Poultry-associated Salmonella enterica subsp. enterica serovar 4,12:d:- reveals high clonality and a distinct pathogenicity gene repertoire

Virulence and antimicrobial resistance factors in Salmonella enterica serotypes isolated from pigs and chickens in central Chile

Salmonella enterica is a food-borne pathogen with a wide host-range that during decades has been of public health concern in developed and developing countries. In Chile, the poultry and pig industries represent the biggest contribution of meat consumption in the population, and sanitary regulations have been imposed for Salmonella control. The aim of this work was to determine and characterize Salmonella strains isolated from pigs and chicken raised on commercials farms in Chile. For this, isolates belonging to pigs (n = 46) and poultry (n = 57) were genotyped by two multiplex PCR reactions and virulotyped by the PCR detection of virulence-associated genes. In addition, isolates were serotyped and analyzed by the Kirby Bauer assay to determine their antimicrobial resistance phenotypes. From these analyses 52 genotypes, six serotypes and several multidrug resistance phenotypes and different combinations of virulence-associated genes were detected. These results suggest that S. enterica in pigs and poultry in central Chile should be monitored due to potential consequences in public and animal health.

Investigation of class 1 integrons and virulence genes in the emergent Salmonella serovar Infantis in Turkey

The emerging situation of Salmonella enterica subsp. enterica serovar Infantis (S. Infantis) in Turkey was investigated in terms of virulence genes and mobile genetic elements such as Salmonella genomic island 1 (SGI1) and class 1 (C1) integron to see whether increased multidrug resistance (MDR) and ability to cause human cases is a consequence of their possession. Screening of SGI1 (and its variants) and C1 integrons was done with conventional PCR, while screening of gene cassettes and virulence genes was conducted with real-time PCR for 70 S. Infantis isolates from poultry products. SGI1 or its variants were not detected in any of the isolates. Sixty-eight of 70 isolates were detected to carry one C1 integron of size 1.0 kb. These integrons were detected to carry ant(3″)-Ia gene cassette explaining the streptomycin/spectinomycin resistance. Sequence analysis of gene cassettes belongs to four representing isolates which showed that, although their difference in isolation date and place, genetically, they are 99.9% similar. Virulence gene screening was introduced as genotypic virulence profiles. The most dominant profile for S. Infantis isolates, among twelve genes, was gatC-tcfA, which are known to be related to colonization at specific hosts. This study revealed the high percentage of C1 integron possession in S. Infantis isolates from poultry products in Turkey. It also showed the potential of S. Infantis strains to be resistant to more antimicrobial drugs. Moreover, a dominant profile of virulence genes that are uncommon for non-typhoidal Salmonella (NTS) serovars was detected, which might explain the enhanced growth at specified hosts.

Iron-Uptake Systems of Chicken-Associated Salmonella Serovars and Their Role in Colonizing the Avian Host

Iron is an essential micronutrient for most bacteria. Salmonella enterica strains, representing human and animal pathogens, have adopted several mechanisms to sequester iron from the environment depending on availability and source. Chickens act as a major reservoir for Salmonella enterica strains which can lead to outbreaks of human salmonellosis. In this review article we summarize the current understanding of the contribution of iron-uptake systems to the virulence of non-typhoidal S. enterica strains in colonizing chickens. We aim to address the gap in knowledge in this field, to help understand and define the interactions between S. enterica and these important hosts, in comparison to mammalian models.

Pheno and genotyping of Salmonella from slaughtered pigs in a Portuguese abattoir reveal differential persistence ability

Pork is one of the most common vehicles of non-typhoid foodborne Salmonella, with the slaughterhouse representing a key point for the infection of pigs and carcass contamination. By comparing matching samples taken from animals at the dirty (skin) and clean (inner and outer carcass surface) areas of the slaughterline, this study aimed to assess potential Salmonella contamination routes of pig carcasses within a Portuguese abattoir. Forty-four Salmonella isolates were retrieved from 120 pigs, and further characterized through pheno and genotypical methods. Most frequent serotypes found were Salmonella 4, [5],12:i:- (47.7%), Salmonella Rissen (40.9%) and Salmonella Derby (11.4%). Isolates were most commonly collected from the skin of pigs sampled at the dirty area (59.1%), followed by the inner (38.1%) and outer (9.1%) carcass surface sampled at the clean area. Most isolates (79.5%) were considered to be multidrug resistant and all harbored the virulence associated genes invA, invH, sopB, stn, slyA, phoP, phoQ and agfA. PFGE analysis revealed that most bacterial isolates belonging to the same serotype, recovered from animals from different farms, and slaughtered at separate days were genetically undistinguishable. Furthermore, our findings suggest that Salmonella Rissen might have an increased ability to endure on the slaughterhouse environment when compared with the other serotypes. Concluding, this study shows that the slaughterhouse may be a key point for the dissemination of resistant and virulent Salmonella strains, which stresses the importance of the implementation of good hygiene practices at the slaughterhouse and of the application of corrective measures to avoid cross-contamination.

