Evaluation of Molecular Epidemiology, Clinical Characteristics, Antifungal Susceptibility Profiles, and Molecular Mechanisms of Antifungal Resistance of Iranian Candida parapsilosis Species Complex Blood Isolates

Clonal expansion of fluconazole resistant (FLZ-R) Candida parapsilosis isolates is increasingly being identified in many countries, while there is no study exploring the antifungal susceptibility pattern, genetic diversity, and clinical information for Iranian C. parapsilosis blood isolates. Candida parapsilosis species complex blood isolates (n = 98) were recovered from nine hospitals located in three major cities, identified by MALDI-TOF MS, and their genetic relatedness was examined by AFLP fingerprinting. Antifungal susceptibility testing followed CLSI-M27-A3 and ERG11, MRR1 and hotspots 1/2 (HS1/2) of FKS1 were sequenced to assess the azole and echinocandin resistance mechanisms, respectively. Ninety-four C. parapsilosis and four Candida orthopsilosis isolates were identified from 90 patients. Only 43 patients received systemic antifungal drugs with fluconazole as the main antifungal used. The overall mortality rate was 46.6% (42/90) and death mostly occurred for those receiving systemic antifungals (25/43) relative to those not treated (17/47). Although, antifungal-resistance was rare, one isolate was multidrug-resistant (FLZ = 16 μg/ml and micafungin = 8 μg/ml) and the infected patient showed therapeutic failure to FLZ prophylaxis. Mutations causing azole and echinocandin resistance were not found in the genes studied. AFLP revealed five genotypes (G) and G1 was the main one (59/94; 62.7%). Clinical outcome was significantly associated with city (P = 0.02, α <0.05) and Mashhad was significantly associated with mortality (P = 0.03, α <0.05). Overall, we found a low level of antifungal resistance for Iranian C. parapsilosis blood isolates, but the noted MDR strain can potentially become the source of future infections and challenge the antifungal therapy in antifungal-naïve patients. AFLP typing results warrants confirmation using other resolutive typing methods.

Accurate detection of chimeric contigs via Bionano optical maps

SUMMARY

A chimeric contig is contig that has been incorrectly assembled, i.e. a contig that contains one or more mis-joins. The detection of chimeric contigs can be carried out either by aligning assembled contigs to genome-wide maps (e.g. genetic, physical or optical maps) or by mapping sequenced reads to the assembled contigs. Here, we introduce a software tool called Chimericognizer that takes advantage of one or more Bionano Genomics optical maps to accurately detect and correct chimeric contigs. Experimental results show that Chimericognizer is very accurate, and significantly better than the chimeric detection method offered by the Bionano Hybrid Scaffold pipeline. Chimericognizer can also detect and correct chimeric optical molecules.

AVAILABILITY AND IMPLEMENTATION

https://github.com/ucrbioinfo/Chimericognizer.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Enhanced stability of quantum Hall skyrmions under radio-frequency radiations

We present in this paper the results from a recent study on the stability of the quantum Hall skyrmions state at a Landau level filling factor (ν) close to ν = 1 in a narrow GaAs quantum well. Consistent with previous work, a resonant behavior is observed in the resistively detected NMR measurements. In the subsequent current-voltage (I-V) measurements to examine its breakdown behavior under radio frequency radiations, we observe that the critical current assumes the largest value right at the ⁷⁵As nuclear resonant frequency. We discuss possible origin for this unexpectedly enhanced stability.

Transcription factor Liv4 is required for growth and pathogenesis of Cryptococcus neoformans

Cryptococcus neoformans is an important invasive fungal pathogen that causes life-threatening meningoencephalitis in humans. Its biological and pathogenic regulatory mechanisms remain largely unknown, particularly due to the presence of those core transcription factors (TFs). Here, we conducted a detailed characterization of the TF Liv4 in the biology and virulence of C. neoformans. Deletion of TF Liv4 protein resulted in growth defect under both normal and stress conditions (such as high temperature and cell wall/membrane damaging agents), drastic morphological damage and also attenuated virulence in C. neoformans. These phenotypic changes might be contributed to transcriptional abnormality in the liv4Δ mutant, in which several cryptococcal genes involved in energy metabolism and cell wall integrity were downregulated. Furthermore, ChIP-seq and ChIP-qPCR assays suggested TF Liv4 might exert its regulatory function in transcription by its activation of RBP1 in C. neoformans. Taken together, our work highlights the importance of TF Liv4 in the growth and virulence of C. neoformans, and it facilitates a better understanding of cryptococcal pathogenesis mechanisms.

Epidemiology of yeast species causing bloodstream infection in Tehran, Iran (2015-2017); superiority of 21-plex PCR over the Vitek 2 system for yeast identification

Introduction. Given the limited number of candidaemia studies in Iran, the profile of yeast species causing bloodstream infections (BSIs), especially in adults, remains limited. Although biochemical assays are widely used in developing countries, they produce erroneous results, especially for rare yeast species.Aim. We aimed to assess the profile of yeast species causing BSIs and to compare the accuracy of the Vitek 2 system and 21-plex PCR.Methodology. Yeast blood isolates were retrospectively collected from patients recruited from two tertiary care training hospitals in Tehran from 2015 to 2017. Relevant clinical data were mined. Identification was performed by automated Vitek 2, 21-plex PCR and sequencing of the internal transcribed spacer region (ITS1-5.8S-ITS2).Results. In total, 137 yeast isolates were recovered from 107 patients. The overall all-cause 30-day mortality rate was 47.7 %. Fluconazole was the most widely used systemic antifungal. Candida albicans (58/137, 42.3 %), Candida glabrata (30/137, 21.9 %), Candida parapsilosis sensu stricto (23/137, 16.8 %), Candida tropicalis (10/137, 7.3 %) and Pichia kudriavzevii (Candida krusei) (4/137, 2.9 %) constituted almost 90 % of the isolates and 10 % of the species detected were rare yeast species (12/137; 8.7 %). The 21-plex PCR method correctly identified 97.1 % of the isolates, a higher percentage than the Vitek 2 showed (87.6 %).Conclusion. C. albicans was the main cause of yeast-derived fungaemia in this study. Future prospective studies are warranted to closely monitor the epidemiological landscape of yeast species causing BSIs in Iran. The superiority of 21-plex PCR over automated Vitek 2 indicates its potential clinical utility as an alternative identification tool use in developing countries.

Long term outcomes of cataract surgery in severe and end stage primary angle closure glaucoma with controlled IOP: a retrospective study

Background

To investigate the long term surgical outcomes of cataract surgery in severe and end stage glaucoma patients with preoperative intraocular pressure less than 21 mmHg, and to detect the associated factors.

Methods

A retrospective study of primary angle closure glaucoma patients was conducted on who underwent cataract surgery or combined with goniosynechialysis from March 2015 to April 2018. Main outcome measures were visual acuity, intraocular pressure, number of glaucoma medications and complications.

Results

Sixteen patients (19 eyes) were included. The mean age was 64.89 ± 11.68 years and the mean followed up duration was 21.89 ± 7.85 months. The final visual acuity was significantly improved from 0.69 ± 0.55 to 0.46 ± 0.52 logMAR, within 12 (63.2%) eyes improved, 4 (21.1%) eyes kept unchanged, and 3 (15.8%) eyes reduced. Linear regression analysis indicated that higher mean deviation, higher visual field index and lower glaucoma stage associated with better final visual acuity (r = − 0.511, r = − 0.493, r = 0.537 respectively). Moreover, the final number of medications were reduced from 1.26 ± 0.99 to 0.26 ± 0.56 (p < 0.01). The mean intraocular pressure was not significantly reduced with the final IOP of 14.48 ± 3.74 mmHg (p = 0.97). While the eyes with intraocular pressure above 15 mmHg was decreased to 6 (31.6%) eyes compared to 10 (52.6%) eyes at baseline. Moreover, the number of eyes free of medications was increased from 4 (21.1%) preoperatively to 15 (78.9%) eyes postoperatively.

