Abstract:
:Clostridium difficile PCR ribotype (RT) 014 is well-established in both human and porcine populations in Australia, raising the possibility that C. difficile infection (CDI) may have a zoonotic or foodborne etiology. Here, whole genome sequencing and high-resolution core genome phylogenetics were performed on a contemporaneous collection of 40 Australian RT014 isolates of human and porcine origin. Phylogenies based on MLST (7 loci, STs 2, 13, and 49) and core orthologous genes (1260 loci) showed clustering of human and porcine strains indicative of very recent shared ancestry. Core genome single nucleotide variant (SNV) analysis found 42% of human strains showed a clonal relationship (separated by ≤2 SNVs in their core genome) with one or more porcine strains, consistent with recent inter-host transmission. Clones were spread over a vast geographic area with 50% of the human cases occurring without recent healthcare exposure. These findings suggest a persistent community reservoir with long-range dissemination, potentially due to agricultural recycling of piggery effluent. We also provide the first pan-genome analysis for this lineage, characterizing its resistome, prophage content, and in silico virulence potential. The RT014 is defined by a large "open" pan-genome (7587 genes) comprising a core genome of 2296 genes (30.3% of the total gene repertoire) and an accessory genome of 5291 genes. Antimicrobial resistance genotypes and phenotypes varied across host populations and ST lineages and were characterized by resistance to tetracycline [tetM, tetA(P), tetB(P) and tetW], clindamycin/erythromycin (ermB), and aminoglycosides (aph3-III-Sat4A-ant6-Ia). Resistance was mediated by clinically important mobile genetic elements, most notably Tn6194 (harboring ermB) and a novel variant of Tn5397 (harboring tetM). Numerous clinically important prophages (Siphoviridae and Myoviridae) were identified as well as an uncommon accessory gene regulator locus (agr3). Conservation in the pathogenicity locus and S-layer correlated with ST affiliation, further extending the concept of clonal C. difficile lineages. This study provides novel insights on the genetic variability and strain relatedness of C. difficile RT014, a lineage of emerging One Health importance. Ongoing molecular and genomic surveillance of strains in humans, animals, food, and the environment is imperative to identify opportunities to reduce the overall CDI burden.
journal_name
Front Microbioljournal_title
Frontiers in microbiologyauthors
Knight DR,Squire MM,Collins DA,Riley TVdoi
10.3389/fmicb.2016.02138subject
Has Abstractpub_date
2017-01-11 00:00:00pages
2138issn
1664-302Xjournal_volume
7pub_type
杂志文章abstract::There is a concerted understanding of the accumulation of soil pathogens as the major driving factor of negative plant-soil feedback (NPSF). However, our knowledge of the connection between plant growth, pathogen build-up and soil microbiome assemblage is limited. In this study, significant negative feedback between t...
journal_title:Frontiers in microbiology
pub_type: 杂志文章
doi:10.3389/fmicb.2019.01597
更新日期:2019-07-26 00:00:00
abstract::Nowadays food preservation, quality maintenance, and safety are major growing concerns of the food industry. It is evident that over time consumers' demand for natural and safe food products with stringent regulations to prevent food-borne infectious diseases. Antimicrobial packaging which is thought to be a subset of...
journal_title:Frontiers in microbiology
pub_type: 杂志文章,评审
doi:10.3389/fmicb.2015.00611
更新日期:2015-06-16 00:00:00
abstract::Sutterella species have been frequently associated with human diseases, such as autism, Down syndrome, and inflammatory bowel disease (IBD), but the impact of these bacteria on health still remains unclear. Especially the interactions of Sutterella spp. with the host are largely unknown, despite of the species being h...
journal_title:Frontiers in microbiology
pub_type: 杂志文章
doi:10.3389/fmicb.2016.01706
更新日期:2016-10-26 00:00:00
abstract::The 1940s and 1950s witnessed a diverse search for not just natural product antibiotics but also for synthetic and semisynthetic compounds. This review revisits this epoch, using the research by a Danish pharmaceutical company, LEO Pharma, as an example. LEO adopted a strategy searching for synthetic antibiotics towar...
