Occurrence and identification of hemotropic mycoplasmas (Hemoplasmas) in free ranging and laboratory rats (Rattus norvegicus) from two Brazilian zoos.

BACKGROUND: Hemotropic mycoplasmas (hemoplasmas), bacteria belonging to the class Mollicutes, are obligatory red blood cell pathogens of a variety of animal species. They may cause acute anemia that is life-threatening or chronic disease that is clinically silent, but may interfere with results of experimental studies when using infected animals. Since these bacteria cannot be cultivated, molecular techniques are the gold standard for diagnosing an infection, investigating its prevalence, and describing new species. Mycoplasma coccoides and M. haemomuris are the most commonly recognized hemoplasmas in the blood of wild and laboratory rodents. Neither the epidemiology nor clinical and molecular characterization of hemoplasma infection in free-ranging rodents in Brazil has been previously reported. The aims of this study were to investigate the occurrence of hemoplasmas in free-ranging rats (Rattus norvegicus) captured in the Passeio Público and Curitiba Zoo and compare hematologic parameters of infected and non-infected animals. RESULTS: Anti-coagulated blood samples collected from 43 free-ranging and 20 nursery rats were included in the study. Overall 63.5% were positive using SYBR® Green quantitative PCR (qPCR) of the 16S rRNA gene to screen for hemoplasma infection (72% among free-ranging rats; 45% among laboratory-raised rats). Sequencing of the qPCR products showed that all but one sample had >98% identity to M. haemomuris. Phylogenetic analysis based on a fragment of approximately 1300 bp of the 16S rRNA gene showed 99% identity to a new hemoplasma from European rats and 98% identity to a hemotropic mycoplasma described infecting a European harvest mouse (Micromys minutus). No statistically significant changes in hematologic parameters between infected and non-infected rats were found, confirming the low pathogenicity and/or silent characteristics of the infection. CONCLUSIONS: Our findings suggest that hemoplasmas are likely endemic in rodent species in this region. The epidemiology, especially as it relates to the mode of transmission, needs to be further investigated as well as the possibility that other animal species, including humans, might become infected.

Glanders Diagnosis in an Asymptomatic Mare from Brazil: Insights from Serology, Microbiological Culture, Mass Spectrometry, and Genome Sequencing.

This manuscript elucidates the occurrence of glanders in an asymptomatic mare from Brazil presenting positive Burkholderia mallei antibody titers. The diagnosis was established through a multi-pronged approach encompassing microbiological culture, mass spectrometry, and genome sequencing. The outbreak occurred in 2019 in Tatuí, São Paulo, Brazil, and the infected mare, despite displaying no clinical symptoms, had multiple miliary lesions in the liver, as well as intense catarrhal discharge in the trachea. Samples were collected from various organs and subjected to bacterial isolation, molecular detection, and identification. The strain was identified as B. mallei using PCR and confirmed by MALDI-TOF mass spectrometry. Whole-genome sequencing revealed a genome size of 5.51 Mb with a GC content of 65.8%, 5871 genes (including 4 rRNA and 53 tRNA genes), and 5583 coding DNA sequences (CDSs). Additionally, 227 predicted pseudogenes were detected. In silico analysis of different genomic loci that allow for differentiation with Burkholderia pseudomallei confirmed the identity of the isolate as B. mallei, in addition to the characteristic genome size. The BAC 86/19 strain was identified as lineage 3, sublineage 2, which includes other strains from Brazil, India, and Iran. The genome sequencing of this strain provides valuable information that can be used to better understand the pathogen and its epidemiology, as well as to develop diagnostic tools for glanders.

The rate and role of pseudogenes of the Mycobacterium tuberculosis complex.