Conclusions

Final visual acuity was significantly improved in the severe and end stage primary angle closure glaucoma patients and the number of eyes came off medications increased by 57.8% after cataract surgery. Preoperatively, the glaucoma stage, mean deviation and visual field index are important parameters to predict the final visual acuity after cataract surgery.

Particle-Hole Symmetry and the Fractional Quantum Hall Effect in the Lowest Landau Level

We report on detailed experimental studies of a high-quality heterojunction insulated-gate field-effect transistor (HIGFET) to probe the particle-hole symmetry of the fractional quantum Hall effect (FQHE) states about half-filling in the lowest Landau level. The HIGFET is specially designed to vary the density of a two-dimensional electronic system under constant magnetic fields. We find in our constant magnetic field, variable density measurements that the sequence of FQHE states at filling factors ν=1/3,2/5,3/7… and its particle-hole conjugate states at filling factors 1-ν=2/3,3/5,4/7… have a very similar energy gap. Moreover, a reflection symmetry can be established in the magnetoconductivities between the ν and 1-ν states about half-filling. Our results demonstrate that the FQHE states in the lowest Landau level are manifestly particle-hole symmetric.

Candida tropicalis is the most prevalent yeast species causing candidemia in Algeria: the urgent need for antifungal stewardship and infection control measures

Background

Despite being associated with a high mortality and economic burden, data regarding candidemia are scant in Algeria. The aim of this study was to unveil the epidemiology of candidemia in Algeria, evaluate the antifungal susceptibility pattern of causative agents and understand the molecular mechanisms of antifungal resistance where applicable. Furthermore, by performing environmental screening and microsatellite typing we sought to identify the source of infection.

Methods

We performed a retrospective epidemiological-based surveillance study and collected available blood yeast isolates recovered from the seven hospitals in Algiers. To identify the source of infection, we performed environmental screening from the hands of healthcare workers (HCWs) and high touch areas. Species identification was performed by API Auxa-Color and MALDI-TOF MS and ITS sequencing was performed for species not reliably identified by MALDI-TOF MS. Antifungal susceptibility testing followed CLSI M27-A3/S4 and included all blood and environmental yeast isolates. ERG11 sequencing was performed for azole-resistant Candida isolates. Microsatellite typing was performed for blood and environmental Candida species, where applicable.

Results

Candida tropicalis (19/66) was the main cause of candidemia in these seven hospitals, followed by Candida parapsilosis (18/66), Candida albicans (18/66), and Candida glabrata (7/66). The overall mortality rate was 68.6% (35/51) and was 81.2% for C. tropicalis-infected patients (13/16). Fluconazole was the main antifungal drug used (12/51); 41% of the patients (21/51) did not receive any systemic treatment. Candida parapsilosis was isolated mainly from the hands of HCWs (7/28), and various yeasts were collected from high-touch areas (11/47), including Naganishia albida, C. parapsilosis and C. glabrata. Typing data revealed interhospital transmission on two occasions for C. parapsilosis and C. glabrata, and the same clone of C. parapsilosis infected two patients within the same hospital. Resistance was only noted for C. tropicalis against azoles (6/19) and fluconazole-resistant C. tropicalis isolates (≥8 μg/ml) (6/19) contained a novel P56S (5/6) amino acid substitution and a previously reported one (V234F; 1/6) in Erg11p.

Conclusions

Collectively, our data suggest an urgent need for antifungal stewardship and infection control strategies to improve the clinical outcome of Algerian patients with candidemia. The high prevalence of C. tropicalis joined by fluconazole-resistance may hamper the therapeutic efficacy of fluconazole, the frontline antifungal drug used in Algeria.

Molecular Hydrogen Protects Human Melanocytes from Oxidative Stress by Activating Nrf2 Signaling

Oxidative stress is proven to be critical for the initiation and progression of vitiligo. Molecular hydrogen (H₂) possesses potent antioxidant activity and has been shown to protect against various oxidative stress-related diseases. In this study, we first investigated the effects and mechanisms of H₂ in human melanocytes damaged by hydrogen peroxide. We initially found that H₂ reduced intracellular ROS accumulation and malondialdehyde levels in both vitiligo specimens and hydrogen peroxide-treated melanocytes in vitro in a concentration- and time-dependent manner, concomitant with the enhancement of antioxidant enzyme activity. Correspondingly, H₂ reversed hydrogen peroxide-induced apoptosis and dysfunction in both normal and vitiligo melanocytes. H₂ protected mitochondrial morphology and function in melanocytes under stress and promoted the activation of Nrf2 signaling, whereas Nrf2 deficiency abolished the protective effect of H₂ against hydrogen peroxide-induced oxidative damage. Furthermore, H₂ positively modulated β-catenin in hydrogen peroxide-treated melanocytes, and the β-catenin pathway was implicated in H₂-induced Nrf2 activation. Collectively, our results indicate that H₂ could be a promising therapeutic agent for vitiligo treatment via attenuating oxidative damage, and its beneficial effect in human melanocytes might involve Wnt/β-catenin-mediated activation of Nrf2 signaling.

First-principles calculations of oxygen octahedral distortions in LaAlO3/SrTiO3(001) superlattices

The size, shape and connectivity of oxide octahedra are essential for understanding and controlling the emergent functional properties of ABO₃ perovskites. Using first-principles calculations, we systematically studied the oxygen octahedral rotation and deformation in LaAlO₃/SrTiO₃(001) superlattices. Superlattices with electron- or hole-doped interfaces, or both, are compared. The results showed that there are at least three different types of oxygen octahedral distortions in these superlattices, which is more than what had previously been reported in the literature. We demonstrate that interfacial oxygen octahedral coupling and hole-doping, in addition to epitaxial strain, are the key factors underlying the formation of multiple types of oxygen octahedral rotations in these systems. We confirm that oxygen octahedral rotations and deformations play an essential role in insulator-metal transitions. Furthermore, octahedral distortion leads to ferroelectricity like dipole formation with the polarization vector always pointing to the positively charged interfaces.

Three-color risk stratification for improving the diagnostic accuracy for biliary atresia

OBJECTIVES

It is challenging to early differentiate biliary atresia from other causes of cholestasis. We aimed to develop an algorithm with risk stratification to distinguish biliary atresia from infantile cholestasis.

METHODS

In this study, we enrolled infants with cholestasis into 2 subgroups from January 2010 to April 2019. A prospective cohort (subgroup 2) of 187 patients (107 with biliary atresia and 80 without biliary atresia) underwent acoustic radiation force impulse elastography. Stepwise regression was used to identify significant predictors of biliary atresia. A sequential algorithm with risk stratification was constructed.

