Genomic heterogeneity underlies multidrug resistance in Pseudomonas aeruginosa: A population-level analysis beyond susceptibility testing

BACKGROUND

Pseudomonas aeruginosa is a persistent and difficult-to-treat pathogen in many patients, especially those with Cystic Fibrosis (CF). Herein, we describe a longitudinal analysis of a series of multidrug resistant (MDR) P. aeruginosa isolates recovered in a 17-month period, from a young female CF patient who underwent double lung transplantation. Our goal was to understand the genetic basis of the observed resistance phenotypes, establish the genomic population diversity, and define the nature of sequence evolution over time.

METHODS

Twenty-two sequential P. aeruginosa isolates were obtained within a 17-month period, before and after a double-lung transplant. At the end of the study period, antimicrobial susceptibility testing, whole genome sequencing (WGS), phylogenetic analyses and RNAseq were performed in order to understand the genetic basis of the observed resistance phenotypes, establish the genomic population diversity, and define the nature of sequence changes over time.

RESULTS

The majority of isolates were resistant to almost all tested antibiotics. A phylogenetic reconstruction revealed 3 major clades representing a genotypically and phenotypically heterogeneous population. The pattern of mutation accumulation and variation of gene expression suggested that a group of closely related strains was present in the patient prior to transplantation and continued to change throughout the course of treatment. A trend toward accumulation of mutations over time was observed. Different mutations in the DNA mismatch repair gene mutL consistent with a hypermutator phenotype were observed in two clades. RNAseq performed on 12 representative isolates revealed substantial differences in the expression of genes associated with antibiotic resistance and virulence traits.

CONCLUSIONS

The overwhelming current practice in the clinical laboratories setting relies on obtaining a pure culture and reporting the antibiogram from a few isolated colonies to inform therapy decisions. Our analyses revealed significant underlying genomic heterogeneity and unpredictable evolutionary patterns that were independent of prior antibiotic treatment, highlighting the need for comprehensive sampling and population-level analysis when gathering microbiological data in the context of CF P. aeruginosa chronic infection. Our findings challenge the applicability of antimicrobial stewardship programs based on single-isolate resistance profiles for the selection of antibiotic regimens in chronic infections such as CF.

Quantifying movement of multiple threatened species to inform adaptive management of environmental flows

There is a growing need for water managers to refine and optimise environmental flow strategies (e-flows) to balance water requirements for humans and nature. With increasing demands for freshwater and consequent declines in biodiversity, managers are faced with the problem of how to adaptively manage e-flows for multiple stakeholders and species whose flow requirements may overlap or vary. This study assessed the effectiveness of a regulated e-flow release strategy from a dam, aimed at providing movement opportunities and facilitating reproductive processes for multiple threatened species. Movements of 24 Mary River cod (Maccullochella mariensis), 20 Australian lungfish (Neoceratodus forsteri) and 13 Mary River turtle (Elusor macrurus) were quantified using acoustic telemetry over a three-year period. The influence of regulated e-flow releases, season, river depth, water temperature and rainfall on animal movements was assessed using Generalised linear mixed models (GLMMs). Models showed that hydraulic connectivity provided by both natural flows and regulated e-flow releases facilitated movement of all three species between pool habitats, throughout the year. Mary River turtles made extensive use of regulated e-flow releases when moving between habitats, whereas Mary River cod and Australian lungfish required additional natural rises in river height above the regulated e-flows to trigger movements. Significant movement activity was also recorded for cod and turtles during the dry season (winter and spring), broadly coinciding with breeding periods for these species. The effectiveness of, and potential improvements to, current e-flow strategies to sustain key life-history requirements of these species is discussed. Findings suggest a revised e-flow strategy with relatively minor increases in the magnitude of e-flow releases throughout winter and spring, would be effective in providing movement opportunities and supporting reproductive success for all three species. This study demonstrates that by quantifying movement behaviour in an e-flow context, ecological risk assessment frameworks can then be used to assess and provide for critical life-history requirements of multiple species within the context of a highly regulated system under increasing water use demands.

Diabetic nephropathy in type 1 diabetes: has the outlook improved since the 1980s?

