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

2020 ◽  
Vol 20 (1) ◽  
Author(s):  
Dong Liu ◽  
Ji Zhang ◽  
Bo Wu ◽  
Feng Liu ◽  
Shugao Ye ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Lung Transplantation ◽  
Bacterial Culture ◽  
Lower Lobe ◽  
Next Generation ◽  
Culture Methods ◽  
Term Outcome ◽  
Donor Lung ◽  
Lung Transplants ◽  
Generation Sequencing

Abstract Background The effect of donor lung colonized bacteria on the prognosis of lung transplantation is not clear. We used the technique of next-generation sequencing (NGS) to detect the colonized bacteria from the lower respiratory tract and analyzed whether the colonized bacteria of donor lung could affect the outcomes of lung transplantation. Methods Seventeen 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 were transplanted with donor lungs with detected bacteria by NGS before surgery, only one patient (1/9) developed the same bacteria after lung transplantation. Based on results of NGS and bacterial culture, there was no association between the colonized bacteria in donor lungs and the patients’ 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 Impact of donor lung colonized 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 ◽  
Bacterial Culture ◽  
Lower Lobe ◽  
Next Generation ◽  
Culture Methods ◽  
Term Outcome ◽  
Donor Lung ◽  
Lung Transplants ◽  
Generation Sequencing

Abstract Background: The effect of donor lung colonized bacteria on the prognosis of lung transplantation is not clear. We used the technique of next-generation sequencing (NGS) to detect the colonized bacteria from the lower respiratory tract and analyzed whether the colonized bacteria of donor lung could affect the outcomes of lung transplantation.Methods: 17 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 was no association between the colonized bacteria in donor lungs and the patients’ 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 Case Report: About a Case of Hyperammonemia Syndrome Following Lung Transplantation: Could Metagenomic Next-Generation Sequencing Improve the Clinical Management?

2021 ◽  
Vol 8 ◽  
Author(s):  
Charlotte Michel ◽  
Michela Raimo ◽  
Vladimir Lazarevic ◽  
Nadia Gaïa ◽  
Nina Leduc ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Antibiotic Therapy ◽  
Lung Transplantation ◽  
Bacterial Culture ◽  
Opportunistic Infections ◽  
Ureaplasma Urealyticum ◽  
Added Value ◽  
Next Generation ◽  
Positive Bacterial Culture ◽  
Generation Sequencing

Background:Mycoplasma hominis and Ureaplasma spp. are responsible for opportunistic infections in transplant patients, sometimes causing a life-threatening hyperammonemia syndrome. Both pathogens are not identified with standard microbiology techniques, resulting in missed or delayed diagnosis. We present a clinical case that illustrates the added value that next-generation sequencing (NGS) may offer in the diagnosis of respiratory infections in immune-compromised patients.Results: A 55 years-old man with idiopathic pulmonary fibrosis underwent double lung transplantation. He received antibiotic prophylaxis with piperacillin-tazobactam and azythromycin. At day 4 post-transplantation (PTx), the patient presented an acute respiratory distress. A broncho-alveolar lavage (BAL) was performed. At day 5 PTx, the patient presented a status epilepticus due to diffuse cerebral oedema. Serum ammonia concentration was 661 μg/dL. BAL bacterial culture was negative. Because of the clinical presentation, special cultures were performed and identified 100.000 CFU/mL of M. hominis and Ureaplasma spp. and specific PCRs were positive for M. hominis and Ureaplasma parvum. Antibiotic therapy was shifted to therapeutic dose of azithromycin and doxycycline; within 48 h ammonia serum concentrations returned to normal but the coma persisted several weeks, followed by a persistent frontal lobe syndrome. A follow-up BAL was performed on day 11 Ptx. The Mycoplasma/Ureaplasma culture was negative, yet the specific PCRs remained positive. Bacterial culture found 100 CFU/mL of Staphylococcus aureus and viral culture was positive for Herpes Simplex Virus-1. These results were confirmed by metagenomic next-generation sequencing (mNGS). In the bacterial fraction, the majority of reads belonged to Corynebacterium propinquum (34.7%), S. aureus (24.1%) and Staphylococcus epidermidis (17.1%). Reads assigned to M. hominis, Ureaplasma urealyticum and parvum represented 0.71, 0.13, and 0.04% of the bacterial fraction and corresponded to 6.9 × 103, 9.7 × 102, and 3.7 × 102 genome equivalents per mL of BAL fluid, respectively. These results are in favor of a cure of the atypical infection.Conclusions: mNGS offered added diagnostic and quantitative values compared to PCR tests, which can remain positive after resolved infections. The initiation of appropriate antibiotic therapy would have occurred earlier on, possibly resulting in a better clinical outcome if mNGS had been performed in a routine fashion.

