Explore the vast range of titles available.

A gold standard diagnostic for Clostridioides difficile infection (CDI) does not exist. An area of controversy is how to manage patients whose stool tests positive by nucleic acid amplification tests but negative by toxin enzyme immunoassay. Clostridioides difficile infection (CDI) is most commonly diagnosed using nucleic acid amplification tests (NAAT); the low positive predictive value of these assays results in patients colonized with C. difficile unnecessarily receiving CDI treatment antibiotics. The risks and benefits of antibiotic treatment in individuals with such cases are unknown. Fecal samples of NAAT-positive, toxin enzyme immunoassay (EIA)-negative patients were collected before, during, and after randomization to vancomycin ( n  = 8) or placebo ( n  = 7). C. difficile and antibiotic-resistant organisms (AROs) were selectively cultured from fecal and environmental samples. Shotgun metagenomics and comparative isolate genomics were used to understand the impact of oral vancomycin on the microbiome and environmental contamination. Overall, 80% of placebo patients and 71% of vancomycin patients were colonized with C. difficile posttreatment. One person randomized to placebo subsequently received treatment for CDI. In the vancomycin-treated group, beta-diversity ( P =  0.0059) and macrolide-lincosamide-streptogramin (MLS) resistance genes ( P =  0.037) increased after treatment; C. difficile and vancomycin-resistant enterococci (VRE) environmental contamination was found in 53% of patients and 26% of patients, respectively. We found that vancomycin alters the gut microbiota, does not permanently clear C. difficile , and is associated with VRE colonization/environmental contamination. (This study has been registered at ClinicalTrials.gov under registration no. NCT03388268.) IMPORTANCE A gold standard diagnostic for Clostridioides difficile infection (CDI) does not exist. An area of controversy is how to manage patients whose stool tests positive by nucleic acid amplification tests but negative by toxin enzyme immunoassay. Existing data suggest most of these patients do not have CDI, but most are treated with oral vancomycin. Potential benefits to treatment include a decreased risk for adverse outcomes if the patient does have CDI and the potential to decrease C. difficile shedding/transmission. However, oral vancomycin perturbs the intestinal microbiota and promotes antibiotic-resistant organism colonization/transmission. We conducted a double-blinded randomized controlled trial to assess the risk-benefit of oral vancomycin treatment in this population. Oral vancomycin did not result in long-term clearance of C. difficile , perturbed the microbiota, and was associated with colonization/shedding of vancomycin-resistant enterococci. This work underscores the need to better understand this population of patients in the context of C. difficile /ARO-related outcomes and transmission.

Vancomycin-resistant enterococci (VRE) are both of medical and public health importance associated with serious multidrug-resistant infections and persistent colonization. Enterococci are opportunistic environmental inhabitants with a remarkable adaptive capacity to evolve and transmit antimicrobial-resistant determinants. The VRE gene operons show distinct genetic variability and apparently continued evolution leading to a variety of antimicrobial resistance phenotypes and various environmental and livestock reservoirs for the most common van genes. Such complex diversity renders a number of important therapeutic options including “last resort antibiotics” ineffective and poses a particular challenge for clinical management. Enterococci resistance to glycopeptides and multidrug resistance warrants attention and continuous monitoring.

Patients with hematological malignancies or undergoing hematopoietic stem cell transplantation are vulnerable to colonization and infection with multidrug-resistant organisms, including vancomycin-resistant Enterococcus faecium (VREfm). Over a 10-y period, we collected and sequenced the genomes of 110 VREfm isolates from gastrointestinal and blood cultures of 24 pediatric patients undergoing chemotherapy or hematopoietic stem cell transplantation for hematological malignancy at St. Jude Children’s Research Hospital. We used patient-specific reference genomes to identify variants that arose over time in subsequent gastrointestinal and blood isolates from each patient and analyzed these variants for insight into how VREfm adapted during colonization and bloodstream infection within each patient. Variants were enriched in genes involved in carbohydrate metabolism, and phenotypic analysis identified associated differences in carbohydrate utilization among isolates. In particular, a Y585C mutation in the sorbitol operon transcriptional regulator gutR was associated with increased bacterial growth in the presence of sorbitol. We also found differences in biofilm-formation capability between isolates and observed that increased biofilm formation correlated with mutations in the putative E. faecium capsular polysaccharide (cps) biosynthetic locus, with different mutations arising independently in distinct genetic backgrounds. Isolates with cps mutations showed improved survival following exposure to lysozyme, suggesting a possible reason for the selection of capsule-lacking bacteria. Finally, we observed mutations conferring increased tolerance of linezolid and daptomycin in patients who were treated with these antibiotics. Overall, this study documents known and previously undescribed ways that VREfm evolve during intestinal colonization and subsequent bloodstream infection in immunocompromised pediatric patients.

