News Scan for Feb 22, 2022

News brief

ECDC warns that Italian Candida auris outbreak could spread

The European Centre for Disease Prevention and Control (ECDC) yesterday issued a warning about an ongoing outbreak of the multidrug-resistant yeast Candida auris in Italy.

The outbreak began with a single case detected in a hospital in Liguria in July 2019. In February 2020, a case was detected in the same hospital's intensive care unit for COVID-19 patients, and C auris case numbers continued to increase at the facility through 2020 and 2021. Whole-genome sequencing of isolates from 10 of the early cases showed that the isolates belonged to the South Asian clade and that all except one were part of the same cluster originating from the index case.

To date at least 277 cases have been detected at eight hospitals in Liguria, 210 of them at the initial hospital. An additional 11 cases have been detected in facilities in the neighboring region of Emilia-Romagna.

C auris was first identified in Japan in 2009 and since then has been detected in 40 countries on six continents. It can cause severe invasive infections in patients who have underlying disease or immunosuppression, and clinicians have limited treatment options. Nearly all C auris isolates described worldwide have been reported as resistant to fluconazole, with varying levels of resistance to other azoles, echinocandins, and amphotericin B.

The ECDC says that, given the high number of cases and the inter-regional spread, the risk of further spread within Italy is considered high.
Feb 21 ECDC rapid risk assessment

VA study finds most dental antibiotic prophylaxis prescriptions improper

Another study of antibiotic prescribing by Veterans' Affairs (VA) dentists found that five of every six prescriptions for antibiotic prophylaxis were inconsistent with guidelines, researchers reported today in Infection Control & Hospital Epidemiology.

The cross-sectional study of visits to VA dentists from 2015 through 2019 examined all antibiotics prescribed within 7 days of a visit in the absence of an oral infection. In the primary analysis, antibiotic prophylaxis was considered appropriate only if it was associated with a visit that involved manipulation of gingival tissue and if the patient had a cardiac condition at the highest risk of an adverse outcome from infective endocarditis according to guidelines.

In the secondary analysis, antibiotic prophylaxis was considered appropriate if it was associated with tooth extractions or implants and the patients had a cardiac condition or was immunocompromised.

The investigators analyzed data on 369,102 prophylaxis prescriptions for 358,078 visits. Over 90% of the visits were categorized as gingival manipulation. The median prescription duration was 7 days; only 6.5% were prescribed for 1 day.

In the primary analysis, using a narrow definition of appropriate, 15% of prophylaxis prescriptions were considered appropriate. In the secondary analysis, with a broader definition, 72% of prophylaxis prescriptions were considered appropriate. Prophylaxis inconsistent with guidelines increased over time.

For the narrow definition, multivariable analysis found that Black (vs White) race, Latino (vs non-Latino) ethnicity, and visits located in the West census region were associated with unnecessary prophylaxis. Variables associated with a lower risk for inappropriate prophylaxis were older age, prosthetic joints, immunocompromising condition, and rural location. Similar predictors were identified on multivariable analysis for the broad definition, although Latino ethnicity was less likely to be associated with inappropriate prophylaxis and dental visits in the Northeast more likely.

The study authors say pressure for dentists to prescribe antibiotics by medical clinicians may play a role in the lack of guideline concordance.

"Other factors that may be associated with potentially unnecessary prescribing by dentists include time constraints, an aging population, dental implant placements, underinsurance, and procedural skills during emergencies," they write.
Feb 22 Infect Control Hosp Epidemiol abstract

WHO survey finds gaps in global infection prevention and control

A World Health Organization (WHO) survey of infection prevention and control (IPC) professionals found significant gaps in IPC implementation, WHO researchers reported yesterday in The Lancet Infectious Diseases.

From Jan 16 to Dec 31, 2019, 4,440 IPC professionals from 81 countries completed the WHO online IPC assessment framework (IPCAF), a questionnaire that scores responses to questions about eight WHO IPC core components: (1) IPC program; (2) IPC guidelines; (3) IPC education and training; (4) healthcare-associated infection (HAI) surveillance; (5) multimodal strategies; (6) monitoring and audit of IPC practices and feedback; (7) workload, staffing, and bed occupancy; and (8) materials and equipment for IPC. Each section generates a score from 0 to 100.

The overall weighted IPCAF median score indicated an advanced level of IPC implementation (605), but significantly lower scores were found in low-income (385) and lower-middle-income (500) countries, as well as in public healthcare facilities (515). Core component 8 (90) and core component 2 (87.5) scored the highest, and core component 7 (70) and core component 3 (70) scored the lowest.

Overall, only 15.2% (588 of 3,873) of facilities met all IPCAF minimum requirements, ranging from 0% (0 of 417) in low-income countries to 25.6% (278 of 1,087) in primary facilities, 9% (24 of 268) in secondary facilities, and 19% (18 of 95) in tertiary facilities in high-income countries.

The authors of the paper say the findings identify key opportunities to inform ongoing global IPC improvement efforts, particularly in low-income and lower-middle-income countries, and note that improvements will be needed to reduce the global burden of HAIs and antimicrobial resistance (AMR).

"The endemic burden of HAIs and AMR continues to affect patient safety, hamper high standards of quality of care, and impede the achievement of universal health coverage," they wrote.

