1
|
Moretti M, Vanstokstraeten R, Crombé F, Barbé K, Wybo I, Allard SD, Jonckheer J, De Geyter D. Five-year VIM-producing Pseudomonas aeruginosa outbreak in four Belgian ICUs, an investigation report (2019-2023). Am J Infect Control 2024:S0196-6553(24)00689-8. [PMID: 39218401 DOI: 10.1016/j.ajic.2024.08.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2024] [Revised: 08/25/2024] [Accepted: 08/25/2024] [Indexed: 09/04/2024]
Abstract
BACKGROUND Verona integron-encoded metallo-β-lactamase-producing Pseudomonas aeruginosa (VIM-PA) outbreaks are frequently linked to contaminated sink-drains in the intensive care unit (ICU). This study aims to investigate a VIM-PA outbreak occurring at 4 ICUs in a Belgian university center. METHODS Between 01/01/2019 and 30/07/2023, data were retrospectively retrieved. Whole-genome sequencing of VIM-PA was carried out for available isolates and the core genome multilocus sequencing typing (cgMLST) was used to confirm clonality. New case incidence was estimated by analyzing the weekly data of at-risk and VIM-PA-colonized patients, fitting a regression model. RESULTS Fifty-one patients were colonized, among them, 32 (63%) were infected by VIM-PA, which contributed to 7 deaths. The outbreak investigation showed that 19 (47%) of the examined sink-drains grew at least once a VIM-PA. Two major clusters were observed by cgMLST: ST111 (59 clones with 40 clinical isolates), and ST17 (8 clones with 6 clinical isolates). The estimated incidence rate of new cases was significantly higher in one unit. CONCLUSIONS A 5-year prolonged outbreak at the UZ Brussel ICUs was caused by only 2 VIM-PA clones, both linked to sink-drains, with minimal mutations occurring throughout the years. Statistical modeling found different incidence rates between units. Tailored interventions were hence prioritized.
Collapse
Affiliation(s)
- Marco Moretti
- Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), Department of Internal Medicine and Infectious Diseases, Brussels, Belgium.
| | - Robin Vanstokstraeten
- Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), Department of Microbiology and Infection Control, Brussels, Belgium
| | - Florence Crombé
- Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), Department of Microbiology and Infection Control, Brussels, Belgium
| | - Kurt Barbé
- Vrije Universiteit Brussel (VUB), Department of Statistic: Support for Quantitative and Qualitative Research (SQUARE), Brussels, Belgium
| | - Ingrid Wybo
- Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), Department of Microbiology and Infection Control, Brussels, Belgium
| | - Sabine D Allard
- Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), Department of Internal Medicine and Infectious Diseases, Brussels, Belgium
| | - Joop Jonckheer
- Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), Department of Intensive Care Medicine, Brussels, Belgium
| | - Deborah De Geyter
- Vrije Universiteit Brussel (VUB), Department of Statistic: Support for Quantitative and Qualitative Research (SQUARE), Brussels, Belgium
| |
Collapse
|
2
|
Rath A, Kieninger B, Hahn J, Edinger M, Holler E, Kratzer A, Fritsch J, Eichner A, Caplunik-Pratsch A, Schneider-Brachert W. Retrospective genome-oriented analysis reveals low transmission rate of multidrug-resistant Pseudomonas aeruginosa from contaminated toilets at a bone marrow transplant unit. J Hosp Infect 2024; 150:96-104. [PMID: 38830540 DOI: 10.1016/j.jhin.2024.05.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Revised: 05/17/2024] [Accepted: 05/28/2024] [Indexed: 06/05/2024]
Abstract
BACKGROUND Prevention of toilet-to-patient transmission of multidrug-resistant Pseudomonas aeruginosa (MDR PA) poses management-related challenges at many bone marrow transplant units (BMTUs). AIM To conduct a longitudinal retrospective analysis of the toilet-to-patient transmission rate for MDR PA under existing infection control (IC) measures at a BMTU with persistent MDR PA toilet colonization. METHODS The local IC bundle comprised: (1) patient education regarding IC; (2) routine patient screening; (3) toilet flushing volume of 9 L; (4) bromination of toilet water tanks, and (5) toilet decontamination using hydrogen peroxide. Toilet water was sampled periodically between 2016 and 2021 (minimum every three months: 26 intervals). Upon MDR PA detection, disinfection and re-sampling were repeated until ≤3 cfu/100 mL was reached. Whole-genome sequencing (WGS) was performed retrospectively on all available MDR PA isolates (90 out of 117 positive environmental samples, 10 out of 14 patients, including nine nosocomial). FINDINGS WGS of patient isolates identified six sequence types (STs), with ST235/CT1352/FIM-1 and ST309/CT3049/no-carbapenemase being predominant (three isolates each). Environmental sampling consistently identified MDR PA ST235 (65.5% ST235/CT1352/FIM-1), showing low genetic diversity (difference of ≤29 alleles by core-genome multi-locus sequence typing (cgMLST)). This indicates that direct toilet-to-patient transmission was infrequent although MDR PA was widespread (detection on 79 occasions, detection in every toilet). Only three MDR PA patient isolates can be attributed to the ST235/CT1352/FIM-1 toilet MRD PA population over six years. CONCLUSION Stringent targeted toilet disinfection can reduce the potential risk for MDR PA acquisition by patients.
Collapse
Affiliation(s)
- A Rath
- Department of Infection Prevention and Infectious Diseases, University Hospital Regensburg, Regensburg, Germany.
