Evolution and genomic profile of Salmonella enterica serovar Gallinarum biovar Pullorum isolates from Brazil.

Salmonella enterica subspecies enterica serovar Gallinarum biovar Pullorum (S. Pullorum) is a pathogenic bacterium that causes Pullorum disease (PD). PD is an acute systemic disease that affects young chickens, causing white diarrhea and high mortality. Although many sanitary programs have been carried out to eradicate S. Pullorum, PD outbreaks have been reported in different types of birds (layers, broilers, breeders) worldwide. This study aimed to evaluate the evolution and genetic characteristics of S. Pullorum isolated from PD in Brazil. Phylogenetic analysis of S. Pullorum genomes sequenced in this study and available genomic databases demonstrated that all isolates from Brazil are from sequence type 92 (ST92) and cluster into two lineages (III and IV). ColpVC, IncFIC(FII), and IncFII(S) were plasmid replicons frequently found in the Brazilian lineages. Two resistance genes (aac(6')-Iaa, conferring resistance to aminoglycoside, disinfecting agents, and antiseptics (mdf(A)) and tetracycline (mdf(A)) were detected frequently. Altogether, these results are important to understand the circulation of S. Pullorum and, consequently, to develop strategies to reduce losses due to PD.

Evolución y perfil genómico de aislados de Salmonella enterica serovar Gallinarum biovar Pullorum de Brasil. Salmonella enterica subespecie enterica serovar Gallinarum biovar Pullorum (S. Pullorum) es una bacteria patógena que causa la enfermedad de Pullorum (EP). La EP es una enfermedad sistémica aguda que afecta a los pollos jóvenes causando diarrea blanca y alta mortalidad. Aunque se han llevado a cabo muchos programas sanitarios para erradicar S. Pullorum, se han informado brotes de EP en diferentes tipos de aves (ponedoras, pollos de engorde, reproductoras) en todo el mundo. Este estudio tuvo como objetivo evaluar la evolución y las características genéticas de S. Pullorum aislado de EP en Brasil. El análisis filogenético de los genomas de S. Pullorum secuenciados en este estudio y las bases de datos genómicas disponibles demostraron que todos los aislamientos de Brasil son del tipo de secuencia 92 (ST92) y se agrupan en dos linajes (III y IV). ColpVC, IncFIC (FII) e IncFII(S) fueron replicones de plásmidos frecuentemente encontrados en los linajes brasileños. Dos genes de resistencia (aac(6')-Iaa, que confiere resistencia a aminoglucósidos, desinfectantes y antisépticos (mdf(A)), y tetraciclina (mdf(A)) fueron detectados con frecuencia. En conjunto, estos resultados son importantes para comprender la circulación de S. Pullorum y, en consecuencia, desarrollar estrategias para reducir las pérdidas por EP.

Epidemiological Insights into Feline Leukemia Virus Infections in an Urban Cat (Felis catus) Population from Brazil.

Feline leukemia virus (FeLV) is a retrovirus distributed worldwide in domestic cats and with different outcomes (progressive, regressive, abortive, focal). The present study reports an epidemiological survey of FeLV frequency and the evaluation of some risk factors and the two main disease outcomes (progressive and regressive) in an urban cat population from Brazil. A total of 366 cats with sociodemographic information and p27 FeLV antigen test performed were included in the study. FeLV DNA (provirus) in the blood samples of all cats was detected via real-time polymerase chain reaction (qPCR). Plasma samples from 109 FeLV-positive and FeLV-negative cats were also submitted to reverse transcription (RT-qPCR) to determine the FeLV viral load. The results demonstrated that 112 (30.6%) cats were positive through the p27 antigen and/or qPCR. A risk factor analysis demonstrated that cats without vaccination against FeLV (OR 9.9, p < 0.001), clinically ill (OR 2.9, p < 0.001), with outdoors access (OR 2.7, p < 0.001), and exhibiting apathetic behavior (OR 3.1, p < 0.001) were more likely to be infected with FeLV. FeLV-infected cats were also more likely to present with anemia (OR 13, p < 0.001) and lymphoma (OR 13.7, p = 0.001). A comparative analysis of the different detection methods in a subset of 109 animals confirmed FeLV infection in 58 cats, including 38 (65.5%) with progressive, 16 (27.6%) with regressive, and 4 (6.9%) with probably focal outcome diseases. In conclusion, this study demonstrates a high prevalence of FeLV in this urban cat population from Brazil and highlights the need to establish more effective prevention strategies (such as viral testing, vaccination programs, specific care for FeLV-positive cats) to reduce diseases associated with this virus in Brazil.

