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Antimicrobial resistance (AMR) is a major global public threat, now largely reported in natural environments. Seabirds are carriers of extended-spectrum ß-lactamase-producing Escherichia coli (ESBL-E. coli), but different foraging and breeding behaviour could impact ESBL-E. coli circulation. We compared the prevalence and genetic determinants of ESBL-E. coli from resident Kelp gulls (Larus dominicanus, Ld), migratory Franklin's gulls (Larus pipixcan, Lp), and endemic Peruvian pelicans (Pelecanus thagus, Pt) from the Humboldt Current Ecosystem (HCE) of central Chile. From 2020 to 2022, we collected 699 fresh faecal samples (Ld = 449, Lp = 116, Pt = 134), and isolated 271 ESBL-E. coli (39 %). Whole-genome-sequencing (WGS) was performed on 85 E. coli selected isolates to identify their Sequence Type (ST), AMR genes, virulence genes, mobile genetic elements (MGE), and to assess potential interspecies transmission. ESBL-genes were detected in the remaining ESBL-E. coli isolates by PCR. ESBL-E. coli prevalence in Ld (46 % [CI: 42-51 %]) and Pt (34 % [CI: 27-43 %]) was higher than in Lp (15 % [CI: 9-22 %]). WGS revealed 41 ESBL-E. coli STs including pandemic clones ST10, ST58, ST131 and ST410. The blaCTX-M-1 and blaCTX-M-15 genes were the most prevalent among ESBL genes, and were mostly associated with MGE IncI1-I(Alpha) and ISEc9. We also report the pAmpC blaCMY-2 gene associated to MGE Inc1-I(Alpha) and IS640 in two E. coli from a Ld and a Lp. Eight ESBL-E. coli of the same ST were shared by at least two seabird species, including ST10 (Ld and Pt); ST88, ST410 and ST617 (Pt and Lp); ST38, ST58, ST131, and SST1722 (three species). Single nucleotide polymorphism (SNP) phylogenetic analyses of ST38, ST617 and ST1722 showed a low difference of SNPs between STs found in different seabird species, suggesting ESBL-E. coli clonal exchanges. Our results highlight ESBL-E. coli dissemination across seabirds of the HCE, including species that unusually forage on human waste like pelicans.

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Bacterial antibiotic resistance is a public health problem affecting humans and animals. This study focuses on identifying Gram-negative bacilli (GNB) (MALDI-TOF MS and Klebsiella MALDI TypeR) resistant to antimicrobials in freshly emitted feces of healthy captive and rescued wild birds from a zoo in Brazil. Birds from the zoo and rescued from sixteen different orders were investigated. Resistant bacteria from feces were selected (MacConkey agar with 2 µg/mL cefotaxime). Genomic similarity and plasmid were investigated by Pulsed-Field Gel Electrophoresis of XbaI fragments (XbaI-PFGE) and S1-PFGE. Polymerase Chain Reaction (PCR) was performed to search for beta-lactamase genes. From 80 birds included, 26 from the zoo (50 %) and 18 rescued wild birds (64 %) presented cefotaxime-resistant GNB. E. coli and Klebsiella spp were the most prevalent species. Among 65 isolates from the zoo and rescued wild birds, 75 % were considered multidrug-resistant (MDR). The majority of the isolates were extended-spectrum beta-lactamases (ESBL) producing and resistant to enrofloxacin. blaCTX-M-GROUP-1, blaTEM, and blaSHV were the most detected genes, and blaKPC was detected in K. pneumoniae complex. According to genomic similarity results, some identical profiles were found in birds with no known contact among the zoo or rescued birds. Several isolates carried one to three plasmids (15-350 kb). The presence of multidrug-resistant (MDR) isolates from healthy captive and wild birds brings novel data on the dissemination of these elements to the environment.

