Mortality in sea lions is associated with the introduction of the H5N1 clade 2.3.4.4b virus in Brazil October 2023: whole genome sequencing and phylogenetic analysis.

Clade 2.3.4.4b highly pathogenic avian influenza (HPAI) H5N1 virus was detected in the South American sea lions found dead in Santa Catarina, Brazil, in October 2023. Whole genome sequencing and comparative phylogenetic analysis were conducted to investigate the origin, genetic diversity, and zoonotic potentials of the H5N1 viruses. The H5N1 viruses belonged to the genotype B3.2 of clade 2.3.4.4b H5N1 virus, which was identified in North America and disseminated to South America. They have acquired new amino acid substitutions related to mammalian host affinity. Our study provides insights into the genetic landscape of HPAI H5N1 viruses in Brazil, highlighting the continuous evolutionary processes contributing to their possible adaptation to mammalian hosts.

Escherichia coli carrying blaNDM-1 obtained from a migratory penguin (Spheniscus magellanicus) in the Brazilian seacoast.

The reservoirs for NDM-producing Enterobacterales are increasing, not only in hospitals, but also in the environment and in the community, challenging the therapeutic efficacy of carbapenems. We aimed to characterize an isolate of Escherichia coli harboring the blaNDM-1 gene recovered from the bloodstream of a penguin (Spheniscus magellanicus) in Southern Brazil. A total of 74 bacterial isolates recovered from arterial blood samples from dead birds were submitted to species identification and antibiotic susceptibility evaluation. One isolate presented resistance to carbapenems (E. coli 89PenNDM) and proved to harbor the blaNDM-1 gene by multiplex high-resolution melting real-time PCR (PCR-HRM). Conjugation experiments indicated that the blaNDM-1 was transmissible to E. coli J53. Whole genome sequencing (WGS) confirmed the presence of the blaNDM-1 gene in a conjugative plasmid (IncA/C2 plasmid) in both the E. coli 89PenNDM and its transconjugants. The isolate was classified as ST 156 and many other resistance genes (e.g., sul1, sul,2, strA, floR, tet(A)) were identified, all carried in the same IncA/C2 plasmid. This is the first report of blaNDM-1-producing E. coli isolated from a penguin in the Brazilian seacoast. The presence of a carbapenemase gene in wildlife animals is of concern as they may become reservoirs of multidrug-resistant bacteria and disseminate them to the environment.

Survey of pathogens in threatened wild red-tailed Amazon parrot (Amazona brasiliensis) nestlings in Rasa Island, Brazil.

The red-tailed Amazon parrot (Amazona brasiliensis) is a threatened species of psittacine bird that inhabit coastal regions of Brazil. In view of the threat of this species, the aim of this study was to perform a health evaluation in wild nestlings in Rasa Island, determining the prevalence of enterobacteria and infectious agents according to type of nest. Blood samples were collected from 64 birds and evaluated for antibodies of Chlamydia psittaci by commercial dot-blot ELISA. Cloacal and oropharyngeal swabs samples were collected from 23 birds from artificial wooden nests, 15 birds from PVC nests and 2 birds from natural nests for microbiological analysis. Swab samples were collected from 58 parrots for C. psittaci detection by PCR and from 50 nestlings for Avian Influenza, Newcastle Disease and West Nile viruses' detection analysis by real-time RT-PCR. Ten bacterial genera and 17 species were identified, and the most prevalent were Escherichia coli and Klebsiella oxytoca. There was no influence of the type of nest in the nestlings' microbiota. All samples tested by ELISA and PCR were negative. There is currently insufficient information available about the health of A. brasiliensis and data of this study provide a reference point for future evaluations and aid in conservation plans.

