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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 -
Science Advances May 2023The rise of antimicrobial resistance poses a substantial threat to our health system, and, hence, development of drugs against novel targets is urgently needed. The...
The rise of antimicrobial resistance poses a substantial threat to our health system, and, hence, development of drugs against novel targets is urgently needed. The natural peptide thanatin kills Gram-negative bacteria by targeting proteins of the lipopolysaccharide transport (Lpt) machinery. Using the thanatin scaffold together with phenotypic medicinal chemistry, structural data, and a target-focused approach, we developed antimicrobial peptides with drug-like properties. They exhibit potent activity against Enterobacteriaceae both in vitro and in vivo while eliciting low frequencies of resistance. We show that the peptides bind LptA of both wild-type and thanatin-resistant and strains with low-nanomolar affinities. Mode of action studies revealed that the antimicrobial activity involves the specific disruption of the Lpt periplasmic protein bridge.
Topics: Enterobacteriaceae; Lipopolysaccharides; Peptidomimetics; Escherichia coli; Anti-Bacterial Agents; Carrier Proteins; Escherichia coli Proteins
PubMed: 37224246
DOI: 10.1126/sciadv.adg3683 -
EcoSal Plus Nov 2020Plasmids are autonomously replicating sequences that help cells adapt to diverse stresses. Theta plasmids are the most frequent plasmid class in enterobacteria. They... (Review)
Review
Plasmids are autonomously replicating sequences that help cells adapt to diverse stresses. Theta plasmids are the most frequent plasmid class in enterobacteria. They co-opt two host replication mechanisms: replication at , a DnaA-dependent pathway leading to replisome assembly (theta class A), and replication fork restart, a PriA-dependent pathway leading to primosome assembly through primer extension and D-loop formation (theta classes B, C, and D). To ensure autonomy from the host's replication and to facilitate copy number regulation, theta plasmids have unique mechanisms of replication initiation at the plasmid origin of replication (). Tight plasmid copy number regulation is essential because of the major and direct impact plasmid gene dosage has on gene expression. The timing of plasmid replication and segregation are also critical for optimizing plasmid gene expression. Therefore, we propose that plasmid replication needs to be understood in its biological context, where complex origins of replication (redundant origins, mosaic and cointegrated replicons), plasmid segregation, and toxin-antitoxin systems are often present. Highlighting their tight functional integration with function, we show that both partition and toxin-antitoxin systems tend to be encoded in close physical proximity to the in a large collection of plasmids. We also propose that adaptation of plasmids to their host optimizes their contribution to the host's fitness while restricting access to broad genetic diversity, and we argue that this trade-off between adaptation to host and access to genetic diversity is likely a determinant factor shaping the distribution of replicons in populations of enterobacteria.
Topics: Adaptation, Physiological; Bacterial Proteins; DNA Replication; DNA-Binding Proteins; Enterobacteriaceae; Escherichia coli; Escherichia coli Proteins; Host Microbial Interactions; Plasmids; Replication Origin; Replicon
PubMed: 33210586
DOI: 10.1128/ecosalplus.ESP-0026-2019 -
Microbiology Spectrum Jun 2022The advent of multidrug-resistant bacteria has hampered the development of new antibiotics, exacerbating their morbidity and mortality. In this context, the...
The advent of multidrug-resistant bacteria has hampered the development of new antibiotics, exacerbating their morbidity and mortality. In this context, the gastrointestinal tract reveals a valuable source of novel antimicrobials. Microcins are bacteriocins produced by members of the family which are endowed with a wide diversity of structures and mechanisms of action, and exert potent antibacterial activity against closely related bacteria. In this study, we investigated the antibacterial activities of four microcins against 54 isolates from three species (Escherichia coli, Klebsiella pneumoniae, and Salmonella enterica). The selected microcins, microcin C (McC, nucleotide peptide), microcin J25 (MccJ25, lasso peptide), microcin B17 (MccB17, linear azol(in)e-containing peptide), and microcin E492 (MccE492, siderophore peptide) carry different post-translational modifications and have distinct mechanisms of action. MICs and minimal bactericidal concentrations (MBC) of the microcins were measured and the efficacy of combinations of the microcins together or with antibiotics was assessed to identify potential synergies. Every isolate showed sensitivity to at least one microcin with MIC values ranging between 0.02 μM and 42.5 μM. Among the microcins tested, McC exhibited the broadest spectrum of inhibition with 46 strains inhibited, closely followed by MccE492 with 38 strains inhibited, while MccJ25 showed the highest activity. In general, microcin activity was observed to be independent of antibiotic resistance profile and strain genus. Of the 42 tested combinations, 20 provided enhanced activity (18 out of 20 being microcin-antibiotic combinations), with two being synergetic. With their wide range of structures and mechanisms of action, microcins are shown to exert antibacterial activities against resistant to antibiotics together with synergies with antibiotics and in particular colistin.
