Molecular typing of Salmonella serotypes prevalent in animals in England: assessment of methodology

Antimicrobial resistance and genotypic profiles of Salmonella Saintpaul isolated along beef processing and distribution continuum

Salmonella Saintpaul (SSa) is increasingly reported from food and foodborne outbreak cases. Pulsed field gel electrophoresis (PFGE) is used for screening and tracking of Salmonella infections. Widespread use of antimicrobial agents in humans and food animals could result in antimicrobial resistant Salmonella serotypes. The aim of this study was to characterize S. Saintpaul (n = 28) isolated from various sampling locations at abattoir and meat processing plant lines in Ethiopia for phenotypic antimicrobial resistance and genotypic diversity, and to track its transfer routes. Sampling location, steps and occasions were considered for each isolate description. Antimicrobial sensitivity testing was performed against seven different antimicrobial agents using disc diffusion method. PFGE with XbaI^® enzymatic genomic digestion with BioNumerics^® analysis was used for genotypic diversity. Of all the isolates tested, only 17.9% were pan susceptible, and 82.1% were resistant to at least one and at most to three antimicrobials. All isolates were susceptible to gentamycin, trimethoprim-sulfamethoxazol and trimethoprim. Resistance to oxytetracycline (82.2%) was predominant followed by 3.6% resistance to each of chloramphenicol, neomycin and polymyxin B. PFGE analysis revealed three distinguishable clusters of pulsotypes but the majority of the isolates (25/28) belonged to cluster-I (SSaX1-4) pulsotype. Indistinguishable/similar cluster of (SSaX 1-4) isolates among and between sampling location, steps and occasions were observed. Majorities of S. Saintpaul (88%) in the cluster-I pulsotype were resistant to oxytetracycline. Our study indicated that oxytetracycline resistance is very common among the S. Saintpaul isolates studied; and the isolates were diverse with similar resistance profiles within the same genomic pulsotypes. Transfer of S. Saintpaul within, between and across sampling locations, during the same or different occasion were determined from SSaX 1-4 pulsotype while cluster-II (SSaX5) indicates transfer from abattoir to butchery. The unique isolate in cluster-III (SSaX6) shows the presence of other possible source of S. Saintpaul for the beef chain contamination.

Phenotypic and Genotypic Eligible Methods for Salmonella Typhimurium Source Tracking

Salmonellosis is one of the most common causes of foodborne infection and a leading cause of human gastroenteritis. Throughout the last decade, Salmonella enterica serotype Typhimurium (ST) has shown an increase report with the simultaneous emergence of multidrug-resistant isolates, as phage type DT104. Therefore, to successfully control this microorganism, it is important to attribute salmonellosis to the exact source. Studies of Salmonella source attribution have been performed to determine the main food/food-production animals involved, toward which, control efforts should be correctly directed. Hence, the election of a ST subtyping method depends on the particular problem that efforts must be directed, the resources and the data available. Generally, before choosing a molecular subtyping, phenotyping approaches such as serotyping, phage typing, and antimicrobial resistance profiling are implemented as a screening of an investigation, and the results are computed using frequency-matching models (i.e., Dutch, Hald and Asymmetric Island models). Actually, due to the advancement of molecular tools as PFGE, MLVA, MLST, CRISPR, and WGS more precise results have been obtained, but even with these technologies, there are still gaps to be elucidated. To address this issue, an important question needs to be answered: what are the currently suitable subtyping methods to source attribute ST. This review presents the most frequently applied subtyping methods used to characterize ST, analyses the major available microbial subtyping attribution models and ponders the use of conventional phenotyping methods, as well as, the most applied genotypic tools in the context of their potential applicability to investigates ST source tracking.

Antimicrobial Susceptibility and Molecular Typing of Salmonella Senftenberg Isolated from Humans and Other Sources in Shanghai, China, 2005 to 2011

Salmonella Senftenberg is an important nontyphoidal Salmonella serovar that causes gastrointestinal disease worldwide. In total, 130 Salmonella Senftenberg strains obtained from humans, food, and the environment in Shanghai, People's Republic of China, were characterized for antimicrobial susceptibility and subjected to molecular typing. Our findings indicated that most (96 of 130, 73.8%) of the strains were susceptible to all 13 antimicrobial compounds tested, whereas only two strains (1.5%) were resistant to two antimicrobial compounds. In total, 56 pulsed-field gel electrophoresis profiles were identified, including four main pulsed-field gel electrophoresis profiles (X2, X3, X4, and X5) that showed 95.7% genetic similarity. Our study revealed that the strains of Salmonella Senftenberg from food and the environment shared a high correlation of genetic similarity with those from humans, highlighting the potential links that exist among the strains recovered from different sources in Shanghai.

A novel procedure on next generation sequencing data analysis using text mining algorithm

Background

Next-generation sequencing (NGS) technologies have provided researchers with vast possibilities in various biological and biomedical research areas. Efficient data mining strategies are in high demand for large scale comparative and evolutional studies to be performed on the large amounts of data derived from NGS projects. Topic modeling is an active research field in machine learning and has been mainly used as an analytical tool to structure large textual corpora for data mining.

Methods

We report a novel procedure to analyse NGS data using topic modeling. It consists of four major procedures: NGS data retrieval, preprocessing, topic modeling, and data mining using Latent Dirichlet Allocation (LDA) topic outputs. The NGS data set of the Salmonella enterica strains were used as a case study to show the workflow of this procedure. The perplexity measurement of the topic numbers and the convergence efficiencies of Gibbs sampling were calculated and discussed for achieving the best result from the proposed procedure.

Results

The output topics by LDA algorithms could be treated as features of Salmonella strains to accurately describe the genetic diversity of fliC gene in various serotypes. The results of a two-way hierarchical clustering and data matrix analysis on LDA-derived matrices successfully classified Salmonella serotypes based on the NGS data. The implementation of topic modeling in NGS data analysis procedure provides a new way to elucidate genetic information from NGS data, and identify the gene-phenotype relationships and biomarkers, especially in the era of biological and medical big data.