Whole-genome sequence analyses have significantly contributed to the understanding of virulence and evolution of the Mycobacterium tuberculosis complex (MTBC), the causative pathogens of tuberculosis. Most MTBC evolutionary studies are focused on single nucleotide polymorphisms and deletions, but rare studies have evaluated gene content, whereas none has comprehensively evaluated pseudogenes. Accordingly, we describe an extensive study focused on quantifying and predicting possible functions of MTBC and Mycobacterium canettii pseudogenes. Using NCBI's PGAP-detected pseudogenes, we analysed 25 837 pseudogenes from 158 MTBC and M. canetii strains and combined transcriptomics and proteomics of M. tuberculosis H37Rv to gain insights about pseudogenes' expression. Our results indicate significant variability concerning rate and conservancy of in silico predicted pseudogenes among different ecotypes and lineages of tuberculous mycobacteria and pseudogenization of important virulence factors and genes of the metabolism and antimicrobial resistance/tolerance. We show that in silico predicted pseudogenes contribute considerably to MTBC genetic diversity at the population level. Moreover, the transcription machinery of M. tuberculosis can fully transcribe most pseudogenes, indicating intact promoters and recent pseudogene evolutionary emergence. Proteomics of M. tuberculosis and close evaluation of mutational lesions driving pseudogenization suggest that few in silico predicted pseudogenes are likely capable of neofunctionalization, nonsense mutation reversal, or phase variation, contradicting the classical definition of pseudogenes. Such findings indicate that genome annotation should be accompanied by proteomics and protein function assays to improve its accuracy. While indels and insertion sequences are the main drivers of the observed mutational lesions in these species, population bottlenecks and genetic drift are likely the evolutionary processes acting on pseudogenes' emergence over time. Our findings unveil a new perspective on MTBC's evolution and genetic diversity.

Unraveling the metabolism of Mycobacterium caprae using comparative genomics.

In our laboratory, Mycobacterium caprae has poor growth in standard medium (SM) 7H9-OADC supplemented with pyruvate and Tween-80. Our objectives were to identify mutations affecting M. caprae metabolism and use this information to design a culture medium to improve its growth. We selected 77 M. caprae genomes and sequenced M. caprae NLA000201913 used in our experiments. Mutations present in >95% of the strains compared to Mycobacterium tuberculosis H37Rv were analyzed in silico for their deleterious effects on proteins of metabolic pathways. Apart from the known defect in the pyruvate kinase, M. caprae has important lesions in enzymes of the TCA cycle, methylmalonyl cycle, B12 metabolism, and electron-transport chain. We provide evidence of enzymatic redundancy elimination and epistatic mutations, and possible production of toxic metabolites hindering M. caprae growth in vitro. A newly designed SM supplemented with l-glutamate allowed faster growth and increased final microbial mass of M. caprae. However, possible accumulation of metabolic waste-products and/or nutritional limitations halted M. caprae growth prior to a M. tuberculosis-like stationary phase. Our findings suggest that M. caprae relies on GABA and/or glyoxylate shunts for in vitro growth in routine media. The newly developed medium will improve experiments with this bacterium by allowing faster growth in vitro.

Genetic Diversity and Potential Paths of Transmission of Mycobacterium bovis in the Amazon: The Discovery of M. bovis Lineage Lb1 Circulating in South America.

Bovine tuberculosis (bTB) has yet to be eradicated in Brazil. Herds of cattle and buffalo are important sources of revenue to people living in the banks of the Amazon River basin. A better understanding of Mycobacterium bovis (M. bovis) populational structure and transmission dynamics affecting these animals can significantly contribute in efforts to improve their sanitary status. Herein, we sequenced the whole genome of 22 M. bovis isolates (15 from buffalo and 7 from cattle) from 10 municipalities in the region of the Lower Amazon River Basin in Brazil and performed phylogenomic analysis and Single Nucleotide Polymorphism (SNP)-based transmission inference to evaluate population structure and transmission networks. Additionally, we compared these genomes to others obtained in unrelated studies in the Marajó Island (n = 15) and worldwide (n = 128) to understand strain diversity in the Amazon and to infer M. bovis lineages. Our results show a higher genomic diversity of M. bovis genomes obtained in the Lower Amazon River region when compared to the Marajó Island, while no significant difference was observed between M. bovis genomes obtained from cattle and buffalo (p ≥ 0.05). This high genetic diversity is reflected by the weak phylogenetic clustering of M. bovis from the Lower Amazon River region based on geographic proximity and in the detection of only two putative transmission clusters in the region. One of these clusters is the first description of inter-species transmission between cattle and buffalo in the Amazon, bringing implications to the bTB control program. Surprisingly, two M. bovis lineages were detected in our dataset, namely Lb1 and Lb3, constituting the first description of Lb1 in South America. Most of the strains of this study (13/22) and all 15 strains of the Marajó Island carried no clonal complex marker, suggesting that the recent lineage classification better describe the diversity of M. bovis in the Amazon.

