Molecular evolutionary genetics of the cattle-adapted serovar Salmonella dublin

First report of Bickerstaff's brainstem encephalitis caused by Salmonella Dublin: a case report

Background

Diseases caused by nontyphoid Salmonella can range from mild, to self-limiting gastroenteritis and severe invasive infection. Relatively rarely, Salmonella may cause severe encephalopathy.

Case presentation

We report a suspected case of Bickerstaff’s brainstem encephalitis caused by Salmonella Dublin. A young man presented with impaired consciousness, ataxia, dysarthria, limb weakness, and restricted eyeball abduction. His clinical symptoms were consistent with Bickerstaff’s brainstem encephalitis.

Conclusions

This is the first case report of Bickerstaff’s brainstem encephalitis caused by Salmonella Dublin in the literature. After treatment, he recovered and was discharged. Early antibiotic treatment of sepsis may control the disease and avoid serious encephalopathy.

Comparison of cell invasion, macrophage survival and inflammatory cytokines profiles between Salmonella enterica serovars Enteritidis and Dublin from Brazil

AIMS

This study compared the capacity of strains of Salmonella enterica serovars Enteritidis and Dublin isolated in Brazil to invade epithelial cells, to be internalized by and survive within macrophages, and to stimulate cytokine release in vitro.

METHODS AND RESULTS

Both serovars infected 75 and 73% Caco-2 (human) and MDBK (bovine) epithelial cells respectively. Salmonella Dublin and S. Enteritidis (i) were internalized at the respective rates of 79·6 and 65·0% (P ≤ 0·05) by U937 (human) macrophages, and 70·4 and 66·9% by HD11 (chicken) macrophages; and (ii) multiplied at the respective rates of 3·2- and 2·7-fold within U937 cells, and 1·9- and 1·1-fold (P ≤ 0·05) within HD11 cells respectively. Seventy per cent of 10 S. Dublin strains stimulated IL-8 production, while 70% of S. Enteritidis strains enhanced production of IL-1β, IL-6, IL-8, IL-10, IL-12p70 and TNF in Caco-2 cells.

CONCLUSIONS

Compared with S. Enteritidis, S. Dublin had stronger ability to survive within macrophages and induced weak cytokine production, which may explain the higher incidence of invasive diseases caused by S. Dublin in humans.

SIGNIFICANCE AND IMPACT OF THE STUDY

This study compared S. enterica serovars Enteritidis and Dublin to provide comparative data about the profile of the two serovars in cells from humans, the common host and their respective natural animal hosts and vice versa in order to check the differences between these two phylogenetically closely related serovars that share antigenic properties but present different phenotypic behaviours.

Disentangling a complex nationwide Salmonella Dublin outbreak associated with raw-milk cheese consumption, France, 2015 to 2016

On 18 January 2016, the French National Reference Centre for Salmonella reported to Santé publique France an excess of Salmonella enterica serotype Dublin (S. Dublin) infections. We investigated to identify the source of infection and implement control measures. Whole genome sequencing (WGS) and multilocus variable-number tandem repeat analysis (MLVA) were performed to identify microbiological clusters and links among cases, animal and food sources. Clusters were defined as isolates with less than 15 single nucleotide polymorphisms determined by WGS and/or with identical MLVA pattern. We compared different clusters of cases with other cases (case–case study) and controls recruited from a web-based cohort (case–control study) in terms of food consumption. We interviewed 63/83 (76%) cases; 2,914 controls completed a questionnaire. Both studies’ findings indicated that successive S. Dublin outbreaks from different sources had occurred between November 2015 and March 2016. In the case–control study, cases of distinct WGS clusters were more likely to have consumed Morbier (adjusted odds ratio (aOR): 14; 95% confidence interval (CI): 4.8–42) or Vacherin Mont d’Or (aOR: 27; 95% CI: 6.8–105), two bovine raw-milk cheeses. Based on these results, the Ministry of Agriculture launched a reinforced control plan for processing plants of raw-milk cheeses in the production region, to prevent future outbreaks.

Highly Sensitive and Specific Detection and Serotyping of Five Prevalent Salmonella Serovars by Multiple Cross-Displacement Amplification

Salmonella is a common cause of foodborne disease worldwide, including Australia. More than 85% of outbreaks of human salmonellosis in Australia were caused by five Salmonella serovars. Rapid, accurate, and sensitive identification of Salmonella serovars is vital for diagnosis and public health surveillance. Recently, an isothermal amplification technique, termed multiple cross-displacement amplification (MCDA), has been employed to detect Salmonella at the species level. Herein, seven MCDA assays were developed and evaluated for rapid detection and differentiation of the five most common Salmonella serovars in Australia: Typhimurium, Enteritidis, Virchow, Saintpaul, and Infantis. MCDA primer sets were designed by targeting seven serovar/lineage-specific gene markers identified through genomic comparisons. The sensitivity and specificity of the seven MCDA assays were evaluated using 79 target strains and 32 nontarget strains. The assays were all highly sensitive and specific to target serovars, with the sensitivity ranging from 92.9% to 100% and the specificity from 93.3% to 100%. The limit of detection of the seven MCDA assays was 50 fg per reaction (10 copies) from pure DNA, and positive results were detected in as little as 8 minutes. These seven MCDA assays offer a rapid, accurate, and sensitive serotyping method. With further validation in clinically relevant conditions, these assays could be used for culture-independent serotyping of common Salmonella serovars directly from clinical samples.

Mechanisms to Evade the Phagocyte Respiratory Burst Arose by Convergent Evolution in Typhoidal Salmonella Serovars

Typhoid fever caused by Salmonella enterica serovar (S.) Typhi differs in its clinical presentation from gastroenteritis caused by S. Typhimurium and other non-typhoidal Salmonella serovars. The different clinical presentations are attributed in part to the virulence-associated capsular polysaccharide (Vi antigen) of S. Typhi, which prevents phagocytes from triggering a respiratory burst by preventing antibody-mediated complement activation. Paradoxically, the Vi antigen is absent from S. Paratyphi A, which causes a disease that is indistinguishable from typhoid fever. Here, we show that evasion of the phagocyte respiratory burst by S. Paratyphi A required very long O antigen chains containing the O2 antigen to inhibit antibody binding. We conclude that the ability to avoid the phagocyte respiratory burst is a property distinguishing typhoidal from non-typhoidal Salmonella serovars that was acquired by S. Typhi and S. Paratyphi A independently through convergent evolution.

Comprehensive Analysis Reveals Two Distinct Evolution Patterns of Salmonella Flagellin Gene Clusters

Salmonella is one of the primary causes of foodborne disease, especially Salmonella enterica subsp. enterica (I) which has caused ~99% of clinical salmonellosis cases for humans and domestic mammals. The flagella genes, fliC and fljB, which encode the Salmonella phase 1 and phase 2 antigens respectively, are considered as the Salmonella serotype determinant genes, and contribute to the virulence of Salmonella. However, the evolution of the two flagellin genes is still not well-understood. In this study, the fliC and fljB gene clusters were analyzed among 205 S. enterica subspecies I genomes. The dataset covered 87 different serovars of S. enterica subsp. enterica and included 9 genomes (six serovars) of four other Salmonella subspecies. Based on a pan-genome definition and flanked gene linkages, the fliC and fljB gene clusters were identified in 207 (91 serovars) and 138 (61 serovars) genomes, respectively. A phylogenetic tree constructed based on SNPs (Single Nucleotide Polymorphisms) of core genes were used to reflect the essential evolutionary relationships among various serovars. Congruence analysis was performed among the core genome and each gene of fliC and fljB gene clusters, with only fliA and fliS showing congruence to Salmonella core genome. Congruence was also observed among fliB, fliC/fljB, and fliD genes, and their phylogeny revealed a division into two major groups, which strongly corresponded to monophasic and biphasic serovars. Besides, homologous recombination events referring fliB, fliC, and fliD were found to have mainly occurred within each group. These results suggested two distinct evolutionary patterns of Salmonella flagellin gene clusters. Further insight on the evolutionary implication of the two patterns and a framework for phase variation mechanism are needed to be further processed.

