Transmission Dynamics of Shiga Toxin-Producing Escherichia coli in New Zealand Cattle from Farm to Slaughter.

Cattle are asymptomatic carriers of Shiga toxin-producing Escherichiacoli (STEC) strains that can cause serious illness or death in humans. In New Zealand, contact with cattle feces and living near cattle populations are known risk factors for human STEC infection. Contamination of fresh meat with STEC strains also leads to the potential for rejection of consignments by importing countries. We used a combination of PCR/matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF) and whole-genome sequencing (WGS) to evaluate the presence and transmission of STEC on farms and in processing plants to better understand the potential pathways for human exposure and thus mitigate risk. Animal and environmental samples (n = 2,580) were collected from six farms and three meat processing plants in New Zealand during multiple sampling sessions in spring of 2015 and 2016. PCR/MALDI-TOF analysis revealed that 6.2% were positive for "Top 7" STEC. Top 7 STEC strains were identified in all sample sources (n = 17) tested. A marked increase in Top 7 STEC prevalence was observed between calf hides on farm (6.3% prevalence) and calf hides at processing plants (25.1% prevalence). Whole-genome sequencing was performed on Top 7 STEC bacterial isolates (n = 40). Analysis of STEC O26 (n = 25 isolates) revealed relatively low genetic diversity on individual farms, consistent with the presence of a resident strain disseminated within the farm environment. Public health efforts should focus on minimizing human contact with fecal material on farms and during handling, transport, and slaughter of calves. Meat processing plants should focus on minimizing cross-contamination between the hides of calves in a cohort during transport, lairage, and slaughter.IMPORTANCE Cattle are asymptomatic carriers of Shiga toxin-producing E. coli (STEC) strains, which can cause serious illness or death in humans. Contact with cattle feces and living near cattle are known risk factors for human STEC infection. This study evaluated STEC carriage in young calves and the farm environment with an in-depth evaluation of six farms and three meat processing plants over 2 years. An advanced molecular detection method and whole-genome sequencing were used to provide a detailed evaluation of the transmission of STEC both within and between farms. The study revealed widespread STEC contamination within the farm environment, but no evidence of recent spread between farms. Contamination of young dairy calf hides increased following transport and holding at meat processing plants. The elimination of STEC in farm environments may be very difficult given the multiple transmission routes; interventions should be targeted at decreasing fecal contamination of calf hides during transport, lairage, and processing.

Use of Genomics to Investigate Historical Importation of Shiga Toxin-Producing Escherichia coli Serogroup O26 and Nontoxigenic Variants into New Zealand.

Shiga toxin-producing Escherichia coli serogroup O26 is an important public health pathogen. Phylogenetic bacterial lineages in a country can be associated with the level and timing of international imports of live cattle, the main reservoir. We sequenced the genomes of 152 E. coli O26 isolates from New Zealand and compared them with 252 E. coli O26 genomes from 14 other countries. Gene variation among isolates from humans, animals, and food was strongly associated with country of origin and stx toxin profile but not isolation source. Time of origin estimates indicate serogroup O26 sequence type 21 was introduced at least 3 times into New Zealand from the 1920s to the 1980s, whereas nonvirulent O26 sequence type 29 strains were introduced during the early 2000s. New Zealand's remarkably fewer introductions of Shiga toxin-producing Escherichia coli O26 compared with other countries (such as Japan) might be related to patterns of trade in live cattle.

Molecular Epidemiology of Shiga Toxin-Producing Escherichia coli (STEC) on New Zealand Dairy Farms: Application of a Culture-Independent Assay and Whole-Genome Sequencing.