Global Distribution and Evolution of Mycobacterium bovis Lineages.

Mycobacterium bovis is the main causative agent of zoonotic tuberculosis in humans and frequently devastates livestock and wildlife worldwide. Previous studies suggested the existence of genetic groups of M. bovis strains based on limited DNA markers (a.k.a. clonal complexes), and the evolution and ecology of this pathogen has been only marginally explored at the global level. We have screened over 2,600 publicly available M. bovis genomes and newly sequenced four wildlife M. bovis strains, gathering 1,969 genomes from 23 countries and at least 24 host species, including humans, to complete a phylogenomic analyses. We propose the existence of four distinct global lineages of M. bovis (Lb1, Lb2, Lb3, and Lb4) underlying the current disease distribution. These lineages are not fully represented by clonal complexes and are dispersed based on geographic location rather than host species. Our data divergence analysis agreed with previous studies reporting independent archeological data of ancient M. bovis (South Siberian infected skeletons at ∼2,000 years before present) and indicates that extant M. bovis originated between 715 and 3,556 years BP, with later emergence in the New World and Oceania, likely influenced by trades among countries.

Mycobacterium bovis in a European bison (Bison bonasus) raises concerns about tuberculosis in Brazilian captive wildlife populations: a case report.

BACKGROUND: Tuberculosis caused by Mycobacterium bovis is an important worldwide zoonosis and has been reported to cause clinical disease in several animal species, including captive wildlife. This report describes a case of M. bovis infection in a European bison from a Brazilian zoo and compiles a number of literature reports that raise concern regarding tuberculosis among captive wildlife in Brazil. CASE PRESENTATION: A 13 year-old captive-born male bison (Bison bonasus) from a Brazilian zoo began presenting weight loss, diarrhea and respiratory symptoms, which inevitably led to his death. At the animal's necropsy, inspection of the thoracic and abdominal cavities revealed multiple enlarged lymph nodes, ranging from 4 to 10 cm, and pulmonary nodules containing caseous masses with firm white materials consistent with mineralization. Histopathology findings showed a significant amount of acid-alcohol resistant bacilli compatible with Mycobacterium spp. Specimens from lymph nodes and lungs were cultured on Petragnani and Stonebrink media, and specific PCR assays of the bacterial isolate identified it as M. bovis. CONCLUSION: The European bison reported herein died from a severe form of disseminated tuberculosis caused by M. bovis. A review of the available literature indicates possible widespread occurrence of clinical disease caused by M. bovis or M. tuberculosis affecting multiple animal species in Brazilian wildlife-related institutions. These likely underestimated numbers raise concern regarding the control of the disease in captive animal populations from Brazil.

Complete Genome Sequencing of Mycobacterium bovis SP38 and Comparative Genomics of Mycobacterium bovis and M. tuberculosis Strains.

