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Li Q, Song M, Hu Z, Ding Y, Huang C, Liu J. Pediatric respiratory pathogen dynamics in Southern Sichuan, China: a retrospective analysis of gender, age, and seasonal trends. Front Pediatr 2024; 12:1374571. [PMID: 39086626 PMCID: PMC11288815 DOI: 10.3389/fped.2024.1374571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Accepted: 07/01/2024] [Indexed: 08/02/2024] Open
Abstract
Objective To address the research gap in the epidemiology of pediatric respiratory tract infections (RTIs) in Luzhou, Southern Sichuan, China, by analyzing respiratory pathogens in a large pediatric cohort from 2018 to 2021, covering the pre- and during-COVID-19 periods. Methods This study conducted a retrospective analysis of children with RTIs in Luzhou from July 2018 to January 2021. Strict exclusion criteria were applied to ensure an accurate representation of the pediatric population. Pathogen detection included viruses, bacteria, and atypical agents. Results Pathogens were identified in 52.8% of 12,546 cases. Viruses accounted for 32.2% of infections, bacteria for 29.8%, and atypical agents for 29.7%, with significant findings of Staphylococcus aureus, Moraxella catarrhalis, and Mycoplasma pneumoniae. Age-related analysis indicated a higher incidence of bacterial infections in infants and viral infections in preschool-aged children, with atypical pathogens being most prevalent in 3-5-year-olds. Gender-based analysis, adjusted for age, revealed similar overall pathogen presence; however, females were more susceptible to viral infections, while males were more prone to Streptococcus pneumoniae. Notably, there was an unusual increase in pathogen cases during spring, potentially influenced by behavioral changes and public health measures related to COVID-19. Co-infections were identified as a significant risk factor for the development of pneumonia. Conclusion The study provides essential insights into the epidemiology of respiratory pathogens in pediatric populations, emphasizing the need for healthcare strategies tailored to age, gender, and seasonality. The findings highlight the impact of environmental and public health factors, including COVID-19 measures, on respiratory pathogen prevalence, underscoring the importance of targeted diagnostic and treatment protocols in pediatric respiratory infections.
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Affiliation(s)
- Qing Li
- Department of Laboratory Medicine, The Affiliated Hospital of Southwest Medical University, Luzhou, China
- Sichuan Province Engineering Technology Research Center of Molecular Diagnosis of Clinical Diseases, The Affiliated Hospital of Southwest Medical University, Luzhou, China
- Molecular Diagnosis of Clinical Diseases Key Laboratory of Luzhou, The Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Min Song
- Department of Laboratory Medicine, The Affiliated Hospital of Southwest Medical University, Luzhou, China
- Sichuan Province Engineering Technology Research Center of Molecular Diagnosis of Clinical Diseases, The Affiliated Hospital of Southwest Medical University, Luzhou, China
- Molecular Diagnosis of Clinical Diseases Key Laboratory of Luzhou, The Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Zhi Hu
- Department of Medical Laboratory, Southwest Medical University, Luzhou, China
| | - Yinhuan Ding
- Department of Laboratory Medicine, The Affiliated Hospital of Southwest Medical University, Luzhou, China
- Sichuan Province Engineering Technology Research Center of Molecular Diagnosis of Clinical Diseases, The Affiliated Hospital of Southwest Medical University, Luzhou, China
- Molecular Diagnosis of Clinical Diseases Key Laboratory of Luzhou, The Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Chengliang Huang
- Department of Respiratory and Critical Care Medicine, The Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Jinbo Liu
- Department of Laboratory Medicine, The Affiliated Hospital of Southwest Medical University, Luzhou, China
- Sichuan Province Engineering Technology Research Center of Molecular Diagnosis of Clinical Diseases, The Affiliated Hospital of Southwest Medical University, Luzhou, China
- Molecular Diagnosis of Clinical Diseases Key Laboratory of Luzhou, The Affiliated Hospital of Southwest Medical University, Luzhou, China
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Arena F, Bernaschi P, Mencacci A. Editorial: Clinical impact of fast platforms and laboratory automation for the rapid diagnosis of infectious diseases and detection of antimicrobial resistance determinants. Front Cell Infect Microbiol 2023; 13:1321663. [PMID: 38239509 PMCID: PMC10794890 DOI: 10.3389/fcimb.2023.1321663] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2023] [Accepted: 11/27/2023] [Indexed: 01/22/2024] Open
Affiliation(s)
- Fabio Arena
- Department of Clinical and Experimental Medicine, University of Foggia, Foggia, Italy
| | - Paola Bernaschi
- Microbiology and Diagnostic Immunology Unit, Bambino Gesù Children’s Hospital, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Rome, Italy
| | - Antonella Mencacci
- Microbiology and Clinical Microbiology, Department of Medicine and Surgery, University of Perugia, Perugia, Italy
- Microbiology, Perugia General Hospital, Perugia, Italy
