Journal of Microbiology and Biotechnology

The Korean Society for Microbiology and Biotechnology (한국미생물·생명공학회)
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Sequencing Methods to Study the Microbiome with Antibiotic Resistance Genes in Patients with Pulmonary Infections

  • Tingyan Dong (Integrated Diagnostic Centre for Infectious Diseases, Guangzhou Huayin Medical Laboratory Center) ;
  • Yongsi Wang (Immunology and Reproduction Biology Laboratory & State Key Laboratory of Analytical Chemistry for Life Sciences, Medical School, Nanjing University) ;
  • Chunxia Qi (Department of Hospital Infection Management, NanFang Hospital, Southern Medical University) ;
  • Wentao Fan (Immunology and Reproduction Biology Laboratory & State Key Laboratory of Analytical Chemistry for Life Sciences, Medical School, Nanjing University) ;
  • Junting Xie (Immunology and Reproduction Biology Laboratory & State Key Laboratory of Analytical Chemistry for Life Sciences, Medical School, Nanjing University) ;
  • Haitao Chen (Immunology and Reproduction Biology Laboratory & State Key Laboratory of Analytical Chemistry for Life Sciences, Medical School, Nanjing University) ;
  • Hao Zhou (Department of Hospital Infection Management, NanFang Hospital, Southern Medical University) ;
  • Xiaodong Han (Immunology and Reproduction Biology Laboratory & State Key Laboratory of Analytical Chemistry for Life Sciences, Medical School, Nanjing University)
  • Received : 2024.02.02
  • Accepted : 2024.05.29
  • Published : 2024.08.28
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Abstract

Various antibiotic-resistant bacteria (ARB) are known to induce repeated pulmonary infections and increase morbidity and mortality. A thorough knowledge of antibiotic resistance is imperative for clinical practice to treat resistant pulmonary infections. In this study, we used a reads-based method and an assembly-based method according to the metagenomic next-generation sequencing (mNGS) data to reveal the spectra of ARB and corresponding antibiotic resistance genes (ARGs) in samples from patients with pulmonary infections. A total of 151 clinical samples from 144 patients with pulmonary infections were collected for retrospective analysis. The ARB and ARGs detection performance was compared by the reads-based method and assembly-based method with the culture method and antibiotic susceptibility testing (AST), respectively. In addition, ARGs and the attribution relationship of common ARB were analyzed by the two methods. The comparison results showed that the assembly-based method could assist in determining pathogens detected by the reads-based method as true ARB and improve the predictive capabilities (46% > 13%). ARG-ARB network analysis revealed that assembly-based method could promote determining clear ARG-bacteria attribution and 101 ARGs were detected both in two methods. 25 ARB were obtained by both methods, of which the most predominant ARB and its ARGs in the samples of pulmonary infections were Acinetobacter baumannii (ade), Pseudomonas aeruginosa (mex), Klebsiella pneumoniae (emr), and Stenotrophomonas maltophilia (sme). Collectively, our findings demonstrated that the assembly-based method could be a supplement to the reads-based method and uncovered pulmonary infection-associated ARB and ARGs as potential antibiotic treatment targets.

Keywords

Acknowledgement

The authors thank all patients and their families who participated in this study. They also thank Dr. Yuhua Ye for his helpful suggestions.

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