Canine parvovirus type 2 (CPV-2) serological and molecular patterns in dogs with viral gastroenteritis from southern Brazil.

Canine Parvovirus type 2 (CPV-2) is a highly contagious virus that can cause severe systemic disease with gastroenteric symptoms in dogs, particularly in young puppies. Originating from the feline parvovirus in the late 1970s, it swiftly propagated globally, instigating a pandemic in dogs. Despite vaccination advancements, CPV-2 remains a substantial challenge for veterinary professionals and pet owners. This study aimed to contribute knowledge about the current situation of CPV-2 among dogs in southern Brazil. In this study, the sera of 125 dogs (mostly with gastroenteritis symptoms) were screened for antibodies against CPV-2 and their faeces for the virus itself. The results showed that 40% (50/125) of dogs were infected with CPV-2. Most animals (65.5%) had previously been exposed to CPV-2 (with serotitres equal or above 1:40), and only 37.6% had protective antibody titres equal or above 1:80. The findings have also demonstrated that vaccination against CPV-2 significantly reduced the risk of infection, with positive cases decreasing from 56.9% (unvaccinated) to 2.0% (fully vaccinated). Furthermore, the prevalence of CPV-2 decreased as dogs aged, with younger dogs and those with an incomplete or non-existent vaccination history at the highest risk of infection. In conclusion, this study provides valuable insight into the prevalence and risk factors associated with CPV-2 infection in dogs in southern Brazil, thereby providing valuable knowledge for the improvement of veterinary care and pet health.

Antiviral alternatives against important members of the subfamily Parvovirinae: a review.

Parvoviruses are responsible for multiple diseases, and there is a critical need for effective antiviral therapies. Specific antiviral treatments for parvovirus infections are currently lacking, and the available options are mostly supportive and symptomatic. In recent years, significant research efforts have been directed toward understanding the molecular mechanisms of parvovirus replication and identifying potential targets for antiviral interventions. This review highlights the structure, pathogenesis, and treatment options for major viruses of the subfamily Parvovirinae, such as parvovirus B19 (B19V), canine parvovirus type 2 (CPV-2), and porcine parvovirus (PPV) and also describes different approaches in the development of antiviral alternatives against parvovirus, including drug repurposing, serendipity, and computational tools (molecular docking and artificial intelligence) in drug discovery. These advances greatly increase the likelihood of discoveries that will lead to potent antiviral strategies against different parvovirus infections.

Antimicrobial activity of essential oils against Staphylococcus aureus and Staphylococcus chromogenes isolated from bovine mastitis.

Staphylococcus aureus and Staphylococcus chromogenes are pathogens frequently detected in bovine mastitis. Treatment and prevention of this disease have been usually carried on with antimicrobials. However, the emergence of bacterial isolates with antimicrobial resistance has aroused interest in new therapeutic alternatives. Plant essential oils (EOs) have been largely studied as antibacterial treatments. In the present study, EOs from five plants were evaluated for their antibacterial activities against S. aureus and S. chromogenes. Bacterial isolates were obtained in a previous study of clinical cases of bovine mastitis. EOs from lemongrass, eucalyptus, lavender, peppermint, and thyme were obtained by hydrodistillation and their chemical compositions were evaluated by gas chromatography (GC). Minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) were evaluated for all EOs. The results demonstrated that citral (40.9%), myrcene (24.7%), and geraniol (1.9%) were detected in lemongrass EO; 1,8-cineole (76.9%), α-pinene (8.2%), and ledene (5.1%) in eucalyptus EO; 1,8-cineole (45.2%), camphor (18.2%), and fenchone (14.6%) in lavender EO; L-menthol (38.5%), menthofuran (16.3%), and citronellal (10.6%) in peppermint EO; and thymol (44.2%), p-cymene (24.6%) and 1,8-cineole (9.9%) in thyme EO. More effective antibacterial activities were observed only with the use of lemongrass (MIC and MBC ranging from 0.39 to 3.12 mg/mL and 0.39 to 6.35 mg/mL, respectively) and thyme (MIC and MBC ranging from 0.39 to 1.56 mg/mL and 0.39 to 3.12 mg/mL, respectively). Peppermint, lavender and eucalyptus EOs did not show bactericidal activities. In conclusion, lemongrass and thyme EOs are promising antibacterial alternatives against Staphylococcus species associated with bovine mastitis.

