ABSTRACT
Linezolid resistance in Enterococcus spp. is increasingly considered critically important and a public health threat which mandates the need to understand their genomic contents and dissemination patterns. Here, we used whole-genome sequencing to characterize the resistome, virulome and mobile genetic elements of nine linezolid-resistant (LZDR) enterococci (seven optrA-E. faecalis, one poxtA-E. faecium and one optrA-E. casseliflavus) previously obtained from the nares of healthy dogs, pigs, pig farmers and tracheal samples of nestling storks in Spain. Also, the relatedness of the isolates with publicly available genomes was accessed by core-genome single nucleotide polymorphism (SNP) analysis. The optrA gene of the E. faecalis and E. casseliflavus isolates was located downstream of the fexA gene. The optrA gene in the E. casseliflavus isolate was carried in a plasmid (pURX4962), while those in the seven E. faecalis isolates were chromosomally located. The OptrA proteins were mostly variants of wild type (DP-2: Y176D/T481P; RDK: I104R/Y176D/E256K; DD-3: Y176D/G393D; and EDD: K3E/Y176D/G393D), except two that were wild type (one E. faecalis and one E. casseliflavus). The poxtA gene in the E. faecium isolate was found alone within its contig. The cfrD was upstream of ermB gene in the E. casseliflavus isolate and flanked by ISNCY and IS1216. All the LZDR enterococci carried plasmid rep genes (2-3) containing tetracycline, chloramphenicol and aminoglycoside resistance genes. All isolates except E. casseliflavus carried at least one intact prophage, of which E. faecalis-ST330 (X4957) from a pig carried the highest (n = 5). Tn6260 was associated with lnuG in E. faecalis-ST330 while Tn554 was with fexA in E. feaecalis-ST59 isolates. All except E. casseliflavus (n = 0) carried at least two metal resistance genes (MRGs), of which poxtA-carrying E. faecium-ST1739 isolate contained the most (arsA, copA, fief, ziaA, znuA, zosA, zupT, and zur). SNP-based analyses identified closely related optrA-E. faecalis isolates from a pig and a pig farmer on the same farm (SNP = 4). Moreover, optrA- carrying E. faecalis-ST32, -ST59, and -ST474 isolates from pigs were related to those previously described from humans (sick and healthy) and cattle in Spain, Belgium, and Switzerland (SNP range 43-86). These findings strongly suggest the transmission of LZDR-E. faecalis between a pig and a pig farmer and potential inter-country dissemination. These highlight the need to strengthen molecular surveillance of LZDR enterococci in all ecological niches and body parts to direct appropriate control strategies.
Subject(s)
Anti-Bacterial Agents , Drug Resistance, Bacterial , Enterococcus , Genome, Bacterial , Linezolid , Phylogeny , Animals , Linezolid/pharmacology , Swine/microbiology , Drug Resistance, Bacterial/genetics , Dogs , Anti-Bacterial Agents/pharmacology , Enterococcus/genetics , Enterococcus/drug effects , Enterococcus/isolation & purification , Enterococcus/classification , Gram-Positive Bacterial Infections/microbiology , Gram-Positive Bacterial Infections/transmission , Gram-Positive Bacterial Infections/veterinary , Humans , Whole Genome Sequencing , Spain , Polymorphism, Single Nucleotide , Microbial Sensitivity Tests , Bacterial Proteins/genetics , Genomics , Plasmids/geneticsABSTRACT
BACKGROUND: Vancomycin-resistant Enterococcus faecium (VREfm) are significant nosocomial pathogens. Sequence type (ST) 80 vanA-encoding VREfm predominate in Irish hospitals, but their transmission is poorly understood. AIMS: To investigate transmission and persistence of predominant complex type (CT) VREfm in two wards of an Irish hospital (H1) using whole-genome sequencing, and their intra- and inter-hospital dissemination. METHODS: Rectal screening (N = 330, September 2019 to December 2022) and environmental (N = 48, November 2022 to December 2022) E. faecium were investigated. Isolate relatedness was assessed by core-genome multi-locus sequence typing (cgMLST) and core-genome single nucleotide polymorphism (cgSNP) analysis. Likely transmission chains were identified using SeqTrack (https://graphsnp.fordelab.com/graphsnp) using cgSNP data and recovery location. Well-characterized E. faecium (N = 908) from seven Irish hospitals including H1 (June 2017 to July 2022) were also investigated. FINDINGS: Conventional MLST assigned isolates to nine STs (ST80, 82%). cgMLST identified three predominant ST80 CTs (CT2933, CT2932 and CT1916) (55% of isolates) of related isolates (≤20 allelic differences). cgSNP analysis differentiated these CTs into multiple distinct closely related genomic clusters (≤10 cgSNPs). Parisimonious network construction identified 55 likely inter- and intra-ward transmissions with epidemiological support between patients ≤30 days involving 73 isolates (≤10 cgSNPs) from seven genomic clusters. Numerous other likely transmissions over longer time periods without evident epidemiological links were identified, suggesting persistence and unidentified reservoirs contribute to dissemination. The three CTs predominated among E. faecium (N = 1286) in seven hospitals, highlighting inter-hospital spread without known epidemiological links. CONCLUSION: This study revealed the long-term intra- and inter-hospital dominance of three major CT ST80 VREfm lineages, widespread transmission and persistence, implicating unidentified reservoirs.
