H5N1

Branswell: Antibiotic under threat, as new superbug emerges in China

Right in the middle of World Antibiotic Awareness Week, Helen Branswell writes in Stat: Antibiotic under threat, as new superbug emerges in China. Excerpt:

Experts have been warning for a while that the bell is tolling for the end of the antibiotic era, presaging a time when infections won’t be treatable with the drugs that have changed modern medicine. On Wednesday, that ominous knell got a little bit louder.

Chinese and British scientists reported that they have found a strain of Escherichia coli that is resistant to colistin, the antibiotic of last resort for gram-negative bacteria such as E. coli. The resistant bacteria were found in pigs, raw pork meat, and in a small number of people in China.

It’s not the first time colistin resistance has been spotted, but this time the phenomenon comes with a nasty twist. The resistance is conferred by a gene found on a plasmid, a portable piece of DNA. That’s alarming because plasmids can both transfer within a family of bugs and to other families of bacteria as well.

If the resistance spreads, it will seriously limit the treatment options available to doctors facing antibiotic-resistant infections, said Dr. Jean Patel, acting director of the office of antimicrobial resistance at the Centers for Disease Control and Prevention in Atlanta. Patel was not involved in the study.

The scientists — from the South China Agricultural University in Guangzhou, the China Agricultural University in Beijing, and other institutions — called the resistance gene mcr-1. Reporting in the journal Lancet Infectious Diseases, they described the emergence of mcr-1 as “the breach of the last group of antibiotics” by plasmid-mediated resistance.

The mcr-1 gene can move among E. coli bacteria, the scientists reported. But it can also go into other bacteria — Klebsiella pneumoniae and Pseudomonas aeruginosa — and give those bugs the capacity to resist colistin, too.

A member of the polymyxin class of antibiotics, colistin is an old drug that was rarely used for decades because there were other antibiotic options that have fewer side effects.

But as antibiotic resistance has increased, the drug has become a critical part of the armamentarium; in 2012 the World Health Organization designated it as critically important for human medicine.

Experts have insisted it should be preserved for people and should not be employed in agricultural operations, where vast quantities of antibiotics are fed to animals as growth promoters. And yet, in China, the drug is used more in animal production than it is on people, said Timothy Walsh, a medical microbiologist from Cardiff University in Wales, and one of the authors of this paper.

“We needed to have definitive borders between antibiotics that are used in human medicine and those that are used in the veterinary sector,” said Walsh, who was also involved in the discovery of another dangerous plasmid-mediated resistance gene, NDM-1. “That mantra should be universal and strictly adhered to.”

Walsh told STAT in an interview that he and his co-authors will meet next week with government officials to try to persuade China to ban agricultural use of colistin.

Hong Kong: NDM-1 case under CHP investigation

The Centre for Health Protection has published Case of NDM-1 Carbapenemase-producing Enterobacteriaceae under CHP investigation. Excerpt:

The Public Health Laboratory Services Branch (PHLSB) of the Centre for Health Protection (CHP) of the Department of Health confirmed today (December 31) a case of New Delhi metallo-β-lactamase-1 (NDM-1) Carbapenemase-producing Enterobacteriaceae in an 86-year-old woman.      

The patient, with chronic medical condition, lives in Hong Kong. She travelled to Guangdong on December 14 and was admitted to a local hospital between December 16 and 20 for shortness of breath. She was subsequently admitted to United Christian Hospital for further treatment upon her return to Hong Kong on December 20. Her current condition is stable.      

The patient's rectal swab yielded NDM-1 Carbapenemase-producing Enterobacteriaceae as confirmed by the PHLSB.      

CHP's investigation is on-going.      

This is the 36th detected case of NDM Carbapenemase-producing Enterobacteriaceae in Hong Kong.      

NDM is an enzyme which can inactivate carbapenems and other beta-lactams such as penicillins. Bacteria harbouring this NDM gene are commonly resistant to multiple antimicrobials, limiting therapeutic options and rendering severe clinical infections difficult to treat. Most bacteria with the NDM enzyme remain susceptible to two types of antibiotics, colistin and tigecycline.      

