Clones. Antibiotics (Basel) 2021; 10:antibiotics10010035. [PMID: 33401446 PMCID: PMC7824207 DOI: 10.3390/antibiotics10010035] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 12/21/2020] [Accepted: 12/28/2020] [Indexed: 11/16/2022] Open
Abstract
The population structure of Pseudomonas aeruginosa is panmictic-epidemic in nature, with the prevalence of some high-risk clones. These clones are often linked to virulence, antibiotic resistance, and more morbidity. The clonal success of these lineages has been linked to acquisition and spread of mobile genetic elements. The main aim of the study was to explore other molecular markers that explain their global success. A comprehensive set of 528 completely sequenced P. aeruginosa genomes was analyzed. The population structure was examined using Multilocus Sequence Typing (MLST). Strain relationships analysis and diversity analysis were performed using the geoBURST Full Minimum Spanning Tree (MST) algorithm and hierarchical clustering. A phylogenetic tree was constructed using the Unweighted Pair Group Method with Arithmetic mean (UPGMA) algorithm. A panel of previously investigated resistance markers were examined for their link to high-risk clones. A novel panel of molecular markers has been identified in relation to risky clones including armR, ampR, nalC, nalD, mexZ, mexS, gyrAT83I, gyrAD87N, nalCE153Q, nalCS46A, parCS87W, parCS87L, ampRG283E, ampRM288R, pmrALeu71Arg, pmrBGly423Cys, nuoGA890T, pstBE89Q, phoQY85F, arnAA170T, arnDG206C, and gidBE186A. In addition to mobile genetic elements, chromosomal variants in membrane proteins and efflux pump regulators can play an important role in the success of high-risk clones. Finding risk-associated markers during molecular surveillance necessitates applying more infection-control precautions.
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Affiliation(s)
- Wedad Nageeb
- Medical Microbiology and Immunology Department, Faculty of Medicine, Suez Canal University, Ismailia 41111, Egypt
- Correspondence:
| | - Dina H. Amin
- Microbiology Department, Faculty of Science, Ain Shams University, Cairo 11566, Egypt;
| | - Zuhair M. Mohammedsaleh
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, University of Tabuk, Tabuk 71491, Saudi Arabia;
| | - Rabab R. Makharita
- Botany and Microbiology Department, Faculty of Science, Suez Canal University, Ismailia 41522, Egypt;
- Biology Department, Faculty of Science and Arts, Khulais, University of Jeddah, Jeddah 21959, Saudi Arabia
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75
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Coppola PE, Gaibani P, Sartor C, Ambretti S, Lewis RE, Sassi C, Pignatti M, Paolini S, Curti A, Castagnetti F, Ursi M, Cavo M, Stanzani M. Ceftolozane-Tazobactam Treatment of Hypervirulent Multidrug Resistant Pseudomonas aeruginosa Infections in Neutropenic Patients. Microorganisms 2020; 8:microorganisms8122055. [PMID: 33371496 PMCID: PMC7767535 DOI: 10.3390/microorganisms8122055] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 12/07/2020] [Accepted: 12/11/2020] [Indexed: 12/28/2022] Open
Abstract
The effectiveness of ceftolozane/tazobactam for the treatment of infections in neutropenic patients caused by hypervirulent multidrug-resistant (MDR) Pseudomonas aeruginosa has not been previously reported. We identified seven cases of MDR P. aeruginosa infection in neutropenic patients over a four-month period within the same hematology ward. Four cases were associated with rapid progression despite piperacillin-tazobactam or meropenem therapy, and three patients developed sepsis or extensive skin/soft tissue necrosis. In three of the four cases, patients were empirically switched from meropenem to ceftolozane/avibactam before carbapenem susceptibility test results were available, and all four patients underwent extensive surgical debridement or amputation of affected tissues and survived. Further investigation revealed a common bathroom source of MDR P. aeruginosa clonal subtypes ST175 and ST235 that harbored genes for type III secretion system expression and elaboration of ExoU or ExoS exotoxin. We conclude that ceftolozane/tazobactam plus early source control was critical for control of rapidly progressing skin and soft infection in these neutropenic patients caused by highly virulent ST175 and ST235 clones of MDR P. aeruginosa.
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Affiliation(s)
- Paolo E. Coppola
- Institute of Hematology “Seràgnoli”, IRCCS-Azienda Ospedaliero Policlinico Sant’Orsola-Universitaria di Bologna, 40138 Bologna, Italy; (P.E.C.); (C.S.); (S.P.); (A.C.); (F.C.); (M.U.); (M.C.)
| | - Paolo Gaibani
- Microbiology, IRCCS-Azienda Ospedaliero Policlinico Sant’Orsola-Universitaria di Bologna, 40138 Bologna, Italy; (P.G.); (S.A.)
| | - Chiara Sartor
- Institute of Hematology “Seràgnoli”, IRCCS-Azienda Ospedaliero Policlinico Sant’Orsola-Universitaria di Bologna, 40138 Bologna, Italy; (P.E.C.); (C.S.); (S.P.); (A.C.); (F.C.); (M.U.); (M.C.)
| | - Simone Ambretti
- Microbiology, IRCCS-Azienda Ospedaliero Policlinico Sant’Orsola-Universitaria di Bologna, 40138 Bologna, Italy; (P.G.); (S.A.)
| | - Russell E. Lewis
- Infectious Diseases, IRCCS-Azienda Ospedaliero Policlinico Sant’Orsola-Universitaria di Bologna, 40138 Bologna, Italy;
- Department of Medical and Surgical Sciences (DIMEC)- Università di Bologna, Alma Mater Studiorum, 40138 Bologna, Italy
| | - Claudia Sassi
- Radiology, IRCCS-Azienda Ospedaliero Policlinico Sant’Orsola-Universitaria di Bologna, 40138 Bologna, Italy;
- Department of Diagnostic and Experimental Medicine Specialty (DIMES)- Università di Bologna, Alma Mater Studiorum, 40138 Bologna, Italy;
| | - Marco Pignatti
- Department of Diagnostic and Experimental Medicine Specialty (DIMES)- Università di Bologna, Alma Mater Studiorum, 40138 Bologna, Italy;
- Plastic Surgery, IRCCS-Azienda Ospedaliero Policlinico Sant’Orsola-Universitaria di Bologna, 40138 Bologna, Italy
| | - Stefania Paolini
- Institute of Hematology “Seràgnoli”, IRCCS-Azienda Ospedaliero Policlinico Sant’Orsola-Universitaria di Bologna, 40138 Bologna, Italy; (P.E.C.); (C.S.); (S.P.); (A.C.); (F.C.); (M.U.); (M.C.)
| | - Antonio Curti
- Institute of Hematology “Seràgnoli”, IRCCS-Azienda Ospedaliero Policlinico Sant’Orsola-Universitaria di Bologna, 40138 Bologna, Italy; (P.E.C.); (C.S.); (S.P.); (A.C.); (F.C.); (M.U.); (M.C.)
| | - Fausto Castagnetti
- Institute of Hematology “Seràgnoli”, IRCCS-Azienda Ospedaliero Policlinico Sant’Orsola-Universitaria di Bologna, 40138 Bologna, Italy; (P.E.C.); (C.S.); (S.P.); (A.C.); (F.C.); (M.U.); (M.C.)
- Department of Diagnostic and Experimental Medicine Specialty (DIMES)- Università di Bologna, Alma Mater Studiorum, 40138 Bologna, Italy;
| | - Margherita Ursi
- Institute of Hematology “Seràgnoli”, IRCCS-Azienda Ospedaliero Policlinico Sant’Orsola-Universitaria di Bologna, 40138 Bologna, Italy; (P.E.C.); (C.S.); (S.P.); (A.C.); (F.C.); (M.U.); (M.C.)
| | - Michele Cavo
- Institute of Hematology “Seràgnoli”, IRCCS-Azienda Ospedaliero Policlinico Sant’Orsola-Universitaria di Bologna, 40138 Bologna, Italy; (P.E.C.); (C.S.); (S.P.); (A.C.); (F.C.); (M.U.); (M.C.)
- Department of Diagnostic and Experimental Medicine Specialty (DIMES)- Università di Bologna, Alma Mater Studiorum, 40138 Bologna, Italy;
| | - Marta Stanzani
- Institute of Hematology “Seràgnoli”, IRCCS-Azienda Ospedaliero Policlinico Sant’Orsola-Universitaria di Bologna, 40138 Bologna, Italy; (P.E.C.); (C.S.); (S.P.); (A.C.); (F.C.); (M.U.); (M.C.)
