Plasma Cell-Free DNA and Caspase-3 Levels in Patients with Chronic Kidney Disease.

BACKGROUND: Cell-free plasma DNA (cfDNA) is circulating extracellular DNA arising from cell death mechanisms (apoptosis, necrosis, etc.). It is commonly existent in healthy individuals, but its ranks increase in diverse clinical circumstances, such as kidney disease, sepsis, myocardial infarction, trauma and cancer. In patients with advanced chronic kidney disease, cfDNA is connected to inflammation, and it has been associated with higher mortality. Caspase-3 plays a dominant role in apoptosis, a mechanism of programmed cell death involved in the pathogenesis and progression of chronic kidney disease (CKD). The aim of this pilot study was the evaluation of cfDNA levels and caspase-3 concentrations in patients with chronic kidney disease, in order to investigate the potential role of these molecules, deriving from inflammatory and apoptotic mechanisms, in the progression of renal damage. METHODS: We compared cfDNA and caspase-3 levels in 25 CKD patients and in 10 healthy subjects, evaluating their levels based on CKD stage. We also explored correlations between cfDNA and caspase-3 levels in CKD patients and between cfDNA and caspase-3 levels and serum creatinine and urea in this population. RESULTS: We observed that cfDNA and caspase-3 levels were higher in patients with CKD compared to healthy subjects, in particular in patients with advanced renal disease (CKD stage 5). A positive correlation between cfDNA and caspase-3 levels and between cfDNA and caspase-3 and creatinine and urea were also noticed. CONCLUSIONS: Patients with chronic kidney disease show higher levels of cfDNA and caspase-3 levels compared to the control group. Based on these preliminary results, we speculated that the worsening of renal damage and the increase in uremic toxin concentration could be associated with higher levels of cfDNA and caspase-3 levels, thus reflecting the potential role of inflammation and apoptosis in the progression of CKD. Future studies should focus on the validation of these promising preliminary results.

Eryptosis in Peritoneal Dialysis-Related Peritonitis: The Potential Role of Inflammation in Mediating the Increase in Eryptosis in PD.

Background: Peritonitis and exit site infections are the main complications of patients treated with peritoneal dialysis (PD). Erythrocytes (red blood cells­RBCs) are very sensitive cells, and they are characterized by eryptosis (programmed cell death). The purpose of this research was to assess eryptosis in PD patients with PD-related peritonitis and its connection to inflammatory markers in vivo and in vitro. Material and Methods: In this study, we included 65 PD patients: 34 PD patients without systemic inflammation nor PD-related peritonitis in the previous 3 months, and 31 PD patients with an acute episode of PD-related peritonitis. We measured C-reactive protein (CRP) and cytokine (IL-1ß, IL-6, and IL-18) levels as systemic inflammatory markers. Eryptosis was evaluated by flow cytometric analyses in freshly isolated RBCs. The induction of eryptosis due to in vitro exposure to IL-1ß, IL-6, and IL-18 was verified. Results: Eryptosis was significantly higher in PD patients with peritonitis (9.6%; IQR 4.2−16.7), compared to the those in the other group (2.7%; IQR 1.6−3.9) (p < 0.0001). Significant positive correlations were noticed between eryptosis and CRP, IL-1ß, and IL-6. RBCs, incubated with greater concentrations of all cytokines in vitro, resulted in significantly higher occurrences of eryptosis in comparison with those incubated with lower concentration and with untreated cell (p < 0.05), and for those with extensive exposure (p < 0.05). Conclusion: In conclusion, we investigated a potential relationship between systemic eryptosis and the in vivo and in vitro inflammatory damage of the peritoneal membrane during peritonitis. Thus, the presented results revealed that upregulated inflammatory markers and immune system dysregulation could be the cause of high levels of systemic eryptosis during PD-related peritonitis.

Eryptosis in Patients with Chronic Kidney Disease: A Possible Relationship with Oxidative Stress and Inflammatory Markers.