This edition of Then and Now discusses three papers published in Diabetologia in the 1980s relating to diabetic nephropathy. Two epidemiological papers by Andersen et al (1983; 25:496-501) and Borch-Johnsen et al (1985; 28:590-596) described in graphic detail the ravages of diabetic nephropathy in type 1 diabetes. After 40 years of diabetes, 41% of their cohort had developed persistent proteinuria. The median time from first appearance of proteinuria to death was 7-8 years, the majority dying of uraemia or cardiovascular disease. The third paper, by Mathiesen et al (1984; 26:406-410), identified individuals with microalbuminuria, a much earlier stage of diabetic nephropathy, and analysed the risk of progression to persistent proteinuria at various levels of urine albumin excretion. Since the description of microalbuminuria, clinicians have hoped that earlier identification of individuals at high risk of end-stage kidney disease, coupled with aggressive use of reno-protective therapies, would prevent, or at the very least significantly delay, the development of end-stage renal disease. Recent data suggest that the outlook has indeed improved since the 1980s, at least in some populations. However, we may be delaying rather than preventing the development of microalbuminuria, proteinuria and kidney failure. Whilst a delay of 10 or more years in the appearance of end-stage renal disease is very welcome, further work is needed to understand why rates of chronic kidney disease vary substantially between cohorts and to develop novel therapies.

Impact of biomarkers for endothelial dysfunction and procoagulant state on 10-year cardiovascular risk in Type 2 diabetes

AIMS

To estimate the coronary heart disease and cardiovascular disease risk associated with novel biomarkers in Type 2 diabetes mellitus.

METHODS

We measured baseline peripheral blood concentrations of soluble E-selectin, factor XIIa, thrombin-antithrombin III complex and plasminogen activator inhibitor-1 in 86 patients with Type 2 diabetes free of known coronary heart disease. We used Cox proportional hazard models to estimate multivariable-adjusted hazard ratios associated with biomarker levels for 10-year coronary heart disease risk (n = 33 events) or total cardiovascular disease risk (n = 45 events).

RESULTS

At baseline, mean (sd) age was 62 years (7 years); 62 were men; and 43 had microalbuminuria. Soluble E-selectin demonstrated cross-sectional relationships with glucose and factor XIIa was related to plasminogen activator inhibitor-1 and triglycerides (all P < 0.05). Baseline log soluble E-selectin was significantly related to incident coronary heart disease and cardiovascular disease. Hazard ratios (95% CIs) associated with a 1-unit increase in log soluble E-selectin in age- and sex-adjusted models were: coronary heart disease : 4.6 (95% CI 1.9-11.3), P = 0.001; cardiovascular disease: 3.6 (95% CI 1.7-7.4, P = 0.001); and in multivariable-adjusted models were: coronary heart disease: 2.9 (95% CI 1.2-7.1, P = 0.02); cardiovascular disease: 2.3 (95% CI 1.1-4.8), P = 0.02. Factor XIIa was significantly related to incident cardiovascular disease. The hazard ratios associated with a 1-unit increase in factor XIIa in age- and sex-adjusted models was 1.5 (95% CI 1.1-1.9, P = 0.003) and in a multivariable-adjusted model was 1.3 (95% CI 1.0-1.6, P = 0.047). Plasminogen activator inhibitor-1 and thrombin-antithrombin III complex were not related to cardiovascular disease events.

CONCLUSIONS

In our study, soluble E-selectin and factor XIIa were significantly related to 10-year incident macrovascular events in patients with Type 2 diabetes. These preliminary findings call for replication in larger studies.

Non-invasive investigation of kidney disease in type 1 diabetes by magnetic resonance imaging

AIMS/HYPOTHESIS

Pathophysiological abnormalities in early diabetic nephropathy are poorly understood. We employed MRI to characterise renal perfusion, tissue oxygenation and kidney size in non-diabetic volunteers and type 1 diabetic patients without and with early renal disease.

METHODS

We studied ten control participants (C; age 40.0 [range 31-54] years), nine longstanding normotensive type 1 diabetic patients (T1Normo; age 40.1 [31-50] years, estimated glomerular filtration rate [eGFR] 83.4 ± 10.6 ml min(-1) 1.73 m(-2)) and eight microalbuminuric type 1 diabetic patients (T1Micro; age 42.4 [33-52] years, eGFR 71.6 ± 13.7 ml min(-1) 1.73 m(-2)). Six microalbuminuric patients were restudied after 4 weeks without renin-angiotensin-aldosterone system inhibitors. Phase contrast angiography and kidney blood oxygen level dependent (BOLD) (R(2)(*)) MRI were performed, before and during water diuresis. Contrast-enhanced MRI was performed at baseline urine flow rate. Renal artery flow, renal vascular resistance (RVR), cortical and medullary volumes, and R(2)(*) were determined.

