Leptospira spp., rotavirus, norovirus, and hepatitis E virus surveillance in a wild invasive golden-headed lion tamarin (Leontopithecus chrysomelas; Kuhl, 1820) population from an urban park in Niterói, Rio de Janeiro, Brazil.

The world currently faces severe biodiversity losses caused by anthropogenic activities such as deforestation, pollution, the introduction of exotic species, habitat fragmentation, and climate changes. Disease ecology in altered environments is still poorly understood. The golden-headed lion tamarin (GHLT, Leontopithecus chrysomelas) is an endangered species that became invasive in an urban park in Niterói, Rio de Janeiro, Brazil. The initially few invasive GHLT individuals became hundreds, adapted to living in proximity to humans and domestic animals. These GHLTs were captured as part of a conservation project; some animals were translocated to Bahia and some were kept in captivity. This study tested 593 GHLT for Leptospira serology; 100 and 95 GHLT for polymerase chain reaction (PCR) toLeptospira and hepatitis E virus genotype 3 (HEV-3), respectively, and 101 familiar groups for PCR to viruses (rotavirus A, norovirus GI and GII, and HEV-3). One animal had antibodies for Leptospira serovar Shermani and another for serovar Hebdomadis. One saprophyticLeptospira was found by the 16S PCR and sequencing. Viruses were not detected in samples tested. Findings suggest that the epidemiological importance of such pathogens in this GHLT population is either low or nonexistent. These data are important to understand the local disease ecology, as well as monitoring a translocation project, and to contribute data for species conservation.

Genomic characterisation of Leptospira inadai serogroup Lyme isolated from captured rat in Brazil and comparative analysis with human reference strain.

Leptospira inadai is classified as a species of the Leptospira intermediate group that has been poorly studied due to its apparent insignificance to human and animal health. Nevertheless, over the last two decades the species has been described in human cases in India and in carrier animals in Ecuador. Here, we present the first identification and genomic characterisation of L. inadai serogroup Lyme isolated from captured rodent in Brazil. Even though the M34/99 strain was not pathogenic for hamsters, it was able to establish renal colonisation. The M34/99 strain presented high similarity with L. inadai serogroup Lyme human reference indicating that animal strain could also infect humans, although it does not represent high risk of severe disease. An extrachromosomal sequence was also identified in M34/99 strain and presented high identity with previously described L. inadai phage LinZ_10, suggesting that phage-like extrachromosomal sequence may be another feature of this understudied species.

Comparative genomics of pathogenic Leptospira interrogans serovar Canicola isolated from swine and human in Brazil.

Leptospira interrogans serovar Canicola is one of the most important pathogenic serovars for the maintenance of urban leptospirosis. Even though it is considered highly adapted to dogs, serovar Canicola infection has already been described in other animals and even a few human cases. Here, we present the genomic characterisation of two Brazilian L. interrogans serovar Canicola strains isolated from slaughtered sows (L0-3 and L0-4) and their comparison with human strain Fiocruz LV133. It was observed that the porcine serovar Canicola strains present the genetic machinery to cause human infection and, therefore, represent a higher risk to public health. Both human and porcine serovar Canicola isolates also presented sequences with high identity to the Chinese serovar Canicola published plasmids pGui1 and pGui2. The plasmids identification in the Brazilian and Chinese serovar Canicola strains suggest that extra-chromosomal elements are one more feature of this serovar that was previously unnoticed.

Vancomycin-intermediate livestock-associated methicillin-resistant Staphylococcus aureus ST398/t9538 from swine in Brazil.

Livestock-associated methicillin-resistant Staphylococcus aureus (LA-MRSA) has been mainly related with pig farming, in Europe and North America, with the ST398 as the most commonly identified type of LA-MRSA. Here we present the draft genome of the first vancomycin-intermediate MRSA ST398/t9538 isolated from a swine presenting exudative epidermitis in Brazil.

Comparative genomic analysis of Brazilian Leptospira kirschneri serogroup Pomona serovar Mozdok.