Background. Eryptosis is the programmed death of red blood cells; it may contribute to worsening anemia in chronic kidney disease (CKD). In this clinical condition, different factors induce eryptosis, such as oxidative stress, energy depletion and uremic toxins. In our study, we investigated if the progression of CKD may influence erythrocyte death levels and its relationship with oxidative stress and inflammation. Methods. We evaluated eryptosis levels in 25 CKD patients (five for each stage), as well as markers of oxidative stress and inflammation: myeloperoxidase (MPO), copper/zinc superoxide dismutase (Cu/Zn SOD) and interleukin-6 (IL-6) were evaluated in plasma samples. Results. Higher cell death rate was reported in the highest CKD stages (p < 0.05). Furthermore, we divided CKD patients into two groups (eGFR< or ≥60 mL/min/1.73 m2). Patients with eGFR < 60 mL/min/1.73 m2 had higher eryptosis levels (p < 0.001). MPO, CU/Zn SOD and IL-6 resulted significantly differently between groups (p < 0.001). Significant positive correlations were reported between eryptosis and MPO (Spearman's rho = 0.77, p = 0.01) and IL-6 (Spearman's rho = 0.52, p = 0.05) and Cu/Zn SOD. Spearman's rho = 0.6, p = 0.03). Conclusions. In patients with CKD, different factors are involved in the pathogenesis of eryptosis, in particular uremic toxins and oxidative stress and inflammatory markers. The progressive impairment of renal function may be associated with the increase in eryptosis levels, probably due to the accumulation of oxidative stress factors, inflammatory cytokines and uremic toxins.

In Vitro Induction of Eryptosis by Uremic Toxins and Inflammation Mediators in Healthy Red Blood Cells.

Eryptosis is the stress-induced RBC (red blood cell) death mechanism. It is known that eryptosis is largely influenced by plasma and blood composition, and that it is accelerated in patients affected by chronic kidney disease (CKD). The aim of this study is to evaluate the eryptosis rate in healthy RBCs treated with different concentration of IL-6, IL-1ß, urea and p-cresol, comparable to plasmatic level of CKD patients, at different time points. We exposed healthy RBCs to increasing concentrations of IL-6, IL-1ß, urea and p-cresol. Morphological markers of eryptosis (cell membrane scrambling, cell shrinkage and PS exposure at RBC surface) were evaluated by flow cytometric analyses. The cytotoxic effect of cytokines and uremic toxins were analyzed in vitro on healthy RBCs at 4, 8 and 24 h. Morphology of treated RBCs was dramatically deranged, and the average cell volume was significantly higher in RBCs exposed to higher concentration of all molecules (all, p < 0.001). Furthermore, healthy RBCs incubated with each molecules demonstrated a significant increase in eryptosis. Cytofluorimetric analysis of eryptosis highlighted significantly higher cell death rate in RBCs incubated with a higher concentration of both cytokines compared with RBCs incubated with a lower concentration (all, p < 0.05). In conclusion, our data show that cytokines and uremic toxins have a harmful effect on RBCs viability and trigger eryptosis. Further studies are necessary to validate these results in vivo and to associate abnormal eryptosis with cytokine levels in CKD patients. The eryptosis pathway could, moreover, become a new promising target for anemia management in CKD patients.

[Impact of the Covid-19 pandemic on kidney transplantation: focus on the Sicilian experience].

The COronaVIrus Disease 2019 (Covid-19) pandemic has rapidly changed hospital structures in our country, radically modifying clinical activity. Nephrology, and kidney transplant in particular, has been heavily influenced by it, with a reduced number of organ donations and, consequently, transplantations. Here we report the data on kidney transplants in our region, Sicily, for the period 2019-July 2021, and we analyze the effects of the pandemic.

The Role of Cell-Free Plasma DNA in Patients with Cardiorenal Syndrome Type 1.

BACKGROUND: Recent research highlighted the potential role of circulating cell-free DNA (cfDNA), resulted by apoptosis or cell necrosis, as a prognostic marker in the setting of different clinical conditions. Cardiorenal syndrome type 1 (CRS type 1) is characterized by a rapid worsening of cardiac function leading to acute kidney injury (AKI). Apoptosis of renal epithelial cells is proposed as a mechanism involved in CRS type 1. In this study, we investigated cfDNA levels in patients with acute heart failure (AHF) and CRS type 1 and the possible correlation between cfDNA levels and inflammatory and apoptotic parameters. METHODS: We enrolled 17 AHF patients and 15 CRS type 1 who exhibited AKI at the time of admission (caused by AHF) or developed AKI during the first 48 h from admission. cfDNA was extracted from plasma and quantified by real-time polymerase chain reaction. Plasma levels of NGAL, tumor necrosis factor-α, interleukin (IL)-6, IL-18, and caspase-3 were measured. RESULTS: We observed significantly higher levels of cfDNA in patients with CRS type 1 than patients with AHF. Caspase-3, IL-6, IL-18, and NGAL levels resulted significantly increased in patients with CRS type 1. Moreover, a positive correlation between cfDNA levels and caspase-3 levels was found, as well as between cfDNA levels and IL-6 and renal parameters. CONCLUSION: Our study explores the premise of cfDNA as a marker for apoptosis and inflammation in CRS type 1 patients. cfDNA could potentially serve as an index for noninvasive monitoring of tissue damage and apoptosis in patients with AKI induced by AHF.