The Changing Role of the Clinical Microbiology Laboratory in Defining Resistance in Gram-negatives

The evolution of resistance in Gram-negatives has challenged the clinical microbiology laboratory to implement new methods for their detection. Multidrug-resistant strains present major challenges to conventional and new detection methods. More rapid pathogen identification and antimicrobial susceptibility testing have been developed for use directly on specimens, including fluorescence in situ hybridization tests, automated polymerase chain reaction systems, microarrays, mass spectroscopy, next-generation sequencing, and microfluidics. Review of these methods shows the advances that have been made in rapid detection of resistance in cultures, but limited progress in direct detection from specimens.

Phenotypic and Molecular Characterization of Salmonella 1,4,[5],12:i:- R-Type ASSuT Isolates from Humans, Animals, and Environment in Portugal, 2006-2011

The increase in prevalence of Salmonella 1,4,[5],12:i:- related infections over the last few years has been considered a public health issue in many European countries, especially as this serovar may be associated with tetraresistance to ampicillin, streptomycin, sulfonamides, and tetracyclines (R-type ASSuT). Salmonella 1,4,[5],12:i:- isolates (n = 187) obtained by the Portuguese National Laboratory from different sources, including human clinical cases (n = 170), veterinary (n = 10), environmental (n = 6), and food samples (n = 1), were collected from 15 districts between 2006 and 2011. All isolates were serotyped using the slide agglutination method and results were confirmed by multiplex PCR for the monophasic variant. From the confirmed Salmonella 1,4,[5],12:i:-, R-type ASSuT isolates were selected by disc diffusion and minimal inhibitory concentration (MIC) determination for further characterization by pulsed-field gel electrophoresis restriction with XbaI, virulence genes determination by PCR, additional antimicrobial resistance profiling by disc diffusion, and epidemiological distribution evaluation. Out of the 187 serotyped isolates, 133 were confirmed as Salmonella 1,4,[5],12:i:- with a R-type ASSuT occurrence of 61.7%. Distribution among Portuguese districts showed a higher percentage of reported cases in coastal areas, in particular, in Porto (24.8%), Setúbal (13.5%), and Aveiro (12.8%), probably due to the higher population density. Clonality analysis revealed a high diversity of pulsotypes with the majority of human salmonellosis cases being attributed to sporadic events. All isolates harbored 14 out of the 18 virulence genes evaluated and 87.8% of the isolates showed all the resistance genes frequently associated with the European clone, blaTEM⁺sul2⁺straA-straB⁺tetB⁺. This study shows that Salmonella 1,4,[5],12:i:- resistant isolates are widely distributed in Portugal. This may be related to a selective advantage offered by R-type ASSuT profile, the presence of multiple virulent features, including the ability to form biofilms, which along with a high diversity of pulsotypes may be responsible for the dissemination through the country.

Comparative genomic analysis and virulence differences in closely related salmonella enterica serotype heidelberg isolates from humans, retail meats, and animals

Salmonella enterica subsp. enterica serovar Heidelberg (S. Heidelberg) is one of the top serovars causing human salmonellosis. Recently, an antibiotic-resistant strain of this serovar was implicated in a large 2011 multistate outbreak resulting from consumption of contaminated ground turkey that involved 136 confirmed cases, with one death. In this study, we assessed the evolutionary diversity of 44 S. Heidelberg isolates using whole-genome sequencing (WGS) generated by the 454 GS FLX (Roche) platform. The isolates, including 30 with nearly indistinguishable (one band difference) Xbal pulsed-field gel electrophoresis patterns (JF6X01.0032, JF6X01.0058), were collected from various sources between 1982 and 2011 and included nine isolates associated with the 2011 outbreak. Additionally, we determined the complete sequence for the chromosome and three plasmids from a clinical isolate associated with the 2011 outbreak using the Pacific Biosciences (PacBio) system. Using single-nucleotide polymorphism (SNP) analyses, we were able to distinguish highly clonal isolates, including strains isolated at different times in the same year. The isolates from the recent 2011 outbreak clustered together with a mean SNP variation of only 17 SNPs. The S. Heidelberg isolates carried a variety of phages, such as prophage P22, P4, lambda-like prophage Gifsy-2, and the P2-like phage which carries the sopE1 gene, virulence genes including 62 pathogenicity, and 13 fimbrial markers and resistance plasmids of the incompatibility (Inc)I1, IncA/C, and IncHI2 groups. Twenty-one strains contained an IncX plasmid carrying a type IV secretion system. On the basis of the recent and historical isolates used in this study, our results demonstrated that, in addition to providing detailed genetic information for the isolates, WGS can identify SNP targets that can be utilized for differentiating highly clonal S. Heidelberg isolates.

