“Friendly reminder: hi! It is that time again ☺”: understanding PMTCT care text message design preferences amongst pre- and post-partum women and their male partners

Background Prevention of mother-to-child HIV transmission (PMTCT) services in Kenya can be strengthened through the delivery of relevant and culturally appropriate SMS messages. Methods This study reports on the results of focus groups conducted with pre and postnatal women living with HIV (5 groups, n = 40) and their male partners (3 groups, n = 33) to elicit feedback and develop messages to support HIV+ women’s adherence to ART medication, ANC appointments and a facility-based birth. The principles of message design informed message development. Results Respondents wanted ART adherence messages that were low in verbal immediacy (ambiguous), came from an anonymous source, and were customized in timing and frequency. Unlike other studies, low message immediacy was prioritized over customization of message content. For retention, participants preferred messages with high verbal immediacy—direct appointment reminders and references to the baby—sent infrequently from a clinical source. Conclusion Overall, participants favored content that was brief, cheerful, and emotionally appealing.

Antimicrobial Activity of the Circular Bacteriocin AS-48 against Clinical Multidrug-Resistant Staphylococcus aureus

The treatment and hospital-spread-control of methicillin-resistant Staphylococcus aureus (MRSA) is an important challenge since these bacteria are involved in a considerable number of nosocomial infections that are difficult to treat and produce prolonged hospitalization, thus also increasing the risk of death. In fact, MRSA strains are frequently resistant to all β-lactam antibiotics, and co-resistances with other drugs such as macrolides, aminoglycosides, and lincosamides are usually reported, limiting the therapeutical options. To this must be added that the ability of these bacteria to form biofilms on hospital surfaces and devices confer high antibiotic resistance and favors horizontal gene transfer of genetic-resistant mobile elements, the spreading of infections, and relapses. Here, we genotypically and phenotypically characterized 100 clinically isolated S. aureus for their resistance to 18 antibiotics (33% of them were OXA resistant MRSA) and ability to form biofilms. From them, we selected 48 strains on the basis on genotype group, antimicrobial-resistance profile, and existing OXA resistance to be assayed against bacteriocin AS-48. The results showed that AS-48 was active against all strains, regardless of their clinical source, genotype, antimicrobial resistance profile, or biofilm formation capacity, and this activity was enhanced in the presence of the antimicrobial peptide lysozyme. Finally, we explored the effect of AS-48 on formed S. aureus biofilms, observing a reduction in S. aureus S-33 viability. Changes in the matrix structure of the biofilms as well as in the cell division process were observed with scanning electron microscopy in both S-33 and S-48 S. aureus strains.

Genomic Insights into a Colistin-Resistant Uropathogenic Escherichia coli Strain of O23:H4-ST641 Lineage Harboring mcr-1.1 on a Conjugative IncHI2 Plasmid from Egypt

The reintroduction of colistin, a last-resort antibiotic for multidrug-resistant pathogens, resulted in the global spread of plasmid-mediated mobile colistin resistance (mcr) genes. Our study investigated the occurrence of colistin resistance among Escherichia coli isolated from patients with urinary tract infections admitted to a teaching hospital in Egypt. Out of 67 isolates, three isolates were colistin-resistant, having a minimum inhibitory concentration of 4 µg/mL and possessing the mcr-1 gene. A double mechanism of colistin resistance was detected; production of mcr-1 along with amino acid substitution in PmrB (E123D and Y358N) and PmrA (G144S). Broth mating experiments inferred that mcr-1 was positioned on conjugative plasmids. Whole-genome sequencing of EC13049 indicated that the isolate belonged to O23:H4-ST641 lineage and to phylogroup D. The mcr-1-bearing plasmid corresponded to IncHI2 type with a notable similarity to other E. coli plasmids previously recovered from Egypt. The unbanned use of colistin in the Egyptian agriculture sector might have created a potential reservoir for the mcr-1 gene in food-producing animals that spread to humans. More proactive regulations must be implemented to prevent further dissemination of this resistance. This is the first characterization of mcr-1-carrying IncHI2:ST4 plasmid recovered from E. coli of a clinical source in Egypt.

Establishment of Optimal Housekeeping Genes for Urinary Extracellular Vesicle Based Biomarker Development: A Step Towards Non-Invasive Diagnostics.

