A classification system for plasmids from enterococci and other Gram-positive bacteria

A classification system for plasmids isolated from enterococci and other Gram-positive bacteria was developed based on 111 published plasmid sequences from enterococci and other Gram-positive bacteria; mostly staphylococci. Based on PCR amplification of conserved areas of the replication initiating genes (rep), alignment of these sequences and using a cutoff value of 80% identity on both protein and DNA level, 19 replicon families (rep-families) were defined together with several unique sequences. The prevalence of these rep-families was tested on 79 enterococcal isolates from a collection of isolates of animal and human origin. Difference in prevalence of the designed rep-families were detected with rep(9) being most prevalent in Enterococcus faecalis and rep(2) in Enterococcus faecium. In 33% of the tested E. faecium and 32% of the tested E. faecalis no positive amplicons were detected. Furthermore, conjugation experiments were performed obtaining 30 transconjugants when selecting for antimicrobial resistance. Among them 19 gave no positive amplicons indicating presence of rep-families not tested for in this experimental setup.

Characterization of vancomycin-resistant Enterococcus faecium isolates from broiler poultry and pig farms in England and Wales

This study aimed to investigate the occurrence and molecular epidemiology of vancomycin-resistant Enterococcus faecium (VREF) isolates on poultry and pig farms in England and Wales. A total of 217 VREF isolates were obtained from fresh feces and environmental swabs collected from conventional and organic farms. A predominant pulsed-field gel electrophoresis (PFGE) profile was found for each VREF-positive farm, together with less frequent types. All isolates presented the vanA genotype and were esp negative. Seventy-six percent of the VREF isolates were additionally resistant to nine or more antimicrobials, presenting a diverse range of resistance phenotypes. The multiresistance traits did not appear to be specific to individual farms or sample types (i.e., environmental or fecal), nor did they correlate with any specific PFGE type. Ninety-three percent of the isolates were resistant to penicillin, 89% were resistant to tetracycline, 87.5% were resistant to erythromycin, and 50% were resistant to quinupristin-dalfospristin (Synercid). The lack of clonality among these populations may suggest the horizontal transfer of resistance genes and/or a dynamic replacement of clonal lines rather than persistence.

Molecular fingerprinting evidence of the contribution of wildlife vectors in the maintenance of Salmonella Enteritidis infection in layer farms

AIMS

To provide molecular fingerprinting evidence of the contribution of wildlife vectors in the on-farm epidemiology of Salmonella Enteritidis infections.

METHODS AND RESULTS

Salmonella Enteritidis strains were isolated from wildlife and from farm environment samples collected in 10 egg layer farms. Isolates were typed using plasmid profiling, XbaI-pulsed field gel electrophoresis and PstI-SphI ribotyping. In all 10 farms we were able to identify the same S. Enteritidis clones in wildlife vectors and farm environment. On several occasions the same clones were found before and after cleansing and disinfecting the farm premises. Also in some instances the same clones were present in mice samples, egg contents and spent hens.

CONCLUSIONS

Definitive molecular evidence for the involvement of several wildlife species (mice, rats, flies, litter beetles and foxes) in the maintenance of S. Enteritidis infection on farms has been presented. Failures in biosecurity seriously compromise the control of this pathogen on laying farms.

SIGNIFICANCE AND IMPACT OF THE STUDY

This paper reports on the use of molecular tools for the study of the epidemiology of S. Enteritidis. It gives useful information to be considered in control programmes for this organism on poultry farms.

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 Enteritidis phage types 4, 7, 6, 8, 13a, 29 and 34: a comparative analysis of genomic fingerprints from geographically distant isolates

AIMS

To evaluate genetic heterogeneity in the most common phage types of Salmonella enterica serovar Enteritidis.

METHODS AND RESULTS

A total of 233 isolates of Salm. Enteritidis from England, Northern Ireland, Spain, Hong Kong and the USA belonging to phage types (PT) 4 (n=88), PT7 (n=12), PT6 (n=72), PT8 (n=14), PT13a (n=29), PT29 (n=14) and PT34 (n=4) were characterized by PstI-SphI (PS) ribotyping and pulsed-field gel electrophoresis after digestion of DNA with XbaI. PS ribotyping differentiated the isolates into 53 different PS types and PFGE showed 14 different macrorestriction profiles; with the combination of both methods, 73 combined types were identified. Some of these clones appeared to be present within several countries. Movement of foodstuffs, animals or people may have been involved in the spread of these strains. On the other hand, some clones were only found in specific locations.

CONCLUSIONS

Several well defined clonal lines seem to co-exist within the different phage types included in this study, and a combined typing approach may constitute a useful tool for epidemiological investigations. Clustering analysis of ribotypes and PFGE types agree with previous studies and suggest that phage types that share receptor binding properties can be distinguished as two families: the PT4 family including PT7 and PT6, and the PT8 family including PT13a. The other phage types are difficult to place in a family unless the geographical site of isolation is known.

