H5N1

Canada: Winnipeg’s National Microbiology Laboratory prepares for next big outbreak

Via The Star: Winnipeg’s National Microbiology Laboratory prepares for next big outbreak. Excerpt from a long, informative article by Jennifer Yang:

In late November, a strange envelope turned up at the Canadian embassy in Lebanon. Its suspicious contents — wood shavings, according to local reports — sparked alarm: did it contain dangerous pathogens? Could this be a bioterrorist attack? The building was closed until the package could be investigated. 

In snowy Winnipeg, 9,600 kilometres away, Dr. Cindi Corbett received the call: she was going to Beirut. In the hours before sunrise on Nov. 30, Corbett and her team drove to a nondescript warehouse and grabbed four black bags — inside were the components of a mobile laboratory, capable of handling some of the world’s deadliest pathogens. 

The team was soon en route to Lebanon. Within hours of arriving at the embassy, they had set up their lab, investigated the package and deemed it to be harmless. 

The episode drew little attention, both at home and in Lebanon, and nowhere on Google will you find any mention of Corbett in Beirut. For the mother of two, it was just another day on the job as one of Canada’s top bioterrorism scientists. For the National Microbiology Laboratory where Corbett works, the Beirut incident was just another example of how Public Health Agency of Canada scientists work behind the scenes to protect people from microscopic dangers. 

Public-health practitioners sometimes mutter that people only notice them when things go wrong. Canadians may remember reading about the National Microbiology Laboratory during SARS, the 2009 H1N1 flu pandemic or the recent XL Foods E. coli outbreak. 

But even in the long, quiet stretches between crises, the lab is working every day to keep pathogens at bay. The Next Big One is always simmering; whether it boils over depends on a mixture of chance and preparedness. 

Ten years after SARS, considered by some to be the first pandemic of the 21st century, the Toronto Star travelled to Winnipeg to meet the people whose job it is to keep pathogens from gaining the upper hand.

Coston on revised NCoV surveillance recommendations

Mike Coston at Avian Flu Diary has a good discussion about the World Health Organization's Revised NCoV Surveillance Recommendations, which were published yesterday.

CRE: How strong is our first line of detection?

Few things cheer me up more than a crabby health expert who is past being tactful and diplomatic about life-or-death concerns. So I'm enjoying the posts at the blog Controversies in Hospital Infection Prevention. Today we have a blast from Dan Diekema: How strong is our first line of detection? Click through for the full, link-rich post. Excerpt:

I feel like I should expand on this recent post about why relying upon prompt laboratory detection of CRE carriers is unlikely to help contain spread (aside from during local outbreak responses). Why shouldn’t screening be a pillar of our prevention efforts, particularly given the inspiring stories of local and regional CRE control that utilized screening to detect carriers? 

Leaving aside the question of how important screening was among multiple simultaneous interventions, these two reports are from academic tertiary care centers with robust on-site laboratory support and external funding to provide financial support for state-of-the-art screening approaches (such as rapid PCR detection of KPC producers). 

The sad fact is that this level of clinical microbiology laboratory support is far from the norm. The trend over the past two decades has been toward consolidation and outsourcing of laboratory services, and reducing local resources available for diagnostic microbiology labs. I spoke about this trend, and some of the consequences, at the 5th Decennial conference a few years ago (you can view the slide set here). 

In the decade that has passed since we noted frequent errors in testing and reporting of blood culture results in a sample of 14 hospital laboratories, I doubt that much has improved. Yes, there are CAP proficiency surveys, but for several reasons these are not good indicators of actual laboratory performance. 

And while outsourcing microbiology to a regional lab may make short-term financial and technical sense for some hospitals, it also removes lab support further from the front line of patient care and infection prevention, prolongs turnaround times, and comes with a host of pre- and post-analytic problems. 

If current fiscal and political trends continue, with additional cuts to public health infrastructure and CDC’s budget, it is difficult to imagine that we can do much in the short term to shore up our surveillance capabilities to respond to the CRE threat.

Still another doctor's take on CRE

Via the blog Controversies in Hospital Infection Prevention, Dr. Eli Perencevich has some Further thoughts on CRE. Click through for the full post and a lot of links. Excerpt:

I have some further thoughts on where we should go. First, as I said earlier this week, we need a national response to CRE and antimicrobial resistance in general. This response needs to be horizontal in approach, as Mike Edmond and Dick Wenzel recommended several years ago. For it is quite clear that if we follow the vertical approach recommended by the CDC and others, swab for CRE and isolate, that this will bankrupt hospitals and ultimately fail. 