Conclusion

The implementation of topic modeling in NGS data analysis provides a new way to elucidate genetic information from NGS data, and identify the gene-phenotype relationships and biomarkers, especially in the era of biological and medical big data.

Electronic supplementary material

The online version of this article (doi:10.1186/s12859-016-1075-9) contains supplementary material, which is available to authorized users.

Antibiotic resistance determinants and genetic analysis of Salmonella enterica isolated from food in Morocco

Antimicrobial-resistant non-typhoidal Salmonella (NTS) are an important cause of infection in Africa, but there is a lack of information on their molecular mechanisms of resistance and epidemiology. This study contributes to fill this gap through the characterization by pulsed-field gel electrophoresis (PFGE), multilocus sequence typing (MLST), plasmid profiling and analysis of antibiotic-resistance determinants of 94 Salmonella enterica strains isolated from food in Morocco. PFGE revealed considerable heterogeneity among the strains, showing 32 pulsotypes. MLST of strains representative of the different serovars evidenced 13 sequence types (STs), three of which were newly identified (ST1694, ST1768 and ST1818) and nine not previously reported in Morocco. Thirty-four strains harbored from one to four plasmids, of IncI1 group in S. Mbandaka, IncFIIA in S. Typhimurium, IncL/M in S. Hadar and S. Blockley. For the first time in Morocco an intact Salmonella Genomic Island 1 (SGI1) carrying the resistance genes aadA2, floR, tetG, blaPSE-1 and sul1 was detected in S. Typhimurium DT104. In serovar Hadar resistance to ampicillin, tetracycline and streptomycin was associated to blaTEM-1, tetA and strA genes respectively, whereas one mutation in gyrA (Asp87Asn) and one in parC (Thr54Ser) genes conferred resistance to nalidixic acid. These findings improve the information on foodborne Salmonella in Morocco, evidencing the presence of MDR strains potentially dangerous to humans, and provide useful data for future studies.

TRS-based PCR as a potential tool for inter-serovar discrimination of Salmonella Enteritidis, S. Typhimurium, S. Infantis, S. Virchow, S. Hadar, S. Newport and S. Anatum

Salmonella enterica subsp. enterica comprises a number of serovars, many of which pose an epidemiological threat to humans and are a worldwide cause of morbidity and mortality. Most reported food infection outbreaks involve the serovars Salmonella Enteritidis and Salmonella Typhimurium. Rapid identification to determine the primary sources of the bacterial contamination is important to the improvement of public health. In recent years, many DNA-based techniques have been applied to genotype Salmonella. Herein, we report the use of a manual TRS-PCR approach for the differentiation of the Salmonella enterica subspecies enterica serovars in a single-tube assay. One hundred seventy Salmonella strains were examined in this work. These consisted of serovars S. Enteritidis, S. Typhimurium, S. Infantis, S. Virchow, S. Hadar, S. Newport and S. Anatum. Five of the TRS-primers, N6(GTG)4, N6(CAC)4, N6(CGG)4, N6(CCG)4 and N6(CTG)4, perfectly distinguished the S. Enteritidis and S. Typhimurium serovars, and the N6(GTG)4 primer additionally grouped the other five frequently isolated serovars. In our opinion, the TRS-PCR methodology could be recommended for a quick and simple DNA-based test for inter-serovar discrimination of Salmonella strains.

A composite model for subgroup identification and prediction via bicluster analysis

Background

A major challenges in the analysis of large and complex biomedical data is to develop an approach for 1) identifying distinct subgroups in the sampled populations, 2) characterizing their relationships among subgroups, and 3) developing a prediction model to classify subgroup memberships of new samples by finding a set of predictors. Each subgroup can represent different pathogen serotypes of microorganisms, different tumor subtypes in cancer patients, or different genetic makeups of patients related to treatment response.

Methods

This paper proposes a composite model for subgroup identification and prediction using biclusters. A biclustering technique is first used to identify a set of biclusters from the sampled data. For each bicluster, a subgroup-specific binary classifier is built to determine if a particular sample is either inside or outside the bicluster. A composite model, which consists of all binary classifiers, is constructed to classify samples into several disjoint subgroups. The proposed composite model neither depends on any specific biclustering algorithm or patterns of biclusters, nor on any classification algorithms.

Results

The composite model was shown to have an overall accuracy of 97.4% for a synthetic dataset consisting of four subgroups. The model was applied to two datasets where the sample’s subgroup memberships were known. The procedure showed 83.7% accuracy in discriminating lung cancer adenocarcinoma and squamous carcinoma subtypes, and was able to identify 5 serotypes and several subtypes with about 94% accuracy in a pathogen dataset.

Conclusion

The composite model presents a novel approach to developing a biclustering-based classification model from unlabeled sampled data. The proposed approach combines unsupervised biclustering and supervised classification techniques to classify samples into disjoint subgroups based on their associated attributes, such as genotypic factors, phenotypic outcomes, efficacy/safety measures, or responses to treatments. The procedure is useful for identification of unknown species or new biomarkers for targeted therapy.

Laboratory monitoring of bacterial gastroenteric pathogens Salmonella and Shigella in Shanghai, China 2006-2012

In 2006 we initiated an enhanced laboratory-based surveillance of Salmonella and Shigella infections in Shanghai, China. A total of 4483 Salmonella and 2226 Shigella isolates were recovered from stool specimens by 2012. In 80 identified Salmonella serovars, Enteritidis (34·5%) and Typhimurium (26·2%) were the most common. Shigella (S.) sonnei accounted for 63·9% of human Shigella infections over the same time period, and replaced S. flexneri to become the primary cause of shigellosis since 2010. Overall, a high level of antimicrobial resistance was observed in Salmonella and Shigella, particularly to nalidixic acid, ampicillin, and tetracycline. Ciprofloxacin resistance was common in Salmonella Typhimurium (21·0%) and S. flexneri (37·6%). The cephalosporin resistance in both pathogens also increased over the years, ranging from 3·4% to 7·0% in Salmonella, and from 10·4% to 28·6% in Shigella. Resistance to multiple antimicrobials was also identified in a large number of the isolates. This study provides insight into the distribution of Salmonella and Shigella in diarrhoeal diseases.

