Microbiology of bloodstream infections in Ontario, Canada during COVID-19 pandemic.

Background: Bloodstream infections (BSI) caused by a wide range of bacterial and fungal pathogens are associated with high rates of morbidity and mortality. Based on an estimate in 2017, the number of BSI incidences in Ontario is 150 per 100,000 population. The epidemiology of BSIs may be affected by many factors, including the social and travel restrictions and increased rates of hospitalizations in Ontario during the coronavirus disease 2019 (COVID-19) pandemic. Objectives: This study aimed to assess the changes in the microbiology of BSIs in Ontario during the COVID-19 pandemic compared to the pre-pandemic period. Methods: Retrospective blood culture data (n=189,106) from LifeLabs Ontario (July 2018 to December 2021) were analyzed. Blood culture positivity rates for common bacterial pathogens were compared between pre-COVID-19 (July 2018 to March 2020) and COVID-19 (April 2020 to December 2021) periods in community and hospital settings, using the chi-square test for significance. Results: During the COVID-19 period, blood culture positivity rates in the community remained the same, while hospital rates increased by approximately threefold (p=0.00E-00). In the community, the isolation rates of most bacterial species remained unchanged, except for an increase in Enterococcus spp. and a decrease in Salmonella spp. The rates of antibiotic-resistant organisms (AROs) also significantly decreased in the community. In hospitals, all bacterial species, including AROs, showed significant increases in isolation rates during the COVID-19 period. Conclusion: The study revealed shifts in the microbiology of BSIs and suggests changes in the epidemiology of BSIs during the COVID-19 pandemic in Ontario, both in hospitals and in the community.

Chronic COVID-19 infection in an immunosuppressed patient shows changes in lineage over time: a case report.

BACKGROUND: The COVID-19 pandemic, caused by the Severe Acute Respiratory Syndrome Coronavirus 2 virus, emerged in late 2019 and spready globally. Many effects of infection with this pathogen are still unknown, with both chronic and repeated COVID-19 infection producing novel pathologies. CASE PRESENTATION: An immunocompromised patient presented with chronic COVID-19 infection. The patient had history of Hodgkin's lymphoma, treated with chemotherapy and stem cell transplant. During the course of their treatment, eleven respiratory samples from the patient were analyzed by whole-genome sequencing followed by lineage identification. Whole-genome sequencing of the virus present in the patient over time revealed that the patient at various timepoints harboured three different lineages of the virus. The patient was initially infected with the B.1.1.176 lineage before coinfection with BA.1. When the patient was coinfected with both B.1.1.176 and BA.1, the viral populations were found in approximately equal proportions within the patient based on sequencing read abundance. Upon further sampling, the lineage present within the patient during the final two timepoints was found to be BA.2.9. The patient eventually developed respiratory failure and died. CONCLUSIONS: This case study shows an example of the changes that can happen within an immunocompromised patient who is infected with COVID-19 multiple times. Furthermore, this case demonstrates how simultaneous coinfection with two lineages of COVID-19 can lead to unclear lineage assignment by standard methods, which are resolved by further investigation. When analyzing chronic COVID-19 infection and reinfection cases, care must be taken to properly identify the lineages of the virus present.

Trends in the Rates of Extended-Spectrum-ß-Lactamase-Producing Enterobacterales Isolated from Urine Cultures during the COVID-19 Pandemic in Ontario, Canada.

