H5N1

Canada: E.coli outbreak hits grain industry

Via National Newswatch: Mysterious E.coli outbreak hits grain industry. Excerpt:

A string of flour product recalls this spring has cost the milling sector millions of dollars and costly research may still be needed to find the source of the contamination, say grain industry officials.  

The outbreak of E.coli 0121 is so mysterious that few people connected to the investigation are willing to discuss it on the record. 

Fred Jamieson of the Office of Food Safety and Recall at the Canadian Food Inspection Agency “we’re working back through the grain supply system to find the answer. We’re looking at all sorts of different possibilities.” 

Among them is the contaminated wheat comes from a particular region of the country or that it’s the result of a weather anomaly, he said. He couldn’t estimate how long it would take to solve the mystery.  

CFIA has issued 22 product recall notices covering bags of baking flour, various unbaked pie and tart shells and cookie dough. No deaths have been reported in connection with the recall but the agency said 26 people were initially infected with E. coli and at least six required hospital care. One of the ill people told investigators he still had a bag of flour. It was tested and found to be contaminated with E.coli 0121. 

The latest recalls were on June 24 and 25 involving tart shells for meat pieces and flour distributed by Ontario firms. The industry hopes the recalls are finished. While a number of small food companies have been hit with recalls, Robin Hood and its supplier Ardent Mills of Brampton appear to have suffered the most.  

The first outbreak of E.coli in flour occurred in the United States last year leading to a major investigation by the Center for Disease Control. CFIA has inspected all the flour mills in Canada and found nothing wrong in their operations, which makes wheat the main suspect. 

The mystery deepens when it comes to how the wheat could be contaminated with bacteria most consumers would think of terms of undercooked ground meat.  

While CFIA says all recalled products should be thrown out or returned to the store, properly cooked bakery products show no trace of the E.coli.

E. coli in Canada: National flour recall expands to additional products

Via The Globe and Mail, a report by The Canadian Press: National flour recall expands to additional products. Excerpt:

A national recall of flour due to E. coli contamination, which was first announced last month and is the subject of a class-action lawsuit, is being expanded to cover additional products. 

The Canadian Food Inspection Agency’s recall on March 28 affected Robin Hood flour sold in four provinces in Western Canada and was later expanded across the country. 

The recall now covers products produced by Ardent Mills of Brampton, Ont. They include one-kilogram bags of Brodie self-raising cake and pastry flour; Creative Baker all-purpose flour in 20-kilogram bags; Creative Baker whole wheat flour in 10-kilogram packages; and Golden Temple Sooji creamy wheat in two-kilogram packages – each with various best-before dates. 

The initial recall affected Robin Hood flour in 10-kilogram bags but the CFIA says the recall now includes Robin Hood flour in one-kilogram bags with best-before dates of April 14, 15 and 18, 2018. 

The CFIA says all recalled products should be thrown out or returned to the store.

Canada: Robin Hood flour recall expanded nationwide due to E. coli contamination

Via CBC News Calgary: Robin Hood flour recall expanded nationwide due to E. coli contamination. Excerpt:

The recall of Robin Hood brand flour linked to an E. coli outbreak has been expanded to the entire country. 

The original recall issued last month by the Canadian Food Inspection Agency on 10-kilogram bags of flour was limited to B.C., Alberta, Saskatchewan and Manitoba.  

One illness has been confirmed from consuming the flour, and 24 other cases are being investigated.

The recall was triggered during an investigation into an outbreak of E. coli O121 that found 25 cases with a matching genetic fingerprint in four provinces — 12 in B.C., four in Alberta, four in Saskatchewan and five in Newfoundland and Labrador.  ​

Several of those who fell ill reported having contact with Robin Hood flour.  

The illness onset dates ranged from November 2016 to late February. Six people were hospitalized but are recovering.  

Food inspection agency officials say any 10-kilogram bags of Robin Hood brand all-purpose flour with a best-before date of April 17, 2018, should be thrown out or returned to the store where they were purchased.

ECDC: WHO publishes list of bacteria for which new antibiotics are urgently needed

ECDC has published WHO publishes list of bacteria for which new antibiotics are urgently needed.