[Phosphorus binders: trigger for intestinal diverticula formation in an ADPKD patient].

Hyperphosphoremia is common in patients with chronic kidney disease and is an important risk factor in this patient population. Phosphate binding drugs are a key therapeutic strategy to reduce phosphoremia levels, although they have significant side effects especially in the gastrointestinal tract, such as gastritis, diarrhoea and constipation. We report the case of a haemodialysis-dependent patient suffering from chronic kidney disease stage V KDIGO secondary to polycystic autosomal dominant disease; treated with phosphate binders, the case was complicated by the appearance of diverticulosis, evolved into acute diverticulitis.

Feasibility of routine ultrasound-guided percutaneous transluminal angioplasty in the treatment of native arteriovenous fistula dysfunction.

BACKGROUND: Stenosis is the main cause of arteriovenous fistula failure and is due to neointimal hyperplasia. Percutaneous transluminal angioplasty is the gold standard for patients with vascular access stenosis. The aim of the study was to evaluate the efficacy and safety of ultrasound-guided percutaneous transluminal angioplasty in the treatment of native arteriovenous fistula venous stenosis. METHODS: The need for intervention was determined by physical examination and duplex ultrasound in 162 patients. All patients with failing or not maturing arteriovenous fistula were treated in the outpatient setting under ultrasound guidance. Procedural success was assessed with repeated post-procedural ultrasound examinations. All procedures were performed under local anesthesia by a single nephrologist and were performed in a single vascular laboratory, while follow-up ultrasound was performed in the dialysis unit of destination. RESULTS: Early technical success was obtained in 95.6% of cases (154 of 162). Complications occurred in 22 patients (13.5%) with no major complication requiring surgical or fluoroscopic endovascular intervention. Primary patency at 6 and 12 months was 84% and 69.8%, respectively. Risk factors for arteriovenous fistula failure/secondary percutaneous transluminal angioplasty were vascular access low blood flow rate and vintage, as well as the need for thrombolysis during the first percutaneous transluminal angioplasty. CONCLUSION: Ultrasound-guided percutaneous transluminal angioplasty is a valuable tool to treat vascular access stenosis.

Holistic vision of the patient with chronic kidney disease in a universalistic healthcare system.

Chronic kidney disease (CKD) is an increasing public health problem. Aging is one of the leading causes, particularly in Western countries, but several comorbidities, such as hypertension and diabetes are involved in its pathogenesis. Thus, the treatment of CKD patient is very complex and requires an integrated strategy. In this context, the holistic approach to the CKD patient and not to the disease itself should be the answer. General practitioners, specialists, voluntary associations, and nonprofit organizations, in addition to the family of the patient, all contribute to the patient care. Moreover, due to the low sensitivity of creatinine values in the early stages of renal failure, its diagnosis often occurs in the advanced phases of the disease. Therefore, the health costs for CKD patients are hardly sustainable by health systems. The reorganization of economic and epidemiological data through new models is necessary to allow the sustainability of the system and to ensure medical care for all patients. In this review, we aim to deal with all the issues about patient care, standards of care, and the impact of chronicity from a global perspective in light of the current state of the Italian healthcare system.

[Therapeutic options to reduce arterial stiffness in chronic kidney disease].

Chronic kidney disease is associated with an increased cardiovascular risk. Several uremic toxins are also vascular toxins and may contribute to the increase of the cardiovascular risk through the development of aortic stiffening. In this process, oxidative stress and endothelial dysfunction play an important role. Considering that aortic stiffness is a known cardiovascular risk factor and a vascular biomarker involved in the development of chronic cardiac dysfunction, and that the reduction of aortic stiffness is associated with an improved survival of patients with end-stage kidney disease, we aim at reviewing the therapeutic options to reduce aortic stiffness and potentially the cardiovascular risk.

