1
|
LiaX is a surrogate marker for cell envelope stress and daptomycin non-susceptibility in Enterococcus faecium. Antimicrob Agents Chemother 2024; 68:e0106923. [PMID: 38289081 PMCID: PMC10916372 DOI: 10.1128/aac.01069-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Accepted: 12/20/2023] [Indexed: 02/12/2024] Open
Abstract
Daptomycin (DAP) is often used as a first-line therapy to treat vancomycin-resistant Enterococcus faecium infections, but emergence of DAP non-susceptibility threatens the effectiveness of this antibiotic. Moreover, current methods to determine DAP minimum inhibitory concentrations (MICs) have poor reproducibility and accuracy. In enterococci, DAP resistance is mediated by the LiaFSR cell membrane stress response system, and deletion of liaR encoding the response regulator results in hypersusceptibility to DAP and antimicrobial peptides. The main genes regulated by LiaR are a cluster of three genes, designated liaXYZ. In Enterococcus faecalis, LiaX is surface-exposed with a C-terminus that functions as a negative regulator of cell membrane remodeling and an N-terminal domain that is released to the extracellular medium where it binds DAP. Thus, in E. faecalis, LiaX functions as a sentinel molecule recognizing DAP and controlling the cell membrane response, but less is known about LiaX in E. faecium. Here, we found that liaX is essential in E. faecium with an activated LiaFSR system. Unlike E. faecalis, E. faecium LiaX is not detected in the extracellular milieu and does not appear to alter phospholipid architecture. We further postulated that LiaX could be used as a surrogate marker for cell envelope activation and non-susceptibility to DAP. For this purpose, we developed and optimized a LiaX enzyme-linked immunosorbent assay (ELISA). We then assessed 86 clinical E. faecium bloodstream isolates for DAP MICs and used whole genome sequencing to assess for substitutions in LiaX. All DAP-resistant clinical strains of E. faecium exhibited elevated LiaX levels. Strikingly, 73% of DAP-susceptible isolates by standard MIC determination also had elevated LiaX ELISAs compared to a well-characterized DAP-susceptible strain. Phylogenetic analyses of predicted amino acid substitutions showed 12 different variants of LiaX without a specific association with DAP MIC or LiaX ELISA values. Our findings also suggest that many E. faecium isolates that test DAP susceptible by standard MIC determination are likely to have an activated cell stress response that may predispose to DAP failure. As LiaX appears to be essential for the cell envelope response to DAP, its detection could prove useful to improve the accuracy of susceptibility testing by anticipating therapeutic failure.
Collapse
|
2
|
LiaX is a surrogate marker for cell-envelope stress and daptomycin non-susceptibility in Enterococcus faecium. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.18.553907. [PMID: 37645818 PMCID: PMC10462152 DOI: 10.1101/2023.08.18.553907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
Daptomycin (DAP) is often used as a first line therapy to treat vancomycin-resistant Enterococcus faecium (VR Efm ) infections but emergence of DAP non-susceptibility threatens the effectiveness of this antibiotic. Moreover, current methods to determine DAP MICs have poor reproducibility and accuracy. In enterococci, DAP resistance is mediated by the LiaFSR cell membrane stress response system and deletion of liaR encoding the response regulator results in hypersusceptibility to DAP and antimicrobial peptides. The main genes regulated by LiaR are a cluster of three genes, designated liaXYZ . In Enterococcus faecalis , LiaX is surface exposed with a C-terminus that functions as a negative regulator of cell membrane remodeling and an N-terminal domain that is released to the extracellular medium where it binds DAP. Thus, in E. faecalis , LiaX functions as a sentinel molecule recognizing DAP and controlling the cell membrane response, but less is known about LiaX in E. faecium . Here, we found that liaX is essential in E. faecium ( Efm ) with an activated LiaFSR system. Unlike E. faecalis , Efm LiaX is not detected in the extracellular milieu and does not appear to alter phospholipid architecture. We further postulated that LiaX could be used as a surrogate marker for cell envelope activation and non-susceptibility to DAP. For this purpose, we developed and optimized a LiaX ELISA. We then assessed 86 clinical E. faecium BSI isolates for DAP MICs and used whole genome sequencing to assess for substitutions in LiaX. All DAP-R clinical strains of E. faecium exhibited elevated LiaX levels. Strikingly, 73% of DAP-S isolates by standard MIC determination had elevated LiaX ELISAs above the established cut-off. Phylogenetic analyses of predicted amino acid substitutions showed 12 different variants of LiaX without a specific association with DAP MIC or LiaX ELISA values. Our findings also suggest that many Efm isolates that test DAP susceptible by standard MIC determination are likely to have an activated cell stress response that may predispose to DAP failure. As LiaX appears to be essential for the cell envelope response to DAP, its detection could prove useful to improve the accuracy of susceptibility testing by anticipating therapeutic failure.