The World Health Organization (WHO) published a list of antibiotic-resistant pathogens for which new and effective antibiotics are urgently needed. The list aims at guiding the prioritization of funding and incentives, and promoting and aligning research and development initiatives with existing public health needs.   

The pathogens have been divided in three priority categories depending on their respective need for new antibiotics to treat them: critical, high and medium. Pathogens with a critical need for new antibiotics include bacteria that have become resistant to a large number of antibiotics, including the carbapenems, a last-resort antibiotic group. Pathogens in the second and third groups include other bacteria that are increasingly becoming antibiotic-resistant and cause more common diseases such as gonorrhoea and salmonellosis.   

According to the latest data from the European Antimicrobial Resistance Surveillance Network (EARS-Net), antibiotic resistance continued to increase for bacteria such as Klebsiella pneumoniae and Escherichia coli, amongst others, in the European Union in 2015. This was also the case for common types of Salmonella in humans, as reported by ECDC and the European Food Safety Authority earlier this month.    

ECDC welcomes this list, and highlights the need of increased efforts on the area of research and development of new antibiotics. Nevertheless, to address the challenge posed by antimicrobial resistance, the development of effective antibiotics needs to be supported by prudent use of existing antibiotics, both in human and veterinary medicine, as well as the implementation of proper infection prevention and control measures.   

WHO publishes list of bacteria for which new antibiotics are urgently needed

A news release: WHO publishes list of bacteria for which new antibiotics are urgently needed. Excerpt:

WHO today published its first ever list of antibiotic-resistant "priority pathogens" – a catalogue of 12 families of bacteria that pose the greatest threat to human health.  

The list was drawn up in a bid to guide and promote research and development (R&D) of new antibiotics, as part of WHO’s efforts to address growing global resistance to antimicrobial medicines.  

The list highlights in particular the threat of gram-negative bacteria that are resistant to multiple antibiotics. These bacteria have built-in abilities to find new ways to resist treatment and can pass along genetic material that allows other bacteria to become drug-resistant as well.  

"This list is a new tool to ensure R&D responds to urgent public health needs," says Dr Marie-Paule Kieny, WHO's Assistant Director-General for Health Systems and Innovation. "Antibiotic resistance is growing, and we are fast running out of treatment options. If we leave it to market forces alone, the new antibiotics we most urgently need are not going to be developed in time."  

The WHO list is divided into three categories according to the urgency of need for new antibiotics: critical, high and medium priority. 

The most critical group of all includes multidrug resistant bacteria that pose a particular threat in hospitals, nursing homes, and among patients whose care requires devices such as ventilators and blood catheters. They include Acinetobacter, Pseudomonas and various Enterobacteriaceae (including Klebsiella, E. coli, Serratia, and Proteus). They can cause severe and often deadly infections such as bloodstream infections and pneumonia.  

These bacteria have become resistant to a large number of antibiotics, including carbapenems and third generation cephalosporins – the best available antibiotics for treating multi-drug resistant bacteria. 

The second and third tiers in the list – the high and medium priority categories – contain other increasingly drug-resistant bacteria that cause more common diseases such as gonorrhoea and food poisoning caused by salmonella.

Trends in carbapenemase-producing enterobacteriaceae, France, 2012 to 2014

Via Eurosurveillance: Trends in carbapenemase-producing enterobacteriaceae, France, 2012 to 2014. The abstract:

In 2014, a total of 2,976 Enterobacteriaceae isolates with decreased susceptibility to carbapenems were received at the French Associated National Reference Center for Antibiotic Resistance (NRC) and were characterised for their molecular resistance mechanism to carbapenems and compared with results obtained during 2012 and 2013.

The overall number of enterobacterial isolates with decreased susceptibility to carbapenems received at the NRC rapidly increased (more than twofold in two years) with a growing proportion of carbapenemase producers (23.1% in 2012 vs 28.6% in 2013 vs 36.2% in 2014). 

Between 2012 and 2014, the main carbapenemase type was OXA-48, with an increase in OXA-48 variants (mostly OXA-181) and NDM producers, whereas the number KPC producers decreased. We identified a potential spread of OXA-181 producers in the tropical region of Africa. Finally, OXA-48 and OXA-48-related enzymes remained the predominant carbapenemases in France. 