- Correspondence:
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76
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Hong JS, Song W, Park MJ, Jeong S, Lee N, Jeong SH. Molecular Characterization of the First Emerged NDM-1-Producing Pseudomonas aeruginosa Isolates in South Korea. Microb Drug Resist 2020; 27:1063-1070. [PMID: 33332204 DOI: 10.1089/mdr.2020.0374] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Carbapenemase-producing Pseudomonas aeruginosa (CPPA) is a threat to public health. This study aimed to describe the first emergence and molecular characterization of NDM-1-producing P. aeruginosa in South Korea. A total of 183 carbapenem-resistant P. aeruginosa (CRPA) isolates were recovered from patients at a university hospital in Seoul, South Korea. The antimicrobial resistance genes and their genetic environments were determined through molecular sequencing. Antimicrobial susceptibility testing was performed using the VITEK 2 system and broth microdilution method. Genetic relatedness was assessed using multilocus sequence typing and pulsed-field gel electrophoresis. Whole genome sequencing (WGS) was carried out to analyze the entire genome of a CPPA isolated from the index patient; the first identified infected patient. All 16 CPPA isolates from the 183 CRPA carried the blaNDM-1 gene and exhibited a high level of resistance to β-lactams, aminoglycosides, and ciprofloxacin. Fifteen of the 16 isolates were recovered from urine samples. They were attributed to ST773 and showed high clonal similarity (>86%). Post-WGS analysis revealed that the blaNDM-1 gene and the 16S rRNA methyltransferase gene rmtB4 were located in the integrative and conjugative element (ICE) on the chromosome. This ICE6660-like region was very similar to the ICE6660 region carrying the blaNDM-1 gene and the 16S rRNA methyltransferase gene rmtD3 in a previously described P. aeruginosa strain. This study described the first emergence and clonal spread of the NDM-1-producing P. aeruginosa ST773 isolates possessing rmtB4, at a university hospital in South Korea, suggesting that continuous surveillance is necessary to prevent infection and transmission of these CRPAs, which can endanger public health.
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Affiliation(s)
- Jun Sung Hong
- Department of Laboratory Medicine and Research, Institute of Bacterial Resistance, Yonsei University College of Medicine, Seoul, South Korea
| | - Wonkeun Song
- Department of Laboratory Medicine, Hallym University College of Medicine, Chuncheon, South Korea
| | - Min-Jeong Park
- Department of Laboratory Medicine, Hallym University College of Medicine, Chuncheon, South Korea
| | - Seri Jeong
- Department of Laboratory Medicine, Hallym University College of Medicine, Chuncheon, South Korea
| | - Nuri Lee
- Department of Laboratory Medicine, Hallym University College of Medicine, Chuncheon, South Korea
| | - Seok Hoon Jeong
- Department of Laboratory Medicine and Research, Institute of Bacterial Resistance, Yonsei University College of Medicine, Seoul, South Korea
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77
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Gregorova M, Morse D, Brignoli T, Steventon J, Hamilton F, Albur M, Arnold D, Thomas M, Halliday A, Baum H, Rice C, Avison MB, Davidson AD, Santopaolo M, Oliver E, Goenka A, Finn A, Wooldridge L, Amulic B, Boyton RJ, Altmann DM, Butler DK, McMurray C, Stockton J, Nicholls S, Cooper C, Loman N, Cox MJ, Rivino L, Massey RC. Post-acute COVID-19 associated with evidence of bystander T-cell activation and a recurring antibiotic-resistant bacterial pneumonia. eLife 2020; 9:e63430. [PMID: 33331820 PMCID: PMC7775105 DOI: 10.7554/elife.63430] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 12/16/2020] [Indexed: 12/24/2022] Open
Abstract
Here, we describe the case of a COVID-19 patient who developed recurring ventilator-associated pneumonia caused by Pseudomonas aeruginosa that acquired increasing levels of antimicrobial resistance (AMR) in response to treatment. Metagenomic analysis revealed the AMR genotype, while immunological analysis revealed massive and escalating levels of T-cell activation. These were both SARS-CoV-2 and P. aeruginosa specific, and bystander activated, which may have contributed to this patient's persistent symptoms and radiological changes.
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Affiliation(s)
- Michaela Gregorova
- School of Cellular and Molecular Medicine, University of BristolBristolUnited Kingdom
| | - Daniel Morse
- School of Cellular and Molecular Medicine, University of BristolBristolUnited Kingdom
| | - Tarcisio Brignoli
- School of Cellular and Molecular Medicine, University of BristolBristolUnited Kingdom
| | - Joseph Steventon
- School of Cellular and Molecular Medicine, University of BristolBristolUnited Kingdom
| | | | | | | | | | - Alice Halliday
- School of Cellular and Molecular Medicine, University of BristolBristolUnited Kingdom
| | - Holly Baum
- School of Cellular and Molecular Medicine, University of BristolBristolUnited Kingdom
| | - Christopher Rice
- School of Cellular and Molecular Medicine, University of BristolBristolUnited Kingdom
| | - Matthew B Avison
- School of Cellular and Molecular Medicine, University of BristolBristolUnited Kingdom
| | - Andrew D Davidson
- School of Cellular and Molecular Medicine, University of BristolBristolUnited Kingdom
| | - Marianna Santopaolo
- School of Cellular and Molecular Medicine, University of BristolBristolUnited Kingdom
| | - Elizabeth Oliver
- School of Cellular and Molecular Medicine, University of BristolBristolUnited Kingdom
| | - Anu Goenka
- School of Cellular and Molecular Medicine, University of BristolBristolUnited Kingdom
| | - Adam Finn
- School of Cellular and Molecular Medicine, University of BristolBristolUnited Kingdom
| | - Linda Wooldridge
- Bristol Veterinary School in the Faculty of Health SciencesBristolUnited Kingdom
| | - Borko Amulic
- School of Cellular and Molecular Medicine, University of BristolBristolUnited Kingdom
| | - Rosemary J Boyton
- Department of Infectious Disease, Imperial College LondonLondonUnited Kingdom
- Lung Division, Royal Brompton & Harefield NHS Foundation TrustLondonUnited Kingdom
| | - Daniel M Altmann
- Department of Infectious Disease, Imperial College LondonLondonUnited Kingdom
| | - David K Butler
- Department of Infectious Disease, Imperial College LondonLondonUnited Kingdom
| | - Claire McMurray
- Institute of Microbiology and Infection, University of BirminghamBirminghamUnited Kingdom
| | - Joanna Stockton
- Institute of Microbiology and Infection, University of BirminghamBirminghamUnited Kingdom
| | - Sam Nicholls
- Institute of Microbiology and Infection, University of BirminghamBirminghamUnited Kingdom
| | - Charles Cooper
- Institute of Microbiology and Infection, University of BirminghamBirminghamUnited Kingdom
| | - Nicholas Loman
- Institute of Microbiology and Infection, University of BirminghamBirminghamUnited Kingdom
| | - Michael J Cox
- Lung Division, Royal Brompton & Harefield NHS Foundation TrustLondonUnited Kingdom
| | - Laura Rivino
- School of Cellular and Molecular Medicine, University of BristolBristolUnited Kingdom
| | - Ruth C Massey
- School of Cellular and Molecular Medicine, University of BristolBristolUnited Kingdom
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78
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Phenotypic and Genomic Comparison of the Two Most Common ExoU-Positive Pseudomonas aeruginosa Clones, PA14 and ST235. mSystems 2020; 5:5/6/e01007-20. [PMID: 33293405 PMCID: PMC7743143 DOI: 10.1128/msystems.01007-20] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [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.
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79
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Pseudomonas aeruginosa epidemic high-risk clones and their association with horizontally-acquired β-lactamases: 2020 update. Int J Antimicrob Agents 2020; 56:106196. [DOI: 10.1016/j.ijantimicag.2020.106196] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 07/30/2020] [Accepted: 09/26/2020] [Indexed: 01/17/2023]
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80
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Sit bath systems: A new source of Legionella infection. PLoS One 2020; 15:e0241756. [PMID: 33147266 PMCID: PMC7641379 DOI: 10.1371/journal.pone.0241756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 10/21/2020] [Indexed: 11/19/2022] Open
Abstract
Sit Bath Systems (SBSs) are the most common hygiene method for patients who are not self-sufficient. Therefore, the water quality of SBSs in the nosocomial environment plays a fundamental role in controlling infections for both patients and health-care workers. A long-term study on Legionella and Pseudomonas aeruginosa (P. aeruginosa) contamination was performed in SBSs (n = 20) of six Health Care Facilities (HCFs). A total of 254 water samples were analyzed following ISO procedures. The samples were positive for P. aeruginosa (46.85%) and Legionella (53.54%), respectively, both over the directive limits. Legionella isolates were identified as: Legionella pneumophila (L. pneumophila) serogroups 1, 3, and 6 and Legionella non-pneumophila species (L. anisa, L. londiniensis, L. rubrilucens, and L. nagelii). Moreover, the contamination found was studied with respect to median temperature measured (42 °C), from which two groups (A and B) could be distinguished. P. aeruginosa was found in both groups (100% of SBSs), while a higher percentage of Legionella positive samples was found in group A (75% of SBSs), compared to group B (50% of SBSs), showing how Legionella control could be carried out by using temperatures above 42 °C. An analysis of SBS water pipelines, maintenance, and disinfection treatments indicates SBSs as a new source of infection risk for both patients and health-care workers.