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This study aimed to investigate the presence of Mycoplasma spp. and identify the species of mycoplasma isolates obtained from seabirds found on Brazilian coastal beaches. Tracheal and cloacal swab samples were collected from 50 seabirds rescued by three conservation and marine animal rehabilitation centers located in Brazil. The tracheal and cloacal samples were subjected to mycoplasma culture and the isolates were identified through PCR. A "Mollicutes-specific" 16S rRNA PCR reaction was employed for triage. Four species-specific PCR reactions were used to detect Mycoplasma gallisepticum, Mycoplasma synoviae, Mycoplasma meleagridis, or M. gallinarum. The Mollicutes positive and species negative samples were submitted do 16S rRNA sequencing. Eighteen (36%) of 50 seabirds tested positive for mycoplasma by culture. In the PCR for the genus, 28 (56%) of 50 seabirds were positive for Mycoplasma spp., with 13 (26%) detected in the trachea, one (2%) in the cloaca, and 14 (28%) in both sites. In the species-specific PCR, M. gallisepticum was detected in 17.8%, and M. meleagridis in 17.8%. Both species were detected in 14.3%. Of the isolates not characterized at species level, we obtained ten sequences and they were divided into three clusters. The first cluster was closely related to M. meleagridis, the second to M. synoviae, and the third grouped M. tully, M. gallisepticum, and M. imitans. Four and five of nine species of seabirds studied had mycoplasma detected by culture or PCR, respectively. Mycoplasmas were found in the majority of the animals studied, with the highest prevalence proportionally found in Sula leucogaster, and the lowest in Fregata magnificens. The phylogenetic analysis identified Mycoplasma spp. adapted to aquatic birds.

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Despite the worldwide occurrence of bartonellae in a broad range of mammal species, in which they usually cause a long-lasting erythrocytic bacteremia, few studies reported Bartonella spp. in avian hosts. The present work aimed to investigate the occurrence and molecular identity of Bartonella spp. infecting birds in the Pantanal wetland, central-western Brazil using a multigene approach. For this purpose, blood samples were collected from 517 individuals from 13 avian orders in the states of Mato Grosso and Mato Groso do Sul. DNA was extracted from avian blood and 500/517 (96.7%) samples were positive in a conventional PCR targeting the avian ß-actin gene. Nineteen (3.8%) out of 500 avian blood samples were positive in a qPCR assay for Bartonella spp. based on the nuoG gene. Among 19 avian blood DNA samples positive in the qPCR for Bartonella spp., 12 were also positive in the qPCR for Bartonella based on the 16S-23S RNA Intergenic region (ITS). In the PCR assays performed for molecular characterization, one 16S rRNA, three ribC, and one nuoG sequences were obtained. Based on BLASTn results, while 1 nuoG, 2 ribC, and 2 ITS sequences showed high identity to Bartonella henselae, one 16S rRNA and 2 ITS showed high similarity to Bartonella machadoae in the sampled birds. Bartonella spp. related to B. henselae and B. machadoae were detected, for the first time, in wild birds from the Brazilian Pantanal.

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We assessed soil fungal and fungal-like diversity using metabarcoding in ornithogenically influenced soils around nests of the bird species Phalacrocorax atriceps, Macronectes giganteus, Pygoscelis antarcticus, and Pygoscelis adelie on the South Shetland Islands, maritime Antarctic. A total of 1,392,784 fungal DNA reads was obtained and assigned to 186 amplicon sequence variants (ASVs). The dominant fungal phylum was Ascomycota, followed by Basidiomycota, Chytridiomycota, Blastocladiomycota, Rozellomycota, Mortierellomycota, Monoblepharomycota, Aphelidiomycota, Basidiobolomycota, Mucoromycota, and the fungal-like Oomycota (Stramenopila), in rank order. Antarctomyces sp., Blastocladiomycota sp., Pseudogymnoascus pannorum, Microascaceae sp., Mortierella sp., Lobulomycetales sp., Sordariomycetes sp., Fungal sp., Rhizophydiales sp., Pseudeurotiaceae sp., Chytridiomycota sp. 1, Filobasidiella sp., Tausonia pullulans, Betamyces sp., and Leucosporidium sp. were the most abundant assigned taxa. The fungal assemblages present in the different ornithogenically influenced soils displayed different diversity indices. However, in general, we detected high fungal diversity and few taxa shared between the samples. Despite the polyextreme environmental conditions experienced in these Antarctic soils, the metabarcoding approach detected a rich and complex fungal community dominated by saprophytes, but with some pathogenic taxa also present. The community was dominated by psychrophilic and psychrotolerant taxa, some apparently endemic to Antarctica, and those identified only at higher taxonomic levels, which may represent currently undescribed fungi. The mycobiome detected included taxa characterized by different ecological roles, including saprotrophic, human- and animal-associated, phytopathogenic, mutualistic, and cosmopolitan. These fungi may potentially be dispersed by birds or in the air column over great distances, including between different regions within Antarctica and from South America, Africa, and Oceania.

