International Journal of Microbiology

This systematic review (PROSPERO registration number: CRD42021282476) aims to collect and analyse current evidence on real-world performance based on clinical accuracy of instrument-read rapid antigen diagnostic tests (Ag-IRRDTs) for SARS-CoV-2 identification. We used PRISMA Checklist and searched databases (PubMed, Web of Science Core Collection and FIND) for publications evaluating the accuracy of SARS-CoV-2 Ag-IRRDTs as of 30 September 2021, and included 40 independent clinical studies resulting in 48 Ag-IRRDT datasets with 137,770 samples. Across all datasets, pooled Ag-IRRDT sensitivity was 67.1% (95% CI: 65.9%–68.3%) and specificity was 99.4% with a tight CI. Pooled sensitivity and specificity of SARS-CoV-2 Ag-IRRDTs did not demonstrate a significant superiority over SARS-CoV-2 rapid antigen tests which do not require a reader instrument, even in the case where surveillance and screening datasets were excluded from the analysis. Nevertheless, they provide connectivity advantages and remove operator interface (in results-reading) issues. The lower sensitivity of certain brands of Ag-IRRDTs can be overcome in high prevalence areas with high frequency of testing. New SARS-CoV-2 variants are major concern for current and future diagnostic performance of these tests.

Cultivation of specialty mushrooms on lignocellulosic wastes represents one of the most economic and cost-effective organic recycling processes. Solid-state cultivation (SSC) was carried out to evaluate the feasibility of using coffee waste (husk and parchment) as substrate for cultivation of oyster mushroom (Pleurotus species). The periods for spawn running, pinhead and fruit body formation, number of flushes, yield, and biological efficiency of the four Pleurotus species (P. citrinopileatus, P. eryngii, P. ostreatus, and P. sapidus) grown on coffee husk and parchment were studied. The results revealed that the time for the first appearance of pinhead was shortest for P. ostreatus (20–21) days followed by P. sapidus (22–23) days on coffee husks, while P. eryngii and P. citrinopileatus required 26–27 days and 23–24 days, respectively, on the some substrate. All the four Pleurotus species recorded at least four flushes and three flushes on coffee husk and parchment, respectively; flush 1 gave the highest yield while flush 3 and 4 gave the lowest yield. The biological efficiency (B.E.) for P. citrinopileatus, P. eryngii, P. ostreatus and P. sapidus obtained from fresh coffee husk was 26.54, 40.94, 60.33, and 55.72, respectively. Significant differences () in yield and % B.E. of the four mushrooms species were recorded. The results also showed that the B.E. (61.92%) of P. ostreatus grown on composted coffee husk was insignificantly higher () than that grown on noncomposted coffee husk (60.33). The yields of P. sapidus obtained from the two substrates were almost comparable with that of P. ostreatus. There was a significant difference at () observed between noncomposted and composted coffee husk and coffee parchment as well as between coffee husk and coffee parchment on yield and biological efficiency (B.E.). Composted coffee waste is more efficient than noncomposted one. Pectinase enzymes productions by these mushrooms were also studied. They are known to produce extracellular enzymes, particularly pectinase, which contribute to the biochemical decomposition of pectin-rich lignocellulosic wastes biomass. Accordingly, P. sapidus showed more pectolytic activities followed by P. ostreatus. But the pectolytic activity showed by P. eryngii and P. citrinopileatus was relatively lower. The implications of this study are the feasibility of using composted coffee husks and coffee parchment with the supplementary substrate to cultivate very protein-rich mushrooms for food in solid-state cultivation (SSC) while at the same time promoting environmental sustainability.

Staphylococcus aureus (S. aureus) is responsible for several disorders including skin and soft tissue infections, bacteremia, pulmonary infections, septic arthritis, osteomyelitis, meningitis, gastroenteritis, toxic-shock syndrome, and urinary tract infections. Methicillin-resistant S. aureus (MRSA) contains penicillin-binding protein 2a (SauPBP2a) responsible for catalyzing the peptidoglycan production within the bacterial cell wall. The binding affinity of SauPBP2a to beta-lactam antibiotics is low, and thus, it is necessary to discover new effective SauPBP2a inhibitors to combat mortality and morbidity in patients affected by MRSA. The binding affinity of 46 natural flavonoids to the SauPBP2a active site was examined via molecular docking analysis. The stability of docked poses associated with the top-ranked flavonoids was tested by performing molecular dynamics (MD) in 10 nanoseconds (ns) computer simulations. Kaempferol 3-rutinoside-7-sophoroside and rutin demonstrated a considerable binding affinity to the SauPBP2a active site (Δ_binding < 11 kcal/mol). Their docked poses were found to be stable for 10 ns MD simulations. Kaempferol 3-rutinoside-7-sophoroside and rutin also exhibited salient binding affinity to the enzyme’s allosteric site. This study suggests that kaempferol 3-rutinoside-7-sophoroside and rutin may be considered as drug candidates for therapeutic aims in several human infections associated with MRSA. Nevertheless, in vitro and in vivo confirmations are warranted.

