Whole metagenomic sequencing reveals different compositions of pathogenic bacteria in patients with appendicitis:Bacterial culture is not suitable as the only therapeutic guidance

2020 ◽  
Author(s):  
Jie Yuan ◽  
Enming Qiu ◽  
Shuai Han ◽  
Zhou Li
Keyword(s):  
Next Generation Sequencing ◽  
Pathogenic Bacteria ◽  
Antimicrobial Agents ◽  
Bacterial Culture ◽  
Treatment Guidelines ◽  
Case Series ◽  
Sequencing Analysis ◽  
Metagenomic Sequencing ◽  
Next Generation ◽  
Generation Sequencing

Abstract Background Appendicitis is the result of a combination of factors, including bacterial infection, anatomy, blood supply, and intestinal contents. Previous diagnosis and treatment guidelines have suggested that bacteria are associated with the severity of appendicitis, and the use of postoperative antibiotics should be guided according to the results of intraoperative sample culture. However, this approach has many limitations. Therefore, in the present study, the relationship between pathogenic bacteria and appendicitis was assessed. Result We conducted a nonconsecutive case series analysis from January to July 2017. Nineteen patients were divided into two groups according to their intraoperative gross pathology and postoperative histological and bacterial culture results. During appendectomy, the diseased appendices were collected, and whole metagenomic sequencing was performed to identify the pathogenic bacteria in the specimens. We identified 361 species in the appendix samples. Six species in the appendix samples had relative abundances > 5%. No significant differences were observed in the bacterial composition of the three assayed groups. In particular, according to the grouping of culture results, the sequencing analysis results were completely different from those of the culture-based method. Conclusion Bacterial culture results are not suitable for exclusively guiding the use of antimicrobial agents after appendicitis. Next-generation sequencing has numerous advantages, such as in precisely characterizing the profiles of microbiota and their antibiotic resistance in appendicitis patients. Based on the above results, we propose that a combination of bacterial culture and next-generation sequencing should be used to improve the efficacy of guiding antibiotic therapy.

scholarly journals Impact of donor lung pathogenic bacteria detected by next-generation sequencing on early post-transplant outcomes in lung transplant recipients

2020 ◽  
Author(s):  
Dong Liu ◽  
Ji Zhang ◽  
Bo Wu ◽  
Feng Liu ◽  
Shugao Ye ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Lung Transplantation ◽  
Pathogenic Bacteria ◽  
Bacterial Culture ◽  
Lower Lobe ◽  
Next Generation ◽  
Culture Methods ◽  
Term Outcome ◽  
Donor Lung ◽  
Generation Sequencing

Abstract Background: The effect of donor lung pathogenic bacteria on the prognosis of lung transplantation is not clear. We used the technique of next-generation sequencing (NGS) to detect the pathogenic bacteria from the lower respiratory tract and analyzed whether the colonized bacteria of donor lung could affect the outcomes of lung transplantation.Methods: All patients who underwent lung transplantation from March 2018 to June 2018 at Wuxi People's Hospital affiliated to Nanjing Medical University were included in this study. Twelve cases of donor lung were obtained, and 17 lung transplants were performed, including 12 single lung transplantation and 5 bilateral lung transplantation. The colonized bacteria in the lower lobe tissue of donor lung were detected by NGS, and the bacteria culture method was used to detect the bacteria in the airway secretion before and after the operation. The information of length of extracorporeal membrane oxygenation (ECMO) support, mechanical ventilation time, length of intensive care unit (ICU) stay, duration of fever and length of hospital stay were collected for prognostic analysis.Results: Compared with bacterial culture methods, the positive rate by using NGS in the lungs were higher (52.9% vs 41.2%). Among the patients who had detected bacteria by NGS in donor lungs before surgery, only one patient (1/9) developed the same bacteria after lung transplantation. Based on results of NGS and bacterial culture, there is no association between the colonized bacteria in donor lungs and the patient outcomes of immediate posttransplant period. Conclusion: NGS showed more sensitive than bacterial culture for detection of bacteria. The colonized bacteria in different parts of the lung are inconsistent. There is no association between the colonized bacteria in donor lungs and short-term outcome of lung transplantation patients.

scholarly journals Clinical Analysis of Metagenomic Next-generation Sequencing Confirmed Chlamydia psittaci Pneumonia: A Case Series and Literature Review

2021 ◽  
Author(s):  
Xin-Qi Teng ◽  
Wen-Cheng Gong ◽  
Ting-Ting Qi ◽  
Guo-Hua Li ◽  
Qiang Qu ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Literature Review ◽  
Clinical Characteristics ◽  
Pathogenic Bacteria ◽  
False Negative ◽  
False Negative Rate ◽  
Case Series ◽  
Chlamydia Psittaci ◽  
Next Generation ◽  
Generation Sequencing