The number of carbapenemase-producing Escherischia coli isolates was multiplied by fivefold between 2012 and 2014, suggesting a possible dissemination in the community.

Measuring changes in transmission of neglected tropical diseases, malaria, and enteric pathogens from quantitative antibody levels

Via bioRxiv: Measuring changes in transmission of neglected tropical diseases, malaria, and enteric pathogens from quantitative antibody levels. The abstract:

Background: 

Serological antibody levels are a sensitive marker of pathogen exposure, and advances in multiplex assays have created enormous potential for large-scale, integrated infectious disease surveillance. Most methods to analyze antibody measurements reduce quantitative antibody levels to seropositive and seronegative groups, but this can be difficult for many pathogens and may provide lower resolution information than quantitative levels in low transmission settings. Analysis methods have predominantly maintained a single disease focus, yet integrated surveillance platforms would benefit from methodologies that work across diverse pathogens included in multiplex assays. 

Methods/Principal Findings: 

We developed an approach to measure changes in transmission from quantitative antibody levels that can be applied to diverse pathogens of global importance. We compared age-dependent immunoglobulin G curves in repeated cross-sectional surveys between populations with differences in transmission for multiple pathogens, including: lymphatic filariasis (Wuchereria bancrofti) measured before and after mass drug administration on Mauke, Cook Islands, malaria (Plasmodium falciparum) before and after a combined insecticide and mass drug administration intervention in the Garki project, Nigeria, and enteric protozoans (Cryptosporidium parvum, Giardia intestinalis, Entamoeba histolytica), bacteria (enterotoxigenic Escherichia coli, Salmonella spp.), and viruses (norovirus groups I and II) in children living in Haiti and the USA. 

Age-dependent antibody curves fit with ensemble machine learning followed a characteristic shape across pathogens that aligned with predictions from basic mechanisms of humoral immunity. Differences in pathogen transmission led to shifts in fitted antibody curves that were remarkably consistent across pathogens, assays, and populations. Mean antibody levels correlated strongly with traditional measures of transmission intensity, such as the entomological inoculation rate for P. falciparum (Spearman's rho=0.75). Seroprevalence estimates recapitulated patterns observed in quantitative antibody levels, albeit with lower resolution. 

Conclusions/Significance: 

Age-dependent antibody curves and summary means provided a robust and sensitive measure of changes in transmission, with greatest sensitivity among young children. The method generalizes to pathogens that can be measured in high-throughput, multiplex serological assays, and scales to surveillance activities that require high spatiotemporal resolution. The approach represents a new opportunity to conduct integrated serological surveillance for neglected tropical diseases, malaria, and other infectious diseases with well-defined antigen targets.

ECDC: Antimicrobial resistance surveillance in Europe 2015

ECDC has published Antimicrobial resistance surveillance in Europe 2015. Click or tap through to download the PDF. The abstract: 

This report presents antimicrobial resistance data for seven microorganisms of major public health importance: Escherichia coli, Klebsiella pneumoniae, Pseudomonas aeruginosa, Acinetobacter species, Streptococcus pneumoniae, Staphylococcus aureus, and Enterococci. For 2015, data were reported by 29 countries. The report also presents trend analyses for the period 2012–2015.  

The tables below are available in a downloadable format: 

E. coli, Tables 3-1 to 3-7 Klebsiella, Tables 3-8 to 3-13 Pseudomonas, Tables 3-14 to 3-20 Acinetobacter, Tables 3-21 to 3-25 Streptococcus, Tables 3-26 to 3-28 Staphylococcus, Table 3-29 Enterococci, Tables 3-30 and 3-31

Branswell: Superbug resistant to last-resort antibiotic arises in China

Via Scientific American, Helen Branswell writes in STAT: Superbug Resistant to Last-Resort Antibiotic Arises in China. This will definitely be on the final exam, so you'd better read it all. Excerpt:

A wide variety of E. coli bacteria in China have developed resistance to a key antibiotic of last resort, a new study has revealed, a worrying development in the rise of so-called superbugs. 