Infections vary from being asymptomatic to potentially life-threatening or fatal. The level of risk depends on which part of the body is affected by the infection, and the general health of the patient.

Eurosurveillance: How NDM-1 moved from Egypt to the Netherlands

Via Eurosurveillance: Latent introduction to the Netherlands of multiple antibiotic resistance including NDM-1 after hospitalisation in Egypt, August 2013. The abstract:

We describe the introduction of various multi-drug resistant bacterial strains, including an NDM-1-producing Klebsiella pneumoniae, through a traveller returning from Egypt, where they had been admitted to a private hospital. All family members of the patient were colonised with one or more extended-spectrum beta-lactamase producing strains. These findings emphasise the importance of adherence to isolation precautions for returning patients and suggest the need for inclusion of Enterobacteriaceae in admission screening.

India launches drive to fight antibiotic-resistant germs

Via The Times of India: Rs 30 crore drive to fight antibiotic-resistant germs. Excerpt:

With rising resistance of first and second generation antibiotic resistance in common bugs, the health ministry has approved a Rs 30-crore [US$4.88 million] surveillance plan that includes setting up of 30 laboratories. The project will be undertaken initially in Delhi and then expanded to other states in a phased manner. The surveillance programme will include training of microbiologists, lab technicians, clinicians, pharmacists and others. 

Indiscriminate use of antibiotics has resulted in many pathogens turning unresponsive to first and second generation drugs. Stemming from this need is the establishment of the national programme on containment of anti-microbial resistance. 

According to a senior health ministry official, "Under this programme a network of 30 quality assured laboratories for anti-microbial resistance surveillance would be established. Each laboratory will be provided Rs 15-20 lakh [US$24,000-$32,000] for equipment, reagents and manpower per year." 

India's antibiotic policy drafted in 2011 in the wake of reports on enzyme metallo-beta lactamase 1 — first detected in a Swedish patient of Indian origin — has not been implemented. There have since been numerous reports on drug resistance, including claims by a Mumbai doctor of total drug resistance in TB bacteria that did not eventually pass scrutiny by the Indian health establishment and the World Health Organisation (WHO).

It's amazing that India's gone for over two years since the identification of NDM-1 without implementing an antibiotic policy. 

Hong Kong: Case of NDM-1 Carbapenemase-producing Enterobacteriaceae under CHP investigation

Via the Centre for Health Protection: Case of NDM-1 Carbapenemase-producing Enterobacteriaceae under CHP investigation. Excerpt:

The Public Health Laboratory Services Branch (PHLSB) of the Centre for Health Protection (CHP) of the Department of Health confirmed today (August 7) a case of New Delhi metallo-β-lactamase-1 (NDM-1) Carbapenemase-producing Enterobacteriaceae in a 58-year-old woman.      

The woman, with chronic illness, lives in Hong Kong and travelled to the Mainland on July 5. She had fractured her right femur and was admitted to a hospital in the Mainland on July 11, with an operation done on July 13. She returned to Hong Kong on July 29 and was admitted to Prince of Wales Hospital for further management the next day. Her condition has been stable all along, and she was discharged today.      

The patient's rectal swab yielded NDM-1 Carbapenemase-producing Enterobacteriaceae as confirmed by the PHLSB.      

Her family contacts are asymptomatic. Investigations by the CHP are under way.      

This is the 31st detected case of NDM Carbapenemase-producing Enterobacteriaceae in Hong Kong.      

NDM is an enzyme which can inactivate carbapenems and other beta-lactams such as penicillins. Bacteria harbouring this NDM gene are commonly resistant to multiple antimicrobials, limiting therapeutic options and rendering severe clinical infections difficult to treat. Most bacteria with the NDM enzyme remain susceptible to two types of antibiotics, colistin and tigecycline.      

Infections have varied from being asymptomatic to potentially life-threatening or fatal. The level of risk depends on which part of the body is affected by the infection, and the general health of the patient.

