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Multiple interlinked factors are associated with the global resistome, whereas multidrug-resistant (MDR) pathogens have been related to increased mortality rates in humans and animals. CTX-M-type is the most prevalent extended-spectrum β-lactamase (ESBL) among Enterobacteriaceae, which raises concern worldwide. Zoological gardens have a high density of animals that live very close to each other and to humans. Therefore, this study aimed to investigate through the whole-genome sequencing (WGS) MDR Escherichia coli lineages obtained from captivity wild animals in a zoo. Genetic background showed a wide resistome for antimicrobials (e.g., blaCTX-M-65, blaCTX-M-8, blaCMY-2, qnrB19), metals (e.g., pcoABCDERS, silABCEP, merACDEPRT), and antibacterial biocides (e.g., sugE, mdfA) among MDR CTX-M-producing E. coli belonging to CC155 and CC156. Mobilome analysis revealed several plasmids, and eight of them were completely characterized, which showed different backbone-encoding genes. Comparative analysis of plasmids blaCTX-M-65/IncHI2-ST3, blaCTX-M-8/IncI1-ST113, and IncQ1 showed a high identity among plasmids obtained from humans and animals worldwide distributed. Besides, several virulence genes, CRISPR, and prophage-related sequences were also detected. The occurrence of MDR E. coli belonging to CCs closely related to humans and food-producing animals and the high similarity among the plasmids from MDR E. coli carrying clinically significant antimicrobial resistance genes may indicate intercontinental dissemination of these lineages and plasmids. Therefore, these findings contribute to the monitoring of antimicrobial resistance and the human-animal-environment interface worldwide.Key Points• Wide resistome for antimicrobials, metals, and antibacterial biocides.• Multidrug resistance plasmids (blaCTX-M-65/IncHI2-ST3, blaCTX-M-8/IncI1-ST113).• Co-occurrence of plasmid-mediated resistance and virulence genes.

Trypanosoma cruzi is a multi-host parasite that infects dozens of mammalian species in the most variable wild environments in Americas. Between 2013 and 2018, autochthonous infections by T. cruzi were suspected in three European wolves (Canis lupus) and an orange dwarf porcupine (Coendou spinosus) from Fundação Parque Zoológico de São Paulo (FPZSP), Brazil, current Coordenadoria de Fauna Silvestre (CFS), which is inserted in a remnant of the Atlantic rainforest inside one of the biggest and most populous municipality of the world. This study aims to detect T. cruzi infections in captive mammals, triatomines and free-living opossums from surrounding areas of FPZSP/CFS. Blood samples from captive and free-living mammals from surrounding areas were collected for parasitological (direct examination and culture), serological (IFAT) and molecular diagnosis using Nested-PCR 18SrDNA followed by DNA sequence analysis. Triatomines (Panstrongylus megistus) found in FPZSP/CFS were also examined by culture of the digestive tract and PCR. Trypanosoma cruzi infection was detected in 35.7% (n = 60/168 - 106 captive and 62 free-living) of the mammals that belonged to nine different families. From captive mammals, positive T. cruzi serology was observed in 29.6% (n = 27/91). Twenty-six positive hemocultures were obtained, from which parasite isolation was achieved in 69.2%, while positive PCR was observed in 40% of them, including nine free-living individuals that were also positive in hemoculture. Of 28 individuals in which T. cruzi characterization was successful, 89.3% were genotyped as DTU TcI, 7.2% as TcII and 3.5% as TcI/TcII mixed infection. Besides, 29 of 30 collected triatomines were infected, and infection by T. cruzi DTU TcI was confirmed in 16 of them. The confirmed autochthonicity of at least 68.9% of cases demonstrates that captive mammals from FPZSP are immersed in the T. cruzi enzootic cycle that involves the vector species P. megistus, and the reservoir hosts C. spinosus and Didelphis aurita from the wild surrounding areas.

Parasites are key players in ecosystems, influencing population sizes and food webs, yet the impact of environmental factors on their diversity is not well understood. The Atlantic rainforest in Brazil, particularly the Parque Estadual das Fontes do Ipiranga (PEFI), exemplifies a biodiversity hotspot facing significant deforestation, housing diverse animal species such as the synanthropic Brazilian common opossum (Didelphis aurita), which serves as a reservoir for multiple zoonotic pathogens. In this study, we investigated parasite diversity, abundance, prevalence, and richness in free-living D. aurita in the PEFI, São Paulo, Brazil. From January 2015 to January 2017, 101 fecal samples of D. aurita were collected in two areas of PEFI, at the Instituto de Pesquisas Ambientais (IPA) and the Parque de Ciência e Tecnologia (Cientec), and analyzed using three different parasitological methods. In total, 99% of the samples were positive for at least one parasite. The most prevalent parasite belonged to the order Strongylida (82%), followed by Cruzia sp. (77%), the latter having a significantly higher prevalence at IPA. In contrast, Acanthocephala showed greater prevalence at Cientec. Co-infections were common, with some individuals harboring up to seven different parasites. Our findings reveal significant parasite diversity in the D. aurita population at PEFI, including both helminths and protozoan trophozoites, some of which are reported for the first time in this host species. Further research is essential for accurate species identification of the observed parasites.

