Exploring bacterial diversity and antimicrobial resistance gene on a southern Brazilian swine farm.

The bacterial composition of and the circulation of antimicrobial resistance genes (ARGs) in waste from Brazilian swine farms are still poorly understood. Considering that antimicrobial resistance (AMR) is one of the main threats to human, animal, and environmental health, the need to accurately assess the load of ARGs released into the environment is urgent. Therefore, this study aimed to characterize the microbiota in a swine farm in southern Brazil and the resistome in swine farm wastewater treated in a series of waste stabilization ponds (WSPs). Samples were collected from farm facilities and the surrounding environment, representing all levels of swine manure within the treatment system. Total metagenomic sequencing was performed on samples from WSPs, and 16S-rDNA sequencing was performed on all the collected samples. The results showed increased bacterial diversity in WSPs, characterized by the presence of Caldatribacteriota, Cloacimonadota, Desulfobacterota, Spirochaetota, Synergistota, and Verrucomicrobiota. Furthermore, resistance genes to tetracyclines, lincosamides, macrolides, rifamycin, phenicol, and genes conferring multidrug resistance were detected in WSPs samples. Interestingly, the most abundant ARG was linG, which confers resistance to the lincosamides. Notably, genes conferring macrolide (mphG and mefC) and rifamycin (rpoB_RIF) resistance appeared in greater numbers in the late WSPs. These drugs are among the high-priority antibiotic classes for human health. Moreover, certain mobile genetic elements (MGEs) were identified in the samples, notably tnpA, which was found in high abundance. These elements are of particular concern due to their potential to facilitate the dissemination of ARGs among bacteria. In summary, the results indicate that, in the studied farm, the swine manure treatment system could not eliminate ARGs and MGEs. Our results validate concerns about Brazil's swine production system. The misuse and overuse of antimicrobials during animal production must be avoided to mitigate AMR.

Carrier state of enterotoxigenic Escherichia coli virulence markers in pigs: effects on gut microbiota modulation and immune markers transcription.

Enterotoxigenic Escherichia coli (ETEC) causes diarrhea in pigs at early age, leading to high mortality rates and significant economic losses in the swine industry. ETEC effect on gut microbiota and immune system is mostly studied in diarrheic model under controlled laboratory conditions, however its impact on asymptomatic carriers remains unknown. Thus, we investigated whether ETEC can modulate gut microbiota or regulate the transcription of immune markers in asymptomatic pigs in farm environment. Stool samples from newborn piglets, nursery and growing pigs, and sows were screened for ETEC markers, then submitted to 16S-rDNA sequencing to explore gut microbiota composition in carriers (ETEC+) and non-carriers (ETEC-) animals. We observed a reduced α-diversity in ETEC+ animals (p<0.05), while bacterial compositions were mostly driven by ageing (p>0.05). Prevotella marked ETEC-carrier group, while Rikenellaceae RC9 gut group was a marker for a healthy gut microbiota, suggesting being biomarker candidates for surveillance and supplementation purposes. Furthermore, we observed transcription regulation of il6 and tff2 genes in ETEC+ in newborn and nursery stages, respectively. Our findings indicate that ETEC presence modulate gut microbiota and the immune response in asymptomatic pigs; nevertheless, further studies using a probabilistic design must be performed to assess the effect of ETEC presence on gut imbalance in pigs despite the age bias.

Effect of Probiotic Lacticaseibacillus rhamnosus LB1.5 on Anxiety-like Behavior, Neuroprotection and Neuroinflammation Markers of Male Mice Fed a High-Fat Diet.