"To address these challenges and make substantial durable progress in IPC, a greater emphasis must be placed on developing and enforcing stronger policies and regulations, supported by leadership and accountability mechanisms at the highest levels, as well as by an appropriately trained IPC workforce at the facility level."
Feb 21 Lancet Infect Dis study

WHO adds details to deadly UK Lassa cluster reports

The WHO yesterday fleshed out more details on the family cluster of imported Lassa fever cases—one of them fatal—recently reported from the United Kingdom.

The first patient got sick after returning from a trip in late 2021 to Mali, where Lassa fever is endemic. He or she was hospitalized and has recovered. The second and third case involved family members who did not travel.

The WHO notes that the cases mark the second known instance of secondary Lassa transmission in Europe. The last secondary Lassa cases in Europe were reported in 2016 in Germany in an individual who performed postmortem care of a person who died from Lassa virus infection.

In the UK cluster, the other two family members were hospitalized, and one died. British media reports said the patient who died was a newborn.

Contact tracers have identified people who were exposed and are being monitored for 21 days. Those with high-risk exposure have been offered postexposure prophylaxis.

Lassa fever is endemic in a number of West African countries where Mastomys rats spread the virus, which can cause a hemorrhagic illness in humans who consume food or water contaminated with feces or urine from infected animals. Human-to-human infections can occur through contact with an infected patient's body fluids.
Feb 21 WHO statement
Feb 16 BBC story

COVID-19 Scan for Feb 22, 2022

News brief

Study highlights rare BA.2 subvariant reinfections after Omicron COVID-19

Infection with the SARS-CoV-2 Omicron BA.2 subvariant shortly after an initial infection with the Omicron BA.1 subvariant—the original Omicron strain—is rare, occurring mostly in young, unvaccinated people with mild symptoms, according to a non–peer-reviewed Danish study.

In the study, published today on the medRxiv preprint server, researchers at the Statens Serum Institut in Denmark analyzed the subgenomic and genomic RNA of viruses responsible for a randomly selected group of 263 paired samples from more than 1.8 million COVID-19 patients. The study period was Nov 22, 2021, when Omicron was first identified in that country, to Feb 11, 2022. The BA.2 variant now accounts for most COVID-19 cases in Denmark.

Of the 263 virus samples, 187 COVID-19 reinfections (71%) were identified, 47 (18%) of which were BA.2 cases after initial BA.1 infections. The severity of both types of infections was similarly mild, and no patients were hospitalized.

Median patient age was 15 years, none were older than 38, 89% were unvaccinated, 6% had received two COVID-19 vaccine doses, and 4% had received one dose.

Overall, viral load was significantly lower in patients with BA.2 reinfections than during the initial infection.

"This may indicate a more superficial and transient secondary infection that could be explained by T cell-mediated immunity obtained during the first infection," the researchers wrote.
Feb 22 medRxiv study

US researchers confirm SARS-CoV-2 Alpha, Delta variants in deer

A new preprint study describes detection of both Alpha and Delta SARS-CoV-2 variants in white-tailed deer in Pennsylvania—the first known detections of those strains in deer—with 18 of 93 nasal swab samples (19.3%) testing positive, adding to growing evidence that deer are a reservoir for the virus in the United States.

The study was published on medRxiv and has not been peer-reviewed.

All deer samples were collected in the fall and winter 2021, after Delta became the prominent variant in the United States but before Omicron emerged. The authors said samples collected from road-killed animals were significantly more likely to be positive than all other sample types (hunter harvested, 11 of 66; road-killed, 6/13; and other, 1/14 [P=0.002]).

Of the 18 positive nasal swabs, researchers performed whole-genome sequencing on seven, which were annotated as Alpha and Delta variants, the first reported observations of these lineages in deer, the authors said. This finding indicates at least four independent spillover events between humans and deer in the last year.

"Given that there are estimated to be 30 deer [per] square mile in PA, and over a million deer total, this suggests an enormous number of spillovers and infected deer in the state" the authors said.

Last year, research conducted in Iowa and Ohio showed that a significant proportion of white-tailed deer were SARS-CoV-2–positive.
Feb 21 medRxiv study

COVID-19 patient ZIP codes may affect disease severity

A pooled cross-sectional study in the Annals of Internal Medicine finds that COVID-19 patients' ZIP codes may affect clinical outcomes, with patients from high-vulnerability neighborhoods more likely to be hospitalized for infections.

The study is based on data from 2,309 patients hospitalized with COVID-19 at 38 Michigan hospitals. Medical history was compared with patients' social vulnerability index (SVI), which takes into account the local area's average income, education level, household density to percentage of households led by single parents, and homes in which English is the not the primary language.

Though once hospitalized, patients from high-vulnerability ZIP codes had similar outcomes to patients from low-vulnerability neighborhoods, they tended to present with more severe clinical symptoms, including lower pulse oximetry readings and higher respiratory rates.

When controlled for age, sex, and comorbidities, patients from high-vulnerability neighborhoods had more acute organ dysfunction (increase of 2.8 percentage points) and acute organ failure (increase of 2.8 percentage points) at hospitalization. But intensive care unit stay, mortality, and discharge disposition were similar across ZIP codes.

"What leads to the initial disparities in seriousness of illness that they arrive with?" said Renuka Tipirneni, MD, the lead study author, in a press release. "Are people not getting access to testing or treatment early in their illness? Are there other individual patient-level social risks such as ongoing difficulties with transportation, housing, or sick leave at work? Did they delay seeking care because of lack of access?"

The authors suggest SVIs will be a useful tool to predict trends in COVID-19 illness in the future.
Feb 21 Ann Intern Med study
Feb 21 University of Michigan press release