Genome-wide methylation patterns in Salmonella enterica Subsp. enterica Serovars

The methylation of DNA bases plays an important role in numerous biological processes including development, gene expression, and DNA replication. Salmonella is an important foodborne pathogen, and methylation in Salmonella is implicated in virulence. Using single molecule real-time (SMRT) DNA-sequencing, we sequenced and assembled the complete genomes of eleven Salmonella enterica isolates from nine different serovars, and analysed the whole-genome methylation patterns of each genome. We describe 16 distinct N⁶-methyladenine (m6A) methylated motifs, one N⁴-methylcytosine (m4C) motif, and one combined m6A-m4C motif. Eight of these motifs are novel, i.e., they have not been previously described. We also identified the methyltransferases (MTases) associated with 13 of the motifs. Some motifs are conserved across all Salmonella serovars tested, while others were found only in a subset of serovars. Eight of the nine serovars contained a unique methylated motif that was not found in any other serovar (most of these motifs were part of Type I restriction modification systems), indicating the high diversity of methylation patterns present in Salmonella.

Drinking water from dug wells in rural ghana--salmonella contamination, environmental factors, and genotypes

Salmonellosis is an important but neglected disease in sub-Saharan Africa. Food or fecal-oral associated transmissions are the primary cause of infections, while the role of waterborne transmission is unclear. Samples were collected from different dug wells in a rural area of Ghana and analyzed for contamination with bacteria, and with Salmonella in particular. In addition, temporal dynamics and riks factors for contamination were investigated in 16 wells. For all Salmonella isolates antibiotic susceptibility testing was performed, serovars were determined and strains from the same well with the same serovar were genotyped. The frequency of well water contamination with Gram-negative rod-shaped bacteria was 99.2% (n = 395). Out of 398 samples, 26 (6.5%) tested positive for Salmonella spp. The serovar distribution was diverse including strains not commonly isolated from clinical samples. Resistance to locally applied antibiotics or resistance to fluoroquinolones was not seen in the Salmonella isolates. The risk of Salmonella contamination was lower in wells surrounded by a frame and higher during the rainy season. The study confirms the overall poor microbiological quality of well water in a resource-poor area of Ghana. Well contamination with Salmonella poses a potential threat of infection, thus highlighting the important role of drinking water safety in infectious disease control.

Comparative analysis of virulence and resistance profiles of Salmonella Enteritidis isolates from poultry meat and foodborne outbreaks in northern Jordan

This study was conducted to isolate Salmonella Enteritidis from poultry samples and compare their virulence and antibiotic resistance profiles to S. Enteritidis isolated from outbreaks in northern Jordan. Two hundred presumptive isolates were obtained from 302 raw poultry samples and were subjected to further analysis and confirmation. A phylogenic tree based on 16S rRNA sequencing was constructed and selected isolates representing each cluster were further studied for their virulence in normal adult Swiss white mice. The most virulent strains were isolated from poultry samples and had an LD 50 of 1.55 × 10 (5) CFU, while some of the outbreak isolates were avirulent in mice. Antibiotic resistance profiling revealed that the isolates were resistant to seven of eight antibiotics screened with each isolate resistant to multiple antibiotics (from two to six). Of the poultry isolates, 100%, 88.9%, 77.8%, 66.7%, and 50% showed resistance to nalidixic acid, ciprofloxacin, ampicillin, cephalothin, and cefoperazone, respectively. Two outbreak isolates were sensitive to all tested antibiotics, while 71.4% were resistant to cefoperazone and only 28.6% showed resistance to nalidixic acid. Salmonella outbreak isolates were genetically related to poultry isolates as inferred from the 16S rRNA sequencing, yet were phenotypically different. Although outbreak strains were similar to poultry isolates, when tested in the mouse model, some of the outbreak isolates were highly virulent while others were avirulent. This might be due to a variation in susceptibility of the mouse to different S. Enteritidis isolates.

Molecular epidemiology of Salmonella enterica serovar Kottbus isolated in Germany from humans, food and animals

Salmonella enterica serovar Kottbus has been continuously isolated from poultry and poultry meat, especially from turkey. We investigated by comparative molecular typing 95 S. Kottbus isolates obtained in Germany between 2000 and 2011 from poultry/poultry meat, pig/pork, cattle, reptiles, the environment as well as from human cases to identify potential infection sources for humans, especially the role of poultry and poultry products as vehicle in transmission of S. Kottbus isolates to humans. Multilocus sequence typing analysis detected three main genetic lineages. Most human isolates belonged to lineage 1 represented by sequence types ST212 and ST808. Part of the isolates isolated from cattle and pork were also linked to this lineage. Nevertheless, human isolates and especially isolates from poultry/poultry meat, and with less extend from other livestock, grouped in lineage 2 represented by ST582. Four additional isolates from reptiles and humans belonging to ST1669 represented the third lineage. The three lineages were also reflected by pulsed-field gel electrophoresis typing data and DNA microarray analysis of 102 pathogenicity genes. Antimicrobial resistance especially to nalidixic acid and ciprofloxacin was predominantly observed in isolates assigned to lineage 2, which contains predominantly resistant isolates compared to lineage 1 and 3. Sequencing of the quinolone resistance-determining region of gyrA revealed a point mutation in codon 83 or 87 responsible for nalidixic acid resistance and MIC values for ciprofloxacin between 0.125 and 0.25mg/l. Overall, this study showed that in Germany a specific S. Kottbus lineage (ST582), which is well-established in poultry, can be transmitted to humans by poultry meat and, consequently, poses a risk for human health.

