1
|
Abstract
PURPOSE OF REVIEW The coronavirus disease 2019 pandemic demonstrated broad utility of pathogen sequencing with rapid methodological progress alongside global distribution of sequencing infrastructure. This review considers implications for now moving clinical metagenomics into routine service, with respiratory metagenomics as the exemplar use-case. RECENT FINDINGS Respiratory metagenomic workflows have completed proof-of-concept, providing organism identification and many genotypic antimicrobial resistance determinants from clinical samples in <6 h. This enables rapid escalation or de-escalation of empiric therapy for patient benefit and reducing selection of antimicrobial resistance, with genomic-typing available in the same time-frame. Attention is now focussed on demonstrating clinical, health-economic, accreditation, and regulatory requirements. More fundamentally, pathogen sequencing challenges the traditional culture-orientated time frame of microbiology laboratories, which through automation and centralisation risks becoming increasingly separated from the clinical setting. It presents an alternative future where infection experts are brought together around a single genetic output in an acute timeframe, aligning the microbiology target operating model with the wider human genomic and digital strategy. SUMMARY Pathogen sequencing is a transformational proposition for microbiology laboratories and their infectious diseases, infection control, and public health partners. Healthcare systems that link output from routine clinical metagenomic sequencing, with pandemic and antimicrobial resistance surveillance, will create valuable tools for protecting their population against future infectious diseases threats.
Collapse
Affiliation(s)
- Jonathan D Edgeworth
- Department of Infectious Diseases, Guy's & St Thomas' NHS Foundation Trust & Department of Infectious Diseases, Kings College London, UK
| |
Collapse
|
2
|
Papanikolopoulou A, Maltezou HC, Stoupis A, Pangalis A, Kouroumpetsis C, Chronopoulou G, Kalofissoudis Y, Kostares E, Boufidou F, Karalexi M, Koumaki V, Pantazis N, Tsakris A, Kantzanou M. Ventilator-Associated Pneumonia, Multidrug-Resistant Bacteremia and Infection Control Interventions in an Intensive Care Unit: Analysis of Six-Year Time-Series Data. Antibiotics (Basel) 2022; 11:antibiotics11081128. [PMID: 36009998 PMCID: PMC9405435 DOI: 10.3390/antibiotics11081128] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 08/10/2022] [Accepted: 08/16/2022] [Indexed: 12/28/2022] Open
Abstract
Ventilator-associated pneumonia (VAP) occurs more than 48h after mechanical ventilation and is associated with a high mortality rate. The current hospital-based study aims to investigate the association between VAP rate, incidence of bacteremia from multidrug-resistant (MDR) pathogens, and infection control interventions in a single case mix ICU from 2013 to 2018. Methods: The following monthly indices were analyzed: (1) VAP rate; (2) use of hand hygiene disinfectants; (3) isolation rate of patients with MDR bacteria; and (4) incidence of bacteremia/1000 patient-days (total cases, total carbapenem-resistant cases, and carbapenem-resistant Acinetobacter baumannii, Pseudomonas aeruginosa, and Klebsiella pneumoniae cases separately). Results: Time trends of infection control interventions showed increased rates in isolation of patients with MDR pathogens (p <0.001) and consumption of hand disinfectant solutions (p =0.001). The last four years of the study an annual decrease of VAP rate by 35.12% (95% CI: −53.52 to −9.41; p =0.01) was recorded, which significantly correlated not only with reduced trauma and cardiothoracic surgery patients (IRR:2.49; 95% CI: 2.09−2.96; p <0.001), but also with increased isolation rate of patients with MDR pathogens (IRR: 0.52; 95% CI: 0.27−0.99; p = 0.048), and hand disinfectants use (IRR: 0.40; 95% CI: 0.18−0.89; p =0.024). Conclusions: Infection control interventions significantly contributed to the decrease of VAP rate. Constant infection control stewardship has a stable time-effect and guides evidence-based decisions.