Antibiotic resistance represents one of the biggest challenges, and there is an urgent need for plant-based antimicrobial agents that enable managing this crisis effectively. In this work, we aimed to investigate the antibacterial activity of Astragalus candolleanus (A. candolleanus) hydromethanolic root extract against Gram-positive (Bacillus subtilis and Staphylococcus aureus) and Gram-negative (Escherichia coli, Salmonella typhimurium, Pseudomonas aeruginosa, Klebsiella pneumoniae, and Kocuria rhizophila) strains by the cup-plate method. The root was powdered and extracted with 70% methanol by cold maceration for 5 days. Preliminary phytochemical screening was performed with different solvents in the order of increasing polarity. Pure compounds were isolated by column chromatography and were characterized through liquid chromatography-mass spectrometry. Targeted predictions of the isolated compounds were also studied using Swiss Target prediction software and prediction of activity spectra for substances. The extract showed a broad zone of inhibition against pathogenic bacteria. Four pure compounds were isolated, of which a novel terpenoid compound has been identified as stemmadenine along with scillirosidin, cephalotaxine, and myxoxanthophyll. The structures of the isolated phytoconstituents were elucidated by spectral analysis. The four pure components isolated from the roots of A. candolleanus are suggested to be effective against tested pathogens. Overall results of drug design suggest that myxoxanthophyll is a promising bioactive compound endowed with antibacterial activity.

Periodontal diseases are initiated by the shift from microbe-host symbiosis to dysbiosis, and the disrupted host response predominantly contributes to tissue destruction. This study investigated whether and to what extent human oral keratinocytes (HOKs) challenged by a periodontal commensal or pathogen could differentially affect the chemotactic activity of THP-1 monocytes. A selected periodontal commensal (Streptococcus sanguinis ATCC 10556) and a pathogen (Porphyromonas gingivalis ATCC 33277) were cultured and inoculated, respectively, into the lower chamber of Transwell® Permeable Supports with HOKs and incubated for 2 h or 18 h at 37°C under appropriate cell growth conditions. HOKs alone served as the control for the transwell migration assay. Well-stained THP-1 monocytes were seeded in the top chamber of the device, incubated for 2 h and then collected from the lower well for quantitation of the migrated fluorescence-labeled cells by the FACSCalibur™ flow cytometer. The statistical significance was determined using one-way ANOVA. The HOKs challenged by S. sanguinis attracted a significantly higher number of THP-1 cell migration as compared with the control after 2 h or 18 h interaction (). By contrast, P. gingivalis-treated HOKs exhibited a markedly reduced chemotactic effect on THP-1 cells (, 2 h; , 18 h). There was no significant difference in THP-1 cell migration among the groups with either S. sanguinis or P. gingivalis alone. The current findings on P. gingivalis-HOKs interactions with resultant paralysis of THP-1 cell chemotaxis provide further evidence that the keystone periodontopathogen P. gingivalis can evade innate defense and contribute to periodontal pathogenesis.

Escherichia coli (E. coli) is a zoonotic pathogen that showed growing resistance to antibiotics. No descriptive analysis highlights the threat of antimicrobial-resistant (AMR) of E. coli among livestock in the United Arab Emirates (UAE). Herein, we conducted phenotypic and genotypic resistance studies on E. coli isolates from livestock samples in the Emirate of Abu Dhabi based on routine diagnosis between the periods 2014–2019. Bacterial culture and disk diffusion methods were used for bacterial isolation and phenotypic resistance analysis. Resistance mechanism was studied by PCR targeting the most commonly resistance genes: ampicillin (bla_SHV, bla_CMY, and blaTEM-1B), tetracyclines (tetA and tetB), co-trimoxazole [sulfamethoxazole (sul1, sul2, and sul3) + trimethoprim (dfrA1 and dfrA17)], aminoglycosides [aph(3'')-Ia, aph(6)-Id, and aac(3)-IV], and fluoroquinolones (qnrA and aac(6’)-Ib-cr). Analysis of 165 E. coli isolates showed resistant to ampicillin, tetracycline, co-trimoxazole, gentamicin, and enrofloxacin by 157/165 (95.4%), 154/165 (93.6%), 141/165 (86%), 139/165 (85%), and 135/165 (82.7%), respectively. Predominant resistance gene/s detected by PCR were bla_CMY (119/160, 72%) and blaTEM-1B (154/160, 96.3%) for ampicillin; tetA (162/164, 98.8%) and tetB (112/164, 68.3%) for tetracyclines; sul2 (156/164, 95%), sul3 (138/164, 84%), and dfra17 (74/164, 44.5%) for co-trimoxazole; aph(3'')-Ia (134/164, 82.1%) and aph(6)-Id (161/164, 98.2%) for aminoglycosides; and aac(6’)-Ib-cr (61/61, 100%) for enrofloxacin. Both phenotypic and genotypic analyses revealed that all E. coli isolates were multidrug-resistant (resistance to 3, 4, and 5 antibiotics classes by 3.6%, 57.6%, and 38.8%, respectively) carrying one or more resistance gene/s for the same antibiotic. PCR profiling confirmed the presence of resistance genes corresponding to their antibiotic profile. Results of the study will highlight the knowledge based on E. coli AMR related to livestock in UAE that may call for interventions.