Specific discrimination of three pathogenic Salmonella enterica subsp. enterica serotypes by carB-based oligonucleotide microarray

It is important to rapidly and selectively detect and analyze pathogenic Salmonella enterica subsp. enterica in contaminated food to reduce the morbidity and mortality of Salmonella infection and to guarantee food safety. In the present work, we developed an oligonucleotide microarray containing duplicate specific capture probes based on the carB gene, which encodes the carbamoyl phosphate synthetase large subunit, as a competent biomarker evaluated by genetic analysis to selectively and efficiently detect and discriminate three S. enterica subsp. enterica serotypes: Choleraesuis, Enteritidis, and Typhimurium. Using the developed microarray system, three serotype targets were successfully analyzed in a range as low as 1.6 to 3.1 nM and were specifically discriminated from each other without nonspecific signals. In addition, the constructed microarray did not have cross-reactivity with other common pathogenic bacteria and even enabled the clear discrimination of the target Salmonella serotype from a bacterial mixture. Therefore, these results demonstrated that our novel carB-based oligonucleotide microarray can be used as an effective and specific detection system for S. enterica subsp. enterica serotypes.

Prevalence and counts of Salmonella and enterohemorrhagic Escherichia coli in raw, shelled runner peanuts

Three major outbreaks of salmonellosis linked to consumption of peanut butter during the last 6 years have underscored the need to investigate the potential sources of Salmonella contamination in the production process flow. We conducted a study to determine the prevalence and levels of Salmonella in raw peanuts. Composite samples (1,500 g, n = 8) of raw, shelled runner peanuts representing the crop years 2009, 2010, and 2011 were drawn from 10,162 retained 22-kg lot samples of raw peanuts that were negative for aflatoxin. Subsamples (350 g) were analyzed for the presence of Salmonella and enterohemorrhagic Escherichia coli. Salmonella was found in 68 (0.67%) of 10,162 samples. The highest prevalence rate (P < 0.05) was for 2009 (1.35%) compared with 2010 (0.36%) and 2011 (0.14%). Among four runner peanut market grades (Jumbo, Medium, No. 1, and Splits), Splits had the highest prevalence (1.46%; P < 0.05). There was no difference (P > 0.05) in the prevalence by region (Eastern versus Western). Salmonella counts in positive samples (most-probable-number [MPN] method) averaged 1.05 (range, 0.74 to 5.25) MPN per 350 g. Enterohemorrhagic E. coli was found in only three samples (0.030%). Typing of Salmonella isolates showed that the same strains found in Jumbo and Splits peanuts in 2009 were also isolated from Splits in 2011. Similarly, strains isolated in 2009 were also isolated in 2010 from different peanut grades. These results indicated the persistence of environmental sources throughout the years. For five samples, multiple isolates were obtained from the same sample that had different pulsed-field gel electrophoresis types. This multistrain contamination was primarily observed in Splits peanuts, in which the integrity of the kernel is usually compromised. The information from the study can be used to develop quantitative microbial risk assessments models.

Comparison of five molecular subtyping methods for differentiation of Salmonella Kentucky isolates in Tunisia

Salmonellosis is one of the most common causes of food-borne infection worldwide. In the last decade, Salmonella enterica serovar Kentucky has shown an increase in different parts of the world with the concurrent emergence of multidrug-resistant isolates. These drug-resistant types spread from Africa and the Middle East to Europe and Asia. Although S. Kentucky serovar is of potential human relevance, there is currently no standardized fingerprinting method for it, in Tunisia. In the present study, a collection of 57 Salmonella Kentucky isolates were analyzed using plasmid profiling, pulsed-field gel electrophoresis (PFGE), ribotyping, enterobacterial repetitive intergenic consensus (ERIC) fingerprinting, and Random Amplification of Polymorphic DNA. Plasmid profiling showed a discriminatory index (D) of 0.290, and only 9 out of 57 (16%) isolates carried plasmids, which represents a limitation of this technique. Fingerprinting of genomic DNA by PFGE and ribotyping produced 4 and 5 patterns, respectively. Distinct PFGE patterns (SX1, SX2, SX3, and SX4) were generated for only 28 strains out of 57 (49.1%) with a D value of 0.647. RAPD fingerprinting with primers RAPD1 and RAPD2 produced 4 and 20 patterns, respectively. ERIC fingerprinting revealed 14 different patterns with a high discriminatory index (D) of 0.903. When the methods were combined, the best combination of two methods was ERIC-2 with RAPD2. These results indicates that a single method cannot be relied upon for discriminating between S. Kentucky strains, and a combination of typing methods such ERIC2 and RAPD2 allows further discrimination.

Serovars and antimicrobial resistance of non-typhoidal Salmonella from human patients in Shanghai, China, 2006–2010

We conducted a retrospective study on non-typhoidal Salmonella isolates from patients with diarrhoea in Shanghai, China, 2006–2010. A total of 1484 isolates of 70 Salmonella serovars were recovered from about 18 000 stool specimens. Serovars Enteritidis and Typhimurium were the most prevalent with isolation rates of 27·6% and 25·5%, respectively. The majority (1151, 77·6%) of the isolates were resistant to at least one antimicrobial, and 598 (40·3%) to more than three antimicrobials. Approximately half (50·9%) of the isolates were resistant to nalidixic acid and other resistance rates were sulfisoxazole (47·9%), streptomycin (37·6%), ampicillin (31·3%) and tetracycline (30·5%). Co-resistance to fluoroquinolones and the third- and fourth-generation cephalosporins was also identified.