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81
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Pappa O, Kefala AM, Tryfinopoulou K, Dimitriou M, Kostoulas K, Dioli C, Moraitou E, Panopoulou M, Vogiatzakis E, Mavridou A, Galanis A, Beloukas A. Molecular Epidemiology of Multi-Drug Resistant Pseudomonas aeruginosa Isolates from Hospitalized Patients in Greece. Microorganisms 2020; 8:microorganisms8111652. [PMID: 33114400 PMCID: PMC7693957 DOI: 10.3390/microorganisms8111652] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 10/21/2020] [Accepted: 10/22/2020] [Indexed: 12/13/2022] Open
Abstract
Resistant Pseudomonas aeruginosa isolates are one of the major causes of both hospital-acquired infections (HAIs) and community-acquired infections (CAIs). However, management of P. aeruginosa infections is difficult as the bacterium is inherently resistant to many antibiotics. In this study, a collection of 75 P. aeruginosa clinical isolates from two tertiary hospitals from Athens and Alexnadroupolis in Greece was studied to assess antimicrobial sensitivity and molecular epidemiology. All P. aeruginosa isolates were tested for susceptibility to 11 commonly used antibiotics, and the newly introduced Double Locus Sequence Typing (DLST) scheme was implemented to elucidate the predominant clones. The tested P. aeruginosa isolates presented various resistant phenotypes, with Verona Integron-Mediated Metallo-β-lactamase (VIM-2) mechanisms being the majority, and a new phenotype, FEPR-CAZS, being reported for the first time in Greek isolates. DLST revealed two predominant types, 32-39 and 8-37, and provided evidence for intra-hospital transmission of the 32-39 clone in one of the hospitals. The results indicate that DLST can be a valuable tool when local outbreaks demand immediate tracking investigation with limited time and financial resources.
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Affiliation(s)
- Olga Pappa
- Department of Biomedical Sciences, University of West Attica, 12243 Egaleo, Greece; (A.M.K.); (M.D.); (C.D.); (A.M.)
- Central Public Health Laboratory, National Public Health Organization, 16672 Athens, Greece;
- Correspondence: or (O.P.); or (A.B.)
| | - Anastasia Maria Kefala
- Department of Biomedical Sciences, University of West Attica, 12243 Egaleo, Greece; (A.M.K.); (M.D.); (C.D.); (A.M.)
| | - Kyriaki Tryfinopoulou
- Central Public Health Laboratory, National Public Health Organization, 16672 Athens, Greece;
| | - Marios Dimitriou
- Department of Biomedical Sciences, University of West Attica, 12243 Egaleo, Greece; (A.M.K.); (M.D.); (C.D.); (A.M.)
| | - Kostas Kostoulas
- Laboratory of Microbiology, ‘Sotiria’ General Hospital, 152 Mesogeion Avenue, 11527 Athens, Greece; (K.K.); (E.M.); (E.V.)
| | - Chrysa Dioli
- Department of Biomedical Sciences, University of West Attica, 12243 Egaleo, Greece; (A.M.K.); (M.D.); (C.D.); (A.M.)
| | - Eleni Moraitou
- Laboratory of Microbiology, ‘Sotiria’ General Hospital, 152 Mesogeion Avenue, 11527 Athens, Greece; (K.K.); (E.M.); (E.V.)
| | - Maria Panopoulou
- Laboratory of Microbiology, School of Medicine, Democritus University of Thrace, Dragana, 68100 Alexandroupolis, Greece;
| | - Evaggelos Vogiatzakis
- Laboratory of Microbiology, ‘Sotiria’ General Hospital, 152 Mesogeion Avenue, 11527 Athens, Greece; (K.K.); (E.M.); (E.V.)
| | - Athena Mavridou
- Department of Biomedical Sciences, University of West Attica, 12243 Egaleo, Greece; (A.M.K.); (M.D.); (C.D.); (A.M.)
| | - Alex Galanis
- Department of Molecular Biology and Genetics, Health Science School, Democritus University of Thrace, 68100 Alexandroupolis, Greece;
| | - Apostolos Beloukas
- Department of Biomedical Sciences, University of West Attica, 12243 Egaleo, Greece; (A.M.K.); (M.D.); (C.D.); (A.M.)
- Institute of Infection & Global Health, University of Liverpool, Liverpool L69 7BE, UK
- Correspondence: or (O.P.); or (A.B.)
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Efflux Pump-Driven Antibiotic and Biocide Cross-Resistance in Pseudomonas aeruginosa Isolated from Different Ecological Niches: A Case Study in the Development of Multidrug Resistance in Environmental Hotspots. Microorganisms 2020; 8:microorganisms8111647. [PMID: 33114277 PMCID: PMC7690850 DOI: 10.3390/microorganisms8111647] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 10/16/2020] [Accepted: 10/19/2020] [Indexed: 12/11/2022] Open
Abstract
Pseudomonas aeruginosa is an opportunistic pathogen displaying high intrinsic antimicrobial resistance and the ability to thrive in different ecological environments. In this study, the ability of P. aeruginosa to develop simultaneous resistance to multiple antibiotics and disinfectants in different natural niches were investigated using strains collected from clinical samples, veterinary samples, and wastewater. The correlation between biocide and antimicrobial resistance was determined by employing principal component analysis. Molecular mechanisms linking biocide and antimicrobial resistance were interrogated by determining gene expression using RT-qPCR and identifying a potential genetic determinant for co- and cross-resistance using whole-genome sequencing. A subpopulation of P. aeruginosa isolates belonging to three sequence types was resistant against the common preservative benzalkonium chloride and showed cross-resistance to fluoroquinolones, cephalosporins, aminoglycosides, and multidrug resistance. Of these, the epidemiological high-risk ST235 clone was the most abundant. The overexpression of the MexAB-OprM drug efflux pump resulting from amino acid mutations in regulators MexR, NalC, or NalD was the major contributing factor for cross-resistance that could be reversed by an efflux pump inhibitor. This is the first comparison of antibiotic-biocide cross-resistance in samples isolated from different ecological niches and serves as a confirmation of laboratory-based studies on biocide adapted isolates. The isolates from wastewater had a higher incidence of multidrug resistance and biocide-antibiotic cross-resistance than those from clinical and veterinary settings.
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Slizen MV, Galzitskaya OV. Comparative Analysis of Proteomes of a Number of Nosocomial Pathogens by KEGG Modules and KEGG Pathways. Int J Mol Sci 2020; 21:ijms21217839. [PMID: 33105850 PMCID: PMC7660090 DOI: 10.3390/ijms21217839] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Revised: 10/12/2020] [Accepted: 10/15/2020] [Indexed: 01/13/2023] Open
Abstract
Nosocomial (hospital-acquired) infections remain a serious challenge for health systems. The reason for this lies not only in the local imperfection of medical practices and protocols. The frequency of infection with antibiotic-resistant strains of bacteria is growing every year, both in developed and developing countries. In this work, a pangenome and comparative analysis of 201 genomes of Staphylococcus aureus, Enterobacter spp., Pseudomonas aeruginosa, and Mycoplasma spp. was performed on the basis of high-level functional annotations—KEGG pathways and KEGG modules. The first three organisms are serious nosocomial pathogens, often exhibiting multidrug resistance. Analysis of KEGG modules revealed methicillin resistance in 25% of S. aureus strains and resistance to carbapenems in 21% of Enterobacter spp. strains. P. aeruginosa has a wide range of unique efflux systems. One hundred percent of the analyzed strains have at least two drug resistance systems, and 75% of the strains have seven. Each of the organisms has a characteristic set of metabolic features, whose impact on drug resistance can be considered in future studies. Comparing the genomes of nosocomial pathogens with each other and with Mycoplasma genomes can expand our understanding of the versatility of certain metabolic features and mechanisms of drug resistance.