Mycobacterium bovis causes bovine tuberculosis and is the main organism responsible for zoonotic tuberculosis in humans. We performed the sequencing, assembly and annotation of a Brazilian strain of M. bovis named SP38, and performed comparative genomics of M. bovis genomes deposited in GenBank. M. bovis SP38 has a traditional tuberculous mycobacterium genome of 4,347,648 bp, with 65.5% GC, and 4,216 genes. The majority of CDSs (2,805, 69.3%) have predictive function, while 1,206 (30.07%) are hypothetical. For comparative analysis, 31 M. bovis, 32 M. bovis BCG, and 23 Mycobacterium tuberculosis genomes available in GenBank were selected. M. bovis RDs (regions of difference) and Clonal Complexes (CC) were identified in silico. Genome dynamics of bacterial groups were analyzed by gene orthology and polymorphic sites identification. M. bovis polymorphic sites were used to construct a phylogenetic tree. Our RD analyses resulted in the exclusion of three genomes, mistakenly annotated as virulent M. bovis. M. bovis SP38 along with strain 35 represent the first report of CC European 2 in Brazil, whereas two other M. bovis strains failed to be classified within current CC. Results of M. bovis orthologous genes analysis suggest a process of genome remodeling through genomic decay and gene duplication. Quantification, pairwise comparisons and distribution analyses of polymorphic sites demonstrate greater genetic variability of M. tuberculosis when compared to M. bovis and M. bovis BCG (p ≤ 0.05), indicating that currently defined M. tuberculosis lineages are more genetically diverse than M. bovis CC and animal-adapted MTC (M. tuberculosis Complex) species. As expected, polymorphic sites annotation shows that M. bovis BCG are subjected to different evolutionary pressures when compared to virulent mycobacteria. Lastly, M. bovis phylogeny indicates that polymorphic sites may be used as markers of M. bovis lineages in association with CC. Our findings highlight the need to better understand host-pathogen co-evolution in genetically homogeneous and/or diverse host populations, considering the fact that M. bovis has a broader host range when compared to M. tuberculosis. Also, the identification of M. bovis genomes not classified within CC indicates that the diversity of M. bovis lineages may be larger than previously thought or that current classification should be reviewed.

Draft Genome Sequence of Marine-Derived Aeromonas caviae CHZ306, a Potential Chitinase Producer Strain.

We report here a draft genome sequence of Aeromonas caviae CHZ306, a marine-derived bacterium with the ability to hydrolyze chitin and express high levels of chitinases. The assembly resulted in 65 scaffolds with approximately 4.78 Mb. Genomic analysis revealed different genes encoding chitin-degrading enzymes that can be used for chitin derivative production.

Draft Genome Sequence of Aeromonas caviae CH129, a Marine-Derived Bacterium Isolated from the Coast of São Paulo State, Brazil.

We report here the draft genome sequence of Aeromonas caviae CH129, a marine-derived bacterium isolated from the coast of São Paulo state, Brazil. Genomic analysis revealed genes encoding enzymes involved in binding, transport, and chitin metabolism and different virulence-associated factors.

Draft Genome Sequence of Mycobacterium bovis Strain SP38, a Pathogenic Bacterium Isolated from a Bovine in Brazil.

We report a draft genome sequence of Mycobacterium bovis strain SP38, isolated from the lungs of a cow in Brazil. The assembly of reads resulted in 36 contigs in a total of approximately 4.37 Mb. Comparison of M. bovis strains sequenced to date will aid in understanding bovine tuberculosis in Brazil.

Occurrence of antibodies anti -Toxoplasma gondii, Neospora caninum and Leptospira interrogans in a captive deer herd in Southern Brazil.

A large number of Brazilian zoos keep many endangered species of deer, however, very few disease surveillance studies have been conducted among captive cervids. Blood samples from 32 Brazilian deer (Blastocerus dichotomus, Mazama nana and Mazama americana) kept in captivity at Bela Vista Biological Sanctuary (Foz do Iguaçu, Brazil) were investigated for 10 ruminant pathogens, with the aims of monitoring deer health status and evaluating any potential zoonotic risk. Deer serum samples were tested for Brucella abortus, Leptospira (23 serovars), Toxoplasma gondii, Neospora caninum, bovine viral diarrhea virus, infectious bovine rhinotracheitis virus, foot-and-mouth disease virus, western equine encephalitis virus, eastern equine encephalitis virus and Venezuelan equine encephalitis virus. Antibodies against T. gondii (15.6%), N. caninum (6.2%) and L. interrogans serogroup Serjoe (3.1%) were detected. The serological results for all other infectious agents were negative. The deer were considered to be clinically healthy and asymptomatic regarding any disease. Compared with studies on free-ranging deer, the prevalences of the same agents tested among the captive deer kept at the Sanctuary were lower, thus indicating good sanitary conditions and high-quality management practices at the zoo.