Stingless bees are vital pollinators in tropical and neotropical regions, emphasizing the need to conserve these species. However, resource scarcity, particularly pollen, during certain periods negatively impacts bee health and pollination efficiency. To address this, we developed a fermented protein feed using microorganisms from pollen of Melipona quadrifasciata, a species commonly found in the Brazilian Atlantic Forest. The fermented feed consisted of a protein bran mixture, sugar syrup, and an inoculant derived from species’ fermented pollen. To assess the feed quality, nutritional evaluation and metabolomic analyses were conducted (UHPLC/DAD-HRMS/MS and GC-MS). The metabolomic analysis identified 85 compounds in positive and 102 in negative ionization modes. Shared metabolites, such as isoquercetin and palatinose, highlighted similarities between the feed and natural fermented pollen. Laboratory tests with caged bees showed comparable consumption between the feed and fermented pollen with no statistical difference (mean: 0.067 g vs. 0.060 g; p = 0.53). The feed exhibited a favorable pH transition (5.30 pre-fermentation to 4.41 after the fermentation process) and remained stable for six months at ±2 °C. These findings demonstrate a biotechnological advance in stingless bee nutrition, offering a viable solution during resource scarcity and promoting the health of M. quadrifasciata.

Acinetobacter bereziniae has recently gained medical notoriety due to its emergence as a multidrug resistance and healthcare-associated pathogen. In this study, we report the whole-genome characterization of an A. bereziniae strain (A321) recovered from an infected semiaquatic turtle, as well as a comparative analysis of A. bereziniae strains circulating at the human-animal-environment interface. Strain A321 displayed a multidrug resistance profile to medically important antimicrobials, which was supported by a wide resistome. The novel Tn 5393m transposon and a qnrB19 -bearing ColE1-like plasmid were identified in A321 strain. Novel OXA-229-like β-lactamases were detected and expression of OXA-931 demonstrated a 2–64-fold increase in the minimum inhibitory concentration for β-lactam agents. Comparative genomic analysis revealed that most A. bereziniae strains did not carry any antimicrobial resistance genes (ARGs); however, some strains from China, Brazil, and India harbored six or more ARGs. Furthermore, A. bereziniae strains harbored conserved virulence genes. These results add valuable information regarding the spread of ARGs and mobile genetic elements that could be shared not only between A. bereziniae but also by other bacteria of clinical interest. This study also demonstrates that A. bereziniae can spill over from anthropogenic sources into natural environments and subsequently be transmitted to non-human hosts, making this a potential One Health bacteria that require close surveillance.

Composting is a promising source of new organisms and thermostable enzymes that may be helpful in environmental management and industrial processes. Here we present results of metagenomic- and metatranscriptomic-based analyses of a large composting operation in the São Paulo Zoo Park. This composting exhibits a sustained thermophilic profile (50 °C to 75 °C), which seems to preclude fungal activity. The main novelty of our study is the combination of time-series sampling with shotgun DNA, 16S rRNA gene amplicon, and metatranscriptome high-throughput sequencing, enabling an unprecedented detailed view of microbial community structure, dynamics, and function in this ecosystem. The time-series data showed that the turning procedure has a strong impact on the compost microbiota, restoring to a certain extent the population profile seen at the beginning of the process; and that lignocellulosic biomass deconstruction occurs synergistically and sequentially, with hemicellulose being degraded preferentially to cellulose and lignin. Moreover, our sequencing data allowed near-complete genome reconstruction of five bacterial species previously found in biomass-degrading environments and of a novel biodegrading bacterial species, likely a new genus in the order Bacillales. The data and analyses provided are a rich source for additional investigations of thermophilic composting microbiology.