RESULTS

Among 187 patients, shear wave speed > 1.35 m/s and presence of the triangular cord sign were considered high risk for biliary atresia (red), in which 73 of 78 patients (accuracy of 93.6%) with biliary atresia were identified. Afterwards, γ-GT, abnormal gallbladder, and clay stool were introduced into the algorithm and 55 intermediate-risk infants were identified (yellow) with a diagnostic accuracy of 60% for biliary atresia. Of the remaining 54 infants who were classified as low-risk patients (green), the accuracy for excluding biliary atresia was 98.1%. By applying a three-color risk stratification tool, 70.6% patients were identified as either high risk or low risk for biliary atresia (area under the curve, 0.983; sensitivity, 98.7%; specificity, 91.4%). We also estimated the risk of biliary atresia in different color groups, which was 94.7% (95%CI, 94.3-95.5%) in the red group and 7.2% (95%CI, 6.6-8.3%) in the green group.

CONCLUSIONS

Our simple noninvasive approach was able to identify biliary atresia with high accuracy.

KEY POINTS

• Five predictors, namely shear wave speed, triangle cord sign, γ-glutamyl transferase, abnormal gallbladder, and clay stool, were selected to identify biliary atresia in cholestasis. • Shear wave speed > 1.35 m/s and presence of the triangle cord sign were considered high-risk patients with a diagnostic accuracy of 93.6% for biliary atresia. • Risk for biliary atresia was high (red), intermediate (yellow), or low (green). In the red and green group, we achieved an extremely high diagnostic performance (area under the curve, 0.983; sensitivity, 98.7%; specificity, 91.4%).

Unequivocal identification of an underestimated opportunistic yeast species, Cyberlindnera fabianii, and its close relatives using a dual-function PCR and literature review of published cases

Although Cyberlindnera fabinaii is a rare opportunist yeast species, its ability to cause septicemia, produce biofilm, and rapid acquisition of resistance to fluconazole and voriconazole, reinforced the urge for its identification from its closely related species. Widely used biochemical assays mainly identify Cyberlindnera fabinaii as Cyberlindnera jadinii and Wickerhamomyces anomalus, resulting in underestimation of this yeast in clinical settings. Moreover, the urge for a reliable molecular means of identification remains unsolved for 28 years. In order to unequivocally differentiate Cy. fabianii, Cy. mississipiensis, Cy. jadinii, and W. anomalus, we designed a dual-function multiplex polymerase chain reaction (PCR) assay. Challenging our dual-function multiplex PCR assay with 30 most clinically important yeast species, proved its specificity. Although conventional PCR could differentiate four target species, the real-time PCR counterpart due to Tm overlap misidentified Cy. mississipiensis as Cy. jadinii. Alongside of presenting a comprehensive literature review of published cases of Cy. fabianii from 1990 to 2018, we collected various clinical isolates from Tehran, Shiraz, and Fasa (July 1, 2017, to December 31, 2017) to find a passive relative distribution of these closely-related species in Iran. Subjecting our Iranian collection of yeast isolates to matrix-assisted laser desorption/ionization–time of flight (MALDI-TOF) MS and LSU and ITS rDNA sequencing revealed six isolates of Cy. fabianii (central venous catheter n = 2 and vaginal swabs n = 4) and one isolate of Cy. jadinii (vaginal swabs). Due to the use of biochemical assays in global ARTEMIS study, we encourage reidentification of clinical isolates of Cy. jadinii and Cy. jadinii using MALDI-TOF or Sanger sequencing that might lead to correcting the distribution of this fungus.

Development and Validation of a Rapid, Single-Step Reverse Transcriptase Loop-Mediated Isothermal Amplification (RT-LAMP) System Potentially to Be Used for Reliable and High-Throughput Screening of COVID-19

Objectives: Development and validation of a single-step and accurate reverse transcriptase loop-mediated isothermal amplification technique (RT-LAMP) for rapid identification of SARS-CoV-2 relative to commercial quantitative reverse transcriptase real-time PCR (qRT-PCR) assays to allow prompt initiation of proper medical care and containment of virus spread. Methods: Primers showing optimal in-silico features were subjected to analytical sensitivity and specificity to assess the limit of detection (LOD) and cross-reaction with closely- and distantly-related viral species, and clinically prominent bacterial and fungal species. In order to evaluate the clinical utility, our RT-LAMP was subjected to a large number of clinical samples, including 213 negative and 47 positive patients, relative to two commercial quantitative RT-PCR assays. Results: The analytical specificity and sensitivity of our assay was 100% and 500 copies/ml when serial dilution was performed in both water and sputum. Subjecting our RT-LAMP assay to clinical samples showed a high degree of specificity (99.5%), sensitivity (91.4%), positive predictive value (97.7%), and negative predictive value (98.1%) when used relative to qRT-PCR. Our RT-LAMP assay was two times faster than qRT-PCR and is storable at room temperature. A suspected case that later became positive tested positive using both our RT-LAMP and the two qRT-PCR assays, which shows the capability of our assay for screening purposes. Conclusions: We present a rapid RT-LAMP assay that could extend the capacity of laboratories to process two times more clinical samples relative to qRT-PCR and potentially could be used for high-throughput screening purposes when demand is increasing at critical situations.

Diagnostic Value of Serum Procollagen III N-Terminal Peptide for Liver Fibrosis in Infantile Cholestasis

Background: Several non-invasive markers have been reported as being effective for the assessment of fibrosis in adults with chronic viral hepatitis. The infantile liver is more susceptible to cholestasis, and it is important to promptly evaluate liver fibrosis to guide the clinical treatment. However, the clinical value of these markers in infants with cholestasis remains unknown. Aim: To investigate the correlation between serum laminin (LN), hyaluronic acid (HA), procollagen III N-terminal peptide (PIIINP) level, and liver fibrosis stage in infants with cholestasis. Methods: One hundred and thirty-seven term infants with cholestasis were included. Laparoscopic exploration and cholangiography were performed to diagnose or rule out biliary atresia. Serum LN, HA, and PIIINP were measured prior to laparoscopic exploration. Liver biopsy was performed for all patients. Liver fibrosis was staged on a five-point scale (F0-F4) according to the METAVIR scoring system. The correlation between serum markers and liver fibrosis stage was assessed. A receiver operator characteristic analysis was performed to determine the accuracy of serum markers for predicting the liver fibrosis stage. Results: Serum PIIINP and HA were positively correlated with liver fibrosis stage (r = 0.622, P < 0.001, and r = 0.41, P < 0.001, respectively). There was no significant correlation between serum LN and liver fibrosis stage (P > 0.05). Serum aspartate aminotransferase, total bilirubin, direct bilirubin, and PIIINP were independently correlated with the fibrosis stage on multivariate ordinal regression analysis. Receiver operating curve (ROC) analysis showed that serum PIIINP was the most effective for the diagnosis of fibrosis grade. The area under the ROC curves (AUROCs) for serum PIIINP for diagnosing fibrosis stages ≥F1, ≥F2, ≥F3, and F4 (cirrhosis) were 0.843, 0.789, 0.82, and 0.891, respectively. The cut-off serum PIIINP value for predicting fibrosis stage ≥F1 was 242.3 ng/mL, with 73.8% sensitivity and 90% specificity. The cut-off value for predicting cirrhosis was 698.7 ng/mL, with 75% sensitivity and 96% specificity. Conclusion: Serum PIIINP is a promising biomarker for predicting liver fibrosis stage, especially cirrhosis. Its assessment is a simple and non-invasive diagnostic method for liver fibrosis in infants with cholestasis.