RESULTS

Renal cortical and medullary volumes were similar in all groups (cortex: C 108 ± 16, T1Normo 112 ± 21, T1Micro 111 ± 10 cm(3)/1.73 m(2); medulla: C 35 ± 14, T1Normo 29 ± 10, 33 ± 6 cm(3)/1.73 m(2)). RVR increased from control to normoalbuminuric to microalbuminuric type 1 diabetic patients (C 0.061 ± 0.018, T1Normo 0.077 ± 0.014, T1Micro 0.093 ± 0.024 mmHg ml(-1) min(-1) 1.73 m(-2), ANOVA p = 0.012). RVR correlated inversely with eGFR in normoalbuminuric, but not in microalbuminuric diabetic patients. Renal artery flow was lower in the whole diabetes cohort (control 740 ± 205 vs diabetes 591 ± 128 ml min(-1) 1.73 m(-2), p = 0.035).

CONCLUSIONS/INTERPRETATION

Cortical and medullary volumes remain normal in early diabetic nephropathy. Decreased renal flow in longstanding normoalbuminuric type 1 diabetic patients may reflect intrarenal vascular stiffening, whereas in the microalbuminuric patients it may also reflect increased intraglomerular pressure.

The ARUBA trial: current status, future hopes

BACKGROUND AND PURPOSE

Report on the status of an on-going National Institutes of Neurological Disorders and Stroke (NINDS)-supported clinical trial of management of unbled brain arteriovenous malformations.

SUMMARY OF REVIEW

Begun in April 2007 with 3 centers, the trial has grown to 65 centers, and has randomized 124 patients through mid-June 2010 en route to the planned 400. The current literature continues to support the rationale for the trial.

CONCLUSIONS

ARUBA is steadily approaching its monthly randomization goals and has already reached the number needed to test the maximum published interventional complication rates against the minimum hemorrhage rates for natural history.

Intrauterine growth rate in pregnancies complicated by type 1, type 2 and gestational diabetes

Fetal macrosomia is a feature of all subtypes of maternal diabetes. The intrauterine time course of development of macrosomia in type 1, type 2 and gestational diabetes (GDM) could identify the times of more rapid growth, which differ as a result of different influences in subtypes of diabetes. Higher maternal weight in type 2 and GDM may be expected to contribute to macrosomia and the blood glucose control will exert an additional influence. Information was collected prospectively on 217 pregnancies in insulin-treated women at a single centre over a six-year period. All women were managed by a single team of obstetricians and diabetologists at a Joint Obstetric Medical Clinic. The rate of increase in abdominal circumference from 28 weeks was identical in each subtype of diabetes and there were no differences between subtypes at the earliest gestation assessed. Use of customized growth centiles showed rates of macrosomia to be similar in type 1, type 2 and GDM (43.0%, 50.0% and 41.8%, respectively). The intrauterine time course to macrosomia is similar in type 1, type 2 and GDM. The relationship of macrosomia to extent of elevation of mean blood glucose control is weak, implying a low threshold for maximal effect on the rate of fetal growth.

Genetic association analyses of non-synonymous single nucleotide polymorphisms in diabetic nephropathy

AIMS/HYPOTHESIS

Diabetic nephropathy, characterised by persistent proteinuria, hypertension and progressive kidney failure, affects a subset of susceptible individuals with diabetes. It is also a leading cause of end-stage renal disease (ESRD). Non-synonymous (ns) single nucleotide polymorphisms (SNPs) have been reported to contribute to genetic susceptibility in both monogenic disorders and common complex diseases. The objective of this study was to investigate whether nsSNPs are involved in susceptibility to diabetic nephropathy using a case-control design.

METHODS

White type 1 diabetic patients with (cases) and without (controls) nephropathy from eight centres in the UK and Ireland were genotyped for a selected subset of nsSNPs using Illumina's GoldenGate BeadArray assay. A chi (2) test for trend, stratified by centre, was used to assess differences in genotype distribution between cases and controls. Genomic control was used to adjust for possible inflation of test statistics, and the False Discovery Rate method was used to account for multiple testing.