Longitudinal study of distributions of similar antimicrobial-resistant Salmonella serovars in pigs and their environment in two distinct swine production systems

The aim of this longitudinal study was to determine and compare the prevalences and genotypic profiles of antimicrobial-resistant (AR) Salmonella isolates from pigs reared in antimicrobial-free (ABF) and conventional production systems at farm, at slaughter, and in their environment. We collected 2,889 pig fecal and 2,122 environmental (feed, water, soil, lagoon, truck, and floor swabs) samples from 10 conventional and eight ABF longitudinal cohorts at different stages of production (farrowing, nursery, finishing) and slaughter (postevisceration, postchill, and mesenteric lymph nodes [MLN]). In addition, we collected 1,363 carcass swabs and 205 lairage and truck samples at slaughter. A total of 1,090 Salmonella isolates were recovered from the samples; these were isolated with a significantly higher prevalence in conventionally reared pigs (4.0%; n = 66) and their environment (11.7%; n = 156) than in ABF pigs (0.2%; n = 2) and their environment (0.6%; n = 5) (P < 0.001). Salmonella was isolated from all stages at slaughter, including the postchill step, in the two production systems. Salmonella prevalence was significantly higher in MLN extracted from conventional carcasses than those extracted from ABF carcasses (P < 0.001). We identified a total of 24 different serotypes, with Salmonella enterica serovar Typhimurium, Salmonella enterica serovar Anatum, Salmonella enterica serovar Infantis, and Salmonella enterica serovar Derby being predominant. The highest frequencies of antimicrobial resistance (AR) were exhibited to tetracycline (71%), sulfisoxazole (42%), and streptomycin (17%). Multidrug resistance (resistance to ≥ 3 antimicrobials; MDR) was detected in 27% (n = 254) of the Salmonella isolates from the conventional system. Our study reports a low prevalence of Salmonella in both production systems in pigs on farms, while a higher prevalence was detected among the carcasses at slaughter. The dynamics of Salmonella prevalence in pigs and carcasses were reciprocated in the farm and slaughter environment, clearly indicating an exchange of this pathogen between the pigs and their surroundings. Furthermore, the phenotypic and genotypic fingerprint profile results underscore the potential role played by environmental factors in dissemination of AR Salmonella to pigs.

Meta-analysis of pulsed-field gel electrophoresis fingerprints based on a constructed Salmonella database

A database was constructed consisting of 45,923 Salmonella pulsed-field gel electrophoresis (PFGE) patterns. The patterns, randomly selected from all submissions to CDC PulseNet during 2005 to 2010, included the 20 most frequent serotypes and 12 less frequent serotypes. Meta-analysis was applied to all of the PFGE patterns in the database. In the range of 20 to 1100 kb, serotype Enteritidis averaged the fewest bands at 12 bands and Paratyphi A the most with 19, with most serotypes in the 13−15 range among the 32 serptypes. The 10 most frequent bands for each of the 32 serotypes were sorted and distinguished, and the results were in concordance with those from distance matrix and two-way hierarchical cluster analyses of the patterns in the database. The hierarchical cluster analysis divided the 32 serotypes into three major groups according to dissimilarity measures, and revealed for the first time the similarities among the PFGE patterns of serotype Saintpaul to serotypes Typhimurium, Typhimurium var. 5-, and I 4,[5],12:i:-; of serotype Hadar to serotype Infantis; and of serotype Muenchen to serotype Newport. The results of the meta-analysis indicated that the pattern similarities/dissimilarities determined the serotype discrimination of PFGE method, and that the possible PFGE markers may have utility for serotype identification. The presence of distinct, serotype specific patterns may provide useful information to aid in the distribution of serotypes in the population and potentially reduce the need for laborious analyses, such as traditional serotyping.

Combined genomarkers approach to Salmonella characterization reveals that nucleotide sequence differences in the phase 1 flagellin gene fliC are markers for variation within serotypes

The characterization and tracking of pathogenic micro-organisms in the clinical laboratory and public health environment demand schemes that are easy to standardize and use, are automated and high-throughput, and provide portable data. A combined genomarkers approach for Salmonella enterica based on comparative sequence analysis by mass spectrometry has been developed. The scheme targets genes encoding synthesis and assembly of antigens, metabolic pathway enzymes, virulence factors and fluoroquinolone resistance, covering the essential sequences that distinguish between and identify variation within serotypes. This study demonstrated how this single method could replace the combination of methods currently required to determine serotypes, subtypes, antibiotic resistance profiles and the genomic relatedness of Salmonella isolates. The results revealed genomic variation within seven serotypes previously unreported. This variation can be detected by using nucleotide sequence differences in the Salmonella flagellin gene fliC as markers that are not detected by traditional serotyping methods.

Significance of the bacteriophage treatment schedule in reducing Salmonella colonization of poultry

Salmonella remains the major cause of food-borne diseases worldwide, with chickens known to be the main reservoir for this zoonotic pathogen. Among the many approaches to reducing Salmonella colonization of broilers, bacteriophage offers several advantages. In this study, three bacteriophages (UAB_Phi20, UAB_Phi78, and UAB_Phi87) obtained from our collection that exhibited a broad host range against Salmonella enterica serovar Enteritidis and Salmonella enterica serovar Typhimurium were characterized with respect to morphology, genome size, and restriction patterns. A cocktail composed of the three bacteriophages was more effective in promoting the lysis of S. Enteritidis and S. Typhimurium cultures than any of the three bacteriophages alone. In addition, the cocktail was able to lyse the Salmonella enterica serovars Virchow, Hadar, and Infantis. The effectiveness of the bacteriophage cocktail in reducing the concentration of S. Typhimurium was tested in two animal models using different treatment schedules. In the mouse model, 50% survival was obtained when the cocktail was administered simultaneously with bacterial infection and again at 6, 24, and 30 h postinfection. Likewise, in the White Leghorn chicken specific-pathogen-free (SPF) model, the best results, defined as a reduction of Salmonella concentration in the chicken cecum, were obtained when the bacteriophage cocktail was administered 1 day before or just after bacterial infection and then again on different days postinfection. Our results show that frequent treatment of the chickens with bacteriophage, and especially prior to colonization of the intestinal tract by Salmonella, is required to achieve effective bacterial reduction over time.

