Molecular epidemiology of two international sprout-borne Salmonella outbreaks

Phylogenomic Analysis of Salmonella enterica subsp. enterica Serovar Bovismorbificans from Clinical and Food Samples Using Whole Genome Wide Core Genes and kmer Binning Methods to Identify Two Distinct Polyphyletic Genome Pathotypes

Salmonella enterica subsp. enterica serovar Bovismorbificans has caused multiple outbreaks involving the consumption of produce, hummus, and processed meat products worldwide. To elucidate the intra-serovar genomic structure of S. Bovismorbificans, a core-genome analysis with 2690 loci (based on 150 complete genomes representing Salmonella enterica serovars developed as part of this study) and a k-mer-binning based strategy were carried out on 95 whole genome sequencing (WGS) assemblies from Swiss, Canadian, and USA collections of S. Bovismorbificans strains from foodborne infections. Data mining of a digital DNA tiling array of legacy SARA and SARB strains was conducted to identify near-neighbors of S. Bovismorbificans. The core genome analysis and the k-mer-binning methods identified two polyphyletic clusters, each with emerging evolutionary properties. Four STs (2640, 142, 1499, and 377), which constituted the majority of the publicly available WGS datasets from >260 strains analyzed by k-mer-binning based strategy, contained a conserved core genome backbone with a different evolutionary lineage as compared to strains comprising the other cluster (ST150). In addition, the assortment of genotypic features contributing to pathogenesis and persistence, such as antimicrobial resistance, prophage, plasmid, and virulence factor genes, were assessed to understand the emerging characteristics of this serovar that are relevant clinically and for food safety concerns. The phylogenomic profiling of polyphyletic S. Bovismorbificans in this study corresponds to intra-serovar variations observed in S. Napoli and S. Newport serovars using similar high-resolution genomic profiling approaches and contributes to the understanding of the evolution and sequence divergence of foodborne Salmonellae. These intra-serovar differences may have to be thoroughly understood for the accurate classification of foodborne Salmonella strains needed for the uniform development of future food safety mitigation strategies.

An outbreak and case-control study of Salmonella Havana linked to alfalfa sprouts in South Australia, 2018

An epidemiological investigation and a retrospective case-control study were conducted into an outbreak of Salmonella Havana in alfalfa sprouts, in Adelaide, Australia. In total, 31 cases of S. Havana were notified during June and July 2018 and linked to the outbreak. Eighteen cases and 54 unmatched controls were included in a case-control study. Results from the case-control study indicated an increased risk of illness linked to the consumption of alfalfa sprouts; this was supported by trace-back, sampling and environmental investigations. This outbreak of S. Havana was caused by consumption of alfalfa sprouts from one local sprouts producer. It is unclear as to when in the production of alfalfa sprouts the contamination occurred. However, contaminated seeds and poor pest control are the most likely causes. This investigation highlights the importance of ensuring that producers take appropriate action to minimise the likelihood of contamination and to comply with legislation and standards for primary production and food safety.

Outbreak of Salmonella Bovismorbificans associated with the consumption of uncooked ham products, the Netherlands, 2016 to 2017

In January 2017, an increase in reported Salmonellaenterica serotype Bovismorbificans cases in the Netherlands was observed since October 2016. We implemented a case-control study to identify the source, including all cases after December 2016. Adjusted odds ratios were calculated using logistic regression analysis. We traced back the distribution chain of suspected food items and sampled them for microbiological analysis. Human and food isolates were sequenced using whole genome sequencing (WGS). From October 2016 to March 2017, 54 S. Bovismorbificans cases were identified. Sequencing indicated that all were infected with identical strains. Twenty-four cases and 37 controls participated in the study. Cases were more likely to have consumed ham products than controls (aOR = 13; 95% CI: 2.0-77) and to have shopped at a supermarket chain (aOR = 7; 95% CI: 1.3-38). Trace-back investigations led to a Belgian meat processor: one retail ham sample originating from this processor tested positive for S. Bovismorbificans and matched the outbreak strain by WGS. All ham products related to the same batch were removed from the market to prevent further cases. This investigation illustrates the importance of laboratory surveillance for all Salmonella serotypes and the usefulness of WGS in an outbreak investigation.

Evaluation of molecular typing of foodborne pathogens in European reference laboratories from 2012 to 2013

In 2012, the European Centre for Disease Prevention and Control (ECDC) initiated external quality assessment (EQA) schemes for molecular typing including the National Public Health Reference Laboratories in Europe. The overall aim for these EQA schemes was to enhance the European surveillance of food-borne pathogens by evaluating and improving the quality and comparability of molecular typing. The EQAs were organised by Statens Serum Institut (SSI) and included Salmonella enterica subsp. enterica, verocytotoxin-producing Escherichia coli (VTEC) and Listeria monocytogenes. Inter-laboratory comparable pulsed-field gel electrophoresis (PFGE) images were obtained from 10 of 17 of the participating laboratories for Listeria, 15 of 25 for Salmonella, but only nine of 20 for VTEC. Most problems were related to PFGE running conditions and/or incorrect use of image acquisition. Analysis of the gels was done in good accordance with the provided guidelines. Furthermore, we assessed the multilocus variable-number tandem repeat analysis (MLVA) scheme for S. Typhimurium. Of 15 laboratories, nine submitted correct results for all analysed strains, and four had difficulties with one strain only. In conclusion, both PFGE and MLVA are prone to variation in quality, and there is therefore a continuous need for standardisation and validation of laboratory performance for molecular typing methods of food-borne pathogens in the human public health sector.

Genomic characterisation of invasive non-typhoidal Salmonella enterica Subspecies enterica Serovar Bovismorbificans isolates from Malawi

Background

Invasive Non-typhoidal Salmonella (iNTS) are an important cause of bacteraemia in children and HIV-infected adults in sub-Saharan Africa. Previous research has shown that iNTS strains exhibit a pattern of gene loss that resembles that of host adapted serovars such as Salmonella Typhi and Paratyphi A. Salmonella enterica serovar Bovismorbificans was a common serovar in Malawi between 1997 and 2004.

Methodology

We sequenced the genomes of 14 Malawian bacteraemia and four veterinary isolates from the UK, to identify genomic variations and signs of host adaptation in the Malawian strains.