Collapse
|
3
|
156. Using Whole Genome Sequencing to Genetically Profile and Analyze Escherichia coli Isolates with Varying Resistance to β-Lactam/β-lactamase Inhibitor Combinations. Open Forum Infect Dis 2022. [DOI: 10.1093/ofid/ofac492.234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Abstract
Background
Whole-genome sequencing has gained interest for assessing antimicrobial resistance (AMR). However, multiple studies have shown a poor correlation between the β-lactam/β-lactamase inhibitor (BL/BLI) phenotype and β-lactamase gene presence/absence. In a recent publication, we found that amplification of β-lactamase encoding genes potentially contribute to BL/BLI resistance and here we explore if gene amplifications allow for better BL/BLI genotype/phenotype correlations.
Methods
We selected 109 E. coli bacteremia isolates and performed ETests (bioMerieux, Inc) to determine AST profiles using the following BL/BLI antibiotics: ampicillin/sulbactam (SAM), amoxicillin/clavulanic acid (AMC), and piperacillin/tazobactam (TZP). CLSI M100 guidelines (2018) were used to stratify isolates into 4 groups: SAM/AMC/TZP susceptible (Group 1), SAM resistant only (Group 2), SAM/AMC resistant (Group 3), and SAM/AMC/TZP resistant (Group 4). Short-read whole genome sequencing was performed on these isolates and analyzed by identifying AMR genes, establishing multi-locus sequence type (MLST), estimating copy number variants (CNV), and investigating blaTEM-1 promoter regions in relation to phenotype. A t-Distributed Stochastic Neighbor Embedding (t-SNE) clustering method and a core-genome, maximum-likelihood phylogeny was generated to group isolates based on AMR gene content and CNV data.
Results
We found 34 different MLST groups with the three most common sequence types ST131 (n=41), ST1193 (n=12), and ST648 (n=6). Group 1 and Group 2 isolates had similar copy number estimates of β-lactamase blaTEM-1 (1.8X and 1.5X respectively) while there was an increase for both Group 3 (3.7X) and Group 4 (8.2X) isolates (Table 1). Additionally, blaOXA-1 was primarily present in Group 4 isolates (63%) with elevated copy numbers (5.2X). We did not observe associations of blaTEM-1 promoter regions with each of the BL/BLI Groups. Our t-SNE analysis shows that Group 1, Group 3, and Group 4 isolates cluster independently.
Core Genome Maximum-likelihood Phylogeny.
Midpoint-rooted core-genome maximum-likelihood phylogeny comparing core elements (MLST) to non core elements (CNV). AMR CNV and presence/absence associate better with BL/BLI phenotypes than do core elements.
Conclusion
There is a clear delineation between fully susceptible and fully resistant BL/BLI E. coli isolates when gene amplification and presence/absence of narrow-spectrum β-lactamases are considered, which should be considered for BL/BLI resistance prediction models.
Disclosures
David E. Greenberg, MD, Shionogi: Grant/Research Support.