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Bonaiuto C, Baccani I, Chilleri C, Antonelli A, Giani T, Rossolini GM. Evaluation of the Liquid Colony™ Produced by the FAST System for Shortening the Time of Bacterial Identification and Phenotypic Antimicrobial Susceptibility Testing and Detection of Resistance Mechanisms from Positive Blood Cultures. Diagnostics (Basel) 2023; 13:diagnostics13111849. [PMID: 37296699 DOI: 10.3390/diagnostics13111849] [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: 03/23/2023] [Revised: 05/17/2023] [Accepted: 05/20/2023] [Indexed: 06/12/2023] Open
Abstract
BACKGROUND the aim of this study was to evaluate the performance of the Liquid Colony™ (LC) generated directly from positive blood cultures (PBCs) by the FAST System (Qvella, Richmond Hill, ON, Canada) for rapid identification (ID) and antimicrobial susceptibility testing (AST) compared with the standard of care (SOC) workflow. METHODS Anonymized PBCs were processed in parallel by the FAST System and FAST PBC Prep cartridge (35 min runtime) and SOC. ID was performed by MALDI-ToF mass spectrometry (Bruker, Billerica, MA, USA). AST was performed by reference broth microdilution (Merlin Diagnostika, Bornheim, Germany). Carbapenemase detection was carried out with the lateral flow immunochromatographic assay (LFIA) RESIST-5 O.O.K.N.V. (Coris, Gembloux, Belgium). Polymicrobial PBCs and samples containing yeast were excluded. RESULTS 241 PBCs were evaluated. ID results showed 100% genus-level concordance and 97.8% species-level concordance between LC and SOC. The AST results for Gram-negative bacteria showed a categorical agreement (CA) of 99.1% (1578/1593), with minor error (mE), major error (ME), and very major error (VME) rates of 0.6% (10/1593), 0.3% (3/1122), and 0.4% (2/471), respectively. The results from Gram-positive bacteria showed a CA of 99.6% (1655/1662), with mE, ME, and VME rates of 0.3% (5/1662), 0.2% (2/1279), and 0.0% (0/378), respectively. Bias evaluation revealed acceptable results for both Gram-negatives and Gram-positives (-12.4% and -6.5%, respectively). The LC yielded the detection of 14/18 carbapenemase producers by LFIA. In terms of turnaround time, the ID, AST, and carbapenemase detection results were generally obtained one day earlier with the FAST System compared with the SOC workflow. CONCLUSIONS The ID, AST, and carbapenemase detection results generated with the FAST System LC were highly concordant with the conventional workflow. The LC allowed species ID and carbapenemase detection within around 1 h after blood culture positivity and AST results within approximately 24 h, which is a significant reduction in the turnaround time of the PBC workflow.
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Affiliation(s)
- Chiara Bonaiuto
- Department of Experimental and Clinical Medicine, University of Florence, 50134 Florence, Italy
- Clinical Microbiology and Virology Unit, Careggi University Hospital, 50134 Florence, Italy
| | - Ilaria Baccani
- Department of Experimental and Clinical Medicine, University of Florence, 50134 Florence, Italy
- Clinical Microbiology and Virology Unit, Careggi University Hospital, 50134 Florence, Italy
| | - Chiara Chilleri
- Department of Experimental and Clinical Medicine, University of Florence, 50134 Florence, Italy
- Clinical Microbiology and Virology Unit, Careggi University Hospital, 50134 Florence, Italy
| | - Alberto Antonelli
- Department of Experimental and Clinical Medicine, University of Florence, 50134 Florence, Italy
- Clinical Microbiology and Virology Unit, Careggi University Hospital, 50134 Florence, Italy
| | - Tommaso Giani
- Department of Experimental and Clinical Medicine, University of Florence, 50134 Florence, Italy
- Clinical Microbiology and Virology Unit, Careggi University Hospital, 50134 Florence, Italy
| | - Gian Maria Rossolini
- Department of Experimental and Clinical Medicine, University of Florence, 50134 Florence, Italy
- Clinical Microbiology and Virology Unit, Careggi University Hospital, 50134 Florence, Italy
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Donnars A, Eveillard M. [Rapid diagnosis of bacteremia by genomic identification]. ANNALES PHARMACEUTIQUES FRANÇAISES 2022; 81:425-432. [PMID: 36464071 DOI: 10.1016/j.pharma.2022.11.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 11/23/2022] [Accepted: 11/28/2022] [Indexed: 12/03/2022]
Abstract
Our objective was to make a focus on the methods for rapid diagnosis of bacteremia by genomic identification. We also aimed to evaluate the interest of using them in the laboratory practice. The different methods currently available have been presented according to their technologic approach. It is also possible to classify these methods according to the data provided, only bacterial and/or resistance gene identification or also bacterial susceptibility to antibiotics. In case of mono-microbial blood cultures, the performances recorded with these methods are very good as compared to the subcultures on agar media. Nevertheless, they are better for identifications (>90%) than for susceptibility to antibiotics (>80%). Numerous studies demonstrated the positive impact of these methods for decreasing the time necessary to the prescription of an appropriate antimicrobial treatment. However, it is noteworthy that an appropriate organization of the laboratory and a strategy of antimicrobial stewardship in the hospital are necessary. Concurrently, the impact on the patient outcome has not been clearly demonstrated. Lastly, few medico-economic studies have been reported. However, as these methods have a substantial cost, their utilization strategy must be economically viable.