A Naturally Occurring Deletion in FliE from Salmonella enterica Serovar Dublin Results in an Aflagellate Phenotype and Defective Proinflammatory Properties

Salmonella enterica serovar Dublin is adapted to cattle but is able to infect humans with high invasiveness. An acute inflammatory response at the intestine helps to prevent Salmonella dissemination to systemic sites. Flagella contribute to this response by providing motility and FliC-mediated signaling through pattern recognition receptors. In a previous work, we reported a high frequency (11 out of 25) of S Dublin isolates lacking flagella in a collection obtained from humans and cattle. The aflagellate strains were impaired in their proinflammatory properties in vitro and in vivo The aim of this work was to elucidate the underlying cause of the absence of flagella in S Dublin isolates. We report here that class 3 flagellar genes are repressed in the human aflagellate isolates, due to impaired secretion of FliA anti-sigma factor FlgM. This phenotype is due to an in-frame 42-nucleotide deletion in the fliE gene, which codes for a protein located in the flagellar basal body. The deletion is predicted to produce a protein lacking amino acids 18 to 31. The aflagellate phenotype was highly stable; revertants were obtained only when fliA was artificially overexpressed combined with several successive passages in motility agar. DNA sequence analysis revealed that motile revertants resulted from duplications of DNA sequences in fliE adjacent to the deleted region. These duplications produced a FliE protein of similar length to the wild type and demonstrate that amino acids 18 to 31 of FliE are not essential. The same deletion was detected in S Dublin isolates obtained from cattle, indicating that this mutation circulates in nature.

Draft Genome Sequences of Yersinia frederiksenii, Yersinia intermedia, and Yersinia kristensenii Strains from Brazil

Yersinia enterocolitica-like strains are usually understudied. In this work, we reported the draft genome sequences of two Yersinia frederiksenii, two Yersinia intermedia, and two Yersinia kristensenii strains isolated from humans, animals, food, and the environment in Brazil. These draft genomes will provide better molecular characterizations of these species.

Isolation, Identification, and Antibiotic Susceptibility Testing of Salmonella from Slaughtered Bovines and Ovines in Addis Ababa Abattoir Enterprise, Ethiopia: A Cross-Sectional Study

Salmonellae are ubiquitous, found in animals, humans, and the environment, a condition which facilitates transmission and cross contamination. Salmonella enterica serotypes exert huge health and economic impacts due to their virulence or carriage of antibiotic resistance traits. To address this significant issues with regard to public health, availability of adequate information on the prevalence and antibiotic resistance patterns of Salmonella, and establishment of adequate measures to control contamination and infection are needed. A cross-sectional study was conducted to assess the level of Salmonella infection in slaughtered bovines and ovines at Addis Ababa abattoir. Samples were collected randomly and processed for identification and antimicrobial susceptibility testing of Salmonella spp. From 280 animals examined, 13 (4.64%) (8 bovines and 5 ovines) were positive, with most samples (12/13, 92%) comprising Salmonella Dublin. Very high level of resistance to some antibiotics used in human medicine was detected. Most isolates were susceptible to gentamycin and amikacin. Nine (69%) of all isolates were resistant to multiple antibiotics. Serotyping revealed 12 of 13 isolates to be of the Dublin serotype with 9,12:g,p:- antigenic formula. This study emphasizes the importance of improving the evisceration practice during slaughtering and restricting the use of antibiotics in farm animals.

Invasive Salmonellosis in Humans

Human salmonellosis is generally associated with Salmonella enterica from subspecies enterica (subspecies I). Acute infections can present in one of four ways: enteric fever, gastroenteritis, bacteremia, or extraintestinal focal infection. As with other infectious diseases, the course and outcome of the infection depend on a variety of factors, including the infecting organism, the inoculating dose, and the immune status and genetic background of the host. For serovarsTyphi and Paratyphi A there is a clear association between the genetic background of the serovar and systemic infection in humans. For serovars Paratyphi B and Paratyphi C, a good clinical description of the host and detailed population genetics of the pathogen are necessary before more detailed genetic studies of novel virulence factors,or host factors,can be initiated. For the nontyphoidalserovars (NTS) the situation is less clear. Serovars Typhimurium and Enteritidis are the most common within the food chain, and so the large number of invasive infections associated with these serovars is most likely due to exposure rather than to increased virulence of the pathogen. In Africa, however, a closely related group of strains of serovar Typhimurium, associated with HIV infection, may have become host adapted tohumans, suggesting that not all isolates called "Typhimurium" should be considered as a single group. Here we review current knowledge of the salmonellae for which invasive disease in humans is an important aspect of their population biology.

Genomic Comparison of the Closely-Related Salmonella enterica Serovars Enteritidis, Dublin and Gallinarum

The Salmonella enterica serovars Enteritidis, Dublin, and Gallinarum are closely related but differ in virulence and host range. To identify the genetic elements responsible for these differences and to better understand how these serovars are evolving, we sequenced the genomes of Enteritidis strain LK5 and Dublin strain SARB12 and compared these genomes to the publicly available Enteritidis P125109, Dublin CT 02021853 and Dublin SD3246 genome sequences. We also compared the publicly available Gallinarum genome sequences from biotype Gallinarum 287/91 and Pullorum RKS5078. Using bioinformatic approaches, we identified single nucleotide polymorphisms, insertions, deletions, and differences in prophage and pseudogene content between strains belonging to the same serovar. Through our analysis we also identified several prophage cargo genes and pseudogenes that affect virulence and may contribute to a host-specific, systemic lifestyle. These results strongly argue that the Enteritidis, Dublin and Gallinarum serovars of Salmonella enterica evolve by acquiring new genes through horizontal gene transfer, followed by the formation of pseudogenes. The loss of genes necessary for a gastrointestinal lifestyle ultimately leads to a systemic lifestyle and niche exclusion in the host-specific serovars.

The Pyromaniac Inside You: Salmonella Metabolism in the Host Gut

A metabolically diverse microbial community occupies all available nutrient-niches in the lumen of the mammalian intestine, making it difficult for pathogens to establish themselves in this highly competitive environment. Salmonella serovars sidestep the competition by using their virulence factors to coerce the host into creating a novel nutrient-niche. Inflammation-derived nutrients available in this new niche support a bloom of Salmonella serovars, thereby ensuring transmission of the pathogen to the next susceptible host by the fecal-oral route. Here we review the anaerobic food chain that characterizes resident gut-associated microbial communities along with the winning metabolic strategy Salmonella serovars use to edge out competing microbes in the inflamed intestine.

Salmonella phages and prophages: genomics, taxonomy, and applied aspects

Since this book was originally published in 2007 there has been a significant increase in the number of Salmonella bacteriophages, particularly lytic virus, and Salmonella strains which have been fully sequenced. In addition, new insights into phage taxonomy have resulted in new phage genera, some of which have been recognized by the International Committee of Taxonomy of Viruses (ICTV). The properties of each of these genera are discussed, along with the role of phage as agents of genetic exchange, as therapeutic agents, and their involvement in phage typing.

