RESUMO
PURPOSE: Tumor necrosis factor inhibitors (TNFi) are known to increase the risk of tuberculosis (TB) reactivation, though cases involving Mycobacterium bovis are rarely reported. CASE PRESENTATION/RESULTS: We describe a case of disseminated TB with M. bovis in a 78-year-old woman with a negative Interferon-Gamma-Release Assay (IGRA), taking adalimumab due to rheumatoid polyarthritis, which resulted in a fatal outcome. The atypical clinical and histopathological features were initially interpreted as sarcoidosis. The case occurred in Switzerland, an officially bovine tuberculosis-free country. The whole genome sequence of the patient's cultured M. bovis isolate was identified as belonging to the animal lineage La1.2, the main genotype in continental Europe, but showed significant genetic distance from previously sequenced Swiss cattle strains. In a literature review, four cases of bovine tuberculosis reactivation under TNFi treatment were identified, with pulmonal, oral and intestinal manifestations. Similar to our patient, two cases presented a negative IGRA before TNFi initiation, which later converted to positive upon symptomatic presentation of M. bovis infection. CONCLUSION: This case highlights the diagnostic challenges of TB in immunosuppressed patients, the limited sensitivity of IGRA, and the importance of considering TB reactivation even in regions declared free of bovine tuberculosis. Detailed patient histories, including potential exposure to unpasteurized dairy products, are essential for guiding preventive TB treatment before TNFi initiation.
RESUMO
Infections with Mycobacterium microti, a member of the M. tuberculosis complex, have been increasingly reported in humans and in domestic and free-ranging wild animals. At postmortem examination, infected animals may display histopathologic lesions indistinguishable from those caused by M. bovis or M. caprae, potentially leading to misidentification of bovine tuberculosis. We report 3 cases of M. microti infections in free-ranging red deer (Cervus elaphus) from western Austria and southern Germany. One diseased animal displayed severe pyogranulomatous pleuropneumonia and multifocal granulomas on the surface of the pericardium. Two other animals showed alterations of the lungs and associated lymph nodes compatible with parasitic infestation. Results of the phylogenetic analysis including multiple animal strains from the study area showed independent infection events, but no host-adapted genotype. Personnel involved in bovine tuberculosis-monitoring programs should be aware of the fastidious nature of M. microti, its pathogenicity in wildlife, and zoonotic potential.
Assuntos
Cervos , Mycobacterium bovis , Tuberculose Bovina , Animais , Animais Selvagens , Áustria , Bovinos , Alemanha/epidemiologia , Mycobacterium bovis/genética , FilogeniaRESUMO
The occurrence of nontuberculous mycobacteria in different hosts and their implication as obligate or opportunistic pathogens remain mainly unclear. Mycobacteriosis in pigs is usually associated with members of the Mycobacterium avium complex and, in particular, with 'Mycobacterium avium subsp. hominissuis'. Here we describe a novel slow-growing mycobacterial species isolated from lymph nodes obtained from two sows housed in different Swiss farms. The animals presented chronic inappetence and mild diarrhoea. Gross pathology revealed focal caseous lymphadenopathy of the mesenteric lymph nodes. Complete genome sequencing of the two isolates from the two sows was performed. The genomes comprised 5.76 Mb and an average nucleotide identity score of 99.97â%. Whole genome sequence, mycolic acid and matrix-assisted laser desorption ionization-time of flight mass spectrometry analyses revealed that the two isolates were not related to any previously described Mycobacterium species. The closest related species was Mycobacterium parmense, a slow-growing scotochromogenic mycobacterium first isolated from a cervical lymph node of a 3-year-old child. The name proposed for the new species is Mycobacterium helveticum sp. nov. and 16-83T (=DSM 109965T= LMG 2019-02457T) is the type strain.
Assuntos
Linfonodos/microbiologia , Mycobacterium/classificação , Filogenia , Suínos/microbiologia , Animais , Técnicas de Tipagem Bacteriana , Composição de Bases , DNA Bacteriano/genética , Ácidos Graxos/química , Feminino , Genoma Bacteriano , Mycobacterium/isolamento & purificação , Infecções por Mycobacterium/microbiologia , Infecções por Mycobacterium/veterinária , Ácidos Micólicos/química , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , SuíçaRESUMO
Animal tuberculosis significantly challenges global health, agriculture, and wildlife conservation efforts. Mycobacterial cultures are resource-intensive, time-consuming, and challenged by heterogeneous populations. In this study, we employed a culture-independent approach, using targeted long-read-based next-generation sequencing (tNGS), to investigate the mycobacterial composition in 60 DNA samples extracted from Mycobacterium bovis infected culture-confirmed African buffalo tissue. We detected mycobacterial DNA in 93.3% of the samples and the sensitivity for detecting Mycobacterium tuberculosis complex (MTBC) was 91.7%, demonstrating a high concordance of our culture-independent tNGS approach with mycobacterial culture results. In five samples, we identified heterogenous mycobacterial populations with various non-tuberculous mycobacteria, including members of the Mycobacterium avium complex (MAC), M. smegmatis, and M. komaniense. The latter Mycobacterium species was described in South Africa from bovine nasal swabs and environmental samples from the Hluhluwe-iMfolozi Park, which was the origin of the buffalo samples in the present study. This finding suggests that exposure to environmental mycobacteria may confound detection of MTBC in wildlife. In conclusion, our approach represents a promising alternative to conventional methods for detecting mycobacterial DNA. This high-throughput technique enables rapid differentiation of heterogeneous mycobacterial populations, which will contribute valuable insights into the epidemiology, pathogenesis, and microbial synergy during mycobacterial infections.
Assuntos
Búfalos , Sequenciamento de Nucleotídeos em Larga Escala , Mycobacterium bovis , Tuberculose , Animais , Búfalos/microbiologia , Mycobacterium bovis/genética , Mycobacterium bovis/isolamento & purificação , Tuberculose/microbiologia , Tuberculose/veterinária , Tuberculose/diagnóstico , África do Sul/epidemiologia , DNA Bacteriano/genética , Bovinos , Microbiota/genéticaRESUMO
Hypervariable region sequencing of the 16S ribosomal RNA (rRNA) gene plays a critical role in microbial ecology by offering insights into bacterial communities within specific niches. While providing valuable genus-level information, its reliance on data from targeted genetic regions limits its overall utility. Recent advances in sequencing technologies have enabled characterisation of the full-length 16S rRNA gene, enhancing species-level classification. Although current short-read platforms are cost-effective and precise, they lack full-length 16S rRNA amplicon sequencing capability. This study aimed to evaluate the feasibility of a modified 150 bp paired-end full-length 16S rRNA amplicon short-read sequencing technique on the Illumina iSeq 100 and 16S rRNA amplicon assembly workflow by utilising a standard mock microbial community and subsequently performing exploratory characterisation of captive (zoo) and free-ranging African elephant (Loxodonta africana) respiratory microbiota. Our findings demonstrate that, despite generating assembled amplicons averaging 869 bp in length, this sequencing technique provides taxonomic assignments consistent with the theoretical composition of the mock community and respiratory microbiota of other mammals. Tentative bacterial signatures, potentially representing distinct respiratory tract compartments (trunk and lower respiratory tract) were visually identified, necessitating further investigation to gain deeper insights into their implication for elephant physiology and health.
Assuntos
Bactérias , Elefantes , Microbiota , RNA Ribossômico 16S , Animais , Elefantes/microbiologia , Elefantes/genética , RNA Ribossômico 16S/genética , Bactérias/genética , Bactérias/classificação , Microbiota/genética , Sequenciamento de Nucleotídeos em Larga Escala/métodos , Sistema Respiratório/microbiologia , Animais de Zoológico/microbiologia , Análise de Sequência de DNA/métodos , Animais Selvagens/microbiologia , FilogeniaRESUMO
This study investigated the presence of Mycobacterium bovis (M. bovis) DNA in archived human sputum samples previously collected from residents who reside adjacent to the M. bovis-endemic Hluhluwe-iMfolozi wildlife park, South Africa (SA). Sixty-eight sputum samples were GeneXpert MTB/RIF Ultra-positive for M. tuberculosis complex (MTBC) DNA but culture negative for M. tuberculosis. Amplification and Sanger sequencing of hsp65 and rpoB genes from DNA extracted from stored heat-inactivated sputum samples confirmed the presence of detectable amounts of MTBC from 20 out of the 68 sputum samples. Region of difference PCR, spoligotyping and gyrB long-read amplicon deep sequencing identified M. bovis (n = 10) and M. tuberculosis (n = 7). Notably, M. bovis spoligotypes SB0130 and SB1474 were identified in 4 samples, with SB0130 previously identified in local cattle and wildlife and SB1474 exclusively in African buffaloes in the adjacent park. M. bovis DNA in sputum, from people living near the park, underscores zoonotic transmission potential in SA. Identification of spoligotypes specifically associated with wildlife only and spoligotypes found in livestock as well as wildlife, highlights the complexity of TB epidemiology at wildlife-livestock-human interfaces. These findings support the need for integrated surveillance and control strategies to curb potential spillover and for the consideration of human M. bovis infection in SA patients with positive Ultra results.
