High-throughput whole-genome sequencing (WGS) is a revolutionary tool in public health microbiology and is gradually substituting classical typing methods in surveillance of infectious diseases. In combination with epidemiological methods, WGS is able to identify both sources and transmission-pathways during disease outbreak investigations.
This review provides the current state of knowledge on the application of WGS in the epidemiology of Campylobacter jejuni, the leading cause of bacterial gastroenteritis in the European Union.
We describe how WGS has improved surveillance and outbreak detection of C. jejuni infections and how WGS has increased our understanding of the evolutionary and epidemiological dynamics of this pathogen. However, the full implementation of this methodology in real-time is still hampered by a few hurdles. The limited insight into the genetic diversity of different lineages of C. jejuni impedes the validity of assumed genetic relationships. Furthermore, efforts are needed to reach a consensus on which analytic pipeline to use and how to define the strains cut-off value for epidemiological association while taking the needs and realities of public health microbiology in consideration.
Even so, we claim that ample evidence is available to support the benefit of integrating WGS in the monitoring of C. jejuni infections and outbreak investigations.
Use of whole-genome sequencing in the epidemiology of Campylobacter jejuni infections: state-of-knowledge
Ahead of print, doi: http://dx.doi.org/10.1101/078550
A survey carried out by a team of scientists of the Microbiology, Fermentation and Biotechnology Division of Central Institute of Fisheries Technology (CIFT) Kochi, found Salmonella in 29 per cent of seafood samples.
During the screening process, the researchers collected as many as 150 fresh seafood samples including popular varieties like sardine, mackerel, prawns and crabs from the markets in and around Kochi.
The study was conducted by a team of scientists including S.S. Greeshma, M.M. Prasad, K.V. Lalitha, Toms C. Joseph, and V. Murugadas.
The presence of salmonella in seafood indicates contamination with human and animal excreta. Fishes and shellfish normally do not harbour micro-organisms like salmonella but can get contaminated with through the use of contaminated ice, water, containers and poor hygienic handling practices, explained Dr. Greeshma.
Samples were collected over a period of nine months. Once salmonella reaches soil and aquatic environments, it can survive there for long periods.
While cooking kills the micro-organism, there exists the risk of cross-contamination with other food items that are consumed raw when handled along with seafood contaminated with salmonella.
Humans who come into direct contact with salmonella-contaminated seafoods face health risk, she explained.
The study underscores the need to hygienic handling of fish in the markets, said C.N. Ravishankar, Director of the Institute in a communication.
The researchers are planning a source study to identify the routes and points of possible contamination of the fish.
Materials and Methods: Sixty blood samples were collected from finished pigs at slaughter and their sera was evaluated by an indirect-IgG ELISA. Matched muscle samples were obtained from the tongue and loin. Whole blood and tissue samples were evaluated to search for T. gondii DNA using a nested-polymerase chain reaction.
Results: Seroprevalence of T. gondii was 96.6% (58/60) of sampled pigs. Meanwhile, T. gondii DNA was present in 23.21% of tongue tissue samples (13/56), 7% of loin tissues (4/57), and 0% in blood samples (0/44), respectively. Two pigs were serologically indeterminate.
Conclusion: This is the first report of the presence of T. gondii DNA in tissue samples obtained from finalized pigs. Results from the present study suggest a high exposure to T. gondii in pigs intended for human consumption from the tropical region of Mexico. Thus, the consumption of some undercooked pork meat meals typical from the southern region of Mexico could represent a significant risk for acquiring infection for the human population.
Presence of Toxoplasma gondii in pork intended for human consumption in tropical southern of Mexico
Foodborne Pathogens and Disease. September 2016, ahead of print. doi:10.1089/fpd.2016.2165.
IB Hernández-Cortazar, KY Acosta-Viana, E Guzmán-Marin, A Ortega-Pacheco, JF de Jesus Torres-Acosta, M Jimenez-Coello
Product was distributed in New York and Connecticut through retail stores and restaurants between 9/6/2016 to 9/16/2016.
The whole product is packed in an unlabeled paper box and delivered to restaurants. The sliced product is sold in a clear plastic package and labeled on the back with lot and use by date.
No illnesses have been reported to date in connection with this problem.
The potential for contamination was noted after routine testing by the FDA inspection revealed the presence of Listeria monocytogenes in floor drains and cracks in the floor.
I went through an extremely brief Ted Nugent phase when I was 16.
I was driving my then-girlfriend and her mom somewhere, and thought it’d be cool to put Wango Tango on the 8-track (a prehistoric device used to play music).
And kissing kittens increases the risk of being infected.
“The scope and impact of the disease is a little bit larger than we thought,” says Dr. Christina Nelson, a medical epidemiologist with the Centers for Disease Control and Prevention and lead author on the study. It’s the first large-scale evaluation of the illness in the United States in over 15 years.
While the total number of people infected with the disease has gone down, the number of people becoming seriously ill has increased. Symptoms typically involve fatigue, fever and swollen lymph nodes. But in a small number of cases, cat-scratch disease can cause the brain to swell or infect the heart. Infections like those can be fatal if they aren’t properly treated.
