Systems biology applications to study mechanisms of human immunodeficiency virus latency and reactivation

Eradication of human immunodeficiency virus (HIV) in infected individuals is currently not possible because of the presence of the persistent cellular reservoir of latent infection. The identification of HIV latency biomarkers and a better understanding of the molecular mechanisms contributing to regulation of HIV expression might provide essential tools to eliminate these latently infected cells. This review aims at summarizing gene expression profiling and systems biology applications to studies of HIV latency and eradication. Studies comparing gene expression in latently infected and uninfected cells identify candidate latency biomarkers and novel mechanisms of latency control. Studies that profiled gene expression changes induced by existing latency reversing agents (LRAs) highlight uniting themes driving HIV reactivation and novel mechanisms that contribute to regulation of HIV expression by different LRAs. Among the reviewed gene expression studies, the common approaches included identification of differentially expressed genes and gene functional category assessment. Integration of transcriptomic data with other biological data types is presently scarce, and the field would benefit from increased adoption of these methods in future studies. In addition, designing prospective studies that use the same methods of data acquisition and statistical analyses will facilitate a more reliable identification of latency biomarkers using different model systems and the comparison of the effects of different LRAs on host factors with a role in HIV reactivation. The results from such studies would have the potential to significantly impact the process by which candidate drugs are selected and combined for future evaluations and advancement to clinical trials.

Three-dimensional models of antigens with serodiagnostic potential for leprosy: An in silico study

BACKGROUND

Leprosy is a disease caused by Mycobacterium leprae (M. leprae), an intracellular pathogen that has tropism and affects skin and nervous system cells. The disease has two forms of presentation: Paucibacillary and multibacillary, with different clinical and immunological manifestations. Unlike what occurs in the multibacillary form , the diagnostic tests for the paucibacillary form are nonspecific and not very sensitive, allowing the existence of infected individuals without treatment, which contributes to the spread of the pathogen in the population. To mitigate this contamination, more sensitive diagnostic tests capable of detecting paucibacillary patients are needed.

AIM

To predict the three-dimensional structure models of M. leprae antigens with serodiagnostic potential for leprosy.

METHODS

In this in silico study, satisfactory templates were selected in the Protein Data Bank (PDB) using Basic Local Alignment Search Tool to predict the structural templates of ML2038, ML0286, ML0050, and 85B antigens by comparative modeling. The templates were selected according to general criteria such as sequence identity, coverage, X-ray resolution, Global Model Quality Estimate value and phylogenetic relationship; Clustal X 2.1 software was used in this analysis. Molecular modeling was completed using the software Modeller 9v13. Visualization of the models was made using ViewerLite 4.2 and PyMol software, and analysis of the quality of the predicted models was performed using the QMEAN score and Z-score. Finally, the three-dimensional moels were validated using the MolProbity and Verify 3D platforms.

RESULTS

The three-dimensional structure models of ML2038, ML0286, ML0050, and 85B antigens of M. leprae were predicted using the templates PDB: 3UOI (90.51% identity), PDB: 3EKL (87.46% identity), PDB: 3FAV (40.00% identity), and PDB: 1F0N (85.21% identity), respectively. The QMEAN and Z-score values indicated the good quality of the structure models. These data refer to the monomeric units of antigens, since some of these antigens have quaternary structure. The validation of the models was performed with the final three-dimensional structure - monomer (ML0050 and 85B antigens) and quaternary structures (ML2038 and ML0286). The majority of amino acid residues were observed in favorable and allowed regions in the Ramachandran plot, indicating correct positioning of the side chain and absence of steric impediment. The MolProbity score value and Verify 3D results of all models indicated a satisfactory prediction.

CONCLUSION

The polarized immune response against M. leprae creates a problem in leprosy detection. The selection of immunodominant epitopes is essential for the development of more sensitive serodiagnostic tests, for this it is important to know the three-dimensional structure of the antigens, which can be predicted with bioinformatics tools.

Brucellosis, a diagnostic dilemma, presenting atypically in a child with terminal ileitis: A case report

BACKGROUND

Brucellosis is endemic in India with seropositivity rates as high as 10% in children in the eastern states, yet the disease is not on the radar when a differential diagnosis of pyrexia of unknown origin (PUO) is being considered, especially in children in urban set-up. This may be because of the non-specific multitude of systemic symptoms seen in this disease and the lack of awareness among clinicians.

