A validated pangenome-scale metabolic model for the Klebsiella pneumoniae species complex

The Klebsiella pneumoniae species complex (KpSC) is a major source of nosocomial infections globally with high rates of resistance to antimicrobials. Consequently, there is growing interest in understanding virulence factors and their association with cellular metabolic processes for developing novel anti-KpSC therapeutics. Phenotypic assays have revealed metabolic diversity within the KpSC, but metabolism research has been neglected due to experiments being difficult and cost-intensive. Genome-scale metabolic models (GSMMs) represent a rapid and scalable in silico approach for exploring metabolic diversity, which compile genomic and biochemical data to reconstruct the metabolic network of an organism. Here we use a diverse collection of 507 KpSC isolates, including representatives of globally distributed clinically relevant lineages, to construct the most comprehensive KpSC pan-metabolic model to date, KpSC pan v2. Candidate metabolic reactions were identified using gene orthology to known metabolic genes, prior to manual curation via extensive literature and database searches. The final model comprised a total of 3550 reactions, 2403 genes and can simulate growth on 360 unique substrates. We used KpSC pan v2 as a reference to derive strain-specific GSMMs for all 507 KpSC isolates, and compared these to GSMMs generated using a prior KpSC pan-reference (KpSC pan v1) and two single-strain references. We show that KpSC pan v2 includes a greater proportion of accessory reactions (8.8 %) than KpSC pan v1 (2.5 %). GSMMs derived from KpSC pan v2 also generate more accurate growth predictions, with high median accuracies of 95.4 % (aerobic, n=37 isolates) and 78.8 % (anaerobic, n=36 isolates) for 124 matched carbon substrates. KpSC pan v2 is freely available at https://github.com/kelwyres/KpSC-pan-metabolic-model, representing a valuable resource for the scientific community, both as a source of curated metabolic information and as a reference to derive accurate strain-specific GSMMs. The latter can be used to investigate the relationship between KpSC metabolism and traits of interest, such as reservoirs, epidemiology, drug resistance or virulence, and ultimately to inform novel KpSC control strategies.

A curated collection of Klebsiella metabolic models reveals variable substrate usage and gene essentiality

The Klebsiella pneumoniae species complex (KpSC) is a set of seven Klebsiella taxa that are found in a variety of niches and are an important cause of opportunistic health care-associated infections in humans. Because of increasing rates of multi-drug resistance within the KpSC, there is a growing interest in better understanding the biology and metabolism of these organisms to inform novel control strategies. We collated 37 sequenced KpSC isolates isolated from a variety of niches, representing all seven taxa. We generated strain-specific genome-scale metabolic models (GEMs) for all 37 isolates and simulated growth phenotypes on 511 distinct carbon, nitrogen, sulfur, and phosphorus substrates. Models were curated and their accuracy was assessed using matched phenotypic growth data for 94 substrates (median accuracy of 96%). We explored species-specific growth capabilities and examined the impact of all possible single gene deletions using growth simulations in 145 core carbon substrates. These analyses revealed multiple strain-specific differences, within and between species, and highlight the importance of selecting a diverse range of strains when exploring KpSC metabolism. This diverse set of highly accurate GEMs could be used to inform novel drug design, enhance genomic analyses, and identify novel virulence and resistance determinants. We envisage that these 37 curated strain-specific GEMs, covering all seven taxa of the KpSC, provide a valuable resource to the Klebsiella research community.

A large-scale genomic snapshot of Klebsiella spp. isolates in Northern Italy reveals limited transmission between clinical and non-clinical settings

The Klebsiella group, found in humans, livestock, plants, soil, water and wild animals, is genetically and ecologically diverse. Many species are opportunistic pathogens and can harbour diverse classes of antimicrobial resistance genes. Healthcare-associated Klebsiella pneumoniae clones that are non-susceptible to carbapenems can spread rapidly, representing a high public health burden. Here we report an analysis of 3,482 genome sequences representing 15 Klebsiella species sampled over a 17-month period from a wide range of clinical, community, animal and environmental settings in and around the Italian city of Pavia. Northern Italy is a hotspot for hospital-acquired carbapenem non-susceptible Klebsiella and thus a pertinent setting to examine the overlap between isolates in clinical and non-clinical settings. We found no genotypic or phenotypic evidence for non-susceptibility to carbapenems outside the clinical environment. Although we noted occasional transmission between clinical and non-clinical settings, our data point to a limited role of animal and environmental reservoirs in the human acquisition of Klebsiella spp. We also provide a detailed genus-wide view of genomic diversity and population structure, including the identification of new groups.