RESULTS

We assessed 1,111 nsSNPs for association with diabetic nephropathy in 1,711 individuals with type 1 diabetes (894 cases, 817 controls). A number of SNPs demonstrated a significant difference in genotype distribution between groups before but not after correction for multiple testing. Furthermore, neither subgroup analysis (diabetic nephropathy with ESRD or diabetic nephropathy without ESRD) nor stratification by duration of diabetes revealed any significant differences between groups.

CONCLUSIONS/INTERPRETATION

The nsSNPs investigated in this study do not appear to contribute significantly to the development of diabetic nephropathy in patients with type 1 diabetes.

Are glomerular volume differences between type 1 and type 2 diabetic patients pathologically significant?

The observation that patients with type 2 diabetes tend to have larger glomeruli than patients with type 1 diabetes was first made more than 10 years ago. It has also been noted that type 2 diabetic patients with nephropathy often have more heterogeneous renal function and structure than type 1 patients. However, whether these observations are linked or have any bearing on the progression of nephropathy in the two types of diabetes remains uncertain. Here we put forward several hypotheses as to why glomerular volume in type 1 differs from that in type 2 diabetes. We suggest that although type 1 and type 2 diabetic patients appear to progress through similar stages of diabetic nephropathy, the route they take may differ. Differences in the way in which the glomeruli respond to the diabetic milieu may enable some type 2 diabetic patients to preserve their filtration surface in the face of an expanding mesangium.

The effect of intrauterine environment and low glomerular number on the histological changes in diabetic glomerulosclerosis

AIMS/HYPOTHESIS

We tested the hypothesis that diabetic glomerulosclerosis would develop more rapidly in animals with fewer glomeruli.

METHODS

We studied the female offspring of Wistar rats that had been fed a low-protein diet (LPD) containing 6% protein or a normal-protein diet (NPD) containing 18% protein during pregnancy. Streptozotocin diabetes was induced at 12 weeks and animals were killed at 40 weeks.

RESULTS

Non-diabetic LPD offspring were of lower birthweight than the NPD offspring (5.19+/-0.64 vs 6.45+/-0.67 g, p<0.001) and had fewer glomeruli (27,402+/-3,137 vs 34,203+/-6,471, p<0.05). Glomerular volume correlated inversely with glomerular number (r=-0.64, p=0.035), but total glomerular filtration surface area was reduced in the LPD animals (4,770+/-541 vs 5,779+/-1,302 mm(2), p=0.05). Other renal structural and functional parameters were similar. In LPD and NPD diabetic animals, glomerular volume and basement membrane width were significantly increased compared to their respective controls. Podocyte density was lowest in the LPD diabetic animals (not significant), and the area covered by each podocyte was greater in the LPD diabetic group (2.40+/-0.693 x10(-3) mm(2)) than in the LPD control group (1.68+/-0.374 x10(-3) mm(2), p<0.001) and in the NPD diabetic animals (1.71+/-0.291 x 10(-3) mm(2), p<0.05). There was no difference in any other structural or functional parameter between the LPD and NPD diabetic animals.

CONCLUSIONS/INTERPRETATION

A decrease in glomerular number was not deleterious to renal structure and function over 40 weeks in this animal model. Further work in models with progressive renal impairment and hypertension is necessary to clarify the impact of glomerular number on the development of renal disease.

The podocyte: a major player in the development of diabetic nephropathy?

Although abnormalities in the glomerular epithelial cell, the podocyte, have been appreciated for some time, it is only recently that their significance and the underlying mechanisms for the changes have begun to be explored. There is a decrease in podocyte number early in diabetes, with further decreases as albuminuria increases. The number of podocytes is inversely related to the degree of albuminuria in both cross-sectional and longitudinal studies. Foot process width is increased in proteinuria, the width correlating with albuminuria. Loss of nephrin - both mRNA and protein - occurs some time after the onset of diabetes and is also inversely related to proteinuria. The amount of the alpha3beta1 integrin on the basement-membrane surface of the foot process of the podocyte is also reduced in diabetes. Loss of nephrin and alpha3beta1 integrin is induced by both hyperglycaemia and mechanical stretch. Agents that inhibit the renin-angiotensin system, but not other agents that reduce proteinuria, restore nephrin expression and prevent the structural changes seen in the podocyte in diabetes. Thus, changes in the podocyte contribute to the proteinuria of diabetic nephropathy and can be ameliorated by inhibition of the renin-angiotensin system.