Abstract Introduction: Chlamydia psittaci infection is a zoonotic infectious disease, which mainly inhaled through the lungs when exposed to the secretions of poultry that carry pathogenic bacteria. The traditional respiratory specimens or serological antibody testing is slow and the false-negative rate is high. Metagenomic next-generation sequencing gives a promising rapid diagnosis tool. Methods: We retrospective summarized the clinical characteristics of five C. psittaci pneumonia patients diagnosed by mNGS, conducted a literature review summarizing the clinical characteristics of patients with C. psittaci pneumonia reported since 2010.Results: Five C. psittaci. pneumonia patients confirmed by mNGS aged from 36 to 66 years with three males. 60% of patients had type 2 diabetes mellitus. And 60% of patients had a history of contact with avian or poultry. All patients had a high fever over 38.5 °C, cough, hypodynamia, hypoxemia, and dyspnea on admission. Two patients had invasive ventilator support and Extracorporeal Membrane Oxygenation support. The levels of C-reactive protein, procalcitonin, and erythrocyte sedimentation rate on admission and follow-up were all higher than normal values. Doxycycline or moxifloxacin monotherapy was accounted for 1/5 (20%) and 2/5 (40%) patients, and combination therapy was accounted for 2/5(40%) patients. Four patients improved and were discharged, and one patient died due to multiple organ failure and disseminated intravascular coagulation.Conclusions: mNGS can increase the detection rate of C. psittaci, shorten the diagnosis time of C. psittaci pneumonia and improve the prognosis of patients.

scholarly journals Impact of donor lung pathogenic bacteria detected by next-generation sequencing on early post-transplant outcomes in lung transplant recipients

2020 ◽  
Author(s):  
Dong Liu ◽  
Ji Zhang ◽  
Bo Wu ◽  
Feng Liu ◽  
Shugao Ye ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Lung Transplantation ◽  
Pathogenic Bacteria ◽  
Bacterial Culture ◽  
Lower Lobe ◽  
Next Generation ◽  
Culture Methods ◽  
Time Duration ◽  
Donor Lung ◽  
Generation Sequencing

Abstract Background: The effect of donor lung pathogenic bacteria on the prognosis of lung transplantation is not clear. We used the technique of next-generation sequencing (NGS) to detect the pathogenic bacteria from the lower respiratory tract and analyzed whether the colonized bacteria of donor lung affect the outcomes of lung transplantation.Methods: All patients who underwent lung transplantation from March 2018 to June 2018 at the Wuxi People's Hospital affiliated to Nanjing Medical University were included in this study. Twelve cases of donor lung were obtained, and 17 lung transplants were performed, including 12 single lung transplantation and 5 bilateral lung transplantation. The colonized bacteria in the lower lobe tissue of donor lung were detected by NGS, and the bacteria culture method was used to detect the bacteria in the airway secretion before and after the operation. The information of extracorporeal membrane oxygenation (ECMO) support time, mechanical ventilation time, intensive care unit (ICU) stay time,duration of fever and hospital length of staywere collected for prognostic analysis.Results: Compared with bacterial culture methods, the positive rate of bacteriaby using NGS in the lungs were higher (52.9% vs 41.2%). Among the patients who had detected bacteria by NGS in donor lungs before surgery, only one patient (1/9) developed the same bacteria after lung transplantation.Either NGS or bacterial culture methods, there is no association between the colonized colonization bacteria in donor lungs and the patient outcomes of immediate posttransplant period.Conclusion: The detection of bacteria by using NGS is more sensitive than normal bacterial culture. The colonized bacteria in different parts of the lung are inconsistent. There is no association between the colonized bacteria in donor lungs and short-term outcome of lung transplantation patients.

scholarly journals 670. Rapid, Non-invasive Detection of Invasive Mycoplasma hominis Infection using the Karius Test, A Next-Generation Sequencing Test for Microbial Cell-free DNA in Plasma

2020 ◽  
Vol 7 (Supplement_1) ◽  
pp. S390-S390
Author(s):  
Priya Edward ◽  
William V La Via ◽  
Mehreen Arshad ◽  
Kiran Gajurel
Keyword(s):  
Next Generation Sequencing ◽  
Case Series ◽  
Mycoplasma Hominis ◽  
Microbial Cell ◽  
Next Generation ◽  
Cell Free Dna ◽  
Non Invasive ◽  
Free Dna ◽  
Hominis Infection ◽  
Generation Sequencing