Eryptosis Is Altered in Peritoneal Dialysis Patients.

BACKGROUND: Red blood cells (RBCs) undergo programmed cell death known as eryptosis. Triggers of eryptosis include increased cytosolic Ca(2+) concentration, oxidative stress, osmotic shock, energy depletion and several uremic toxins. Little is known about the pathogenesis of eryptosis in peritoneal dialysis (PD) patients; furthermore, its relevance in worsening clinical conditions in these patients is still not completely defined. OBJECTIVES: We investigated eryptosis levels in PD patients and its association with inflammatory and clinical parameters. MATERIAL AND METHODS: A total of 46 PD patients and 17 healthy subjects (CTR) were enrolled. All eryptosis measurements were made in freshly isolated RBCs using the flow cytometer. RESULTS: Eryptosis was significantly higher in PD patients than that in CTR (p < 0.001). Eryptosis levels did not differ significantly between PD patients with and without diabetes, with and without hypertension, and with and without cardiovascular disease. Eryptosis showed no significant differences between patients treated with continuous ambulatory PD/automated PD, with Kt/Vurea value ≤1.7 and >1.7, with a negative or positive history of peritonitis. On the contrary, eryptosis showed significantly lower levels in PD patients with weekly creatinine clearance ≥45 L/week/1.73 m2 (2.8%, 1.7-4.9 vs. 5.6%, 5.0-13.5; p= 0.049). Eryptosis showed significantly lower levels in PD patients with residual diuresis (n = 23) than that in patients without (3.7%, 2.6-5.6 vs. 5%, 3.1-16; p = 0.03). In these 23 patients, significant negative correlations between percentage of eryptosis and residual glomerular filtration rate (rGFR; Spearman's rho = -0.51, p = 0.01) and diuresis volume (Spearman's rho = -0.43, p = 0.05) were found. CONCLUSIONS: The present study demonstrated higher eryptosis levels in PD patients compared to corresponding levels in CTR. Furthermore, important PD comorbidity and main PD parameters do not influence eryptosis. Importantly, our data have reported an increase in eryptosis levels with progressive residual diuresis and rGFR loss, probably due to decreased uremic toxins clearance.

Neurohormonal, Endocrine, and Immune Dysregulation and Inflammation in Cardiorenal Syndrome.

"Organ crosstalk" is the complex physiological communication between different body systems, and it is necessary for the optimal equilibrium and functioning of the organism. In particular, heart and kidney function is tightly connected, and interplay between these two organs occurs through a vast array of dynamic and bidirectional mechanisms. The term cardiorenal syndrome (CRS) indicates an interaction between the heart and kidneys in acute and chronic disease settings. In all types of CRS, multiple pathophysiological processes are implicated in the initiation and progression of organ injury. In addition to hemodynamic parameters, endothelial injury, immunological imbalance, cell death, inflammatory cascades, oxidative stress, neutrophil migration, leukocyte trafficking, caspase-mediated apoptosis, extracellular vesicles, small noncoding RNAs, and epigenetics play pivotal roles in the development of CRS. In this review, we will focus on neurohormonal, endocrine, and immune dysregulation and inflammation as mechanisms involved in the pathogenesis of CRS.

Multi-Omics Approach: New Potential Key Mechanisms Implicated in Cardiorenal Syndromes.

Cardiorenal syndromes (CRS) include a scenario of clinical interactions characterized by the heart and kidney dysfunction. The crosstalk between cardiac and renal systems is clearly evidenced but not completely understood. Multi-factorial mechanisms leading to CRS do not involve only hemodynamic parameters. In fact, in recent works on organ crosstalk endothelial injury, the alteration of normal immunologic balance, cell death, inflammatory cascades, cell adhesion molecules, cytokine and chemokine overexpression, neutrophil migration, leukocyte trafficking, caspase-mediated induction of apoptotic mechanisms and oxidative stress has been demonstrated to induce distant organ dysfunction. Furthermore, new alternative mechanisms using the multi-omics approach may be implicated in the pathogenesis of cardiorenal crosstalk. The study of "omics" modifications in the setting of cardiovascular and renal disease represents an emerging area of research. Over the last years, indeed, many studies have elucidated the exact mechanisms involved in gene expression and regulation, cellular communication and organ crosstalk. In this review, we analyze epigenetics, gene expression, small non-coding RNAs, extracellular vesicles, proteomics, and metabolomics in the setting of CRS.