Patterns of genome evolution that have accompanied host adaptation in Salmonella

Many bacterial pathogens are specialized, infecting one or few hosts, and this is often associated with more acute disease presentation. Specific genomes show markers of this specialization, which often reflect a balance between gene acquisition and functional gene loss. Within Salmonella enterica subspecies enterica, a single lineage exists that includes human and animal pathogens adapted to cause infection in different hosts, including S. enterica serovar Enteritidis (multiple hosts), S. Gallinarum (birds), and S. Dublin (cattle). This provides an excellent evolutionary context in which differences between these pathogen genomes can be related to host range. Genome sequences were obtained from ∼ 60 isolates selected to represent the known diversity of this lineage. Examination and comparison of the clades within the phylogeny of this lineage revealed signs of host restriction as well as evolutionary events that mark a path to host generalism. We have identified the nature and order of events for both evolutionary trajectories. The impact of functional gene loss was predicted based upon position within metabolic pathways and confirmed with phenotyping assays. The structure of S. Enteritidis is more complex than previously known, as a second clade of S. Enteritidis was revealed that is distinct from those commonly seen to cause disease in humans or animals, and that is more closely related to S. Gallinarum. Isolates from this second clade were tested in a chick model of infection and exhibited a reduced colonization phenotype, which we postulate represents an intermediate stage in pathogen-host adaptation.

Repression of flagella is a common trait in field isolates of Salmonella enterica serovar Dublin and is associated with invasive human infections

The nontyphoidal Salmonella enterica serovar Dublin is adapted to cattle but infrequently infects humans, very often resulting in invasive infections with high levels of morbidity and mortality. A Salmonella-induced intestinal acute inflammatory response is postulated as a mechanism to prevent bacterial dissemination to systemic sites. In S. enterica serovar Typhimurium, flagella contribute to this response by providing motility and FliC-mediated activation of pattern recognition receptors. In this study, we found 4 Salmonella enterica isolates, with the antigenic formula 9,12:-:-, that, based on fliC sequence and multilocus sequence type (MLST) analyses, are aflagellate S. Dublin isolates. Interestingly, all were obtained from human bloodstream infections. Thus, we investigated the potential role of flagella in the unusual invasiveness exhibited by S. Dublin in humans by analyzing flagellation and proinflammatory properties of a collection of 10 S. Dublin human clinical isolates. We found that 4 of 7 blood isolates were aflagellate due to significantly reduced levels of fliC expression, whereas all 3 isolates from other sources were flagellated. Lack of flagella correlated with a reduced ability of triggering interleukin-8 (IL-8) and CCL20 chemokine expression in human intestinal Caco-2 cells and with reduced early inflammation in the ceca of streptomycin-pretreated C57/BL6 mice. These results indicate that flagella contribute to the host intestinal inflammatory response to Salmonella serovar Dublin and suggest that their absence may contribute to its systemic dissemination through dampening of the gut immune response. Analysis of FliC production in a collection of cattle isolates indicated that the aflagellate phenotype is widely distributed in field isolates of S. Dublin.

Loss of very-long O-antigen chains optimizes capsule-mediated immune evasion by Salmonella enterica serovar Typhi

Expression of capsular polysaccharides is a variable trait often associated with more-virulent forms of a bacterial species. For example, typhoid fever is caused by the capsulated Salmonella enterica serovar Typhi, while nontyphoidal Salmonella serovars associated with gastroenteritis are noncapsulated. Here we show that optimization of the immune evasive properties conferred by the virulence-associated (Vi) capsular polysaccharide involved an additional alteration to the cell envelope of S. Typhi, namely inactivation of the fepE gene, encoding the regulator of very-long O-antigen chains. Introduction of the capsule-encoding viaB locus into the nontyphoidal S. enterica serovar Typhimurium reduced complement deposition in vitro and intestinal inflammation in a mouse colitis model. However, both phenotypes were markedly enhanced when the viaB locus was introduced into an S. Typhimurium fepE mutant, which lacks very-long O-antigen chains. Collectively, these data suggest that during the evolution of the S. Typhi lineage, loss of very-long O-antigen chains by pseudogene formation was an adaptation to maximize the anti-inflammatory properties of the Vi capsular polysaccharide.

Genomic comparison illustrates that acquisition of virulence factors by horizontal gene transfer is an important contributor to the evolution of enteric pathogens. Acquisition of complex virulence traits commonly involves horizontal transfer of a large gene cluster, and integration of the gene cluster into the host genome results in the formation of a pathogenicity island. Acquisition of the virulence-associated (Vi) capsular polysaccharide encoded by SPI7 (Salmonella pathogenicity island 7) was accompanied in the human-adapted Salmonella enterica serovar Typhi by inactivation of the fepE gene, encoding the regulator of very-long O-antigen chains. We show that the resulting loss of very-long O-antigen chains was an important mechanism for maximizing immune evasion mediated by the Vi capsular polysaccharide. These data suggest that successful incorporation of a capsular polysaccharide requires changes in the cell envelope of the hosting pathogen.

Salmonella enterica diversity in central Californian coastal waterways

Salmonella enterica is one of the most important bacterial enteric pathogens worldwide. However, little is known about its distribution and diversity in the environment. The present study explored the diversity of 104 strains of Salmonella enterica isolated over 2 years from 12 coastal waterways in central California. Pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing were used to probe species diversity. Seventy-four PFGE patterns and 38 sequence types (STs) were found, including 18 newly described STs. Nineteen of 25 PFGE patterns were indistinguishable from those of clinical isolates in PulseNet. The most common ST was consistent with S. enterica serovar Typhimurium, and other frequently detected STs were associated with the serovars Heidelberg and Enteritidis; all of these serovars are important etiologies of salmonellosis. An investigation into S. enterica biogeography was conducted at the level of ST and subspecies. At the ST and subspecies level, we found a taxon-time relationship but no taxon-area or taxon-environmental distance relationships. STs collected during wet versus dry conditions tended to be more similar; however, STs collected from waterways adjacent to watersheds with similar land covers did not tend to be similar. The results suggest that the lack of dispersal limitation may be an important factor affecting the diversity of S. enterica in the region.

The importance of motility and chemotaxis for extra-animal survival of Salmonella enterica serovar Typhimurium and Dublin

AIMS

This study investigated the importance of flagella and motility of Salmonella enterica serovar Typhimurium and Dublin in models of extra-animal survival.

METHODS AND RESULTS

The study was performed using transposon mutants in flagella genes fliC and fljB and in chemotaxis genes cheA, cheB and cheR. Flagella and chemotaxis were found to be of minor importance for attachment to plant leaves, survival in liquid manure and interaction with the nematode C. elegans, while differences were observed between the fliC mutant and the wild-type strain of S. Dublin in interactions with amoebae.

CONCLUSIONS

The study shows that flagella and chemotaxis play a minor role in extra-animal survival of these two serovars of Salmonella under the conditions tested.

SIGNIFICANCE AND IMPACT OF THE STUDY

Extra-animal survival is important in the full infection cycle for zoonotic salmonellae. Such serovars are motile. Even though the current study was only based on the characterization of two serovars, it strongly suggests that motility and chemotaxis are of minor importance during the spread of Salmonella from one animal to the next through the external environment.