Collapse
Affiliation(s)
| | - Helena C. Maltezou
- Directorate of Research, Studies and Documentation, National Public Health Organization, 15123 Athens, Greece
| | - Athina Stoupis
- Clinical Infectious Diseases Department, Athens Medical Center, 15125 Athens, Greece
| | - Anastasia Pangalis
- Biopathology Department Athens Medical Center, Marousi, 15125 Athens, Greece
| | | | | | - Yannis Kalofissoudis
- Quality Assurance Department, Athens Medical Center, Marousi, 15125 Athens, Greece
| | - Evangelos Kostares
- Department of Microbiology, School of Medicine, National and Kapodistrian University of Athens, 75 Mikras Asias Street, 11527 Athens, Greece
| | - Fotini Boufidou
- Neurochemistry and Biological Markers Unit, 1st Department of Neurology, School of Medicine, Eginition Hospital, National and Kapodistrian University of Athens, 11528 Athens, Greece
| | - Maria Karalexi
- Department of Microbiology, School of Medicine, National and Kapodistrian University of Athens, 75 Mikras Asias Street, 11527 Athens, Greece
| | - Vasiliki Koumaki
- Department of Microbiology, School of Medicine, National and Kapodistrian University of Athens, 75 Mikras Asias Street, 11527 Athens, Greece
| | - Nikos Pantazis
- Department of Hygiene, Epidemiology and Medical Statistics, Faculty of Medicine, School of Health Sciences, National and Kapodistrian University of Athens, 11527 Athens, Greece
| | - Athanasios Tsakris
- Department of Microbiology, School of Medicine, National and Kapodistrian University of Athens, 75 Mikras Asias Street, 11527 Athens, Greece
- Correspondence: ; Tel.: +30-210-7462011
| | - Maria Kantzanou
- Department of Microbiology, School of Medicine, National and Kapodistrian University of Athens, 75 Mikras Asias Street, 11527 Athens, Greece
| |
Collapse
|
3
|
Ceccato A, Dominedò C, Ferrer M, Martin-Loeches I, Barbeta E, Gabarrús A, Cillóniz C, Ranzani OT, De Pascale G, Nogas S, Di Giannatale P, Antonelli M, Torres A. Prediction of ventilator-associated pneumonia outcomes according to the early microbiological response: a retrospective observational study. Eur Respir J 2021; 59:13993003.00620-2021. [PMID: 34475230 DOI: 10.1183/13993003.00620-2021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 08/12/2021] [Indexed: 11/05/2022]
Abstract
Ventilator-associated pneumonia is a leading infectious cause of morbidity in critically ill patients; yet current guidelines offer no indications for follow-up cultures.We aimed to evaluate the role of follow-up cultures and microbiological response 3 days after diagnosing ventilator-associated pneumonia as predictors of short- and long-term outcomes.We performed a retrospective analysis of a cohort prospectively collected from 2004 to 2017. Ventilator-associated pneumonia was diagnosed based on clinical, radiographic, and microbiological criteria. For microbiological identification, a tracheobronchial aspirate was performed at diagnosis and repeated after 72 h. We defined three groups when comparing the two tracheobronchial aspirate results: persistence, superinfection, and eradication of causative pathogens.One-hundred-fifty-seven patients were enrolled in the study, among whom microbiological persistence, superinfection, and eradication was present in 67 (48%), 25 (16%), and 65 (41%), respectively, after 72hs. Those with superinfection had the highest mortalities in the intensive care unit (p=0.015) and at 90 days (p=0.036), while also having the fewest ventilation-free days (p=0.024). Multivariable analysis revealed shock at VAP diagnosis (odds ratios [OR] 3.43; 95% confidence interval [CI] 1.25 to 9.40), Staphylococcus aureus isolation at VAP diagnosis (OR 2.87; 95%CI 1.06 to 7.75), and hypothermia at VAP diagnosis (OR 0.67; 95%CI 0.48 to 0.95, per +1°C) to be associated with superinfection.Our retrospective analysis suggests that ventilator-associated pneumonia short-term and long-term outcomes may be associated with superinfection in follow-up cultures. Follow-up cultures may help guiding antibiotic therapy and its duration. Further prospective studies are necessary to verify our findings.
