Blog Archives

Illegal marijuana grows threaten fishers in the southern Sierra Nevada

June 27, 2013 — Rat poison used on illegal marijuana grows is killing fishers in the southern Sierra Nevada, according to a recent study conducted by a team of scientists from the U.S. Forest Service’s Pacific Southwest Research Station (PSW), University of California, Davis, University of California, Berkeley, and the Integral Ecology Research Center.

A previous study published last summer by the research team documented that rodenticides were being found in the tissues of the cat-sized, weasel-like critters which live in rugged portions of the southern Sierra Nevada. The authors speculated that the most likely source of the poisons was the illegal marijuana grows found throughout the Sierra Nevada. This new study solidifies that link, documenting that female fishers who live in areas with a higher number of marijuana sites had more exposure to rodenticides, and subsequently had lower survival rates. The findings concern scientists because the fisher is a candidate for listing under federal, Oregon, and California endangered species acts, and is considered a sensitive species in the western United States by the U.S. Forest Service.

The researchers deduced that illegal marijuana grows are a likely source of the poison, because the fishers in this study were radio-tracked and many were not observed venturing into rural, urban or agricultural areas where rodenticides are often used legally. Illegal marijuana cultivation on public lands is widespread, and some growers apply large quantities of numerous pesticides to deter a wide range of animals and insects from encroaching on their crops. While the exposure of wildlife to rodenticides and insecticides near agricultural fields is not uncommon, the amount and variety of poisons found at the illegal marijuana plots is a new threat.

According to co-author PSW wildlife biologist Dr. Kathryn Purcell, “exposure of wildlife to pesticides has been widely documented, but this is a fundamentally different scenario.

“In marijuana cultivation sites, regulations regarding proper use of pesticides are completely ignored and multiple compounds are used to target any and all threats to the crop, including compounds illegal in the U.S.,” she says.

While some fishers have died from either directly consuming flavored rodenticides or by consuming prey that had recently ingested the poisons, exposure may also predispose animals to dying from other causes. Exposure to lower doses — or to combinations — of the poisons, results in slower reflexes, reduced ability to heal from injuries, and neurological impairment. Consequently, this leads to death from other sources, such as predation or road kill.

Fishers in the southern Sierra Nevada are highly susceptible to pesticide exposure because, unlike their larger bodied relatives in other parts of the country that eat larger prey, their diet consists of small mammals, birds, carrion, insects, fungi, and other plant material. In the vicinity of illegal marijuana sites, numerous dead or dying insects and small mammals are often found. In this study, scientists reported on the amount of poisons found at over 300 illegal plots and compared the locations of these sites with the home ranges and survival of 46 adult female fishers.

The conservation implications of this study are far-reaching.

“By increasing the number of animals that die from supposedly natural causes, these pesticides may be tipping the balance of recovery for fishers” says Dr. Craig Thompson, a PSW wildlife ecologist and the study’s lead author.

This new threat may also impact other species already facing declining populations, including the wolverine, marten, great gray owl, California spotted owl, and Sierra Nevada red fox, which may also be exposed to the poisons, say the scientists.

The full report can be found at http://treesearch.fs.fed.us/pubs/43761

Headquartered in Albany, Calif., the Pacific Southwest Research Station develops and communicates science needed to sustain forest ecosystems and other benefits to society. It has research facilities in California, Hawai’i and the U.S.-affiliated Pacific Islands.

ScienceDaily: Agriculture and Food News

How Culture-Independent Diagostics Threaten Public Health Surveillance

Traditional methods for diagnosing foodborne illness infections such as Salmonella, Campylobacter and E. coli involve cultivating patient samples in an artificial nutrient medium. But tests that don’t require isolates from pure culture are becoming increasingly popular.

There are different kinds of culture-independent diagnostic tests (CIDTs), but they all take a broad look at the DNA in samples, screening for the general types of pathogens that are present. The type of CIDT public health folks think will really overtake culture tests are syndrome-based panels that can test for multiple agents at once. There are five such tests currently licensed for gastrointestinal illnesses, with more expected to follow in coming years.

These CIDTs are particularly attractive to clinicians because, in addition to testing for many different pathogens, they can be faster than traditional methods and can detect bugs that would otherwise be difficult to find. They also don’t need as much equipment or highly trained technicians, so they can save labs money.

“It represents a major departure from what we used to see and we’re anticipating: that there’s going to be very rapid adoption,” says Dr. John Besser, deputy chief of the enteric Diseases Laboratory Branch within the Centers for Disease Control and Prevention’s Division of Foodborne, Waterborne, and Environmental Diseases.

Despite all the positives, there is real concern about what CIDT adoption will mean for public health surveillance.

By definition, these types of tests don’t result in any bacterial or viral isolate, despite the fact that PulseNet, the current government pathogen database, is isolate-based. PulseNet is the national network of public health laboratories that use pulsed-field gel electrophoresis (PFGE) to connect illnesses that have the same pattern, or DNA “fingerprint.”

Information from PFGE tests are uploaded to CDC’s central server, where they can monitor trends nationwide and track illness clusters that may indicate an outbreak. This is how most outbreaks are identified in the U.S.; but without isolates, public health can’t detect the clusters.

“The irony is that the adoption of new tests that are arguably better for patient management may actually be a negative for our ability to detect and investigate clusters of disease,” Besser says.

Using the example of Shiga toxin-producing E. coli (STEC), a CIDT can tell you if the pathogen is present or not and possibly if it has toxin genes Stx1 or Stx2. “PFGE will tell you if it’s one of a thousand different strains in our database, and it’s that level of specificity that we use to connect cases together,” Besser says. “Without that, the cases pretty much all look alike.”