Leptospira kirschneri is one of the pathogenic species of the Leptospira genus. Human and animal infection from L. kirschneri gained further attention over the last few decades. Here we present the isolation and characterisation of Brazilian L. kirschneri serogroup Pomona serovar Mozdok strain M36/05 and the comparative genomic analysis with Brazilian human strain 61H. The M36/05 strain caused pulmonary hemorrhagic lesions in the hamster model, showing high virulence. The studied genomes presented high symmetrical identity and the in silico multilocus sequence typing analysis resulted in a new allelic profile (ST101) that so far has only been associated with the Brazilian L. kirschneri serogroup Pomona serovar Mozdok strains. Considering the environmental conditions and high genomic similarity observed between strains, we suggest the existence of a Brazilian L. kirschneri serogroup Pomona serovar Mozdok lineage that could represent a high public health risk; further studies are necessary to confirm the lineage significance and distribution.

Draft genome of the Leptospira interrogans strains, Acegua, RCA, Prea, and Capivara, obtained from wildlife maintenance hosts and infected domestic animals.

In the present paper, we announce new draft genomes of four Leptospira interrogans strains named Acegua, RCA, Prea, and Capivara. These strains were isolated in the state of Rio Grande do Sul, Brazil, from cattle, dog, Brazilian guinea pig, and capybara, respectively.

Characterization of Aeromonas Isolates from Ornamental Fish: Species, Virulence Genes, and Antimicrobial Susceptibility.

This study aimed to characterize 300 Aeromonas spp. strains isolated from 123 ornamental fish of 32 different species presenting with septicemia, skin lesions, and/or eye lesions. Within the 300 strains, 53.0% were identified as A. veronii, 41.3% as A. hydrophila, and 5.7% as A. caviae. Among the six virulence genes investigated, the most frequent were act (90.3%) and aer (79.3%). More than 50% of A. hydrophila strains were positive for all the studied genes. A total of 30 virulence profiles were identified, with the five main profiles identified comprising 75% of strains. Only five strains were negative for all genes and were identified as A. caviae and A. veronii. The antimicrobial susceptibility profile was performed for 234 strains, with sulfonamides presenting more than 50% of the resistance rates. Susceptibility was observed mainly for cephalosporins, aminoglycosides, chloramphenicol and piperacillin-tazobactam. Multidrug resistance was detected in 82.5% of the studied strains, including A. caviae with 100% multidrug resistance, and A. hydrophila with 90.9% multidrug resistance. The SE-AFLP analysis resulted in 66 genotypes of A. hydrophila, 118 genotypes of A. veronii, and 14 genotypes of A. caviae, demonstrating the greater heterogeneity of A. veronii and A. caviae. However, no direct correlation was observed between the genotypes and the strains' origins or virulence and resistance profiles.

Characterization of Escherichia coli Isolated from Sows Presenting Purulent Vulvar Discharge.

Purulent vulvar discharge is a clinical sign of genitourinary tract infections, which are a significant concern in swine facilities, leading to sow culling and mortality. Escherichia coli is one of the main agents involved in these diseases. This study aimed to characterize the virulence and antimicrobial resistance profiles as well as the phylotype of Escherichia coli strains isolated from sows with purulent vulvar discharge. The results showed that at least 2 of the 29 tested virulence genes related to extraintestinal pathogenic E. coli were present in all strains tested. The most frequent gene was iutA, present in all strains, followed by the genes iucD, csgA, iss2, and irp2. Associations between iron uptake genes, genes related to adhesion, attachment, and serum resistance, as well as genes related to toxin release and bacteriocin, were frequent. The most prevalent phylotype was B1 (40.0%), followed by A (18.5%), D (11.9%), C (9.6%), B2 (7.4%), E (4.4%), F (1.5%), and Clade I (0.7%), with B2 being related to highly virulent traits. The strains presented elevated resistance to antimicrobials such as ciprofloxacin, streptomycin, cephalexin, florfenicol, and ampicillin. More than 90% of the strains were identified as multidrug-resistant, indicating the selection that is induced by the high use of antimicrobials in swine farming.

