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Current Issues in Molecular Biology Apr 2022Gut microbiome balance plays a key role in human health and maintains gut barrier integrity. Dysbiosis, referring to impaired gut microbiome, is linked to a variety of...
Gut microbiome balance plays a key role in human health and maintains gut barrier integrity. Dysbiosis, referring to impaired gut microbiome, is linked to a variety of diseases, including cancers, through modulation of the inflammatory process. Most studies concentrated on adenocarcinoma of different sites with very limited information on gastroenteropancreatic neuroendocrine neoplasms (GEP-NENs). In this study, we have analyzed the gut microbiome (both fungal and bacterial communities) in patients with metastatic GEP-NENs. Fecal samples were collected and compared with matched healthy control samples using logistic regression distances utilizing R package MatchIt (version 4.2.0, Daniel E. Ho, Stanford, CA, USA). We examined differences in microbiome profiles between GEP-NENs and control samples using small subunit (SSU) rRNA (16S), ITS1, ITS4 genomic regions for their ability to accurately characterize bacterial and fungal communities. We correlated the results with different behavioral and dietary habits, and tumor features including differentiation, grade, primary site, and therapeutic response. All tests are two-sided and -values ≤ 0.05 were considered statistically significant. Gut samples of 34 patients (12 males, 22 females, median age 64 years) with metastatic GEP-NENs (22 small bowel, 10 pancreatic, 1 gall bladder, and 1 unknown primary) were analyzed. Twenty-nine patients had well differentiated GEP-neuroendocrine tumors (GEP-NETs), (G1 = 14, G2 = 12, G3 = 3) and five patients had poorly differentiated GEP-neuroendocrine carcinomas (GEP-NECs). Patients with GEP-NENs had significantly decreased bacterial species and increased fungi (notably species, Ascomycota, and species belonging to saccharomycetes) compared to controls. Patients with GEP-NECs had significantly enriched populations of specific bacteria and fungi (such as , and ) compared to those with GEP-NETs ( = 0.048, 0.0022 and 0.034, respectively). In addition, higher grade GEP-NETs were associated with significantly higher ( = 0.022), and ( = 0.00018) species compared to lower grade tumors. There were substantial differences associated with dietary habits and therapeutic responses. This is the first study to analyze the role of the microbiome environment in patients with GEP-NENs. There were significant differences between GEP-NETs and GEP-NECs, supporting the role of the gut microbiome in the pathogenesis of these two distinct entities.
PubMed: 35678665
DOI: 10.3390/cimb44050136 -
Journal of Infection Prevention Sep 2022Free online tools for bacterial genome analyses are available for local infection surveillance at hospitals. The tools do not require bioinformatic expertise and provide...
Free online tools for bacterial genome analyses are available for local infection surveillance at hospitals. The tools do not require bioinformatic expertise and provide rapid actionable results. Within half a year carbapenemase producing was reported in clinical samples from three patients who had been hospitalized at the same ward. The aim of this outbreak investigation was to characterize and compare genomes of the isolated bacteria in order to determine molecular evidence of hospital transmission. The three isolates and two isolates reported as susceptible to carbapenems were locally analyzed by whole genome sequencing (WGS). Draft genome assembly, species identification, phylogenetic analyses, typing, resistance gene determination, and plasmid analyses were carried out using free online tools from the Center for Genomic Epidemiology (CGE). Genome analyses identified all three suspected outbreak isolates as carrying gene. Two of the suspected outbreak isolates were closely related, while one was substantially different from them. Horizontal transfer of plasmid may have taken place in the ward. Detailed knowledge on the genomic composition of bacteria in suspected hospital outbreaks can be obtained by free online tools and may reveal transfer of resistance genes between different strains in addition to dissemination of specific clones.
PubMed: 36003132
DOI: 10.1177/17571774221107293 -
Frontiers in Cellular and Infection... 2022Transmission of colistin-resistant from companion animals to humans poses a clinical risk as colistin is a last-line antimicrobial agent for treatment of...