CIDRAP: News scan for August 1

Via CIDRAP: News Scan for Aug 01, 2013. Excerpt:

Scientists writing in Eurosurveillance today detailed the first outbreak of carbapenem-resistant New Delhi metallo-beta-lactamase 1 (NDM-1)–producing Acinetobacter baumannii in Europe, in a French intensive care unit (ICU) from January to May. Bacteria that produce NDM-1 are usually resistant to most antibiotics. 

The index patient was a woman in her 80s who was transferred from Algeria for care of end-stage cirrhosis. On Jan 18 she was admitted to a Paris hospital and, in line with guidance, was screened for carriage of multidrug-resistant (MDR) bacteria, which turned up the NDM-1 A baumannii. 

From then to Feb 2 an additional three patients in that ICU were confirmed to have the same drug-resistant strain. Meanwhile, another woman in her 80s arrived from the same region in Algeria and was found to be NDM-positive with the same strain on admission to the same ICU. 

Two months after this first cluster of five patients, two additional patients who were free of MDR bacteria on admission to the ICU also acquired the NDM-1–producing A baumannii outbreak strain during their stay in this unit. 

The authors conclude, "Taking in account the relationship between North African countries and many European countries, it is possible that the spread of NDM-1 carbapenemase may occur rapidly, mostly through A baumannii rather than Enterobacteriacae, since A baumannii may become much more difficult to eradicate."

India: Extensive use of antibiotics may lead Kolkata to a disaster

Via The Times of India: Extensive use of antibiotics may lead Kolkata to a disaster. Excerpt:

KOLKATA: Multi-drug resistant bacteria - triggered by rampant and injudicious use of antibiotics - are on the prowl in the city. They're affecting more than half of the patients across city hospitals and can lead to a crisis unless measures are taken immediately to identify the bacteria and regulate the prescription of antibiotics, according to the "Task Force for Antibiotic Stewardship" formed by doctors from five hospitals in Kolkata. 

Samples collected by the task force reveal that a bacteria similar to the metallo-beta-lactamese-1 or NDM 1, that wreaked havoc in New Delhi a few years ago, could be prevalent in Kolkata as well. The 'superbug' is resistant to all known antibiotics. 

Analysis of data and bacteria samples collected by the task force from KPC Medical College, Medica Superspecialty, Fortis, DM Hospital, Ruby Hospital and the Saroj Gupta Cancer Research Centre has revealed the presence of several drug-resistant bugs. It's alarming, say members of the task force who are now busy identifying the resistance pattern among bacteria. 

"There is a very high prevalence of drug-resistant bacteria, particularly in the tertiary care hospitals where patients are treated with multiple anti-biotics. We have identified one that is either NDM 1 or very similar to it. Conventional treatment would be futile if such bacteria are allowed to flourish. The only solution is to restrict the use of anti-biotics through a comprehensive policy that would be adopted across all city hospitals," said Bhaskar Narayan Chaudhuri, consultant microbiologist at Fortis Hospital who is a member of the task force. 

An IT firm is collecting the data from treatment records of the hospitals. While the task force is trying to rope in the government hospitals as well, none has yet joined the task force. 

"We are trying to collect their data as well for they treat the largest number of patients in the city. An anti-biotic policy can't be framed unless we include government hospitals," said Chaudhuri.

Hong Kong: New NDM-1 case under investigation

Via the Centre for Health Protection: Case of NDM-1 Carbapenemase-producing Enterobacteriaceae under CHP investigation. Excerpt:

The Public Health Laboratory Services Branch (PHLSB) of the Centre for Health Protection (CHP) of the Department of Health confirmed today (June 25) a case of New Delhi metallo-β-lactamase-1 (NDM-1) Carbapenemase-producing Enterobacteriaceae in a 15-month-old baby boy.      

The boy, with good past health, lives in Guangzhou. He presented with fever, running nose and cough on June 8, and developed convulsion on June 11. He was admitted to a hospital in the Mainland and was subsequently admitted to Kwong Wah Hospital on June 16. He was diagnosed as having pneumonia and febrile convulsion. His condition has been stable all along, and he was discharged on June 19.      