Infection of chickens with antimicrobial-resistant Salmonella enterica Typhimurium DT193 and monophasic Salmonella Typhimurium-like variants: an emerging risk to the poultry industry?

Antimicrobial-resistant Salmonella enterica poses a particular risk to public health, and in particular isolates belonging to clonal lineages such as Salmonella Typhimurium DT104 cause epidemics across species including poultry. In recent years, antimicrobial-resistant S. Typhimurium DT193 and specifically the monophasic S. Typhimurium-like variants of this phage type, serotypes 4,12:i:- and 4,5,12:i:-, have become an increasing risk to public health in Europe and the USA and now account for nearly one-half of human S. Typhimurium infections in the UK. Unlike S. Typhimurium that possesses two forms of flagella which can vary between phase 1 and phase 2 during infection, monophasic variants possess only phase 1 flagella. These monophasic antimicrobial-resistant variants have become a major problem in pig production but human cases have also been associated with poultry consumption and have been found in UK flocks through surveillance schemes since 2010. In this study we determined the ability of antimicrobial-resistant DT193 serotype 4,12:i:- and 4,5,12:i:- isolates from pigs to infect chickens. All isolates were found to colonize the caeca and liver. All but one isolate of serotype 4,5,12:i:- also infected the spleen. Levels of infection and pathology were comparable with those found with the virulent S. Typhimurium isolate 4/74. These findings indicate that both S. Typhimurium DT193 and monophasic variants of this phage type usually associated with pigs are capable of colonizing the chicken. This shows that both S. Typhimurium DT193 and monophasic variants represent a significant and potential emerging threat to poultry production from "spill-over" of these isolates from the pig industry or other sources.

Population structure of Salmonella enterica serovar 4,[5],12:b:- strains and likely sources of human infection

Salmonella enterica serovar 4,[5],12:b:- is a monophasic serovar not able to express the second-phase flagellar antigen (H2 antigen). In Germany, the serovar is occasionally isolated from poultry, reptiles, fish, food, and humans. In this study, a selection of 67 epidemiologically unrelated Salmonella enterica serovar 4,[5],12:b:- strains isolated in Germany between 2000 and 2011 from the environment, animal, food, and humans was investigated by phenotypic and genotypic methods to better understand the population structure and to identify potential sources of human infections. Strains of this monophasic serovar were highly diverse. Within the 67 strains analyzed, we identified 52 different pulsed-field gel electrophoresis XbaI profiles, 12 different multilocus sequence types (STs), and 18 different pathogenicity array types. The relatedness of strains based on the pathogenicity gene repertoire (102 markers tested) was in good agreement with grouping by MLST. S. enterica serovar 4,[5],12:b:- is distributed across multiple unrelated eBurst groups and consequently is highly polyphyletic. Two sequence types (ST88 and ST127) were linked to S. enterica serovar Paratyphi B (d-tartrate positive), two single-locus variants of ST1583 were linked to S. enterica serovar Abony, and one sequence type (ST1484) was associated with S. enterica serovar Mygdal, a recently defined, new serovar. From the characterization of clinical isolates and those of nonhuman origin, it can be concluded that the potential sources of sporadic human infections with S. enterica serovar 4,[5],12:b:- most likely are mushrooms, shellfish/fish, and poultry.

Genetic types, gene repertoire, and evolution of isolates of the Salmonella enterica serovar 4,5,12:i:- Spanish clone assigned to different phage types

Salmonella enterica subsp. enterica 4,[5],12:i:- is one of the most prevalent serovars associated with human infections worldwide. Two multidrug-resistant clones, designated Spanish and European clones, are recognized as having importance for public health and are subject to control measures in the European Union. In this study, 23 clinical isolates belonging to the Spanish clone were characterized by multilocus sequence typing, multiple-locus variable number tandem repeat analysis (MLVA), PCR amplification and sequencing, and a DNA microarray targeting 263 genes, in order to provide new insights into their origins and further evolution. The derived data were compared with information available from other studies for S. 4,[5],12:i:- isolates of both the Spanish and the European clones, to identify differential molecular markers which could be potentially used as surveillance tools in the control of dissemination of this serovar. The isolates analyzed were assigned to sequence type 19 and to 17 MLVA patterns, with 3-13-16-NA-311 being the most prevalent. Highly similar virulence, metabolic, and prophage-associated gene profiles were identified, but DNA mobility markers distinguished five genotypes. Two types of deletions, caused by insertion of IS26, presumably donated by pUO-STmR/RV1-like plasmids typically found in the Spanish clone, affected the fljAB operon and surrounding DNA. The Spanish and European clones differ in sequence type, MLVA patterns, gene repertoire, and fljAB deletion type. The observed variability supports an independent evolution of the two successful monophasic clones from different Salmonella enterica serovar Typhimurium ancestors and can be taken into consideration for epidemiological surveillance.

