Stewardship / Resistance Scan for Feb 17, 2021

News brief

Study finds herbicides increase antibiotic resistance genes in soil

New research by scientists from China and the United Kingdom shows that three widely used herbicides increase the prevalence of antibiotic resistance genes in soil bacteria, along with the mobile genetic elements that enable those genes to move between bacteria. The research appeared yesterday in Molecular Biology and Evolution.

In a series of experiments, the scientists showed that application of the herbicides glyphosate, glufosinate, and dicamba to soil microcosms over 60 days significantly increased the total abundance of antibiotic resistance genes in soil bacteria, with glyphosate showing a ninefold increase in antibiotic resistance genes compared with control soil samples. In addition, glufosinate and glyphosate significantly increased total abundances of mobile genetic elements, with glyphosate and glufosinate having more of an impact than dicamba.

Further experiments suggest that the herbicides may promote antibiotic tolerance by changing bacterial gene expression, or by selecting for mutations that increase tolerance to antibiotics during prolonged herbicide exposure. The scientists also found that herbicide exposure increased bacterial cell membrane permeability and conjugation of multidrug-resistant plasmids, which promote the movement of antibiotic resistance genes between bacteria.

To assess whether these laboratory findings translated to real-world settings, the scientists sampled soil from 21 agricultural sites across China and compared soil exposed to glyphosate with soil that had been free of herbicide use for 5 years. They found that glyphosate application was associated with higher relative abundances of both antibiotic resistance genes and mobile genetic elements.

The authors of the study note that although the presence of antimicrobial resistance genes and mobile genetic elements in harmless soil bacteria may not pose a health threat, fertilization of fields with untreated animal manure that typically contains opportunistic pathogens could result in those bacteria acquiring resistance genes and spreading. The authors say that the effect of herbicides on soil microbiomes should be re-evaluated.

"While antibiotic resistance genes are not harmful per se, they will reduce the efficiency of antibiotics during clinical treatments," study author Ville Friman, PhD, of the University of York, said in a university press release. "Keeping the frequency of resistance genes low will hence prolong the long-efficiency of antibiotics. As resistance genes can easily move between environments, agricultural fields could be globally important sources for resistance genes."
Feb 16 Mol Biol Evol abstract
Feb 16 University of York press release

UK study shows sustained drop in outpatient antibiotics during pandemic

A decline in community antibiotic prescribing in North West London that began before the first COVID-19 peak in March 2020 was sustained for 8 months, UK researchers reported this week in Clinical Microbiology and Infection.

In the study, researchers from the UK National Institute for Health Research and Imperial College London analyzed individual prescribing records for 2 million people in North West London from January 2015 through November 2020 and conducted an interrupted time series analysis to determine whether there was a measurable change in antibiotic prescribing in primary care associated with the pandemic and the national response. Antibiotic prescriptions in 2020 were stratified by gender, age-group, ethnic group, and socioeconomic deprivation level, and prescribing records were linked to SARS-CoV-2 test results.

From January through November 2020, 730,001 primary care antibiotic prescriptions were identified. The interrupted time series analysis showed that the antibiotic prescribing volume in North West London had been declining before March 2020 at a rate of 584 items per month, but the rate of decline climbed to 3,504 items per month after March 2020.

The rate of decline was sustained beyond the initial peak of COVID-19 cases, with the antibiotic prescribing volume reaching its lowest level in August 2020. Reduced antibiotic prescribing continued into the second COVID-19 peak, which began in late September. The observed decline, which occurred despite primary care consultation rates returning to normal, was seen across all gender, age, ethnic, and socioeconomic groups.

From January through August 2020, prescribing of penicillins declined the most (57.2% of March levels), followed by macrolides (54.6%) and tetracyclines (45.0%). Among 6,158 COVID-19 patients, the most commonly prescribed antibiotics within 14 days of a positive test were amoxicillin (34.9%) and doxycycline (27.4%).

"The reduction in community prescribing associated with COVID-19 and the national pandemic response could potentially have a favourable impact on antimicrobial resistance," the study authors wrote. "Our results need to be seen in the context of all antibiotic prescribing, and further monitoring is required to see whether this reduction persists and the impact that it will have."
Feb 15 Clin Microbiol Infect study

News Scan for Feb 17, 2021

News brief

Interventions tied to lower COVID rates in meat processing plants

Almost one in five meat processing workers in Nebraska contracted COVID-19 from April to July 2020, but after facility-wide mitigations and strategies were put in place, new cases appeared to decrease, according to an Emerging Infectious Diseases report yesterday. The researchers found that men and Hispanic/Latinos showed the highest burden in case numbers and severity.

Facility information was available for 13 meat processing sites, and 8 showed significant decreases in case incidence, ranging from 1.22 to 16.58 fewer cases per 1,000 people (median 3.20) 10 days after implementing universal mask policies and physical barriers. Four facilities showed no statistically significant change, including the two that added mask policies only, and another showed a significant increase, from 0.48 to 2.09 cases per 1,000 people (P = 0.008).

Out of 5,200 total COVID patients among approximately 26,000 meat processing workers, 225 (5.3%) needed hospitalization for symptoms, 83 (1.6%) were admitted to the intensive care unit (ICU), and 21 (0.4%) died. At least 501 cases (9.6%) were asymptomatic, although the lack of information for 264 as well as a general lack of mass testing means more probably went unrecorded.

