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Dan Li,1– 3,* Qingling Li,4,* Zhen Huang,2 Wenhao Wu,2 Xinyuan Fan,2 Jing Liu,2 Ruoran Li,2 Qi Zhang,2 Xin Su1 1Department of Respiratory and Critical Care Medicine, Nanjing Drum Tower Hospital, Clinical College of Nanjing Medical University, Nanjing, Jiangsu, 210000, People’s Republic of China; 2Department of Respiratory and Critical Care Medicine, Xuzhou Central Hospital, Xuzhou, Jiangsu, 221000, People’s Republic of China; 3Department of Respiratory and Critical Care Medicine, Jinling Hospital, Nanjing Medical University, Nanjing, 210002, People’s Republic of China; 4Department of Respiratory and Critical Care Medicine, Xuzhou First People’s Hospital, The Affiliated Xuzhou Municipal Hospital of Xuzhou Medical University, Xuzhou, Jiangsu, 221000, People’s Republic of China*These authors contributed equally to this workCorrespondence: Xin Su, Department of Respiratory and Critical Care Medicine, Nanjing Drum Tower Hospital, Clinical College of Nanjing Medical University, Nanjing, Jiangsu, 210000, People’s Republic of China, Email suxinjs@163.com Qi Zhang, Department of Respiratory and Critical Care Medicine, Xuzhou Central Hospital, Xuzhou, Jiangsu, 221000, People’s Republic of China, Email zhangqi1107@126.comBackground: tNGS and mNGS are valuable tools for diagnosing pathogens in lower respiratory tract infections (LRTIs), which subsequently influence treatment strategies. However, the impact of tNGS and mNGS on antimicrobial stewardship in patients with LRTIs remains unclear.Methods: Patients diagnosed with LRTIs who underwent tNGS or mNGS between June 2021 and January 2024 were included. Patients who underwent both tNGS and conventional microbiologic tests (CMTs) were grouped into the tNGS group, the others were divided into the mNGS group. Then, the diagnostic efficacy of tNGS and mNGS was compared, along with their impact on antimicrobial management and clinical outcomes.Results: 548 patients with an initial diagnosis of LRTIs who underwent tNGS or mNGS were evaluated. Finally, 321 patients were analyzed, with 117 patients in tNGS group and 204 patients in mNGS group. The overall pathogen detection rates for tNGS and mNGS were 89.74% and 89.71% (P=0.991). The distribution of detected pathogens was similar between tNGS and mNGS, with bacteria being the predominant microorganisms. The proportions of patients who underwent antimicrobial agent changes and received targeted therapy were not significantly different between tNGS and mNGS groups (P=0.270; P=0.893). Additionally, no significant differences were noted in the rates of antibiotic de-escalation, escalation, or changes in the opposite direction (all P> 0.05). The same results was observed in the proportions of patients with addition or reductions in antiviral, antifungal, and antibacterial agents (all P> 0.05). Hospital stays, improvement rate and mortality rate were also similar (all P> 0.05).Conclusion: tNGS and mNGS demonstrate comparable overall pathogen yield rates in patients with LRTIs. Furthermore, tNGS is also comparable to mNGS in terms of adjusting antimicrobial treatments and clinical outcomes, tNGS meets the clinical needs of most patients with LRTIs and can be firstly used for these patients.Keywords: tNGS, mNGS, antimicrobial management, lower respiratory tract infection

