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Rath A, Kieninger B, Caplunik-Pratsch A, Fritsch J, Mirzaliyeva N, Holzmann T, Bender JK, Werner G, Schneider-Brachert W. Concerning emergence of a new vancomycin-resistant Enterococcus faecium strain ST1299/CT1903/vanA at a tertiary university centre in South Germany. J Hosp Infect 2024; 143:25-32. [PMID: 37852539 DOI: 10.1016/j.jhin.2023.10.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 09/22/2023] [Accepted: 10/08/2023] [Indexed: 10/20/2023]
Abstract
BACKGROUND vanB-carrying vancomycin-resistant Enterococcus faecium (VREfm) of the sequence types 80 (ST80) and ST117 have dominated Germany in the past. In 2020, our hospital witnessed a sharp increase in the proportion of vanA-positive VREfm. AIM To attempt to understand these dynamics through whole-genome sequencing (WGS) and analysis of nosocomial transmissions. METHODS At our hospital, the first VREfm isolate per patient, treated during 2020, was analysed retrospectively using specific vanA/vanB PCR, WGS, multi-locus sequence typing (MLST), and core-genome (cg) MLST. Epidemiologic links between VRE-positive patients were assessed using hospital occupancy data. FINDINGS Isolates from 319 out of 356 VREfm patients were available for WGS, of which 181 (56.7%) fulfilled the ECDC definition for nosocomial transmission. The high load of nosocomial cases is reflected in the overall high clonality rate with only three dominating sequence (ST) and complex types (CT), respectively: the new emerging strain ST1299 (100% vanA, 77.4% CT1903), and the well-known ST80 (90.0% vanB, 81.0% CT1065) and ST117 (78.0% vanB, 65.0% CT71). The ST1299 isolates overall, and the subtype CT1903 in particular, showed high isolate clonality, which demonstrates impressively high spreading potential. Overall, 152 out of 319 isolates had an allelic cgMLST difference of ≤3 to another, including 91 (59.6%) ST1299. Occupancy data identified shared rooms (3.7%), shared departments (6.2%), and VRE-colonized prior room occupants (0.6%) within 30 days before diagnosis as solid epidemiological links. CONCLUSION A new emerging VREfm clone, ST1299/CT1903/vanA, dominated our institution in 2020 and has been an important driver of the increasing VREfm rates.
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Affiliation(s)
- A Rath
- Department of Infection Prevention and Infectious Diseases, University Hospital Regensburg, Regensburg, Germany.
| | - B Kieninger
- Department of Infection Prevention and Infectious Diseases, University Hospital Regensburg, Regensburg, Germany
| | - A Caplunik-Pratsch
- Department of Infection Prevention and Infectious Diseases, University Hospital Regensburg, Regensburg, Germany
| | - J Fritsch
- Department of Infection Prevention and Infectious Diseases, University Hospital Regensburg, Regensburg, Germany
| | - N Mirzaliyeva
- Department of Infection Prevention and Infectious Diseases, University Hospital Regensburg, Regensburg, Germany
| | - T Holzmann
- Department of Infection Prevention and Infectious Diseases, University Hospital Regensburg, Regensburg, Germany
| | - J K Bender
- Department of Infectious Diseases, Division of Nosocomial Pathogens and Antibiotic Resistances, Robert Koch Institute, Wernigerode, Germany
| | - G Werner
- Department of Infectious Diseases, Division of Nosocomial Pathogens and Antibiotic Resistances, Robert Koch Institute, Wernigerode, Germany
| | - W Schneider-Brachert
- Department of Infection Prevention and Infectious Diseases, University Hospital Regensburg, Regensburg, Germany
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2
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DuPont HL. The potential for development of clinically relevant microbial resistance to rifaximin-α: a narrative review. Clin Microbiol Rev 2023; 36:e0003923. [PMID: 37971270 PMCID: PMC10732030 DOI: 10.1128/cmr.00039-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2023] Open
Abstract
Rifaximin-α is a gut-targeted antibiotic indicated for numerous gastrointestinal and liver diseases. Its multifaceted mechanism of action goes beyond direct antimicrobial effects, including alterations in bacterial virulence, cytoprotective effects on host epithelial cells, improvement of impaired intestinal permeability, and reduction of proinflammatory cytokine expression via activation of the pregnane X receptor. Rifaximin-α is virtually non-absorbed, with low systemic drug levels contributing to its excellent safety profile. While there are high concentrations of drug in the colon, low water solubility leads to low colonic drug bioavailability, protecting the gut microbiome. Rifaximin-α appears to be more active in the bile-rich small bowel. Its important biologic effects are largely at sub-inhibitory concentration. Although in vitro testing of clinical isolates from rifaximin recipients has revealed rifaximin-resistant strains in some studies, the risk of emergent rifaximin-α resistance appears to be lower than for many other antibiotics. Rifaximin-α has been used for many years for traveler's diarrhea with no apparent increase in resistance levels in causative pathogens. Further, rifaximin-α retains its efficacy after long-term and recurrent usage in chronic gastrointestinal disorders. There are numerous reasons why the risk of microbial resistance to rifaximin-α may be lower than that for other agents, including low intestinal bioavailability in the aqueous colon, the mechanisms of action of rifaximin-α not requiring inhibitory concentrations of drug, and the low risk of cross transmission of rifaximin-α resistance between bacterial species. Reported emergence of vancomycin-resistant Enterococcus in liver-disease patients maintained on rifaximin needs to be actively studied. Further studies are required to assess the possible correlation between in vitro resistance and rifaximin-α efficacy.
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Affiliation(s)
- Herbert L. DuPont
- School of Public Health and McGovern Medical School, Baylor College of Medicine, Kelsey Research Foundation, University of Texas Health Science Center Houston, Houston, Texas, USA
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3
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Yoon YK, Moon C, Kim J, Heo ST, Lee MS, Lee S, Kwon KT, Kim SW. Korean Guidelines for Use of Antibiotics for Intra-abdominal Infections in Adults. Infect Chemother 2022; 54:812-853. [PMID: 36596690 PMCID: PMC9840951 DOI: 10.3947/ic.2022.0156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 12/12/2022] [Indexed: 12/24/2022] Open
Abstract
The guidelines are intended to provide practical information for the correct use of antibiotics for intra-abdominal infections in Korea. With the aim of realizing evidence-based treatment, these guidelines for the use of antibiotics were written to help clinicians find answers to key clinical questions that arise in the course of patient care, using the latest research results based on systematic literature review. The guidelines were prepared in consideration of the data on the causative pathogens of intra-abdominal infections in Korea, the antibiotic susceptibility of the causative pathogens, and the antibiotics available in Korea.
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Affiliation(s)
- Young Kyung Yoon
- Division of Infectious Diseases, Department of Internal Medicine, Korea University College of Medicine, Seoul, Korea.,Korean Society for Antimicrobial Therapy, Seoul, Korea
| | - Chisook Moon
- Korean Society for Antimicrobial Therapy, Seoul, Korea.,Division of Infectious Diseases, Department of Internal Medicine, Inje University College of Medicine, Busan, