Identification and characterisation of SARS-CoV-2 and Human alphaherpesvirus 1 from a productive coinfection in a fatal COVID-19 case

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.

A novel Betacoronavirus characterised in collared peccaries from the Rio de Janeiro Zoo (Brazil) killed by unknown disease

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.

Salmonella Panama: genetic diversity of the isolates collected from human and non-human sources

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.

Virulence genes and genetic relationship of L. monocytogenes isolated from human and food sources in Brazil

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.

Antibiotic resistance of Vibrio parahaemolyticus isolated from pond-reared Litopenaeus vannamei marketed in Natal, Brazil

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 percent) presented multiple antibiotic resistance to ampicillin (90 percent) and amikacin (60 percent), while two strains (20 percent) 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 percent, 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.

Plesiomonasshigelloides and Aeromonadaceae family pathogens isolated from marine mammals of Southern and Southeastern Brazilian coast / Plesiomonasshigelloides e patógenos da família Aeromonadaceae isolados de mamíferos marinhos da costa sul e sudeste do Brasil

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 percent of sodium chloride (NaCl), APW plus 3 percent 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 percent), A. caviae (12.3 percent), A. hydrophila (9.6 percent) and P.shigelloides (7 percent). 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.

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 por cento de cloreto de sódio (NaCl) e APA com 3 por cento 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 por cento), A. caviae (12,2 por cento), A. hydrophila (9,6 por cento) e Plesiomonasshigelloides (7 por cento). 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.

Caracterização de Aeromonas spp isoladas de neonatos hospitalizados / Characterization of Aeromonas spp isolates from newborns hospitalized

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 por cento de cloreto de sódio (NaCl) e água peptonada alcalina adicionada de 3 por cento 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 por cento), Aeromonas media (25 por cento), Aeromonas veronii biogrupo sobria (10,7 por cento), Aeromonas hydrophila (9 por cento), Aeromonas veronii biogrupo veronii (5,3 por cento), Aeromonas sobria (1,8 por cento), Aeromonas jandaei (1,8 por cento), Aeromonas schubertii (1,8 por cento) e Aeromonas sp (1,8 por cento). Foi observada resistência a uma ou mais drogas antimicrobianas em 26,8 por cento 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 percent sodium chloride (NaCl) and alkaline peptonated water plus 3 percent 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 percent), Aeromonas media (25 percent), Aeromonas veronii biogroup sobria (10.7 percent), Aeromonas hydrophila (9 percent), Aeromonas veronii biogroup veronii (5.3 percent), Aeromonas sobria (1.8 percent), Aeromonas jandaei (1.8 percent), Aeromonas schubertii (1.8 percent) and Aeromonas sp (1.8 percent). Resistance to one or more antimicrobial drugs was observed in 26.8 percent of the strains. Considering the importance of Aeromonas, there is an urgent need to warn about this in relation to nosocomial infection control.

Resenha histórica / Historic report

A Liga de Assistência Médico-Social (LAMS) do Centro Acadêmico "Rocha Lima" (CARL) surgiu em 1961, sendo posteriomente dividida , em 1994, em três frentes de atuação: Puericultura, Saúde Reprodutiva e Geriatria. Ao longo de sua existência, a LAMS tem desenvolvido atividades diversas envolvendo ensino médico, pesquisa e assistência, com enfoque na atencao à saúde de populações de diferentes faixas etárias: crianças, jovens e idosos