A comparative study of the bacterial diversity and composition of nursery piglets' oral fluid, feces, and housing environment

The oral cavity is the portal of entry for many microorganisms that affect swine, and the swine oral fluid has been used as a specimen for the diagnosis of several infectious diseases. The oral microbiota has been shown to play important roles in humans, such as protection against non-indigenous bacteria. In swine, studies that have investigated the microbial composition of the oral cavity of pigs are scarce. This study aimed to characterize the oral fluid microbiota of weaned pigs from five commercial farms in Brazil and compare it to their respective fecal and environmental microbiotas. Bacterial compositions were determined by 16S rRNA gene sequencing and analyzed in R Studio. Oral fluid samples were significantly less diverse (alpha diversity) than pen floor and fecal samples (P < 0.01). Alpha diversity changed among farms in oral fluid and pen floor samples, but no differences were observed in fecal samples. Permutational ANOVA revealed that beta diversity was significantly different among sample types (P = 0.001) and farms (P = 0.001), with separation of sample types (feces, pen floor, and oral fluid) on the principal coordinates analysis. Most counts obtained from oral fluid samples were classified as Firmicutes (80.4%) and Proteobacteria (7.7%). The genera Streptococcus, members of the Pasteurellaceae family, and Veillonella were differentially abundant in oral fluid samples when compared to fecal samples, in which Streptococcus was identified as a core genus that was strongly correlated (SparCC) with other taxa. Firmicutes and Bacteroidota were the most relatively abundant phyla identified in fecal and pen floor samples, and Prevotella_9 was the most classified genus. No differentially abundant taxa were identified when comparing fecal samples and pen floor samples. We concluded that under the conditions of our study, the oral fluid microbiota of weaned piglets is different (beta diversity) and less diverse (alpha diversity) than the fecal and environmental microbiotas. Several differentially abundant taxa were identified in the oral fluid samples, and some have been described as important colonizers of the oral cavity in human microbiome studies. Further understanding of the relationship between the oral fluid microbiota and swine is necessary and would create opportunities for the development of innovative solutions that target the microbiota to improve swine health and production.

Microbiological Quality of Pig Carcasses in a Slaughterhouse under Risk-Based Inspection System

Meat product inspection is one of the procedures adopted more than a century ago to guarantee food quality and safety for consumption. Due to technology and regulation advancement for farming and slaughtering pigs, a change in zoonotic profile attributed to pork has been identified. Thus, a global movement began to establish inspection parameters based on epidemiological risk profiles, culminating in the publication of a new regulation in Brazil in 2018. This normative instruction establishes that slaughterhouses under federal inspection must implement risk-based inspection until 2028. Changes in the inspection system can generate questions and objections on the part of customers and consumer markets. In order to assess microbiological contamination when adopting a risk-based inspection system, the occurrence of Salmonella spp. and the quantification of Enterobacteriaceae and mesophilic aerobic counts were compared in pig carcasses slaughtered under traditional and risk-based inspection systems. A statistical significance reduction was identified regarding the quantification of Enterobacteriaceae (log -0.18 to -1.61 CFU/cm²) and mesophilic aerobic counts (log 4.60 to 3.49 CFU/cm²). The occurrence of Salmonella spp. did not show a significant difference (4% to 5.3%). The results allowed us to conclude that adopting risk-based inspection systems improves food safety through Enterobacteriaceae and mesophilic aerobic counts reduction.

Vaginal Microbiota Diversity in Response to Lipopolysaccharide in Gilts Housed Under Three Housing Systems

