rapid identification
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Molecules ◽  
2022 ◽  
Vol 27 (2) ◽  
pp. 549
Mariana Santos-Rivera ◽  
Amelia R. Woolums ◽  
Merrilee Thoresen ◽  
Florencia Meyer ◽  
Carrie K. Vance

Bovine respiratory syncytial virus (BRSV) is a major contributor to respiratory disease in cattle worldwide. Traditionally, BRSV infection is detected based on non-specific clinical signs, followed by reverse transcriptase-polymerase chain reaction (RT-PCR), the results of which can take days to obtain. Near-infrared aquaphotomics evaluation based on biochemical information from biofluids has the potential to support the rapid identification of BRSV infection in the field. This study evaluated NIR spectra (n = 240) of exhaled breath condensate (EBC) from dairy calves (n = 5) undergoing a controlled infection with BRSV. Changes in the organization of the aqueous phase of EBC during the baseline (pre-infection) and infected (post-infection and clinically abnormal) stages were found in the WAMACS (water matrix coordinates) C1, C5, C9, and C11, likely associated with volatile and non-volatile compounds in EBC. The discrimination of these chemical profiles by PCA-LDA models differentiated samples collected during the baseline and infected stages with an accuracy, sensitivity, and specificity >93% in both the calibration and validation. Thus, biochemical changes occurring during BRSV infection can be detected and evaluated with NIR-aquaphotomics in EBC. These findings form the foundation for developing an innovative, non-invasive, and in-field diagnostic tool to identify BRSV infection in cattle.

Diagnostics ◽  
2022 ◽  
Vol 12 (1) ◽  
pp. 196
Junji Hosokawa-Muto ◽  
Yukiko Sassa-O’Brien ◽  
Yoshihito Fujinami ◽  
Hiroaki Nakahara

When examining infectious samples, rapid identification of the pathogenic agent is required for diagnosis and treatment or for investigating the cause of death. In our previous study, we applied exhaustive amplification using non-specific primers (the rapid determination system of viral genome sequences, the RDV method) to identify the causative virus via swab samples from a cat with a suspected viral infection. The purpose of the current study is to investigate suitable methods for the rapid identification of causative pathogens from infected tissue samples. First, the influenza virus was inoculated into mice to prepare infected tissue samples. RNA extracted from the mouse lung homogenates was transcribed into cDNA and then analyzed using the RDV method and next-generation sequencing, using MiSeq and MinION sequencers. The RDV method was unable to detect the influenza virus in the infected tissue samples. However, influenza virus reads were detected using next-generation sequencing. Comparing MiSeq and MinION, the time required for library and sequence preparation was shorter for MinION sequencing than for MiSeq sequencing. We conclude that when a causative virus needs to be rapidly identified from an infectious sample, MinION sequencing is currently the method of choice.

PLoS ONE ◽  
2022 ◽  
Vol 17 (1) ◽  
pp. e0262551
Ayman Elbehiry ◽  
Musaad Aldubaib ◽  
Osamah Al Rugaie ◽  
Eman Marzouk ◽  
Marwan Abaalkhail ◽  

Brucellae are intracellular sneaky bacteria and they can elude the host’s defensive mechanisms, resulting in therapeutic failure. Therefore, the goal of this investigation was to rapid identification of Brucella species collected from animals and humans in Saudi Arabia, as well as to evaluate their resistance to antibiotics. On selective media, 364 animal samples as well as 70 human blood samples were cultured. Serological and biochemical approaches were initially used to identify a total of 25 probable cultured isolates. The proteomics of Brucella species were identified using the MALDI Biotyper (MBT) system, which was subsequently verified using real-time polymerase chain reaction (real-time PCR) and microfluidic electrophoresis assays. Both Brucella melitensis (B. melitensis) and Brucella abortus (B. abortus) were tested for antimicrobial susceptibility using Kirby Bauer method and the E-test. In total, 25 samples were positive for Brucella and included 11 B. melitensis and 14 B. abortus isolates. Twenty-two out of 25 (88%) and 24/25 (96%) of Brucella strains were recognized through the Vitek 2 Compact system. While MBT was magnificently identified 100% of the strains at the species level with a score value more than or equal to 2.00. Trimethoprim-sulfamethoxazole, rifampin, ampicillin-sulbactam, and ampicillin resistance in B. melitensis was 36.36%, 31.82%, 27.27%, and 22.70%, respectively. Rifampin, trimethoprim-sulfamethoxazole, ampicillin, and ampicillin-sulbactam resistance was found in 35.71%, 32.14%, 32.14%, and 28.57% of B. abortus isolates, correspondingly. MBT confirmed by microfluidic electrophoresis is a successful approach for identifying Brucella species at the species level. The resistance of B. melitensis and B. abortus to various antibiotics should be investigated in future studies.