Multilocus sequence typing as a replacement for serotyping in Salmonella enterica

Salmonella enterica subspecies enterica is traditionally subdivided into serovars by serological and nutritional characteristics. We used Multilocus Sequence Typing (MLST) to assign 4,257 isolates from 554 serovars to 1092 sequence types (STs). The majority of the isolates and many STs were grouped into 138 genetically closely related clusters called eBurstGroups (eBGs). Many eBGs correspond to a serovar, for example most Typhimurium are in eBG1 and most Enteritidis are in eBG4, but many eBGs contained more than one serovar. Furthermore, most serovars were polyphyletic and are distributed across multiple unrelated eBGs. Thus, serovar designations confounded genetically unrelated isolates and failed to recognize natural evolutionary groupings. An inability of serotyping to correctly group isolates was most apparent for Paratyphi B and its variant Java. Most Paratyphi B were included within a sub-cluster of STs belonging to eBG5, which also encompasses a separate sub-cluster of Java STs. However, diphasic Java variants were also found in two other eBGs and monophasic Java variants were in four other eBGs or STs, one of which is in subspecies salamae and a second of which includes isolates assigned to Enteritidis, Dublin and monophasic Paratyphi B. Similarly, Choleraesuis was found in eBG6 and is closely related to Paratyphi C, which is in eBG20. However, Choleraesuis var. Decatur consists of isolates from seven other, unrelated eBGs or STs. The serological assignment of these Decatur isolates to Choleraesuis likely reflects lateral gene transfer of flagellar genes between unrelated bacteria plus purifying selection. By confounding multiple evolutionary groups, serotyping can be misleading about the disease potential of S. enterica. Unlike serotyping, MLST recognizes evolutionary groupings and we recommend that Salmonella classification by serotyping should be replaced by MLST or its equivalents.

Microbiologists have used serological and nutritional characteristics to subdivide pathogenic bacteria for nearly 100 years. These subdivisions in Salmonella enterica are called serovars, some of which are thought to be associated with particular diseases and epidemiology. We used MultiLocus Sequence-based Typing (MLST) to identify clusters of S. enterica isolates that are related by evolutionary descent. Some clusters correspond to serovars on a one to one basis. But many clusters include multiple serovars, which is of public health significance, and most serovars span multiple, unrelated clusters. Despite its broad usage, serological typing of S. enterica has resulted in confusing systematics, with a few exceptions. We recommend that serotyping for strain discrimination of S. enterica be replaced by a DNA-based method, such as MLST. Serotyping and other non-sequence based typing methods are routinely used for detecting outbreaks and to support public health responses. Moving away from these methods will require a major shift in thinking by public health microbiology laboratories as well as national and international agencies. However, a transition to the routine use of MLST, supplemented where appropriate by even more discriminatory sequence-based typing methods based on entire genomes, will provide a clearer picture of long-term transmission routes of Salmonella, facilitate data transfer and support global control measures.

Genomic Comparison of the Closely Related Salmonella enterica Serovars Enteritidis and Dublin

The Enteritidis and Dublin serovars of Salmonella enterica are closely related, yet they differ significantly in pathogenicity and epidemiology. S. Enteritidis is a broad host range serovar that commonly causes gastroenteritis and infrequently causes invasive disease in humans. S. Dublin mainly colonizes cattle but upon infecting humans often results in invasive disease.To gain a broader view of the extent of these differences we conducted microarray-based comparative genomics between several field isolates from each serovar. Genome degradation has been correlated with host adaptation in Salmonella, thus we also compared at whole genome scale the available genomic sequences of them to evaluate pseudogene composition within each serovar.Microarray analysis revealed 3771 CDS shared by both serovars while 33 were only present in Enteritidis and 87 were exclusive to Dublin. Pseudogene evaluation showed 177 inactive CDS in S. Dublin which correspond to active genes in S. Enteritidis, nine of which are also inactive in the host adapted S. Gallinarum and S. Choleraesuis serovars. Sequencing of these 9 CDS in several S. Dublin clinical isolates revealed that they are pseudogenes in all of them, indicating that this feature is not peculiar to the sequenced strain. Among these CDS, shdA (Peyer´s patch colonization factor) and mglA (galactoside transport ATP binding protein), appear also to be inactive in the human adapted S. Typhi and S. Paratyphi A, suggesting that functionality of these genes may be relevant for the capacity of certain Salmonella serovars to infect a broad range of hosts.

Removal of Salmonella and indicator micro-organisms in integrated constructed wetlands treating agricultural wastewater

The purpose of this study was to investigate the removal of pathogenic and indicator micro-organisms in integrated constructed wetland (ICW) systems treating agricultural wastewater. Nine ICW's treating piggery (3) or dairy (6) wastewaters were sampled and indicator micro-organisms were enumerated in the influent as well as the effluent from the first, mid- and final cells. The presence/absence of Salmonella was also determined and any Salmonella isolates recovered were characterized. Mean counts of coliform, E. coli and Enterococcus across all nine ICW systems were lower in the final effluent than in the effluent from cell 1 (P < 0.001). An antibiotic susceptible isolate of Salmonella Dublin, a bovine-adapted serotype, was isolated from the influent to one dairy ICW but was not detected in any of the ICW cells. An antibiotic sensitive Salmonella Dublin isolate with the same molecular fingerprint was also recovered from the cell 1 effluent of another dairy ICW but was absent from the influent and the mid-cell and final effluents. Salmonella Typhimurium DT104b was detected in the liquid fraction of anaerobically digested pig manure as well as in the effluent from the first cell and mid-cell of an ICW treating this material, but was absent in the final effluent. Molecular fingerprinting by pulsed field gel electrophoresis demonstrated that the recovered isolates were highly related. However, they had different antimicrobial resistance profiles, with some highly resistant isolates recovered. In conclusion, counts of indicator micro-organisms were reduced significantly within ICW, with E. coli and Enterococcus non-detectable in the final effluent. Moreover, Salmonella, when present in the influent, appears to have been removed.

Identification by PCR of non-typhoidal Salmonella enterica serovars associated with invasive infections among febrile patients in Mali

Background

In sub-Saharan Africa, non-typhoidal Salmonella (NTS) are emerging as a prominent cause of invasive disease (bacteremia and focal infections such as meningitis) in infants and young children. Importantly, including data from Mali, three serovars, Salmonella enterica serovar Typhimurium, Salmonella Enteritidis and Salmonella Dublin, account for the majority of non-typhoidal Salmonella isolated from these patients.

Methods

We have extended a previously developed series of polymerase chain reactions (PCRs) based on O serogrouping and H typing to identify Salmonella Typhimurium and variants (mostly I 4,[5],12:i:-), Salmonella Enteritidis and Salmonella Dublin. We also designed primers to detect Salmonella Stanleyville, a serovar found in West Africa. Another PCR was used to differentiate diphasic Salmonella Typhimurium and monophasic Salmonella Typhimurium from other O serogroup B, H:i serovars. We used these PCRs to blind-test 327 Salmonella serogroup B and D isolates that were obtained from the blood cultures of febrile patients in Bamako, Mali.

Principal Findings

We have shown that when used in conjunction with our previously described O-serogrouping PCR, our PCRs are 100% sensitive and specific in identifying Salmonella Typhimurium and variants, Salmonella Enteritidis, Salmonella Dublin and Salmonella Stanleyville. When we attempted to differentiate 171 Salmonella Typhimurium (I 4,[ 5],12:i:1,2) strains from 52 monophasic Salmonella Typhimurium (I 4,[5],12:i:-) strains, we were able to correctly identify 170 of the Salmonella Typhimurium and 51 of the Salmonella I 4,[5],12:i:- strains.

Conclusion

We have described a simple yet effective PCR method to support surveillance of the incidence of invasive disease caused by NTS in developing countries.