Collapse
Affiliation(s)
- Adrian Ceccato
- August Pi i Sunyer Biomedical Research Institute (IDIBAPS), University of Barcelona; Biomedical Research Networking Centres in Respiratory Diseases (CIBERES), Barcelona, Spain.,Intensive Care Unit, Hospital Universitari Sagrat Cor, Barcelona, Spain.,Equal Contribution
| | - Cristina Dominedò
- Department of Anesthesiology and Intensive Care Medicine, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy.,Università Cattolica del Sacro Cuore, Rome, Italy.,Equal Contribution
| | - Miquel Ferrer
- August Pi i Sunyer Biomedical Research Institute (IDIBAPS), University of Barcelona; Biomedical Research Networking Centres in Respiratory Diseases (CIBERES), Barcelona, Spain.,Department of Pneumology, Hospital Clinic of Barcelona, Barcelona, Spain
| | - Ignacio Martin-Loeches
- August Pi i Sunyer Biomedical Research Institute (IDIBAPS), University of Barcelona; Biomedical Research Networking Centres in Respiratory Diseases (CIBERES), Barcelona, Spain.,Department of Intensive Care Medicine, Multidisciplinary Intensive Care Research Organization (MICRO), St James's Hospital, Trinity College Dublin, Dublin, Ireland
| | - Enric Barbeta
- August Pi i Sunyer Biomedical Research Institute (IDIBAPS), University of Barcelona; Biomedical Research Networking Centres in Respiratory Diseases (CIBERES), Barcelona, Spain.,Intensive Care Unit, Hospital Universitari Sagrat Cor, Barcelona, Spain.,Department of Pneumology, Hospital Clinic of Barcelona, Barcelona, Spain
| | - Albert Gabarrús
- August Pi i Sunyer Biomedical Research Institute (IDIBAPS), University of Barcelona; Biomedical Research Networking Centres in Respiratory Diseases (CIBERES), Barcelona, Spain.,Department of Pneumology, Hospital Clinic of Barcelona, Barcelona, Spain
| | - Catia Cillóniz
- August Pi i Sunyer Biomedical Research Institute (IDIBAPS), University of Barcelona; Biomedical Research Networking Centres in Respiratory Diseases (CIBERES), Barcelona, Spain.,Department of Pneumology, Hospital Clinic of Barcelona, Barcelona, Spain
| | - Otavio T Ranzani
- Barcelona Institute for Global Health, ISGlobal, Barcelona, Spain.,Pulmonary Division, Heart Institute (InCor), Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de Sao Paulo, Sao Paulo, Brazil
| | - Gennaro De Pascale
- Department of Anesthesiology and Intensive Care Medicine, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy.,Università Cattolica del Sacro Cuore, Rome, Italy
| | - Stefano Nogas
- Department of Surgical Sciences and Integrated Diagnostics, University of Genoa, Ospedale Policlinico San Martino-IRCCS per l'Oncologia, Genoa, Italy
| | - Pierluigi Di Giannatale
- University of Chieti-Pescara 'Gabriele D'Annunzio', Hospital of Chieti 'SS. Annunziata', Chieti, Italy
| | - Massimo Antonelli
- Department of Anesthesiology and Intensive Care Medicine, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy.,Università Cattolica del Sacro Cuore, Rome, Italy
| | - Antoni Torres
- August Pi i Sunyer Biomedical Research Institute (IDIBAPS), University of Barcelona; Biomedical Research Networking Centres in Respiratory Diseases (CIBERES), Barcelona, Spain .,Department of Pneumology, Hospital Clinic of Barcelona, Barcelona, Spain
| |
Collapse
|
4
|
Vergara A, Moreno-Morales J, Roca I, Pitart C, Kostyanev T, Rodriguez-Baño J, Goossens H, Marco F, Vila J. A comparative study between real-time PCR and loop-mediated isothermal amplification to detect carbapenemase and/or ESBL genes in Enterobacteriaceae directly from bronchoalveolar lavage fluid samples. J Antimicrob Chemother 2021; 75:1453-1457. [PMID: 32073602 DOI: 10.1093/jac/dkaa031] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Revised: 01/13/2020] [Accepted: 01/16/2020] [Indexed: 12/23/2022] Open
Abstract
OBJECTIVES To evaluate and compare the efficacy of real-time PCR (Xpert Carba-R) and loop-mediated isothermal amplification (Eazyplex® SuperBug CRE) for detecting carbapenemase carriage in Enterobacteriaceae directly from bronchoalveolar lavage (BAL). METHODS Negative BAL samples were spiked with 21 well-characterized carbapenemase-producing Enterobacteriaceae strains to a final concentration of 102-104 cfu/mL. Xpert Carba-R (Cepheid, Sunnyvale, CA, USA), which detects five targets (blaKPC, blaNDM, blaVIM, blaOXA-48 and blaIMP-1), and the Eazyplex® SuperBug CRE system (Amplex-Diagnostics GmbH, Germany), which detects seven genes (blaKPC, blaNDM, blaVIM, blaOXA-48, blaOXA-181, blaCTXM-1 and blaCTXM-9), were evaluated for the detection of these genes directly from BAL samples. RESULTS Xpert Carba-R showed 100% agreement with carbapenemase characterization by PCR and sequencing for all final bacteria concentrations. Eazyplex® SuperBug CRE showed 100%, 80% and 27% agreement with PCR and sequencing when testing 104, 103 and 102 cfu/mL, respectively. False negative results for Eazyplex® SuperBug CRE matched the highest cycle threshold values for Xpert Carba-R. Hands-on time for both assays was about 15 min, but Eazyplex® SuperBug CRE results were available within 30 min, whereas Xpert Carba-R took around 50 min. CONCLUSIONS We here describe the successful use of two commercial diagnostic tests, Xpert Carba-R and Eazyplex® SuperBug CRE, to detect bacterial carbapenem resistance genes directly in lower respiratory tract samples. Our results could be used as proof-of-concept data for validation of these tests for this indication.
