Abstract:
Background:Enterobacter hormaechei is an important emerging pathogen and a key member of the highly diverse Enterobacter cloacae complex. E. hormaechei strains can persist and spread in nosocomial environments, and often exhibit resistance to multiple clinically important antibiotics. However, the genomic regions that harbour resistance determinants are typically highly repetitive and impossible to resolve with standard short-read sequencing technologies. Results:Here we used both short- and long-read methods to sequence the genome of a multidrug-resistant hospital isolate (C15117), which we identified as E. hormaechei. Hybrid assembly generated a complete circular chromosome of 4,739,272 bp and a fully resolved plasmid of 339,920 bp containing several antibiotic resistance genes. The strain also harboured a 34,857 bp repeat encoding copper resistance, which was present in both the chromosome and plasmid. Long reads that unambiguously spanned this repeat were required to resolve the chromosome and plasmid into separate replicons. Conclusion:This study provides important insights into the evolution and potential spread of antimicrobial resistance in a nosocomial E. hormaechei strain. More broadly, it further exemplifies the power of long-read sequencing technologies, particularly the Oxford Nanopore platform, for the characterisation of bacteria with complex resistance loci and large repeat elements.
journal_name
Gut Pathogjournal_title
Gut pathogensauthors
Monahan LG,DeMaere MZ,Cummins ML,Djordjevic SP,Roy Chowdhury P,Darling AEdoi
10.1186/s13099-019-0288-7subject
Has Abstractpub_date
2019-02-13 00:00:00pages
3issn
1757-4749pii
288journal_volume
11pub_type
相关文献
Gut Pathogens文献大全abstract:BACKGROUND:There are multiple etiologies responsible for infectious gastroenteritis causing acute diarrhea which are often under diagnosed. Also acute diarrhea is one of the major causes of morbidity and mortality among children less than 5 years of age. METHODS:In our study, fecal samples (n = 130) were collected fro...
journal_title:Gut pathogens
pub_type: 杂志文章
doi:10.1186/s13099-017-0166-0
更新日期:2017-04-11 00:00:00
abstract:BACKGROUND:Shiga toxin (Stx) producing Escherichia coli (E. coli) (STEC) is the most frequent cause of diarrhoea-positive haemolytic uraemic syndrome (D + HUS) in humans. In 2011, a huge outbreak with an STEC O104:H4 strain in Germany highlighted the limited possibilities for causative treatment of this syndrome. The r...
journal_title:Gut pathogens
pub_type: 杂志文章
doi:10.1186/s13099-017-0179-8
更新日期:2017-05-25 00:00:00
abstract::Rapid scientific and technological advances have allowed for a more detailed understanding of the relevance of intestinal microbiota, and the entire body-wide microbiome, to human health and well-being. Rodent studies have provided suggestive evidence that probiotics (e.g. lactobacillus and bifidobacteria) can influen...
journal_title:Gut pathogens
pub_type: 杂志文章
doi:10.1186/1757-4749-5-4
更新日期:2013-03-16 00:00:00
abstract:BACKGROUND:Helicobacter pylori infection is associated with risk for chronic gastritis (CG), gastric ulcer (GU), duodenal ulcer (DU), and gastric cancer (GC). The H. pylori Cag type IV secretion system (TFSS) translocates the virulence factor cytotoxin-associated gene A protein into host cells and plays an important ro...
journal_title:Gut pathogens
pub_type: 杂志文章
doi:10.1186/s13099-017-0165-1
更新日期:2017-04-21 00:00:00
abstract:BACKGROUND:Shigellosis is an acute form of gastroenteritis caused by the bacteria belonging to the genus Shigella. It is the most common cause of morbidity and mortality in children. Shigella belongs to the family Enterobactericeae, which is a Gram-negative and rod shaped bacterium. In the present study, we report the ...
journal_title:Gut pathogens
pub_type: 杂志文章
doi:10.1186/1757-4749-6-28
更新日期:2014-07-11 00:00:00
abstract::Of 19 environmental Escherichia coli (n = 12) and Klebsiella pneumoniae (n = 7) tested for quinolone resistance-related genes qnrA, qnrB, qnrC, qnrS and qepA, four each of E. coli and K. pneumoniae possessed qnrS, and another E. coli isolate possessed a new variant of qepA. This is the first detection of qepA in envir...
journal_title:Gut pathogens
pub_type: 杂志文章
doi:10.1186/s13099-017-0207-8
更新日期:2017-10-23 00:00:00
abstract:Background:The root extract of Rhodiola rosea has historically been used in Europe and Asia as an adaptogen, and similar to ginseng and Shisandra, shown to display numerous health benefits in humans, such as decreasing fatigue and anxiety while improving mood, memory, and stamina. A similar extract in the Rhodiola fami...
journal_title:Gut pathogens
pub_type: 杂志文章
doi:10.1186/s13099-018-0239-8
更新日期:2018-03-20 00:00:00
abstract:Background:After an environmental disaster, the affected community is at increased risk for persistent abdominal pain but mechanisms are unclear. Therefore, our study aimed to determine association between abdominal pain and poor water, sanitation and hygiene (WaSH) practices, and if small intestinal bacterial overgrow...