“We haven’t seen a drastic reduction in the number of isolates coming in yet, but it’s something we are anticipating,” said CDC’s Jean Whichard at a National Antimicrobial Resistance Monitoring System (NARMS) conference in August.

While they may not be able to be logged in PulseNet, positive CIDT results that were confirmed by culture are included in the Foodborne Diseases Active Surveillance Network’s (FoodNet) statistics every year. But in the network’s most recent foodborne illness report card, the agencies identified an additional 1,487 reports of positive CIDTs that were not confirmed by culture, either because the specimen was not cultured or because a culture did not yield the pathogen.

FoodNet decided to start tracking these tests in 2013 to better understand their uptake, calling them “a trend that will chal­lenge the ability to identify cases, monitor trends, detect out­breaks, and characterize pathogens.”

How to Proceed

The currently-licensed tests do not result in the destruction of the original patient sample, so one temporary solution to the need for an isolate is reflex testing — proceeding to culture after a CIDT shows a positive result.

Another option is to send the positive sample on to a public health laboratory for them to do the isolation. The problem there is that the state and local public health agencies don’t have the resources to do this.

Furthermore, it slows down the process of obtaining detailed information about the pathogen when a lot of the success in detecting and solving outbreaks comes from the ability to do these things quickly. The longer it takes to get information into PulseNet, the longer it takes to identify illness clusters, and the longer it takes for health departments to contact patients about what they ate and where. The more time that passes between a patient consuming a contaminated meal and the epidemiological interview, the less they’re going to remember.

“While we’re probably going to have to go the route of reflex culture because we don’t have any alternative, it’s not optimal,” Besser says.

Many food safety experts are excited about whole-genome sequencing because of the increased level of detail it can provide. CDC and the U.S. Food and Drug Administration are in the process of implementing the technology. The program began with Listeria and has so far sequenced hundreds of clinical and environmental isolates and begun real-time sequencing of every Listeria isolate across the country.

But, as it’s currently used, whole-genome sequencing also requires an isolate, so it’s also threatened by changing testing practices in clinical labs.

The long-range solution for testing is to develop culture-independent methods that function the same as PulseNet.

“Those new tests will almost certainly be DNA sequence-based,” Besser says.

By developing whole-genome sequencing, he adds, the agencies are putting together the infrastructure that will be needed for culture-independent tests, taking advantage of the current technology to get more accurate detection of illnesses and building a large library of bacterial genomes that can help in the development of these new CIDTs.

“Whole genome sequencing is the first phase of our long-term plan,” Besser says.

In September, CDC launched a “No-Petri-Dish” Diagnostic Test Challenge , which offered a $ 200,000 prize to encourage researchers to straintype and characterize Shiga toxin-producing E. coli (STEC) without using culture-based methods. The contest is open until Nov. 30 and the agency will notify the winner by mid-December.

Food Safety News

How Culture-Independent Diagostics Threaten Public Health Surveillance

Traditional methods for diagnosing foodborne illness infections such as Salmonella, Campylobacter and E. coli involve cultivating patient samples in an artificial nutrient medium. But tests that don’t require isolates from pure culture are becoming increasingly popular.

There are different kinds of culture-independent diagnostic tests (CIDTs), but they all take a broad look at the DNA in samples, screening for the general types of pathogens that are present. The type of CIDT public health folks think will really overtake culture tests are syndrome-based panels that can test for multiple agents at once. There are five such tests currently licensed for gastrointestinal illnesses, with more expected to follow in coming years.

These CIDTs are particularly attractive to clinicians because, in addition to testing for many different pathogens, they can be faster than traditional methods and can detect bugs that would otherwise be difficult to find. They also don’t need as much equipment or highly trained technicians, so they can save labs money.

“It represents a major departure from what we used to see and we’re anticipating: that there’s going to be very rapid adoption,” says Dr. John Besser, deputy chief of the enteric Diseases Laboratory Branch within the Centers for Disease Control and Prevention’s Division of Foodborne, Waterborne, and Environmental Diseases.

Despite all the positives, there is real concern about what CIDT adoption will mean for public health surveillance.

By definition, these types of tests don’t result in any bacterial or viral isolate, despite the fact that PulseNet, the current government pathogen database, is isolate-based. PulseNet is the national network of public health laboratories that use pulsed-field gel electrophoresis (PFGE) to connect illnesses that have the same pattern, or DNA “fingerprint.”

Information from PFGE tests are uploaded to CDC’s central server, where they can monitor trends nationwide and track illness clusters that may indicate an outbreak. This is how most outbreaks are identified in the U.S.; but without isolates, public health can’t detect the clusters.

“The irony is that the adoption of new tests that are arguably better for patient management may actually be a negative for our ability to detect and investigate clusters of disease,” Besser says.

Using the example of Shiga toxin-producing E. coli (STEC), a CIDT can tell you if the pathogen is present or not and possibly if it has toxin genes Stx1 or Stx2. “PFGE will tell you if it’s one of a thousand different strains in our database, and it’s that level of specificity that we use to connect cases together,” Besser says. “Without that, the cases pretty much all look alike.”

“We haven’t seen a drastic reduction in the number of isolates coming in yet, but it’s something we are anticipating,” said CDC’s Jean Whichard at a National Antimicrobial Resistance Monitoring System (NARMS) conference in August.

