Diagnostic performance of four lateral flow immunoassays for COVID-19 antibodies in Peruvian population.

Serological assays have been used in seroprevalence studies to inform the dynamics of COVID-19. Lateral flow immunoassay (LFIA) tests are a very practical technology to use for this objective; however, one of their challenges may be variable diagnostic performance. Given the numerous available LFIA tests, evaluation of their accuracy is critical before real-world implementation. We performed a retrospective diagnostic evaluation study to independently determine the diagnostic accuracy of 4 different antibody-detection LFIA tests: Now Check (Bionote), CareStart (Access bio), Covid-19 BSS (Biosynex) and OnSite (CTK Biotech). The sample panel was comprised of specimens collected and stored in biobanks; specifically, specimens that were RT-PCR positive for SARS-CoV-2 collected at various times throughout the COVID-19 disease course and those that were collected before the pandemic, during 2018 or earlier, from individuals with upper respiratory symptoms but were negative for tuberculosis. Clinical performance (sensitivity and specificity) was analyzed overall, and subset across individual antibody isotypes, and days from symptoms onset. A very high specificity (98% - 100%) was found for all four tests. Overall sensitivity was variable, ranging from 29% [95% CI: 21%-39%] to 64% [95% CI: 54%-73%]. When considering detection of IgM only, the highest sensitivity was 42% [95% CI: 32%-52%], compared to 57% [95% CI: 47%-66%] for IgG only. When the analysis was restricted to at least 15 days since symptom onset, across any isotype, the sensitivity reached 90% for all four brands. All four LFIA tests proved effective for identifying COVID-19 antibodies when two conditions were met: 1) at least 15 days have elapsed since symptom onset and 2) a sample is considered positive when either IgM or IgG is present. With these considerations, the use of this assays could help in seroprevalence studies or further exploration of its potential uses.

Comparative genomic analysis of two novel plasmids from Acidithiobacillus ferrivorans strain PQ33 / Análisis genómico comparativo de dos nuevos plásmidos de la cepa PQ33 de Acidithiobacillus ferrivorans

Abstract Acidithiobacillus ferrivorans is a psychrotolerant acidophile capable of growing and oxidizing ferrous and sulphide substrates at low temperatures. To date, six genomes of this organism have been characterized; however, evidence of a plasmid in this species has been reported only once, whereby there is no conclusive role of the plasmids in the species. Herein, two novel plasmids of A. ferrivorans PQ33 were molecularly characterized and compared at a genomic scale. The genomes of two plasmids (12 kbp and 10 kbp) from A. ferrivorans PQ33 (NZ_LVZL01000000) were sequenced and annotated. The plasmids, named pAfPQ33-1 (NZ_CP021414.1) and pAfPQ33-2 (NZ_CP021415.1), presented 9 CDS and 13 CDS, respectively. In silico analysis showed proteins involved in conjugation (TraD, MobA, Eep and XerD), toxin-antitoxin systems (HicA and HicB), replication (RepA and DNA binding protein), transcription regulation (CopG), chaperone DnaJ, and a virulence gene (vapD). Furthermore, the plasmids contain sequences similar to phosphate-selective porins O and P and a diguanylate cyclase-phosphodiesterase protein. The presence of these genes suggests the possibility of horizontal transfer, a regulatory system of plasmid maintenance, and adhesion to substrates for A. ferrivorans species and PQ33. This is the first report of plasmids in this strain.

Resumen Acidithiobacillus ferrivorans es un acidófilo psicrotolerante capaz de hacer crecer y oxidar sustratos ferrosos y sulfurosos a bajas temperaturas. Hasta la fecha se han caracterizado seis genomas de este organismo; sin embargo, la evidencia de un plásmido en esta especie ha sido informado solo una vez, por lo que no hay un rol concluyente de los plásmidos en la especie. Aquí, dos plásmidos novedosos de A. ferrivorans PQ33 se caracterizaron molecularmente y se compararon a escala genómica. Se secuenciaron y anotaron los genomas de dos plásmidos (12 kpb y 10 kpb) de A. ferrivorans PQ33 (NZ_LVZL01000000). Los plásmidos, denominados pAfPQ33-1 (NZ_CP021414.1) y pAfPQ33-2 (NZ_CP021415.1), presentaron 9 CDS y 13 CDS, respectivamente. El análisis in silico mostró proteínas involucradas en la conjugación (TraD, MobA, Eep y XerD), sistemas de toxina-antitoxina (HicA y HicB), replicación (RepA y proteína de unión al ADN), regulación de la transcripción (CopG), chaperona DnaJ y un gen de virulencia (vapD). Además, los plásmidos contienen secuencias similares a las porinas selectivas de fosfato O y P y una proteína diguanilato ciclasa-fosfodiesterasa. La presencia de estos genes sugiere la posibilidad de transferencia horizontal, un sistema regulador de mantenimiento de plásmidos y adhesión a sustratos para especies de A. ferrivorans y PQ33. Este es el primer informe de plásmidos en esta cepa.

