Exploring the Bacteriome and Resistome of Humans and Food-Producing Animals in Brazil.

The epidemiology of antimicrobial resistance (AMR) is complex, with multiple interfaces (human-animal-environment). In this context, One Health surveillance is essential for understanding the distribution of microorganisms and antimicrobial resistance genes (ARGs). This report describes a multicentric study undertaken to evaluate the bacterial communities and resistomes of food-producing animals (cattle, poultry, and swine) and healthy humans sampled simultaneously from five Brazilian regions. Metagenomic analysis showed that a total of 21,029 unique species were identified in 107 rectal swabs collected from distinct hosts, the highest numbers of which belonged to the domain Bacteria, mainly Ruminiclostridium spp. and Bacteroides spp., and the order Enterobacterales. We detected 405 ARGs for 12 distinct antimicrobial classes. Genes encoding antibiotic-modifying enzymes were the most frequent, followed by genes related to target alteration and efflux systems. Interestingly, carbapenemase-encoding genes such as blaAIM-1, blaCAM-1, blaGIM-2, and blaHMB-1 were identified in distinct hosts. Our results revealed that, in general, the bacterial communities from humans were present in isolated clusters, except for the Northeastern region, where an overlap of the bacterial species from humans and food-producing animals was observed. Additionally, a large resistome was observed among all analyzed hosts, with emphasis on the presence of carbapenemase-encoding genes not previously reported in Latin America. IMPORTANCE Humans and food production animals have been reported to be important reservoirs of antimicrobial resistance (AMR) genes (ARGs). The frequency of these multidrug-resistant (MDR) bacteria tends to be higher in low- and middle-income countries (LMICs), due mainly to a lack of public health policies. Although studies on AMR in humans or animals have been carried out in Brazil, this is the first multicenter study that simultaneously collected rectal swabs from humans and food-producing animals for metagenomics. Our results indicate high microbial diversity among all analyzed hosts, and several ARGs for different antimicrobial classes were also found. As far as we know, we have detected for the first time ARGs encoding carbapenemases, such as blaAIM-1, blaCAM-1, blaGIM-2, and blaHMB-1, in Latin America. Thus, our results support the importance of metagenomics as a tool to track the colonization of food-producing animals and humans by antimicrobial-resistant bacteria. In addition, a network surveillance system called GUARANI, created for this study, is ready to be expanded and to collect additional data.

Large Scale Genome-Centric Metagenomic Data from the Gut Microbiome of Food-Producing Animals and Humans.

The One Health concept is a global strategy to study the relationship between human and animal health and the transfer of pathogenic and non-pathogenic species between these systems. However, to the best of our knowledge, no data based on One Health genome-centric metagenomics are available in public repositories. Here, we present a dataset based on a pilot-study of 2,915 metagenome-assembled genomes (MAGs) of 107 samples from the human (N = 34), cattle (N = 28), swine (N = 15) and poultry (N = 30) gut microbiomes. Samples were collected from the five Brazilian geographical regions. Of the draft genomes, 1,273 were high-quality drafts (≥90% of completeness and ≤5% of contamination), and 1,642 were medium-quality drafts (≥50% of completeness and ≤10% of contamination). Taxonomic predictions were based on the alignment and concatenation of single-marker genes, and the most representative phyla were Bacteroidota, Firmicutes, and Proteobacteria. Many of these species represent potential pathogens that have already been described or potential new families, genera, and species with potential biotechnological applications. Analyses of this dataset will highlight discoveries about the ecology and functional role of pathogens and uncultivated Archaea and Bacteria from food-producing animals and humans. Furthermore, it also represents an opportunity to describe new species from underrepresented taxonomic groups.

First case report of non-human primates (Alouatta clamitans) with the hypervirulent Klebsiella pneumoniae serotype K1 strain ST 23: A possible emerging wildlife pathogen.

BACKGROUND: Hypervirulent strain of Klebsiella pneumoniae genotype K1 isolates have recently emerged, causing severe pyogenic liver abscess complicated by devastating metastatic infections in humans. METHODS: We describe a short outbreak of the non-human primate (NHP) research center, associated with a hypervirulent K. pneumoniae. The genetic similarity of the strains was evaluated by pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing (MLST) techniques, and virulence encoding genes were detected by polymerase chain reaction (PCR). RESULTS: The isolates were phenotypically like strains causing community-acquired invasive liver abscess syndrome in humans. All strains exhibited identical PFGE patterns and were found to belong to ST23 and presented a hypermucovisity phenotype and possessed magA and rmpA gene. CONCLUSION: This is the first case report of NHPs caused by K. pneumoniae displaying a hypermucoviscosity phenotype and belonging to capsular serotypes K1 and ST23.

