News Scan for May 11, 2021

News brief

CARB-X to fund development of rapid test for chlamydia, gonorrhea

CARB-X announced today that it is awarding Australian diagnostics company SpeeDx up to $1.8 million to develop a rapid molecular diagnostic test for chlamydia and gonorrhea infections.

The money will aid development of SpeeDx's InSignia technology, which is able to detect whether an active infection is associated with Chlamydia trachomatis or Neisseria gonorrhoeae within 60 minutes. The technology will also be able to perform antibiotic susceptibility testing to identify the most appropriate antibiotic for gonorrhea infections.

SpeeDx, of Sydney, Australia, plans to combine the test with a battery powered, easy-to-use device developed by QuantuMDx that can be used in remote or low-resource settings such as sub-Saharan Africa, where the vast majority of gonorrhea infections go undetected and untreated. If the project achieves certain milestones, it could be eligible for $1.9 million in additional funding from CARB-X (the Combating Antibiotic Resistant Bacteria Biopharmaceutical Accelerator).

"SpeeDx's technology is in the early stages of development and, if successful, could be used to help healthcare providers rapidly diagnose chlamydia and gonorrhea, and to identify antibiotics that could be effective, thus improving treatment decisions, and mitigating the devastating effects of these diseases," CARB-X Research and Development Chief Erin Duffy, PhD, said in a CARB-X press release. "Faster diagnostics have the potential to help inform treatment decisions, and those diagnostics that can be deployed in low-resource settings are sorely needed."
May 11 CARB-X press release

Hospital pathogens in Vietnam show increasing resistance levels

Analysis of surveillance data from hospitals in Vietnam found alarmingly high and increasing levels of antibiotic resistance in clinically important organisms, researchers reported yesterday in Antimicrobial Resistance and Infection Control.

Among the 42,553 bacterial isolates collected from 13 Vietnamese hospitals in 2016-17 by Vietnam's national antimicrobial resistance (AMR) surveillance network, 71% were gram-negative and 29% were gram-positive. Escherichia coli (21%) and Staphylococcus aureus (11%) were the most frequently detected species, followed by Klebsiella pneumoniae (9.1%) and Acinetobacter baumannii (9%).

Antibiotic susceptibility data showed that, among gram-positive bacteria, 73% of S aureus isolates were methicillin-resistant, 34% of Enterococcus faecium were resistant to vancomycin, and 58% of Streptococcus pneumoniae had reduced susceptibility to penicillin.

Among gram-negative bacteria, 59% of E coli and 40% of K pneumoniae produced extended-spectrum beta-lactamase (ESBL) enzymes, and 29% and 11% were resistant to carbapenems, respectively. In addition, 79% of Acinetobacter spp. and 45% of Pseudomonas aeruginosa were carbapenem resistant, and 88% of Haemophilus influenzae were resistant to ampicillin.

When compared with data collected from the same hospitals in 2012-13, the proportion of antibiotic-resistant isolates were higher in 2016-17 for most pathogen-antibiotic combinations of interest, including imipenem-resistant A baumannii, P aeruginosa, and Enterobacterales. The proportion of multidrug-resistant E coli, A baumannii, and P aeruginosa was also higher.

The study authors note that the findings may not reflect the true prevalence of antibiotic resistance because of sampling biases and because they did not know whether the isolates were from hospital- or community-acquired infections.
May 10 Antimicrob Resist Infect Control study

Uganda reports Crimean-Congo fever cluster at refugee camp

Uganda has reported a Crimean-Congo hemorrhagic fever (CCHF) outbreak, which involves two confirmed cases at a refugee settlement in Kikuube region in the country's western region, the World Health Organization (WHO) African regional office said in its latest weekly outbreaks and health emergencies report.

The first case was confirmed on Apr 28 in a 16-year-girl who sought care at a healthcare facility after experiencing fever with hemorrhagic symptoms that included vomiting and nosebleeds. An investigation found that her family raises goats. The virus that causes CCHF is known to circulate in the country's livestock.

A second epidemiologically linked case was detected and involves a 13-year-old boy who had similar symptoms. Both patients are recovering and are listed in stable condition.

No other suspected cases have been reported, and so far, 144 contacts are being monitored. The outbreak response includes mass spraying of livestock, managing human cases, and increasing supplies of ribavirin and personal protective equipment.

The CCHF virus is carried by ticks, which can pass the disease to cattle, sheep, goats, and rabbits. People can contract infections through tick bites or contact with the blood of infected animals. The virus can also spread from person to person by body fluids.
May 10 WHO African regional office weekly outbreaks and emergencies bulletin

COVID-19 Scan for May 11, 2021

News brief

COVID-19 death rates low in pregnant, hospitalized women, study finds

Compared with non-pregnant women hospitalized with COVID-19, pregnant women with COVID-19 had lower in-hospital death rates, according to a research letter in the Annals of Internal Medicine today.