Probiotic supplementation has been identified as a potential target to reduce inflammatory mediators associated with obesity. Therefore, this study assessed the effect of probiotic Lacticaseibacillus rhamnosus LB1.5 on anxiety-like behavior, gene expression in the prefrontal cortex, and neuroinflammation in the cerebral cortex and hippocampus of male mice fed a high-fat diet. Mice aged 21 days were divided into four groups: control (CONT), control plus probiotic (CONT + PROB), high-fat diet (HFD), and high-fat diet plus probiotic (HFD + PROB), and fed for 13 weeks. The probiotic Lact. rhamnosus 1.5 (3.1 × 108 CFU/mL, derived from raw buffalo milk) was administered by gavage three times a week. Probiotic supplementation provided an anxiolytic effect in CONT and HFD. The IL-6 showed lower levels after probiotic supplementation in the HFD. Regarding immunoreactivity for GFAP in the cerebral cortex, we demonstrated that animals HFD-fed had a reduction in cells number compared to CONT. In the hippocampus, we found an interaction between diet and supplementation, as well as an effect of probiotic supplementation. A higher number of Th positive cells was observed in the cerebral cortex in mice fed HFD. Lact. rhamnosus LB1.5 supplementation decreased serum IL-6 levels in HFD-fed mice and promoted a reduction in anxiety-like behavior.

Comparative Analysis of How the Fecal Microbiota of Green-Winged Saltator (Saltator similis) Diverge among Animals Living in Captivity and in Wild Habitats.

The microbiota's alteration is an adaptive mechanism observed in wild animals facing high selection pressure, especially in captive environments. The objective of this study is to compare and predict the potential impact of habitat on the fecal bacterial community of Saltator similis, a songbird species that is a victim of illegal trafficking, living in two distinct habitats: wild and captivity. Nine wild and nine captive S. similis were sampled, and total bacterial DNA was obtained from the feces. Each DNA sample was employed to the amplification of the V4 region of the 16S rDNA following high-throughput sequencing. The most predominant phyla in all songbirds, irrespective of habitat, were Firmicutes, Bacteroidota, Proteobacteria, and Actinobacteriota. Interestingly, a microbiota profile (phylogenetic and abundance relationship) related to habitat was identified. The genera "Candidatus Arthromitus", Acinetobacter, Kocuria, and Paracoccus were exclusively identified in animals living in captivity, which can be a potential biomarker associated with birds in captive environments. This study presents the first description of the fecal bacterial community composition of S. similis living two different lifestyles. Finally, our results suggest that the lifestyle of S. similis birds significantly impacts the composition of the fecal microbiota. The animals living in captivity showed dysbiosis in the microbiota, with some bacteria genera being indicated as biological markers of environmental behavior. Thus, the present research provides a new concept of life quality measure for songbirds.

Genotypic characterization of Streptococcus didelphis causative of fatal infection in white-eared opossums.

Streptococcus didelphis was once reported as related to severe infections in opossums. Thus, we present the first comprehensive whole-genome characterization of clinical S. didelphis strains isolated from white-eared opossums (Didelphis albiventris). Long-read whole-genome sequencing was performed using the MinION platform, which allowed the prediction of several genomic features. We observed that S. didelphis genomes harbor a cluster for streptolysin biosynthesis and a conserved genomic island with genes involved in transcriptional regulation (arlR) and transmembrane transport (bcrA). Antimicrobial resistance genes for several drug classes were found, including beta-lactam, which is the main antimicrobial class used in Streptococcus spp. infections; however, no phenotypical resistance was observed. In addition, we predicted the presence of 33 virulence factors in the analyzed genomes. High phylogenetic similarity was observed between clinical and reference strains, yet no clonality was suggested. We also proposed dnaN, gki, pros, and xpt as housekeeping candidates to be used in S. didelphis sequence typing. This is the first whole-genome characterization of S. didelphis, whose data provide important insights into its pathogenicity.

A cross-sectional study on Campylobacter fetus subsp. venerealis prevalence and associated factors in Brazilian southern cattle farms.