This surveillance approach will bankrupt us, because CRE isn't the only "nightmare" in our hospitals. Back in 2010, when Dan was discussing MRSA on NPR, he said so eloquently: "MRSA is not the only bad bug out there. It's just the most famous." 

And along with MRSA, we have VRE and ESBL and C. difficile and Acinetobacter and MDR-Pseudomonas. You see, we might not be able to take this single-hospital outbreak approach and extrapolate it to the entire country and 10+ pathogens. 

And if there is one lesson we should be taking away from the NIH CRE outbreak it's not that new-fangled whole genome sequence stopped the outbreak (because it didn't), it's that the outbreak spread and killed many patients despite herculean efforts to detect and eliminate it. 

Furthermore, if we target MRSA like many hospitals are now doing with chlorhexidine (CHG) baths, this approach could select for Gram-negative bacteria like CRE. 

My recommendations: 

(1) Invest significantly in antimicrobial discovery. Apart from the need for new treatment options, optimal control of resistant pathogens may depend on availability of effective antibiotics. 

(2) Invest in studies to improve compliance with hand hygiene – only 4 studies on this topic since 1980 per a recent Cochrane Review. Compliance is terrible, but currently the approach is to blame healthcare workers and not figure out how to help them easily clean their hands. 

(3) Study universal gowning and gloving (several studies are ongoing). Dentists wear gloves with every patient, why not doctors? 

(4) Undertake studies to further optimize environmental source control 

(5) Actually study antimicrobial stewardship. Stop yelling at patients and clinicians to not use antimicrobials. Actually fund studies that use advertising and other other messaging techniques that have a chance to be effective.

This is the most interesting online debate I've seen in ages.

The legacy of SARS

Via The Lancet, a fascinating and informative article: SARS legacy: outbreak reporting is expected and respected. By all means register with The Lancet so you can read the whole thing (registration is free). Excerpt:

The new disease was transmitted from person to person for about 8 months and then disappeared after an unprecedented level of international cooperation and collaboration. By July 5, 2003, WHO was able to declare that “all known chains of person-to-person transmission of the SARS coronavirus” had been broken. 

Whether SARS would have become endemic in people or in an animal reservoir without this determined global health response will never be known. One clear lesson that emerged from the outbreak, however, was that inadequate surveillance and response capacity in one country can endanger not only its population, but also global public health security. 

As happened with smallpox—another disease that has disappeared from people—later cases did occur because of laboratory accidents. Additionally, investigation in the emergence of SARS identified small mammals sold for human consumption within live animal markets in Guangdong, China, as a milieu in which coronaviruses can be amplified and repeatedly cross the species barrier to human beings. 

Four cases of SARS were reported from Guangdong between December, 2003, and January, 2004; at least some patients were thought to have been to live animal markets. But the virus that had spread around the world earlier in 2003 seemed to have a mutation, with an important 29 base-pair deletion in ORF8 that created a novel genetic sublineage. This deletion was absent in virus isolates from civets and in the later four human cases. 

Perhaps the most important legacy of the SARS outbreak resulted from the courage of the WHO Director-General, Gro Harlem Brundtland. Concerned about delays in official reporting and ineffective outbreak containment that led to the global outbreak, she publicly accused a WHO Member State of placing the world at risk. 

Official reporting and effective national outbreak control followed, and, in what became perhaps the greatest legacy of SARS, disease reporting changed almost overnight from being approached with hesitancy and preoccupation with concern about the potential economic fallout from such transparency, to something that was simply expected and respected. 

This development was enshrined in an international agreement after the World Health Assembly—concerned about the emergence and rapid spread of SARS—urged WHO to give high priority to the work on the revision of the International Health Regulations “using experiences, knowledge, and learning acquired during the SARS response”. 

4 years later, in 2007, the new International Health Regulations (IHR 2005)13 came into force and now provide the legal framework with which reporting and risk assessments for public health emergencies of international concern are required. Now, countries are expected to report unusual and unexplained outbreaks of disease despite any potential economic effects, and reporting is respected internationally. 

The first cases of severe human pneumonia caused by influenza A (H5N1)—detected and reported in Vietnam and Thailand between late 2003, and early 2004—were probably identified partly because of enhanced alertness after the SARS outbreak, and led to the recognition and reporting of disease in poultry. Human infections with influenza A (H5N1) virus continue to be reported, despite severe and often uncompensated culling and decreased travel, trade, and tourism. 