[The new frontier in endovascular treatment of arteriovenous fistula stenosis: the role of ultrasound-guided percutaneous transluminal angioplasty].

Native arteriovenous fistula is the preferred vascular access because of it does not usually cause infections and seems to be closely related with prolonged patient survival, compared to prosthetic grafts and central venous catheters; it also is cost effective. Venous stenosis is one of the main causes of AVF failure. It is caused by a number of upstream and downstream events. The former group comprises hemodynamic and surgical stressors, inflammatory stimuli and uraemia, while downstream events involve the proliferation of smooth muscle cells and myofibroblasts and the development of neo-intimal hyperplasia. Percutaneous transluminal angioplasty is the gold standard for arteriovenous fistula stenosis. It allows the visualization of the whole vascular circuit and the immediate use of the vascular access for the next dialysis session. Ultrasound-guided percutaneous endovascular angioplasty is a feasible and safe alternative to conventional fluoroscopic technique: it is equally effective in treating arteriovenous fistula stenosis, but it presents the advantage of not using contrast media or ionizing radiation. The aim of this review is to report the latest evidence on cellular and molecular mechanisms that contribute to the development of neo-intimal hyperplasia, as well as the current and future therapeutic perspectives, especially concerning the use of anti-proliferative drugs, and the efficacy of the ultrasound-guided angioplasty in restoring and maintaining the vascular access patency over time.

Effects of valsartan, benazepril and their combination in overt nephropathy of type 2 diabetes: A prospective, randomized, controlled trial.

AIMS: To evaluate whether angiotensin-converting enzyme (ACE) inhibitor and angiotensin II receptor blocker (ARB) combination therapy is more nephroprotective than ACE inhibitor or ARB monotherapy in people with type 2 diabetes and overt nephropathy. MATERIALS AND METHODS: In this prospective, randomized, open, blind-endpoint phase III trial sponsored by the Italian Drug Agency, 103 consenting patients with type 2 diabetes, aged >40 years, with serum creatinine levels 159 to 309 µmol/L, spot morning urinary albumin-creatinine ratio > 1000 mg/g (or > 500 mg/g in those on ACE inhibitor or ARB therapy at inclusion) were stratified by centre and randomized to 4.5-year treatment with valsartan 320 mg/d (n = 36), benazepril 20 mg/d (n = 34) or halved doses of both medications (n = 33). The primary endpoint was end-stage renal disease (ESRD). Modified intention-to-treat analyses were performed. RESULTS: Recruitment took place between June 2007 and February 2013 at 10 centres in Italy and one in Slovenia. A total of 77 participants completed the study and 26 were prematurely withdrawn. During a median (interquartile range) of 41 (18-54) months, 12 participants on benazepril (35.3%) and nine on combination therapy (27.3%) progressed to ESRD, versus five on valsartan (13.9%). Differences between benazepril (hazard ratio [HR] 3.59, 95% confidence interval [CI] 1.25-10.30; P = 0.018) or combination therapy (HR 3.28, 95% CI 1.07-10.0; P = 0.038) and valsartan were significant, even after adjustment for age, gender and baseline serum creatinine, systolic blood pressure and 24-hour proteinuria (HR 5.16, 95% CI 1.50-17.75, P = 0.009 and HR 4.75, 95% CI 1.01-22.39, P = 0.049, respectively). Adverse events were distributed similarly among the groups. CONCLUSIONS: In people with type 2 diabetes with nephropathy, valsartan (320 mg/d) safely postponed ESRD more effectively than benazepril (20 mg/d) or than halved doses of both medications.

Presepsin and Procalcitonin Levels as Markers of Adverse Postoperative Complications and Mortality in Cardiac Surgery Patients.