Human infections attributable to the D-tartrate-fermenting variant of Salmonella enterica serovar Paratyphi B in Germany originate in reptiles and, on rare occasions, poultry

In this study, the population structure, incidence, and potential sources of human infection caused by the d-tartrate-fermenting variant of Salmonella enterica serovar Paratyphi B [S. Paratyphi B (dT+)] was investigated. In Germany, the serovar is frequently isolated from broilers. Therefore, a selection of 108 epidemiologically unrelated S. enterica serovar Paratyphi B (dT+) strains isolated in Germany between 2002 and 2010 especially from humans, poultry/poultry meat, and reptiles was investigated by phenotypic and genotypic methods. Strains isolated from poultry and products thereof were strongly associated with multilocus sequence type ST28 and showed antimicrobial multiresistance profiles. Pulsed-field gel electrophoresis XbaI profiles were highly homogeneous, with only a few minor XbaI profile variants. All strains isolated from reptiles, except one, were strongly associated with ST88, another distantly related type. Most of the strains were susceptible to antimicrobial agents, and XbaI profiles were heterogeneous. Strains isolated from humans yielded seven sequence types (STs) clustering in three distantly related lineages. The first lineage, comprising five STs, represented mainly strains belonging to ST43 and ST149. The other two lineages were represented only by one ST each, ST28 and ST88. The relatedness of strains based on the pathogenicity gene repertoire (102 markers tested) was mostly in agreement with the multilocus sequence type. Because ST28 was frequently isolated from poultry but rarely in humans over the 9-year period investigated, overall, this study indicates that in Germany S. enterica serovar Paratyphi B (dT+) poses a health risk preferentially by contact with reptiles and, to a less extent, by exposure to poultry or poultry meat.

Rapid detection, characterization, and enumeration of foodborne pathogens

As food safety management further develops, microbiological testing will continue to play an important role in assessing whether Food Safety Objectives are achieved. However, traditional microbiological culture-based methods are limited, particularly in their ability to provide timely data. The present review discusses the reasons for the increasing interest in rapid methods, current developments in the field, the research needs, and the future trends. The advent of biotechnology has introduced new technologies that led to the emergence of rapid diagnostic methods and altered food testing practices. Rapid methods are comprised of many different detection technologies, including specialized enzyme substrates, antibodies and DNA, ranging from simple differential plating media to the use of sophisticated instruments. The use of non-invasive sampling techniques for live animals especially came into focus with the 1990s outbreak of bovine spongiform encephalopathy that was linked to the human outbreak of Creutzfeldt Jakob's Disease. Serology is still an important tool in preventing foodborne pathogens to enter the human food supply through meat and milk from animals. One of the primary uses of rapid methods is for fast screening of large number of samples, where most of them are expected to be test-negative, leading to faster product release for sale. This has been the main strength of rapid methods such as real-time Polymerase Chain Reaction (PCR). Enrichment PCR, where a primary culture broth is tested in PCR, is the most common approach in rapid testing. Recent reports show that it is possible both to enrich a sample and enumerate by pathogen-specific real-time PCR, if the enrichment time is short. This can be especially useful in situations where food producers ask for the level of pathogen in a contaminated product. Another key issue is automation, where the key drivers are miniaturization and multiple testing, which mean that not only one instrument is flexible enough to test for many pathogens but also many pathogens can be detected with one test. The review is mainly based on the author's scientific work that has contributed with the following new developments to this field: (i) serologic tests for large-scale screening, surveillance, or eradication programs, (ii) same-day detection of Salmonella that otherwise was considered as difficult to achieve, (iii) pathogen enumeration following a short log-phase enrichment, (iv) detection of foodborne pathogens in air samples, and finally (v) biotracing of pathogens based on mathematical modeling, even in the absence of isolate. Rapid methods are discussed in a broad global health perspective, international food supply, and for improvement of quantitative microbial risk assessments. The need for quantitative sample preparation techniques, culture-independent, metagenomic-based detection, online monitoring, a global validation infrastructure has been emphasized. The cost and ease of use of rapid assays remain challenging obstacles to surmount.

Microbial Diagnostic Microarrays for the Detection and Typing of Food- and Water-Borne (Bacterial) Pathogens

Reliable and sensitive pathogen detection in clinical and environmental (including food and water) samples is of greatest importance for public health. Standard microbiological methods have several limitations and improved alternatives are needed. Most important requirements for reliable analysis include: (i) specificity; (ii) sensitivity; (iii) multiplexing potential; (iv) robustness; (v) speed; (vi) automation potential; and (vii) low cost. Microarray technology can, through its very nature, fulfill many of these requirements directly and the remaining challenges have been tackled. In this review, we attempt to compare performance characteristics of the microbial diagnostic microarrays developed for the detection and typing of food and water pathogens, and discuss limitations, points still to be addressed and issues specific for the analysis of food, water and environmental samples.