BackgroundRecent years have witnessed a growing interest in employing urine as a clinical source of renal pathology biomarkers. Urinary extracellular vesicles(UEVs) hold cellular RNAs, including small RNA and micro RNA. Quantitative polymerase chain reaction (qPCR) is one of the most sensitive methods for evaluating gene expression, which depends on comparative analysis with reference/house-keeping genes. However, reliable interpretation of UEVs gene expression data is biased due to the lack of reported ideal house-keeping reference-genes in UEVs.MethodsUEVs were isolated from 40 healthy human controls using Polyethylene glycol (P.E.G. Mn6000) based precipitation. UEVs were characterized by biophysical and biochemical assays. At the molecular biology level, the expression and stability of five commonly used housekeeping genes B2M, RPL13A, PPIA, HMBS, and GAPDH, were considered for comparing and finding out ideal reference gene. Data were analyzed using four practical algorithmic approaches, including Norm Finder, GeNorm, Best Keeper, and the Delta Ct for reference gene evaluation integrated with RefFinder. The final ranking of stable genes is derived from the weighted geometric means of all the above algorithms.Results12% PEG isolated UEVs were round and cup-shaped, ranging from 30 - 100nm, as per electron microscopy, nanoparticle-tracking-analysis, and dynamic-light-scattering profile. The functional purity of UEVs was determined with their acetylcholine esterase and Dipeptidyl peptidase-IV activity. RefFinder established the stability index of housekeeping genes. B2M and RPL13A genes were identified as stable genes with a mean stability score of 1.5(Genorm) and below 1 (Norm finder), indicating a reduced gene expression variation. ConclusionsThe comprehensive ranking analysis identified B2M and RPL13A as optimal reference genes for UEVs based gene expression studies.

Patient Cohort Identification on Time Series Data Using the OMOP Common Data Model

Background The identification of patient cohorts for recruiting patients into clinical trials requires an evaluation of study-specific inclusion and exclusion criteria. These criteria are specified depending on corresponding clinical facts. Some of these facts may not be present in the clinical source systems and need to be calculated either in advance or at cohort query runtime (so-called feasibility query). Objectives We use the Observational Medical Outcomes Partnership (OMOP) Common Data Model (CDM) as the repository for our clinical data. However, Atlas, the graphical user interface of OMOP, does not offer the functionality to perform calculations on facts data. Therefore, we were in search for a different approach. The objective of this study is to investigate whether the Arden Syntax can be used for feasibility queries on the OMOP CDM to enable on-the-fly calculations at query runtime, to eliminate the need to precalculate data elements that are involved with researchers' criteria specification. Methods We implemented a service that reads the facts from the OMOP repository and provides it in a form which an Arden Syntax Medical Logic Module (MLM) can process. Then, we implemented an MLM that applies the eligibility criteria to every patient data set and outputs the list of eligible cases (i.e., performs the feasibility query). Results The study resulted in an MLM-based feasibility query that identifies cases of overventilation as an example of how an on-the-fly calculation can be realized. The algorithm is split into two MLMs to provide the reusability of the approach. Conclusion We found that MLMs are a suitable technology for feasibility queries on the OMOP CDM. Our method of performing on-the-fly calculations can be employed with any OMOP instance and without touching existing infrastructure like the Extract, Transform and Load pipeline. Therefore, we think that it is a well-suited method to perform on-the-fly calculations on OMOP.

The Inhibition Potentials of Different Honey against Staphylococcus aureus, Escherichia coli and Bacillus species Isolated from Clinical Source

As a result of the increased prevalence of antibiotic resistance among different bacteria, different plants and other natural products have been studied and found to be highly effective against pathogenic bacteria. Honey, over the years has been used as an antibacterial agent to treat certain infections caused by bacteria and is believed to be effective especially in rural areas. This study was thus aimed at comparing the effect of different honey samples against some pathogenic bacteria (Escherichia coli, Staphylococcus aureus and Bacillus cereus) isolated from clinical source. This study was carried out in the microbiology laboratory, department of microbiology Rivers State University Nigeria from January 2018 to August 2019. The antibacterial sensitivity test was carried out using agar well diffusion method while the Minimum inhibitory concentration and Minimum bactericidal concentration were determined using broth tube micro dilution technique in two fold dilution. The inhibition efficiency of the honey samples on the test organisms increased with increasing concentration from 20 to 100% as 100% concentration had the highest zone of inhibition. Staphylococcus aureus (6.33 mm – 26.33 mm) was the most sensitive to the honey samples while Bacillus cereus (0.00 – 19.67 mm) was less sensitive. At concentrations of 20 – 80%, raw and Rowse honey were more effective on E. coli compared to Princenic Global honey, while at 100%, Princenic Global honey was more effective on Staphylococcus aureus. Raw and Rowse honey were more effective at 20 -60% concentrations followed by Princenic Global honey; whereas at 80 -100% concentrations, Raw and Princenic Global honey were more effective. Bacillus cereus was resistancet to the honey samples at 20 – 60% but sensitive at 80 – 100% concentrations to Rowse, Raw and Princenic Global honey. The inhibition efficiency of the honey samples on the growth of the tested organisms was found to be dependent on the concentration and type of honey used, as well as they type of organism tested. The result of the minimum inhibitory and minimum bactericidal concentration showed that Staphylococcus aureus was inhibited most at a lower concentration of 25% compared to other bacteria isolates. All honey samples tested did not show any bactericidal effect but was bacteriostatic to some of the tested organisms. Pharmacological standardization and clinical evaluation on the effect of honey is essential before honey can be used as a preventive and curative measure to common diseases related to the tested bacterial species.

