Plasmid-encoded tetracycline resistance in Salmonella enterica subsp. enterica serovars choleraesuis and typhimurium: identification of complete and truncated Tn1721 elements

During routine screening of Salmonella enterica subsp., S. enterica isolates of animal origin for plasmid-encoded tetracycline resistance, two tetracycline resistance plasmids, the 50 kbp plasmid pGFT3 of Salmonella choleraesuis and the 9.5 kbp plasmid pGFT4 of Salmonella typhimurium var. Copenhagen DT002, were detected. The respective tetracycline resistance genes (tet) were identified by hybridization and PCR analysis to belong to hybridization class A. Conjugation experiments identified plasmid pGFT3 as a conjugative plasmid. Molecular analysis of the tet(A) gene area and the flanking regions identified a complete Tn1721-like transposon on plasmid pGFT3 and a truncated Tn1721-like element on plasmid pGFT4. The complete Tn1721-like element was integrated into a transposase reading frame of a truncated Tn3 transposon also located on plasmid pGFT3. The truncated Tn1721-like element of plasmid pGFT4 lacked the entire transposase part. This Tn1721-relic was integrated in an unknown reading frame which on amino acid level showed homology to the Rop protein of Escherichia coli. A model for the deletion of the transposase part was developed on the basis of the sequences present at the termini of the truncated Tn1721-like element.

Discrimination between endemic and feedborne Salmonella Infantis infection in cattle by molecular typing

Salmonella enterica serovar Infantis is endemic in Finnish cattle. Feed contaminated with S. Infantis was distributed to cattle farms in May 1995. Following increased sampling, S. Infantis was detected on 242 farms in 1995. Molecular typing was used to differentiate the farms that were infected by the feed-related Infantis from those infected by other endemic strains. Twenty-three isolates from feed in 1995 and 413 from cattle (72 from 19924, 324 from 1995, 17 from 1996-7) were analysed. The feed-related Infantis was clonally related to the endemic infection by the ribotype, IS200-type and XbaI-profile. The feed isolates had a distinctive plasmid that appeared in pulsed-field gel electrophoresis as a 60 kb band when cleaved with XbaI or linearized by S1-nuclease. This plasmid appeared in cattle only since the outbreak and seemed stable on the follow-up farms. In addition to contact farms, the feedborne strain was found on 19% of the farms infected with S. Infantis in 1995 but not having bought suspected feedstuffs, possibly as secondary infections.

Typing of Salmonella enterica serotype paratyphi C isolates from various countries by plasmid profiles and pulsed-field gel electrophoresis

Pulsed-field gel electrophoresis (PFGE) of 61 Salmonella enterica serotype Paratyphi C isolates from six countries gave five distinct clusters. Twenty-four isolates from five countries were susceptible to 10 antimicrobials tested and gave similar restriction endonuclease digest patterns of the 38-MDa plasmid. In contrast, plasmid and PFGE profiles of 37 multidrug-resistant isolates from Zaire were different from those from other countries.

Comparative physical and genetic maps of the virulence plasmids of Salmonella enterica serovars typhimurium, enteritidis, choleraesuis, and dublin

Using fragment profiling, PCR, and Southern hybridization, we found that Salmonella enterica serovar Choleraesuis harbored virulence plasmids of various sizes, whereas serovars Typhimurium, Enteritidis, and Dublin carried a plasmid of a unique size. Also, the virulence plasmid of Typhimurium contained genes in the same order detected in the other three plasmids, all of which contained deletions.

Resistance of Escherichia coli and Salmonella against nisin and curvacin A

We have determined the effects of the following factors on the resistance of Gram-negative bacteria against nisin and curvacin A: (i) chemotype of the lipopolysaccharide (LPS), (ii) addition of agents permeabilizing the outer membrane, (iii) the fatty acid supply of the growth medium, and (iv) the adaptation to acid and salt stress. Bacteriocin activity was determined against growing and resting cells as well as protoplasts. All smooth strains of Escherichia coli and Salmonella enterica serovar Typhimurium were highly resistant towards the bacteriocins, whereas mutants that possess the core of the LPS, but not the O antigen, as well as deep rough LPS mutants were sensitive. Antibiotics with outer membrane permeabilizing activity, polymyxin B and polymyxin B nonapeptide, increased the sensitivity of smooth E. coli towards nisin, but not that of deep rough mutants. Incorporation of 1 g l(-1) of either oleic acid or linoleic acid to the growth media greatly increased the susceptibility of E. coli LTH1600 and LTH4346 towards bacteriocins. Both strains of E. coli were sensitive to nisin and curvacin A at a pH of less than 5.5 and more than 3% (w/v) NaCl. Adaptation to sublethal pH or higher NaCl concentrations (pH 4.54 and 5.35 or 4.5% (w/v) NaCl) provided only limited protection against the bacteriocidal activity of nisin and curvacin A. Adaptation to 4.5% (w/v) NaCl did not result in cross protection to bacteriocin activity at pH 4.4, but rendered the cells more sensitive towards bacteriocins.