Reporting expectations were clearly demonstrated by the emergence of another novel coronavirus in Saudi Arabia in 2012. Under the framework of the IHR 2005, Saudi Arabia, Qatar, and Jordan—countries where people infected with this novel virus lived—worked together with other countries where patients had been admitted to hospital, such as the UK and Germany, and with a global network of laboratories and WHO to review the available evidence and assess and communicate the risk globally to help prevent an irrational response.

The requirement to report is not always honoured—Cuba seems to have been unfortunately reticent in telling us the full truth about cholera, and Indonesia was famously silent about human H5N1 for a long time. Still, we owe WHO (and Gro Harlem Brundtland) a great deal for their response.

ECDC: Annual Epidemiological Report 2012

ECDC has published Annual Epidemiological Report 2012. Click through to download the report. The summary:

Released today, ECDC’s new Annual Epidemiological Report provides a comprehensive review of more than 50 communicable diseases currently notifiable under EU legislation. 

European communicable disease surveillance lies firmly in the hand of the European Centre for Disease Prevention and Control and its database system known as ‘TESSy’ (The European Surveillance System). Through data calls to 27 EU Member States as well as Iceland, Liechtenstein and Norway, the resulting report offers a near-complete picture of the state of European health with regard to infectious diseases. 

The Annual Epidemiological Report 2012 – which is based on 2010 surveillance data – also shows that meaningful disease surveillance in Europe is not easily accomplished. Surveillance systems in the EU still have a long way to go before disease data will be comparable and compatible between Member States or even between the regions within each State. 

In addition, the 2012 report gives an overview of antimicrobial consumption in the Member States and offers a summary of ‘potential communicable disease threats’ recorded in 2011, demonstrating once again the usefulness of epidemic intelligence as a tool for the early detection of disease outbreaks.

Haiti: High tech versus cholera

Via PAHO's Haiti page (not its moribund Hispaniola cholera page): Information System via SMS. Excerpt:

SYMO is an information transmission system that streamlines geographically dispersed data into a single management center. The technology can be used even where Internet may not be working or where there are connection problems. Previously encoded SMS messages transmit information from the field to a central post where it automatically undertakes the following. 

• Evaluates content consistency, notifying the sender via SMS of any error 

• Sets up an alert when the value of the parameter being monitored exceeds the predefined alarm level 

• Stores in a database the information received. Historical reports, statistics can be subsequently performed etc. 

Success stories have been: 

• Monitoring of water quality through the residual chlorine in Dominican Republic and Haiti. An alert is sent when it detects that it is 0 mg/liter. The system automatically notifies operators and health officials via SMS and email. 

• Surveillance of cholera cases (hospitalizations and deaths) in Haiti, such that each day the number of cases and deaths in all the communities are reported from across the country - including from those with difficult access where information has not been readily available.

So the question arises: If a daily tally of hospitalizations and deaths is coming in from all over the country, including the mysteriously silent department of Grande Anse, why doesn't MSPP post a routine, complete, daily update on its Documentation page?

And another question: How many people in Haiti and the Dominican Republic have access to chlorinated water even at the best of times?

Butler: When Google got flu wrong

Via Nature News & Comment, a fascinating report by Declan Butler: When Google got flu wrong. Excerpt (but read the whole thing):

When influenza hit early and hard in the United States this year, it quietly claimed an unacknowledged victim: one of the cutting-edge techniques being used to monitor the outbreak. A comparison with traditional surveillance data showed that Google Flu Trends, which estimates prevalence from flu-related Internet searches, had drastically overestimated peak flu levels. 

The glitch is no more than a temporary setback for a promising strategy, experts say, and Google is sure to refine its algorithms. But as flu-tracking techniques based on mining of web data and on social media proliferate, the episode is a reminder that they will complement, but not substitute for, traditional epidemiological surveillance networks. 

“It is hard to think today that one can provide disease surveillance without existing systems,” says Alain-Jacques Valleron, an epidemiologist at the Pierre and Marie Curie University in Paris, and founder of France’s Sentinelles monitoring network. 

“The new systems depend too much on old existing ones to be able to live without them,” he adds.

WHO: Polio in Niger

Via its Global Alert and Response page, WHO has published Polio in Niger.

Following the notification on 3 January 2013 of a wild poliovirus type 1 (WPV1) case in Niger, outbreak response is continuing in the country. 