Subject(s)
Cross Infection , Enterococcus faecium , Gram-Positive Bacterial Infections , Hospitals , Vancomycin-Resistant Enterococci , Whole Genome Sequencing , Humans , Ireland/epidemiology , Enterococcus faecium/genetics , Enterococcus faecium/isolation & purification , Enterococcus faecium/drug effects , Enterococcus faecium/classification , Vancomycin-Resistant Enterococci/genetics , Vancomycin-Resistant Enterococci/isolation & purification , Vancomycin-Resistant Enterococci/classification , Gram-Positive Bacterial Infections/microbiology , Gram-Positive Bacterial Infections/transmission , Gram-Positive Bacterial Infections/epidemiology , Cross Infection/microbiology , Cross Infection/epidemiology , Cross Infection/transmission , Multilocus Sequence Typing , Polymorphism, Single Nucleotide , Genome, Bacterial , GenotypeSubject(s)
Cross Infection , Genome, Bacterial , Gram-Positive Bacterial Infections , Vancomycin-Resistant Enterococci , Humans , Vancomycin-Resistant Enterococci/genetics , Vancomycin-Resistant Enterococci/isolation & purification , Vancomycin-Resistant Enterococci/drug effects , Cross Infection/microbiology , Cross Infection/transmission , Cross Infection/epidemiology , Gram-Positive Bacterial Infections/transmission , Gram-Positive Bacterial Infections/microbiology , Gram-Positive Bacterial Infections/epidemiology , Anti-Bacterial Agents/pharmacologyABSTRACT
Outbreaks caused by vancomycin-resistant enterococci that transcend jurisdictional boundaries are occurring worldwide. This study focused on a vancomycin-resistant enterococcus outbreak that occurred between 2018 and 2021 across two cities in Hiroshima, Japan. The study involved genetic and phylogenetic analyses using whole-genome sequencing of 103 isolates of vancomycin-resistant enterococci to identify the source and transmission routes of the outbreak. Phylogenetic analysis was performed using core genome multilocus sequence typing and core single-nucleotide polymorphisms; infection routes between hospitals were inferred using BadTrIP. The outbreak was caused by Enterococcus faecium sequence type (ST) 80 carrying the vanA plasmid, which was derived from strain A10290 isolated in India. Of the 103 isolates, 93 were E. faecium ST80 transmitted across hospitals. The circular vanA plasmid of the Hiroshima isolates was similar to the vanA plasmid of strain A10290 and transferred from E. faecium ST80 to other STs of E. faecium and other Enterococcus species by conjugation. The inferred transmission routes across hospitals suggest the existence of a central hospital serving as a hub, propagating vancomycin-resistant enterococci to multiple hospitals. Our study highlights the importance of early intervention at the key central hospital to prevent the spread of the infection to small medical facilities, such as nursing homes, with limited medical resources and a high number of vulnerable individuals.
Subject(s)
Disease Outbreaks , Enterococcus faecium , Gram-Positive Bacterial Infections , Multilocus Sequence Typing , Phylogeny , Plasmids , Vancomycin-Resistant Enterococci , Whole Genome Sequencing , Enterococcus faecium/genetics , Enterococcus faecium/drug effects , Enterococcus faecium/isolation & purification , Japan/epidemiology , Humans , Vancomycin-Resistant Enterococci/genetics , Vancomycin-Resistant Enterococci/drug effects , Vancomycin-Resistant Enterococci/isolation & purification , Plasmids/genetics , Gram-Positive Bacterial Infections/transmission , Gram-Positive Bacterial Infections/microbiology , Gram-Positive Bacterial Infections/epidemiology , Cross Infection/microbiology , Cross Infection/transmission , Cross Infection/epidemiology , Bacterial Proteins/genetics , Anti-Bacterial Agents/pharmacology , Carbon-Oxygen Ligases/genetics , Microbial Sensitivity Tests , Polymorphism, Single Nucleotide , Hospitals , Vancomycin/pharmacology , Genome, Bacterial/geneticsABSTRACT
Worldwide outbreaks make infections with pathogenic strains of Enterococcus cecorum (EC) one of the most important diseases in the broiler industry. Although research has increased knowledge about the pathogen, the transmission is not fully understood. Samples from different locations were collected from two broiler farms in Germany over a total of six production cycles. Samples were collected at days 1, 5, 10, 15, 21, 27, 34, 41 post-hatch and after cleaning and disinfection (C&D). A total of 1017 samples were collected from 25 different locations on the farms. Samples were analysed in the laboratory for EC by quantitative real-time PCR. Overall, 7.5% of the samples were positive. The probabilities for positive and negative samples did not differ between the farms. The number of findings differed significantly between the cycles. Compared to other samples, the chances of detecting EC in faecal samples were significantly higher. Most positive samples were found in the last week of the production periods, indicating an accumulation of EC in the barn environment. After C&D, positive PCR results were obtained in four out of 14 locations. A re-introduction from contaminated environment seemed possible. However, one pooled faecal sample was positive 1 day post-hatch. The locations that showed positive results after C&D and the positive faecal sample 1 day post-hatch indicated the persistence of EC in broiler houses of clinically healthy flocks that could lead to potential horizontal transmission routes. The present study detected potential EC sources and may help to improve hygienic measures to avoid transmissions.RESEARCH HIGHLIGHTSMethodology is suitable to detect EC during production and after C&D.Locations were detected that may serve as a reservoir for EC.Cycles with fewer positive samples were observed.Cleaning and disinfection had a major impact on the detection of EC.