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Affiliation(s)
- Mikhail V. Slizen
- Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Moscow Region, Russia;
| | - Oxana V. Galzitskaya
- Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Moscow Region, Russia;
- Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, 142290 Pushchino, Moscow Region, Russia
- Correspondence:
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Rodrigues YC, Furlaneto IP, Maciel AHP, Quaresma AJPG, de Matos ECO, Conceição ML, Vieira MCDS, Brabo GLDC, Sarges EDSNF, Lima LNGC, Lima KVB. High prevalence of atypical virulotype and genetically diverse background among Pseudomonas aeruginosa isolates from a referral hospital in the Brazilian Amazon. PLoS One 2020; 15:e0238741. [PMID: 32911510 PMCID: PMC7482967 DOI: 10.1371/journal.pone.0238741] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2020] [Accepted: 08/21/2020] [Indexed: 12/23/2022] Open
Abstract
Pseudomonas aeruginosa is an opportunistic pathogen causing different types of infections, particularly in intensive care unit patients. Characteristics that favor its persistence artificial environments are related to its high adaptability, wide arsenal of virulence factors and resistance to several antimicrobial classes. Among the several virulence determinants, T3SS stands as the most important due to the clinical impact of exoS and exoU genes in patient’s outcome. The molecular characterization of P. aeruginosa isolates helps in the comprehension of transmission dynamics and enhance knowledge of virulence and resistance roles in infection process. In the present study, we investigated virulence and resistance properties and the genetic background of P. aeruginosa isolated from ICUs patients at a referral hospital in Brazilian Amazon. A total of 54 P. aeruginosa isolates were characterized by detecting 19 virulence-related genes, antimicrobial susceptibility testing, molecular detection of β-lactamase-encoding genes and genotyping by MLST and rep-PCR. Our findings showed high prevalence of virulence-related markers, where 53.7% of the isolates presented at least 17 genes among the 19 investigated (P = 0.01). The rare exoS+/exoU+ cytotoxic virulotype was detected in 55.6% of isolates. Antimicrobial susceptibility testing revealed percentages of antibiotic resistance above 50% to carbapenems, cephalosporins and fluoroquinolones associated to MDR/XDR isolates. Isolates harboring both blaSPM-1 and blaOXA genes were also detected. Genotyping methods demonstrated a wide genetic diversity of strains spread among the different intensive care units, circulation of international MDR/XDR high-risk clones (ST111, ST235, ST244 and ST277) and emergence of seven novel MLST lineages. Finally, our findings highlight the circulation of strains with high virulence potential and resistance to antimicrobials and may be useful on comprehension of pathogenicity process, treatment guidance and establishment of strategies to control the spread of epidemic P. aeruginosa strains.
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Affiliation(s)
- Yan Corrêa Rodrigues
- Programa de Pós-graduação em Biologia Parasitária na Amazônia, Centro de Ciências Biológicas e da Saúde, Universidade do Estado do Pará (UEPA), Belém, Pará, Brazil
- * E-mail: (YCR); (KVBL)
| | - Ismari Perini Furlaneto
- Programa de Pós-graduação em Educação em Saúde, Centro Universitário do Pará (CESUPA), Belém, Pará Brazil
| | - Arthur Henrique Pinto Maciel
- Laboratório de Biologia Molecular, Seção de Bacteriologia e Micologia, Instituto Evandro Chagas (IEC), Ministério da Saúde, Ananindeua, Pará, Brazil
| | - Ana Judith Pires Garcia Quaresma
- Laboratório de Biologia Molecular, Seção de Bacteriologia e Micologia, Instituto Evandro Chagas (IEC), Ministério da Saúde, Ananindeua, Pará, Brazil
| | - Eliseth Costa Oliveira de Matos
- Departamento de Patologia, Centro de Ciências Biológicas e da Saúde, Universidade do Estado do Pará (UEPA), Belém, Pará, Brazil
| | - Marília Lima Conceição
- Programa de Pós-graduação em Biologia Parasitária na Amazônia, Centro de Ciências Biológicas e da Saúde, Universidade do Estado do Pará (UEPA), Belém, Pará, Brazil
| | - Marcelo Cleyton da Silva Vieira
- Laboratório de Biologia Molecular, Seção de Bacteriologia e Micologia, Instituto Evandro Chagas (IEC), Ministério da Saúde, Ananindeua, Pará, Brazil
| | - Giulia Leão da Cunha Brabo
- Laboratório de Biologia Molecular, Seção de Bacteriologia e Micologia, Instituto Evandro Chagas (IEC), Ministério da Saúde, Ananindeua, Pará, Brazil
| | | | - Luana Nepomuceno Godim Costa Lima
- Programa de Pós-graduação em Biologia Parasitária na Amazônia, Centro de Ciências Biológicas e da Saúde, Universidade do Estado do Pará (UEPA), Belém, Pará, Brazil
- Laboratório de Biologia Molecular, Seção de Bacteriologia e Micologia, Instituto Evandro Chagas (IEC), Ministério da Saúde, Ananindeua, Pará, Brazil
| | - Karla Valéria Batista Lima
- Programa de Pós-graduação em Biologia Parasitária na Amazônia, Centro de Ciências Biológicas e da Saúde, Universidade do Estado do Pará (UEPA), Belém, Pará, Brazil
- Laboratório de Biologia Molecular, Seção de Bacteriologia e Micologia, Instituto Evandro Chagas (IEC), Ministério da Saúde, Ananindeua, Pará, Brazil
- * E-mail: (YCR); (KVBL)
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Del Barrio-Tofiño E, Zamorano L, Cortes-Lara S, López-Causapé C, Sánchez-Diener I, Cabot G, Bou G, Martínez-Martínez L, Oliver A. Spanish nationwide survey on Pseudomonas aeruginosa antimicrobial resistance mechanisms and epidemiology. J Antimicrob Chemother 2020; 74:1825-1835. [PMID: 30989186 DOI: 10.1093/jac/dkz147] [Citation(s) in RCA: 84] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2019] [Revised: 03/11/2019] [Accepted: 03/11/2019] [Indexed: 12/30/2022] Open
Abstract
OBJECTIVES To undertake a Spanish nationwide survey on Pseudomonas aeruginosa molecular epidemiology and antimicrobial resistance. METHODS Up to 30 consecutive healthcare-associated P. aeruginosa isolates collected in 2017 from each of 51 hospitals were studied. MICs of 13 antipseudomonal agents were determined by broth microdilution. Horizontally acquired β-lactamases were detected by phenotypic methods and PCR. Clonal epidemiology was evaluated through PFGE and MLST; at least one XDR isolate from each clone and hospital (n = 185) was sequenced. RESULTS The most active antipseudomonals against the 1445 isolates studied were colistin and ceftolozane/tazobactam (both 94.6% susceptible, MIC50/90 = 1/2 mg/L) followed by ceftazidime/avibactam (94.2% susceptible, MIC50/90 = 2/8 mg/L). Up to 252 (17.3%) of the isolates were XDR. Carbapenemases/ESBLs were detected in 3.1% of the isolates, including VIM, IMP, GES, PER and OXA enzymes. The most frequent clone among the XDR isolates was ST175 (40.9%), followed by CC235 (10.7%), ST308 (5.2%) and CC111 (4.0%). Carbapenemase production varied geographically and involved diverse clones, including 16.5% of ST175 XDR isolates. Additionally, 56% of the sequenced XDR isolates showed horizontally acquired aminoglycoside-modifying enzymes, which correlated with tobramycin resistance. Two XDR isolates produced QnrVC1, but fluoroquinolone resistance was mostly caused by QRDR mutations. Beyond frequent mutations (>60%) in OprD and AmpC regulators, four isolates showed AmpC mutations associated with resistance to ceftolozane/tazobactam and ceftazidime/avibactam. CONCLUSIONS ST175 is the most frequent XDR high-risk clone in Spanish hospitals, but this nationwide survey also indicates a complex scenario in which major differences in local epidemiology, including carbapenemase production, need to be acknowledged in order to guide antimicrobial therapy.
