False-positive detection of Group B Streptococcus (GBS) in chromogenic media due to presence of Enterococcus faecalis in High Vaginal Swabs

Background Group B Streptococcus (GBS) is a gram-positive bacterium and its vaginal colonization is associated with preterm births and neonatal sepsis. Thus, routine screening of GBS in prenatal care before the onset of labour is recommended. Recently chromogenic media have been develop and are found to be useful in rapid and sensitive screening for GBS in vaginal swabs. In the present study we evaluated the performance of chromogenic media for the detection of GBS in vaginal swabs of pregnant Indian women near term. Methodology In this study 201 vaginal swab samples were collected from pregnant women. Swabs were inoculated in chromogenic media (carrot broth).The positive and negative cultures were inoculated on Blood agar and Crome agar plates. The colonies were subjected to 16S rRNA sequencing and gene-specific PCR for confirmation. CAMP and BEA were used for biochemical confirmation. PCR was done on genomic DNA isolated from uncultured vaginal swabs. Result 20/201(9.9%) vaginal swab samples were positive in the carrot broth. 17/20 (85%) and 19/20 (95%) of these samples yielded colonies on Blood agar and Crome agar respectively. Of the 181 carrot broth negative samples 1(0.5%) and 38 (20.9%) yielded colonies on Blood agar and crome agar plates respectively. However 16s rRNA sequencing revealed that none of the 20 carrot broth positive cultures were that of GBS and had sequence similarities to the Enterococcus faecalis. This was also confirmed by using gene specific PCR and BEA positivity. Furthermore, Enterococcus faecalis was detected by PCR in DNA isolated from 57 uncultured vaginal swabs samples, GBS could be detected by PCR only in 4 samples. Conclusion Carrot Broth-based culture can lead to false-positive detection due to the presence of Enterococcus faecalis. Keywords: Streptococcus agalactiae, Infection, PCR, pregnant women, Carrot Broth, Blood agar, Crome agar, Preterm birth, Sepsis

Head-mounted accelerometry accurately detects prey capture in California sea lions

Detecting when and where animals feed is key to understanding their ecophysiology, but our ability to collect these data in marine mammals remains limited. Here, we test a tag-based accelerometry method to detect prey capture in California sea lions. From synchronized underwater video and acceleration data of two trained sea lions, we isolated a combined acceleration and Jerk pattern that reliably indicated prey capture in training datasets. We observed a stereotyped feeding motion in underwater video that included (1) mouth opening while approaching prey; (2) head deceleration to allow initial suction or prey engulfment, and (3) jaw closure. This motion (1–3) was repeated if a prey item was not initially engulfed. This stereotyped feeding motion informed a signal pattern phrase that accurately detected feeding in a training dataset. This phrase required (1) an initial heave-axis Jerk signal surpassing a threshold based on sampling rate; (2) an estimated dynamic surge-axis deceleration signal surpassing −0.7 g beginning within 0.2 s of the initial Jerk signal; and (3) an estimated dynamic surge-axis acceleration signal surpassing 1.0 g within 0.5 s of the beginning of the prior deceleration signal. We built an automated detector in MATLAB to identify and quantify these patterns. Blind tests of this detector on non-training datasets found high true-positive detection rates (91%–100%) with acceleration sampled at 50–333 Hz and low false-positive detection rates (0%–4.8%) at all sampling rates (16–333 Hz). At 32 Hz and below, true-positive detection rates decreased due to attenuation of signal detail. A detector optimized for an adult female was also accurate at 32–100 Hz when tested on an adult male’s data, suggesting the potential future use of a generalized detector in wild subjects. When tested on the same data, a published triaxial Jerk method produced high true-positive detection rates (91–100%) and low-to-moderate false-positive detection rates (15–43%) at ≥ 32 Hz. Using our detector, larger prey elicited longer prey capture duration in both animals at almost all sampling rates 32 Hz or faster. We conclude that this method can accurately detect feeding and estimate relative prey length in California sea lions.

Segmentation Analysis in Powdery Mildew Infested (Sphaerotheca Fuliginea) Cucumber Leaves

In this document, we propose the recognition of powdery mildew in cucumber leaves based on image processing. Two cucumber cycles were established and infested with powdery mildew. As the disease developed, photos were taken to perform the analysis. Two hundred photographs were manually preprocessed eliminating the background and leaving only leaves infested with the disease. The images were segmented using three threshold binarization techniques: gray scale binarization, RGB binarization and K-means algorithm with initially located centroids. The results were compared between the different methods. The gray scale binarization as well as the RGB binarization allowed locating the disease based on a percentage of the lighter shades, although the latter method analyzes each one of the different color layers. The K-means algorithm identified groups with similar characteristics around provided centers. A false positive detection test was also performed with 25 previously processed photographs. The experimental results show that the proposed gray scale binarization method better results for the recognition of the disease than the other methods.

Person Recognition Using Soft Biometric

Global security concerns raised the multiplication of video surveillance devices. Intelligent systems identify the person captured at the different cameras, angles, views, background, and wearing different accessories. Gait is measured at a distance without human cooperation. In this work, gait recognition is increased by concatenating semantic features with traditional features. Combining features are dimensionally reduced and classified using classifiers. This method motivates in future to increase the gait recognition with less false positive detection.

