RESUMO
Group B Streptococcus (GBS) is a major human and animal pathogen that threatens public health and food security. Spill-over and spill-back between host species is possible due to adaptation and amplification of GBS in new niches but the evolutionary and functional mechanisms underpinning those phenomena are poorly known. Based on analysis of 1,254 curated genomes from all major GBS host species and six continents, we found that the global GBS population comprises host-generalist, host-adapted and host-restricted sublineages, which are found across host groups, preferentially within one host group, or exclusively within one host group, respectively, and show distinct levels of recombination. Strikingly, the association of GBS genomes with the three major host groups (humans, cattle, fish) is driven by a single accessory gene cluster per host, regardless of sublineage or the breadth of host spectrum. Moreover, those gene clusters are shared with other streptococcal species occupying the same niche and are functionally relevant for host tropism. Our findings demonstrate (1) the heterogeneity of genome plasticity within a bacterial species of public health importance, enabling the identification of high-risk clones; (2) the contribution of inter-species gene transmission to the evolution of GBS; and (3) the importance of considering the role of animal hosts, and the accessory gene pool associated with their microbiota, in the evolution of multi-host bacterial pathogens. Collectively, these phenomena may explain the adaptation and clonal expansion of GBS in animal reservoirs and the risk of spill-over and spill-back between animals and humans.
Assuntos
Genoma Bacteriano , Infecções Estreptocócicas , Streptococcus agalactiae , Streptococcus agalactiae/genética , Streptococcus agalactiae/patogenicidade , Infecções Estreptocócicas/microbiologia , Infecções Estreptocócicas/genética , Animais , Humanos , Bovinos , Especificidade de Hospedeiro/genética , Genômica , Peixes/microbiologia , FilogeniaRESUMO
We describe group B Streptococcus linked to disease in farmed pigs and wild porcupines in Italy. Occurrence in pigs was attributed to transmission from nonpasteurized bovine milk whey. Antimicrobial-resistance profiles in isolates from porcupines suggest no common source of infection. Our findings expand the known host range for group B Streptococcus disease.
Assuntos
Porcos-Espinhos , Infecções Estreptocócicas , Streptococcus agalactiae , Doenças dos Suínos , Animais , Infecções Estreptocócicas/veterinária , Infecções Estreptocócicas/microbiologia , Infecções Estreptocócicas/epidemiologia , Infecções Estreptocócicas/transmissão , Itália/epidemiologia , Suínos , Doenças dos Suínos/microbiologia , Doenças dos Suínos/epidemiologia , Doenças dos Suínos/transmissão , Streptococcus agalactiae/isolamento & purificação , Streptococcus agalactiae/efeitos dos fármacos , Streptococcus agalactiae/classificação , Porcos-Espinhos/microbiologia , Antibacterianos/farmacologia , Antibacterianos/uso terapêutico , Bovinos , Doenças Transmissíveis Emergentes/microbiologia , Doenças Transmissíveis Emergentes/veterinária , Doenças Transmissíveis Emergentes/epidemiologia , Doenças Transmissíveis Emergentes/transmissãoRESUMO
Group B Streptococcus sequence type 103 is known primarily as a bovine mastitis pathogen. In Brazil, it has circulated in cattle and humans since the 1990s. It lacks scpB and, in humans, was found only among carriage isolates. Bovine-human interspecies transmission may have contributed to its evolution and spread.
Assuntos
Infecções Estreptocócicas , Bovinos , Humanos , Brasil/epidemiologia , Animais , Infecções Estreptocócicas/microbiologia , Infecções Estreptocócicas/veterinária , Infecções Estreptocócicas/epidemiologia , Infecções Estreptocócicas/transmissão , Streptococcus agalactiae/genética , Streptococcus agalactiae/classificação , Streptococcus agalactiae/isolamento & purificação , Feminino , Mastite Bovina/microbiologia , Doenças dos Bovinos/microbiologia , Doenças dos Bovinos/epidemiologia , FilogeniaRESUMO
Campylobacteriosis and antimicrobial resistance (AMR) are global public health concerns. Africa is estimated to have the world's highest incidence of campylobacteriosis and a relatively high prevalence of AMR in Campylobacter spp. from humans and animals. Few studies have compared Campylobacter spp. isolated from humans and poultry in Africa using whole-genome sequencing and antimicrobial susceptibility testing. We explored the population structure and AMR of 178 Campylobacter isolates from East Africa, 81 from patients with diarrhea in Kenya and 97 from 56 poultry samples in Tanzania, collected during 2006-2017. Sequence type diversity was high in both poultry and human isolates, with some sequence types in common. The estimated prevalence of multidrug resistance, defined as resistance to >3 antimicrobial classes, was higher in poultry isolates (40.9%, 95% credible interval 23.6%-59.4%) than in human isolates (2.5%, 95% credible interval 0.3%-6.8%), underlining the importance of antimicrobial stewardship in livestock systems.