“Most of the people who get seriously sick from cat-scratch are immunocompromised. The classic example is patients with HIV,” says Dr. Aaron Glatt, chairman of medicine and hospital epidemiology of South Nassau Community Hospital in New York. Glatt was not involved in the study
The fact that there are more people with suppressed immune systems today may be why a larger number of patients are getting dangerously ill, Glatt says. But Nelson thinks that severe cases of cat-scratch disease may have been misdiagnosed in the past. Either way, she says, this study, which was published Wednesday in Emerging Infectious Diseases, is a good first step.
“Cat-scratch is preventable,” Nelson says. “If we can identify the populations at risk and the patterns of disease, we can focus the prevention efforts.”
It’s preventable because you need direct contact with a cat to get it. The disease is caused by bacteria, usually Bartonella henselae, and passed between cats by fleas. The bacteria are also present in flea dirt — the official name for flea feces — which build up in the cats’ fur. It gets on their paws and in their mouths when they groom themselves. If a person is scratched by contaminated claws, they’re at risk of getting the disease.
The study combed health insurance claims from 2005 to 2013, and charted when and where cat-scratch disease is most likely to strike. It found that about 12,000 people will be diagnosed with cat-scratch disease each year, and 500 of them will be sick enough to be hospitalized.
Many of those infected will be children, probably because of the ways kids play with cats. And most of the infections will occur in the South, where heat-and-moisture-loving fleas are more common.
If you want to avoid cat-scratch disease altogether, says Nelson, go somewhere arid —like Colorado or Utah.
But moving to the Rockies isn’t an option for everyone. If you’re stuck in the South, how can you skip cat-scratch?
“Stay away from cats,” says Glass, although he acknowledges that in a country full of cat-lovers, this isn’t really realistic.
“Use adequate flea control and keep your cats indoors,” suggests Nelson. The bacteria can also enter your body through your nose, eyes or mouth, so the CDC recommends washing your hands after touching a cat. Kissing their flea dirt-filled fur probably isn’t a good idea, either. Neither is letting them lick you if you have any scrapes, scabs or open wounds.
Oh. And avoid kittens.
“Younger cats are more likely to have bacteria in their blood,” explains Nelson. Kittens aren’t immune to cat-scratch, so they’re an easy target for the bacteria.
So try to keep from kissing Felix … at least until he’s flea-free.
In a newly published study, researchers artificially contaminated food with salmonella. They then tested the food samples using Salmonella-specific antibodies combined with a unique signal amplification technique. Their test found salmonella present after 15 hours and removed other microorganisms that sometimes clutter laboratory results. This is shorter than the two to three days it takes to detect salmonella in a culture, the study shows.
“The test has great potential as a simple monitoring system for foodborne pathogens in food samples, which can improve food safety and public health,” said Soohyoun Ahn, a UF/IFAS assistant professor of food science and human nutrition and lead author of the study. “Even with all the strategies used to minimize contamination of beef and poultry, they are still one of the major food vehicles for salmonella.”
The test would be suitable for any government research laboratory or industry that routinely tests for Salmonella, Ahn said.
Ahn sees the salmonella test showing similar potential for faster detection of other pathogens you can get from eating certain contaminated foods. A similar test has been developed for E. coli in milk and ground beef, and it performed well, she said.
The study is published in the Journal of Food Safety.
Attempts to reduce the human risk for acquiring EHEC infections should include strategies to control such STEC strains persisting in cattle. We therefore aimed to identify genetic patterns associated with the STEC colonization type in the bovine host. We included 88 persistent colonizing STEC (STECper) (shedding for ≥4 months) and 74 sporadically colonizing STEC (STECspo) (shedding for ≤2 months) isolates from cattle and 16 bovine STEC isolates with unknown colonization types. Genoserotypes and multilocus sequence types (MLSTs) were determined, and the isolates were probed with a DNA microarray for virulence-associated genes (VAGs). All STECper isolates belonged to only four genoserotypes (O26:H11, O156:H25, O165:H25, O182:H25), which formed three genetic clusters (ST21/396/1705, ST300/688, ST119). In contrast, STECspo isolates were scattered among 28 genoserotypes and 30 MLSTs, with O157:H7 (ST11) and O6:H49 (ST1079) being the most prevalent. The microarray analysis identified 139 unique gene patterns that clustered with the genoserotypes and MLSTs of the strains. While the STECper isolates possessed heterogeneous phylogenetic backgrounds, the accessory genome clustered these isolates together, separating them from the STECspo isolates.
Given the vast genetic heterogeneity of bovine STEC strains, defining the genetic patterns distinguishing STECper from STECspo isolates will facilitate the targeted design of new intervention strategies to counteract these zoonotic pathogens at the farm level.
The accessory genome of Shiga toxin-producing Escherichia coli defines a persistent colonization type in cattle
Appl Environ Microbiol 82:5455–5464. doi:10.1128/AEM.00909-16.
