Nigeria's big Lassa outbreak blamed on rats, not human-human spread

A genomic analysis indicates that Nigeria’s big Lassa fever outbreak this year has been driven by transmission from rats, not by human-to-human spread, easing worries about a possible Lassa superbug, according to a study described yesterday in the New England Journal of Medicine (NEJM).

Nigeria recorded 523 Lassa cases with 135 deaths from Jan 1 through Oct 7 of this year, according to a press release from the US National Institute of Allergy and Infectious Diseases (NIAID), which supported the study.

The Lassa virus is spread in West Africa by Mastomys natalensis rodents, also known as African soft-furred rats. People can become infected through contact with the rats’ urine or feces, and the virus can spread from person to person through contact with bodily fluids.

Public health officials were concerned that the Nigerian outbreak could be driven by a new or more virulent Lassa strain, possibly fueling increased human transmission, NIAID said. To find out, researchers analyzed Lassa virus genomes from 129 patients in this year's outbreak and 91 patients infected from 2015 through 2017.

"They discovered that Lassa genomes from 2018 were drawn from a diverse range of viruses previously observed in Nigeria rather than from a single dominant strain," NIAID said. "This indicates that a single virus strain was not driving the surge in cases in 2018." In addition, dating of the most recent ancestors of the 2018 samples suggested the outbreak involved many independent transmissions from rats to humans rather than from humans to humans.

Further, phylogenetic analysis revealed that viral diversity was affected by geography, with major rivers appearing to serve as barriers to migration of different strains, the NEJM report said.

A Nature news story yesterday said the "unprecedented speed" of the genomic analysis has helped health officials fight the spread of Lassa virus. The study was led by Christian Happi, PhD, director of the African Center of Excellence for Genomics of Infectious Diseases at Redeemer's University in Ede, Nigeria.
Oct 17 NEJM report
Oct 17 NIAID press release
Oct 17 Nature news story


CDC notes Jamestown Canyon and Powassan virus infections

In a review of arbovirus illness activity in the United States for 2017, researchers from the US Centers for Disease Control and Prevention (CDC) today said more cases of Jamestown Canyon and Powassan virus neuroinvasive disease were reported than in any previous year. They published their findings today in Morbidity and Mortality Weekly Report (MMWR).

Of 2,291 arbovirus cases reported to the CDC, 70% were neuroinvasive. West Nile virus was responsible for 92% (2,097), with a rate of neuroinvasive disease that was similar to the average for previous years. Others included Jamestown Canyon (75), La Crosse (63), Powassan (34), St. Louis encephalitis (11), unspecified California serogroup (6), and eastern equine encephalitis (5). The cases were reported from 641 counties in 47 states and the District of Columbia. Rates of neuroinvasive disease were highest in South Dakota, Mississippi, Arizona, Texas, and Illinois.

The Jamestown Canyon virus cases, two of which were fatal, were reported in 10 states, mainly in the Northeast and Upper Midwest, with Louisiana, Maine, and North Carolina reporting their first cases in 2017.

Powassan virus cases were reported in 10 states, also mainly in the Northeast and Midwest. Increases in both illnesses could be due to increased awareness and testing, but increased virus activity can't be ruled out, researchers said.

In another notable finding for 2017, eastern equine encephalitis from organ transplantation was reported for the first time and occurred in three patients.
Oct 18 MMWR report


APIC, CDC unveil tools to quickly identify infection prevention gaps

To help health facilities quickly spot infection prevention gaps and take action in real time, the Association for Professionals in Infection Control and Epidemiology (APIC) and the CDC today released free, downloadable Quick Observation Tools (QUOTs).

In a statement, APIC said the QUOTs are a set of ready-to-use assessment forms arranged around common themes, environments, and patient populations. The tools are designed to allow healthcare workers to check infection prevention at the patient-care level in a matter of minutes. The 20 sets of QUOTs are based on scientific recommendations, and each contains as many as 10 individual observation worksheets for use separately or together.

Ryan Fagan, MD, medical officer at the CDC, said the goal is to empower a range of health professionals, not just infection preventionists, to curb infections in their own patient care areas. "These tools are designed to be completed in just a few minutes each with a simple set of observations and should be repeated over time to track improvements."

The tools, funded by a CDC contract, are available on the APIC website and were introduced during International Infection Prevention Week.
Oct 18 APIC press release

Stewardship / Resistance Scan for Oct 18, 2018

News brief

Paper lays out hurdles for developing rapid antibiotic susceptibility tests

An international group of specialists from hospitals, research institutes, public health agencies, and diagnostics firms yesterday published a paper outlining the challenges to developing novel and rapid antibiotic susceptibility tests (ASTs). The consensus statement was published in Nature Reviews Microbiology.

ASTs are necessary to ensure that patients with bacterial infections get the most appropriate treatment. They also enable healthcare facilities to collect data on local patterns of antibiotic resistance; this data can be used to craft policies guiding empiric antibiotic therapy and to design strategic actions to control the spread of antibiotic-resistant pathogens. But current AST methods are time consuming (between 12 and 48 hours), and even currently available rapid tests take several hours and lack full automation. And when infections are severe, a delay in appropriate treatment can be the difference between life and death.