Antimicrobial resistance and virulence determinants in European Salmonella genomic island 1-positive Salmonella enterica isolates from different origins

Salmonella genomic island 1 (SGI1) contains a multidrug resistance region conferring the ampicillin-chloramphenicol-streptomycin-sulfamethoxazole-tetracycline resistance phenotype encoded by bla(PSE-1), floR, aadA2, sul1, and tet(G). Its increasing spread via interbacterial transfer and the emergence of new variants are important public health concerns. We investigated the molecular properties of SGI1-carrying Salmonella enterica serovars selected from a European strain collection. A total of 38 strains belonging to S. enterica serovar Agona, S. enterica serovar Albany, S. enterica serovar Derby, S. enterica serovar Kentucky, S. enterica serovar Newport, S. enterica serovar Paratyphi B dT+, and S. enterica serovar Typhimurium, isolated between 2002 and 2006 in eight European countries from humans, animals, and food, were subjected to antimicrobial susceptibility testing, molecular typing methods (XbaI pulsed-field gel electrophoresis [PFGE], plasmid analysis, and multilocus variable-number tandem-repeat analysis [MLVA]), as well as detection of resistance and virulence determinants (PCR/sequencing and DNA microarray analysis). Typing experiments revealed wide heterogeneity inside the strain collection and even within serovars. PFGE analysis distinguished a total of 26 different patterns. In contrast, the characterization of the phenotypic and genotypic antimicrobial resistance revealed serovar-specific features. Apart from the classical SGI1 organization found in 61% of the strains, seven different variants were identified with antimicrobial resistance properties associated with SGI1-A (S. Derby), SGI1-C (S. Derby), SGI1-F (S. Albany), SGI1-L (S. Newport), SGI1-K (S. Kentucky), SGI1-M (S. Typhimurium), and, eventually, a novel variant similar to SGI1-C with additional gentamicin resistance encoded by aadB. Only minor serovar-specific differences among virulence patterns were detected. In conclusion, the SGI1 carriers exhibited pathogenetic backgrounds comparable to the ones published for susceptible isolates. However, because of their multidrug resistance, they may be more relevant in clinical settings.

A multiplex ligation detection assay for the characterization of Salmonella enterica strains

A proof of principle of a multi-target assay for genotyping Salmonella has been developed targeting 62 genomic marker sequences of Salmonella related to pathogenicity. The assay is based on multiplex ligation detection reaction (LDR) followed by customized ArrayTube® microarray detection. The feasibility of the developed assay was verified in a method comparison study with conventional PCR using 16 Salmonella 'test' strains comprising eight serovars. Subsequently, the feasibility of the LDR microarray assay was also tested by analyzing 41 strains belonging to 23 serovars. With the exception of four serovars each serovar was characterized by a unique virulence associated gene repertoire. The LDR microarray platform proved to be a convenient, rapid and easy to use tool with potential in tracing a Salmonella contamination in the food chain, for outbreak studies, and to provide data for risk assessors that support bio-traceability models.

Relative prevalence of Salmonella Sofia on broiler chickens pre- and postprocessing in Australia

A survey was conducted to determine the relative prevalence of Salmonella serovars on whole chicken carcasses before and after processing in 3 Australian poultry abattoirs. Ninety and 180 whole chicken carcasses were tested for Salmonella serovars before and after processing, respectively. Each carcass was subjected to a buffered peptone water rinse according to Australian Standard methodologies and Salmonella prevalence was determined using Australian Standard methodologies. After isolation, Salmonella isolates were serotyped and results were analyzed to determine the relative percentage of each serovar at both processing points. Salmonella Sofia was shown to significantly increase its relative prevalence (P < or = 0.05) after processing and proved to be the dominant serovar accounting for 45/89 (51%) isolations before processing and 51/69 (74%) isolations after processing. The reasons for the increased relative prevalence of Salmonella Sofia are currently unknown and require further investigation but may involve factors related to prevalence and numbers on chickens and the ability of Salmonella Sofia to respond to environmental stressors and attach to surfaces.