Can early surgery improve the outcome of patients with meconium peritonitis? A single-center experience over 16 years

BACKGROUND

In the last century, meconium peritonitis(MP)was once a highly fatal gastrointestinal. disease With the development of fetal radiological technology, abnormal signs, such as pseudocysts, can. be detected during the fetal period so that more patients can be diagnosed prenatally and receive surgery. in the early stage of life. The survival rate of MP has increased up to 80% in recent years. According to. a review of the treatment and outcomes of patients diagnosed with MP, we evaluated the influence of. early operation on survival rate and discussed the risk factors of prognosis.

METHODS

We collected 79 cases of patients diagnosed with MP who were treated in our department. from October 2001 to December 2017. They were divided into 2 groups. Patients in group A were born. in our hospital. Patients in group B were born in a local hospital with suspicion of MP and then transferred. to our department.

RESULTS

The birth weight (BW) and gestational age (GA) of patients were higher in group A than in. group B. There was no significant difference in the proportion of premature and low birth weight (LBW). patients between the two groups (p = 0.422, p = 0.970). Their age at the time of surgery was younger in. group A than in group B (1.4 ± 2.0 vs. 6.9 ± 14.9, p < 0.001). The overall survival rate of group A was higher. than that of group B (95.0% vs. 79.5%, p = 0.038). The prognosis of premature patients was worse than. that of full-term infants for both groups (p = 0.012).

CONCLUSIONS

Prematurity is a significant risk factor related to death for MP patients. The survival rate. of MP patients can be improved by early operation during the neonatal period.

Gut microbiota differences during metamorphosis in sick and healthy giant spiny frogs (Paa spinosa) tadpoles

Gut microbiota plays important roles in host nutrition, immunity, development and health; therefore, disruption of the gut microbiota is closely associated with development of diseases in the host. In amphibians, metamorphosis is associated not only with extensive changes in the gut microbiota, but also with high mortality. Therefore, we hypothesized that unsuccessful restructuring of the gut microbiota during metamorphosis was an important factor that caused the fatalities. To test this hypothesis, we investigated the gut microbiota of apparently sick and healthy giant spiny frog tadpoles during metamorphosis, using high-throughput sequencing of the 16S rRNA gene. Our results showed that most dominant phyla differed significantly among developmental stages of sick and healthy Paa spinosa tadpoles. The differences in the dominant genera in sick and healthy tadpoles were the highest at the stage of degeneration of cloacal tube (TDCT). After the metamorphosis, the composition of the gut microbiota was more alike between healthy and sick tadpoles at the stage of forelimb emergence than at TDCT. These results imply that failed restructuring of the gut microbiota during metamorphosis caused the death of P. spinosa tadpoles. These results provided an important reference to prevent the high actual of P. spinosa tadpoles during metamorphosis. SIGNIFICANCE AND IMPACT OF THE STUDY: We investigated the gut microbiota of apparently sick and healthy giant spiny frog (Paa spinosa) tadpoles during metamorphosis, using high-throughput sequencing of the 16S rRNA gene. Our results showed that the differences in the dominant genera in sick and healthy tadpoles were the highest at the stage of degeneration of cloacal tube. After the metamorphosis, the composition of the gut microbiota was alike between healthy and sick tadpoles. These results imply that failed restructuring of the gut microbiota during metamorphosis caused the death of P. spinosa tadpoles.

[One-stage posterior correction and second-stage anterior debridement and fusion in treating children with thoracic tuberculosis complicated with kyphoscoliosis]

Objective: To investigate the clinical outcomes of one-stage posterior correction surgery and second-stage anterior debridement and fusion in treating children with thoracic tuberculosis complicated with kyphoscoliosis. Methods: From January 2008 to December 2014, a total of 17 children with thoracic vertebral tuberculosis complicated with kyphoscoliosis who underwent a one-stage posterior correction and second-stage anterior debridement and complementary fusion were included. There were 8 males and 9 females with an average age of (8±4) years (5-14 years). All patients underwent posterior correction and anterior debridement and bone graft fusion surgery. The neurological function was determined by Frankel grade. The operation time, estimated blood loss (EBL), levels fused and numbers of screws were recorded. The following radiographic parameters were measured: Cobb angle of the coronal curve, regional kyphosis and sagittal vertical axis (SVA). The incidence of intraoperative and postoperative complications was recorded. The data before and after the operation were compared with paired sample t test. Results: The tuberculosis lesions located in the thoracic vertebrae, and the abscess involved 2 to 4 vertebral segments. The average operation time was (4.1±0.8) h, the EBL was (526±275) ml, the levels fused were 7.6±2.3, and 173 pedicle screws were placed. The preoperative coronal curve averaged 12.6°±6.2°, and it was corrected to 4.2°±1.9° postoperatively (t=4.628, P<0.01), the regional kyphosis was 67.2°±19.4°, and it was corrected to 15.7°±8.2° postoperatively (t=8.192, P<0.01). The SVA improved from (8.1±5.0) mm to (3.0±1.7) mm postoperatively. The mean duration of follow-up for all the patients were (38±11) months. At final follow-up, SVA was reduced to (2.4±2.0) mm and the other parameter kept stable. Thirteen patients had more than one grade improvement of Frankel grade. The VAS score for all patients improved from 4.7±2.8 to 2.2±0.5 postoperatively (t=3.973, P=0.01), and improved to 0.5±0.5 at final follow-up (t=-7.880, P<0.01). No recurrence of primary spinal tuberculosis was seen at final follow-up of all patients. Conclusions: One-stage posterior correction and second-stage anterior complementary debridement and fusion is an effective procedure for children with thoracic tuberculosis complicated with kyphoscoliosis. Significant postoperative deformity correction could be achieved with satisfactory improvement of neurological function. Solid fusion and satisfactory correction maintenance were observed at mid-to long-term follow-up.

Outcomes of Congenital Diaphragmatic Hernia in One of the Twins

OBJECTIVE

Congenital diaphragmatic hernia (CDH) occurred in one of the twins is rarely seen. This study aims to describe the clinical features and outcomes of this special CDH.

STUDY DESIGN

The medical records of all CDH neonates treated in our institution between 2010 and 2016 were retrospectively reviewed. Data were analyzed using parametric and nonparametric tests, appropriately. Association between the twin pregnancy and outcomes was assessed.

RESULTS

Eighty-nine patients met the inclusion criteria. In the multivariate analysis, liver herniation, observed/expected lung-to-head circumference ratio, and lower birth weight were independently related to the survival rate of CDH. Eleven patients were identified with CDH occurred in only one of the twins. Among them, seven patients (63.6%) were premature and six (54.5%) were found with low birth weight. Compared with CDH patients with singleton pregnancy, they had significantly higher rates of prematurity (p < 0.001) and lower birth weight (p < 0.001). Additionally, they had worse outcomes with a shorter duration of mechanical ventilation (p = 0.015) and lower survival rate at discharge (p = 0.024).

CONCLUSION

Preterm birth and low birth weight are more common in CDH patients with twin pregnancy, which may lead to worse outcomes.

P916The effect of a novel, user-friendly, transcatheter edge-to-edge mitral valve repair device in a porcine model of mitral regurgitation

Objective

A new technique has been devised to treat mitral regurgitation (MR) through the transapical route by replicating the edge-to-edge repair surgery. This system encompasses an easy-to-use leaflet clamp and a smaller-sized delivery system (14F–16F). We aimed to evaluate the effectiveness of this device in a porcine model of acute MR.

Methods

Acute MR was induced in 36 anesthetized porcine subjects by severing the major chordae supporting the corresponding segment of the leaflet. This device was then transapically implanted on the prolapsing segment under 3D epicardial echocardiographic guidance. All of the animals were killed 30 days after the procedure to verify the proper location of the implanted devices.

