Comparison of a real-time multiplex PCR and sequetyping assay for pneumococcal serotyping

BACKGROUND: Pneumococcal serotype identification is essential to monitor pneumococcal vaccine effectiveness and serotype replacement. Serotyping by conventional serological methods are costly, labour-intensive, and require significant technical expertise. We compared two different molecular methods to serotype pneumococci isolated from the nasopharynx of South African infants participating in a birth cohort study, the Drakenstein Child Health Study, in an area with high 13-valent pneumococcal conjugate vaccine (PCV13) coverage. METHODS: A real-time multiplex PCR (rmPCR) assay detecting 21 different serotypes/-groups and a sequetyping assay, based on the sequence of the wzh gene within the pneumococcal capsular locus, were compared. Forty pneumococcal control isolates, with serotypes determined by the Quellung reaction, were tested. In addition, 135 pneumococcal isolates obtained from the nasopharynx of healthy children were tested by both serotyping assays and confirmed by Quellung testing. Discordant results were further investigated by whole genome sequencing of four isolates. RESULTS: Of the 40 control isolates tested, 25 had a serotype covered by the rmPCR assay. These were all correctly serotyped/-grouped. Sequetyping PCR failed in 7/40 (18%) isolates. For the remaining isolates, sequetyping assigned the correct serotype/-group to 29/33 (88%) control isolates. Of the 132/135 (98%) nasopharyngeal pneumococcal isolates that could be typed, 69/132 (52%) and 112/132 (85%) were assigned the correct serotype/-group by rmPCR and sequetyping respectively. The serotypes of 63/132 (48%) isolates were not included in the rmPCR panel. All except three isolates (serotype 25A and 38) were theoretically amplified and differentiated into the correct serotype/-group with some strains giving ambigous results (serotype 13/20, 17F/33C, and 11A/D/1818F). Of the pneumococcal serotypes detected in this study, 69/91 (76%) were not included in the current PCV13. The most frequently identified serotypes were 11A, 13, 15B/15C, 16F and 10A. CONCLUSION: The rmPCR assay performed well for the 21 serotypes/-groups included in the assay. However, in our study setting, a large proportion of serotypes were not detected by rmPCR. The sequetyping assay performed well, but did misassign specific serotypes. It may be useful for regions where vaccine serotypes are less common, however confirmatory testing is advisable

Carbapenem resistance expressed by Gram-negative bacilli isolated from a cohort of Libyan patients

Background and objectives: Carbapenem-resistant Enterobacteriaceae (CRE) and other Gram-negative bacteria are among the most common pathogens responsible for both community and hospital acquired infection. The global spread of cephalosporinases in Enterobacteriaceae has led to the increased use of carbapenems resulting in the emergence and rapid spread of CRE. This has become an alarming public health concern, yet the condition in Libya remains unclear. The aim of this study was to obtain a better understanding of CRE strains prevalent in Libyan patients by investigating their phenotypic characteristics and antibiograms. Methods: Gram-negative bacterial species were collected from Misrata Central Hospital, Misrata Cancer Centre and Privet Pathology Laboratories. Clinical samples and swabs were obtained from hospitalised and non-hospitalised patients and from mechanical ventilation and suction machines. Patients who had received antibiotic therapy for at least three days prior to the study were excluded. The identification and characterization of the isolated species were achieved using the growth characteristics on MacConkey and blood agar, spot tests and API 20E or API 20NE biochemical testing systems. Screening for carbapenem resistance was performed using the disk diffusion method with carbapenem 10 μg and cephalosporin 30 μg disks and minimum inhibitory concentrations (MIC) determined using the Sensititre Gram-negative Xtra plate format (GNX2F). All strains demonstrating resistance or reduced susceptibility to one of the four carbapenems were subjected to carbapenememase activity detection using the RAPIDEC CARBA NP test, Modified Hodge test and carbapenem inactivation methods. Results: A total of one hundred and forty isolates representing fourteen bacterial species were isolated from 140 non-duplicated specimens. Clinical specimens included urine samples (96/140, 68.57%), sputum (15/140, 10.71%), surgical wound swabs (18/140, 12.85%), foot swabs from diabetes mellitus (DM) patients (6/140, 4.29%), ear swabs (3/140, 2.14%) and wound swabs (2/140, 1.43%). Thirty-four (24.29%) isolates demonstrated resistance to at least one of the four carbapenems with Klebsiella pneumoniae representing 73.53% (25 isolates) of all carbapenem resistant species, followed by 8.82% for Pseudomonas aeruginosa (3 isolates), 5.88% for both Proteus mirabilis (2 isolates) and Escherichia coli (2 isolates) and 2.94% for both Citrobacter koseri (1 isolate) and Rahnella aquatilis (1 isolate). The other isolates were either susceptible or cephalosporinase producers. Conclusion: This study has revealed the high rate of carbapenem resistance amongst Libyan patients and emphasizes the crucial need for accurate screening, identification and susceptibility testing to prevent further spread of nosocomial and community acquired resistance. This may be achieved through the establishment of antibiotic stewardship programmes along with firm infection control practices.National Research Foundation of South Africa; Libyan GovernmentWeb of Scienc