A periplasmic D-alanyl-D-alanine dipeptidase in the gram-negative bacterium Salmonella enterica

The VanX protein is a D-alanyl-D-alanine (D-Ala-D-Ala) dipeptidase essential for resistance to the glycopeptide antibiotic vancomycin. While this enzymatic activity has been typically associated with vancomycin- and teicoplainin-resistant enterococci, we now report the identification of a D-Ala-D-Ala dipeptidase in the gram-negative species Salmonella enterica. The Salmonella enzyme is only 36% identical to VanX but exhibits a similar substrate specificity: it hydrolyzes D-Ala-D-Ala, DL-Ala-DL-Phe, and D-Ala-Gly but not the tripeptides D-Ala-D-Ala-D-Ala and DL-Ala-DL-Lys-Gly or the dipeptides L-Ala-L-Ala, N-acetyl-D-Ala-D-Ala, and L-Leu-Pro. The Salmonella dipeptidase gene, designated pcgL, appears to have been acquired by horizontal gene transfer because pcgL-hybridizing sequences were not detected in related bacterial species and the G+C content of the pcgL-containing region (41%) is much lower than the overall G+C content of the Salmonella chromosome (52%). In contrast to wild-type Salmonella, a pcgL mutant was unable to use D-Ala-D-Ala as a sole carbon source. The pcgL gene conferred D-Ala-D-Ala dipeptidase activity upon Escherichia coli K-12 but did not allow growth on D-Ala-D-Ala. The PcgL protein localizes to the periplasmic space of Salmonella, suggesting that this dipeptidase participates in peptidoglycan metabolism.

Molecular typing of Salmonella serotype Thompson strains isolated from human and animal sources

One-hundred-and-thirteen isolates of Salmonella serotype Thompson from diverse sources in seven countries were characterized by PvuII ribotyping and IS200 fingerprinting. Ten PvuII ribotypes were observed. The predominant PvuII ribotype 1 represented a major clone of world-wide distribution but was not found in Australia; PvuII ribotypes 2 and 3 represented minor clones. HincII ribotyping discriminated subtypes within PvuII ribotype 1: HincII ribotype 1 was distributed widely but HincII ribotype 2 was found mainly in Scottish isolates. None of 101 isolates of PvuII ribotypes 1-3 contained copies of IS200. All 12 isolates of PvuII ribotypes 4-10 were from Australia and 7 of them contained copies of IS200 of 5 different profiles. These results suggest the existence of at least two lineages of Salmonella Thompson with a different geographical distribution. The finding that most isolates from man and poultry in Scotland belonged to the same ribotype (PvuII 1/HincII 2) and were IS200-negative suggests that poultry is an important source of human infection in Scotland.

The SPI-3 pathogenicity island of Salmonella enterica

Pathogenicity islands are chromosomal clusters of pathogen-specific virulence genes often found at tRNA loci. We have determined the molecular genetic structure of SPI-3, a 17-kb pathogenicity island located at the selC tRNA locus of Salmonella enterica serovar Typhimurium. The G+C content of SPI-3 (47.5%) differs from that of the Salmonella genome (52%), consistent with the notion that these sequences have been horizontally acquired. SPI-3 harbors 10 open reading frames organized in six transcriptional units, which include the previously described mgtCB operon encoding the macrophage survival protein MgtC and the Mg2+ transporter MgtB. Among the newly identified open reading frames, one exhibits sequence similarity to the ToxR regulatory protein of Vibrio cholerae and one is similar to the AIDA-I adhesin of enteropathogenic Escherichia coli. The distribution of SPI-3 sequences varies among the salmonellae: the right end of the island, which harbors the virulence gene mgtC, is present in all eight subspecies of Salmonella; however, a four-gene cluster at the center of SPI-3 is found in only some of the subspecies and is bracketed by remnants of insertion sequences, suggesting a multistep process in the evolution of SPI-3 sequences.

Increasing incidence and comparison of nalidixic acid-resistant Salmonella enterica subsp. enterica serotype typhimurium isolates from humans and animals

We determined the resistance to quinolone of 309 Salmonella enterica subsp. enterica serotype Typhimurium strains isolated from humans and animals (cattle, pigs, or poultry) in 1995 or 1996. Nalidixic acid resistance increased from 8.5% in 1995 to 18.6% in 1996. The highest resistance levels correlated with a mutation at Ser-83 (or Asp-82). All strains remained ciprofloxacin susceptible. Human and animal isolates were compared by pulsed-field gel electrophoresis, and the banding patterns of the human isolates most closely matched those of the bovine isolates.