Two thirds of COVID infections were in Hispanic or Latino people, and the researchers found that this subgroup represented 73% of workers who needed hospitalization, 78% who needed ICU care, and 68% of deaths. Men made up 58% of the cases, 72% of those hospitalized, 78% of those in the ICU, and 81% of deaths.

"Our results indicate significantly reduced incidence of COVID-19 cases in 62% of studied facilities following adoption of universal masking and physical barrier interventions," the researchers write, although they also emphasized the importance of enhanced ventilation. "Increased multilayered IPC [infection prevention and control] strategies, rapid contact tracing, and accessible testing are critical to identifying asymptomatic and presymptomatic cases and interrupting silent transmission."
Feb 16 Emerg Infect Dis study

Experts highlight best imaging for COVID-related musculoskeletal issues

Computed tomography, magnetic resonance imaging (MRI), and ultrasound scans should be used to help diagnose and treat COVID-19 symptoms, according to a review published today in Skeletal Radiology.

While COVID-19 infection is most known for its respiratory ailments, musculoskeletal symptoms such as muscle pain and inflammation, peripheral neuropathy, joint pain, and clotting issues can cause short- or long-term issues, the researchers write.

The authors discuss symptoms caused or related to COVID-19 infection across muscles, nerves, joints, soft tissues, and bones, as well as which imaging techniques may be best to identify them.

For example, myositis (muscle inflammation) and its more severe complication, rhabdomyolysis, can best be detected via MRI, but electromyography, nerve conduction studies, creatine phosphokinase levels, and reported weakness can also help. Radiologists should look for muscle edema as well as disease patterns on the scan including homogeneous hyperintense signals or "stipple signs" of myonecrosis.

"Many patients with COVID-related musculoskeletal disorders recover, but for some individuals, their symptoms become serious, are deeply concerning to the patient or impact their quality of life, which leads them to seek medical attention and imaging," said corresponding author Swati Deshmukh, MD, in a Northwestern University press release. "That imaging allows us to see if COVID-related muscle and joint pain, for example, are not just body aches similar to what we see from the flu—but something more insidious."

The researchers also note in the paper that some conditions may be associated with ICU treatment, such as corticosteroid use, which can cause myopathy, and prone positioning, which they speculate could be related to some peripheral neuropathy because of stretch and traction injuries.

"Familiarity with incidence, etiology, and imaging findings of COVID-19 related musculoskeletal manifestations is important for radiologists in order to optimize imaging report interpretation and patient care," they conclude.
Feb 17 Northwestern University press release

Emergency funds for Ebola outbreaks; DRC virus tied to earlier outbreak

In the latest Ebola outbreak developments, Mark Lowcock, head of the United Nations Central Emergency Response Fund, announced today on Twitter that he allocated $15 million for responses to new outbreaks in the Democratic Republic of the Congo (DRC) and Guinea.

In the DRC, preliminary genetic analysis suggests that the virus is related to an earlier outbreak, Reuters journalist Fiston Mahamba said yesterday on Twitter. The result suggests that the source is likely related to contact with a survivor of the earlier event and not a new virus introduction from an animal or other source.

So far, four infections and two deaths have been reported in the DRC flare-up, which is occurring in the region where a large 2-year outbreak was declared over in June. The index patient in the cluster is a woman who was married to an Ebola survivor. In rare instances, survivors can harbor the virus in "immune-protected" body sites such as the eyes or testes.

The World Health Organizaton's (WHO's) African regional office said in its latest weekly health emergencies update that the DRC outbreak is concerning, because the virus has spread to other health zones and areas and that one healthcare worker is among the confirmed cases.

Regarding the Guinea outbreak, based on data as of Feb 14, it said the reemergence is gravely concerning, and though health officials have responded quickly, they face challenges of unsecure burials, inadequate infection prevention and control measures, and lack of rapid tests at the hospital in the outbreak region. Yesterday, the Africa Centers for Disease Control and Prevention (Africa CDC) said Guinea had 17 cases, 5 of them fatal.
Feb 17 Mark Lowcock tweet
Feb 16 Fiston Mahamba tweet
Feb 16 WHO African regional office weekly report
Feb 16 CIDRAP News scan

Global flu detections still spotty, mostly from flu B

Over the last half of January, flu activity across the world stayed mainly at sporadic levels, despite increased testing to assess if the virus is circulating along with COVID-19, the WHO said in its latest update.

Most of the Northern Hemisphere, where the flu season would normally be under way, only reported sporadic cases. In China, flulike activity was well below usual levels, with southern China reporting another small rise in influenza B detections.

Western Africa's flu activity continued, with different countries reporting different stains, and in Eastern Africa, Kenya has reported H3N2 and influenza B in recent weeks.

In Southeast Asia, H3N2 activity continues to be reported from Laos.

Globally, of the few respiratory samples that tested for positive for flu at WHO-affiliated labs, 81.1% were influenza B, and of the subtyped influenza A samples, 61.8% were H3N2.

The WHO's flu vaccine strain advisors began their virtual deliberations today to assess and recommend the strains to include in vaccines for the Northern Hemisphere's 2021-22 flu season. They will also review zoonotic flu strains to see if any candidate vaccine strains are needed for pandemic preparedness.
Feb 15 WHO global flu update
WHO flu vaccine strain selection meeting information