journal_title:Frontiers in microbiology
pub_type: 杂志文章,评审
doi:10.3389/fmicb.2020.00976
更新日期:2020-06-12 00:00:00
abstract::We have characterized the single subunit RNA polymerase from Klebsiella phage KP34. The enzyme is unique among known bacteriophage RNA polymerases in that it recognizes two unrelated promoter sequences, which provided clues for the evolution of phage single-subunit RNA polymerases. As the first representative enzyme f...
journal_title:Frontiers in microbiology
pub_type: 杂志文章
doi:10.3389/fmicb.2019.02487
更新日期:2019-10-31 00:00:00
abstract::Interactions between plants and microbes can affect ecosystem functions, and many studies have demonstrated that plant properties influence mutualistic microorganisms. Here, high-throughput sequencing was used to investigate rhizosphere and phyllosphere fungal communities during different plant development stages. Res...
journal_title:Frontiers in microbiology
pub_type: 杂志文章
doi:10.3389/fmicb.2020.556002
更新日期:2020-09-29 00:00:00
abstract::Accurately identifying bacteriophage virion proteins from uncharacterized sequences is important to understand interactions between the phage and its host bacteria in order to develop new antibacterial drugs. However, identification of such proteins using experimental techniques is expensive and often time consuming; ...
journal_title:Frontiers in microbiology
pub_type: 杂志文章
doi:10.3389/fmicb.2018.00476
更新日期:2018-03-16 00:00:00
abstract::Microorganisms perform countless tasks on Earth and they are expected to be essential for human space exploration. Despite the interest in the responses of bacteria to space conditions, the findings on the effects of microgravity have been contradictory, while the effects of Martian gravity are nearly unknown. We perf...
journal_title:Frontiers in microbiology
pub_type: 杂志文章
doi:10.3389/fmicb.2020.579156
更新日期:2020-10-14 00:00:00
abstract::Random transposon mutagenesis is a powerful technique used to generate libraries of genetic insertions in many different bacterial strains. Here we develop a system facilitating random transposon mutagenesis in a range of different Gram-negative bacterial strains, including Pectobacterium atrosepticum, Citrobacter rod...
journal_title:Frontiers in microbiology
pub_type: 杂志文章
doi:10.3389/fmicb.2015.01442
更新日期:2015-12-22 00:00:00
abstract::Low phosphorus soils are thought to constitute the majority of soils worldwide and cannot support intensive agriculture without high fertilizer inputs. Rhizobacteria are well-known to modify P dynamics and an increased bacterial diversity normally has a positive impact on various process rates. However, it is not know...
journal_title:Frontiers in microbiology
pub_type: 杂志文章
doi:10.3389/fmicb.2018.01990
更新日期:2018-09-05 00:00:00
abstract::Many bacteria produce cytolytic toxins that target host cells or other competing microbes. It is well known that environmental factors control toxin expression, however, recent work suggests that some bacteria manipulate the fold of these protein toxins to control their function. The β-sheet rich amyloid fold is a hig...
journal_title:Frontiers in microbiology
pub_type: 杂志文章,评审
doi:10.3389/fmicb.2014.00401
更新日期:2014-08-01 00:00:00
abstract::Microorganisms play a significant role in the evolution and functioning of the eukaryotes with which they interact. Much of our understanding of beneficial host-microbe interactions stems from studying already established associations; we often infer the genotypic and environmental conditions that led to the existing ...
journal_title:Frontiers in microbiology
pub_type: 杂志文章,评审
doi:10.3389/fmicb.2016.01444
更新日期:2016-09-13 00:00:00
abstract::The ability of human enteric pathogens to colonize plants and use them as alternate hosts is now well established. Salmonella, similarly to phytobacteria, appears to be capable of producing the plant hormone auxin via an indole-3-pyruvate decarboxylase (IpdC), a key enzyme of the IPyA pathway. A deletion of the Salmon...