journal_title:Gut pathogens
pub_type: 杂志文章
doi:10.1186/s13099-017-0224-7
更新日期:2017-12-14 00:00:00
abstract:BACKGROUND:Campylobacter enteritis represents a risk factor for the development of inflammatory bowel disease (IBD) via unknown mechanisms. As IBD patients exhibit inflammatory responses to their commensal intestinal microflora, factors that induce translocation of commensal bacteria across the intestinal epithelium ma...
journal_title:Gut pathogens
pub_type: 杂志文章
doi:10.1186/1757-4749-1-2
更新日期:2009-02-03 00:00:00
abstract:BACKGROUND:Although antimicrobial resistance and persistence of resistant bacteria in humans and animals are major health concerns worldwide, the impact of antimicrobial resistance on bacterial intestinal colonization in healthy domestic animals has only been rarely studied. We carried out a retrospective analysis of t...
journal_title:Gut pathogens
pub_type: 杂志文章
doi:10.1186/1757-4749-1-18
更新日期:2009-10-08 00:00:00
abstract:Background:Campylobacter jejuni is considered as a chicken commensal. The gut microbiota and the immune status of the host may affect its colonization. Infectious bursal disease virus (IBDV) is an immunosuppressive virus of chickens, which allows secondary pathogens to invade or exacerbates their pathogenesis. To inves...
journal_title:Gut pathogens
pub_type: 杂志文章
doi:10.1186/s13099-018-0241-1
更新日期:2018-03-30 00:00:00
abstract:BACKGROUND:The human and animal intestinal tract harbors a complex community of microbes which enables bacteria to inherit antibiotic resistance genes. The aims of this study were to investigate clonality, antimicrobial resistance, prevalence and gene cassette arrays of class I and II integrons among commensal Escheric...
journal_title:Gut pathogens
pub_type: 杂志文章
doi:10.1186/s13099-016-0123-3
更新日期:2016-08-30 00:00:00
abstract:BACKGROUND:Widely considered probiotic organisms, Bifidobacteria are common inhabitants of the alimentary tract of animals including insects. Bifidobacteria identified from the honey bee are found in larval guts and throughout the alimentary tract, but attain their greatest abundance in the adult hind gut. To further u...
journal_title:Gut pathogens
pub_type: 杂志文章
doi:10.1186/1757-4749-5-42
更新日期:2013-12-18 00:00:00
abstract:BACKGROUND:Campylobacter jejuni, a gram-negative bacterium, is a frequent cause of gastrointestinal food-borne illness in humans throughout the world. There are several reports that the virulence of C. jejuni might be modulated by non-flagellar proteins that are secreted through the filament. Recently, FspA (Flagella s...
journal_title:Gut pathogens
pub_type: 杂志文章
doi:10.1186/1757-4749-3-11
更新日期:2011-07-12 00:00:00
abstract::We evaluated the effects of the probiotic Escherichia coli Nissle 1917 (EcN) and the antibiotic Ciprofloxacin (Cipro) on mRNA expression of intestinal epithelial cells (IEC) in gnotobiotic (Gn) piglets colonized with a defined commensal microflora (DMF) and inoculated with human rotavirus (HRV) that infects IECs. We a...
journal_title:Gut pathogens
pub_type:
doi:10.1186/s13099-016-0148-7
更新日期:2016-12-13 00:00:00
abstract:BACKGROUND:Cronobacter sakazakii is an emerging opportunistic pathogen that is associated with rare but life-threatening cases of severe diseases: meningitis, necrotizing enterocolitis, and sepsis in premature and full-term infants. However, the pathogenesis mechanism of this pathogen remains largely unknown. To determ...
journal_title:Gut pathogens
pub_type:
doi:10.1186/s13099-016-0150-0
更新日期:2017-01-04 00:00:00
abstract:BACKGROUND:In 2007, a nationwide Salmonella Tennessee outbreak occurred via contaminated peanut butter. Here, we developed a single-nucleotide polymorphism (SNP)-typing method for S. Tennessee to determine the clonal subtypes of S. Tennessee that were associated with the peanut butter outbreak. METHODS AND RESULTS:One...
journal_title:Gut pathogens
pub_type: 杂志文章
doi:10.1186/s13099-017-0176-y
更新日期:2017-05-01 00:00:00
abstract::As the associations between the gut microbiota and numerous health outcomes become more evident, it is important to conduct longitudinal microbiome research to advance the field beyond the identification of associations. It is also necessary to include individuals who have historically been underrepresented in biomedi...
journal_title:Gut pathogens
pub_type: 杂志文章
doi:10.1186/s13099-019-0324-7
更新日期:2019-08-26 00:00:00
abstract:BACKGROUND:Salmonella enterica serovar Typhi (S. Typhi) exhibits unique characteristics as an intracellular human pathogen. It causes both acute and chronic infection with various disease manifestations in the human host only. The principal factors underlying the unique lifestyle of motility and biofilm forming ability...