Collapse
Affiliation(s)
- A Vergara
- Department of Clinical Microbiology - CDB, Hospital Clínic, University of Barcelona, Barcelona, Spain
| | - J Moreno-Morales
- Institute for Global Health (ISGlobal), Hospital Clínic - Universitat de Barcelona, Barcelona, Spain
| | - I Roca
- Institute for Global Health (ISGlobal), Hospital Clínic - Universitat de Barcelona, Barcelona, Spain
| | - C Pitart
- Department of Clinical Microbiology - CDB, Hospital Clínic, University of Barcelona, Barcelona, Spain
| | - T Kostyanev
- Department of Medical Microbiology, Vaccine & Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
| | - J Rodriguez-Baño
- Unidad Clínica de Enfermedades Infecciosas, Microbiología y Medicina Preventiva, Hospital Universitario Virgen Macarena/Departamento de Medicina, Universidad de Sevilla/Instituto de Biomedicina de Sevilla (IBiS), Sevilla, Spain
| | - H Goossens
- Department of Medical Microbiology, Vaccine & Infectious Disease Institute, University of Antwerp, Antwerp, Belgium.,Laboratory of Medical Microbiology, University Hospital Antwerp, Antwerp, Belgium
| | - F Marco
- Department of Clinical Microbiology - CDB, Hospital Clínic, University of Barcelona, Barcelona, Spain.,Institute for Global Health (ISGlobal), Hospital Clínic - Universitat de Barcelona, Barcelona, Spain
| | - J Vila
- Department of Clinical Microbiology - CDB, Hospital Clínic, University of Barcelona, Barcelona, Spain.,Institute for Global Health (ISGlobal), Hospital Clínic - Universitat de Barcelona, Barcelona, Spain
| |
Collapse
|
5
|
Pérez-Granda MJ, Alonso B, Zavala R, Latorre MC, Hortal J, Samaniego R, Bouza E, Muñoz P, Guembe M. Selective digestive decontamination solution used as "lock therapy" prevents and eradicates bacterial biofilm in an in vitro bench-top model. Ann Clin Microbiol Antimicrob 2020; 19:44. [PMID: 32972419 PMCID: PMC7513905 DOI: 10.1186/s12941-020-00387-7] [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: 06/24/2020] [Accepted: 09/10/2020] [Indexed: 02/07/2023] Open
Abstract
Background Most preventing measures for reducing ventilator-associated pneumonia (VAP) are based mainly on the decolonization of the internal surface of the endotracheal tubes (ETTs). However, it has been demonstrated that bacterial biofilm can also be formed on the external surface of ETTs. Our objective was to test in vitro the efficacy of selective digestive decontamination solution (SDDs) onto ETT to prevent biofilm formation and eradicate preformed biofilms of three different microorganisms of VAP. Methods We used an in vitro model in which we applied, at the subglottic space of ETT, biofilms of either P. aeruginosa ATCC 15442, or E. coli ATCC 25922, or S. aureus ATCC 29213, and the SDDs at the same time (prophylaxis) or after 72 h of biofilm forming (treatment). ETT were incubated during 5 days with a regimen of 2 h-locks. ETT fragments were analyzed by sonication and confocal laser scanning microscopy to calculate the percentage reduction of cfu and viable cells, respectively. Results Median (IQR) percentage reduction of live cells and cfu/ml counts after treatment were, respectively, 53.2% (39.4%—64.1%) and 100% (100%–100.0%) for P. aeruginosa, and 67.9% (46.7%–78.7%) and 100% (100%–100.0%) for E. coli. S. aureus presented a complete eradication by both methods. After prophylaxis, there were absence of live cells and cfu/ml counts for all microorganisms. Conclusions SDDs used as “lock therapy” in the subglottic space is a promising prophylactic approach that could be used in combination with the oro-digestive decontamination procedure in the prevention of VAP.
Collapse
Affiliation(s)
- María Jesús Pérez-Granda
- Cardiac Surgery Postoperative Care Unit, Hospital General Universitario Gregorio Marañón, Madrid, 28007, Spain.,Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, 28009, Spain.,CIBER Enfermedades Respiratorias-CIBERES, CB06/06/0058), Madrid, Spain
| | - Beatriz Alonso
- Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, 28009, Spain. .,Department of Clinical Microbiology and Infectious Diseases, Hospital General Universitario Gregorio Marañón, Madrid, 28007, Spain. .,Servicio de Microbiología Clínica y Enfermedades Infecciosas, Instituto de Investigación Sanitaria Gregorio Marañón, Hospital General Universitario "Gregorio Marañón", C/. Dr. Esquerdo, 46, Madrid, 28007, Spain.
