Diagnosis of infectious diseases

With advances in sequencing technologies, high-throughput next-generation sequencing (NGS) has triggered increased attention on its application in clinical laboratories and facilitates the molecular diagnosis and treatment of infectious diseases. Compared with conventional microbiology laboratory methods, NGS has greatly increased the sensitivity and accuracy of diagnosis, and reduced detection time for infectious pathogens, especially for diagnosis of complex and mixed infections. However, there are still some problems that hamper the NGS application in infections diagnosis, including lack of standardization, cost, and variation in data interpretation, etc. In recent years, with the developing of policies and legislation, and guidance and supports from Chinese government, the sequencing industry has gained continuously healthy development and sequencing application market gradually becomes mature. Meanwhile, worldwide microbiology experts are striving to develop the standards and reach the consensus, there are more and more clinical laboratories equipped with sequencing instruments and personnel with expertise. All of these measures would certainly promote the clinical application of NGS, and making full use of high-throughput NGS could contribute to the accurate clinical diagnosis and appropriate treatment. The current article describes the application of high-throughput next-generation sequencing technology in the laboratory diagnosis of clinical microbial infectious diseases, as well as the policy system support and development direction.

Recently, metagenomic next-generation sequencing (mNGS) has been used in the diagnosis of infectious diseases (IDs) as an emerging and powerful tool. However, whether the complicated methodological variation in mNGS detections makes a difference in their clinical performance is still unknown. Here we conducted a method study on the clinical application of mNGS tests in the DNA detection of IDs. We analyzed the effect of several potential factors in the whole process of mNGS for DNA detection on microorganism identification in 98 samples of suspected ID patients by amplification-based mNGS. The amplification-based and amplification-free mNGS tests were successfully performed in 41 samples. Then we compared the clinical application of the two mNGS methods in the DNA detection of IDs. We found that a higher concentration of extracted nucleic acid was more conducive to detecting microorganisms. Other potential factors, such as read depth and proportion of human reads, might not be attributed to microorganism identification. The concordance rate of amplification-based and amplification-free mNGS results was 80.5% (33/41) in the patients with suspected IDs. Amplification-based mNGS showed approximately 16.7% higher sensitivity than amplification-free mNGS. However, 4 cases with causative pathogens only detected by amplification-based mNGS were finally proved false-positive. In addition, empirical antibiotic treatments were adjusted in 18 patients following mNGS testing with unexpected pathogens. Amplification-based and amplification-free mNGS tests showed their specific advantages and disadvantages in the diagnosis of IDs. The clinical application of mNGS still needs more exploration from a methodological perspective. With advanced technology and standardized procedure, mNGS will play a promising role in the diagnosis of IDs and help guide the use of antibiotics.

Strengthening the BTWC: The role of the Biological and Toxin Weapons Convention in combating natural and deliberate disease outbreaks

Infectious Diseases in the Pediatric Intensive Care Unit is a comprehensive collection of infectious disease topics in the paediatric intensive care unit (PICU) and in the neonatal intensive care unit (NICU) written by different experts. The chapters cover a broad range of interest, from the development of the immune system to diagnosis, treatment and prophylaxis of various infectious diseases including sepsis. The chapters on immunology, including the immunosuppressed host – with abundant information about congenital immunodeficiencies and HIV – are more comprehensive than other topics covered. There is further emphasis on potentially life-threatening tropical infections such as malaria, dengue, tetanus and Japanese encephalitis. The purpose of the book is to provide a comprehensive overview of infectious diseases in critically ill neonates and infants. The scope of the book is broad, and it aims to provide information on pathophysiology as well as to serve as a practical manual on diagnosis, therapy and prevention of infectious diseases in the PICU and the NICU. Infectious Diseases in the Pediatric Intensive Care Unit is primarily directed at physicians working with children in intensive care facilities who are not infectious diseases specialists. Most chapters of the book could also reach out to a larger audience, including medical students and infectious disease fellows who are not paediatricians. The short chapter on infection control might be of interest for nonspecialists; however, several of its paragraphs and references (for example, hand hygiene, epidemiology, antibiotic control) are outdated. Most chapters of the book are quite basic and therefore cannot replace currently available standard textbooks or state-of-the-art reviews. Overall, this book does a good job of summarising and presenting the essentials of infectious diseases in the PICU and in the NICU in 580 pages. Moreover, it gives useful and practical information about diagnostic and therapeutic challenges. While some chapters are excellent, however, others are less so and – as the one about fungal infections – are partially outdated and somewhat inaccurate due to recent publications in this field. Furthermore, the merged discussion of issues related to the NICU and the PICU makes some chapters difficult to read because there is considerable variation among differential diagnoses, therapies and prevention strategies among neonates versus older children. Finally, several chapters could have benefited from more illustrations and summary tables to facilitate quick reading. This first edition of the Infectious Diseases in the Pediatric Intensive Care Unit provides comprehensive information about infectious diseases in paediatric and neonatal intensive care facilities. It is a useful guide for paediatric intensive care fellows and physicians in order to gain an overview of specific infectious disease topics in their daily practice.