Subject(s)
Chickens , Enterococcus , Feces , Gram-Positive Bacterial Infections , Housing, Animal , Poultry Diseases , Animals , Chickens/microbiology , Feces/microbiology , Enterococcus/isolation & purification , Enterococcus/genetics , Poultry Diseases/microbiology , Poultry Diseases/epidemiology , Gram-Positive Bacterial Infections/veterinary , Gram-Positive Bacterial Infections/microbiology , Gram-Positive Bacterial Infections/epidemiology , Gram-Positive Bacterial Infections/transmission , Germany/epidemiology , Real-Time Polymerase Chain Reaction/veterinary , Disinfection , Environmental MicrobiologyABSTRACT
BACKGROUND: To establish effective infection control protocols, understanding pathogen transmission pathways is essential. Non-infectious surrogate tracers may safely explore these pathways and challenge pre-existing assumptions. We used silica nanoparticles with encapsulated DNA (SPED) for the first time in a real-life hospital setting to investigate potential transmission routes of vancomycin-resistant enterococci in the context of a prolonged outbreak. METHODS: The two study experiments took place in the 900-bed University Hospital Zurich, Switzerland. A three-run 'Patient experiment' investigated pathogen transmission via toilet seats in a two-patient room with shared bathroom. First, various predetermined body and fomite sites in a two-bed patient room were probed at baseline. Then, after the first patient was contaminated with SPED at the subgluteal region, both patients sequentially performed a toilet routine. All sites were consequently swabbed again for SPED contamination. Eight hours later, further spread was tested at predefined sites in the patient room and throughout the ward. A two-run 'Mobile device experiment' explored the potential transmission by mobile phones and stethoscopes in a quasi-realistic setting. All SPED contamination statuses and levels were determined by real-time qPCR. RESULTS: Over all three runs, the 'Patient experiment' yielded SPED in 59 of 73 (80.8%) predefined body and environmental sites. Specifically, positivity rates were 100% on subgluteal skin, toilet seats, tap handles, and entertainment devices, the initially contaminated patients' hands; 83.3% on patient phones and bed controls; 80% on intravenous pumps; 75% on toilet flush plates and door handles, and 0% on the initially not contaminated patients' hands. SPED spread as far as doctor's keyboards (66.6%), staff mobile phones (33.3%) and nurses' keyboards (33.3%) after eight hours. The 'Mobile device experiment' resulted in 16 of 22 (72.7%) positive follow-up samples, and transmission to the second patient occurred in one of the two runs. CONCLUSIONS: For the first time SPED were used to investigate potential transmission pathways in a real hospital setting. The results suggest that, in the absence of targeted cleaning, toilet seats and mobile devices may result in widespread transmission of pathogens departing from one contaminated patient skin region.
Subject(s)
Cross Infection/transmission , Gram-Positive Bacterial Infections/transmission , Infection Control , Nanoparticles/chemistry , Patients' Rooms , Vancomycin-Resistant Enterococci/physiology , DNA , Equipment Contamination , Fomites , Hospitals , Silicon Dioxide/chemistry , SwitzerlandABSTRACT
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.
Subject(s)
Cross Infection/transmission , Delivery of Health Care , Enterococcus faecium/genetics , Genome, Bacterial , Gram-Positive Bacterial Infections/transmission , Vancomycin-Resistant Enterococci/genetics , Anti-Bacterial Agents , Bacterial Proteins/genetics , Bacterial Typing Techniques , Carbon-Oxygen Ligases/genetics , Cross Infection/epidemiology , Disease Outbreaks , Enterococcus faecium/classification , Enterococcus faecium/isolation & purification , Genomics , Gram-Positive Bacterial Infections/epidemiology , Gram-Positive Bacterial Infections/microbiology , Humans , Multilocus Sequence Typing , Phylogeny , Vancomycin , Vancomycin-Resistant Enterococci/classification , Vancomycin-Resistant Enterococci/isolation & purification , Whole Genome SequencingABSTRACT
BACKGROUND/OBJECTIVES: We investigated whether behavioral precautions adopted during Coronavirus disease (COVID-19) pandemic also influenced the spreading and multidrug resistance (MDR) of ESKAPEEc (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii [AB], Pseudomonas aeruginosa, Enterobacter spp and Escherichia Coli, [EC]) among Intensive Care Unit (ICU) patients. SUBJECTS/METHODS: We performed a single-center retrospective study in adult patients admitted to our COVID-19-free surgical ICU. Only patients staying in ICU for more than 48 hours were included. The ESKAPEEc infections recorded during the COVID-19 period (June 1, 2020 - February 28, 2021) and in the corresponding pre-pandemic period (June 1, 2019 - February 28, 2020) were compared. An interrupted time series analysis was performed to rule out possible confounders. RESULTS: Overall, 173 patients in the COVID-19 period and 132 in the pre-COVID-19 period were investigated. The ESKAPEEc infections were documented in 23 (13.3%) and 35 (26.5%) patients in the pandemic and the pre-pandemic periods, respectively (p = 0.005). Demographics, diagnosis, comorbidities, type of surgery, Simplified Acute Physiology Score II, length of mechanical ventilation, hospital and ICU length of stay, ICU death rate, and 28-day hospital mortality were similar in the two groups. In comparison with the pre-pandemic period, no AB was recorded during COVID-19 period, (p = 0.017), while extended-spectrum beta-lactamase-producing EC infections significantly decreased (p = 0.017). Overall, the ESKAPEEc isolates during pandemic less frequently exhibited multidrug-resistant (p = 0.014). CONCLUSIONS: These findings suggest that a robust adherence to hygiene measures together with human contact restrictions in a COVID-19 free ICU might also restrain the transmission of ESKAPEEc pathogens.