Backgound: This study was aimed at evaluating the presepsin and procalcitonin levels to predict adverse postoperative complications and mortality in cardiac surgery patients. METHODS: A total of 122 cardiac surgery patients were enrolled for the study. Presepsin and procalcitonin levels were measured 48 h after the procedure. The primary endpoints were adverse renal, respiratory, and cardiovascular outcomes and mortality. RESULTS: Presepsin and procalcitonin levels were significantly higher in patients with adverse renal and respiratory outcome (p < 0.001 and 0.0081). The presepsin levels were significantly higher in patients with adverse cardiovascular outcome (p = 0.023) and the procalcitonin values in patients with sepsis (p = 0.0013). Presepsin levels were significantly higher in patients who died during hospitalization (382 pg/mL, interquartile range [IQR] 243-717.5 vs. 1,848 pg/mL, IQR 998-5,451.5, p = 0.049). In addition, the predictive value for in-hospital, 30-days, and 6-months mortality was higher for presepsin, with a significant difference between the 2 biomarkers (p = 0.025, p = 0.035, p = 0.003; respectively). Presepsin and procalcitonin seem to have comparable predictive value for adverse renal, cardiovascular, and respiratory outcome in cardiac surgery patients. Although a positive trend was notable for presepsin and adverse renal outcome (area under the ROC [receiver operating characteristic] curves [AUC] of 0.760, 95% CI 0.673-0.833 versus procalcitonin: AUC 0.692; 95% CI 0.601-0.773): no statistically significant difference was evident between the AUC of the 2 biomarkers (p = 0.25). CONCLUSIONS: Presepsin and -procalcitonin seem to have comparable predictive value for -adverse renal, cardiovascular, and respiratory outcome in cardiac surgery patients. Also, presepsin possesses a better predictive value for in-hospital, 30-days, and 6-months mortality.

[Methodology for determining workforce in health nephrologic unit in ITALY. Update of lows].

Nephrology continues to be in transition. While rates of kidney diseases and injury continue to rise, changes in the general health care system and the delivery of kidney care make it unclear how increases in need will be translated into demand for nephrologists. The changes in the delivery system also raise questions as to the future roles and career paths for nephrologists. There a major interrelated workforce issues to be watched closely : how many nephrologists are needed ? The supply of nephrologists does not reflect the distribution of patients with kidney diseases or the activity and job description related to end stage renal disease (ESRD) patients. Looking forward, more needs to be done to systematically measure need and access, and to identify clinical areas and activity of high need for nephrologists. This review examines the laws that govern the measure of work and the needs of personnel of the Italian state and in particular in health care. Therefore, once the method is accepted and established, it will be possible communicate those findings to policy makers and fellows and to involve the politicians.

Systemic AA amyloidosis as a unique manifestation of a combined mutation of TNFRSF1A and MEFV genes.

We report the case of a 22-year-old Caucasian woman presenting with a new-onset nephrotic syndrome with normal renal function during the 35th week of pregnancy. AA (secondary) amyloidosis was further diagnosed at the renal biopsy. Extensive genetic testing revealed that the patient was heterozygous for both TNFRSF1A p.R92Q and MEFV p.M694I mutations leading to an autoinflammatory syndrome characterized by amyloid deposition as the sole manifestation.

Mobilomics in Saccharomyces cerevisiae strains.

BACKGROUND: Mobile Genetic Elements (MGEs) are selfish DNA integrated in the genomes. Their detection is mainly based on consensus-like searches by scanning the investigated genome against the sequence of an already identified MGE. Mobilomics aims at discovering all the MGEs in a genome and understanding their dynamic behavior: The data for this kind of investigation can be provided by comparative genomics of closely related organisms. The amount of data thus involved requires a strong computational effort, which should be alleviated. RESULTS: Our approach proposes to exploit the high similarity among homologous chromosomes of different strains of the same species, following a progressive comparative genomics philosophy. We introduce a software tool based on our new fast algorithm, called regender, which is able to identify the conserved regions between chromosomes. Our case study is represented by a unique recently available dataset of 39 different strains of S.cerevisiae, which regender is able to compare in few minutes. By exploring the non-conserved regions, where MGEs are mainly retrotransposons called Tys, and marking the candidate Tys based on their length, we are able to locate a priori and automatically all the already known Tys and map all the putative Tys in all the strains. The remaining putative mobile elements (PMEs) emerging from this intra-specific comparison are sharp markers of inter-specific evolution: indeed, many events of non-conservation among different yeast strains correspond to PMEs. A clustering based on the presence/absence of the candidate Tys in the strains suggests an evolutionary interconnection that is very similar to classic phylogenetic trees based on SNPs analysis, even though it is computed without using phylogenetic information. CONCLUSIONS: The case study indicates that the proposed methodology brings two major advantages: (a) it does not require any template sequence for the wanted MGEs and (b) it can be applied to infer MGEs also for low coverage genomes with unresolved bases, where traditional approaches are largely ineffective.