News Scan for Feb 17, 2022

News brief

H5 avian flu strikes third Indiana poultry farm

The Indiana Board of Animal Health (IBAH) said today that initial tests at a third turkey farm in the state are positive for H5 avian flu. The new detection marks the United States' fifth recent outbreak in poultry. Further testing is under way to assess if the virus is the same highly pathogenic H5N1 strain that struck the first Indiana farm.

The newly infected farm is in Greene County, the second county to be affected. Indiana's other two events occurred at turkey farms in Dubois County, located about 60 miles to the south. The IBAH said in an email notice that the Greene County outbreak is outside the surveillance zone for the Dubois County outbreaks, so officials have added another 10-kilometer zone that includes the northern portion of Daviess County, which lies between Greene and Dubois counties. Both affected counties are in southwestern Indiana.

Officials said a high mortality in birds at the Greene County facility led to testing, adding that depopulation of about 48,000 birds is under way.

In January, federal officials reported several detections of the highly pathogenic Eurasian H5N1 in waterfowl across a wide swath of the East Coast, which was followed by poultry outbreaks in Indiana, Kentucky, and Virginia. In Canada's Nova Scotia and Newfoundland provinces, H5N1 was also detected in wild birds and in poultry.

The virus is fueling detections and poultry outbreaks in several parts of the world and has been linked to a few illnesses in people who had close contact with poultry. So far, no onward transmission among people has been found.
IBAH avian flu page

Chinese study highlights spread of MCR-1 colistin resistance gene in E coli

A study of fecal samples from patients at hospitals in Shanghai found the mobile colistin resistance gene MCR-1 in nearly 4% of Escherichia coli strains, most of them from children, Chinese researchers reported today in the Journal of Global Antimicrobial Resistance.

In the study, researchers from China's Center for Disease Control and Prevention collected fecal samples from patients with diarrhea and healthy individuals treated at Shanghai hospitals from 2012 through 2015. They isolated E coli bacteria from the samples, then screened the E coli strains, using polymerase chain reaction, to detect MCR-1, a gene that was first discovered in China in 2015 and is known to be widely distributed in E coli and other pathogens that cause diarrhea. They also conducted whole-genome sequencing (WGS) and antimicrobial susceptibility testing on the isolates.

A total of 1,204 E coli strains were isolated from the fecal samples, and 40 strains (3.9%) carried MCR-1. The MCR-1–positive rates climbed from 1.20% in 2012 to 3.94% in 2015. Most strains harboring MCR-1 were isolated from children younger than 7 years of age, and the gene was found in four types of E coli: atypical enteropathogenic, typical enteropathogenic, enterotoxigenic, and enteroaggregative.

Antimicrobial susceptibility testing found that all 40 strains carrying MCR-1 were resistant to colistin, 36 were resistant to three or more antibiotic classes, and 27 were resistant to five or more classes. WGS revealed that nearly half of the strains also carried quinolone-resistance genes or beta-lactam–resistance genes and were multidrug-resistant (MDR). The predominant type of plasmid in MCR-1–positive E coli was IncX4 and IncI12.

"These results indicate that more attention should be paid to the spread of mcr-1 in various types of E. coli," the study authors wrote. "Strengthening the surveillance of mcr-1-positive strains and investigating their prevalence and distribution will help us actively respond to the challenge of MDR gram-negative Enterobacteriaceae."
Feb 17 J Glob Antimicrob Resist study

Previously approved antibiotic could be used against plague, melioidosis

The UK government says its scientists, working in collaboration with industry and academia, have found that a fluoroquinolone antibiotic used to treat ear infections may also work against plague and melioidosis.

The antibiotic, finafloxacin, was approved by the US Food and Drug Administration in 2014 for the treatment of acute otitis externa (infection of the outer ear canal) and is also in clinical trials for use in patients with complicated urinary tract infections. But German pharmaceutical company Merlion Pharma says finafloxacin has also demonstrated efficacy against Burkholderia pseudomallei, the bacterium that causes melioidosis, and Yersinia pestis, which causes plague, in mouse models of infection.

In a project funded by the US Defense Threat Reduction Agency (DTRA), scientists from the UK's Defence Science and Technology Laboratory (Dstl) have been working with MerLion to further investigate whether finafloxacin can be used to treat infections caused by these pathogens, which are endemic in several parts of the world but are also considered potential bioweapons.