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Affiliation(s)
- A Donnars
- Laboratoire de bactériologie, département de biologie des agents infectieux, centre hospitalier universitaire d'Angers, Angers, France
| | - M Eveillard
- Laboratoire de bactériologie, département de biologie des agents infectieux, centre hospitalier universitaire d'Angers, Angers, France.
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Åkerlund A, Petropoulos A, Malmros K, Tängdén T, Giske CG. Blood culture diagnostics: a Nordic multicentre survey comparison of practices in clinical microbiology laboratories. Clin Microbiol Infect 2021; 28:731.e1-731.e7. [PMID: 34537364 DOI: 10.1016/j.cmi.2021.09.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 08/17/2021] [Accepted: 09/04/2021] [Indexed: 11/19/2022]
Abstract
OBJECTIVES Accurate and rapid microbiological diagnostics are crucial to tailor treatment and improve outcomes in patients with severe infections. This study aimed to assess blood culture diagnostics in the Nordic countries and to compare them with those of a previous survey conducted in Sweden in 2013. METHODS An online questionnaire was designed and distributed to the Nordic clinical microbiology laboratories (CMLs) (n = 76) in January 2018. RESULTS The response rate was 64% (49/76). Around-the-clock incubation of blood cultures (BCs) was supported in 82% of the CMLs (40/49), although in six of these access to the incubators around the clock was not given to all of the cabinets in the catchment area, and 41% of the sites (20/49) did not assist with satellite incubators. Almost half (49%, 24/49) of the CMLs offered opening hours for ≥10 h during weekdays, more commonly in CMLs with an annual output ≥30 000 BCs. Still, positive BCs were left unprocessed for 60-70% of the day due to restrictive opening hours. Treatment advice was given by 23% of CMLs (11/48) in ≥75% of the phone contacts. Rapid analyses (species identification and susceptibility testing with short incubation), performed on aliquots from positive cultures, were implemented in 18% of CMLs (9/49). Compared to 2013, species identification from subcultured colonies (<6 h) had become more common. CONCLUSIONS CMLs have taken action to improve aspects of BC diagnostics, implementing satellite incubators, rapid species identification and susceptibility testing. However, the limited opening hours and availability of clinical microbiologists are confining the advantages of these changes.
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Affiliation(s)
- Anna Åkerlund
- Division of Clinical Microbiology, Laboratory Medicine, Jönköping, Region Jönköping County, and Department of Clinical and Experimental Medicine, Linköping University, Sweden; Division of Clinical Microbiology, Department of Clinical and Experimental Medicine, Linköping University Hospital, Linköping, Sweden.
| | - Alexandros Petropoulos
- Department of Microbiology, Tumour and Cell Biology, Karolinska Institutet, Stockholm, Sweden; Department of Clinical Microbiology, Karolinska University Hospital, Stockholm, Sweden
| | - Karin Malmros
- Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Thomas Tängdén
- Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Christian G Giske
- Department of Clinical Microbiology, Karolinska University Hospital, Stockholm, Sweden; Department of Laboratory Medicine, Division of Clinical Microbiology, Karolinska Institutet, Stockholm, Sweden
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Hill C. Microbiome and Infection: A Case for "Selective Depletion". ANNALS OF NUTRITION & METABOLISM 2021; 77:1-6. [PMID: 34038906 DOI: 10.1159/000516399] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Accepted: 04/08/2021] [Indexed: 11/19/2022]
Abstract
In most instances where a pathogen has initiated an infection, the primary goal of the treating physician or pharmacist is to eliminate the pathogen. In the absence of knowledge of the precise identity of the problem-causing microbe, a broad-spectrum antimicrobial gives the best chance of success. This approach has saved many lives and is an invaluable tool in fighting infections. However, perhaps our current appreciation of the importance of the microbiome in human health should give us pause. We can regard the microbiome as a virtual organ within the human body, and we would surely hesitate to advance any therapeutic approach that would cause substantial damage to one of our organs. This is one consequence of many broad-spectrum antimicrobial therapies. There may be instances where a more precise approach would be useful. I have termed this "selective depletion"; a concept where pathogen numbers are curtailed by a narrow-spectrum inhibitor but the microbiome is protected and can play a role in restoring health and suppressing the outgrowth of the pathogen in the infected patient. It may well be that the best reservoir of microbiome-friendly antimicrobial agents is the microbiome itself, and I provide examples of where the microbiome has been mined for novel precision antimicrobials.
