The Complete Genome Sequence of the Pathogenic Intestinal Spirochete Brachyspira pilosicoli and Comparison with Other Brachyspira Genomes

Background: The anaerobic spirochete Brachyspira pilosicoli colonizes the large intestine of various species of birds and mammals, including humans. It causes ''intestinal spirochetosis'', a condition characterized by mild colitis, diarrhea and reduced growth. This study aimed to sequence and analyse the bacterial genome to investigate the genetic basis of its specialized ecology and virulence. Methodology/Principal Findings: The genome of B. pilosicoli 95/1000 was sequenced, assembled and compared with that of the pathogenic Brachyspira hyodysenteriae and a near-complete sequence of Brachyspira murdochii. The B. pilosicoli genome was circular, composed of 2,586,443 bp with a 27.9 mol% G+C content, and encoded 2,338 genes. The three Brachyspira species shared 1,087 genes and showed evidence of extensive genome rearrangements. Despite minor differences in predicted protein functional groups, the species had many similar features including core metabolic pathways. Genes distinguishing B. pilosicoli from B. hyodysenteriae included those for a previously undescribed bacteriophage that may be useful for genetic manipulation, for a glycine reductase complex allowing use of glycine whilst protecting from oxidative stress, and for aconitase and related enzymes in the incomplete TCA cycle, allowing glutamate synthesis and function of the cycle during oxidative stress. B. pilosicoli had substantially fewer methyl-accepting chemotaxis genes than B. hyodysenteriae and hence these species are likely to have different chemotactic responses that may help to explain their different host range and colonization sites. B. pilosicoli lacked the gene for a new putative hemolysin identified in B. hyodysenteriae WA1. Both B. pilosicoli and B. murdochii lacked the rfbBADC gene cluster found on the B. hyodysenteriae plasmid, and hence were predicted to have different lipooligosaccharide structures. Overall, B. pilosicoli 95/1000 had a variety of genes potentially contributing to virulence. Conclusions/Significance: The availability of the complete genome sequence of B. pilosicoli 95/1000 will facilitate functional genomics studies aimed at elucidating host-pathogen interactions and virulence

Clinical and virological characteristics of hospitalised COVID-19 patients in a German tertiary care centre during the first wave of the SARS-CoV-2 pandemic: a prospective observational study

Purpose: Adequate patient allocation is pivotal for optimal resource management in strained healthcare systems, and requires detailed knowledge of clinical and virological disease trajectories. The purpose of this work was to identify risk factors associated with need for invasive mechanical ventilation (IMV), to analyse viral kinetics in patients with and without IMV and to provide a comprehensive description of clinical course. Methods: A cohort of 168 hospitalised adult COVID-19 patients enrolled in a prospective observational study at a large European tertiary care centre was analysed. Results: Forty-four per cent (71/161) of patients required invasive mechanical ventilation (IMV). Shorter duration of symptoms before admission (aOR 1.22 per day less, 95% CI 1.10-1.37, p < 0.01) and history of hypertension (aOR 5.55, 95% CI 2.00-16.82, p < 0.01) were associated with need for IMV. Patients on IMV had higher maximal concentrations, slower decline rates, and longer shedding of SARS-CoV-2 than non-IMV patients (33 days, IQR 26-46.75, vs 18 days, IQR 16-46.75, respectively, p < 0.01). Median duration of hospitalisation was 9 days (IQR 6-15.5) for non-IMV and 49.5 days (IQR 36.8-82.5) for IMV patients. Conclusions: Our results indicate a short duration of symptoms before admission as a risk factor for severe disease that merits further investigation and different viral load kinetics in severely affected patients. Median duration of hospitalisation of IMV patients was longer than described for acute respiratory distress syndrome unrelated to COVID-19