2022 ◽  
Vol 7 (1) ◽  
pp. 7
Rizza Antoinette Yap So ◽  
Romina A. Danguilan ◽  
Eric Chua ◽  
Mel-Hatra I. Arakama ◽  
Joann Kathleen B. Ginete-Garcia ◽  

Rapid identification of patients likely to develop pulmonary complications in severe leptospirosis is crucial to prompt aggressive management and improve survival. The following article is a cohort study of leptospirosis patients admitted at the National Kidney and Transplant Institute (NKTI). Logistic regression was used to predict pulmonary complications and obtain a scoring tool. The Kaplan–Meir method was used to describe survival rates. Among 380 patients with severe leptospirosis and kidney failure, the overall mortality was 14%, with pulmonary hemorrhage as the most common cause. In total, there were 85 (22.4%) individuals who developed pulmonary complications, the majority (95.3%) were observed within three days of admission. Among the patients with pulmonary complications, 56.5% died. Patients placed on mechanical ventilation had an 82.1% mortality rate. Multivariate analyses showed that dyspnea (OR = 28.76, p < 0.0001), hemoptysis (OR = 20.73, p < 0.0001), diabetes (OR = 10.21, p < 0.0001), renal replacement therapy (RRT) requirement (OR = 6.25, p < 0.0001), thrombocytopenia (OR = 3.54, p < 0.0029), and oliguria/anuria (OR = 3.15, p < 0.0108) were significantly associated with pulmonary complications. A scoring index was developed termed THe-RADS score (Thrombocytopenia, Hemoptysis, RRT, Anuria, Diabetes, Shortness of breath). The odds of developing pulmonary complications were 13.90 times higher among patients with a score >2 (63% sensitivity, 88% specificity). Pulmonary complications in severe leptospirosis with kidney failure have high mortality and warrant timely and aggressive management.

2022 ◽  
Xinsheng Nan ◽  
Sven Hoehn ◽  
Patrick Hardinge ◽  
Shrinivas N Dighe ◽  
John Ukeri ◽  

The COVID-19 pandemic continues to pose a threat to the general population. The ongoing vaccination programs provide protection to individuals and facilitate the opening of society and a return to normality. However, emergent and existing SARS-CoV-2 variants capable of evading the immune system endanger the efficacy of the vaccination strategy. To preserve the efficacy of SARS-CoV-2 vaccination globally, aggressive and effective surveillance for known and emerging SARS-CoV-2 Variants of Concern (VOC) is required. Rapid and specific molecular diagnostics can provide speed and coverage advantages compared to genomic sequencing alone, benefitting the public health response and facilitating VOC containment. In this work, we expand the recently developed SARS-CoV-2 CRISPR-Cas detection technology (SHERLOCK) to allow rapid and sensitive discrimination of VOCs, that can be used at point of care and/or implemented in the pipelines of small or large testing facilities, and even determine proportion of VOCs in pooled population-level wastewater samples. This technology aims to complement the ongoing sequencing efforts to allow facile and, crucially, rapid identification of individuals infected with VOCs to help break infection chains. Here, we show the optimisation of our VarLOCK assays (Variant-specific SHERLOCK) for multiple specific mutations in the S gene of SARS-CoV-2 and validation with samples from the Cardiff University Testing Service. We also show the applicability of VarLOCK to national wastewater surveillance of SARS-CoV-2 variants. In addition, we show the rapid adaptability of the technique for new and emerging VOCs such as Omicron.

Sensors ◽  
2022 ◽  
Vol 22 (2) ◽  
pp. 439
Jinjun Duan ◽  
Zhouchi Liu ◽  
Yiming Bin ◽  
Kunkun Cui ◽  
Zhendong Dai

In the robot contact operation, the robot relies on the multi-dimensional force/torque sensor installed at the end to sense the external contact force. When the effective load and speed of the robot are large, the gravity/inertial force generated by it will have a non-negligible impact on the output of the force sensor, which will seriously affect the accuracy and effect of the force control. The existing identification algorithm time is often longer, which also affects the efficiency of force control operations. In this paper, a self-developed multi-dimensional force sensor with integrated gravity/inertial force sensing function is used to directly measure the resultant force. Further, a method for the rapid identification of payload based on excitation trajectory is proposed. Firstly, both a gravity compensation algorithm and an inertial force compensation algorithm are introduced. Secondly, the optimal spatial recognition pose based on the excitation trajectory was designed, and the excitation trajectory of each joint is represented by a finite Fourier series. The least square method is used to calculate the identification parameters of the load, the gravity, and inertial force. Finally, the experiment was verified on the robot. The experimental results show that the algorithm can quickly identify the payload, and it is faster and more accurate than other algorithms.