Assuntos
Antibacterianos , Infecções por Campylobacter , Campylobacter coli , Campylobacter jejuni , Diarreia , Testes de Sensibilidade Microbiana , Aves Domésticas , Humanos , Campylobacter jejuni/efeitos dos fármacos , Campylobacter jejuni/genética , Campylobacter jejuni/isolamento & purificação , Animais , Diarreia/microbiologia , Diarreia/epidemiologia , Diarreia/tratamento farmacológico , Infecções por Campylobacter/microbiologia , Infecções por Campylobacter/epidemiologia , Infecções por Campylobacter/tratamento farmacológico , Infecções por Campylobacter/veterinária , Aves Domésticas/microbiologia , Antibacterianos/farmacologia , Campylobacter coli/efeitos dos fármacos , Campylobacter coli/genética , Campylobacter coli/isolamento & purificação , Farmacorresistência Bacteriana , Doenças das Aves Domésticas/microbiologia , Doenças das Aves Domésticas/epidemiologia , Doenças das Aves Domésticas/tratamento farmacológico , Sequenciamento Completo do Genoma , África Oriental/epidemiologia , Farmacorresistência Bacteriana Múltipla , FilogeniaRESUMO
Bovine digital dermatitis (BDD) is an important cause of lameness in dairy cows worldwide. However, very little is known about this disease in Australian herds, which are predominantly managed on pasture. The primary objectives of this cross-sectional study were to describe the presence and prevalence of BDD in Australian dairy herds and to characterize the microbiota of healthy skin and M4 lesions of BDD-affected, pasture-managed cows. Cows from 71 dairy herds were examined at milking time to identify the presence of BDD lesions. True prevalence was estimated using Bayesian methods with informative priors for sensitivity and specificity. Biopsy samples (n = 60) were collected from cows with and without BDD lesions in 7 pasture-based herds. The microbiota in the superficial and deep strata of each tissue biopsy were characterized via sequencing of the V3-V4 region of the bacterial ribosomal RNA gene. Lesions were detected in 1,817 (11.5%) of 15,813 cows and in 68 of 71 (95.8%) herds. The median herd-level apparent and true prevalences of BDD were 8.5% and 18.1%, respectively, but prevalences varied considerably between farms. On farms with BDD, M4 lesions accounted for 70% to 100% of all lesions (interquartile range = 95.1%-100%, median = 100%); M2 lesions (i.e., large ulcerative lesions) were observed at low prevalence (<2.2%) in the few herds (7/71, 9.9%) where they were found. There was a significant difference in the composition of the microbiota between healthy skin and M4 lesions but not between superficial and deep tissue layers. Several gut- and effluent-associated bacterial taxa, including Lentimicrobium and Porphyromonas, which have previously been associated with BDD, were abundant in BDD lesions but not in control biopsies. Our study supports the idea that such taxa are involved in, although possibly not essential to, lesion development and persistence in pasture-managed cows in Australia. Our results also suggest that Dichelobacter may contribute to the disease process. We conclude that BDD is likely to occur in most Australian dairy farms, but that further studies are needed to identify its effect on cow welfare and productivity. Further investigation of the etiology of BDD in Australian dairy herds is also necessary to inform prevention and control strategies.