Collapse
|
4
|
735. Contribution of the Oral Cavity and Gastrointestinal Microbiome on Bloodstream Infections inLeukemia Patients. Open Forum Infect Dis 2022. [PMCID: PMC9752037 DOI: 10.1093/ofid/ofac492.026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Background Blood stream infections (BSI) are a common cause of morbidity and mortality in immunocompromised patients. It was previously reported that intestinal domination (defined as occupation of ≥ 30% of the microbiota by a single bacterial taxon) by Enterococcus and Proteobacteria often preceded enterococcal and gram-negative BSI. Methods 16s rRNA sequencing was used to analyze the saliva and stool of 73 acute leukemia patients with BSIs to determine the correlation between the taxa present ( > 0% relative abundance), colonizing ( > 3%) or dominating ( > 30%) a patient’s microbiome and the BSI agent. Species level confirmation of these findings was performed via digital droplet PCR (ddPCR) and LEfSe analysis was used to determine enrichment of infectious taxa at either collection site. Whole genome sequencing and antimicrobial susceptibilities on all BSI isolates. Results We collected simultaneous patient stool and blood isolates from 11 Pseudomonas aeruginosa, 14 Escherichia coli, 4 Klebsiella sp., 8 Enterococcus sp., 18 viridans group streptococci (VGS), 13 Staphylococcus epidermidis, and 5 Staphylococcus aureus BSIs. Mann-Whitney testing confirmed that individuals with P. aeruginosa (oral P =.004, stool P < .001), E. coli (stool P < .001), and VGS infections (oral P =.001) had significantly higher relative abundance of those respective genera compared to other BSI patients, and this appeared to be site specific. LEfSe analysis confirmed enrichment of Pseudomonas in the saliva and stool, Escherichia in the stool, and Streptococcus in the saliva of respective infections. However, while 64 patients showed presence of the infectious genera in the stool and/or saliva at time of BSI, only 7 exhibited domination. ddPCR was used to confirm not only species specificity, but the detection of those antibiotic resistance determinants (CTX-14, CTX-15, Van A and CfrA) found in the BSI isolates within concurrent stool samples. Conclusion It appears that GI domination by the infecting organism was not present at the time of most BSIs. However, in scenarios where the etiological agent was detectable in the saliva or stool, so were the antibiotic resistant determinants. Furthermore, certain infections exhibited a significant difference in oral or stool presence by the same bacteria they were infected with. Disclosures All Authors: No reported disclosures.
Collapse
|
5
|
Oral and Stool Microbiome Coalescence and Its Association With Antibiotic Exposure in Acute Leukemia Patients. Front Cell Infect Microbiol 2022; 12:848580. [PMID: 35433514 PMCID: PMC9010033 DOI: 10.3389/fcimb.2022.848580] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 03/08/2022] [Indexed: 11/16/2022] Open
Abstract
Failure to maintain segregation of oral and gut microbial communities has been linked to several diseases. We sought to characterize oral-fecal microbiome community coalescence, ectopic extension of oral bacteria, clinical variables contributing to this phenomenon, and associated infectious consequences by analyzing the 16S rRNA V4 sequences of longitudinal fecal (n=551) and oral (n=737) samples from 97 patients with acute myeloid leukemia (AML) receiving induction chemotherapy (IC). Clustering observed in permutation based multivariate analysis of variance (PERMANOVA) of Bray-Curtis dissimilarity and PCoA plot of UniFrac distances between intra-patient longitudinal oral-stool sample pairs suggested potential oral-stool microbial community coalescence. Bray-Curtis dissimilarities and UniFrac distances were used to create an objective definition of microbial community coalescence. We determined that only 23 of the 92 patients exhibited oral-stool community coalescence. This was validated through a linear mixed model which determined that patients who experienced coalescence had an increased proportion of shared to unique OTUs between their oral-stool sample pairs over time compared to non-coalesced patients. Evaluation of longitudinal microbial characteristics revealed that patients who experienced coalescence had increased stool abundance of Streptococcus and Stenotrophomonas compared to non-coalesced patients. When treated as a time-varying covariate, each additional day of linezolid (HR 1.15, 95% CI 1.06 – 1.24, P <0.001), meropenem (HR 1.13, 95% CI 1.05 – 1.21, P = 0.001), metronidazole (HR 1.13, 95% CI 1.05 – 1.21, P = 0.001), and cefepime (HR 1.10, 95% CI 1.01 – 1.18, P = 0.021) increased the hazard of oral-stool microbial community coalescence. Levofloxacin receipt was associated with a lower risk of microbiome community coalescence (HR 0.75, 95% CI 0.61 – 0.93, P = 0.009). By the time of neutrophil recovery, the relative abundance of Bacteroidia (P<0.001), Fusobacteria (P=0.012), and Clostridia (P=0.013) in the stool were significantly lower in patients with oral-gut community coalescence. Exhibiting oral-stool community coalescence was associated with the occurrence of infections prior to neutrophil recovery (P=0.002), as well as infections during the 90 days post neutrophil recovery (P=0.027). This work elucidates specific antimicrobial effects on microbial ecology and furthers the understanding of oral/intestinal microbial biogeography and its implications for adverse clinical outcomes.