Impact of intracellular location of and antigen display by intracellular bacteria: implications for vaccine development

Intracellular bacteria are primarily controlled by T-lymphocytes. The 'phagosomal' bacteria such as Salmonella enterica and Mycobacterium bovis BCG remain in the phagosome. These microbes primarily stimulate CD4 T-cells via antigen presentation through MHC class II molecules. In contrast, Listeria monocytogenes egresses from the phagosome into the cytoplasm by virtue of listeriolysin. This 'cytoplasmic' pathogen is controlled by CD8 T-cells through MHC class I antigen presentation. Some bacterial pathogens such as Mycobacterium tuberculosis presumably remain in the phagosome but apparently 'perforate' the phagosomal membrane and thus stimulate both CD4 and CD8 T-cells. We have constructed S. enterica and M. bovis BCG vaccine carriers which secrete listeriolysin. Such constructs are capable of introducing antigens into the MHC class II and MHC class I pathway, resulting in stimulation of both CD4 and CD8 T-cells. Moreover, we constructed S. enterica vaccines which display one and the same listerial antigen in secreted and somatic form. Secreted antigen display was found to be superior to somatic antigen display. Hence, we consider antigen secretion a major prerequisite of an effective vaccine against intracellular bacteria.

Comparison of ribotyping and arbitrarily primed PCR for molecular typing of Salmonella enterica and relationships between strains on the basis of these molecular markers

Arbitrarily primed PCR (AP-PCR) using a discriminatory 10-mer primer and an automated EcoRI ribotyping technique (Riboprinter) were compared for their ability to discriminate between 100 serovars of Salmonella, including multiple isolates representing Salm. Enteritidis PT4 and Salm. Typhimurium DT104. Profiles generated by each method were subjected to numerical analysis using GelCompar software, resulting in the construction of phylogenetic trees and calculation of Simpson's numerical index of diversity (DI). Both methods were highly discriminatory for isolates of Salmonella (Ribotype DI = 0.990, AP-PCR DI = 0.997) with EcoRI ribotyping proving more discriminatory than AP-PCR for isolates of Typhimurium DT104. The population structure was found to be clonal by numerical analysis of markers generated by both methods with serovars being polyphyletic in some cases and grouped in a single cluster in others. No absolute correlation was observed in the relationships between strains formed on the basis of ribo- and AP-PCR markers and serological characteristics.

Extraintestinal salmonellosis in a general hospital (1991 to 1996): relationships between Salmonella genomic groups and clinical presentations

Episodes of extraintestinal salmonellosis treated at a general hospital (1,522 beds) over a 6-year period (1991 to 1996) were characterized by the analysis of phenotypic and genotypic traits of Salmonella organisms and clinical data from medical reports. Extraintestinal salmonellosis accounted for 8% of all salmonellosis episodes. Fifty-two medical reports, dealing with 6 cases of typhoid fever, 32 cases of bacteremia, and 14 focal infections, were reviewed. All cases of typhoid fever except 1, 7 cases of bacteremia, and 5 focal infections were not related to any underlying disease or predisposing factors, while 25 cases of bacteremia and 9 focal infections were associated with some of these risk factors. All typhoid isolates and 65.4% of the nontyphoid isolates were susceptible to antimicrobials. Fifty-one nontyphoid strains were analyzed and assigned to 21 genomic groups, which were defined by serotype, combined ribotype, and combined randomly amplified polymorphic DNA type (each genomic group could include organisms differing in some phenotypic traits). The relationships between genomic groups and clinical presentations were traced. Organisms causing 22 episodes (17 episodes of bacteremia, 2 of pneumonia, 1 of peritonitis, 1 of pyelonephritis, and 1 of cystitis) belonged to a prevalent Salmonella enterica serotype Enteritidis genomic group, which included organisms assigned to four phage types, five biotypes, and four resistance patterns, causing infections in patients with and without risk factors. Seven other genomic groups, 4 Enteritidis groups (associated with both bacteremia and focal infections), 2 Typhimurium groups (one associated with bacteremia and the other with focal infections) and 1 Brandenburg group (associated with bacteremia) included two or more strains, and the remaining 13 genomic groups consisted of only one strain each.

Pathogenicity in isolates of Salmonella enterica serotype Enteritidis PT4 which differ in RpoS expression: effects of growth phase and low temperature

Experiments with 2 wild type isolates of Salmonella enterica serotype Enteritidis PT4, which differed in RpoS expression, tolerance to certain hostile environments and pathogenicity, found that changes in in vitro acid, heat, or peroxide tolerance had no effect on the ability of the isolates to multiply in the spleens of C57/BL7/J mice infected orally. Thus, with the pathogenic RpoS-positive isolate, the infectivity of log phase chilled cells, which are profoundly acid-sensitive, was the same as that of non-chilled stationary phase cells which are acid-tolerant. Similarity the infectivity of the RpoS-negative, sensitive isolate, was not enhanced by increases in any tolerance. The ability to survive on surfaces, like infectivity, was also largely unaffected by either growth phase or cold exposure. These two attributes may thus be related and, given that the pathogenic PT4 isolate is capable of prolonged survival and the nonpathogenic isolate survives poorly, survival could serve as a potential marker of pathogenicity. Although the pathogenicity of the two isolates was very different, they showed an almost identical increase in acid tolerance following culture at pH 4.0 for up to 60 min.