Heterogeneity of persistence of Salmonella enterica serotype Senftenberg strains could explain the emergence of this serotype in poultry flocks

Salmonella enterica serotype Senftenberg (S. Senftenberg) has recently become more frequent in poultry flocks. Moreover some strains have been implicated in severe clinical cases. To explain the causes of this emergence in farm animals, 134 S. Senftenberg isolates from hatcheries, poultry farms and human clinical cases were analyzed. Persistent and non-persistent strains were identified in chicks. The non-persistent strains disappeared from ceca a few weeks post inoculation. This lack of persistence could be related to the disappearance of this serotype from poultry farms in the past. In contrast, persistent S. Senftenberg strains induced an intestinal asymptomatic carrier state in chicks similar to S. Enteritidis, but a weaker systemic infection than S. Enteritidis in chicks and mice. An in vitro analysis showed that the low infectivity of S. Senftenberg is in part related to its low capacity to invade enterocytes and thus to translocate the intestinal barrier. The higher capacity of persistent than non-persistent strains to colonize and persist in the ceca of chickens could explain the increased persistence of S. Senftenberg in poultry flocks. This trait might thus present a human health risk as these bacteria could be present in animals before slaughter and during food processing.

Prediction system for rapid identification of Salmonella serotypes based on pulsed-field gel electrophoresis fingerprints

A classification model is presented for rapid identification of Salmonella serotypes based on pulsed-field gel electrophoresis (PFGE) fingerprints. The classification model was developed using random forest and support vector machine algorithms and was then applied to a database of 45,923 PFGE patterns, randomly selected from all submissions to CDC PulseNet from 2005 to 2010. The patterns selected included the top 20 most frequent serotypes and 12 less frequent serotypes from various sources. The prediction accuracies for the 32 serotypes ranged from 68.8% to 99.9%, with an overall accuracy of 96.0% for the random forest classification, and ranged from 67.8% to 100.0%, with an overall accuracy of 96.1% for the support vector machine classification. The prediction system improves reliability and accuracy and provides a new tool for early and fast screening and source tracking of outbreak isolates. It is especially useful to get serotype information before the conventional methods are done. Additionally, this system also works well for isolates that are serotyped as "unknown" by conventional methods, and it is useful for a laboratory where standard serotyping is not available.

Escherichia coli and selected veterinary and zoonotic pathogens isolated from environmental sites in companion animal veterinary hospitals in southern Ontario

Hospital-based infection control in veterinary medicine is emerging and the role of the environment in hospital-acquired infections (HAI) in veterinary hospitals is largely unknown. This study was initiated to determine the recovery of Escherichia coli and selected veterinary and zoonotic pathogens from the environments of 101 community veterinary hospitals. The proportion of hospitals with positive environmental swabs were: E. coli--92%, Clostridium difficile--58%, methicillin-resistant Staphylococcus aureus (MRSA)--9%, CMY-2 producing E. coli--9%, methicillin-resistant Staphylococcus pseudintermedius--7%, and Salmonella--2%. Vancomycin-resistant Enterococcus spp., canine parvovirus, and feline calicivirus were not isolated. Prevalence of antimicrobial resistance in E. coli isolates was low. Important potential veterinary and human pathogens were recovered including Canadian epidemic strains MRSA-2 and MRSA-5, and C. difficile ribotype 027. There is an environmental reservoir of pathogens in veterinary hospitals; therefore, additional studies are required to characterize risk factors associated with HAI in companion animals, including the role of the environment.

Evaluation of pulsed-field gel electrophoresis profiles for identification of Salmonella serotypes

Pulsed-field gel electrophoresis (PFGE) is a standard typing method for isolates from Salmonella outbreaks and epidemiological investigations. Eight hundred sixty-six Salmonella enterica isolates from eight serotypes, including Heidelberg (n = 323), Javiana (n = 200), Typhimurium (n = 163), Newport (n = 93), Enteritidis (n = 45), Dublin (n = 25), Pullorum (n = 9), and Choleraesuis (n = 8), were subjected to PFGE, and their profiles were analyzed by random forest classification and compared to conventional hierarchical cluster analysis to determine potential predictive relationships between PFGE banding patterns and particular serotypes. Cluster analysis displayed only the underlying similarities and relationships of the isolates from the eight serotypes. However, for serotype prediction of a nonserotyped Salmonella isolate from its PFGE pattern, random forest classification provided better accuracy than conventional cluster analysis. Discriminatory DNA band class markers were identified for distinguishing Salmonella serotype Heidelberg, Javiana, Typhimurium, and Newport isolates.

Epidemiology and interaction of Salmonella enterica serovar Derby, Infantis and Typhimurium with porcine alveolar macrophages

In this study we were interested in the serovars which are frequently isolated from pigs, i.e. S. Typhimurium, S. Derby and S. Infantis. First we collected different isolates of S. Infantis and S. Derby and compared them by macrorestriction analysis. In the second part of the study we infected porcine alveolar macrophages (PAMs) with representative strains of these serovars and S. Typhimurium and determined intracellular survival, cytotoxicity and cytokine response. In S. Derby, 17 different profiles in 51 isolates have been identified and in S. Infantis, 12 different profiles in 37 isolates have been identified. Four hours post-addition of bacteria to PAMs, higher numbers of intracellular S. Typhimurium than S. Derby or S. Infantis were observed. However, within next 24h, counts of S. Typhimurium did not change while S. Derby and S. Infantis increased their counts 10 and 5 times, respectively. The apparent inability of S. Typhimurium to multiply inside PAMs was caused by its higher cytotoxicity because PAMs infected with S. Typhimurium released LDH 24h post-infection to a significantly higher level than when infected with the other two serovars. The IL-1β, IL-8, IL-12p40, IL-23p19 and TNFα response to S. Derby and S. Infantis was always higher than to S. Typhimurium and the differences among the serovars were more significant at 4 than 24h post-infection. The lower cytokine signaling but higher cytotoxicity of S. Typhimurium for macrophages correlates with the higher virulence for pigs of this serotype when compared with S. Derby or S. Infantis.