New Zealand has a relatively high incidence of human cases of Shiga toxin-producing Escherichia coli (STEC), with 8.9 STEC cases per 100,000 people reported in 2016. Previous research showed living near cattle and contact with cattle feces as significant risk factors for STEC infections in humans in New Zealand, but infection was not linked to food-associated factors. During the 2014 spring calving season, a random, stratified, cross-sectional study of dairy farms (n = 102) in six regions across New Zealand assessed the prevalence of the "Top 7" STEC bacteria (serogroups O157, O26, O45, O103, O111, O121, and O145) in young calves (n = 1,508), using a culture-independent diagnostic test (PCR/MALDI-TOF). Twenty percent (306/1,508) of calves on 75% (76/102) of dairy farms were positive for at least one of the "Top 7" STEC bacteria. STEC carriage by calves was associated with environmental factors, increased calf age, region, and increased number of calves in a shared calf pen. The intraclass correlation coefficient (ρ) indicated strong clustering of "Top 7" STEC-positive calves for O157, O26, and O45 serogroups within the same pens and farms, indicating that if one calf was positive, others in the same environment were likely to be positive as well. This finding was further evaluated with whole-genome sequencing, which indicated that a single E. coli O26 clonal strain could be found in calves in the same pen or farm, but different strains existed on different farms. This study provides evidence that would be useful for designing on-farm interventions to reduce direct and indirect human exposure to STEC bacteria.IMPORTANCE Cattle are asymptomatic carriers of Shiga toxin-producing E. coli (STEC) bacteria that can cause bloody diarrhea and kidney failure in humans if ingested. New Zealand has relatively high numbers of STEC cases, and contact with cattle feces and living near cattle are risk factors for human infection. This study assessed the national prevalence of STEC in young dairy cattle by randomly selecting 102 farms throughout New Zealand. The study used a molecular laboratory method that has relatively high sensitivity and specificity compared to traditional methods. "Top 7" STEC was found in 20% of calves on 75% of the farms studied, indicating widespread prevalence across the country. By examining the risk factors associated with calf carriage, potential interventions that could decrease the prevalence of "Top 7" STEC bacteria at the farm level were identified, which could benefit both public health and food safety.

Using chemical and DNA marker analysis to authenticate a high-value food, manuka honey.

Ensuring the authenticity of food is a rapidly emerging issue, especially in regard to high-value products that are marketed through increasingly complex global food chains. With the ever-increasing potential for mislabeling, fraud and adulteration, governments are increasingly having to invest in, and assure, the authenticity of foods in international trade. This is particularly the case for manuka honey, an iconic New Zealand food product. We show how the authenticity of a specific type of honey can be determined using a combination of chemicals derived from nectar and DNA derived from pollen. We employ an inter-disciplinary approach to evaluate a selection of authenticity markers, followed by classification modelling to produce criteria that consistently identify manuka honey from New Zealand. The outcome of our work provides robust identification criteria that can be applied in a regulatory setting to authenticate a high-value natural food. Our approach can transfer to other foods where assurance of authenticity must take into account a high level of natural variability.

Geographic divergence of bovine and human Shiga toxin­producing Escherichia coli O157:H7 genotypes, New Zealand.

Shiga toxin-producing Escherichia coli (STEC)O157:H7 is a zoonotic pathogen of public health concern worldwide. To compare the local and large-scale geographic distributions of genotypes of STEC O157:H7 isolates obtained from various bovine and human sources during 2008­2011, we used pulsed-field gel electrophoresis and Shiga toxin­encoding bacteriophage insertion (SBI) typing. Using multivariate methods, we compared isolates from the North and South Islands of New Zealand with isolates from Australia and the United States. The STEC O157:H7 population structure differed substantially between the 2 islands and showed evidence of finer scale spatial structuring, which is consistent with highly localized transmission rather than disseminated foodborne outbreaks. The distribution of SBI types differed markedly among isolates from New Zealand, Australia, and the United States. Our findings also provide evidence for the historic introduction into New Zealand of a subset of globally circulating STEC O157:H7 strains that have continued to evolve and be transmitted locally between cattle and humans.

A prospective case-control and molecular epidemiological study of human cases of Shiga toxin-producing Escherichia coli in New Zealand.