In vitro effects of cinnamon, oregano, and thyme essential oils against Escherichia coli and Trueperella pyogenes isolated from dairy cows with clinical endometritis.

Clinical endometritis causes serious economic losses in dairy farms, mainly due to its negative health impact on fertility and milk production, as well as the additional costs of medicines used to treat the affected animals. The therapy for uterine diseases is principally performed with antibiotic treatment; however, its indiscriminate use in dairy herds can favor the increase in the resistance of pathogenic bacteria, leading to treatment failures. In this regard, the use of unconventional treatment may be a good option to reduce the use of antimicrobials in milk production. The objective of the present study was to evaluate the antibacterial activity of cinnamon, oregano, and thyme essential oils, and their combinations, against bovine uterine pathogens. The antibacterial activities of these essential oils were evaluated by the Minimum Inhibitory Concentration (MIC) and Minimum Bactericidal Concentration (MBC), and Fractional Inhibitory Concentration (FIC) indices against Escherichia coli and Trueperella pyogenes, which were isolated from dairy cows with clinical endometritis. Among the essential oils evaluated, the lowest MIC and MBC values observed were obtained with cinnamon essential oil alone. The association among essential oils showed different kinds of interactions, and in some situations, antagonism was observed. This study demonstrated a promising antimicrobial activity of cinnamon's essential oil, indicating that it has excellent potential to be explored as a possible alternative in the treatment of clinical endometritis in dairy cows.

Characterization of Salmonella enterica Contamination in Pork and Poultry Meat from São Paulo/Brazil: Serotypes, Genotypes and Antimicrobial Resistance Profiles.

Salmonellosis is a zoonosis of major relevance to global public health. Here we present the assessment of Salmonella enterica contamination in pork and poultry meat sold at retail markets in São Paulo, Brazil. A total of 780 meat samples (386 poultry meat and 394 pork samples) were collected from 132 markets. From these, 57 samples (7.3%) were positive for S. enterica isolation, including 32 (8.3%) poultry meat and 25 (6.3%) pork samples. S. enterica isolates were further characterized for serotyping, antimicrobial resistance and genotyping by amplified fragment length polymorphism and pulsed field gel electrophoresis. Antimicrobial resistance analysis demonstrated two main profiles: pork isolates were more resistant to macrolides, ß-lactams, tetracycline, phenicols, and fluoroquinolones, and poultry meat isolates presented higher resistance to fluoroquinolones, sulfonamides, tetracycline, and ß-lactams. A total of 72.4% of poultry meat isolates were identified as S. Heidelberg, while most of pork isolates were S. Typhimurium (31.7%) and S. Give (16.7%). Genotyping resulted in most clusters consisting exclusively of pork or poultry meat, no cross-contamination was detected, and a tendency to differentiate isolates according to their serotypes and markets of origin. High resistance rates to critically important antimicrobials reinforce the importance of controlling Salmonella contamination in meat production chains.

Neobenedenia melleni from reef ornamental fish species in a retailer of Southeastern Brazil and its possible role as a mechanical vector of bacterial infection.

Annually, more than 2500 ornamental fish species are traded worldwide. Forty percent of these are from marine water. Some 98% of marine species are wild-caught from their natural habitat, and the majority subsequently exported. Wild fish frequently carry pathogens, which could induce diseases after the stress of capture. Neobenedenia melleni is a platyhelminth that mainly attaches to the skin and eyes of the host. It provokes dermal inflammation, epidermal loss, skin depigmentation, reduction in the number of mucous cells, and, consequently, decreased mucus protection, and declining immunological barriers. This makes fish susceptible to secondary infections. A total of 47 wild reef fish from a retailer were examined, suspected to be infected with ectoparasites. The morphological identification revealed N. melleni as a monogenean agent. One monogenean specimen was collected from the eye of each of the 40 fish analyzed to evaluate possible bacterial secondary infections using the matrix-assisted laser desorption ionization-time-of-flight mass spectrometry (MALDI-TOF MS) technique. The MALDI-TOF MS identified that 59% of monogenean collected from the eyes had bacteria, including some pathogenic to fish. This led us to believe that the ectoparasite can be a possible mechanical vector of pathogenic bacteria for fish culture and maintenance. The use of praziquantel as an antiparasitic agent is also discussed.