Subject(s)
COVID-19/prevention & control , Cross Infection/epidemiology , Gram-Negative Bacterial Infections/epidemiology , Gram-Positive Bacterial Infections/epidemiology , Infection Control , Acinetobacter Infections/epidemiology , Acinetobacter Infections/microbiology , Acinetobacter Infections/transmission , Acinetobacter baumannii , Aged , Cross Infection/microbiology , Cross Infection/transmission , Drug Resistance, Multiple, Bacterial , Enterobacter , Enterobacteriaceae Infections/epidemiology , Enterobacteriaceae Infections/microbiology , Enterobacteriaceae Infections/transmission , Enterococcus faecium , Escherichia coli Infections/epidemiology , Escherichia coli Infections/microbiology , Escherichia coli Infections/transmission , Female , Gram-Negative Bacterial Infections/microbiology , Gram-Negative Bacterial Infections/transmission , Gram-Positive Bacterial Infections/microbiology , Gram-Positive Bacterial Infections/transmission , Hand Disinfection , Humans , Intensive Care Units , Interrupted Time Series Analysis , Klebsiella Infections/epidemiology , Klebsiella Infections/microbiology , Klebsiella Infections/transmission , Klebsiella pneumoniae , Male , Methicillin-Resistant Staphylococcus aureus , Middle Aged , Organizational Policy , Personal Protective Equipment , Pseudomonas Infections/epidemiology , Pseudomonas Infections/microbiology , Pseudomonas Infections/transmission , Pseudomonas aeruginosa , Retrospective Studies , SARS-CoV-2 , Staphylococcal Infections/epidemiology , Staphylococcal Infections/microbiology , Staphylococcal Infections/transmission , Staphylococcus aureus , Visitors to PatientsABSTRACT
Gardnerella vaginalis in association with anaerobes has been linked to bacterial vaginosis in women, while urinary tract infections (UTIs) in men have rarely been reported. The aim of the review was to reveal the significance of G. vaginalis UTIs in men. Prevalence of G. vaginalis UTIs in men varied from 0.5 to >27% according to patients' groups. Most patients had comorbidity such as urolithiasis or stents, transplants, tumors and diabetes, however, infections can also affect immunocompetent patients. We observed G. vaginalis-associated bacteriuria and leukocyturia in a kidney transplant man. Complications of the UTIs such as bacteremia (in 9/11 cases), hydronephrosis (4/11) and abscesses or septic emboli have been reported. Bacterial vaginosis in female partners has been a risk factor for UTIs in males. In women, biofilm Gardnerella phenotype, stabilized by Atopobium vaginae and Prevotella bivia was linked to ≥6-fold higher antibiotic resistance rates compared with the planktonic phenotype. Non-susceptibility to metronidazole and levofloxacin was found also in males. Therefore, if aerobic urine cultures are negative, urine and blood samples from male patients with predisposing factors and clinical signs of UTIs and bacteremia, can be taken. Plates should be incubated for 2-4 days in capnophilic/microaerophilic conditions, however only anaerobic incubation can help with detecting G. vaginalis strains which grow only anaerobically. Susceptibility testing of the isolates is highly important. Briefly, adherent G. vaginalis phenotype can be sexually transmissible. Despite the infrequency of G. vaginalis UTIs in men, the infections should be considered since they are often linked to severe complications.
Subject(s)
Gardnerella vaginalis , Gram-Positive Bacterial Infections/microbiology , Gram-Positive Bacterial Infections/transmission , Urinary Tract Infections/microbiology , Disease Management , Disease Susceptibility , Female , Gardnerella vaginalis/drug effects , Gram-Positive Bacterial Infections/diagnosis , Gram-Positive Bacterial Infections/epidemiology , Humans , Male , Prevalence , Risk Factors , Sex Factors , Sexually Transmitted Diseases, Bacterial/diagnosis , Sexually Transmitted Diseases, Bacterial/epidemiology , Sexually Transmitted Diseases, Bacterial/microbiology , Sexually Transmitted Diseases, Bacterial/transmission , Urinary Tract Infections/diagnosis , Urinary Tract Infections/epidemiology , Urinary Tract Infections/transmission , Vaginosis, Bacterial/microbiologyABSTRACT
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 Tn1546 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.