Transmission of colistin-resistant from companion animals to humans poses a clinical risk as colistin is a last-line antimicrobial agent for treatment of multidrug-resistant Gram-negative bacteria including . In this study, we investigated the colistin susceptibility of 285 (including 140 , 86 spp., and 59 spp.) isolated from companion animals in Japan. We further characterized colistin-resistant isolates by multilocus sequence typing (MLST), phylogenetic analysis of sequences, and population analysis profiling, to evaluate the potential clinical risk of companion animal-derived colistin-resistant to humans in line with the One Health approach. All isolates were susceptible to colistin, and only one spp. isolate (1.2%, 1/86 isolates) was colistin resistant. spp. isolates were frequently colistin resistant (20.3%, 12/59 isolates). In colistin-resistant spp., all except one isolate exhibited colistin heteroresistance by population analysis profiling. These colistin-heteroresistant isolates belonged to clusters I, II, IV, VIII, and XII based on phylogeny. MLST analysis revealed that 12 colistin-resistant spp. belonged to the complex; five (four ST591 and one ST1577), three (one ST562 and two ST1578), two (ST606 and ST1576), and (ST1579) and (ST765) (each one strain). Forty-two percent of the colistin-resistant complex isolates (predominantly ST562 and ST591) belonged to lineages with human clinical isolates. Four ST591 isolates were resistant to third-generation cephalosporines, aminoglycosides, and fluroquinolones but remained susceptible to carbapenems. In conclusion, our study is the first to our knowledge to report the frequent isolation of the colistin-resistant complex from companion animals. Furthermore, a subset of isolates belonged to human-associated lineages with resistance to multiple classes of antibiotics. These data warrant monitoring carriage of the colistin-resistant complex in companion animals as part of a domestic infection control procedure in line with the One Health approach.
Topics: Animals; Anti-Bacterial Agents; Bacterial Proteins; Colistin; Enterobacter cloacae; Enterobacteriaceae Infections; Escherichia coli; Humans; Japan; Klebsiella; Microbial Sensitivity Tests; Multilocus Sequence Typing; Pets; Phylogeny; beta-Lactamases
PubMed: 35873176
DOI: 10.3389/fcimb.2022.946841 -
Microbiology (Reading, England) Dec 2008Enterobacter hormaechei is a Gram-negative bacterium within the Enterobacter cloacae complex, and has been shown to be of clinical significance by causing nosocomial...
Characterization of an extended-spectrum beta-lactamase Enterobacter hormaechei nosocomial outbreak, and other Enterobacter hormaechei misidentified as Cronobacter (Enterobacter) sakazakii.
Enterobacter hormaechei is a Gram-negative bacterium within the Enterobacter cloacae complex, and has been shown to be of clinical significance by causing nosocomial infections, including sepsis. Ent. hormaechei is spread via horizontal transfer and is often associated with extended-spectrum beta-lactamase production, which increases the challenges associated with treatment by limiting therapeutic options. This report considers 10 strains of Ent. hormaechei (identified by 16S rDNA sequencing) that had originally been identified by phenotyping as Cronobacter (Enterobacter) sakazakii. Seven strains were from different neonates during a nosocomial outbreak in a California hospital. PFGE analysis revealed a clonal relationship among six of the seven isolates and therefore a previously unrecognized Ent. hormaechei outbreak had occurred over a three-month period. Antibiotic-resistance profiles were determined and extended-spectrum beta-lactamase activity was detected. The association of the organism with powdered infant formula, neonatal hosts and Cr. sakazakii suggested that the virulence of these organisms may be similar. Virulence traits were tested and all strains were shown to invade both gut epithelial (Caco-2) and blood-brain barrier endothelial cells (rBCEC4), and to persist in macrophages (U937). Due to misidentification we suggest that Ent. hormaechei may be an under-reported cause of bacterial infection, especially in neonates. Also, its isolation from various sources, including powdered infant milk formula, makes it a cause for concern and merits further investigation.
Topics: Animals; Bacterial Typing Techniques; Caco-2 Cells; California; Cronobacter sakazakii; Cross Infection; DNA, Bacterial; Diagnostic Errors; Disease Outbreaks; Drug Resistance, Bacterial; Electrophoresis, Gel, Pulsed-Field; Endothelial Cells; Enterobacter; Enterobacteriaceae Infections; Humans; Infant, Newborn; Microbial Sensitivity Tests; Molecular Sequence Data; Phenotype; Rats; Sequence Analysis, DNA; U937 Cells; beta-Lactamases
PubMed: 19047733
DOI: 10.1099/mic.0.2008/021980-0 -
Journal of Global Antimicrobial... Sep 2023Carbapenems are among the few effective antibiotics against multidrug-resistant Enterobacteriaceae. This study aimed at characterizing the plasmid content and resistome...
OBJECTIVES
Carbapenems are among the few effective antibiotics against multidrug-resistant Enterobacteriaceae. This study aimed at characterizing the plasmid content and resistome of clinical carbapenem-resistant Enterobacteriaceae (CRE) recovered from 2016 to 2019 from hospitalized patients in Lebanon.
METHODS
Plasmid typing and whole-genome sequencing were used to study the genomic characteristics of 65 clinical CREs including 27 Escherichia coli, 24 Klebsiella pneumoniae, one Klebsiella quasipneumoniae, three Morganella morganii, three Citrobacter freundii, five Enterobacter hormaechei, and two Serratia marcescens.
