Typing ofSalmonella entericaserovar Saintpaul: An outbreak investigation

Whole-Genome-Based Survey for Polyphyletic Serovars of Salmonella enterica subsp. enterica Provides New Insights into Public Health Surveillance

Serotyping has traditionally been considered the basis for surveillance of Salmonella, but it cannot distinguish distinct lineages sharing the same serovar that vary in host range, pathogenicity and epidemiology. However, polyphyletic serovars have not been extensively investigated. Public health microbiology is currently being transformed by whole-genome sequencing (WGS) data, which promote the lineage determination using a more powerful and accurate technique than serotyping. The focus in this study is to survey and analyze putative polyphyletic serovars. The multi-locus sequence typing (MLST) phylogenetic analysis identified four putative polyphyletic serovars, namely, Montevideo, Bareilly, Saintpaul, and Muenchen. Whole-genome-based phylogeny and population structure highlighted the polyphyletic nature of Bareilly and Saintpaul and the multi-lineage nature of Montevideo and Muenchen. The population of these serovars was defined by extensive genetic diversity, the open pan genome and the small core genome. Source niche metadata revealed putative existence of lineage-specific niche adaptation (host-preference and environmental-preference), exhibited by lineage-specific genomic contents associated with metabolism and transport. Meanwhile, differences in genetic profiles relating to virulence and antimicrobial resistance within each lineage may contribute to pathogenicity and epidemiology. The results also showed that recombination events occurring at the H1-antigen loci may be an important reason for polyphyly. The results presented here provide the genomic basis of simple, rapid, and accurate identification of phylogenetic lineages of these serovars, which could have important implications for public health.

Genetic and resistance phenotypic subtyping of Salmonella Saintpaul isolates from various food sources and humans: Phylogenetic concordance in combinatory analyses

Bacterial pathogen subtyping for public health traceback of foodborne outbreaks has increasingly produced a number of disparate molecular techniques of varying resolution. Here, we bridge the molecular divide across three methodologies, transform data types for cross-comparison, and test phylogenetic concordance. Single nucleotide polymorphism (SNP) discovery was combined with pulsed-field gel electrophoresis (PFGE) and antimicrobial susceptibility profiles for identifying and differentiating 183 strains of closely related Salmonella enterica serovar Saintpaul isolates from retail meats, produce-associated outbreaks, and clinical sources. Fifty-six SNPs across 30 different genes were identified by comparative genomic analysis. These SNPs stratified general, monophyletic S. Saintpaul serovar specific signatures down to informative strain-specific markers. This SNP panel resulted in 17 distinct genotypes that, in concert with standard PFGE profiling, generated additional discriminatory power among clonal swarms of isolates when the data were transformed into a cross-comparable binary format. In a limited number of cases, antimicrobial susceptibility profiles (ASP) provided additional attributes for some strains when combined similarly. However, as expected from presumably acquired elements, resistant and susceptible populations produced some conflicting signals in most clonal complexes but they remained largely undisruptive to the general concordance. Taken in concert together, the three datasets (SNPs, PFGE,ASP) yielded a matrix of 156 independent phylogenetic characters that were statistically evaluated and found to be largely congruent, resulting in a consistently structured, non-homoplastic, phylogenetic signal and tree topology.

Comparison of sampling methods to detect Salmonella infection of turkey flocks

AIMS

To compare the efficiency of various sampling methods for detection of Salmonella in turkey flocks.

METHODS AND RESULTS

In a field study that compared various sampling methods one pair of boot swabs taken from the whole turkey house provided suitably sensitive results for fattening and rearing flocks and was no less sensitive than two pairs, each from half the house, tested as a pooled sample. The sensitivity was further enhanced by adding a dust sample. The dust sample appeared to be particularly useful in flocks with a low prevalence, especially in breeding flocks, and was more sensitive than a method which used five pairs of boot swabs per flock. Combined incubation of a boot swab and a dust sample showed no interference between the two sample types and a maximum sensitivity of detection. Litter samples and commercial sponge drag swabs provided a lower level of detection.

CONCLUSIONS

A single pair of boot swabs taken from the whole house is recommended for routine sampling of commercial rearing or fattening flocks. An additional dust sample could be added to increase detection in flocks with a low prevalence or in breeding flocks, but adding an additional pair of boot swabs would not increase detection compared with a single pair.