Results

Cutting the major chordae induced an eccentric MR jet (MR grade: 3+, 27.8%/4+, 72.2%) in all of the animals. Every single pig was then successfully implanted with one clamp. The duration of catheterization ranged from 18 to 40 minutes. Overt MR reduction was observed following the procedure through echocardiography; residual MR was mild in 8 cases, trivial in 19 cases, and absent in 9 cases. In terms of hemodynamic parameters, the mean and maximum mitral valve pressure gradients were increased significantly (p<0.01), but these values were less than 4 mmHg in all of the cases. Autopsy demonstrated that all but one device were precisely placed to clip the prolapsing segment of the mitral valve, and there was no evidence of thrombosis, thromboembolism or impairment of the cardiac structure.

Table 1. Changes in hemodynamic parameters, cardiac size, and functional parameters after the procedure Preoperation Postoperation P value MR-maxA (mm2) 7.27±2.13 1.54±1.29 0.000 MVPG-max (mmHg) 1.95±0.47 3.66±0.62 0.000 MVPG-mean (mmHg) 0.87±0.31 1.7±0.28 0.000 LVEDD (mm) 46.08±2.85 46.44±3.53 0.239 LVESD (mm) 29.11±3.44 29.08±3.62 0.940 LVEF (%) 66.53±6.4 67.14±4.93 0.256 LAD (mm) 35.75±2.24 36.42±1.99 0.057 LAA (mm2) 12.95±2.22 12.64±1.55 0.301

Figure 1

Conclusions

Transapical implantation of the novel mitral valve repair device is effective and safe in reducing acutely induced MR in pigs; thus, suggesting that it has great potential for clinical benefit in patients with MR.

Acknowledgement/Funding

Shanghai Science and Technology Committee

Identification of Mycoses in Developing Countries

Extensive advances in technology offer a vast variety of diagnostic methods that save time and costs, but identification of fungal species causing human infections remains challenging in developing countries. Since the echinocandins, antifungals widely used to treat invasive mycoses, are still unavailable in developing countries where a considerable number of problematic fungal species are present, rapid and reliable identification is of paramount importance. Unaffordability, large footprints, lack of skilled personnel, and high costs associated with maintenance and infrastructure are the main factors precluding the establishment of high-precision technologies that can replace inexpensive yet time-consuming and inaccurate phenotypic methods. In addition, point-of-care lateral flow assay tests are available for the diagnosis of Aspergillus and Cryptococcus and are highly relevant for developing countries. An Aspergillus galactomannan lateral flow assay is also now available. Real-time PCR remains difficult to standardize and is not widespread in countries with limited resources. Isothermal and conventional PCR-based amplification assays may be alternative solutions. The combination of real-time PCR and serological assays can significantly increase diagnostic efficiency. However, this approach is too expensive for medical institutions in developing countries. Further advances in next-generation sequencing and other innovative technologies such as clustered regularly interspaced short palindromic repeats (CRISPR)-based diagnostic tools may lead to efficient, alternate methods that can be used in point-of-care assays, which may supplement or replace some of the current technologies and improve the diagnostics of fungal infections in developing countries.

Predictive value of gestational age at diagnosis for outcomes in prenatally diagnosed congenital diaphragmatic hernia

OBJECTIVE

To assess the value and accuracy of gestational age at diagnosis in predicting postnatal outcomes of prenatally diagnosed congenital diaphragmatic hernia (CDH).

STUDY DESIGN

The medical records of 158 prenatally diagnosed neonates with CDH from 2008 to 2018 were retrospectively reviewed. Data were analyzed using parametric and nonparametric tests, appropriately.

RESULTS

Gestational age at diagnosis predicted postnatal survival independently. Survival rate at discharge increased when gestational age at diagnosis increased (p < .001). Area under the receiver operator curve for survival for gestational age at diagnosis was 0.74, observed-to-expected lung to head ratio 0.74, and liver herniation 0.76. Patients diagnosed with CDH before 25 gestational weeks had a larger size of the diaphragmatic defect, more need for patch repair, longer duration of mechanical ventilation and hospital stay than those after 25 gestational weeks.

CONCLUSIONS

Gestational age at diagnosis is an independent predictor of CDH prognosis. It has a similar ability to predict survival compared to observed-to-expected lung to head ratio and liver herniation.

Novo&Stitch: accurate reconciliation of genome assemblies via optical maps

Motivation

De novo genome assembly is a challenging computational problem due to the high repetitive content of eukaryotic genomes and the imperfections of sequencing technologies (i.e. sequencing errors, uneven sequencing coverage and chimeric reads). Several assembly tools are currently available, each of which has strengths and weaknesses in dealing with the trade-off between maximizing contiguity and minimizing assembly errors (e.g. mis-joins). To obtain the best possible assembly, it is common practice to generate multiple assemblies from several assemblers and/or parameter settings and try to identify the highest quality assembly. Unfortunately, often there is no assembly that both maximizes contiguity and minimizes assembly errors, so one has to compromise one for the other.

Results

The concept of assembly reconciliation has been proposed as a way to obtain a higher quality assembly by merging or reconciling all the available assemblies. While several reconciliation methods have been introduced in the literature, we have shown in one of our recent papers that none of them can consistently produce assemblies that are better than the assemblies provided in input. Here we introduce Novo&Stitch, a novel method that takes advantage of optical maps to accurately carry out assembly reconciliation (assuming that the assembled contigs are sufficiently long to be reliably aligned to the optical maps, e.g. 50 Kbp or longer). Experimental results demonstrate that Novo&Stitch can double the contiguity (N50) of the input assemblies without introducing mis-joins or reducing genome completeness.

Availability and implementation

Novo&Stitch can be obtained from https://github.com/ucrbioinfo/Novo_Stitch.

Molecular Identification, Genotypic Diversity, Antifungal Susceptibility, and Clinical Outcomes of Infections Caused by Clinically Underrated Yeasts, Candida orthopsilosis, and Candida metapsilosis: An Iranian Multicenter Study (2014-2019)

Despite the increasing occurrence of Candida orthopsilosis and Candida metapsilosis in clinical settings, little is known about their microbiological and clinical properties. Herein, we conducted a national retrospective study (2014–2019) from multiple centers in Iran. Among the 1,770 Candida isolates collected, we identified 600 Candida parapsilosis species complex isolates. Isolate identification was performed by 9-plex PCR, matrix-assisted laser desorption-time of flight mass spectrometry (MALDI-TOF MS), and rDNA sequencing, and antifungal susceptibility testing (AFST) followed CLSI M27-A3/S4; genotyping was performed by amplified fragment length polymorphism (AFLP) analysis; and clinical information was mined. Thirty-one isolates of C. orthopsilosis from various clinical sources, one mixed sample (blood) concurrently containing C. orthopsilosis and C. parapsilosis and one isolate of C. metapsilosis from a nail sample were identified. Although both 9-plex PCR and MALDI-TOF successfully identified all isolates, only 9-plex PCR could identify the agents in a mixed sample. For the C. orthopsilosis isolates, resistance (non-wild type) was noted only for itraconazole (n = 4; 12.5%). Anidulafungin and fluconazole showed the highest and voriconazole had the lowest geometric mean values. AFLP analysis showed three main and four minor genotypes. Interestingly, 90% of nail isolates clustered with 80% of the blood isolates within two clusters, and four blood isolates recovered from four patients admitted to a hospital clustered into two genotypes and showed a high degree of similarity (>99.2%), which suggests that C. orthopsilosis disseminates horizontally. Supported by our data and published case studies, C. orthopsilosis and C. metapsilosis can be linked to challenging clinical failures, and successful outcomes are not always mirrored by in vitro susceptibility. Accordingly, conducting nationwide studies may provide more comprehensive data, which is required for a better prognosis and clinical management of patients.

