Role of Multiplex PCR in CAP

Molecular Methods for Identifying Bacteria in Lower Respiratory Tract Specimens Among Patients With Pneumonia by Multiplex PCR

1. role of multiplex PCR in early identifying bacteria in patients with lower respiratory tract infection.
2. effect of early starting targeted antibiotics on outcome

Study Overview

• Status: Not yet recruiting
• Conditions: Community-acquired Pneumonia
• Intervention / Treatment: Diagnostic test: MultiplexPCR

Detailed Description

Pneumonia remains a worldwide health problem with a high rate of morbidity and mortality. Identification of microbial pathogens which cause pneumonia is an important area for optimum clinical management of pneumonia patients and is a big challenge for conventional microbiological methods. The development and implementation of molecular diagnostic tests for pneumonia has been a major advance in the microbiological diagnosis of respiratory pathogens in recent years. Targeted antibiotic selection and more effective de-escalation and improved stewardship for pneumonia patients.

PCR is a simple, yet elegant, enzymatic assay, which allows for the amplification of a specific DNA fragment from a complex pool of DNA.. Only trace amounts of DNA are needed for PCR to generate enough copies to be analyzed using conventional laboratory methods. For this reason, PCR is a sensitive assay.

Each PCR assay requires the presence of template DNA, primers, nucleotides, and DNA polymerase .The DNA polymerase is the key enzyme that links individual nucleotides together to form the PCR product. The nucleotides include the four bases - adenine, thymine, cytosine, and guanine (A, T, C, G) - that are found in DNA. These act as the building blocks that are used by the DNA polymerase to create the resultant PCR product. The primers in the reaction specify the exact DNA product to be amplified. The primers are short DNA fragments with a defined sequence complementary to the target DNA that is to be detected and amplified. These serve as an extension point for the DNA polymerase to build on.There are multiple advantages to PCR. First, it is a simple technique to understand and to use, a nd it produces results rapidly. It is a highly sensitive technique with the potential to produce millions to billions of copies of a specific product for sequencing, cloning, and analysis. Although PCR is a valuable technique, it does have limitations. Because PCR is a highly sensitive technique, any form of contamination of the sample by even trace amounts of DNA can produce misleading results . In addition, in order to design primers for PCR, some prior sequence data is needed. Therefore, PCR can only be used to identify the presence or absence of a known pathogen or gene

• Study Type: Observational
• Enrollment (Estimated): 66

Contacts and Locations

• Study Contact: Name: Asmaa Saleh Mousa, resident physician; Phone Number: 01149227845; Email: asmaa241.saleh@gmail.com
• Study Contact Backup: Name: Lamia Hasan Shaaban, prof; Phone Number: 01002681478; Email: Lamiashaban@yahoo.com

Participation Criteria

Eligibility Criteria

• Ages Eligible for Study: Adult; Older Adult
• Accepts Healthy Volunteers: No

• Sampling Method: Non-Probability Sample

Study Population

patients with CAP will divided in two groups (1:1), one group undergoes multiplex PCR and treatment will be started according targeted antibiotics, the other group undergoes simple culture and sensitivity and empirical antibiotics will be started until results appear and according results ,treatment will be completed or shifted to another treatment or be narrowed ,later on detect outcome of both groups.

Sample Size Calculation: 66 cases

Description

Inclusion Criteria:

• male and female
• Age >18 years Old

Adult patients were included if they fulfilled:

• radiographic and clinical criteria.
• Radiographic findings included chest imaging with an airspace opacity, lobar consolida-tion, or interstitial opacities

• new or worsening compared to available baseline. In addition, at least 2 of the following clinical criteria had to be fulfilled:

  1. reported or documented fever > 37.5
  2. new worsening productive cough or increase in respiratory secretions in intubated patients

  3. pleuritic chest pain 4) new/worsening dyspnea or hypoxia, defined as documented blood oxygen saturation <92%.

     Exclusion Criteria:

     Patients under 18 years old. Patients who refuse to participate in the study

Study Plan

How is the study designed?

Number of groups / cohorts

2

Cohorts and Interventions

Group / Cohort	Intervention / Treatment
one group undergoes multiplex PCR; treatment will be started according targeted antibiotics	Diagnostic test: MultiplexPCR; PCR is a simple, yet elegant, enzymatic assay, which allows for the amplification of a specific DNA fragment from a complex pool of DNA.. Only trace amounts of DNA are needed for PCR to generate enough copies to be analyzed using conventional laboratory methods. For this reason, PCR is a sensitive assay.
the other group undergoes simple culture and sensitivity; empirical antibiotics will be started until results appear and according results ,treatment will be completed or shifted to another treatment or be narrowed ,later on detect outcome of both groups.

What is the study measuring?

Primary Outcome Measures

Outcome Measure	Measure Description	Time Frame
detect Antimicrobial therapy duration in CAP in comparison in both groups	Antimicrobial therapy duration in patients with CAP in comparison of two groups	1 year
detect clinical improvement in both groups	detection of clinical improvement in both groups (subsided of bronchial symptoms as productive cough ,colored sputum, relieve of dysnea and pleuritic chest pain , subsided of fever	1 year

Collaborators and Investigators

• Sponsor: Assiut University

Publications and helpful links

Helpful Links

• . Timsit J-F, Bassetti M, Cremer O, et al. Rationalizing antimicrobial therapy in the ICU: a narrative review. Intensive Care Med. 2019;45(2):172-89
• . Peiffer-Smadja N, Rawson TM, Ahmad R, et al. Machine learning for clinical decision support in infectious diseases: a narrative review of current applications. Clin Microbiol Infect Published online September 17. 2019

Study record dates

Study Major Dates

• Study Start (Estimated): November 1, 2023
• Primary Completion (Estimated): October 1, 2024
• Study Completion (Estimated): December 1, 2024

Study Registration Dates

• First Submitted: September 1, 2023
• First Submitted That Met QC Criteria: October 20, 2023
• First Posted (Actual): October 24, 2023

Study Record Updates

• Last Update Posted (Actual): October 24, 2023
• Last Update Submitted That Met QC Criteria: October 20, 2023
• Last Verified: October 1, 2023

More Information

Terms related to this study

• Additional Relevant MeSH Terms: Infections; Respiratory Tract Infections; Respiratory Tract Diseases; Lung Diseases; Pneumonia
• Other Study ID Numbers: role of multiplex PCR in CAP

Drug and device information, study documents

• Studies a U.S. FDA-regulated drug product: No
• Studies a U.S. FDA-regulated device product: No