Distribution and genotypic characterization of Salmonella serovars isolated from tropical seafood of Cochin, India

AIMS

To determine the distribution of Salmonella serovars in seafood and to examine the intraserovar genetic variations in Salmonella enterica subsp. enterica serovar Rissen and Salmonella Weltevreden by polymerase chain reaction (PCR)-ribotyping and enterobacterial repetitive intergenic consensus (ERIC)-PCR methods.

METHOD AND RESULTS

A total of 417 seafood samples collected over 2003-2006 from fishing harbours and fish markets of Cochin (India) was studied for presence of Salmonella serovars. Seafood samples were analysed for the presence of Salmonella by Bacteriological Analytical Manual (BAM), U.S. Food & Drug Administration (USFDA) method. The study indicated that 23.2% of the seafood samples were positive for Salmonella and a total of 241 Salmonella isolates comprising of 27 different serovars were isolated from seafood. S. Weltevreden, Salmonella Rissen, Salmonella Typhimurium and Salmonella Derby were found to be the most predominant serovars in seafood. PCR-ribotypes and ERIC-PCR profiles showed multiple genotypic profiles for S. Rissen and S. Weltevreden in seafood and the level of discrimination indices obtained was at 0.974 for S. Rissen and 0.988 for S. Weltevreden, respectively.

CONCLUSION

The study highlighted the major Salmonella serovars in the seafood of Cochin (India) and molecular fingerprinting pattern revealed genetic variation among S. Rissen and S. Weltevreden.

SIGNIFICANCE AND IMPACT OF THE STUDY

Widespread occurrence of Salmonella contamination in seafood and multiple clones of S. Rissen and S. Weltevreden detected in seafood, thus, indicated the diverse routes of Salmonella contamination in seafood.

Salmonella in broiler flocks in the republic of Ireland

In order to obtain an estimation of the prevalence of Salmonella spp. in flocks of broilers in the Republic of Ireland, a study was conducted in 2006 in a total of 362 broiler flocks associated with four integrated companies. Salmonella spp. was isolated from 27.3% of flocks, and eight Salmonella serovars were identified, none of which were Salmonella Enteritidis or Salmonella Typhimurium. The most prevalent serovar was Salmonella Mbandaka, followed by Salmonella Kentucky, which respectively accounted for 61.6% and 27.0% of positive samples. Notable differences were observed among the flocks associated with different integrated companies, both in the Salmonella spp. prevalence and in the serovar distribution. Results from routine official Salmonella testing in broiler production in 2006 showed similar serovar distribution within each integrated company from the associated hatchery and factory samples. In our study, differences in the prevalence of Salmonella at farm level did not correlate with differences in the percentages of positive chicken carcasses officially tested, which were low, for all the four companies investigated. Given the high prevalence of Salmonella Mbandaka, all human isolates obtained in the Republic of Ireland from 2003 to 2006 were compared to a subset of poultry isolates by pulsed-field gel electrophoresis, but an epidemiological link between the animal and the human strains could not be established. Finally the antimicrobial resistance analysis indicated a low proportion of resistant strains among the broiler flock isolates.

Molecular typing of Salmonella enterica serovar Sofia in Australia by pulsed-field gel electrophoresis and repetitive element PCR typing

AIMS

In this study, we used two molecular fingerprinting methods to investigate the genetic and clonal relationship shared by Australian Salmonella Sofia isolates.

METHODS AND RESULTS

A total of 84 Australian Salm. Sofia isolates from various states in Australia were typed using pulsed-field gel electrophoresis (PFGE) (XbaI and SpeI) and repetitive element PCR (REP1R-I primer). The previous problem of DNA degradation of Salm. Sofia strains was solved by modifying the lysis solution used to treat the bacterial plugs, allowing Salm. Sofia to be subtyped using PFGE. Molecular typing of isolates resulted in the generation of eight XbaI, six SpeI and five REP1 pattern profiles. Individual typing methods showed low discrimination index values (<0·5), indicating the poor discriminatory ability of the methods. However, the combination of the typing methods was able to improve the discrimination of isolates, further dividing them into 16 subtypes and raising the index value to 0·721.

CONCLUSIONS

The combination of typing methods was shown to be the best approach to fingerprint Salm. Sofia. The Australian Salm. Sofia isolates only showed limited genetic diversity and probably share a clonal relationship. A majority of the Salm. Sofia isolates were not geographically restricted with the predominant pattern subtype observed amongst the isolates from various states.

SIGNIFICANCE AND IMPACT OF THE STUDY

We have successfully devised a PFGE protocol that counteracts DNase activity of Salm. Sofia, enabling typing of this serovar.

Occurrence and characterization of Salmonella Hiduddify from chickens and poultry meat in Nigeria

The objective of this study was to determine the prevalence of Salmonella serovars and the antimicrobial susceptibility in chickens and poultry meat products in rural areas in Nigeria. The study was an observational cross-sectional investigation in which the target population included exotic and local chickens in Maiduguri main markets, chickens from farms, and free-range local chickens. A total of 865 samples were collected from feces, kidney, lungs, cecum, intestine, liver, heart, gizzard, and cloacal swabs from 525 different chickens. Salmonella was isolated from 130 of the samples. A stratified random sampling technique was used to select 41 isolates out of the 130 strains for serotyping, pulsed-field gel electrophoresis (PFGE), and antimicrobial susceptibility testing. Thirty-nine out of the 41 samples serotyped yielded Salmonella Hiduddify; two yielded a rough Salmonella serovar. The 39 Salmonella Hiduddify isolates and the two rough isolates were highly similar by PFGE typing, indicating that all of the isolates were of the same serovar. A low frequency of resistance was found among the isolates, except for resistance to ciprofloxacin for which 23 (56%) of the isolates tested exhibited resistance. This study documents for the first time the isolation of Salmonella Hiduddify in chickens and shows that this serovar is widespread in rural areas in Nigeria. It also documents a high frequency of fluoroquinone resistance in the isolates indicating the presence of selective pressure in the environment. Further studies should be conducted to reveal if the serovar is present in eggs and causes salmonellosis among the general population.

