RESUMO

Bacteria of the genus Brucella are facultative intracellular parasites that cause brucellosis, a severe animal and human disease. Recently, a group of taxonomists merged the brucellae with the primarily free-living, phylogenetically related Ochrobactrum spp. in the genus Brucella. This change, founded only on global genomic analysis and the fortuitous isolation of some opportunistic Ochrobactrum spp. from medically compromised patients, has been automatically included in culture collections and databases. We argue that clinical and environmental microbiologists should not accept this nomenclature, and we advise against its use because (i) it was presented without in-depth phylogenetic analyses and did not consider alternative taxonomic solutions; (ii) it was launched without the input of experts in brucellosis or Ochrobactrum; (iii) it applies a non-consensus genus concept that disregards taxonomically relevant differences in structure, physiology, population structure, core-pangenome assemblies, genome structure, genomic traits, clinical features, treatment, prevention, diagnosis, genus description rules, and, above all, pathogenicity; and (iv) placing these two bacterial groups in the same genus creates risks for veterinarians, medical doctors, clinical laboratories, health authorities, and legislators who deal with brucellosis, a disease that is particularly relevant in low- and middle-income countries. Based on all this information, we urge microbiologists, bacterial collections, genomic databases, journals, and public health boards to keep the Brucella and Ochrobactrum genera separate to avoid further bewilderment and harm.

Assuntos

RESUMO

The intracellular pathogens of the genus Brucella are phylogenetically close to Ochrobactrum, a diverse group of free-living bacteria with a few species occasionally infecting medically compromised patients. A group of taxonomists recently included all Ochrobactrum organisms in the genus Brucella based on global genome analyses and alleged equivalences with genera such as Mycobacterium. Here, we demonstrate that such equivalencies are incorrect because they overlook the complexities of pathogenicity. By summarizing Brucella and Ochrobactrum divergences in lifestyle, structure, physiology, population, closed versus open pangenomes, genomic traits, and pathogenicity, we show that when they are adequately understood, they are highly relevant in taxonomy and not unidimensional quantitative characters. Thus, the Ochrobactrum and Brucella differences are not limited to their assignments to different "risk-groups", a biologically (and hence, taxonomically) oversimplified description that, moreover, does not support ignoring the nomen periculosum rule, as proposed. Since the epidemiology, prophylaxis, diagnosis, and treatment are thoroughly unrelated, merging free-living Ochrobactrum organisms with highly pathogenic Brucella organisms brings evident risks for veterinarians, medical doctors, and public health authorities who confront brucellosis, a significant zoonosis worldwide. Therefore, from taxonomical and practical standpoints, the Brucella and Ochrobactrum genera must be maintained apart. Consequently, we urge researchers, culture collections, and databases to keep their canonical nomenclature.

RESUMO

Objetivos: El muestreo de hisopado nasofaríngeo para la detección de SARS CoV-2 es un método estándar para el diagnóstico de COVID-19, pero su recolección generalmente ocasiona incomodidad en el paciente y expone a un mayor riesgo al personal de salud. La muestra de saliva parece ser una buena alternativa con respecto a las muestras de hisopado nasofaringeo, no es invasiva, reduce el riesgo de contaminación del personal sanitario y permite la auto recolección. Este estudio tiene por objetivo comparar la capacidad de detectar al SARS CoV-2 por RT-PCR en un mismo paciente, a partir de muestras de saliva y de hisopado nasofaríngeo para analizar la concordancia de los resultados obtenidos entre ambas muestras. Métodos: Treinta muestras de saliva y de HNF de pacientes con síntomas de COVID-19 que ingresaron al servicio de emergencia del Hospital Clínico Viedma fueron tomadas en paralelo. Ambas muestras fueron analizadas por RT-PCR para la detección de SARS CoV-2. La concordancia de resultados fue calculada por el coeficiente de kappa de Cohen. Resultados: Nuestros resultados muestran que existe una buena concordancia (Índice Kappa 0,730; IC del 95%: 0,486 - 0,974) entre los dos tipos de muestras analizadas. Conclusiones: La saliva parece ser una muestra fiable y efectiva para la detección del SARS CoV-2.

Objectives: Nasopharyngeal swab sampling for the detection of SARS-CoV-2 is a standard method for the diagnosis of COVID-19, but its collection usually causes discomfort in the patient and exposes healthcare workers to a higher risk. Saliva seems to be a good alternative to nasopharyngeal swabs, as it is non-invasive, reduces the risk of contamination of healthcare workers, and allows self-collection. This study aims to compare the ability to detect SARS-CoV-2 by RT-PCR in the same patient using saliva and nasopharyngeal swab samples to analyze the concordance of the results obtained between the two samples. Methods: Thirty saliva and nasopharyngeal swab samples from patients with COVID-19 symptoms who were admitted to the emergency department of the Viedma Clinical Hospital were taken in parallel. Both samples were analyzed by RT-PCR for the detection of SARS-CoV-2. The concordance of results was calculated using the Cohen's Kappa coefficient. Results: Our results show that there is good concordance (Kappa index 0.730; 95% CI: 0.486-0.974) between the two types of samples analyzed. Conclusions: Saliva seems to be a reliable and effective sample for the detection of SARS-CoV-2.