A second study released Friday, like the first published in the journal Lancet Infectious Diseases, found the superbug is still uncommon in Chinese hospitals—though not a rare as experts might like. 

The gene known as mcr-1—which has the capacity to move from one bacterium to another—was found in about 1 percent of E. coli bacteria and 1 percent of a bacteria, known as Klebsiella pneumoniae, that can cause pneumonia, bloodstream infections, and wound infections. 

Although that incidence was described as rare, it wasn’t especially reassuring to Lance Price, director of the Antibiotic Resistance Action Center at George Washington University. 

“One percent doesn’t sound huge, but for something that we didn’t know about a little more than a year ago and that is clearly a recently evolved [drug resistance] element, it’s pretty substantial,” said Price, who was not involved in the study. 

The mcr-1 gene gives bacteria the ability to withstand treatment with a drug called colistin. It’s an old antibiotic that wasn’t used much for years because it has unpleasant side effects; other newer drugs were simply better. But with resistance to better drugs on the rise, colistin has taken on increasing importance in medicine. 

In many places is it reserved for human use—and even then, only when absolutely needed. But China has been using it in agriculture, to speed growth of animals raised for meat. 

In November 2015 scientists reported finding this gene in China, raising alarms around the world. Within a short span of time researchers elsewhere revealed they had looked for and found the gene in their stored bacteria collections. 

An alarming feature of mcr-1 is that the gene moves easily from bug to bug and also from a family like E. coli to others, like Klebsiella pneumoniae. 

The authors of the new paper reporting the incidence of the gene in hospital infections are from Sir Run Run Shaw Hospital, College of Medicine, Zhejiang University, in Hangzhou. 

Professor Timothy Walsh of the University of Cardiff was one of the discoverers of mcr-1 and is also an author of the paper that tracked the gene’s spread among E. coli bacteria. 

“I think the take away message is that mcr-1 is very, very widely spread among many different types of E. coli and therefore is kind of pervasive, really, throughout Chinese communities,” Walsh told STAT. 

And that picture could be about to get a lot worse. 

China has agreed to ban use of colistin for growth promotion purposes. That policy comes into effect on April 1, Walsh said. But it also plans to license the drug for human use there. 

China is making that move, Walsh said, because it realizes it is morally unacceptable to use the drug in animal feed. But there’s another reason: It needs colistin to deal with the rapid spread of other superbugs in China.

Branswell: Dangerous superbug CRE appears to be spreading stealthily in US hospitals

Via STAT, Helen Branswell writes: Dangerous superbug appears to be spreading stealthily in US hospitals. Excerpt:

A dangerous type of superbug has more tricks up its sleeves than we may be giving it credit for, a new study suggests. 

The researchers found that this class of bacteria, CREs — that’s short for carbapenem-resistant Enterobacteriaceae — has more ways to evade antibiotics than have been currently identified, and that these bugs share their tricks readily across the families of bacteria that make up this grouping. 

Further, the authors suggest these bacteria may be spreading more stealthily than existing surveillance can detect.

“You know the phrase ‘Shutting the stable door after the horse has bolted?’ The horse has not only bolted, the horse has had a lot of ponies, and they’re eating all our carrots,” said Bill Hanage, an infectious diseases epidemiologist at the Harvard T.H. Chan School of Public Health and senior author of the study.  

Hanage and colleagues from Harvard and the Broad Institute of MIT and Harvard took an in-depth look at CREs recovered from patients in three Boston hospitals and a hospital in Irvine, Calif. Their findings are published this week in the Proceedings of the National Academy of Sciences. 

Dr. Tom Frieden, director of the Centers for Disease Control and Prevention, has dubbed CREs “nightmare bacteria.”  That’s because they are resistant to many, and sometimes most, antibiotics, including carbapenems, an important class of last-resort drugs.  

They also have the capacity to transfer resistance genes from one family to the next — for instance from E. coli bacteria to Klebsiella pneumoniae. Think of it as gangs in a neighborhood teaching each other all their worst tricks.  

According to CDC estimates, CREs cause 9,300 infections a year in the US and 600 deaths. They vary in their ability to fend off antibiotics; a report last week revealed a woman in Nevada died last September from a CRE infection that could not be treated with the antibiotics available in the United States.