The United Kingdom and European Union have banned crates for pregnant sows. However, animals are kept in a restrictive environment for up to four weeks after mating, leading to stress and different responses of the animals’ immune system. Here, we used vaginal flushing of gilts to investigate whether housing systems or an experimental inflammatory challenge with lipopolysaccharide (LPS) can modify the gilt vaginal microbiome. Alpha-diversity indices showed differences in the microbiota of gilts housed under different systems (q = 0.04). Shannon alpha-diversity richness was higher in gilts group-housed in pens than in gilts housed in crates (q = 0.035), but not higher than in other groups. The relative abundance of the operational taxonomic unit (OTU) (q < 0.05) revealed specific differences in housing systems before a LPS or saline (SAL control) challenge. We found different abundances in taxa of Actinobacteria, Bacteroidetes, Cyanobacteria, Firmicutes, and Proteobacteria in gilts housed in the different systems before challenge. After the LPS challenge, significant differences were detected in the relative abundance of OTUs (q < 0.05) for the LPS-challenged group compared with SAL animals for each housing system. The phylum Staphylococcus showed higher abundance among the LPS-challenged gilts than in SAL-challenged animals. Furthermore, Enterobacter was more abundant in the LPS-challenged gilts housed in crates than in SAL-challenged gilts housed in crates. Streptococcus suis, Conchiformibius, Globicatella and Actinobacillus were more abundant in LPS-challenged gilts in indoor group housing than in SAL gilts in the same housing system. Gilts kept outdoors did not show changes in vaginal microbiota after an LPS challenge. Gilts housed in crates showed clinical signs of urogenital infection, whereas gilts housed outdoors and in indoor group housing did not. The relationship between environment, immune response, and microbiota suggested that animals in a poor environments experience difficulties responding to a challenge and their vaginal microbiota is altered as a consequence, with decreased richness of normal vaginal microbiota, and increased opportunistic bacteria. Welfare indicators measured by gilts’ responses to housing systems however, do not fully explain mechanisms associated with the unique signature in vaginal microbiota encountered in the different housing systems.

First isolation and whole-genome sequencing of a Shewanella algae strain from a swine farm in Brazil

BACKGROUND

Infections caused by Shewanella spp. have been increasingly reported worldwide. The advances in genomic sciences have enabled better understanding about the taxonomy and epidemiology of this agent. However, the scarcity of DNA sequencing data is still an obstacle for understanding the genus and its association with infections in humans and animals.

RESULTS

In this study, we report the first isolation and whole-genome sequencing of a Shewanella algae strain from a swine farm in Brazil using the boot sock method, as well as the resistance profile of this strain to antimicrobials. The isolate was first identified as Shewanella putrefaciens, but after whole-genome sequencing it showed greater similarity with Shewanella algae. The strain showed resistance to 46.7% of the antimicrobials tested, and 26 resistance genes were identified in the genome.

CONCLUSIONS

This report supports research made with Shewanella spp. and gives a step forward for understanding its taxonomy and epidemiology. It also highlights the risk of emerging pathogens with high resistance to antimicrobial formulas that are important to public health.

Leishmaniasis in cat shelters: A serological, molecular and entomological study

An epidemiological Leishmania spp. and entomological Phlebotomine sandflies survey was performed in cat shelters at leishmaniasis endemic area of Brazil. Blood and conjunctival swab (CS) samples were collected from 94 cats in two animal protection shelters. These samples were subjected to serological tests using the indirect immunofluorescence antibody test (IFAT) and indirect enzyme-linked immunosorbent assay (ELISA) and to molecular test by polymerase chain reaction (PCR). In addition, a Phlebotomine sandflies survey was performed in the same shelters. The analyses revealed a positivity of 31.91% (30/94) through ELISA and 29.79% (28/94) through IFAT. The two serological tests showed a positive association with perfect agreement (k = 0.925). None of the cats were positive by Leishmania spp. DNA. One Lutzomyia (Lutzomyia) longipalpis male was found in one of the cat shelters. The results and the implications of our findings are discussed below.