Vaginal microbiota signatures in healthy and purulent vulvar discharge sows.

Purulent vulvar discharges, primarily caused by genito-urinary tract infections, are an important source of economic loss for swine producers due to sow culling and mortality. However, the agents that compose the vaginal microbiota of sows and their changes during infections are not well understood. The first goal of this study was to characterize and compare the vaginal bacterial content of healthy (HE, n = 40) and purulent vulvar discharge sows (VD, n = 270) by a culture-dependent method and MALDI-TOF MS identification. Secondly, we performed 16S rRNA targeted metagenomic approach (n = 72) to compare the vaginal microbiota between these groups. We found a wide variety of bacteria, with Proteobacteria, Firmicutes, and Bacteroidota being the most abundant phyla in both groups, as well as Escherichia-Shigella, Streptococcus, and Bacteroides at the genus level. Most agents identified in the sequencing method also grew in the culture-dependent method, showing the viability of these bacteria. Alpha diversity did not differ between HE and VD sows, regarding sample richness and diversity, but a beta-diversity index showed a different microbiota composition between these groups in two tested herds. ANCOM analysis revealed that Bacteroides pyogenes were more abundant in VD females and can be a marker for this group. Other agents also require attention, such as the Streptococcus dysgalactiae and Staphylococcus hyicus found in remarkably greater relative abundance in VD sows. Network analysis revealed important positive correlations between some potentially pathogenic genera, such as between Escherichia-Shigella, Trueperella, Streptococcus, Corynebacterium, and Prevotella, which did not occur in healthy sows. We conclude that the alteration of the vaginal microbiota between healthy and purulent vulvar discharge sows, although not extreme, could be due to the increase in the relative abundance of specific agents and to associations between potentially pathogenic bacteria.

Main bacterial species causing clinical disease in ornamental freshwater fish in Brazil.

Bacterial diseases are common in ornamental fish, more frequently associated with ubiquitous bacteria from the aquarium environment. The disease can lead to fish mortality and cause high economic losses if not rapidly controlled. The aim of this study was to identify the main causative bacterial agents of infection in ornamental fish with different clinical signs. A total of 126 freshwater fish, from 12 families and 38 species, with clinical signs were collected in a wholesaler in São Paulo, SP, Brazil. Samples were taken from the eye, skin ulcers, kidneys, and gills, plated on MacConkey, CHROMagar Orientation, and blood agar and incubated under aerobic and anaerobic conditions. Bacterial identification was performed by MALDI-TOF mass spectrometry. From the 126 studied animals, 112 were positive for bacterial isolation. Among the positive animals, 32.1% presented infection caused by a single bacterial species, while in the remaining 67.9%, two to six different bacterial species were identified. A total of 259 bacterial strains were obtained and classified among 46 bacterial species. The species of higher frequency were Aeromonas veronii (26.3%), Aeromonas hydrophilla (16.2%), Shewanella putrefaciens (7.3%), Citrobacter freundii (8.1%), Vibrio albensis (5.8%), and Klebsiella pneumoniae (4.2%). MALDI-TOF MS showed to be a rapid method for diagnosis of bacterial disease outbreaks in ornamental fish establishments.

Salmonella enterica in Invasive Lizard from Fernando de Noronha Archipelago: Serotyping, Antimicrobial Resistance and Molecular Epidemiology.

