BACKGROUND During routine Coronavirus disease 2019 (COVID-19) diagnosis, an unusually high viral load was detected by reverse transcription real-time polymerase chain reaction (RT-qPCR) in a nasopharyngeal swab sample collected from a patient with respiratory and neurological symptoms who rapidly succumbed to the disease. Therefore we sought to characterise the infection. OBJECTIVES We aimed to determine and characterise the etiological agent responsible for the poor outcome. METHODS Classical virological methods, such as plaque assay and plaque reduction neutralisation test combined with amplicon-based sequencing, as well as a viral metagenomic approach, were performed to characterise the etiological agents of the infection. FINDINGS Plaque assay revealed two distinct plaque phenotypes, suggesting either the presence of two severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) strains or a productive coinfection of two different species of virus. Amplicon-based sequencing did not support the presence of any SARS-CoV-2 genetic variants that would explain the high viral load and suggested the presence of a single SARS-CoV-2 strain. Nonetheless, the viral metagenomic analysis revealed that Coronaviridae and Herpesviridae were the predominant virus families within the sample. This finding was confirmed by a plaque reduction neutralisation test and PCR. MAIN CONCLUSIONS We characterised a productive coinfection of SARS-CoV-2 and Herpes simplex virus 1 (HSV-1) in a patient with severe symptoms that succumbed to the disease. Although we cannot establish the causal relationship between the coinfection and the severity of the clinical case, this work serves as a warning for future studies focused on the interplay between SARS-CoV-2 and HSV-1 coinfection and COVID-19 severity.

RESUMO Os viróides infectam plantas de grande importância econômica como os citros. Objetivando detectar a presença de viróides através de métodos moleculares em árvores cítricas, cinco propriedades em Araruama, no Estado do Rio de Janeiro foram avaliadas. Vinte e duas amostras foram coletadas a partir de plantas com nanismo, rachadura no tronco e epinastia, sendo realizada a extração de RNA das folhas e empregado a técnica de RT-PCR com primers específicos para cinco espécies de viróide que infectam citros. O resultado da eletroforese em gel de agarose mostrou-se positivo para os viróides Citrus exocortis viroid (CEVd); Citrus bent leaf viroid (CBLVd); Hop stunt viroid (HSVd) e Citrus dwarfing viroid (CDVd), sendo o último encontrado em todas as propriedades e na combinação com outros viróides, o HSVd e o CBLVd estavam presentes em duas propriedades e o CEVd isoladamente em apenas uma propriedade. Não foi detectada a presença do Citrus viroid IV (CVd-IV) nas amostras avaliadas. Foram observadas diferenças na expressão dos sintomas associados ao CEVd o que pode ter ocorrido devido a interferências entre as espécies de viróides que infectavam uma mesma planta. A transmissão pode ter sido mecanicamente através da poda das plantas cítricas ou através de mudas infectadas com viróide. A utilização de métodos moleculares mostrou-se eficiente na identificação da presença de viróides em plantas cítricas no Estado do Rio de Janeiro.

ABSTRACT Viroids infect plants of great economic importance such as citrus. With the aim of detecting the presence of viroids by molecular methods in citrus trees, five farms in Araruama, Rio de Janeiro State, were evaluated. Twenty-two samples were collected from plants showing dwarfism, trunk cracking and hyponastic response; RNA was extracted from their leaves and the RT-PCR technique was used with specific primers for five viroid species that infect citrus. The result of agarose gel electrophoresis was positive for Citrus exocortis viroid (CEVd), Citrus bent leaf viroid (CBLVd), Hop stunt viroid (HSVd) and Citrus dwarfing viroid (CDVd); the latter was found in all farms and in combination with other viroids. HSVd and CBLVd were present in two farms and CEVd alone in only one farm. Citrus viroid IV (CVd-IV) was not detected in the evaluated samples. Differences in the expression of CEVd-associated symptoms were observed, which may have occurred due to interference of viroid species infecting the same plant. Transmission may have been mechanical through pruning of citrus plants or through viroid-infected seedlings. The use of molecular methods was efficient in identifying the presence of viroids in citrus plants in the state of Rio de Janeiro.

In an enclosure with nine collared peccaries (Pecari tajacu) from the Rio de Janeiro city Zoo, Brazil, one specimen was found dead and two others developed prostration, apathy and dehydration, resulting on its death. Necropsy of two animals pointed to pulmonary and renal damage. Histological examination revealed vasculitis in spleen from both P. tajacu, suggesting a systemic viral infection. Lungs from one specimen showed fibrinoid vasculitis, alveolar damage with hyaline membrane, and interstitial lymphocytes infiltration. Virome analysis in anal wash samples from the latter two animals revealed a new type of Betacoronavirus, lineage A, provisionally named Ptajacu-CoV.