In a prospective genomic surveillance study of liver transplant patients, we found that temporal dynamics differed between multidrug-resistant organisms with respect to onset of intestinal colonization, clearance, and infections. Whole-genome sequencing revealed an unexpected diversity of carbapenem-resistant Enterobacteriaceae. Abstract Background Multidrug-resistant organisms (MDROs) are an important cause of morbidity and mortality after solid organ transplantation. We aimed to characterize MDRO colonization dynamics and infection in liver transplant (LT) recipients through innovative use of active surveillance and whole-genome sequencing (WGS). Methods We prospectively enrolled consecutive adult patients undergoing LT from March 2014 to March 2016. Fecal samples were collected at multiple timepoints from time of enrollment to 12 months posttransplant. Samples were screened for carbapenem-resistant Enterobacteriaceae (CRE), Enterobacteriaceae resistant to third-generation cephalosporins (Ceph-RE), and vancomycin-resistant enterococci. We performed WGS of CRE and selected Ceph-RE isolates. We also collected clinical data including demographics, transplant characteristics, and infection data. Results We collected 998 stool samples and 119 rectal swabs from 128 patients. MDRO colonization was detected in 86 (67%) patients at least once and was significantly associated with subsequent MDRO infection (0 vs 19.8%, P = .002). Child-Turcotte-Pugh score at LT and duration of post-LT hospitalization were independent predictors of both MDRO colonization and infection. Temporal dynamics differed between MDROs with respect to onset of colonization, clearance, and infections. We detected an unexpected diversity of CRE colonizing isolates and previously unrecognized transmission that spanned Ceph-RE and CRE phenotypes, as well as a cluster of mcr-1-producing isolates. Conclusions Active surveillance and WGS showed that MDRO colonization is a highly dynamic and complex process after LT. Understanding that complexity is crucial for informing decisions regarding MDRO infection control, use of therapeutic decolonization, and empiric treatment regimens.

Vancomycin-resistant Enterococcus faecium (VREfm) is a major nosocomial pathogen. Identifying VREfm transmission dynamics permits targeted interventions, and while genomics is increasingly being utilised, methods are not yet standardised or optimised for accuracy. We aimed to develop a standardized genomic method for identifying putative VREfm transmission links. Using comprehensive genomic and epidemiological data from a cohort of 308 VREfm infection or colonization cases, we compared multiple approaches for quantifying genetic relatedness. We showed that clustering by core genome multilocus sequence type (cgMLST) was more informative of population structure than traditional MLST. Pairwise genome comparisons using split k-mer analysis (SKA) provided the high-level resolution needed to infer patient-to-patient transmission. The more common mapping to a reference genome was not sufficiently discriminatory, defining more than three times more genomic transmission events than SKA (3729 compared to 1079 events). Here, we show a standardized genomic framework for inferring VREfm transmission that can be the basis for global deployment of VREfm genomics into routine outbreak detection and investigation. Vancomycin-resistant Enterococcus faecium is an important healthcare-associated pathogen and genomic analyses could inform targeted interventions. Here, the authors optimise an analysis pipeline for identification of putative transmission events using core genome multilocus sequence type clustering and split kmer analysis.

Vancomycin-resistant Enterococci (VRE) are major pathogens causing nosocomial infections globally. This study investigated the genetic characteristics of vancomycin-resistant Enterococcus faecium (VREfm) in Thailand between June and November 2022. Fifty-two clinical VREfm isolates from Bangkok hospitals were analyzed for antimicrobial susceptibility, resistance genes, virulence factors, and genotypes using multilocus sequence typing (MLST). Phylogenetic analysis and goeBURST assessed genetic relationships and population structure. The VRE detection rate was 14.5%, with 97.1% E. faecium and 2.9% E. faecalis , likely reflecting the impact of an active case-finding program. All isolates exhibited resistance to penicillin, ampicillin, vancomycin, levofloxacin, ciprofloxacin, and rifampin. Resistance to erythromycin, high-level streptomycin, teicoplanin, and tetracycline occurred in 98.1%, 53.8%, 51.9%, and 17.3% of isolates, respectively. Chloramphenicol, linezolid, and high-level gentamicin remained effective against all isolates. The van A gene was the sole resistance determinant detected. Virulence genes esp and hyl were present in 100% and 88.5% of isolates, respectively. MLST identified five sequence types (STs), with ST17 (86.5%) as the dominant lineage, followed by ST262 (7.7%), ST202, ST787, and ST80 (1.9% each). All isolates belonged to Clonal Complex 17. Genome analysis revealed various resistance genes (VanHAX, aac (6')-Ii, aad (6), ant(6)-Ia , msr C, and tet M) and virulence factors ( acm , bop D, cps A/ upp S, cps B/ cds A, ebp A, ebp B, ebp C, efa A, esp , sgr A, and srt C). The van A gene primarily drives vancomycin resistance in Thailand’s VREfm. Genome analysis reveals antibiotic resistance genes, virulence factors, and mobile genetic elements that may drive antimicrobial resistance, increase diversity, and support adaptation in hospital settings. Ongoing infection control and active surveillance are essential.