The genus Salmonella has more than 2500 serological variants (serovars), such as Salmonella enterica serovar Typhi and Salmonella Paratyphi A and B, that cause, respectively, typhoid and paratyphoid fevers (enteric fevers), and a large number of non-typhoidal Salmonella (NTS) serovars that cause gastroenteritis in healthy hosts. In young infants, the elderly and immunocompromised hosts, NTS can cause severe, fatal invasive disease. Multiple studies of pediatric patients in sub-Saharan Africa have documented the important role of NTS, in particular Salmonella Typhimurium and Salmonella Enteritidis (and to a lesser degree Salmonella Dublin), as invasive bacterial pathogens. Salmonella spp. are isolated from blood and identified by standard microbiological techniques and the serovar is ascertained by agglutination with commercial antisera. PCR-based typing techniques are becoming increasingly popular in developing countries, in part because high quality typing sera are difficult to obtain and expensive and H serotyping is technically difficult. We have developed a series of polymerase chain reactions (PCRs) to identify Salmonella Typhimurium and variants, Salmonella Enteritidis and Salmonella Dublin. We successfully identified 327 Salmonella isolates using our multiplex PCR. We also designed primers to detect Salmonella Stanleyville, a serovar found in West Africa. Another PCR generally differentiated diphasic Salmonella Typhimurium and monophasic Salmonella Typhimurium variant strains from other closely related strains. The PCRs described here will enable more laboratories in developing countries to serotype NTS that have been isolated from blood.

Identification of Salmonella enterica serovar Dublin-specific sequences by subtractive hybridization and analysis of their role in intestinal colonization and systemic translocation in cattle

Salmonella enterica serovar Dublin is a host-restricted serovar associated with typhoidal disease in cattle. In contrast, the fowl-associated serovar S. enterica serovar Gallinarum is avirulent in calves, yet it invades ileal mucosa and induces enteritis at levels comparable to those induced by S. enterica serovar Dublin. Suppression subtractive hybridization was employed to identify S. enterica serovar Dublin strain SD3246 genes absent from S. enterica serovar Gallinarum strain SG9. Forty-one S. enterica serovar Dublin fragments were cloned and sequenced. Among these, 24 mobile-element-associated genes were identified, and 12 clones exhibited similarity with sequences of known or predicted function in other serovars. Three S. enterica serovar Dublin-specific regions were homologous to regions from the genome of Enterobacter sp. strain 638. Sequencing of fragments adjacent to these three sequences revealed the presence of a 21-kb genomic island, designated S. enterica serovar Dublin island 1 (SDI-1). PCR analysis and Southern blotting showed that SDI-1 is highly conserved within S. enterica serovar Dublin isolates but rarely found in other serovars. To probe the role of genes identified by subtractive hybridization in vivo, 24 signature-tagged S. enterica serovar Dublin SD3246 mutants lacking loci not present in Salmonella serovar Gallinarum SG9 were created and screened by oral challenge of cattle. Though attenuation of tagged SG9 and SD3246 Salmonella pathogenicity island-1 (SPI-1) and SPI-2 mutant strains was detected, no obvious defects of these 24 mutants were detected. Subsequently, a DeltaSDI-1 mutant was found to exhibit weak but significant attenuation compared with the parent strain in coinfection of calves. SDI-1 mutation did not impair invasion, intramacrophage survival, or virulence in mice, implying that SDI-1 does not influence fitness per se and may act in a host-specific manner.

Rapid detection of Salmonella dublin by PCR amplification of the SopE gene and its cloning

This study is directed towards the method of amplifying and cloning the SopE gene, that encodes Salmonella outer protein E. Strains used in this study were S. dublin collected from Kermanshah province. Genomic DNA was extracted by the general boiling method. Using the specific primers, a part of SopE gene was multiplied. The PCR product was inserted into the cloning vector (pTZ57R/T). Furthermore, E. coli DH5alpha bacteria were transformed to amplify the recombinant plasmid. Recombinant clones were identified by blue/white selection. Recombinant plasmids were purified by alkaline lysis procedure. Moreover, identity of the SopE/pTZ57R/T product was confirmed by restriction enzyme digestion assay and sequencing. Finally, the cloned gene was compared with that published by the NCBI Genbank (L78932). The results showed that the obtained sequence differed in four nucleotides which resulted in two amino acid differences. The cloned SopE was submitted to the NCBI Genbank (EU399750).

Salmonella phages and prophages--genomics and practical aspects

Numerous bacteriophages specific to Salmonella have been isolated or identified as part of host genome sequencing projects. Phylogenetic analysis of the sequenced phages, based on related protein content using CoreGenes, reveals that these viruses fall into five groupings (P27-like, P2-like, lambdoid, P22-like, and T7-like) and three outliers (epsilon15, KS7, and Felix O1). The P27 group is only represented by ST64B; the P2 group contains Fels-2, SopEphi, and PSP3; the lambdoid Salmonella phages include Gifsy-1, Gifsy-2, and Fels-1. The P22-like viruses include epsilon34, ES18, P22, ST104, and ST64T. The only member of the T7-like group is SP6. The properties of each of these phages are discussed, along with their role as agents of genetic exchange and as therapeutic agents and their involvement in phage typing.

Salmonella Epidemiology and Pathogenesis in Food-Producing Animals

This review reviews the pathogenesis of different phases of Salmonella infections. The nature of Salmonella infections in several domesticated animal species is described to highlight differences in the epidemiology and pathogenesis of salmonellosis in different hosts. The biology of Salmonella serovar host specificity is discussed in the context of our current understanding of the molecular basis of pathogenesis and the potential impact of different virulence determinants on Salmonella natural history. The ability to colonize the intestine, as evidenced by the shedding of relatively large numbers of bacteria in the feces over a long period, is shared unequally by Salmonella serovars. Studies probing the molecular basis of Salmonella intestinal colonization have been carried out by screening random transposon mutant banks of serovar Typhimurium in a range of avian and mammalian species. It is becoming increasingly clear that Salmonella pathogenicity island 2 (SPI2) is a major virulence factor during infection of food-producing animals, including cattle and poultry. The prevalence of Salmonella serovars in domestic fowl varies in different countries and with time. Although chickens are the natural hosts of serovars Gallinarum and Pullorum, natural outbreaks caused by these serovars in turkeys, guinea fowl, and other avian species have been described. There are two possible explanations to account for the apparent host specificity of certain Salmonella serovars. Environmental factors may increase exposure of particular animal species to certain serovars. Alternatively, there are genetic differences between these serovars, which allow them to survive and/or grow in specific niches only found within ruminants or pigs.

DNA sequence-based subtyping and evolutionary analysis of selected Salmonella enterica serotypes

While serotyping and phage typing have been used widely to characterize Salmonella isolates, sensitive subtyping methods that allow for evolutionary analyses are essential for examining Salmonella transmission, ecology, and evolution. A set of 25 Salmonella enterica isolates, representing five clinically relevant serotypes (serotypes Agona, Heidelberg, Schwarzengrund, Typhimurium, and Typhimurium var. Copenhagen) was initially used to develop a multilocus sequence typing (MLST) scheme for Salmonella targeting seven housekeeping and virulence genes (panB, fimA, aceK, mdh, icdA, manB, and spaN). A total of eight MLST types were found among the 25 isolates sequenced. A good correlation between MLST types and Salmonella serotypes was observed; only one serotype Typhimurium var. Copenhagen isolate displayed an MLST type otherwise typical for serotype Typhimurium isolates. Since manB, fimA, and mdh allowed for the highest subtype discrimination among the initial 25 isolates, we chose these three genes to perform DNA sequencing of an additional 41 Salmonella isolates representing a larger diversity of serotypes. This "three-gene sequence typing scheme" allowed discrimination of 25 sequence types (STs) among a total of 66 isolates; STs correlated well with serotypes and allowed within-serotype differentiation for 9 of the 12 serotypes characterized. Phylogenetic analyses showed that serotypes Kentucky and Newport could each be separated into two distinct, statistically well supported evolutionary lineages. Our results show that a three-gene sequence typing scheme allows for accurate serotype prediction and for limited subtype discrimination among clinically relevant serotypes of Salmonella. Three-gene sequence typing also supports the notion that Salmonella serotypes represent both monophyletic and polyphyletic lineages.