Worldwide, extended-spectrum ß-lactamase (ESBL) rates are increasing at an alarming level with increasing rates of health care exposures, international travel, and antibiotic usage. In this study, we investigated whether enhanced social isolation, travel restrictions, and the reduced use of antibiotics in Ontario, Canada during coronavirus disease 2019 (COVID-19) pandemic had an impact on ESBL rates in urine cultures collected from the community and long-term-care (LTC) facilities across the province. Data from a total of 8.6 million urine cultures performed at LifeLabs Ontario from 2016 to 2021 were utilized for analysis. ESBL-producing Escherichia coli (ESBL Escherichia coli) and ESBL Klebsiella pneumoniae were identified using standard operating procedures. Data trends were estimated by interrupted time series (ITS) regression analysis. Among 2.3 million positive urine cultures, 48.9% and 7.2% grew E. coli and K. pneumoniae, of which 5.8% and 3.3% produced ESBLs, respectively. While the overall rate of ESBL isolation was higher in the pandemic period than in the prepandemic period, by ITS regression analysis of the monthly rates of ESBL isolation, decreasing trends were noted for ESBL E. coli in both the community and LTC facilities and for ESBL K. pneumoniae in the community. The ESBL K. pneumoniae rates in LTC facilities continued to increase throughout the COVID-19 period. By subgroup analysis for different genders, age groups, and local health integration network (LHIN) units, similar trends were seen in most cases (P < 0.05), except for a few densely populated LHINs where rate changes were not statistically significant. IMPORTANCE Community-onset urinary tract infections (UTIs) caused by ESBL-producing Enterobacterales, particularly E. coli and K. pneumoniae, are a major public health concern. In this study, we assessed the impact of COVID-19 on ESBL rates in urine cultures in Ontario, Canada. Our results show the recent epidemiology of ESBL-producing Enterobacterales in urine cultures from both the community and LTC facilities in Ontario, Canada, and the impact of COVID-19 restrictions on ESBL trends for the entire province as well as different subgroups of the population based on demographic and geographic characteristics. Our results may have important public health implications in the context of the gradual easing of COVID-19 restrictions.

Secondary Analysis of a Systematic Review: Are Antifungal Noninferiority Trials at Risk of Eroding Effectiveness Because of Biocreep?

Noninferiority randomized controlled trial (RCT) effectiveness may erode when results favor the active control over time and when a decreasingly effective control arm is used in serial trials. We analyzed 32 antifungal noninferiority RCTs (NI-RCTs) for these scenarios in this secondary analysis of a systematic review. Our exploratory analysis suggests that the erosion risk in the effectiveness of antifungal noninferiority trials is uncommon. Findings are limited by small sample size and overall risk of bias.

Listeria pericarditis in a lymphoma patient: Case report and literature review.

We present a case of pericarditis with pericardial effusion secondary to Listeria monocytogenes. A 56-year-old man presented with signs of acute pericarditis, but with prior chronic lymphocytic leukemia treated with stem cell transplantation, chronic graft-versus-host disease, and a recent diagnosis of untreated diffuse large B-cell lymphoma. He developed cardiac tamponade requiring pericardiocentesis. Blood and pericardial cultures grew Listeria monocytogenes. He responded to ampicillin but later died from gram-negative sepsis. A systematic review found 10 other published English-language cases of pericarditis caused by Listeria. The most common risk factors were cirrhosis and malignancy. Only three patients survived both the listeriosis and their underlying infections. Listeria monocytogenes is a rare and often fatal cause of pericarditis, typically occurring in immunocompromised patients. Cultures showing gram-positive bacilli in the context of pericarditis in an immunocompromised patient should prompt consideration of this rare cause.

Les auteurs présentent un cas de péricardite avec effusion secondaire au Listeria monocytogenes. Un homme de 56 ans a consulté à cause de signes de péricardite aiguë. Il souffrait déjà d'une leucémie lymphoïde chronique traitée par une greffe de cellules souches et d'une réaction chronique du greffon contre l'hôte et avait récemment reçu un diagnostic de lymphome diffus à grandes cellules B non traité. Il a développé une tamponnade cardiaque exigeant une péricardiocentèse. Les cultures sanguine et péricardique ont révélé la présence de Listeria monocytogenes. Le patient a répondu à l'ampicilline, mais a fini par mourir d'un sepsis à Gram négatif. Une analyse systématique a révélé dix autres cas de péricardite causés par la Listeria dans des publications en langue anglaise. La cirrhose et les tumeurs en étaient les principaux facteurs de risque. Seulement trois patients ont survécu à la fois à la listériose et à ses infections sous-jacentes. Le Listeria monocytogenes est une cause de péricardite rare et souvent fatale, qui se déclare généralement chez des hôtes immunodéprimés. Des cultures révélant des bacilles à Gram positif dans le contexte d'une péricardite chez un hôte immunodéprimé doivent inciter à envisager cette cause rare.