Hongyuan Zhou,* Jian Zhang* Department of Respiratory and Critical Care Medicine, Yuyao People’s Hospital, Ningbo City, Zhejiang Province, People’s Republic of China*These authors contributed equally to this workCorrespondence: Jian Zhang, Department of Respiratory and Critical Care Medicine, Yuyao People’s Hospital, No. 800 Chengdong Road, Fengshan District, Ningbo City, Zhejiang Province, People’s Republic of China, Tel +8615068756296, Email 514041632@qq.comBackground: Tropheryma whipplei (T. whipplei) is a rod-shaped, Gram-positive, acid-fast bacterium. Classical Whipple’s disease, a rare chronic infectious condition affecting multiple systems, is traditionally attributed to T. whipplei infection. The conventional treatment regimen consists of a one-year course of oral doxycycline (100 mg twice daily) and hydroxychloroquine (600 mg daily), followed by lifelong doxycycline maintenance therapy. However, the literature lacks discussion on short-term antimicrobial treatment for acute T. whipplei infections, such as pulmonary abscesses caused by this pathogen.Presentation: This case report describes a 57-year-old male presenting with a pulmonary abscess. The patient underwent bronchoscopic alveolar lavage and pus cavity irrigation. The collected sample was subjected to pathogen targeted next-generation sequencing (tNGS) analysis. The tNGS results indicated that T. whipplei was the primary etiological agent responsible for the pulmonary abscess. Treatment with 6 weeks amoxicillin clavulanate led to a favorable clinical outcomes.Conclusion: Existing case reports typically employ treatment protocols for classic Whipple’s disease, such as oral doxycycline combined with hydroxychloroquine or trimethoprim/sulfamethoxazole for a one-year duration. The use of amoxicillin/clavulanic acid for short-term antimicrobial treatment of T. whipplei-induced pulmonary abscesses achieved favorable clinical outcomes. This case study explores the feasibility of short-term antimicrobial therapy for an acute T. whipplei infection.Keywords: Tropheryma whipplei, pulmonary abscess, tNGS, bronchoscopic lavage

Background: Parvimonas micra (P. micra) has been identified as a pathogen capable of causing lung abscesses; however, its identification poses challenges due to the specialized culture conditions for anaerobic bacterial isolation. Only a few cases of lung abscesses caused by P. micra infection have been reported. Therefore, we describe the clinical characteristics of lung abscesses due to P. micra based on our case series. Methods: A retrospective analysis was conducted on eight patients who were diagnosed with lung abscesses attributed to P. micra. Detection of P. micra was accomplished through target next-generation sequencing (tNGS). A systematic search of the PubMed database using keywords "lung abscess" and "Parvimonas micra/Peptostreptococcus micros" was performed to review published literature pertaining to similar cases. Results: Among the eight patients reviewed, all exhibited poor oral hygiene, with four presenting with comorbid diabetes. Chest computed tomography (CT) showed high-density mass shadows with necrosis and small cavities in the middle. Bronchoscopic examination revealed purulent sputum and bronchial mucosal inflammation. Thick secretions obstructed the airway, leading to the poor drainage of pus, and the formation of local abscesses leading to irresponsive to antibiotic therapy, which finally protracted recovery time. P. micra was successfully identified in bronchoalveolar lavage fluid (BALF) samples from all eight patients using tNGS; in contrast, sputum and BALF bacterial cultures yielded negative results, with P. micra cultured from only one empyema sample. Following appropriate antibiotic therapy, seven patients recovered. In previously documented cases, favorable outcomes were observed in 77.8% of individuals treated with antibiotics and 22.2% were cured after surgical interventions for P. micra lung abscesses. Conclusions: This study enriches our understanding of the clinical characteristics associated with lung abscesses attributed to P. micra. Importantly, tNGS has emerged as a rapid and effective diagnostic test in scenarios where traditional sputum cultures are negative. Encouragingly, patients with lung abscesses caused by P. micra infection exhibit a favorable prognosis with effective airway clearance and judicious anti-infective management. [ABSTRACT FROM AUTHOR]

BackgroundPsittacosis is a zoonotic infectious disease caused by Chlamydia psittaci (C. psittaci) infection, which can be transmitted by birds, poultry and wild animals. The symptoms and imaging findings of C. psittaci pneumonia are atypical and primarily rely on etiological diagnosis. The incidence of C. psittaci infection has been significantly underestimated because of the low sensitivity and poor timeliness of traditional diagnostic methods. Therefore, early and accurate diagnosis of psittacosis remains a challenge.Case presentationA case series with six pneumonia patients who were admitted to our hospital in the period from January 2023 to June 2023 is presented. These patients exhibited acute onset and symptoms, including fever, cough, poor appetite, dry mouth, dizziness, chills, and chest tightness. Despite comprehensive laboratory and radiological examinations, the cause of the pneumonia remained unidentified. Therefore, a sample of bronchoalveolar lavage fluid (BALF) was tested via target next-generation sequencing (tNGS), which revealed a positive result for C. psittaci. Prompt adjustment of the treatment regimens upon identification of the pathogen led to favorable outcomes in all patients.ConclusiontNGS is a novel diagnostic technology that enables rapid, accurate and cost-effective detection of C. psittaci pneumonia. Early detection of C. psittaci can improve patient outcomes through timely adjustment of therapies.