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Affiliation(s)
- Colin Hill
- APC Microbiome Ireland and School of Microbiology, University College Cork, Cork, Ireland
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Tiseo G, Arena F, Borrè S, Campanile F, Falcone M, Mussini C, Pea F, Sganga G, Stefani S, Venditti M. Diagnostic stewardship based on patient profiles: differential approaches in acute versus chronic infectious syndromes. Expert Rev Anti Infect Ther 2021; 19:1373-1383. [PMID: 33970746 DOI: 10.1080/14787210.2021.1926986] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Introduction: New diagnostics may be useful in clinical practice, especially in contexts of high prevalence of multidrug-resistant organisms (MDRO). However, misuse of diagnostic tools may lead to increased costs and worse patient outcome. Conventional and new techniques should be appropriately positioned in diagnostic algorithms to guide an appropriate use of antimicrobial therapy.Areas covered: A panel of experts identified 4 main areas in which the implementation of diagnostic stewardship is needed. Among chronic infections, bone and prosthetic joint infections and subacute-chronic intravascular infections and endocarditis represent common challenges for clinicians. Among acute infections, bloodstream infections and community-acquired pneumonia may be associated with high mortality and require appropriate diagnostic approach.Expert opinion: Diagnostic stewardship aims to improve the appropriate use of microbiological diagnostics to guide therapeutic decisions through appropriate and timely diagnostic testing. Here, diagnostic algorithms based on different patient profiles are proposed for chronic and acute clinical syndromes. In each clinical scenario, combining conventional and new diagnostic techniques is crucial to make a rapid and accurate diagnosis and to guide the selection of antimicrobial therapy. Barriers related to the implementation of new rapid diagnostic tools, such as high initial costs, may be overcome through their rational and structured use.
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Affiliation(s)
- Giusy Tiseo
- Infectious Disease Unit, Azienda Ospedaliera Universitaria Pisana, Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - Fabio Arena
- Infectious Disease Unit, Azienda Ospedaliera Universitaria Pisana, Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy.,IRCCS Fondazione Don Carlo Gnocchi, Florence, Italy
| | - Silvio Borrè
- Infectious Diseases Unit, Sant'Andrea Hospital Vercelli, Vercelli, Italy
| | - Floriana Campanile
- Department of Biomedical and Biotechnological Sciences, University of Catania, Catania, Italy
| | - Marco Falcone
- Infectious Disease Unit, Azienda Ospedaliera Universitaria Pisana, Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - Cristina Mussini
- Department of Infectious Diseases, Azienda Ospedaliero-Universitaria, Policlinico of Modena, Modena, Italy
| | - Federico Pea
- Department of Medical and Surgical Sciences, Alma Mater Studiorum, University of Bologna, Bologna, Italy.,SSD Clinical Pharmacology, University Hospital IRCCS Policlinico Sant'Orsola, Bologna, Italy
| | - Gabriele Sganga
- Emergency Surgery, Fondazione Policlinico Agostino Gemelli IRCCS of Rome, Rome, Italy
| | - Stefania Stefani
- Department of Biomedical and Biotechnological Sciences, University of Catania, Catania, Italy
| | - Mario Venditti
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, Rome, Italy
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Performance evaluation of Alfred 60AST rapid susceptibility testing directly from positive blood cultures in the routine laboratory workflow. Eur J Clin Microbiol Infect Dis 2021; 40:1487-1494. [PMID: 33598828 DOI: 10.1007/s10096-021-04191-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Accepted: 02/09/2021] [Indexed: 12/16/2022]
Abstract
The aim of this study was to evaluate the performance of the new automated system Alfred60AST which is based on light scattering technology for rapid susceptibility testing directly from positive blood cultures as well as its applicability in the routine laboratory workflow. We evaluated 176 significant episodes of bacteremia due to 92 Gram-negative and 84 Gram-positive bacteria. The antimicrobial agents tested were ceftriaxone, ciprofloxacin, gentamicin, meropenem, piperacillin-tazobactam, and colistin for Gram negatives and cefoxitin, vancomycin, linezolid, and daptomycin for Gram positives. Concordance assessment was performed in comparison with our routine method, Vitek2 (bioMérieux). Discrepancies were resolved with MICRONAUT-S (Merlin) or E-test (bioMérieux). Out of 690 susceptibility determinations, 94.05% showed categorical agreement (CA) with the routine method and this percentage increased to 94.49 after discrepancy analysis. There were 1.45% very major errors, 3.33% major errors, and 1.16% minor errors (decreased to 1.45, 3.04, and 1.01 after discrepancy analysis). The CA for most of the antibiotics was above 90% except for daptomycin for Gram positives (87.30%) and ceftriaxone for Gram negatives (88.23%). The concordance was slightly better for Gram negative than for Gram-positive bacteria (94.30 versus 93.70%, respectively). The total turnaround time for a complete Alfred60AST result was 6-6.5h. The evaluated method gave rapid and reliable results in a few hours, versus 48h for the conventional one. Implementing this technology in routine workflow allows clinicians to optimize the treatment on the same day of blood culture positivity with potential positive clinical benefits and impact on antibiotic stewardship.