SIGNIFICANCE AND IMPACT OF THE STUDY

This study demonstrates that significant efficiencies can be made in sampling programmes for detection of Salmonella in turkey flocks without detracting from the sensitivity. Similar studies are recommended for other poultry sectors, particularly in chicken breeding flocks.

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

OBJECTIVE

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

MATERIALS AND METHODS

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

RESULTS

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

CONCLUSION

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

An outbreak of Salmonella serotype Saintpaul in a children's hospital

OBJECTIVES

To describe a nosocomial outbreak of Salmonella serotype Saintpaul gastroenteritis and to explore risk factors for infection.

DESIGN

Case-control study.

SETTING

A 208-bed, university-affiliated children's hospital.

PARTICIPANTS

Patients hospitalized at Children's Hospital and Regional Medical Center, Seattle, Washington, during February 2001 who had stool specimens obtained for culture at least 24 hours after admission. Case-patients (n = 11) were patients with an indistinguishable strain of Salmonella Saintpaul cultured from their stool. Control-patients (n = 41) were patients hospitalized for problems other than gastroenteritis whose stool cultures were negative for Salmonella.

METHODS

Risk factors were evaluated using the chi-square test or Fisher's exact test. Continuous variables were compared using the Mann-Whitney U test. A multivariable analysis was performed using logistic regression. The predictor of interest was the receipt of enteral feeding formula mixed by the hospital.

RESULTS

Case-patients were more likely than control-patients to have received formula mixed by the hospital (OR, 4.2; 95% confidence interval, 1.04 to 17.16). Other variables evaluated were not significant predictors of Salmonella Saintpaul infection.

CONCLUSIONS

Formula mixed by the hospital appears to have been the source of this Salmonella outbreak. Strict sanitation measures must be ensured in formula preparation and delivery, and bacterial pathogens should be included in the differential diagnosis for nosocomial gastroenteritis.

Modified pulsed-field gel electrophoresis method for DNA degradation-sensitive Salmonella enterica and Escherichia coli strains

A number of S. enterica and E. coli strains appeared sensitive to a rapid DNA degradation during the course of PFGE pattern analysis. This kind of DNA degradation could not be stopped by intensive treatment with proteinase K, formalin treatment, or other modifications of the protocol for the isolation of intact chromosomal DNA. However, the application of 100 microM thiourea into the running buffer gave rise to clear-cut PFGE patterns and in turn to an overall typeability.

Typing of Salmonella enterica subsp. enterica serovar Mbandaka isolates

Recently, Salmonella enterica subsp. enterica serovar Mbandaka (S. Mbandaka) has gained some importance in the epidemiology of salmonellosis in Poland. Since biotyping, resistance typing, and plasmid profiling were insufficient for strain differentiation, genome macrorestriction by means of pulse-field gel electrophoresis (PFGE) was applied and proved to be the method of choice in S. Mbandaka epidemiological studies. XbaI and BcuI macrorestriction produced 15 and 14 pulse-field profiles (PFP), respectively, but in the case of each enzyme one profile was prevalent. When macrorestriction profiles were combined, a total 24 patterns were found. Based on the similarity of the profiles, four clonal lineages were identified. One clonal lineage contained the majority of poultry, feed and human isolates. Poultry was concluded to be an important source of S. Mbandaka for humans in Poland. Complementary use of various typing techniques improved efficacy of epidemiological studies giving possibility to subdivide S. Mbandaka into 35 types and the index of discrimination reached 0.947.

Salmonella serotypes isolated from turkey meat in Albania

Eleven (11) Salmonella strains were recovered from 11 (8.2%) out of 134 turkey meat samples in Albania, for the period of time 1996-1998. The percentage of Salmonella positive turkey meat samples varied with 5% in 1996 (3 out of 60), 14.7% in 1997 (5 out of 34) and 7.5% in 1998 (3 out of 40). The isolated strains were found to belong to 3 different Salmonella serogroups; 6 isolates to serogroup B, 4 isolates to serogroup D and 1 isolate to serogroup C. Five (5) different serotypes were encountered; Salmonella enteritidis (4 isolates), Salmonella agona (3 isolates), S. saint-paul, S. reading and S. blockley with only one isolate each. One Salmonella strain, belonging to serogroup B, was not completely serotyped.