Virulotyping and antimicrobial resistance typing of Salmonella enterica serovars relevant to human health in Europe

The combination of virulence gene and antimicrobial resistance gene typing using DNA arrays is a recently developed genomics-based approach to bacterial molecular epidemiology. We have now applied this technology to 523 Salmonella enterica subsp. enterica strains collected from various host sources and public health and veterinary institutes across nine European countries. The strain set included the five predominant Salmonella serovars isolated in Europe (Enteritidis, Typhimurium, Infantis, Virchow, and Hadar). Initially, these strains were screened for 10 potential virulence factors (avrA, ssaQ, mgtC, siiD, sopB, gipA, sodC1, sopE1, spvC, and bcfC) by polymerase chain reaction. The results indicated that only 14 profiles comprising these genes (virulotypes) were observed throughout Europe. Moreover, most of these virulotypes were restricted to only one (n = 9) or two (n = 4) serovars. The data also indicated that the virulotype did not vary significantly with host source or geographical location. Subsequently, a representative subset of 77 strains was investigated using a microarray designed to detect 102 virulence and 49 resistance determinants. The results confirmed and extended the previous observations using the virulo-polymerase chain reaction screen. Strains belonging to the same serovar grouped together, indicating that the broader virulence-associated gene complement corresponded with the serovar. There were, however, some differences in the virulence gene profiles between strains belonging to an individual serovar. This variation occurred primarily within those virulence genes that were prophage encoded, in fimbrial clusters or in the virulence plasmid. It seems likely that such changes enable Salmonella to adapt to different environmental conditions, which might be reflected in serovar-specific ecology. In this strain subset a number of resistance genes were detected and were serovar restricted to a varying degree. Once again the profiles of those genes encoding resistance were similar or the same for each serovar in all hosts and countries investigated.

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.

Microarray-based genotyping of Salmonella: inter-laboratory evaluation of reproducibility and standardization potential

Bacterial food-borne infections in humans caused by Salmonella spp. are considered a crucial food safety issue. Therefore, it is important for the risk assessments of Salmonella to consider the genomic variation among different isolates in order to control pathogen-induced infections. Microarray technology is a promising diagnostic tool that provides genomic information on many genes simultaneously. However, standardization of DNA microarray analysis is needed before it can be used as a routine method for characterizing Salmonella isolates across borders and laboratories. A comparative study was designed in which the agreement of data from a DNA microarray assay used for typing Salmonella spp. between two different labs was assessed. The study was expected to reveal the possibility of obtaining the same results in different labs using different equipment in order to evaluate the reproducibility of the microarray technique as a first step towards standardization. The low-density array contains 281 57-60-mer oligonucleotide probes for detecting a wide range of specific genomic marker genes associated with antibiotic resistance, cell envelope structures, mobile genetic elements and pathogenicity. Several critical methodology parameters that differed between the two labs were identified. These related to printing facilities, choice of hybridization buffer, wash buffers used following the hybridization and choice of procedure for purifying genomic DNA. Critical parameters were randomized in a four-factorial experiment and statistical measures of inter-lab consistency and agreement were performed based on the kappa coefficient. A high level of agreement (kappa=0.7-1.0) in microarray results was obtained even when employing different printing and hybridization facilities, different procedures for purifying genomic DNA and different wash buffers. However, less agreement (Kappa=0.2-0.6) between microarray results were observed when using different hybridization buffers, indicating this parameter as being highly critical when transferring a standard microarray assay between laboratories. In conclusion, this study indicates that DNA microarray assays can be reproduced in at least two different facilities, which is a pre-requisite for the development of standard guidelines.

Association between phylogeny, virulence potential and serovars of Salmonella enterica

Salmonella enterica subsp. enterica is one of the leading causes of zoonotic food-borne disease worldwide. The consequence of these infections is a serious impact on economics of the society in the form of lost productivity and expenses for medical care. The objective of this study was to analyze the difference in genomic content between selected serovars, especially the content of pathogenicity genes and this was done with a DNA microarray. Furthermore, we investigated the phylogenetic relationship between serovars using multilocus sequence typing (MLST). We chose serovars Typhimurium and Enteritidis as they are responsible for 75% of human infections in Europe. Additionally, we included serovars Derby, Dublin, Saintpaul, 4,5,12:i:-, Java and 4,5,12:b:- which are suspected to have different degrees of virulence to humans. MLST analysis clustered strains according to serovar with the exception of Java and Derby. DNA microarray clustered strains according to serovar and serogroup except for serovar 4,5,12:b:-. Differences in content of pathogenicity related genes between serovars with various host preferences and virulence towards humans were not observed. However, our strains from the supposedly less virulent serovar Derby lacked a combination of genes important for virulence. It might be speculated that other serovars can sustain their pathogenicity lacking one or two of these genes, whereas lack of many virulence genes will result in reduced virulence. A partial lack of concordance between MLST and microarray was found and this can be explained by the underlying data. On one hand, microarray data include highly variable regions which are known to be involved in horizontal gene transfer. On the other hand, MLST data is restricted to seven sequences and disregards contribution of horizontally acquired genes when evaluating evolution. The DNA microarray and MLST analysis complement each other giving a clearer image of evolution of these serovars and, furthermore, a visualization of the horizontally acquired genes.