Assuntos
Doenças dos Bovinos , Dermatite Digital , Bovinos , Animais , Doenças dos Bovinos/epidemiologia , Doenças dos Bovinos/microbiologia , Feminino , Estudos Transversais , Dermatite Digital/epidemiologia , Dermatite Digital/microbiologia , Austrália/epidemiologia , Indústria de Laticínios , Coxeadura Animal/epidemiologia , PrevalênciaRESUMO
To support antimicrobial stewardship in livestock production, there is a growing array of point-of-care diagnostics to guide antimicrobial treatment. The primary objective of this observational study was to evaluate the diagnostic performance of 5 point-of-care tests currently available in Australia for guiding lactational treatment of nonsevere clinical mastitis. A secondary objective was to describe the pathogen profiles of mastitis-causing organisms in cows managed in barns ("intensive") and on pasture ("nonintensive"). Foremilk samples (n = 641) were collected by farm staff in dairy herds in Australia (n = 30) and tested at a university laboratory using a reference test and 5 index tests. The reference test was aerobic culture on trypticase soy agar with 5% sheep blood followed by MALDI-TOF for identification of isolates. The following point-of-care tests were evaluated as index tests: Accumast, biplate, Check-Up, Mastatest (with AUP3-2022 product), and 3M Petrifilm. We found that 23% of samples were contaminated, with the median herd contamination prevalence being 22%. After excluding contaminated samples, the most common diagnoses (according to the reference test) in intensive herds were no growth (31.7%), Klebsiella spp. (28.1%), Escherichia coli (15.0%), and Streptococcus uberis (8.4%). The most common diagnoses in noncontaminated samples from cows in nonintensive herds were Strep. uberis (35.0%), no growth (26.9%), and E. coli (13.3%). After 24 h of incubation, all index tests demonstrated limited diagnostic sensitivity for identification of pathogens of interest (range: 0.06-0.63). Diagnostic performance was better at the group-level, with sensitivity and specificity for identification of noncontaminated gram-positive growths (i.e., cases that are widely considered to be candidates for antimicrobial treatment) being 0.84 and 0.75, respectively (biplate), 0.76 and 0.90 (Accumast), 0.89 and 0.79 (Check-Up), 0.67 and 0.83 (Petrifilm), and 0.55 and 0.81 (Mastatest). In intensive herds, 22.7% to 40% of cases were classified as antimicrobial treatment candidates by index tests, which was less than for cows in nonintensive herds (41.3%-61.0%). Despite limited diagnostic reliability at the genus level and species level, and the need to ensure samples are collected aseptically, our findings indicate that implementation of selective treatment protocols using the tests evaluated in this study would likely reduce antimicrobial usage in Australian herds.
Assuntos
Mastite Bovina , Bovinos , Animais , Mastite Bovina/diagnóstico , Mastite Bovina/microbiologia , Mastite Bovina/tratamento farmacológico , Feminino , Austrália , Sistemas Automatizados de Assistência Junto ao Leito , Indústria de Laticínios , Lactação , Leite/microbiologiaRESUMO
Our objectives were to quantify the dimensions of a fully 'closed' teat canal in dry cows and to describe recovery of the teat canal between milkings in lactating cows to assess whether and when full closure is attained, since this is an important determinant of udder health. Using an ultrasound scanner, teat canal length and diameter (proximal, midpoint and distal), teat cistern width, teat end width, whole teat width and teat wall thickness in 77 dry and 39 lactating dairy cows were measured. The dry cows represented a cross section of the dry population, with days since dry off ranging from 0 to 69 (median: 27). Data from lactating cows were recorded just before milking, and every 3 h post-milking. To control for location a cross-over (parlour vs. barn) study design was used. In dry cows, teat canal length and diameter did not vary by quarter or days since dry off, but multiparous cows had significantly wider teat canals than primiparous cows. The dry cow measurements can be used as baseline for dimensions for closed teats. In lactating cows, all teat dimensions except teat end width changed significantly during the 12-h milking cycle. Location (parlour vs. barn) did not affect the measurements, except teat end width and teat wall thickness. Teat canal length increased after milking and returned to pre-milking values by 9 h. Proximal and midpoint teat canal diameters decreased slightly just after milking and then progressively increased to above the pre-milking values by 9 h. Distal teat canal diameter increased after milking, partially contracting by 9 h. We found that during the dry period the teat canal is in a steady state, but its diameter is not zero, while during the lactation, the teat canal is in a near constant state of remodelling.