A WPV1 case had been detected from Tahoua region, with onset of paralysis on 15 November 2012 (the first case in the country since December 2011). Genetic sequencing confirmed that the virus was a new importation into Niger, most closely related to virus circulating in Kaduna state, Nigeria. 

The Government of Niger is continuing to implement a comprehensive response in line with international outbreak response guidelines issued by the World Health Assembly (WHA) in Resolution WHA59.1. 

Following an initial supplementary immunization activity (SIA) on 15 January 2013 to reach approximately two million children with bivalent oral polio vaccine (OPV), nationwide SIAs were conducted from 2-5 February 2013, targeting more than five million children with trivalent OPV. A second nationwide SIA is planned for 2-5 March with bivalent OPV. 

Previously, nationwide SIAs had been conducted on 23 November 2012 with bivalent OPV. A joint national and international team of epidemiologists and public health experts has been deployed by the World Health Organization’s (WHO) Regional Office for Africa to assist the Government of Niger in the investigations, help plan response activities and support active searches for additional cases of paralytic polio. 

This event confirms the risk of ongoing international spread of a pathogen (WPV) slated for eradication. In May 2012, the completion of polio eradication was declared a programmatic emergency for global public health by the WHA in Resolution WHA65.5. Given the history of international spread of polio from northern Nigeria across west Africa, WHO assesses the risk of further international spread from Nigeria as high. 

Based on the history of previous importations to Niger and the ongoing response, WHO assesses the risk of further international spread from Niger as moderate to high. This risk is currently magnified by large-scale population movements across the region associated with insecurity in Mali. 

To minimize this risk, multi-country synchronized SIAs are planned across 13 countries of west Africa in late April and late May, using a combination of bivalent and trivalent OPV. 

Due to the persistence of subnational surveillance gaps in some areas of west Africa, undetected further circulation cannot be ruled out at this time. Investigations are ongoing to more clearly identify surveillance gaps in the region, including among mobile, migrant and underserved populations. Measures are being implemented to strengthen sub-national surveillance, to ensure that all groups and areas, particularly high-risk populations, are covered by high-quality surveillance. 

As per recommendations outlined in WHO's International travel and health, travellers to and from Niger, and other polio-affected countries, should be fully protected by vaccination. 

It is important that all countries, in particular those with frequent travel and contacts with polio-infected countries, strengthen surveillance for cases of acute flaccid paralysis (AFP), in order to rapidly detect any new poliovirus importations and facilitate a rapid response. 

Countries should also analyse routine immunization coverage data to identify any subnational gaps in population immunity to guide catch-up immunization activities and thereby minimize the consequences of any new virus introduction. Priority should be given to areas at high-risk of importations and where OPV3/DPT3 coverage is <80%.

Cambodia: H5N1 surveillance in live poultry markets, 2011

Via this month's Emerging Infectious Diseases, a very timely article: Influenza A(H5N1) Virus Surveillance at Live Poultry Markets, Cambodia, 2011. The introduction:

Highly pathogenic avian influenza (HPAI) A(H5N1) virus was first detected in 2004 in Cambodia. Since then, outbreaks of subtype H5N1 infection among poultry have been regularly detected, and 21 human cases associated with 19 deaths have been recorded. In Cambodia, where poultry vaccination is not allowed, illegal poultry trade has been a repeated source of reintroduction of the virus. 

Surveillance for subtype H5N1 virus at live poultry markets (LPMs) has been conducted in Cambodia by inoculating cloacal or throat swab specimens from poultry into embryonated chicken eggs; however, virus has rarely been detected by this method (S. Sorn, unpub. data). 

After outbreaks of subtype H5N1 virus in poultry, the viral genome can be detected for >1 week in environmental samples from the outbreak area; thus, environmental surfaces are potential sources of virus transmission to humans and animals. 

LPMs have also been reported as sources of virus involved in human subtype H5N1 infection (7–9). Birds sold at LPMs can originate from many regions of a country; thus, conducting surveillance for subtype H5N1 virus at these markets would probably be an effective way to monitor the circulation of virus within a country. 

It has been recommended that samples of drinking water shared by birds maintained within the same cage and samples of poultry feces be used to detect virus within LPMs. We performed this study to determine whether subtype H5N1 virus circulation in Cambodia could be better monitored by using environmental sampling in LPMs.

I suspect that the rapid response teams around Phnom Penh are doing something very much like this.