Species-specific Bacterial Detector for Fast Pathogen Diagnosis of Severe Pneumonia

Species-specific Bacterial Detector for Fast Pathogen Diagnosis of Severe Pneumonia Patients in Intensive Care Uint: a Multicentre, Randomised Controlled Trial

This study is a multicenter randomized controlled trial. The purpose of this study is to assess the efficacy of the combination of PCR and CRISPR/Cas12a (SSBD)in tract secretion from lower respiratory for early targeted anti-infective therapy for patients with severe pneumonia. 5 adult ICU units from 5 hospitals in Jiangsu province participate the study and the hosted unit is the Department of Critical Care Medicine, Affiliated Drum Tower Hospital of Nanjing University Medical College. All patients are randomly assigned to the experiment group and the control group. For experiment group, the combined detection of PCR andCRISPR/Cas12a is carried out in the early stage, and the antibiotic scheme is changed base on the results of PCR-CRISPR/Cas12a. The patients in the control group are adjusted according to the traditional microbial detection methods. Some clinical parameters and outcomes are recorded.

ICU patients have a high incidence of bacterial infection in the lower respiratory tract, mainly with severe pneumonia, often causing severe sepsis and septic shock, which is one of the main causes of death in patients. At present, the biggest difficulty faced by clinicians is the continuous increase of bacterial resistance rate and the increase of patient mortality due to the early inadequacy empirical anti-infective treatment. Studies have shown that patients with VAP(Ventilator Associated Pneumonia) have irrational drug use in the early stage, with a mortality rate of more than 50%. When the rate of appropriate drug use has dropped to 33%, while mechanical ventilation time and ICU hospitalization time have been significantly shortened. Therefore, identifying pathogenes as early as possible and shortening the time of empirical anti-infective treatment are very important for improving the prognosis of patients with severe pneumonia and reducing the incidence of bacterial resistance. There are three traditional methods for detecting pathogenic microorganisms: 1. microbial culture method is the most traditional means of identifying pathogen. It is necessary to inoculate the patient's body fluid, blood, etc. in a suitable medium, incubate in a suitable incubator, and then pass the drug. Sensitivity tests determine the resistance of microorganisms, usually takes 3-7 days. For some specific types of pathogenic microorganisms or microorganisms with harsh growth conditions, there may be negative culture results. Therefore, the traditional culture methods have disadvantages such as poor timeliness, relatively high requirements, and low positive culture rate (30-40%). 2. time-of-flight mass spectrometry: the mass spectrometry technique is used to analyze and detect the protein components of the strain, and the characteristic peak spectrum is obtained. Compared with the bacterial map in the database, the bacteria can be judged by matching. The method can be shortened by about 6-8 hours compared with the conventional culture method, but since the detection of the colony needs to reach a certain amount, the specimen can not be directly detected after obtaining the specimen, and the preliminary microbial culture is required. Therefore, the detection time still takes 1-2 days or more, and there is also the disadvantage of low timeliness. In addition, it is necessary to compare the expansion and standardization of the database, and the inability to analyze the resistance of microorganisms is also the inadequacy of the detection technology. 3. High-throughput sequencing technology: With the rapid development of molecular biology in recent years, high-throughput sequencing technology is widely used in the early diagnosis of clinical microbiology, the principle is mainly through the connection of the universal linker to the fragmentation to be sequenced. Genomic DNA, which produces tens of millions of single-molecule polyclonal polymerase chain reaction arrays, then performs large-scale primer hybridization and enzyme extension reactions, and obtains complete DNA sequence information by computer analysis. However, this technology is difficult to effectively distinguish between pathogenic bacteria and background bacteria, technology and database to be standardized, detection time still takes about 2 days, can not obtain microbial resistance, expensive and other shortcomings At the office. In summary, the current time limit for targeted anti-infective treatment is stopped 2 days after the specimen is taken. Therefore, the search for new, pathogenic microbial detection technology that is faster, more accurate and more sensitive is a hotspot and a difficult point in the field of microbial and anti-infective research in recent years. CRISPR/Cas12a has trans-cleavage activity, which could be developed as a new molecular method for testing specific nucleotide sequences with high specificity and sensitivity . We thus initiatively designed the Species-Specific Bacterial Detector (SSBD) system basing on CRISPR/Cas12a. In theory, the method is prominent with rapidity, high sensitivity and specificity, and variable detection targets, which is an innovation in microorganism identification and maybe bring benefits to sepsis treatment. As some particular bacteria account of most of sepsis, 12 common bacteria are chosen as the initial panel according to previous studies and local epidemic data from our hospital. Our aim of the study is to establish and validate the effectiveness of the SSBD system through comparing with culture results, and then evaluate the possible clinical values in therapy adjustments and clinical outcomes of severe pneumonia in ICU, which was the major causes of sepsis.

Based on 1791 microorganism genomes of 232 species from the public database, we identified species-specific DNA-tags for 12 common pathogenic bacteria, which allowed us to design our Cas12a system for using the trans-cleavage activity and judging whether bacterium infects the patient or not by fluorescence value.

the time taken from collecting the specimen for the investigation to initiating appropriate treatment on the results available

The incidence of antibiotic-associated diarrhea is the index of side effects of anti-infective treatment from randomization to day 28.

rate of multi-drug resistant bacteria colonization or infection is the index of side effects of anti-infective treatment from randomization to day 28

Inclusion Criteria: age ≥ 18 years; Pneumonia with undetermined pathogen and lower respiratory tract specimens can be obtained ; signed informed consent; the expected length of staying in ICU is more than 3 days Exclusion Criteria: pregnant women lactating women Those who specimens of lower respiratory tract cannot be obtained; Those who have submitted for other microbiological examination within 72 hours before enrollment; The main responsibility of infection was not in the lung, but outside the lung; Clinical diagnosis of non-bacterial pneumonia, such as Pneumocystis carinii pneumonia, viral pneumonia and fungal pneumonia; Those who are estimated to die or give up treatment within 72 hours; patients have participated in other clinical studies.