A time-resolved proteomic and prognostic map of COVID-19

COVID-19 is highly variable in its clinical presentation, ranging from asymptomatic infection to severe organ damage and death. We characterized the time-dependent progression of the disease in 139 COVID-19 inpatients by measuring 86 accredited diagnostic parameters, such as blood cell counts and enzyme activities, as well as untargeted plasma proteomes at 687 sampling points. We report an initial spike in a systemic inflammatory response, which is gradually alleviated and followed by a protein signature indicative of tissue repair, metabolic reconstitution, and immunomodulation. We identify prognostic marker signatures for devising risk-adapted treatment strategies and use machine learning to classify therapeutic needs. We show that the machine learning models based on the proteome are transferable to an independent cohort. Our study presents a map linking routinely used clinical diagnostic parameters to plasma proteomes and their dynamics in an infectious disease

Co-Infection with SARS-COV-2 and Parainfluenza in a young adult patient with pneumonia: Case Report

Coronavirus 2 (SARS-CoV-2) is now considered a pandemic causing Coronavirus disease (COVID-19), multiple fatalities and morbidities which have been associated with it worldwide. We report a severe pneumonia causing acute respiratory distress syndrome due to a coinfection with SARS-COV-2 and Parainfluenza 4 virus in a Hispanic 21 year old male in Florida, USA. The case represents the importance of prompt diagnosis and awareness of the potential co-infection with other respiratory viruses and this novel deadly virus

COVID-19 Coinfection with Mycobacterium abscessus in a Patient with Multiple Myeloma

Background. Coronavirus disease (COVID-19) is a worldwide pandemic causing multiple fatalities and morbidities worldwide. We report a case of severe pneumonia causing acute respiratory distress syndrome due to a coinfection with SARS-CoV-2 and Mycobacterium abscessus in an elderly patient with multiple myeloma in Florida, USA. Case Presentation. An 84-year-old male with a medical history significant for multiple myeloma not in remission was sent to the emergency department to rule out COVID-19 infection prior to continuing his chemotherapy sessions. At presentation, he had nonspecific mild symptoms and an unremarkable physical examination. He had significant blood test findings including serum lactate dehydrogenase 373 U/L, high sensitive C-reactive protein 17.40 mg/l, and ferritin 415 ng/ml. Xpert-SARS-CoV-2 was positive. Chest radiograph revealed patchy areas of interstitial infiltrates in mid to lower lung zones. During his hospitalization course, his oxygenation deteriorated, requiring mechanical intubation. Repeat chest radiograph showed worsening bilateral infiltrates. He was started on broad-spectrum antibiotics and eventually weaned off mechanical intubation and extubated. On the 11th day of admission, he was found to be bradycardic and in shock, and he was reintubated. His labs showed worsening inflammatory markers along with kidney dysfunction to the point of requiring renal replacement therapy. He received both convalescent plasma and remdesivir for treatment of COVID-19 pneumonia. Eventually, repeat blood cultures came back positive for the growth of acid-fast beaded bacilli. While awaiting final culture and sensitivity reports, his antibiotics were upgraded to cover possible nocardia infection. Repeat blood and sputum cultures resulted in growth of AFB bacilli Mycobacterium abscessus 1 week after. Conclusions. This case report highlights the importance of keeping a broad differential and considering multiple coinfections, including atypical ones during this COVID-19 pandemic, such as the one that was discussed above, Mycobacterium abscessus, in order to provide goal-directed therapy

Effect of mobile text messages on antiretroviral medication adherence and patient retention in early HIV care: An open-label, randomized, single center study in south Florida