Restriction fragment length polymorphism analysis of some flagellin genes of Salmonella enterica

Salmonellae often have the ability to express two different flagellar antigen specificities (phase 1 and phase 2). At the cell level, only one flagellar phase is expressed at a time. Two genes, fliC, encoding phase-1 flagellin, and fljB, encoding phase-2 flagellin, are alternatively expressed. Flagellin genes from 264 serovars of Salmonella enterica were amplified by two phase-specific PCR systems. Amplification products were subjected to restriction fragment length polymorphism (RFLP) analysis by using endonucleases HhaI and HphI. RFLP with HhaI and HphI yielded 64 and 42 different restriction profiles, respectively, among 329 flagellin genes coding for 26 antigens. The phase-1 gene showed 46 patterns with HhaI and 30 patterns with HphI. The phase-2 gene showed 23 patterns with HhaI and 17 patterns with HphI. When the data from both enzymes were combined, 116 patterns were obtained: 74 for fliC, 47 for fljB, and 5 shared by both genes. Of these combined patterns, 80% were specifically associated with one flagellar antigen and 20% were associated with more than one antigen. Each flagellar antigen was divided into 2 to 18 different combined patterns. In the sample of strains used, determination of the phase-1 and phase-2 flagellin gene RFLP, added to the knowledge of the O antigen, allowed identification of all diphasic serovars. Overall, the diversity uncovered by flagellin gene RFLP did not precisely match that evidenced by flagellar agglutination.

Molecular fingerprinting defines a strain of Salmonella enterica serotype Anatum responsible for an international outbreak associated with formula-dried milk

Molecular analyses based on plasmid profile typing and pulsed-field gel electrophoresis have defined a strain of Salmonella enterica serotype Anatum associated with the consumption of a particular brand of formula-dried milk responsible for an outbreak in late 1996/early 1997 involving 15 infants and 2 relatives in the UK, and 2 infants in France. The study has demonstrated the value of laboratory-based surveillance involving identification of the outbreak strain at the molecular level coupled with food microbiology and targeted epidemiological investigations, and has highlighted the importance of rapid communication and subsequent international collaboration through the European Union-funded Salm-Net salmonella surveillance network.

Expression of the O antigen gene cluster is regulated by RfaH through the JUMPstart sequence

O antigen genes are clustered, with a JUMPstart sequence located upstream. JUMPstart is a 39-bp sequence, present upstream of many polysaccharide gene clusters and also upstream of haemolysin and F factor gene clusters. RfaH is known to regulate the expression of E. coli group II capsule, haemolysin, F factor and the outer core of lipopolysaccharide all of which have the JUMPstart sequence, and has been shown to function as a transcriptional antiterminator in some cases. Using lacZ fusions to genes in the O antigen gene cluster of Salmonella enterica serovar Typhimurium, we found that RfaH also regulates the expression of O antigen. We showed that RfaH enhances expression of the 18-kb O antigen gene cluster, with promoter-distal genes affected more dramatically. We also showed that the JUMPstart sequence was required for RfaH function.

Identification and sequence analysis of a 27-kilobase chromosomal fragment containing a Salmonella pathogenicity island located at 92 minutes on the chromosome map of Salmonella enterica serovar typhimurium LT2

Using a genomic approach, we have identified a new Salmonella pathogenicity island, SPI-4, which is the fourth Salmonella pathogenicity island to be identified. SPI-4 was located at 92 min on the chromosome map and was flanked by the ssb and soxSR loci. The DNA sequence covering the entire SPI-4 and both boundaries was determined. The size of SPI-4 was about 25 kb and it contains 18 putative open reading frames (ORFs). Three of these ORFs encode proteins that have significant homology with proteins involved in toxin secretion. Another five ORFs encode proteins that have significant homology with hypothetical proteins from Synechocystis sp. strain PCC6803 or Acinetobacter calcoaceticus. The rest of the ORFs encode novel proteins, one of which has five membrane-spanning domains. SPI-4 is likely to carry a type I secretion system involved in toxin secretion. Furthermore, a previously identified locus (ims98), which is required for intramacrophage survival, was also mapped within the SPI-4 region. These findings suggested that SPI-4 is needed for intramacrophage survival.

Salmonella virulence plasmid. Modular acquisition of the spv virulence region by an F-plasmid in Salmonella enterica subspecies I and insertion into the chromosome of subspecies II, IIIa, IV and VII isolates

The spv operon is common to all Salmonella virulence plasmids. DNA hybridization analysis indicates that the spv region is limited in distribution to serovars of Salmonella enterica subspecies I, II, IIIa, IV, and VII and is absent from Salmonella bongori isolates. Among strains of subspecies II, IIIa, and VII, all isolates examined contained sequences that hybridized with the spv region. However, among isolates of subspecies I, DNA sequences capable of hybridizing with the spv region were found in some isolates of certain serovars. Furthermore, in isolates of subspecies I, the virulence plasmid was found in the same set of isolates as an F-related plasmid, as determined by the presence of the spv region of the virulence plasmid and the finO, traD, and repA sequences of the F-plasmid. The concordance of the virulence plasmid and all three F-plasmid sequences in subspecies I serovar Choleraesuis, Paratyphi, and Typhimurium is most easily explained if the spv region is carried in an F-related plasmid in these isolates. In contrast, among S. enterica subspecies II, IIIa, IV, and VII, the isolates that contain spv sequences did not hybridize with an F-related plasmid or any other identifiable plasmid. With the use of pulse-field gel electrophoresis, the spv region in subspecies II, IIIa, and VII was found to be encoded on the chromosome. Analysis of the phylogenetic distribution of spv among Salmonella isolates and comparative nucleotide sequence analysis of spvA and spvC suggests that the spv region was acquired very recently, after speciation of the salmonellae.

