Chicken or egg?

The Salmonella Enteritidis challenge

This article has been written exclusively for Food New Zealand by the New Zealand Food Safety Science & Research Centre. It describes the recent detection of food-borne Salmonellosis in New Zealand, and the subsequent steps taken by authorities.

First cases

In October 2019, 38 diners at a very nice Auckland restaurant became ill: 17 were confirmed to have an infection with Salmonella, of the serotype Enteritidis (SE). Two of the confirmed cases ended up in hospital. Follow-up interviews by the health authority pointed to two desserts. One was a panna cotta, but the vanilla pods which were an ingredient in that dish were ruled out as a possible source of the bacteria. The other dessert was a semi-freddo – this is short and posh-sounding Italian for a partly frozen ice cream. It seems likely that the bacteria were harboured by raw eggs in the dessert, as the same strain was subsequently identified at the farm supplying the restaurant. However, this is speculation as no samples of the ice cream were tested at the time. There is still an outside possibility that a food handler may have contaminated the food.

Until 2019, there were typically 1000-1200 cases of salmonellosis (all serotypes) per year, and roughly one third of these were acquired overseas. Sixty-two percent of all cases were foodborne and a fifth of these attributed to poultry. Ironically, despite the SE outbreak spikes, total cases actually declined significantly between 2020 and 2022 because of the sudden death of overseas travel and eating out, and many other factors directly or indirectly connected to the pandemic.

Advances in gene sequencing

Up until November 2019, just after the Auckland restaurant outbreak, phage typing was routinely used by ESR to type clinical isolates, but this method has a number of limitations. It classifies bacteria based on their susceptibility to a subset of bacteriophages (these are viruses that infect bacteria). The same phage types are not necessarily genomically related and the method cannot resolve specific strains down to single DNA bases.

The replacement of phage typing with whole genome sequencing by the team at ESR revolutionised our ability to recognise, track and trace outbreaks – and just in time for COVID-19. Using the powerful new sequencing technology, ESR linked the SE strain from the Auckland restaurant outbreak with isolates from three other North Island outbreaks. The first of these had occurred in May 2019, and from that time on, the same strain kept showing up.

An expanding situation

Eighteen months later, in February 2021, SE was isolated during routine testing of chicken carcasses in a processing plant. There was a direct match between this strain and isolates from the ongoing cluster of SE human infections. SE has been ubiquitous on Earth for a very long time, but until then, not in New Zealand’s poultry industry, as far as we knew anyway. This was not good news. Unlike most other Salmonella serotypes, certain strains of SE, including the one isolated from the chicken carcass, can sometimes infect a hen’s reproductive system. This can lead to egg contents becoming contaminated with SE while the egg is being produced by the chicken. Any SE present in the yolk then has the potential to grow to high concentrations if eggs are not stored in the fridge, causing human infection if they are eaten raw or undercooked. Contaminated eggs and poultry meat are the dominant sources of foodborne SE infection in the UK, Europe and America. Like New Zealand, Australian poultry had been free of SE, but in 2018, SE associated with laying hens caused a big outbreak in New South Wales.

The identification of SE in poultry, and the direct links with the human cases, triggered an alarm at New Zealand Food Safety (NZFS), setting off a comprehensive formal response and sampling blitz along the supply chain. Environmental sampling uncovered SE in a large North Island hatchery which supplies the poultry industry with about 50% of its layer hens, and approximately 10% of the different breed of chickens reared for meat. The two stocks can overlap in hatchery environments, so it was possible that the bacteria had spread to both layer and meat flocks. While the October 2019 Auckland restaurant outbreak may have been associated with eggs, subsequent infections have implicated both eggs and chicken meat, and SE has now been found in both layer and chicken meat farms. There was an uptick in cases of infection in February 2021 after the chicken meat from the broiler flock, later found to be positive for SE by routine testing, entered the food chain.

Response to detection

While it was possible for carcasses from positive broiler flocks to be treated to kill SE prior to sale to the public, e.g. a proven antimicrobial wash or heat treatment, it was impractical at the time. Sadly, the only option for the broiler and egg industry, which had determined from the outset to eradicate the strain, was to destroy the entire flock on farms where it was isolated. Once the premises were disinfected and retesting returned negative results, they could then re-stock.

Dr Kerry Mulqueen, who is veterinary science adviser to the Poultry Industry Association of NZ (PIANZ), said the action for affected flocks depends on the products they produce. Breeder flocks and their eggs have been destroyed and buried, while affected meat chicken flocks have been destroyed, buried, or heated to destroy the Salmonella present before being used for animal or human food (rendered).

Says Kerry, “There was no compensation for the loss of stock and cost of disinfection, which in each case amounted to about $300,000 in costs for a meat chicken shed – not including profit loss. It has been a pretty devastating event for the producers concerned.”