SARS-CoV-2 seroprevalence in pregnant women in Kilifi, Kenya from March 2020 to March 2022

BackgroundSeroprevalence studies are an alternative approach to estimating the extent of transmission of SARS-CoV-2 and the evolution of the pandemic in different geographical settings. We aimed to determine the SARS-CoV-2 seroprevalence from March 2020 to March 2022 in a rural and urban setting in Kilifi County, Kenya.MethodsWe obtained representative random samples of stored serum from a pregnancy cohort study for the period March 2020 to March 2022 and tested for antibodies against the spike protein using a qualitative SARS-CoV-2 ELISA kit (Wantai, total antibodies). All positive samples were retested for anti-SARS-CoV-2 anti-nucleocapsid antibodies (Euroimmun, ELISA kits, NCP, qualitative, IgG) and anti-spike protein antibodies (Euroimmun, ELISA kits, QuantiVac; quantitative, IgG).ResultsA total of 2,495 (of 4,703 available) samples were tested. There was an overall trend of increasing seropositivity from a low of 0% [95% CI 0–0.06] in March 2020 to a high of 89.4% [95% CI 83.36–93.82] in Feb 2022. Of the Wantai test-positive samples, 59.7% [95% CI 57.06–62.34] tested positive by the Euroimmun anti-SARS-CoV-2 NCP test and 37.4% [95% CI 34.83–40.04] tested positive by the Euroimmun anti-SARS-CoV-2 QuantiVac test. No differences were observed between the urban and rural hospital but villages adjacent to the major highway traversing the study area had a higher seroprevalence.ConclusionAnti-SARS-CoV-2 seroprevalence rose rapidly, with most of the population exposed to SARS-CoV-2 within 23 months of the first cases. The high cumulative seroprevalence suggests greater population exposure to SARS-CoV-2 than that reported from surveillance data

Development of a real-time ECG signal transmission monitoring algorithm

This research will focus on the creation of a simulated real-time ECG signal transmission Algorithm. A MATLAB program would be created to implement the algorithm and monitor the heart rate of the patient. The study focuses on the implementation of Electrocardiograms (ECG) through simulation and would receive the data through a transmitter to a receiver in real-time. The researchers tackled this topic because of its timeliness in present time society wherein most people neglect their physical health. The researchers will solve this problem through a simulation of an ECG signal using the Matrix Laboratory (MATLAB) software. The system will utilize an ECG sampled signal that was converted digitally so that it could be manipulated by MATLAB. An FSK line encoder will be used, and an additive white Gaussian noise will be applied to simulate real-life noise. The expected results will show that the simulation that will be carried out will create an accurate result with a good signal resolution. This study will prove that the MATLAB software is capable of transmitting and receiving ECG signals. © 2020, World Academy of Research in Science and Engineering. All rights reserved