| | - B Kieninger
- Department of Infection Prevention and Infectious Diseases, University Hospital Regensburg, Regensburg, Germany
| | - J Hahn
- Department of Internal Medicine III, Haematology and Oncology, University Hospital Regensburg, Regensburg, Germany
| | - M Edinger
- Department of Internal Medicine III, Haematology and Oncology, University Hospital Regensburg, Regensburg, Germany
| | - E Holler
- Department of Internal Medicine III, Haematology and Oncology, University Hospital Regensburg, Regensburg, Germany
| | - A Kratzer
- Hospital Pharmacy, University Hospital Regensburg, Regensburg, Germany
| | - J Fritsch
- Department of Infection Prevention and Infectious Diseases, University Hospital Regensburg, Regensburg, Germany
| | - A Eichner
- Department of Infection Prevention and Infectious Diseases, University Hospital Regensburg, Regensburg, Germany
| | - A Caplunik-Pratsch
- Department of Infection Prevention and Infectious Diseases, University Hospital Regensburg, Regensburg, Germany
| | - W Schneider-Brachert
- Department of Infection Prevention and Infectious Diseases, University Hospital Regensburg, Regensburg, Germany
| |
Collapse
|
3
|
Volling C, Mataseje L, Graña-Miraglia L, Hu X, Anceva-Sami S, Coleman BL, Downing M, Hota S, Jamal AJ, Johnstone J, Katz K, Leis JA, Li A, Mahesh V, Melano R, Muller M, Nayani S, Patel S, Paterson A, Pejkovska M, Ricciuto D, Sultana A, Vikulova T, Zhong Z, McGeer A, Guttman DS, Mulvey MR. Epidemiology of healthcare-associated Pseudomonas aeruginosa in intensive care units: are sink drains to blame? J Hosp Infect 2024; 148:77-86. [PMID: 38554807 DOI: 10.1016/j.jhin.2024.03.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 02/23/2024] [Accepted: 03/04/2024] [Indexed: 04/02/2024]
Abstract
BACKGROUND Pseudomonas aeruginosa (PA) is a common cause of healthcare-associated infection (PA-HAI) in the intensive care unit (ICU). AIM To describe the epidemiology of PA-HAI in ICUs in Ontario, Canada, and to identify episodes of sink-to-patient PA transmission. METHODS This was a prospective cohort study of patients in six ICUs from 2018 to 2019, with retrieval of PA clinical isolates, and PA-screening of antimicrobial-resistant organism surveillance rectal swabs, and of sink drain, air, and faucet samples. All PA isolates underwent whole-genome sequencing. PA-HAI was defined using US National Healthcare Safety Network criteria. ICU-acquired PA was defined as PA isolated from specimens obtained ≥48 h after ICU admission in those with prior negative rectal swabs. Sink-to-patient PA transmission was defined as ICU-acquired PA with close genomic relationship to isolate(s) previously recovered from sinks in a room/bedspace occupied 3-14 days prior to collection date of the relevant patient specimen. FINDINGS Over ten months, 72 PA-HAIs occurred among 60/4263 admissions. The rate of PA-HAI was 2.40 per 1000 patient-ICU-days; higher in patients who were PA-colonized on admission. PA-HAI was associated with longer stay (median: 26 vs 3 days uninfected; P < 0.001) and contributed to death in 22/60 cases (36.7%). Fifty-eight admissions with ICU-acquired PA were identified, contributing 35/72 (48.6%) PA-HAIs. Four patients with five PA-HAIs (6.9%) had closely related isolates previously recovered from their room/bedspace sinks. CONCLUSION Nearly half of PA causing HAI appeared to be acquired in ICUs, and 7% of PA-HAIs were associated with sink-to-patient transmission. Sinks may be an under-recognized reservoir for HAIs.
Collapse
Affiliation(s)
- C Volling
- Department of Microbiology, Sinai Health, Toronto, Canada.
| | - L Mataseje
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Canada
| | - L Graña-Miraglia
- Department of Cell & Systems Biology, University of Toronto, Toronto, Canada
| | - X Hu
- Department of Cell & Systems Biology, University of Toronto, Toronto, Canada
| | - S Anceva-Sami
- Department of Microbiology, Sinai Health, Toronto, Canada
| | - B L Coleman
- Department of Microbiology, Sinai Health, Toronto, Canada
| | | | - S Hota
- Department of Medicine, University Health Network, Toronto, Canada
| | - A J Jamal
- Department of Microbiology, Sinai Health, Toronto, Canada
| | - J Johnstone
- Department of Microbiology, Sinai Health, Toronto, Canada
| | - K Katz
- Department of Medicine, North York General Hospital, Toronto, Canada
| | - J A Leis
- Department of Medicine, Sunnybrook Health Sciences Centre, Toronto, Canada
| | - A Li
- Department of Microbiology, Sinai Health, Toronto, Canada
| | - V Mahesh
- Department of Microbiology, Sinai Health, Toronto, Canada
| | - R Melano
- Pan American Health Organization, Washington, USA
| | - M Muller
- Department of Medicine, Unity Health Toronto, Toronto, Canada
| | - S Nayani
- Department of Microbiology, Sinai Health, Toronto, Canada
| | - S Patel
- Public Health Ontario Laboratory, Toronto, Canada
| | - A Paterson
- Department of Microbiology, Sinai Health, Toronto, Canada
| | - M Pejkovska
- Department of Microbiology, Sinai Health, Toronto, Canada
| | - D Ricciuto
- Department of Medicine, Lakeridge Health, Oshawa, Canada
| | - A Sultana
- Department of Microbiology, Sinai Health, Toronto, Canada
| | - T Vikulova
- Department of Microbiology, Sinai Health, Toronto, Canada
| | - Z Zhong
- Department of Microbiology, Sinai Health, Toronto, Canada
| | - A McGeer
- Department of Microbiology, Sinai Health, Toronto, Canada
| | - D S Guttman
- Department of Cell & Systems Biology, University of Toronto, Toronto, Canada; Centre for the Analysis of Genome Evolution and Function, Department of Cell and Systems Biology, University of Toronto, Toronto, Canada
| | - M R Mulvey
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Canada
| |
Collapse
|
4
|
Ahmadi N, Salimizand H, Zomorodi AR, Abbas JE, Ramazanzadeh R, Haghi F, Hassanzadeh S, Jahantigh M, Shahin M. Genomic diversity of β-lactamase producing Pseudomonas aeruginosa in Iran; the impact of global high-risk clones. Ann Clin Microbiol Antimicrob 2024; 23:5. [PMID: 38218982 PMCID: PMC10790247 DOI: 10.1186/s12941-024-00668-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Accepted: 01/04/2024] [Indexed: 01/15/2024] Open
Abstract
BACKGROUND Hospital-acquired infections caused by multidrug-resistant Pseudomonas aeruginosa incline hospital stay and costs of treatment that resulted in an increased mortality rate. The frequency of P. aeruginosa high-risk clones producing carbapenemases was investigated in our clinical samples. METHODS In this cross-sectional study, 155 non-repetitive P. aeruginosa isolates were included from different medical centers of Iran. Antibiotic susceptibility testing was determined, and the presence of β-lactamases were sought by phenotypic and genotypic methods. The clonal relationship of all isolates was investigated, and multi-locus sequence typing (MLST) was used for finding the sequence types of carbapenemase-producers. RESULTS The agent with highest percent susceptibility rate was recorded for colistin (94.9%). MOX and FOX were found both as low as 1.95% (3/155). The most frequent narrow spectrum β-lactamase was SHV with 7.7% (12/155) followed by PER, OXA-1, and TEM with the frequency of 7.1% (11/155), 3.2% (5/155), and 1.3% (2/155), respectively. Carbapenemases were detected in 28 isolates (18%). The most frequent carbapenemase was IMP with 9% (14/155) followed by NDM, 8.4% (13/155). OXA-48 and VIM were also detected both per one isolate (0.65%). MLST of carbapenem resistant P. aeruginosa isolates revealed that ST244, ST664, ST235, and ST357 were spread in subjected clinical settings. REP-PCR uncovered high genomic diversity in our clinical setting. CONCLUSION Clonal proliferation of ST235 strain plays a key role in the propagation of MDR pattern in P. aeruginosa. Our data showed that high-risk clones has distributed in Iran, and programs are required to limit spreading of these clones.