Assuntos
Lactação , Glândulas Mamárias Animais , Animais , Lactação/fisiologia , Feminino , Glândulas Mamárias Animais/anatomia & histologia , Glândulas Mamárias Animais/diagnóstico por imagem , Bovinos/anatomia & histologia , Bovinos/fisiologia , Ultrassonografia/veterinária , ParidadeRESUMO
Most diseases in aquaculture are caused by opportunistic pathogens. One of them, Vibrio harveyi, is a widespread Gram-negative bacterium that has become an important pathogen of aquatic species in marine environments. Here, we propose the use of the causal pie model as a framework to conceptualize the causation of vibriosis in juvenile barramundi (Lates calcarifer) and to establish an effective challenge model. In the model, a sufficient cause, or the causal pie, is a constellation of component causes that lead to an outcome (e.g. vibriosis). In the pilot study, a high cumulative mortality (63.3% ± 10.0%, mean ± SE) was observed when V. harveyi was administered by intraperitoneal injection using a high challenge dose [107 colony-forming units (CFU) fish-1 ], but low or no mortality was observed in fish subject to cold stress or fish with intact skin when challenged by immersion. We, therefore, tested the use of a skin lesion (induced with a 4-mm biopsy punch) combined with cold temperature stress to induce vibriosis following the causal pie model. After challenge, fish were immediately subject to cold stress (22°C) or placed at an optimal temperature of 30°C. All groups were challenged with 108 CFU mL-1 for 60 min. A considerably higher mortality level (72.7% ± 13.9%) was observed in fish challenged with both a skin lesion and cold stress compared with mortality in fish only having a skin lesion (14.6% ± 2.8%). V. harveyi was re-isolated from all moribund fish and was detected by species-specific real-time PCR in gills, head kidney and liver, regardless of challenge treatment confirming vibriosis as the cause of disease. Parenchymal tissues had histopathological changes consistent with vibriosis. Whole-genome sequence (WGS) is provided for the Vibrio harveyi isolate examined in this study. Overall, the causal pie model was a useful framework to conceptualize the design of the experimental challenge model, in which both cold stress and skin damage were identified as component causes of vibriosis with high mortality. This conceptual framework can be applied to other opportunistic pathogens in aquaculture or to the study of co-infections in fish.
Assuntos
Doenças dos Peixes , Perciformes , Vibrioses , Vibrio , Animais , Temperatura Baixa , Temperatura , Resposta ao Choque Frio , Projetos Piloto , Doenças dos Peixes/microbiologia , Vibrioses/veterinária , Vibrioses/microbiologia , PeixesRESUMO
We report here on an outbreak of mastitis caused by Streptococcus agalactiae, or group B Streptococcus, in a northern Italy (Lombardy Region) free stall dairy farm. This outbreak was unusual because it occurred in a closed dairy herd and proved to be extremely difficult to resolve even after the application of the classical control procedures, which are specifically focused on the contagious nature of S. agalactiae. In order to better understand the potential origins of the pathogen and the critical points that could impair the eradication program and to investigate the possible presence of S. agalactiae in sources outside the mammary gland, we collected 656 individual composite milk samples, 577 samples from extramammary body sites (289 rectal, 284 vaginal, and four throat samples from milking cows, dry cows, heifers, and calves), and 81 samples from the cattle environment, including the milking parlor and the barn. Twenty-two S. agalactiae isolates were obtained from lactating cows or their environment. Of these, nine were isolated from milk, two were from rectal swabs, and two were from vaginal swabs, while nine were isolated from environmental samples. Based on molecular serotyping, pilus island (PI) typing and multilocus sequence typing, all isolates belonged to serotype III, pilus type PI-1/2b, and sequence type 103 (ST103), a type previously described to have an environmental transmission cycle and a potential human origin. Once the classical mastitis control measures were supplemented with environmental hygiene measures, herd monitoring using bulk tank milk revealed no further positive results for S. agalactiae, and the outbreak was considered resolved. IMPORTANCE Streptococcus agalactiae is an important pathogen in humans and cattle. Bovine mastitis caused by this bacterium and its control are generally associated with contagious transmission between animals. More recently, the presence of a fecal-oral transmission cycle in cattle has been proposed, linked to the ability of some S. agalactiae strains to survive in the bovine gastrointestinal tract and environment. Based on analysis of 1,316 specimens from cattle and their environment on a single dairy farm, we demonstrate the presence of sequence type 103 (ST103), which may have an environmental mode of transmission. This possibility was supported by the fact that the mastitis outbreak could not be controlled through measures to prevent contagious transmission alone and required additional environmental hygiene measures to be brought to a halt. This case study highlights that measures to control animal disease need to evolve alongside the microorganisms that cause them.