Principal Findings

Whole genome phylogeny of invasive and veterinary S. Bovismorbificans isolates showed that the isolates are highly related, belonging to the most common international S. Bovismorbificans Sequence Type, ST142, in contrast to the findings for S. Typhimurium, where a distinct Sequence Type, ST313, is associated with invasive disease in sub-Saharan Africa. Although genome degradation through pseudogene formation was observed in ST142 isolates, there were no clear overlaps with the patterns of gene loss seen in iNTS ST313 isolates previously described from Malawi, and no clear distinction between S. Bovismorbificans isolates from Malawi and the UK.

The only defining differences between S. Bovismorbificans bacteraemia and veterinary isolates were prophage-related regions and the carriage of a S. Bovismorbificans virulence plasmid (pVIRBov).

Conclusions

iNTS S. Bovismorbificans isolates, unlike iNTS S. Typhiumrium isolates, are only distinguished from those circulating elsewhere by differences in the mobile genome. It is likely that these strains have entered a susceptible population and are able to take advantage of this niche. There are tentative signs of convergent evolution to a more human adapted iNTS variant. Considering its importance in causing disease in this region, S. Bovismorbificans may be at the beginning of this process, providing a reference against which to compare changes that may become fixed in future lineages in sub-Saharan Africa.

Bacteraemia and meningitis caused by non-typhoidal Salmonella (including serovars Typhimurium, Enteritidis and Bovismorbificans) are a serious health issue in sub-Saharan Africa, particularly in young children and HIV-infected adults. Previous work has indicated that a distinct S. Typhimurium sequence type, ST313, has evolved and spread in these countries, and may be more human-adapted than isolates found in the developed world. We therefore investigated the genomes of Salmonella enterica serovar Bovismorbificans bacteraemia isolates from Malawi and compared them to genomes of veterinary S. Bovismorbificans isolates from the UK using Next Generation Sequencing Technology and subsequent genomic comparisons to establish if there is a genetic basis for this increase in invasive disease observed among African NTS. Contrary to the previous findings for S. Typhimurium, where a distinct ST is found only in sub-Saharan Africa, we discovered that the S. Bovismorbificans isolates from Malawi belong to the most common ST of the serovar and the genome is highly conserved across all sequenced isolates. The major differences between UK veterinary and African human isolates were due to prophage regions inserted into the genomes of African isolates, coupled with a higher prevalence of a virulence plasmid compared to the UK isolates.

Interrelationships of food safety and plant pathology: the life cycle of human pathogens on plants

Bacterial food-borne pathogens use plants as vectors between animal hosts, all the while following the life cycle script of plant-associated bacteria. Similar to phytobacteria, Salmonella, pathogenic Escherichia coli, and cross-domain pathogens have a foothold in agricultural production areas. The commonality of environmental contamination translates to contact with plants. Because of the chronic absence of kill steps against human pathogens for fresh produce, arrival on plants leads to persistence and the risk of human illness. Significant research progress is revealing mechanisms used by human pathogens to colonize plants and important biological interactions between and among bacteria in planta. These findings articulate the difficulty of eliminating or reducing the pathogen from plants. The plant itself may be an untapped key to clean produce. This review highlights the life of human pathogens outside an animal host, focusing on the role of plants, and illustrates areas that are ripe for future investigation.

Oral priming with Salmonella Typhi vaccine strain CVD 909 followed by parenteral boost with the S. Typhi Vi capsular polysaccharide vaccine induces CD27+IgD-S. Typhi-specific IgA and IgG B memory cells in humans

Attenuated live oral typhoid vaccine candidate CVD 909 constitutively expresses Salmonella Typhi capsular polysaccharide antigen (Vi). A randomized, double-blind, heterologous prime-boost clinical study was conducted to determine whether immunity to licensed parenteral Vi vaccine could be enhanced by priming with CVD 909. Priming with CVD 909 elicited higher and persistent, albeit not significant, anti-Vi IgG and IgA following immunization with Vi, than placebo-primed recipients. Vi-specific IgA B memory (B(M)) cells were significantly increased in CVD 909-primed subjects. S. Typhi-specific LPS and flagella IgA B(M) cells were observed in subjects immunized with CVD 909 or with the licensed Vi-negative oral typhoid vaccine Ty21a. CVD 909-induced B(M) cells exhibited a classical B(M) phenotype (i.e., CD3(-)CD19(+)IgD(-)CD27(+)). This is the first demonstration of classical B(M) cells specific for bacterial polysaccharide or protein antigens following typhoid immunization. The persistent IgA B(M) responses demonstrate the capacity of oral typhoid vaccines to prime mucosally relevant immune memory.

Molecular and pathogenic characterization of Salmonella enterica serovar Bovismorbificans strains of animal, environmental, food, and human origin in Hungary

In this study, we characterized 110 strains of Salmonella enterica serovar Bovismorbificans contaminating environment, animals, food of animal origin, and human, to assess their significance along the food chain in Hungary. Additionally, five strains from Germany were tested for comparative purposes. Characterization involved antibiotic susceptibility testing, class 1 integron detection by polymerase chain reaction, plasmid profiling, virulotyping (using virulence gene-specific polymerase chain reactions), and pulsed-field gel electrophoresis. Pathogenic potential of selected strains was tested in orally infected 1-day-old specific pathogen-free chicks. Eighty-two percent of the strains were susceptible to the 16 antibiotics tested, and none of them had class 1 integron. A multidrug-resistant human isolate harbored a bla(SHV5)-type extended-spectrum beta-lactamase gene, first reported in this serotype. All the strains possessed avrA, ssaQ, mgtC, spi4, and sopB genes indicating the presence of Salmonella pathogenicity islands 1-5, respectively, missed the phage-related genes sopE and gipA, but retained the phage-related gene sodC1. An approximately 90 kb large plasmid was characteristic to 80% of the strains, all of which carried the spvC gene. In vivo colonization testing of four selected strains in 1-day-old chicks resulted in significantly reduced liver and spleen colonization ability as compared with the Salmonella Enteritidis control strain, whereas their caecal colonization ability differed less from that of Salmonella Enteritidis. Pulsed-field gel electrophoresis data revealed the dominance of two pulsotypes (C2 and C5) without any specific temporal, geographical, and/or source-related linkages. The results show that Salmonella Bovismorbificans studied here are less invasive than Salmonella Enteritidis, but they may colonize and persist in several animal species and successfully contaminate meat products of different animal origin in Hungary.