RESUMO
Dermatophytosis is an important zoonotic disease in pet rabbits. While common clinical signs of dermatophytosis can occur, rabbits can also be asymptomatically infected. This case report describes a rabbit from Switzerland, with a focal alopecic area on one forepaw. Dermatophyte culture of a hair and skin sample taken from the lesion revealed growth of a dermatophyte, that was identified as the recently described species Arthroderma (A.) lilyanum by sequencing of the internal transcribed spacer (ITS) and ß-tubulin genes. After local treatment with a disinfectant containing octenidine dihydrochloride and phenoxyethanol twice daily for two weeks, the lesion fully healed. Although it is not clear whether the dermatophyte was responsible for the lesion or if it was an incidental finding with an asymptomatic infection, the current report shows, that the host spectrum and geographical distribution of A. lilyanum are broader than previously thought.
RESUMO
Glaesserella parasuis, Mycoplasma hyorhinis, and Mycoplasma hyosynoviae are important porcine pathogens responsible for polyserositis, polyarthritis, meningitis, pneumonia, and septicemia causing significant economic losses in the swine industry. A new multiplex quantitative polymerase chain reaction (qPCR) was designed on one hand for the detection of G. parasuis and the virulence marker vtaA to distinguish between highly virulent and non-virulent strains. On the other hand, fluorescent probes were established for the detection and identification of both M. hyorhinis and M. hyosynoviae targeting 16S ribosomal RNA genes. The development of the qPCR was based on reference strains of 15 known serovars of G. parasuis, as well as on the type strains M. hyorhinis ATCC 17981T and M. hyosynoviae NCTC 10167T . The new qPCR was further evaluated using 21 G. parasuis, 26 M. hyorhinis, and 3 M. hyosynoviae field isolates. Moreover, a pilot study including different clinical specimens of 42 diseased pigs was performed. The specificity of the assay was 100% without cross-reactivity or detection of other bacterial swine pathogens. The sensitivity of the new qPCR was demonstrated to be between 11-180 genome equivalents (GE) of DNA for M. hyosynoviae and M. hyorhinis, and 140-1200 GE for G. parasuis and vtaA. The cut-off threshold cycle was found to be at 35. The developed sensitive and specific qPCR assay has the potential to become a useful molecular tool, which could be implemented in veterinary diagnostic laboratories for the detection and identification of G. parasuis, its virulence marker vtaA, M. hyorhinis, and M. hyosynoviae.
