Animal Disease Research Unit, USDA Agricultural Research Service,1 College of Veterinary Medicine, Washington State University, Pullman, Washington,2 Seoul National University, Seoul, Korea,3 Massachusetts State Laboratory Institute, Massachusetts Department of Public Health, Boston, Massachusetts,4 Bureau of Microbial Hazards, Health Products and Food Branch, Health Canada, Ottawa, Ontario, Canada5
Received 13 February 2004/ Returned for modification 14 April 2004/ Accepted 31 July 2004
| ABSTRACT |
|---|
|
|
|---|
| INTRODUCTION |
|---|
|
|
|---|
Although 13 serotypes of L. monocytogenes have been described (25), only three serotypes (1/2a, 1/2b, and 4b) cause the vast majority of clinical cases (26). Interestingly, although serotype 1/2a is most frequently isolated from food, serotype 4b causes the majority of human epidemics (12). Thus, many have suggested that there may be a link between serotype and virulence potential.
Numerous molecular subtyping techniques have identified two major phylogenetic divisions within the species. Division I consists of serotypes 1/2b, 3b, 4b, 4d, and 4e, and Division II consists of serotypes 1/2a, 1/2c, 3a, and 3c (1-3, 5, 15, 21). A third division, consisting of serotypes 4a and 4c and a subset of 4b strains, has also been described (8, 22, 27).
Epidemiological investigation of epidemic and sporadic cases of listeriosis requires molecular characterization to allow the identification of specific subtypes. L. monocytogenes subtypes are usually characterized by serotyping and then further subtyped by using the current "gold standard," pulsed-field gel electrophoresis (PFGE) (16) or ribotyping. Multilocus sequence typing (MLST) has been described as a novel, reproducible, and potentially discriminatory subtyping method (10, 18, 23, 24), and Revazishvili et al. (23) recently demonstrated that MLST was able to differentiate most of the L. monocytogenes strains examined better than PFGE with AscI restriction endonuclease digestion.
DNA subtyping with DNA microarrays may provide an improved alternative to resolve genetic differences that exist among isolates (4, 9, 28). This technique has the added advantage that, unlike PFGE, ribotyping, and MLST, it can identify specific or unique genes associated with strains of interest. For example, Call and colleagues (9) demonstrated that certain strains of L. monocytogenes contained genes responsible for repairing UV-damaged DNA, salt tolerance, and biofilm formation, which would confer an advantage in certain ecological niches such as food production environments.
In the present study, a 629-probe "condensed" microarray was constructed using exclusively polymorphic probes. Fifty-two strains of L. monocytogenes were genotyped using the condensed array to compare the resolution of microarray subtyping to that of PFGE, MLST, and ribotyping and to identify genetic regions that characterize subtypes.
| MATERIALS AND METHODS |
|---|
|
|
|---|
|
MLST.
Loci were identified by searching for housekeeping genes from both L. monocytogenes and L. innocua via GenBank (http://www.ncbi.nlm.nih.gov). These genes were mapped against the L. monocytogenes EGD genome sequence (13) to provide adequate genome coverage, and primers were chosen to amplify coding regions of 500 to 750 bp under common conditions (3 mM MgCl2 and an annealing temperature of 58°C). Nucleotide sequences were obtained by PCR amplification of coding regions from the following genes: ahs, O-acetylhomoserine sulfhydralase homolog; pstI, phosphenolpyruvate-dependent phosphotransferase enzyme I; lisK, histidine kinase homolog; lhkA, histidine kinase; dhk, dihydroxyacetone kinase; and abcZ, ABC transporter homolog Z. PCR products were purified by using QIAquick 96 PCR purification kits (Qiagen, Valencia, Calif.) and were eluted in
60 µl of water; 96-well plates were stored at 20°C. Dye terminator cycle sequencing was performed with the CEQ cycle sequencing kit (Beckman Coulter, Fullerton, Calif.) in 10-µl reaction volumes with 10 to 20 ng of DNA. Sequencing reaction products were ethanol precipitated and dried, and samples were resuspended in 20 µl of formamide prior to separation by capillary electrophoresis with a CEQ2000XL DNA sequencer (Beckman Coulter). Sequence alignment and editing were performed with BioNumerics version 2.5 (Applied Maths, Kortrijk, Belgium). Allele sequence types were identified from 450 to 550 bp from each locus. Unweighted pair group method using arithmetic averages (UPGMA) analysis of categorical information based on the six different allele sequence types for each isolate was performed.