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Abstract Introduction: Trypanosomes are hemoparasites that can be observed circulating in the peripheral blood of birds. Parasitological studies in birds in their natural environment are neglected, but are important for research relating to transmission, maintenance of the biological cycle, and abundance, among other parasitological aspects. Objective: To describe infections by Trypanosoma sp. in birds in the Brazilian Amazon, as well as the prevalence, morphological and morphometric characteristics of this hemoparasite. Methods: In the Tapajós National Forest, we captured a total of 125 birds, mostly from the order Passeriformes. We obtained blood samples from the ulnar vein using sterile insulin needles, and aliquots of blood using a microhematocrit capillary tube. We made blood smears in triplicate and stained with the Giemsa method. We viewd the morphotypes of the Trypanosoma sp. under the light microscope with objective lenses of 40 X and 100 X. To determine the morphometric characteristics of Trypanosomatidae, we used the Zen Blue Edition 2 software package. Results: We observed the presence of hemoparasites in the trypomastigote form in specimens of Thamnophilidae, Dendrocolaptidae and Conopophagidae, with low prevalence. Only one morphotype of Trypanosoma sp. was detected and measurement. Conclusions: We report the infection by Trypanosoma sp. in species of ecological importance, such as Phlegopsis nigromaculata, endangered in Brazil. The morphology and morphometry of the morphotype found could contribute to more detailed descriptions of these hemoparasites.

Resumen Introducción: Los tripanosomas son hemoparásitos que pueden observarse circulando en la sangre periférica de las aves. Los estudios parasitológicos en aves en el medio natural son escasos, pero son importantes para la investigación relacionada con la transmisión, el mantenimiento del ciclo biológico y la abundancia, entre otros aspectos parasitológicos. Objetivo: Describir infecciones por Trypanosoma sp. en aves de la Amazonia brasileña, así como la prevalencia, características morfológicas y morfométricas de este hemoparásito. Métodos: En la Floresta Nacional de Tapajós, capturamos un total de 125 aves, la mayoría del orden Passeriformes. Obtuvimos muestras de sangre por punción de la vena cubital del ala con agujas estériles de insulina. Con un tubo capilar microhematocrito, obtuvimos alícuotas de sangre. Realizamos frotis de sangre por triplicado y teñimos con el método de Giemsa. Visualizamos los morfotipos de Trypanosoma sp. al microscopio óptico con lentes objetivos de 40 X y 100 X. Para determinar las características morfométricas de Trypanosomatidae, usamos el paquete informático Zen Blue Edition 2. Resultados: Observamos la presencia de hemoparásitos en la forma tripomastigote en ejemplares de la familia de aves Thamnophilidae, Dendrocolaptidae y Conopophagidae, con baja prevalencia. Solo detectamos un morfotipo de Trypanosoma sp. Conclusión: Reportamos la infección por Trypanosoma sp. en especies de importancia ecológica, como Phlegopsis nigromaculata en peligro de extinción en Brasil. La morfología y morfometría del morfotipo encontrado puede contribuir con descripciones más detalladas de estos hemoparásitos.

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Escherichia coli is a part of both animal and human commensal microbiota. Avian pathogenic E. coli (APEC) is responsible for colibacillosis in poultry, an economically important disease. However, the close similarities among APEC isolates make it difficult to differentiate between pathogenic and commensal bacteria. The aim of this study was to determine phenotypic and molecular characteristics of APEC isolates and to compare them with their in vivo pathogenicity indices. A total of 198 APEC isolates were evaluated for their biofilm-producing ability and extended-spectrum ß-lactamase (ESBL) production phenotypes. In addition, 36 virulence-associated genes were detected, and the isolates were classified into seven phylogenetic groups using polymerase chain reaction. The sources of the isolates were not associated with biofilms, ESBL, genes, or phylogroups. Biofilm and ESBL production were not associated with pathogenicity. Group B2 had the highest pathogenicity index. Groups B2 and E were positively associated with high-pathogenicity isolates and negatively associated with low-pathogenicity isolates. In contrast, groups A and C were positively associated with apathogenic isolates, and group B1 was positively associated with low-pathogenicity isolates. Some virulence-associated genes showed positive or negative associations with specific phylogenetic groups. None of the individual techniques produced results that correlated with the in vivo pathogenicity index. However, the combination of two techniques, namely, detection of virulence-associated genes and the phylogenetic groups, could help the classification of the isolates as pathogenic or commensal.