Suitability of repetitive-DNA-sequence-based PCR fingerprinting for characterizing epidemic isolates of Salmonella enterica serovar Saintpaul

Three molecular typing methods, repetitive-sequence-based PCR (rep-PCR) fingerprinting, plasmid profiling, and arbitrarily primed PCR fingerprinting, were used to characterize isolates of Salmonella enterica serovar Saintpaul. Most of the isolates were obtained from epidemic human cases of food-borne salmonellosis, together with some from the food material suspected to be the source of infection, and a few were obtained from other cases apparently not related to the epidemic. All three methods adequately discriminated the epidemic strain from other strains of the serovar. In addition several isolates from human cases which are not identical to the epidemic strain were found. These isolates therefore must have been responsible for some sporadic infections, which were only temporally related to the epidemic. These strains showed a high degree of similarity to a strain isolated from a turkey. rep-PCR fingerprinting with REP-Dt primers and primer ERIC1R, applicable even to crude cell lysates, offers an attractive choice as a primary method for the discrimination of various Salmonella serotypes as well as isolates within serotype Saintpaul.

Tetracycline resistance in Salmonella enterica subsp. enterica serovar Dublin

The 47-kbp plasmid pGFT1 from Salmonella enterica subsp. enterica serovar Dublin mediated tetracycline resistance via a tet(A) gene located on an integrated copy of a Tn1721-analogous transposon. The integration site of the transposon was located within the reading frame of a fip gene. Plasmid pGFT1 was shown to be conjugative and to be able to replicate and express tetracycline resistance in Escherichia coli.

The assembly system for the lipopolysaccharide R2 core-type of Escherichia coli is a hybrid of those found in Escherichia coli K-12 and Salmonella enterica. Structure and function of the R2 WaaK and WaaL homologs

In Escherichia coli F632, the 14-kilobase pair chromosomal region located between waaC (formerly rfaC) and waaA (kdtA) contains genes encoding enzymes required for the synthesis of the type R2 core oligosaccharide portion of lipopolysaccharide. Ten of the 13 open reading frames encode predicted products sharing greater than 90% total similarity with homologs in E. coli K-12. However, the products of waaK (rfaK) and waaL (rfaL) each resemble homologs in Salmonella enterica serovar Typhimurium but share little similarity with E. coli K-12. The F632 WaaK and WaaL proteins therefore define differences between the type R2 and K-12 outer core oligosaccharides of E. coli lipopolysaccharides. Based on the chemical structure of the core oligosaccharide of an E. coli F632 waaK::aacC1 mutant and in vitro glycosyltransferase analyses, waaK encodes UDP-N-acetylglucosamine:(glucose) lipopolysaccharide alpha1, 2-N-acetylglucosaminyltransferase. The WaaK enzyme adds a terminal GlcNAc side branch substituent that is crucial for the recognition of core oligosaccharide acceptor by the O-polysaccharide ligase, WaaL. Results of complementation analyses of E. coli K-12 and F632 waaL mutants suggest that structural differences between the WaaL proteins play a role in recognition of, and interaction with, terminal lipopolysaccharide core moieties.

Mosaic structure of the smpB-nrdE intergenic region of Salmonella enterica

The Salmonella enterica smpB-nrdE intergenic region contains about 45 kb of DNA that is not present in Escherichia coli. This DNA region was not introduced by a single horizontal transfer event, but was generated by multiple insertions and/or deletions that gave rise to a mosaic structure in this area of the chromosome.

Phylogenetic relationships of Salmonella based on rRNA sequences

To establish the phylogenetic relationships between the subspecies of Salmonella enterica (official name Salmonella choleraesuis), Salmonella bongori and related members of Enterobacteriaceae, sequence comparison of rRNA was performed by maximum-likelihood analysis. The two Salmonella species were separated by 16S rRNA analysis and found to be closely related to the Escherichia coli and Shigella complex by both 16S and 23S rRNA analyses. The diphasic serotypes S. enterica subspp. I and VI were separated from the monophasic serotypes subspp. IIIa and IV, including S. bongori, by 23S rRNA sequence comparison.

