RESUMEN
BACKGROUND: Coronavirus disease 2019 (COVID-19) is highly infectious causing millions of deaths worldwide. Nasopharyngeal swabs are the primary sample of choice for the diagnosis of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), thus, to decrease the exposure to potentially infected samples through the collection is a key point to reduce the risk of infection in healthcare workers. OBJECTIVES: This study aimed to evaluate the sensitivity and viral load of saliva specimens by days of symptoms onset comparing to nasopharyngeal swabs in subjects with mild symptoms. METHODS: Saliva and nasopharyngeal swabs samples were collected from São Paulo Hospital workers presenting mild symptoms, such as fever, cough, sore throat, rhinorrhea, myalgia, headaches, anosmia, ageusia, and fatigue. To understand the positivity and viral load, reverse transcription-polymerase chain reaction (RT-PCR) was performed. FINDINGS: Saliva specimens presented a sensitivity of 98.6% compared to nasopharyngeal swabs. Overall, saliva showed lower viral load compared to nasopharyngeal swabs, regarding days of symptoms onset on diagnosis, the first four days had significant changes in viral load and no significant difference was reported in the days five to nine. MAIN CONCLUSIONS: Although RT-PCR of saliva has presented a lower viral load compared to nasopharyngeal swabs, saliva specimens are a potential and reliable candidate for COVID-19 diagnosis through RT-PCR.
Asunto(s)
COVID-19 , ARN Viral , Prueba de COVID-19 , Humanos , Nasofaringe , SARS-CoV-2 , Saliva , Carga ViralAsunto(s)
Infecciones por Acinetobacter , Acinetobacter baumannii , Bacteriemia , Infección Hospitalaria , Trasplante de Células Madre Hematopoyéticas , Infecciones por Acinetobacter/tratamiento farmacológico , Antibacterianos/farmacología , Antibacterianos/uso terapéutico , Bacteriemia/diagnóstico , Bacteriemia/tratamiento farmacológico , Brasil , Infección Hospitalaria/tratamiento farmacológico , Farmacorresistencia Bacteriana Múltiple , Humanos , Pruebas de Sensibilidad MicrobianaRESUMEN
OBJECTIVES: To analyze the relationship of ribosomal protein mutations and clonality of high-risk clones Acinetobacter baumannii. METHODS: Seventy-nine carbapenem-resistant A. baumannii were subjected to whole-genome sequencing (Illumina NextSeq), and codifying sequences of ribosomal proteins were extracted and screened for mutations. MALDI-TOF MS analysis (Bruker Biotyper) and Spectra data from MALDI-TOF was employed to generate a dendrogram based on principal component analysis (PCA) data. Clones were identified by Multilocus sequencing typing (MLST) based on WGS. RESULTS: Ribosomal RNA protein sequences extracted from the genomes identified mutations that were associated with clonal complexes, but most of them were silent. PCA did not cluster the isolates according to their clonality identified by MLST. CONCLUSIONS: By comparing the nucleotide and amino acid sequences of diversified A. baumannii, and Bruker Biotyper profiles, we showed that silent mutations in ribosomal RNA nucleotides are associated with clonal complexes, but since most of the mutations were silent, MALDI-TOF MS raw data was not a useful tool for typing the high-risk clones of this species.
Asunto(s)
Infecciones por Acinetobacter/microbiología , Acinetobacter baumannii/genética , Proteínas Ribosómicas/genética , Infecciones por Acinetobacter/epidemiología , Acinetobacter baumannii/clasificación , Acinetobacter baumannii/efectos de los fármacos , Antibacterianos/farmacología , Brasil/epidemiología , Carbapenémicos/farmacología , ADN Bacteriano , Farmacorresistencia Bacteriana , Humanos , Pruebas de Sensibilidad Microbiana , Tipificación de Secuencias Multilocus , Mutación Silenciosa , Espectrometría de Masa por Láser de Matriz Asistida de Ionización Desorción , Secuenciación Completa del GenomaRESUMEN
Dissemination of carbapenem-resistant Acinetobacter baumannii (CRAB) is mainly driven by the spread of clonal lineages. High frequencies of CRAB are reported in South America, and clonal complexes CC1, CC15, CC79 and CC25 are predominant. A total of 79 non-redundant CRAB recovered from 26 Brazilian hospitals were selected for antimicrobial susceptibility testing by microdilution and whole-genome sequencing (WGS). Multilocus sequence typing (MLST), acquired antimicrobial resistance genes and phylogeny based on high-quality SNPs were extracted from WGS data. XDR (86.1%), MDR (12.7%) and one PDR isolate from CC15 (1.3%) were identified. Colistin resistance was more frequent in CC25 isolates (P < 0.01). Prevalence of CC79 (n = 22; 27.8%) CC1 (n = 21; 26.6%), CC15 (n = 21; 26.6%) and CC25 (n = 12; 15.2%) was observed. Regarding carbapenem-hydrolysing class D ß-lactamases (CHDLs), blaOXA-23 was frequently detected in CC1, CC15 and CC25 isolates, whereas blaOXA-72 was the most frequent CHDL in CC79 isolates [n = 12/22 (54.5%); P < 0.01]. High-quality SNP analysis correlated well with sequence type and revealed that CRAB clones are highly conversed and present some clone-specific resistance determinants. This study provides essential information to understand the antimicrobial resistance patterns of CRAB in Brazilian hospitals, where hyperendemic XDR-CRAB clones are disseminated. Phenotypic and genomic analysis of CRAB recovered from Brazilian hospitals revealed the predominance of XDR phenotype in the majority of international clonal complex CC79, CC1, CC15 and CC25. Dissemination of specific CRAB lineages in Brazil is suggested to be driven by their resistance determinants under antimicrobial selective pressure.
Asunto(s)
Acinetobacter baumannii/efectos de los fármacos , Acinetobacter baumannii/genética , Antibacterianos/farmacología , Carbapenémicos/farmacología , Farmacorresistencia Bacteriana Múltiple/genética , Polimixinas/farmacología , Acinetobacter baumannii/aislamiento & purificación , Proteínas Bacterianas/genética , Brasil , Genoma Bacteriano/genética , Hospitales , Humanos , Pruebas de Sensibilidad Microbiana , Epidemiología Molecular , Tipificación de Secuencias Multilocus , Filogenia , Polimorfismo de Nucleótido Simple/genética , Secuenciación Completa del Genoma , beta-Lactamasas/genéticaRESUMEN
Acinetobacter baumannii is the main species of the Acinetobacter genus; however, non-baumannii Acinetobacter (NBA) species causing infections have been described for the past years, as well as antimicrobial resistance. In this study, we describe the occurrence of two multidrug-resistant (MDR) IMP-1-producing Acinetobacter bereziniae isolates recovered from bloodstream infections in different patients but in the same intensive care unit among 134 carbapenem-resistant Acinetobacter screened. Antimicrobial susceptibility testing revealed resistance to carbapenems, extended spectrum, and antipseudomonad cephalosporins, amikacin, and trimethoprim-sulfamethoxazole. Both A. bereziniae isolates shared the same ApaI-pulsed-field gel electrophoresis (PFGE) pattern. Whole-genome sequencing of both isolates revealed that blaIMP-1 was embedded into an In86 Class I integron carrying also sul1, aac(6')-31, and aadA genes. A new sequence type (ST1309 Pasteur) was deposited. The virulence genes lpxC and ompA, seen in A. baumannii, were detected in the A. bereziniae strains. Recognition of A. bereziniae causing invasive MDR infection underscores the role of NBA species as human pathogens especially in at-risk patients.