Antimicrobial drug resistance and molecular characterization of Salmonella isolated from domestic animals, humans, and meat products

OBJECTIVES

1) To characterize and determine genotypic relatedness of Salmonella serovars commonly isolated from domestic animals and humans in North Dakota, and 2) to assess their role in transferring antimicrobial resistance (AMR) to humans.

MATERIALS AND METHODS

A total of 434 Salmonella isolates obtained from 1) feces of apparently healthy feedlot, range, and dairy cattle in North Dakota; 2) clinical samples from sick or dead animals submitted to North Dakota State University-Veterinary Diagnostic Laboratory (2000-2005); 3) previous meat product surveillance studies in North Dakota; and 4) 179 samples from human patients in North Dakota (2000-2005) by the North Dakota Department of Health were studied. The isolates were initially serotyped and later genotyped by pulsed-field gel electrophoresis (PFGE) to investigate their relatedness. The National Antimicrobial Resistance Monitoring Systems panel was used to compare AMR profiles of animal and human isolates to assess a possible role of domestic animals in transfer of AMR to humans.

RESULTS

Salmonella Typhimurium was the predominant serotype in both humans (13.4%) and domestic animals (34.3%), followed by Newport in animals (2.6%) and human (3.9%). Salmonella Arizona (0.7%), Salmonella Give (0.9%), and Salmonella Muenster (3.5%) were isolated from sick or dead animals. PFGE results confirmed occurrence of similar Salmonella genotypes in both domestic animals and humans. AMR profiles showed that most animal strains were multidrug resistant. A single human isolate had PFGE and multidrug resistance profiles similar to a major cattle genotype, suggesting a possible AMR transmission from cattle to humans. CONCLUSION AND APPLICATION: Similar Salmonella genotypes were infecting domestic animals and humans in North Dakota. The AMR levels were higher in domestic animal isolates than in humans, implying that the occurrence of AMR in animal isolates may not translate directly into AMR in human isolates in North Dakota. This is helpful in determining future policies regarding antimicrobial drug use in domestic animals and humans.

Outbreak of Salmonella Thompson infections linked to imported rucola lettuce

On November 15, 2004, a cluster of three cases of Salmonella Thompson infection was registered by the Norwegian reference laboratory. In the following days further cases occurred, prompting a case-control study among the first 13 cases and 26 matched controls. By December 31, 21 cases had been reported, with the first onset on October 24. Consumption of rucola lettuce (Eruca sativa, also known as rocket salad or arugula) (OR 8,8 [1,2-infinity]) and mixed salad (OR 5,0 [1,0-infinity]) was associated with illness. On November 26, Swedish authorities notified the finding of Salmonella Thompson in rucola lettuce through the EU Rapid Alert System for Food and Feed. Later, several countries reported finding this and other Salmonella serovars and Campylobacter in rucola produced in Italy. In response to our alert through the international Enter-net surveillance network, Sweden and England also reported an increase of cases. Salmonella Thompson isolates from products and patients from several countries showed high similarity by pulsed-field gel electrophoresis, but some isolates showed significant differences. We think that the outbreak in Norway reflected a larger international outbreak caused by rucola imported from one Italian producer. Findings of other pathogens indicate a massive contamination, possibly caused by irrigation with nonpotable water. Rapid international information exchange is invaluable when investigating outbreaks caused by internationally marketed products.

Causes and consequences of plant-associated biofilms

The rhizosphere is the critical interface between plant roots and soil where beneficial and harmful interactions between plants and microorganisms occur. Although microorganisms have historically been studied as planktonic (or free-swimming) cells, most are found attached to surfaces, in multicellular assemblies known as biofilms. When found in association with plants, certain bacteria such as plant growth promoting rhizobacteria not only induce plant growth but also protect plants from soil-borne pathogens in a process known as biocontrol. Contrastingly, other rhizobacteria in a biofilm matrix may cause pathogenesis in plants. Although research suggests that biofilm formation on plants is associated with biological control and pathogenic response, little is known about how plants regulate this association. Here, we assess the biological importance of biofilm association on plants.

Linking healthcare associated norovirus outbreaks: a molecular epidemiologic method for investigating transmission

BACKGROUND

Noroviruses are highly infectious pathogens that cause gastroenteritis in the community and in semi-closed institutions such as hospitals. During outbreaks, multiple units within a hospital are often affected, and a major question for control programs is: are the affected units part of the same outbreak or are they unrelated transmission events? In practice, investigators often assume a transmission link based on epidemiological observations, rather than a systematic approach to tracing transmission.Here, we present a combined molecular and statistical method for assessing:1) whether observed clusters provide evidence of local transmission and2) the probability that anecdotally|linked outbreaks truly shared a transmission event.

METHODS

76 healthcare associated outbreaks were observed in an active and prospective surveillance scheme of 15 hospitals in the county of Avon, England from April 2002 to March 2003. Viral RNA from 64 out of 76 specimens from distinct outbreaks was amplified by reverse transcription-PCR and was sequenced in the polymerase (ORF 1) and capsid (ORF 2) regions. The genetic diversity, at the nucleotide level, was analysed in relation to the epidemiological patterns.

RESULTS

Two out of four genetic and epidemiological clusters of outbreaks were unlikely to have occurred by chance alone, thus suggesting local transmission. There was anecdotal epidemiological evidence of a transmission link among 5 outbreaks pairs. By combining this epidemiological observation with viral sequence data, the evidence of a link remained convincing in 3 of these pairs. These results are sensitive to prior beliefs of the strength of epidemiological evidence especially when the outbreak strains are common in the background population.

CONCLUSION

The evidence suggests that transmission between hospitals units does occur. Using the proposed criteria, certain hypothesized transmission links between outbreaks were supported while others were refuted. The combined molecular/epidemiologic approach presented here could be applied to other viral populations and potentially to other pathogens for a more thorough view of transmission.

Comparison of primers for the detection of pathogenic Escherichia coli using real-time PCR

AIMS

To evaluate PCR primers for the detection of pathogenic Escherichia coli in a real-time PCR assay and determine their utility in produce irrigation water testing.