Subject(s)
Bacterial Proteins/genetics , Carbon-Oxygen Ligases/genetics , Cross Infection/microbiology , Gram-Positive Bacterial Infections/transmission , Vancomycin-Resistant Enterococci/classification , Aged , Antimicrobial Stewardship , Case-Control Studies , Cross Infection/transmission , Disease Outbreaks , Electrophoresis, Gel, Pulsed-Field , Endemic Diseases , Female , Humans , Japan , Male , Phylogeny , Plasmids/genetics , Population Surveillance , Vancomycin-Resistant Enterococci/genetics , Vancomycin-Resistant Enterococci/isolation & purificationABSTRACT
BACKGROUND: Enterococcus faecium is a commensal of the gastrointestinal tract of animals and humans but also a causative agent of hospital-acquired infections. Resistance against glycopeptides and to vancomycin has motivated the inclusion of E. faecium in the WHO global priority list. Vancomycin resistance can be conferred by the vanA gene cluster on the transposon Tn1546, which is frequently present in plasmids. The vanA gene cluster can be disseminated clonally but also horizontally either by plasmid dissemination or by Tn1546 transposition between different genomic locations. METHODS: We performed a retrospective study of the genomic epidemiology of 309 vancomycin-resistant E. faecium (VRE) isolates across 32 Dutch hospitals (2012-2015). Genomic information regarding clonality and Tn1546 characterization was extracted using hierBAPS sequence clusters (SC) and TETyper, respectively. Plasmids were predicted using gplas in combination with a network approach based on shared k-mer content. Next, we conducted a pairwise comparison between isolates sharing a potential epidemiological link to elucidate whether clonal, plasmid, or Tn1546 spread accounted for vanA-type resistance dissemination. RESULTS: On average, we estimated that 59% of VRE cases with a potential epidemiological link were unrelated which was defined as VRE pairs with a distinct Tn1546 variant. Clonal dissemination accounted for 32% cases in which the same SC and Tn1546 variants were identified. Horizontal plasmid dissemination accounted for 7% of VRE cases, in which we observed VRE pairs belonging to a distinct SC but carrying an identical plasmid and Tn1546 variant. In 2% of cases, we observed the same Tn1546 variant in distinct SC and plasmid types which could be explained by mixed and consecutive events of clonal and plasmid dissemination. CONCLUSIONS: In related VRE cases, the dissemination of the vanA gene cluster in Dutch hospitals between 2012 and 2015 was dominated by clonal spread. However, we also identified outbreak settings with high frequencies of plasmid dissemination in which the spread of resistance was mainly driven by horizontal gene transfer (HGT). This study demonstrates the feasibility of distinguishing between modes of dissemination with short-read data and provides a novel assessment to estimate the relative contribution of nested genomic elements in the dissemination of vanA-type resistance.
Subject(s)
Bacterial Proteins/metabolism , Gram-Positive Bacterial Infections/microbiology , Gram-Positive Bacterial Infections/transmission , Hospitals , Vancomycin Resistance , Base Sequence , Enterococcus faecium/genetics , Enterococcus faecium/physiology , Humans , Netherlands/epidemiology , Plasmids/genetics , Reproducibility of Results , Time Factors , Vancomycin-Resistant Enterococci/genetics , Vancomycin-Resistant Enterococci/isolation & purificationABSTRACT
Nosocomial acquisition and transmission of vancomycin-resistant Enterococcus faecium (VREfm) is the driver for E. faecium carriage in hospitalized patients, which, in turn, is a risk factor for invasive infection in immunocompromised patients. In the present study, we provide a comprehensive picture of E. faecium transmission in an entire sampled patient population using a sequence-driven approach. We prospectively identified and followed 149 haematology patients admitted to a hospital in England for 6 months. Patient stools (n = 376) and environmental swabs (n = 922) were taken at intervals and cultured for E. faecium. We sequenced 1,560 isolates (1,001 stool, 559 environment) and focused our genomic analyses on 1,477 isolates (95%) in the hospital-adapted clade A1. Of 101 patients who provided two or more stool samples, 40 (40%) developed E. faecium carriage after admission based on culture, compared with 64 patients (63%) based on genomic analysis (73% VREfm). Half of 922 environmental swabs (447, 48%) were positive for VREfm. Network analysis showed that, of 111 patients positive for the A1 clade, 67 had strong epidemiological and genomic links with at least one other patient and/or their direct environment, supporting nosocomial transmission. Six patients (3.4%) developed an invasive E. faecium infection from their own gut-colonizing strain, which was preceded by nosocomial acquisition of the infecting isolate in half of these. Two informatics approaches (subtype categorization to define phylogenetic clusters and the development of an SNP cut-off for transmission) were central to our analyses, both of which will inform the future translation of E. faecium sequencing into routine outbreak detection and investigation. In conclusion, we showed that carriage and environmental contamination by the hospital-adapted E. faecium lineage were hyperendemic in our study population and that improved infection control measures will be needed to reduce hospital acquisition rates.
Subject(s)
Cross Infection/epidemiology , Enterococcus faecium/genetics , Gram-Positive Bacterial Infections/transmission , Infection Control/methods , Vancomycin-Resistant Enterococci/genetics , Adult , Aged , Aged, 80 and over , Alcohols/pharmacology , Anti-Bacterial Agents/pharmacology , Chlorhexidine/pharmacology , Cross Infection/transmission , Disease Outbreaks , Disinfectants/pharmacology , Enterococcus faecium/isolation & purification , Genome, Bacterial/genetics , Gram-Positive Bacterial Infections/pathology , Humans , Microbial Sensitivity Tests , Middle Aged , Prospective Studies , Vancomycin/pharmacology , Vancomycin-Resistant Enterococci/isolation & purification , Whole Genome Sequencing , Young AdultABSTRACT
Vancomycin-resistant Enterococcus faecium (VREfm) belonging to sequence type (ST)80 has become the predominant clonal lineage in Stockholm in the last three years. ST80 accounted for 75% and 46% of VRE cases in 2018 and 2019, respectively, and gave rise to both vanA-type and vanB-type outbreaks. Non-duplicate ST80-VREfm isolates (N = 188) were subjected to whole genome sequencing. Genomic analysis revealed three distinct transmission clusters. Our study indicated that difficulties in detecting low-grade vancomycin-resistant isolates by phenotypic testing might be one of the explanatory factors for the prolonged course of vanB-type outbreaks. Herein, we also report the first optrA-positive linezolid-resistant VRE isolate in Stockholm.