journal_title:Frontiers in microbiology
pub_type: 杂志文章
doi:10.3389/fmicb.2017.02668
更新日期:2018-01-12 00:00:00
abstract::Cyanobacteria are major primary producers in the polar and alpine regions contributing significantly to nitrogen and carbon cycles in the cryosphere. Recent advancements in environmental sequencing techniques have revealed great molecular diversity of microorganisms in cold environments. However, there are no comprehe...
journal_title:Frontiers in microbiology
pub_type: 杂志文章
doi:10.3389/fmicb.2015.01070
更新日期:2015-10-13 00:00:00
abstract::Biogenic transformation of Fe minerals, associated with extracellular electron transfer (EET), allows microorganisms to exploit high-potential refractory electron acceptors for energy generation. EET-capable thermophiles are dominated by hyperthermophilic archaea and Gram-positive bacteria. Information on their EET pa...
journal_title:Frontiers in microbiology
pub_type: 杂志文章
doi:10.3389/fmicb.2020.597818
更新日期:2021-01-11 00:00:00
abstract::High-throughput sequencing (HTS) techniques are of great value for the investigation of microbial communities, and have been extensively used to study the gut microbiome. While most studies focus on the human gut, many others have investigated insects. However, because of the rapid spread of HTS techniques, a lot of v...
journal_title:Frontiers in microbiology
pub_type: 杂志文章
doi:10.3389/fmicb.2019.02833
更新日期:2019-12-13 00:00:00
abstract::The development of antibiotic resistance poses an increasing threat to global health. Understanding how resistance develops in bacteria is critical for the advancement of new strategies to combat antibiotic resistance. In the 1980s, it was discovered that certain antibiotics induce elevated rates of mutation in bacter...
journal_title:Frontiers in microbiology
pub_type: 杂志文章,评审
doi:10.3389/fmicb.2020.585175
更新日期:2020-10-22 00:00:00
abstract::Acinetobacter baumannii, a Gram-negative opportunistic pathogen, is known to cause multidrug resistant infections. This organism has primarily been isolated from clinical environments and its environmental reservoirs remain largely unknown. In the present study, we recovered seven isolates of A. baumannii growing unde...
journal_title:Frontiers in microbiology
pub_type: 杂志文章
doi:10.3389/fmicb.2016.01871
更新日期:2016-11-18 00:00:00
abstract::Haemophilus parasuis is known as a commensal organism discovered in the upper respiratory tract of swine where the pathogenic bacteria survive in various adverse environmental stress. QseC, a histidine protein kinase of the two-component regulatory systems CheY/QseC, is involved in the environmental adaptation in bact...
journal_title:Frontiers in microbiology
pub_type: 杂志文章
doi:10.3389/fmicb.2018.00212
更新日期:2018-02-13 00:00:00
abstract::Maintenance of Borrelia burgdorferi within its enzootic cycle requires a complex regulatory pathway involving the alternative σ factors RpoN and RpoS and two ancillary trans-acting factors, BosR and Rrp2. Activation of this pathway occurs within ticks during the nymphal blood meal when RpoS, the effector σ factor, tra...
journal_title:Frontiers in microbiology
pub_type: 杂志文章
doi:10.3389/fmicb.2019.01923
更新日期:2019-08-21 00:00:00
abstract::Lower-termites are one of the best studied symbiotic systems in insects. Their ability to feed on a nitrogen-poor, wood-based diet with help from symbiotic microbes has been under investigation for almost a century. A unique microbial consortium living in the guts of lower termites is essential for wood-feeding. Host ...