METHODS AND RESULTS

Three previously published PCR primer sets and one set designed for this study were tested for their ability to produce amplification products for several pathogenic E. coli serotypes from whole cells as template. Two of the previously published primer sets were chosen for real-time PCR detection limit determination. The coneaeA and PEH detection limit of E. coli O157:H7 was 10(0) and 10(1) CFU rxn(-1) in sterile water respectively. To detect E. coli O157:H7 in sprout irrigation water, the water required dilution due to PCR inhibitors. The detection limit of the coneaeA and PEH was 10(1) and between 10(2) and 10(3) CFU rxn(-1) in diluted sprout irrigation water respectively.

CONCLUSIONS

The primer set coneaeA was able to produce an amplification product from each E. coli serotype, except O128:H7 and most sensitive for real-time PCR detection of pathogenic E. coli in diluted sprout irrigation water.

SIGNIFICANCE AND IMPACT OF THE STUDY

The necessity of a dissociation analysis to distinguish positive samples from those with fluorescence of random dsDNA generation for real-time PCR in a complex background was established.

Characterization of the binding of diarrheagenic strains of E. coli to plant surfaces and the role of curli in the interaction of the bacteria with alfalfa sprouts

Diarrheagenic Escherichia coli were able to bind to plant surfaces, including alfalfa sprouts and open seed coats, and tomato and Arabidopsis thaliana seedlings incubated in water. The characteristics of the binding differed with the bacterial strain examined. Laboratory K12 strains of E. coli failed to show significant binding to any of the plant surfaces examined, suggesting that some of the genes present and expressed in pathogenic strains and absent or unexpressed in K12 strains may be required for binding to plants. When a plasmid carrying the mlrA gene (a positive regulator of curli biosynthesis) or a plasmid carrying the operons that encode the synthesis of curli (csgA-G) was introduced into K12 strains, the bacteria acquired the ability to bind to sprouts. CsgA mutants of an avian pathogenic E. coli and an O157:H7 strain showed no reduction in their ability to bind to sprouts. Thus, the production of curli appears to be sufficient to allow K12 strains to bind, but curli are not necessary for the binding of pathogenic strains, suggesting that pathogenic strains may have more than one mechanism for binding to plant surfaces.

Monte Carlo simulation of pathogen behavior during the sprout production process

Food-borne disease outbreaks linked to the consumption of raw sprouts have become a concern over the past decade. A Monte Carlo simulation model of the sprout production process was created to determine the most-effective points for pathogen control. Published literature was reviewed, and relevant data were compiled. Appropriate statistical distributions were determined and used to create the Monte Carlo model with Analytica software. Factors modeled included initial pathogen concentration and prevalence, seed disinfection effectiveness, and sampling of seeds prior to sprouting, sampling of irrigation water, or sampling of the finished product. Pathogen concentration and uniformity of seed contamination had a large effect on the fraction of contaminated batches predicted by the simulation. The model predicted that sprout sampling and irrigation water sampling at the end of the sprouting process would be more effective in pathogen detection than seed sampling prior to production. Day of sampling and type of sample (sprout or water) taken had a minimal effect on rate of detection. Seed disinfection reduced the proportion of contaminated batches, but in some cases it also reduced the ability to detect the pathogen when it was present, because cell numbers were reduced below the detection limit. Both the amount sampled and the pathogen detection limit were shown to be important variables in determining sampling effectiveness. This simulation can also be used to guide further research and compare the levels of effectiveness of different risk reduction strategies.

Application of molecular genetic methods in diagnostics and epidemiology of food-borne bacterial pathogens

Salmonella enterica, Campylobacter and Yersinia species, Shiga toxin-producing Escherichia coli (STEC), Listeria monocytogenes and Clostridium perfringens are the bacterial pathogens constituting the greatest burden of food-borne disease in Finland. Several molecular genetic methods have been applied to diagnose, discriminate and survey these bacteria. PCR, PCR-RFLP and PFGE are the most widely and successfully used. However, these methods are unable to replace conventional and internationally standardised phenotyping. Electronic database libraries of the different genomic profiles will enable continuous surveillance of infections and detection of possible infection clusters at an early stage. Furthermore, whole-genome sequence data have opened up new insights into epidemiological surveillance. Laboratory-based surveillance performed in a timely manner and exploiting adequate methods, and co-operation at local, national and international levels are among the key elements in preventing food-borne diseases. This paper reviews different applications of molecular genetic methods for investigating enteric bacterial pathogens and gives examples of the methods successfully used in diagnostics and epidemiological studies in Finland.

Molecular epidemiologic surveillance of salmonellosis in Arkansas

OBJECTIVES

Salmonella serotype Newport and Salmonella serotype Typhimurium are the most commonly identified serotypes of Salmonella causing human disease in the state of Arkansas. The purpose of our study was to compare the results of standard and molecular epidemiologic methods of investigating human salmonellosis cases due to Salmonella serotype Newport and Salmonella serotype Typhimurium.

METHODS

All isolates of Salmonella serotype Newport and Salmonella serotype Typhimurium collected and submitted to the Arkansas Department of Health between July 1, 1997 and June 30, 1998 were gathered and underwent pulsed-field gel electrophoresis (PFGE). Patients from whom the isolates were collected were contacted and completed a questionnaire.

RESULTS

There were 84 patients from whom Salmonella serotype Newport was isolated and 83 from whom Salmonella serotype Typhimurium was isolated during the study period. In the 124 patients (74%) who completed the questionnaire, Salmonella serotype Newport was more likely to be the infecting agent in younger, white, and pet-owning patients (P < 0.05). The use of PFGE confirmed that approximately 20% of the organisms had genetic fingerprint patterns identical to those of at least one other individual in the state. One third of the patients from whom these isolates were obtained were linked by standard epidemiologic methods.

CONCLUSIONS

The use of PFGE on our state's most common isolates provides additional confirmation that despite being linked by time of onset and location of residence, the majority of the human salmonellosis cases in our region are still sporadic. Low-level, intermittent transmission of these organisms through environmental contamination and contact with asymptomatically infected individuals would be likely vehicles of transmission in our state. Molecular techniques are important in surveillance systems that investigate human salmonellosis. Eighty-one percent of the Salmonella serotype Newport and 92% of the Salmonella serotype Typhimurium cases that appeared to be outbreak-related based upon time of onset and location were actually found not to be outbreak-related by PFGE. Using techniques such as PFGE will allow for more focused evaluations of potential outbreaks and will save the already limited financial and human resources that would otherwise be spent on investigations that are not warranted.