Background People with HIV (PHIV) with limited access to health services often experience suboptimal antiretroviral therapy (ART) adherence. We investigated whether a daily text messaging intervention improves ART adherence and retention in early HIV care in PHIV in a south Florida hospital-based clinic. Methods ART-naïve PHIV receiving care through the clinic’s Ryan White HIV/AIDS Program were enrolled and randomly assigned to the intervention or control groups with a 1:1 ratio. The intervention group received a 1-way text message daily and the control group received standard care without receiving text message reminders for 6 months. HIV RNA and CD4 cell count were measured at baseline and post-intervention. Adherence to ART was defined as a visual analog scale of ≥ 90%. Retention in care was defined as continued engagement at study end. Results 94 ART-naïve patients were randomized and 83 (85.6%) completed the study, of which 44 were in the intervention group and 39 were in the control group. At the end of the 6-month study period, adherence to ART was 84.4% in the intervention group versus 73.5% in the control group (OR, 1.9; 95% CI 0.7–5.0; p = 0.194). Retention in care significantly improved in the intervention group compared to the control group with the odds of retention increasing by 20% (OR, 1.2; 95% CI 1.1–1.5; p = 0.006). Undetectable HIV RNA (< 50 copies/mL) was 86.7% in the intervention group versus 73.5% in the control group (OR, 2.3; 95% CI 0.8–6.9; p = 0.112). A significant increase in CD4 cell count and a decrease in HIV RNA were found at study end, with no differences between the two groups. Conclusions In this pilot study, a one-way daily text messaging intervention did not improve ART adherence over a 6-month study period, but significantly enhanced patient retention in early HIV care. Implementation of interventions to improve adherence in this population is required.This work was supported by the Nova Southeastern University Health Professions Division Research Grant and the Nova Southeastern University President's Faculty Research and Development Grant.Scopu

A retrospective study on 198 mpox cases in South Florida: Clinical characteristics and outcomes with focus on human immunodeficiency virus status

Background Men who have sex with men (MSM) and persons living with human immunodeficiency virus (PLWH) were disproportionately affected by global mpox outbreak in 2022. In this retrospective review, we describe epidemiology and clinical characteristics of mpox infection in South Florida with a focus on human immunodeficiency virus (HIV) status. Methods This was a retrospective observational study of 198 adult patients with confirmed diagnosis of mpox between 01 January 2020, and 10 September 2022, in two large health systems in South Florida. A descriptive analysis was performed to summarize demographic, clinical and laboratory characteristics, and outcomes of the patients. Results Young male patients and PLWH were disproportionately represented among patients with mpox. HIV positive patients were less likely to have adenopathy and myalgia and were more likely to have oral or facial lesions. 22.7% of studied patients were diagnosed with one or more concurrent STI at the time of mpox diagnosis. Conclusions We suggest screening for sexually transmitted infections and HIV for patients diagnosed with mpox. We suggest prompt consultation or referral to infectious disease specialist if needed for the patients who are diagnosed with mpox especially in the severely immunocompromised host

Distinct Clinical Presentations and Outcomes of Hospitalized Adults with the SARS-CoV-2 Infection Occurring during the Omicron Variant Surge

The COVID-19 Omicron variant has imposed a tremendous burden on healthcare services. We characterized the types of the Omicron variant-associated hospitalizations and their associations with clinical outcomes. Consecutive adults hospitalized with COVID-19 during the Omicron variant surge period of 1–14 January 2022, were classified into one of three groups based on their clinical presentations on admission: Group 1—primary COVID-19; Group 2—extrapulmonary manifestations of COVID-19; and Group 3—incidental COVID-19. Of the 500 patients who were hospitalized, 51.4% fell into Group 1, 16.4% into Group 2, and 32.2% into Group 3. The patients in Groups 1 and 2 were older, with higher proportions of comorbidities than patients in Group 3. The Group 1 patients had the highest mortality rate (15.6%), followed by Group 2 (8.5%), and Group 3 (0.6%), with adjusted odds ratios (OR) of 22.65 (95% confidence interval [CI], 2.75–239.46; p = 0.004) and 10.95 (95% CI, 1.02–117.28; p = 0.048), respectively, compared to Group 3. Those in Group 1 showed a greater utilization of intensive care services (15.9%), followed by Group 2 (10.9%), and Group 3 (2.5%), with adjusted ORs of 7.95 (95% CI, 2.52–25.08; p p = 0.017), respectively, compared to Group 3. The patients in Groups 1 and 2 had longer hospitalization stays than the patients in Group 3 (p p = 0.002, respectively). Older age (≥65 years) was an independent factor associated with longer hospital stays (OR = 1.72, 95% CI, 1.07–2.77). These findings can help hospitals prioritize patient care and service planning for future SARS-CoV-2 variants