Unleashing the power of artificial intelligence for diagnosing and treating infectious diseases: A comprehensive review

Background. Nanopore‐based sequencing by Oxford Nanopore Technologies (ONT) offers rapid, cost‐effective and portable sequencing. As an emerging technology, ONT must be evaluated for efficacy and practical application in both high‐ and low‐resource settings. This scoping review (SR) aimed to (1) describe how nanopore technology is used in Africa for surveillance and diagnosis of human infectious diseases, (2) describe how nanopore technology aids in the real-time detection of infectious pathogens in Africa and (3) identify challenges and opportunities for utilizing nanopore technology in Africa to study infectious diseases.Methods. This SR followed the Joanna Briggs Institute Reviewer’s Manual framework for SRs. English language studies published from 1 January 2008 to 30 April 2024 that used ONT on human specimens collected in Africa and targeted ≥1 microbial agent were included. Searches were performed in Embase, Medline, PubMed, CINAHL and the Cochrane Library. The protocol was publicly available on the Open Science Framework Bastug et al. (Nanopore Sequencing for Infectious Diseases Surveillance and Diagnostics in Africa: a Scoping Review 2024) prior to data collection. Two independent reviewers screened studies using Covidence, and data was extracted using a custom REDCap instrument. Descriptive statistics and data visualization were performed in Microsoft Excel.Results. One thousand one hundred sixty-two studies were identified and 93 (8%) underwent full-text review. The portable MinION Mk1B was the most common ONT device (65% of studies). Eighty-eight studies analysed specimens from a single African country. Of these, 45% were sequenced in the same country, 7% in a different African country and 11% in a non-African country, while 32% did not specify the location. Specimen types included direct patient specimens (62%) and cultured isolates (35%), or a combination of both. Blood, serum or plasma was most common (35%), followed by naso- or oropharyngeal specimens (27%). Forty-four studies used ONT during an active infectious disease outbreak, 25 of which studied severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Seventy-two studies used ONT for genomic surveillance of infectious pathogens or antibiotic resistance genes, and one study used ONT for a direct clinical application. African-affiliated authors were included as first, middle and last authors in 46% of studies, and 15% were published by entirely African-affiliated teams. Ten studies published information on workflow timeline, and five studies published the per-specimen cost.Conclusions. ONT can enable timely and affordable sequencing in African countries as demonstrated through a small number of studies that accomplished these goals individually. Most studies used ONT for genomic surveillance of pathogens or antimicrobial resistance genes, while only one study used ONT directly for a real-time clinical application. A small number of studies described a short interval between specimen collection and sequence result, supporting that clinical applications are possible. There is a need for improved reporting of ONT methodology including pipeline timelines, cost, use of barcoding, flow cell models and the use of negative controls. Publications that provide these details will enhance reproducibility and support the development of new studies using ONT for the diagnosis and surveillance of infectious diseases in low-resource settings.