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Walsh TL, Bremmer DN, Moffa MA, Trienski TL, Buchanan C, Stefano K, Hand C, Taylor T, Kasarda K, Shively NR, Bhanot N, Cheronis N, DiSilvio BE, Cho CY, Carr DR. Impact of an Antimicrobial Stewardship Program-bundled initiative utilizing Accelerate Pheno™ system in the management of patients with aerobic Gram-negative bacilli bacteremia. Infection 2021; 49:511-519. [PMID: 33528813 PMCID: PMC8159835 DOI: 10.1007/s15010-021-01581-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Accepted: 01/18/2021] [Indexed: 12/01/2022]
Abstract
Purpose Gram-negative bacteria (GNB) are a leading cause of bloodstream infections (BSI) and management is complicated by antibiotic resistance. The Accelerate Pheno™ system (ACC) can provide rapid organism identification and antimicrobial susceptibility testing (AST). Methods A retrospective, pre-intervention/post-intervention study was conducted to compare management of non-critically ill patients with GNB BSI before and after implementation of a bundled initiative. This bundled initiative included dissemination of a clinical decision algorithm, ACC testing on all GNB isolated from blood cultures, real-time communication of results to the Antimicrobial Stewardship Program (ASP), and prospective audit with feedback by the ASP. The pre-intervention period was January 2018 through December 2018, and the post-intervention period was May 2019 through February 2020. Results Seventy-seven and 129 patients were included in the pre-intervention and post-intervention cohorts, respectively. When compared with the pre-intervention group, the time from Gram stain to AST decreased from 46.1 to 6.9 h (p < 0.001), and the time to definitive therapy (TTDT) improved from 32.6 to 10.5 h (p < 0.001). Implementation led to shorter median total duration of antibiotic therapy (14.2 vs 9.5 days; p < 0.001) and mean hospital length of stay (7.9 vs 5.3 days; p = 0.047) without an increase in 30-day readmissions (22.1% vs 14%; p = 0.13). Conclusion Implementation of an ASP-bundled approach incorporating the ACC aimed at optimizing antibiotic therapy in the management GNB BSI in non-critically ill patients led to reduced TTDT, shorter duration of antibiotic therapy, and shorter hospital length of stay without adversely affecting readmission rates.
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Affiliation(s)
- Thomas L Walsh
- Medicine Institute and Division of Infectious Diseases, Allegheny Health Network, Allegheny General Hospital, 320 East North Ave. East Wing Office Building, Suite 406, Pittsburgh, PA, 15212, USA.
| | - Derek N Bremmer
- Department of Pharmacy, Allegheny Health Network, Pittsburgh, PA, USA
| | - Matthew A Moffa
- Medicine Institute and Division of Infectious Diseases, Allegheny Health Network, Allegheny General Hospital, 320 East North Ave. East Wing Office Building, Suite 406, Pittsburgh, PA, 15212, USA.
| | - Tamara L Trienski
- Department of Pharmacy, Allegheny Health Network, Pittsburgh, PA, USA
| | - Carley Buchanan
- Department of Pharmacy, Allegheny Health Network, Pittsburgh, PA, USA
| | - Kelly Stefano
- Department of Microbiology, Allegheny Health Network, Pittsburgh, PA, USA
| | - Catharine Hand
- Department of Microbiology, Allegheny Health Network, Pittsburgh, PA, USA
| | - Tricia Taylor
- Department of Microbiology, Allegheny Health Network, Pittsburgh, PA, USA
| | - Karen Kasarda
- Department of Microbiology, Allegheny Health Network, Pittsburgh, PA, USA
| | - Nathan R Shively
- Medicine Institute and Division of Infectious Diseases, Allegheny Health Network, Allegheny General Hospital, 320 East North Ave. East Wing Office Building, Suite 406, Pittsburgh, PA, 15212, USA
| | - Nitin Bhanot
- Medicine Institute and Division of Infectious Diseases, Allegheny Health Network, Allegheny General Hospital, 320 East North Ave. East Wing Office Building, Suite 406, Pittsburgh, PA, 15212, USA
| | - Nicholas Cheronis
- Medicine Institute and Division of Infectious Diseases, Allegheny Health Network, Allegheny General Hospital, 320 East North Ave. East Wing Office Building, Suite 406, Pittsburgh, PA, 15212, USA.,Medicine Institute and Division of Pulmonary and Critical Care Medicine, Allegheny Health Network, Pittsburgh, PA, USA
| | - Briana E DiSilvio
- Medicine Institute and Division of Pulmonary and Critical Care Medicine, Allegheny Health Network, Pittsburgh, PA, USA
| | - Christian Y Cho
- Department of Pharmacy, Allegheny Health Network, Pittsburgh, PA, USA
| | - Dustin R Carr
- Department of Pharmacy, Allegheny Health Network, Pittsburgh, PA, USA
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Peiffer-Smadja N, Bouadma L, Mathy V, Allouche K, Patrier J, Reboul M, Montravers P, Timsit JF, Armand-Lefevre L. Performance and impact of a multiplex PCR in ICU patients with ventilator-associated pneumonia or ventilated hospital-acquired pneumonia. Crit Care 2020; 24:366. [PMID: 32560662 PMCID: PMC7303941 DOI: 10.1186/s13054-020-03067-2] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Accepted: 06/04/2020] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Early appropriate antibiotic therapy reduces morbidity and mortality of severe pneumonia. However, the emergence of bacterial resistance requires the earliest use of antibiotics with the narrowest possible spectrum. The Unyvero Hospitalized Pneumonia (HPN, Curetis) test is a multiplex PCR (M-PCR) system detecting 21 bacteria and 19 resistance genes on respiratory samples within 5 h. We assessed the performance and the potential impact of the M-PCR on the antibiotic therapy of ICU patients. METHODS In this prospective study, we performed a M-PCR on bronchoalveolar lavage (BAL) or plugged telescoping catheter (PTC) samples of patients with ventilated HAP or VAP with Gram-negative bacilli or clustered Gram-positive cocci. This study was conducted in 3 ICUs in a French academic hospital: the medical and infectious diseases ICU, the surgical ICU, and the cardio-surgical ICU. A multidisciplinary expert panel simulated the antibiotic changes they would have made if the M-PCR results had been available. RESULTS We analyzed 95 clinical samples of ventilated HAP or VAP (72 BAL and 23 PTC) from 85 patients (62 males, median age 64 years). The median turnaround time of the M-PCR was 4.6 h (IQR 4.4-5). A total of 90/112 bacteria were detected by the M-PCR system with a global sensitivity of 80% (95% CI, 73-88%) and specificity of 99% (95% CI 99-100). The sensitivity was better for Gram-negative bacteria (90%) than for Gram-positive cocci (62%) (p = 0.005). Moreover, 5/8 extended-spectrum beta-lactamases (CTX-M gene) and 4/4 carbapenemases genes (3 NDM, one oxa-48) were detected. The M-PCR could have led to the earlier initiation of an effective antibiotic in 20/95 patients (21%) and to early de-escalation in 37 patients (39%) but could also have led to one (1%) inadequate antimicrobial therapy. Among 17 empiric antibiotic treatments with carbapenems, 10 could have been de-escalated in the following hours according to the M-PCR results. The M-PCR also led to 2 unexpected diagnosis of severe legionellosis confirmed by culture methods. CONCLUSIONS Our results suggest that the use of a M-PCR system for respiratory samples of patients with VAP and ventilated HAP could improve empirical antimicrobial therapy and reduce the use of broad-spectrum antibiotics.
