Antonio Vieira

Global Monitoring of Salmonella Serovar Distribution from the World Health Organization Global Foodborne Infections Network Country Data Bank: Results of Quality Assured Laboratories from 2001 to 2007

Salmonella enterica is commonly acquired from contaminated food and is an important cause of illness worldwide. Interventions are needed to control Salmonella; subtyping Salmonella by serotyping is useful for targeting such interventions. We, therefore, analyzed the global distribution of the 15 most frequently identified serovars of Salmonella isolated from humans from 2001 to 2007 in laboratories from 37 countries that participated in World Health Organization Global Foodborne Infections Network and demonstrated serotyping proficiency in the Global Foodborne Infections Network External Quality Assurance System. In all regions throughout the study period, with the exception of the Oceania and North American regions, Salmonella serovars Enteritidis and Typhimurium ranked as the most common and second most common serovar, respectively. In the North American and Oceania (Australia and New Zealand) regions, Salmonella serovar Typhimurium was the most common serovar reported, and Salmonella serovar Enteritidis was the second most common serovar. During the study period, the proportion of Salmonella isolates reported from humans that were Salmonella serovar Enteritidis was 43.5% (range: 40.6% [2007] to 44.9% [2003]), and Salmonella serovar Typhimurium was 17.1% (range: 15% [2007] to 18.9% [2001]). Salmonella serovars Newport (mainly observed in Latin and North American and European countries), Infantis (dominating in all regions), Virchow (mainly observed in Asian, European, and Oceanic countries), Hadar (profound in European countries), and Agona (intense in Latin and North American and European countries) were also frequently isolated with an overall proportion of 3.5%, 1.8%, 1.5%, 1.5%, and 0.8%, respectively. There were large differences in the most commonly isolated serovars between regions, but lesser differences between countries within the same region. The results also highlight the complexity of the global epidemiology of Salmonella and the need and importance for improving monitoring data of those serovars of highest epidemiologic importance.

Attributing human foodborne illness to food sources and water in Latin America and the Caribbean using data from outbreak investigations

Foodborne pathogens are responsible for an increasing burden of disease worldwide. Knowledge on the contribution of different food sources and water for disease is essential to prioritize food safety interventions and implement appropriate control measures. Source attribution using outbreak data utilizes readily available data from outbreak surveillance to estimate the contribution of different sources to human disease. We developed a probabilistic model based on outbreak data that attributes human foodborne disease by various bacterial pathogens to sources in Latin America and the Caribbean (LA&C). Foods implicated in outbreaks were classified by their ingredients as simple foods (i.e. belonging to one single food category), or complex foods (i.e. belonging to multiple food categories). For each agent, the data from simple-food outbreaks were summarized, and the proportion of outbreaks caused by each category was used to define the probability that an outbreak was caused by a source. For the calculation of the number of outbreaks attributed to each source, simple-food outbreaks were attributed to the single food category in question, and complex-food outbreaks were partitioned to each category proportionally to the estimated probability. We analysed all bacterial pathogens together, focused on important bacterial pathogens separately, and, when data were sufficient, performed analyses by country, decade and location. Between 1993 and 2010, 6313 bacterial outbreaks were reported by 20 countries. In general, the most important sources of bacterial disease were meat, dairy products, water and vegetables in the 1990s, and eggs, vegetables, and grains and beans in the 2000s. We observed fluctuations of the most important sources of disease for each pathogen between decades and countries, which may be a consequence of changes in the control of zoonotic disease over the years, of changes in food consumption habits, or of changes in public health focus and availability of data of different pathogens. This study identified data gaps in the region and highlighted the importance of effective surveillance systems to identify sources of disease. Still, the application of this method for source attribution in the LA&C region was successful, and we concluded that this approach can be used to attribute disease to food sources and water in other regions, including developing regions with limited data on the public health impact of foodborne diseases.