Abstract Background Mycoplasma hominis is typically associated with genital infections in women and is a rare cause of musculoskeletal infections often in immunocompromised hosts. Diagnosis of invasive Mycoplasma hominis infections are difficult due to challenges in culturing these organisms. Molecular diagnostics require an index of suspicion which may not be present at the time of tissue sampling. Accurate, rapid diagnosis of Mycoplasma hominis infections are important for antibiotic management. Methods Two cases of invasive Mycoplasma hominis infections are presented in which the Karius test (KT) was used to make the diagnosis. The KT is a CLIA certified/CAP-accredited next-generation sequencing (NGS) plasma test that detects microbial cell-free DNA (mcfDNA). After mcfDNA is extracted and NGS performed, human reads are removed and remaining sequences are aligned to a curated database of > 1400 organisms. Organisms present above a statistical threshold are reported. Case review was performed for clinical correlation. Results A young woman with lupus nephritis status post renal transplant developed persistent fever with progressive multifocal culture-negative osteoarticular infection despite empiric ceftriaxone. An adolescent female presented with an ascending pelvic infection progressing to purulent polymicrobial peritonitis (see table) requiring surgical debridement and cefipime, metronidazole and micafungin therapy; her course was complicated by progressive peritonitis/abscesses. Karius testing detected high-levels of Mycoplasma hominis mcfDNA in both cases – at 3251 molecules/microliter (MPM) in the first case and 3914 MPM in the second case. The normal range of Mycoplasma hominis mcfDNA in a cohort of 684 normal adults is 0 MPM. The patients rapidly improved with atypical coverage with doxycycline and levofloxaxin. Clinical findings in 2 patients with M. hominis infection detected by the Karius Test Conclusion Open-ended, plasma-based NGS for mcfDNA provides a rapid, non-invasive method to diagnose invasive Mycoplasma hominis infection. This case series highlights the potential to diagnose infections caused by fastidious pathogens to better inform antimicrobial therapy and achieve favorable outcomes. Disclosures William V. La Via, MD, Karius (Employee)

scholarly journals Metagenomic Next-Generation Sequencing for Pathogen Detection and Transcriptomic Analysis in Pediatric Central Nervous System Infections

2021 ◽  
Author(s):  
Nanda Ramchandar ◽  
Nicole G Coufal ◽  
Anna S Warden ◽  
Benjamin Briggs ◽  
Toni Schwarz ◽  
...  
Keyword(s):  
Central Nervous System ◽  
Nervous System ◽  
Next Generation Sequencing ◽  
Usual Care ◽  
Transcriptomic Analysis ◽  
Cns Infection ◽  
Metagenomic Sequencing ◽  
Next Generation ◽  
Cns Infections ◽  
Generation Sequencing

Abstract Background Pediatric central nervous system (CNS) infections are potentially life-threatening and may incur significant morbidity. Identifying a pathogen is important, both in terms of guiding therapeutic management, but also in characterizing prognosis. Usual care testing by culture and PCR is often unable to identify a pathogen. We examined the systematic application of metagenomic next-generation sequencing (mNGS) for detecting organisms and transcriptomic analysis of cerebrospinal fluid (CSF) in children with CNS infections. Methods We conducted a prospective multi-site study that aimed to enroll all children with a CSF pleocytosis and suspected CNS infection admitted to one of three tertiary pediatric hospitals during the study timeframe. After usual care testing had been performed, the remaining CSF was sent for mNGS and transcriptomic analysis. Results We screened 221 and enrolled 70 subjects over a 12-month recruitment period. A putative organism was isolated from CSF in 25 (35.7%) subjects by any diagnostic modality. mNGS of the CSF samples identified a pathogen in 20 (28.6%) subjects, which were also all identified by usual care testing. The median time to result was 38 hours. Conclusion Metagenomic sequencing of CSF has the potential to rapidly identify pathogens in children with CNS infections.

scholarly journals Diagnosis of Severe Tetanus Assisted by Next-Generation Sequencing Analysis of Etiology: A Case Report

2020 ◽  
Author(s):  
Yuling An ◽  
Mingming Fan ◽  
Ziyu Li ◽  
You Peng ◽  
Xiaomeng Yi ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Comprehensive Treatment ◽  
Sequencing Analysis ◽  
Next Generation ◽  
Next Generation Sequencing Analysis ◽  
Autonomic Instability ◽  
The Right ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing ◽  
Severe Tetanus

Abstract We shared our successful treatment experience of a severe tetanus patient in China. A 50 year old male patient was admitted to our hospital 10 days after the right arm injury due to pain and masticatory weakness. The pathogen of wound secretion was confirmed to be clostridium tetanus by next-generation sequencing (NGS).The patient's condition rapidly progressed to a severe state with autonomic instability. After debridement and comprehensive treatment in ICU, including deep analgesia and sedation with dexmedetomidine, ventilator support and anti-infection treatment, the patient finally recovered and discharged. This case suggested that early diagnosis and reasonable intervention of severe tetanus could reduce mortality.

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