| | - Ricardo Zavala
- Biology Department, School of Biology, Universidad Complutense de Madrid, Madrid, 28040, Spain
| | - María Consuelo Latorre
- Biology Department, School of Biology, Universidad Complutense de Madrid, Madrid, 28040, Spain
| | - Javier Hortal
- Cardiac Surgery Postoperative Care Unit, Hospital General Universitario Gregorio Marañón, Madrid, 28007, Spain.,CIBER Enfermedades Respiratorias-CIBERES, CB06/06/0058), Madrid, Spain
| | - Rafael Samaniego
- Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, 28009, Spain.,Confocal Laser Scanning Microscopy Unit, Hospital General Universitario Gregorio Marañón, Madrid, 28007, Spain
| | - Emilio Bouza
- Medicine Department, School of Medicine, Universidad Complutense de Madrid, Madrid, 28040, Spain
| | - Patricia Muñoz
- Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, 28009, Spain.,CIBER Enfermedades Respiratorias-CIBERES, CB06/06/0058), Madrid, Spain.,Department of Clinical Microbiology and Infectious Diseases, Hospital General Universitario Gregorio Marañón, Madrid, 28007, Spain.,Medicine Department, School of Medicine, Universidad Complutense de Madrid, Madrid, 28040, Spain
| | - María Guembe
- Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, 28009, Spain. .,Department of Clinical Microbiology and Infectious Diseases, Hospital General Universitario Gregorio Marañón, Madrid, 28007, Spain. .,Servicio de Microbiología Clínica y Enfermedades Infecciosas, Instituto de Investigación Sanitaria Gregorio Marañón, Hospital General Universitario "Gregorio Marañón", C/. Dr. Esquerdo, 46, Madrid, 28007, Spain.
| |
Collapse
|
6
|
Cornejo-Juárez P, González-Oros I, Mota-Castañeda P, Vilar-Compte D, Volkow-Fernández P. Ventilator-associated pneumonia in patients with cancer: Impact of multidrug resistant bacteria. World J Crit Care Med 2020; 9:43-53. [PMID: 32844090 PMCID: PMC7416360 DOI: 10.5492/wjccm.v9.i3.43] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 05/22/2020] [Accepted: 06/14/2020] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Patients with cancer have several risk factors for developing respiratory failure requiring mechanical ventilation (MV). The emergence of multidrug resistant bacteria (MDRB) has become a public health problem, creating a new burden on medical care in hospitals, particularly for patients admitted to the intensive care unit (ICU).
AIM To describe risk factors for ventilator-acquired pneumonia (VAP) in patients with cancer and to evaluate the impact of MDRB.
METHODS A retrospective study was performed from January 2016 to December 2018 at a cancer referral center in Mexico City, which included all patients who were admitted to the ICU and required MV ≥ 48 h. They were classified as those who developed VAP versus those who did not; pathogens isolated, including MDRB. Clinical evolution at 60-d was assessed. Descriptive analysis was carried out; comparison was performed between VAP vs non-VAP and MDRB vs non-MDRB.
RESULTS Two hundred sixty-three patients were included in the study; mean age was 51.9 years; 52.1% were male; 68.4% had solid tumors. There were 32 episodes of VAP with a rate of 12.2%; 11.5 episodes/1000 ventilation-days. The most frequent bacteria isolated were the following: Klebsiella spp. [n = 9, four were Extended-Spectrum Beta-Lactamase (ESBL) producers, one was Carbapenem-resistant (CR)]; Escherichia coli (n = 5, one was ESBL), and Pseudomonas aeruginosa (n = 8, two were CR). One Methicillin-susceptible Staphylococcus aureus was identified. In multivariate analysis, the sole risk factor associated for VAP was length of ICU stay (OR = 1.1; 95%CI: 1.03-1.17; P = 0.003). Sixty-day mortality was 53% in VAP and 43% without VAP (P = 0.342). There was not higher mortality in those patients with MDRB.
CONCLUSION This study highlights the high percentage of Gram-negative bacteria, which allows the initiation of empiric antibiotic coverage for these pathogens. In this retrospective, single center, observational study, MDRB VAP was not directly linked to increased mortality at 60 days.