BackgroundMetagenomic next-generation sequencing (mNGS) technology has been widely used to diagnose various infections. Based on the most common pathogen profiles, targeted mNGS (tNGS) using multiplex PCR has been developed to detect pathogens with predesigned primers in the panel, significantly improving sensitivity and reducing economic burden on patients. However, there are few studies on summarizing pathogen profiles of pulmonary infections in immunocompetent and immunocompromised patients in Jilin Province of China on large scale.MethodsFrom January 2021 to December 2023, bronchoalveolar lavage fluid (BALF) or sputum samples from 546 immunocompetent and immunocompromised patients with suspected community-acquired pneumonia were collected. Pathogen profiles in those patients on whom mNGS was performed were summarized. Additionally, we also evaluated the performance of tNGS in diagnosing pulmonary infections.ResultsCombined with results of mNGS and culture, we found that the most common bacterial pathogens were Pseudomonas aeruginosa, Klebsiella pneumoniae, and Acinetobacter baumannii in both immunocompromised and immunocompetent patients with high detection rates of Staphylococcus aureus and Enterococcus faecium, respectively. For fungal pathogens, Pneumocystis jirovecii was commonly detected in patients, while fungal infections in immunocompetent patients were mainly caused by Candida albicans. Most of viral infections in patients were caused by Human betaherpesvirus 5 and Human gammaherpesvirus 4. It is worth noting that, compared with immunocompetent patients (34.9%, 76/218), more mixed infections were found in immunocompromised patients (37.8%, 14/37). Additionally, taking final comprehensive clinical diagnoses as reference standard, total coincidence rate of BALF tNGS (81.4%, 48/59) was much higher than that of BALF mNGS (40.0%, 112/280).ConclusionsOur findings supplemented and classified the pathogen profiles of pulmonary infections in immunocompetent and immunocompromised patients in Jilin Province of China. Most importantly, our findings can accelerate the development and design of tNGS specifically used for regional pulmonary infections.

Shiying Li,1 Jin Tong,2 Hu Li,1 Chenxue Mao,3 Wei Shen,1 Yu Lei,1 Peng Hu1 1Department of Infectious Diseases, Key Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education), Institute for Viral Hepatitis, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, People’s Republic of China; 2Department of Respiratory Medicine, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, People’s Republic of China; 3Department of Laboratory Diagnosis, ChongQing KingMed Center for Clinical Laboratory Co., Ltd, Chongqing, 400050, People’s Republic of ChinaCorrespondence: Peng Hu, Department of Infectious Diseases, Key Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education), Institute for Viral Hepatitis, The Second Affiliated Hospital, Chongqing Medical University, 74# Linjiang Road, Chongqing, 400010, People’s Republic of China, Email hp_cq@163.com; hupengcq@hospital.cqmu.edu.cnAbstract: We report a case of a 34-year-old lady with multiple joint pain. Autoimmune diseases were considered first with a positive result of anti-Ro antibody and her right knee joint cavity effusion. Later, bilateral interstitial changes in her lungs and mediastinal lymphadenopathy were found after chest CT scanning. Empirical quinolone therapy was given although pathological examinations of blood, sputum and bronchoalveolar lavage fluid (BALF) did not find anything. Finally, Legionella pneumophila was identified by target next-generation sequencing (tNGS) detection. This case highlighted the timely use of tNGS, a new tool with fast speed, high accuracy and effective cost, could help to identify atypical infection and start an early therapy.Keywords: case report, Legionella pneumophila, targeted next-generation sequencing, tNGS, precision treatment, levofloxacin