While they may not be able to be logged in PulseNet, positive CIDT results that were confirmed by culture are included in the Foodborne Diseases Active Surveillance Network’s (FoodNet) statistics every year. But in the network’s most recent foodborne illness report card, the agencies identified an additional 1,487 reports of positive CIDTs that were not confirmed by culture, either because the specimen was not cultured or because a culture did not yield the pathogen.

FoodNet decided to start tracking these tests in 2013 to better understand their uptake, calling them “a trend that will chal­lenge the ability to identify cases, monitor trends, detect out­breaks, and characterize pathogens.”

How to Proceed

The currently-licensed tests do not result in the destruction of the original patient sample, so one temporary solution to the need for an isolate is reflex testing — proceeding to culture after a CIDT shows a positive result.

Another option is to send the positive sample on to a public health laboratory for them to do the isolation. The problem there is that the state and local public health agencies don’t have the resources to do this.

Furthermore, it slows down the process of obtaining detailed information about the pathogen when a lot of the success in detecting and solving outbreaks comes from the ability to do these things quickly. The longer it takes to get information into PulseNet, the longer it takes to identify illness clusters, and the longer it takes for health departments to contact patients about what they ate and where. The more time that passes between a patient consuming a contaminated meal and the epidemiological interview, the less they’re going to remember.

“While we’re probably going to have to go the route of reflex culture because we don’t have any alternative, it’s not optimal,” Besser says.

Many food safety experts are excited about whole-genome sequencing because of the increased level of detail it can provide. CDC and the U.S. Food and Drug Administration are in the process of implementing the technology. The program began with Listeria and has so far sequenced hundreds of clinical and environmental isolates and begun real-time sequencing of every Listeria isolate across the country.

But, as it’s currently used, whole-genome sequencing also requires an isolate, so it’s also threatened by changing testing practices in clinical labs.

The long-range solution for testing is to develop culture-independent methods that function the same as PulseNet.

“Those new tests will almost certainly be DNA sequence-based,” Besser says.

By developing whole-genome sequencing, he adds, the agencies are putting together the infrastructure that will be needed for culture-independent tests, taking advantage of the current technology to get more accurate detection of illnesses and building a large library of bacterial genomes that can help in the development of these new CIDTs.

“Whole genome sequencing is the first phase of our long-term plan,” Besser says.

In September, CDC launched a “No-Petri-Dish” Diagnostic Test Challenge , which offered a $ 200,000 prize to encourage researchers to straintype and characterize Shiga toxin-producing E. coli (STEC) without using culture-based methods. The contest is open until Nov. 30 and the agency will notify the winner by mid-December.

Food Safety News

How Culture-Independent Diagostics Threaten Public Health Surveillance

Traditional methods for diagnosing foodborne illness infections such as Salmonella, Campylobacter and E. coli involve cultivating patient samples in an artificial nutrient medium. But tests that don’t require isolates from pure culture are becoming increasingly popular.

There are different kinds of culture-independent diagnostic tests (CIDTs), but they all take a broad look at the DNA in samples, screening for the general types of pathogens that are present. The type of CIDT public health folks think will really overtake culture tests are syndrome-based panels that can test for multiple agents at once. There are five such tests currently licensed for gastrointestinal illnesses, with more expected to follow in coming years.

These CIDTs are particularly attractive to clinicians because, in addition to testing for many different pathogens, they can be faster than traditional methods and can detect bugs that would otherwise be difficult to find. They also don’t need as much equipment or highly trained technicians, so they can save labs money.

“It represents a major departure from what we used to see and we’re anticipating: that there’s going to be very rapid adoption,” says Dr. John Besser, deputy chief of the enteric Diseases Laboratory Branch within the Centers for Disease Control and Prevention’s Division of Foodborne, Waterborne, and Environmental Diseases.

Despite all the positives, there is real concern about what CIDT adoption will mean for public health surveillance.

By definition, these types of tests don’t result in any bacterial or viral isolate, despite the fact that PulseNet, the current government pathogen database, is isolate-based. PulseNet is the national network of public health laboratories that use pulsed-field gel electrophoresis (PFGE) to connect illnesses that have the same pattern, or DNA “fingerprint.”

Information from PFGE tests are uploaded to CDC’s central server, where they can monitor trends nationwide and track illness clusters that may indicate an outbreak. This is how most outbreaks are identified in the U.S.; but without isolates, public health can’t detect the clusters.

“The irony is that the adoption of new tests that are arguably better for patient management may actually be a negative for our ability to detect and investigate clusters of disease,” Besser says.

Using the example of Shiga toxin-producing E. coli (STEC), a CIDT can tell you if the pathogen is present or not and possibly if it has toxin genes Stx1 or Stx2. “PFGE will tell you if it’s one of a thousand different strains in our database, and it’s that level of specificity that we use to connect cases together,” Besser says. “Without that, the cases pretty much all look alike.”

“We haven’t seen a drastic reduction in the number of isolates coming in yet, but it’s something we are anticipating,” said CDC’s Jean Whichard at a National Antimicrobial Resistance Monitoring System (NARMS) conference in August.

While they may not be able to be logged in PulseNet, positive CIDT results that were confirmed by culture are included in the Foodborne Diseases Active Surveillance Network’s (FoodNet) statistics every year. But in the network’s most recent foodborne illness report card, the agencies identified an additional 1,487 reports of positive CIDTs that were not confirmed by culture, either because the specimen was not cultured or because a culture did not yield the pathogen.

FoodNet decided to start tracking these tests in 2013 to better understand their uptake, calling them “a trend that will chal­lenge the ability to identify cases, monitor trends, detect out­breaks, and characterize pathogens.”