journal_title:Gut pathogens
pub_type: 杂志文章
doi:10.1186/1757-4749-6-2
更新日期:2014-02-05 00:00:00
abstract:UNLABELLED: BACKGROUND:Following Helicobacter pylori eradication in idiopathic parkinsonism (IP), hypokinesia improved but flexor-rigidity increased. Small intestinal bacterial-overgrowth (SIBO) is a candidate driver of the rigidity: hydrogen-breath-test-positivity is common in IP and case histories suggest that Helic...
journal_title:Gut pathogens
pub_type: 杂志文章
doi:10.1186/1757-4749-4-12
更新日期:2012-10-19 00:00:00
abstract::In the present study we demonstrate that the initial attachment of Listeria monocytogenes cells to plastic surfaces was significantly increased by growth in the presence of bile. Improved biofilm formation was confirmed by crystal violet staining, microscopy and bioluminescence detection of a luciferase-tagged strain....
journal_title:Gut pathogens
pub_type: 杂志文章
doi:10.1186/1757-4749-1-11
更新日期:2009-05-28 00:00:00
abstract:Background:Extended spectrum beta lactamase (ESBL)-producing extraintestinal pathogenic Escherichia coli infections are of global interest because of their clinical and economic impact. The ESBL resistance genes disseminate through plasmids, and are found in successful global lineages such as ST131 and ST648. The carri...
journal_title:Gut pathogens
pub_type: 杂志文章
doi:10.1186/s13099-018-0243-z
更新日期:2018-06-15 00:00:00
abstract::Potential biological roles of the Campylobacter jejuni genes cj0641, cj0774c and cj1663 were investigated. The proteins encoded by these genes showed sequence similarities to the phosphonate utilisation PhnH, K and L gene products of Escherichia coli. The genes cj0641, cj0774c and cj1663 were amplified from the pathog...
journal_title:Gut pathogens
pub_type: 杂志文章
doi:10.1186/1757-4749-1-13
更新日期:2009-06-25 00:00:00
abstract:BACKGROUND:Acid treatment is commonly used for controlling or killing pathogenic microorganisms on medical devices and environments; however, inadequate acid treatment may cause acid tolerance response (ATR) and offer cross-protection against environmental stresses, including antimicrobials. This study aimed to charact...
journal_title:Gut pathogens
pub_type: 杂志文章
doi:10.1186/s13099-020-00390-5
更新日期:2020-12-01 00:00:00
abstract:BACKGROUND:The putative H. pylori pathogenicity-associated factor dupA has been associated with IL-8 induction in vitro, and duodenal ulcer (DU) and gastric cancer (GC) development in certain populations, but this association is inconsistent between studies. We aimed to investigate dupA prevalence in clinical isolates ...
journal_title:Gut pathogens
pub_type: 杂志文章
doi:10.1186/1757-4749-1-5
更新日期:2009-03-11 00:00:00
abstract:BACKGROUND:In 2005, the first disease-specific Helicobacter pylori virulence factor that induced duodenal ulcer and had a suppressive action on gastric cancer has been identified, and was named duodenal ulcer promoting gene (dupA). However, the importance of the dupA gene on clinical outcomes is conflicting in subseque...
journal_title:Gut pathogens
pub_type: 杂志文章
doi:10.1186/1757-4749-2-13
更新日期:2010-10-31 00:00:00
abstract:BACKGROUND:One of the working mechanisms of probiotic bacteria is their ability to compete with pathogens. To define the probiotic properties of seven Lactic Acid Bacteria (LAB) strains, we tested them for survival in simulated gastro-intestinal conditions, antimicrobial activities, co-aggregative abilities, and interf...
journal_title:Gut pathogens
pub_type: 杂志文章
doi:10.1186/s13099-017-0162-4
更新日期:2017-03-06 00:00:00
abstract:Background:Recent advances in next-generation sequencing technologies have enabled comprehensive analysis of the gut microbiota, which is closely linked to the health of the host. Consequently, several studies have explored the factors affecting gut microbiota composition. In recent years, increasing number of dog owne...
journal_title:Gut pathogens
pub_type: 杂志文章
doi:10.1186/s13099-017-0218-5
更新日期:2017-11-21 00:00:00
abstract:Background:Shigella has evolved as a result of acquiring extragenetic material through horizontal gene exchange. These aid in the rapid emergence of bacterial inter-strain diversity in virulence factors and serotype variants through O-antigenic switching. Plasmid incompatibility typing of isolates is insightful in unde...
journal_title:Gut pathogens
pub_type: 杂志文章
doi:10.1186/s13099-019-0314-9
更新日期:2019-06-14 00:00:00
abstract:BACKGROUND:Klebsiella pneumoniae is the most common pathogen of community-acquired pyogenic liver abscess in East Asia. Diabetes mellitus (DM) is a well-established risk factor for K. pneumoniae liver abscess (KPLA). However, reports regarding the emergence of KPLA in non-diabetic patients are limited. RESULTS:A total...
journal_title:Gut pathogens
pub_type: 杂志文章
doi:10.1186/s13099-016-0128-y
更新日期:2016-10-18 00:00:00