Evaluation of genome-derived amplicon length polymorphism PCR primers for the genetic evaluation of related strains of Salmonella

AIMS

The intent of this study is to exploit both the genetic diversity and conservation demonstrated between the Salmonella enterica ssp. enterica serovar Typhi CT18 and Salm. enterica ssp. enterica serovar Typhimurium LT2 genomes by utilizing amplicon length polymorphism (ALP) to detect and differentiate various Salmonella strains.

METHODS AND RESULTS

Methods of ALP-PCR analysis were developed based on identifying DNA sequence deletions within highly homologous regions of the Salm. Typhi CT18 and Salm. Typhimurium LT2 genomes. This study describes the application of genome-based ALP-PCR using primer pairs designed to detect genomic differences present within both Salmonella genomes and evaluated against a reference set of Salmonella strains.

CONCLUSIONS

This study defines a collection of primer sequences broadly distributed along the Salmonella genome that can differentiate various Salmonella strains.

SIGNIFICANCE AND IMPACT OF THE STUDY

Genome-based ALP-PCR provides a useful and powerful analytical method to evaluate variability within a group of Salmonella strains independent of serological, phenotypic or other molecular approaches.

Persistence of Salmonella Senftenberg in poultry production environments and investigation of its resistance to desiccation

Most Salmonella serovars, including Salmonella enterica subsp. enterica serovar Senftenberg (S. Senftenberg), are tolerant to desiccation and able to colonize and persist in feed mills. In addition, they may survive cleaning and disinfection procedures used on poultry farms. The present study was conducted to investigate the survival of S. Senftenberg in broiler parent stock farms and broiler farms. The isolates from one of the parent stock farms investigated only differed by a single band in fluorescent amplified fragment-length polymorphism analysis and had identical pulsed-field gel electrophoresis profiles, indicating that a S. Senftenberg clone had persisted for more than 2 years, despite cleaning, disinfection, desiccation and depopulation, and was subsequently able to infect Salmonella-free layers. Isolates from the same house on a different broiler parent stock farm were found to be identical by amplified fragment-length polymorphism analysis and pulsed-field gel electrophoresis although the farm tested negative for Salmonella 55 times over a period of 18 months between the two positive samplings. An assay was developed to investigate the survival of 34 S. Senftenberg isolates during desiccation at approximately 38% relative humidity. On average, the viability of S. Senftenberg isolates decreased by 1000-fold over 35 days. The persistent clones were no more resistant to desiccation than the other isolates investigated. However, S. Senftenberg was more resistant to desiccation than an isolate of Pantoea agglomerans commonly found on poultry feed-processing lines. This study demonstrates the risk of persistence of feed-associated serovars such as S. Senftenberg.

Comparison of molecular typing methods for the differentiation of Salmonella foodborne pathogens

Bacteria belonging to the genus Salmonella are among the leading causes of foodborne disease of bacterial etiology. These bacteria are also widely disseminated throughout the animal kingdom. The ability to identify the food source from which a human pathogen originated would be of great value in reducing the incidence of foodborne disease and the extent of disease outbreaks due to Salmonella. To date, efforts to identify the origin of these pathogens have centered on phenotypic and genotypic characterization of Salmonella isolates. This review focuses molecular or genotypic techniques that are currently being used for typing, and examines their strengths and weaknesses for determining the source of Salmonella foodborne infections.

Testing an ecological model for transmission of Salmonella enterica in swine production ecosystems using genotyping data

An ecological model for transmission of Salmonella enterica in swine production ecosystems was developed, identifying host species, environmental reservoirs, and temporal, spatial, and functional (i.e., stage of production) dimensions. It was hypothesized that transmission was most likely within spatial and functional compartments, between hosts of the same species and abiotic compartments of the same type. Eighteen swine production systems in Illinois, USA, were sampled in four collection cycles (1998, 1999, 2000, 2003). There were 11,873 samples collected, including feces from swine and other mammals and birds, and samples from insects, pen floors, boots, feed, and water. The 460 Salmonella isolates obtained were genotyped using repetitive sequence PCR with three primers-REP, BOX, and ERIC. All isolates from 2000 and 2003 were serotyped, as well as a subsample from 1998 and 1998. Genetic relatedness was estimated from the similarity of fragmentation patterns after gel electrophoresis of PCR products. Cluster analysis identified genetically related isolates. Linking of isolates in tight clusters (similarity >or=85%) was viewed as evidence for transmission. Five farms had a sufficient number of tight clusters for hypothesis testing. The factors most differentiating isolates genetically were farm of origin and time of sampling. Isolates were also differentiated genetically by site, building, room, and pen. There was no consistent association of genotype with stage of production or host/environment reservoir. Serotype analysis confirmed that Salmonella lineages were differentiated by visit and site. Thus, Salmonella transmission was primarily over short distances, i.e., within the same pen or room, with some transmission between rooms and buildings on the same site, but with limited transmission between sites. Transmission was observed across a variety of ecological niches represented by different host species and environmental reservoirs. Genetic differences over time reflected multiple introductions into the ecosystem of different Salmonella genotypes, as well as evolutionary changes within lineages. Intervention strategies to reduce Salmonella prevalence within swine production ecosystems would be best targeted at maintaining spatial barriers to transmission, whereas intervention targeted at specific biological hosts or environmental reservoirs is less likely to be effective.