Assuntos
Reação em Cadeia da Polimerase Multiplex , Infecções por Mycoplasma , Mycoplasma hyorhinis , Mycoplasma hyosynoviae , Infecções por Pasteurellaceae , Pasteurellaceae , Doenças dos Suínos , Reação em Cadeia da Polimerase Multiplex/métodos , Pasteurellaceae/isolamento & purificação , Mycoplasma hyorhinis/isolamento & purificação , Mycoplasma hyosynoviae/isolamento & purificação , Doenças dos Suínos/diagnóstico , Doenças dos Suínos/microbiologia , Animais , Suínos , Infecções por Mycoplasma/diagnóstico , Infecções por Mycoplasma/microbiologia , Infecções por Mycoplasma/veterinária , Infecções por Pasteurellaceae/diagnóstico , Infecções por Pasteurellaceae/microbiologia , Infecções por Pasteurellaceae/veterinária , Projetos Piloto , Sensibilidade e EspecificidadeRESUMO
Campylobacteriosis is the most common cause of acute gastrointestinal bacterial infection in Europe, with most infections linked to the consumption of contaminated food. While previous studies found an increasing rate of antimicrobial resistance (AMR) in Campylobacter spp. over the past decades, the investigation of additional clinical isolates is likely to provide novel insights into the population structure and mechanisms of virulence and drug resistance of this important human pathogen. Therefore, we combined whole-genome sequencing and antimicrobial-susceptibility testing of 340 randomly selected Campylobacter jejuni isolates from humans with gastroenteritis, collected in Switzerland over an 18 year period. In our collection, the most common multilocus sequence types (STs) were ST-257 (n=44), ST-21 (n=36) and ST-50 (n=35); the most common clonal complexes (CCs) were CC-21 (n=102), CC-257 (n=49) and CC-48 (n=33). High heterogeneity was observed among STs, with the most abundant STs recurring over the entire study period, while others were observed only sporadically. Source attribution based on ST assigned more than half of the strains to the 'generalist' category (n=188), 25ââ% as 'poultry specialist' (n=83), and only a few to 'ruminant specialist' (n=11) or 'wild bird' origin (n=9). The isolates displayed an increased frequency of AMR from 2003 to 2020, with the highest rates of resistance observed for ciprofloxacin and nalidixic acid (49.8â%), followed by tetracycline (36.9â%). Quinolone-resistant isolates carried chromosomal gyrA mutations T86I (99.4â%) and T86A (0.6â%), whereas tetracycline-resistant isolates carried tet(O) (79.8â%) or mosaic tetO/32/O (20.2â%) genes. A novel chromosomal cassette carrying several resistance genes, including aph(3')-III, satA and aad(6), and flanked by insertion sequence elements was detected in one isolate. Collectively, our data revealed an increasing prevalence of resistance to quinolones and tetracycline in C. jejuni isolates from Swiss patients over time, linked to clonal expansion of gyrA mutants and acquisition of the tet(O) gene. Investigation of source attribution suggests that infections are most likely related to isolates from poultry or generalist backgrounds. These findings are relevant to guide future infection prevention and control strategies.
Assuntos
Campylobacter jejuni , Gastroenterite , Animais , Humanos , Antibacterianos/farmacologia , Campylobacter jejuni/genética , Prevalência , Farmacorresistência Bacteriana , Aves Domésticas/microbiologia , TetraciclinaRESUMO
Animal tuberculosis is a significant infectious disease affecting both livestock and wildlife populations worldwide. Effective disease surveillance and characterization of Mycobacterium bovis (M. bovis) strains are essential for understanding transmission dynamics and implementing control measures. Currently, sequencing of genomic information has relied on culture-based methods, which are time-consuming, resource-demanding, and concerning in terms of biosafety. This study explores the use of culture-independent long-read whole-genome sequencing (WGS) for a better understanding of M. bovis epidemiology in African buffaloes (Syncerus caffer). By comparing two sequencing approaches, we evaluated the efficacy of Illumina WGS performed on culture extracts and culture-independent Oxford Nanopore adaptive sampling (NAS). Our objective was to assess the potential of NAS to detect genomic variants without sample culture. In addition, culture-independent amplicon sequencing, targeting mycobacterial-specific housekeeping and full-length 16S rRNA genes, was applied to investigate the presence of microorganisms, including nontuberculous mycobacteria. The sequencing quality obtained from DNA extracted directly from tissues using NAS is comparable to the sequencing quality of reads generated from culture-derived DNA using both NAS and Illumina technologies. We present a new approach that provides complete and accurate genome sequence reconstruction, culture independently, and using an economically affordable technique.
RESUMO
A 9-year-old cat was referred with multiple, raised, ulcerative and non-ulcerative nodules in the periocular area, sclera and ear-base region, and on the ventral aspect of the tongue. In addition, a progressive ulcerative skin nodule on the tail was observed. Fine-needle aspirations of multiple nodules from the eyelid and sclera revealed the presence of histiocytes with numerous acid-fast intracellular bacilli. The replication of slowly growing mycobacteria in liquid media was detected from biopsied nodules after three months of incubation. The molecular characterization of the isolate identified Mycobacterium (M.) lepraemurium as the cause of the infection. The cat was treated with a combination of surgical excision and a four-week course of antimicrobial therapy including rifampicin combined with clarithromycin. This is an unusual manifestation of feline leprosy and the first molecularly confirmed M. lepraemurium infection in a cat with ocular involvement in Europe. The successful combination of a surgical and antimycobacterial treatment regimen is reported.