CASE SUMMARY

We present a case of a 13-year-old boy, who came with a history of undulating fever for the past three and a half months, loss of appetite, and abdominal pain. The child had visited several pediatricians and was even admitted to a tertiary care hospital for PUO evaluation, but to no avail. He presented to us after three and half months of suffering and weight loss of more than 10% of body weight. His ultrasonography revealed thickening of the terminal ileum. His blood culture grew Brucella melitensis. A diagnosis of Brucellosis with terminal ileitis was made. Brucella serology by enzyme-linked immunoassay (ELISA) was positive for both IgG and IgM. He was treated with doxycycline and Rifampicin along with syrup multivitamin and zinc, for 6 wk. There was remarkable improvement with gain in 4 kg body weight within 2 mo of completing treatment. History revealed consumption of unpasteurized milk and contact with cattle.

CONCLUSION

Clinical suspicion, detailed history, appropriate laboratory investigations are the three pillars for diagnosing Brucellosis in patients presenting with vague symptoms.

Sub-acute endocarditis by Corynebacterium straitum: An often ignored pathogen

With the emergence of novel etiologic organisms, pan-resistance, and invasive medical care infective endocarditis continues to be evasive, requiring newer approaches and modified treatment guidelines. Presented here is the case of a 75-year-old male with history of systolic heart failure with an automatic internal cardioverter defibrillator (AICD) implantation and a prosthetic mitral valve who presented with generalized malaise and progressive shortness of breath for 6 d. He was found to have positive blood cultures for gram positive rod shaped bacteria identified as Corynebacterium straitum, but was not considered as the etiological pathogen initially as it a usual skin contaminant. Later this bacterium was found to be the causative agent for the patient’s endocarditis. This case highlights the importance of identifying the role of this uncommon commensal in invasive disease. With the use of effective antibiotic regimen and awareness of these new pathogens in invasive disease, mortality and morbidity can be prevented with initiation of early appropriate therapy.

Incidental diagnosis of intestinal spirochetosis in a patient with chronic hepatitis B: A case report

BACKGROUND

Intestinal spirochetosis (IS) is caused by Brachyspira colonization of the gastrointestinal tract. Some patients are asymptomatic, while others present with gastrointestinal complaints such as abdominal pain, diarrhea, or gastrointestinal bleeding. However, the clinical significance of asymptomatic IS is unclear, and guidelines are lacking regarding decision to treat.

CASE SUMMARY

A 73-year-old male with peptic ulcer disease and gastroesophageal reflux was evaluated for elevated liver enzymes. He was diagnosed with chronic hepatitis B virus and prescribed entecavir. Additionally, he was leukopenic and had stage 4 liver fibrosis on transient elastography. After 5 mo, the patient returned for esophagogastroduodenoscopy and screening colonoscopy. He denied any gastrointestinal symptoms at that time. Findings included grade I distal esophageal varices, mild portal hypertensive gastropathy, and patchy nodular gastric antral mucosa. On colonoscopy, several polyps were removed. Hematoxylin and eosin stain of mucosa adjacent to the polyps revealed a “false brush border,” and Steiner stain identified spirochetes adherent to the mucosa. These pathology findings confirmed the diagnosis of IS. He was managed conservatively with careful observation and without antibiotic therapy via a multidisciplinary approach between gastroenterology and infectious disease. He remained asymptomatic at the 7-wk follow-up.

CONCLUSION

This case reports the finding of incidental, asymptomatic IS in a leukopenic patient with hepatitis B virus. Conservative management was appropriate.

Monkeypox in humans: Transmission, pathophysiology, diagnosis, treatment, prevention, and all recent updates

The Centers for Disease Control and Prevention (CDC) is monitoring an epidemic of monkeypox infection in the United States. The outbreak is now global and more than 6900 cases have already been reported. There are 83 confirmed cases among children and adolescents, as shown in the report published on November 3, 2022, in the USA. However, monkeypox in pediatric patients is still infrequent (< 0.3% of total cases). Among cases in the United States, 16 cases were in children < 5 years, 12 in the age group 5-12 years, and 55 cases in adolescents 13-17 years old. In the adolescent age group, 89% were male. For children < 12 years of age, close physical contact with an adult household with monkeypox was the primary exposure, but for adolescents, male-to-male sexual contact was found more frequently. The CDC advised United States healthcare providers to remain vigilant for patients with a rash resembling monkeypox, even if there is no history of travel to a country with high risk. This article summarizes the history and epidemiology of monkeypox with a specific emphasis on clinical features and management in pediatric patients.

