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strains were isolated from poultry and poultry - related sources and were obtained from the center for veterinary medicine and center for food safety and applied nutrition of the us food and drug administration and from the university of georgia . after screening numerous restriction enzymes , the 6 selected were xbai , blni , and spei , all used in pulsenet protocols ( 5 ) ; sfii and paci , previously used to improve resolution in pfge studies involving escherichia coli o157:h7 ( 8,9 ) ; and noti , found to yield an optimal number of cut sites ( 10 ) .
the standard pulsenet pfge protocol for non - typhoidal salmonella was performed as described ( 11,12 ) .
all digestion times were 23 h.  digestions were separated in 1% agarose gels ( cambrex , baltimore , md , usa ) at 6v / cm by using a chef - mapper ( bio - rad , hercules , ca , usa ) .
first , unique pfge patterns or pattern combinations , when analyzing > 2 enzymes , were tallied .
second , the mean number of strains per polytomy ( an unresolved strain cluster ) was calculated as the number of polytomous strains divided by the number of polytomies in the tree .
third , the percentage of polytomous strains ( of 76 s. enteritidis strains ) was calculated .
fourth , the node : strain ratio was calculated as the number of nodes ( bifurcating tree forks ) divided by 76 s. enteritidis strains .
finally , the simpson diversity index was calculated as a numerical assessment of the relative discriminatory potential of each enzyme and enzyme combination ( 13 ) .
xbai - blni patterns from 76 s. enteritidis strains and 74 s. typhimurium strains were analyzed simultaneously for a direct comparison of pfge diversity .
the resultant dendrogram yielded striking topologic differences between the 2 serovars ( figure 1 ) .
s. typhimurium strains were almost entirely resolved ; nearly every strain possessed its own branch on the dendrogram .
in contrast , s. enteritidis strain discrimination was sharply weaker , affirming extensive genetic homogeneity among strains .
for example , 6 polytomies were evident in the s. enteritidis portion of the tree , 5 of which comprised 4 or more strains and 1 of which comprised 24 strains . in total ,
76% of s. enteritidis strains occupied unresolved clusters with an average of 10 strains per cluster .
moreover , the s. typhimurium dendrogram retained a nearly 1:1 ratio of nodes to strains , indicating that almost every strain retained a unique xbai / blni pattern combination . s. enteritidis , however , yielded a node : strain ratio of 1:3 , indicating a relatively poorly bifurcated tree .
together , these observations highlighted the difficulty in differentiating s. enteritidis with conventional pfge approaches .
simultaneous cluster analysis of salmonella enteritidis and s. typhimurium that used a standard xbai / blni combined pfge protocol .
the dendrogram incorporates 76 s. enteritidis strains and 74 s. typhimurium strains and depicts the contrasting ability of pulsed - field gel electrophoresis ( pfge ) to genetically differentiate these 2 salmonella subspecies i serovars .
the dendrogram was generated in bionumerics v.4.061 ( applied maths , sint - martens - latem , belgium ) by using band - matched xbai / blni pfge data in conjunction with an unweighted pair group method with arithmetic mean clustering algorithm and a dice similarity coefficient .
shaded cones to the right of terminal tree branches denote polytomies within the dendrogram ; adjacent numbers ( n ) show the strain totals composing that polytomy .
an arrow near the bottom of the tree denotes the basal branch of the s. enteritidis cluster .
the s. enteritidis portion of the dendrogram comprises strains isolated from georgia ( n = 31 ) , maryland ( n = 8) , pennsylvania ( n = 3 ) , connecticut ( n = 3 ) , north carolina ( n = 2 ) , iowa ( n = 2 ) , tennessee ( n = 2 ) , minnesota ( n = 1 ) , mexico ( n = 11 ) , and the people s republic of china ( n = 6 ) . to develop a more discriminatory scheme for s. enteritidis
, we examined pattern diversity for 4 additional restriction endonucleases ( spei , sfii , paci , and noti ) .
many of the indices designated noti as being effective for discriminating s. enteritidis . among the 6 enzymes , noti yielded the highest number of unique patterns ( n = 26 ) , the fewest average number of strains per polytomy ( 5.2 ) , the lowest percentage of strains captured by polytomies ( 82% ) , the highest node : strain ratio ( 0.47 ) , and the highest simpson diversity value ( 0.92 ) .
noti was followed closely by paci for most indices , which suggests that paci was also useful for s. enteritidis strain discrimination .