Assuntos
Mastite Bovina , Infecções Estreptocócicas , Animais , Bovinos , Indústria de Laticínios/métodos , Fazendas , Feminino , Humanos , Lactação , Mastite Bovina/epidemiologia , Mastite Bovina/microbiologia , Leite/microbiologia , Infecções Estreptocócicas/epidemiologia , Infecções Estreptocócicas/microbiologia , Infecções Estreptocócicas/veterinária , Streptococcus agalactiae/genéticaRESUMO
East Africa is a hotspot for foodborne diseases, including infection by nontyphoidal Salmonella (NTS), a zoonotic pathogen that may originate from livestock. Urbanization and increased demand for animal protein drive intensification of livestock production and food processing, creating risks and opportunities for food safety. We built a probabilistic mathematical model, informed by prior beliefs and dedicated stakeholder interviews and microbiological research, to describe sources and prevalence of NTS along the beef supply chain in Moshi, Tanzania. The supply chain was conceptualized using a bow tie model, with terminal livestock markets as pinch point, and a forked pathway postmarket to compare traditional and emerging supply chains. NTS was detected in 36 (7.7%) of 467 samples throughout the supply chain. After combining prior belief and observational data, marginal estimates of true NTS prevalence were 4% in feces of cattle entering the beef supply and 20% in raw meat at butcheries. Based on our model and sensitivity analyses, true NTS prevalence was not significantly different between supply chains. Environmental contamination, associated with butchers and vendors, was estimated to be the most likely source of NTS in meat for human consumption. The model provides a framework for assessing the origin and propagation of NTS along meat supply chains. It can be used to inform decision making when economic factors cause changes in beef production and consumption, such as where to target interventions to reduce risks to consumers. Through sensitivity and value of information analyses, the model also helps to prioritize investment in additional research.
Assuntos
Carne , Salmonella , Animais , Bovinos , Gado , Carne/microbiologia , Modelos Estatísticos , TanzâniaRESUMO
BACKGROUND: Salmonella Enteritidis and Salmonella Typhimurium are major causes of bloodstream infection and diarrheal disease in East Africa. Sources of human infection, including the role of the meat pathway, are poorly understood. METHODS: We collected cattle, goat, and poultry meat pathway samples from December 2015 through August 2017 in Tanzania and isolated Salmonella using standard methods. Meat pathway isolates were compared with nontyphoidal serovars of Salmonella enterica (NTS) isolated from persons with bloodstream infections and diarrheal disease from 2007 through 2017 from Kenya by core genome multi-locus sequence typing (cgMLST). Isolates were characterized for antimicrobial resistance, virulence genes, and diversity. RESULTS: We isolated NTS from 164 meat pathway samples. Of 172 human NTS isolates, 90 (52.3%) from stool and 82 (47.7%) from blood, 53 (30.8%) were Salmonella Enteritidis sequence type (ST) 11 and 62 (36.0%) were Salmonella Typhimurium ST313. We identified cgMLST clusters within Salmonella Enteritidis ST11, Salmonella Heidelberg ST15, Salmonella Typhimurium ST19, and Salmonella II 42:r:- ST1208 that included both human and meat pathway isolates. Salmonella Typhimurium ST313 was isolated exclusively from human samples. Human and poultry isolates bore more antimicrobial resistance and virulence genes and were less diverse than isolates from other sources. CONCLUSIONS: Our findings suggest that the meat pathway may be an important source of human infection with some clades of Salmonella Enteritidis ST11 in East Africa, but not of human infection by Salmonella Typhimurium ST313. Research is needed to systematically examine the contributions of other types of meat, animal products, produce, water, and the environment to nontyphoidal Salmonella disease in East Africa.
Assuntos
Salmonella typhimurium , Sepse , Animais , Antibacterianos , Bovinos , Diarreia/epidemiologia , Humanos , Carne , Tipagem de Sequências Multilocus , Salmonella enteritidis/genética , Salmonella typhimurium/genética , TanzâniaRESUMO
BACKGROUND: Streptococcus agalactiae (Group B Streptococcus, (GBS)) is the leading cause of mastitis (inflammation of the mammary gland) among dairy camels in Sub-Saharan Africa, with negative implications for milk production and quality and animal welfare. Camel milk is often consumed raw and presence of GBS in milk may pose a public health threat. Little is known about the population structure or virulence factors of camel GBS. We investigated the molecular epidemiology of camel GBS and its implications for mastitis control and public health. RESULTS: Using whole genome sequencing, we analysed 65 camel milk GBS isolates from 19 herds in Isiolo, Kenya. Six sequence types (STs) were identified, mostly belonging to previously described camel-specific STs. One isolate belonged to ST1, a predominantly human-associated lineage, possibly as a result of interspecies transmission. Most (54/65) isolates belonged to ST616, indicative of contagious transmission. Phylogenetic analysis of GBS core genomes showed similar levels of heterogeneity within- and between herds, suggesting ongoing between-herd transmission. The lactose operon, a marker of GBS adaptation to the mammary niche, was found in 75 % of the isolates, and tetracycline resistance gene tet(M) in all but two isolates. Only the ST1 isolate harboured virulence genes scpB and lmb, which are associated with human host adaptation. CONCLUSIONS: GBS in milk from Kenyan camel herds largely belongs to ST616 and shows signatures of adaptation to the udder. The finding of similar levels of within- and between herd heterogeneity of GBS in camel herds, as well as potential human-camel transmission highlights the need for improved internal as well as external biosecurity to curb disease transmission and increase milk production.
