A new approach for the analysis of bacterial microarray-based Comparative Genomic Hybridization: insights from an empirical study

BACKGROUND: Microarray-based Comparative Genomic Hybridization (M-CGH) has been used to characterize the extensive intraspecies genetic diversity found in bacteria at the whole-genome level. Although conventional microarray analytical procedures have proved adequate in handling M-CGH data, data interpretation using these methods is based on a continuous character model in which gene divergence and gene absence form a spectrum of decreasing gene conservation levels. However, whereas gene divergence may yet be accompanied by retention in gene function, gene absence invariably leads to loss of function. This distinction, if ignored, leads to a loss in the information to be gained from M-CGH data. We present here results from experiments in which two genome-sequenced strains of C. jejuni were compared against each other using M-CGH. Because the gene content of both strains was known a priori, we were able to closely examine the effects of sequence divergence and gene absence on M-CGH data in order to define analytical parameters for M-CGH data interpretation. This would facilitate the examination of the relative effects of sequence divergence or gene absence in comparative genomics analyses of multiple strains of any species for which genome sequence data and a DNA microarray are available. RESULTS: As a first step towards improving the analysis of M-CGH data, we estimated the degree of experimental error in a series of experiments in which identical samples were compared against each other by M-CGH. This variance estimate was used to validate a Log Ratio-based methodology for identification of outliers in M-CGH data. We compared two genome strains by M-CGH to examine the effect of probe/target identity on the Log Ratios of signal intensities using prior knowledge of gene divergence and gene absence to establish Log Ratio thresholds for the identification of absent and conserved genes. CONCLUSION: The results from this empirical study validate the Log Ratio thresholds that have been used in other studies to establish gene divergence/absence. Moreover, the analytical framework presented here enhances the information content derived from M-CGH data by shifting the focus from divergent/absent gene detection to accurate detection of conserved and absent genes. This approach closely aligns the technical limitations of M-CGH analysis with practical limitations on the biological interpretation of comparative genomics data

A new approach for the analysis of bacterial microaray-based Comparative Genomic Hybridization : Insights from an empirical study

NRC publication: Ye

Comparative genomic analysis of <it>Campylobacter jejuni </it>associated with Guillain-Barré and Miller Fisher syndromes: neuropathogenic and enteritis-associated isolates can share high levels of genomic similarity

<p>Abstract</p> <p>Background</p> <p><it>Campylobacter jejuni </it>infection represents the most frequent antecedent infection triggering the onset of the neuropathic disorders Guillain-Barré syndrome (GBS) and Miller Fisher syndrome (MFS). Although sialylated ganglioside-mimicking lipo-oligosaccharide (LOS) structures are the strongest neuropathogenic determinants in <it>C. jejuni</it>, they do not appear to be the only requirement for a neuropathic outcome since strains capable of their production have been isolated from patients with uncomplicated cases of enteritis. Consequently, other pathogen and/or host-related factors contribute to the onset of neurological complications. We have used comparative genomic hybridization to perform a detailed genomic comparison of strains isolated from GBS/MFS and enteritis-only patients. Our dataset, in which the gene conservation profile for 1712 genes was assayed in 102 strains, including 56 neuropathogenic isolates, represents the largest systematic search for <it>C. jejuni </it>factors associated with GBS/MFS to date and has allowed us to analyze the genetic background of neuropathogenic <it>C. jejuni </it>strains with an unprecedented level of resolution.</p> <p>Results</p> <p>The majority of GBS/MFS strains can be assigned to one of six major lineages, suggesting that several genetic backgrounds can result in a neuropathogenic phenotype. A statistical analysis of gene conservation rates revealed that although genes involved in the sialylation of LOS structures were significantly associated with neuropathogenic strains, still many enteritis-control strains both bear these genes and share remarkable levels of genomic similarity with their neuropathogenic counterparts. Two capsule biosynthesis genes (Cj1421c and Cj1428c) showed higher conservation rates among neuropathogenic strains compared to enteritis-control strains. Any potential involvement of these genes in neuropathogenesis must be assessed. A single gene (HS:3 Cj1135) had a higher conservation rate among enteritis-control strains. This gene encodes a glucosyltransferase that is found in some of the LOS classes that do not express ganglioside mimics.</p> <p>Conclusion</p> <p>Our findings corroborate that neuropathogenic factors may be transferred between unrelated strains of different genetic background. Our results would also suggest that the failure of some strains isolated from uncomplicated cases of enteritis to elicit a neuropathic clinical outcome may be due to subtle genetic differences that silence their neuropathogenic potential and/or due to host-related factors.</p> <p>The microarray data has been deposited in NCBI's Gene Expression Omnibus under accession number GSE3579.</p