Collapse
Affiliation(s)
- Nazila Ahmadi
- Student Research Committee, Kurdistan University of Medical Sciences, Sanandaj, Iran
| | - Himen Salimizand
- Cellular and Molecular Research Center, Research Institute for Health Development, Kurdistan University of Medical Sciences, Sanandaj, Iran.
| | - Abolfazl Rafati Zomorodi
- Department of Bacteriology and Virology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Jalileh Ebn Abbas
- Department of Microbiology, Faculty of Medicine, Kurdistan University of Medical Sciences, Sanandaj, Iran
| | - Rashid Ramazanzadeh
- Department of Microbiology, Faculty of Medicine, Ardabil University of Medical Sciences, Ardabil, Iran
| | - Fakhri Haghi
- Department of Microbiology, Zanjan University of Medical Sciences, Zanjan, Iran
| | - Sepideh Hassanzadeh
- Department of Microbiology and Virology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mojdeh Jahantigh
- Department of Microbiology, School of Medicine, Zahedan University of Medical Sciences, Zahedan, Iran
| | - Mojtaba Shahin
- Department of Medical Laboratory Sciences, Faculty of Medical Sciences, Arak branch, Islamic Azad University, Arak, Iran
| |
Collapse
|
5
|
Bourdin T, Benoit MÈ, Bédard E, Prévost M, Quach C, Déziel E, Constant P. High-Throughput Short Sequence Typing Schemes for Pseudomonas aeruginosa and Stenotrophomonas maltophilia Pure Culture and Environmental DNA. Microorganisms 2023; 12:48. [PMID: 38257875 PMCID: PMC10819370 DOI: 10.3390/microorganisms12010048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Revised: 12/22/2023] [Accepted: 12/25/2023] [Indexed: 01/24/2024] Open
Abstract
Molecular typing techniques are utilized to determine genetic similarities between bacterial isolates. However, the use of environmental DNA profiling to assess epidemiologic links between patients and their environment has not been fully explored. This work reports the development and validation of two high-throughput short sequence typing (HiSST) schemes targeting the opportunistic pathogens Pseudomonas aeruginosa and Stenotrophomonas maltophilia, along with a modified SM2I selective medium for the specific isolation of S. maltophilia. These HiSST schemes are based on four discriminative loci for each species and demonstrate high discriminating power, comparable to pairwise whole-genome comparisons. Each scheme includes species-specific PCR primers for precise differentiation from closely related taxa, without the need for upstream culture-dependent methods. For example, the primers targeting the bvgS locus make it possible to distinguish P. aeruginosa from the very closely related Pseudomonas paraeruginosa sp. nov. The selected loci included in the schemes are adapted to massive parallel amplicon sequencing technology. An R-based script implemented in the DADA2 pipeline was assembled to facilitate HiSST analyses for efficient and accurate genotyping of P. aeruginosa and S. maltophilia. We demonstrate the performance of both schemes through in silico validations, assessments against reference culture collections, and a case study involving environmental samples.
Collapse
Affiliation(s)
- Thibault Bourdin
- Centre Armand-Frappier Santé Biotechnologie, Institut National de la Recherche Scientifique, 531 Boulevard des Prairies, Laval, QC H7V 1B7, Canada;
| | - Marie-Ève Benoit
- CHU Sainte-Justine Research Center, Montréal, QC H3T 1C5, Canada; (M.-È.B.); (C.Q.)
| | - Emilie Bédard
- Department of Civil Engineering, Polytechnique Montréal, Montréal, QC H3T 1J4, Canada; (E.B.); (M.P.)
| | - Michèle Prévost
- Department of Civil Engineering, Polytechnique Montréal, Montréal, QC H3T 1J4, Canada; (E.B.); (M.P.)
| | - Caroline Quach
- CHU Sainte-Justine Research Center, Montréal, QC H3T 1C5, Canada; (M.-È.B.); (C.Q.)
| | - Eric Déziel
- Centre Armand-Frappier Santé Biotechnologie, Institut National de la Recherche Scientifique, 531 Boulevard des Prairies, Laval, QC H7V 1B7, Canada;
| | - Philippe Constant
- Centre Armand-Frappier Santé Biotechnologie, Institut National de la Recherche Scientifique, 531 Boulevard des Prairies, Laval, QC H7V 1B7, Canada;
| |
Collapse
|
6
|
Benigno V, Carraro N, Sarton-Lohéac G, Romano-Bertrand S, Blanc DS, van der Meer JR. Diversity and evolution of an abundant ICE clc family of integrative and conjugative elements in Pseudomonas aeruginosa. mSphere 2023; 8:e0051723. [PMID: 37902330 PMCID: PMC10732049 DOI: 10.1128/msphere.00517-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Accepted: 09/24/2023] [Indexed: 10/31/2023] Open
Abstract
IMPORTANCE Microbial populations swiftly adapt to changing environments through horizontal gene transfer. While the mechanisms of gene transfer are well known, the impact of environmental conditions on the selection of transferred gene functions remains less clear. We investigated ICEs, specifically the ICEclc-type, in Pseudomonas aeruginosa clinical isolates. Our findings revealed co-evolution between ICEs and their hosts, with ICE transfers occurring within strains. Gene functions carried by ICEs are positively selected, including potential virulence factors and heavy metal resistance. Comparison to publicly available P. aeruginosa genomes unveiled widespread antibiotic-resistance determinants within ICEclc clades. Thus, the ubiquitous ICEclc family significantly contributes to P. aeruginosa's adaptation and fitness in diverse environments.