Assuntos
Biosseguridade/normas , Camelus , Genoma Bacteriano/genética , Leite/microbiologia , Streptococcus agalactiae/genética , Animais , Biosseguridade/tendências , Genômica , Humanos , Quênia , Filogenia , Infecções Estreptocócicas/microbiologia , Streptococcus agalactiae/classificação , Sequenciamento Completo do GenomaRESUMO
To limit the use of antimicrobials in dairy cattle, farmers are increasingly encouraged to adopt targeted treatment decisions based on knowledge of the pathogens causing clinical mastitis (CM), whereby treatment of non-severe CM is generally recommended for gram-positive mastitis but not for gram-negative or culture-negative mastitis. The objectives of this study were to conduct a laboratory-based evaluation of the performance of a simplified slide test as a tool to differentiate gram-positive CM from other cases of CM, and to compare its performance against a commercially available on-farm test that is commonly used in our area (VétoRapid). Test outcomes after 24-48 h incubation were compared to results from bacteriological culture and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-ToF MS). Milk samples (n = 156) were obtained from cases of severe and non-severe CM on seven farms and collected by farm personnel. After removal of small numbers of contaminated samples and organisms with unknown species identity, the simplified slide test showed high sensitivity and accuracy (>80%), similar to the comparator test. For most outcomes of interest (culture positive, Escherichia coli, or gram-positive growth), the specificity of the slide test was higher than the specificity of the comparator test. When considering non-severe cases of CM only, and interpreting detection of gram-positive organisms as indicative of the need for antimicrobial treatment, the simplified test had higher specificity (77.4% v. 60.4%) and higher positive predictive value (79.7% v. 70.0%) than the comparator test and similar sensitivity (83.9% v. 87.5%). The proportion of sampled CM cases, contaminated samples and gram-positive mastitis cases - which affects the positive and negative predictive value, the economic value of diagnostic testing and its potential to reduce antimicrobial use - differed between farms. The simplicity and accuracy of the slide test could make it an attractive tool for farmers to target antimicrobial treatment of non-severe clinical mastitis.
Assuntos
Laboratórios , Mastite Bovina/microbiologia , Mastite Bovina/terapia , Testes Imediatos , Animais , Anti-Infecciosos/uso terapêutico , Técnicas Bacteriológicas/métodos , Bovinos , Fazendas , Feminino , Bactérias Gram-Negativas/isolamento & purificação , Bactérias Gram-Positivas/isolamento & purificação , Leite/microbiologia , Sensibilidade e Especificidade , Espectrometria de Massas por Ionização e Dessorção a Laser Assistida por Matriz/veterináriaRESUMO
The influence that bacterial adaptation (or niche partitioning) within species has on gene spillover and transmission among bacterial populations occupying different niches is not well understood. Streptococcus agalactiae is an important bacterial pathogen that has a taxonomically diverse host range making it an excellent model system to study these processes. Here, we analyze a global set of 901 genome sequences from nine diverse host species to advance our understanding of these processes. Bayesian clustering analysis delineated 12 major populations that closely aligned with niches. Comparative genomics revealed extensive gene gain/loss among populations and a large pan genome of 9,527 genes, which remained open and was strongly partitioned among niches. As a result, the biochemical characteristics of 11 populations were highly distinctive (significantly enriched). Positive selection was detected and biochemical characteristics of the dispensable genes under selection were enriched in ten populations. Despite the strong gene partitioning, phylogenomics detected gene spillover. In particular, tetracycline resistance (which likely evolved in the human-associated population) from humans to bovine, canines, seals, and fish, demonstrating how a gene selected in one host can ultimately be transmitted into another, and biased transmission from humans to bovines was confirmed with a Bayesian migration analysis. Our findings show high bacterial genome plasticity acting in balance with selection pressure from distinct functional requirements of niches that is associated with an extensive and highly partitioned dispensable genome, likely facilitating continued and expansive adaptation.