Cattle farming is a major livestock activity with economic relevance in Rio Grande do Sul (RS), Brazil. However, this activity is still considered of intermediate to low technological level, and in this region, there are few epidemiologic reports of Campylobacter fetus subsp. venerealis (Cfv), the causative agent of bovine genital campylobacteriosis (BGC). Thus, we designed a cross-sectional study to assess the prevalence and Cfv-associated factors in cattle farms in RS, Brazil. In total, 99 farms were randomly selected to participate in the survey. Preputial mucus samples from selected bulls were collected twice (within a 15-day interval) and subjected to Cfv molecular detection. A farm was considered positive when at least one sample was positive for Cfv. Our findings indicate that the farm-level Cfv prevalence in RS is 67.67%. On average, the chance of a farm using natural service to be Cfv-positive increased approximately twice compared to farms that do not use natural service. We also determined that Cfv routine tests reduce the chance of a farm being positive by 92%. Therefore, both Cfv detection tests and the reduction of natural services decrease the chance of a farm being positive for Cfv. Finally, we conclude that Cfv is widely spread in Southern Brazil cattle farms and it is urgent the implementation of control measures to reduce Cfv prevalence in the target population.

Virulent potential of methicillin-resistant and methicillin-susceptible Staphylococcus pseudintermedius in dogs.

Staphylococcus pseudintermedius is a zoonotic pathogen responsible for several infectious diseases in pet animals, yet its pathogenic potential is not fully understood. Thus, this study aims to unravel the virulence profile of S. pseudintermedius from canine origin. Methicillin-resistant (MRSP) and methicillin-susceptible (MSSP) strains were isolated from different infection sites and their genotypic and phenotypic features were compared to determine the clinical implications of MRSP and MSSP strains. Bacterial identification was performed using MALDI-TOF and 16S-rDNA sequencing. In addition, we used multilocus sequence typing (MLST) for strains' sequence type (ST) determination and phylogenetic relationship. The strains were screened for toxin genes, including cytotoxins (lukS, lukF), exfoliative toxin (siet), enterotoxins (sea, seb, sec, secCanine, sel, sem, and seq) and toxic shock syndrome toxin (tst-1). In vitro phenotypic analyses assessing antimicrobial susceptibility profile, biofilm formation ability, and expression of extracellular matrix components were performed. The investigated S. pseudintermedius strains belong to 17 unique ST, most of which were classified as ST71. MSSP and MRSP strains shared siet, lukS, and lukF virulence markers. Our findings showed that some MSSP strains also harbored sel, seq, and sem enterotoxin genes, suggesting a more diverse virulence profile. All MRSP strains and 77% of MSSP strains were classified as multidrug resistant (MDR). Moreover, all investigated S. pseudintermedius strains showed strong biofilm formation ability. In summary, our findings highlight the wide spread of highly virulent and drug-resistant zoonotic S. pseudintermedius strains, being a potential concern for One Health issues.

A high-fat diet changes placental morphology but does not change biochemical parameters, placental oxidative stress or cytokine levels.

INTRODUCTION: The placenta is an organ that forms the bridge between mother and fetus during pregnancy. Changes in the intrauterine environment directly impact the fetus' health, with maternal nutrition determining its development. This study analyzed the effects of different diets and probiotic supplementation during pregnancy on the biochemical parameters of maternal serum and placental morphology, oxidative stress, and cytokine levels in mice. METHODS: Female mice were fed standard (CONT), restrictive (RD), or high-fat (HFD) diets before and during pregnancy. During pregnancy, the CONT and HFD groups were divided into two groups that received the Lactobacillus rhamnosus LB1.5 three times per week (CONT + PROB and HFD + PROB). The RD, CONT, or HFD groups received vehicle control. Maternal serum biochemical parameters (glucose, cholesterol, and triglycerides) were evaluated. The morphology, redox profile (thiobarbituric acid reactive substances, sulfhydryls, catalase, and superoxide dismutase enzyme activity), and inflammatory cytokines (interleukins 1α, 1ß, IL-6, and tumor necrosis factor-alpha) were evaluated in the placenta. RESULTS: The serum biochemical parameters presented no differences between the groups. Regarding placental morphology, the HFD group showed an increased thickness of the labyrinth zone compared to the CONT + PROB group. However, no significant difference was found in the analysis of the placental redox profile and cytokine levels. DISCUSSION: RD and HFD, for 16 weeks before and during pregnancy, as well as probiotic supplementation during pregnancy, caused no change in serum biochemical parameters nor the gestational viability rate, placental redox state, and cytokine levels. However, HFD increased the thickness of the placental labyrinth zone.