Canine Parvovirus 2 in Free-Living Wild Mammals from Southern Brazil.

Pathogens from domestic canines represent a significant and constant threat to wildlife. This study looked for four common canine pathogens, Babesia vogeli, Ehrlichia canis, Leishmania infantum, and canine parvovirus 2 (CPV-2) in mammals from the Pampa Biome, southern Brazil. Animals killed by vehicular trauma on a road traversing this biome were evaluated over a 1-yr period. Tissues collected from 31 wild mammals and six dogs were further analyzed by specific real-time PCR assays for each pathogen. Babesia vogeli and L. infantum were not detected in any investigated animal. Ehrlichia canis was detected in one dog and CPV-2 in nine animals: four dogs, three white-eared opossums (Didelphis albiventris), one pampas fox (Lycalopex gymnocercus), and one brown rat (Rattus norvegicus). These results demonstrate the occurrence of important carnivore pathogens (E. canis and CPV-2) in domestic dogs and wild mammals from the Pampa Biome in southern Brazil.

Evolution and Epidemic Spread of the Avian Infectious Bronchitis Virus (IBV) GI-23 in Brazil.

Infectious bronchitis virus (IBV) is a pathogen affecting poultry flocks worldwide. GI-23 is an IBV lineage with a rapid spread into different continents of the world, and it was reported for the first time in South American/Brazilian broiler farms last year. This study aimed to investigate the recent introduction and epidemic spread of IBV GI-23 in Brazil. Ninety-four broiler flocks infected with this lineage were evaluated from October 2021 to January 2023. IBV GI-23 was detected using real-time RT-qPCR, and the S1 gene hypervariable regions 1 and 2 (HVR1/2) were sequenced. S1 complete and HVR1/2 nucleotide sequence datasets were used to carry out phylogenetic and phylodynamic analyses. Brazilian IBV GI-23 strains clustered into two specific subclades (SA.1 and SA.2), both in tree branches with IBV GI-23 from Eastern European poultry-producing countries, suggesting two independent and recent introductions (around 2018). Viral phylodynamic analysis showed that the IBV GI-23 population increased from 2020 to 2021, remaining constant for one year and declining in 2022. S1 amino acid sequences from Brazilian IBV GI-23 presented specific and characteristic substitutions in the HVR1/2 for subclades IBV GI-23 SA.1 and SA.2. This study brings new insights into the introduction and recent epidemiology of IBV GI-23 in Brazil.

Canine parvovirus type 2 vaccines in Brazil: Viral load in commercial vaccine vials and phylogenetic analysis of the vaccine viruses.

Canine parvovirus type 2 (CPV-2) is the etiological agent of a highly contagious and frequently fatal disease in dogs. Live attenuated vaccines (LAV) are recommended to prevent and control this disease. Commercial vaccines are typically produced with CPV-2 strains adapted to cell culture and usually non-pathogenic. The present study aimed to determine the viral load of CPV-2 vaccines commercially available in Brazil and to characterize the vaccine virus by DNA analysis of its capsid gene. The results demonstrated that all vaccine strains presented high homology of the VP2 gene and they were all closely related to the original CPV-2 strains. However, vaccine strains presented several differences in comparison with field strains currently circulating in Brazil. Seventy-one vials contained viral loads ranging from 7.4E3 to 4.9E10 DNA copies/ml. Nine vials did not contain any detectable CPV-2 DNA. In conclusion, there are genetic and antigenic differences among CPV-2 vaccines and field strains. Additionally, some vaccines have been commercialized with low titers of CPV-2. It is important to improve the quality of the vaccines to prevent or reduce the spread of CPV-2 in Brazil.