Collaborating to eradicate SE

Kerry is part of the expert team quickly assembled by NZFS to deal with the outbreak and come up with an eradication plan. Dr Joanne Kingsbury, a microbiologist at ESR, is a key member of the team, having previously carried out extensive research on pathogens associated with poultry meat and eggs. Massey Distinguished Professor Nigel French*, chief science adviser to the NZ Food Safety Science & Research Centre, is also indispensable to the group, with his track record in helping to halve Campylobacter rates, and pre-eminence in the application of whole genome sequencing. Dr Paul Dansted, Director Food Regulation at NZFS, is in charge of implementing the “Emergency Control Scheme” (ECS) response which mandates regular environmental testing, and tracks and regulates stock movement. The ECS applies to commercial suppliers with over 100 birds. Of course, many other people and agencies, such as Ministry of Health, are playing their part in this team effort.

How do you devise an eradication programme when the pathogen has already had 18 months freedom to move under the radar, and the number of hens is stupendous – in the hundreds of millions? New Zealanders consume more than one billion eggs a year and over 120 million chickens. In addition, there is an export market for poultry meat, eggs and day-old chicks.

Intense sampling.

Instead of directly sampling eggs and birds, all production facilities must collect regular samples of dust or environmental swabs, and boot swabs (which capture both faeces and dust) from breeder, broiler and layer sheds, and hatchery environments. Joanne explains that this approach is much more likely to detect any Salmonella present in the flock than testing eggs and chickens directly, because only a fraction of the birds or eggs from a colonised flock might be carrying the Salmonella. The bacteria are excreted in the faeces of colonised chickens, and can survive in the shed for long periods in dry conditions, such as in dust. Testing is required throughout the entire live poultry production system, from the breeders, hatcheries, rearing farms, egg layer and broiler chicken farms. Fortunately, South Island producers have remained free of SE so far, and the affected hatchery has been able to move most production of layer chicks to the South Island.

Joanne says that most Salmonella serotypes have the potential to infect people via shell surface contamination which, prior to the introduction of SE, was thought to be the common route of egg-associated salmonellosis in New Zealand. The bacteria can be ingested directly (touching eggs, and then the mouth), or get into egg mixes, which might infect people if not cooked. There is high awareness of the need for scrupulous hygiene with chicken, but people are not so cognisant of the need to wash their hands, bench and utensils after handling eggs.

Although there was no evidence of any occurrence of transovarian infection (the bacteria getting inside the yolk before it is laid) NZFS had to err on the safe side and advise consumers to avoid any dish containing uncooked or lightly cooked eggs – mayonnaise, ice-cream made with eggs, meringues, aioli, etc. – and the risk associated with children (and some of their parents!) ‘licking the bowl’. Consumers are also advised to store their eggs in the fridge after purchase and not to take any chances with ‘use by’ dates.

Of the 124 cases confirmed with the outbreak strain since 2019, there have been 46 hospitalisations, but fortunately no deaths. There is evidence that this strain of SE may cause more severe disease, reflected by higher than usual hospitalisation rates – 37% for this outbreak strain compared with about 20% for salmonellosis before May 2019. As with many infectious diseases, the most vulnerable are the very young and old, pregnant women and immune-compromised people – respectfully, YOPIs for short in health parlance. There have been 12 infections with this SE strain so far this year - the last reported human case (as at 20 July 2022) had an infection onset date of 7 May 2022. Numbers of infections are declining, but no one is thinking the outbreak is over yet.

Of course, progeny of the original SE strain that came over the border has diverged in the hundreds of successive generations over the last three years, but the human isolates are still identical or very closely related to the poultry isolates, including isolates from layer, broiler and breeder/hatchery flocks.

Past, now and into the future

Based on the first reported human case in May 2019, and using the so-called molecular clock, which uses average mutation rates to extrapolate the evolution of a bacteria or virus backwards, scientists estimated that the SE had come into the country around April 2019, and was a single lineage introduction. We still don’t know how it arrived and probably never will. The DNA sequence is most closely related, albeit quite distantly, to isolates from pine nuts and infected people in Turkey.

For Joanne, the challenge is translating all the knowledge she has gained about poultry/egg microbiology over the last six years into critical action. “Livelihoods and the health of many vulnerable New Zealanders are at stake,” she says. The same applies to many of her science colleagues at ESR who have been working round the clock on COVID-19. “There’s a huge sense of urgency and responsibility, and that what you do every day really matters,” says Joanne.

The NZFS Response Team has been able to learn a lot from overseas experience, too, especially the 2018 outbreak in Australia. Our production systems and culture are so similar. Parallel experiences with COVID-19 and Mycoplasma bovis have also informed the modus operandi, though each have different challenges and infection pathways.

What are the chances we can get rid of this strain now, and what further measures can we put in place to stop these unwanted pathogens getting into New Zealand? Nigel says, “It may be difficult to eliminate SE from all poultry farms in New Zealand and prevent further strains from crossing our border. As with all emerging pathogens, having a good understanding of likely entry points and effective surveillance systems in place are essential to help reduce the likelihood of future outbreaks.”

*Professor French is the new co-director, with Te Pora Thompson, of the Infectious Diseases Research Platform, granted $36million by MBIE, and hosted by University of Otago and ESR.