Collapse
Affiliation(s)
- Valentina Benigno
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Nicolas Carraro
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Garance Sarton-Lohéac
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Sara Romano-Bertrand
- Hydrosciences Montpellier, IRD, CNRS, University of Montpellier, Hospital Hygiene and Infection Control Team, University Hospital of Montpellier, Montpellier, France
| | - Dominique S. Blanc
- Prevention and Infection Control Unit, Infectious Diseases Service, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | | |
Collapse
|
7
|
Mazzolini R, Rodríguez-Arce I, Fernández-Barat L, Piñero-Lambea C, Garrido V, Rebollada-Merino A, Motos A, Torres A, Grilló MJ, Serrano L, Lluch-Senar M. Engineered live bacteria suppress Pseudomonas aeruginosa infection in mouse lung and dissolve endotracheal-tube biofilms. Nat Biotechnol 2023; 41:1089-1098. [PMID: 36658340 PMCID: PMC10421741 DOI: 10.1038/s41587-022-01584-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Accepted: 10/21/2022] [Indexed: 01/21/2023]
Abstract
Engineered live bacteria could provide a new modality for treating lung infections, a major cause of mortality worldwide. In the present study, we engineered a genome-reduced human lung bacterium, Mycoplasma pneumoniae, to treat ventilator-associated pneumonia, a disease with high hospital mortality when associated with Pseudomonas aeruginosa biofilms. After validating the biosafety of an attenuated M. pneumoniae chassis in mice, we introduced four transgenes into the chromosome by transposition to implement bactericidal and biofilm degradation activities. We show that this engineered strain has high efficacy against an acute P. aeruginosa lung infection in a mouse model. In addition, we demonstrated that the engineered strain could dissolve biofilms formed in endotracheal tubes of patients with ventilator-associated pneumonia and be combined with antibiotics targeting the peptidoglycan layer to increase efficacy against Gram-positive and Gram-negative bacteria. We expect our M. pneumoniae-engineered strain to be able to treat biofilm-associated infections in the respiratory tract.
Collapse
Affiliation(s)
- Rocco Mazzolini
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain
- Pulmobiotics Ltd, Barcelona, Spain
| | - Irene Rodríguez-Arce
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain
- Institute of Agrobiotechnology, CSIC-Navarra Government, Navarra, Spain
| | - Laia Fernández-Barat
- Cellex Laboratory, CibeRes, Institut d'Investigacions Biomèdiques August Pi i Sunyer, University of Barcelona, Barcelona, Spain
- Department of Pneumology, Thorax Institute, Hospital Clinic of Barcelona, SpainICREA, Barcelona, Spain
| | - Carlos Piñero-Lambea
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain
- Pulmobiotics Ltd, Barcelona, Spain
| | - Victoria Garrido
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain
- Institute of Agrobiotechnology, CSIC-Navarra Government, Navarra, Spain
| | - Agustín Rebollada-Merino
- VISAVET Health Surveillance Centre, Complutense University of Madrid, Madrid, Spain
- Department of Internal Medicine and Animal Surgery, Faculty of Veterinary Medicine, Complutense University of Madrid, Madrid, Spain
| | - Anna Motos
- Cellex Laboratory, CibeRes, Institut d'Investigacions Biomèdiques August Pi i Sunyer, University of Barcelona, Barcelona, Spain
- Department of Pneumology, Thorax Institute, Hospital Clinic of Barcelona, SpainICREA, Barcelona, Spain
| | - Antoni Torres
- Cellex Laboratory, CibeRes, Institut d'Investigacions Biomèdiques August Pi i Sunyer, University of Barcelona, Barcelona, Spain
- Department of Pneumology, Thorax Institute, Hospital Clinic of Barcelona, SpainICREA, Barcelona, Spain
| | | | - Luis Serrano
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain.
- Universitat Pompeu Fabra, Barcelona, Spain.
- ICREA, Barcelona, Spain.
| | - Maria Lluch-Senar
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain.
- Pulmobiotics Ltd, Barcelona, Spain.
- Basic Sciences Department, Faculty of Medicine and Health Sciences, Universitat Internacional de Catalunya, Sant Cugat del Vallès, Spain.
| |
Collapse
|
8
|
Patil S, Chen X, Dong S, Mai H, Lopes BS, Liu S, Wen F. Resistance genomics and molecular epidemiology of high-risk clones of ESBL-producing Pseudomonas aeruginosa in young children. Front Cell Infect Microbiol 2023; 13:1168096. [PMID: 37293207 PMCID: PMC10244630 DOI: 10.3389/fcimb.2023.1168096] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 04/24/2023] [Indexed: 06/10/2023] Open
Abstract
Introduction The emergence of multidrug-resistant Pseudomonas aeruginosa poses a global threat, but the distribution and resistance profiling are unclear, especially in young children. Infections due to P. aeruginosa are common, associated with high mortality, and increasingly β-lactam drug resistant. Methods We studied the molecular epidemiology and antibiotic resistance mechanisms in 294 clinicalisolates of P. aeruginosa from a pediatric hospital in China. Non-duplicate isolates were recovered from clinical cases and were identified using an API-20 kit followed by antimicrobial susceptibility testing using the VITEK®2 compact system (BioMerieux, France) and also by broth dilution method. In addition, a double-disc synergy test for the ESBL/E-test for MBL was performed. The presence of beta-lactamases, plasmid types, and sequence types was determined by PCR and sequencing. Results Fifty-six percent (n = 164) of the isolates were resistant to piperacillin-tazobactam, followed by cefepime (40%; n = 117), ceftazidime (39%; n = 115), imipenem (36%; n = 106), meropenem (33%; n = 97), and ciprofloxacin (32%; n = 94). Forty-two percent (n = 126) of the isolates were positive for ESBL according to the double-disc synergy test. The blaCTX-M-15 cephalosporinase was observed in 32% (n = 40/126), while 26% (n = 33/126) werepositive for blaNDM-1 carbapenemase. Aminoglycoside resistance gene aac(3)IIIawas observed in 16% (n = 20/126), and glycylcyclines resistance gene tet(A) was observed in 12% (n = 15/126) of the isolates. A total of 23 sequence types were detected, including ST1963 (12%; n = 16), followed by ST381 (11%; n = 14), ST234 (10%; n = 13), ST145 (58%; n = 10), ST304 (57%; n = 9), ST663 (5%; n = 7), and a novel strain. In ESBL-producing P. aeruginosa, 12 different Incompatibility groups (Inc) were observed, the most common being IncFI, IncFIS, and IncA/C. The MOBP was the most common plasmid type, followed by MOBH, MOBF, and MOBQ. Discussion Our data suggest that the spread of antibiotic resistance is likely due toclonal spread and dissemination of different clinical strains of P. aeruginosa harbouring different plasmids. This is a growing threat in hospitals particularly in young children which needs robust prevention strategies.