RESUMO
ABSTRACT: Clostridium estertheticum and C. estertheticum-like spp. are obligate anaerobic psychrophiles causing "blown pack" spoilage of chilled vacuum-packed meat. The present study aimed at detecting and isolating these spoilage bacteria in fecal samples of cattle of different ages at the slaughterhouse level. One hundred two swab fecal samples were obtained and enriched anaerobically in prereduced peptone-yeast-glucose-starch (PYGS) medium for 3 weeks at 4°C and then screened for C. estertheticum and C. estertheticum-like spp. by using a 16S rRNA gene-based real-time PCR (RT-PCR) assay. The RT-PCR-positive samples were further enriched for 3 weeks in prereduced PYGS medium and then subjected to an ethanol (50%, v/v) and lysozyme (4 mg/mL) treatment. Isolation was carried out anaerobically on Columbia agar with 5% defibrinated sheep blood at 4°C for 3 weeks. Isolated strains were identified morphologically and by the 16S rRNA gene. Forty (39%) of 102 samples were RT-PCR positive. The frequency of positive samples was the following: 9 (45%) of 20 in calves (aged ≤160 days), 23 (43%) of 54 in young cattle (aged 161 to 1,000 days), and 8 (29%) of 28 in cows or bulls (aged >1,000 days). Six strains were isolated from 6 of 40 RT-PCR-positive samples. Of these, five were from the calves (n = 1) and young cattle (n = 4). The six isolates were identified as C. estertheticum (n = 1), Clostridium frigoriphilum (n = 1), and C. estertheticum-like spp. (n = 4). The present findings confirm that feces of cattle are an important source of psychrophilic Clostridium spp. The fecal carriage among livestock animals at slaughter is strongly correlated with the risk of carcass contamination. Therefore, the maintenance of slaughter hygiene is of central importance.
Assuntos
Matadouros , Embalagem de Alimentos , Animais , Bovinos , Clostridium , Fezes , Masculino , Carne , RNA Ribossômico 16S , OvinosRESUMO
Corynebacterium pseudotuberculosis biovar Ovis is the etiological agent of the contagious and chronic disease caseous lymphadenitis (CLA) in sheep and goats. The economic impact of CLA in Switzerland remains largely unknown, and the transmission modalities, as well as the genetic diversity of circulating strains, are poorly understood. This work presents further characterization data for 215 C. pseudotuberculosis isolates from sheep, goats and a dromedary originating from Switzerland and the Principality of Liechtenstein, collected over a 15-year period. The isolates were classified into the two biovars Ovis and Equi, analyzed for the presence of the diphtheria-like toxin gene and characterized using MLSA. All sheep and goat isolates were classified as C. pseudotuberculosis biovar Ovis. The isolate from a dromedary was classified as biovar Equi. No isolates harboring the diphtheria-like toxin gene were detected. Phylogenetic analysis of the concatenated sequences of four genes revealed the existence of 24 clusters. There was no correlation between MLSA sequence types, year of isolation and the geographical origin of the isolates. These findings confirm the presence of several MLSA sequence types in the study area and over a 15-year period. Moreover, no sheep- and goat-specific MLSA sequence types were found.
RESUMO
The interferon-γ assay has been used worldwide as an ancillary test for the diagnosis of bovine tuberculosis (bTB). This study aimed to describe, based on the bTB-free status in Switzerland, the difference of applying a more stringent cutoff point of 0.05 compared with 0.1 for bTB surveillance. Moreover, the effect of time between blood collection and stimulation, culture results, optical density values, and the influence of testing different breeds were evaluated. Blood samples from a total of 118 healthy cows older than 6 months were tested with three commercial interferon-gamma assays. To confirm the bTB-free status of the tested animals and to investigate potential cross-reactions with nontuberculous mycobacteria, pulmonary and abdominal lymph nodes in addition to ileal mucosa from each cattle were used for the detection of viable Mycobacteria spp. by specific culture. Significant differences regarding the proportion of false-positive results between the two Bovigam tests and between Bovigam 2G and ID Screen were found. Samples analyzed with Bovigam 2G were 2.5 [95% confidence interval (CI) 1.6-3.9] times more likely to yield a false-positive test result than samples analyzed with Bovigam TB. Similarly, the odds ratio (OR) for testing samples false-positive with ID Screen compared with Bovigam TB was 1.9 (95% CI 1.21-2.9). The OR for testing false-positive with ID Screen compared with Bovigam 2G was less to equally likely with an OR of 0.75 (95% CI 0.5-1.1). When using a cutoff of 0.05 instead of 0.1, the OR for a false-positive test result was 2.2 (95% CI 1.6-3.1). Samples tested after 6 h compared with a delayed stimulation time of 22-24 h were more likely to yield a false-positive test result with an OR of 3.9 (95% CI 2.7-5.6). In conclusion, applying a more stringent cutoff of 0.05 with the Bovigam 2G kit generates a questionable high number of false-positive results of one of three tested animals. Furthermore, specific breeds might show an increased risk to result false-positive in the Bovigam 2G and the ID Screen assays.