Collapse
|
6
|
Contemporary Clinical and Molecular Epidemiology of Vancomycin-Resistant Enterococcal Bacteremia: A Prospective Multicenter Cohort Study (VENOUS I). Open Forum Infect Dis 2021; 9:ofab616. [PMID: 35155713 PMCID: PMC8830530 DOI: 10.1093/ofid/ofab616] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 12/06/2021] [Indexed: 11/25/2022] Open
Abstract
Background Vancomycin-resistant enterococci (VRE) are major therapeutic challenges. Prospective contemporary data characterizing the clinical and molecular epidemiology of VRE bloodstream infections (BSIs) are lacking. Methods The Vancomycin-Resistant Enterococcal BSI Outcomes Study (VENOUS I) is a prospective observational cohort of adult patients with enterococcal BSI in 11 US hospitals. We included patients with Enterococcus faecalis or Enterococcus faecium BSI with ≥1 follow-up blood culture(s) within 7 days and availability of isolate(s) for further characterization. The primary study outcome was in-hospital mortality. Secondary outcomes were mortality at days 4, 7, 10, 12, and 15 after index blood culture. A desirability of outcome ranking was constructed to assess the association of vancomycin resistance with outcomes. All index isolates were subjected to whole genome sequencing. Results Forty-two of 232 (18%) patients died in hospital and 39 (17%) exhibited microbiological failure (lack of clearance in the first 4 days). Neutropenia (hazard ratio [HR], 3.13), microbiological failure (HR, 2.4), VRE BSI (HR, 2.13), use of urinary catheter (HR, 1.85), and Pitt BSI score ≥2 (HR, 1.83) were significant predictors of in-hospital mortality. Microbiological failure was the strongest predictor of in-hospital mortality in patients with E faecium bacteremia (HR, 5.03). The impact of vancomycin resistance on mortality in our cohort changed throughout the course of hospitalization. Enterococcus faecalis sequence type 6 was a predominant multidrug-resistant lineage, whereas a heterogeneous genomic population of E faecium was identified. Conclusions Failure of early eradication of VRE from the bloodstream is a major factor associated with poor outcomes.
Collapse
|
7
|
Alterations of the Oral Microbiome and Cumulative Carbapenem Exposure Are Associated With Stenotrophomonas maltophilia Infection in Patients With Acute Myeloid Leukemia Receiving Chemotherapy. Clin Infect Dis 2021; 72:1507-1513. [PMID: 32544947 DOI: 10.1093/cid/ciaa778] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Accepted: 06/11/2020] [Indexed: 01/24/2023] Open
Abstract
BACKGROUND Stenotrophomonas maltophilia is increasingly common in patients with acute myeloid leukemia (AML). Little is known about factors that drive S. maltophilia infection. We evaluated the microbiome and cumulative antibiotic use as predictors of S. maltophilia infection in AML patients receiving remission induction chemotherapy (RIC). METHODS Subanalysis of a prospective, observational cohort of patients with AML receiving RIC between September 2013 and August 2015 was performed. Fecal and oral microbiome samples collected from initiation of RIC until neutrophil recovery were assessed for the relative abundance of Stenotrophomonas via 16S rRNA gene quantitation. The primary outcome, microbiologically proven S. maltophilia infection, was analyzed using a time-varying Cox proportional hazards model. RESULTS Of 90 included patients, 8 (9%) developed S. maltophilia infection (pneumonia, n = 6; skin-soft tissue, n = 2); 4/8 (50%) patients were bacteremic; and 7/8 (88%) patients with S. maltophilia infection had detectable levels of Stenotrophomonas vs 22/82 (27%) without infection (P < .01). An oral Stenotrophomonas relative abundance of 36% predicted infection (sensitivity, 96%; specificity, 93%). No association of S. maltophilia infection with fecal relative abundance was found. Cumulative meropenem exposure was associated with increased infection risk (hazard ratio, 1.17; 95% confidence interval, 1.01-1.35; P = .03). CONCLUSIONS Here, we identify the oral microbiome as a potential source for S. maltophilia infection and highlight cumulative carbapenem use as a risk factor for S. maltophilia in leukemia patients. These data suggest that real-time monitoring of the oral cavity might identify patients at risk for S. maltophilia infection.