Collapse
Affiliation(s)
- Sandip Patil
- Department of Haematology and Oncology, Shenzhen Children’s Hospital, Shenzhen, China
- Paediatric Research Institute, Shenzhen Children’s Hospital, Shenzhen, China
| | - Xiaowen Chen
- Paediatric Research Institute, Shenzhen Children’s Hospital, Shenzhen, China
| | - Shaowei Dong
- Paediatric Research Institute, Shenzhen Children’s Hospital, Shenzhen, China
| | - Huirong Mai
- Department of Haematology and Oncology, Shenzhen Children’s Hospital, Shenzhen, China
| | - Bruno Silvester Lopes
- School of Health and Life Sciences, Teesside University, Middlesbrough, United Kingdom
- National Horizons Centre, Teesside University, Darlington, United Kingdom
| | - Sixi Liu
- Department of Haematology and Oncology, Shenzhen Children’s Hospital, Shenzhen, China
| | - Feiqiu Wen
- Department of Haematology and Oncology, Shenzhen Children’s Hospital, Shenzhen, China
- Paediatric Research Institute, Shenzhen Children’s Hospital, Shenzhen, China
| |
Collapse
|
9
|
Soonthornsit J, Pimwaraluck K, Kongmuang N, Pratya P, Phumthanakorn N. Molecular epidemiology of antimicrobial-resistant Pseudomonas aeruginosa in a veterinary teaching hospital environment. Vet Res Commun 2023; 47:73-86. [PMID: 35449493 DOI: 10.1007/s11259-022-09929-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 04/17/2022] [Indexed: 01/27/2023]
Abstract
This study aimed to investigate sites for colonization and molecular epidemiology of antimicrobial-resistant Pseudomonas aeruginosa in a veterinary teaching hospital. Bacterial specimens from surface and liquid samples (n = 165) located in five rooms were collected three times every 2 months, and antimicrobial susceptibility was subsequently determined by minimum inhibitory concentrations. The genomes of resistant strains were further analyzed using whole-genome sequencing. Among 19 P. aeruginosa isolates (11.5%, 19/165), sinks were the most frequent colonization site (53.3%), followed by rubber tubes (44.4%), and anesthesia-breathing circuit (33.3%). The highest resistance to gentamicin (47.4%), followed by piperacillin/tazobactam (36.8%), levofloxacin (36.8%), and ciprofloxacin (36.8%), was observed from 19 P. aeruginosa isolates, of which 10 were resistant strains. Of these 10 antimicrobial-resistant isolates, five were multidrug-resistant isolates, including carbapenem. From the multilocus sequence typing (MLST) analysis, five sequence types (STs), including a high-risk clone of human ST235 (n = 3), and ST244 (n = 3), ST606 (n = 2), ST485 (n = 1), and ST3405 (n = 1) were identified in resistant strains. Multiresistant genes were identified consistent with STs, except ST235. The MLST approach and single nucleotide polymorphism analysis revealed a link between resistant strains from ward rooms and those from examination, wound care, and operating rooms. The improvement of routine cleaning, especially of sink environments, and the continued monitoring of antimicrobial resistance of P. aeruginosa in veterinary hospitals are necessary to prevent the spread of resistant clones and ensure infection control.
Collapse
Affiliation(s)
- Jeerawat Soonthornsit
- Department of Pre-Clinic and Applied Animal Science, Faculty of Veterinary Science, Mahidol University, Salaya Campus, 999 Phutthamonthon Sai 4 Road Salaya, Phutthamonthon Nakhon Pathom, Thailand
| | | | | | - Ploy Pratya
- Faculty of Veterinary Science, Mahidol University, Nakhon Pathom, Thailand
| | - Nathita Phumthanakorn
- Department of Pre-Clinic and Applied Animal Science, Faculty of Veterinary Science, Mahidol University, Salaya Campus, 999 Phutthamonthon Sai 4 Road Salaya, Phutthamonthon Nakhon Pathom, Thailand.
| |
Collapse
|
10
|
Cameron DR, Pitton M, Oberhaensli S, Schlegel K, Prod’hom G, Blanc DS, Jakob SM, Que YA. Parallel Evolution of Pseudomonas aeruginosa during a Prolonged ICU-Infection Outbreak. Microbiol Spectr 2022; 10:e0274322. [PMID: 36342287 PMCID: PMC9769503 DOI: 10.1128/spectrum.02743-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 10/19/2022] [Indexed: 11/09/2022] Open
Abstract
Most knowledge about Pseudomonas aeruginosa pathoadaptation is derived from studies on airway colonization in cystic fibrosis; little is known about adaptation in acute settings. P. aeruginosa frequently affects burned patients and the burn wound niche has distinct properties that likely influence pathoadaptation. This study aimed to genetically and phenotypically characterize P. aeruginosa isolates collected during an outbreak of infection in a burn intensive care unit (ICU). Sequencing reads from 58 isolates of ST1076 P. aeruginosa taken from 23 patients were independently mapped to a complete reference genome for the lineage (H25338); genetic differences were identified and were used to define the population structure. Comparative genomic analysis at single-nucleotide resolution identified pathoadaptive genes that evolved multiple, independent mutations. Three key phenotypic assays (growth performance, motility, carbapenem resistance) were performed to complement the genetic analysis for 47 unique isolates. Population structure for the ST1076 lineage revealed 11 evolutionary sublineages. Fifteen pathoadaptive genes evolved mutations in at least two sublineages. The most prominent functional classes affected were transcription/two-component regulatory systems, and chemotaxis/motility and attachment. The most frequently mutated gene was oprD, which codes for outer membrane porin involved in uptake of carbapenems. Reduced growth performance and motility were found to be adaptive phenotypic traits, as was high level of carbapenem resistance, which correlated with higher carbapenem consumption during the outbreak. Multiple prominent linages evolved each of the three traits in parallel providing evidence that they afford a fitness advantage for P. aeruginosa in the context of human burn infection. IMPORTANCE Pseudomonas aeruginosa is a Gram-negative pathogen causing infections in acutely burned patients. The precise mechanisms required for the establishment of infection in the burn setting, and adaptive traits underpinning prolonged outbreaks are not known. We have assessed genotypic data from 58 independent P. aeruginosa isolates taken from a single lineage that was responsible for an outbreak of infection in a burn ICU that lasted for almost 2.5 years and affected 23 patients. We identified a core set of 15 genes that we predict to control pathoadaptive traits in the burn infection based on the frequency with which independent mutations evolved. We combined the genotypic data with phenotypic data (growth performance, motility, antibiotic resistance) and clinical data (antibiotic consumption) to identify adaptive phenotypes that emerged in parallel. High-level carbapenem resistance evolved rapidly, and frequently, in response to high clinical demand for this antibiotic class during the outbreak.