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Affiliation(s)
- Ester Del Barrio-Tofiño
- Servicio de Microbiología, Hospital Son Espases, Instituto de Investigación Sanitaria Illes Balears (IdISBa), Palma de Mallorca, España
| | - Laura Zamorano
- Servicio de Microbiología, Hospital Son Espases, Instituto de Investigación Sanitaria Illes Balears (IdISBa), Palma de Mallorca, España
| | - Sara Cortes-Lara
- Servicio de Microbiología, Hospital Son Espases, Instituto de Investigación Sanitaria Illes Balears (IdISBa), Palma de Mallorca, España
| | - Carla López-Causapé
- Servicio de Microbiología, Hospital Son Espases, Instituto de Investigación Sanitaria Illes Balears (IdISBa), Palma de Mallorca, España
| | - Irina Sánchez-Diener
- Servicio de Microbiología, Hospital Son Espases, Instituto de Investigación Sanitaria Illes Balears (IdISBa), Palma de Mallorca, España
| | - Gabriel Cabot
- Servicio de Microbiología, Hospital Son Espases, Instituto de Investigación Sanitaria Illes Balears (IdISBa), Palma de Mallorca, España
| | - Germán Bou
- Servicio de Microbiología, Hospital Universitario La Coruña, Instituto Investigación Biomédica A Coruña (INIBIC), La Coruña, España
| | - Luis Martínez-Martínez
- Unidad de Gestión Clínica de Microbiología, Hospital Reina Sofía, Departamento de Microbiología, Universidad de Córdoba, Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), Córdoba, España
| | - Antonio Oliver
- Servicio de Microbiología, Hospital Son Espases, Instituto de Investigación Sanitaria Illes Balears (IdISBa), Palma de Mallorca, España
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De Oliveira DMP, Forde BM, Kidd TJ, Harris PNA, Schembri MA, Beatson SA, Paterson DL, Walker MJ. Antimicrobial Resistance in ESKAPE Pathogens. Clin Microbiol Rev 2020; 23:788-99. [PMID: 32404435 DOI: 10.1111/imb.12124] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/23/2023] Open
Abstract
Antimicrobial-resistant ESKAPE ( Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter species) pathogens represent a global threat to human health. The acquisition of antimicrobial resistance genes by ESKAPE pathogens has reduced the treatment options for serious infections, increased the burden of disease, and increased death rates due to treatment failure and requires a coordinated global response for antimicrobial resistance surveillance. This looming health threat has restimulated interest in the development of new antimicrobial therapies, has demanded the need for better patient care, and has facilitated heightened governance over stewardship practices.
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Affiliation(s)
- David M P De Oliveira
- School of Chemistry and Molecular Biosciences, The University of Queensland, QLD, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, QLD, Australia
| | - Brian M Forde
- School of Chemistry and Molecular Biosciences, The University of Queensland, QLD, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, QLD, Australia
| | - Timothy J Kidd
- School of Chemistry and Molecular Biosciences, The University of Queensland, QLD, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, QLD, Australia
| | - Patrick N A Harris
- Australian Infectious Diseases Research Centre, The University of Queensland, QLD, Australia
- UQ Centre for Clinical Research, The University of Queensland, QLD, Australia
| | - Mark A Schembri
- School of Chemistry and Molecular Biosciences, The University of Queensland, QLD, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, QLD, Australia
| | - Scott A Beatson
- School of Chemistry and Molecular Biosciences, The University of Queensland, QLD, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, QLD, Australia
| | - David L Paterson
- Australian Infectious Diseases Research Centre, The University of Queensland, QLD, Australia
- UQ Centre for Clinical Research, The University of Queensland, QLD, Australia
| | - Mark J Walker
- School of Chemistry and Molecular Biosciences, The University of Queensland, QLD, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, QLD, Australia
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87
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Ohadian Moghadam S, Afshar D, Nowroozi MR, Behnamfar A, Farzin A. Molecular Epidemiology of Carbapenemase-Producing Pseudomonas aeruginosa Isolated from an Iranian University Hospital: Evidence for Spread of High-Risk Clones. Infect Drug Resist 2020; 13:1583-1592. [PMID: 32581561 PMCID: PMC7277578 DOI: 10.2147/idr.s253756] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Purpose Given the importance of treatment failure due to multidrug-resistant (MDR) strains, studies on population structure of these organisms are necessary to improve control strategies. Accordingly, the current study aimed to determine the prevalence of carbapenem-resistant P. aeruginosa (CRPA) at a teaching referral hospital in Iran and to analyz their molecular clonality by multilocus sequence typing (MLST) and pulsed-field gel electrophoresis (PFGE) for epidemiological purposes. Methods In this study, modified Hodge test (MHT) and double-disk synergy test (DDST) were used for carbapenemase production and metallo-β-lactamases (MBLs) screening, respectively. All P. aeruginosa isolates were tested for antimicrobial resistance. Moreover, MBL genes (blaIMP, blaVIM, blaSPM, blaNDM) were detected by multiplex PCR assay. Results Among 68 P. aeruginosa clinical isolates, 38 (55.88%) isolates were CRPA. Antibiotic susceptibility testing revealed that most of these isolates were MDR. PFGE analyses showed 5 common types and 27 single types among CRPA isolates. MLST analysis revealed three major clusters (MLST-sequence types (STs): 235, 357, and 861) among them. The 30 non-CRPA isolates corresponded mainly to MLST-STs 253, 360, and 446. Conclusion Our results showed that internationally distributed MLST-STs with widely genomic diversity have spread in our hospital, and clonal expansion of MDR strains of P. aeruginosa was described as well.
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Affiliation(s)
| | - Davoud Afshar
- Department of Microbiology and Virology, Zanjan University of Medical Sciences, Zanjan, Iran
| | | | - Amir Behnamfar
- Uro-Oncology Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Amirreza Farzin
- Uro-Oncology Research Center, Tehran University of Medical Sciences, Tehran, Iran
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de Sales RO, Migliorini LB, Puga R, Kocsis B, Severino P. A Core Genome Multilocus Sequence Typing Scheme for Pseudomonas aeruginosa. Front Microbiol 2020; 11:1049. [PMID: 32528447 PMCID: PMC7264379 DOI: 10.3389/fmicb.2020.01049] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Accepted: 04/28/2020] [Indexed: 12/15/2022] Open
Abstract
Pseudomonas aeruginosa is a ubiquitous microorganism and an important opportunistic pathogen responsible for a broad spectrum of infections mainly in immunosuppressed and critically ill patients. Molecular investigations traditionally rely on pulsed field gel electrophoresis (PFGE) and multilocus sequence typing (MLST). In this work we propose a core genome multilocus sequence typing (cgMLST) scheme for P. aeruginosa, a methodology that combines traditional MLST principles with whole genome sequencing data. All publicly available complete P. aeruginosa genomes, representing the diversity of this species, were used to establish a cgMLST scheme targeting 2,653 genes. The scheme was then tested using genomes available at contig, chromosome and scaffold levels. The proposed cgMLST scheme for P. aeruginosa typed over 99% (2,314/2,325) of the genomes available for this study considering at least 95% of the cgMLST target genes present. The absence of a certain number gene targets at the threshold considered for both the creation and validation steps due to low genome sequence quality is possibly the main reason for this result. The cgMLST scheme was compared with previously published whole genome single nucleotide polymorphism analysis for the characterization of the population structure of the epidemic clone ST235 and results were highly similar. In order to evaluate the typing resolution of the proposed scheme, collections of isolates belonging to two important STs associated with cystic fibrosis, ST146 and ST274, were typed using this scheme, and ST235 isolates associated with an outbreak were evaluated. Besides confirming the relatedness of all the isolates, earlier determined by MLST, the higher resolution of cgMLST denotes that it may be suitable for surveillance programs, overcoming possible shortcomings of classical MLST. The proposed scheme is publicly available at: https://github.com/BioinformaticsHIAEMolecularMicrobiology/cgMLST-Pseudomonas-aeruginosa.
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Affiliation(s)
- Romário Oliveira de Sales
- Hospital Israelita Albert Einstein, Albert Einstein Research and Education Institute, São Paulo, Brazil
| | - Letícia Busato Migliorini
- Hospital Israelita Albert Einstein, Albert Einstein Research and Education Institute, São Paulo, Brazil
| | - Renato Puga
- Hospital Israelita Albert Einstein, Albert Einstein Research and Education Institute, São Paulo, Brazil
| | - Bela Kocsis
- Institute of Medical Microbiology, Semmelweis University, Budapest, Hungary
| | - Patricia Severino
- Hospital Israelita Albert Einstein, Albert Einstein Research and Education Institute, São Paulo, Brazil
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PÉrez-VÁzquez M, Sola-Campoy PJ, Zurita ÁM, Ávila A, GÓmez-Bertomeu F, SolÍs S, LÓpez-Urrutia L, GÓnzalez-BarberÁ EM, Cercenado E, Bautista V, Lara N, Aracil B, Oliver A, Campos J, Oteo-Iglesias J. Carbapenemase-producing Pseudomonas aeruginosa in Spain: interregional dissemination of the high-risk clones ST175 and ST244 carrying bla VIM-2, bla VIM-1, bla IMP-8, bla VIM-20 and bla KPC-2. Int J Antimicrob Agents 2020; 56:106026. [PMID: 32450200 DOI: 10.1016/j.ijantimicag.2020.106026] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 05/13/2020] [Accepted: 05/14/2020] [Indexed: 12/14/2022]
Abstract
Carbapenemase-producing (CP) Pseudomonas aeruginosa is rare compared with mutation-driven carbapenem-resistance, but this situation may be changing. A collection of CP P. aeruginosa isolates was characterized in this study. In 2016, 232 unduplicated carbapenem-resistant P. aeruginosa isolates, of which 71 (30.6%) carried carbapenemase genes, were submitted to the Spanish antibiotic reference laboratory and were further analysed by whole-genome sequencing (WGS). Of the 71 CP P. aeruginosa, 39 (54.9%) carried blaVIM-2, 14 (19.7%) blaVIM-1, 8 (11.3%) blaIMP-8, 6 (8.5%) blaVIM-20, 2 (2.8%) blaVIM-2 plus blaKPC-2, one (1.4%) blaIMP-13 and one (1.4%) blaVIM-1 plus blaIMP-18. Four sequence types (ST175, ST244, ST815 and ST155) encompassed 83.1% of the 71 CP P. aeruginosa; ST175 was detected in hospitals from seven provinces. Using core genome multilocus sequence typing (cgMLST), four clusters were detected: Cluster 1 included nine ST815/VIM-2 isolates; Cluster 2 included five ST175/VIM-2 isolates; Cluster 3 included seven ST244 isolates (five VIM-2 and two VIM-2 plus KPC-2); and Cluster 4 included 11 ST175 isolates (seven VIM-2 and four IMP-8). The average number of acquired resistance genes was significantly higher in the blaVIM-1-carying isolates (7.1 ± 0.94) than in the blaVIM-2-carrying isolates (4.5 ± 0.20). CP P. aeruginosa isolates are spreading in Spain, mainly due to the dissemination of high-risk clones such as ST175 and ST244 producing VIM and IMP carbapenemases. Emergence of CP P. aeruginosa is a cause of clinical and epidemiological concern.
