COVID-19 Scan for May 08, 2020

News brief

Study: Evidence of COVID-19 virus found in 16% of semen samples

A study yesterday in JAMA Network Open is the first to demonstrate that SARS-CoV-2, the virus that causes COVID-19, is detectable in the semen of recovered and actively infected men, but it does not prove that the virus can be sexually transmitted.

"If it could be proved that SARS-CoV-2 can be transmitted sexually in future studies, sexual transmission might be a critical part of the prevention of transmission, especially considering the fact that SARS-CoV-2 was detected in the semen of recovering patients," the authors write.

The study was based on 38 semen samples collected from China in a small cohort study of male patients who currently had or recovered from COVID-19. Of the 38 participants who provided a semen specimen, 23 participants (60.5%) had achieved clinical recovery and 15 participants (39.5%) were at the acute stage of infection.

The semen of 6 patients (15.8%) tested positive for SARS-CoV-2 via polymerase chain reaction, including 4 of 15 patients (26.7%) who were at the acute stage of infection and 2 of 23 patients (8.7%) who were recovering. There were no clinical difference in patients' ages, days since symptom onset, days since recovery, or urogenital disease. The tests do not detect the presence of infectious virus.
May 7 JAMA Netw Open study


Temperature, humidity, latitude not tied to COVID-19 growth

Public health measures like school closures and mass gathering restrictions were found to have a far greater impact on slowing the spread of the coronavirus than temperature, latitude, and humidity, Canadian and Swiss scientists reported today in the Canadian Medical Association Journal.

To measure whether the epidemic growth of the coronavirus, as with influenza, is slowed by higher temperatures and higher humidity, which are associated with geographic latitude, the researchers performed a prospective cohort study of all 144 countries with at least 10 COVID-19 cases and local transmission by Mar 10. China, Italy, South Korea, and Iran were excluded from the analysis.

The investigators collected latitude, mean temperature, and mean relative humidity for the capital of each country, during an exposure period of 7 days (Mar 7 to Mar 13). They also collected data on school closures, restrictions of mass gatherings, and measures of social (physical) distancing. They then compared cumulative counts of COVID-19 in the 144 countries on Mar 27 with cumulative counts on Mar 20. Epidemic growth from Mar 20 to Mar 27 was expressed as ratios of rate ratios (RRR).

In a univariate analyses, there was no association between epidemic growth and latitude (RRR per 400 degrees2 increase 0.99; 95% confidence interval [CI], 0.96 to 1.03, P = 0.72) or mean temperature (RRR per 5°C increase, 0.97: 95% CI, 0.93 to 1.02). But there was a negative association with relative humidity (RRR per 10% increase 0.91, 95% CI 0.85 to 0.96) and with absolute humidity (RRR per 5 g/m3 increase 0.92; 95% CI, 0.85 to 0.99). Much stronger negative associations were found for restrictions of mass gatherings (RRR 0.65; 95% CI, 0.53 to 0.79), school closures (RRR 0.63; 95% CI, 0.52 to 0.78), and measures of social distancing (RRR 0.62; 95% CI, 0.45 to 0.85).

A multivariable model found a strong association with the number of implemented public health interventions (P for trend = 0.001), whereas the association with absolute humidity was no longer significant.

"Taken together, these findings suggest that seasonality is likely to play only a minor role in the epidemiology of COVID-19, while public health interventions (school closures, restricting mass gatherings, social distancing) appear to have a major impact," the authors write. "The important effect of public health interventions needs to be weighed carefully against potential economic and psychosocial harms when deciding when and how to lift restrictions."
May 8 Can Med Assoc J study


Early New York state coronavirus cases concentrated in households

A new analysis of COVID-19 cases in New York state outside of New York City in the early part of the outbreak found high levels of infections in households, a team of New York researchers reported today in Clinical Infectious Diseases.

During March, officials confirmed 47,326 cases outside of New York City, which reflected a 33% test-positive rate. The highest number of cases were in the metro region counties.

When the authors tracked 229 initial cases, people who were diagnosed through Mar 12, they found that 13% were hospitalized and 2% died. Testing among 498 people in initial patients' households revealed that 57% were positive for COVID-19—excluding the initial patients in each household, 38% were positive.