Salmonella infection can pose serious health issues, especially to children, elders or immunosuppressed humans. Wild populations of reptiles can reach Salmonella prevalence of up to 100% and the direct or indirect transmission from reptiles to humans have been extensively reported. Fernando de Noronha (FN) is an inhabited oceanic archipelago in the northeast coast of Brazil, with an economy based on tourism. The tegu (Salvator merianae) is the largest lizard native to South America and was introduced to the archipelago in the early 20th century. This study determines the prevalence, serotypes, antimicrobial resistance, and molecular epidemiology of Salmonella enterica in the tegu population from FN archipelago. Results show that S. enterica is widely distributed in the FN tegu population, with 43.8% prevalence. The bacteria were isolated from 70.5% of the sampled sites and a total of 15 serotypes were detected in 98 S. enterica isolates. Strains were further classified into 31 genotypes. Recaptured animals presented distinct genotypes in each season, demonstrating a seasonal strain turnover. Most S. enterica isolates from FN tegus presented low antimicrobial resistance. This is possibly due to geographical isolation of the island population, hampering contact with strains from livestock from the continent, where antimicrobial resistance is common.

Molecular epidemiology of Leptospira noguchii reveals important insights into a One Health context.

Leptospirosis presents a complex and dynamic epidemiology. Bovine leptospirosis has been described as a major infectious disease impairing reproductive efficiency. Although infections by Leptospira interrogans, L. santarosai and L. borgpetersenii are frequently reported in cattle, the presence of L. noguchii in these animals should not be neglected. In this study, we describe serological (MAT) and molecular characterization (rrs and secY gene sequencing, multilocus sequence typing [MLST] and pulsed-field gel electrophoresis [PFGE]) of eight L. noguchii strains obtained from slaughtered cows. Intraspecific genetic diversity was evaluated, and haplotype networks were constructed based on hosts and geographical localizations. Strains were characterized as belonging to serogroups Australis, Autumnalis and Panama, and molecular characterization showed a high heterogeneity of these strains. Ten different STs were found (including nine new STs and 39 novel alleles) as well as nine different pulsotypes. Two clonal complexes were found. Phylogenetic trees based on secY locus and concatenated MLST loci showed two main clusters, with sequences from the present study included in the first. In general, there was no relationship between the geographical origin and the secY phylogenetic clusters, as well as between secY phylogenetic clusters and serogroups. Molecular diversity indexes confirmed a high variability (H > 0.8). This high intraspecific variation observed may be related to differences in virulence, pathogenicity and antigenicity or even adaptability of the strains. In addition, haplotype networks clearly demonstrated the circulation of genotypes between humans and animals, confirming the zoonotic potential. The present study provides relevant data for the study of leptospirosis in the One Health context, where human, animal and environmental health is closely connected.

Molecular Typing and Antimicrobial Susceptibility Profile of Staphylococcus aureus Isolates Recovered from Bovine Mastitis and Nasal Samples.

In the present study, we aimed to determine the antimicrobial resistance and molecular typing of Staphylococcus aureus recovered from transient and persistent intramammary infections and nares/muzzles in dairy cows. We investigated the antimicrobial resistance of 189 S. aureus strains using a broad antimicrobial susceptibility profile. Furthermore, 107 S. aureus isolates were strain-typed using staphylococcal protein-A (spa) typing. A large proportion of strains exhibited multidrug resistance to antimicrobials, including resistance to critically important antimicrobials, although no methicillin-resistant S. aureus strains were found. Our study did not strengthen the idea that extramammary niches (i.e., nares/muzzles) are an important source of S. aureus for bovine mastitis. A discrepancy in the antimicrobial resistance between S. aureus strains isolated from nares/muzzles and milk samples was observed. Furthermore, S. aureus isolates from transient and persistent intramammary infections (IMIs) did not differ by spa typing, suggesting that the persistence of bovine IMIs was determined by cow factors. Thus, the high level of multidrug-resistant S. aureus found in the two herds, considered together with the predominance of a well udder-adapted S. aureus strain, may contribute to our knowledge of the history of the high prevalence of mastitis caused by S. aureus, which is of great concern for animal and public health.

Genomic characterization and comparative analysis of Leptospira kirschneri serogroup Grippotyphosa UC5/2011, a strain isolated after mare abortion: Implications for genital animal leptospirosis.