Collapse
|
8
|
605. Identification of a Novel CMY-Variant Enzyme in a Clinical Escherichia coli Strain with Treatment-Emergent Ceftazidime–Avibactam Resistance. Open Forum Infect Dis 2019. [PMCID: PMC6811110 DOI: 10.1093/ofid/ofz360.674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
Background Ceftazidime–avibactam (CZA) is a novel β-lactam / β-lactamase inhibitor with in vitro activity against multidrug-resistant Gram-negatives, including those harboring CMY-2 enzymes. Treatment-emergent resistance to CZA has been described in KPC-producing Klebsiella pneumoniae but has not been described in non-carbapenemase-producing, carbapenem-resistant Enterobacteriaceae (CRE). Methods A patient with an intra-abdominal infection due to a carbapenem-resistant E. coli (ertapenem MIC 16 µg/mL; meropenem MIC 2 µg/mL; CZA MIC 2 µg/mL; carbapenemase negative) was treated with CZA. On day 48 of therapy, a CZA resistant, carbapenem-sensitive E. coli was identified from abdominal drainage (CZA MIC ≥256 µg/mL; meropenem MIC 0.19 µg/mL). Illumina MiSeq whole-genome sequencing (WGS) was performed on both isolates to identify potential resistance mechanisms. The ResFinder database was used to identify known β-lactamase enzymes, and in silico modeling of β-lactamase structure was assessed. Results WGS revealed that both isolates were ST410 E. coli, with the sole difference in β-lactam resistance determinants between the two being a novel CMY β-lactamase harbored on an Inc1-type conjugative plasmid in the second isolate. The novel CMY has 4 amino acid substitutions relative to CMY-2: A134E, Q140K, V231S, and N366Y. The V231S substitution is found in CMY-42 and has previously been associated with increased ceftazidime hydrolysis. The remaining three substitutions have not previously been identified. Previous studies have identified that substitutions at position 366 influence the rate of ceftazidime hydrolysis rate. Preliminary protein structure analysis suggests that positions 140 and 366 are in the active site. No other differences in β-lactam resistance determinants were identified between the first and second isolates. Conclusion To our knowledge, we have identified the first case of CMY-associated CZA resistance. Given the widespread and transferrable nature of CMY enzymes, this finding raises concern for additional cases of resistance with increasing usage of CZA. Further analysis is needed to identify the mechanism by which this enzyme confers CZA resistance. Disclosures Samuel L. Aitken, PharmD, Melinta Therapeutics: Grant/Research Support, Research Grant; Merck, Sharpe, and Dohme: Advisory Board; Shionogi: Advisory Board.