Occurrences of anti-Toxoplasma gondii and anti-Neospora caninum antibodies in Barbary sheep at Curitiba zoo, southern Brazil.

Barbary sheep (Ammotragus lervia) have the potential to act as hosts of important infectious diseases, particularly zoonoses. Blood samples from 17 Barbary sheep at the Curitiba zoo were collected to evaluate occurrences of anti-Toxoplasma gondii and anti-Neospora caninum antibodies, tested using the indirect immunofluorescence antibody test (IFAT). Anti-T. gondii and anti-N. caninum antibodies were detected in 4/17 (23.5%) and 4/17 (23.5%) samples, respectively. The present study has shown that Barbary sheep at Curitiba zoo were exposed to T. gondii and N. caninum and therefore may act as intermediate hosts, spreading toxoplasmosis and neosporosis within and between species in shared areas.

Mycobacterium tuberculosis complex infection in Barbary sheep (Ammotragus lervia) at the Curitiba Zoo, southern Brazil: case report / Infecção pelo complexo Mycobacterium tuberculosis em carneiro da Barbária (Ammotragus lervia) no Zoológico de Curitiba, sul do Brasil: relato de caso

Tuberculosis is one of the most important mandatory notification diseases in the world caused by bacteria of the Mycobacterium tuberculosis complex, infecting both humans and animals. A sudden death of a Barbary sheep in Curitiba Zoo, and presence of multifocal nodules in lungs at necropsy raised suspicion of tuberculosis. Quantitative polymerase chain reaction (qPCR) from organs and fluid was performed and detected M. tuberculosis complex in a lung sample. This research reports the M. tuberculosis complex infection in Barbary sheep, a zoonosis of great relevance to public health and emphasizes the need to implement prevention measures. Furthermore, the research may provide a better understanding for species conservation, occurrence and transmission of diseases in captivity, reservoir potential and public health impact to zoo personnel and visitors.(AU)

A tuberculose é uma das doenças mundiais de notificação obrigatória mais importantes causada pelo complexo Mycobacterium tuberculosis que pode infectar pessoas e animais. A morte repentina de um carneiro da Barbária no Zoológico de Curitiba, que apresentou nódulos multifocais no pulmão à necropsia, levantou a suspeita de tuberculose. Foi realizada a Reação em Cadeia da Polimerase Quantitativa (qPCR) de fragmentos de órgãos e fluido. A qPCR detectou a presença do complexo M. tuberculosis nas amostras de pulmão. Este estudo relata a infecção pelo complexo M. tuberculosis no carneiro da Barbária, uma zoonose de grande relevância para a saúde pública, ressaltando-se a necessidade da implementação de medidas de prevenção. Além disso, pode prover um melhor entendimento sobre conservação de espécies, ocorrência e transmissão de doenças em cativeiro, potencial reservatório e impacto na saúde pública para visitantes e funcionários dos zoológicos.(AU)

Occurrence of antibodies anti -Toxoplasma gondii, Neospora caninum and Leptospira interrogans in a captive deer herd in Southern Brazil / Ocorrência de anticorpos anti -Toxoplasma gondii, Neospora caninum e Leptospira interrogans em um rebanho de cervídeos de cativeiro do sul do Brasil