Abstract Background Organizing pneumonia (OP) is a rare interstitial lung disease. Secondary organizing pneumonia (SOP) caused by Mycobacterium tuberculosis (MTB) is extremely rare. Migratory MTB-associated SOP is more deceptive and dangerous. When insidious tuberculosis (TB) is not recognized, SOP would be misdiagnosed as cryptogenic organizing pneumonia (COP). Use of steroid hormone alone leads to the progression of TB foci or even death. Clues of distinguishing atypical TB at the background of OP is urgently needed. Case presentation A 56-year-old female patient was hospitalized into the local hospital because of cough and expectoration for more than half a month. Her medical history and family history showed no relation to TB or other lung diseases. Community-acquired pneumonia was diagnosed and anti-infection therapy was initialized but invalid. The patient suffered from continuous weigh loss. More puzzling, the lesions were migratory based on the chest computed tomography (CT) images. The patient was then transferred to our hospital. The immunological indexes of infection in blood and pathogenic tests in sputum and the bronchoalveolar lavage fluid were negative. The percutaneous lung puncture biopsy and pathological observation confirmed OP, but without granulomatous lesions. Additionally, pathogen detection of the punctured lung tissues by metagenomics next generation sequencing test (mNGS) were all negative. COP was highly suspected. Fortunately, the targeted next-generation sequencing (tNGS) detected MTB in the punctured lung tissues and MTB-associated SOP was definitely diagnosed. The combined therapy of anti-TB and prednisone was administrated. After treatment for 10 days, the partial lesions were significantly resorbed and the patient was discharged. In the follow-up of half a year, the patient was healthy. Conclusions It is difficult to distinguish SOP from COP in clinical practice. Diagnosis of COP must be very cautious. Transient small nodules and cavities in the early lung image are a clue to consider TB, even though all pathogen tests are negative. tNGS is also a powerful tool to detect pathogen, ensuring prompt diagnosis of TB-related SOP. For clinicians in TB high burden countries, we encourage them to keep TB in mind before making a final diagnosis of COP.

Background: Organizing pneumonia (OP) is a rare interstitial lung disease. Secondary organizing pneumonia (SOP) caused by Mycobacterium tuberculosis (MTB) is extremely rare. Migratory MTB-associated SOP is more deceptive and dangerous. When insidious tuberculosis (TB) is not recognized, SOP would be misdiagnosed as cryptogenic organizing pneumonia (COP). Use of steroid hormone alone leads to the progression of TB foci or even death. Clues of distinguishing atypical TB at the background of OP is urgently needed. Case presentation: A 56-year-old female patient was hospitalized into the local hospital because of cough and expectoration for more than half a month. Her medical history and family history showed no relation to TB or other lung diseases. Community-acquired pneumonia was diagnosed and anti-infection therapy was initialized but invalid. The patient suffered from continuous weigh loss. More puzzling, the lesions were migratory based on the chest computed tomography (CT) images. The patient was then transferred to our hospital. The immunological indexes of infection in blood and pathogenic tests in sputum and the bronchoalveolar lavage fluid were negative. The percutaneous lung puncture biopsy and pathological observation confirmed OP, but without granulomatous lesions. Additionally, pathogen detection of the punctured lung tissues by metagenomics next generation sequencing test (mNGS) were all negative. COP was highly suspected. Fortunately, the targeted next-generation sequencing (tNGS) detected MTB in the punctured lung tissues and MTB-associated SOP was definitely diagnosed. The combined therapy of anti-TB and prednisone was administrated. After treatment for 10 days, the partial lesions were significantly resorbed and the patient was discharged. In the follow-up of half a year, the patient was healthy. Conclusions: It is difficult to distinguish SOP from COP in clinical practice. Diagnosis of COP must be very cautious. Transient small nodules and cavities in the early lung image are a clue to consider TB, even though all pathogen tests are negative. tNGS is also a powerful tool to detect pathogen, ensuring prompt diagnosis of TB-related SOP. For clinicians in TB high burden countries, we encourage them to keep TB in mind before making a final diagnosis of COP. [ABSTRACT FROM AUTHOR]