Subject(s)
Enterococcus faecium , Gram-Positive Bacterial Infections/transmission , Vancomycin-Resistant Enterococci , Anti-Bacterial Agents , Enterococcus faecium/genetics , Genomics , Gram-Positive Bacterial Infections/epidemiology , Humans , Microbial Sensitivity Tests , Sweden , Vancomycin-Resistant Enterococci/geneticsABSTRACT
BACKGROUND: Transplant recipients are at high risk for infections. However, donor-recipient transmission of multidrug-resistant organisms (MDROs) remains mostly unaddressed in the protocols of pre-transplant infection and colonization screening. Vancomycin-resistant enterococci (VRE) are MDROs that colonize the gastrointestinal tract and are associated with a significant burden of disease. Besides the high mortality of invasive VRE infections, chronic colonization leads to costly isolation measures in the hospital setting. Whereas most post-transplantation VRE infections are endogenous and thus preceded by colonization of the recipient, conclusive evidence of VRE transmission via allograft in the context of intestinal transplantation is lacking. CASE PRESENTATION: We describe a donor-derived VRE infection after intestinal transplantation including small bowel and right hemicolon. The recipient, a 54-year old male with history of mesenteric ischemia and small bowel perforation due to generalized atherosclerosis and chronic stenosis of the celiac trunk and the superior mesenteric artery, developed an intra-abdominal infection and bloodstream infection after transplantation. VRE isolates recovered from the patient as well as from the allograft prior to transplantation were analyzed via whole genome sequencing. Isolates showed to be genetically identical, thus confirming the transmission from donor to recipient. CONCLUSIONS: This case underlines the relevance of donor-recipient VRE transmission and invasive infection in the context of intestinal transplantation, highlighting the need for preoperative MDRO screening that facilitates the prompt and effective treatment of possible infections as well as the timely establishment of contact precautions to prevent further spread.
Subject(s)
Bacteremia/etiology , Gram-Positive Bacterial Infections/transmission , Intestines/transplantation , Postoperative Complications/etiology , Tissue Donors , Vancomycin-Resistant Enterococci , Drug Resistance, Multiple, Bacterial , Humans , Male , Middle AgedABSTRACT
Streptococcus mutans is one of the primary pathogens responsible for the development of dental caries. Recent whole-genome sequencing (WGS)-based core genome multilocus sequence typing (cgMLST) approaches have been employed in epidemiological studies of specific human pathogens. However, this approach has not been reported in studies of S. mutans Here, we therefore developed a cgMLST scheme for S. mutans We surveyed 199 available S. mutans genomes as a means of identifying cgMLST targets, developing a scheme that incorporated 594 targets from the S. mutans UA159 reference genome. Sixty-eight sequence types (STs) were identified in this cgMLST scheme (cgSTs) in 80 S. mutans isolates from 40 children that were sequenced in this study, compared to 35 STs identified by multilocus sequence typing (MLST). Fifty-six cgSTs (82.35%) were associated with a single isolate based on our cgMLST scheme, which is significantly higher than in the MLST scheme (11.43%). In addition, 58.06% of all MLST profiles with ≥2 isolates were further differentiated by our cgMLST scheme. Topological analyses of the maximum likelihood phylogenetic trees revealed that our cgMLST scheme was more reliable than the MLST scheme. A minimum spanning tree of 145 S. mutans isolates from 10 countries developed based upon the cgMLST scheme highlighted the diverse population structure of S. mutans This cgMLST scheme thus offers a new molecular typing method suitable for evaluating the epidemiological distribution of this pathogen and has the potential to serve as a benchmark for future global studies of the epidemiological nature of dental caries.IMPORTANCEStreptococcus mutans is regarded as a major pathogen responsible for the onset of dental caries. S. mutans can transmit among people, especially within families. In this study, we established a new epidemiological approach to S. mutans classification. This approach can effectively differentiate among closely related isolates and offers superior reliability relative to that of the traditional MLST molecular typing method. As such, it has the potential to better support effective public health strategies centered around this bacterium that are aimed at preventing and treating dental caries.
Subject(s)
Bacterial Typing Techniques/methods , Genome, Bacterial , Multilocus Sequence Typing/methods , Streptococcus mutans/classification , Streptococcus mutans/genetics , Child, Preschool , China/epidemiology , Genotype , Gram-Positive Bacterial Infections/epidemiology , Gram-Positive Bacterial Infections/microbiology , Gram-Positive Bacterial Infections/transmission , Humans , Phylogeny , Reproducibility of Results , Whole Genome SequencingABSTRACT
Vancomycin-resistant E. faecium (VRE) are an important cause of nosocomial infections, which are rapidly transmitted in hospitals. To identify possible transmission routes, we applied combined genomics and contact-network modeling to retrospectively evaluate routine VRE screening data generated by the infection control program of a hemato-oncology unit. Over 1 year, a total of 111 VRE isolates from 111 patients were collected by anal swabs in a tertiary care hospital in Southern Germany. All isolated VRE were whole-genome sequenced, followed by different in-depth bioinformatics analyses including genotyping and determination of phylogenetic relations, aiming to evaluate a standardized workflow. Patient movement data were used to overlay sequencing data to infer transmission events and strain dynamics over time. A predominant clone harboring vanB and exhibiting genotype ST117/CT469 (n = 67) was identified. Our comprehensive combined analyses suggested intra-hospital spread, especially of clone ST117/CT469, despite of extensive screening, single room placement, and contact isolation. A new interactive tool to visualize these complex data was designed. Furthermore, a patient-contact network-modeling approach was developed, which indicates both the periodic import of the clone into the hospital and its spread within the hospital due to patient movements. The analyzed spread of VRE was most likely due to placement of patients in the same room prior to positivity of screening. We successfully demonstrated the added value for this combined strategy to extract well-founded knowledge from interdisciplinary data sources. The combination of patient-contact modeling and high-resolution typing unraveled the transmission dynamics within the hospital department and, additionally, a constant VRE influx over time.
