News Scan for Nov 03, 2020

News brief

Bacteriophages used in COVID patients with resistant bacterial infections

Eight COVID-19 patients in Texas who have secondary carbapenem-resistant Acinetobacter baumannii (CRAB) infections are receiving investigational bacteriophage therapy from biotechnology company Adaptive Phage Therapeutics (APT), company officials announced yesterday.

In collaboration with the Walter Reed Army Institute of Research, Bacterial Diseases Branch, APT scientists identified two bacteriophages from the company's PhageBank library that were active against bacterial isolates from the hospitalized patients, and they are using those phages to treat the patients under Food and Drug Administration (FDA) emergency Investigational New Drug requests. The company also says it's receiving and analyzing CRAB isolates from new patients daily to identify other potential bacteriophage matches.

The use of bacteriophage therapy in the eight patients came in response to requests in late September from the Rio Grande Valley Collaborative (RGVC), a network of 11 healthcare facilities in south Texas treating COVID-19 patients. RGVC data revealed that mortality rates were more than twice as high in COVID-19 patients with secondary CRAB infections than those without secondary CRAB infections.

"We are pleased to have been able to successfully deploy our investigational PhageBank therapy in response to this outbreak in COVID-19 patients in Texas," Greg Merril, APT's CEO and co-founder, said in a press release. "Our PhageBank deployment represents the first time our technology, originally developed by the Department of Defense, has been used to treat multidrug-resistant secondary bacterial infections in COVID-19 patients."

Merril said the company is working with the FDA to expand early access to PhageBank–based therapies for COVID-19 patients.
Nov 2 APT press release

ED study finds high rate of antibiotics for asymptomatic bacteriuria

A study of hospitalized patients admitted through the emergency department (ED) for asymptomatic bacteriuria (ASB) at more than 40 hospitals found that nearly 75% received antibiotics, US researchers reported today in Open Forum Infectious Diseases.

The study, which included 43 hospitals participating in the Michigan Hospital Medicine Safety Consortium, looked at all patients with ASB who were admitted through the ED February 2018 through February 2020. ASB is frequent among hospitalized patients and is commonly treated with antibiotics, even though national guidelines recommend against antibiotic therapy. Because unnecessary antibiotic treatment is common in EDs, the researchers wanted to evaluate how often antibiotic treatment for ASBs is initiated by emergency medicine (EM) clinicians.

The primary outcomes was the percentage of patients who had antibiotic treatment initiated by an EM clinician, and secondary outcomes included length of hospitalization and Clostridioides difficile infection within 30 days. The researchers also assessed factors associated with antibiotic treatment and length of antibiotic therapy.

Of the 2,461 patients admitted through the ED and ultimately determined to have ASB, 1,830 (74.4%) were treated with antibiotics, with a median treatment duration of 6 days. Urine cultures were ordered by EM clinicians in 1,970 patients (80%), and antibiotic treatment was initiated by an EM clinician in 68.5% of those treated with antibiotics (1,253 of 1,830). When antibiotic treatment was initiated by EM clinicians, 79.2% (993 of 1,253) of patients remained on an antibiotic for 3 or more days.

Predictors of EM clinician treatment of ASB versus no treatment included dementia (odds ratio [OR], 1.43; 95% confidence interval [CI], 1.11 to 1.84), spinal cord injury (OR, 5.92; 95% CI, 1.36 to 25.72), presence of a urinary catheter (OR, 1.54; 95% CI, 1.17 to 2.03), incontinence (OR, 1.81; 95% CI, 1.40 to 2.33), and altered mental status (OR, 2.34; 95% CI, 1.82 to 3.00). Patients treated with antibiotics were more likely to have C difficile infection than those who didn't receive antibiotics (0.9% vs 0%) and have longer hospital stays (5.1 vs 4.2 days).

"These findings identify the ED as a key target to reduce antibiotic use and improve outcomes in hospitalized patients with ASB," the authors wrote.
Nov 3 Open Forum Infect Dis abstract

UK reports high-path H5N8 avian flu at poultry farm

The United Kingdom yesterday announced that H5N8 avian flu has been detected at a broiler breeding farm in Cheshire, which comes just after veterinary officials detailed an unrelated low-pathogenic H5N2 outbreak at a farm in Kent.

Today the Department for Environment, Food, and Rural Affairs (DEFRA) confirmed that the outbreak was caused by a highly pathogenic strain.

The farm's 13,000 birds will be culled to curb the spread of the virus, and control zones have been placed around the affected location. An investigation is under way into the source of the virus, and DEFRA noted that wild birds migrating from the European mainland can spread avian flu to poultry and other captive birds.

Over the past few months, Russia and its neighbor Kazakhstan have reported a small but steady stream of highly pathogenic H5N8 avian flu outbreaks, which prompted earlier warnings from UK animal health officials for farmers to be vigilant and take precautions. The Netherlands recently reported highly pathogenic H5N8 in wild swans and a highly pathogenic H5 outbreak in poultry.
Nov 2 DEFRA update
Nov 3 DEFRA update

COVID-19 Scan for Nov 03, 2020

News brief

Study finds 10% rate of COVID-19 in traced contacts in San Francisco

In a case study of COVID-19 contact tracing during San Francisco's shelter-in-place period, of the 1,124 contacts traced, 1,017 (83.8%) were successfully notified, 457 (37.6%) were tested, and 120 (9.9%) were newly diagnosed.