Follow-Up Report of Laparoscopic Fundoplication in Different Types of Esophageal Hiatal Hernia in Children

Background: Esophageal hiatal hernia can be classified into four types. It has been reported that most complications occurred in type II-IV hernia patients compared with type I hernia. This study aimed to investigate and compare the efficacy, complications, and long-time outcomes after laparoscopic fundoplication between type I and type II-IV hernia patients. Materials and Methods: Medical records of 110 children who underwent laparoscopic fundoplication during 2008-2017 in our institution were retrospectively analyzed. Information of postoperative symptoms, complications, and quality of life (QOL) were compared between different types. Results: All 110 children underwent laparoscopic fundoplication, and none converted to open surgery. Type I and type II-IV each accounted for 50.9% and 42.8%. There was no significant difference in the perioperative data between type I and type II-IV esophageal hiatal hernia. The follow-up information of 81 children was obtained. The scores of postoperative symptoms were comparable between type I and type II-IV group, except the severity score of reflux symptom was higher in type I hernia patients (P = .032). The difference in the incidence of postoperative complications and recurrence after laparoscopic fundoplication between type I and type II-IV hernia was not significant. The QOL in three aspects improved significantly after laparoscopic fundoplication in all types of esophageal hiatal hernia. Conclusions: Laparoscopic fundoplication was an effective approach for all types of esophageal hiatal hernia. Type II-IV hernia could obtain a comparable therapeutic effect and long-time outcome compared with type I hernia despite its increased complexity of the anatomy and the required laparoscopic repair procedure.

TNF-α-Producing Cryptococcus neoformans Exerts Protective Effects on Host Defenses in Murine Pulmonary Cryptococcosis

Tumor necrosis factor alpha (TNF-α) plays a critical role in the control of cryptococcal infection, and its insufficiency promotes cryptococcal persistence. To explore the therapeutic potential of TNF-α supplementation as a booster of host anti-cryptococcal responses, we engineered a C. neoformans strain expressing murine TNF-α. Using a murine model of pulmonary cryptococcosis, we demonstrated that TNF-α-producing C. neoformans strain enhances protective elements of host response including preferential T-cell accumulation and improved Th1/Th2 cytokine balance, diminished pulmonary eosinophilia and alternative activation of lung macrophages at the adaptive phase of infection compared to wild type strain-infected mice. Furthermore, TNF-α expression by C. neoformans enhanced the fungicidal activity of macrophages in vitro. Finally, mice infected with the TNF-α-producing C. neoformans strain showed improved fungal control and considerably prolonged survival compared to wild type strain-infected mice, but could not induce sterilizing immunity. Taken together, our results support that TNF-α expression by an engineered C. neoformans strain while insufficient to drive complete immune protection, strongly enhanced protective responses during primary cryptococcal infection.

Lumbar drainage for the treatment of refractory intracranial hypertension in HIV-negative cryptococcal meningitis

Aim: This study aims to evaluate lumbar drainage (LD) for controlling refractory intracranial hypertension among non-HIV cryptococcal meningitis patients. Patients & methods: A case–control study was designed to compare LD (case) with repeated lumbar puncture (control). Results: Both LD and repeated lumbar puncture can efficiently control refractory intracranial hypertension. LD group showed better clinical symptom remission, such as lower rate of headache, vision disorders, signs of meningeal irritation and conscious disturbance, than control group. LD group was reported with higher intracranial pressure reduction (173.75 ± 17.72 mmH2O) than those among control group (113.50 ± 14.94 mmH2O; p < 0.05). Conclusion: LD is an effective and safe alternative to control refractory intracranial hypertension in HIV-negative cryptococcal meningitis patients.

Validating genome-wide CRISPR-Cas9 function improves screening in the oleaginous yeast Yarrowia lipolytica

Genome-wide mutational screens are central to understanding the genetic underpinnings of evolved and engineered phenotypes. The widespread adoption of CRISPR-Cas9 genome editing has enabled such screens in many organisms, but identifying functional sgRNAs still remains a challenge. Here, we developed a methodology to quantify the cutting efficiency of each sgRNA in a genome-scale library, and in doing so improve screens in the biotechnologically important yeast Yarrowia lipolytica. Screening in the presence and absence of native DNA repair enabled high-throughput quantification of sgRNA function leading to the identification of high efficiency sgRNAs that cover 94% of genes. Library validation enhanced the classification of essential genes by identifying inactive guides that create false negatives and mask the effects of successful disruptions. Quantification of guide effectiveness also creates a dataset from which determinants of CRISPR-Cas9 can be identified. Finally, application of the library identified novel mutations for metabolic engineering of high lipid accumulation.

Molecular characterization and antifungal susceptibility testing of Candida nivariensis from blood samples - an Iranian multicentre study and a review of the literature

PURPOSE

Identification of the emerging yeast species Candida nivariensis among presumptively identified Iranian Candida glabrata isolates.

METHODOLOGY

Clinical C. glabrata species complex isolates from blood (n=71; 33.3 %), urine (n=100; 46.9 %), vaginal swabs (n=20;9.4 %), BAL (n=10; 4.7 %), and sputum (n=12; 5.6 %) from Iran were investigated. Isolates were characterized by CHROMagar, multiplex PCRs, matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS), amplified fragment length polymorphism (AFLP) fingerprinting, internal transcribed spacer (ITS)/large subunit (LSU) rDNA and FKS1/FKS2 sequencing, and the European Committee on Antimicrobial Susceptibility Testing broth microdilution method. A comprehensive literature review was conducted and all the relevant clinical and microbiological data were collected.

RESULTS

Four C. nivariensis isolates were recovered from blood samples of three subjects and were all consistently identified by nine-plex PCR, Bruker MALDI-TOF MS, and LSU and ITS rDNA sequencing. AFLP genotyping clustered the isolates into two groups. Sequencing of the FKS1 and FKS2 hotspots showed no accountable amino acid substitutions. All isolates were susceptible to amphotericin B, fluconazole, itraconazole, posaconazole, voriconazole, anidulafungin and micafungin.

CONCLUSION

In total, 4 out of 213 clinical C. glabrata species complex candidemia isolates were C. nivariensis. Improvement of the BioMerieux Vitek MS database is required to accurately identify C. nivariensis and it is advised to alternatively use CHROMagar and/or PCR-based techniques. As other species within the Nakaseomyces clade may cause infection and showed high MIC values for antifungals, inclusion of their spectra into the MALDI-TOF MS database seems relevant. Due to developing resistance to fluconazole and insufficient efficacy of caspofungin, the combination of catheter removal plus treatment with caspofungin, or voriconazole, or micafungin might be effective for patients.

First fungemia case due to environmental yeast Wickerhamomyces myanmarensis: detection by multiplex qPCR and antifungal susceptibility

AIM

Presenting the first clinical case of Wickerhamomyces myanmarensis.

PATIENTS & METHODS

Yeast cells were isolated from blood and central venous catheter of a 5.5-year-old male subject. API 20C AUX, MALDI-TOF MS, ITS and LSU rDNA sequencing, and our qPCR assay were used for identification and the MIC values were determined by CLSI M27-A3.