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Affiliation(s)
- María PÉrez-VÁzquez
- Reference and Research Laboratory for Antibiotic Resistance and Health Care Infections, National Centre for Microbiology, Institute of Health Carlos III, Majadahonda, Madrid, Spain; Spanish Network for Research in Infectious Diseases (REIPI RD16/0016), Instituto de Salud Carlos III, Madrid, Spain
| | - Pedro J Sola-Campoy
- Reference and Research Laboratory for Antibiotic Resistance and Health Care Infections, National Centre for Microbiology, Institute of Health Carlos III, Majadahonda, Madrid, Spain
| | - Ángela María Zurita
- Reference and Research Laboratory for Antibiotic Resistance and Health Care Infections, National Centre for Microbiology, Institute of Health Carlos III, Majadahonda, Madrid, Spain
| | - Alicia Ávila
- Reference and Research Laboratory for Antibiotic Resistance and Health Care Infections, National Centre for Microbiology, Institute of Health Carlos III, Majadahonda, Madrid, Spain
| | | | - Sonia SolÍs
- Microbiology Department, Hospital Universitario de Guadalajara, Spain
| | - Luis LÓpez-Urrutia
- Microbiology Department, Hospital Universitario Río Hortega, Valladolid, Spain
| | | | - Emilia Cercenado
- Microbiology Department, Hospital Gregorio Marañón, Madrid, Spain
| | - Verónica Bautista
- Reference and Research Laboratory for Antibiotic Resistance and Health Care Infections, National Centre for Microbiology, Institute of Health Carlos III, Majadahonda, Madrid, Spain; Spanish Network for Research in Infectious Diseases (REIPI RD16/0016), Instituto de Salud Carlos III, Madrid, Spain
| | - Noelia Lara
- Reference and Research Laboratory for Antibiotic Resistance and Health Care Infections, National Centre for Microbiology, Institute of Health Carlos III, Majadahonda, Madrid, Spain; Spanish Network for Research in Infectious Diseases (REIPI RD16/0016), Instituto de Salud Carlos III, Madrid, Spain
| | - Belén Aracil
- Reference and Research Laboratory for Antibiotic Resistance and Health Care Infections, National Centre for Microbiology, Institute of Health Carlos III, Majadahonda, Madrid, Spain; Spanish Network for Research in Infectious Diseases (REIPI RD16/0016), Instituto de Salud Carlos III, Madrid, Spain
| | - Antonio Oliver
- Microbiology Department-Research Institute Biomedical Islas Baleares (IdISBa), Hospital Son Espases, Palma de Mallorca, Spain
| | - José Campos
- Reference and Research Laboratory for Antibiotic Resistance and Health Care Infections, National Centre for Microbiology, Institute of Health Carlos III, Majadahonda, Madrid, Spain; Spanish Network for Research in Infectious Diseases (REIPI RD16/0016), Instituto de Salud Carlos III, Madrid, Spain
| | - Jesús Oteo-Iglesias
- Reference and Research Laboratory for Antibiotic Resistance and Health Care Infections, National Centre for Microbiology, Institute of Health Carlos III, Majadahonda, Madrid, Spain; Spanish Network for Research in Infectious Diseases (REIPI RD16/0016), Instituto de Salud Carlos III, Madrid, Spain.
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Abstract
Antimicrobial-resistant ESKAPE ( Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter species) pathogens represent a global threat to human health. The acquisition of antimicrobial resistance genes by ESKAPE pathogens has reduced the treatment options for serious infections, increased the burden of disease, and increased death rates due to treatment failure and requires a coordinated global response for antimicrobial resistance surveillance. This looming health threat has restimulated interest in the development of new antimicrobial therapies, has demanded the need for better patient care, and has facilitated heightened governance over stewardship practices.
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Jeanvoine A, Bouxom H, Leroy J, Gbaguidi-Haore H, Bertrand X, Slekovec C. Resistance to third-generation cephalosporins in Escherichia coli in the French community: The times they are a-changin'? Int J Antimicrob Agents 2020; 55:105909. [DOI: 10.1016/j.ijantimicag.2020.105909] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2019] [Revised: 01/17/2020] [Accepted: 01/18/2020] [Indexed: 10/25/2022]
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Silveira MC, Rocha-de-Souza CM, Albano RM, de Oliveira Santos IC, Carvalho-Assef APD. Exploring the success of Brazilian endemic clone Pseudomonas aeruginosa ST277 and its association with the CRISPR-Cas system type I-C. BMC Genomics 2020; 21:255. [PMID: 32293244 PMCID: PMC7092672 DOI: 10.1186/s12864-020-6650-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Accepted: 03/04/2020] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND The Brazilian endemic clone Pseudomonas aeruginosa ST277 carries important antibiotic resistance determinants, highlighting the gene coding for SPM-1 carbapenemase. However, the resistance and persistence of this clone is apparently restricted to the Brazilian territory. To understand the differences between Brazilian strains from those isolated in other countries, we performed a phylogenetic analysis of 47 P. aeruginosa ST277 genomes as well as analyzed the virulence and resistance gene profiles. Furthermore, we evaluated the distribution of genomic islands and assessed in detail the characteristics of the CRISPR-Cas immunity system in these isolates. RESULTS The Brazilian genomes presented a typical set of resistance and virulence determinants, genomic islands and a high frequency of the CRISPR-Cas system type I-C. Even though the ST277 genomes are closely related, the phylogenetic analysis showed that the Brazilian strains share a great number of exclusively SNPs when compared to other ST277 genomes. We also observed a standard CRISPR spacers content for P. aeruginosa ST277, confirming a strong link between sequence type and spacer acquisition. Most CRISPR spacer targets were phage sequences. CONCLUSIONS Based on our findings, P. aeruginosa ST277 strains circulating in Brazil characteristically acquired In163 and PAGI-25, which can distinguish them from strains that do not accumulate resistance mechanisms and can be found on the Asian, European and North American continents. The distinctive genetic elements accumulated in Brazilian samples can contribute to the resistance, pathogenicity and transmission success that characterize the ST277 in this country.
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Affiliation(s)
- Melise Chaves Silveira
- Laboratório de Pesquisa em Infecção Hospitalar, Oswaldo Cruz Institute, Fiocruz, Avenida Brasil 4365, Manguinhos, Rio de Janeiro, Rio de Janeiro, 21040-360, Brazil
| | - Cláudio Marcos Rocha-de-Souza
- Laboratório de Pesquisa em Infecção Hospitalar, Oswaldo Cruz Institute, Fiocruz, Avenida Brasil 4365, Manguinhos, Rio de Janeiro, Rio de Janeiro, 21040-360, Brazil
| | - Rodolpho Mattos Albano
- Departamento de Bioquímica, Universidade do Estado do Rio de Janeiro, Boulevard Vinte e Oito de Setembro, 87, fundos, andar 4, Vila Isabel, Rio de Janeiro, Rio de Janeiro, 20551-030, Brazil
| | - Ivson Cassiano de Oliveira Santos
- Laboratório de Pesquisa em Infecção Hospitalar, Oswaldo Cruz Institute, Fiocruz, Avenida Brasil 4365, Manguinhos, Rio de Janeiro, Rio de Janeiro, 21040-360, Brazil
| | - Ana Paula D'Alincourt Carvalho-Assef
- Laboratório de Pesquisa em Infecção Hospitalar, Oswaldo Cruz Institute, Fiocruz, Avenida Brasil 4365, Manguinhos, Rio de Janeiro, Rio de Janeiro, 21040-360, Brazil.