Collapse
Affiliation(s)
- David R. Cameron
- Department of Intensive Care Medicine, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Melissa Pitton
- Department of Intensive Care Medicine, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
- Graduate School for Cellular and Biomedical Sciences (GCB), University of Bern, Bern, Switzerland
| | - Simone Oberhaensli
- Interfaculty Bioinformatics Unit and SIB Swiss Institute of Bioinformatics, University of Bern, Bern, Switzerland
| | - Katja Schlegel
- Institute of Psychology, University of Bern, Bern, Switzerland
| | - Guy Prod’hom
- Institute of Microbiology, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Dominique S. Blanc
- Service of Hospital Preventive Medicine, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Stephan M. Jakob
- Department of Intensive Care Medicine, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Yok-Ai Que
- Department of Intensive Care Medicine, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| |
Collapse
|
11
|
A High-Throughput Short Sequence Typing Scheme for Serratia marcescens Pure Culture and Environmental DNA. Appl Environ Microbiol 2021; 87:e0139921. [PMID: 34586910 DOI: 10.1128/aem.01399-21] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Molecular typing methods are used to characterize the relatedness between bacterial isolates involved in infections. These approaches rely mostly on discrete loci or whole-genome sequencing (WGS) analyses of pure cultures. On the other hand, their application to environmental DNA profiling to evaluate epidemiological relatedness among patients and environments has received less attention. We developed a specific, high-throughput short sequence typing (HiSST) method for the opportunistic human pathogen Serratia marcescens. Genes displaying the highest polymorphism were retrieved from the core genome of 60 S. marcescens strains. Bioinformatics analyses showed that use of only three loci (within bssA, gabR, and dhaM) distinguished strains with a high level of efficiency. This HiSST scheme was applied to an epidemiological survey of S. marcescens in a neonatal intensive care unit (NICU). In a first case study, a strain responsible for an outbreak in the NICU was found in a sink drain of this unit, by using HiSST scheme and confirmed by WGS. The HiSST scheme was also applied to environmental DNA extracted from sink-environment samples. Diversity of S. marcescens was modest, with 11, 6, and 4 different sequence types (ST) of gabR, bssA, and dhaM loci among 19 sink drains, respectively. Epidemiological relationships among sinks were inferred on the basis of pairwise comparisons of ST profiles. Further research aimed at relating ST distribution patterns to environmental features encompassing sink location, utilization, and microbial diversity is needed to improve the surveillance and management of opportunistic pathogens. IMPORTANCE Serratia marcescens is an important opportunistic human pathogen, often multidrug resistant and involved in outbreaks of nosocomial infections in neonatal intensive care units. Here, we propose a quick and user-friendly method to select the best typing scheme for nosocomial outbreaks in relating environmental and clinical sources. This method, named high-throughput short sequence typing (HiSST), allows to distinguish strains and to explore the diversity profile of nonculturable S. marcescens. The application of HiSST profile analysis for environmental DNA offers new possibilities to track opportunistic pathogens, identify their origin, and relate their distribution pattern with environmental features encompassing sink location, utilization, and microbial diversity. Adaptation of the method to other opportunistic pathogens is expected to improve knowledge regarding their ecology, which is of significant interest for epidemiological risk assessment and elaborate outbreak mitigation strategies.
Collapse
|
12
|
Catho G, Martischang R, Boroli F, Chraïti MN, Martin Y, Koyluk Tomsuk Z, Renzi G, Schrenzel J, Pugin J, Nordmann P, Blanc DS, Harbarth S. Outbreak of Pseudomonas aeruginosa producing VIM carbapenemase in an intensive care unit and its termination by implementation of waterless patient care. Crit Care 2021; 25:301. [PMID: 34412676 PMCID: PMC8376114 DOI: 10.1186/s13054-021-03726-y] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 08/09/2021] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Long-term outbreaks of multidrug-resistant Gram-negative bacilli related to hospital-building water systems have been described. However, successful mitigation strategies have rarely been reported. In particular, environmental disinfection or replacement of contaminated equipment usually failed to eradicate environmental sources of Pseudomonas aeruginosa. METHODS We report the investigation and termination of an outbreak of P. aeruginosa producing VIM carbapenemase (PA-VIM) in the adult intensive care unit (ICU) of a Swiss tertiary care hospital with active case finding, environmental sampling and whole genome sequencing (WGS) of patient and environmental strains. We also describe the implemented control strategies and their effectiveness on eradication of the environmental reservoir. RESULTS Between April 2018 and September 2020, 21 patients became either infected or colonized with a PA-VIM strain. For 16 of them, an acquisition in the ICU was suspected. Among 131 environmental samples collected in the ICU, 13 grew PA-VIM in sink traps and drains. WGS confirmed the epidemiological link between clinical and environmental strains and the monoclonal pattern of the outbreak. After removing sinks from patient rooms and implementation of waterless patient care, no new acquisition was detected in the ICU within 8 months after the intervention. DISCUSSION Implementation of waterless patient care with removal of the sinks in patient rooms was successful for termination of a PA-VIM ICU outbreak linked to multiple environmental water sources. WGS provides highly discriminatory accuracy to investigate environment-related outbreaks.