Association Between Antimicrobial Resistance in Escherichia coli Isolates from Food Animals and Blood Stream Isolates from Humans in Europe: An Ecological Study

BACKGROUND In addition to medical antimicrobial usage, the use of antimicrobials in food animals contributes to the occurrence of resistance among some bacterial species isolated from infections in humans. Recently, several studies have indicated that a large proportion of Escherichia coli causing infections in humans, especially those resistant to antimicrobials, have an animal origin. METHODS We analyzed the correlation between the prevalence of antimicrobial resistance in E. coli isolates from blood stream infections in humans and in E. coli isolates from poultry, pigs, and cattle between 2005 and 2008 for 11 countries, using available surveillance data. We also assessed the correlation between human antimicrobial usage and the occurrence of resistance in E. coli isolates from blood stream infections. RESULTS Strong and significant correlations between prevalences of resistance to ampicillin (r=0.94), aminoglycosides (r=0.72), third-generation cephalosporins (r=0.76), and fluoroquinolones (r=0.68) were observed for human and poultry E. coli isolates. Similar significant correlations were observed for ampicillin (r=0.91), aminoglycosides (r=0.73), and fluoroquinolone resistance (r=0.74) in pig and human isolates. In cattle isolates, only ampicillin resistance (r=0.72) was significantly correlated to human isolates. When usage of antimicrobials in humans was analyzed with antimicrobial resistance among human isolates, only correlations between fluoroquinolones (r=0.90) and third-generation cephalosporins (r=0.75) were significant. CONCLUSIONS Resistance in E. coli isolates from food animals (especially poultry and pigs) was highly correlated with resistance in isolates from humans. This supports the hypothesis that a large proportion of resistant E. coli isolates causing blood stream infections in people may be derived from food sources.

WHO Global Salm-Surv External Quality Assurance System for Serotyping of Salmonella Isolates from 2000 to 2007

ABSTRACT An international external quality assurance system (EQAS) for the serotyping of Salmonella species was initiated in 2000 by WHO Global Salm-Surv to enhance the capacity of national reference laboratories to obtain reliable data for surveillance purposes worldwide. Seven EQAS iterations were conducted between 2000 and 2007. In each iteration, participating laboratories submitted serotyping results for eight Salmonella isolates. A total of 249 laboratories in 96 countries participated in at least one EQAS iteration. A total of 756 reports were received from the participating laboratories during the seven EQAS iterations. Cumulatively, 76% of participating laboratories submitted data for all eight strains, and 82% of strains were correctly serotyped. In each iteration, 84% to 96% of the laboratories correctly serotyped the Salmonella enterica serovar Enteritidis isolate that was included as an internal quality control strain. Regional differences in performance were observed, with laboratories in Central Asia and the Middle East performing less well overall than those in other regions. Errors that resulted in incorrect serovar identification were typically caused by difficulties in the detection of the phase two flagellar antigen or in differentiation within antigen complexes; some of these errors are likely related to the quality of the antisera available. The results from the WHO Global Salm-Surv EQAS, the largest of its kind in the world, show that most laboratories worldwide are capable of correctly serotyping Salmonella species. However, this study also indicates a continuing need for improvement. Future training efforts should be aimed at enhancing the ability to detect the phase two flagellar antigen and at disseminating information on where to purchase high-quality antisera.

Shigella from Humans in Thailand During 1993 to 2006: Spatial-Time Trends in Species and Serotype Distribution