Recent advances in diabetic nephropathy

Diabetic nephropathy is the leading cause of end stage renal disease worldwide and is associated with increased cardiovascular risk. The earliest clinical manifestation is of microalbuminuria. Tight blood glucose and blood pressure control reduce the risk of microalbuminuria. Once microalbuminuria is present, the rate of progression to end stage renal disease and of cardiovascular disease can be delayed by aggressive management of blood pressure, glucose, and lipids. Inhibition of the renin-angiotensin system is important to reduce intraglomerular pressure but other classes of antihypertensive agent may also be needed to gain adequate control of systemic blood pressure. Such measures can at least half the rate of progression of nephropathy and cardiovascular disease.

Increasing neutrophil F-actin corrects CD11b exposure in Type 2 diabetes

BACKGROUND

Leukocyte dysfunction contributes to the pathogenesis of diabetic vascular complications. Neutrophils adhere to the endothelium through the beta(2)integrin CD11b/CD18. In Type 2 diabetes, neutrophil surface CD11b expression is increased and is associated with impaired actin polymerization. This study aimed to determine whether increasing neutrophil actin polymerization could correct the defect in CD11b exposure.

DESIGN

Neutrophil actin polymerization was stimulated with the tyrosine phosphatase inhibitor phenylarsine oxide (PAO), and cytoskeletal phosphotyrosine was monitored by immunoblotting Triton X-100 insoluble fractions of cells. Neutrophil F-actin was measured with phalloidin-FITC staining, and surface CD11b expression was determined with anti-CD11b-PE before analysis with flow cytometry.

RESULTS

Phenylarsine oxide caused an increase in phosphotyrosine in neutrophils from both patients with Type 2 diabetes (DM) and controls (NC) (-fold increase: NC, 1.43 +/- 0.16; DM, 1.46 +/- 0.10). The response to PAO in terms of phalloidin-binding was impaired in neutrophils from patients [phalloidin-FITC MFI area under the curve, NC 200 +/- 5 (x 10(3)), DM 124 +/- 9 (x 10(3)), P < 0.0001]. Phenylarsine oxide at concentrations < 10 micro mol L(-1) also caused loss of CD11b from neutrophil surfaces that was impaired in samples from patients [CD11b sites area under the curve NC 90 +/- 6 (x 10(3)), DM 121 +/- 9 (x 10(3)), P < 0.002]. However, in neutrophils from patients, incubation with PAO at a concentration of > 10 micro mol L(-1) caused a significant increase in intracellular F-actin and CD11b down-regulation equivalent to that observed in controls.

CONCLUSION

In Type 2 diabetes, impaired neutrophil actin polymerization even in response to increasing cytoskeletal phophotyrosine suggests a downstream defect. Furthermore, increasing actin polymerization, above a minimum threshold level, corrects the defect in integrin exposure. Correction of the actin polymerization defect in Type 2 diabetes could improve the prognosis of diabetic vascular complications.

Impaired neutrophil store-mediated calcium entry in Type 2 diabetes

BACKGROUND

In Type 2 diabetes impaired neutrophil function leads to increased bacterial infection and cardiovascular disease. Many neutrophil functions depend on calcium signalling, which involves release of calcium from intracellular stores and subsequently translocation of stores via the cytoskeleton to the plasma membrane, causing store-mediated calcium entry (SMCE) into the cell. We hypothesized that in Type 2 diabetes there would be a defect in SMCE.

MATERIALS AND METHODS

Neutrophils were prepared from patients with Type 2 diabetes (DM, n=15) and controls (NC, n=15). Free cytosolic calcium [Ca2+]i was measured with Fura-2 in resting cells and after stimulation of calcium release with fMLP and thapsigargin.