Pulsed-Field Gel Electrophoresis Subtyping Database for FoodborneSalmonella entericaSerotype Discrimination

Nontyphoid Salmonella is one of the main causes of bacterial gastroenteritis worldwide and is responsible for 65% of reported outbreaks of foodborne diseases in France. Serotyping is widely used for isolate preliminary identification, but it poorly discriminates strains. Rapid, efficient molecular subtyping tools have therefore been developed for the investigation of outbreaks. We evaluated the performance of the pulsed-field gel electrophoresis (PFGE) method for discrimination of 31 Salmonella serotypes frequently isolated in France. We set up a genomic database of Salmonella strains isolated from food, animals, the environment, and humans to improve the management of contamination and reactions to foodborne disease outbreaks. We studied 1128 isolates by PFGE, according to the standardized PulseNet protocol. We identified 452 PFGE patterns, 67.5% of which corresponded to a single isolate. The ability of this method to distinguish between isolates was estimated by calculating the Simpson index and the 95% confidence interval. Values obtained ranged between 0.33 (0.11-0.54) to 0.99 (0.96-1.00), depending on serotype. Epidemiological information about isolates was used for analyses of intra- and interserotype diversity results and for determining whether PFGE patterns were linked to the source of the isolate. Clustering analysis of the PFGE patterns obtained confirmed that serotype and PFGE genotype were closely linked. Some PFGE patterns were identified as major patterns, each of these patterns being found in at least 10 isolates. The database generated has already proved its effectiveness in epidemiological investigations in livestock production and foodborne outbreaks.

Use of pulsed-field gel electrophoresis of conserved XbaI fragments for identification of swine Salmonella serotypes

Swine Salmonella isolates (n=674) from various locations throughout the United States and Canada were analyzed via pulsed-field gel electrophoresis (PFGE) with XbaI. PFGE subtypes were analyzed by cluster analysis and compared to conventional serotyping results. The analysis showed a correlation of serotype to PFGE subtype. In addition, conserved fragments were identified within the restriction patterns that were unique to each serotype. PFGE using XbaI restriction provided a possible alternative method for screening and identifying swine Salmonella serotypes.

Salmonella isolated in sewage sludge traced back to human cases of salmonellosis

AIM

The main aim of this study was to investigate a possible connection between the Salmonella content in sewage sludge and human cases of salmonellosis. An additional aim was to survey the antimicrobial resistance situation in Salmonella isolated from Swedish sewage sludge.

METHODS AND RESULTS

The Salmonella strains were compared by restriction enzyme analysis combined with pulsed field gel electrophoresis and antimicrobial susceptibility testing. This study suggests a link between Salmonella isolated from sewage sludge and human Salmonella isolates.

CONCLUSIONS

This study demonstrates that Salmonella spp. isolated in sewage treatment plants (STP) originate from infected humans and survive treatment at STP. It also highlights the risk of spreading resistant Salmonella strains from sewage sludge to the environment.

SIGNIFICANCE AND IMPACT OF THE STUDY

As Salmonella spp. originating from infected humans can survive the treatment at STP, the risk of Salmonella spp. being spread with sewage sludge to the environment and then to people and animals is enhanced. The threat to society is even worse if the bacteria are resistant to antimicrobial agents.

Improvement and validation of RAPD in combination with PFGE analysis of Salmonella enterica ssp. enterica serovar Senftenberg strains isolated from feed mills

In 1995 and 1996 a Swedish feed mill had problems due to a persistent contamination of Salmonella enterica spp. enterica serovar Senftenberg that was difficult to eliminate. Forty-eight strains isolated from the feed mill, together with unrelated strains included to evaluate the discriminatory power and reproducibility, were analysed by pulsed-field gel electrophoresis (PFGE). The source of contamination in the feed mill was identified and preventative measures were taken, that led to a resolution of the problem. A previously developed randomly amplified polymorphic DNA (RAPD) protocol was used, to evaluate a rapid and low-cost alternative to PFGE typing. The use of the alternative thermostable DNA polymerase Tth was shown to increase the reproducibility of the RAPD analysis. The reproducibility, in terms of Pearson's and Dice's similarity coefficients for duplicate runs, increased from 72.0 +/- 16.9% and 72.3 +/- 12.9% for Taq to 91.6 +/- 7.5% and 90.9 +/- 5.3% for the fingerprints obtained for the RAPD method employing Tth DNA polymerase. Simpson's index of diversity was calculated and found to be 0.580 for RAPD and 0.896 for PFGE. All of the seven RAPD types could be subdivided into one or more PFGE types, whereas none of the 22 PFGE types was divided into more than one RAPD type. RAPD provides a simple, rapid and powerful screening method that can be used to initially select isolates for further analysis by PFGE.

[Use of molecular subtyping methods to investigate two nosocomial outbreaks due to Salmonella Livingstone in Sfax hospital, Tunisia]

OBJECTIVE

The aim of the study was to investigate two nosocomial outbreaks due to Salmonella Livingstone in a pediatric ward in Sfax hospital using molecular typing techniques.

MATERIALS AND METHODS

We included 84 strains of S. Livingstone isolated from patients hospitalized in a pediatric ward between November 1999 through August 2002 in addition to one environmental sample. Three epidemiological unrelated strains of S. Livingstone were also tested. The molecular typing techniques were: plasmid analysis, enterobacterial repetitive intergenic consensus (ERIC-PCR), random amplification of polymorphic DNA (RAPD-PCR) and pulsed field gel electrophoresis (PFGE).

RESULTS

The plasmid analysis and the ERIC-PCR generated a similar profile for outbreak isolates including the environmental sample while the epidemiologically unrelated strains demonstrated distinct patterns. The RAPD-PCR applied on 20 strains showed three patterns but one profile was predominating. All the strains isolate of S. Livingstone, except the veterinary strain, could not be typed by PFGE.

CONCLUSION

Using the molecular typing techniques, we showed that these two outbreaks in the pediatric ward were due to the clonal spread of a single strain of S. Livingstone. The identification of the source of contamination and the improvement of hygiene conditions are required.