In Thailand during 1993-2006, a total of 9063 Shigella isolates from different medical centers were serotyped and trends over time and spatial clustering analyzed. Of 3583 cases with age information, 1315 (37%) cases were from children between 0 and 4 years and 684 (19%) from children between 5 and 8 years. Most infections were recorded during 1993-1994 (> 1500 per year), decreasing to < 200 in 2006. The relative species distribution also changed. During 1993-1994, Shigella flexneri accounted for 2241 (65%) of 3474 isolations. This proportion decreased to 64 (36%) of 176 infections in 2006. Most infections occurred during July and August, and fewest in December. S. flexneri clustered around Bangkok, and Shigella sonnei in southern Thailand. Most S. flexneri infections were caused by serotype 2a (1590 of 4035) followed by serotype var X (1249). For both serotypes, a pronounced decrease in the number of isolates occurred over time. A much smaller decrease was observed for serotype 3a isolates. Phase I S. sonnei was initially most common, but shifted gradually over phase I, II, to only phase II. No differences in spatial distribution were found. The three most common S. flexneri serotypes all clustered in, around, and west of Bangkok. Serotypes 2a and 3a also clustered in southern Thailand, whereas var X clustered north and northeast of Bangkok. In conclusion, looking at Shigella species, Thailand changed from being a developing country to a developed country between 1995 and 1996. In addition, major shifts in the types of S. sonnei were observed as were differences in spatial clustering of S. flexneri and S. sonnei and S. flexneri serotypes.

Trends in slaughter pig production and antimicrobial consumption in Danish slaughter pig herds, 2002-2008.

Overuse of antimicrobials in food-animal production is thought to be a major risk factor for the development of resistant bacterial populations. Data on non-human antimicrobial usage is essential for planning of intervention strategies to lower resistance levels at the country, region or herd levels. In this study we evaluated Danish national antimicrobial usage data for five antimicrobial classes used in slaughter pigs in different herd sizes and data on the number of slaughter pigs produced per herd, between 2002 and 2008, in Denmark. The objective was to ascertain if there is an association between herd size and amount of antimicrobials consumed. During this period, the overall number of herds with slaughter pigs decreased by 43%, with larger herds becoming more prevalent. The tetracycline treatment incidence (TI) rate increased from 0·28 to 0·70 animal-defined daily dose (ADD)/100 slaughter pig-days at risk while macrolide TI presented a more moderate increase, from 0·40 to 0·44 ADD/100 slaughter pig-days at risk during the study period. Linear regression analyses revealed a significant association between herd size and TI rates for tetracyclines, macrolides, sulfonamides/trimethoprim and cephalosporins, with small herds presenting significantly higher TI than moderate, large and the largest herds. This study highlights the importance of establishing an antimicrobial consumption monitoring programme, integrated with comprehensive food-animal production surveillance. Further research should be performed to address the potential causes of the detected associations between herd sizes and antimicrobial consumption in pigs.

Prevalence of tetracycline resistance and genotypic analysis of populations of Escherichia coli from animals, carcasses and cuts processed at a pig slaughterhouse.

A Danish pig slaughterhouse was visited in this study to investigate the impact of carcass processing on prevalence of tetracycline-resistant Escherichia coli, and to identify the origins of carcass contaminations with E. coli by assessing genetic diversity of E. coli populations on carcasses. A total of 105 carcasses were sampled at five sequential stages: after stunning, after scalding, after splitting, after cooling and after cutting. Total and tetracycline-resistant E. coli were counted for each sample and tetracycline resistance prevalence per sample was calculated by the fraction of tetracycline-resistant E. coli out of total E. coli. From 15 repeatedly sampled carcasses, 422 E. coli isolates from faeces, stunned carcasses, split carcasses and chilled carcasses were examined by pulse-field gel electrophoresis (PFGE) and tested for antimicrobial susceptibility. The results showed that E. coli counts and the prevalence of tetracycline-resistant E. coli per sample were both progressively reduced after each sampling stage. PFGE analysis showed that E. coli populations from stunned carcasses were highly genetically diverse, compared with those from split carcasses and faeces. Thirteen carcasses (87%) were contaminated with E. coli that were also isolated from faeces of either the same or other pigs slaughtered on the same day; and 80% of stunned carcasses shared the same E. coli PFGE subtypes. The results suggest that some carcass processing steps in the slaughterhouse were effective in reducing both E. coli numbers and the tetracycline resistance prevalence in E. coli on carcasses. Faeces from the same or other pigs slaughtered on the same day were likely to be an important source of E. coli carcass contamination. Combined data from E. coli enumeration, PFGE typing and antimicrobial susceptibility testing suggest that tetracycline-susceptible E. coli probably persisted better compared to resistant ones during the carcass processing.