* pfge , pulsed - field gel electrophoresis . absolute tally of unique pfge fingerprints or fingerprint combinations derived from the corresponding enzyme or group of enzymes . 
derived from the formula for assessing discriminatory capability of a subtyping method ( 13 ) .
previous studies that used pfge noted the combining of restriction enzyme data into a single analysis as an approach for improving strain differentiation ( 8,9 ) . in our study , a dendrogram of the combined 6-enzyme s. enteritidis data was highly resolved and yielded 57 unique pattern combinations .
the tree contained , on average , 3.6 strains per polytomy ( n = 8) , and only 38% of the strains in the 6-enzyme tree were associated with unresolved clusters ( table 2 ) .
the node : strain ratio was 0.78 , and the simpson index was 0.98 , surpassing the accepted threshold ( 0.95 ) for a useful subtyping scheme ( 14 ) . although highly effective for s. enteritidis discrimination , 6-enzyme simultaneous analysis would increase the time and resources needed to complete investigations .
first , 2-enzyme combinations were assessed to ascertain a minimal enzyme set for useful discrimination of s. enteritidis .
combinations sfii / noti and paci / noti yielded optimal diversity measures , compared with the others ( table 2 ) .
however , because no 2-enzyme pair rivaled the discriminatory potential of the 6-enzyme analysis , 3-enzyme combinations were explored .
a sfii / paci / noti combination was found to be superior in all diversity categories ( table 2 ) .
it yielded 51 unique pattern combinations , an average of 3.3 strains per unresolved cluster , a node : strain ratio of 0.79 , and a simpson index of 0.98 .
the latter 3 measures matched or exceeded corresponding values in the 6-enzyme analysis , which indicates that most of the diversity in the 6-enzyme analysis was captured by this 3-enzyme combination .
the sfii / paci / noti dendrogram showed a highly resolved tree topology and earmarked this 3-enzyme combination as being particularly effective for differentiating s. enteritidis strains ( figure 2 , panel a ) .
of 11 clusters , 9 comprised 3 or fewer strains , and only 47% of s. enteritidis strains composed these 11 clusters , which , aside from the 6-enzyme analysis , represented the lowest portion of polytomous strains in the study .
a ) dendrogram derived from the combined analysis of pfge data from sfii , paci , and noti . shaded cones to the right of the terminal branches denote polytomies within each dendrogram ; adjacent numbers ( n ) show the strain totals composing their respective polytomies .
b ) examples of s. enteritidis strain differentiation that used sfii , paci , and noti pfge patterns .
the 4 strains are numbered above the gel lanes as follows : 1 , s. enteritidis 9 ; 2 , s. enteritidis 12 ; 3 , 22,704 ; and 4 , 22,705 .
the robust discrimination of s. enteritidis achieved from combining sfii , paci , and noti was attributed to polymorphic band classes that were lacking in other enzymes . as an example , the sfii , paci , and noti pfge patterns for 4 strains ( s. enteritidis 9 , s. enteritidis 12 , 22704 , and 22705 ) that were identical using xbai and blni were examined for band variation .
in contrast to xbai , sfii , paci , and noti , all showed some level of polymorphism among dna fragments ( figure 2 , panel b ) .
band differences for these 3 enzymes partitioned the 4 s. enteritidis strains into disparate dendrogram positions .
on the basis of common geography and xbai / blni pattern homogeneity , several clusters of s. enteritidis strains appeared to exhibit clonal relatedness .
however , the combined analysis of sfii / paci / noti pfge patterns was able to differentiate not only geographically disparate s. enteritidis strains but also s. enteritidis isolates from within a specific geographic locale ( e.g. , georgia s. enteritidis strains 415421 and 434436 ) .
although several parameters , such as variable run conditions and times , likely preclude application to outbreak events in real time , the revised scheme presented here may be useful for retrospective epidemiologic investigations in which a more specific focus is often placed on a limited number of epidemiologically related isolates ( 15 ) . specifically ,
when s. enteritidis strains are tightly linked geographically and temporally by clonal expansion , this 3-enzyme approach should provide an effective differentiation process .
to improve pulsed - field gel electrophoresis  based strain discrimination of 76 salmonella enteritidis strains , we evaluated 6 macro - restriction endonucleases , separately and in various combinations . 
 one 3-enzyme subset , sfii / paci / noti , was highly discriminatory . 
 five different indices , including the simpson diversity index , supported this 3-enzyme combination for improved differentiation of s. enteritidis .