Natural isolates of Salmonella enterica serovar Dublin carry a single nadA missense mutation

Nicotinic acid is required by most isolates of Salmonella enterica (serovar Dublin), a pathogen of cattle. A single nadA missense mutation causes the nutritional requirement of all serovar Dublin isolates tested. Models for persistence of this allele are tested and discussed.

Evolution and Ecology of Salmonella

Over the past 120 to 160 million years, the genus Salmonella has evolved into a complex group of more than 2,300 genetically and phenotypically diverse serovars. Members of this genus are able to infect a wide diversity of vertebrate and invertebrate hosts; disease manifestations in humans range from gastroenteritis to typhoid fever. The evolution of the genus Salmonella and the divergence and radiation of particular lineages within this group have resulted from selection acting on new genetic variation generated by events such as the gain, loss, and/or rearrangement of genetic material. These types of genetic events have contributed to the speciation of Salmonella from its ancestral association with cold-blood animals to a pathogen of warm-blooded hosts. Moreover, adaptive radiation due to changes in gene content within S. enterica subspecies I has impacted host specificity and aided in the selection of host-restricted, host-adapted, and non-host-adapted serovars. In addition to the genetic diversity important for the wide phenotypic heterogeneity within the genus, a subset of core Salmonella-specific genes present in all Salmonella species and serovars has been identified that may contribute to the conserved aspects of the lifestyle of this microorganism, including the ability to survive in nutrient-poor nonhost environments such as soil and water. Whole-genome comparisons of isolates differing in host range and virulence will continue to elucidate the genetic mechanisms that have contributed to the evolution and diverse ecology of the genus Salmonella.

Population structure of Salmonella investigated by amplified fragment length polymorphism

AIMS

This study was undertaken to investigate the usefulness of amplified fragment length polymorphism (AFLP) in determining the population structure of Salmonella.

METHODS AND RESULTS

A total of 89 strains were subjected to AFLP analysis using the enzymes BglII and BspDI, a combination that is novel in Salmonella. Both species S. bongori and S. enterica and all subsp. of S. enterica were represented with emphasis on S. enterica subsp. enterica using a local strain collection and strains from the Salmonella Reference Collection B (SARB). The amplified fragments were used in a band-based cluster analysis. The tree resulting from the subgroup analysis clearly separated all subgroups with high bootstrap values with the species S. bongori being the most distantly related of the subgroups. The tree resulting from the analysis of the SARB collection showed that some serotypes are very clonal whereas others are highly divergent.

CONCLUSIONS

AFLP clearly clustered strains representing the subgroups of Salmonella together with high bootstrap values and the serotypes of subspecies enterica were divided into polyphyletic or monophyletic types corresponding well with multilocus enzyme electrophoresis (MLEE) and sequence-based studies of the population structure in Salmonella.

SIGNIFICANCE AND IMPACT OF THE STUDY

AFLP with the enzyme combination BglII and BspDI allows discrimination of individual strains and provides evidence for the usefulness of AFLP in studies of population structure in Salmonella.

Towards the development of a DNA-sequence based approach to serotyping of Salmonella enterica

Background

The fliC and fljB genes in Salmonella code for the phase 1 (H1) and phase 2 (H2) flagellin respectively, the rfb cluster encodes the majority of enzymes for polysaccharide (O) antigen biosynthesis, together they determine the antigenic profile by which Salmonella are identified. Sequencing and characterisation of fliC was performed in the development of a molecular serotyping technique.

Results

FliC sequencing of 106 strains revealed two groups; the g-complex included those exhibiting "g" or "m,t" antigenic factors, and the non-g strains which formed a second more diverse group. Variation in fliC was characterised and sero-specific motifs identified. Furthermore, it was possible to identify differences in certain H antigens that are not detected by traditional serotyping. A rapid short sequencing assay was developed to target serotype-specific sequence motifs in fliC. The assay was evaluated for identification of H1 antigens with a panel of 55 strains.

Conclusion

FliC sequences were obtained for more than 100 strains comprising 29 different H1 alleles. Unique pyrosequencing profiles corresponding to the H1 component of the serotype were generated reproducibly for the 23 alleles represented in the evaluation panel. Short read sequence assays can now be used to identify fliC alleles in approximately 97% of the 50 medically most important Salmonella in England and Wales. Capability for high throughput testing and automation give these assays considerable advantages over traditional methods.

Differences in the carriage and the ability to utilize the serotype associated virulence plasmid in strains of Salmonella enterica serotype Typhimurium investigated by use of a self-transferable virulence plasmid, pOG669

Most strains of Salmonella enterica subspecies enterica serotype typhimurium (S. typhimurium) naturally harbour a virulence plasmid which carries the salmonella plasmid virulence (spv) genes. However, isolates belonging to certain phage types are generally found without the plasmid. We have utilized a self-transferable virulence plasmid, pOG669 to investigate the effect of introduction of spv genes into strains of such phage types. The use of the co-integrate plasmid, pOG669, was validated on a diverse collection of strains. pOG669 was transferred into strains of serotypes that are normally associated with the possession of virulence plasmids. All strains maintained the wild type level of virulence in a mouse model, except that introduction of pOG669 restored normal virulence levels in an avirulent, plasmid free strain of S. dublin and resulted in a decrease in virulence in a strain of S. dublin from clonal line Du3. S. gallinarum did not become virulent in mice, but pOG669 was functionally interchangeable with the wild type plasmid when strains were tested in a chicken model. Strains of serotypes not normally associated with the carriage of a virulence plasmid did not increase in virulence upon the introduction of pOG669. An IncX plasmid pOG670 that was included as control was incompatible with the virulence plasmid in a strain of S. dublin, demonstrating that the common virulence plasmid of this serotype is of a different incompatibility group than other virulence plasmids. Strains of S. typhimurium from phage types that do not normally carry a virulence plasmid responded differently to attempts to introduce pOG669. No transconjugants were observed with the strains of DT5 and DT21. The introduction of pOG669 did not alter the virulence of JEO3942(DT10), DT35 and JEO3949(DT66) significantly, while DT1 and DT27 became more virulent. DT27 became as virulent as wild type C5, while logVC(10) of DT1 only increased from 4.1 to 5.7. The ability to express spv-genes was measured by use of an spvRAB'-cat fusion. Expression in S. enteritidis was found to be higher than in other serotypes tested. Only serotypes that naturally carry a virulence plasmid expressed spv-genes. The strain of DT1 expressed spv at a very low level, while expression in the strains of DT10 and DT35 was approximately 2-fold lower than in a control strain of S. typhimurium, while the level in the DT66 strain corresponded to the control strain. The plasmid pSTF9, which carried the fusion gene could not be introduced into the strains of DT5, DT21 and DT27. The RpoS level in the strains was measured indirectly by use of a katE-lacZ fusion. In the DT5 strain the level of expression was low, while the strains JEO3942(DT10), DT21, DT27 and DT35 expressed 4-5 fold the level in this strain. An internal fragment of the rpoS gene was sequenced in three strains. These all showed an identical sequence to a published S. typhimurium rpoS gene.