Context—Molecular diagnostics continues to evolve very rapidly, and its impact in the diagnosis of infectious diseases is undeniable. Molecular tools have played a pivotal role in discovering and characterizing several emerging infectious agents and have now become the gold standard for the diagnosis of infectious diseases caused by fastidious or uncultivable agents. Multiple challenges still remain for the widespread use of cost-effective, validated, and commercially available molecular tools. Automated instruments capable of sample processing and multiplex nucleic acid amplification and postamplification analysis have already been approved by the US Food and Drug Administration (FDA) for use in the clinical setting. Nanobiotechnology is beginning to impact laboratory diagnostics in the clinical setting. Objective—To address current nucleic acid techniques used in the clinical laboratory for diagnosis of infectious diseases. FDA-approved tests are listed, as well as molecular techniques (amplifi...

PurposeCRISPR gene-editing technology has the potential to transform the diagnosis and treatment of infectious diseases, but most clinicians are unaware of its broad applicability. Derived from an ancient microbial defence system, these so-called “molecular scissors” enable precise gene editing with a low error rate. However, CRISPR systems can also be targeted against pathogenic DNA or RNA sequences. This potential is being combined with innovative delivery systems to develop new therapeutic approaches to infectious diseases.MethodsWe searched Pubmed and Google Scholar for CRISPR-based strategies in the diagnosis and treatment of infectious diseases. Reference lists were reviewed and synthesized for narrative review.ResultsCRISPR-based strategies represent a novel approach to many challenging infectious diseases. CRISPR technologies can be harnessed to create rapid, low-cost diagnostic systems, as well as to identify drug-resistance genes. Therapeutic strategies, such as CRISPR systems that cleave integrated viral genomes or that target resistant bacteria, are in development. CRISPR-based therapies for emerging viruses, such as SARS-CoV-2, have also been proposed. Finally, CRISPR systems can be used to reprogram human B cells to produce neutralizing antibodies. The risks of CRISPR-based therapies include off-target and on-target modifications. Strategies to control these risks are being developed and a phase 1 clinical trials of CRISPR-based therapies for cancer and monogenic diseases are already underway.ConclusionsCRISPR systems have broad applicability in the field of infectious diseases and may offer solutions to many of the most challenging human infections.

Emerging and relapsing infectious diseases pose a huge health threat to human health and a new challenge to global public health. Rapid, sensitive and simple diagnostic tools are keys to successful management of infectious patients and containment of disease transmission. In recent years, international research on Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) and CRISPR-related proteins (Cas) has revolutionized our understanding of biology. The CRISPR-Cas system has the advantages of high specificity, high sensitivity, simple, rapid, low cost, and has begun to be used for molecular diagnosis and treatment of infectious diseases. In this paper, we described the biological principles, application fields and prospects of CRISPR-Cas system in the molecular diagnosis and treatment of infectious diseases, and compared it with existing molecular diagnosis methods, the advantages and disadvantages were summarized.Supplementary InformationThe online version contains supplementary material available at 10.1007/s11033-022-07752-z.

Rationale:Nocardia farcinica is an opportunistic pathogen that rarely causes ocular infections. This study reviewed a case of N. farcinica-mediated scleritis involving the corneal limbus.Patient concerns:A 56-year-old man was admitted to the Department of Keratology of Jinan Second People’s Hospital due to “a red and swollen right eye accompanied with severe pain for >1 month.” He denied any history of hypertension, diabetes, systemic immune diseases and eye surgery.Diagnoses:Corneal defect and scleral necrosis were observed by slit lamp. Combination of anterior segment optical coherence tomography and ophthalmic ultrasound biomicroscopy was used for diagnosis and evaluation of corneal and scleral conditions. Culture and metagenomic sequencing verified that the pathogen of scleritis was N. farcinica.Interventions:The patient was treated by sulfacetamide sodium eye drops, oral administration of sulfamethoxazole tablets, amikacin anterior chamber flushing, scleral debridement, and allogeneic scleral transplantation.Outcomes:The disease was successfully controlled.Lessons:Infectious scleritis caused by N. farcinica is extremely rare. Culture of pathogenic microorganisms remains to be the gold standard for the diagnosis of infectious eye diseases. Metagenomic sequencing shows potential promise in the diagnosis of infectious eye diseases. N. farcinica is sensitive to sulfonamides and amikacin.