Analysis of published sprout seed sanitization studies shows treatments are highly variable

Consumption of raw sprouts has caused many foodborne illness outbreaks in the last decade, and most outbreaks have been linked to contaminated seeds. Many seed sanitization treatments have been studied as a means to reduce the risk of illness associated with sprouts. Published data on seed sanitization were analyzed collectively to identify factors that influenced the efficacy of seed sanitization and to determine the variability associated with various sanitization processes. Temperature and duration of the sanitization treatment were found to produce a negligible effect on log microbial reductions. Salmonella, Escherichia coli O157:H7, and total aerobic microorganisms were all inactivated at similar rates. Data were fit to triangular or uniform distributions for 16 different chemical treatments. Among the most effective treatments were 8% hydrogen peroxide (uniform distribution [2.5, 4.5]), 20,000 ppm of chlorine (triangular distribution [1, 2.5, 6.5]), and 1% Ca(OH)2 (triangular distribution [0.5, 4, 5]). Chemical treatments where more published data were available showed more variability.

A Bayesian approach to quantify the contribution of animal-food sources to human salmonellosis

Based on the data from the integrated Danish Salmonella surveillance in 1999, we developed a mathematical model for quantifying the contribution of each of the major animal-food sources to human salmonellosis. The model was set up to calculate the number of domestic and sporadic cases caused by different Salmonella sero and phage types as a function of the prevalence of these Salmonella types in the animal-food sources and the amount of food source consumed. A multiparameter prior accounting for the presumed but unknown differences between serotypes and food sources with respect to causing human salmonellosis was also included. The joint posterior distribution was estimated by fitting the model to the reported number of domestic and sporadic cases per Salmonella type in a Bayesian framework using Markov Chain Monte Carlo simulation. The number of domestic and sporadic cases was obtained by subtracting the estimated number of travel- and outbreak-associated cases from the total number of reported cases, i.e., the observed data. The most important food sources were found to be table eggs and domestically produced pork comprising 47.1% (95% credibility interval, CI: 43.3-50.8%) and 9% (95% CI: 7.8-10.4%) of the cases, respectively. Taken together, imported foods were estimated to account for 11.8% (95% CI: 5.0-19.0%) of the cases. Other food sources considered had only a minor impact, whereas 25% of the cases could not be associated with any source. This approach of quantifying the contribution of the various sources to human salmonellosis has proved to be a valuable tool in risk management in Denmark and provides an example of how to integrate quantitative risk assessment and zoonotic disease surveillance.

Growth dynamics of Salmonella enterica strains on alfalfa sprouts and in waste seed irrigation water

Alfalfa sprouts and other seed sprouts have been implicated in numerous outbreaks of salmonellosis. The source of these epidemics appears to have been low-level contamination of seeds by Salmonella bacteria that developed into clinically significant populations during the seed germination process. To test the possibility that Salmonella enterica strains carry host range determinants that allow them to grow on alfalfa, strains isolated from alfalfa or other sources were surveyed for their ability to grow on germinating alfalfa seeds. An S. enterica serovar Cubana strain originally isolated from contaminated alfalfa sprouts multiplied most rapidly during the initial 24 h of the seed germination process. Germinating alfalfa seeds supported the multiplication of S. enterica cells prior to the emergence of the root radicle at 72 h. Thereafter, much lower rates of multiplication were apparent. The ability of S. enterica to grow on germinating alfalfa seeds was independent of the serovar, isolation source, or virulence of the strain. Isolates obtained from alfalfa attained population levels similar to those observed for strains isolated from contaminated meat products or stools. Each of the strains could be detected in the waste irrigation water, with populations being strongly correlated with those detected on the germinating alfalfa seeds. The S. enterica strains were capable of utilizing the waste irrigation water as a sole carbon and nitrogen source. S. enterica strains thus appear to grow saprophytically on soluble organics released from seeds during early phases of germination. The ability to detect S. enterica in the waste irrigation water early in the germination process indicates that this method may be used as a simple way to monitor the contamination of sprouts during commercial operations.

Differences in attachment of Salmonella enterica serovars and Escherichia coli O157:H7 to alfalfa sprouts

Numerous Salmonella enterica and Escherichia coli O157:H7 outbreaks have been associated with contaminated sprouts. We examined how S. enterica serovars, E. coli serotypes, and nonpathogenic bacteria isolated from alfalfa sprouts grow on and adhere to alfalfa sprouts. Growth on and adherence to sprouts were not significantly different among different serovars of S. enterica, but all S. enterica serovars grew on and adhered to alfalfa sprouts significantly better than E. coli O157:H7. E. coli O157:H7 was essentially rinsed from alfalfa sprouts with repeated washing steps, while 1 to 2 log CFU of S. enterica remained attached per sprout. S. enterica Newport adhered to 3-day-old sprouts as well as Pantoea agglomerans and 10-fold more than Pseudomonas putida and Rahnella aquatilis, whereas the growth rates of all four strains throughout seed sprouting were similar. S. enterica Newport and plant-associated bacteria adhered 10- to 1,000-fold more than E. coli O157:H7; however, three of four other E. coli serotypes, isolated from cabbage roots exposed to sewage water following a spill, adhered to sprouts better than E. coli O157:H7 and as well as the Pseudomonas and Rahnella strains. Therefore, attachment to alfalfa sprouts among E. coli serotypes is variable, and nonpathogenic strains of E. coli to be used as surrogates for the study of pathogenic E. coli may be difficult to identify and should be selected carefully, with knowledge of the biology being examined.

Combined effects of water activity, temperature and chemical treatments on the survival of Salmonella and Escherichia coli O157:H7 on alfalfa seeds

AIMS

The objective of this study was to determine the combined effects of water activity (a(w)), chemical treatment and temperature on Salmonella and Escherichia coli O157:H7 inoculated onto alfalfa seeds.

METHODS AND RESULTS

Alfalfa seeds inoculated with Salmonella or E. coli O157:H7 and adjusted to various a(w) values were subjected to simultaneous and separate treatments with chemicals and heat. The rate of death of both pathogens was correlated with increased a(w) (0.15-0.60) and temperature (5-37 degrees C) over a 52-week storage period. Higher seed a(w) enhanced the inactivation of pathogens on seeds heated at 50-70 degrees C for up to 24 h. Treatment of seeds with water, 1% Ca(OH)2, 1% Tween 80, 1% Ca(OH)2 plus 1% Tween 80 or 40 mg l(-1) Tsunami 200 at 23 or 55 degrees C for 2 min significantly (alpha=0.05) reduced populations of Salmonella and E. coli O157:H7.