We investigated genomic evolution of vancomycin-resistant Enterococcus faecium (VREF) during an outbreak in Shenzhen, China. Whole-genome sequencing revealed 2 sequence type 80 VREF subpopulations diverging through insertion sequence-mediated recombination. One subpopulation acquired more antimicrobial resistance and carbohydrate metabolism genes. Persistent VREF transmission underscores the need for genomic surveillance to curb spread.

The spread of vancomycin-resistant enterococci (VRE) is a major threat in nosocomial settings. A large-scale multiclonal VRE outbreak has rarely been reported in Japan due to low VRE prevalence. We evaluated the transmission of vancomycin resistance in a multiclonal VRE outbreak, conducted biological and genomic analyses of VRE isolates, and assessed the implemented infection control measures. In total, 149 patients harboring VanA-type VRE were identified from April 2017 to October 2019, with 153 vancomycin-resistant Enterococcus faecium isolated being grouped into 31 pulsotypes using pulsed-field gel electrophoresis, wherein six sequence types belonged to clonal complex 17. Epidemic clones varied throughout the outbreak; however, they all carried vanA -plasmids (pIHVA). pIHVA is a linear plasmid, carrying a unique structural Tn 1546 containing vanA ; it moves between different Enterococcus spp. by genetic rearrangements. VRE infection incidence among patients in the “hot spot” ward correlated with the local VRE colonization prevalence. Local prevalence also correlated with vancomycin usage in the ward. Transmission of a novel transferrable vanA -plasmid among Enterococcus spp. resulted in genomic diversity in VRE in a non-endemic setting. The prevalence of VRE colonization and vancomycin usage at the ward level may serve as VRE cross-transmission indicators in non-intensive care units for outbreak control.

Enterococci are ubiquitous microorganisms that could be found everywhere; in water, plant, soil, foods, and gastrointestinal tract of humans and animals. They were previously used as starters in food fermentation due to their biotechnological traits (enzymatic and proteolytic activities) or protective cultures in food biopreservation due to their produced antimicrobial bacteriocins called enterocins or as probiotics, live cells with different beneficial characteristics such as stimulation of immunity, anti-inflammatory activity, hypocholesterolemic effect, and prevention/treatment of some diseases. However, in the last years, the use of enterococci in foods or as probiotics caused an important debate because of their opportunistic pathogenicity implicated in several nosocomial infections due to virulence factors and antibiotic resistance, particularly the emergence of vancomycin-resistant enterococci. These virulence traits of some enterococci are associated with genetic transfer mechanisms. Therefore, the development of new enterococcal probiotics needs a strict assessment with regard to safety aspects for selecting the truly harmless enterococcal strains for safe applications. This review tries to give some data of the different points of view about this question.

Vancomycin-resistant enterococci (VRE) are a major public health concern, yet little is known about their circulation in fish. This study investigated the occurrence, glycopeptide resistance genotypes, virulence characteristics, and sequence types (STs) of VRE isolated from diseased fishes and humans. Isolates were identified using multiplex polymerase chain reaction (PCR) assay and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS), and tested for antimicrobial susceptibility. VRE isolates were screened for the presence of glycopeptide resistance genes and eight virulence genes. Multilocus sequence typing (MLST) was determined to assess the clonality of VRE isolates from fishes and humans. Among 60 human samples, 20 Enterococcus species isolates (33.33%) including Enterococcus faecalis and Enterococcus faecium (10 of each), were identified. The overall prevalence of E. faecalis was 42.86% (30/70) in Oreochromis niloticus and 48.0% (24/50) in Clarias gariepinus . E. faecium was found in 15.71% (11/70) of Oreochromis niloticus and 14.0% (7/50) of Clarias gariepinus . Over 50% of human isolates were multidrug resistant (MDR) and 30% exhibited an extensive drug resistant (XDR) phenotype. Fish isolates also displayed high MDR (70.83%) and XDR (29.17%) rates. Forty-nine (53.26%; 34 from fish and 15 from human) isolates were VRE including 30 isolates of E. faecalis (VREfs) and 19 isolates of E. faecium (VREfm). The vanA gene was the most frequent among VREfs (83.33%) and VREfm (100%) isolates. The vanB gene was found in 26.67% of VREfs and 15.79% of VREfm. Three out of 10 VREfm (30%) and 2/24 (8.33%) VREfs isolates of fish origin carried both vanA and vanB genes. vanC gene was found in 13.33% (4/30) of VREfs of human and fish origin. One VREfs isolate from human urine carried both vanA and vanC genes. High frequency of the virulence genes  gelE , sprE , asa1 , esp, and cylA were observed;  efa  and ace gene was more associated with VREfs, while hyl  gene was more frequently detected in VREfm. Different combinations of virulence genes suggesting synergistic pathogenic potential. MLST revealed both overlapping and host-specific STs among the examined Enterococcus isolates from humans and fish. Experimental infection of O. niloticus with VREfs and VREfm caused a 100% and 60% mortality rate within 6 days postinfection, respectively with characteristic disease symptoms. The emergence of VRE and the high prevalence of virulence traits could be regarded as an alarming situation. The call for increased infection control and antibiotic stewardship measures is timely and relevant to combat the spread of VRE in fish and humans.