Life after recovery from SARS, influenza, and Middle East respiratory syndrome: An insight into possible long-term consequences of COVID-19

Viral infectious diseases have become an increased public health issue in the past 20 years. The outbreaks of severe acute respiratory syndrome coronavirus (SARS-CoV-1) in 2002, influenza H1N1 in 2009, Middle East respiratory syndrome-CoV in 2012, and the current new coronavirus SARS-CoV-2 have shown that viral infectious diseases are a major concern in the 21^st century. As the world lives under the pandemic of a new coronavirus (COVID-19), knowing the clinical characteristics from those past diseases and their long-term outcomes is important to understand the current coronavirus pandemic and its complications and consequences better and plan for possible future outbreaks. Several long-term complications have been described with these respiratory viral diseases, such as decreased pulmonary function, pulmonary fibrosis, chronic fatigue syndrome, avascular necrosis of bone, polyneuropathy, encephalitis, posttraumatic stress disorder, depression, and anxiety. This article summarizes several studies describing chronic complications and long-term outcomes of patients recovered from these viral syndromes.

Is it enough to eliminate hepatitis C virus to reverse the damage caused by the infection?

Hepatitis C virus (HCV) infection represents one of the major causes of chronic liver disease, hepatocellular carcinoma and morbidity/mortality worldwide. It is also a major burden to the healthcare systems. A complete elimination of the HCV from the body through treatment is now possible. However, HCV not only alters the hepatic function. Several extra-hepatic manifestations are present in HCV-infected patients, which increase the mortality rate. Liver and gut are closely associated in what is called the “gut-liver axis”. A disrupted gut barrier leads to an increase in bacterial translocation and an activation of the mucosal immune system and secretion of inflammatory mediators that plays a key role in the progression of liver disease towards decompensated cirrhosis in HCV-infected patients. In addition, both qualitative and quantitative changes in the composition of the gut microbiota (GM) and states of chronic inflammation have been observed in patients with cirrhosis. Thus, a successful treatment of HCV infection should be also accompanied by a complete restoration of GM composition in order to avoid activation of the mucosal immune system, persistent inflammation and the development of long-term complications. Evaluation of GM composition after treatment could be of interest as a reliable indicator of the total or partial cure of these patients. However, studies focused on microbiota composition after HCV eradication from the body are lacking, which opens unique opportunities to deeply explore and investigate this exciting field.

Medical errors, infection-control breaches and the use of adulterated and misbranded medical devices

Several well-publicized cases of improper cleaning, disinfection or sterilization of contaminated reusable medical equipment that posed an increased risk of patient-to-patient disease transmission were reported within the past few years, resulting in the notification of approximately 20 000 patients. These medical errors, the specific infection-control standards they breached, and assessments of the risk of infection associated with each are discussed. Other topics discussed include the Food and Drug Administration’s (FDA) regulation of medical devices and infection-control products; the use of adulterated, misbranded, and investigational devices; consent decrees and associated Certificates of Medical Necessity; and informed patient consent. Focus is placed on liquid chemical sterilization, its history, and the FDA’s recent censure and discontinuation of a medical device labeled with this claim, namely, the STERIS System 1 processor. Recommendations are provided for healthcare facilities, regulatory agencies, manufacturers of reusable medical devices, and professional healthcare organizations and administrations to improve public health and prevent healthcare-associated infections.

Origin of de novo daptomycin non susceptible enterococci

The emergence of daptomycin non-susceptible enterococci (DNSE) poses both treatment and infection control challenges. Clinicians should be vigilant that DNSE may be isolated from patients with or without (de novo DNSE) prior use of daptomycin. Recent epidemiological data suggest the presence of a community reservoir for DNSE which may be associated with environmental, foodborne and agricultural exposures. The mechanisms of nonsusceptibility to daptomycin have not been well characterized and may not parallel those for Staphylococcus aureus. The identification of daptomycin resistance genes in anaerobes, in farm animals and in an ecosystem that has been isolated for million years, suggest that the environmental reservoir for de novo DNSE may be larger than previously thought. Herein, the limited available scientific evidence regarding the possible origin of de novo DNSE is discussed. The current existing evidence is not sufficient to draw firm conclusions on the origin of DNSE. Further studies to determine the mechanisms of de novo daptomycin nonsusceptibility among enterococci are needed.