Collapse
|
9
|
2682. Prophylaxis-Driven Molecular Epidemiology of Pseudomonas aeruginosa Bloodstream Infections in Adults With Leukemia. Open Forum Infect Dis 2019. [PMCID: PMC6810113 DOI: 10.1093/ofid/ofz360.2359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Background Fluoroquinolones (FQs) are routinely used as antimicrobial prophylaxis in leukemia patients receiving chemotherapy to prevent Pseudomonas aeruginosa infections. Patients who are intolerant to FQs may receive cefpodoxime (CPD) or other agents. How FQ use affects the resistance profile and epidemiology of breakthrough P. aeruginosa infections is unknown. To determine this, we performed a whole-genome sequencing (WGS)-driven epidemiologic study of leukemia patients with P. aeruginosa bloodstream infections. Methods All adult (age > 17 years) inpatients with leukemia and a first episode of monomicrobial P. aeruginosa bloodstream infection were included. Clinical data were extracted from the electronic medical record. Isolates were sequenced using an Illumina NextSeq and phylogenomics was performed using an in-house analysis pipeline consisting of Bowtie2, SAMtools and bcftools. Results 110 patients were included and most had a diagnosis of acute myeloid leukemia (n = 66). Twenty (18%) patients received FQ prophylaxis, 56 (54%) received CPD, and the remaining 34 (31%) received other agents. 9 (8%) isolates were multidrug-resistant (MDR). MDR was more common in those receiving FQ prophylaxis (20% vs 6%, P = 0.06). 76 sequence types (STs) were represented with ST235 (n = 8) being most common followed by ST244 (n = 7). ST235 strains were genetically distinct, but closely related (>10 but < 250 SNPs) in comparison to other STs. 2 ST244 strains were genetically identical despite being isolated 4 months apart, suggesting horizontal transmission. MDR was more common among ST235 isolates compared with other STs (38% vs 6%, P = 0.02). ST235 strains were more common in patients receiving FQ vs other prophylaxis (20% vs 4%, P = 0.04). 1 ST244 isolate harbored a VIM-2 β-lactamase. In 20 FQ-resistant isolates, 80% had mutations in either parC (S87L) or gyrA (T83I) and 50% had both. FQ-resistance mutations were more common in FQ recipients (50% vs 8%, P < 0.01). Conclusion Most P. aeruginosa infections occurred in non-FQ recipients, while MDR P. aeruginosa infections were more common in FQ recipients. These data suggest that decisions on empiric treatment of patients with P. aeruginosa bacteremia must take antimicrobial prophylaxis history into account. Disclosures Samuel L. Aitken, PharmD, Melinta Therapeutoics: Grant/Research Support, Research Grant; Merck, Sharpe, and Dohme: Advisory Board; Shionogi: Advisory Board.
Collapse
|
10
|
622. The Accessory Genome in Enterococcal Bacteremia: Results from the Vancomycin-Resistant Enterococcal Bacteremia Outcomes Study (VENOUS). Open Forum Infect Dis 2019. [PMCID: PMC6811187 DOI: 10.1093/ofid/ofz360.690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Abstract
Background
Vancomycin-resistant enterococci (VRE) are a major cause of nosocomial bloodstream infections. Enterococci exhibit remarkable genomic plasticity and can recombine through the acquisition of genetic material via mobile genetic elements (MGEs), including resistance genes. The accessory genome plays a major role in the evolution of enterococci within the human host. Thus, dissecting the entire genome (pan-genome) is of paramount importance to characterize the population structure of enterococci causing disease.
Methods
VENOUS is an ongoing prospective, observational study of adults with enterococcal bacteremia. From September 2016 to March 2018, E. faecalis (Efs) and E. faecium (Efm) were collected in 14 hospitals of a single hospital system and a major cancer center in Houston, TX, and a general hospital in Detroit, MI. Short- and long-read genomic sequencing were performed with Illumina MiSeq and Oxford Nanopore Technologies GridION X5, respectively. A proprietary bioinformatics pipeline was utilized for genome assembly and further analyses.
Results
156 Efs and 98 Efm isolates from single patients were analyzed. The average proportion of core genes in each genome was 64.6% (53.0–74.1) and 49.1% (45.2–51.0) for Efs and Efm, respectively. The vanA gene cluster was identified in 5.1% (8/157) of Efs and 57.1% (56/98) of Efm. The plasmid-encoded aac(6′)-Ie-aph(2″)-Ia gene conferring high-level resistance to aminoglycosides was found in 37.6% (59/157) Efs, seven of which also possessed vanA. Long-read sequencing of vanA-harboring plasmids from a subset of VRE revealed that the vanA cluster was carried in plasmids ranging from 31.7 to 132.3 kb. Although the vanA operon was fairly conserved, insertions of MGE were identified in the intergenic regions of vanS/vanH and vanX/vanY. Furthermore, a variety of MGE insertions mediated integration of the vanA operon, including IS1216 and IS256 (figure).