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Affiliation(s)
- Nathan Peiffer-Smadja
- Université de Paris, IAME, INSERM, Paris, F-75018, France.
- Infectious and Tropical Diseases Department, Bichat-Claude Bernard Hospital, AP-HP, Paris, 75018, France.
| | - Lila Bouadma
- Université de Paris, IAME, INSERM, Paris, F-75018, France
- Medical and Infectious Diseases ICU (MI2), Bichat-Claude Bernard Hospital, AP-HP, 75018, Paris, France
| | - Vincent Mathy
- Bacteriology Laboratory, Bichat-Claude Bernard Hospital, AP-HP, Paris, France
| | - Kahina Allouche
- Bacteriology Laboratory, Bichat-Claude Bernard Hospital, AP-HP, Paris, France
| | - Juliette Patrier
- Medical and Infectious Diseases ICU (MI2), Bichat-Claude Bernard Hospital, AP-HP, 75018, Paris, France
| | - Martin Reboul
- Bacteriology Laboratory, Bichat-Claude Bernard Hospital, AP-HP, Paris, France
| | - Philippe Montravers
- Département d'Anesthésie Réanimation, Bichat-Claude Bernard Hospital, AP-HP, Paris, France
- INSERM UMR 1152, Physiopathologie et Epidémiologie des Maladies respiratoires, Paris, France
| | - Jean-François Timsit
- Université de Paris, IAME, INSERM, Paris, F-75018, France
- Medical and Infectious Diseases ICU (MI2), Bichat-Claude Bernard Hospital, AP-HP, 75018, Paris, France
| | - Laurence Armand-Lefevre
- Université de Paris, IAME, INSERM, Paris, F-75018, France
- Bacteriology Laboratory, Bichat-Claude Bernard Hospital, AP-HP, Paris, France
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Belibasakis GN. Grand Challenges in Oral Infections and Microbes. FRONTIERS IN ORAL HEALTH 2020; 1:2. [PMID: 35047975 PMCID: PMC8757780 DOI: 10.3389/froh.2020.00002] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Accepted: 04/06/2020] [Indexed: 12/31/2022] Open
Affiliation(s)
- Georgios N Belibasakis
- Division of Oral Diseases, Department of Dental Medicine, Karolinska Institutet, Huddinge, Sweden
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12
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Cattaneo D, Corona A, De Rosa FG, Gervasoni C, Kocic D, Marriott DJ. The management of anti-infective agents in intensive care units: the potential role of a 'fast' pharmacology. Expert Rev Clin Pharmacol 2020; 13:355-366. [PMID: 32320302 DOI: 10.1080/17512433.2020.1759413] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
INTRODUCTION Patients in intensive care units (ICU) are often developing severe infections in which are associated with significant mortality rates. A number of novel technologies for the rapid microbiological diagnosis of these infections have been developed, introducing the era of 'fast microbiology.' Treatment of bacterial and fungal infections in ICU is however complicated by alterations in the pharmacokinetics of antimicrobial agents. AREAS COVERED We review novel pharmacologic tools that can be used to optimize anti-infective therapies and patient management in ICU. A MEDLINE Pubmed search for articles published from January 1995 to 2019 was completed matching the terms pharmacokinetics and pharmacology with antimicrobial agents and ICU or critically ill patients. Moreover, additional studies were identified from the reference list of retrieved articles. EXPERT OPINION Several tools are in development for the full automation of the analytical methods used for the quantification of antimicrobial concentrations within a few hours after sample collection. Ad hoc software with adaptive feedback is also available for appropriate dose adjustments based on both individual patient covariate data and therapeutic drug monitoring (TDM) data when available. The application of these technological improvements in the clinical practice should open the way to a 'fast pharmacology' at the bedside.