RESULTS

ITS and LSU rDNA sequencing identified both isolates as W. myanmarensis, while API 20C AUX and MALDI-TOF MS did not identify them correctly. Our qPCR specifically distinguished W. myanmarensis from W. anomalus. Isolate obtained from blood showed a higher MIC value for fluconazole, voriconazole and posaconazole.

CONCLUSION

Utilization of reliable identification tools might reveal the genuine spectrum of opportunistic yeast species.

Comparison of 21-Plex PCR and API 20C AUX, MALDI-TOF MS, and rDNA Sequencing for a Wide Range of Clinically Isolated Yeast Species: Improved Identification by Combining 21-Plex PCR and API 20C AUX as an Alternative Strategy for Developing Countries

Occurrence of non-Candida albicans Candida (NCAC) species that are associated with elevated MIC values and therapeutic failures are increasing. As a result, timely and accurate means of identification to the species level is becoming an essential part of diagnostic practices in clinical settings. In this study, 301 clinically isolated yeast strains recovered from various anatomical sites [Blood (n = 145), other sites (n = 156)] were used to assess the accuracy and practicality of API 20C AUX and 21-plex PCR compared to MALDI-TOF MS and large subunit rDNA (LSU rDNA). MALDI-TOF MS correctly identified 98.33% of yeast isolates, 100% of top five Candida species, 95.7% of rare yeast species, while 1.3% of isolates were misidentified. API 20C AUX correctly identified 83.7% of yeast isolates, 97.2% of top five Candida species, 61.8% of rare yeast species, while 16.2% of yeast isolates were misidentified. The 21-plex PCR, accurately identified 87.3% of yeast isolates, 100% of top five Candida species, 72% of rare yeast species, but it misidentified 1.3% of rare yeast species while 9.9% of whole yeast isolates were not identified. The combination of rapidity of 21-plex PCR and comprehensiveness of API 20C AUX, led to correct identification of 92% of included yeast isolates. Due to expensiveness of MALDI-TOF MS and sequencing, this combination strategy could be the most accurate and inexpensive alternative identification strategy for developing countries. Moreover, by the advent and development of cost-effective, reliable, and rapid PCR machines that cost 130 US dollars, 21-plex could be integrated in routine laboratories of developing and resource-limited countries to specifically identify 95% causative agents of yeast-related infections in human. Databases of MALDI-TOF MS, API 20C AUX, and the number of target species identified by 21-plex require further improvement to keep up with the diverse spectrum of yeast species.

Ciliochoroidal detachment after Ahmed glaucoma valve implantation: a retrospective study

Background

To investigate the occurrence of ciliochoroidal detachment (CCD), its risk factors and its impact on the success rate after Ahmed glaucoma valve (AGV) implantation.

Methods

This is a retrospective observational study carried out at Eye Hospital of Wenzhou Medical University, Zhejiang, China. Patients with uncontrolled glaucoma who underwent AGV implantation alone or combined with phacoemulsification (AGV-Phaco) in the hospital from April 1, 2013 to July 31, 2016 were included. The preoperative and postoperative CCD was defined when the detachment between ciliary body and choroid was detected by the ultrasound biomicroscopy (UBM) and anterior segment optical coherence tomography (AS-OCT) respectively. The main outcomes included the incidence of CCD and the success rate at 6 months after surgery.

Results

In total, 97 male and 56 female patients were included. CCD was observed in 92 (57.8%) eyes. The glaucoma diagnosis in the Non-CCD and CCD group included primary open angle glaucoma (21(31.3%) vs 33(35.9%)), primary angle closure glaucoma (10(14.9%) vs 13(14.1%)), secondary glaucoma (25(37.3%) vs (28(30.4%)) and so on. The preoperative median IOP (interquartile range) were 21.7(16.0,32.0) mmHg and 23.0(16.0,33.0) mmHg in the Non-CCD group and CCD group. Previous surgical history (95% confidence interval (CI), 1.24 to 13.34; odds ratio (OR) 4.06; p = 0.02) and shorter axial length (95% CI, 0.62 to 0.97 OR 0.78; p = 0.02) were the two risk factors of CCD. The success rate between the CCD and Non-CCD group was not significantly different (64.3% vs 62.5%, p = 0.86) at 6 months.

Conclusions

The incidence of CCD is 57.8% after AGV surgery. Eyes with previous surgical procedure was prone to CCD occurrence and longer axial length was protective against CCD. But at 6 months postoperatively, CCD did not reduce the success rate of AGV surgery and may not be a worrisome complication.

Strain-induced indirect-to-direct bandgap transition in an np-type LaAlO3/SrTiO3(110) superlattice

By applying uniaxial in-plane strains, an indirect-to-direct bandgap transition occurs in the polar LaAlO₃/SrTiO₃ (110) superlattices.

Novel multiplex real-time quantitative PCR detecting system approach for direct detection of Candida auris and its relatives in spiked serum samples

The multidrug-resistant opportunistic yeast species of Candida auris, Candida haemulonii, Candida duobushaemulonii and Candida pseudohaemulonii continue to endanger the healthcare settings around the globe. Due to the lack of a specific qPCR assay for detection of these species from clinical samples, we developed a multiplex qPCR assay. Analytical specificity and sensitivity showed 100% specificity and the sensitivity of up to ten genomes of target species with a high value of reproducibility (R² >0.99). Subsequently, from spiked serum samples, our qPCR specifically could detect up to ten genomes of C. auris and one genome of C. haemulonii, C. duobushaemulonii and C. pseudohaemulonii (R² >0.98). Lack of cross reaction with the human DNA, a high degree of specificity and sensitivity, showed the potential of our multiplex PCR for direct detection of C. auris and closely related species from serum samples of suspected patients. Future studies are warranted to assure its applicability in clinical settings.

Identification of nine cryptic species of Candida albicans, C. glabrata, and C. parapsilosis complexes using one-step multiplex PCR

Background

Candida albicans, Candida glabrata, and Candida parapsilosis are three prevalent causes of candidiasis, worldwide. These species are considered as nine medically important complex species. Limited knowledge about these newly recognized species prompted us to develop a one-step, multiplex PCR to detect and identify them in clinical settings.

Methods

Primers targeting Hyphal Wall Protein I gene for the C. albicans, C. dubliniensis, C. africana, Intergenic Spacer for the C. glabrata, C. nivariensis, C. bracarensis, and Intein and ITS rDNA for the C. parapsilosis, C. orthopsilosis, and C. metapsilosis were designed. Using 168 CBS reference strains and 280 clinical isolates, the specificity and reproducibility of the developed assay were evaluated.

Results

Our developed assay successfully identified and distinguished all the nine species. No cross-reaction with closely- and distantly-related yeast species, Aspergillus species and human DNA was observed, resulting in 100% specificity. The ambiguous results obtained by MALDI-TOF for C. albicans and C. africana were corrected by our 9-plex PCR assay. This assay identified all the cryptic complex species from two test sets from Iran and China, correctly.

Conclusions

Our developed multiplex assay is accurate, specific, cost/time-saving, and works without the tedious DNA extraction steps. It could be integrated into routine clinical laboratories and as a reliable identification tool and has the potential to be implemented into epidemiological studies to broaden the limited knowledge of cryptic species complexes.

Electronic supplementary material

The online version of this article (10.1186/s12879-018-3381-5) contains supplementary material, which is available to authorized users.