Conclusion
Accessory genes, including AMR genes, comprise a significant proportion of the enterococcal pan-genome, indicating major genetic plasticity within these organisms. Acquired resistance genes seem to have a high degree of recombination and play a substantial role in the expansion of the genomic repertoire in clinical isolates.
Disclosures
Samuel L. Aitken, PharmD, Melinta Therapeutics: Grant/Research Support, Research Grant; Merck, Sharpe, and Dohme: Advisory Board; Shionogi: Advisory Board.
Collapse
|
11
|
Fecal Microbiome, Metabolites, and Stem Cell Transplant Outcomes: A Single-Center Pilot Study. Open Forum Infect Dis 2019; 6:ofz173. [PMID: 31065565 PMCID: PMC6499899 DOI: 10.1093/ofid/ofz173] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Accepted: 03/31/2019] [Indexed: 12/13/2022] Open
Abstract
Background Accumulating evidence suggests that the intestinal microbiome may dramatically affect the outcomes of hematopoietic stem cell transplant (HSCT) recipients. Providing 16S ribosomal RNA based microbiome characterization in a clinically actionable time frame is currently problematic. Thus, determination of microbial metabolites as surrogates for microbiome composition could offer practical biomarkers. Methods Longitudinal fecal specimens (n = 451) were collected from 44 patients before HSCT through 100 days after transplantation, as well as 1-time samples from healthy volunteers (n = 18) as controls. Microbiota composition was determined using 16S ribosomal RNA V4 sequencing. Fecal indole and butyrate levels were determined using liquid chromatography tandem mass spectrometry. Results Among HSCT recipients, both fecal indole and butyrate levels correlated with the Shannon diversity index at baseline (P = .02 and P = .002, respectively) and directly after transplantation (P = .006 and P < .001, respectively). Samples with high butyrate levels were enriched for Clostridiales, whereas samples containing high indole were also enriched for Bacteroidales. A lower Shannon diversity index at the time of engraftment was associated with increased incidence of acute intestinal graft-vs-host disease (iGVHD) (P = .02) and transplant-related deaths (P = .03). Although fecal metabolites were not associated with acute iGVHD or overall survival, patients contracting bloodstream infections within 30 days after transplantation had significantly lower levels of fecal butyrate (P = .03). Conclusions Longitudinal analysis of fecal microbiome and metabolites after HSCT identified butyrate and indole as potential surrogate markers for microbial diversity and specific taxa. Further studies are needed to ascertain whether fecal metabolites can be used as biomarkers of acute iGVHD or bacteremia after HSCT.
Collapse
|
12
|
Associations of inflammation with symptom burden in patients with acute myeloid leukemia. Psychoneuroendocrinology 2018; 89:203-208. [PMID: 29414033 DOI: 10.1016/j.psyneuen.2018.01.018] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Revised: 12/13/2017] [Accepted: 01/18/2018] [Indexed: 12/11/2022]
Abstract
The aim of the study was to assess the association inflammation with symptom burden in patients with acute myeloid leukemia (AML), assessed before and during remission induction chemotherapy (IC). Patients with AML (n = 95) were followed from baseline (before IC) to the third week of IC for severity of self-reported somatic symptoms (assessed with the MD Anderson Symptom Inventory) and plasma levels of 13 inflammation-related biomarkers (n = 64). A composite symptom burden severity score was computed as the average score of the six most severe somatic symptoms i.e., fatigue, disturbed sleep, drowsiness, dry mouth, lack of appetite, and pain. Results from cross-sectional analyses showed that inflammation was weakly associated with symptom burden before IC (multiple regression model, explained variance = 10%) but this association grew stronger during IC (week 3 explained variance = 35%). About half of the sample showed a change over time in symptom severity. These changes were not reflected in similar changes over time in inflammatory markers, suggesting that it is the absolute concentration of a given inflammatory marker at a given time point rather than its relative change over time that is of importance. In conclusion, inflammation was strongly associated with symptom burden only during IC, possibly because expression of cytokines only then becomes relevant for regulation of symptom burden. While the current study does not allow for determination of causality, the results suggest that AML patients might benefit from anti-inflammatory interventions during treatment to alleviate somatic symptom experience.
Collapse
|