"Therefore, to facilitate targeted (and personalized) antimicrobial prescribing practices and to help reduce the increasing global burden of antibiotic resistance, there is an urgent need for the development and implementation of novel and truly rapid AST platforms (that is, results being available in 30 min to 1 h)," the authors write.

But the development of widely used rapid AST platforms has been slow over the past decade, the authors explain, for a variety of reasons. These include complex legal and regulatory landscapes; a complicated, multi-step development process that favors large diagnostics companies over small- and medium-sized enterprises; issues with quality and quality control; and difficulties in demonstrating the clinical utility, validity, and cost-effectiveness of new ASTs.

The authors say they hope that laying out these challenges will lead to increased dialogue between AST developers and end users and, ultimately, improve patient care.

"Better communication about the importance of AST should lead to better collaboration between the public, academia, patient groups, policy makers and industry," they write. "Understanding AST platform development and implementation issues will lead to a better understanding of the barriers and solutions required by public and private entities in maximizing the availability and use of (new and rapid) AST platforms."
Oct 17 Nat Rev Microbiol paper


Report shows results from new South Korean AMR surveillance system

Scientists from South Korea today published the first year of results from the government's new antimicrobial resistance (AMR) surveillance system, Kor-GLASS, which is modeled after the World Health Organization's Global AMR Surveillance System. The findings, along with a description of how Kor-GLASS was established, appear in Eurosurveillance.

From May 2016 through April 2017, non-duplicated isolates of major pathogens from blood, urine, feces, and urethral and cervical swabs were collected from six sentinel hospitals and tested at a central laboratory. Among 67,803 blood cultures, 3,523 target pathogens were recovered; Escherichia coli (1,536 isolates), Klebsiella pneumoniae (597), and Staphylococcus aureus (584) were the predominant bacterial species identified. Among 57,477 urine cultures, 6,394 E coli and 1,097 K pneumoniae isolates were recovered. From 12,782 stool cultures, 77 Salmonella spp. were recovered. None of the 3,111 genital cultures were positive for Neisseria gonorrhoeae.

Analysis of AMR prevalence in the major pathogens showed that 54.3% of the S aureus isolates were methicillin-resistant, 34.7% of E coli blood isolates and 27.0% of K pneumoniae blood isolates were resistant to cefotaxime, and 29.0% of Enterococcus faecium isolates were resistant to vancomycin. While resistance rates in E coli urine isolates were similar to those in blood isolates, K pneumonia urine isolates exhibited higher rates of resistance than K pneumoniae blood isolates. In addition, carbapenem and colistin resistance were identified more frequently in K pneumoniae blood and urine isolates than E coli blood and urine isolates. Among Acinetobacter baumannii isolates, 76.1% were multidrug-resistant, and 13.8% were extensively drug-resistant.

Bloodstream infections in inpatients per 10,000 patient-days were highest for cefotaxime-resistant E coli with 2.1, followed by 1.6 for methicillin-resistant S aureus, 1.1 for imipenem-resistant A baumannii, 0.8 for cefotaxime-resistant K pneumoniae, and 0.4 for vancomycin-resistant E faecium. Urinary tract infections in inpatients were 7.7 and 2,1 per 10,000 patient-days for cefotaxime-resistant E coli and K pneumoniae, respectively.

The authors of the report say that the country's previous AMR surveillance system had two notable limitations: AST methods were not well-harmonized across the participating clinical laboratories, and duplicated isolates were not filtered out. This created problems with reliability and potential overestimation of national AMR rates. They believe the results from the first year of Kor-GLASS show that the system is reliable, devoid of collection bias or isolate duplication, and can be expanded to include more sentinel hospitals and cover more pathogens.

"Beyond monitoring AMR, this system is a useful tool for public health authorities to deal with AMR," they write. "Kor-GLASS's successful AMR monitoring system has encouraged the South Korean government to establish a 'one health' approach for AMR in 2017 and to further develop the project by 2019."
Oct 18 Eurosurveill surveillance and outbreak report
Oct 18 Eurosurveill perspective


Study profiles use of procalcitonin and other biomarkers for sepsis

Researchers who looked at the use of biomarkers to guide clinical assessment and treatment in sepsis patients found that use of procalcitonin (PCT) increased sixfold over the 4-year study period, while lactate and C-reactive protein use remained level. They reported their findings yesterday in Public Library of Science (PLoS) One.

In the US retrospective observational study, the team analyzed adult sepsis discharges from 2012 through 2015. Of 933,591 adult sepsis discharges during the study period, 731,392 (78%) had biomarker testing.

Researchers also found that PCT use was linked to decreased odds of in-hospital mortality but increased hospital costs per day. It was also associated with increased antimicrobial use and increased length of stay. They also noted that serial biomarker monitoring may be connected to improved outcomes in the most critically ill patients
Oct 17 PLoS One report

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