YEAST PANEL multiplex PCR for identification of clinically important yeast species: stepwise diagnostic strategy, useful for developing countries

Identification of opportunistic yeasts in developing countries is mainly performed by phenotypic assays, which are time-consuming and prone to errors. Wrong species identification may result in suboptimal treatment and inaccurate epidemiological data. To improve rapidity and accuracy of species identification, a diagnostic strategy using a stepwise "YEAST PANEL multiplex PCR assays" targeting 21 clinically important yeast species of Candida, Trichosporon, Rhodotorula, Cryptococcus, and Geotrichum was designed. Four hundred CBS reference strains were used for optimization and specificity testing. Eight hundred clinical species were prepared in blinded sets for multiplex polymerase chain reaction (PCR) and matrix-assisted laser desorption time of flight mass spectrophotometry (MALDI-TOF MS) investigation. Results obtained from YEAST PANEL multiplex PCR assay were 100% consistent with those of MALDI-TOF MS. Utilization of pure colony testing showed distinct amplicons for each species, thus eliminating the need for DNA extraction. The targeted yeast species of this assay are responsible for 95% of the yeast infections. In conclusion, due to the high accuracy and coverage of a broad range of yeasts, this assay could be useful for identification in routine laboratories and epidemiological studies.

[Comparison of spontaneous correction in thoracic curves after anterior versus posterior selective fusion in Lenke type 5C adolescent idiopathic scoliosis]

Objective: To analyze the long-term results and the influence factors of spontaneous correction of unfused thoracic curves in anterior and posterior selective fusions in Lenke type 5C adolescent idiopathic scoliosis (AIS). Methods: From January 2005 to December 2011, 89 Lenke type 5C AIS patients with a minimum of 5-year follow-up who underwent thoracolumbar/lumbar (TL/L) selective fusion in Spine Surgery of Nanjing Drum Tower Hospital were reviewed.Forty-six patients underwent anterior fusion (anterior group), while 46 underwent posterior fusion (posterior group). The following radiological parameters were measured and analyzed at pre-operation, post-operation, and latest follow-up: curve magnitude of primary thoracolumbar/lumbar and secondary thoracic curve, trunk shift, thoracic apical vertebral translation, upper instrumented vertebra tilt, thoracic kyphosis, proximal junctional angle, sagittal vertical axis. Independent sample t test was used to compare the above parameters between the two groups. Results: Compared with those in posterior group, anterior group were found with less fusion levels (5.4±0.6 vs 5.9±0.8, t=3.318, P=0.001) and longer operation time[(276±28)min vs (186±36)min, t=13.101, P<0.001]. Immediately after surgery, the spinal deformity was significantly corrected in the two groups. The mean spontaneous correction rates of the minor curve were 50%±21% and 56%±20% in anterior and posterior groups, respectively (t=1.489, P=0.140). After a mean follow-up of (6.8±1.7) years in anterior group and (6.3±1.3) years in posterior group, the spontaneous correction rate of minor curve was maintained at 46%±22% and 49%±19%, respectively (t=0.703, P=0.484), with no significant correction loss. Other radiographic parameters were also stably maintained. According to the correlation analysis, the spontaneous correction rate was significantly correlated with upper instrumented vertebra (UIV) tilt in both groups (anterior: r=-0.526, posterior: r=-0.399, both P<0.05). Conclusions: Both anterior and posterior selective fusion can achieve satisfactory spontaneous correction of unfused thoracic curves in Lenke type 5C AIS, with no significant difference between the two surgical approaches. UIV tilt is a key influence factor of spontaneous correction of thoracic curves.

A Simple Colorimetric System for Detecting Target Antigens by a Three-Stage Signal Transformation-Amplification Strategy

Inexpensive, straightforward, and rapid medical diagnostics are becoming increasingly important for disease identification in time- and resource-limited settings. Previous attempts to link oligonucleotide-based aptamers and hammerhead ribozymes to form ligand-induced ribozymes have been successful in identifying a variety of small molecule and protein targets. Isothermal exponential amplification reactions (EXPAR) amplify minute amounts of nucleic acid templates without requiring special instrumentation. We introduce a colorimetric assay that we engineered using an aptamer, hammerhead ribozyme, EXPAR, and peroxidase activity in conjunction with a 3,3',5,5'-tetramethylbenzidine (TMB) substrate. This is a modular signal enhancer system that can be easily modified to detect virtually any chosen analyte target within 5-10 min with minimal technical requirements. Ligand-aptamer binding causes the ribozyme to change conformation and self-cleave. The cleaved ribozyme triggers exponential amplification of a reporter sequence during EXPAR. The amplification products fold into single-stranded DNA guanine quadruplexes that exhibit peroxidase-like activity and can oxidize a colorless TMB substrate into a colored reaction product for visual detection. As a proof of concept, we examined the bronchodilator theophylline versus its chemical analogue, caffeine. We demonstrate linear changes in absorption readout across a wide range of target concentrations (0.5-1000 μM) and the ability to visually detect theophylline at 0.5 μM with an approximately 35-fold increased specificity versus that of caffeine. This three-stage detection system is a versatile platform that has the potential to improve the rapid identification of target analytes.

Elongation of esophageal segments by bougienage stretching technique for long gap esophageal atresia to achieve delayed primary anastomosis by thoracotomy or thoracoscopic repair: A first experience from China

OBJECTIVES

The treatment of long gap esophageal atresia (LGEA) is one of the most challenging congenital malformations in neonatal surgery. A preoperative bougienage stretching technique for elongation of the two segments of esophagus is applied to achieve utilizing the native esophagus to establish esophageal continuity by open or thoracoscopic approach.

METHODS

From January 2015 to May 2017, 12 neonates who suffered from LGEA were admitted to our department. They were divided into 2 groups (A and B) according to their admission time. They all accepted bougienage stretching technique before esophageal anastomosis.

RESULTS

Initially the lengths of esophageal gap in 12 infants ranged from 4 to 7.5 vertebral bodies (M=5.8±1.1). The gap lengths became -1 to 2.5 vertebral bodies after bougienage stretching technique and tension-free anastomosis were performed successfully for all 12 cases: Group A (n=5) by thoracotomy and group B (n=7) by thoracoscopic approach. 12 cases have been followed up for 1-25 months (M=12.4±8.5) after definitive surgery.

CONCLUSIONS

Bougienage stretching technique for LGEA is feasible with satisfactory clinical results. Thoracoscopic approach is a good choice for primary anastomosis in LGEA.

LEVELS OF EVIDENCE

Treatment Study Level IV.

Low-Cost Tetraplex PCR for the Global Spreading Multi-Drug Resistant Fungus, Candida auris and Its Phylogenetic Relatives

Candida auris, C. haemulonii, C. duobushaemulonii, and C. pseudohaemulonii are closely related and highly multidrug resistant yeast pathogens. The high cost and low accuracy of current diagnostics may underestimate their prevalence, especially in medical resource-limited regions. In this study, we used 172 C. auris stains and its relatives and 192 other fungal strains to establish and validate a novel multiplex end-point PCR. A prospective and a retrospective clinical screenings using this assay were further performed in China and Iran respectively. We identified the first isolate of C. pseudohaemulonii in China and the first isolate of C. haemulonii in Iran from 821 clinical isolates in total, without any false positive. Animal models of C. auris and C. haemulonii were established for validation. The overall positive rates of the assay for mice blood and tissue were 28.6 and 92.9%, respectively. Compared with previously developed assays, our assay is more available and affordable to the developing countries, and may contribute to a better understanding of the epidemiology of C. auris and its relatives in these regions.