Characterization of the cervicovaginal microbiota of female beef cattle harboring Campylobacter fetus subsp. venerealis using 16S rDNA gene sequencing.

Bovine genital campylobacteriosis (BGC) is a leading cause of return to estrus in cows. The etiologic agent, Campylobacter fetus subsp. venerealis (Cfv) is transmitted by venereal route. Hence, the surrounding reproductive tract microenvironment could play a role in return to estrus in cows. The presence of Cfv in cervicovaginal mucus of Angus breed females provide three experimental groups, which were subject to bacteriome analyses: 10 Cfv-positive cows (CVP), 10 Cfv-negative cows (CVN), and 10 nonsexually active heifers (NSA). Cows with return to estrus showed higher bacterial richness than NSA. Beta diversity analysis showed a significant difference (P = 0.006) in bacterial composition among the three groups analyzed (CVP, CVN, and NSA). However, no significant difference was found when comparing the CVP versus CVN groups. Ureaplasma and Pseudomonas were the genera most frequently observed in NSA, being Ureaplasma the predictor genus to that group, whereas Alistipes, Bacteroides, Rikenellaceae_RC9_gut_group, UCG-005, and UCG-10 were both significantly more abundant and predictors genera in cows with return to estrus. Our results provide an overview of the cervicovaginal bacterial microbiota in cows harboring Cfv and improve the knowledge of the pathogenesis of BGC.

Mannheimia varigena as the etiologic agent of lameness and coronary band lesion in cattle / Mannheimia varigena como agente etiológico de claudicação e lesão na banda coronária em bovinos

Mannheimia varigena was identified as the etiologic agent of lameness and coronary band lesion in 30% of cattle in a farm located in Rio Grande do Sul, Brazil. Swab samples from the lesions were cultured in McConkey Agar and Blood Agar for microbiological identification. Culture growth was submitted to Gram staining and Matrix Assisted Laser Desorption Ionization Time of Flight Mass Spectrometry (MALDI-TOF MS) identification. Antimicrobial susceptibility test based on disc diffusion was performed for three antibiotics: ceftiofur, gentamicin and florfenicol. Furthermore, molecular characterization of 16S rDNA gene sequencing was performed and the data was used in a phylogenetic analysis. For that purpose, total DNA was extracted by thermo extraction directly from the bacterial colonies and the polymerase chain reaction (PCR) was performed. Gram-negative Mannheimia varigena strain LBV010/22 was identified as the causative of the lesions. The strain was susceptible to all antibiotics tested. The phylogenetic analysis demonstrated that the analyzed strain is closely related to M. varigena strains from pyelonephritis and respiratory tract. Overall, this is the first report of M. varigena as the causative agent of coronary band injury in bovine. Therefore, our findings show the importance of an accurate microbiological identification of infectious agent in lameness cases in order to prevent the occurrence and perform an appropriate treatment in the future.

Mannheimia varigena foi identificada como agente etiológico de claudicação e lesão de banda coronária em 30% dos bovinos de uma fazenda localizada no Rio Grande do Sul, Brasil. Amostras de swab das lesões foram cultivadas em Ágar McConkey e Ágar Sangue para identificação microbiológica. O crescimento da cultura foi submetido à coloração de Gram e identificação por Espectrometria de Massa de Ionização por Dessorção a Laser Assistida por Matriz (MALDI-TOF MS). O teste de suscetibilidade antimicrobiana baseado na difusão em disco foi realizado para três antibióticos: ceftiofur, gentamicina e florfenicol. Além disso, foi realizada a caracterização molecular do sequenciamento do gene 16S rDNA e o resultado utilizado para análise filogenética. Para tanto, o DNA total foi extraído por termoextração diretamente das colônias bacterianas e uma reação em cadeia da polimerase (PCR) foi realizada. Foi identificada como causadora das lesões a cepa gram-negativa de Mannheimia varigenaLBV010/22. Ela foi suscetível a todos os antibióticos testados. A análise filogenética demonstrou que a cepa analisada está intimamente relacionada às M. varigena presentes em pielonefrite e no trato respiratório. No geral, este é o primeiro relato de M. varigenacomo agente causador de lesão de banda coronária em bovinos. Portanto, nossos achados mostram a importância de uma identificação microbiológica precisa do agente infeccioso nos casos de claudicação, a fim de prevenir a ocorrência e realizar um tratamento adequado no futuro.