Abstract Background Patients with acquired immunodeficiency syndrome (AIDS) tend to suffer from several central nervous system (CNS) infections due to hypoimmunity. However, CNS aspergillosis (CNSAG) is extremely rare and difficult to diagnose. Thus, it is easily misdiagnosed. Case presentation We reported a 47-year-old male AIDS patient with ghosting vision and anhidrosis on the left head and face. He was accordingly diagnosed with Toxoplasma gondii encephalitis (TE) at other hospitals, for which he received regular anti-Toxoplasma gondii and anti-human immunodeficiency virus (anti-HIV) treatment. Then, the patient was transferred to our hospital due to a lack of any improvement with the prescribed treatment. The patient's neurological examination revealed no abnormalities at admission, only a slight change in the cerebrospinal fluid. His cranial magnetic resonance imaging (MRI) revealed multiple abnormal signals in the brain parenchyma, and his blood was positive for Toxoplasma gondii IgG antibody. The initial diagnosis at our hospital was also TE. Considering the poor efficacy of anti-TE treatment, cerebrospinal fluid metagenomics next-generation sequencing (mNGS) was performed, but no pathogenic bacteria were detected. However, Aspergillus fumigatus was detected in the cerebrospinal fluid via targeted next-generation sequencing (tNGS) and bronchoalveolar alveolar lavage fluid via mNGS. The diagnosis was accordingly revised to CNSAG combined with his other clinical manifestations. After administering voriconazole antifungal therapy, the patient’s symptoms were relieved, with improved absorption of the intracranial lesions. Conclusions The present case experience indicates the need for clinicians to strengthen their understanding of CNSAG. Moreover, for patients with diagnostic difficulties, early mNGS and tNGS (using biological samples with only a few pathogens) are helpful for early diagnosis and treatment, potentially allowing patients to achieve favorable outcomes.

Novel germplasm resources are the key to crop breeding, with their genetic diversity and population structure analysis being highly significant for future faba bean breeding. We genotyped 410 global faba bean accessions using the 130K targeted next-generation sequencing (TNGS) genotyping platform, resulting in a total of 38,111 high-quality SNP loci by high-standard filtering. We found the polymorphism information content (PIC) and Nei's gene diversity were 0.0905–0.3750 and 0.0950–0.5000, with averages of 0.2471 and 0.3035, respectively. After evaluating the genetic diversity of 410 accessions using Nei's gene diversity and PIC, on the basis of their geographical origin (continent) and structure-analysis-inferred subpopulations, we found that the faba bean accessions from Asia (except China) and Europe had rich genetic diversity, while those from the winter sowing area of China were low. The 410 faba bean accessions were divided into four subpopulations according to population structure analysis and clustering analysis based on Nei's (1972) genetic distance using the neighbor-joining (NJ) method. However, the same subpopulation contained materials from different geographical origins, thereby indicating that the gene flow or introgression occurred among the accessions. Results from NJ clustering based on shared allele genetic distance indicated that the 410 accessions were divided into three groups according to their dissemination routes. The genetic diversity analysis results demonstrated that the genetic relationships among the faba bean groups with similar ecological environments and geographic origins in neighboring regions or countries were closer and frequently found within the same group, while genetic variation among individuals was the main source of their total genetic variation. [ABSTRACT FROM AUTHOR]