Abstract INTRODUCTION Salmonella enterica serovar Panama belongs to the D1 serogroup and is frequently associated with nontyphoidal salmonellosis in humans. This study aimed to characterize isolates collected from Northeast Brazil by phenotypic and molecular methods. METHODS Forty four S. Panama strains were examined for antimicrobial susceptibility, virulence genes, and pulsed field gel electrophoresis (PFGE) types. RESULTS All strains were susceptible to antibiotics (except for streptomycin), presented classical virulence factors, and could be clustered into four groups and 18 pulsotypes. CONCLUSIONS This work calls for continuous surveillance for the emergence of antibiotic resistance and new clones in a geographical area.

ABSTRACT The herein presented assay provided a bacteriological and molecular characterization of 100 samples of L. monocytogenes isolated from human (43) and food (57) sources, from several regions of Brazil, and collected between 1975 and 2013. Antigenic characterization defined 49% of serotype 4b samples, followed by 28% of serotype 1/2b, 14% of serotype 1/2c, 8% of serotype 1/2a, and 1% of serotype 3b. Both type of samples from human and food origin express the same serotype distribution. Multiplex PCR analysis showed 13 strains of type 4b with the amplification profile 4b-VI (Variant I). Virulence genes hly, inlA, inlB, inlC, inlJ, actA, plcA, and prfA were detected in all samples, highlighting a deletion of 105pb on the actA gene in 23% of serotype 4b samples. Macrorestriction profile with ApaI at PFGE showed 55 pulsotypes, with the occurrence of the same pulsotype in hospitalized patients in São Paulo in 1992 and 1997, and two other highly related pulsotypes in patients hospitalized in Rio de Janeiro in 2008. Recognized pulsotypes in listeriosis cases have also been detected in food. Thus, the prevalence of a serotype and the persistence of certain pulsotypes herald future problems.

Abstract Approximately 185 million people worldwide are chronically infected with hepatitis C virus (HCV). The first-wave of approved NS3 protease inhibitors (PIs) were Telaprevir and Boceprevir, which are currently discontinued. Simeprevir is a second-wave PI incorporated into the Brazilian hepatitis C treatment protocol. Drug resistance plays a key role in patients' treatment regimen. Here, we developed a simple phenotypic assay to evaluate the impact of resistance mutations in HCV NS3 protease to PIs, using a protein expression vector containing wild type NS3 protease domain and NS4A co-factor. We analyzed the impact of five resistance mutations (T54A, V36M, V158I, V170I and T54S+V170I) against Telaprevir, Boceprevir and Simeprevir. Protein purifications were performed with low cost methodology, and enzymatic inhibition assays were measured by FRET. We obtained recombinant proteases with detectable activity, and IC50 and fold change values for the evaluated PIs were determined. The variant T54A showed the highest reduction of susceptibility for the PIs, while the other four variants exhibited lower levels of reduced susceptibility. Interestingly, V170I showed 3.2-fold change for Simeprevir, a new evidence about this variant. These results emphasize the importance of enzymatic assays in phenotypic tests to determine which therapeutic regimen should be implemented.

Ten out of fifty fresh and refrigerated samples of shrimp (Litopenaeus vannamei) collected from retailers in Natal (Rio Grande do Norte, Northeastern Brazil) tested positive for Vibrio parahaemolyticus. The Kanagawa test and multiplex PCR assays were used to detect TDH and TRH hemolysins and the tdh, trh and tlh genes, respectively. All strains were Kanagawa-negative and tlh-positive. Antibiotic susceptibility testing was done for seven antibiotics by the agar diffusion technique. Five strains (50%) presented multiple antibiotic resistance to ampicillin (90%) and amikacin (60%), while two strains (20%) displayed intermediate-level resistance to amikacin. All strains were sensitive to chloramphenicol. Intermediate-level susceptibility and/or resistance to other antibiotics ranged from 10 to 90%, with emphasis on the observed growing intermediate-level resistance to ciprofloxacin. Half our isolates yielded a multiple antibiotic resistance index above 0.2 (range: 0.14-0.29), indicating a considerable risk of propagation of antibiotic resistance throughout the food chain.