The genome of a Brazilian strain of Leptospira kirschneri serogroup Grippotyphosa isolated from a mare post-abortion was sequenced and analyzed. High symmetrical identity and few structural differences were found when compared with a European strain of the same serogroup, L. kirschneri serovar Valbuzzi strain 200702274. Genes associated with virulence and antimicrobial resistance were found. Knowledge of the virulence evolution of Leptospira remains limited, especially in diseases of the reproductive sphere. We highlight the importance of virulence studies in the sphere of genital leptospirosis.

First report of mcr-1-harboring Salmonella enterica serovar Schwarzengrund isolated from poultry meat in Brazil.

Brazilian poultry meat samples were screened for colistin-resistant Salmonella enterica. Sixty Salmonella isolates were tested for in vitro colistin resistance and mcr-1, mcr-2, mcr-3 and mcr-4 genes. Two isolates harbored the mcr-1 gene and whole-genome analysis determined the serovar to be Schwarzengrund, ST96, harboring the IncX4 plasmid. This is the first report of mcr-1-harboring Salmonella enterica serovar Schwarzengrund in Brazil.

Streptococcus suis in Brazil: Genotypic, Virulence, and Resistance Profiling of Strains Isolated from Pigs between 2001 and 2016.

Streptococcus suis remains an important challenge for the worldwide swine industry. Considering that Brazil is a major pork producer and exporter, proper monitoring of the pathogen and resistance rates are required. We present here the characterization of Brazilian S. suis strains isolated over a 15 year period by pulsed-field gel electrophoresis (PFGE) typing, capsular, virulence, and antimicrobial resistance profiling. Serotype prevalence revealed a predominance of serotype 2/½ followed by 3, 7, 1/14, 6, 8, 18, 28, and 27; the latter had not yet been reported in Brazil. Resistance profiling enabled the differentiation of nine profiles presenting resistance to three and up to eight antimicrobial classes. Even though an association between the most resistant strains and isolation year starting from 2009 was observed, a high frequency of multidrug-resistant strains isolated from 2001 to 2003 was also detected. This suggests that despite the isolation period, S. suis strains already presented high resistance selection pressure. A slight association of serotype 2/½ with some virulence profiles and PFGE pulsotypes was also identified. Nevertheless, no clonal dispersion or persistency of clones over the analyzed years and herds was detected.

Genetic diversity, virulence genotype and antimicrobial resistance of uropathogenic Escherichia coli (UPEC) isolated from sows.

BACKGROUND: Urinary tract infections (UTI) cause severe losses to the swine industry worldwide and uropathogenic Escherichia coli (UPEC) are the main agent isolated from UTI in sows. OBJECTIVE: The aim of this study was to investigate the virulence genes, assess the phylogenetic background, clonal diversity, and the pattern of resistance to antimicrobials in 186 isolates of UPEC isolated from sows in Brazil. MATERIALS AND METHODS: Urine samples from 300 sows of three herds with clinical signs from São Paulo State (Brazil) were screened for UTI; samples with suggestive results were submitted to bacterial isolation. E. coli strains isolated were characterized using disk diffusion technique, polymerase chain reaction and Single-enzyme amplification fragment length polymorphism (SE-AFLP). RESULTS: Virulence genes focH and papC were present in 78.5% and 58% of strains, respectively, followed by cnf1 (23.2%), afa (13.4%), sfa (11.3%), iucD (6.9%), and hlyA (1.6%). No clonal relatedness was found by SE-AFLP. A total of 98% of isolates (182/186) were multidrug resistant, and the highest levels of resistance were to sulfonamides, tetracycline, florfenicol, and ampicillin. Isolates were classified in phylogenetic group B1 (34.4%), followed by D (33.9%), E (30.1%) and A (1.6%). CONCLUSIONS: The data obtained suggest that pigs from clinically affected herds may serve as a reservoir of uropathogenic and multidrug-resistant E. coli strains.