Collapse
Affiliation(s)
- Patricia Cornejo-Juárez
- Infectious Diseases Department, Instituto Nacional de Cancerología (INCan), Mexico City 14080, Mexico
| | - Ivan González-Oros
- Infectious Diseases Department, Instituto Nacional de Cancerología (INCan), Mexico City 14080, Mexico
| | - Paola Mota-Castañeda
- Infectious Diseases Department, Instituto Nacional de Cancerología (INCan), Mexico City 14080, Mexico
| | - Diana Vilar-Compte
- Infectious Diseases Department, Instituto Nacional de Cancerología (INCan), Mexico City 14080, Mexico
| | - Patricia Volkow-Fernández
- Infectious Diseases Department, Instituto Nacional de Cancerología (INCan), Mexico City 14080, Mexico
| |
Collapse
|
7
|
Cornejo-Juárez P, González-Oros I, Mota-Castañeda P, Vilar-Compte D, Volkow-Fernández P. Ventilator-associated pneumonia in patients with cancer: Impact of multidrug resistant bacteria. World J Crit Care Med 2020. [DOI: 10.5492/wjccm.v9.i3.0000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
|
8
|
Cai Y, Zhang W, Zhang R, Cui X, Fang J. Combined Use of Three Machine Learning Modeling Methods to Develop a Ten-Gene Signature for the Diagnosis of Ventilator-Associated Pneumonia. Med Sci Monit 2020; 26:e919035. [PMID: 32031163 PMCID: PMC7020762 DOI: 10.12659/msm.919035] [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: 12/14/2022] Open
Abstract
BACKGROUND This study aimed to use three modeling methods, logistic regression analysis, random forest analysis, and fully-connected neural network analysis, to develop a diagnostic gene signature for the diagnosis of ventilator-associated pneumonia (VAP). MATERIAL AND METHODS GSE30385 from the Gene Expression Omnibus (GEO) database identified differentially expressed genes (DEGs) associated with patients with VAP. Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment identified the molecular functions of the DEGs. The least absolute shrinkage and selection operator (LASSO) regression analysis algorithm was used to select key genes. Three modeling methods, including logistic regression analysis, random forest analysis, and fully-connected neural network analysis, also known as also known as the feed-forward multi-layer perceptron (MLP), were used to identify the diagnostic gene signature for patients with VAP. RESULTS Sixty-six DEGs were identified for patients who had VAP (VAP+) and who did not have VAP (VAP-). Ten essential or feature genes were identified. Upregulated genes included matrix metallopeptidase 8 (MMP8), arginase 1 (ARG1), haptoglobin (HP), interleukin 18 receptor 1 (IL18R1), and NLR family apoptosis inhibitory protein (NAIP). Down-regulated genes included complement factor D (CFD), pleckstrin homology-like domain family A member 2 (PHLDA2), plasminogen activator, urokinase (PLAU), laminin subunit beta 3 (LAMB3), and dual-specificity phosphatase 2 (DUSP2). Logistic regression, random forest, and MLP analysis showed receiver operating characteristic (ROC) curve area under the curve (AUC) values of 0.85, 0.86, and 0.87, respectively. CONCLUSIONS Logistic regression analysis, random forest analysis, and MLP analysis identified a ten-gene signature for the diagnosis of VAP.
Collapse
Affiliation(s)
- Yunfang Cai
- Department of Anesthesia, Zhejiang Cancer Hospital, Hangzhou, Zhejiang, China (mainland)
| | - Wen Zhang
- Department of Anesthesia, Zhejiang Cancer Hospital, Hangzhou, Zhejiang, China (mainland)
| | - Runze Zhang
- Department of Anesthesia, Zhejiang Cancer Hospital, Hangzhou, Zhejiang, China (mainland)
| | - Xiaoying Cui
- Department of Anesthesia, Zhejiang Cancer Hospital, Hangzhou, Zhejiang, China (mainland)
| | - Jun Fang
- Department of Anesthesia, Zhejiang Cancer Hospital, Hangzhou, Zhejiang, China (mainland)
| |
Collapse
|
9
|
Assessment of a Loop-Mediated Isothermal Amplification (LAMP) Assay for the Rapid Detection of Pathogenic Bacteria from Respiratory Samples in Patients with Hospital-Acquired Pneumonia. Microorganisms 2020; 8:microorganisms8010103. [PMID: 31940771 PMCID: PMC7022425 DOI: 10.3390/microorganisms8010103] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Revised: 12/24/2019] [Accepted: 01/08/2020] [Indexed: 01/26/2023] Open
Abstract
Rapid identification of the causative agent of hospital-acquired pneumonia (HAP) will allow an earlier administration of a more appropriate antibiotic and could improve the outcome of these patients. The aim of this study was to develop a rapid protocol to identify the main microorganisms involved in HAP by loop-mediated isothermal amplification (LAMP) directly from respiratory samples. First of all, a rapid procedure (<30 min) to extract the DNA from bronchoalveolar lavage (BAL), endotracheal aspirate (EA) or bronchoaspirate (BAS) was set up. A specific LAMP for Staphylococcus aureus, Escherichia coli, Klebsiella pneumoniae, Pseudomonas aeruginosa, Stenotrophomonas maltophilia and Acinetobacter baumannii was performed with the extracted solution at 65 °C for 30–40 min. Overall, 58 positive BAL and 83 EA/BAS samples were tested. The limits of detection varied according to the microorganism detected. Validation of the LAMP assay with BAL samples showed that the assay was 100% specific and 86.3% sensitive (positive predictive value of 100% and a negative predictive value of 50%) compared with culture. Meanwhile for BAS/EA samples, the assay rendered the following statistical parameters: 100% specificity, 94.6% sensitivity, 100% positive predictive value and 69.2% negative predictive value. The turnaround time including sample preparation and LAMP was circa 1 h. LAMP method may be used to detect the most frequent bacteria causing HAP. It is a simple, cheap, sensitive, specific and rapid assay.