Looking at the household cases by age, the investigators found significant differences. The positivity rate was lower (23%) in children younger than 5 and higher (68%) in people age 65 and older. They concluded that New York state's COVID-19 burden was substantial and increased in March, with its earliest cases marked by high levels of infections in households that came with high risks of hospitalization and deaths.
May 8 Clin Infect Dis abstract

News Scan for May 08, 2020

News brief

Afghanistan, Pakistan, Chad, Niger confirm polio cases

Afghanistan, Pakistan, Chad, and Niger have reported new polio cases—14 in all—according to this week's Global Polio Eradication Initiative (GPEI) update.

Afghanistan has confirmed 6 new wild poliovirus type 1 (WPV1) cases, as well as 2 new circulating vaccine-derived poliovirus type 2 (cVDPV2) cases. The WPV1 cases are in Badakhshan, Balkh, Hirat, Kunar, and Kandahar (2 cases) provinces and bring the WPV1 total for the country this year to 11. The 2 cVDPV2 cases are in Nangarhar province and are the first of that type so far this year.

Pakistan reported 2 WVP1 cases, in Balochistan and Sindh provinces, which bring the number of confirmed 2020 cases to 43, compared with 21 at this point last year. Officials also confirmed 2 cVDPV2 cases, in Khyber Pakhtoon and Punjab, raising that number to 44. Pakistan had only 22 cVDPV2 cases in all of 2019, and none at this point in the year.

Chad and Niger each reported 1 cVDPV2 case this week, raising their 2020 totals to 21 and 2, respectively.
May 7 GPEI update


H5N8 avian flu poultry outbreaks affect 3 Hungarian counties

Over the last few days, Hungary has reported 12 more highly pathogenic H5N8 avian flu outbreaks in poultry, according to notifications from the World Organization for Animal Health (OIE).

Ten of the outbreaks occurred in Bacs-Kiskun County and 1 in Csongrad County, both of which have been hit hard, and 1 occurred in Bekes County. All are in southern Hungary.

The outbreaks began from Apr 25 to May 3, killing 909 of 191,593 susceptible poultry. The rest were culled to curb the spread of the virus. Officials did not specify the number of affected or susceptible birds in the Csongrad outbreak.

Hungary is one of a handful of European countries to report a small but steady stream of H5N8 outbreaks during the cool weather months.
May 5 OIE report on H5N8 in Bekes County
May 8 OIE report on H5N8 in Csongrad County
May 8 OIE report on H5N8 in Bacs-Kiskun County

ASP Scan (Weekly) for May 08, 2020

News brief

Our weekly wrap-up of antimicrobial stewardship & antimicrobial resistance scans

IDSA urges changes to national sepsis care measures

Originally published by CIDRAP News May 7

The Infectious Diseases Society of America (IDSA) and five other medical organizations are urging changes to a national set of care measures for sepsis patients, with the aim of reducing unnecessary antibiotic use in patients who may not need them.

In a paper published yesterday in Clinical Infectious Disease, members of the IDSA Sepsis Task Force argued that the Centers for Medicare and Medicaid Services' (CMS's) Severe Sepsis and Septic Shock Early Management Bundle (SEP-1), which was implemented in 2015, has the potential to drive antibiotic overuse because it does not account for the high rate of sepsis overdiagnosis and encourages aggressive antibiotics for all patients with possible sepsis, regardless of the certainty of diagnosis or severity of illness. Of particular concern is that SEP-1 stipulates the same time-to-antibiotic goal for both sepsis and septic shock, even though the association between time-to-antibiotics and mortality is much stronger for septic shock than for sepsis without shock.

"IDSA believes the perception that any delays in antibiotic therapy lead to worse outcomes for patients with sepsis, regardless of the severity of illness, contributes to inappropriate antibiotic prescribing and is the wrong message to communicate to providers," the authors wrote.

Among the recommendations outlined in the paper is removing sepsis without shock from SEP-1 to mitigate the risk of inappropriate antibiotics for patients with signs and symptoms resembling sepsis but with a low likelihood of infection. The recommendations also urge that SEP-1 continue to focus on obtaining blood cultures before giving antibiotics, versus after, and that antibiotics be administered within 1 hour of septic shock being recognized. But they call for the criteria for septic shock to be simplified.