RESULTS

Baseline [Ca2+]i was higher in neutrophils from the patients than the controls (NC 65 +/- 5 nm, DM 80 +/- 4 nm, P<0.05). However, after fMLP-treatment [Ca2+]i was significantly lower in the patients (NC 301 +/- 28 nm, DM 210 +/- 20 nm, P<0.01). The greater increase in controls was not observed when cells were treated with fMLP in the absence of extracellular calcium (-fold increase NC 2.9 +/- 0.5, DM 2.7 +/- 0.3). Treatment of cells with thapsigargin caused a similar greater increase in [Ca2+]i in the controls than in the patients that was not seen in the absence of extracellular calcium (-fold increase with Ca2+ NC 5.2 +/- 1.0, DM 3.0 +/- 0.4, P<0.05; fold increase without Ca2+ NC 2.5 +/- 0.4, DM 2.2 +/- 0.2).

CONCLUSIONS

In Type 2 diabetes there is a defect in neutrophil calcium signalling which results in a lesser increase in free cytosolic calcium owing to impaired influx across the plasma membrane. Abnormal calcium signalling is likely to be important in the pathogenesis of diabetic complications.

Microalbuminuria is more frequent in South Asian than in European origin populations: a comparative study in Newcastle, UK

AIMS

We aimed to compare levels of urinary albumin excretion and the prevalence of microalbuminuria in UK South Asians and Europeans. Microalbuminuria predicts cardiovascular disease in European origin populations, but evidence from the general population of South Asians is lacking. Coronary heart disease (CHD) mortality is 40-50% higher in UK South Asians compared with the whole population, for reasons that are incompletely understood.

METHODS

Microalbuminuria was measured using the albumin-creatinine ratio in an age- and sex-stratified random sample of 1509 adults from European (n = 825), Indian (n = 259), Pakistani (n = 305) and Bangladeshi (n = 120) ethnic groups.

RESULTS

Levels of urinary albumin excretion were substantially higher in South Asians (geometric mean albumin creatinine ratio (95% confidence interval) 0.83 (0.75, 0.91)) than in Europeans (0.55 (0.51, 0.60)). Microalbuminuria was associated with older age, hypertension and diabetes, but independently of these risk factors urinary albumin excretion was higher in South Asians than Europeans.

CONCLUSIONS

Urinary albumin excretion is higher and microalbuminuria more frequent in UK South Asians compared with the majority ethnic population. Microalbuminuria may be relevant to the causal pathways leading to the excess of cardiovascular mortality and possibly renal failure in UK South Asians.

Impaired neutrophil actin assembly causes persistent CD11b expression and reduced primary granule exocytosis in Type II diabetes

AIMS/HYPOTHESIS

Neutrophil dysfunction has a role in the pathogenesis of complications in Type II (non-insulin-dependent) diabetes mellitus. Neutrophils adhere through expression of the beta(2)integrin CD11b/CD18 which closely associates with the actin cytoskeleton. The aim of this study was to investigate the effect of actin polymerisation on CD11b expression and exocytosis of the primary granule marker CD69 in neutrophils from patients with Type II diabetes.

METHODS

Neutrophils were activated with fMLP or PMA, actin polymerisation was inhibited with cytochalasin D. Cells were stained for CD11b and CD69 expression and intracellular F-actin was measured with phalloidin-FITC. Cellular fluorescence was measured by flow cytometry. Actin content of Triton X-100 fractions of cells was measured by SDS-PAGE and Coomassie blue staining.

RESULTS

PMA caused an increase in neutrophil F-actin that was greater in control subjects than in patients with Type II diabetes (50.8% vs 33.4%, p<0.001) and correlated with actin integrated optical density (IOD) by SDS-PAGE ( r=0.74, p=0.01). Loss of CD11b from cell surfaces only occurred in neutrophils with high F-actin. The proportion of cells losing CD11b was lower in patients than in control subjects (23.1% vs 37.5%, p<0.001) and lowest in patients with additional cardiovascular risk markers (20.1% vs 27.7%; p<0.05). Cytochalasin D prevented loss of CD11b ( p<0.001). CD69 expression was reduced in patients with Type II diabetes (22.6% vs 36.4%, p<0.001) and correlated with F-actin content ( r=0.78, p<0.0001).

CONCLUSION/INTERPRETATION

In Type II diabetes impaired neutrophil actin polymerisation leads to persistent expression of CD11b and reduced exocytosis of primary granules and could contribute to the pathogenesis of diabetic complications.