Collapse
|
10
|
Motos A, Yang H, Yang M, Torres A. Perspectives on synthetic pharmacotherapy for the treatment of nosocomial pneumonia. Expert Opin Pharmacother 2019; 20:1439-1448. [PMID: 31095426 DOI: 10.1080/14656566.2019.1617852] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Introduction: Nosocomial pneumonia is the second most common infection in hospital settings, resulting in substantial increases in morbidity, mortality, and length of hospital stay. The rapid increase in resistance of nosocomial pathogens to many antibiotics and the high dissemination of resistance genes highlight the need for innovative approaches to combat difficult-to-treat nosocomial respiratory infections. Areas covered: This review summarizes the synthetic antimicrobials that are currently in development for the treatment of nosocomial pneumonia, focusing on antibiotics in the final phases of clinical development and on the strategies employed by novel synthetic antimicrobial peptides. Expert opinion: Several novel synthetic antimicrobials are currently in the pipeline, and it appears that new antimicrobial peptides or mimetics will soon be made available, expanding the opportunities to treat nosocomial pneumonia. However, the approval process for use in the treatment of nosocomial pneumonia is arduous. Given that significant investments by pharmaceutical companies have ended in failure to obtain the approval of regulatory agencies, novel platforms for antimicrobial discovery are needed. The identification of new and fully synthetic chemical structures with activity against nosocomial pathogens needs to be followed by preclinical studies in large animals and by pharmacokinetic and pharmacodynamic studies in specific critically ill populations to assess lung penetration.
Collapse
Affiliation(s)
- Ana Motos
- Division of Animal Experimentation, Department of Pulmonary and Critical Care Medicine, Hospital Clinic , Barcelona , Spain.,Centro de Investigación Biomédica en Red Enfermedades Respiratorias , Madrid , Spain.,Institut d'Investigacions Biomèdiques August Pi I Sunyer , Barcelona , Spain.,Faculty of Medicine, University of Barcelona , Barcelona , Spain
| | - Hua Yang
- Division of Animal Experimentation, Department of Pulmonary and Critical Care Medicine, Hospital Clinic , Barcelona , Spain
| | - Minlan Yang
- Division of Animal Experimentation, Department of Pulmonary and Critical Care Medicine, Hospital Clinic , Barcelona , Spain.,Faculty of Medicine, University of Barcelona , Barcelona , Spain
| | - Antoni Torres
- Division of Animal Experimentation, Department of Pulmonary and Critical Care Medicine, Hospital Clinic , Barcelona , Spain.,Centro de Investigación Biomédica en Red Enfermedades Respiratorias , Madrid , Spain.,Institut d'Investigacions Biomèdiques August Pi I Sunyer , Barcelona , Spain.,Faculty of Medicine, University of Barcelona , Barcelona , Spain
| |
Collapse
|
11
|
Chen L, Su Y, Quan L, Zhang Y, Du L. Clinical Trials Focusing on Drug Control and Prevention of Ventilator-Associated Pneumonia: A Comprehensive Analysis of Trials Registered on ClinicalTrials.gov. Front Pharmacol 2019; 9:1574. [PMID: 30863312 PMCID: PMC6399618 DOI: 10.3389/fphar.2018.01574] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Accepted: 12/31/2018] [Indexed: 02/05/2023] Open
Abstract
Objective: Clinical trials have emerged as the main force in driving the development of medicine. However, little is known about the current status of clinical trials regarding drug control and prevention of ventilator-associated pneumonia (VAP). This study aimed at providing a comprehensive landscape of these trials on the basis of ClinicalTrials.gov. Methods: A cross-sectional, descriptive study of clinical trials on drug control and prevention of VAP which have been registered on the ClinicalTrials.gov up to 25th August 2018 was conducted. Results: A total of 109 eligible trials were identified. Trials were started from 1998 to 2018, and most trials focused on adult patients. More than half trials were completed, while only 11.9% trials had results available. Sample sizes were relatively large, with a median enrollment of 146. Universities were listed as the primary sponsor for 36.7% trials, industry for 28.4% trials and hospitals for 19.3% trials. Of the 109 VAP trials, 37 trials were from in Europe, 36 in North America and 27 in Asia. Among the 97 interventional trials, 32 were phase 3 trials, 21 were phase 4 trials, and 16 were phase 2 trials. Most interventional trials were randomized trials with a parallel assignment, and 57.7% trials were blinded. Of the 12 observational trials, 9 were cohort studies, and 10 trials were prosepctive studies. Drugs about oral care, preemptive antibiotics and probiotics were most investigated for prevention. A total of 61 trials investigated drugs for the treatment of VAP, mainly focused on antibiotics. A total of 36 kinds of antibiotics were investigated for monotherapy or combination therapy. Beta-lactams were most studied, followed by aminoglycosides and polypeptides. Conclusion: Most clinical trials registered on ClinicalTrials.gov about drugs for VAP were interventional trials with the purpose for treatment. A high proportion of interventional trials were randomized, parallel assigned and masked. Our analysis highlights the need for improvement in completeness of study results on the ClinicalTrials.gov.