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 Next Generation Sequencing for the Prediction of the Antibiotic Resistance in Helicobacter pylori: A Literature Review

Antibiotics ◽  
2021 ◽  
Vol 10 (4) ◽  
pp. 437
Author(s):  
Ilaria Maria Saracino ◽  
Matteo Pavoni ◽  
Angelo Zullo ◽  
Giulia Fiorini ◽  
Tiziana Lazzarotto ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Next Generation Sequencing ◽  
Literature Review ◽  
Molecular Mechanisms ◽  
World Health ◽  
Next Generation ◽  
Culture Methods ◽  
Phenotypic Resistance ◽  
H Pylori ◽  
Generation Sequencing

Background and aims: Only a few antimicrobials are effective against H. pylori, and antibiotic resistance is an increasing problem for eradication therapies. In 2017, the World Health Organization categorized clarithromycin resistant H. pylori as a “high-priority” bacterium. Standard antimicrobial susceptibility testing can be used to prescribe appropriate therapies but is currently recommended only after the second therapeutic failure. H. pylori is, in fact, a “fastidious” microorganism; culture methods are time-consuming and technically challenging. The advent of molecular biology techniques has enabled the identification of molecular mechanisms underlying the observed phenotypic resistance to antibiotics in H. pylori. The aim of this literature review is to summarize the results of original articles published in the last ten years, regarding the use of Next Generation Sequencing, in particular of the whole genome, to predict the antibiotic resistance in H. pylori.Methods: a literature research was made on PubMed. The research was focused on II and III generation sequencing of the whole H. pylori genome. Results: Next Generation Sequencing enabled the detection of novel, rare and complex resistance mechanisms. The prediction of resistance to clarithromycin, levofloxacin and amoxicillin is accurate; for other antimicrobials, such as metronidazole, rifabutin and tetracycline, potential genetic determinants of the resistant status need further investigation.

scholarly journals Case Report: Metagenomic Next-Generation Sequencing in Diagnosis of Talaromycosis of an Immunocompetent Patient

2021 ◽  
Vol 8 ◽  
Author(s):  
Jiejun Shi ◽  
Naibin Yang ◽  
Guoqing Qian
Keyword(s):  
Next Generation Sequencing ◽  
Pathogenic Bacteria ◽  
Clinical Decision Making ◽  
Fungal Infections ◽  
Clinical Manifestations ◽  
Whole Body ◽  
Recurrent Fever ◽  
Next Generation ◽  
Generation Sequencing ◽  
Immunocompetent Patients

Background: Talaromycosis is a serious fungal infection which is rare in immunocompetent people. Since its clinical manifestations lack specificity, it is easy to escape diagnosis or be misdiagnosed leading to high mortality and poor prognosis. It is necessary to be alert to the disease when broad-spectrum antibiotics do not work well in immunocompetent patients.Case Presentation: A 79-year-old man was admitted to our Infectious Diseases Department for recurrent fever and cough. Before admission he has been treated with piperacillin-tazobactam, moxifloxacin followed by antituberculous agents in other hospitals while his symptoms were not thoroughly eased. During the first hospitalization in another hospital, he has been ordered a series of examination including radionuclide whole body bone imaging, transbronchial needle aspiration for subcarinal nodes. However, the results were negative showing no neoplasm. After being admitted to our hospital, he underwent various routine examinations. The initial diagnosis was bacterial pneumonia, and he was given meropenem injection and tigecycline injection successively, but there were no improvement of symptoms and inflammatory indicators. In the end, the main pathogen Talaromyces marneffei was confirmed using Metagenomic Next-Generation Sequencing (mNGS), and his clinical symptoms gradually relieved after targeted antifungal treatment using voriconazole.Conclusion: When empirical anti-infective treatment is ineffective, it is necessary to consider the possibility of opportunistic fungal infections on immunocompetent patients. mNGS, as a new generation of pathogenic testing methods, can often detect pathogenic bacteria faster than traditional methods, providing important help for clinical decision-making.

scholarly journals Bacterial colonization of explanted non-endocarditis cardiac valves: evidence and characterization of the valvular microbiome

2020 ◽  
Author(s):  
Stefano Di Bella ◽  
Giuseppina Campisciano ◽  
Roberto Luzzati ◽  
Enea Gino Di Domenico ◽  
Antonio Lovecchio ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Dna Sequences ◽  
Bacterial Colonization ◽  
Common Finding ◽  
Diabetic Patients ◽  
Next Generation ◽  
Culture Methods ◽  
Bacterial Dna ◽  
Mitral Valves ◽  
Generation Sequencing

Abstract Bacterial colonization has been already demonstrated in heart valve tissues of patients without cardiovascular infections. However, the evidence of a valvular microbiome is still scarce. The next-generation sequencing method was carried out on 34 specimens of aortic (n = 20) and mitral valves (n = 14) explanted from 34 patients having neither evidence nor history of infectious diseases, particularly infective endocarditis. While no bacteria were demonstrated using standard culture methods, bacterial deoxyribonucleic acid (DNA) sequences were found using next-generation sequencing in 15/34 (44%) cases. Escherichia coli was present in 6 specimens and was the most frequently identified bacterium. There was a trend towards a higher rate of bacterial DNA positivity in specimens of calcific valves than in those of non-calcific valves (10/17 vs 5/17, P = 0.17). Based on a quantitative test, E. coli accounted for 0.7% ± 1% in calcific valvular tissue and 0.3% ± 0.3% in non-calcific valvular tissue (P = 0.2), and for 11% ± 27% in the valvular tissue of diabetic patients and 0.3% ± 1% in the valvular tissue of non-diabetic patients (P = 0.08). Detection of bacterial DNA in non-endocarditis valvular tissues could be a relatively common finding. There could be an association between the valvular microbiome and certain models of valve degeneration and common metabolic disorders.

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