Survey of pathogens in threatened wild red-tailed Amazon parrot (Amazona brasiliensis) nestlings in Rasa Island, Brazil

ABSTRACT The red-tailed Amazon parrot (Amazona brasiliensis) is a threatened species of psittacine bird that inhabit coastal regions of Brazil. In view of the threat of this species, the aim of this study was to perform a health evaluation in wild nestlings in Rasa Island, determining the prevalence of enterobacteria and infectious agents according to type of nest. Blood samples were collected from 64 birds and evaluated for antibodies of Chlamydia psittaci by commercial dot-blot ELISA. Cloacal and oropharyngeal swabs samples were collected from 23 birds from artificial wooden nests, 15 birds from PVC nests and 2 birds from natural nests for microbiological analysis. Swab samples were collected from 58 parrots for C. psittaci detection by PCR and from 50 nestlings for Avian Influenza, Newcastle Disease and West Nile viruses' detection analysis by real-time RT-PCR. Ten bacterial genera and 17 species were identified, and the most prevalent were Escherichia coli and Klebsiella oxytoca. There was no influence of the type of nest in the nestlings' microbiota. All samples tested by ELISA and PCR were negative. There is currently insufficient information available about the health of A. brasiliensis and data of this study provide a reference point for future evaluations and aid in conservation plans.

O uso da microbiologia como ferramenta para a conservação de aves ameaçadas: dados preliminares para o papagaio-de-cara-roxa, Amazona brasiliensis (aves: Psittacidae) no Paraná / Use of microbiology as a tool for the preservation of threatened bird species: preliminary data for the red-tailed amazon, Amazona brasiliensis (birds: Psittacidae) in Paraná / El uso de la microbiología como herramienta para la conservación de aves amenazadas: datos preliminares para el loro de cara púrpura, Amazona brasiliensis (aves: Psittacidae) en Paraná

Amazona brasiliensis, também conhecido popularmente como papagaio-de-cara-roxa, é uma espécie de Psittacidae endêmica da Mata Atlântica distribuída entre o litoral sul de São Paulo e o litoral Norte de Santa Catarina. Este estudo foi concentrado no estado do Paraná, visando uma prévia caracterização do perfil sanitário natural em filhotes da população por meio de análises microbiológicas. O estudo epidemiológico de uma espécie ameaçada inicia-se com a determinação dos agentes infecciosos comuns na população, que provavelmente co-evoluíram com a espécie e representam baixo risco aos espécimes de vida livre. Do total de colônias isoladas quase 75% foram positivas para a família Enterobacteriaceae. Normalmente, a microbiota entérica de psitacídeos é composta por micro-organismos Gram-positivos, porém a alta porcentagem de Gram-negativas isoladas pode ser explicada pela diferença entre a composição microbiana de adultos e filhotes. Seria interessante um estudo mais detalhado para uma eventual comparação entre possíveis sinais clínicos e micro-organismos presentes em cada indivíduo amostrado.(AU)

Amazona brasiliensis, also popularly known as Red-tailed Amazon, is an endemic species to the Atlantic Forest. This Psittacidae range goes from the south coast of São Paulo state to the northern coast of Santa Catarina state. This study focuses on the population in the state of Paraná, aiming to perform a preliminary characterization of the prevalence of natural pathogens in nestlings through microbiological analyses. The epidemiological study of an endangered species begins with the determination of common infectious agents within the population, which probably co-evolved with the species and represent a low risk to free-living specimens. Almost 75% of the colonies isolated were positive for Enterobacteriaceae. Usually, the enteric microbiota of psittacidae consists of Gram-positive microorganisms, but the high percentage of isolated Gram-negative bacteria can be explained by differences between the microbial composition of adults and nestlings. It would be interesting to further develop this study into a more detailed comparison between possible clinical signs and microorganisms present in each individual sampled.(AU)

Amazona brasiliensis, popularmente conocido como el loro de cara púrpura, es una especie endémica de Psittacidae de la Mata Atlántica distribuido entre la costa sur de São Paulo y la costa norte de Santa Catarina. Este estudio se concentra en el estado de Paraná, buscando caracterizar preliminarmente el perfil sanitario natural en crías de la población, por medio del análisis microbiológico. El estudio epidemiológico de una especie amenazada comienza con la determinación de agentes infecciosos comunes en la población, que probablemente ha evolucionado con la especie y representan un riesgo bajo para especímenes de vida libre. Del total de colonias aisladas casi el 75% fueron positivos para Enterobacteriaceae. Normalmente, la microbiota entérica de loros se compone de microorganismos Gram positivos, pero el alto porcentaje de aislados Gram negativas se puede explicar por la diferencia entre la composición microbiana de adultos y pichones. Sería interesante un estudio más detallado para una posible comparación entre los síntomas clínicos y los microorganismos presentes en cada individuo muestreado.(AU)