scholarly journals Metagenomic Next-Generation Sequencing Improves the Prognosis of Patients with Infectious Diseases on Mechanical Ventilation in the Intensive Care Unit (ICU)

2020 ◽  
Author(s):  
Yin Xi ◽  
Jing Zhou ◽  
Zhimin Lin ◽  
Weibo Liang ◽  
Chun Yang ◽  
...  
Keyword(s):  
Infectious Disease ◽  
Mechanical Ventilation ◽  
Next Generation Sequencing ◽  
Mortality Rate ◽  
Infectious Diseases ◽  
Apache Ii Score ◽  
Next Generation ◽  
Double Positive ◽  
Conventional Methods ◽  
Generation Sequencing

Abstract Background: Metagenomic Next-Generation Sequencing (mNGS) has gradually shown its advantages in pathogen identification for clinical infectious disease. However, few studies were conducted on the evaluation between this technique and conventional methods like culture and PCR and the prognosis of patients with infectious diseases on mechanical ventilation in ICUMethods: We conducted this retrospective study from March 2018 to May 2020 in the first Affiliated Hospital of Guangzhou Medical University, a total of 228 patients with suspected infectious diseases on mechanical ventilation were included, including 104 cases of mNGS group and 124 cases of non-mNGS. Statistical analyses were performed between the two groups and subgroup of whether were immunocompromised. The concordance between mNGS, culture and PCR was also assessed.Results: The 28-day mortality rate of the patients in the mNGS group was lower after the baseline difference correction (19.23% vs. 29.03%，p=0.039), indicating that mNGS may improve the prognosis of patients in ICU. And subgroup analysis showed that mNGS could improve the 28-day mortality of nonimmunosuppressive patients（14.06% vs. 29.82%, p=0.018）. According to the analysis of Logistic Regression, not performing mNGS, high APACHE II score and hypertension were independent risk factors for 28-day mortality, which strongly suggested that mNGS was one of the key factors affecting prognosis. A total of 157 samples performed mNGS, 116 of them received both mNGS and culture. mNGS presented advantages of positivity (69.8% double positive and 25.0% mNGS positive only) and concordance (79.0%, match and partly match).Conclusions: mNGS may improve the prognosis and reduce the 28-day mortality rate of patients with infectious diseases on mechanical ventilation in ICU. This technique has shown its advantages comparing with conventional methods, and will be wildly used as a promising technology for infectious disease.

scholarly journals Metagenomic Next-Generation Sequencing Improves The Prognosis of Patients With Infectious Diseases on Mechanical Ventilation in The Intensive Care Unit (ICU)

2021 ◽  
Author(s):  
Yin Xi ◽  
Jing Zhou ◽  
Zhimin Lin ◽  
Weibo Liang ◽  
Chun Yang ◽  
...  
Keyword(s):  
Infectious Disease ◽  
Mechanical Ventilation ◽  
Next Generation Sequencing ◽  
Mortality Rate ◽  
Infectious Diseases ◽  
Apache Ii Score ◽  
Next Generation ◽  
Double Positive ◽  
Conventional Methods ◽  
Generation Sequencing

Abstract Background: Metagenomic Next-Generation Sequencing (mNGS) has gradually shown its advantages in pathogen identification for clinical infectious disease. However, few studies were conducted on the evaluation between this technique and conventional methods like culture and PCR and the prognosis of patients with infectious diseases on mechanical ventilation in ICUMethods: We conducted this retrospective study from March 2018 to May 2020 in the first Affiliated Hospital of Guangzhou Medical University, a total of 228 patients with suspected infectious diseases on mechanical ventilation were included, including 104 cases of mNGS group and 124 cases of non-mNGS. Statistical analyses were performed between the two groups and subgroup of whether were immunocompromised. The concordance between mNGS, culture and PCR was also assessed.Results: The 28-day mortality rate of the patients in the mNGS group was lower after the baseline difference correction (19.23% vs. 29.03%，p=0.039), indicating that mNGS may improve the prognosis of patients in ICU. And subgroup analysis showed that mNGS could improve the 28-day mortality of nonimmunosuppressive patients（14.06% vs. 29.82%, p=0.018）. According to the analysis of Logistic Regression, not performing mNGS, high APACHE II score and hypertension were independent risk factors for 28-day mortality, which strongly suggested that mNGS was one of the key factors affecting prognosis. A total of 157 samples performed mNGS, 116 of them received both mNGS and culture. mNGS presented advantages of positivity (69.8% double positive and 25.0% mNGS positive only) and concordance (79.0%, match and partly match).Conclusions: mNGS may improve the prognosis and reduce the 28-day mortality rate of patients with infectious diseases on mechanical ventilation in ICU. This technique has shown its advantages comparing with conventional methods, and will be wildly used as a promising technology for infectious disease.