RESULTS
bla (33.8%; n = 22) and bla-like genes were among the detected resistance determinants, with two isolates co-harbouring bla. Various bla variants, bla (16.9%; n = 11), bla (9.2%; n = 6), bla (9.2%; n = 6), and bla (4.6%; n = 3), different ESBLs, and AmpC β-lactamases were detected. Carbapenem resistance determinants were linked to a variety of incompatibility groups with IncFIB(K) (43.1%; n = 28) being the most prevalent, followed by IncFIA (40.0%), IncL (35.4%), IncX3 (32.3%), IncI1 (32.3%), and IncFIIK (29.2%).
CONCLUSIONS
We analysed the clonality and resistance determinants of 65 multidrug-resistant (MDR) Enterobacteriaceae recovered in the period from 2016 to 2019 from a large tertiary hospital in Lebanon. NDM variants, OXA-48, and OXA-181 were the most prevalent detected carbapenemases and were mostly linked to the dissemination of IncL, IncX3, and IncF. This study reinforces the need to track the spread and dominance of clinically relevant carbapenemase-encoding plasmids in healthcare settings.
Topics: Humans; Carbapenem-Resistant Enterobacteriaceae; Enterobacteriaceae; Escherichia coli; Anti-Bacterial Agents; Sequence Analysis
PubMed: 37437842
DOI: 10.1016/j.jgar.2023.07.004 -
Vaccines Apr 2022is involved in multiple hospital-associated infections and is resistant to beta-lactam and tetracycline antibiotics. Due to emerging antibiotics resistance in and lack...
is involved in multiple hospital-associated infections and is resistant to beta-lactam and tetracycline antibiotics. Due to emerging antibiotics resistance in and lack of licensed vaccine availability, efforts are required to overcome the antibiotics crisis. In the current research study, a multi-epitope-based vaccine against was designed using reverse vaccinology and immunoinformatic approaches. A total number of 50 strains were analyzed from which the core proteome was extracted. One extracellular (curlin minor subunit CsgB) and two periplasmic membrane proteins (flagellar basal-body rod protein (FlgF) and flagellar basal body P-ring protein (FlgI) were prioritized for B and T-cell epitope prediction. Only three filtered TPGKMDYTS, GADMTPGKM and RLSAESQAT epitopes were used when designing the vaccine construct. The epitopes were linked via GPGPG linkers and EAAAK linker-linked cholera toxin B-subunit adjuvant was used to enhance the immune stimulation efficacy of the vaccine. Docking studies of the vaccine construct with immune cell receptors revealed better interactions, vital for generating proper immune reactions. Docked complexes of vaccine with MHC-I, MHC-II and Tool-like receptor 4 (TLR-4) reported the lowest binding energy of -594.1 kcal/mol, -706.7 kcal/mol, -787.2 kcal/mol, respectively, and were further subjected to molecular dynamic simulations. Net binding free energy calculations also confirmed that the designed vaccine has a strong binding affinity for immune receptors and thus could be a good vaccine candidate for future experimental investigations.
PubMed: 35632421
DOI: 10.3390/vaccines10050665 -
Microbiology Spectrum Jun 2022To investigate the contribution of a (A) variant to tigecycline resistance in Enterobacter hormaechei and the recombination events that occurred during transmission of...
To investigate the contribution of a (A) variant to tigecycline resistance in Enterobacter hormaechei and the recombination events that occurred during transmission of this variant. MICs were determined by broth microdilution. G17 was characterized by PCR, transfer assay, S1-PFGE, Southern blot hybridization, and WGS analysis. A (A) variant conferring resistance to tigecycline was present in G17. This strain harbored two resistance plasmids (pG17-1, 264,084 bp and pG17-2, 68,610 bp) and its E. coli transformant T-G17 one resistance plasmid (pTm-G17, 93,013 bp). The comparative analysis of pG17-1, pG17-2, and pTm-G17 showed that a (A) variant-carrying multiresistance gene cluster (~23 kb) originating from pG17-1 had integrated into pG17-2, forming the novel plasmid pTm-G17. In a first step, this multiresistance gene cluster was excised from pG17-1 by recombination of homologous sequences, including △Tn at both termini, thereby generating an unconventional circularizable structure (UCS). In a second step, this UCS integrated into pG17-2 via recombination between homologous sequences, including IS present on both, the UCS and pG17-2, thereby giving rise to the new plasmid pTm-G17. In summary, a (A) variant conferring resistance to tigecycline was reported in . Transfer of a (A) variant-carrying multiresistance gene cluster between plasmids occurred in a two-step recombination process, in which homologous sequences, including either △Tn or IS, were involved. Tigecycline is an important last-resort broad spectrum antimicrobial agent. This study describes the two-step recombination processes resulting in the transfer of the (A) variant gene between different plasmids in , which depicts the role of recombination processes in the generation of UCSs and new plasmids, both carrying a (A) variant conferring resistance to tigecycline. Such processes enhance the dissemination of resistance genes, which is of particular relevance for resistance genes, such as the (A) variant. The presence and transmission of a (A) variant in will compromise the efficacy of tigecycline treatment for associated infection.