The patient's rectal swab yielded NDM-1 Carbapenemase-producing Enterobacteriaceae as confirmed by the PHLSB.      

His family contacts are asymptomatic. Investigations by the CHP are under way.      

This is the 30th detected case of NDM Carbapenemase-producing Enterobacteriaceae in Hong Kong.

nCoV: A new naming battle

Via ScienceInsider, a report by Martin Enserink: International Group Settles on Name for New Coronavirus. As the British say, this will end in tears before bedtime. Excerpt:

New MERS cases. The MERS coronavirus. Or—if things turn really bad—the MERS pandemic. That's how the world may soon be talking about the new virus that surfaced in the Arabian Peninsula last summer and that has been rattling health experts since. In a move that may end more than 7 months of confusion, an international group of scientists and public health officials will soon recommend that the new virus be called Middle East respiratory syndrome coronavirus (MERS-CoV). 

The group plans to publish a paper recommending the new name, says Raoul de Groot, a veterinary virologist at Utrecht University in the Netherlands, who has coordinated the effort. De Groot chairs the Coronavirus Study Group of the International Committee on Taxonomy of Viruses (ICTV), which took the initiative to find a new, widely accepted name. The study group has no power to enforce use of the name, however; it will be up to researchers to decide whether to adopt the moniker. 

News of the name comes as Saudi Arabia has reported 13 new cases of the virus, including seven deaths, in just the past 5 days. The wave—more than a month after the last reported case, a 73-year-old man from Abu Dhabi who died in Munich on 26 March—has sparked fresh worries that the virus might start spreading between humans and trigger a global outbreak. As of today, the total reported number of cases is 30, including 18 deaths. 

Confusion had reigned over the new name since the virus was first reported by Ali Mohamed Zaki, an Egyptian microbiologist who isolated it in June 2012 from a patient at a hospital in Jeddah, Saudi Arabia, where he worked at the time. Zaki sent the virus to Ron Fouchier's virology group at Erasmus MC in Rotterdam, the Netherlands, which characterized it further in a paper published in m Bio in November. Alexander Gorbalenya, a coronavirologist at Leiden University in the Netherlands and ICTV's vice president, was a co-author, and the group provisionally called the virus HCoV-EMC/2012, short for human coronavirus-Erasmus MC. 

The reference to the Dutch lab didn't sit well with Saudi health officials, who said that Zaki lacked authorization to send the virus to Rotterdam in the first place. Still, most researchers have accepted HCoV-EMC as the name to use. Some have dropped the "EMC," however, and called the virus simply HCoV, a name that might cause confusion because there are five other human coronaviruses. 

The World Health Organization (WHO) has adopted the more neutral "novel coronavirus"—abbreviated initially as NCoV but more recently as nCoV—a name that by its very nature was not meant to last.

We've seen this before. The Indians are still sulking about NDM-1, the resistance gene first identified in a sample from New Delhi. Even the most dedicated health experts suddenly become defenders of the local brand when something embarrassing breaks out on their turf.

So never mind that the Middle East is already branded as a sorry mess; naming a virus after it will unite even that fractious region in opposition.

The (still) novel coronavirus is only the latest bug that we can analyze right down to its genes even as we grope for something to call the damn thing. I've been dealing for eight years with "bird flu" and "avian flu," "high-path H5N1" and "low-path H5N1." And don't get me going on "swine flu," "swine fever," "pandemic H1N1" and garden varieties of that wretched virus. I don't want to hear about earlier versions of H7; H7N9 is sufficient to blight my life.

We are also dealing with our innate laziness: It's so much trouble, so time-consuming, to spell out an initialism like Enn-See-Oh-Vee rather than snap out an acronym like SARS. And nCoV is a copy editor's nightmare. My esteemed blogging colleague Dr. Ian Mackay prefers HCoV; fine, it's a Human virus, but so are plenty of others.

