ABSTRACT
Antimicrobial resistance is a major threat to human health that is predicted to impact most heavily on sub-Saharan Africa, however there is a lack of clinical outcome data from drug-resistant infections in this setting. There are reasons to expect the COVID-19 pandemic to have both positive and negative impacts on AMR in Africa. We have recruited a series of prospective longitudinal cohorts from Queen Elizabeth Central Hospital (QECH), Blantyre, Malawi and the surrounding communities in the Southern Region of Malawi. The data from these cohorts has been used to describe the aetiology of febrile illness, the burden of antimicrobial resistance in this setting and the distribution of extended spectrum beta-lactamase producing bacteria in humans, animals and the environment. Amongst a cohort of patients presenting to QECH unwell with febrile illness, 67% were living with human immunodeficiency virus (HIV). We identified a diagnosis in 145 of 225 (64%) participants, most commonly tuberculosis (TB;34%) followed by invasive bacterial infections (17%), arboviral infections (13%), and malaria (9%). In a second cohort with drug resistant infection, resistance to third-generation cephalosporins was associated with an increased probability of in-hospital mortality (hazard ratio [HR] 1.44, 95% CI 1.02-2.04), longer hospital stays (1.5 days, 1.0-2.0) and decreased probability of discharge alive (HR 0.31, 0.22-0.45). In the community cohorts, a paucity of environmental health infrastructure and materials for safe sanitation was identified across all sites and ESBL-Enterobacterales were isolated from 41.8% of human stool, 29.8% of animal stool and 66.2% of river water samples and was associated with the wet season, living in urban areas, advanced age and in household-animal interactions. Life threatening febrile illness is common in Blantyre however, diagnostics are few, however the COVID-19 pandemic has led to rapid expansion of diagnostic capacity. We are, however frequently treating the wrong bugs with ceftriaxone, further there was significant expansion of azithromycin demand and usage during the pandemic. Current management of sepsis has not been optimised and ceftriaxone use is promoting carriage of ESBL bacteria out of the hospital and ESBL E. coli and K. pneumoniae are ubiquitous in the community, where environmental hygiene infrastructure and community antimicrobial stewardship are critically lacking.Copyright © 2023
ABSTRACT
Background: Acinetobacter baumannii can reside in humans without causing infection or symptoms but can opportunistically cause community and nosocomial infections. Few studies from Taiwan have used national-level data to investigate antibiotic resistance rates of A. baumannii infections in the intensive care units (ICUs) of medical centers. Aim(s): This study determined the number of infection sites of A. baumannii and the resistance rates of carbapenem-resistant A. baumannii (CRAB) infections in ICUs in Taiwan, and identified trends over time, variations of infection site, and factors associated with resistance. Method(s): This study used the database provided by Taiwan's Centers for Disease Control. Yearly, Taiwan Nosocomial Infections Surveillance System Surveys from 2008 to 2019 were analyzed, including data on the site of infection and resistance rates of A. baumannii and patient and hospital characteristics. Result(s): On average, 21 hospitals as medical center/year participated in the survey, and 6803 A. baumannii isolates were identified. All isolates were health care-related infections. The most frequent sites of infection were the urinary tract (50.6%), respiratory tract (19.6%), bloodstream (18.2%), surgical wounds (4.3%), and others (7.4%). Infection rates were the highest in the urinary tract in 2019 (63.6%;P < 0.001). On average, the rate of carbapenem resistance was 66.6% (95% confidence interval: 63.1-70.1) among ICU patients at medical centers. Considerable regional differences were observed, with the highest rates of resistance in the central regions. Higher resistance rates were observed between 2019 and 2020 COVID-19 pandemic (74.2%). Conclusion(s): This is the first report on the prevalence of health care-related A. baumannii infection in Taiwan in 2008-2019. Several invasive diseases, such as urinary tract infections, are associated with higher rates of carbapenem resistance. The resistance rate of CRAB in Taiwan is exceptionally high. The current big-data-derived findings may inform future surveillance and research efforts in Taiwan.Copyright © 2023 Wolters Kluwer Medknow Publications. All rights reserved.
ABSTRACT
Since the beginning of detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in 2019, many genetic evolutions of this virus have been reported. The most recent variant that caused the fourth wave of Covid-19 infection worldwide, Omicron, has shown various mutations at its receptor binding domain therefore inducing changes in behavior compared to previous variants. According to published data, major genetic mutations, differences in clinical severity and also resistance to prevention and treatment strategies have been observed. Lower rates of disease severity, hospital and intensive care unit admissions, younger age of contamination with progression to severe disease, resistance to 2 dose vaccination, risk of re-infection and resistance to monoclonal antibodies have been some of the many differences in the recent variant of concern. In the following article some considerations and modifications of the Omicron variant with regard to its general characteristics and treatment will be discussed.
ABSTRACT
Background: Knowing the true incidence of HIV-1 infections (recent infections) among people newly diagnosed is pivotal to monitoring the course of the epidemic. We have developed a Primer ID Next Gen Sequencing (PID-NGS) assay to identify recent infection by measuring within-host viral diversity over multiple regions of the HIV-1 genome. We implemented a state-wide project to identify recent infections and transmitted drug resistance mutations (DRMs) in diagnostic samples in near real time. Methods: Serum samples from individuals with newly HIV-1 diagnoses (diagnostic sample collected within 30 days of diagnosis) were sequenced. PID-NGS libraries were constructed covering the coding regions for protease, a portion of reverse transcriptase, integrase, and the env gene. The use of the PID-NGS strategy allows for significant error correction and also a definition of the sampling depth of the viral population. Recent infection was defined as within 9-month of infection. DRMs were summarized at detection sensitivities of 30%, 10% and 1% based on viral population sampling depth. Results: From Jan 2018 to Jun 2021, we successfully sequenced partial genomes from 743 individuals with new diagnoses. Year 2020 had the lowest number of new diagnoses (Fig 1a, red bar). Overall, 39.2% of samples were inferred to have represented infection within the previous 9 months. Percent of recent infection varied significantly over the years, increasing from 29.6% in late 2018 to 50.9% in early 2020, but decreasing significantly to 32.7% in 2021 (Fig 1a, blue lines). Individuals younger than 30 y/o were more likely to be identified with recent infection (p<0.01). NNRTI DRMs, especially K103N, were the most abundant DRMs. Fig 1b shows the trend of DRMs over the four years. We observed a trend of decrease in the overall NNRTI DRMs and an increase in the NRTI DRMs in the population. Further analysis suggests that the increase in NRTI DRMs were from TAMs and their revertants, while clinically important NRTI DRMs (K65R and M184) were low (<1%). Conclusion: We have demonstrated a state-wide, all-in-one platform to monitor HIV-1 recency and DRMs in new diagnoses. The number of new diagnoses decreased significantly in 2020 in concert with the COVID-19 pandemic which suggests a decrease in overall HIV testing. The decline in the percentage of recent infections in early 2021 signals a return to broader HIV-1 testing and diagnosis. The increase of other NRTI DRMs suggests ongoing evolution at these sites within the viral population.