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93
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Secondary in-hospital epidemiological investigation after an outbreak of Pseudomonas aeruginosa ST357. J Infect Chemother 2020; 26:257-265. [DOI: 10.1016/j.jiac.2019.09.014] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Revised: 09/04/2019] [Accepted: 09/24/2019] [Indexed: 12/27/2022]
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94
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Cabral MP, Correia A, Vilanova M, Gärtner F, Moscoso M, García P, Vallejo JA, Pérez A, Francisco-Tomé M, Fuentes-Valverde V, Bou G. A live auxotrophic vaccine confers mucosal immunity and protection against lethal pneumonia caused by Pseudomonas aeruginosa. PLoS Pathog 2020; 16:e1008311. [PMID: 32040500 PMCID: PMC7034913 DOI: 10.1371/journal.ppat.1008311] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Revised: 02/21/2020] [Accepted: 01/06/2020] [Indexed: 12/28/2022] Open
Abstract
Pseudomonas aeruginosa is one of the leading causes of nosocomial pneumonia and its associated mortality. Moreover, extensively drug-resistant high-risk clones are globally widespread, presenting a major challenge to the healthcare systems. Despite this, no vaccine is available against this high-concerning pathogen. Here we tested immunogenicity and protective efficacy of an experimental live vaccine against P. aeruginosa pneumonia, consisting of an auxotrophic strain which lacks the key enzyme involved in D-glutamate biosynthesis, a structural component of the bacterial cell wall. As the amounts of free D-glutamate in vivo are trace substances in most cases, blockage of the cell wall synthesis occurs, compromising the growth of this strain, but not its immunogenic properties. Indeed, when delivered intranasally, this vaccine stimulated production of systemic and mucosal antibodies, induced effector memory, central memory and IL-17A-producing CD4+ T cells, and recruited neutrophils and mononuclear phagocytes into the airway mucosa. A significant improvement in mice survival after lung infection caused by ExoU-producing PAO1 and PA14 strains was observed. Nearly one third of the mice infected with the XDR high-risk clone ST235 were also protected. These findings highlight the potential of this vaccine for the control of acute pneumonia caused by this bacterial pathogen. Pseudomonas aeruginosa is an opportunistic bacterium and one of the most common causes of healthcare-associated diseases, including acute pneumonia, causing high mortality within immunocompromised hosts. Most of these infections are strikingly difficult to treat using conventional antibiotic therapies, since this microorganism displays high intrinsic resistance to a wide range of antibiotics. Moreover, to date, no vaccine is available for prevention. Here we used a mutated bacterial strain, which is unable to replicate in vivo and to cause disease, as a live vaccine against acute pneumonia caused by this pathogen. When applied intranasally, this vaccine induced immunity both at local and distant body sites, activating immune cells which were recruited into the airway mucosa. This evoked immune response reduced the number of non-surviving mice after infection with two cytotoxic P. aeruginosa strains causing acute lung infection. Some protection was also observed against an internationally disseminated cytotoxic strain. These data indicate that this is a promising vaccine candidate against P. aeruginosa-pneumonia.
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Affiliation(s)
- Maria P. Cabral
- Department of Microbiology, University Hospital A Coruña (CHUAC)–Biomedical Research Institute A Coruña (INIBIC), A Coruña, Spain
| | - Alexandra Correia
- i3S –Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- IBMC–Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal
- Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Porto, Portugal
| | - Manuel Vilanova
- i3S –Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- IBMC–Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal
- Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Porto, Portugal
| | - Fátima Gärtner
- i3S –Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Porto, Portugal
- IPATIMUP—Institute of Molecular Pathology and Immunology, University of Porto, Porto, Portugal
| | - Miriam Moscoso
- Department of Microbiology, University Hospital A Coruña (CHUAC)–Biomedical Research Institute A Coruña (INIBIC), A Coruña, Spain
| | - Patricia García
- Department of Microbiology, University Hospital A Coruña (CHUAC)–Biomedical Research Institute A Coruña (INIBIC), A Coruña, Spain
| | - Juan A. Vallejo
- Department of Microbiology, University Hospital A Coruña (CHUAC)–Biomedical Research Institute A Coruña (INIBIC), A Coruña, Spain
| | - Astrid Pérez
- Department of Microbiology, University Hospital A Coruña (CHUAC)–Biomedical Research Institute A Coruña (INIBIC), A Coruña, Spain
| | - Mónica Francisco-Tomé
- Department of Microbiology, Galicia Sur Health Research Institute (IISGS), Vigo, Spain
| | - Víctor Fuentes-Valverde
- Department of Microbiology, University Hospital A Coruña (CHUAC)–Biomedical Research Institute A Coruña (INIBIC), A Coruña, Spain
| | - Germán Bou
- Department of Microbiology, University Hospital A Coruña (CHUAC)–Biomedical Research Institute A Coruña (INIBIC), A Coruña, Spain
- * E-mail:
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95
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Integrated Genome-Wide Analysis of an Isogenic Pair of Pseudomonas aeruginosa Clinical Isolates with Differential Antimicrobial Resistance to Ceftolozane/Tazobactam, Ceftazidime/Avibactam, and Piperacillin/Tazobactam. Int J Mol Sci 2020; 21:ijms21031026. [PMID: 32033143 PMCID: PMC7037351 DOI: 10.3390/ijms21031026] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Revised: 01/27/2020] [Accepted: 02/02/2020] [Indexed: 01/10/2023] Open
Abstract
Multidrug-resistant (MDR) Pseudomonas aeruginosa is one of the main causes of morbidity and mortality in hospitalized patients and the leading cause of nosocomial infections. We investigated, here, two MDR P. aeruginosa clinical isolates from a hospitalized patient with differential antimicrobial resistance to ceftazidime/avibactam (CZA), ceftolozane/tazobactam (C/T), and piperacillin/tazobactam (P/T). Their assembled complete genomes revealed they belonged to ST235, a widespread MDR clone; and were isogenic with only a single nucleotide variant, causing G183D mutation in AmpC β-lactamase, responsible for a phenotypic change from susceptible to resistant to CZA and C/T. Further epigenomic profiling uncovered two conserved DNA methylation motifs targeted by two distinct putative methyltransferase-containing restriction-modification systems, respectively; more intriguingly, there was a significant difference between the paired isolates in the pattern of genomic DNA methylation and modifications. Moreover, genome-wide gene expression profiling demonstrated the inheritable genomic methylation and modification induced 14 genes being differentially regulated, of which only toxR (downregulated), a regulatory transcription factor, had its promoter region differentially methylate and modified. Since highly expressed opdQ encodes an OprD porin family protein, therefore, we proposed an epigenetic regulation of opdQ expression pertinent to the phenotypic change of P. aeruginosa from resistant to susceptible to P/T. The disclosed epigenetic mechanism controlling phenotypic antimicrobial resistance deserves further experimental investigation.
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96
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Voigt AM, Zacharias N, Timm C, Wasser F, Sib E, Skutlarek D, Parcina M, Schmithausen RM, Schwartz T, Hembach N, Tiehm A, Stange C, Engelhart S, Bierbaum G, Kistemann T, Exner M, Faerber HA, Schreiber C. Association between antibiotic residues, antibiotic resistant bacteria and antibiotic resistance genes in anthropogenic wastewater - An evaluation of clinical influences. CHEMOSPHERE 2020; 241:125032. [PMID: 31622887 DOI: 10.1016/j.chemosphere.2019.125032] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Revised: 09/12/2019] [Accepted: 09/30/2019] [Indexed: 06/10/2023]
Abstract
The high use of antibiotics in human and veterinary medicine has led to a wide spread of antibiotics and antimicrobial resistance into the environment. In recent years, various studies have shown that antibiotic residues, resistant bacteria and resistance genes, occur in aquatic environments and that clinical wastewater seems to be a hot spot for the environmental spread of antibiotic resistance. Here a representative statistical analysis of various sampling points is presented, containing different proportions of clinically influenced wastewater. The statistical analysis contains the calculation of the odds ratios for any combination of antibiotics with resistant bacteria or resistance genes, respectively. The results were screened for an increased probability of detecting resistant bacteria, or resistance genes, with the simultaneous presence of antibiotic residues. Positive associated sets were then compared, with regards to the detected median concentration, at the investigated sampling points. All results show that the sampling points with the highest proportion of clinical wastewater always form a distinct cluster concerning resistance. The results shown in this study lead to the assumption that ciprofloxacin is a good indicator of the presence of multidrug resistant P. aeruginosa and extended spectrum β-lactamase (ESBL)-producing Klebsiella spec., Enterobacter spec. and Citrobacter spec., as it positively relates with both parameters. Furthermore, a precise relationship between carbapenemase genes and meropenem, regarding the respective sampling sites, could be obtained. These results highlight the role of clinical wastewater for the dissemination and development of multidrug resistance.