Variation of the ribosomal operon 16S-23S gene spacer region in representatives of Salmonella enterica subspecies

The 16S-23S spacer regions of two ribosomal operons (rrnA and rrnE) have been sequenced in seven representatives of the Salmonella enterica subspecies. Isolated nucleotide substitutions were found at the same sites as in Escherichia coli but the number of polymorphic sites was much larger, as could be expected for a more heterogeneous species. Still, as in E. coli, most of the variation found was due to insertions and/or deletions affecting blocks of nucleotides generally located at equivalent regions of the putative secondary structure for both species. Isolated polymorphic sites generated phylogenetic trees generally consistent with the subspecies structure and the accepted relationships among the subspecies. However, the sequences of rrnE put subspecies I closer to E. coli K-12 than to the other S. enterica subspecies. The distribution of polymorphisms affecting blocks of nucleotides was much more random, and the presence of equivalent sequences in distantly related subspecies, and even in E. coli, could reflect relatively frequent horizontal transfer. The smallest 16S-23S spacers in other genera of the family Enterobacteriaceae were also sequenced. As expected, the level of variation was much larger. Still, the phylogenetic tree inferred is consistent with those of 16S rRNA or housekeeping genes.

Molecular typing of Salmonella enterica subsp. enterica serovar Hadar: evaluation and application of different typing methods

A highly discriminatory molecular typing system for isolates of Salmonella enterica subsp. enterica (S.) serovar Hadar was developed based on the data obtained from 34 epidemiologically unrelated S. Hadar isolates from Germany and Brazil. Plasmid profile analysis and macrorestriction analysis with the enzymes XbaI, SpeI and BlnI represented the most discriminative typing methods. In contrast, ribotyping as performed with a gene probe that recognized the entire rrn operon did not reveal any differences between the S. Hadar isolates. IS200 typing was not applicable due to the lack of insertion elements of this type in all S. Hadar isolates included in this study. The combination of the results of plasmid analysis and macrorestriction analysis subdivided the 34 S. Hadar isolates into 32 different genomic groups. The high discriminatory power of these methods confirmed their suitability as effective typing methods for epidemiological studies on S. Hadar isolates. The practical application of this molecular typing system to S. Hadar isolates of the same flock obtained during a 15 month period strongly suggested recurring introduction of genomically different S. Hadar isolates instead of a single introduction of S. Hadar followed by subsequent spread within the flock.

IroN, a novel outer membrane siderophore receptor characteristic of Salmonella enterica

Speciation in enterobacteria involved horizontal gene transfer. Therefore, analysis of genes acquired by horizontal transfer that are present in one species but not its close relatives is expected to give insights into how new bacterial species were formed. In this study we characterize iroN, a gene located downstream of the iroBC operon in the iroA locus of Salmonella enterica serotype Typhi. Like iroBC, the iroN gene is present in all phylogenetic lineages of S. enterica but is absent from closely related species such as Salmonella bongori or Escherichia coli. Comparison of the deduced amino acid sequence of iroN with other proteins suggested that this gene encodes an outer membrane siderophore receptor protein. Mutational analysis in S. enterica and expression in E. coli identified a 78-kDa outer membrane protein as the iroN gene product. When introduced into an E. coli fepA cir fiu aroB mutant on a cosmid, iroN mediated utilization of structurally related catecholate siderophores, including N-(2,3-dihydroxybenzoyl)-L-serine, myxochelin A, benzaldehyde-2,3-dihydroxybenzhydrazone, 2-N,6-N-bis(2,3-dihydroxybenzoyl)-L-lysine, 2-N,6-N-bis(2,3-dihydroxybenzoyl)-L-lysine amide, and enterochelin. These results suggest that the iroA locus functions in iron acquisition in S. enterica.

Phylogenetic profiles: a graphical method for detecting genetic recombinations in homologous sequences

Phylogenetic profiles constitute a novel way of graphically displaying the coherence of the sequence relationships over the entire length of a set of aligned homologous sequences. Using a sliding-window technique, this method determines the pairwise distances of all sequences in the windows and evaluates, for each sequence, the degree to which the patterns of distances in these regions agree. This method is suited for exploring data consistency as well as detecting recombinant sequences. A computer program implementing the algorithm has been developed, and examples with simulated and natural sequences are given to demonstrate the sensitivity and accuracy of the method for identifying recombinant sequences and their recombination junctions as well as detecting hot spots of recombinational activity.

Relationships among the O-antigen gene clusters of Salmonella enterica groups B, D1, D2, and D3

The O antigen is an important cell wall antigen of gram-negative bacteria, and the genes responsible for its biosynthesis are located in a gene cluster. We have cloned and sequenced the DNA segment unique to the O-antigen gene cluster of Salmonella enterica group D3. This segment includes a novel O-antigen polymerase gene (wzyD3). The polymerase gives alpha(1-->6) linkages but has no detectable sequence similarity to that of group D2, which confers the same linkage. We find the remnant of a D3-like wzy gene in the O-antigen gene clusters of groups D1 and B and suggest that this is the original wzy gene of these O-antigen gene clusters.