Infecção cervical por papilomavírus humano em mulheres idosas / Cervical human papillomavirus infection in older women

Resumo Objetivo Investigar a presença de infecção cervical pelo papilomavírus humano (HPV, human papillomavirus) em mulheres idosas e fatores relacionados. Método Trata-se de um estudo transversal, retrospectivo e descritivo, com abordagem quantitativa. A amostra foi constituída por 106 mulheres com idade igual ou superior a 60 anos atendidas em serviços de saúde pública de uma cidade do Sul do Brasil, as quais realizaram coleta de material cervical para análise citológica e detecção molecular do DNA do HPV, bem como levantamento de dados clínicos e sociodemográficos por meio de um questionário padronizado e requisição do exame citopatológico. Resultados A idade das pacientes variou entre 60 e 82 anos, com média de 64,9 ± 5,1. O HPV foi detectado em 14 (13,2%) idosas avaliadas no estudo e 8 tipos virais foram identificados, a maioria (n=7; 87,5%) de alto risco oncogênico. Observou-se, por análise de qui-quadrado, que casos HPV positivos possuem associação com maior número de parceiros sexuais (p= 0,018). Na citologia, a maioria das mulheres (n=102; 96,2%) apresentou resultado negativo para lesão intraepitelial ou malignidade e duas (1,8%) apresentaram citologia alterada, mas destas, nenhuma apresentou infecção por HPV no teste molecular. Das 10 mulheres avaliadas em duas visitas, sete (70%) não apresentaram infecção pelo HPV em ambas as avaliações, duas (20%) eliminaram a infecção pelo HPV e uma (10%) apresentou conversão para positividade. Nenhuma delas apresentou infecção persistente. Conclusão Mulheres idosas estão suscetíveis à infecção por HPV e às lesões causadas por esse vírus, por isso devem manter o rastreamento citológico.

Abstract Objective To investigate the presence of cervical infection by human papillomavirus (HPV) and associated factors in older women Method A cross-sectional, retrospective descriptive study with a quantitative approach was conducted. The sample comprised 106 women aged 60 years or over, seen at public health services of a city in southern Brazil, who underwent cervical cell collection for cytological analysis and molecular detection of HPV DNA. Clinical and sociodemographic data were collected using a standardized questionnaire and from Pap test result Results Patient age was 60-82 years, with a mean of 64.9 ± 5.1 years. HPV was detected in 14 (13.2%) of the study participants and 8 viral types were identified, the majority (n=7; 87.5%) of high oncogenic risk. Chi-square analysis revealed that positive HPV cases were associated with a higher number of sexual partners (p= 0.018). On cytology, most of the women (n=102; 96.2%) had a negative result for intraepithelial lesion or malignancy, and two (1.8%) had abnormal cytology, but neither were positive for HPV infection on molecular testing. Of the 10 women evaluated at two visits, seven (70%) tested negative for HPV infection on both evaluations, two (20%) eliminated the HPV infection, and one (10%) showed conversion to positive infection status. None of the cases had persistent infection. Conclusion Older women are susceptible to HPV infection and to the lesions caused by the virus. This group should therefore continue regular cytological screening.

Emergence and molecular characterization of the avian infectious bronchitis virus GI-23 in commercial broiler farms from South America.

Avian infectious bronchitis virus (IBV) is the etiological agent of a highly contagious disease in the poultry industry. The spike protein (S1 subunit) is responsible for the molecular diversity of the virus and many genetic types, and lineages are described worldwide. IBV genetic type I-strain 23 (GI-23) has spread across different continents (including Asia, Europe and Africa), causing multiple outbreaks and severe economic losses throughout the poultry industry in the last decade. The present study aimed to report the emergence and molecular characterization of GI-23 in South Brazil, being detected for the first time in South America. Eighty-two broiler flocks presenting clinical suspicion of infectious bronchitis were selected for this study. Tracheal, renal and intestinal samples were collected for IBV detection and genotyping. A total of 57 flocks were positive for IBV by generic RT-qPCR targeting 5' untranslated region and 31 also tested positive for GI-11 by a specific RT-qPCR targeting S1 gene for this lineage. The remaining 26 IBV-positive samples were genotyped by partial and one by complete S1 gene/protein sequencing. Phylogenetic analysis demonstrated that all of them clustered into a specific branch of the GI-23. S1 protein sequence analysis evidenced that all Brazilian GI-23 IBVs had the two characteristic amino acid substitutions A93T and S/H118P/L, but other changes were also observed, such as S37F (n = 21; 81%), G117S (n = 17, 65%), P122S (n = 16; 61%) and W71R (n = 9; 35%). This study brings new insights into the epidemiology of the IBV GI-23 in the world, highlighting its emergence and molecular characteristics in Brazil, South America.

Emergence, Dissemination and Antimicrobial Resistance of the Main Poultry-Associated Salmonella Serovars in Brazil.