• tNGS identified pathogenic infections in 99.09% of these patients. • 76.36% of children with severe pneumonia had mixed infections. • The main infectious pathogens were MP, HRSV and HHV. • 40% of the severe pneumonia required admission to the ICU. Severe pneumonia in children represents a significant clinical challenge due to its high incidence and associated mortality. This study aimed to assess the distribution of pathogens and patterns of infection in pediatric patients with severe pneumonia. This study included 110 pediatric patients diagnosed with severe pneumonia, who were admitted to Guangxi Maternal and Child Health Hospital between July 2021 and November 2023. Pathogen-targeted next-generation sequencing (tNGS) was employed to identify respiratory pathogens in these cases. Pathogens were detected in 109 out of 110 cases, yielding a positive detection rate of 99.09%. Among these cases, 25 (22.72%) involved single-pathogen infections, while 84 (76.36%) were characterized by mixed infections. The infection pattern in children with severe pneumonia was relatively common with bacterial-viral coinfection (28.2%, 31/110). A total of 39 pathogens were identified from the 110 children with severe pneumonia, with the top three pathogens being Mycoplasma pneumoniae (30.91%, 34/110), Human Respiratory Syncytial Virus Type A (26.36%, 29/110), and Human Herpesvirus (18.18%, 20/110). Notably, 38.2% (13/34) of the cases were found to have macrolide-resistant Mycoplasma pneumoniae (MRMP). Additionally, 40% (44/110) of the children required admission to the intensive care unit (ICU). The application of tNGS demonstrates significant utility in the detection of pathogens in pediatric patients with severe pneumonia. The predominant pathogens identified in this study are Mycoplasma pneumoniae , Human Respiratory Syncytial Virus, and Human Herpesvirus. Furthermore, mixed infections involving multiple pathogens were observed in 76.36% of the cases, and a substantial proportion (40%) of these patients necessitated intensive care. [ABSTRACT FROM AUTHOR]

Background: Patients with acquired immunodeficiency syndrome (AIDS) tend to suffer from several central nervous system (CNS) infections due to hypoimmunity. However, CNS aspergillosis (CNSAG) is extremely rare and difficult to diagnose. Thus, it is easily misdiagnosed. Case presentation: We reported a 47-year-old male AIDS patient with ghosting vision and anhidrosis on the left head and face. He was accordingly diagnosed with Toxoplasma gondii encephalitis (TE) at other hospitals, for which he received regular anti-Toxoplasma gondii and anti-human immunodeficiency virus (anti-HIV) treatment. Then, the patient was transferred to our hospital due to a lack of any improvement with the prescribed treatment. The patient's neurological examination revealed no abnormalities at admission, only a slight change in the cerebrospinal fluid. His cranial magnetic resonance imaging (MRI) revealed multiple abnormal signals in the brain parenchyma, and his blood was positive for Toxoplasma gondii IgG antibody. The initial diagnosis at our hospital was also TE. Considering the poor efficacy of anti-TE treatment, cerebrospinal fluid metagenomics next-generation sequencing (mNGS) was performed, but no pathogenic bacteria were detected. However, Aspergillus fumigatus was detected in the cerebrospinal fluid via targeted next-generation sequencing (tNGS) and bronchoalveolar alveolar lavage fluid via mNGS. The diagnosis was accordingly revised to CNSAG combined with his other clinical manifestations. After administering voriconazole antifungal therapy, the patient's symptoms were relieved, with improved absorption of the intracranial lesions. Conclusions: The present case experience indicates the need for clinicians to strengthen their understanding of CNSAG. Moreover, for patients with diagnostic difficulties, early mNGS and tNGS (using biological samples with only a few pathogens) are helpful for early diagnosis and treatment, potentially allowing patients to achieve favorable outcomes. [ABSTRACT FROM AUTHOR]

Lysosomal storage diseases (LSDs) are a heterogeneous group of rare multisystem metabolic disorders occurring mostly in infancy and childhood, characterized by a gradual accumulation of non-degraded substrates inside the cells. Although biochemical enzymatic assays are considered the gold standard for diagnosis of symptomatic patients, genotyping is a requirement for inclusion in enzyme replacement programs and is a prerequisite for carrier tests in relatives and DNA-based prenatal diagnosis. The emerging next-generation sequencing (NGS) technologies are now offering a powerful diagnostic tool for genotyping LSDs patients by providing faster, cheaper, and higher-resolution testing options, and are allowing to unravel, in a single integrated workflow SNVs, small insertions and deletions (indels), as well as major structural variations (SVs) responsible for the pathology. Here, we summarize the current knowledge about the most recurrent and private SVs involving LSDs-related genes, review advantages and drawbacks related to the use of the NGS in the SVs detection, and discuss the challenges to bring this type of analysis in clinical diagnostics. [ABSTRACT FROM AUTHOR]