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Affiliation(s)
- A M Voigt
- Institute for Hygiene and Public Health, University Hospital Bonn, Medical Faculty University of Bonn, Venusberg-Campus 1, Building 63, 53127, Bonn, Germany.
| | - N Zacharias
- Institute for Hygiene and Public Health, University Hospital Bonn, Medical Faculty University of Bonn, Venusberg-Campus 1, Building 63, 53127, Bonn, Germany
| | - C Timm
- Institute for Hygiene and Public Health, University Hospital Bonn, Medical Faculty University of Bonn, Venusberg-Campus 1, Building 63, 53127, Bonn, Germany
| | - F Wasser
- Institute for Hygiene and Public Health, University Hospital Bonn, Medical Faculty University of Bonn, Venusberg-Campus 1, Building 63, 53127, Bonn, Germany
| | - E Sib
- Institute for Hygiene and Public Health, University Hospital Bonn, Medical Faculty University of Bonn, Venusberg-Campus 1, Building 63, 53127, Bonn, Germany
| | - D Skutlarek
- Institute for Hygiene and Public Health, University Hospital Bonn, Medical Faculty University of Bonn, Venusberg-Campus 1, Building 63, 53127, Bonn, Germany
| | - M Parcina
- Institute of Immunology, Medical Microbiology and Parasitology, University Hospital Bonn, Medical Faculty University of Bonn, Venusberg-Campus 1, Building 63, 53127, Bonn, Germany
| | - R M Schmithausen
- Institute for Hygiene and Public Health, University Hospital Bonn, Medical Faculty University of Bonn, Venusberg-Campus 1, Building 63, 53127, Bonn, Germany
| | - T Schwartz
- Karlsruhe Institute of Technology (KIT), Institute of Functional Interfaces (IFG), Microbiology/Molecular Biology Department, Hermann-von-Helmholtz Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - N Hembach
- Karlsruhe Institute of Technology (KIT), Institute of Functional Interfaces (IFG), Microbiology/Molecular Biology Department, Hermann-von-Helmholtz Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - A Tiehm
- DVGW-Technologiezentrum Wasser (TZW), Karlsruher Straße 84, 76139, Karlsruhe, Germany
| | - C Stange
- DVGW-Technologiezentrum Wasser (TZW), Karlsruher Straße 84, 76139, Karlsruhe, Germany
| | - S Engelhart
- Institute for Hygiene and Public Health, University Hospital Bonn, Medical Faculty University of Bonn, Venusberg-Campus 1, Building 63, 53127, Bonn, Germany
| | - G Bierbaum
- Institute of Immunology, Medical Microbiology and Parasitology, University Hospital Bonn, Medical Faculty University of Bonn, Venusberg-Campus 1, Building 63, 53127, Bonn, Germany
| | - T Kistemann
- Institute for Hygiene and Public Health, University Hospital Bonn, Medical Faculty University of Bonn, Venusberg-Campus 1, Building 63, 53127, Bonn, Germany
| | - M Exner
- Institute for Hygiene and Public Health, University Hospital Bonn, Medical Faculty University of Bonn, Venusberg-Campus 1, Building 63, 53127, Bonn, Germany
| | - H A Faerber
- Institute for Hygiene and Public Health, University Hospital Bonn, Medical Faculty University of Bonn, Venusberg-Campus 1, Building 63, 53127, Bonn, Germany
| | - C Schreiber
- Institute for Hygiene and Public Health, University Hospital Bonn, Medical Faculty University of Bonn, Venusberg-Campus 1, Building 63, 53127, Bonn, Germany
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97
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Whole-Genome Sequences of Two NDM-1-Producing Pseudomonas aeruginosa Strains Isolated in a Clinical Setting in Albania in 2018. Microbiol Resour Announc 2020; 9:9/1/e01291-19. [PMID: 31896642 PMCID: PMC6940294 DOI: 10.1128/mra.01291-19] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Isolation of metallo-β-lactamase-producing, carbapenem-resistant, Pseudomonas aeruginosa strains is increasingly being documented worldwide; their presence constitutes a public health threat. Here, we report draft genome sequences of two New Delhi metallo-β-lactamase-1-producing, multidrug-resistant, P. aeruginosa strains of sequence type 235 that were isolated from the surgical wound of two patients hospitalized in the same ward.
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98
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Pathogenic characteristics of Pseudomonas aeruginosa bacteraemia isolates in a high-endemicity setting for ST175 and ST235 high-risk clones. Eur J Clin Microbiol Infect Dis 2019; 39:671-678. [PMID: 31823150 DOI: 10.1007/s10096-019-03780-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Accepted: 11/27/2019] [Indexed: 12/22/2022]
Abstract
Multidrug-resistant (MDR) Pseudomonas aeruginosa represents a major clinical concern. The interplay between antimicrobial resistance and virulence of P. aeruginosa was investigated in in vitro and in vivo studies. Thirty-eight well-characterized (21 MDR and 17 non-MDR) P. aeruginosa strains from patients with bacteraemia were analysed. Resistance phenotype, carbapenemase production, clonal relatedness, type III secretion system genotype, O-antigen serotype, cytotoxicity (ability to lyse cells) on A549 cells, and virulence (lethality in nematodes) in a Caenorhabditis elegans model were investigated. MDR strains showed lower cytotoxicity (35.4 ± 21.30% vs. 45.0 ± 18.78 %; P = 0.044) and virulence (66.7% vs. 100%; P = 0.011) than non-MDR strains. However, the pathogenicity of MDR high-risk clones varied broadly, with ST235 and ST175 clones being the most and least cytotoxic (51.8 ± 10.59% vs. 11.0 ± 1.25%; P < 0.0001) and virulent ([100% vs. 73.1; P = 0.075] and [0% vs. 93.9%; P < 0.0001], respectively). The pathogenicity of the ST235 clone was similar to that of non-MDR strains, and its ability to lyse cells and high virulence were related with the exoU-positive genotype. Furthermore, the O11 serotype was more frequent among the ST235 clone and exoU-positive genotype strains and was also essential for the pathogenicity of P. aeruginosa. Our data suggest that the pathogenicity of MDR high-risk clones is the result not only of the resistance phenotype but also of the virulence genotype. These findings have implications for the clinical management of patients and infection control programmes.
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99
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High-Risk International Clones of Carbapenem-Nonsusceptible Pseudomonas aeruginosa Endemic to Indonesian Intensive Care Units: Impact of a Multifaceted Infection Control Intervention Analyzed at the Genomic Level. mBio 2019; 10:mBio.02384-19. [PMID: 31719179 PMCID: PMC6851282 DOI: 10.1128/mbio.02384-19] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
In low-to-middle-income countries such as Indonesia, work in intensive care units (ICUs) can be hampered by lack of resources. Conducting large epidemiological studies in such settings using genomic tools is rather challenging. Still, we were able to systematically study the transmissions of carbapenem-nonsusceptible strains of P. aeruginosa (CNPA) within and between ICUs, before and after an infection control intervention. Our data show the importance of the broad dissemination of the internationally recognized CNPA clones, the relevance of environmental reservoirs, and the mixed effects of the implemented intervention; it led to a profound change in the clonal make-up of CNPA, but it did not reduce the patients’ risk of CNPA acquisitions. Thus, CNPA epidemiology in Indonesian ICUs is part of a global expansion of multiple CNPA clones that remains difficult to control by infection prevention measures. Infection control effectiveness evaluations require detailed epidemiological and microbiological data. We analyzed the genomic profiles of carbapenem-nonsusceptible Pseudomonas aeruginosa (CNPA) strains collected from two intensive care units (ICUs) in the national referral hospital in Jakarta, Indonesia, where a multifaceted infection control intervention was applied. We used clinical data combined with whole-genome sequencing (WGS) of systematically collected CNPA to infer the transmission dynamics of CNPA strains and to characterize their resistome. We found that the number of CNPA transmissions and acquisitions by patients was highly variable over time but that, overall, the rates were not significantly reduced by the intervention. Environmental sources were involved in these transmissions and acquisitions. Four high-risk international CNPA clones (ST235, ST823, ST375, and ST446) dominated, but the distribution of these clones changed significantly after the intervention was implemented. Using resistome analysis, carbapenem resistance was explained by the presence of various carbapenemase-encoding genes (blaGES-5, blaVIM-2-8, and blaIMP-1-7-43) and by mutations within the porin OprD. Our results reveal for the first time the dynamics of P. aeruginosa antimicrobial resistance (AMR) profiles in Indonesia and additionally show the utility of WGS in combination with clinical data to evaluate the impact of an infection control intervention. (This study has been registered at www.trialregister.nl under registration no. NTR5541).
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100
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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] [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.
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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 ()
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