Prevalence of Salmonella enterica in poultry and eggs in Uruguay during an epidemic due to Salmonella enterica serovar Enteritidis

Salmonella enterica serovar Enteritidis (S. Enteritidis) is frequently associated with food-borne disease worldwide. Poultry-derived products are a major source. An epidemic of human infection with S. Enteritidis occurred in Uruguay, and to evaluate the extent of poultry contamination, we conducted a nationwide survey over 2 years that included the analysis of sera from 5,751 birds and 12,400 eggs. Serological evidence of infection with Salmonella group O:9 was found in 24.4% of the birds. All positive sera were retested with a gm flagellum-based enzyme-linked immunosorbent assay, and based on these results, the national prevalence of S. Enteritidis infection was estimated to be 6.3%. Salmonellae were recovered from 58 of 620 pools made up of 20 eggs each, demonstrating a prevalence of at least 1 in every 214 eggs. Surprisingly, the majority of the isolates were not S. Enteritidis. Thirty-nine isolates were typed as S. Derby, 9 as S. Gallinarum, 8 as S. Enteritidis, and 2 as S. Panama. Despite the highest prevalence in eggs, S. Derby was not isolated from humans in the period of analysis, suggesting a low capacity to infect humans. Microarray-based comparative genomic hybridization analysis of S. Derby and S. Enteritidis revealed more than 350 genetic differences. S. Derby lacked pathogenicity islands 13 and 14, the fimbrial lpf operon, and other regions encoding metabolic functions. Several of these regions are present not only in serovar Enteritidis but also in all sequenced strains of S. Typhimurium, suggesting that these regions might be related to the capacity of Salmonella to cause food-borne disease.

Pork contaminated with Salmonella enterica serovar 4,[5],12:i:-, an emerging health risk for humans

Salmonella enterica subsp. enterica serovar 4,[5],12:i:- is a monophasic variant of S. enterica serovar Typhimurium (antigenic formula 4,[5],12:i:1,2). Worldwide, especially in several European countries and the United States, it has been reported among the 10 most frequently isolated serovars in pigs and humans. In the study reported here, 148 strains of the monophasic serovar isolated from pigs, pork, and humans in 2006 and 2007 in Germany were characterized by various phenotypic and genotypic methods. This characterization was done in order to investigate their clonality, the prevalence of identical subtypes in pigs, pork, and humans, and the genetic relatedness to other S. enterica serovar Typhimurium subtypes in respect to the pathogenic and resistance gene repertoire. Two major clonal lineages of the monophasic serovar were detected which can be differentiated by their phage types and pulsed-field gel electrophoresis (PFGE) profiles. Seventy percent of the strains tested belonged to definite phage type DT193, and those strains were mainly assigned to PFGE cluster B. Nineteen percent of the strains were typed to phage type DT120 and of these 86% belonged to PFGE cluster A. Sixty-five percent of the isolates of both lineages carried core multiresistance to ampicillin, streptomycin, tetracycline, and sulfamethoxazole encoded by the genes bla(TEM1-like), strA-strB, tet(B), and sul2. No correlation to the source of isolation was observed in either lineage. Microarray analysis of 61 S. enterica serovar 4,[5],12:i:- and 20 S. enterica serovar Typhimurium isolates tested determining the presence or absence of 102 representative pathogenicity genes in Salmonella revealed no differences except minor variations in single strains within and between the serovars, e.g., by presence of the virulence plasmid in four strains. Overall the study indicates that in Germany S. enterica serovar 4,[5],12:i:- strains isolated from pig, pork, and human are highly related, showing their transmission along the food chain. Since the pathogenicity gene repertoire is highly similar to that of S. enterica serovar Typhimurium, it is essential that interventions are introduced at the farm level in order to limit human infection.

DNA microarray analysis of Salmonella serotype Typhimurium strains causing different symptoms of disease

Background

Salmonella enterica subsp. enterica is one of the leading food-borne pathogens in the USA and European countries. Outcome of human Salmonella serotype Typhimurium infections ranges from mild self-limiting diarrhoea to severe diarrhoea that requires hospitalization. Increased knowledge of the mechanisms that are responsible for causing infection and especially the severity of infection is of high interest.

Results

Strains were selected from patients with mild infections (n = 9) and patients with severe infections (n = 9) and clinical data allowed us to correct for known underlying diseases. Additionally, outbreak isolates (n = 3) were selected. Strains were analyzed on a DNA-DNA microarray for presence or absence of 281 genes covering marker groups of genes related to pathogenicity, phages, antimicrobial resistance, fimbriae, mobility, serotype and metabolism. Strains showed highly similar profiles when comparing virulence associated genes, but differences between strains were detected in the prophage marker group. The Salmonella virulence plasmid was present in 72% of the strains, but presence or absence of the virulence plasmid did not correspond to disease symptoms. A dendrogram clustered strains into four groups. Clustering confirmed DT104 as being a clonal phagetype. Clustering of the remaining strains was mainly correlated to presence or absence of the virulence plasmid and mobile elements such as transposons. Each of the four clusters in the tree represented an almost equal amount of strains causing severe or mild symptoms of infection.

Conclusions

We investigated clinical significance of known virulence factors of Salmonella serotype Typhimurium strains causing different disease symptoms, and conclude that the few detected differences in Salmonella serotype Typhimurium do not affect outcome of human disease.