Subject(s)
Contact Tracing/methods , Cross Infection/transmission , Gram-Positive Bacterial Infections/transmission , High-Throughput Nucleotide Sequencing/methods , Population Surveillance/methods , Tertiary Care Centers/statistics & numerical data , Algorithms , Anti-Bacterial Agents/pharmacology , Cross Infection/microbiology , Cross Infection/prevention & control , Enterococcus faecium/classification , Enterococcus faecium/drug effects , Enterococcus faecium/genetics , Germany/epidemiology , Gram-Positive Bacterial Infections/epidemiology , Gram-Positive Bacterial Infections/microbiology , Humans , Infection Control/methods , Models, Theoretical , Phylogeny , Population Dynamics , Retrospective Studies , Vancomycin/pharmacology , Vancomycin-Resistant Enterococci/drug effects , Vancomycin-Resistant Enterococci/genetics , Vancomycin-Resistant Enterococci/physiologyABSTRACT
Vagococcus salmoninarum was identified as the causative agent of a chronic epizootic in broodstock "coaster" brook trout (Salvelinus fontinalis) at the Iron River National Fish Hatchery. The epizootic spanned more than a year, was unresponsive to multiple florfenicol treatments, and resulted in >50% mortality of the affected fish. The decision was made to cull the remaining fish during spawning, which presented an opportunity to more thoroughly examine V. salmoninarum sampling methods, organ tropism and vertical transmission. A newly developed qPCR targeting the pheS gene was used in concert with bacterial culture to show that V. salmoninarum indeed disproportionately affects females and has a tropism for female reproductive tissues. The study demonstrates that some female reproductive tissues (e.g. ovarian fluid, unfertilized eggs) are also an effective option for non-lethal detection. Despite the widespread presence of V. salmoninarum in ovarian fluid and on egg surfaces, we found no evidence of intra-ova transmission.
Subject(s)
Enterococcaceae/isolation & purification , Fish Diseases/epidemiology , Gram-Positive Bacterial Infections/veterinary , Polymerase Chain Reaction/veterinary , Trout , Animals , Aquaculture , Female , Fish Diseases/microbiology , Fish Diseases/transmission , Gram-Positive Bacterial Infections/epidemiology , Gram-Positive Bacterial Infections/microbiology , Gram-Positive Bacterial Infections/transmission , Male , Ovum/microbiology , Polymerase Chain Reaction/methods , Prevalence , Viral Tropism , Wisconsin/epidemiologyABSTRACT
Enterococcus faecium is a gut commensal of humans and animals but is also listed on the WHO global priority list of multidrug-resistant pathogens. Many of its antibiotic resistance traits reside on plasmids and have the potential to be disseminated by horizontal gene transfer. Here, we present the first comprehensive population-wide analysis of the pan-plasmidome of a clinically important bacterium, by whole-genome sequence analysis of 1,644 isolates from hospital, commensal, and animal sources of E. faecium Long-read sequencing on a selection of isolates resulted in the completion of 305 plasmids that exhibited high levels of sequence modularity. We further investigated the entirety of all plasmids of each isolate (plasmidome) using a combination of short-read sequencing and machine-learning classifiers. Clustering of the plasmid sequences unraveled different E. faecium populations with a clear association with hospitalized patient isolates, suggesting different optimal configurations of plasmids in the hospital environment. The characterization of these populations allowed us to identify common mechanisms of plasmid stabilization such as toxin-antitoxin systems and genes exclusively present in particular plasmidome populations exemplified by copper resistance, phosphotransferase systems, or bacteriocin genes potentially involved in niche adaptation. Based on the distribution of k-mer distances between isolates, we concluded that plasmidomes rather than chromosomes are most informative for source specificity of E. faeciumIMPORTANCEEnterococcus faecium is one of the most frequent nosocomial pathogens of hospital-acquired infections. E. faecium has gained resistance against most commonly available antibiotics, most notably, against ampicillin, gentamicin, and vancomycin, which renders infections difficult to treat. Many antibiotic resistance traits, in particular, vancomycin resistance, can be encoded in autonomous and extrachromosomal elements called plasmids. These sequences can be disseminated to other isolates by horizontal gene transfer and confer novel mechanisms to source specificity. In our study, we elucidated the total plasmid content, referred to as the plasmidome, of 1,644 E. faecium isolates by using short- and long-read whole-genome technologies with the combination of a machine-learning classifier. This was fundamental to investigate the full collection of plasmid sequences present in our collection (pan-plasmidome) and to observe the potential transfer of plasmid sequences between E. faecium hosts. We observed that E. faecium isolates from hospitalized patients carried a larger number of plasmid sequences compared to that from other sources, and they elucidated different configurations of plasmidome populations in the hospital environment. We assessed the contribution of different genomic components and observed that plasmid sequences have the highest contribution to source specificity. Our study suggests that E. faecium plasmids are regulated by complex ecological constraints rather than physical interaction between hosts.