Multicentre post-implementation assessment of the positive-predictive value of SARS-CoV-2 antigen-based point-of-care tests used for asymptomatic screening of continuing care staff

Frequent screening of SARS-CoV-2 among asymptomatic populations using antigen-based point of care tests (APOCT) is occurring globally with limited clinical performance data. The positive predictive value (PPV) of two APOCT used in the asymptomatic screening of SARS-CoV-2 among healthcare workers (HCW) at continuing care (CC) sites across Alberta, Canada was evaluated. Between February 22 and May 2, 2021, CC sites implemented SARS-CoV-2 voluntary screening of their asymptomatic HCW. Onsite testing with Abbott Panbio or BD Veritor occurred on a weekly or twice weekly basis. Positive APOCT were confirmed with a real-time reverse-transcriptase polymerase chain reaction (rRT-PCR) reference method. A total of 71,847 APOCT (17,689 Veritor and 54,158 Panbio) were performed among 369 CC sites. Eighty-seven (0.12%) APOCT were positive, of which 39 (0.05%) confirmed as true positives using rRT-PCR. Use of the Veritor and Panbio resulted in a 76.6% and 30.0% false positive detection, respectively (p<0.001). This corresponded to a 23.4% and 70.0% PPV for the Veritor and Panbio, respectively. Frequent screening of SARS-CoV-2 among asymptomatic HCW in CC, using APOCT, resulted in a very low detection rate and a high detection of false positives. Careful assessment between the risks vs benefits of APOCT programs and prevalence of infection in this population needs to be thoroughly considered before implementation.

Multi-centre post-implementation evaluation of SARS-CoV-2 antigen-based point of care tests used for asymptomatic screening of continuing care healthcare workers

Frequent screening of SARS-CoV-2 among asymptomatic populations using antigen-based point of care tests (APOCT) is occurring globally with limited clinical performance data. The positive predictive value (PPV) of two APOCT used in the asymptomatic screening of SARS-CoV-2 among healthcare workers (HCW) at continuing care (CC) sites across Alberta, Canada was evaluated. Between February 22 and May 2, 2021, CC sites implemented SARS-CoV-2 voluntary screening of their asymptomatic HCW. Onsite testing with Abbott Panbio or BD Veritor occurred on a weekly or twice weekly basis. Positive APOCT were confirmed with a real-time reverse-transcriptase polymerase chain reaction (rRT-PCR) reference method. A total of 71,847 APOCT (17,689 Veritor and 54,158 Panbio) were performed among 369 CC sites. Eighty-seven (0.12%) APOCT were positive, of which 39 (0.05%) confirmed as true positives using rRT-PCR. Use of the Veritor and Panbio resulted in a 76.6% and 30.0% false positive detection, respectively (p<0.001). This corresponded to a 23.4% and 70.0% PPV for the Veritor and Panbio, respectively. Frequent screening of SARS-CoV-2 among asymptomatic HCW in CC, using APOCT, resulted in a very low detection rate and a high detection of false positives. Careful assessment between the risks vs benefits of APOCT programs in this population needs to be thoroughly considered before implementation.

Evaluation of the BD Phoenix CPO detect panel for prediction of Ambler class carbapenemases

Rapid detection of carbapenemases as a cause of resistance is beneficial for infection control and antimicrobial therapy. The BD Phoenix NMIC-502 panel and CPO detect test identifies presence of carbapenemases in Enterobacterales such as Klebsiella pneumoniae and assigns them to Ambler classes. To evaluate the performance of the CPO detect panel, we employed a European collection of 1222 K. pneumoniae including carbapenem non-susceptible and susceptible clinical isolates from 26 countries, for which draft genomes were available after Illumina sequencing and the presence of carbapenemase genes had been identified by ARIBA gene calling. The CPO panel detected 488 out of 494 carbapenemase-encoding isolates as positive and six as negative. One-hundred and two isolates were tested positive for carbapenemase in the absence of any carbapenemase gene. The CPO panel identified 229 out of 230 KPC-positive isolates as carbapenemase producing and classified 62 of these as class A enzyme. Similarly, the CPO panel correctly specified 167 of 182 as class D. Regarding metallo-beta-lactamases, the CPO panel assigned 78 of 90 MBL positive isolates to class B enzymes. The sensitivity of the CPO panel in detecting carbapenemase activity was 99.5%, 97.7% and 98.3% for class A, B and D enzymes, respectively. The sensitivity in assignation to Ambler class A, B and D was 27%, 86% and 91%, respectively. An overall sensitivity of 98.8% and specificity of 86% in unclassified detection of carbapenemases was observed, with frequent false positive detection of carbapenemase producing organisms, thus rendering further confirmatory tests necessary.

Locating Macromolecular Assemblies in Cells by 2D Template Matching with cisTEM

For a more complete understanding of molecular mechanisms, it is important to study macromolecules and their assemblies in the broader context of the cell. This context can be visualized at nanometer resolution in three dimensions (3D) using electron cryo-tomography, which requires tilt series to be recorded and computationally aligned, currently limiting throughput. Additionally, the high-resolution signal preserved in the raw tomograms is currently limited by a number of technical difficulties, leading to an increased false-positive detection rate when using 3D template matching to find molecular complexes in tomograms. We have recently described a 2D template matching approach that addresses these issues by including high-resolution signal preserved in single-tilt images. A current limitation of this approach is the high computational cost that limits throughput. We describe here a GPU-accelerated implementation of 2D template matching in the image processing software cisTEM that allows for easy scaling and improves the accessibility of this approach. We apply 2D template matching to identify ribosomes in images of frozen-hydrated Mycoplasma pneumoniae cells with high precision and sensitivity, demonstrating that this is a versatile tool for in situ visual proteomics and in situ structure determination. We benchmark the results with 3D template matching of tomograms acquired on identical sample locations and identify strengths and weaknesses of both techniques, which offer complementary information about target localization and identity.