Intra-species variation within Lactobacillus rhamnosus correlates to beneficial or harmful outcomes: lessons from the oral cavity

Background The origin of most of the Lactobacillus rhamnosus genome sequences lodged in NCBI can be traced to food and faecal isolates followed by blood and tissue sites but with minimal representation from oral and vaginal isolates. However, on the L. rhamnosus phylogenetic tree no apparent clade is linked to the origin of isolation or to the relevant clinical source, except for a distinct clade exclusively shared by L. rhamnosus isolates from early stages of dental pulp infection (LRHMDP2 and LRHMDP3) and from bronchoalveolar lavage (699_LRHA and 708_LRHA) from a critical care patient. These L. rhamnosus strains, LRHMDP2, LRHMDP3, 699_LRHA and 708_LRHA isolated from different continents, display closest genome neighbour gapped identity of 99.95%. The aim of this study was to define a potentially unique complement of genes of clinical relevance shared between these L. rhamnosus clinical isolates in comparison to probiotic L. rhamnosus strains. Results In this analysis we used orthologous protein identification tools such as ProteinOrtho followed by tblastn alignments to identify a novel tyrosine protein phosphatase (wzb)-tyrosine-protein kinase modulator EpsC (wzd)- synteny exopolysaccharide (EPS) cluster. This EPS cluster was specifically conserved in a clade of 5 clinical isolates containing the four L. rhamnosus clinical isolates noted above and Lactobacillus spp. HMSC077C11, a clinical isolate from a neck abscess. The EPS cluster was shared with only two other strains, L. rhamnosus BPL5 and BPL15, which formed a distant clade on the L. rhamnosus phylogenetic tree, with a closest genome neighbour gapped identity of 97.51% with L. rhamnosus LRHMDP2 and LRHMDP3. Exclusivity of this EPS cluster (from those identified before) was defined by five EPS genes, which were specifically conserved between the clade of 5 clinical isolates and L. rhamnosus BPL5 and BPL15 when compared to the remaining L. rhamnosus strains. Comparative genome analysis between the clade of 5 clinical isolates and L. rhamnosus BPL5 and BPL15 showed a set of 58 potentially unique genes characteristic of the clade of 5. Conclusion The potentially unique functional protein orthologs associated with the clade of 5 clinical isolates may provide understanding of fitness under selective pressure.

Self-audits as alternatives to travel-audits for improving data quality in the Caribbean, Central and South America network for HIV epidemiology

Introduction:Audits play a critical role in maintaining the integrity of observational cohort data. While previous work has validated the audit process, sending trained auditors to sites (“travel-audits”) can be costly. We investigate the efficacy of training sites to conduct “self-audits.”Methods:In 2017, eight research groups in the Caribbean, Central, and South America network for HIV Epidemiology each audited a subset of their patient records randomly selected by the data coordinating center at Vanderbilt. Designated investigators at each site compared abstracted research data to the original clinical source documents and captured audit findings electronically. Additionally, two Vanderbilt investigators performed on-site travel-audits at three randomly selected sites (one adult and two pediatric) in late summer 2017.Results:Self- and travel-auditors, respectively, reported that 93% and 92% of 8919 data entries, captured across 28 unique clinical variables on 65 patients, were entered correctly. Across all entries, 8409 (94%) received the same assessment from self- and travel-auditors (7988 correct and 421 incorrect). Of 421 entries mutually assessed as “incorrect,” 304 (82%) were corrected by both self- and travel-auditors and 250 of these (72%) received the same corrections. Reason for changing antiretroviral therapy (ART) regimen, ART end date, viral load value, CD4%, and HIV diagnosis date had the most mismatched corrections.Conclusions:With similar overall error rates, findings suggest that data audits conducted by trained local investigators could provide an alternative to on-site audits by external auditors to ensure continued data quality. However, discrepancies observed between corrections illustrate challenges in determining correct values even with audits.