Microarray construction. A genomic library was constructed from 20 strains representing six serotypes (1/2a [n = 5], 1/2b [n = 4], 1/2c [n = 4], 3a [n = 1], 4b [n = 5], and 4c [n = 1]) and obtained from a variety of sources (human sporadic [n = 10], epidemic [n = 2], environmental [n = 7], and veterinary [n = 1]). Genomic DNA was extracted from the 20 strains by using an Easy DNA kit (Invitrogen, Carlsbad, Calif.). DNA was quantified by UV spectrophotometry, and equal amounts of genomic DNA from each strain were mixed. This pooled genomic DNA was used to construct a random shotgun library (Amplicon Express, Pullman, Wash.). Briefly, 10 µg of DNA was cut with the restriction enzyme CviJI (Chimerx, Milwaukee, Wis.) or by sonification, and fragments of approximately 600 bp were gel isolated, extracted, and ligated into pUC18. Ligation products were transformed into Escherichia coli, and 12,000 positive recombinant clones were picked and arrayed into 96-well plates. Clone inserts were amplified by PCR with M13 primers (55 pmol each), 1.5 µl of bacterial culture (template DNA), 4 U of Taq polymerase with 1x reaction buffer (Fisher, Pittsburgh, Pa.), a 0.2 mM concentration of each deoxynucleoside triphosphate (Eppendorf, Westbury, N.Y.), and 2.5 mM MgCl2 in a 100-µl reaction volume. PCR cycle conditions were 95°C for 5 min; followed by 35 cycles of 95°C for 30 s, 52°C for 30 s, and 72°C for 1 min; followed by 72°C for 10 min after cycling was completed. The insert size was determined by using gel electrophoresis (1% agarose). PCR products of the correct size (500 to 1,000 bp) were purified with a Montage PCR96 Cleanup kit (Millipore Corp., Bedford, Mass.) and stored at 20°C until ready for printing.
PCR products were purified by sodium acetate precipitation, resuspended in 100 µl of H2O, quantified by UV spectrophotometry, and air dried. Probe DNA was then suspended in print buffer (200 mM Na2HPO4 plus 0.4 M NaCl [pH 11.5]) at a final concentration of 100 ng/µl, using a BIO-ROBOT 8000 instrument (Qiagen). Probes were then printed onto epoxy-coated slides (TeleChem International, Inc., Sunnyvale, Calif.) by using an Omnigrid spotter (GeneMachines, San Carlos, Calif.). PCR products from cloned fragments of L. monocytogenes ribosomal and listeriolysin genes were used as positive controls, and PCR products from a mouse cDNA library were used as negative controls. After printing, the slides were UV cross-linked (120,000 µJ) and stored at room temperature in the dark.
Target preparation and hybridization. Genomic DNA was extracted from target strains by using a DNeasy tissue kit (Qiagen) and quantified by using UV spectrophotometry. Target DNA (1.5 µg) was nick translated in the presence of biotin-dATP (BioNick labeling system; Invitrogen). The labeled DNA was then ethanol precipitated, resuspended in 150 µl of hybridization buffer consisting of 4x SSC (60 mM NaCl, 0.6 mM Na citrate [pH 7.0]) and 5x Denhardt's solution (0.1% Ficoll, 0.1% polyvinylpyrrolidone, 0.1% bovine serum albumin), and added to the slide for overnight hybridizations at 55°C. Hybridizations and subsequent amplification steps were done in a GeneTAC hybridization station (Genomic Solutions, Ann Arbor, Mich.). Following target hybridization, the signal was amplified with a Tyramide signal amplification kit (Perkin-Elmer, Boston, Mass.). The slides were washed twice at 23°C for 30 s with TNT buffer (100 mM Tris-HCl [pH 7.5], 150 mM NaCl, 0.05% Tween 20). Subsequent wash steps used two washes (30 s each) in TNT buffer, and all subsequent manipulations occurred at approximately 23°C. Streptavidin conjugated to horseradish peroxidase (1:100 in hybridization buffer) was incubated on the slide for 30 min, followed by washing and incubation with 10% equine serum (Sigma-Aldrich) in 2x SSC for 30 min. Biotinyl tyramide (1:50 in amplification buffer [tyramide signal amplification biotin system]) was then incubated on each slide for 10 min, followed by washing and a 30-min incubation with 2 µg of streptavidin per ml conjugated to Alexa Fluor 546 (Molecular Probes, Eugene, Oreg.) in 1x SSC-5x Denhardt's solution. The slides were given a final wash, followed by drying and imaging with a ScanArray 4000XL laser scanner (Packard BioChip Technologies, Downers Grove, Ill.).