Salmonella infects poultry, and it is also a human foodborne pathogen. This bacterial genus is classified into several serovars/lineages, some of them showing high antimicrobial resistance (AMR). The ease of Salmonella transmission in farms, slaughterhouses, and eggs industries has made controlling it a real challenge in the poultry-production chains. This review describes the emergence, dissemination, and AMR of the main Salmonella serovars and lineages detected in Brazilian poultry. It is reported that few serovars emerged and have been more widely disseminated in breeders, broilers, and layers in the last 70 years. Salmonella Gallinarum was the first to spread on the farms, remaining as a concerning poultry pathogen. Salmonella Typhimurium and Enteritidis were also largely detected in poultry and foods (eggs, chicken, turkey), being associated with several human foodborne outbreaks. Salmonella Heidelberg and Minnesota have been more widely spread in recent years, resulting in frequent chicken/turkey meat contamination. A few more serovars (Infantis, Newport, Hadar, Senftenberg, Schwarzengrund, and Mbandaka, among others) were also detected, but less frequently and usually in specific poultry-production regions. AMR has been identified in most isolates, highlighting multi-drug resistance in specific poultry lineages from the serovars Typhimurium, Heidelberg, and Minnesota. Epidemiological studies are necessary to trace and control this pathogen in Brazilian commercial poultry production chains.

Molecular survey of porcine respiratory disease complex pathogens in Brazilian wild boars.

Wild boar (Sus scrofa) is an exotic invasive species in Brazil and may be a reservoir for several pathogens, including those related to the porcine respiratory disease complex (PRDC), a critical infectious disease in pig production. The objective of this study was to investigate viral and bacterial pathogens related to PRDC in free-living wild boars from Brazil. Eighty animals were examined in search of genomes of porcine circovirus 2 (PCV2), Torque teno Sus virus 1a (TTSuV1a) and 1b (TTSuV1b), Influenza A virus (IAV), Actinobacillus pleuropneumoniae, Glaesserella parasuis, Pasteurella multocida, and Mycoplasma hyopneumoniae. The results demonstrated that 57.5% (46/80) of the animals had at least one detected pathogen, and 11.3% of them (9/80) were co-infected. TTSuV1a was the most prevalent genome, for which risk factors were associated with increased contact between wild boars and other animals. The other pathogens were detected at much lower frequencies or not detected (M. hyopneumoniae and IAV). An additional IAV serology search identified H1N1pdm09 antibodies in 35.5% (16/45) of the wild boars, bringing concern related to public health. In conclusion, wild boars are infected with pathogens that cause swine diseases, so their eventual contact with domestic pigs might risk animal production in Brazil.

Polymerase chain reaction and loop-mediated isothermal amplification targeting lic13162, lic20239, and lipL32 genes for leptospirosis diagnosis.

Leptospirosis is a zoonotic disease caused by pathogenic species of Leptospira. Due to the similarity with clinical signs of other febrile diseases, early diagnosis remains challenging. Real-time PCR has been used for direct detection of Leptospira, but it requires thermocyclers and highly trained personnel. Loop-mediated isothermal amplification (LAMP) is a simple and rapid DNA-based assay. Therefore, here we have developed PCR and LAMP assays targeting two novel genes, lic13162 and lic20239, and also lipL32 gene to detect pathogenic Leptospira. Analytical and diagnostic performances were compared with bacterial isolates (including different Leptospira species and serovars) and clinical samples. The results demonstrated that PCR assays targeting lic13162 and lic20239 were successful to amplify Leptospira, but LAMP not. However, both PCR and LAMP targeting lipL32 could detect pathogenic Leptospira. LAMP lipL32 could be performed in 30 min with a detection limit of 156 cells/mL. Diagnostic performance of lipL32-LAMP presented 84.2% sensitivity and 93.2% specificity. In conclusion, lipL32 PCR and LAMP are effective methods to detect pathogenic Leptospira directly from clinical samples.

Molecular phylogenetic assessment of the canine parvovirus 2 worldwide and analysis of the genetic diversity and temporal spreading in Brazil.