SA Barth, C Menge, I Eichhorn, T Semmier, LH Wieler, D Pickard, A Belka, C Berens, L Geue
We quantified and examined trends in reptile-associated salmonellosis in the Netherlands during a 30-year period, from 1985 to 2014. Using source attribution analysis, we estimated that 2% (95% confidence interval: 1.3–2.8) of all sporadic/domestic human salmonellosis cases reported in the Netherlands during the study period (n = 63,718) originated from reptiles.
The estimated annual fraction of reptile-associated salmonellosis cases ranged from a minimum of 0.3% (corresponding to 11 cases) in 1988 to a maximum of 9.3% (93 cases) in 2013. There was a significant increasing trend in reptile-associated salmonellosis cases (+ 19% annually) and a shift towards adulthood in the age groups at highest risk, while the proportion of reptile-associated salmonellosis cases among those up to four years-old decreased by 4% annually and the proportion of cases aged 45 to 74 years increased by 20% annually.
We hypothesise that these findings may be the effect of the increased number and variety of reptiles that are kept as pets, calling for further attention to the issue of safe reptile–human interaction and for reinforced hygiene recommendations for reptile owners.
Increase in reptile-associated human Salmonellosis and shift toward adulthood in the age groups at risk, The Netherlands, 1985 to 2014
Eurosurveillance, Volume 21, Issue 34, 25 August 2016, DOI: http://dx.doi.org/10.2807/1560-7917.ES.2016.21.34.30324
One of my daughters got married on the weekend. I have two grandsons. The Tragically Hip may never play live again (it’s a Canadian thing, but 1-in-3 Canadians watched the concert Saturday night from Kingston).
We had a top-10 list of conclusions to be applied in whatever risky business might come along:
a risk information vacuum is a primary factor in the social amplification of risk;
regulators are responsible for effective risk communication;
industry is responsible for effective risk communication;
if you are responsible for communicating about risks, do it early and often;
there is always more to a risk issue than what science says;
always put the science in a policy context;
educating the public about science is no substitute for good risk communication practice;
banish no risk messages;
risk messages should address directly the contest of opinion in society; and,
communicating well has spinoff benefits for good risk management.
I watch these microbial food safety risk shitfests, document them in barfblog.com, and sigh-a-sigh worthy of someone who didn’t just fall off the turnip truck.
At the time, I applauded Jeni’s CEO John Lowe for the proactive steps they announced after finding Listeria in their ice cream, but also wondered why they weren’t looking before?
Lowe also said, “Finally, let me reiterate: we will not make or serve ice cream again until we can ensure it is 100% safe. Until we know more about reopening, we are going to continue to keep our heads down and to work hard to get this issue resolved. But know this: you’ll be hearing from us soon.”
Sounds like some cookie-cutter MBA approach to crisis.
“Two of 75 samples were found to have listeria by the FDA’s lab. Those two samples came from:
* The floor adjacent to the prep room, nine feet from a prep table where the base for Intelligentsia Black Cat Espresso was being processed and packaged.
* The floor of the wash room by a drain, two feet from a sink used to wash, rinse and sanitize equipment parts, utensils and containers used in production.”
Jeni’s said it took immediate corrective actions and prevented any spread to food contact surfaces or areas around food contact surfaces. It also noted that it has taken more than 2,000 environmental swabs in the past year and listeria has never been detected on food contact surfaces or around food contact surfaces and that its “test-and-hold” procedures, which have been in place for a year, have not turned up a single positive test for listeria.
Dan Eaton of Columbus Business First quotes founder Jeni Britton Bauer, CEO John Lowe and Quality Leader Mary Kamm as jointly writing in a Wednesday blog post, “As a result of our sanitation and other food safety procedures, our environmental testing program and our test-and-hold procedures, we can assure everyone that the food we produce is absolutely 100 percent safe.”
Alex Black of FG Insight reports the UK Association of Independent Meat Suppliers (AIMS) has claimed the Food Standards Agency (FSA) ’appears to continue to undermine the meat processing sector’ with misleading campylobacter figures.
An article in The Meat Trades Journal quoted figures published on the Food Standards Agency website stated campylobacter was believed to cause 100 deaths a year.
However, AIMS pointed out the figure was an extract from a FSA funded paper which said ’We could not estimate deaths attributable to foodborne illness, due to the lack of reliable data sources on pathogen-specific mortality rates’.
AIMS head of policy, Norman Bagley, said: “Selectively quoting from its own commissioned report on its own website has once again undermined the excellent work and progress the industry has made on combating campylobacter.
“Stating that campylobacter causes 100 deaths a year is just not based on science and leads to continuing scary, misleading stories being carried in both the trade and consumer media, which once again, undermines our sector.
“This is far from helpful and needs to stop.”
A FSA spokesman said: “We explain on our website that the campylobacter deaths figure is a previous estimate, and that we are continuing to analyse the full impact that campylobacter has.
“We are determining which updated figures to use in the future.”
This review provides the current state of knowledge on the application of WGS in the epidemiology of Campylobacter jejuni, the leading cause of bacterial gastroenteritis in the European Union.