Topics: Anti-Bacterial Agents; Enterobacter; Escherichia coli; Microbial Sensitivity Tests; Plasmids; Recombination, Genetic; Tigecycline
PubMed: 35579466
DOI: 10.1128/spectrum.00496-22 -
Pathogens (Basel, Switzerland) Sep 2022Wild animals may act as efficient antimicrobial-resistance reservoirs and epidemiological links between humans, livestock, and natural environments. By using phenotypic...
Wild animals may act as efficient antimicrobial-resistance reservoirs and epidemiological links between humans, livestock, and natural environments. By using phenotypic and genotypic characterization, the present study highlighted the occurrence of an antimicrobial-resistant (i.e., amoxicillin, amoxicillin-clavulanic acid, cephalothin, and colistin) subsp. strain in wild boar () from France. The molecular analysis conducted showed non-synonymous mutations in the and operons and the regulator gene, leading to colistin resistance. The present data highlight the need for continuous monitoring of multidrug-resistant bacteria in wild animals to limit the spread of these threatening pathogens.
PubMed: 36145454
DOI: 10.3390/pathogens11091022 -
Antimicrobial Agents and Chemotherapy Apr 2017International data on the molecular epidemiology of with IMP carbapenemases are lacking. We performed short-read (Illumina) whole-genome sequencing on a global...
International data on the molecular epidemiology of with IMP carbapenemases are lacking. We performed short-read (Illumina) whole-genome sequencing on a global collection of 38 IMP-producing clinical (2008 to 2014). IMP-producing (7 varieties within 11 class 1 integrons) were mainly present in the South Pacific and Asia. Specific -containing integrons (In809 with , In722 with , and In687 with ) were circulating among different bacteria in countries such as Australia, Japan, and Thailand. In1312 with was present in from Japan and from Brazil. ( = 22) was the most common species; clonal complex 14 (CC14) from Philippines and Japan was the most common clone and contained In1310 with and In1321 with The complex ( = 9) consisted of and cluster III. CC78 (from Taiwan) containing In73 with was the most common clone among the complex. This study highlights the importance of surveillance programs using the latest molecular techniques for providing insight into the characteristics and global distribution of with genes.
Topics: Brazil; Citrobacter freundii; Enterobacteriaceae; Inosine Monophosphate; Klebsiella pneumoniae; Microbial Sensitivity Tests; Molecular Epidemiology; beta-Lactamases
PubMed: 28167555
DOI: 10.1128/AAC.02729-16 -
Microbial Cell Factories Jun 2009Trehalose synthase (TreS) which converts maltose to trehalose is considered to be a potential biocatalyst for trehalose production. This enzymatic process has the...
BACKGROUND
Trehalose synthase (TreS) which converts maltose to trehalose is considered to be a potential biocatalyst for trehalose production. This enzymatic process has the advantage of simple reaction and employs an inexpensive substrate. Therefore, new TreS producing bacteria with suitable enzyme properties are expected to be isolated from extreme environment.
RESULTS
Six TreS producing strains were isolated from a specimen obtained from soil of the Tibetan Plateau using degenerate PCR. A novel treS gene from Enterobacter hormaechei was amplified using thermal asymmetric interlaced PCR. The gene contained a 1626 bp open reading frame encoding 541 amino acids. The gene was expressed in Escherichia coli, and the recombinant TreS was purified and characterized. The purified TreS had a molecular mass of 65 kDa and an activity of 18.5 U/mg. The optimum temperature and pH for the converting reaction were 37 degrees C and 6, respectively. Hg2+, Zn2+, Cu2+and SDS inhibited the enzyme activity at different levels whereas Mn2+ showed an enhancing effect by 10%.
CONCLUSION
In this study, several TreS producing strains were screened from a source of soil bacteria. The characterization of the recombinant TreS of Enterobacter hormaechei suggested its potential application. Consequently, a strategy for isolation of TreS producing strains and cloning of novel treS genes from natural sources was demonstrated.
PubMed: 19523196
DOI: 10.1186/1475-2859-8-34