Canine parvovirus type 2 (CPV-2) is a relevant pathogen for dogs and causes a severe disease in carnivore species. CPV-2 reached pandemic proportions after the 1970s with the worldwide dissemination, generating antigenic and genetic variants (CPV-2a, CPV-2b, and CPV-2c) with different pathobiology in comparison with the original type CPV-2. The present study aimed to assess the current global CPV-2 molecular phylogeny and to analyze genetic diversity and temporal spreading of variants from Brazil. A total of 284 CPV-2 whole-genome sequences (WGS) and 684 VP2 complete genes (including 23 obtained in the present study) were compared to analyze phylogenetic relationships. Bayesian coalescent analysis estimated the time to the most recent common ancestor (tMRCA) and the population dynamics of the different CPV-2 lineages in the last decades. The WGS phylogenetic tree demonstrated two main clades disseminated worldwide today. The VP2 gene tree showed a total of four well-defined clades distributed in different geographic regions, including one with CPV-2 sequences exclusive from Brazil. These clades do not have a relationship with the previous classification into CPV-2a, CPV-2b, and CPV-2c, despite some having a predominance of one or more antigenic types. Temporal analysis demonstrated that the main CPV-2 clades evolved within a few years (from the 1980s to 1990s) in North America and they spread worldwide afterwards. Population dynamics analysis demonstrated that CPV-2 presented a major dissemination increase at the end of the 1980s / beginning of the 1990s followed by a period of stability and a second minor increase from 2000 to 2004.

Molecular detection of respiratory coinfections in pig herds with enzootic pneumonia: a survey in Brazil.

Mycoplasma hyopneumoniae is the primary etiologic agent of swine enzootic pneumonia (EP), in which the immune response is reduced, making pigs susceptible to secondary infections. We surveyed commercial pig herds in Brazil for viral and bacterial respiratory coinfections that could complicate EP. Over a 2-y period (2015-2016), we found that 854 of 2,206 pigs (38.7%) were positive for M. hyopneumoniae in herds from various production systems in 3 Brazilian regions (Central-West, Southeast, South). We collected samples of 321 lungs positive for M. hyopneumoniae from 169 farms to also screen for Pasteurella multocida, Actinobacillus pleuropneumoniae, Glaesserella parasuis, influenza A virus (IAV), and porcine circovirus 2 (PCV2) by real-time PCR. The prevalence of pathogens found in addition to M. hyopneumoniae varied: P. multocida (141; 43.9%), G. parasuis (71; 22.1%), PCV2 (50; 15.6%), IAV (23; 7.2%), and A. pleuropneumoniae (18; 5.6%). G. parasuis was more frequent in farrowing or nursery herds (48.7%) than in breeding and fattening herds (10% and 18.6%, respectively; p < 0.01); A. pleuropneumoniae was found only in herds on farrow-to-finish and fattening farms.

Recent molecular evolution of hepatitis B virus genotype F in Latin America.

The evolution of hepatitis B virus genotype F (HBV-F) in Latin America is not completely understood. The aim of this study was to evaluate the molecular evolution of HBV-F in Latin America by comparing 224 whole-genome sequences. Bayesian coalescent analysis was performed to estimate the time to the most recent common ancestor. Four main clades were found, dating from between 1245 and 1730. In addition, four subclades were identified, dating to between 1705 and 1801. The overall effective population size of HBV-F grew in the 18th century and showed an initial expansion outward from Venezuela to other countries from Latin America. Although HBV-F originated thousands of years ago, circulating strains of HBV-F appear to have spread in recent centuries, particularly in the 18th and 19th centuries. The new molecular data provide valuable information for characterizing the evolution of Native American HBV-F in recent centuries.

Temporal spread and evolution of SARS-CoV-2 in the second pandemic wave in Brazil.

Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) pandemic spread rapidly and this scenario is concerning in South America, mainly in Brazil that presented more than 21 million coronavirus disease 2019 cases and 590 000 deaths. The recent emergence of novel lineages carrying several mutations in the spike protein has raised additional public health concerns worldwide. The present study describes the temporal spreading and evolution of SARS-CoV2 in the beginning of the second pandemic wave in Brazil, highlighting the fast dissemination of the two major concerning variants (P.1 and P.2). A total of 2507 SARS-CoV-2 whole-genome sequences (WGSs) with available information from the country (Brazil) and sampling date (July 2020-February 2021), were obtained and the frequencies of the lineages were evaluated in the period of the growing second pandemic wave. The results demonstrated the increasing prevalence of P.1 and P.2 lineages in the period evaluated. P.2 lineage was first detected in the middle of 2020, but a high increase occurred only in the last trimester of this same year and the spreading to all Brazilian regions. P.1 lineage emerged even later, first in the North region in December 2020 and really fast dissemination to all other Brazilian regions in January and February 2021. All SARS-CoV-2 WGSs of P.1 and P.2 were further separately evaluated with a Bayesian approach. The rates of nucleotide and amino acid substitutions were statistically higher in P.1 than P.2 (p < 0.01). The phylodynamic analysis demonstrated that P.2 gradually spread in all the country from September 2020 to January 2021, while P.1 disseminated even faster from December 2020 to February 2021. Skyline plots of both lineages demonstrated a slight rise in the spreading for P.2 and exponential growth for P.1. In conclusion, these data demonstrated that the P.1 (recently renamed as Gamma) and P.2 lineages have predominated in the second pandemic wave due to the very high spreading across all geographic regions in Brazil at the end of 2020 and beginning of 2021.