SIGNIFICANCE AND IMPACT OF THE STUDY

This paper reports on an extensive assessment of the use of molecular tools for the study of the epidemiology of the enteric pathogen Salm. Enteritidis. It also gives new information regarding relationships among some common phage types.

Use of molecular fingerprinting to assist the understanding of the epidemiology of Salmonella contamination within broiler production

1. We analysed Salmonella isolates by conventional sero- and phage-typing, as well as by molecular techniques within the broiler production chain in two integrated companies. The most prevalent serovars were selected for genetic fingerprinting. 2. Isolates were first screened by plasmid profiling; subsequently, the most common plasmid types within the prevalent zoonotic serovars (enteritidis and typhimurium) and S. agama were further characterised by PstI-SphI ribotyping, and XbaI pulsed field gel electrophoresis (PFGE). 3. Salmonella binza, S. kedougou, and S. 4,12:d:- were endemic in the feed mills over long periods of time, and a variety of plasmid types for each of the serovars were found in the premises. 4. A similar situation was found with S. binza and S. senftenberg within the hatchery in company B. The Salmonella serovars which were resident in those locations were also the ones most widely distributed throughout the broiler flocks. 5. Plasmid profiling was useful to subdivide clusters of isolates within serovars, but for each serovar a high percentage (36 to 79%) of the isolates tested fall within a prevalent plasmid type. 6. A more detailed genetic analysis of the isolates by a multiple typing approach allowed for further strain differentiation, and allowed some epidemiological conclusions to be drawn.

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

Salmonella enterica serotypes Derby, Mbandaka, Montevideo, Livingstone, and Senftenberg were among the 10 most prevalent serotypes isolated from farm animals in England and Wales in 1999. These serotypes are of potential zoonotic relevance; however, there is currently no "gold standard" fingerprinting method for them. A collection of isolates representing the former serotypes and serotype Gold Coast were analyzed using plasmid profiling, pulsed-field gel electrophoresis (PFGE), and ribotyping. The success of the molecular methods in identifying DNA polymorphisms was different for each serotype. Plasmid profiling was particularly useful for serotype Derby isolates, and it also provided a good level of discrimination for serotype Senftenberg. For most serotypes, we observed a number of nontypeable plasmid-free strains, which represents a limitation of this technique. Fingerprinting of genomic DNA by ribotyping and PFGE produced a significant variation in results, depending on the serotype of the strain. Both PstI/SphI ribotyping and XbaI-PFGE provided a similar degree of strain differentiation for serotype Derby and serotype Senftenberg, only marginally lower than that achieved by plasmid profiling. Ribotyping was less sensitive than PFGE when applied to serotype Mbandaka or serotype Montevideo. Serotype Gold Coast isolates were found to be nontypeable by XbaI-PFGE, and a significant proportion of them were found to be plasmid free. A similar situation applies to a number of serotype Livingstone isolates which were nontypeable by plasmid profiling and/or PFGE. In summary, the serotype of the isolates has a considerable influence in deciding the best typing strategy; a single method cannot be relied upon for discriminating between strains, and a combination of typing methods allows further discrimination.

Diversity of strains of Salmonella enterica serotype enteritidis from English poultry farms assessed by multiple genetic fingerprinting

Reliable and sufficiently discriminative methods are needed for differentiating individual strains of Salmonella enterica serotype Enteritidis beyond the phenotypic level; however, a consensus has not been reached as to which molecular method is best suited for this purpose. In addition, data are lacking on the molecular fingerprinting of serotype Enteritidis from poultry environments in the United Kingdom. This study evaluated the combined use of classical methods (phage typing) with three well-established molecular methods (ribotyping, macrorestriction analysis of genomic DNA, and plasmid profiling) in the assessment of diversity within 104 isolates of serotype Enteritidis from eight unaffiliated poultry farms in England. The most sensitive technique for identifying polymorphism was PstI-SphI ribotyping, distinguishing a total of 22 patterns, 10 of which were found among phage type 4 isolates. Pulsed-field gel electrophoresis of XbaI-digested genomic DNA segregated the isolates into only six types with minor differences between them. In addition, 14 plasmid profiles were found among this population. When all of the typing methods were combined, 54 types of strains were differentiated, and most of the poultry farms presented a variety of strains, which suggests that serotype Enteritidis organisms representing different genomic groups are circulating in England. In conclusion, geographical and animal origins of Salmonella serotype Enteritidis isolates may have a considerable influence on selecting the best typing strategy for individual programs, and a single method cannot be relied on for discriminating between strains.