BACKGROUND: Shiga toxin-producing Escherichia coli (STEC) O157:H7 and related non-O157 STEC strains are enteric pathogens of public health concern worldwide, causing life-threatening diseases. Cattle are considered the principal hosts and have been shown to be a source of infection for both foodborne and environmental outbreaks in humans. The aims of this study were to investigate risk factors associated with sporadic STEC infections in humans in New Zealand and to provide epidemiological information about the source and exposure pathways. METHODS: During a national prospective case-control study from July 2011 to July 2012, any confirmed case of STEC infection notified to regional public health units, together with a random selection of controls intended to be representative of the national demography, were interviewed for risk factor evaluation. Isolates from each case were genotyped using pulsed-field gel electrophoresis (PFGE) and Shiga toxin-encoding bacteriophage insertion (SBI) typing. RESULTS: Questionnaire data from 113 eligible cases and 506 controls were analysed using multivariate logistic regression. Statistically significant animal and environmental risk factors for human STEC infections were identified, notably 'Cattle livestock present in meshblock' (the smallest geographical unit) (odds ratio 1.89, 95% CI 1.04-3.42), 'Contact with animal manure' (OR 2.09, 95% CI 1.12-3.90), and 'Contact with recreational waters' (OR 2.95, 95% CI 1.30-6.70). No food-associated risk factors were identified as sources of STEC infection. E. coli O157:H7 caused 100/113 (88.5%) of clinical STEC infections in this study, and 97/100 isolates were available for molecular analysis. PFGE profiles of isolates revealed three distinctive clusters of genotypes, and these were strongly correlated with SBI type. The variable 'Island of residence' (North or South Island of New Zealand) was significantly associated with PFGE genotype (p = 0.012). CONCLUSIONS: Our findings implicate environmental and animal contact, but not food, as significant exposure pathways for sporadic STEC infections in humans in New Zealand. Risk factors associated with beef and dairy cattle suggest that ruminants are the most important sources of STEC infection. Notably, outbreaks of STEC infections are rare in New Zealand and this further suggests that food is not a significant exposure pathway.

Molecular epidemiology of Campylobacter jejuni in a geographically isolated country with a uniquely structured poultry industry.

In New Zealand the number of campylobacteriosis notifications increased markedly between 2000 and 2007. Notably, this country's poultry supply is different than that of many developed countries as the fresh and frozen poultry available at retail are exclusively of domestic origin. To examine the possible link between human cases and poultry, a sentinel surveillance site was established to study the molecular epidemiology of Campylobacter jejuni over a 3-year period from 2005 to 2008 using multilocus sequence typing. Studies showed that 60.1 to 81.4% of retail poultry carcasses from the major suppliers were contaminated with C. jejuni. Differences were detected in the probability and level of contamination and the relative frequency of genotypes for individual poultry suppliers and humans. Some carcasses were contaminated with isolates belonging to more than one sequence type (ST), and there was evidence of both ubiquitous and supplier-associated strains, an epidemiological pattern not recognized yet in other countries. The common poultry STs were also common in human clinical cases, providing evidence that poultry is a major contributor to human infection. Both internationally rare genotypes, such as ST-3069 and ST-474, and common genotypes, such as ST-45 and ST-48, were identified in this study. The dominant human sequence type in New Zealand, ST-474, was found almost exclusively in isolates from one poultry supplier, which provided evidence that C. jejuni has a distinctive molecular epidemiology in this country. These results may be due in part to New Zealand's geographical isolation and its uniquely structured poultry industry.

Assigning the source of human campylobacteriosis in New Zealand: a comparative genetic and epidemiological approach.

Integrated surveillance of infectious multi-source diseases using a combination of epidemiology, ecology, genetics and evolution can provide a valuable risk-based approach for the control of important human pathogens. This includes a better understanding of transmission routes and the impact of human activities on the emergence of zoonoses. Until recently New Zealand had extraordinarily high and increasing rates of notified human campylobacteriosis, and our limited understanding of the source of these infections was hindering efforts to control this disease. Genetic and epidemiological modeling of a 3-year dataset comprising multilocus sequence typed isolates from human clinical cases, coupled with concurrent data on food and environmental sources, enabled us to estimate the relative importance of different sources of human disease. Our studies provided evidence that poultry was the leading cause of human campylobacteriosis in New Zealand, causing an estimated 58-76% of cases with widely varying contributions by individual poultry suppliers. These findings influenced national policy and, after the implementation of poultry industry-specific interventions, a dramatic decline in human notified cases was observed in 2008. The comparative-modeling and molecular sentinel surveillance approach proposed in this study provides new opportunities for the management of zoonotic diseases.

Source attribution of food-borne zoonoses in New Zealand: a modified Hald model.

A Bayesian approach was developed by Hald et al.((1)) to estimate the contribution of different food sources to the burden of human salmonellosis in Denmark. This article describes the development of several modifications that can be used to adapt the model to different countries and pathogens. Our modified Hald model has several advantages over the original approach, which include the introduction of uncertainty in the estimates of source prevalence and an improved strategy for identifiability. We have applied our modified model to the two major food-borne zoonoses in New Zealand, namely, campylobacteriosis and salmonellosis. Major challenges were the data quality for salmonellosis and the inclusion of environmental sources of campylobacteriosis. We conclude that by modifying the Hald model we have improved its identifiability, made it more applicable to countries with less intensive surveillance, and feasible for other pathogens, in particular with respect to the inclusion of nonfood sources. The wider application and better understanding of this approach is of particular importance due to the value of the model for decision making and risk management.