CONCLUSIONS

Overall, at the combinations of temperature and concentrations of chemicals tested, 1% Ca(OH)2 was most effective in killing Salmonella and E. coli O157:H7 without reducing seed viability.

SIGNIFICANCE AND IMPACT OF THE STUDY

None of the treatments evaluated in this study, whether applied separately or in combination, eliminated Salmonella or E. coli O157:H7 on alfalfa seeds without sacrificing the viability of the seeds. It remains essential that practices to prevent the contamination of alfalfa seeds be strictly followed in order to minimize the risk of Salmonella and E. coli O157:H7 infections associated with sprouts produced from these seeds.

Differences in growth of Salmonella enterica and Escherichia coli O157:H7 on alfalfa sprouts

Sprout producers have recently been faced with several Salmonella enterica and Escherichia coli O157:H7 outbreaks. Many of the outbreaks have been traced to sprout seeds contaminated with low levels of human pathogens. Alfalfa seeds were inoculated with S. enterica and E. coli O157:H7 strains isolated from alfalfa seeds or other environmental sources and sprouted to examine growth of these human pathogens in association with sprouting seeds. S. enterica strains grew an average of 3.7 log(10) on sprouting seeds over 2 days, while E. coli O157:H7 strains grew significantly less, an average of 2.3 log(10). The initial S. enterica or E. coli O157:H7 inoculum dose and seed-sprouting temperature significantly affected the levels of both S. enterica and E. coli O157:H7 on the sprouts and in the irrigation water, while the frequency of irrigation water replacement affected only the levels of E. coli O157:H7. Colonization of sprouting alfalfa seeds by S. enterica serovar Newport and E. coli O157:H7 strains transformed with a plasmid encoding the green fluorescent protein was examined with fluorescence microscopy. Salmonella serovar Newport colonized both seed coats and sprout roots as aggregates, while E. coli O157:H7 colonized only sprout roots.

Salmonella serotypes isolated from nonhuman sources in São Paulo, Brazil, from 1996 through 2000

A total of 4,581 Salmonella strains isolated from nonhuman sources, including foodstuffs associated with foodborne Salmonella outbreaks, from January 1996 through December 2000 were serotyped at the Enteropathogens Laboratory, Instituto Adolfo Lutz, São Paulo, Brazil. Among the 123 different serotypes identified, Salmonella enterica subsp. enterica serotype Enteritidis (Salmonella Enteritidis) was the most prevalent (32.7%), ranking first for almost every kind of source. The next most common serotypes were Salmonella Senftenberg (10.3%), Salmonella Hadar (6.8%), Salmonella Agona (5.1%), and Salmonella Typhimurium (2.4%). Rough strains belonging to the subspecies S. enterica subsp. enterica (4.8%), S. enterica subsp. arizonae (<1%), S. enterica subsp. diarizonae (<1%), and S. enterica subsp. houtenae (<1%) were also detected. Foodstuffs (including poultry meat for consumption) contained 38.1% of the studied Salmonella strains, poultry flocks (from several farms under salmonellosis control by the owners) contained 21.7%, the environment contained 10.6%, sewage contained 9.4%, water contained 6.6%, animal feed contained 4.4%, chill water from poultry-processing operations contained 2.2%, and other sources contained 7.0%. Foodstuffs extensively contaminated with Salmonella strains were poultry meat (40%), cow meat (11%), desserts (8%), mayonnaise (6%), sausage (5%), and unpasteurized shell eggs (4%), and there were several other food sources (26%). Homemade mayonnaise was the most common vehicle for Salmonella foodborne outbreaks, and Salmonella Enteritidis was the serotype most isolated (95%) from that source. According to these data and previously published data concerning Salmonella strains isolated in São Paulo State, almost the same serotypes have predominated among nonhuman sources for the last decade.

Foodborne outbreaks in Canada linked to produce

Examples of foodborne outbreaks traced to fresh fruits and vegetables can be found worldwide. The quantity of produce eaten per capita has been increasing steadily over the past two decades, creating a heightened potential for produce-related foodborne disease. A number of outbreaks identified during this time period were reviewed, with particular emphasis placed on incidents that have occurred in Canada. The collective information highlights the diversity of infectious agents and produce items involved, with a view to the prevention of fresh produce-related foodborne disease in the future.

Multistate outbreak of Salmonella serovar Muenchen infections associated with alfalfa sprouts grown from seeds pretreated with calcium hypochlorite

During September 1999, a multistate outbreak of Salmonella serovar Muenchen infection associated with eating raw alfalfa sprouts was identified in Wisconsin. Despite use of a calcium hypochlorite sanitizing procedure to pretreat seeds before sprouting, at least 157 outbreak-related illnesses were identified in seven states having sprouters who received alfalfa seed from a specific lot. The continued occurrence of sprout-related outbreaks despite presprouting disinfection supports the concern that no available treatment will eliminate pathogens from seeds before sprouting and reinforces the need for additional safeguards to protect the public. A lack of consumer knowledge regarding exposure to sprouts documented in this investigation suggests that more-targeted outreach to high-risk individuals may be needed to reduce their risk.

Wrinkled alfalfa seeds harbor more aerobic bacteria and are more difficult to sanitize than smooth seeds

At least 14 separate outbreaks of food poisoning attributed to either Salmonella enterica or Escherichia coli O157:H7 have been traced to sprouts in the past decade. Seeds contaminated with human pathogens caused most of these outbreaks, thus many sprout growers are now treating alfalfa seeds with the sanitizing agent, calcium hypochlorite (Ca[OCl]2), prior to sprouting. The efficacy of alfalfa seed sanitation varies between seed lots and between seeds within each lot. Alfalfa seeds from different seed lots were sorted by type in an effort to determine if certain seed types carry more aerobic bacteria than other seed types. Seeds with a wrinkled type, characteristic of lygus bug damage, had significantly higher levels of culturable aerobic bacteria and were more difficult to sanitize than smooth, healthy seeds. After sanitation, wrinkled alfalfa seeds that had been inoculated with S. enterica ser. Newport carried significantly higher levels of Salmonella Newport than smooth seeds. If S. enterica is present on wrinkled seeds in naturally contaminated seed lots, it may be difficult to chemically sanitize the seed lot. Removal of the wrinkled alfalfa seeds from the seed lots, perhaps by adapting color sorting equipment similar to that used to sort rice grains and other seeds, should reduce the level of aerobic bacteria in seed lots and may result in lower levels of human pathogens on contaminated alfalfa seeds.