Association between tetracycline consumption and tetracycline resistance in Escherichia coli from healthy Danish slaughter pigs.

It has been recognized that exposure to antimicrobial agents can exert a selective pressure for the emergence of antimicrobial resistance. The objective of this study was to investigate an association between the probability of isolating a tetracycline-resistant Escherichia coli isolate from the intestinal tract of healthy pigs and patterns of tetracycline consumption in the herds of origin, together with other risk factors. Data on antimicrobial resistance, antimicrobial consumption, and pig herd demographics were obtained from different Danish surveillance programs. Descriptive statistics were performed for the risk factors in relation to the susceptibility status. Logistic regression analysis was performed to identify risk factors with significant effect on the log odds of tetracycline resistance of E. coli isolates. The model showed that an increase in the interval between last prescription and sampling date would decrease the probability of isolating a resistant E. coli isolate (p-value = 0.01). Also, a direct association between treatment incidence rate in a herd and probability of resistance was detected (p-value = 0.03). Other risk factors found to have a significant effect in the isolate susceptibility status were number of produced animals in the year and year of sampling. Other antimicrobial consumption risk factors, such as number of prescriptions and amount prescribed, although not included in the final model, presented indirect impact in the tetracycline resistance probability. From this study, we can infer that tetracycline usage, the time span between last treatment and sampling date, together with herd size and the proportion of animals being treated in a herd, increase the probability of obtaining a resistant isolate.

Spatio-temporal analysis of Salmonella surveillance data in Thailand

This study evaluates the usefulness of spatio-temporal statistical tools to detect outbreaks using routine surveillance data where limited epidemiological information is available. A dataset from 2002 to 2007 containing information regarding date, origin, source and serotype of 29,586 Salmonella isolates from Thailand was analysed. Data was grouped into human and non-human categories and the analysis was performed for the top five occurring serovars for each year of the study period. A total 91 human and 39 non-human significant spatio-temporal clusters were observed, accounting for 11% and 16% of the isolates, respectively. Serovar-specific associations between human and non-human clusters were also evaluated. Results show that these statistical tools can provide information for use in outbreak prevention and detection, in countries where only limited data is available. Moreover, it is suggested that monitoring non-human reservoirs can be relevant in predicting future Salmonella human cases.

Spatial Scan Statistics to Assess Sampling Strategy of Antimicrobial Resistance Monitoring Program

The collection and analysis of data on antimicrobial resistance in human and animal populations are important for establishing a baseline of the occurrence of resistance and for determining trends over time. In animals, targeted monitoring with a stratified sampling plan is normally used. However, to our knowledge it has not previously been analyzed whether animals have a random chance of being sampled by these programs, regardless of their spatial distribution. In this study, we used spatial scan statistics, based on a Poisson model, as a tool to evaluate the geographical distribution of animals sampled by the Danish Integrated Antimicrobial Resistance Monitoring and Research Programme (DANMAP), by identifying spatial clusters of samples and detecting areas with significantly high or low sampling rates. These analyses were performed for each year and for the total 5-year study period for all collected and susceptibility tested pig samples in Denmark between 2002 and 2006. For the yearly analysis, both high and low sampling rates areas were significant, with two clusters in 2002 (relative risk [RR]: 2.91, p < 0.01 and RR: 0.06, p < 0.01) and one in 2005 (RR: < 0.01, p < 0.01). For the 5-year analysis, one high sampling rate cluster was detected (RR: 2.56, p = 0.01). These findings allowed subsequent investigation to clarify the source of the sampling clusters. Overall, the detected clusters presented different spatial locations over the years and we can conclude that they were more associated to temporary sampling problems than to a failure in the sampling strategy adopted by the monitoring program. Spatial scan statistics proved to be a useful tool for assessment of the randomness of the sampling distribution, which is important when evaluating the validity of the results obtained by an antimicrobial monitoring program.