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Affiliation(s)
- Dario Cattaneo
- Unit of Clinical Pharmacology, ASST Fatebenefratelli Sacco University Hospital , Milan, Italy.,Gestione Ambulatoriale Politerapie (GAP) Outpatient Clinic, ASST Fatebenefratelli Sacco University Hospital , Milan, Italy
| | - Alberto Corona
- Intensive Care Unit, ASST Fatebenefratelli Sacco, University Hospital , Milan, Italy
| | | | - Cristina Gervasoni
- Gestione Ambulatoriale Politerapie (GAP) Outpatient Clinic, ASST Fatebenefratelli Sacco University Hospital , Milan, Italy.,Department of Infectious Diseases, ASST Fatebenefratelli Sacco University Hospital , Milan, Italy
| | - Danijela Kocic
- Department of Clinical Pharmacology and Toxicology, St Vincent's Hospital Sydney , Sydney, Australia
| | - Deborah Je Marriott
- Department of Clinical Microbiology and Infectious Diseases, St Vincent's Hospital , Sydney, Australia
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13
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Innovative and rapid antimicrobial susceptibility testing systems. Nat Rev Microbiol 2020; 18:299-311. [PMID: 32055026 DOI: 10.1038/s41579-020-0327-x] [Citation(s) in RCA: 163] [Impact Index Per Article: 40.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/13/2020] [Indexed: 12/21/2022]
Abstract
Antimicrobial resistance (AMR) is a major threat to human health worldwide, and the rapid detection and quantification of resistance, combined with antimicrobial stewardship, are key interventions to combat the spread and emergence of AMR. Antimicrobial susceptibility testing (AST) systems are the collective set of diagnostic processes that facilitate the phenotypic and genotypic assessment of AMR and antibiotic susceptibility. Over the past 30 years, only a few high-throughput AST methods have been developed and widely implemented. By contrast, several studies have established proof of principle for various innovative AST methods, including both molecular-based and genome-based methods, which await clinical trials and regulatory review. In this Review, we discuss the current state of AST systems in the broadest technical, translational and implementation-related scope.
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14
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Arena F, Argentieri M, Bernaschi P, Fortina G, Kroumova V, Pecile P, Rassu M, Spanu T, Rossolini GM, Fontana C. Compliance of clinical microbiology laboratories with recommendations for the diagnosis of bloodstream infections: Data from a nationwide survey in Italy. Microbiologyopen 2020; 9:e1002. [PMID: 32012494 PMCID: PMC7142361 DOI: 10.1002/mbo3.1002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Revised: 01/09/2020] [Accepted: 01/09/2020] [Indexed: 12/17/2022] Open
Abstract
In 2014, the Italian Working Group for Infections in Critically Ill Patient of the Italian Association of Clinical Microbiologists updated the recommendations for the diagnostic workflow for bloodstream infections (BSI). Two years after publication, a nationwide survey was conducted to assess the compliance with the updated recommendations by clinical microbiology laboratories. A total of 168 microbiologists from 168 laboratories, serving 204 acute care hospitals and postacute care facilities, were interviewed during the period January–October 2016 using a questionnaire consisting of nineteen questions which assessed the level of adherence to various recommendations. The most critical issues were as follows: (a) The number of sets of blood cultures (BC) per 1,000 hospitalization days was acceptable in only 11% of laboratories; (b) the minority of laboratories (42%) was able to monitor whether BCs were over or under‐inoculated; (c) among the laboratories monitoring BC contamination (80%), the rate of contaminated samples was acceptable in only 12% of cases;(d) the Gram‐staining results were reported within 1 hr since BC positivity in less than 50% of laboratories. By contrast, most laboratories received vials within 2–4 hr from withdrawal (65%) and incubated vials as soon as they were received in the laboratory (95%). The study revealed that compliance with the recommendations is still partial. Further surveys will be needed to monitor the situation in the future.