In an editorial, authors from CMS, the University of California, San Francisco School of Medicine, and Wayne State University say the IDSA has not met the burden of proof to establish that SEP-1 has increased unnecessary antibiotic usage, or shown that delaying antibiotics in patients with severe sepsis is safe.

"We are open to considering alternative antibiotic measurement strategies in severe sepsis and septic shock, but we cannot support a strategy of leaving severe sepsis patients without timely and appropriate antibiotic coverage," the authors wrote. CMS requires hospitals to publicly report their compliance with SEP-1 in order to receive additional payments.
May 6 Clin Infect Dis paper
May 6 Clin Infect Dis editorial


Randomized trial shows stewardship benefits of rapid ID, susceptibility test

Originally published by CIDRAP News May 7

In another study published yesterday in Clinical Infectious Diseases, the results of a randomized controlled trial found that use of a rapid organism identification and phenotypic antibiotic susceptibility test (AST) led to faster changes in antibiotic therapy in patients with gram-negative bloodstream infections (BSIs) when compared with conventional testing.

In the prospective trial, US researchers randomized 500 patients who had a positive blood culture showing gram-negative bacteria at two US academic medical centers to receive either standard-of-care (SOC) culture and AST or rapid organism identification and phenotypic AST using the Accelerate Pheno System (RAPID). All patients in both arms underwent prospective audit and feedback from antibiotic stewardship programs at the hospitals. The primary outcome was time to first antibiotic modification within 72 hours of randomization.

Among the 448 participants included in the final analysis, the mean time to organism identification was faster in the RAPID arm than in the SOC arm (2.7 hours vs 11.7 hours, P < 0.001), as was time to susceptibility results (13.5 hours vs 44.9 hours, P < 0.001). Median (interquartile range, [IQR]) hours to first antibiotic modification was faster in the RAPID vs SOC arm for overall antibiotics (8.6 hours vs 14.9 hours, difference 6.3 hours, P = 0.02) and for gram-negative antibiotics (17.3 hours vs 42.1 hours, difference 24.8, P < 0.001). Median (IQR) time to antibiotic escalation was also faster in the RAPID arm than the SOC arm for antibiotic-resistant BSIs (18.4 vs 61.7 hours, difference 43.3 hours, P = 0.01).

Analysis of patient outcomes found no statistically significant differences between the two arms for mortality, time to death, or length of hospital stay.

The authors of the National Institutes of Health–funded study say the results indicate that rapid ID and AST, implemented along with antibiotic stewardship measures, can help clinicians provide timely, effective therapy while also promoting more appropriate antibiotic use.

"Development of rapid, innovative methods for detection of microorganisms and drug resistance in blood cultures is an important component in the fight against antimicrobial resistance," they wrote.
May 6 Clin Infect Dis abstract 


Study describes C auris bloodstream infections in Colombian kids

Originally published by CIDRAP News May 6

In a study today in the Journal of the Pediatric Infectious Diseases Society, US and Colombian researchers report that nearly one-third of the pediatric invasive Candida bloodstream infections (BSIs) analyzed at two Colombian pediatric hospitals were caused by Candida auris.

Of the 110 pediatric BSIs caused by Candida species at the two hospitals from July 2014 through October 2017, the researchers found that 34 (31%) were caused by C auris, a multidrug-resistant fungus that has primarily been identified in hospitalized and immunocompromised adults and rarely among children. Twenty-one percent of the children were younger than 28 days, 47% were 1 year old and younger, and 32% were over 1 year old. Underlying conditions included preterm birth (26%), being malnourished (59%), cancer (3%), solid-organ transplant (3%), and kidney disease (3%). All patients had at least one indwelling device, and 82% had a central venous catheter.

Thirty-three of the children (97%) received specific antifungal treatment for C auris. Analysis of 13 isolates found that 7 (54%) were resistant to amphotericin-B, 2 (15%) were resistant to fluconazole, and 1 (8%) was resistant to anidulafungin. In-hospital mortality was 41%.

