scholarly journals Characterization of Leishmania Ulcers Microbiota Using Next Generation Sequencing: Leishmania Ulcers Microbiota

2021 ◽  
Vol 01 (1) ◽  
pp. 68-78
Author(s):  
Suheir Ereqat
Keyword(s):  
Next Generation Sequencing ◽  
Bacterial Communities ◽  
Pathogenic Bacteria ◽  
Healing Process ◽  
Leishmania Infection ◽  
Skin Microbiome ◽  
Next Generation ◽  
Subsequent Formation ◽  
Acinetobacter Species ◽  
Generation Sequencing

The human skin microbiome is a major source of bacteria in cutaneous leishmaniasis (CL) ulcers following the fall of the crust and the subsequent formation of a shallow depression in the epidermis and dermis of the skin. As a result, secondary bacterial infections are frequently observed which impair the healing process. Our study aimed at studying the bacterial communities in CL lesions using next-generation sequencing. A total of 298 patients (178 males and 120 females; median age of 17) presenting ulcerated skin lesions suspected with CL were included in this study. CL was confirmed in 153 (51%) cases by ITS1-PCR and/ or microscopy. Based on bacterial 16S rRNA-PCR, 92 samples were positive for the presence of bacteria, while 206 samples were negative and excluded from the microbiome study. A total of 925 Operational Taxonomic Units (OTUs) were identified and assigned to 215 genera. Despite insignificant difference in the microbiome composition between CL and non-CL lesions, the phylum level analysis revealed that Actinobacteria was significantly higher in CL ulcers while Protoeobacteria was significantly higher in non-CL ulcers (X2, P=0.039). The relative abundance of the most commonly encountered skin pathogens i. e E coli, Pseudomonas aeruginosa, Enterobacter, Enterococcus and Acinetobacter species were significantly higher in non-CL ulcers (X2, P<0.05) compared to Staphylococcus aureus and Proteus mirabilis which were higher in CL ulcers (P<0.05). Our data showed that bacterial communities did not cluster according to the Leishmania infection. Nonetheless, bacterial diversity was lower in CL compared to non-CL lesions. Presence of pathogenic bacteria in CL lesions such as S. aureus might exacerbate lesions, hinder diagnosis, and delay healing.

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 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 Profiling of the Causative Bacteria in Infected Lymphocysts after Lymphadenectomy for Gynecologic Cancer by Pyrosequencing the 16S Ribosomal RNA Gene Using Next-Generation Sequencing Technology

2019 ◽  
Vol 2019 ◽  
pp. 1-5 ◽  
Author(s):  
Yuya Nogami ◽  
Kouji Banno ◽  
Masataka Adachi ◽  
Haruko Kunitomi ◽  
Yusuke Kobayashi ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Pathogenic Bacteria ◽  
Sequence Data ◽  
Bacterial Flora ◽  
Gynecologic Cancer ◽  
False Negative ◽  
Enteric Bacteria ◽  
Next Generation ◽  
Single Strain ◽  
Generation Sequencing

Background. Surgery for gynecologic cancer with lymphadenectomy and pelvic radiotherapy can produce lymphoceles that sometimes complicate with infection, resulting in abscesses. The true pathogenic bacteria of abscesses are not always found because of false-negative results due to administered antibiotics and difficulty with detection, including for anaerobic bacteria. Analyzing bacteria flora by next-generation sequencing (NGS) using 16S ribosomal DNA may reveal the true pathogenic bacteria in abscesses. This is the first report on causative pathogens for infectious lymphocele using this technology. Methods. The subjects were patients who developed infectious lymphocele after surgery for gynecologic cancer at our hospital from July 2015 to September 2016. NGS analyses of bacterial flora were performed using specimens preserved at -80°C. Two steps of PCR were performed for purified DNA samples to obtain sequence libraries. Processing of sequence data, including operational taxonomic unit (OTU) definition, taxonomy assignment, and an OTU BLAST search were performed. All patients gave written informed consent and the study was approved by the institutional research ethics committee. Results. Six patients underwent puncture and drainage. The result in most cases indicated a single causative pathogen, including Staphylococcus lugdunensis, Streptococcus dysgalactiae, Streptococcus equinus, Enterococcus saccharolyticus, and Escherichia coli. Conclusions. NGS revealed that the causative bacteria in lymphocele infection are normally a single strain, such as a surface Gram-positive coccus or enteric bacteria. Antibiotics should be chosen as appropriate for elimination of these respective bacteria.

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.

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