Treatment of urinary tract infections in the era of antimicrobial resistance and new antimicrobial agents.

Urinary tract infections (UTIs) caused by antibiotic-resistant Gram-negative bacteria are a growing concern due to limited treatment options. Knowledge of the common uropathogens in addition to local susceptibility patterns is essential in determining appropriate empiric antibiotic therapy of UTIs. The recommended first-line empiric antibiotic therapy for acute uncomplicated bacterial cystitis in otherwise healthy adult nonpregnant females is a 5-day course of nitrofurantoin, a 3-g single dose of fosfomycin tromethamine, or a 5-day course of pivmecillinam. High rates of resistance for trimethoprim-sulfamethoxazole and ciprofloxacin preclude their use as empiric treatment of UTIs in several communities, particularly if patients who were recently exposed to them or in patients who are at risk of infections with extended-spectrum ß-lactamases (ESBLs)-producing Enterobacteriales. Second-line options include oral cephalosporins such as cephalexin or cefixime, fluoroquinolones and ß-lactams, such as amoxicillin-clavulanate. Current treatment options for UTIs due to AmpC- ß -lactamase-producing Enterobacteriales include nitrofurantoin, fosfomycin, pivmecillinam, fluoroquinolones, cefepime, piperacillin-tazobactam and carbapenems. Treatment oral options for UTIs due to ESBLs-E coli include nitrofurantoin, fosfomycin, pivmecillinam, amoxicillin-clavulanate, finafloxacin, and sitafloxacin while pivmecillinam, fosfomycin, finafloxacin, and sitafloxacin are treatment oral options for ESBLs- Klebsiella pneumoniae. Parenteral treatment options for UTIs due to ESBLs-producing Enterobacteriales include piperacillin-tazobactam (for ESBL-E coli only), carbapenems including meropenem/vaborbactam, imipenem/cilastatin-relebactam, and sulopenem, ceftazidime-avibactam, ceftolozane-tazobactam, aminoglycosides including plazomicin, cefiderocol, fosfomycin, sitafloxacin, and finafloxacin. Ceftazidime-avibactam, meropenem/vaborbactam, imipenem/cilastatin-relebactam, colistin, fosfomycin, aztreonam and ceftazidime-avibactam, aztreonam and amoxicillin-clavulanate, aminoglycosides including plazomicin, cefiderocol, tigecycline are treatment options for UTIs caused by carbapenem-resistant Enterobacteriales (CRE). Treatment options for UTIs caused by multidrug resistant (MDR)-Pseudomonas spp. include fluoroquinolones, ceftazidime, cefepime, piperacillin-tazobactam, carbapenems including imipenem-cilastatin/relebactam, meropenem, and fosfomycin, ceftolozane-tazobactam, ceftazidime-avibactam, aminoglycosides including plazomicin, aztreonam and ceftazidime-avibactam, cefiderocol, and colistin. It is important to use the new antimicrobials wisely for treatment of UTIs caused by MDR-organisms to avoid resistance development.

Seminal reservoirs during an HIV type 1 eradication trial.

Despite dramatic reduction of the levels of human immunodeficiency virus type I (HIV-1) virions in blood and seminal plasma of infected patients, highly active antiretroviral therapy (HAART) does not eradicate HIV-1. Three patients, with less than 50 copies/ml of plasma viral RNA, were enrolled in this eradication protocol. Didanosine (DDI) and hydroxyurea (HU) were added to their baseline HAART and after a month of therapy, low dose OKT3, followed by a 2-week course of interleukin 2 (IL-2), was administrated. All antiretroviral therapy was then interrupted and the three patients developed viral rebound in the peripheral blood. The V3 loop region of the HIV-1 gp120 from cell-free viral RNA and proviral DNA in blood and seminal compartments was sequenced in one patient. The two major viral isolates in semen cells were macrophage- tropic (R5) and dual-tropic (R5X4), and these isolates were also present in the PBMCs. Six months after the viral rebound, we demonstrated a shift toward dual tropism in semen cell-associated HIV-1 proviral DNA, with the first appearance of a T-lymphotropic (X4) provirus solely in this compartment. The virus responsible for the blood plasma viral rebound was never found in the semen microenvironment. This study suggests viral compartmentalization of the semen microenvironment after an intensification and stimulatory HIV-1 eradication protocol, with evidence of viral evolution.