Subject(s)
Cross Infection/microbiology , Enterococcus faecium/genetics , Enterococcus faecium/pathogenicity , Genome, Bacterial , Plasmids/genetics , Anti-Bacterial Agents/pharmacology , DNA Transposable Elements/genetics , Enterococcus faecium/drug effects , Gene Transfer, Horizontal , Genomics , Gram-Positive Bacterial Infections/microbiology , Gram-Positive Bacterial Infections/transmission , Hospitals , Humans , Phylogeny , Sequence Analysis, DNA , Whole Genome SequencingABSTRACT
BACKGROUND: Athletic training rooms have a high prevalence of bacteria, including multidrug-resistant organisms, increasing the risk for both local and systematic infections in athletes. There are limited data outlining formal protocols or standardized programs to reduce bacterial and viral burden in training rooms as a means of decreasing infection rate at the collegiate and high school levels. HYPOTHESIS: Adaptation of a hygiene protocol would lead to a reduction in bacterial and viral pathogen counts in athletic training rooms. STUDY DESIGN: Cohort study. LEVEL OF EVIDENCE: Level 3. METHODS: Two high school and 2 collegiate athletic training rooms were studied over the course of the 2017-2018 academic year. A 3-phase protocol, including introduction of disinfectant products followed by student-athlete and athletic trainer education, was implemented at the 4 schools. Multiple surfaces in the athletic training rooms were swabbed at 4 time points throughout the investigation. Bacterial and viral burden from swabs were analyzed for overall bacterial aerobic plate count (APC), bacterial adenosine triphosphate activity, influenza viral load, and multidrug-resistant organisms such as methicillin-resistant Staphylococcus aureus (MRSA) and vancomycin-resistant enterococcus (VRE). RESULTS: Overall bacterial load, as measured by APC, was reduced by 94.7% (95% CI, 72.6-99.0; P = 0.003) over the course of the investigation after protocol implementation. MRSA and VRE were found on 24% of surfaces prior to intervention and were reduced to 0% by the end of the study. Influenza was initially detected on 25% of surfaces, with no detection after intervention. No cases of athletic training room-acquired infections were reported during the study period. CONCLUSION: A uniform infection control protocol was effective in reducing bacterial and viral burden, including multidrug-resistant organisms, when implemented in the athletic training rooms of 2 high schools and 2 colleges. CLINICAL RELEVANCE: A standardized infection control protocol can be utilized in athletic training rooms to reduce bacterial and viral burden.
Subject(s)
Community-Acquired Infections/prevention & control , Disease Reservoirs/microbiology , Infection Control/methods , Schools , Community-Acquired Infections/transmission , Disinfectants/administration & dosage , Gram-Positive Bacterial Infections/prevention & control , Gram-Positive Bacterial Infections/transmission , Hand Disinfection , Health Education , Humans , Influenza, Human/prevention & control , Influenza, Human/transmission , Methicillin-Resistant Staphylococcus aureus/isolation & purification , Orthomyxoviridae/isolation & purification , Risk Reduction Behavior , Staphylococcal Infections/prevention & control , Staphylococcal Infections/transmission , Vancomycin-Resistant Enterococci/isolation & purificationABSTRACT
Background: Vancomycin-resistant enterococci (VRE) are a serious antimicrobial resistant threat in the healthcare setting. We assessed the cost-effectiveness of VRE screening and isolation for patients at high-risk for colonisation on a general medicine ward compared to no VRE screening and isolation from the healthcare payer perspective. Methods: We developed a microsimulation model using local data and VRE literature, to simulate a 20-bed general medicine ward at a tertiary-care hospital with up to 1000 admissions, approximating 1 year. Primary outcomes were accrued over the patient's lifetime, discounted at 1.5%, and included expected health outcomes (VRE colonisations, VRE infections, VRE-related bacteremia, and deaths subsequent to VRE infection), quality-adjusted life years (QALYs), healthcare costs, and incremental cost-effectiveness ratio (ICER). Probabilistic sensitivity analysis (PSA) and scenario analyses were conducted to assess parameter uncertainty. Results: In our base-case analysis, VRE screening and isolation prevented six healthcare-associated VRE colonisations per 1000 admissions (6/1000), 0.6/1000 VRE-related infections, 0.2/1000 VRE-related bacteremia, and 0.1/1000 deaths subsequent to VRE infection. VRE screening and isolation accrued 0.0142 incremental QALYs at an incremental cost of $112, affording an ICER of $7850 per QALY. VRE screening and isolation practice was more likely to be cost-effective (> 50%) at a cost-effectiveness threshold of $50,000/QALY. Stochasticity (randomness) had a significant impact on the cost-effectiveness. Conclusion: VRE screening and isolation can be cost-effective in majority of model simulations at commonly used cost-effectiveness thresholds, and is likely economically attractive in general medicine settings. Our findings strengthen the understanding of VRE prevention strategies and are of importance to hospital program planners and infection prevention and control.