Lysosomal storage diseases (LSDs) are a heterogeneous group of rare multisystem metabolic disorders occurring mostly in infancy and childhood, characterized by a gradual accumulation of non-degraded substrates inside the cells. Although biochemical enzymatic assays are considered the gold standard for diagnosis of symptomatic patients, genotyping is a requirement for inclusion in enzyme replacement programs and is a prerequisite for carrier tests in relatives and DNA-based prenatal diagnosis. The emerging next-generation sequencing (NGS) technologies are now offering a powerful diagnostic tool for genotyping LSDs patients by providing faster, cheaper, and higher-resolution testing options, and are allowing to unravel, in a single integrated workflow SNVs, small insertions and deletions (indels), as well as major structural variations (SVs) responsible for the pathology. Here, we summarize the current knowledge about the most recurrent and private SVs involving LSDs-related genes, review advantages and drawbacks related to the use of the NGS in the SVs detection, and discuss the challenges to bring this type of analysis in clinical diagnostics.

Abstract Computational neuroscience attempts to understand the nervous system functions by using realistic models in large-scale simulations. This work is inspired by the Theory of Neural Group Selection (TNGS) and by the theory of Central Pattern Generators (CPGs). The TNGS states that neural connection topology generates strongly connected neuronal groups which are the smallest functional unit of the nervous system responsible for the most basic processing activities. The CPGs are neuronal circuits, located in the spinal cord of vertebrate animals, responsible for breathing, rhythm generation, motor behaviors, as well as other oscillatory functions. In this work, the oscillatory dynamics of neuronal groups and CPGs is modeled by using spiking neural networks. The aim is to analyze how the relationship between the parameters of the neural network influences its oscillatory frequency. The neurons are implemented by using the Izhikevich neuron model due to its low computational cost and biological plausibility. The methodology used in this analysis consists of four steps. In the first step, the influence of the constructive parameters in the oscillation frequency of the neural network is studied using the 2 k Factorial Design. In the second step, the statistical relevance of the parameters a and b of the Izhikevich equation as well as the synaptic weight s was verified by the Friedman test, demonstrating their influence in determining the network oscillation frequency. In the third step, the parameters of the second step were adjusted to build systems at frequencies of 5, 20 and 40 Hz, proving the hypothesis established in the Friedman test, i.e. , that the oscillation frequency can be set by the parameters a, b and s. In the fourth step, a mathematical formulation is presented to relate the oscillation frequency of the neural network with its constructive parameters. These results contribute to building spiking neural networks oscillating at desired frequencies, which may be used as the building blocks of CPGs and neuronal groups, as proposed in the TNGS. [ABSTRACT FROM AUTHOR]

In July 2023, the World Health Organization (WHO) began recommending targeted next-generation sequencing (tNGS), due to its ability to detect resistance to many drugs with a single test. In March 2023, South Africa further adopted the GeneXpert XDR cartridge, which detects mutations associated with resistance to second-line injectable drugs. Here, we consider the feasibility for implementing tNGS in South Africa, what such a facility might look like and the specific context of this upper-middle-income country. Whilst the WHO now recommends tNGS for TB diagnostics and DST, there are many economic and infrastructural challenges opposing its deployment. In lieu of this, we instead recommend a stratified diagnostic pipeline that utilizes South Africa's existing GeneXpert technologies, attempting to reduce the costs associated with implementation of tNGS., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (© 2024 The Authors.)