Cows' reproductive performances and parity order influences the cervicovaginal fungal community.

Fungi have already been described as etiological agents of reproductive diseases such as endometritis and infertility in cows. However, few studies have been developed to elucidate the entire cervicovaginal fungal communities in cows. Therefore, our study aimed to characterize the fungal community present in the cervix of cows with different reproductive performances. Cervicovaginal mucus was collected from 36 Angus breed cows (1.5-12 years old) on a commercial beef cattle ranch. Twenty-one cows had a history of infertility in the year prior to the collection, showing early return to estrus. Ten cows were sampled at 60-70 days postpartum being considered fertile cows. Additionally, five non-sexually active heifers were employed as control group. Ascomycota and Basidiomycota were the predominant fungal phyla in the analyzed animals. Diversity metrics of the cervicovaginal fungal community revealed statistical differences in the composition of the fungal community among infertile cows, fertile cows and non-sexually active heifers. In addition, the cervicovaginal fungal microbiota had significative increased richness and evenness in nulliparous cows and non-sexually active heifers, while in multiparous cows a decreased richness and evenness of the fungal microbiota were identified. These results provide an unprecedented understanding of the cervicovaginal fungal structure associated with infertility and parity order.

Characterization of Lactic Acid Bacteria in Raw Buffalo Milk: a Screening for Novel Probiotic Candidates and Their Transcriptional Response to Acid Stress.

Lactic acid bacteria (LAB) are important microorganisms for the food industry due to their functional activity, as starters and potential probiotic strains. With that in mind, we explored the LAB diversity in raw buffalo milk, screening for novel potential probiotic strains. A total of 11 strains were identified by combination of MALDI-TOF and partial 16S rDNA sequencing and selected as potential probiotic candidates. Bacteria innocuity assessment was performed by determining antimicrobial susceptibility and the presence of virulence factors. Antagonism activity against Escherichia coli, Pseudomonas aeruginosa, Listeria monocytogenes and Staphylococcus aureus was assessed, as well as milk proteolytic activity and exopolysaccharides production. Seven strains were identified as innocuous and two of them, Lactobacillus rhamnosus LB1.5 and Lactobacillus paracasei LB6.4 were selected for further probiotic potential analyses. Both strains demonstrated adhesion ability to Caco-2 cells, coaggregated with S. aureus and E. coli and maintained cell viability after gastrointestinal simulation in vitro, suggesting their probiotic potential. Furthermore, the transcriptional response of Lact. rhamnosus LB1.5 and Lact. paracasei LB6.4 to in vitro acid stress was assessed by RT-qPCR targeting seven genes related to adhesion, aggregation, stress tolerance, DNA repair and central metabolism. The association between the transcriptional responses and the maintenance of cell viability after gastrointestinal simulation highlights the genetic ability as probiotic of the two selected strains. Finally, we have concluded that Lact. rhamnosus LB1.5 and Lact. paracasei LB6.4 are important probiotic candidates to further in vivo studies.

