News Scan for Nov 14, 2017

Real-time resistance tracker
Salmonella in calves
Drug-resistant malaria controversy
Hepatitis A in California

FDA launches Resistome Tracker to monitor antibiotic resistance

The US Food and Drug Administration (FDA) today launched an interactive research tool called Resistome Tracker to track antibiotic-resistance genes.

"Resistome Tracker is one of the first publicly available tools to provide visually informative displays of antibiotic resistance genes in bacteria," the FDA said in a news release. Designed mainly for public health officials, academics, and researchers who are using new genomics technologies, the tool allows users to identify new resistance genes, customize visualizations by antibiotic drug class, compare resistance genes across different sources, and map resistance genes to geographic region.

By using whole-genome sequencing (WGS), Resistome Tracker represents a major advancement in resistance monitoring that will enhance the evaluation of the impact of antibiotic use on the evolution and spread of antibiotic resistance, the agency said.

Resistome Tracker has launched with a focus on Salmonella. Scientists upload Salmonella genome sequences from the National Center for Biotechnology Information (NCBI) public databases Resistome Tracker each week, allowing near real-time monitoring of antibiotic resistance. Resistome Tracker includes WGS data on 97,390 genomes from NCBI, 27,512 of which are US isolates and 8,900 are isolates from the National Antimicrobial Resistance Monitoring System (NARMS).

Later the tool will include data on pathogens like Escherichia coli and Campylobacter as well as additional gene categories such as serotype, sequence type, and virulence genes.
Nov 14 FDA news release
Resistome Tracker


CDC reports more cases of drug-resistant Salmonella tied to dairy calves

A multistate outbreak of Salmonella Heidelberg infections linked to contact with dairy calves has grown by 8 cases, to 54 cases, the Centers for Disease Control and Prevention (CDC) said today in an update.

Of the 54 cases, 17 have required hospitalization, the CDC said, but no deaths have been reported. The latest cases were in six states, including Virginia, which had its first case and increase the number of infected states to 15, 1 more than the agency reported in its previous outbreak update on Aug 2. Wisconsin has had the most cases (19), followed by Missouri (7), Minnesota (6), and South Dakota (5).

Officials have interviewed every patient, and 34 of them (63%) reported contact with dairy calves or other cattle in the week before they fell ill.

The CDC said, "Ongoing surveillance in veterinary diagnostic laboratories showed that calves in several states continue to get sick with the outbreak strains of multidrug resistant Salmonella Heidelberg. Information collected earlier in the outbreak indicated that most of the calves came from Wisconsin. Regulatory officials in several states are now tracing the origin of the calves that are linked to the newer illnesses."

The update said WGS has identified multiple resistance genes in 43 outbreak-related isolates from patients, 87 from cattle, and 11 from animal environments. All 8 isolates from people that were tested were resistant to amoxicillin-clavulanic acid, ampicillin, cefoxitin, ceftriaxone, streptomycin, sulfisoxazole, and tetracycline, and had reduced susceptibility to ciprofloxacin. Seven isolates were also resistant to trimethoprim-sulfamethoxazole, 5 to nalidixic acid, and 3 to chloramphenicol. All eight isolates, however, were susceptible to azithromycin and meropenem.
Nov 14 CDC update


Controversy simmers over drug-resistant malaria threat

Researchers concerned about alarming levels of treatment failures of preferred malaria drugs in the Greater Mekong region are at odds over whether stronger actions should be taken to head off the threat, such as declaring a public health emergency of international concern (PHEIC), according to a Nov 10 report from BMJ.

On Sep 21, researchers writing in a letter to The Lancet Infectious Diseases described a multidrug-resistant parasite lineage that has now been detected in southern Vietnam, following spread in Cambodia, Thailand, and Laos. They said that, over 8 years, the lineage, resistant to the piperaquine component of combination therapy, has now been found in all four Greater Mekong countries.

The report from Mahidol Oxford Tropical Medicine Research Unit (MORU) triggered calls for greater action, including from its top funder, the Wellcome Trust. One of the concerns is the impact that drug-resistant malaria would have if it spread to Africa, which carries 90% of the world's malaria death burden. And some experts said they worried that the development might undo steady progress in battling the disease.

In a response to the letter and calls for action in late September, the World Health Organization (WHO) said the research is sound, though it questioned the group's interpretation. It said resistance to malarial drugs is a big concern, but warned against creating unnecessary alarm. The WHO also said current malaria elimination efforts have had a big impact.

Nicholas White, MD, DSc, one of the researchers at MORU, told BMJ that the group doesn't see any new strategies taking shape that address heightened concerns over the spread of drug-resistant malaria and that the WHO may be overly optimistic about current combination treatments and new ones to be developed.

Other global health experts, however, discounted the need for a PHEIC, noting continued progress against the disease and the need to focus efforts on access to treatment for populations who need it. Yet others said the uncertainty over whether to declare an emergency shows weakness in the current system for responding to infectious disease threats.

Ed Whiting, policy director at Wellcome Trust, told BMJ, "A new, graded system that triggers a concerted international response at scale, before reaching crisis status, would enable serious threats like artemisinin resistance to be tackled sooner, and may prevent them from becoming a global health emergency."
Nov 10 BMJ extract
Sep 21 Lancet Infect Dis letter
Sep 29 WHO Q and A on Lancet Infect Dis letter


Vaccine shortage limits hepatitis A campaign in California

A hepatitis A vaccination campaign planned in California is postponed until a national shortage of hepatitis A vaccine can be resolved. The vaccination campaign was meant to provide the second of two inoculations against the liver disease, Kaiser Health News (KHN) reported today.

As of Nov 6, 544 people have gotten sick with hepatitis A and 20 have died in San Diego County. According to KHN, 90,735 people have received vaccinations in San Diego County, most of them the first of the two shots administered 6 months apart.

The outbreak in San Diego County and another outbreak in Michigan—which has sickened 486 and killed 19—have squeezed the national stockpile of hepatitis A vaccines. Both Merck and GlaxoSmithKline manufacture a hepatitis A vaccine.

The outbreaks in California and Michigan are deadlier than previously reported outbreaks, according to public health officials.
Nov 14 KHN story

Newsletter Sign-up

Get CIDRAP news and other free newsletters.

Sign up now»


Unrestricted financial support provided by

Bentson Foundation Gilead 
Grant support for ASP provided by


  Become an underwriter»