Background and Aims An expanding number of monogenic defects have been identified as causative of severe forms of very early-onset inflammatory bowel diseases [VEO-IBD]. The present study aimed at defining how next-generation sequencing [NGS] methods can be used to improve identification of known molecular diagnosis and to adapt treatment. Methods A total of 207 children were recruited in 45 paediatric centres through an international collaborative network [ESPGHAN GENIUS working group] with a clinical presentation of severe VEO-IBD [ n = 185] or an anamnesis suggestive of a monogenic disorder [ n = 22]. Patients were divided at inclusion into three phenotypic subsets: predominantly small bowel inflammation, colitis with perianal lesions, and colitis only. Methods to obtain molecular diagnosis included functional tests followed by specific Sanger sequencing, custom-made targeted NGS, and in selected cases whole exome sequencing [WES] of parents-child trios. Genetic findings were validated clinically and/or functionally. Results Molecular diagnosis was achieved in 66/207 children [32%]: 61% with small bowel inflammation, 39% with colitis and perianal lesions, and 18% with colitis only. Targeted NGS pinpointed gene mutations causative of atypical presentations, and identified large exonic copy number variations previously missed by WES. Conclusions Our results lead us to propose an optimised diagnostic strategy to identify known monogenic causes of severe IBD. [ABSTRACT FROM AUTHOR]

Background: Phenotypic drug susceptibility testing (pDST) for Mycobacterium tuberculosis can take up to 8 weeks, while conventional molecular tests identify a limited set of resistance mutations. Targeted next-generation sequencing (tNGS) offers rapid results for predicting comprehensive drug resistance, and this study sought to explore its operational feasibility within a public health laboratory in Mumbai, India., Methods: Pulmonary samples from consenting patients testing Xpert MTB-positive were tested for drug resistance by conventional methods and using tNGS. Laboratory operational and logistical implementation experiences from study team members are shared below., Results: Of the total number of patients tested, 70% (113/161) had no history of previous TB or treatment; however, 88.2% ( n = 142) had rifampicin-resistant/multidrug-resistant TB (RR/MDR-TB). There was a high concordance between resistance predictions of tNGS and pDST for most drugs, with tNGS more accurately identifying resistance overall. tNGS was integrated and adapted into the laboratory workflow; however, batching samples caused significantly longer result turnaround time, fastest at 24 days. Manual DNA extraction caused inefficiencies; thus protocol optimisations were performed. Technical expertise was required for analysis of uncharacterised mutations and interpretation of report templates. tNGS cost per sample was US$230, while for pDST this was US$119., Conclusions: Implementation of tNGS is feasible in reference laboratories. It can rapidly identify drug resistance and should be considered as a potential alternative to pDST., Competing Interests: Conflicts of interest: none declared., (© 2023 The Union.)

Based on the Theory of Neuronal Group Selection (TNGS), we have investigated the emergence of synchronicity in a network composed of spiking neurons via genetic algorithm. The TNGS establishes that a neuronal group is the most basic unit in the cortical area of the brain and, as a rule, it is not formed by a single neuron, but by a cluster of tightly coupled neural cells which fire and oscillate in synchrony at a predefined frequency. Thus, this paper describes a method of tuning the parameters of the Izhikevich spiking neuron model through genetic algorithm in order to enable the self-organization of the neural network. Computational experiments were performed considering a network composed of neurons of the same type and another composed of neurons of different types. [ABSTRACT FROM AUTHOR]

Proprotein convertase 1 (PCSK1, PC1/3) deficiency is an uncommon cause of neonatal malabsorptive diarrhoea associated with endocrinopathies that are due to the disrupted processing of a large number of prohormones, including proinsulin. To date, only 26 cases have been reported. Herein, we describe two siblings with typical features including severe congenital diarrhoea, central diabetes insipidus, growth hormone deficiency, and hypoadrenalism. Next generation sequencing found a homozygous missense mutation in exon 5 of PCSK1 gene, c.500A>C (p.Asp167Ala), located within the catalytic domain. Both patients presented a high level of proinsulin. In the first years of life they required parenteral nutrition and hormone replacement therapy. The patients, aged 3 and 1.5 years, experienced several infectious episodes associated with septic shocks. While the mechanism underlying intestinal failure remains poorly investigated, parenteral nutrition is essential in order to ensure normal growth in early childhood., (Copyright © 2021. Published by Elsevier Masson SAS.)