scholarly journals A Case of Streptococcus Suis Meningitis With Visual Impairment and Hearing Loss Diagnosed by Metagenomic Next-generation Sequencing

2021 ◽  
Author(s):  
Haina Zhao ◽  
Lanlan Chen ◽  
Lin Zhu ◽  
Tingting Qiao ◽  
Peipei Liu ◽  
...  
Keyword(s):  
Cerebrospinal Fluid ◽  
Hearing Loss ◽  
Next Generation Sequencing ◽  
Infectious Diseases ◽  
Visual Impairment ◽  
Vision Loss ◽  
Streptococcus Suis ◽  
Next Generation ◽  
The Right ◽  
Generation Sequencing

Abstract Background: Streptococcus suis is responsible for several kinds of zoonosis worldwide. It can cause meningitis, sepsis, osteoarthritis, endocarditis, endophthalmitis, and other diseases. Human infection typically occurs in occupational settings associated with pig husbandry or pork processing. At present, metagenomic next-generation sequencing (mNGS) is prominent testing method for achieving an early and rapid diagnosis of some infectious diseases. Case presentation: A 48-year-old Chinese man who denied exposure to pigs or pork was to admitted the hospital because he had experienced a fever for three days, visual impairment, and hearing loss for one day. After a series of examinations and laboratory tests, Streptococcus suis was detected in the aqueous humor culture as well as the vitreous humor and cerebrospinal fluid with mNGS. But bacteria were not detected in the blood or cerebrospinal fluid culture. The patient's condition improved, and he was discharged after 2 weeks of active treatment. However, at present, poor vision in the right eye, poor hearing in the right ear and recurrent vertigo remain.Conclusions: In a patient presenting with meningitis, vision loss, and/or hearing loss, Streptococcus suis infection should be strongly suspected regardless of the patient's occupation. mNGS has excellent diagnostic value to determine which was the etiological agent for infectious diseases.

scholarly journals Etiology of fever in Ugandan children: identification of microbial pathogens using metagenomic next-generation sequencing and IDseq, a platform for unbiased metagenomic analysis

2018 ◽  
Author(s):  
Akshaya Ramesh ◽  
Sara Nakielny ◽  
Jennifer Hsu ◽  
Mary Kyohere ◽  
Oswald Byaruhanga ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Pilot Study ◽  
Infectious Diseases ◽  
Parvovirus B19 ◽  
Human Herpesvirus ◽  
Febrile Illness ◽  
Microbial Pathogens ◽  
Next Generation ◽  
Syncytial Virus ◽  
Generation Sequencing