Management of periprosthetic infections

Periprosthetic joint infection (PJI) is considered one of the most challenging complications compromising patient health and is considered an economic burden. Despite all strategies PJI prevalence is between 1%-2%. Considerable efforts have been investigated in the past decade to diminish or erradicate PJI prevalence. This article manages the definition of PJI and the new major and minor criteria from Parvizi et al Then a scientific analysis of every minor and major criteria. Multidisciplinary management is reccommended according to guidelines. A numerous of surgical options exist each and everyone with its indications, contraindications and specific antibiotic therapy regimen. Surgical options are: (1) irrigation and cleaning with retention of the prosthesis with a success rate 0%-89%; (2) single-stage revision surgery with a succes rate of > 80%; and (3) two-stage revision surgery (authors preferred method) with a succes rate of 87%. Radical treatment options like arthrodesis and amputation are reserved for specific group of patients, with a succes rate varying from 60%-100%. The future of PJI is focused on improving the diagnostic tools and to combat biofilm. The cornerstone of management consists in a rapid diagnosis and specific therapy. This article presents the most current diagnostic and treatment criteria as well as the different surgical treatment options depending on the type of infection, bacterial virulence and patient comorbidities.

Predictors of severe and critical COVID-19: A systematic review

BACKGROUND

Coronavirus disease 2019 (COVID-19) has emerged as a public health crisis that was declared as a global pandemic by the World Health Organization. Although most cases have no or mild symptoms, around 10% of patients develop severe or critical illness that necessitates hospitalization and intensive care unit admission.

AIM

To assess the literature for the predictive factors that can identify patients having severe/critical COVID-19 disease.

METHODS

A Preferred Reporting Items for Systematic Reviews and Meta-Analyses-compliant systematic search of the literature was conducted. Electronic databases including PubMed/MEDLINE, Scopus, and Cochrane Library were queried. The main outcome measures were the predictors of severe/critical COVID-19 and mortality.

RESULTS

Five studies including 583 patients of a median age of 50.5 years were reviewed. Patients were 346 (59.4%) male and 237 (40.6%) female. Of 583 hospitalized patients, 242 (41.5%) had critical illness. Acute respiratory distress disease occurred in 291 patients, accounting for 46.7% of total complications. One-hundred (17.1%) mortalities were recorded. The most commonly reported predictors of severe COVID-19 were older age, medical comorbidities, lymphopenia, elevated C-reactive protein, increased D-dimer, and increased neutrophil ratio. Findings on computed tomography (CT) scanning predictive of severe disease were bronchial wall thickening, CT score > 7, linear opacities, consolidation, right upper lobe affection, and crazy paving pattern.

CONCLUSION

Several demographic, clinical, laboratory, and radiologic factors can help predict severe and critical COVID-19 along with the potential need for mechanical ventilation. Factors that were more commonly reported were older age, medical comorbidities, lymphopenia, increased neutrophil ratio, elevated C-reactive protein, and increased D-dimer.

Can the detection of IgA anti-Mycoplasma pneumoniae added to IgM increase diagnostic accuracy in patients with infections of the lower respiratory airways?

AIM

To evaluate the increase in diagnostic yield, by using IgA in addition to IgM, instead of IgM alone, in relation to the age of the patients.

METHODS

The study considered 1067 blood samples from patients with clinical signs of lower respiratory tract infections, tested for anti-Mycoplasma IgG, IgM and IgA antibody.

RESULTS

The increase in diagnostic yield with IgA, compared to IgM detection alone was of 3.5% with statistically significant differences between age groups (0.8% for those equal/under 50 years of age and 4.3% for those over 50).

CONCLUSION

Our findings demonstrate that IgA detection lead to a twofold increase in the number of diagnoses among the older age groups, but it did not result in relevant increase among the younger age groups.