journal_title:Frontiers in microbiology
pub_type: 杂志文章,评审
doi:10.3389/fmicb.2016.00422
更新日期:2016-04-08 00:00:00
abstract::Aerobic granular sludge (AGS) is based on self-granulated flocs forming mobile biofilms with a gel-like consistence. Bacterial and structural dynamics from flocs to granules were followed in anaerobic-aerobic sequencing batch reactors (SBR) fed with synthetic wastewater, namely a bubble column (BC-SBR) operated under ...
journal_title:Frontiers in microbiology
pub_type: 杂志文章
doi:10.3389/fmicb.2013.00175
更新日期:2013-07-10 00:00:00
abstract::Variation among animals in their host-associated microbial communities is increasingly recognized as a key determinant of important life history traits including growth, metabolism, and resistance to disease. Quantitative estimates of the factors shaping the stability of host microbiomes over time at the individual le...
journal_title:Frontiers in microbiology
pub_type: 杂志文章
doi:10.3389/fmicb.2019.02883
更新日期:2019-12-20 00:00:00
abstract::Cronobacter spp. are bacterial pathogens that cause neonatal meningitis, septicemia, and necrotizing enterocolitis in infants with a lethality rate of 40-80%. Powdered infant formulas (PIF) have been implicated as the main vehicles of transmission. This pathogen can also cause infection through contaminated expressed ...
journal_title:Frontiers in microbiology
pub_type: 杂志文章
doi:10.3389/fmicb.2018.02206
更新日期:2018-09-27 00:00:00
abstract::The dlt operon of Gram-positive bacteria is required for the incorporation of D-alanine esters into cell wall-associated teichoic acids (TAs). Addition of D-alanine to TAs reduces the negative charge of the cell envelope thereby preventing cationic antimicrobial peptides (CAMPs) from reaching their target of action on...
journal_title:Frontiers in microbiology
pub_type: 杂志文章
doi:10.3389/fmicb.2017.01437
更新日期:2017-08-03 00:00:00
abstract::Recent studies of bacterial speciation have claimed to support the biological species concept-that reduced recombination is required for bacterial populations to diverge into species. This conclusion has been reached from the discovery that ecologically distinct clades show lower rates of recombination than that which...
journal_title:Frontiers in microbiology
pub_type: 杂志文章
doi:10.3389/fmicb.2015.01540
更新日期:2016-01-14 00:00:00
abstract::Grapevine downy mildew, caused by oomycete fungus Plasmopara viticola, is one of the most devastating diseases of grapes across the major production regions of the world. Although many putative effector molecules have been identified from this pathogen, the functions of the majority of these are still unknown. In this...
journal_title:Frontiers in microbiology
pub_type: 杂志文章
doi:10.3389/fmicb.2020.00692
更新日期:2020-04-21 00:00:00
abstract::In bacteria, the GntR family is a widespread family of transcription factors responsible for the regulation of a myriad of biological processes. In contrast, despite their occurrence in archaea only a little information is available on the function of GntR-like transcription factors in this domain of life. The thermoa...
journal_title:Frontiers in microbiology
pub_type: 杂志文章
doi:10.3389/fmicb.2019.02084
更新日期:2019-09-10 00:00:00
abstract::Chagas disease is one of the prevalent neglected tropical diseases, affecting at least 6-7 million individuals in Latin America. It is caused by the protozoan parasite Trypanosoma cruzi, which is transmitted to vertebrate hosts by blood-sucking insects. After infection, the parasite invades and multiplies in the myoca...
journal_title:Frontiers in microbiology
pub_type: 杂志文章,评审
doi:10.3389/fmicb.2016.00388
更新日期:2016-03-31 00:00:00
abstract::Human life expectancy is rapidly increasing with an associated increasing burden of chronic diseases, such as neurodegenerative diseases and cancer. However, there is limited progress in finding effective treatment for these conditions. For this reason, members of the genus Streptomyces have been explored extensively ...
journal_title:Frontiers in microbiology
pub_type: 杂志文章,评审
doi:10.3389/fmicb.2017.02065
更新日期:2017-11-01 00:00:00