How to Proceed

The currently-licensed tests do not result in the destruction of the original patient sample, so one temporary solution to the need for an isolate is reflex testing — proceeding to culture after a CIDT shows a positive result.

Another option is to send the positive sample on to a public health laboratory for them to do the isolation. The problem there is that the state and local public health agencies don’t have the resources to do this.

Furthermore, it slows down the process of obtaining detailed information about the pathogen when a lot of the success in detecting and solving outbreaks comes from the ability to do these things quickly. The longer it takes to get information into PulseNet, the longer it takes to identify illness clusters, and the longer it takes for health departments to contact patients about what they ate and where. The more time that passes between a patient consuming a contaminated meal and the epidemiological interview, the less they’re going to remember.

“While we’re probably going to have to go the route of reflex culture because we don’t have any alternative, it’s not optimal,” Besser says.

Many food safety experts are excited about whole-genome sequencing because of the increased level of detail it can provide. CDC and the U.S. Food and Drug Administration are in the process of implementing the technology. The program began with Listeria and has so far sequenced hundreds of clinical and environmental isolates and begun real-time sequencing of every Listeria isolate across the country.

But, as it’s currently used, whole-genome sequencing also requires an isolate, so it’s also threatened by changing testing practices in clinical labs.

The long-range solution for testing is to develop culture-independent methods that function the same as PulseNet.

“Those new tests will almost certainly be DNA sequence-based,” Besser says.

By developing whole-genome sequencing, he adds, the agencies are putting together the infrastructure that will be needed for culture-independent tests, taking advantage of the current technology to get more accurate detection of illnesses and building a large library of bacterial genomes that can help in the development of these new CIDTs.

“Whole genome sequencing is the first phase of our long-term plan,” Besser says.

In September, CDC launched a “No-Petri-Dish” Diagnostic Test Challenge , which offered a $ 200,000 prize to encourage researchers to straintype and characterize Shiga toxin-producing E. coli (STEC) without using culture-based methods. The contest is open until Nov. 30 and the agency will notify the winner by mid-December.

Food Safety News

How Culture-Independent Diagostics Threaten Public Health Surveillance

Traditional methods for diagnosing foodborne illness infections such as Salmonella, Campylobacter and E. coli involve cultivating patient samples in an artificial nutrient medium. But tests that don’t require isolates from pure culture are becoming increasingly popular.

There are different kinds of culture-independent diagnostic tests (CIDTs), but they all take a broad look at the DNA in samples, screening for the general types of pathogens that are present. The type of CIDT public health folks think will really overtake culture tests are syndrome-based panels that can test for multiple agents at once. There are five such tests currently licensed for gastrointestinal illnesses, with more expected to follow in coming years.

These CIDTs are particularly attractive to clinicians because, in addition to testing for many different pathogens, they can be faster than traditional methods and can detect bugs that would otherwise be difficult to find. They also don’t need as much equipment or highly trained technicians, so they can save labs money.

“It represents a major departure from what we used to see and we’re anticipating: that there’s going to be very rapid adoption,” says Dr. John Besser, deputy chief of the enteric Diseases Laboratory Branch within the Centers for Disease Control and Prevention’s Division of Foodborne, Waterborne, and Environmental Diseases.

Despite all the positives, there is real concern about what CIDT adoption will mean for public health surveillance.

By definition, these types of tests don’t result in any bacterial or viral isolate, despite the fact that PulseNet, the current government pathogen database, is isolate-based. PulseNet is the national network of public health laboratories that use pulsed-field gel electrophoresis (PFGE) to connect illnesses that have the same pattern, or DNA “fingerprint.”

Information from PFGE tests are uploaded to CDC’s central server, where they can monitor trends nationwide and track illness clusters that may indicate an outbreak. This is how most outbreaks are identified in the U.S.; but without isolates, public health can’t detect the clusters.

“The irony is that the adoption of new tests that are arguably better for patient management may actually be a negative for our ability to detect and investigate clusters of disease,” Besser says.

Using the example of Shiga toxin-producing E. coli (STEC), a CIDT can tell you if the pathogen is present or not and possibly if it has toxin genes Stx1 or Stx2. “PFGE will tell you if it’s one of a thousand different strains in our database, and it’s that level of specificity that we use to connect cases together,” Besser says. “Without that, the cases pretty much all look alike.”

“We haven’t seen a drastic reduction in the number of isolates coming in yet, but it’s something we are anticipating,” said CDC’s Jean Whichard at a National Antimicrobial Resistance Monitoring System (NARMS) conference in August.

While they may not be able to be logged in PulseNet, positive CIDT results that were confirmed by culture are included in the Foodborne Diseases Active Surveillance Network’s (FoodNet) statistics every year. But in the network’s most recent foodborne illness report card, the agencies identified an additional 1,487 reports of positive CIDTs that were not confirmed by culture, either because the specimen was not cultured or because a culture did not yield the pathogen.

FoodNet decided to start tracking these tests in 2013 to better understand their uptake, calling them “a trend that will chal­lenge the ability to identify cases, monitor trends, detect out­breaks, and characterize pathogens.”

How to Proceed

The currently-licensed tests do not result in the destruction of the original patient sample, so one temporary solution to the need for an isolate is reflex testing — proceeding to culture after a CIDT shows a positive result.

Another option is to send the positive sample on to a public health laboratory for them to do the isolation. The problem there is that the state and local public health agencies don’t have the resources to do this.

