PMC:5374366 / 9148-15716 JSONTXT

{"target":"https://pubannotation.org/docs/sourcedb/PMC/sourceid/5374366","sourcedb":"PMC","sourceid":"5374366","source_url":"https://www.ncbi.nlm.nih.gov/pmc/5374366","text":"3. Recent Work Describing the Use of the Cronobacter Microarray to Data Mine Specific Alleles\nThe data shown in Figure 1 support and complement the phylogenic sequence divergence of the genus as described by others [18,19] and Stephan et al. [23], who used phylogenetic analyses using whole genome sequencing. Microarray analysis clearly captures and emphasizes the genomic diversity among each species member of the genus. Recently, Yan et al. [24] utilized this microarray to characterize the phylogenetic relatedness among Cronobacter strains obtained during an environmental surveillance study of several European PIF production facilities. Results from this study showed that the microarray was able to accurately assess each strain’s identity, could differentiate Cronobacter species from their nearest neighbors, and it further defined two phylogenetic lineages among the C. sakazakii sequence type (ST) ST-4 strains. Microarray analysis separated these groups of C. sakazakii isolates into multiple clusters which were also segregated according to sequence type. Interestingly, the microarray grouped 25 ST-4 isolates into two distinct subclusters. Strains from lineage 1 differed from those in lineage 2 by 24–71 genes, seven of which were phage-related and 17 were associated with the pESA3-harbored type 6 secretion system (T6SS) gene cluster. Using PCR assays described by Franco et al. [25], Yan et al. [24] were able to confirm that these unique ST-4 lineages were segregated according to differences ascribing to the strain’s type 6 secretion system which is found on the common virulence plasmid pESA3. This illustrates that the microarray improved and more accurately defined the phylogenetic genomic content of genes associated with pESA3 found in this important meningitis-causing group [25]. Together, these examples emphasize the many attributes of the Cronobacter microarray, the most powerful of which is its ability to assess the dispensable genome within and among each of the Cronobacter species. This enables one to further elucidate the evolutionary associations among disproportionately dispersed but vertically obtained genomic features, as well as horizontally acquired mobile elements.\nPreviously, Iversen et al. [16] showed that of the three subspecies (subsp.) of C. dublinensis, C. dublinensis subsp. dublinensis can utilize both malonate and myo-inositol, while C. dublinensis ssp. lactaridi utilizes only myo-inositol, and C. dublinensis subsp. lausannensis cannot utilize either of the two substrates. Grim et al. [19] showed that the alleles represented on the microarray for malonate utilization were associated with genome region (GR) 34 and the alleles for myo-inositol utilization were located in GR29. Microarray analysis of the species type strain C. dublinensis subsp. dublinensis LMG23823T (synonyms: CFS237 or E187) confirmed that this strain possessed genes associated with both malonate and myo-inositol utilization operons, which augments and confirms the molecular presence of these operons involved in the phenotype described by Iversen et al. [16] for C. dublinensis subsp. dublinensis [18]. Furthermore, Tall et al. [18] used the microarray to mine the genomic content for both sets of these genes in 18 other C. dublinensis strains and demonstrated that C. dublinensis subsp. dublinensis strains contained both sets of gene clusters and that only C. dublinensis subsp. lactaridi possessed the myo-inositol utilization operon. Conversely, microarray analysis of C. dublinensis subsp. lausannensis strains confirmed that these strains lacked both gene clusters.\nAnother example of the usefulness of the microarray to mine phylogenetically-related information is demonstrated by performing the microarray analysis on 240 Cronobacter and phylogenetically-related species to determine sequence divergence among outer-membrane protein (OMP) genes which encode for several OMPs such as OmpA; OmpX; porins OmpC, D, E, and F; a conjugative plasmid transfer protein (CTP); molecular chaperon GroEL; and an OM autotransporter protein (Omatp) [26]. The microarray contains 58 OMP alleles (probe sets) representing these genes among the seven Cronobacter species (summarized in Supplementary Table S3). Microarray analysis demonstrated that particular alleles such as the omatp gene (NCBI Reference number: ABU77334) from C. sakazakii present on the microarray are more species-specific in that all 204 C. sakazakii strains and only one of 12 C. turicensis strains were positive for omatp, while representative strains of the other five species were microarray-negative. A similar sequence divergence trend was observed for ompC (NCBI Reference number: ABU76243) and ompF (NCBI Reference number: ABU77659) from C. malonaticus and