Signal analysis. Quantarray software (Packard Biochip Technologies) was used to quantify signal intensity. The final output included median intensity values, and data were normalized by dividing the median signal intensity by the median signal intensity of the ribosomal positive control. Data were managed by using MS Excel (Microsoft Corp., Redmond, Wash.) spreadsheets.
Data analysis. Our analysis was limited to only those probes that were bimodally distributed such that both positive hybridizations (high signal) and negative hybridizations (low signal) were clearly identified. The selection process was based on a previously published algorithm (14). Briefly, for each probe, intensity values were assigned to either a "low" or a "high" cluster. After intensity values for all hybridization experiments were assigned to these two clusters, cluster averages and standard deviations were calculated. If cluster averages were different by greater than three standard deviations, the probe was considered bimodal. Ninety bimodal probes were selected for analysis by this technique. An additional 30 bimodal probes were selected for analysis as described previously (4).
For dendrogram construction, probes with normalized intensity readings of less than 0.2 were assigned a score of 1, probes with normalized intensity readings of greater than 0.2 but less than 0.4 were scored as 2 (and treated as ambiguous data in the phylogenetic analysis), and probes with normalized intensity readings of greater than 0.4 were scored as 3. A matrix was constructed and processed with PAUP (version 4.0b8a; Sinauer Associates, Inc., Sunderland, Mass.). UPGMA and Treeview (20) were used to construct a dendrogram that summarized genetic relationships between samples. Stepwise discriminant function analysis (DFA) (NCSS 2001 statistical software; NCSS, Kaysville, Utah) was used to identify probes characteristic of divisions and subtypes. Data were also examined by using a spreadsheet (Microsoft Excel) to identify probes that consistently discriminated between various dendrogram clusters.
Sequence analysis. Probes of interest were retrieved from the clone library and sequenced by using two-pass automated sequencing, and data were analyzed by using DNASTAR (DNASTAR, Madison, Wis.). Nucleotide sequences were compared to existing nucleotide and protein sequences present in the GenBank database by using BLASTn and BLASTx searches. Seven of these probe sequences were selected to identify how sequence divergence was reflected by signal intensity on the microarray. PCR primers were designed to amplify a 500- to 600-bp region of the corresponding sequences from 15 L. monocytogenes isolates representing the two primary phylogenetic divisions. The resulting PCR products were sequenced, and percent sequence similarity was calculated.
Nucleotide sequence accession numbers. The DNA sequences of the MLST loci have been deposited in GenBank under accession numbers AY622010 through AY622039 (abcZ), AY622040 through AY622069 (ahs), AY622070 through AY622099 (dhk), AY622100 through AY622129 (lhkA), AY622130 through AY622159 (lisK), and AY622160 through AY622189 (ptsI).
| RESULTS |
|---|
|
|
|---|
Fifty-two L. monocytogenes strains were hybridized to the condensed array, and subsequent data analysis identified 130 bimodally distributed probes. Data analyses were limited to these probes to maximize the likelihood of identifying subtype- or division-specific DNA sequences.
Phylogenetic divisions and subgroups. Comparative microarray analysis grouped strains according to previously described phylogenetic divisions, and all strains were grouped by serotype (Fig. 1). Division I (D1) consisted of two main subgroups (D1a and D1b). Interestingly, the D1b subgroup, consisting of human sporadic and environmental serotype 1/2b strains, clustered more closely to Division II (D2) strains than to D1a strains. However, DFA and subsequent sequence analysis were unable to identify probes with sequences unique to D2 and D1b. Indeed, sequence analysis of 13 of the 14 probes revealed that the majority of sequence differences occurred between the major divisions (D1 and D2). Three probes that differentiated between serovars 1 and 4 (probes 55 and 205) or between serotypes (probe 1083) were identified, and it is likely that serovar-specific probes may have influenced the topological position of the D1b subcluster.
|
Stepwise DFA was used to identify 22 probes that differed among divisions and subclusters. Thirteen of these probes were further investigated by PCR and sequence analysis (Table 2). Sequence data revealed that five of the probes were division specific, four were subcluster specific, and four were serovar or serotype specific.