RESUMO
Rodents represent a natural reservoir of several Bartonella species, including zoonotic ones. In this study, small wild rodents, collected from two sites in rural areas of Switzerland, were screened for Bartonella spp. using molecular detection methods. In brief, 346 rodents were trapped in two rural sites in the Gantrisch Nature Park of Switzerland (Plasselb, canton of Fribourg, and Riggisberg, canton of Bern). Pools of DNA originating from three animals were tested through a qPCR screening and an end-point PCR, amplifying the 16S-23S rRNA gene intergenic transcribed spacer region and citrate synthase (gltA) loci, respectively. Subsequently, DNA was extracted from spleen samples belonging to single animals of gltA positive pools, and gltA and RNA polymerase subunit beta (rpoB) were detected by end-point PCR. Based on PCR results and sequencing, the prevalence of infection with Bartonella spp. in captured rodents, was 21.10% (73/346): 31.78% in Apodemus sp. (41/129), 10.47% in Arvicola scherman (9/86), 17.05% in Myodes glareolus (22/129), and 50% in Microtus agrestis (1/2). A significant association was observed between Bartonella spp. infection and rodent species (p < 0.01) and between trapping regions and positivity to Bartonella spp. infection (p < 0.001). Similarly, prevalence of Bartonella DNA was higher (p < 0.001) in rodents trapped in woodland areas (66/257, 25.68%) compared to those captured in open fields (9/89, 10.11%). Sequencing and phylogenetic analysis demonstrated that the extracted Bartonella DNA belonged mainly to B. taylorii and also to Candidatus "Bartonella rudakovii", B. grahamii, B. doshiae, and B. birtlesii. In conclusion, the present study could rise public health issues regarding Bartonella infection in rodents in Switzerland.
RESUMO
The occurrence of mycobacterial infections in different hosts and their implication as obligate or opportunistic pathogens remain mainly unclear. In addition to the well-known pathogenic members of the Mycobacterium tuberculosis - complex (MTBC), over 180 non-tuberculous mycobacteria (NTM) species have been described. Although the large majority of the NTM is assumed to be non-pathogenic to most individuals, an increasing trend in NTM infections has been observed over the last decades. The reasons of such augmentation are probably more than one: improved laboratory diagnostics, an increasing number of immunocompromised patients and individuals with lung damage are some of the possible aspects. Mandibular lymph nodes of 176 hunted wild boars from the pre-Alpine region of Canton Ticino, Switzerland, were collected. Following gross inspection, each lymph node was subjected to culture and to an IS6110 based real-time PCR specific for MTBC members. Histology was performed of a selection of lymph nodes (n = 14) presenting gross visible lesions. Moreover, accuracy of matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) species identification was compared with sequence analysis of a combination of housekeeping genes. Mycobacteria of the MTBC were detected in 2.8% of the wild boars (n = 5; CI95% 1.2-6.5) and were all confirmed to be Mycobacterium microti by molecular methods. In addition, based on the examined lymph nodes, NTM were detected in 57.4% (n = 101; CI95% 50.0-64.5) of the wild boars originating from the study area. The 111 isolates belonged to 24 known species and three potentially undescribed Mycobacterium species. M. avium subsp. hominissuis thereby predominated (22.5%) and was found in lymph nodes with and without macroscopic changes. Overall, the present findings show that, with the exception of undescribed Mycobacterium species where identification was not possible (3.6%; 4/111), MALDI-TOF MS had a high concordance rate (90.1%; 100/111 isolates) to the sequence-based reference method.
