News Scan for Aug 15, 2018

News brief

USDA finalizes compensation plan for high-path avian flu damages

The US Department of Agriculture (USDA) Animal and Plant Health Inspection Service (APHIS) announced yesterday that it has issued a final rule spelling out USDA indemnity pay to farms hit by highly pathogenic avian influenza outbreaks.

The final rule updates a 2016 interim rule and allows indemnity payments to be split, based on a provided formula, between poultry and egg owners and their contracted growers. It also adopts biosecurity principles set by the National Poultry Improvement Plan and requires larger operations to have auditable biosecurity plans in place to receive indemnity payments.

According to its statement on the final rules, the USDA said the split payments for highly pathogenic avian influenza are in line with the existing program for low pathogenic avian influenza.

In the final rule, officials address stakeholder concerns that followed the release of the interim rules, including if self-certification of biosecurity was adequate. In the final rule, operations that meet minimum size requirements must have an auditable plan that addresses 14 biosecurity principles that comply with the NPIP.
Aug 14 APHIS press release
Feb 8, 2016, CIDRAP News scan "USDA expands regulations for compensating avian flu damages"

Recommendations tackle steps to keep, increase ID physician-scientists

In new recommendations geared toward retaining and boosting the numbers of physician scientists specializing in infectious diseases, three medical societies said the main factors needed are improved compensation, expanded mentorship and training opportunities, and steps to improve workforce diversity.

The three groups include the Infectious Diseases Society of America (IDSA), the HIV Medicine Association (HIVMA), and the Pediatric Infectious Diseases Society (PIDS). The groups published their policy recommendations in a Journal of Infectious Diseases supplement.

They acknowledge the challenges that infectious disease physicians face balancing their clinical and scientific roles and that efforts to address attrition and bring new people into the field will require efforts of federal, university, and professional sectors.

Among the current problems are inadequate funding for fellowship opportunities and big compensation disparities, with median pay 20% less for infectious disease researchers when compared to infectious disease clinicians working at hospitals or clinics. According to the report, infectious disease physician-researchers make 27% less than their peers working in private practice.

The report covers ways to increase the number and quality of training opportunities, which includes expanding entry criteria for federal grant opportunities and collaborations with research and advocacy groups.
Aug 14 IDSA press release
Aug 14 J Infect Dis abstract

Stewardship / Resistance Scan for Aug 15, 2018

News brief

MCR-3 detected in study of English pigs

A study of pigs has detected the presence of the MCR-3 colistin-resistance gene in England for the first time, United Kingdom researchers reported yesterday in the Journal of Antimicrobial Chemotherapy. But the study also found that stopping the use of colistin can mitigate long-term on-farm persistence.

To gain a better understanding of the molecular epidemiology of MCR-positive Enterobacteriaceae, circulating plasmids, and their on-farm persistence, researchers from the UK's Animal and Plant Health Agency used whole-genome sequencing to analyze MCR-1-positive Enterobacteriaceae isolates from pig samples on a single pig farm. They collected fecal samples from three cohorts of pigs: one that was initially treated with colistin following diarrhea, a younger cohort that was untreated but overlapped with the first cohort over a period of 5 months, and a third cohort on the same farm 20 months after the initial diagnostic submission.

The results showed that Escherichia coli harboring MCR-1 and multiple resistance genes were detected in the colistin-treated cohort of pigs as well as the untreated cohort. The researchers theorize that the presence of MCR-1 in the untreated pigs may have been because these pigs had moved into accommodations previously occupied by the treated pigs and had been exposed to environmental contamination with MCR-1 E coli. Additionally, the researchers found MCR-3 in seven of the E coli isolates from the treated cohort, with some isolates also harboring multiple copies of MCR-1 on different plasmids.

Neither MCR-1 nor MCR-3 were detected when the farm was re-sampled after 20 months.

"In conclusion, this study indicated that although mcr E. coli had become widespread on a farm in England, measures taken to mitigate on-farm risk were successful," the authors wrote.
Aug 14 J Antimicrob Chemother study

Study shows emergence of E coli ST131 clade in Europe

In another study yesterday in the Journal of Antimicrobial Chemotherapy, a team of European researchers report the emergence of an extended-spectrum beta-lactamase (ESBL)-producing E coli ST131 clade in European hospital patients.

In the study, 688 ESBL E coli isolates were obtained from rectal swabs of patients in hospitals in Berlin, Geneva, Madrid, and Utrecht. The researchers were looking to assess the prevalence, geographical distribution, and microbiological characteristics of E coli ST13—a multidrug-resistant pandemic clone causing urinary tract and bloodstream infections—and its dominant sublineage, C/H30.

The analysis found that the ST131 detection rate among ESBL E coli carriers was 20.5% (141/688), with 16% (46/295) prevalence in Madrid, 18% (31/172) prevalence in Utrecht, 23% (31/135) in Berlin, and 38% (33/86) in Geneva. Subclone typing further revealed that C/H30 subset compromised the majority of the ST131 isolates (70.2%, 99/141). But there was significant difference in subclone prevalence, with C1/H30R1 isolates more prevalent in Geneva (49%, 16/33) and C2/H30Rx more prevalent in Madrid (67%, 31/46). While the C2/H30Rx isolates were significantly associated with the CTX-M-15 enzyme, the C1/H30R1 isolates were more associated with the CTX-M-27 enzyme.

Isolates belonging to this new ST131-C1-M27 clade have previously been detected among Japanese, French, and German isolates, but the detection of isolates from this clade in all four hospitals suggest it is circulating throughout Europe. The authors of the study say the findings demonstrate a changing epidemiology of ESBLs in Europe caused by ST131 subclones.
Aug 14 J Antimicrob Chemother abstract