AbstractBackgroundFebrile illness is a major burden in African children, and non-malarial causes of fever are uncertain. We built and employed IDseq, a cloud-based, open access, bioinformatics platform and service to identify microbes from metagenomic next-generation sequencing of tissue samples. In this pilot study, we evaluated blood, nasopharyngeal, and stool specimens from 94 children (aged 2-54 months) with febrile illness admitted to Tororo District Hospital, Uganda.ResultsThe most common pathogens identified were Plasmodium falciparum (51.1% of samples) and parvovirus B19 (4.4%) from blood; human rhinoviruses A and C (40%), respiratory syncytial virus (10%), and human herpesvirus 5 (10%) from nasopharyngeal swabs; and rotavirus A (50% of those with diarrhea) from stool. Among other potential pathogens, we identified one novel orthobunyavirus, tentatively named Nyangole virus, from the blood of a child diagnosed with malaria and pneumonia, and Bwamba orthobunyavirus in the nasopharynx of a child with rash and sepsis. We also identified two novel human rhinovirus C species.ConclusionsThis exploratory pilot study demonstrates the utility of mNGS and the IDseq platform for defining the molecular landscape of febrile infectious diseases in resource limited areas. These methods, supported by a robust data analysis and sharing platform, offer a new tool for the surveillance, diagnosis, and ultimately treatment and prevention of infectious diseases.

scholarly journals Precision Medicine and Precision Public Health in the Era of Pathogen Next-Generation Sequencing

2019 ◽  
Vol 221 (Supplement_3) ◽  
pp. S289-S291 ◽  
Author(s):  
Mariana Leguia ◽  
Anton Vila-Sanjurjo ◽  
Patrick S G Chain ◽  
Irina Maljkovic Berry ◽  
Richard G Jarman ◽  
...  
Keyword(s):  
Public Health ◽  
Next Generation Sequencing ◽  
Infectious Diseases ◽  
Next Generation ◽  
The Past ◽  
Infectious Disease Research ◽  
History Of ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing ◽  
Health Applications

Abstract This brief report serves as an introduction to a supplement of the Journal of Infectious Diseases entitled “Next-Generation Sequencing (NGS) Technologies to Advance Global Infectious Disease Research.” We briefly discuss the history of NGS technologies and describe how the techniques developed during the past 40 years have impacted our understanding of infectious diseases. Our focus is on the application of NGS in the context of pathogen genomics. Beyond obvious clinical and public health applications, we also discuss the challenges that still remain within this rapidly evolving field.

scholarly journals Next Generation Sequencing and Bioinformatics Methodologies for Infectious Disease Research and Public Health: Approaches, Applications, and Considerations for Development of Laboratory Capacity

2019 ◽  
Author(s):  
Irina Maljkovic Berry ◽  
Melanie C Melendrez ◽  
Kimberly A Bishop-Lilly ◽  
Wiriya Rutvisuttinunt ◽  
Simon Pollett ◽  
...  
Keyword(s):  
Public Health ◽  
Infectious Disease ◽  
Next Generation Sequencing ◽  
Next Generation ◽  
Human Pathogens ◽  
Sequencing Platform ◽  
Disease Research ◽  
Infectious Disease Research ◽  
Pathogen Discovery ◽  
Generation Sequencing

Abstract Next generation sequencing (NGS) combined with bioinformatics has successfully been used in a vast array of analyses for infectious disease research of public health relevance. For instance, NGS and bioinformatics approaches have been used to identify outbreak origins, track transmissions, investigate epidemic dynamics, determine etiological agents of a disease, and discover novel human pathogens. However, implementation of high-quality NGS and bioinformatics in research and public health laboratories can be challenging. These challenges mainly include the choice of the sequencing platform and the sequencing approach, the choice of bioinformatics methodologies, access to the appropriate computation and information technology infrastructure, and recruiting and retaining personnel with the specialized skills and experience in this field. In this review, we summarize the most common NGS and bioinformatics workflows in the context of infectious disease genomic surveillance and pathogen discovery, and highlight the main challenges and considerations for setting up an NGS and bioinformatics-focused infectious disease research public health laboratory. We describe the most commonly used sequencing platforms and review their strengths and weaknesses. We review sequencing approaches that have been used for various pathogens and study questions, as well as the most common difficulties associated with these approaches that should be considered when implementing in a public health or research setting. In addition, we provide a review of some common bioinformatics tools and procedures used for pathogen discovery and genome assembly, along with the most common challenges and solutions. Finally, we summarize the bioinformatics of advanced viral, bacterial, and parasite pathogen characterization, including types of study questions that can be answered when utilizing NGS and bioinformatics.

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