Characterization of the nonlamellar cubic and HII structures of lipid A from Salmonella enterica serovar Minnesota by X-ray diffraction and freeze-fracture electron microscopy

The aggregate structures of lipid A, the 'endotoxic principle' of bacterial lipopolysaccharide (LPS), from rough mutant Salmonella enterica sv. Minnesota R595 was analyzed at different water content, cation (Mg2+) concentration, and temperature applying synchrotron radiation X-ray diffraction and, in selected cases, freeze-fracture electron microscopy. The X-ray diffraction spectra prove the existence of different lamellar, mixed lamellar/cubic, various cubic, and inverted hexagonal (HII) structures depending on ambient conditions. The three mainly bicontinuous cubic phases Q224, Q229, and Q230 can be observed between 30 and 50 degrees C in narrow water and cation concentration ranges. Above 50 degrees C, Q212 an intermediate phase between bicontinuous and micellar is adopted. In freeze-fracture electron microscopic experiments, cubic structures of these symmetries are not readily detected, which can be understood in the light of changes in hydration during freezing and the metastability of these phases. However, 'lipidic particles' closely related to cubic phases are observed. Above 65-70 degrees C, the existence of the HII phase with hexagonal periodicities dH between 4.0 and 6.0 nm for different hydration states is shown using both techniques. Possible biological implications for the preference of lipid A for nonlamellar structures are discussed.

Levels of expression and immunogenicity of attenuated Salmonella enterica serovar typhimurium strains expressing Escherichia coli mutant heat-labile enterotoxin

The effects of heterologous gene dosage as well as Salmonella typhimurium strain variability on immune response toward both the heterologous antigen, the nontoxic mutant of the Escherichia coli heat-labile enterotoxin LTK63, and the carrier Salmonella strain have been analyzed. Effects of a single integration into the host DNA and different-copy-number episomal vectors were compared in S. typhimurium delta cya delta crp delta asd strains of two different serotypes, UK-1 and SR-11. Expression of the enterotoxin in the different Salmonella isolates in vitro was found to vary considerably and, for the episomal vectors, to correlate with the plasmid copy number. LTK63-specific serum immunoglobulin G (IgG) and mucosal immunoglobulin A (IgA) antibodies were highest in mice immunized with the high-level-expression strain. High anti-LTK63 IgG and IgA titers were found to correspond to higher anti-Salmonella immunity, suggesting that LTK63 exerts an adjuvant effect on response to the carrier. Statistically significant differences in anti-LTK63 immune response were observed between groups of mice immunized with the attenuated delta cya delta crp UK-1 and SR-11 derivatives producing the antigen at the same rate. These data indicate that the same attenuation in S. typhimurium strains of different genetic backgrounds can influence significantly the immune response toward the heterologous antigen. Moreover, delivery of the LTK63 enterotoxin to the immune system by attenuated S. typhimurium strains is effective only when synthesis of the antigen is very high during the initial phase of invasion, while persistence of the S. typhimurium strain in deep tissues has only marginal influence.

Size and sequence polymorphism in the isocitrate dehydrogenase kinase/phosphatase gene (aceK) and flanking regions in Salmonella enterica and Escherichia coli

The sequence of aceK, which codes for the regulatory catalytic enzyme isocitrate dehydrogenase kinase/phosphatase (IDH K/P), and sequences of the 5' flanking region and part or all of the 3' flanking region were determined for 32 strains of Salmonella enterica and Escherichia coli. In E. coli, the aceK gene was 1734 bp long in 13 strains, but in three strains it was 12 bp shorter and the stop codon was TAA rather than TGA. Strains with the shorter aceK lacked an open reading frame (f728) downstream between aceK and iclR that was present, in variable length, in the other strains. Among the 72 ECOR strains, the truncated aceK gene was present in all isolates of the B2 group and half of those of the D group. Other variant conditions included the presence of IS1 elements in two strains and large deletions in two strains. The aceK-aceA intergenic region varied in length from 48 to 280 bp in E. coli, depending largely on the number of repetitive extragenic palindromic (REP) sequences present. Among the ECOR strains, the number of REP elements showed a high degree of phylogenetic association, and sequencing of the region in the ECOR strains permitted partial reconstruction of its evolutionary history. In S. entica, the normal length of aceK was 1752 bp, but three other length variants, ranging from 1746 to 1785 bp, were represented in five of the 16 strains examined. The flanking intergenic regions showed relatively minor variation in length and sequence. The occurrence of several nonrandom patterns of distribution of polymorphic synonymous nucleotide sites indicated that intragenic recombination of horizontally exchanged DNA has contributed to the generation of allelic diversity at the aceK locus in both species.

Evolutionary genetics of the isocitrate dehydrogenase gene (icd) in Escherichia coli and Salmonella enterica