Campylobacter fetus in abomasal fluid from spontaneously aborted bovine and ovine fetuses

Pregnancy losses are a major concern in livestock industry due to their economic impact on producers. Campylobacter fetus subspecies fetus (Cff) and C. fetus subspecies venerealis (Cfv) are directly related to reproductive failures in ruminants. Cff colonizes the gastrointestinal tract of a wide range of hosts leading to abortion, while Cfv is restricted to genital tract being generally associated to infertility in bovine. Considering the great economic losses related to campylobacteriosis in cattle and ovine herds, this study aims to investigate the occurrence of C. fetus, considering Cff and Cfv subspecies, in bovine and ovine spontaneously aborted fetuses in state of Rio Grande do Sul, Brazil. In this study, samples of abomasal fluid collected from 30 spontaneously aborted bovine (n = 18) and ovine (n = 12) fetuses were investigated for the detection of Campylobacter fetus throughout conventional PCR. Positive fetuses for C. fetus presence were further analyzed by molecular assays for Cff and Cfv detection, in order to determine subspecies identification. When available, samples of the main organs of the thoracic and abdominal cavities, as well as the brain, skeletal muscle, eyelid, skin, and placenta were collected for further histopathological analyses and bacterial culture, aiming to assess the presence of infection lesions and pathogens in those sites, respectively. Additionally, RT-qPCR assays were also performed for the detection of ruminant pestivirus, in order to detect bovine viral diarrhea cases. Throughout the present methodology, C. fetus was detected in the abomasal fluid samples of 2 bovine fetuses, being both identified as Cfv subspecies by PCR. Histopathological analyses demonstrated that macroscopic and microscopic changes found in the Cfv-positive animals were not either specific or directly related to Campylobacter infections. Moreover, no significant bacterial growth was observed in microbiological culture from the collected tissues, and both fetuses were negative for ruminant pestivirus. Differently, there was no detection of C. fetus in any of the analyzed ovine fetuses. Considering that abortion diagnosis rates reported in cattle and sheep industry are highly variable among the published studies, and that abortion diagnoses are commonly inconclusive due to difficulties in sampling methodology and inadequate identification of the pathogen involved, it is important to investigate the etiological causes of abortion the herds for better understanding the causes of pregnancy issues and monitoring their occurrence. In addition, the absence of pathognomonic lesions in the tissues investigated in the histopathological analyses observed in this study strongly suggests that well-known etiological agents commonly associated to abortion, such as Leptospira spp., Toxoplasma spp., Chlamydia spp. and Neospora caninum, are unlikely to be the cause of infection of the analyzed fetuses. Taking this into account, the presence of C. fetus in the abomasal fluid samples from two bovine fetuses demonstrated in the present study suggests the possible association of Cfv not only with infertility, but also with cases of bovine abortion, highlighting the importance of investigating unusual causal agents of abortions in sheep and cattle. Overall, an adequate diagnosis is essential for establishing better prevention strategies to avoid the circulation of abortion-related infectious agents in the herds.(AU)

Mycoplasma non-coding RNA: identification of small RNAs and targets.

BACKGROUND: Bacterial non-coding RNAs act by base-pairing as regulatory elements in crucial biological processes. We performed the identification of trans-encoded small RNAs (sRNA) from the genomes of Mycoplama hyopneumoniae, Mycoplasma flocculare and Mycoplasma hyorhinis, which are Mycoplasma species that have been identified in the porcine respiratory system. RESULTS: A total of 47, 15 and 11 putative sRNAs were predicted in M. hyopneumoniae, M. flocculare and M. hyorhinis, respectively. A comparative genomic analysis revealed the presence of species or lineage specific sRNA candidates. Furthermore, the expression profile of some M. hyopneumoniae sRNAs was determined by a reverse transcription amplification approach, in three different culture conditions. All tested sRNAs were transcribed in at least one condition. A detailed investigation revealed a differential expression profile for two M. hyopneumoniae sRNAs in response to oxidative and heat shock stress conditions, suggesting that their expression is influenced by environmental signals. Moreover, we analyzed sRNA-mRNA hybrids and accessed putative target genes for the novel sRNA candidates. The majority of the sRNAs showed interaction with multiple target genes, some of which could be linked to pathogenesis and cell homeostasis activity. CONCLUSION: This study contributes to our knowledge of Mycoplasma sRNAs and their response to environmental changes. Furthermore, the mRNA target prediction provides a perspective for the characterization and comprehension of the function of the sRNA regulatory mechanisms.