Prevalence of antibodies to HHV-8 in the general population and in individuals at risk for sexually transmitted and blood-borne infections in Catania, Eastern Sicily.

BACKGROUND: Human herpes virus 8 (HHV-8) is the putative infectious agent of multifactorial diseases, such as Kaposi's sarcoma (KS), primary effusion lymphoma and multicentric Castleman's disease. However, its exact mode of action as well as its transmission is still under investigation. Besides, little is known about its seroprevalence in the population. HHV-8 epidemiology has been widely studied all over the world, demonstrating significant differences in distribution among various geographical areas and various population communities. Very few studies of HHV-8 seroprevalence have been conducted in Italy, particularly in Sicily which, along with other Mediterranean areas, is known to have high rates of KS incidence. Between January 2001 and April 2002, 424 patients were consecutively recruited from three treatment facilities. An Infectious Diseases Clinic provided 196 anti-HIV positive patients, both affected by AIDS and not. A further 122 anti-HIV negative intravenous drug users were recruited from drug treatment clinics, while as a control group from the Blood Bank 126 blood donors were recruited. Base-line serum samples were assayed for antibodies to HHV-8 latency-associated nuclear antigen (anti-LANA) by IFA (Viramed Biotech AG, Planneg/Steinkirken--Germany). Anti-HHV-8 antibodies were found in 98 individuals (23.1%). HHV-8 reactivity was more common among anti-HIV positive patients (89/196, 45.4%, 95 C.I. 38.4-52.4) than in IDUs (6/102, 5.9%, 95 C.I. 1.2-16.2) and the control group (3/126, 2.4%, 95 C.I. 0.7-10.1). Overall, anti-HHV-8 antibodies were found in all three groups with large differences between groups.

Peripheral blood Dendritic cells are not a major reservoir for HIV type 1 in infected individuals on virally suppressive HAART.

Dendritic cells (DCs) are potent antigen-presenting cells, and their physiological localization in tissues that interact with the external environment is important as a first barrier against pathogens such as human immunodeficiency virus type I (HIV-1). Several models have been proposed to explain the possible role of DCs as a reservoir for HIV-1 in patients on virally suppressive highly active antiretroviral therapy (HAART). However, the low yield of cell isolates has made this evaluation a difficult task. The present study analyzes whether peripheral blood DCs from HIV-1-infected individuals on virally suppressive HAART, with plasma HIV-1 RNA levels of less than 50 copies/ml, carry either HIV-1 provirus and/or HIV-1 virions. Peripheral blood DCs were isolated from a cohort of 10 HIV-1-seropositive men taking suppressive HAART. In five patients, plasmacytoid and myeloid dendritic cells were isolated to attempt to identify their respective roles in HIV-1 residual disease. Viral out-growth assays were performed in vitro, as well as gag and R/U5 polymerase chain reaction (PCR) amplification of viral RNA and DNA, respectively, from DC and peripheral blood mononuclear cell (PBMC) extracts. Fluorescence activated cell-sorting (FACS) data revealed cellular yields from 85.90 to 95.18%, of relatively pure DCs isolated from patients' PBMCs. Although HIV-1 RNA gag and DNA RU/5 were detected in all PBMC samples isolated from the patients, proviral DNA and viral RNA forms were not detected in any of the DC isolates. In addition, no replication-competent virus was demonstrated in DC coculture assays, while virus was isolated from each patients' CD8+ T-lymphocyte-depleted PBMC cocultures. Furthermore, HIV-1 gag proviral DNA was not detected in either plasmacytoid or myeloid DC subfractions. The current study suggests that in HIV-1-infected individuals treated with suppressive HAART, peripheral blood DCs do not carry HIV-1 proviral DNA or viral particles attached to their surface. These populations of peripheral blood DCs are likely not a major HIV-1 reservoir in patients on HAART with clinically undetectable plasma viral RNA.