|
Resolution of the condensed array was compared to that of the current gold standard, PFGE with AscI and ApaI restriction endonuclease digestion (16), by characterizing a panel of 28 strains by using both techniques. Resolution was similar for the two techniques, with both microarray analysis and PFGE dividing the 28 strains into 10 distinct subtypes (Fig. 1). Additionally, nine epidemiologically unrelated strains were grouped into four subtypes by using ribotyping and MLST with six housekeeping genes (Table 3). These strains separated into five distinct groups when characterized by microarray analysis and PFGE (with AscI and ApaI).
|
| DISCUSSION |
|---|
|
|
|---|
D1 strains were separated into four main subclusters, with D1a containing three subclusters and D1b consisting of a single 1/2b subcluster. One of the subclusters within D1a included 15 of the 17 serotype 4b strains associated with epidemics (Fig. 1). DFA was used to identify three probes that are most useful in defining this subcluster, and further analysis of these probes is under way.
Strains epidemiologically linked to particular epidemics were included in the microarray analysis to determine whether microarray subtyping did indeed group these strains together. Isolates obtained from patients and implicated foods from the 1981 Halifax epidemic (F495E and F496E), the 1994 Illinois epidemic (B507E and B508B), and the 1998 multistate epidemic (F470E, F581E, and F584E) grouped according to epidemic (Fig. 1). Two of the three strains associated with the 1988 to 1990 United Kingdom epidemic also grouped together. Investigation of the later outbreak identified pÂté as the likely source of an observed upsurge in listeriosis cases; however, no samples of pÂté eaten by patients with listeriosis were available for subtyping (19). Interestingly, the two strains from this outbreak that did cluster together were both obtained from patients, whereas strain F497E, a strain also associated with this epidemic but in a separate cluster, was a food isolate.
Strain A503E, a serotype 1/2a isolate that caused a multistate deli meat-associated epidemic in 2000, clustered with three other 1/2a strains (Fig. 1). Two of these strains are particularly interesting, because one (A501N) was isolated from the same food-processing plant in 1988 as A503E and another (A502S) was from a human sporadic case associated with A501N (17).
The resolutions of four different subtyping methods were compared using a subset of strains (Fig. 1; Table 3). Microarray analysis and PFGE subtyping showed the highest resolution, MLST had moderate subtyping resolution, and ribotyping had the lowest resolution. The microarray analysis subtyping resolution was similar to that of PFGE with two enzymes, the current gold standard for molecular subtyping of L. monocytogenes strains (16). Nevertheless, occasionally the two techniques placed strains in different groups (Fig. 1; Table 3). This is not surprising, because the two techniques sample the genome differently.
Microarray analysis and subsequent DFA processing of data resulted in the identification of 22 subtype-specific probes. Thirteen of these probes were further analyzed by PCR and sequence analysis (Table 2). Sequence analysis indicated that the microarray hybridization was capable of detecting approximately 10% sequence divergence between strains. These data agree with the microarray sensitivity threshold reported previously (9), although microarray sensitivity is obviously dependent on hybridization conditions, sequence content, and signal analysis.
The 22 probes identified as important for division and subtype definition included seven probes with sequence similarity to cell wall-associated proteins (probes 119, 205, 265, 321, 553, 657, 891, and 951). Three of these were serovar or serotype specific (Table 2). Five probes had sequence similarity to proteins important for survival in the environment or host (probes 57, 837, 1133, 1229, and 1263), and four probes were similar in sequence to virulence-associated proteins (probes 55, 875, 887, and 1117).
In conclusion, these data indicate that microarray analysis has a resolution similar to that of PFGE and better than those of MLST with housekeeping genes and ribotyping. Microarray analysis accurately clustered epidemiologically linked strains. Most epidemic-related strains formed a monophyletic cluster within Division I. Additionally, microarray analysis allowed identification of 22 probes that simultaneously distinguish divisions, serotypes, and subtypes.
| ACKNOWLEDGMENTS |
|---|
We gratefully acknowledge the excellent technical assistance provided by James Reynolds, Kevin Tyler, Edith Orozco, Dave Tibbals, and Melissa Krug. L. monocytogenes isolates were kindly provided by Lewis Graves (Centers for Disease Control and Prevention), Jinxin Hu (Washington State Department of Health), Karen Jinneman (U.S. Food and Drug Administration), Lisa Gorski (USDA Agricultural Research Service), and Martin Wiedmann (Cornell University).
| FOOTNOTES |
|---|
| REFERENCES |
|---|
|
|
|---|
This article has been cited by other articles:
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Antimicrob. Agents Chemother. | Clin. Microbiol. Rev. |
|---|---|
| Clin. Vaccine Immunol. | ALL ASM JOURNALS |
|---|