Large-Scale Comparative Genomics Meta-Analysis of Campylobacter jejuni Isolates Reveals Low Level of Genome Plasticity

We have used comparative genomic hybridization (CGH) on a full-genome Campylobacter jejuni microarray to examine genome-wide gene conservation patterns among 51 strains isolated from food and clinical sources. These data have been integrated with data from three previous C. jejuni CGH studies to perform a meta-analysis that included 97 strains from the four separate data sets. Although many genes were found to be divergent across multiple strains (n = 350), many genes (n = 249) were uniquely variable in single strains. Thus, the strains in each data set comprise strains with a unique genetic diversity not found in the strains in the other data sets. Despite the large increase in the collective number of variable C. jejuni genes (n = 599) found in the meta-analysis data set, nearly half of these (n = 276) mapped to previously defined variable loci, and it therefore appears that large regions of the C. jejuni genome are genetically stable. A detailed analysis of the microarray data revealed that divergent genes could be differentiated on the basis of the amplitudes of their differential microarray signals. Of 599 variable genes, 122 could be classified as highly divergent on the basis of CGH data. Nearly all highly divergent genes (117 of 122) had divergent neighbors and showed high levels of intraspecies variability. The approach outlined here has enabled us to distinguish global trends of gene conservation in C. jejuni and has enabled us to define this group of genes as a robust set of variable markers that can become the cornerstone of a new generation of genotyping methods that use genome-wide C. jejuni gene variability data

Comparative genomic analysis of associated with Guillain-Barré and Miller Fisher syndromes: neuropathogenic and enteritis-associated isolates can share high levels of genomic similarity-4

<p><b>Copyright information:</b></p><p>Taken from "Comparative genomic analysis of associated with Guillain-Barré and Miller Fisher syndromes: neuropathogenic and enteritis-associated isolates can share high levels of genomic similarity"</p><p>http://www.biomedcentral.com/1471-2164/8/359</p><p>BMC Genomics 2007;8():359-359.</p><p>Published online 5 Oct 2007</p><p>PMCID:PMC2174954.</p><p></p> neuropathogenic strains. Both types of strains can show substantial similarities in genomic background, which includes similarities at several hypervariable regions. The lineage (LIN) of the 56 neuropathogenic strains is shown. Highly similar enteritis-control/neuropathogenic strain pairs (boxes a through d) are shown in expanded form in Figure 3. Legend: Hypervariable loci (L – LOS locus; F – flagellar modification locus; C – capsular locus; R/M – restriction-modification locus); Strain sets (DG: Dutch GBS; DM: Dutch MFS; DE: Dutch enteritis; JG: Japanese GBS; JM: Japanese MFS; JE: Japanese enteritis; CG: Curaçao GBS; CE: Curaçao enteritis)

Comparative genomic analysis of associated with Guillain-Barré and Miller Fisher syndromes: neuropathogenic and enteritis-associated isolates can share high levels of genomic similarity-0

<p><b>Copyright information:</b></p><p>Taken from "Comparative genomic analysis of associated with Guillain-Barré and Miller Fisher syndromes: neuropathogenic and enteritis-associated isolates can share high levels of genomic similarity"</p><p>http://www.biomedcentral.com/1471-2164/8/359</p><p>BMC Genomics 2007;8():359-359.</p><p>Published online 5 Oct 2007</p><p>PMCID:PMC2174954.</p><p></p>how unique gene conservation profiles and fail to cluster robustly with any major lineage. Branches with greater than 75% bootstrap support are shown in red. Although data is displayed including capsular genes (gray box), these genes were removed during cluster analysis to avoid biasing results. Highly divergent/Absent genes shown in red; Moderately Divergent genes are shown in blue. Legend: Hypervariable loci (L – LOS locus; F – flagellar modification locus; C – capsular locus; R/M – restriction-modification locus); Strain sets (DG: Dutch GBS; DM: Dutch MFS; JG: Japanese GBS; JM: Japanese MFS; CG: Curaçao GBS)

Comparative genomic analysis of associated with Guillain-Barré and Miller Fisher syndromes: neuropathogenic and enteritis-associated isolates can share high levels of genomic similarity-1