University of Texas (UTHealth) and University of Maryland researchers looked at 1,062 pregnant and 9,815 non-pregnant patients hospitalized with COVID-19 and viral pneumonia from April to November 2020. All were 15 to 45 years old.

Pregnant women had a 0.8% mortality rate, compared with 3.5% in the non-pregnant group, and this difference was seen across sensitivity analyses looking only at intensive care unit patients (3.5% vs 14.9%) and those needing mechanical ventilation (8.6% vs 31.4%). The median time from admission to death was 18 days in pregnant women and 12 days in non-pregnant women.

Pregnant women tended to be younger, healthier, and on public health insurance, but no conclusions could be drawn due to the low death count. The researchers also note that pregnancy status was only available for 36% of patients in the Premier Healthcare Database.

Of the 9 pregnant patients who died, they were between the ages of 23 to 44, 8 were Black or Hispanic, 6 were obese, and 7 had at least one comorbidity. All died from April to July, and 7 of 9 of the pregnancies resulted in live births.

"We had expected to confirm the results of the CDC and other U.S. researchers showing that pregnancy increases the risk for dying from COVID-19," said first author Beth Pineles, MD, PhD, in a UTHealth press release. "However, once we compared our results to data from the UK and reviewed the CDC reports more carefully, we found confirmation that our results were likely to represent the true risks of COVID-19 in these populations, despite the limitation of pregnant women being younger and healthier than non-pregnant women."
May 11 Ann Intern Med study
May 11 UTHealth press release

Data show 2% of COVID patients may carry 90% of community's virus

Just 2% of COVID-19–infected individuals could carry 90% of the SARS-CoV-2 virions circulating within communities, according to a Proceedings of the National Academy of Science study comparing presymptomatic and asymptomatic patients with hospitalized patients.

The results, published yesterday, included 1,405 positive COVID-19 cases from the University of Colorado Boulder's 2020 fall semester testing program and compared them with 404 data points from previous research on hospitalized COVID-19 patients. Overall, more than 72,500 saliva samples were tested for COVID-19 on the college campus, all from people who were asymptomatic or presymptomatic.

The average viral load from campus collections was 2.1 x 10⁷ virions per milliliter (mL), with a median of 1.1 x 10⁶ virions/mL. In comparison, hospitalized patients had an average viral load of 2.5 x 10⁷ virions/mL and a median of 9.4 x 10⁵ virions/mL.

Past research has shown that it's rare for infectious virions to be isolated from biosamples with less than 1 million (10⁶) virions per mL, and the researchers say that approximately half of the patients in both cohorts had lower amounts. While this portion of the study population makes up less than 0.02% of the total virions, the researchers note that the individual with the highest viral load made up 5%.

"By summing the viral load across individuals based on the interpolated probability density function representing each population starting with those with the highest viral loads, we find that just 2% of individuals harbor 90% of the circulating virions," the researchers write. "This is true in both the university (i.e., asymptomatic) and hospitalized (i.e., symptomatic) populations. Further, 99% of community-circulating virions are accounted for by just 10% of the asymptomatic and 14% of the symptomatic population."

The researchers conclude that viral supercarriers are likely also superspreaders, and they advocate for screening strategies that target asymptomatic and presymptomatic COVID patients.
May 10 Proc Natl Acad Sci study

COVID-19 antibody rates go up in association with UK vaccine rollout

Real-world effects from the United Kingdom's vaccine rollout began after the first dose: From late February to late March, 94% of 70- to 84-year-old blood donors had COVID-19 antibodies, but only about 5% were from natural infection, according to a Journal of Infection letter to the editor yesterday.

Out of 7,720 blood donor samples available from Feb 22 to Mar 21, 3,224 (44.7%) were positive for Roche S, which indicates COVID-19 antibodies from either natural infection or vaccine, and 1,111 (14.4%) were Roche N positive, which indicates antibodies only from natural infection. The researchers say the overall weighted seropositivity among blood donors was 46.4% with the Roche S assay, compared with the 54.7% all-cause antibodies reported by the UK Office of National Statistics Infections Survey from Feb 18 to Mar 14.

During this 4-week period, weighted seroprevalence for 70- to 84-year-old blood donors was estimated to be 93.5% (95% confidence interval [CI], 90.9% to 95.4%), with 4.7% caused by natural infection (95% CI, 3.1% to 7.1%). The researchers attribute the rest of the antibodies in this age-group to the first dose of either the Pfizer/BioNTech or the AstraZeneca/Oxford vaccines. (At this time, less than 1% of those 70 to 84 had received a second dose.)

The researchers note that natural-infection antibodies in this older age-group had stabilized at least since the month of January, when it was at 5.2%.
May 10 J Infect study