Comparative genomic survey of Bacillus cereus sensu stricto isolates from the dairy production chain in Brazil

The genomes of 262 Bacillus cereus isolates were analyzed including 69 isolates sampled from equipment, raw milk and dairy products from Brazil. The population structure of isolates showed strains belonging to known phylogenetic groups II, III, IV, V and VI. Almost all the isolates obtained from dairy products belonged to group III. Investigation of specific alleles revealed high numbers of isolates carrying toxin-associated genes including cytK (53.62%), hblA (59.42%), hblC (44.93%), hblD (53.62%), nheA (84.06%), nheB (89.86%) and nheC (84.06%) with isolates belonging to groups IV and V having significant higher prevalence of hblACD and group IV of CytK genes. Strains from dairy products had significantly lower prevalence of CytK and hblACD genes compared to isolates from equipment and raw milk/bulk tanks. Genes related to sucrose metabolism were detected at higher frequency in isolates obtained from raw milk compared to strains from equipment and utensils. The population genomic analysis demonstrated the diversity of strains and variability of putative function among B. cereus group isolates in Brazilian dairy production, with large numbers of strains potentially able to cause foodborne illness. This detailed information will contribute to targeted interventions to reduce milk contamination and spoilage associated with B. cereus in Brazil.

EFFECT OF BACTERIAL AGENTS OF PORCINE RESPIRATORY DISEASE COMPLEX ON PRODUCTIVE INDICES AND SLAUGHTER WEIGHT

Abstract Porcine respiratory disease complex comprises the interaction of two or more infectious agents. The major bacterial agents involved were investigated in 115 finishing pigs at a farm in São Paulo State, Brazil: Actinobacillus pleuropneumoniae (serology, bacterial culture, and multiplex PCR), Mycoplasma hyopneumoniae (Mhyo) (nested PCR), Pasteurella multocida (multiplex PCR), Haemophilus parasuis (PCR multiplex), and Streptococcus sp. (bacterial culture). Macroscopic and microscopic lung lesions were evaluated, and zootechnical indices were recorded. Mhyo occurred in 113 animals (98.3%), seventeen of which were co-infected with Streptococcus sp. The finding of emphysematous lung was associated with significantly lower final and carcass weight at slaughter. Although vaccinated against Mhyo with an inactivated immunogen, almost 100% of the animals were infected. Mhyo infection with and without Streptococcus sp. co-infection was related to lung lesions of varying degrees and lower slaughter and carcass weight.

Micoplasma hyopneumoniae associado ao circovírus suíno tipo 2 em plantéis não vacinados para micoplasmose

RESUMO: A síndrome circovirose suína e doenças associadas (PCVAD) tem sido descrita em diversas regiões do mundo. Seu agente primário, o circovírus suíno tipo 2 (PCV2), está associado a elevados índices de refugagem nas granjas e a vultuosos prejuízos econômicos. Diversos fatores de risco estão relacionados à manifestação dos quadros clínicos da síndrome, nomeadamente deficiências de manejo, presença de coinfecções e imunização diante do agente. Entre os agentes frequentemente relatados associados ao PCV2 está o Mycoplasma hyopneumoniae. Este estudo objetivou verificar a ocorrência de M. hyopneumoniae em animais diagnosticados estarem acometidos pela PCVAD, em sistemas intensivos de produção de suínos do estado de Goiás. Amostras de secreção nasal de 40 animais foram analisadas para a pesquisa do DNA de M. hyopneumoniae. Do total das amostras de secreção nasal, 6 (15%) foram positivas na reação em cadeia da polimerase (PCR) para o M. hyopneumoniae, apenas em granjas que não praticavam a vacinação contra esse agente. Os resultados relacionados à presença de micoplasma estão de acordo com os achados clínicos dos animais analisados que apresentavam sintomatologia de doenças respiratórias e lesões relacionadas ao trato respiratório. Este é o primeiro relato da associação de PCV2 com M. hyopneumoniae em suínos identificados com PCVAD no estado de Goiás.

Ocorrência de coronavírus entérico de ferrets no Brasil: nota prévia

Coronavírus entérico de furões (FECV) é associado à enterite catarral epizoótica (ECE) em furões (Mustela putorius furo). Neste estudo, relatamos a ocorrência deste agente em quatro amostras fecais diarreicas de furões domésticos, analisadas por microscopia eletrônica de transmissão (contrastação negativa) e RT-PCR específica e direcionada ao gene de nucleocapsídeo (N). Estes achados constituem o primeiro relato de FECV no Brasil e remetem para a importância deste vírus na etiologia de quadros entéricos nestes animais.