C. turicensis where only seven of nine C. malonaticus and two of 12 C. turicensis strains were positive for ompC and ompF, respectively, while representative strains of the other species were negative for these species-specific OMP probe sets [27]. However, the ompC allele (NCBI Reference number: ABU76243) from C. muytjensii was determined to be present in approximately 99% (239 out of 240) of the strains. A similar trend was also seen with the ompA allele (NCBI Reference number: ABU79362) from C. turicensis which was found to be present in 99% of the strains, whereas the ompA allele (NCBI Reference number: ABU76166) from C. dublinensis subsp. lausannensis was only found in the C. dublinensis and the C. universalis strains. The probe set for the groEL allele (NCBI Reference number: ABU75458) from C. turicensis captured 99% of the strains analyzed except for C. condimenti, demonstrating that this allele is common among six of the seven species. Interestingly, the ctp probe set (NCBI Reference number: ABU77334) from C. sakazakii was also present in a high percentage of strains (96%) from all species except for C. condimenti, whereas the mipA probe sets from C. dublinensis subsp. lausannensis and C. condimenti (NCBI Reference number: ABU77421) only were positive in C. dublinensis and C. condimenti strains and mipA was not found in any other strain (species). These results again support the phylogenetic relationships generated using whole genome sequence information [19,23], and demonstrate the utility of the microarray to study the phylogenetic relationship of a specific set of alleles [11,18,19]. Outer-membrane protein genes have been submitted to NCBI under a Cronobacter GenomeTrakr Project: FDA-Center for Food Safety and Applied Nutrition Bioproject 258403 [27,26].","divisions":[{"label":"Title","span":{"begin":0,"end":93}}],"tracks":[{"project":"2_test","denotations":[{"id":"28273858-26284227-69474758","span":{"begin":216,"end":218},"obj":"26284227"},{"id":"28273858-23724777-69474759","span":{"begin":219,"end":221},"obj":"23724777"},{"id":"28273858-25028159-69474760","span":{"begin":243,"end":245},"obj":"25028159"},{"id":"28273858-25911470-69474761","span":{"begin":446,"end":448},"obj":"25911470"},{"id":"28273858-21421789-69474762","span":{"begin":1400,"end":1402},"obj":"21421789"},{"id":"28273858-25911470-69474763","span":{"begin":1417,"end":1419},"obj":"25911470"},{"id":"28273858-21421789-69474764","span":{"begin":1807,"end":1809},"obj":"21421789"},{"id":"28273858-18523192-69474765","span":{"begin":2246,"end":2248},"obj":"18523192"},{"id":"28273858-23724777-69474766","span":{"begin":2553,"end":2555},"obj":"23724777"},{"id":"28273858-18523192-69474767","span":{"begin":3098,"end":3100},"obj":"18523192"},{"id":"28273858-26284227-69474768","span":{"begin":3141,"end":3143},"obj":"26284227"},{"id":"28273858-26284227-69474769","span":{"begin":3172,"end":3174},"obj":"26284227"},{"id":"28273858-28232819-69474770","span":{"begin":5017,"end":5019},"obj":"28232819"},{"id":"28273858-23724777-69474771","span":{"begin":6261,"end":6263},"obj":"23724777"},{"id":"28273858-25028159-69474772","span":{"begin":6264,"end":6266},"obj":"25028159"},{"id":"28273858-26000266-69474773","span":{"begin":6384,"end":6386},"obj":"26000266"},{"id":"28273858-26284227-69474774","span":{"begin":6387,"end":6389},"obj":"26284227"},{"id":"28273858-23724777-69474775","span":{"begin":6390,"end":6392},"obj":"23724777"},{"id":"28273858-28232819-69474776","span":{"begin":6561,"end":6563},"obj":"28232819"}],"attributes":[{"subj":"28273858-26284227-69474758","pred":"source","obj":"2_test"},{"subj":"28273858-23724777-69474759","pred":"source","obj":"2_test"},{"subj":"28273858-25028159-69474760","pred":"source","obj":"2_test"},{"subj":"28273858-25911470-69474761","pred":"source","obj":"2_test"},{"subj":"28273858-21421789-69474762","pred":"source","obj":"2_test"},{"subj":"28273858-25911470-69474763","pred":"source","obj":"2_test"},{"subj":"28273858-21421789-69474764","pred":"source","obj":"2_test"},{"subj":"28273858-18523192-69474765","pred":"source","obj":"2_test"},{"subj":"28273858-23724777-69474766","pred":"source","obj":"2_test"},{"subj":"28273858-18523192-69474767","pred":"source","obj":"2_test"},{"subj":"28273858-26284227-69474768","pred":"source","obj":"2_test"},{"subj":"28273858-26284227-69474769","pred":"source","obj":"2_test"},{"subj":"28273858-28232819-69474770","pred":"source","obj":"2_test"},{"subj":"28273858-23724777-69474771","pred":"source","obj":"2_test"},{"subj":"28273858-25028159-69474772","pred":"source","obj":"2_test"},{"subj":"28273858-26000266-69474773","pred":"source","obj":"2_test"},{"subj":"28273858-26284227-69474774","pred":"source","obj":"2_test"},{"subj":"28273858-23724777-69474775","pred":"source","obj":"2_test"},{"subj":"28273858-28232819-69474776","pred":"source","obj":"2_test"}]}],"config":{"attribute types":[{"pred":"source","value type":"selection","values":[{"id":"2_test","color":"#93afec","default":true}]}]}}