Salmonella enterica serovar Dublin strains which are Vi antigen-positive use type IVB pili for bacterial self-association and human intestinal cell entry

Some strains of Salmonella enterica serovar Dublin are Vi antigen-positive. S. enterica serovar Typhi uses Type IVB pili, encoded adjacent to the viaB locus required for Vi antigen synthesis, to facilitate both eukaryotic cell attachment and bacterial self-association under conditions that favour DNA supercoiling. These pilus-mediated events may be important in typhoid fever pathogenesis. A survey of 17 isolates of S. enterica serovar Dublin showed that all strains which carried the viaB region also carried a serovar Typhi-like Type IVB pil operon, and all serovar Dublin Vi antigen-negative isolates lacked the pil operon. The pil operon was completely sequenced from one of the Vi(+) serovar Dublin strains, and was almost identical (4 nt changes; 3 aa changes, in over 10 kb) to that of serovar Typhi. A pilS mutant of one serovar Dublin strain was constructed, and shown to invade cultured human intestinal INT407 cells to an extent only 20% that of the wild-type parent. Purified prePilS protein inhibited INT407 cell entry by serovar Dublin. The wild-type serovar Dublin strain, but not the pilS mutant, self-associated. The data suggest that the serovar Dublin Type IVB pil operon may increase the human-invasiveness of serovar Dublin, compared to pil-free strains.

Investigation of the genetic diversity among isolates of Salmonella enterica serovar Dublin from animals and humans from England, Wales and Ireland

AIMS

To assess the degree of genetic diversity among animal Salmonella Dublin UK isolates, and to compare it with the genetic diversity found among human isolates from the same time period.

METHODS AND RESULTS

One hundred isolates (50 human and 50 animal) were typed using plasmid profiling, XbaI-pulsed field gel electrophoresis (PFGE) and PstI-SphI ribotyping. Antimicrobial resistance data to 16 antibiotics was presented, and the presence of class-I integrons was investigated by real-time PCR. Seven different plasmid profiles, 19 ribotypes and 21 PFGE types were detected. A combination of the three methods allowed clear differentiation of 43 clones or strains. Eighteen isolates were resistant to at least one antimicrobial; five of them were multi-resistant and of these, only three presented class I integrons.

CONCLUSIONS

Ribotyping data suggest the existence of at least three very different clonal lines; the same distribution in well-defined groups was not evident from the PFGE data. The existence of a variety of clones in both animals and humans has been demonstrated. A few prevalent clones seem to be widely disseminated among different animal species and show a diverse geographical and temporal distribution. The same clones were found in animals and humans, which may infer that both farm and pet animals may act as potential vehicles of infection for humans. Some other clones seem to be less widely distributed. Clustering analysis of genomic fingerprints of Salmonella Dublin and Salm. Enteritidis isolates confirms the existence of a close phylogenetic relationship between both serotypes.

SIGNIFICANCE AND IMPACT OF THE STUDY

This paper describes the utility of a multiple genetic typing approach for Salm. Dublin. It gives useful information on clonal diversity among human and animal isolates.

Salmonella enterica serotype Dublin infection: an emerging infectious disease for the northeastern United States

Salmonella enterica subspecies enterica serotype Dublin (S. enterica Dublin) emerged for the first time in New York, Pennsylvania, and Ohio in 1988. Since that time this host-adapted serotype has spread throughout the veal- and dairy beef-raising operations in the region; very few dairy farms have experienced clinical S. enterica Dublin infections. This study details the epidemiology of the outbreaks in cattle. During the period 1988 through 1995, nine New York and four Pennsylvania counties have been affected; 13 different locations were involved in New York, and 10 were involved in Pennsylvania. The morbidity and mortality and seasonal distribution of outbreaks, which totaled 35, is described. The antimicrobial susceptibility pattern of isolates revealed that many of the strains were resistant to a number of commonly used drugs. Clinical case details and pathology information are provided, with a caution to clinicians and microbiologists presented with suspect animals, i.e., most cases occurred in older calves, which is atypical for salmonellosis for this region (calves were 8 or more weeks old) and presented as pneumonia and septicemia rather than the primarily diarrheal syndrome that is more typically recognized for the region. The epidemiology of cases is analyzed through cluster analysis of bacterial isolates and their fatty acid methyl ester profiles; at least six clones appeared in the region during the study period. Results of the epidemiology analysis are used to support a hypothesis regarding the source of S. enterica Dublin for the region and its manner of dissemination.

Multiphasic analysis of xanthomonads causing bacterial spot disease on tomato and pepper in the Caribbean and central america: evidence for common lineages within and between countries

ABSTRACT Four hundred thirty-three xanthomonad strains isolated from tomato or pepper plants from 32 different fields in four Caribbean and Central American countries were screened for the ability to hydrolyze starch and sodium polypectate and for resistance to copper and streptomycin. Of these, 95 representative strains were further characterized by various phnetic tests, and 63 of these strains were then analyzed by genomic fingerprinting. Most of the strains (>90%) were tolerant to copper. However, there was much more variability in sensitivity to streptomycin. All strains in Guadeloupe and 93% of the strains in Barbados were sensitive to streptomycin. The majority of strains were typical Xanthomonas campestris pv. vesicatoria group A strains. In Barbados, however, a unique group of strains was identified that was serologically similar to group A strains but was amylolytic. These strains were designated A1. The occurrence of X. campestris pv. vesicatoria group B strains in Central America was found to be limited to two fields in Costa Rica and one in Guatemala. No group B strains were identified in the Caribbean, in contrast to common occurrence in the central United States and in South America. T3 strains were not found in this study, despite the recent increase of such strains in Florida and Mexico. Unique strains from Costa Rica belonging to the X. gardneri group were identified. Little linkage was found among phenotypic and rep-polymerase chain reaction (rep-PCR) genomic fingerprinting profiles of the pathogens except at the species/pathovar level; strains displaying virtually identical fingerprint profiles were found to correspond to distinct races and vice versa. The rep-PCR genomic fingerprinting analyses suggest that certain lineages may have evolved or predominated in specific regions or specific countries.

Amplification of rfbE and fliC genes by polymerase chain reaction for identification and detection of Salmonella serovar Enteritidis, Dublin and Gallinarum-Pullorum

Polymerase chain reaction (PCR) primers for O9 antigen (rfbE) and phase 1 flagellin antigen (fliC) were designed for the rapid identification and detection of Salmonella serovar Enteritidis and Dublin. The rfbE primer pairs selectively amplified the rfbE region of group O9 Salmonella serovars. The fliC primer pairs amplified the DNAs of g,m and g,p-type flagellar antigen; Salmonella serovar Enteritidis, Dublin, and Essen. However, DNA from flagellar-negative Salmonella serovar Gallinarum-Pullorum was also amplified. The sensitivity of PCR primer pairs was 10(4) CFU/assay by boiled DNA preparation and 10(2) CFU/assay by proteinase K-treated DNA preparation.

Mapping of the H7-serospecific domain of Escherichia coli flagellin

The amino acid sequences responsible for H7 and H23 flagellum serology have been identified by using a genetic approach. The H7-specific domain was located between amino acids 352 and 374 of the H7 flagellin. The sequencing data also demonstrated that the difference between the H7 and H23 flagellins in this region results from a single substitution at amino acid 366 (Ser-->Thr). The common epitopes for H7 and H23 were located between amino acids 284 and 366.