Molecular epidemiological analysis of Salmonella enterica serotype Derby infections in Hong Kong

OBJECTIVES

We aimed to study the antimicrobial susceptibilities and molecular epidemiology of Salmonella enterica serotype Derby, a unique and common salmonella serotype in Hong Kong.

METHODS

Salmonella Derby strains isolated from stools of patients in a large general hospital in Hong Kong from 1989 to 1994 and from food samples isolated in the Public Health Laboratory were randomly selected and investigated for the antimicrobial susceptibilities by determining the minimal inhibitory concentrations of 19 antimicrobial agents and their relatedness using plasmid analysis, ribotyping, pulsed-field gel electrophoresis (PFGE) and total DNA fingerprinting.

RESULTS

About 50% of the 127 isolates studied were susceptible to all the 19 antibiotics tested, although resistance to tetracycline (49%) and sulfamethoxazole (38%) was high. Only 12% did not harbour any detectable plasmids, while the rest contained plasmids in 51 profiles. There were two predominant clones, one comprising of 35% of isolates that could not be pulsotyped because discrete bands were not discernible after PFGE and another comprising 34% of isolates that could be pulsotyped. The remaining 31% belonged to a variety of types.

CONCLUSIONS

Approximately 70% of S. Derby belonging to two clones were endemic in the community, while the remaining isolates belonged to a variety of types which were probably a result of sporadic infection. The sources of human infections were foods, since most isolates from foods also belonged to the two endemic clones. Typing of S. Derby isolates from other sources such as animals or the environment would help elucidate how foods were contaminated. PFGE might not be universally applicable to all salmonella strains.

Comparison of aqueous chemical treatments to eliminate Salmonella on alfalfa seeds

Several outbreaks of salmonellosis associated with alfalfa sprouts have been documented in the United States since 1995. This study was undertaken to evaluate various chemical treatments for their effectiveness in killing Salmonella on alfalfa seeds. Immersing inoculated seeds in solutions containing 20,000 ppm free chlorine (Ca[OCl]2), 5% Na3PO4, 8% H2O2, 1% Ca(OH)2, 1% calcinated calcium, 5% lactic acid, or 5% citric acid for 10 min resulted in reductions of 2.0 to 3.2 log10 CFU/ g. Treatment with 1,060 ppm Tsunami or Vortex, 1,200 ppm acidified NaClO2, or 5% acetic acid were less effective in reducing Salmonella populations. With the exceptions of 8% H2O2, 1% Ca(OH)2, and 1% calcinated calcium that reduced populations by 3.2, 2.8, and 2.9 log10 CFU/g, respectively, none of treatments reduced the number of Salmonella by more than 2.2 log10 CFU/g without significantly reducing the seed germination percentage. Treatment with 5% acetic, lactic, or citric acids substantially reduced the ability of seeds to germinate. Treatment with 1% Ca(OH)2 in combination with 1% Tween 80, a surfactant, enhanced inactivation by 1.3 log10 CFU/g compared to treatment with 1% Ca(OH)2 alone. Presoaking seeds in water, 0.1% EDTA, 1% Tween 80, or 1% Tween 80 plus 0.1% EDTA for 30 min before treatment with water, 2,000 ppm NaOCl, or 2% lactic acid had a minimal effect on reducing populations of Salmonella. Results indicate that, although several chemical treatments cause reductions in Salmonella populations of up to 3.2 log10 CFU/g initially on alfalfa seeds when analyzed by direct plating, no treatment eliminated the pathogen, as evidenced by detection in enriched samples.

Genotypes of multidrug-resistant Salmonella enterica serotype typhimurium from two regions of Kenya

A combination of phage typing and pulsed-field gel electrophoresis of Xbal-digested chromosomal DNA has been used to study the epidemiological relationships of multidrug-resistant Salmonella enterica serotype typhimurium from Nairobi (64 isolates) and Kilifi (40 isolates) collected over the period 1994-1997. Isolates from Nairobi belonged to 11 definitive phage types (DTs) encompassing eight different PFGE patterns. In contrast, isolates from Kilifi were mainly DT 56 (60%) and all fell into a single PFGE pattern. The remaining isolates did not conform to a recognisable phage type. We conclude that multidrug-resistant S. typhimurium infections from Nairobi were caused by multiple strains while those from Kilifi were likely to be from a microepidemic caused by a single clone.

A variation of the amplified-fragment length polymorphism (AFLP) technique using three restriction endonucleases, and assessment of the enzyme combination BglII-MfeI for AFLP analysis of Salmonella enterica subsp. enterica isolates

We have performed amplified-fragment length polymorphism (AFLP) fingerprinting on a collection of Salmonella enterica subsp. enterica serovar typhimurium strains with a restriction endonuclease combination (BglII and MfeI) that has previously been used successfully for typing Campylobacter jejuni isolates with high resolution. Additionally, a variation of the AFLP assay in which two rare cutting restriction enzymes (XbaI and BsrGI) in combination with the frequent cutter (HinP1I) was examined. The BglII and MfeI enzyme combination offered low resolution for genotyping Salmonella typhimurium isolates and is not recommended for this common serovar. The three-enzyme combination gave a higher discrimination, and is thus a new alternate way of performing AFLP fingerprinting of S. typhimurium.