Furthermore, it slows down the process of obtaining detailed information about the pathogen when a lot of the success in detecting and solving outbreaks comes from the ability to do these things quickly. The longer it takes to get information into PulseNet, the longer it takes to identify illness clusters, and the longer it takes for health departments to contact patients about what they ate and where. The more time that passes between a patient consuming a contaminated meal and the epidemiological interview, the less they’re going to remember.

“While we’re probably going to have to go the route of reflex culture because we don’t have any alternative, it’s not optimal,” Besser says.

Many food safety experts are excited about whole-genome sequencing because of the increased level of detail it can provide. CDC and the U.S. Food and Drug Administration are in the process of implementing the technology. The program began with Listeria and has so far sequenced hundreds of clinical and environmental isolates and begun real-time sequencing of every Listeria isolate across the country.

But, as it’s currently used, whole-genome sequencing also requires an isolate, so it’s also threatened by changing testing practices in clinical labs.

The long-range solution for testing is to develop culture-independent methods that function the same as PulseNet.

“Those new tests will almost certainly be DNA sequence-based,” Besser says.

By developing whole-genome sequencing, he adds, the agencies are putting together the infrastructure that will be needed for culture-independent tests, taking advantage of the current technology to get more accurate detection of illnesses and building a large library of bacterial genomes that can help in the development of these new CIDTs.

“Whole genome sequencing is the first phase of our long-term plan,” Besser says.

In September, CDC launched a “No-Petri-Dish” Diagnostic Test Challenge , which offered a $ 200,000 prize to encourage researchers to straintype and characterize Shiga toxin-producing E. coli (STEC) without using culture-based methods. The contest is open until Nov. 30 and the agency will notify the winner by mid-December.

Food Safety News

How Culture-Independent Diagostics Threaten Public Health Surveillance

Traditional methods for diagnosing foodborne illness infections such as Salmonella, Campylobacter and E. coli involve cultivating patient samples in an artificial nutrient medium. But tests that don’t require isolates from pure culture are becoming increasingly popular.

There are different kinds of culture-independent diagnostic tests (CIDTs), but they all take a broad look at the DNA in samples, screening for the general types of pathogens that are present. The type of CIDT public health folks think will really overtake culture tests are syndrome-based panels that can test for multiple agents at once. There are five such tests currently licensed for gastrointestinal illnesses, with more expected to follow in coming years.

These CIDTs are particularly attractive to clinicians because, in addition to testing for many different pathogens, they can be faster than traditional methods and can detect bugs that would otherwise be difficult to find. They also don’t need as much equipment or highly trained technicians, so they can save labs money.

“It represents a major departure from what we used to see and we’re anticipating: that there’s going to be very rapid adoption,” says Dr. John Besser, deputy chief of the enteric Diseases Laboratory Branch within the Centers for Disease Control and Prevention’s Division of Foodborne, Waterborne, and Environmental Diseases.

Despite all the positives, there is real concern about what CIDT adoption will mean for public health surveillance.

By definition, these types of tests don’t result in any bacterial or viral isolate, despite the fact that PulseNet, the current government pathogen database, is isolate-based. PulseNet is the national network of public health laboratories that use pulsed-field gel electrophoresis (PFGE) to connect illnesses that have the same pattern, or DNA “fingerprint.”

Information from PFGE tests are uploaded to CDC’s central server, where they can monitor trends nationwide and track illness clusters that may indicate an outbreak. This is how most outbreaks are identified in the U.S.; but without isolates, public health can’t detect the clusters.

“The irony is that the adoption of new tests that are arguably better for patient management may actually be a negative for our ability to detect and investigate clusters of disease,” Besser says.

Using the example of Shiga toxin-producing E. coli (STEC), a CIDT can tell you if the pathogen is present or not and possibly if it has toxin genes Stx1 or Stx2. “PFGE will tell you if it’s one of a thousand different strains in our database, and it’s that level of specificity that we use to connect cases together,” Besser says. “Without that, the cases pretty much all look alike.”

“We haven’t seen a drastic reduction in the number of isolates coming in yet, but it’s something we are anticipating,” said CDC’s Jean Whichard at a National Antimicrobial Resistance Monitoring System (NARMS) conference in August.

While they may not be able to be logged in PulseNet, positive CIDT results that were confirmed by culture are included in the Foodborne Diseases Active Surveillance Network’s (FoodNet) statistics every year. But in the network’s most recent foodborne illness report card, the agencies identified an additional 1,487 reports of positive CIDTs that were not confirmed by culture, either because the specimen was not cultured or because a culture did not yield the pathogen.

FoodNet decided to start tracking these tests in 2013 to better understand their uptake, calling them “a trend that will chal­lenge the ability to identify cases, monitor trends, detect out­breaks, and characterize pathogens.”

How to Proceed

The currently-licensed tests do not result in the destruction of the original patient sample, so one temporary solution to the need for an isolate is reflex testing — proceeding to culture after a CIDT shows a positive result.

Another option is to send the positive sample on to a public health laboratory for them to do the isolation. The problem there is that the state and local public health agencies don’t have the resources to do this.

Furthermore, it slows down the process of obtaining detailed information about the pathogen when a lot of the success in detecting and solving outbreaks comes from the ability to do these things quickly. The longer it takes to get information into PulseNet, the longer it takes to identify illness clusters, and the longer it takes for health departments to contact patients about what they ate and where. The more time that passes between a patient consuming a contaminated meal and the epidemiological interview, the less they’re going to remember.

“While we’re probably going to have to go the route of reflex culture because we don’t have any alternative, it’s not optimal,” Besser says.