RESUMO
Mastitis, inflammation of the bovine mammary gland, is generally caused by intramammary infection with bacteria, and antimicrobials have long been a corner stone of mastitis control. As societal concern about antimicrobial use in animal agriculture grows, there is pressure to reduce antimicrobial use in dairy farming. Point-of-care tests for on-farm use are increasingly available as tools to support this. In this Research Reflection, we consider available culture-dependent and culture-independent tests in the context of ASSURED criteria for low-resource settings, including convenience criteria, scientific criteria and societal criteria that can be used to evaluate test performance. As tests become more sophisticated and sensitive, we may be generating more data than we need. Special attention is given to the relationship between test outcomes and treatment decisions, including issues of diagnostic refinement, antimicrobial susceptibility testing, and detection of viable organisms. In addition, we explore the role of technology, big data and people in improved performance and uptake of point-of-care tests, recognising that societal barriers may limit uptake of available or future tests. Finally, we propose that the 3Rs of reduction, refinement and replacement, which have been used in an animal welfare context for many years, could be applied to antimicrobial use for mastitis control on dairy farms.
Assuntos
Mastite Bovina/diagnóstico , Testes Imediatos , Animais , Anti-Infecciosos/efeitos adversos , Anti-Infecciosos/uso terapêutico , Bovinos , Indústria de Laticínios/métodos , Resistência Microbiana a Medicamentos , Feminino , Mastite Bovina/tratamento farmacológico , Mastite Bovina/microbiologiaRESUMO
The aim of this study was to analyze bacterial profiles of bovine mastitic milk samples and samples from healthy quarters using Next Generation Sequencing of amplicons from 16S rRNA genes and to compare results with microbiological results by PCR assays of the same samples. A total of 49 samples were collected from one single dairy herd during the same day. The samples were divided in two sample sets, which were used in this study. The DNA extraction as well as the library preparation and sequencing of these two sets were performed separately, and results of the two datasets were then compared. The vast majority of genera detected appeared with low read numbers and/or in only a few samples. Results of PCR and microbiome analyses of samples infected with major pathogens Staphylococcus aureus or Streptococcus uberis were consistent as these genera also covered the majority of reads detected in the microbiome analysis. Analysis of alpha diversity revealed a much higher species richness in set 1 than in set 2. The dominating bacterial genera with the highest read numbers clearly differed between datasets, especially in PCR negative samples and samples positive for minor pathogens. In addition to this, linear discriminant analysis (LDA) was conducted between the two sets to identify significantly different genera/family level microbes. The genus Methylobacterium was much more common in set 2 compared to set 1, and genus Streptococcus more common in set 1. Our results indicate amplification of contaminating bacteria in excess in samples with no or minor amounts of pathogen DNA in dataset 2. There is a need for critical assessment of results of milk microbiome analyses.
Assuntos
Sequenciamento de Nucleotídeos em Larga Escala/métodos , Microbiota , Leite/microbiologia , Reação em Cadeia da Polimerase/métodos , Animais , Bovinos , Feminino , Mastite Bovina/microbiologia , RNA Bacteriano/análise , RNA Ribossômico 16S/análiseRESUMO
Here we describe a new species of the genus Streptococcus that was isolated from a dairy cow with mastitis in New Zealand. Strain NZ1587T was Gram-positive, coccus-shaped and arranged as chains, catalase and coagulase negative, γ-haemolytic and negative for Lancefield carbohydrates (A-D, F and G). The 16S rRNA sequence did not match sequences in the NCBI 16S rRNA or GreenGenes databases. Taxonomic classification of strain NZ1587T was investigated using 16S rRNA and core genome phylogeny, genome-wide average nucleotide identity (ANI) and predicted DNA-DNA hybridisation (DDH) analyses. Phylogeny based on 16S rRNA was unable to resolve the taxonomic position of strain NZ1587T, however NZ1587T shared 99.4â% identity at the 16S rRNA level with a distinct branch of S. pseudoporcinus. Importantly, core genome phylogeny demonstrated that NZ1587T grouped amongst the 'pyogenic' streptococcal species and formed a distinct branch supported by a 100â% bootstrap value. In addition, average nucleotide identity and inferred DNA-DNA hybridisation analyses showed that NZ1587T represents a novel species. Biochemical profiling using the rapid ID 32 strep identification test enabled differentiation of strain NZ1587T from closely related streptococcal species. In conclusion, strain NZ1587T can be classified as a novel species, and we propose a novel taxon named Streptococcus bovimastitidis sp. nov.; the type strain is NZ1587T. NZ1587T has been deposited in the Culture Collection University of Gothenburg (CCUG 69277T) and the Belgian Co-ordinated Collections of Micro-organisms/LMG (LMG 29747).