Collapse
Affiliation(s)
- Lingmin Chen
- Department of Anesthesiology and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China.,West China School of Medicine, Sichuan University, Chengdu, China
| | - Yanling Su
- Unit of General Practice, West China Hospital, Sichuan University, Chengdu, China
| | - Liuliu Quan
- West China School of Medicine, Sichuan University, Chengdu, China
| | - Yonggang Zhang
- Department of Periodical Press and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China.,Chinese Evidence-Based Medicine Center, West China Hospital, Sichuan University, Chengdu, China
| | - Liang Du
- Department of Periodical Press and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China.,Chinese Evidence-Based Medicine Center, West China Hospital, Sichuan University, Chengdu, China
| |
Collapse
|
12
|
Bonell A, Azarrafiy R, Huong VTL, Viet TL, Phu VD, Dat VQ, Wertheim H, van Doorn HR, Lewycka S, Nadjm B. A Systematic Review and Meta-analysis of Ventilator-associated Pneumonia in Adults in Asia: An Analysis of National Income Level on Incidence and Etiology. Clin Infect Dis 2019; 68:511-518. [PMID: 29982303 PMCID: PMC6336913 DOI: 10.1093/cid/ciy543] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Accepted: 06/29/2018] [Indexed: 01/31/2023] Open
Abstract
Background Ventilator-associated pneumonia (VAP) is the commonest hospital-acquired infection (HAI) in intensive care. In Asia, VAP is increasingly caused by resistant gram-negative organisms. Despite the global antimicrobial resistance crisis, the epidemiology of VAP is poorly documented in Asia. Methods We systematically reviewed literature published on Ovid Medline, Embase Classic, and Embase from 1 January 1990 to 17 August 2017 to estimate incidence, prevalence, and etiology of VAP. We performed a meta-analysis to give pooled rates and rates by country income level. Results Pooled incidence density of VAP was high in lower- and upper-middle-income countries and lower in high-income countries (18.5, 15.2, and 9.0 per 1000 ventilator-days, respectively). Acinetobacter baumannii (n = 3687 [26%]) and Pseudomonas aeruginosa (n = 3176 [22%]) were leading causes of VAP; Staphylococcus aureus caused 14% (n = 1999). Carbapenem resistance was common (57.1%). Conclusions VAP remains a common cause of HAI, especially in low- and middle-income countries, and antibiotic resistance is high.
Collapse
Affiliation(s)
- Ana Bonell
- Oxford Clinical Research Unit Hanoi, National Hospital for Tropical Diseases, Vietnam
| | | | - Vu Thi Lan Huong
- Oxford Clinical Research Unit Hanoi, National Hospital for Tropical Diseases, Vietnam
| | - Thanh Le Viet
- Oxford Clinical Research Unit Hanoi, National Hospital for Tropical Diseases, Vietnam
| | | | | | - Heiman Wertheim
- Department of Medical Microbiology, Radboud Center of Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands
- Nuffield Department of Medicine, University of Oxford, United Kingdom
| | - H Rogier van Doorn
- Oxford Clinical Research Unit Hanoi, National Hospital for Tropical Diseases, Vietnam
| | - Sonia Lewycka
- Oxford Clinical Research Unit Hanoi, National Hospital for Tropical Diseases, Vietnam
| | - Behzad Nadjm
- Oxford Clinical Research Unit Hanoi, National Hospital for Tropical Diseases, Vietnam
| |
Collapse
|