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Emergence of zoonotic infectious diseases represent one of the main threats to people worldwide. To properly understand and prevent zoonoses is fundamental to study their epidemiology and the possibility of spillover events, especially for commercially intensive domestic animals and humans. Here, we studied 210 wild birds from the "Ipucas" region, which consists of fragments of the Amazon Forest interspersed with fragments of the "Cerrado" that is subject to seasonal flooding and 75 domestic birds from neighboring poultry farming. Then, we molecularly diagnosed Salmonella and Chlamydia from wild birds and poultry. Among the wild birds, four were diagnosed with Chlamydia psittaci and 23 with Salmonella spp., while we detected 15 poultry infected by Salmonella spp. and no poultry with C. psittaci. We highlighted the common infections of wild and domestic birds in an anthropologically modified environment and potential spillover of Salmonella pathogens among wild and livestock birds. Those infections can harm the health of native and domestic species.

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Salmonellosis is an important gastrointestinal infection in humans and cause of foodborne outbreaks in the world. In this context, molecular characterization is essential to understand how the strains circulate. The aim of this study was to evaluate the genotypic distribution of S. Heidelberg according to the source of isolation. The genetic relatedness of the S. Heidelberg isolates was determined by pulsed-field gel electrophoresis (PFGE). The most prevalent pulsotypes of cluster A were BRJF6X01.006 (27/95 = 28,42%) related between 1995 and 2011 in broilers, poultry meat and poultry farms, meat product and human, and BRJF6X01.001 (21/95 = 22,10%) related between 2011 and 2017 in wild animals, broilers, poultry meat, poultry farms, meat product, animal feed, and pork meat. The pulsotype BRJF6X01.001 shows a high distribution in the environmental and productive chain. The degree of similarity between pulsotypes BRJF6X01.006 and BRJF6X01.001 is 88%. To ensure the safety of human and animal health, holistic approaches, including surveillance of Salmonella throughout the environment and in the production chain, together with control measures, are critical. As transmission of Salmonella from food producing animals to wildlife and to the environment is considered potential public health problem, information on the survival and persistence of Salmonella in the environment and in potential reservoirs is of considerable importance.(AU)

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The control of Salmonella in the poultry production chain combined with biosecurity measures is an important tool to maintain and guarantee the sanitary status of Brazilian flocks. The aim of this work was to compare official laboratory data on molecular typification of Salmonella isolates from poultry breeding flocks in different Brazilian states between 2016 and 2018 and identify the production category with the most positive flocks, in light of current legislation. Surveillance data of positive samples from the official Brazilian Salmonella Control Programme sent to Federal Agricultural Defence Laboratory of São Paulo (LFDA-SP) after molecular characterization were analysed. These data were subject to an exploratory study, undergoing a descriptive statistical analysis followed by the use of frequency and non-parametric hypothesis tests. Overall, 49 serovars were detected in poultry broiler-breeder and layer-breeder flocks. Salmonella ser. Heidelberg, Salmonella ser. Anatum, Salmonella ser. Newport, Salmonella ser. Schwarzengrund and Salmonella ser. Mbandaka were the five most common isolated serovars. The data shows that there is an opportunity to improve biosecurity measures in parent breeder flocks. A total of 16 serovars were identified in turkey-breeders. Salmonella ser. Anatum, Salmonella ser. Newport, Salmonella ser. Brandenburg, Salmonella ser. Litchfield, and Salmonella ser. Livingstone were the most common ones. The four official controlled serovars represented a small part of the isolated strains. These data demonstrate the importance of an official program in Brazil for Salmonella surveillance in breeder flocks combined with biosecurity measures.(AU)

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