Multilocus enzyme electrophoretic (MEE) analysis of Australian isolates of Salmonella enteritidis

Seventy-three Australian isolates of Salmonella Enteritidis (SE) were analysed by multilocus enzyme electrophoresis (MEE) using a polyacrylamide gel system. Analysis of 11 enzyme loci identified eight electrophoretic types (ETs), with 61 of the isolates assigned to ET1, and 72 isolates considered to represent a clonal lineage. Representative isolates of each of the Australian ETs were then compared with isolates from England, Germany and the United States, using a starch gel system and 13 enzyme loci. The overseas isolates formed a single ET with representatives of the major Australian ET. It is concluded that Australian isolates of SE are closely related genetically to those from countries in which egg-borne transmission is common.

Molecular epidemiological tools for Salmonella Dublin typing

A total of 32 strains of Salmonella Dublin recovered from cattle were differentiated by electrophoretic typing of their esterases (zymotyping), restriction fragment length polymorphism of ribosomal DNA (ribotyping), arbitrarily primed PCR (AP-PCR) using five primers, PCR based on repetitive extragenic palindromic sequences (REP-PCR) and PCR based on enterobacterial repetitive intergenic consensus sequences (ERIC-PCR). ERIC-PCR and REP-PCR each gave one type, zymotyping gave three, AP-PCR gave five and ribotyping gave seven types. Combination of ribotyping and AP-PCR produced a total of 11 types, whereas 14 different types were obtained by all five methods. Thus a combination of several methods enhanced the discrimination of cattle-adapted strains among the genotypically homogeneous serovar Salmonella Dublin.

Molecular analysis of Salmonella enterica serotype Dublin: building bridges between population genetic and molecular epidemiological studies

Population genetic studies of Salmonella enterica serotype Dublin using multilocus enzyme electrophoresis have recognised two dominant clones termed Du1 and Du3. The characterisation of plasmids in Dublin suggests greater strain diversity. The application of restriction enzyme fragmentation pattern (REFP) analysis of genomic DNA using Sau3A and HincII together with plasmid subtractive analysis can resolve anomalies in earlier comparisons. Twenty-six isolates were selected for inclusion in the study. All had been previously characterised with respect to their plasmids, and were isolated from the USA, Canada and five European countries. On the basis of plasmid profiles, 17 were predicted to correspond with Du1 and Du3. Sau3A digestion generated two distinct REFPs (A and B) of < 70% similarity, which corresponded with Du1 and Du3. After the contribution of plasmid-derived bands was subtracted, two variants of A (A1 and A2) and four of B (B1, B2, B3 and B4) were recognised. Seventeen were concordant with predictions from population genetic studies. Nine that could not be predicted on the basis of atypical plasmid profiles all showed REFP A1 (Du1) and were consistent with the incursion of additional plasmids or plasmid cointegration. REFPs from HincII digests generally corroborated Sau3A data but showed greater overall similarity between the strains and more influence from plasmid DNA.

Application of random amplified polymorphic DNA analysis to differentiate strains of Salmonella enteritidis

A random amplified polymorphic DNA (RAPD) fingerprinting method has been developed to differentiate Salmonella enteritidis isolates. A total of 65 arbitrary primers were screened with S. enteritidis isolates of different phage types. This allowed selection of a panel of primers capable of detecting DNA polymorphisms among S. enteritidis isolates. This panel was used to examine a panel of 29 isolates of S. enteritidis which had been previously characterized by other subtyping methods, including phage typing (PT) (n = 7), ribotyping (RT) (n = 13), and pulsed-field gel electrophoresis (PFGE). Applied collectively, these three methods resolved the collection into 20 different subtypes. However, by the RAPD fingerprinting method alone, 14 RAPD subtypes were revealed. Eight isolates of S. enteritidis phage type 8 that failed to be discriminated by other typing methods (PT, RT, and PFGE) were resolved into three different subtypes by RAPD analysis. In contrast, isolates that were derived from the same sources were not differentiated by any of the subtyping methods employed, including PT, RT, PFGE, and RAPD analysis. This RAPD approach to S. enteritidis subtyping provided more discriminatory power than did any of several other subtyping methods applied individually. Once the challenging step of primer identification was accomplished, determinations of the appropriate concentrations of arbitrary primer, DNA template, and MG2+ ion were also necessary for optimal discriminatory power. The bacterial DNA used in this RAPD protocol was obtained by boiling the bacterial sample. This simple procedure yielded DNA that produced fingerprint patterns as consistent as those obtained from phenol-chloroform-extracted DNA. Clearly, when appropriately constituted primer sets are identified and employed, RAPD analysis provides a simple, rapid, and powerful subtyping method for S. enteritidis.

Electrophoretic variation in adenylate kinase of Neisseria meningitidis is due to inter- and intraspecies recombination

In prokaryotic and eukaryotic organisms, the electrophoretic variation in housekeeping enzymes from natural populations is assumed to have arisen by the accumulation of stochastic predominantly neutral mutations. In the naturally transformable bacterium Neisseria meningitidis, we show that variation in the electrophoretic mobility of adenylate kinase is due to inter- and intraspecies recombination rather than mutation. The nucleotide sequences of the adenylate kinase gene (adk) from isolates that express the predominant slow electrophoretic variant were rather uniform, differing in sequence at an average of 1.1% of nucleotide sites. The adk sequences of rare isolates expressing the fast migrating variant were identical to each other but had a striking mosaic structure when compared to the adk genes from strains expressing the predominant variant. Thus the sequence from the fast variants was identical to those of typical slow variants in the first 158 bp of the gene but differed by 8.4% in the rest of the gene (nt 159-636). The fast electrophoretic variant appears to have arisen by the replacement of most of the meningococcal gene with the corresponding region from the adk gene of a closely related Neisseria species. The adk genes expressing the electrophoretic variant with intermediate mobility were perfect, or almost perfect, recombinants between the adk genes expressing the fast and slow variants. Recombination may, therefore, play a major role in the generation of electrophoretically detectable variation in housekeeping enzymes of some bacterial species.

Diversity and molecular variation among plasmids in Salmonella enterica serotype Dublin based on restriction enzyme fragmentation pattern analysis

Molecular variation within and between plasmids of Salmonella enterica serotype Dublin was analysed. Such variation has been demonstrated in the serotype-specific plasmids (SSP's) of Typhimurium and Enteritidis. The two aims of this study were to determine the plasmid diversity in a host-adapted serotype and also the incidence of molecular variation in the SSP among strains of Dublin using restriction endonuclease fragmentation pattern (REFP) analysis with Pst1, Sma1 and EcoRV. Sixty-five strains were examined from seven countries. Plasmid profile and REFP analysis showed that none of the strains was plasmid-free. Seventy-seven percent of the strains possessed the 72 kb SSP either alone or in combination with another plasmid; 23% harboured plasmids which were molecular variants of the SSP. Four of the variants were more closely related to each other than to the reference SSP and were harboured by Dublin isolated from both the USA and Europe. A further three were shown to be cointegrate plasmids and were similarly distributed. Thirty-two percent of strains possessed the SSP alone. None of the UK strains was resistant to any of the antimicrobial agents tested whereas 74% of the remaining strains were resistant to between one and five antimicrobial agents. This study corroborates previous findings concerning the high degree of stability of the SSP and confirmed the clonal nature of Dublin. Co-resident plasmids provided evidence of sub-clones within localized geographical areas.

Identification of the domain which determines the g,m serotype of the flagellin of Salmonella enteritidis

Clones expressing fragments of the flagellin protein of Salmonella enteritidis were constructed and screened with a g,m-specific monoclonal antibody. Results showed that the g,m epitope is localized between amino acids 258 and 348 of the flagellin. The fliC gene, encoding the flagellin of S. enteritidis, was proven to be the only flagellin gene present in S. enteritidis.