O ambiente aquático é o habitat de vários microrganismos, incluindo Plesiomonasshigelloides e espécies de Aeromonas, os quais são patogênicos para o homem e os animais. Na presente investigação, foi avaliada a ocorrência destes patógenos a partir de swabs coletados de mamíferos marinhos encalhados ou capturados acidentalmente em redes de pesca nas regiões costeiras do sudeste (RJ) e sul (RS) do Brasil. O total de 198 swabs de 27 espécimes de mamíferos marinhos, incluindo 11 espécies distintas, foi coletado por profissionais dos institutos DEENSP, GEMARS-CECLIMAR/UFRGS e enviado ao LRNCEB/IOC/FIOCRUZ. Em seguida, as amostras foram submetidas a enriquecimento em Água Peptonada Alcalina (APA) adicionada de 1% de cloreto de sódio (NaCl) e APA com 3% de NaCl (37ºC/18-24 h). Posteriormente, as amostras foram semeadas em meio Agar Seletivo para Pseudomonas-Aeromonas (Agar GSP) e as colônias suspeitas submetidas à caracterização bioquímica. Um total de 114 cepas foram identificadas, incluindo dez espécies de Aeromonas e P.shigelloides. Os principais patógenos isolados foram A.veronii biogrupo veronii (19,3%), A. caviae (12,2%), A. hydrophila (9,6%) e Plesiomonasshigelloides (7%). Os patógenos foram encontrados tanto em espécies de mamíferos marinhos costeiros como oceânicos. Esses dados apontam para a importância da vigilância epidemiológica e monitoramento microbiológico, além de reforçar a necessidade de implantação de programas de proteção ambiental, particularmente relacionados aos mamíferos marinhos ameaçados de extinção.

The aquatic environment is the habitat of many microorganisms, including Plesiomonasshigelloides and Aeromonas species which are pathogenic to human and animals. In the present investigation, we evaluated the occurrence of these pathogens from marine mammals beached or accidentally captured by fishing net in southeastern (RJ) and southern (RS) coastal Brazilian regions. A total of 198 swabs from 27 specimens of marine mammals, including 11 different species, were collected by DEENSP and GEMARS-CECLIMAR/UFRGS Institutes and sent to LRNCEB/IOC/FIOCRUZ. The samples were enriched in Alkaline Peptone Water (APW) added with 1% of sodium chloride (NaCl), APW plus 3% NaCl and incubated at 37ºC for 18-24 hours. Following, samples were streaked onto Pseudomonas-Aeromonas Selective Agar Base (GSP Agar) and suspected colonies were biochemically characterized. The results revealed 114 strains, including ten Aeromonas species and P.shigelloides. The main pathogens isolated were A.veronii biogroup veronii (19.3%), A. caviae (12.3%), A. hydrophila (9.6%) and P.shigelloides (7%). The pathogens were isolated in both coastal and offshore marine mammals. These data point the importance of epidemiological surveillance and microbiological monitoring and reinforce the need to implement environmental protection programs, especially related to endangered cetacean species.

Aeromonas spp é reconhecida como patogênica para o homem após o consumo de água e alimentos contaminados. Na presente investigação, foram avaliadas 2.323 amostras de swabs retais de neonatos hospitalizados no Rio de Janeiro objetivando o isolamento de Aeromonas. As amostras foram coletadas e enviadas ao Laboratório de Referência Nacional de Cólera e outras enteroinfecções bacterianas, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz. Os swabs foram submetidos ao enriquecimento em água peptonada alcalina adicionada de 1% de cloreto de sódio (NaCl) e água peptonada alcalina adicionada de 3% de NaCl (37ºC/18-24h) e semeadas em agar seletivo para Pseudomonas aeromonas (Agar GSP). Foram isoladas 56 cepas de Aeromonas assim distribuídas: Aeromonas caviae (42,8%), Aeromonas media (25%), Aeromonas veronii biogrupo sobria (10,7%), Aeromonas hydrophila (9%), Aeromonas veronii biogrupo veronii (5,3%), Aeromonas sobria (1,8%), Aeromonas jandaei (1,8%), Aeromonas schubertii (1,8%) e Aeromonas sp (1,8%). Foi observada resistência a uma ou mais drogas antimicrobianas em 26,8% das cepas. Considerando a relevância de Aeromonas torna-se urgente alertar sobre sua importância para o controle de infecções hospitalares.

Aeromonas spp is recognized as pathogenic to humans after consumption of contaminated water and food. In the present investigation, 2,323 rectal swab samples from newborns hospitalized in Rio de Janeiro were evaluated with a view to isolating Aeromonas. The samples were collected and sent to the national reference laboratory for cholera and other bacterial intestinal infections, at the Oswaldo Cruz Institute of the Oswaldo Cruz Foundation. The swabs were subjected to enrichment in alkaline peptonated water with the addition of 1% sodium chloride (NaCl) and alkaline peptonated water plus 3% NaCl (37°C/18-24h) and were streaked onto agar that was selective for Pseudomonas-Aeromonas (GSP Agar). Fifty-six Aeromonas strains were isolated, distributed as follows: Aeromonas caviae (42.8%), Aeromonas media (25%), Aeromonas veronii biogroup sobria (10.7%), Aeromonas hydrophila (9%), Aeromonas veronii biogroup veronii (5.3%), Aeromonas sobria (1.8%), Aeromonas jandaei (1.8%), Aeromonas schubertii (1.8%) and Aeromonas sp (1.8%). Resistance to one or more antimicrobial drugs was observed in 26.8% of the strains. Considering the importance of Aeromonas, there is an urgent need to warn about this in relation to nosocomial infection control.