Minimally invasive surgery for pediatric dumbbell neuroblastoma: systematic literature review and report of a single-stage neurosurgical and thoracoscopic approach

INTRODUCTION

Traditional surgical strategies for dumbbell neuroblastoma entail, among others, high risk of spinal deformity. Less invasive procedures might reduce these sequelae, however, there is small evidence comparing different strategies. Indications of minimally invasive surgery in neuroblastoma are still developing. Our aim is to identify and analyze different surgical approaches described in the recent literature and to suggest a minimally invasive option.

METHODS

A systematic review of the literature was conducted in PubMed (Jan 2000-Dec 2021) to identify reports describing surgical resection of dumbbell neuroblastoma in children, according to the PRISMA guidelines. Only full-text articles were included.

RESULTS

7 articles met the inclusion criteria which, added to the present case, represent a total of 43 patients. All were retrospective studies, most of them small series. Tumor location was mostly thoracic. Most of combined approaches were performed in two stages. Spinal deformity after surgery was reported in 3 patients. Minimally invasive approach was described in only one paper, with no reported cases of its use in a single-stage combined surgery. We also report, to our knowledge, the first single-stage posterior neurosurgical approach combined with thoracoscopy for resection of a dumbbell neuroblastoma in an infant.

CONCLUSION

Surgical resection of dumbbell neuroblastomas is challenging. There is no consensus on best surgical approach. Dumbbell tumors should not be considered a contraindication for minimally invasive surgery. A single stage and minimally invasive strategy is proposed.

[Pilot experience with indocyanine green navigation in pediatric surgery]

INTRODUCTION

Indocyanine Green (ICG) fluorescence is a new tool for navigated minimal invasive and open surgery, with multiple possible uses, that can increase safety and improve surgical results, facilitating intraoperative decision making. We hereby present our pilot series using ICG navigation in different procedures of pediatric surgery.

MATERIAL AND METHODS

As a proof of concept, between May 2017 and March 2019, we have used this technique as a help for decision making in these scenarios: visualization of the biliary tract, vascular and lymphatic structures, neoplastic tissue and other anatomic landmarks. The route of administration, timing and dosage changed depending on the indication. A 30º optic, with a conventional and near-infrared light emitter, connected to a high definition system specially equipped was used.

RESULTS

We considered that the technique might be useful in 20 patients (22 procedures): 6 involving the biliary tract (5 cholecystectomies, 1 choledochal stenosis), 9 oncologic procedures (5 laparoscopic and 4 open), 7 miscellanea (pulmonary nodule resections, long-gap esophageal atresia, anastomotic leak, etc). There were no complications regarding ICG administration. We considered that the system provided relevant information or affected intraoperative decision making in 90% of the cases.

CONCLUSIONS

ICG navigation was easy to perform and complication free. Our preliminary results suggest that ICG navigation, in open and endoscopic procedures, might provide a qualitative leap regarding safety and facilitate the performance of certain pediatric surgical procedures, particularly in oncology, liver surgery and neonatal surgery.

[Endovascular embolization in the treatment of the pulmonary intralobar sequestration]

INTRODUCTION

Up to date the classical therapeutic approach for intralobar sequestrations (IS) has been surgical excision. However, systemic arteries embolization is presented as an alternative, and even constitutes the first line of treatment in some centers. We summarize our experience in selected cases with the aim of preserving the maximum lung parenchyma.

MATERIAL AND METHODS

Retrospective study of IS who underwent endovascular embolization at our institution between 2013 and 2014.

RESULTS

Three patients of 12, 14 and 21 months old were treated. Two patients had unilateral IS, one in the left lower lobe (LLL) and the other in the right lower lobe (RLL); the third one had bilateral lesions (a CAM-S complex in the RLL and a IS in the LII). The embolization of the four lesions was performed via right femoral artery. The case with bilateral lesions underwent thoracoscopic lobectomy of the CAM-S 7 months after embolization, finding adherences to the diaphragm. None of the patients had immediate complications and were discharged within 48 hours after embolization. In successive ultrasound and plain radiographs controls, with a follow-up of 6, 18 and 30 months, no complications were found.

CONCLUSIONS

Systemic vessels embolization is a treatment option for the treatment of IS that avoids surgery, preserves lung parenchyma and does not preclude surgical resection in case of treatment failure or presence of parenchymal lesions. Longer follow-up is needed to determine long-term effectiveness.

[Nissen fundoplication in children under 1 year of age: is age important?]

AIM

Nissen fundoplication (NF) is a procedure with technical difficulties and variable functional prognosis the lower the patient's age is. Our objective is to analyze the peculiarities of this procedure when performed in children under 1 year.