Between the virologists worried about next year's tourism statistics and the complications inherent in defining various hemagglutinins and neuroaminidases, it looks as if one effect of influenza, even before you catch it, is to make you tongue-tied.

Maybe, as a recovering English major, I'm taking this too seriously. But my own modest proposal is a new term for all influenzas since H5N1 appeared in Hong Kong in 1997: Nyfia. Capitalize the whole thing if you like; you can pronounce it either niff-ee-uh or knife-ee-uh.

Nyfia stands for "Not Yet Found In Antarctica," where the penguins have little access to the media and the human residents don't consider themselves residents with a stake in tourism. So H5N1 could be Nyfia1; pandemic H1N1 could be Nyfia2; H7N9 could be Nyfia3; and this stupid new coronavirus can be Nyfia4. (Hyphens are deleted to make it easier to hashtag these terms.) SARS is already a politically acceptable term and therefore exempt.

If we accept this nomenclature, we can number many new health threats without offending the sensibilities of political leaders or presidents of hoteliers' associations. If the numbers get too big, we can switch to Nyfom (Not Yet Found on Mars).

Then we can get on with trying to keep these stupid viruses from killing people, and talking about it at the same time.

India "has lost" superbug war

Via India Real Time, a blog of the Wall Street Journal: India ‘Has Lost’ Superbug War. Excerpt:

India has lost the war against the toughest forms of antibiotic resistance, largely because of poor sanitation, unregulated use of antibiotics and an absence of drug resistance monitoring, according to the man who discovered a type of drug resistance in bacteria in New Delhi. 

“All these factors add to why it’s going to be so difficult to deal with or even tackle [resistance], you won’t solve it, it’s over,” said Tim Walsh, professor of medical microbiology at Cardiff University in Wales. 

In 2010, Mr. Walsh discovered an enzyme that made disease-causing bacteria resistant to antibiotics.  He named the enzyme “New Delhi Metallo 1” (NDM-1) and claims he was banned from working in India after the discovery. 

Bacteria carrying the NDM-1 enzyme are highly resistant to the most powerful group of antibiotics, known as carbopenems, making infections caused by them extremely difficult to treat. 

They can also transfer their resilience to other bacteria, including those that cause infections. “The rapidity and frequency of that transfer is something that we have never seen before in antibiotic resistance,” Mr. Walsh said. 

He estimates that up to 200 million Indians carry NDM-1 on the benign bacteria in their intestines. But a lack of research and scarcity of data make it difficult to gauge in terms of its transfer to disease causing bacteria. 

“We’ve failed to understand how NDM-1 spreads in the community,” Mr. Walsh said, adding that there is also very little understanding about the risks associated with being infected by a bacteria carrying NDM-1. 

“We’ve failed to understand what dominant clones are in hospital and we’ve failed to understand the risk post surgical infections,” he said. 

In almost three years since he published his research in the Lancet medical journal, Mr. Walsh says that India has failed to respond to the “urgent” need to regulate the sale and use of antibiotics, track the incidence of resistance or improve sanitation. 

Antibiotics are for sale without prescription in pharmacies in India and there are no national guidelines for clinicians on their use in hospitals. Bacterial diseases develop resistance to treatment with antibiotics when the drugs are wrongly used to treat viral infections or when a full course of drugs isn’t completed. 

Resistance makes infectious diseases more difficult or impossible to treat. Even simple urinary tract infections when caused by an NDM-1 carrying bacteria cannot be eradicated with antibiotics, Mr. Walsh said. 

When he published his findings in 2010 Walsh says his name “became mud” in political and scientific circles in India. 

“I named the gene after the capital of India which they [the government] weren’t too thrilled about,” he said. It is normal scientific practice to name genes after the cities in which they are found, he added. 

“We were banned from India and India had a massive clamp down on sending [biological] strains out,” Mr. Walsh said. “Indians were banned from working with me, or anybody in Europe the whole thing was a systematic campaign to control research into antibiotic resistance in India.” 

Neither the Ministry of Health nor the Central Drugs Standard Control Organization responded to requests for comment.