<p><b>Copyright information:</b></p><p>Taken from "Comparative genomic analysis of associated with Guillain-Barré and Miller Fisher syndromes: neuropathogenic and enteritis-associated isolates can share high levels of genomic similarity"</p><p>http://www.biomedcentral.com/1471-2164/8/359</p><p>BMC Genomics 2007;8():359-359.</p><p>Published online 5 Oct 2007</p><p>PMCID:PMC2174954.</p><p></p> neuropathogenic strains. Both types of strains can show substantial similarities in genomic background, which includes similarities at several hypervariable regions. The lineage (LIN) of the 56 neuropathogenic strains is shown. Highly similar enteritis-control/neuropathogenic strain pairs (boxes a through d) are shown in expanded form in Figure 3. Legend: Hypervariable loci (L – LOS locus; F – flagellar modification locus; C – capsular locus; R/M – restriction-modification locus); Strain sets (DG: Dutch GBS; DM: Dutch MFS; DE: Dutch enteritis; JG: Japanese GBS; JM: Japanese MFS; JE: Japanese enteritis; CG: Curaçao GBS; CE: Curaçao enteritis)

Hospital case volume and clinical outcomes in critically ill patients with acute kidney injury treated with dialysis

PurposeTo determine whether patients with severe acute kidney injury who receive dialysis (AKI-D) experience better outcomes at centres that care for more patients with AKI-D.Materials and methodsLinked administrative datasets where used to perform a retrospective cohort study of all critically ill patients in Ontario, Canada, who had a first episode of AKI-D between 2002 and 2011. Centre volume for a given year, was designated by calculating the mean number of patients treated with acute dialysis at that centre during that year and the one preceding it. Patients treated at that centre were then assigned to a centre volume quartile for that year.ResultsWe identified 19,658 critically ill patients with AKI-D treated at 54 Ontario hospitals. Mortality and dialysis dependence at 90-days were 46% and 31%, respectively. Centre volume was not associated with mortality at 90 days (with quartile 1 as the reference, adjusted odds ratio (aOR) 1.16 (95% CI, 0.87 - 1.54) in quartile 2, aOR 1.17 (95% CI, 0.91 - 1.50) in quartile 3, and aOR 1.06 (95% CI, 0.81 - 1.41) in quartile 4).ConclusionsThere are no Centre volume survival associations in the management of AKI-D despite high mortality and dependence rate

Perioperative aspirin and clonidine and risk of acute kidney injury: a randomized clinical trial.

IMPORTANCE: Acute kidney injury, a common complication of surgery, is associated with poor outcomes and high health care costs. Some studies suggest aspirin or clonidine administered during the perioperative period reduces the risk of acute kidney injury; however, these effects are uncertain and each intervention has the potential for harm. OBJECTIVE: To determine whether aspirin compared with placebo, and clonidine compared with placebo, alters the risk of perioperative acute kidney injury. DESIGN, SETTING, AND PARTICIPANTS: A 2 × 2 factorial randomized, blinded, clinical trial of 6905 patients undergoing noncardiac surgery from 88 centers in 22 countries with consecutive patients enrolled between January 2011 and December 2013. INTERVENTIONS: Patients were assigned to take aspirin (200 mg) or placebo 2 to 4 hours before surgery and then aspirin (100 mg) or placebo daily up to 30 days after surgery, and were assigned to take oral clonidine (0.2 mg) or placebo 2 to 4 hours before surgery, and then a transdermal clonidine patch (which provided clonidine at 0.2 mg/d) or placebo patch that remained until 72 hours after surgery. MAIN OUTCOMES AND MEASURES: Acute kidney injury was primarily defined as an increase in serum creatinine concentration from the preoperative concentration by either an increase of 0.3 mg/dL or greater (≥26.5 μmol/L) within 48 hours of surgery or an increase of 50% or greater within 7 days of surgery. RESULTS: Aspirin (n = 3443) vs placebo (n = 3462) did not alter the risk of acute kidney injury (13.4% vs 12.3%, respectively; adjusted relative risk, 1.10; 95% CI, 0.96-1.25). Clonidine (n = 3453) vs placebo (n = 3452) did not alter the risk of acute kidney injury (13.0% vs 12.7%, respectively; adjusted relative risk, 1.03; 95% CI, 0.90-1.18). Aspirin increased the risk of major bleeding. In a post hoc analysis, major bleeding was associated with a greater risk of subsequent acute kidney injury (23.3% when bleeding was present vs 12.3% when bleeding was absent; adjusted hazard ratio, 2.20; 95% CI, 1.72-2.83). Similarly, clonidine increased the risk of clinically important hypotension. In a post hoc analysis, clinically important hypotension was associated with a greater risk of subsequent acute kidney injury (14.3% when hypotension was present vs 11.8% when hypotension was absent; adjusted hazard ratio, 1.34; 95% CI, 1.14-1.58). CONCLUSIONS AND RELEVANCE: Among patients undergoing major noncardiac surgery, neither aspirin nor clonidine administered perioperatively reduced the risk of acute kidney injury. TRIAL REGISTRATION: clinicaltrials.gov Identifier: NCT01082874