Many food safety experts are excited about whole-genome sequencing because of the increased level of detail it can provide. CDC and the U.S. Food and Drug Administration are in the process of implementing the technology. The program began with Listeria and has so far sequenced hundreds of clinical and environmental isolates and begun real-time sequencing of every Listeria isolate across the country.

But, as it’s currently used, whole-genome sequencing also requires an isolate, so it’s also threatened by changing testing practices in clinical labs.

The long-range solution for testing is to develop culture-independent methods that function the same as PulseNet.

“Those new tests will almost certainly be DNA sequence-based,” Besser says.

By developing whole-genome sequencing, he adds, the agencies are putting together the infrastructure that will be needed for culture-independent tests, taking advantage of the current technology to get more accurate detection of illnesses and building a large library of bacterial genomes that can help in the development of these new CIDTs.

“Whole genome sequencing is the first phase of our long-term plan,” Besser says.

In September, CDC launched a “No-Petri-Dish” Diagnostic Test Challenge , which offered a $ 200,000 prize to encourage researchers to straintype and characterize Shiga toxin-producing E. coli (STEC) without using culture-based methods. The contest is open until Nov. 30 and the agency will notify the winner by mid-December.

Food Safety News

How Culture-Independent Diagostics Threaten Public Health Surveillance

Traditional methods for diagnosing foodborne illness infections such as Salmonella, Campylobacter and E. coli involve cultivating patient samples in an artificial nutrient medium. But tests that don’t require isolates from pure culture are becoming increasingly popular.

There are different kinds of culture-independent diagnostic tests (CIDTs), but they all take a broad look at the DNA in samples, screening for the general types of pathogens that are present. The type of CIDT public health folks think will really overtake culture tests are syndrome-based panels that can test for multiple agents at once. There are five such tests currently licensed for gastrointestinal illnesses, with more expected to follow in coming years.

These CIDTs are particularly attractive to clinicians because, in addition to testing for many different pathogens, they can be faster than traditional methods and can detect bugs that would otherwise be difficult to find. They also don’t need as much equipment or highly trained technicians, so they can save labs money.

“It represents a major departure from what we used to see and we’re anticipating: that there’s going to be very rapid adoption,” says Dr. John Besser, deputy chief of the enteric Diseases Laboratory Branch within the Centers for Disease Control and Prevention’s Division of Foodborne, Waterborne, and Environmental Diseases.

Despite all the positives, there is real concern about what CIDT adoption will mean for public health surveillance.

By definition, these types of tests don’t result in any bacterial or viral isolate, despite the fact that PulseNet, the current government pathogen database, is isolate-based. PulseNet is the national network of public health laboratories that use pulsed-field gel electrophoresis (PFGE) to connect illnesses that have the same pattern, or DNA “fingerprint.”

Information from PFGE tests are uploaded to CDC’s central server, where they can monitor trends nationwide and track illness clusters that may indicate an outbreak. This is how most outbreaks are identified in the U.S.; but without isolates, public health can’t detect the clusters.

“The irony is that the adoption of new tests that are arguably better for patient management may actually be a negative for our ability to detect and investigate clusters of disease,” Besser says.

Using the example of Shiga toxin-producing E. coli (STEC), a CIDT can tell you if the pathogen is present or not and possibly if it has toxin genes Stx1 or Stx2. “PFGE will tell you if it’s one of a thousand different strains in our database, and it’s that level of specificity that we use to connect cases together,” Besser says. “Without that, the cases pretty much all look alike.”

“We haven’t seen a drastic reduction in the number of isolates coming in yet, but it’s something we are anticipating,” said CDC’s Jean Whichard at a National Antimicrobial Resistance Monitoring System (NARMS) conference in August.

While they may not be able to be logged in PulseNet, positive CIDT results that were confirmed by culture are included in the Foodborne Diseases Active Surveillance Network’s (FoodNet) statistics every year. But in the network’s most recent foodborne illness report card, the agencies identified an additional 1,487 reports of positive CIDTs that were not confirmed by culture, either because the specimen was not cultured or because a culture did not yield the pathogen.

FoodNet decided to start tracking these tests in 2013 to better understand their uptake, calling them “a trend that will chal­lenge the ability to identify cases, monitor trends, detect out­breaks, and characterize pathogens.”

How to Proceed

The currently-licensed tests do not result in the destruction of the original patient sample, so one temporary solution to the need for an isolate is reflex testing — proceeding to culture after a CIDT shows a positive result.

Another option is to send the positive sample on to a public health laboratory for them to do the isolation. The problem there is that the state and local public health agencies don’t have the resources to do this.

Furthermore, it slows down the process of obtaining detailed information about the pathogen when a lot of the success in detecting and solving outbreaks comes from the ability to do these things quickly. The longer it takes to get information into PulseNet, the longer it takes to identify illness clusters, and the longer it takes for health departments to contact patients about what they ate and where. The more time that passes between a patient consuming a contaminated meal and the epidemiological interview, the less they’re going to remember.

“While we’re probably going to have to go the route of reflex culture because we don’t have any alternative, it’s not optimal,” Besser says.

Many food safety experts are excited about whole-genome sequencing because of the increased level of detail it can provide. CDC and the U.S. Food and Drug Administration are in the process of implementing the technology. The program began with Listeria and has so far sequenced hundreds of clinical and environmental isolates and begun real-time sequencing of every Listeria isolate across the country.

But, as it’s currently used, whole-genome sequencing also requires an isolate, so it’s also threatened by changing testing practices in clinical labs.

The long-range solution for testing is to develop culture-independent methods that function the same as PulseNet.