Background Trypanosoma cruzi is a multi-host parasite that infects dozens of mammalian species in the most variable wild environments in Americas. Between 2013 and 2018, autochthonous infections by T. cruzi were suspected in three European wolves (Canis lupus) and an orange dwarf porcupine (Coendou spinosus) from Fundação Parque Zoológico de São Paulo (FPZSP), Brazil, current Coordenadoria de Fauna Silvestre (CFS), which is inserted in a remnant of the Atlantic rainforest inside one of the biggest and most populous municipality of the world. This study aims to detect T. cruzi infections in captive mammals, triatomines and free-living opossums from surrounding areas of FPZSP/CFS. Methodology/Principal Findings Blood samples from captive and free-living mammals from surrounding areas were collected for parasitological (direct examination and culture), serological (IFAT) and molecular diagnosis using Nested-PCR 18SrDNA followed by DNA sequence analysis. Triatomines (Panstrongylus megistus) found in FPZSP/CFS were also examined by culture of the digestive tract and PCR. Trypanosoma cruzi infection was detected in 35.7% (n = 60/168 - 106 captive and 62 free-living) of the mammals that belonged to nine different families. From captive mammals, positive T. cruzi serology was observed in 29.6% (n = 27/91). Twenty-six positive hemocultures were obtained, from which parasite isolation was achieved in 69.2%, while positive PCR was observed in 40% of them, including nine free-living individuals that were also positive in hemoculture. Of 28 individuals in which T. cruzi characterization was successful, 89.3% were genotyped as DTU TcI, 7.2% as TcII and 3.5% as TcI/TcII mixed infection. Besides, 29 of 30 collected triatomines were infected, and infection by T. cruzi DTU TcI was confirmed in 16 of them. Conclusions/Significance The confirmed autochthonicity of at least 68.9% of cases demonstrates that captive mammals from FPZSP are immersed in the T. cruzi enzootic cycle that involves the vector species P. megistus, and the reservoir hosts C. spinosus and Didelphis aurita from the wild surrounding areas.

The bioprospection for cellulase and protease producers is a promise strategy for the discovery of potential biocatalysts for use in hydrolysis of lignocellulosic materials as well as proteic residues. These enzymes can increment and turn viable the production of second generation ethanol from different and alternative sources. In this context, the goal of this study was the investigation of cellulolytic and proteolytic abilities of bacteria isolated from the gastrointestinal tract of a hippopotamus as well as from its composting process. It is important to highlight that hippopotamus gastrointestinal samples were a non-typical sources of efficient hydrolytic bacteria with potential for application in biotechnological industries, like biofuel production. Looking for this, a total of 159 bacteria were isolated, which were submitted to qualitative and quantitative enzymatic assays. Proteolytic analyzes were conducted through the evaluation of fluorescent probes. Qualitative assays for cellulolytic abilities revealed 70 positive hits. After quantitative analyzes, 44 % of these positive hits were selected, but five (5) strains showed cellulolytic activity up to 11,8 FPU/mL. Regarding to proteolytic activities, six (6) strains showed activity above 10 %, which overpassed results described in the literature. Molecular analyzes based on the identification of 16S rDNA, revealed that all the selected bacterial isolates were affiliated to Bacillus genus. In summary, these results strongly indicate that the isolated bacteria from a hippopotamus can be a potential source of interesting biocatalysts with cellulolytic and proteolytic activities, with relevance for industrial applications.

Halophilic microorganisms are able to grow in the presence of salt and are also excellent source of enzymes and biotechnological products, such as exopolysaccharides (EPSs) and polyhydroxyalkanoates (PHAs). Salt-tolerant bacteria were screened in the Organic Composting Production Unit (OCPU) of São Paulo Zoological Park Foundation, which processes 4 ton/day of organic residues including plant matter from the Atlantic Rain Forest, animal manure and carcasses and mud from water treatment. Among the screened microorganisms, eight halotolerant bacteria grew at NaCl concentrations up to 4 M. These cultures were classified based on phylogenetic characteristics and comparative partial 16S rRNA gene sequence analysis as belonging to the genera Staphylococcus, Bacillus and Brevibacterium. The results of this study describe the ability of these halotolerant bacteria to produce some classes of hydrolases, namely, lipases, proteases, amylases and cellulases, and biopolymers. The strain characterized as of Brevibacterium avium presented cellulase and amylase activities up to 4 M NaCl and also produced EPSs and PHAs. These results indicate the biotechnological potential of certain microorganisms recovered from the composting process, including halotolerant species, which have the ability to produce enzymes and biopolymers, offering new perspectives for environmental and industrial applications.

Halophilic microorganisms are able to grow in the presence of salt and are also excellent source of enzymes and biotechnological products, such as exopolysaccharides (EPSs) and polyhydroxyalkanoates (PHAs). Salt-tolerant bacteria were screened in the Organic Composting Production Unit (OCPU) of São Paulo Zoological Park Foundation, which processes 4 ton/day of organic residues including plant matter from the Atlantic Rain Forest, animal manure and carcasses and mud from water treatment. Among the screened microorganisms, eight halotolerant bacteria grew at NaCl concentrations up to 4 M. These cultures were classified based on phylogenetic characteristics and comparative partial 16S rRNA gene sequence analysis as belonging to the genera Staphylococcus, Bacillus and Brevibacterium. The results of this study describe the ability of these halotolerant bacteria to produce some classes of hydrolases, namely, lipases, proteases, amylases and cellulases, and biopolymers. The strain characterized as of Brevibacterium avium presented cellulase and amylase activities up to 4 M NaCl and also produced EPSs and PHAs. These results indicate the biotechnological potential of certain microorganisms recovered from the composting process, including halotolerant species, which have the ability to produce enzymes and biopolymers, offering new perspectives for environmental and industrial applications.