The development of management tactics for pregnant women with congenital infections is the most important medical and social task, since it determines the prognosis and outcome of the disease for the mother and her children. The lack of standardized approaches to the diagnosis and treatment of congenital infectious diseases, as well as the insufficient level of interaction between obstetric and gynecological and infectious diseases services necessitate a comprehensive multidisciplinary approach to the early diagnosis and treatment of congenital infectious diseases in the antenatal period. The article presents our own cases of management of pregnant women with congenital cytomegalovirus and parvovirus B19 infections. Key words: pregnancy, diagnosis, infections, treatment, parvovirus B19, cytomegalovirus

As US public health faces increasing threats from outbreaks, impending changes to the healthcare landscape in the United States may alter the way that health departments are able to detect and control some of the most common infectious diseases. The Patient Protection and Affordable Care Act (ACA) has made significant changes in the way health care is provided in the United States. While many of the clinical, economic, and policy implications of the ACA are well described, there has been limited analysis of changes, if any, in the surveillance and control of infectious diseases of public health importance-such as tuberculosis, sexually transmitted infections, and HIV-that are anticipated or occurring as the ACA is implemented across the United States. To address these questions, we reviewed the literature for evidence of changing trends and conducted 66 semi-structured, not-for-attribution interviews with 82 participants from healthcare systems; academia; federal, state, and local public health agencies; and professional and nongovernmental organizations across the United States. This analysis identifies several ways in which ACA implementation has not fully addressed the public health needs associated with diagnosis, treatment, surveillance, and control of infectious diseases of public health importance.

Some advanced methods and multi-platform technologies have been used for diagnosis of infectious diseases. We reviewed the advanced technologies, such as rapid antigen and antibody detection, rapid molecular detection, integrated automate platform, rapid microorganism identification systems, novel biomarker for sepsis, and the automaton and digitization technologies in this article. It may provide guidance for the future application of new technology in clinical microbiology laboratory, as to provide reference for the construction of clinical microbiology laboratories in the future. Key words: Clinical microbiology; Laboratory; Molecular diagnosis; Automaton

This chapter describes general concepts of diagnosis of viral, bacterial, protozoal and arthropod-borne, and fungal infectious diseases with an overview of the most common diagnostic methods employed for these infections. It discusses specific diagnostic features of common infectious diseases in dogs and cats, geographic distribution, main transmission modes, chief clinical signs, clinicopathologic abnormalities, treatment, prognosis, and prevention. The most commonly employed techniques for the diagnosis of infectious diseases in small animals include microscopic examination of microorganisms in cytologic preparations or histopathologic specimens, serology, polymerase chain reaction, and culture of the organism in appropriate medium are also described. The chapter lists the advantages and disadvantages of these diagnostic techniques. It outlines sample collection, transport, and preservation of specimens for the different diagnostic tests and pathogens.

Serological laboratory diagnosis of infectious diseases is inflicted with several kinds of basic problems. One difficulty relates to the fact that the serological diagnosis of infectious diseases is double indirect: The first indirect aim in diagnosing an infectious disease is to identify the microbial agent that caused the disease. The second indirect aim is to identify this infectious agent by measuring the patient's immune response to the potential agent. Thus, the serological test is neither measuring directly disease nor the cause of the disease, but the patient's immune system. The latter poses another type of problem, because each person's immune system is unique. The immune response to an infectious agent is usually of polyclonal nature, and the exact physicochemical properties of antibodies are unique for each clone of antibody. The clonal makeup and composition and, therefore, the way an individual's immune system sees an infectious agent, depends not only on the genetic background of the person but also on the individual experience from former encounters with various infectious agents. In consequence, the reaction of a patient's serum in an analytical system is not precisely predictable. Also, the antigenic makeup of an infectious agent is not always foreseeable. Antigenic variations leading to different serotypes is a quite common phenomenon. Altogether, these biological problems lead to complexities in selecting the appropriate tests and strategies for testing, in interpreting the results, and in standardizing serological test systems. For that reason, a close collaboration of the laboratory with the clinic is mandatory to avoid erroneous conclusions from serological test results, which might lead to wrong decisions in patient care.