Isolation of leptospira Serovars Canicola and Copenhageni from cattle urine in the state of Paraná, Brazil / Isolamento de leptospiras dos Sorovares Canicola e Copenhageni em amostras de urina de bovinos no estado do Paraná, Brasil

In 2001, 698 urine samples were randomly collected from cattle at a slaughterhouse in the State of Paraná, Brazil. Direct examination using dark field microscopy was carried out immediately after collection. Five putative positive samples were cultured in modified EMJH medium, yielding two positive cultures (LO-14 and LO-10). Typing with monoclonal antibodies revealed that the two isolates were similar to Canicola (LO-14) and Copenhageni (LO-10). Microscopic agglutination test results show that Hardjo is the most common serovar in cattle in Brazil. Rats and dogs are the common maintenance hosts of serovars Copenhageni and Canicola. The excretion of highly pathogenic serovars such as Copenhageni and Canicola by cattle can represent an increasing risk for severe leptospirosis is large populations, mainly living in rural areas.

No ano de 2001, 698 amostras de urina foram colhidas aleatoriamente, durante o abate em um frigorífico do Estado do Paraná, Brasil. O exame direto em microscópio de campo escuro foi realizado imediatamente após a colheita. As cinco amostras de urina positivas neste exame foram semeadas em meio EMJH modificado, sendo possível o crescimento de leptospiras em duas (LO-14 e LO-10). As estirpes isoladas foram tipificadas, por painel de anticorpos monoclonais, como mais similares ao perfil das amostras de referência dos sorovares Canicola (LO-14) e Copenhageni (LO-10). No Brasil, inquéritos sorológicos utilizando a prova de soroaglutinação microscópica mostram o predomínio de reações para o sorovar Hardjo em bovinos. Roedores e cães são os reservatórios mais comuns dos sorovares Copenhageni e Canicola, respectivamente. A eliminação dos sorovares Canicola e Copenhageni pela espécie bovina pode resultar em um aumento na ocorrência de casos graves de leptospirose humana, principalmente na população rural.

Isolation of leptospira Serovars Canicola and Copenhageni from cattle urine in the state of ParanÁ, Brazil.

In 2001, 698 urine samples were randomly collected from cattle at a slaughterhouse in the State of Paraná, Brazil. Direct examination using dark field microscopy was carried out immediately after collection. Five putative positive samples were cultured in modified EMJH medium, yielding two positive cultures (LO-14 and LO-10). Typing with monoclonal antibodies revealed that the two isolates were similar to Canicola (LO-14) and Copenhageni (LO-10). Microscopic agglutination test results show that Hardjo is the most common serovar in cattle in Brazil. Rats and dogs are the common maintenance hosts of serovars Copenhageni and Canicola. The excretion of highly pathogenic serovars such as Copenhageni and Canicola by cattle can represent an increasing risk for severe leptospirosis is large populations, mainly living in rural areas.

Leptospires detection in kidney, liver and uterus of cows slaughtered in Paraná State, Brazil

O objetivo deste trabalho foi detectar leptospiras em fragmentos de rim, fígado e útero de 96 fêmeas bovinas com histórico sanitário desconhecido, escolhidas aleatoriamente durante o abate em um frigorífico no Estado do Paraná, Brasil. Todas as 96 amostras de urina foram submetidas ao exame direto em microscópio de campo escuro. As amostras positivas neste exame e todos os fragmentos de rim, fígado e útero foram semeados nos meios de cultura EMJH modificado e Tween 80/40/LH. Os cortes histológicos de rim, fígado e útero foram submetidos à coloração de Hematoxilina-Eosina (HE) e a prova de imunoperoxidase indireta com soros hiperimunes contra o sorovar Hardjo (Hardjoprajitno) e contra a estirpe Londrina (LO14), do sorovar Canicola, isolada no norte do Paraná, Brasil, utilizados como anticorpo primário. O exame direto detectou leptospiras na urina de quatro animais. Todas as tentativas de isolamento das urinas e fragmentos de rim, fígado e útero foram negativas após 16 semanas de incubação. No exame histopatológico foi observado infiltrado focal de células mononucleares no interstício renal da maioria dos animais. Na prova de imunoperoxidase indireta com o soro hiperimune contra a estirpe LO14, o rim de um animal foi o único a apresentar resultado positivo. Todos os fragmentos de rim, fígado e útero testados com o soro hiperimune contra o sorovar Hardjo foram negativos.