Assuntos
Mastite Bovina/microbiologia , Filogenia , Infecções Estreptocócicas/veterinária , Streptococcus/classificação , Animais , Técnicas de Tipagem Bacteriana , Composição de Bases , Bovinos , DNA Bacteriano/genética , Feminino , Nova Zelândia , Hibridização de Ácido Nucleico , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Streptococcus/genética , Streptococcus/isolamento & purificaçãoRESUMO
Klebsiella pneumoniae is now recognized as an urgent threat to human health because of the emergence of multidrug-resistant strains associated with hospital outbreaks and hypervirulent strains associated with severe community-acquired infections. K. pneumoniae is ubiquitous in the environment and can colonize and infect both plants and animals. However, little is known about the population structure of K. pneumoniae, so it is difficult to recognize or understand the emergence of clinically important clones within this highly genetically diverse species. Here we present a detailed genomic framework for K. pneumoniae based on whole-genome sequencing of more than 300 human and animal isolates spanning four continents. Our data provide genome-wide support for the splitting of K. pneumoniae into three distinct species, KpI (K. pneumoniae), KpII (K. quasipneumoniae), and KpIII (K. variicola). Further, for K. pneumoniae (KpI), the entity most frequently associated with human infection, we show the existence of >150 deeply branching lineages including numerous multidrug-resistant or hypervirulent clones. We show K. pneumoniae has a large accessory genome approaching 30,000 protein-coding genes, including a number of virulence functions that are significantly associated with invasive community-acquired disease in humans. In our dataset, antimicrobial resistance genes were common among human carriage isolates and hospital-acquired infections, which generally lacked the genes associated with invasive disease. The convergence of virulence and resistance genes potentially could lead to the emergence of untreatable invasive K. pneumoniae infections; our data provide the whole-genome framework against which to track the emergence of such threats.
Assuntos
Variação Genética , Genoma Bacteriano/genética , Infecções por Klebsiella/microbiologia , Klebsiella pneumoniae/genética , Animais , Anti-Infecciosos/farmacologia , Proteínas de Bactérias/classificação , Proteínas de Bactérias/genética , Infecção Hospitalar/microbiologia , Farmacorresistência Bacteriana Múltipla/genética , Genes Bacterianos/genética , Genômica/métodos , Humanos , Klebsiella pneumoniae/classificação , Klebsiella pneumoniae/patogenicidade , Filogenia , Dinâmica Populacional , Saúde Pública/estatística & dados numéricos , Saúde Pública/tendências , Análise de Sequência de DNA , Especificidade da Espécie , Virulência/genéticaRESUMO
BACKGROUND: Bovine tuberculosis (bTB), caused by Mycobacterium bovis, is an important livestock disease raising public health and economic concerns around the world. In New Zealand, a number of wildlife species are implicated in the spread and persistence of bTB in cattle populations, most notably the brushtail possum (Trichosurus vulpecula). Whole Genome Sequenced (WGS) M. bovis isolates sourced from infected cattle and wildlife across New Zealand were analysed. Bayesian phylogenetic analyses were conducted to estimate the substitution rate of the sampled population and investigate the role of wildlife. In addition, the utility of WGS was examined with a view to these methods being incorporated into routine bTB surveillance. RESULTS: A high rate of exchange was evident between the sampled wildlife and cattle populations but directional estimates of inter-species transmission were sensitive to the sampling strategy employed. A relatively high substitution rate was estimated, this, in combination with a strong spatial signature and a good agreement to previous typing methods, acts to endorse WGS as a typing tool. CONCLUSIONS: In agreement with the current knowledge of bTB in New Zealand, transmission of M. bovis between cattle and wildlife was evident. Without direction, these estimates are less informative but taken in conjunction with the low prevalence of bTB in New Zealand's cattle population it is likely that, currently, wildlife populations are acting as the main bTB reservoir. Wildlife should therefore continue to be targeted if bTB is to be eradicated from New Zealand. WGS will be a considerable aid to bTB eradication by greatly improving the discriminatory power of molecular typing data. The substitution rates estimated here will be an important part of epidemiological investigations using WGS data.