In the study, published yesterday in JAMA Internal Medicine, the authors noted that contact tracers identified secondary cases within a median of 6 days from the person's symptom onset.

The city's sheltering in place lasted from Apr 13 to Jun 8, and officials recommended universal testing for all close contacts on May 5 whether or not they displayed COVID-19 symptoms. Of the 791 people the researchers interviewed after this new recommendation, 404 (51.1%) had a contact not previously diagnosed as having COVID-19, 356 (45.0%) had at least 1 contact notified, 206 (26%) had at least 1 contact that got tested, and 72 (9.1%) had at least 1 contact receive a positive test result for COVID-19.

Excluding long-term care facility outbreaks, the researchers reported 1,633 cases overall.

The researchers found that, similar to other studies, the secondary attack rate was higher for household contacts (11.3% vs 3.9%). Because of this, they hope that the period for testing and contact tracing can be decreased to prevent presymptomatic spread.

Also similar to other studies, minorities showed disproportionate rates of infection. Although San Francisco's population is 15% Latino, they made up 70% of the study's interviewed, infected people.
Nov 2 JAMA Intern Med study

Less distancing, higher COVID-19 burden in low-income neighborhoods

A study in Nature Human Behavior today finds a strong association between neighborhood income and physical distancing, with financial constraints and inability to work from home contributing to a higher COVID-19 burden in low-income neighborhoods.

Physical distancing—reducing close contacts between non-household members—is one of the primary strategies to mitigate the transmission of COVID-19 and was the impetus for state-level stay-at-home orders in the early months of the US pandemic. Data suggest that stay-at-home orders helped to reduce cases but reveal unequal declines and higher mortality rates among racial and ethnic minorities, who disproportionately live in low-income neighborhoods.

The study authors used cellphone mobility data from 19 million users in all 50 states and the District of Columbia from Jan 6 to May 3 to assess neighborhood-level physical distancing, finding increased physical distancing for all income groups, but lower increases for low-income communities. The highest income neighborhoods increased days at home 16.0 percentage points more than the lowest-income neighborhoods (P < 0.001, 95% confidence interval [CI], 16.0 to 16.1), inverting the pre-pandemic pattern of people in high income neighborhoods staying home less than those in low-income communities.

"The rapid inversion in the relationship between mobility and income during the COVID-19 pandemic illustrates how higher socioeconomic position affords greater opportunity to achieve good health," the authors write.

Residents of low-income neighborhoods were more likely to work outside the home, showing only a 6.6-percentage-point reduction in days at work versus a 13.7-percentage-point reduction for the highest income areas. Non-work activities outside the home declined in all groups, with low- and high-income communities curtailing non-work activities at similar rates.

"Although lower-income individuals had the knowledge and motivation to avoid exposure to COVID-19, as their reductions in non-work activities suggest, they were less able to stop reporting to work outside the home," the study authors conclude. "Our findings indicate that state policies did little to level the disparities in distancing between low- and high-income communities in Spring 2020."
Nov 3 Nat Hum Behav study

Higher COVID-19 rates and mortality tied to substandard housing

Poor housing conditions are associated with higher US COVID-19 incidence and mortality rates, a PLOS One study yesterday showed, highlighting the need for health policies supporting individuals living in substandard housing.

Veterans Administration researchers conducted a cross-sectional nationwide analysis of 3,135 US counties used data from the US Centers for Disease Control and Prevention, the US Census Bureau, and John Hopkins Coronavirus Resource Center, identifying an average of 14.2% of US households living in substandard housing.

The authors defined poor housing as households that included one or more of the following characteristics: overcrowding (more than one person per room), high housing cost (greater than 50% of household monthly income), incomplete kitchen facilities (lacking a sink with running water, stove, range, or refrigerator), or incomplete plumbing facilities (lacking hot and cold piped water, a flush toilet, or a bathtub/shower).

The researchers calculated incidence rate ratios (IRR) and mortality rate ratios (MRR) for county-level COVID-19 cases and deaths on Apr 21, finding a 50% higher risk of COVID-19 incidence (IRR, 1.50, 95% CI, 1.38 to 1.62) and a 42% higher risk of COVID-19 mortality (MRR, 1.42, 95% CI, 1.25 to 1.61) for each 5% increase in percent of households with one or more substandard housing characteristics, with similar results for two earlier time points (Mar 31 and Apr 10).

The authors point to repeated exposure and potentially higher viral inoculum due to overcrowding and a lack of access to adequate plumbing and sanitation as the most likely factors responsible for the higher incidence and mortality. They advocate for the need for public health messaging to improve hygiene, surface cleaning, and ventilation in crowded housing.

"Our study adds to a robust body of evidence for other disease processes, which has shown that inadequate housing is a public health hazard especially in relation to infectious diseases and highlights the importance of finding short (e.g. better access to clean water and bathrooms) and long-term (e.g. overcrowding, cost) solutions to problems surrounding poor housing to help contain or mitigate the spread of COVID-19," the authors wrote.
Nov 2 PLOS One study