MATERIALS AND METHODS

Retrospective study of the NF in our center from 1999 to 2014. We review the differences between children under 1 year of age and the leftover of the series: history, indications, surgical approach and postoperative outcomes.

RESULTS

A total of 233 patients (57.1% male) were operated at a median age of 2.3years (1 month-17.31years), of which 82 (35.2%) were younger than 1 year. It Open surgery was performed in 118 patients (86.6% of children under 1 year and 31.1% over 1 year, p <0.05) and laparoscopic in 115. The median follow-up was 3.92 ± 3.24 years. Patients under 1 year had a higher number of comorbidities (91.5% vs 81.5%), respiratory symptoms (76.8% vs 49.7%) and postoperative complications (20.7% vs 9.9% OR = 2.4), with statistically significant differences (p <0.05). There were not differences in the Nissen's failure rate (15.9% vs 8.6%) or the need of reoperation (15.9% vs 7.9%).

CONCLUSIONS

Patients under 1 year operated by NF form a group with particular indications and comorbidities. Although the outcomes among these patients are favourable, surgical complications are more frequent than in older children.

[Current anesthesia risk of anterior mediastinal masses]

AIM

To analyze the current risk of an anesthetic event during surgical acts in pediatric patients with anterior mediastinal masses (AMM) in a tertiary oncology center, using the previously published risk factors to plan the procedure.

MATERIALS AND METHODS

Retrospective study (2009-2015) of pediatric patients with AMM who underwent surgical procedures at debut. Published risk factors (symptoms, radiological findings), with special focus on the statistically significant ones, diagnosis, surgical and anesthetic procedure, special measures, and anesthetic events were recorded. Patients were classified as high or low-risk when airway or vascular compression or severe symptoms were present.

MAIN RESULTS

Retrospective study (2009-2015) of pediatric patients with AMM who underwent surgical procedures at debut. Published risk factors (symptoms, radiological findings), with special focus on the statistically significant ones, diagnosis, surgical and anesthetic procedure, special measures, and anesthetic events were recorded. Patients were classified as high or low-risk when airway or vascular compression or severe symptoms were present.

CONCLUSIONS

Preoperative evaluation of risk in AMM through clinical history and CT/MRI and surgical/anesthetic planning leads to excellent outcomes. The least aggressive procedures should be favored, but if needed, planned general anesthesia under experienced hands is safe even in risk patients.

[Autologous blood pleurodesis for treatment of spontaneous pneumothorax and persistent air leak in pediatric patients]

AIM OF THE STUDY

Recurrent spontaneous pneumothorax (SP) and persistent air leak (PAL) are a therapeutic challenge in some patients. Autologous blood pleurodesis (ABP) is an alternative treatment, but its usefulness in pediatric patients has not been determined yet.

MATERIAL AND METHODS

Retrospective study of pediatric patients treated with ABP at our institution between 2010 and 2014, with special assessment of its indications, description of the technique, volume of blood used, complications and outcomes.

RESULTS

During this period, 29 patients were treated for SP. 5 of them (17.2%) received ABP. Indications were: 2 patients with recurrent SP after thoracoscopic bullae resection and pleurodesis and 3 patients with PAL (1 after thoracoscopic bullae resection and 2 in lung transplantation candidates who were not suitable for surgery). Median age was 14.3 years (11.9-16.6) and volume of blood used was 50 ml (26-60). The air leak stopped in a median of 2.6 days (1-7). One patient needed a second ABP for PAL and another one presented an ipsilateral recurrence of SP after ABP. Follow up time was 2.21 years (0.49-3.42). No complications were observed.

CONCLUSIONS

ABP is a cheap, safe and easy to perform procedure and may be considered as a therapeutic option in some pediatric patients with SP or PAL.

[Spontaneous pneumothorax in children: factors associated with their recurrence]

INTRODUCTION

Recurrence of spontaneous pneumothorax (SP) is more frequent in pediatric patients. The purpose of our study was to identify factors associated with this recurrence.

MATERIAL AND METHODS

Retrospective review of the chart of patients with SP treated at our institution between 2004 and 2014. Statistic methods (χ2 and logistic regression) were used analyzing age, gender, side and size of pneumothorax and therapeutic approach as possible predictive factors of SP recurrence.