Collapse
Affiliation(s)
- Gaud Catho
- Infection Control Program, WHO Collaborating Center for Patient Safety, Faculty of Medicine, Geneva University Hospitals, Rue Gabrielle Perret-Gentil, 4, CH-1205, Geneva, Switzerland.
| | - R Martischang
- Infection Control Program, WHO Collaborating Center for Patient Safety, Faculty of Medicine, Geneva University Hospitals, Rue Gabrielle Perret-Gentil, 4, CH-1205, Geneva, Switzerland
| | - F Boroli
- Division of Critical Care, Faculty of Medicine, Geneva University Hospitals, Geneva, Switzerland
| | - M N Chraïti
- Infection Control Program, WHO Collaborating Center for Patient Safety, Faculty of Medicine, Geneva University Hospitals, Rue Gabrielle Perret-Gentil, 4, CH-1205, Geneva, Switzerland
| | - Y Martin
- Infection Control Program, WHO Collaborating Center for Patient Safety, Faculty of Medicine, Geneva University Hospitals, Rue Gabrielle Perret-Gentil, 4, CH-1205, Geneva, Switzerland
| | - Z Koyluk Tomsuk
- Division of Critical Care, Faculty of Medicine, Geneva University Hospitals, Geneva, Switzerland
| | - G Renzi
- Bacteriology Laboratory, Faculty of Medicine, Geneva University Hospitals, Geneva, Switzerland
| | - J Schrenzel
- Bacteriology Laboratory, Faculty of Medicine, Geneva University Hospitals, Geneva, Switzerland
| | - J Pugin
- Division of Critical Care, Faculty of Medicine, Geneva University Hospitals, Geneva, Switzerland
| | - P Nordmann
- Emerging Antibiotic Resistance Unit, Medical and Molecular Microbiology, Department of Medicine, Faculty of Science and Medicine, University of Fribourg, Fribourg, Switzerland
- Swiss National Reference Center for Emerging Antibiotic Resistance, Fribourg, Switzerland
| | - D S Blanc
- Swiss National Reference Center for Emerging Antibiotic Resistance, Fribourg, Switzerland
- Service of Hospital Preventive Medicine, Lausanne University Hospital, University of Lausanne, Lausanne, Switzerland
| | - S Harbarth
- Infection Control Program, WHO Collaborating Center for Patient Safety, Faculty of Medicine, Geneva University Hospitals, Rue Gabrielle Perret-Gentil, 4, CH-1205, Geneva, Switzerland
| |
Collapse
|
13
|
Establishment and Evaluation of a Core Genome Multilocus Sequence Typing Scheme for Whole-Genome Sequence-Based Typing of Pseudomonas aeruginosa. J Clin Microbiol 2021; 59:JCM.01987-20. [PMID: 33328175 DOI: 10.1128/jcm.01987-20] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 12/07/2020] [Indexed: 01/04/2023] Open
Abstract
The environmental bacterium Pseudomonas aeruginosa, particularly multidrug-resistant clones, is often associated with nosocomial infections and outbreaks. Today, core genome multilocus sequence typing (cgMLST) is frequently applied to delineate sporadic cases from nosocomial transmissions. However, until recently, no cgMLST scheme for a standardized typing of P. aeruginosa was available. To establish a novel cgMLST scheme for P. aeruginosa, we initially determined the breadth of the P. aeruginosa population based on MLST data with a Bayesian approach (BAPS). Using genomic data of representative isolates for the whole population and all 12 serogroups, we extracted target genes and further refined them using a random data set of 1,000 P. aeruginosa genomes. Subsequently, we investigated reproducibility and discriminatory ability with repeatedly sequenced isolates and isolates from well-defined outbreak scenarios, respectively, and compared clustering applying two recently published cgMLST schemes. BAPS generated seven P. aeruginosa groups. To cover these and all serogroups, 15 reference strains were used to determine genes common in all strains. After refinement with the data set of 1,000 genomes, the cgMLST scheme consisted of 3,867 target genes, which are representative of the P. aeruginosa population and highly reproducible using biological replicates. We finally evaluated the scheme by reanalyzing two published outbreaks where the authors used single-nucleotide polymorphism (SNP) typing. In both cases, cgMLST was concordant with the previous SNP results and the results of the two other cgMLST schemes. In conclusion, the highly reproducible novel P. aeruginosa cgMLST scheme facilitates outbreak investigations due to the publicly available cgMLST nomenclature.
Collapse
|
14
|
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.
Collapse
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
| |
Collapse
|
15
|
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.
Collapse
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
| |
Collapse
|
16
|
Dylus D, Pillonel T, Opota O, Wüthrich D, Seth-Smith HMB, Egli A, Leo S, Lazarevic V, Schrenzel J, Laurent S, Bertelli C, Blanc DS, Neuenschwander S, Ramette A, Falquet L, Imkamp F, Keller PM, Kahles A, Oberhaensli S, Barbié V, Dessimoz C, Greub G, Lebrand A. NGS-Based S. aureus Typing and Outbreak Analysis in Clinical Microbiology Laboratories: Lessons Learned From a Swiss-Wide Proficiency Test. Front Microbiol 2020; 11:591093. [PMID: 33424794 PMCID: PMC7793906 DOI: 10.3389/fmicb.2020.591093] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 10/19/2020] [Indexed: 12/31/2022] Open
Abstract
Whole genome sequencing (WGS) enables high resolution typing of bacteria up to the single nucleotide polymorphism (SNP) level. WGS is used in clinical microbiology laboratories for infection control, molecular surveillance and outbreak analyses. Given the large palette of WGS reagents and bioinformatics tools, the Swiss clinical bacteriology community decided to conduct a ring trial (RT) to foster harmonization of NGS-based bacterial typing. The RT aimed at assessing methicillin-susceptible Staphylococcus aureus strain relatedness from WGS and epidemiological data. The RT was designed to disentangle the variability arising from differences in sample preparation, SNP calling and phylogenetic methods. Nine laboratories participated. The resulting phylogenetic tree and cluster identification were highly reproducible across the laboratories. Cluster interpretation was, however, more laboratory dependent, suggesting that an increased sharing of expertise across laboratories would contribute to further harmonization of practices. More detailed bioinformatic analyses unveiled that while similar clusters were found across laboratories, these were actually based on different sets of SNPs, differentially retained after sample preparation and SNP calling procedures. Despite this, the observed number of SNP differences between pairs of strains, an important criterion to determine strain relatedness given epidemiological information, was similar across pipelines for closely related strains when restricting SNP calls to a common core genome defined by S. aureus cgMLST schema. The lessons learned from this pilot study will serve the implementation of larger-scale RT, as a mean to have regular external quality assessments for laboratories performing WGS analyses in a clinical setting.