Computer vision on a parking management and vehicle inventory system

Over time, scientists and engineers have developed technology that has improved everyday living. For every invention, they have found to reinvent it and create a better version of it. An example would be parking lots. From the usual time-in-time-out system; window cashier to parking spot back to window cashier, the hassle of this cycle was reduced through the use of license plate recognition which this study tackled. License plate identification technology has become a useful factor in different issues like parking management, vehicle owner recognition, etc. Computer vision has provided a means to reduce manual labor in parking lots by replacing them with sensors and scanners which would take over. This would be beneficial to the company as this technology would require minimal maintenance. Through image processing and enhancement, the license plates of these cars could be taken account of in real-time and this data could be used to generate the parking bills given the time-in and a time-out of the vehicle. This paper aimed to tackle the problems of car management and to further simplify the parking system. © 2020, World Academy of Research in Science and Engineering. All rights reserved

Design and evaluation of a multiple amplitude shift keyed bit to audio tone line encoder and decoder for ASCII character communications

This paper focused on the integration of line coding and nonlinear mixing in digital communication systems. The researcher\u27s implementation of a bit-to-audio-tone encoder with a respective decoder. The encoder received a message from the user. The message that was inputted could be a symbol, and after it was fed into the system, it then produced audio. If the receiving end has the decoder, the audio when then be translated back to the original message. This study has benefits in the field of security systems because data can be accessed or hacked by those that have the skillset to do so. This digital communication system could be used to send information to a certain person, and since only that person has the digital decoder, only he/she can access the data. To others, the system would only produce an audio tune that would be unrecognizable by those receive it if they do not have the decoder. This research aimed to create a safer way to send and receive sensitive information without unwanted third parties to decipher it. © 2020 Asian Research Publishing Network (ARPN)

Effect of dielectric substrate on dipole antenna directivity

© 2019, World Academy of Research in Science and Engineering. All rights reserved. This paper aimed to determine how the directivity was affected by the dielectric substrate in the dipole antenna. The researchers had to choose different substrates and specific property of antennas in order to produce this study. Given all these substrates, the study focused on which of these would produce the best results that would be beneficial to antennas of a certain function. For this case, it is the directivity of the antenna that is being researched on. Through the use of the Matrix Laboratory (MATLAB) software, the researchers were able to conduct a comparative study on these different substrates to obtain their directivities. After the researchers conducted the simulation, the dielectric substrate, Fused Quartz was found to have the least value in directivity while Air had the highest directivity. Additionally, the researchers were able to deduce that the lower the constant of the material, the higher the directivity of the material. This showed that the relationship between the two variables was inversely proportional

NGS data and assembly metrics.

<p>NGS data and assembly metrics.</p

Concordance of molecular serotyping results of pneumococcal control strains.

<p>^armPCR: real-time Multiplex PCR.</p><p>N/A* = serotype not included in the rmPCR panel.</p><p>No ID ^b. = sequence identity of ≤98% with sequences in GenBank.</p><p>Neg^c = negative sequetyping PCR result.</p><p>^dThe Sequetyping assay mistyped serotype 18C as 18B.</p><p>Concordance of molecular serotyping results of pneumococcal control strains.</p

Similarity of 16F-like capsular polysaccharide (<i>cps</i>) gene loci.

<p>Sequences from pneumococci serotyped as 16F Quellung but sequetyped as 9V was compared to reference 9V (CR931648) and 16F (CR931668) <i>cps</i> sequences. Artemis Comparison Tool (ACT) was used to generate and view gene homology. The top lines represent the forward and reverse strand of a serotype 9v reference, the middle lines represent the queried 16F strain and the bottom lines shows the 16F reference. The portion of the <i>wzh</i> gene that is amplified by the sequetyping assay is shown by the blue rectangle. The clear blocks below the blue box shows regions were the genes that are not similar. BLASTN matches are shown as red bands between sequences, indicating the degree of similarity between the sequences.</p