"Finding an antibiotic that works against a range of pathogens is really exciting," Dstl associate professor Sarah Harding, PhD, said in a news release. "It has been almost 10 years of research, which would not have been possible without the collaboration between Dstl, MerLion Pharmaceuticals and DTRA."
Feb 17 UK.gov news release

COVID-19 Scan for Feb 17, 2022

News brief

Study: COVID-19 vaccination protective against developing long COVID

A new review of 15 studies analyzed by the UK Health Security Agency (UKHSA) shows COVID-19 vaccination is protective against developing symptoms of long COVID, or symptoms lasting longer than 4 weeks after the initial infection.

The UKHSA said approximately 2% of people in the United Kingdom with COVID-19 have gone on to develop long COVID, with the most common symptoms being lingering fatigue, shortness of breath, and muscle and joint pain.

In a new rapid evidence review, the agency says eight studies show strong evidence that people who received two doses of COVID-19 vaccine are half as likely to develop long COVID. Another four studies demonstrate evidence that people who are vaccinated after receiving a long COVID diagnosis see their symptoms improve.

Mary Ramsay, MD, the head of Immunization at UKHSA, said in a press release, "These studies add to the potential benefits of receiving a full course of the COVID-19 vaccination. Vaccination is the best way to protect yourself from serious symptoms when you get infected and may also help to reduce the longer-term impact."
Feb 15 UKHSA rapid review
Feb 15 UKHSA press release

In a related development, the European Society of Clinical Microbiology and Infectious Diseases (ESCMID) yesterday published in Clinical Microbiology and Infection new rapid guidelines for the assessment and treatment of patients with long COVID.

ESCMID recommends that patients experiencing respiratory symptoms at 3 months post initial infection may benefit from routine blood tests, chest imaging, and pulmonary function tests.
Feb 16 Clin Microbiol Infect paper

Nirmatrelvir-ritonavir cut risk of severe COVID by 89% in phase 2/3 trial

A phase 2/3 trial of 2,246 symptomatic, unvaccinated, high-risk COVID-19 outpatients finds that a combination of the antivirals nirmatrelvir and ritonavir lowered the risk of progression to severe illness by 89%.

Results of the trial, led by scientists from nirmatrelvir maker Pfizer, were published yesterday in the New England Journal of Medicine (NEJM).

The researchers randomly assigned 2,246 COVID-19 patients to receive either 300 milligrams (mg) of oral nirmatrelvir and 100 mg of ritonavir (1,120 patients) or a placebo every 12 hours for 5 days (1,126).

An interim analysis of 774 patients treated within 3 days of symptom onset showed that nirmatrelvir recipients' incidence of COVID-related hospitalization or death by day 28 was 6.32 percentage points lower than in the placebo group (95% confidence interval [CI], -9.04 to -3.59; relative risk reduction [RR], 89.1%).

Three of 389 nirmatrelvir patients (0.77%) were hospitalized, but none died. In contrast, 27 of 385 placebo patients (7.01%) were hospitalized, and 7 of them died.

The final analysis of 1,379 patients showed similar efficacy, with a difference in incidence of 5.81 percentage points (95% CI, -7.78 to -3.84) and a relative RR of 88.9%. All 13 deaths were among placebo recipients.

The SARS-CoV-2 viral load was lower in the nirmatrelvir than in the placebo group at day 5 of treatment. Treatment-emergent adverse events occurred in similar proportions in both groups (22.6% with nirmatrelvir vs 23.9% with placebo). Serious adverse events occurred in 1.6% of the nirmatrelvir group, compared with 6.6% in the placebo group, and adverse events leading to treatment discontinuation occurred in 2.1% vs. 4.2%, respectively.

Two adverse effects were reported more often in the nirmatrelvir than in the placebo group, with 5.6% versus 0.3% having an abnormal sense of taste and 3.1% versus 1.6% reporting diarrhea.

A related editorial by Eric Rubin, MD, PhD, NEJM editor-in-chief, and Deputy Editor Lindsey Baden, MD, said that the antiviral combination should be reserved for high-risk COVID-19 patients no more than 5 days after symptom onset. "Until we have a better idea of the potential for the emergence of resistance, we need to be good stewards of this medication," they wrote.
Feb 16 NEJM study and editorial