Assuntos
Infecções por Mycobacterium/veterinária , Mycobacterium/isolamento & purificação , Animais , Mycobacterium/classificação , Infecções por Mycobacterium/diagnóstico , Infecções por Mycobacterium/epidemiologia , Infecções por Mycobacterium/microbiologia , Infecções por Mycobacterium não Tuberculosas/diagnóstico , Infecções por Mycobacterium não Tuberculosas/epidemiologia , Infecções por Mycobacterium não Tuberculosas/microbiologia , Infecções por Mycobacterium não Tuberculosas/veterinária , Micobactérias não Tuberculosas/classificação , Micobactérias não Tuberculosas/isolamento & purificação , Prevalência , Sus scrofa , Suínos , Doenças dos Suínos , Suíça/epidemiologiaRESUMO
Background: The bacteria that compose the Mycobacterium tuberculosis complex (MTBC) cause tuberculosis (TB) in humans and in different animals, including livestock. Much progress has been made in understanding the population structure of the human-adapted members of the MTBC by combining phylogenetics with genomics. Accompanying the discovery of new genetic diversity, a body of operational nomenclature has evolved to assist comparative and molecular epidemiological studies of human TB. By contrast, for the livestock-associated MTBC members, Mycobacterium bovis, M. caprae and M. orygis, there has been a lack of comprehensive nomenclature to accommodate new genetic diversity uncovered by emerging phylogenomic studies. We propose to fill this gap by putting forward a new nomenclature covering the main phylogenetic groups within M. bovis, M. caprae and M. orygis. Methods: We gathered a total of 8,736 whole-genome sequences (WGS) from public sources and 39 newly sequenced strains, and selected a subset of 829 WGS, representative of the worldwide diversity of M. bovis, M. caprae and M. orygis. We used phylogenetics and genetic diversity patterns inferred from WGS to define groups. Results: We propose to divide M. bovis, M. caprae and M. orygis in three main phylogenetic lineages, which we named La1, La2 and La3, respectively. Within La1, we identified several monophyletic groups, which we propose to classify into eight sublineages (La1.1-La1.8). These sublineages differed in geographic distribution, with some being geographically restricted and others globally widespread, suggesting different expansion abilities. To ease molecular characterization of these MTBC groups by the community, we provide phylogenetically informed, single nucleotide polymorphisms that can be used as barcodes for genotyping. These markers were implemented in KvarQ and TB-Profiler, which are platform-independent, open-source tools. Conclusions: Our results contribute to an improved classification of the genetic diversity within the livestock-associated MTBC, which will benefit future molecular epidemiological and evolutionary studies.
RESUMO
PURPOSE OF REVIEW: Among the nontuberculous mycobacteria (NTM), Mycobacterium avium complex (MAC) is the leading cause of pulmonary disease in humans. Innate and acquired immunodeficiencies have been associated with an increased host susceptibility to NTM infections. The underlying mechanisms predisposing humans and dogs to MAC infections is being elucidated. RECENT FINDINGS: Although MAC infection is infrequently diagnosed in dogs, a strong breed predisposition particularly for Miniature Schnauzer and Basset Hound dogs is evident. A recessively inherited defect of the adaptor protein CARD9 has recently been documented to be responsible for the increased susceptibility to MAC in the Miniature Schnauzer breed. SUMMARY: Given the zoonotic potential of a MAC infected dog particularly to immunocompromised human patients, diseased dogs pose a public health risk. While not a reportable disease, treatment of systemic mycobacteriosis is generally not effective and discouraged in dogs. The collaborative efforts by microbiologists, veterinary clinicians, dog breeders, primary care physicians, and infectious disease specialists applying the One Health approach is therefore crucial for the best management and prevention of MAC infection.
RESUMO
Clostridium algidicarnis causes blown-pack spoilage of vacuum-packed meat. Here, we report the draft genome sequences of C. algidicarnis strains CM002 and CM003, isolated from unspoiled chilled vacuum-packed lamb. The genome sequences of CM002 and CM003 comprise 2,950,326 and 2,870,995 bp, respectively, and each have a GC content of 30.1%.
RESUMO
We present the draft genome sequence of Psychrobacter okhotskensis strain 5179-1A, which was isolated from a raw cured ham storage crate. Its size and GC content are 3.4 Mb and 43.4%, respectively. The 16S rRNA sequences of strain 5179-1A and P. okhotskensis MD17T are 100% identical.