Topics: Amino Acid Sequence; Anti-Bacterial Agents; Bacteriocins; Drug Resistance, Multiple, Bacterial; Enterobacteriaceae; Escherichia coli; Peptides
PubMed: 35543514
DOI: 10.1128/spectrum.02752-21 -
European Journal of Clinical... Aug 2021One hundred forty-nine carbapenem-resistant Enterobacterales from clinical samples obtained between April 2014 and November 2017 were subjected to whole genome...
One hundred forty-nine carbapenem-resistant Enterobacterales from clinical samples obtained between April 2014 and November 2017 were subjected to whole genome sequencing and multi-locus sequence typing. Klebsiella pneumoniae (81, 54.4%) and Escherichia coli (38, 25.5%) were the most common species. Genes encoding metallo-β-lactamases were detected in 68 (45.8%) isolates, and OXA-48-like enzymes in 60 (40.3%). bla (45; 30.2%) and bla (29; 19.5%) were the most frequent. KPC-encoding genes were identified in 5 (3.6%) isolates. Most common sequence types were E. coli ST410 (8; 21.1%) and ST38 (7; 18.4%), and K. pneumoniae ST147 (13; 16%) and ST231 (7; 8.6%).
Topics: Adolescent; Adult; Aged; Aged, 80 and over; Anti-Bacterial Agents; Child; Child, Preschool; Drug Resistance, Multiple, Bacterial; Enterobacteriaceae; Enterobacteriaceae Infections; Female; Humans; Infant; Male; Middle Aged; Qatar; Young Adult
PubMed: 33616788
DOI: 10.1007/s10096-021-04185-7 -
Journal of Applied Microbiology Sep 2022The purpose of the work was to investigate bacterial levels and diversity as well as survival of Salmonella in used dish washing sponges and brushes and identify...
AIMS
The purpose of the work was to investigate bacterial levels and diversity as well as survival of Salmonella in used dish washing sponges and brushes and identify consumer practices that can potentially explain bacterial status of these items.
METHODS AND RESULTS
Used washing up utensils were collected from consumers. The bacterial numbers (TVC) were very variable with an extremely high median level (10.3 log cfu/item) in Portuguese sponges and lower levels in Norwegian items (7.3 and 7.0 cfu/item for sponges and brushes). No self-reported practices or household composition could explain differences found in TVC levels among the collected sponges. Lower mean TVC levels were found in unworn brushes and brushes regularly cleaned with soap, but the differences were modest (1.5 log or less). A common set of bacteria was found in brushes and sponges, dominated by Acinetobacter, Chryseobacterium, Enhydrobacter, Enterobacteriaceae and Pseudomonas. There was no difference in TVC or bacterial diversity between conventional and antimicrobial sponges containing silver after 4 weeks of use. For used brushes inoculated with Salmonella and allowed to dry overnight, a significant reduction in Salmonella numbers was observed. No reduction was observed for brushes stored in humid conditions (in a plastic bag) or for sponges regardless of storing conditions.
CONCLUSIONS
Overall, lower bacterial levels were observed in used brushes than in sponges, and Salmonella died more rapidly in brushes. A common set of non-pathogenic bacteria dominated in brushes and sponges.
SIGNIFICANCE AND IMPACT OF STUDY
The study demonstrates that the use of brushes may be more hygienic than the use of sponges.
Topics: Bacteria; Enterobacteriaceae; Hygiene; Salmonella
PubMed: 35560961
DOI: 10.1111/jam.15621 -
Sheng Wu Gong Cheng Xue Bao = Chinese... Apr 2021The enterobacterial common antigen (ECA) is a polysaccharide composed of polysaccharide repeats that are located in the outer membrane of almost all Enterobacteriaceae... (Review)
Review
The enterobacterial common antigen (ECA) is a polysaccharide composed of polysaccharide repeats that are located in the outer membrane of almost all Enterobacteriaceae bacteria and has diverse biological functions. ECA is synthesized by the synergistic action of multiple genes that are present in clusters on the genome of Enterobacteriaceae bacteria, forming the ECA antigen gene cluster, an important virulence factor that plays a role in host invasion and survival of Enterobacteriaceae in vivo. ECA also plays an important role in the maintenance of the bacterial outer membrane permeability barrier, flagella gene expression, swarming motility, and bile salts resistance. In addition, ECALPS, anchored in the core region of bacterial lipopolysaccharide, is an important surface antigen for bacteria, stimulating high levels of antibody production in the host and could be a target for vaccine research. This review summarizes ECA purification, genes involved in ECA biosynthesis, its immunological characteristics, biological functions and clinical applications.