Sequences of the icd gene, encoding isocitrate dehydrogenase (IDH), were obtained for 33 strains representing the major phylogenetic lineages of Escherichia coli and Salmonella enterica. Evolutionary relationships of the strains based on variation in icd are generally similar to those previously obtained for several other housekeeping and for invasion genes, but the sequences of S. enterica subspecies V strains are unusual in being almost intermediate between those of the other S. enterica subspecies and E. coli. For S. enterica, the ratio of synonymous (silent) to nonsynonymous (replacement) nucleotide substitutions between pairs of strains was larger than comparable values for 12 other housekeeping and invasion genes, reflecting unusually strong purifying selection against amino acid replacement in the IDH enzyme. All amino acids involved in the catalytic activity and conformational changes of IDH are strictly conserved within and between species. In E. coli, the level of variation at the 3' end of the gene is elevated by the presence in some strains of a 165-bp replacement sequence supplied by the integration of either lambdoid phage 21 or defective prophage element e14. The 72 members of the E. coli Reference Collection (ECOR) and five additional E. coli strains were surveyed for the presence of phage 21 (as prophage) by PCR amplification of a phage 21-specific fragment in and adjacent to the host icd, and the sequence of the phage 21 segment extending from the 3' end of icd through the integrase gene (int) was determined in nine strains of E. coli. Phage 21 was found in 39% of E. coli strains, and its distribution among the ECOR strains is nonrandom. In two ECOR strains, the phage 21 int gene is interrupted by a 1,313-bp insertion element that has 99.3% nucleotide sequence identity with IS3411 of E. coli. The phylogenetic relationships of phage 21 strains derived from sequences of two different genomic regions were strongly incongruent, providing evidence of frequent recombination.

Genetic typing methods applied to the differentiation of clonal lines among Salmonella enterica serogroup G strains causing human salmonellosis

In Spain, in November 1995, an epidemiological alert recommended the surveillance of Salmonella serogroup G. The nine clinical isolates collected after and the four collected before the alert in Asturias were differentiated into six clonal lines by the combination of results from HincII ribotyping, PCR ribotyping, and RAPD typing using primers named A and S. The seven Gumpensis isolates showed identical DNA fingerprinting with the four typing procedures falling into a line. Six of these were collected during May-August from people living in a single health area suggesting that they could be associated with a community outbreak. The four Worthington isolates fell into three other lines, one Poona isolate into another line and one Havana isolate into another. 100% typeability was shown with all methods. The reproducibility of HincII ribotyping was better than that of PCR-based methods, although these were less time-consuming. The highest discriminatory power was obtained with HincII ribotyping and RAPD typing using primer A.

Evaluation of a fluorescence-labelled oligonucleotide probe targeting 23S rRNA for in situ detection of Salmonella serovars in paraffin-embedded tissue sections and their rapid identification in bacterial smears

A method for the detection of Salmonella based on fluorescence in situ hybridization (FISH) has been developed and applied for the direct detection of Salmonella in pure cultures and in formalin-fixed, paraffin-embedded tissue sections. On the basis of the 23S rRNA gene sequences representing all of the S. enterica subspecies and S. bongori, an 18-mer oligonucleotide probe was selected. The specificity of the probe was tested by in situ hybridization to bacterial cell smears of pure cultures. Forty-nine of 55 tested Salmonella serovars belonging to subspecies I, II, IIIb, IV, and VI hybridized with the probe. The probe did not hybridize to serovars from subspecies IIIa (S. arizonae) or to S. bongori. No cross-reaction to 64 other strains of the family Enterobacteriaceae or 18 other bacterial strains outside this family was observed. The probe was tested with sections of formalin-fixed, paraffin-embedded tissue from experimentally infected mice or from animals with a history of clinical salmonellosis. In these tissue sections the probe hybridized specifically to Salmonella serovars, allowing for the detection of single bacterial cells. The development of a fluorescence-labelled specific oligonucleotide probe makes the FISH technique a promising tool for the rapid identification of S. enterica in bacterial smears, as well as for the detection of S. enterica in histological tissue sections.

Molecular epidemiology of two international sprout-borne Salmonella outbreaks

Sprout-borne Salmonella outbreaks in Finland have increased during the last 10 years. The latest two were caused by Salmonella enterica serovar Bovismorbificans (antigenic structure 6,8:r:1,5) in 1994 and S. enterica serovar Stanley (4,5, 12:d:1,2) in 1995. In this study, the restriction fragment length polymorphism of genomic DNA after pulsed-field gel electrophoresis (PFGE) and antimicrobial resistance profiles of the outbreak and nonoutbreak strains were compared. In each separate outbreak, the PFGE patterns of the outbreak strains (40 strains of S. enterica serovar Bovismorbificans and 28 strains of S. enterica serovar Stanley) after digestion of genomic DNA with restriction enzyme XbaI were indistinguishable from each other but differed clearly from those of the nonoutbreak strains (26 strains of S. enterica serovar Bovismorbificans and 40 strains of S. enterica serovar Stanley). The restriction enzyme XhoI did not differentiate the outbreak and nonoutbreak strains. The S. enterica serovar Stanley strains associated with the outbreak also had a unique antimicrobial resistance pattern, whereas all S. enterica serovar Bovismorbificans strains, both outbreak and nonoutbreak strains, were sensitive to all antimicrobial agents tested. Thus, the molecular typing confirmed that the S. enterica serovar Bovismorbificans outbreak isolates from humans and sprout salad were identical and strongly supported the epidemiological finding that S. enterica serovar Stanley outbreak isolates also originated from contaminated alfalfa seeds. It also confirmed that the sources of similar outbreaks in Sweden in 1994 caused by S. enterica serovar Bovismorbificans and in the United States in 1995 caused by S. enterica serovar Stanley and the source of the Finnish outbreaks were common.