Avian Reoviruses in Poultry Farms from Brazil.

Avian reovirus (ARV) is highly disseminated in commercial Brazilian poultry farms, causing arthritis/tenosynovitis, runting-stunting syndrome, and malabsorption syndrome in different meat- and egg-type birds (breeders, broilers, grillers, and layers). In Brazil, ARV infection was first described in broilers in the 1970s but was not considered an important poultry health problem for decades. A more concerning outcome of field infections has been observed in recent years, including condemnations at slaughterhouses because of the unsightly appearance of chicken body parts, mainly the legs. Analyses of the performance of poultry flocks have further evidenced economic losses to farms. Genetic and antigenic characterization of ARV field strains from Brazil demonstrated a high diversity of lineages circulating in the entire country, including four of the five main phylogenetic groups previously described (I, II, III, and V). It is still unclear if all of them are associated with different diseases affecting flocks' performance in Brazilian poultry. ARV infections have been controlled in Brazilian poultry farms by immunization of breeders and young chicks with classical commercial live vaccine strains (S1133, 1733, 2408, and 2177) used elsewhere in the Western Hemisphere. However, genetic and antigenic variations of the field isolates have prevented adequate protection against associated diseases, so killed autogenous vaccines are being produced from isolates obtained on specific farms. In conclusion, ARV field variants are continuously challenging poultry farming in Brazil. Epidemiological surveillance combined with molecular biological analyses from the field samples, as well as the development of vaccine strains directed toward the ARV circulating variants, are necessary to control this economically important poultry pathogen.

Reovirus aviares en granjas avícolas de Brasil. El reovirus aviar (ARV) está muy diseminado en las granjas avícolas comerciales brasileñas y causa artritis/tenosinovitis viral, síndrome de retraso de enanismo infeccioso y síndrome de malabsorción en diferentes tipos de aves de carne y huevos (reproductoras, pollos de engorde, parrillas y ponedoras). En Brasil, la infección por reovirus aviares se describió por primera vez en pollos de engorde en la década de 1970, pero no se consideró un problema importante de salud avícola durante décadas. En los últimos años se ha observado un resultado más preocupante de las infecciones de campo, incluidos los decomisos en las plantas de procesamiento debido a la apariencia antiestética de las partes del cuerpo de los pollos, principalmente las patas. Los análisis del desempeño de las parvadas avícolas han evidenciado pérdidas económicas adicionales para las granjas. La caracterización genética y antigénica de las cepas de campo de reovirus aviares de Brasil demostró una gran diversidad de linajes que circulan en todo el país, incluidos cuatro de los cinco grupos filogenéticos principales descritos anteriormente (I, II, III y V). Todavía no está claro si todos ellos están asociados con diferentes enfermedades que afectan el rendimiento de las parvadas en las aves de corral brasileñas. Las infecciones por reovirus aviares se han controlado en granjas avícolas brasileñas mediante la inmunización de reproductores y pollitos jóvenes con cepas vacunales vivas comerciales clásicas (S1133, 1733, 2408 y 2177) utilizadas en otras partes del hemisferio occidental. Sin embargo, las variaciones genéticas y antigénicas de los aislamientos de campo han impedido una protección adecuada contra enfermedades asociadas, por lo que se están produciendo vacunas autógenas inactivadas a partir de aislamientos obtenidos en granjas específicas. En conclusión, las variantes de campo de ARV son un desafío continuo para la avicultura en Brasil. La vigilancia epidemiológica combinada con análisis de biología molecular de las muestras de campo, así como el desarrollo de cepas de vacunas dirigidas a las variantes circulantes de los reovirus aviares, son necesarias para controlar este patógeno avícola económicamente importante.

