Classification and Drug Resistance Analysis of Pathogenic Bacteria in Patients with Bacterial Pneumonia in Emergency Intensive Care Unit
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Kai Yin1, Ling Liu2, Guofeng Fan1
1Department of Emergency, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing 210008, China.
Objective:
This study aimed to compare the identification efficiency of metagenome next generation sequencing (mNGS) and traditional methods in detecting pathogens in patients with severe bacterial pneumonia (BP) and further analyze the drug resistance of common pathogens.
Methods:
A total of 180 patients with severe BP who were admitted to our hospital from June 2017 to July 2020 were selected as the research objects. Alveolar lavage fluid from the patients were collected, and pathogens were detected by the mNGS technology and traditional etiological detection technology. Common pathogens detected by mNGS were tested for the drug sensitivity test. The difference between mNGS and traditional detection method in the identification of pathogenic bacteria in severe BP patients was compared, and the distribution characteristics and drug resistance of pathogenic bacteria were analyzed.
Results:
The positive rate of mNGS detection was 92.22%, which was significantly higher than that of the traditional culture method (58.33%, P < 0.05). 347 strains of pathogenic bacteria were detected by mNGS, including 256 strains of Gram-negative bacteria (G-), 89 strains of Gram-positive bacteria (G+), and 2 strains of fungi. Among G- bacteria, Acinetobacter baumannii had higher resistance to piperacillin/tazobactam, ceftazidime, imipenem, levofloxacin, amikacin, ciprofloxacin, gentamicin, and the lowest resistance to tigecycline. The resistance of Klebsiella pneumoniae to piperacillin/tazobactam and ceftazidime was higher. Pseudomonas aeruginosa had low resistance to all the drugs. Escherichia coli had high drug resistance to most drugs, and the drug resistant rates to cefoperazone/sulbactam, piperacillin/tazobactam, ceftazidime, imipenem, and gentamicin were all more than 50.00%. G+ bacteria had high resistance to penicillin, azithromycin, amoxicillin and levofloxacin, and amoxicillin and levofloxacin had high resistance, up to 100.00%.
Conclusion:
mNGS has high sensitivity for the identification of pathogenic bacteria in patients with BP. G- bacteria were the main pathogens of BP, but both G- and G+ bacteria had high resistance to a variety of antibacterial drugs.
Insights
Metagenome next generation sequencing (mNGS) significantly improves pathogen identification in severe bacterial pneumonia compared to traditional methods. Both Gram-negative and Gram-positive bacteria show high antimicrobial resistance, necessitating careful treatment selection.
Area of Science:
- Medical Microbiology
- Infectious Diseases
- Genomics
Background:
- Severe bacterial pneumonia (BP) poses a significant global health challenge.
- Accurate and rapid pathogen identification is crucial for effective treatment and antimicrobial stewardship.
- Traditional culture-based methods have limitations in sensitivity and speed for complex infections.
Purpose of the Study:
- To compare the diagnostic efficiency of metagenome next generation sequencing (mNGS) against traditional methods for pathogen detection in severe BP.
- To analyze the antimicrobial resistance patterns of common pathogens identified in severe BP patients.
Main Methods:
- A cohort of 180 severe BP patients was studied.
- Alveolar lavage fluid was analyzed using both mNGS and traditional culture techniques.
- Pathogens identified by mNGS underwent drug sensitivity testing.
Main Results:
- mNGS achieved a significantly higher positive detection rate (92.22%) compared to traditional culture (58.33%).
- Gram-negative bacteria were the predominant pathogens, with notable resistance observed in *Acinetobacter baumannii*, *Klebsiella pneumoniae*, and *Escherichia coli*.
- Gram-positive bacteria exhibited high resistance to several common antibiotics, including penicillin, azithromycin, amoxicillin, and levofloxacin.
Conclusions:
- mNGS demonstrates superior sensitivity for identifying bacterial pathogens in severe BP.
- Both Gram-negative and Gram-positive bacteria prevalent in BP cases display substantial resistance to a wide range of antibacterial agents.
- Findings highlight the need for advanced diagnostic tools like mNGS and careful consideration of resistance profiles in guiding antibiotic therapy for severe BP.
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