Topics: Antigens, Bacterial; Enterobacteriaceae; Lipopolysaccharides; Polysaccharides
PubMed: 33973426
DOI: 10.13345/j.cjb.200334 -
Nature Communications Nov 2021Child undernutrition is a global health issue associated with a high burden of infectious disease. Undernourished children display an overabundance of intestinal...
Child undernutrition is a global health issue associated with a high burden of infectious disease. Undernourished children display an overabundance of intestinal pathogens and pathobionts, and these bacteria induce enteric dysfunction in undernourished mice; however, the cause of their overgrowth remains poorly defined. Here, we show that disease-inducing human isolates of Enterobacteriaceae and Bacteroidales spp. are capable of multi-species symbiotic cross-feeding, resulting in synergistic growth of a mixed community in vitro. Growth synergy occurs uniquely under malnourished conditions limited in protein and iron: in this context, Bacteroidales spp. liberate diet- and mucin-derived sugars and Enterobacteriaceae spp. enhance the bioavailability of iron. Analysis of human microbiota datasets reveals that Bacteroidaceae and Enterobacteriaceae are strongly correlated in undernourished children, but not in adequately nourished children, consistent with a diet-dependent growth synergy in the human gut. Together these data suggest that dietary cross-feeding fuels the overgrowth of pathobionts in undernutrition.
Topics: Animals; Bacteroidetes; Child; Coculture Techniques; Diet; Enterobacteriaceae; Escherichia coli; Feces; Gastrointestinal Microbiome; Humans; Intestines; Malnutrition; Mice; Nutrients; Symbiosis
PubMed: 34824233
DOI: 10.1038/s41467-021-27191-x -
Journal of Global Antimicrobial... Mar 2020
Topics: Aged; Carbapenem-Resistant Enterobacteriaceae; Ceftriaxone; Disk Diffusion Antimicrobial Tests; Drug Resistance, Multiple, Bacterial; Escherichia coli; Escherichia coli Infections; Feces; Humans; Malawi; Male; Whole Genome Sequencing; beta-Lactamases
PubMed: 31899349
DOI: 10.1016/j.jgar.2019.12.017 -
MSphere Jul 2020The order of Gram-negative bacteria includes the common nosocomial pathogens , , , and species. Intestinal domination by some colonizing bacterial taxa is associated...
The order of Gram-negative bacteria includes the common nosocomial pathogens , , , and species. Intestinal domination by some colonizing bacterial taxa is associated with subsequent infection, but 16S rRNA gene sequencing is too costly and slow to be used in a clinical setting. The objectives of this study were to develop a PCR-based assay that can measure density, validate it against 16S rRNA gene sequencing, and measure the association between dominance and subsequent infection. Two quantitative PCR (qPCR) assays that were developed to quantify the absolute and relative abundance of had good correlation with 16S rRNA sequence analysis ( 0.0001). Using both PCR assays and 16S sequencing, a matched case-control study was performed comparing rectal swabs from hospitalized patients who later developed bloodstream, urinary tract, or respiratory infections ( = 95) to swabs from patients who remained uninfected ( = 189). abundance measured by sequencing was high in both cases and controls (means, 31.1% and 27.5%, respectively; 0.322). We observed an increased risk of infection that depended on both the absolute and relative abundance of as measured by qPCR assay A ( 0.012). After adjustment for albumin levels, central venous catheter presence, and use of cephalosporins at the time of swab collection, this association still approached significance ( 0.061). These results demonstrate that using qPCR to measure intestinal colonization dominance is feasible, indicate that hospitalized patients have high levels of colonization, and suggest that both relative and absolute abundance may be associated with subsequent infection. Increasing antibiotic resistance has resulted in infections that are life-threatening and difficult to treat. Interventions that prevent these infections, particularly without using antibiotics, could save lives. Intestinal colonization by pathogens, including vancomycin-resistant and carbapenem-resistant (part of the order ) is associated with subsequent infection, and increased colonization density is associated with increased infection risk. Therefore, colonization offers a window of opportunity for infection prevention if (i) there are rapid and inexpensive assays to detect colonization, (ii) there are safe and effective interventions, and (iii) the risk of infection outweighs the risk of the treatment. Fecal transplants are proof of principle that manipulating the microbiome can reduce such colonization and prevent infections. This study demonstrates the feasibility of implementing rapid and inexpensive assays to quantify colonization and measures the strength of association between dominance and subsequent infection. The approach described here could be a valuable tool in the prevention of antibiotic-resistant infections.
Topics: Adult; Aged; Case-Control Studies; Colony Count, Microbial; Cross Infection; Enterobacteriaceae; Enterobacteriaceae Infections; Female; Hospitalization; Humans; Intestines; Male; Middle Aged; Polymerase Chain Reaction; RNA, Ribosomal, 16S; Rectum
PubMed: 32699120
DOI: 10.1128/mSphere.00450-20