“Those new tests will almost certainly be DNA sequence-based,” Besser says.

By developing whole-genome sequencing, he adds, the agencies are putting together the infrastructure that will be needed for culture-independent tests, taking advantage of the current technology to get more accurate detection of illnesses and building a large library of bacterial genomes that can help in the development of these new CIDTs.

“Whole genome sequencing is the first phase of our long-term plan,” Besser says.

In September, CDC launched a “No-Petri-Dish” Diagnostic Test Challenge , which offered a $ 200,000 prize to encourage researchers to straintype and characterize Shiga toxin-producing E. coli (STEC) without using culture-based methods. The contest is open until Nov. 30 and the agency will notify the winner by mid-December.

Food Safety News

US (CA): Extreme heat and birds threaten Valley grapes

US (CA): Extreme heat and birds threaten Valley grapes

Some Valley growers are in a race against time. The heat is ripening grapes on the vine while labourers work shorter hours because of the high heat. Bright reflective foil strips fly over a Madera vineyard to keep the birds away from the red flame seedless grapes.

Michelle Shackelford of Robert Johnson Farms explained, “Hopefully the wind scares the birds away by flapping the tape.” But Shackelford said the strips don’t keep enough of the hungry birds away. “No, they don’t. It lasts for about a day. Helps for about a day.”

Fortunately the grape crop was healthy and heavy. Shackelford said the red flame harvest started a little early this year. In another week all of the bunches will be a nice red colour because of the intense heat.

Michelle said, “This heat is pushing them to colour. They’re colouring much faster.”

The leafy canopy helps protect the grapes from sunburn as does the grass growing in each row. Shackelford said, “Grapes need circulation, air circulation to prevent mildew growth but on top they like a nice umbrella.”

Shackelford added the hot streak will damage some of her varieties.

“It’s also going to impact I think the Thompson crop, “said Shackelford. “I think we’re going to see some burn on 5-10% of the crop.”

The red flames are sold locally at The Market and Whole Foods under the Robert Johnson Farms label as well as the Jenelle brand, which combines the names of Michelle and her sister Jennifer.

Please click here to view the video report.

Source: abc30.com

Publication date: 7/9/2014


FreshPlaza.com

US (CA): Extreme heat and birds threaten Valley grapes

US (CA): Extreme heat and birds threaten Valley grapes

Some Valley growers are in a race against time. The heat is ripening grapes on the vine while labourers work shorter hours because of the high heat. Bright reflective foil strips fly over a Madera vineyard to keep the birds away from the red flame seedless grapes.

Michelle Shackelford of Robert Johnson Farms explained, “Hopefully the wind scares the birds away by flapping the tape.” But Shackelford said the strips don’t keep enough of the hungry birds away. “No, they don’t. It lasts for about a day. Helps for about a day.”

Fortunately the grape crop was healthy and heavy. Shackelford said the red flame harvest started a little early this year. In another week all of the bunches will be a nice red colour because of the intense heat.

Michelle said, “This heat is pushing them to colour. They’re colouring much faster.”

The leafy canopy helps protect the grapes from sunburn as does the grass growing in each row. Shackelford said, “Grapes need circulation, air circulation to prevent mildew growth but on top they like a nice umbrella.”

Shackelford added the hot streak will damage some of her varieties.

“It’s also going to impact I think the Thompson crop, “said Shackelford. “I think we’re going to see some burn on 5-10% of the crop.”

The red flames are sold locally at The Market and Whole Foods under the Robert Johnson Farms label as well as the Jenelle brand, which combines the names of Michelle and her sister Jennifer.

Please click here to view the video report.

Source: abc30.com

Publication date: 7/9/2014


FreshPlaza.com

Oil palm plantations threaten water quality, scientists say

If you’ve gone grocery shopping lately, you’ve probably bought palm oil.

Found in thousands of products, from peanut butter and packaged bread to shampoo and shaving cream, palm oil is a booming multibillion-dollar industry. While it isn’t always clearly labeled in supermarket staples, the unintended consequences of producing this ubiquitous ingredient have been widely publicized.

The clearing of tropical forests to plant oil palm trees releases massive amounts of carbon dioxide, a greenhouse gas fueling climate change. Converting diverse forest ecosystems to these single-crop “monocultures” degrades or destroys wildlife habitat. Oil palm plantations also have been associated with dangerous and abusive conditions for laborers.

Significantly eroded water quality now joins the list of risks associated with oil palm cultivation, according to new research co-authored by researchers from Stanford University and the University of Minnesota, who warn of threats to freshwater streams that millions ofpeople depend on for drinking water, food and livelihoods. The new study in the Journal of Geophysical Research: Biogeosciences contains surprising findings about the intensity and persistence of these impacts, even in areas fully forested with mature oil palm trees.

Land clearing, plantation management (including fertilizer and pesticide application) and processing of oil palm fruits to make crude palm oil can all send sediment, nutrients and other harmful substances into streams that run through plantations. Vegetation removal along stream banks destroys plant life that stream organisms depend on for sustenance and shade.

“Although we previously documented carbon emissions from land use conversion to oil palm, we were stunned by how these oil palm plantations profoundly alter freshwater ecosystems for decades,” said study co-author and team leader Lisa M. Curran, a professor of ecological anthropology at Stanford and a senior fellow at the Stanford Woods Institute for the Environment.

Palm oil epicenter

Indonesia produces almost half of the world’s palm oil. Home to the world’s third-largest tropical forest, the country is also one of the principal emitters of greenhouse gases, due to the rapid conversion of carbon-rich forests and peatlands to other uses.