The authors of the study note that the two hospitals were part of a large C auris outbreak investigation in Colombia, and that environmental and patient sampling at the hospitals showed extensive C auris contamination. They suspect that the infections were acquired during hospitalization.

"Rapid and accurate identification of C. auris is needed to guide treatment decisions, as are infection-control measures to stop the spread of the organism," they write. "Pediatricians need to be vigilant for C. auris infections in pediatric populations."
May 6 J Pediatric Infect Dis Soc abstract


Review finds low rate of co-infections in COVID-19 patients

Originally published by CIDRAP News May 4

Rates of bacterial or fungal co-infection reported in patients with COVID-19 are low, according to a new review of medical literature published in Clinical Infectious Diseases. But use of broad-spectrum antibiotics in these patients is common.

The review, led by researchers from Imperial College London, looked at all medical literature on coronavirus infections and bacterial or fungal co-infections published from 2000 through April 2020. The researchers included literature on other coronaviruses, such as severe acute respiratory syndrome (SARS) and Middle East respiratory syndrome (MERS), because of the lack of data on COVID-19 and a desire to explore whether similar observations have been made between these infections. To date, early reports from China have suggested a high rate of bacterial co-infection in COVID-19 patients.

Of the 1,007 abstracts identified, a total of 18 that reported bacterial/fungal coinfection were included in the final analysis. Nine of the studies reported on COVID-19, 5 on SARS-1, 1 on MERS, and 3 on other coronaviruses. Studies on COVID-19 reported that 8% of patients (62/806) had bacterial/fungal co-infection. A secondary analysis of the COVID-19 studies found that 72% of patients (1,450/2,010) received antibiotic therapy, with most therapy tending to be broad-spectrum.

The authors say potential stewardship interventions to support reduced antibiotic prescribing during the COVID-19 pandemic should be considered, and that prospective studies on antibiotic use and stewardship in COVID-19 patients are needed to develop evidence-based strategies.

"Despite the extensive reporting of broad-spectrum empirical antibiotic prescribing in patients with coronavirus respiratory infections, there is a paucity of data to support their association with bacterial/fungal co-infection," the authors wrote. "With increasing pressure on healthcare infrastructure during the COVID-19 pandemic, a general evidence-base on which to develop antimicrobial prescribing and stewardship strategies is required to support optimal treatment outcomes and prevention of the unintended consequences of antimicrobial usage on the individual and wider society." 
May 2 Clin Infect Dis abstract


Web tool for antibiotic prescribing proving popular among French GPs

Originally published by CIDRAP News May 4

French researchers report in the Journal of Antimicrobial Chemotherapy that the use of Antibioclic, a web-based computerized decision support system (CDSS) to aid appropriate antibiotic prescribing in primary care in France, has seen steadily increasing in use since its introduction in 2011.

Designed by a team of French general practitioners (GPs), Antibioclic is a stand-alone web application that allows clinicians to access guideline-based recommendations for treatment of common infections seen in primary care settings. In an analysis of queries made to Antibioclic by French GPs from 2012 through 2018, the researchers found that the number of queries increased from a median of 796 per day in 2012 to 11,125/day in 2018, while unique users increased from 414/day to 5,365/day. Among more than 3.5 million queries in 2018, 78% were for adult patients, with six conditions—cystitis, acute otitis media, acute sinusitis, community-acquired pneumonia, sore throat, and pyelonephritis—accounting for more than 50% of queries.

Among 4,016 GPs who responded to surveys conducted in 2014 and 2019, 96% reported using Antibioclic during a consultation with patients, with 24% systematically using the CDSS to initiate an antibiotic course and 93% following the program's recommendation for the latest prescription. In addition, 43% of GPs reported using Antibioclic to explain to patients why they did not prescribe an antibiotic.

The authors conclude, "This study demonstrates that Antibioclic has been successfully implemented and adopted by French GPs, with data indicating sustained use and a continuous increase in users. Antibioclic may have a positive impact on users’ prescriptions, antibiotic consumption, AMR [antimicrobial resistance] and patient care. In an era in which AMR is increasing while therapeutic innovation is rare, such systems should be promoted and developed through a global collaborative approach."
May 1 J Antimicrob Chemother abstract

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