Incidence of Salmonella in fish and seafood

Field laboratories of the U.S. Food and Drug Administration collected and tested 11,312 import and 768 domestic seafood samples over a 9-year period (1990 to 1998) for the presence of Salmonella. The overall incidence of Salmonella was 7.2% for import and 1.3% for domestic seafood. Nearly 10% of import and 2.8% of domestic raw seafood were positive for Salmonella. The overall incidence of Salmonella in ready-to-eat seafood and shellfish eaten raw was 0.47% for domestic--one shucked oyster and one shark cartilage powder. The incidence in the 2,734 ready-to-eat import seafood was 2.6%--cooked shrimp, shellfish or fish paste, smoked fish, salted/dried fish, and caviar. The incidence in import shellfish consumed raw was 1% in oyster, 3.4% in clams, and 0% in mussels. The incidence in raw, import fish was 12.2%. Distribution of Salmonella in seafood on a regional basis indicated the incidence to be highest in central Pacific and Africa and lowest in Europe/Russia and North America (12% versus 1.6%). Data on a country basis indicated Vietnam to have the highest (30%) and Republic of Korea the lowest (0.7%). While the most frequent serotypes in import seafood were Salmonella Weltevreden (1st), Salmonella Senftenberg (2nd), Salmonella Lexington, and Salmonella Paratyphi-B (3rd, equal numbers for each serotype), the top 20 list included Salmonella enteritidis (5th), Salmonella Newport (6th), Salmonella Thompson (7th), Salmonella typhimurium (12th), and Salmonella anatum (13th), commonly involved in foodborne illness in the United States. Because the incidence in the present study is based on only a small fraction of the seafood imported into the United States, efforts should be directed toward implementation of hazard analysis and critical control points to reduce the incidence of Salmonella in seafood without relying on testing for Salmonella.

Naturally occurring biofilms on alfalfa and other types of sprouts

Scanning electron microscopy was used to examine the cotyledons, hypocotyls, and roots of alfalfa, broccoli, clover, and sunflower sprouts purchased from retail outlets as well as alfalfa sprouts grown in the laboratory using a tray system equipped with automatic irrigation. Biofilms were observed on all plant parts of the four types of commercially grown sprouts. Biofilms were also commonly observed on alfalfa sprouts grown in the laboratory by 2 days of growth. Rod-shaped bacteria of various sizes were predominant on all sprouts examined both as free-living cells and as components of biofilms. Occasionally, cocci-shaped bacteria as well as yeast cells were also present in biofilms. The microbes contained in the biofilms appeared to be attached to each other and to the plant surface by a matrix, most likely composed of bacterial exopolysaccharides. Biofilms were most abundant and of the largest dimensions on cotyledons, sometimes covering close to the entire cotyledon surface (approximately 2 mm in length). Naturally occurring biofilms on sprouts may afford protected colonization sites for human pathogens such as Salmonella and Escherichia coli O157:H7, making their eradication with antimicrobial compounds difficult.

Microbiological safety evaluations and recommendations on sprouted seeds. National Advisory Committee on Microbiological Criteria for Foods

In 1997, the National Advisory Committee on Microbiological Criteria for Foods (NACMCF/the Committee) was asked to review the current literature on sprout-associated outbreaks: identify the organisms and production practices of greatest public health concern: prioritize research needs: and provide recommendations on intervention and prevention strategies. In response to this charge, the Fresh Produce Work Group (FPWG) documented the relevant epidemiology and microbial ecology of sprout-associated outbreaks and reviewed current industry practices and initiatives related to the growing of seed and the production of sprouts. Sprouts have been identified as a special problem because of the potential for pathogen growth during the sprouting process. If pathogens are present on or in the seed, sprouting conditions may favor their proliferation. There is no inherent step in the production of raw sprouts to reduce or eliminate pathogens. Contaminated seed is the likely source for most reported sprout-associated outbreaks. Research has been initiated on methods to reduce or eliminate pathogenic bacteria on seeds and sprouts and some treatments show promise. However, to date, no single treatment has been shown to completely eliminate pathogens under experimental conditions used. Finally, the Committee found that, at the time of the charge, there was a lack of fundamental food safety knowledge along the continuum from seed production through sprout consumption. More recently, many have become aware of the potential for this food to be a vehicle for foodborne illness and the need for appropriate controls: however, such awareness is not universal. Although seed appears to be the most likely source of contamination in sprout associated outbreaks, practices and conditions at the sprouting facility may also impact on the safety of the finished product. In recent sprout-associated outbreak investigations, facilities associated with outbreaks did not consistently apply seed disinfection treatments prior to sprouting. Conversely, facilities that used seed from the same lot as an implicated facility, but had not been associated with reported illnesses, appear to have been consistently using seed disinfection treatments, such as 20,000 ppm calcium hypochlorite, to disinfect seed prior to sprouting. The Committee has developed a number of specific recommendations, including: 1. The knowledge of all interested parties pertaining to the microbiological safety of sprouted seeds must be enhanced; government and industry should develop education programs for seed and sprout producers on basic principles for microbiological food safety, good agricultural practices, good manufacturing practices, and hazard analysis and critical control point (HACCP) systems. 2. Good agricultural practices should be systematically implemented to reduce the potential for microbial contamination of seeds for sprout production. 3. Seed cleaning, storage, and handling practices that minimize the potential for microbial contamination should be developed and implemented. 4. Seeds should be treated with one or more treatments that have been shown to reduce pathogenic bacteria that may be present. Intervention strategies that deliver less than a given reduction (at this time, 5-log) in levels of Salmonella spp. and enterohemorrhagic Escherichia coli O157 should be coupled with a microbiological testing program. 5. Establish good manufacturing practices and food safety systems, including regulatory oversight, microbial testing, adoption of HACCP, and improved traceback, that systematically look for means to prevent seeds from serving as the vehicle for foodborne disease, and 6. Conduct research related to the microbiological safety of sprouted seeds, particularly in the areas of pathogen reduction or elimination, sources of contamination and its prevention, and preventing or retarding pathogen growth during sprouting.

Infections associated with eating seed sprouts: an international concern

Recent outbreaks of Salmonella and Escherichia coli O157:H7 infections associated with raw seed sprouts have occurred in several countries. Subjective evaluations indicate that pathogens can exceed 107 per gram of sprouts produced from inoculated seeds during sprout production without adversely affecting appearance. Treating seeds and sprouts with chlorinated water or other disinfectants fails to eliminate the pathogens. A comprehensive approach based on good manufacturing practices and principles of hazard analysis and critical control points can reduce the risk of sprout-associated disease. Until effective measures to prevent sprout-associated illness are identified, persons who wish to reduce their risk of foodborne illness from raw sprouts are advised not to eat them; in particular, persons at high risk for severe complications of infections with Salmonella or E. coli O157:H7, such as the elderly, children, and those with compromised immune systems, should not eat raw sprouts.