2022 ◽  
Vol 21 (1) ◽  
Vanessa S. Terra ◽  
Marta Mauri ◽  
Thippeswamy H. Sannasiddappa ◽  
Alexander A. Smith ◽  
Mark P. Stevens ◽  

Abstract Background Campylobacter is an animal and zoonotic pathogen of global importance, and a pressing need exists for effective vaccines, including those that make use of conserved polysaccharide antigens. To this end, we adapted Protein Glycan Coupling Technology (PGCT) to develop a versatile Escherichia coli strain capable of generating multiple glycoconjugate vaccine candidates against Campylobacter jejuni. Results We generated a glycoengineering E. coli strain containing the conserved C. jejuni heptasaccharide coding region integrated in its chromosome as a model glycan. This methodology confers three advantages: (i) reduction of plasmids and antibiotic markers used for PGCT, (ii) swift generation of many glycan-protein combinations and consequent rapid identification of the most antigenic proteins or peptides, and (iii) increased genetic stability of the polysaccharide coding-region. In this study, by using the model glycan expressing strain, we were able to test proteins from C. jejuni, Pseudomonas aeruginosa (both Gram-negative), and Clostridium perfringens (Gram-positive) as acceptors. Using this pgl integrant E. coli strain, four glycoconjugates were readily generated. Two glycoconjugates, where both protein and glycan are from C. jejuni (double-hit vaccines), and two glycoconjugates, where the glycan antigen is conjugated to a detoxified toxin from a different pathogen (single-hit vaccines). Because the downstream application of Live Attenuated Vaccine Strains (LAVS) against C. jejuni is to be used in poultry, which have a higher body temperature of 42 °C, we investigated the effect of temperature on protein expression and glycosylation in the E. coli pgl integrant strain. Conclusions We determined that glycosylation is temperature dependent and that for the combination of heptasaccharide and carriers used in this study, the level of PglB available for glycosylation is a step limiting factor in the glycosylation reaction. We also demonstrated that temperature affects the ability of PglB to glycosylate its substrates in an in vitro glycosylation assay independent of its transcriptional level.

2022 ◽  
Vol 9 ◽  
Maoyi Zhang ◽  
Changqing Ding ◽  
Shuli Guo

Tracheobronchial diverticula (TD) is a common cystic lesion that can be easily neglected; hence accurate and rapid identification is critical for later diagnosis. There is a strong need to automate this diagnostic process because traditional manual observations are time-consuming and laborious. However, most studies have only focused on the case report or listed the relationship between the disease and other physiological indicators, but a few have adopted advanced technologies such as deep learning for automated identification and diagnosis. To fill this gap, this study interpreted TD recognition as semantic segmentation and proposed a novel attention-based network for TD semantic segmentation. Since the area of TD lesion is small and similar to surrounding organs, we designed the atrous spatial pyramid pooling (ASPP) and attention mechanisms, which can efficiently complete the segmentation of TD with robust results. The proposed attention model can selectively gather features from different branches according to the amount of information they contain. Besides, to the best of our knowledge, no public research data is available yet. For efficient network training, we constructed a data set containing 218 TD and related ground truth (GT). We evaluated different models based on the proposed data set, among which the highest MIOU can reach 0.92. The experiments show that our model can outperform state-of-the-art methods, indicating that the deep learning method has great potential for TD recognition.

Derek T. Armstrong ◽  
Stefanie Fisher ◽  
Marissa Totten ◽  
Matthew Schwartz ◽  
Devasena Gnanashanmugam ◽  

The identification of the M. tuberculosis complex (MTBC) from smear positive broth cultures can be achieved using several methods including both lab-developed and commercially available molecular assays. In the United States, a commercially available probe-based assay has been used for over a decade by many laboratories for identification of MTBC directly from AFB smear positive broth cultures, including those recovered from the MGIT 960 system. However, recent difficulties in obtaining probe kits for identification resulted in mycobacteriology laboratories looking for alternative platforms to provide for rapid identification of MTBC and detection of rifampicin resistance. The Xpert® MTB/RIF test (Cepheid, Sunnyvale, Ca) has shown high sensitivity for the diagnosis of MTBC from pulmonary specimens but is not often used for identification directly from smear positive, MGIT 960 broth cultures (Becton Dickinson, Sparks, Md). We sought to validate the Xpert MTB/RIF test for use with AFB smear positive MGIT 960 cultures in a clinical hospital setting. Overall, the assay showed a categorical agreement of 100% for identification of MTBC and detection of rifampin resistance. No false positive results or cross-reactivity were noted. Findings indicate that the Xpert MTB/RIF test may be suitable as a rapid replacement for identification of MTBC and detection of rifampicin resistance from AFB smear positive MGIT 960 broth cultures.

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