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Affiliation(s)
- Fabio Arena
- Department of Clinical and Experimental Medicine, University of Foggia, Foggia, Italy.,IRCCS Don Carlo Gnocchi Foundation, Florence, Italy
| | - Marta Argentieri
- Microbiology Unit, Children's Hospital Bambino Gesù, Rome, Italy
| | - Paola Bernaschi
- Microbiology Unit, Children's Hospital Bambino Gesù, Rome, Italy
| | - Giacomo Fortina
- Italian Work Group for Infections in Critically Ill Patient (GliPac-AMCLI), Milan, Italy
| | - Vesselina Kroumova
- Infection Control Unit, University Hospital "Maggiore della Carità", Novara, Italy
| | - Patrizia Pecile
- Clinical Microbiology and Virology Unit, Florence Careggi University Hospital, Florence, Italy
| | - Mario Rassu
- Microbiology and Virology Lab, AULS 8 Berica, S. Bortolo Hospital, Vicenza, Italy
| | - Teresa Spanu
- Institute of Microbiology, Università Cattolica del Sacro Cuore, Fondazione Policlinico Universitario Agostino Gemelli, Rome, Italy
| | - Gian Maria Rossolini
- Clinical Microbiology and Virology Unit, Florence Careggi University Hospital, Florence, Italy.,Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Carla Fontana
- Department Experimental Medicine, University of Rome Tor Vergata, Rome, Italy.,Microbiology and Virology Lab, Tor Vergata University Hospital, Rome, Italy
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15
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Comparison of rapid BACpro® II, Sepsityper® kit and in-house preparation methods for direct identification of bacteria from blood cultures by MALDI-TOF MS with and without Sepsityper® module analysis. Eur J Clin Microbiol Infect Dis 2019; 38:2133-2143. [PMID: 31494828 PMCID: PMC6800852 DOI: 10.1007/s10096-019-03654-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Accepted: 07/21/2019] [Indexed: 01/24/2023]
Abstract
There are several approaches available for purifying microorganisms prior to matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS) analysis. In the present study, rapid BACpro® II (Nittobo Medical Co., Ltd., Tokyo, Japan), a new application, has been compared with Sepsityper® kit (Bruker Daltonics, Billerica, USA) and an in-house method. Samples were also tested with two modules, standard and Sepsityper®, identified in the Bruker MALDI-TOF MS. The bottles having monomicrobial growth were included in the study according to Gram staining results. In total, two hundred blood culture bottles were included but there was no growth in one of the subcultures so 199 blood culture bottles were studied prospectively. With the standard MALDI-TOF MS analysis, rapid BACpro® II could successfully identify microorganisms in 174/199 (87.4%) of the bottles where Sepsityper® kit and in-house method were successful in 136/199 (68.3%) and 114/199 (57.3%), respectively. When the MALDI-TOF MS data were analysed by Sepsityper® module, the identification rates were increased to 94.4%, 82.1% and 69.8% (p < 0.001), respectively. In the Sepsityper® module, 72/73 (98.6%) of Gram-negative and 97/106 (91.5%) of Gram-positive microorganisms were detected by rapid BACpro® II method. The present study shows that rapid BACpro® II is a reliable preparation procedure and has higher rates of identification compared with Sepsityper® kit and in-house method. The use of the Sepsityper® module in blood cultures increases the chance of identification for all three methods studied.
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16
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Schneider JG, Wood JB, Smith NW, Emery CL, Davis TE, Manaloor JJ, Bocian B, Schmitt BH. Direct antimicrobial susceptibility testing of positive blood cultures: a comparison of the Accelerate Pheno™ and VITEK® 2 systems. Diagn Microbiol Infect Dis 2019; 95:114841. [PMID: 31422873 DOI: 10.1016/j.diagmicrobio.2019.05.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Revised: 05/14/2019] [Accepted: 05/18/2019] [Indexed: 12/22/2022]
Abstract
OBJECTIVES To compare the performance and time-to-result (TTR) for antimicrobial susceptibility testing (AST) of positive blood cultures (PBC) using the Accelerate Pheno™ system (AXDX) and both a direct VITEK® 2 card inoculation workflow (DV2) and traditional FDA-approved VITEK® 2 workflow using subcultured isolates (V2). METHODS Patient samples with monomicrobial Gram-negative rod bacteremia were tested on AXDX and DV2 in tandem and compared to V2 AST results. Categorical agreement (CA) errors were adjudicated using broth microdilution. Instrumentation times and AST TTR were compared. RESULTS AXDX and DV2 had a CA of 93.4% and 97.4%, respectively, compared to V2. Postadjudication, AXDX, DV2, and V2 had CA of 94.7%, 95.7%, and 96.5%, respectively. Instrument run times were 6.6 h, 9.4 h, and 9.2 h, and AST TTR were 8.9 h, 12.9 h and 35.5 h, respectively. CONCLUSIONS AXDX and DV2 ASTs are fast and reliable, which may have significant antimicrobial stewardship implications.
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Affiliation(s)
- Jack G Schneider
- Ryan White Center for Pediatric Infectious Diseases and Global Health, Indiana University School of Medicine, Indianapolis, Indiana, USA.
| | - James B Wood
- Ryan White Center for Pediatric Infectious Diseases and Global Health, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | | | - Christopher L Emery
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Thomas E Davis
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - John J Manaloor
- Ryan White Center for Pediatric Infectious Diseases and Global Health, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Brittany Bocian
- Indiana University Health Methodist and University Hospitals, Indianapolis, Indiana, USA
| | - Bryan H Schmitt
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, Indiana, USA
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Microfluidics-Based Organism Isolation from Whole Blood: An Emerging Tool for Bloodstream Infection Diagnosis. Ann Biomed Eng 2019; 47:1657-1674. [PMID: 30980291 DOI: 10.1007/s10439-019-02256-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Accepted: 03/27/2019] [Indexed: 12/11/2022]
Abstract
The diagnosis of bloodstream infections presents numerous challenges, in part, due to the low concentration of pathogens present in the peripheral bloodstream. As an alternative to existing time-consuming, culture-based diagnostic methods for organism identification, microfluidic devices have emerged as rapid, high-throughput and integrated platforms for bacterial and fungal enrichment, detection, and characterization. This focused review serves to highlight and compare the emerging microfluidic platforms designed for the isolation of sepsis-causing pathogens from blood and suggest important areas for future research.
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