Development of Food Safety Risk Assessment Guidelines for Foods of Animal Origin in International Trade †.

The international food safety environment is currently in a unique period of reevaluation and change. In an emerging trading environment regulated more according to food safety requirements than nontariff trade protection barriers, food safety risk analysis is pivotal to future Codex activities and implementation of the World Trade Organisation (WTO) Sanitary and Phytosanitary (SPS) Agreement. Development of guidelines for food safety risk assessment requires determination of scope, internationally agreed definitions, general principles, guidelines tailored for each class of foodborne hazards, and linkages and interactions with risk management and risk communication. Food safety risk assessments need to be soundly based on science, should incorporate the four analytical steps of the risk assessment paradigm, and should be documented in a transparent and readily understandable form. The particular needs of Codex, the WTO, national governments, industry, and consumers need to be taken into account, and this includes identification of the essential linkages between risk assessment and the design of HACCP plans. With respect to chemical hazards in food, a risk assessment approach provides the opportunity to broaden the understanding of acceptable daily intakes, maximum residue levels, and their public health significance. Guidelines for chemicals in foods will inevitably have to address the differences between safety evaluation and a genuine risk assessment approach. With respect to microbiological hazards, the unique problems associated with risk assessment of living organisms in food make it likely that application of guidelines in the medium term will more commonly use qualitative approaches. In the absence of a history of safety evaluation according to a notionally zero risk baseline, as is the case with chemicals, the objective of microbiological risk analysis to reduce microbial risks to "the minimum which is technologically feasible and practical" represents a genuine focus for risk assessment. As risk assessment is increasing applied and internationally accepted guidelines become established, decision criteria for risk management arguably present the greatest challenge in establishing and maintaining quantitative SPS measures for food in international trade and judging their equivalence. However, the desire of all interested parties for scientifically justified food safety measures may be tempered according to the ability of the global scientific community to generate the necessary data and the political will to accept food safety programmes in different countries that have equivalent outputs.

Risk Assessment Model for Human Infection with the Cestode Taenia saginata.

A probabilistic risk assessment model was developed to estimate the risk to human health of Taenia saginata in the New Zealand cattle population. A standardized monitoring program was established to determine the number of suspect cysts detected during postmortem inspection and the scenario set was applied to risks in both the domestic and export markets. The mean number of human infections per year as a result of consumption in the export and the domestic market was estimated as 0.50 and 1.10 respectively. Estimations for expression of specific clinical symptoms were even less. In a scenario set where postmortem inspection procedures for T. saginata were not applied, the mean number of human infections per year was estimated to increase from 0.50 to 0.61 in the export market and from 1.10 to 1.30 in the domestic market. Given that T. saginata infection in humans results in mild and readily treatable symptoms, these risk estimates are extremely low on any scale of food-borne disease and bring the value of specific postmortem inspection procedures for T. saginata in the New Zealand situation into question. The Monte Carlo model developed to calculate these probabilities is presented here in detail to illustrate the potential of Monte Carlo methods for modeling risk.

Postmortem Meat Inspection Programs; Separating Science and Tradition.

Although a traditional approach to postmortem meat inspection dominates current programs, scientific evidence increasingly suggests that some practices are inappropriately focused. Allocation of inspection resources in modern meat production and processing systems should reflect a distribution according to risk, rather than a distribution according to the classical rules of meat inspection. Postmortem inspection procedures are not usually differentiated according to the class of livestock presented for slaughter, and they may be inappropriate to the spectrum and prevalence of diseases and defects present in a particular geographical region. A risk assessment model can provide the methodology for scientific evaluation of different postmortem inspection procedures, and allow the recognition of equivalent rather than replicated programs by international trading partners. The threat to human (and animal) health posed by various grossly evident diseases detectable by routine meat inspection procedures has been overemphasized relative to the threat posed by inadvertent microbiological contamination of the carcass and offals. The Hazard Analysis Critical Control Point approach (HACCP) identifies and ranks microbiological and other hazards that can arise at each operational step in a food processing system and is a scientifically based system for process control. It has yet to be introduced as a formal method for regulatory control of slaughter and dressing. The networking of slaughterhouse information back to the farm enhances the preventative approach of HACCP.