Phase variable switching of in vivo and environmental phenotypes of Salmonella typhimurium

Previously it was shown that S. typhimurium strain 798, which is known to cause persistent asymptomatic infections in pigs, exists in two phenotypes. One phenotype, which is called adhesive, was shown to produce pili, is adhesive to porcine enterocytes, is readily phagocytized, and then survives intracellularly in phagocytes. The other phenotype, termed non-adhesive, does not produce pili, does not attach to enterocytes, is phagocytized less efficiently, and does not survive within the phagocyte. Cells in each phenotype can freely switch to the other phenotype at a fairly high frequency and thus the shift between each phenotype is phase variation. Further analysis of these phenotypes identified 4 additional characteristics that were co-regulated by phase variation. The first is the enterocyte-specific adhesin, which was shown to be type 1 fimbriae. Mutations in fimA, the major pilin molecule, led to a decreased ability to colonize the gut of pigs and mice. The second characteristic is O-antigen production. Adhesive cells produce a long O-antigen (up to 18 subunits) while non-adhesive cells do not (only 1-2 subunits). The long O-antigen produced by the adhesive cells leads to resistance to serum and appears to be the result of phase variable expression of rfaL. A third locus, ebu, has been identified based on differential color production of colonies growing on Evans blue-Uranine plates. The relationship of this trait to in vivo survival or virulence is not known but ebu is genetically related to a family of transcriptional activators. The fourth locus, prv is located on the virulence plasmid and a mutation in prv results in delayed time to death in mice. It is hypothesized that the adhesive phenotype is the in vivo, virulent form, while the non-adhesive phenotype is the environmental, avirulent form. By modulating the fraction of cells in each phase, persistent asymptomatic infections can be promoted.

Phenotyping and genotyping methods applied to investigate the relatedness of Brazilian isolates of Enterobacter cloacae

In order to evaluate the resolving power of several typing methods to identify relatedness among Brazilian strains of Enterobacter cloacae, we selected twenty isolates from different patients on three wards of a University Hospital (Orthopedics, Nephrology, and Hematology). Traditional phenotyping methods applied to isolates included biotyping, antibiotic sensitivity, phage-typing, and O-serotyping. Plasmid profile analysis, ribotyping, and macrorestriction analysis by pulsed-field gel electrophoresis (PFGE) were used as genotyping methods. Sero- and phage-typing were not useful since the majority of isolates could not be subtyped by these methods. Biotyping, antibiogram and plasmid profile permitted us to classify the samples into different groups depending on the method used, and consequently were not reliable. Ribotyping and PFGE were significantly correlated with the clinical epidemiological analysis. PFGE did not type strains containing nonspecific DNase. Ribotyping was the most discriminative method for typing Brazilian isolates of E. cloacae.

Random amplification of polymorphic DNA (RAPD), pulsed-field gel electrophoresis (PFGE) and phage-typing in the analysis of a hospital outbreak of Salmonella enteritidis

Isolates of Salmonella Enteritidis from 81 patients from Herlev Hospital or from Copenhagen County were analysed by random amplification of polymorphic DNA (RAPD), pulsed-field gel electrophoresis (PFGE) and phage-typing. Fourteen polymorphic markers from five decamer primers unambiguously placed all isolates into six RAPD groups: 65 isolates of phagetype 6 (PFGE type I) were resolved into three RAPD groups constituting 86, 12, and 2%, respectively. A fourth RAPD group of 10 isolates was coincident with phage type 8 (PFGE type II) and two isolates, one phage-type 1, the other phage-type 4 (both PFGE type I) formed the fifth group. The sixth group of four isolates was not phage typeable and was PFGE type III. Forty outbreak-related isolates of phage-type 6 were resolved into three strains. No diversity of phage-type 6 was found among isolates unrelated to the outbreak. It is concluded that RAPD is useful as a tool in investigations of microbial outbreaks in its own right, or to supplement phage-typing and PFGE of Salmonella Enteritidis.