Collapse
Affiliation(s)
- David Dylus
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland.,Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland.,SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Trestan Pillonel
- Institute of Microbiology, Lausanne University Hospital, University of Lausanne, Lausanne, Switzerland
| | - Onya Opota
- Institute of Microbiology, Lausanne University Hospital, University of Lausanne, Lausanne, Switzerland
| | - Daniel Wüthrich
- Division of Clinical Bacteriology and Mycology, University Hospital of Basel, Basel, Switzerland.,Applied Microbiology Research, Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Helena M B Seth-Smith
- Division of Clinical Bacteriology and Mycology, University Hospital of Basel, Basel, Switzerland.,Applied Microbiology Research, Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Adrian Egli
- Division of Clinical Bacteriology and Mycology, University Hospital of Basel, Basel, Switzerland.,Applied Microbiology Research, Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Stefano Leo
- Bacteriology Laboratory, Division of Laboratory Medicine, Department of Genetics Laboratory Medicine and Pathology, Geneva University Hospitals, Geneva, Switzerland
| | - Vladimir Lazarevic
- Bacteriology Laboratory, Division of Laboratory Medicine, Department of Genetics Laboratory Medicine and Pathology, Geneva University Hospitals, Geneva, Switzerland
| | - Jacques Schrenzel
- Bacteriology Laboratory, Division of Laboratory Medicine, Department of Genetics Laboratory Medicine and Pathology, Geneva University Hospitals, Geneva, Switzerland
| | - Sacha Laurent
- Institute of Microbiology, Lausanne University Hospital, University of Lausanne, Lausanne, Switzerland
| | - Claire Bertelli
- Institute of Microbiology, Lausanne University Hospital, University of Lausanne, Lausanne, Switzerland
| | - Dominique S Blanc
- Service of Hospital Preventive Medicine, Lausanne University Hospital, University of Lausanne, Lausanne, Switzerland
| | | | - Alban Ramette
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Laurent Falquet
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland.,Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Frank Imkamp
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
| | - Peter M Keller
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
| | - Andre Kahles
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland.,Biomedical Informatics, Swiss Federal Institute of Technology (ETH Zürich), ETH Zürich, Zurich, Switzerland
| | - Simone Oberhaensli
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland.,Interfaculty Bioinformatics Unit, University of Bern, Bern, Switzerland
| | - Valérie Barbié
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Christophe Dessimoz
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland.,Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland.,SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland.,Department of Genetics, Evolution and Environment, University College London, London, United Kingdom.,Department of Computer Science, University College London, London, United Kingdom
| | - Gilbert Greub
- Institute of Microbiology, Lausanne University Hospital, University of Lausanne, Lausanne, Switzerland
| | - Aitana Lebrand
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| |
Collapse
|
17
|
Blanc DS, Magalhães B, Koenig I, Senn L, Grandbastien B. Comparison of Whole Genome (wg-) and Core Genome (cg-) MLST (BioNumerics TM) Versus SNP Variant Calling for Epidemiological Investigation of Pseudomonas aeruginosa. Front Microbiol 2020; 11:1729. [PMID: 32793169 PMCID: PMC7387498 DOI: 10.3389/fmicb.2020.01729] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Accepted: 07/02/2020] [Indexed: 12/29/2022] Open
Abstract
Whole genome sequencing (WGS) is increasingly used for epidemiological investigations of pathogens. While SNP variant calling is currently considered as the most suitable method, the choice of a representative reference genome and the isolate dependency of results limit standardization and affect resolution in an unknown manner. Whole or core genome Multi Locus Sequence Typing (wg-, cg-MLST) represents an attractive alternative. Here, we assess the accuracy of wg- and cg-MLST by comparing results of four Pseudomonas aeruginosa datasets for which epidemiological and genomic data were previously described. Three datasets included 155 isolates from three different sequence types (ST) of P. aeruginosa collected in our ICUs over a 5-year period. The fourth dataset consisted of 10 isolates from an investigation of P. aeruginosa contaminated hand soap. All isolates were previously analyzed by a core SNP approach. In this study, wg- and cg-MLST were performed in BioNumericsTM using a scheme developed by Applied-Maths. Correlation between SNP calling and wg- or cg-MLST results were evaluated by calculating linear regressions and their coefficient of correlations (R2) between the number of SNPs and the number of allele differences in pairwise comparison of isolates. The number of SNPs and allele difference between isolates with close epidemiological linkage varies between 0–26 and 0–13, respectively. When compared to core-SNP calling, a higher coefficient of correlation was obtained with cgMLST (R2 of 0.92–0.99) than with wgMLST (0.78–0.99). In one dataset, a putative homologous recombination of a large DNA fragment (202 loci) was identified among these isolates, affecting its phylogeny, but with no impact on the epidemiological analysis of outbreak isolates. In conclusion, we showed that the P. aeruginosa wgMLST scheme in BioNumericsTM is as discriminatory as the core-SNP calling approach and apparently useful for outbreak investigations. We also showed that epidemiological linked isolates showed less than 26 SNPs or 13 allele differences. These are important figures for the distinction between outbreak and non-outbreak isolates when interpreting WGS results. However, as P. aeruginosa is highly recombinant, a cgMLST approach is preferable and caution should be addressed to possible recombination of large DNA fragments.
Collapse
Affiliation(s)
- Dominique S Blanc
- Service of Hospital Preventive Medicine, Lausanne University Hospital, University of Lausanne, Lausanne, Switzerland
| | - Bárbara Magalhães
- Service of Hospital Preventive Medicine, Lausanne University Hospital, University of Lausanne, Lausanne, Switzerland
| | - Isabelle Koenig
- Service of Hospital Preventive Medicine, Lausanne University Hospital, University of Lausanne, Lausanne, Switzerland
| | - Laurence Senn
- Service of Hospital Preventive Medicine, Lausanne University Hospital, University of Lausanne, Lausanne, Switzerland
| | - Bruno Grandbastien
- Service of Hospital Preventive Medicine, Lausanne University Hospital, University of Lausanne, Lausanne, Switzerland
| |
Collapse
|