RESULTS

A total of 81 SP cases in 43 patients (29 men, 14 women) were reviewed: 50 primary (PSP) and 31 secondary (SSP). Median age at presentation was 15,1 years (0.5-18.59). Follow up was 3.52 years (0.21-18.59). Twenty-three cases (28.4%) underwent surgery (22 thoracoscopies, 1 thoracotomy), consisting of bleb resection with abrasive and chemical pleurodesis. Ipsilateral recurrence after surgery was 21.7% (22.2% in PSP, 20% in SSP, p = 0.096) and 41.4% after non-surgical treatment. Age was a risk factor for recurrence (p= 0.049; OR = 1.16), especially between 10 and 15 years (44.6% in front of 19%, p = 0.013). Male gender and size >20% were associated with higher recurrence risk in SSP that received non-surgical treatment (p<0.05).

CONCLUSIONS

Recurrences of SP in children are frequent even after surgical treatment. Age (preadolescence and early adolescence), male gender and initial size of pneumothorax may be factors associated with higher recurrence risk.

[Laryngotracheal traumatic injuries (LTI) in children: when to operate?]

INTRODUCTION

Paediatric LTI is associated with significant morbid-mortality. Although historically first line treatment was surgical, conservative management is making headway. The purpose of this study was to analyze the management and surgical indications of LTI treated at our institution.

MATERIAL AND METHODS

Retrospective study of patients with LTI treated between 2007 and 2014.

RESULTS

Six out of seven patients, with a median age of 4 years (2-15), had blunt traumas and one had an open trauma. Respiratory distress, pain and subcutaneous emphysema were presented in 71.4% of the patients. Five children were intubated (3 pre-hospital care and 2 after reaching the hospital), all of them underwent fibrobronchoscopy, determining the location, the extention, and assessing the possibility of extubation. Esophagoscopy was made in 2 cases. The remaining 2 cases were bounded to observation as they did not have respiratory symptoms or progressive emphysema, precluding bronchoscopy. Conservative management was followed in 71.4% of the patients, with a 100% success rate. Conservative management criteria were no progression of emphysema or respiratory distress, regardless the degree and location of the lesions. Two patients needed surgery: one tracheoesophageal fistula caused by a button battery, and the other was a tracheal open section associated with vascular injury. Both of them recovered uneventfully.

CONCLUSIONS

If the respiratory symptoms or the emphysema do not progress, patients with LTI can be managed conservatively, regardless of size or location of the injury. Associated esophageal lesions and open injuries require surgical management. An early diagnosis is mandatory in order to minimize morbidity and mortality.

[Experimental model of amniotic band in rats: model description and initial morphological study]

PURPOSE

Our objective is to describe a new experimental model of amniotic band in rats and to show the initial morphological results.

METHODS

The model was created by ligation of a hind limb with silk on day 17 of gestation; in selected fetuses ligation was withdrawn on day 19 of gestation. Fetuses were removed by cesarean section on day 21 of gestation, analyzing their weights and morphological characteristics of their hind legs. We used 10 pregnant SD rats, weighing 263 g (231-279). One hundred and thirteen fetuses were analyzed divided into 6 groups: fetuses from control rats (n=28), uterine opening and closing (n=7), band creation (n=28), band creation and subsequent removal (n=14) and not intervened fetuses of the litters in which the band was created (n=19) and that the band was created and removed (n=17). Comparisons between groups were made using parametric tests considering p<0.05 as a threshold for significance.

RESULTS

Operated fetuses (band creation and band creation and removal) showed statistically significant differences in weight (mean=4.56 g and 4.4 g) and length of their hind limbs (mean=3.97 mm and 5.34 mm) compared to the rest of the groups. The rate of abortions in operated fetuses was 16.6% and the rate of amputations was 8.3%.

DISCUSSION

A viable and reproducible experimental model of amniotic band is described, with potential applications in both the study of the disease and the role of fetal surgery thereon.

[Technical aspects of experimental intestinal transplant]

PURPOSE

Our objective is to analyze the variables that influence the outcome of Small Bowel Transplantation (SBT) in rats in an experimental microsurgery program. The surgical technique and perioperative care are described in detail.

METHODS

Retrospective study of the SBT in rats conducted in our experimental surgery laboratory from 2002 to 2010. The animals were divided into group A (those who survived more than 48 hours) and group B (those who died earlier without justificable cause). We compared in both groups: number of transplants performed by the surgeon, warm ischemia time, cold ischemia time and duration of the procedure.

RESULTS

Five surgeons with different degrees of microsurgical training participated in the study. A total of 521 SBT were performed with an overall survival of 48%. The first successful transplant was performed after a median of 46 (25-68) transplants. Total procedure time (3.5 vs 2.9 hours) and warm ischemia time (51 vs 35 minutes) were higher in group B (p < 0.05).

DISCUSSION

The number of transplants required for learning the technique is high. However, survival is acceptable when the time needed for vascular anastomosis is reduced. The SBT in rats is a valuable model for surgical training and research of the phenomena related to SBT.