Species identification and antimicrobial susceptibility profile of bacteria associated with cow mastitis in southern Brazil / Identificação de espécies e perfil de suscetibilidade aos antimicrobianos de bactérias associadas à mastite bovina no sul do Brasil

Bovine mastitis is the most common disease in dairy cattle and responsible for economic losses in the milk industry. The present study aimed to identify the main species and to evaluate the antimicrobial susceptibility of bacterial isolates from cow herds with mastitis in dairy farms from southern Brazil. A total of 107 milk samples were collected from different cow herds in one important dairy producing region in southern Brazil, including farms located in ten cities from the Northeast region in the Rio Grande do Sul state. Bacterial strains were isolated and submitted to presumptive identification by classical bacteriological methods. Bacterial species were also identified by MALDI-TOF MS and antimicrobial susceptibility testing was performed with 12 antimicrobials commonly used in dairy farms. Fifty-one bacterial strains were isolated and the presumptive identification demonstrated the occurrence of Staphylococcus spp. (82.3%), Bacillus spp. (3.9%), Klebsiella spp. (3.9%), Streptococcus spp. (3.9%), Corynebacterium sp. (2%), Enterococcus sp. (2%) and Serratia sp. (2%). Forty-one isolates were successfully identified in the MALDI-TOF analysis, including 35 isolates from eleven different bacterial species. Importantly, there were eight different Staphylococcus species, with a high frequency of Staphylococcus chromogenes (48.6%) and Staphylococcus aureus (20%). Overall, bacterial isolates demonstrated resistance to penicillin (46.3%), tetracycline (39%), amoxicillin (36.6%), ampicillin (34.1%) and sulfamethoxazole/trimethoprim (31.7%). Enrofloxacin was the unique antimicrobial that all isolates were susceptible. In addition, there were six multidrug resistant isolates (five S. chromogenes and one S. aureus). This study highlights that bacterial pathogens with resistance to several antimicrobials were identified in cows from dairy farms in a very important milk producing region located in southern Brazil. Microbial identification of the bovine mastitis pathogens and determination of the antimicrobial profile is necessary for the rational use of the medicines.

A mastite bovina é a doença mais comum em gado leiteiro e responsável por perdas econômicas na indústria de laticínios. O presente estudo teve como objetivo identificar as principais espécies e avaliar a suscetibilidade antimicrobiana de isolados bacterianos de rebanhos bovinos com mastite em fazendas leiteiras no sul do Brasil. Um total de 107 amostras de leite foram coletadas em diferentes rebanhos bovinos em uma importante região produtora de leite do sul do Brasil, incluindo fazendas localizadas em 10 cidades da região Nordeste do estado do Rio Grande do Sul. As cepas bacterianas foram isoladas e submetidas à identificação presuntiva por métodos bacteriológicos clássicos. A identificação bacteriana foi confirmada por MALDI-TOF MS e o teste de sensibilidade antimicrobiana foi realizado com antimicrobianos comumente usados em fazendas leiteiras. Cinquenta e uma cepas bacterianas foram isoladas e a identificação presuntiva demonstrou a ocorrência de Staphylococcus spp. (82,3%), Bacillus spp. (3,9%), Klebsiella spp. (3,9%), Streptococcus spp. (3,9%), Corynebacterium sp. (2%), Enterococcus sp. (2%) e Serratia sp. (2%). Os 41 isolados foram identificados com sucesso na análise MALDI-TOF, incluindo 35 isolados de onze espécies bacterianas diferentes. É importante ressaltar que houve a ocorrência de oito espécies diferentes de Staphylococcus, com alta frequência de Staphylococcus chromogenes (48,6%) e Staphylococcus aureus (20%). No geral, os isolados bacterianos tiveram alta resistência à penicilina (46,3%), tetraciclina (39%), amoxicilina (36,6%), ampicilina (34,1%) e sulfametoxazol/trimetoprima (31,7%). A enrofloxacina foi o único antimicrobiano que todos os isolados foram suscetíveis. Além disso, havia seis isolados multirresistentes (cinco S. chromogenes e um S. aureus). Este estudo destaca que os patógenos bacterianos com resistência aos antimicrobianos estão presentes em fazendas leiteiras de subsistência em uma importante região produtora no sul do Brasil. É necessário o monitoramento constante dos patógenos da mastite bovina e a determinação de seu perfil antimicrobiano para o uso racional dos medicamentos.