From 2000 to 2013, Indonesia’s land used for oil palm cultivation more than tripled. About 35 percent of Indonesian Borneo’s unprotected lowlands may be cleared for oil palm in coming years, according to previous research by Curran and the study’s lead author, Kimberly Carlson, a former Stanford graduate student who is now a postdoctoral scholar at the University of Minnesota’s Institute on the Environment.

Curran, Carlson and their colleagues focused on small streams flowing through oil palm plantations, smallholder agriculture and forests in and around Gunung Palung National Park, a federally protected area that Curran was instrumental in establishing in 1990. They found that water temperatures in streams draining recently cleared plantations were almost 4 degrees Celsius (more than 7 degrees Fahrenheit) warmer than forest streams. Sediment concentrations were up to 550 times greater. They also recorded a spike in stream metabolism — the rate at which a stream consumes oxygen and an important measure of a stream’s health — during a drought.

Possible solutions

The impact of these land use changes on fisheries, coastal zones and coral reefs — potentially many miles downstream — remains unclear because this study is one of the first to examine the oil palm’s effects on freshwater ecosystems. “Local communities are deeply concerned about their freshwater sources. Yet the long-term impact of oil palm plantations on freshwater streams has been completely overlooked until now,” Curran said. “We hope this work will highlight these issues and bring a voice to rural communities’ concerns that directly affect their livelihoods.”

Potential management solutions, according to Carlson and Curran, include maintaining natural vegetative cover next to streams and designing oil palm plantations so that dense road networks do not intersect directly with waterways. These kinds of improved practices are being pioneered by the Roundtable on Sustainable Palm Oil and other organizations that certify palm oil production as sustainable. Yet, Carlson said, “Our findings suggest that converting logged forests and diverse smallholder agricultural lands to oil palm plantations may be almost as harmful to stream ecosystems as clearing intact forests.” Very few protections for such non-intact forest ecosystems exist.

According to Curran, extensive land conversion to oil palm plantations could lead to a “perfect storm” combining the crop’s environmental effects with those from a massive El Niño-associated drought. (One is predicted this fall.) “This could cause collapse of freshwater ecosystems and significant social and economic hardships in a region,” Curran said.

Story Source:

The above story is based on materials provided by Stanford University. The original article was written by Rob Jordan. Note: Materials may be edited for content and length.

Agriculture and Food News — ScienceDaily

US: H-2A delays threaten winter vegetable harvest

US: H-2A delays threaten winter vegetable harvest

America’s nearly $ 4 billion winter vegetable harvest is in jeopardy if the Obama administration doesn’t immediately speed up foreign guest worker visa applications that have been stalled during the government shutdown, the Western Growers Association warns.

The Office of Foreign Labor Certification at the U.S. Department of Labor has been closed since Oct. 1 and processing of H-2A guest worker applications was halted just when the growing season for winter vegetables was getting underway, the association said in a news release.

Federal workers who were furloughed under the partial government shutdown were to return to work Oct. 17.

It usually takes at least eight weeks to process H-2A applications and if workers are not in place by Nov. 18, consequences will be dire, said Tom Nassif, president and CEO of Western Growers. “The H-2A program has never been efficient or responsive to needs of employers or workers even in the best of times,” Nassif said. “Inaction by Congress on immigration reform has forced farmers to turn to H-2A in desperation, but if these applications are not processed in an expedited manner, the Yuma and Imperial winter vegetable harvest, which relies on thousands of H-2A workers, will suffer and consumers will face a shortage of domestic fresh produce. Prices will surely rise as supplies diminish.”

Desert regions of Arizona and California produce 90 percent of the country’s vegetables in winter. Applications have not been processed for more than two weeks and a backlog has grown. Some 30 to 50 percent of agricultural workers in Yuma County, Ariz., and Imperial County, Calif., are H-2A guest workers during the winter, the association said.

Source: capitalpress.com

Publication date: 10/18/2013


FreshPlaza.com

Weeds threaten carbon offset programs

Aug. 12, 2013 — Researchers have identified gamba grass and other invasive weeds as a potential threat to landholder involvement in environmental offset programs such as the Carbon Farming Initiative.

Strategic savanna burning is one way to reduce Australia’s carbon emissions and create new markets in northern Australia, but the increased fuel load and emissions from weed infestations could make it unfeasible.

Dr Vanessa Adams says that late dry season wildfires in Australia’s tropical north generate about 3% of the country’s annual greenhouse gas emissions, so strategic burning could be an important abatement activity.

“But when native savannas are invaded by weeds such as gamba grass, fuel loads are dramatically increased and fires can burn up to five times hotter than a native wildfire,” Dr Adams said.

“We examined the spatial and financial extent of the threat of gamba grass and found that 75% of the area across northern Australia suitable for savanna burning is also highly suitable for gamba grass.

“There’s a large disparity between the profits generated from savanna burning — $ 1.92 per hectare — and the costs of managing gamba grass — $ 40 per hectare — meaning that much more savanna needs to be enrolled for carbon farming to cover the costs of weed eradication.

“The good news is that in the Northern Territory, only about 20% of properties that could run profitable savanna burning programs had gamba grass, and of these, about 16% had small infestations.

“A one-off investment of $ 200,000 would eradicate these infestations, and for the majority of properties that are gamba free, an effective control program would safeguard them into the future.

“It’s really important we look at how these types of barriers might prevent landholders from getting involved in environmental offset programs and that we strategically manage weeds so that they don’t become an intractable problem in the future.”

ScienceDaily: Agriculture and Food News