Abstract A large number of Brazilian zoos keep many endangered species of deer, however, very few disease surveillance studies have been conducted among captive cervids. Blood samples from 32 Brazilian deer (Blastocerus dichotomus, Mazama nana and Mazama americana) kept in captivity at Bela Vista Biological Sanctuary (Foz do Iguaçu, Brazil) were investigated for 10 ruminant pathogens, with the aims of monitoring deer health status and evaluating any potential zoonotic risk. Deer serum samples were tested for Brucella abortus, Leptospira (23 serovars), Toxoplasma gondii, Neospora caninum, bovine viral diarrhea virus, infectious bovine rhinotracheitis virus, foot-and-mouth disease virus, western equine encephalitis virus, eastern equine encephalitis virus and Venezuelan equine encephalitis virus. Antibodies against T. gondii (15.6%), N. caninum (6.2%) and L. interrogans serogroup Serjoe (3.1%) were detected. The serological results for all other infectious agents were negative. The deer were considered to be clinically healthy and asymptomatic regarding any disease. Compared with studies on free-ranging deer, the prevalences of the same agents tested among the captive deer kept at the Sanctuary were lower, thus indicating good sanitary conditions and high-quality management practices at the zoo.

Resumo Um grande número de zoológicos brasileiros abriga espécies de cervídeos ameaçados de extinção, entretanto, estudos de vigilância de doenças em cervídeos de cativeiro são escassos. Amostras de sangue de 32 cervídeos brasileiros (Blastocerus dichotomus, Mazama nana e Mazama americana), mantidos em cativeiro no Refúgio Biológico Bela Vista (Foz do Iguaçu, Brasil), foram investigados para 10 patógenos de ruminantes, visando monitorar o estado de saúde dos cervídeos e avaliar a presença de agentes zoonóticos. As amostras de soro foram testadas para Brucella abortus, Leptospira (23 sorovares), Toxoplasma gondii, Neospora caninum, diarreia viral bovina, rinotraqueíte infecciosa bovina, febre aftosa, encefalomielite equina do oeste, encefalomielite equina do leste e encefalomielite equina venezuelana. Foram detectados anticorpos para T. gondii (15,6%), N. caninum (6,2%) e para L. interrogans sorogrupo Serjoe (3,1%). As sorologias apresentaram resultado negativo para as demais doenças. Os cervídeos foram considerados clinicamente sadios e assintomáticos para doenças. Comparados aos estudos de populações de vida livre, as soroprevalências para os mesmos agentes testados foram menores para os cervídeos mantidos no Refúgio, indicando as boas condições sanitárias e a qualidade das práticas de manejo no zoológico.

Occurrences of anti-Toxoplasma gondii and anti-Neospora caninum antibodies in Barbary sheep at Curitiba zoo, southern Brazil / Ocorrências de anticorpos anti-Toxoplasma gondii e anti-Neospora caninum em aoudads no zoológico de Curitiba, sul do Brasil

Barbary sheep (Ammotragus lervia) have the potential to act as hosts of important infectious diseases, particularly zoonoses. Blood samples from 17 Barbary sheep at the Curitiba zoo were collected to evaluate occurrences of anti-Toxoplasma gondii and anti-Neospora caninum antibodies, tested using the indirect immunofluorescence antibody test (IFAT). Anti-T. gondii and anti-N. caninum antibodies were detected in 4/17 (23.5%) and 4/17 (23.5%) samples, respectively. The present study has shown that Barbary sheep at Curitiba zoo were exposed to T. gondii and N. caninum and therefore may act as intermediate hosts, spreading toxoplasmosis and neosporosis within and between species in shared areas.

Aoudads (Ammotragus lervia) têm o potencial para atuar como hospedeiros de importantes doenças infecciosas, em particular as zoonoses. Amostras de sangue de 17 aoudads do zoológico de Curitiba foram coletadas para avaliar ocorrências de anticorpos anti-Toxoplasma gondii e anti-Neospora caninum, testados pela reação de imunofluorescência indireta (RIFI). Anticorpos anti-T. gondii e anti-N. caninum foram detectados em 4/17 (23,5%) e 4/17 (23,5%) das amostras dos aoudads, respectivamente. O presente estudo revelou que os aoudads no zoológico de Curitiba estão expostos a T. gondii e N. caninum e, portanto, podem atuar como hospedeiros intermediários e fatores de difusão da toxoplasmose e da neosporose intra e interespécies em áreas compartilhadas.