Physiological and comparative genomic analysis of Acidithiobacillus ferrivorans PQ33 provides psychrotolerant fitness evidence for oxidation at low temperature.

Friendly environmental hydrometallurgy at low temperatures is principally promoted by Acidithiobacillus ferrivorans. Until recently, the synergy between cold tolerance and the molecular mechanism of ferrous iron (Fe2+) oxidation was unknown. In the present paper, we conducted a physiological and comparative genomics analysis of the new strain A. ferrivorans PQ33 to elucidate the oxidation mechanism at low temperatures, with emphasis placed on trehalose and the Rus operon. PQ33 exhibited a doubling time of 66.6 h in Fe2+ at pH 1.6 and 63.6 h in CuS at 5 °C. Genomic island (GI) identification and comparative genome analysis were performed with four available genomes of Acidithiobacillus sp. The genome comprised 3,298,172 bp and 56.55% GC content. In contrast to ATCC Acidithiobacillus ferrooxidans strains, the genome of A. ferrivorans PQ33 harbors one GI, which contains a RusB gene. Moreover, five genes of peptidyl-prolyl cis-trans isomerase (PPIases) were observed. Furthermore, comparative analysis of the trehalose operon suggested the presence of a horizontal transfer event. In addition, comparison of rusticyanin proteins revealed that RusB has better intrinsic flexibility than RusA. This comparison suggests psychrotolerant fitness and supports the genetic canalization of A. ferrivorans PQ33 for oxidation at low temperature.

Actividad inhibitoria del crecimiento bacteriano por cobre nanoestructurado obtenido de minerales de la región Marañón: comparación con cobre comercial / Bacterial growth inhibitory activity for nanostructured copper minerals obtained from the Marañon region: comparison with commercial copper

En el presente trabajo se reporta la actividad inhibitoria del crecimiento bacteriano por nanopartículas de cobre cementado y de cobre comercial. Se utilizaron las cepas de Staphylococcus aureus ATCC 6538 (Gram positiva) y Escherichia coli ATCC 35218 (Gram negativa) para determinar el efecto inhibitorio mediante la concentración mínima inhibitoria de las nanopartículas diluidas en caldo de cultivo nutritivo y distribuidas en placas de ELISA. Las muestras de cobre cementado (obtenidas por procesos hidrometalúrgicos) y de cobre comercial fueron nanoestructuradas empleando un equipo de molienda mecánica. Los resultados indican que las nanopartículas de cobre comercial (a 2.5 horas de molienda) muestran acción inhibitoria del crecimiento de la cepa S. aureus y no así en la cepa E. coli. Asimismo, se determinó que la concentración mínima inhibitoria de la muestra de cobre comercial fue de 20 μg/mL frente a S. aureus. El cobre cementado (en su forma sólida y nanoestructurada) no mostró efecto inhibitorio del crecimiento en ninguna de las dos cepas estudiadas.

In this paper, we report on the bacterial growth inhibitory activity of nanoparticles of cemented and commercial copper. Strains of Staphylococcus aureus ATCC 6538 (Gram positive) and Escherichia coli ATCC 35218 (Gram negative) were used to determine the inhibitory effect by the minimal inhibitory concentration of the nanoparticles diluted in nutrient culture broth and distributed in ELISA plates. The copper cements (obtained from hydrometallurgical processes) and the commercial one were nanostructured employing a mechanical milling equipment. The results indicate that commercial copper nanoparticles (after 2.5 hours of milling) show growth inhibitory action of S. aureus strain. However, in the case of E. coli strains no inhibitory action has been observed. It was also determined that the minimal inhibitory concentration of the commercial copper is 20 μg/mL against S. aureus. On the other hand, copper cements (in solid and nanostructured form) do not show inhibitory effects.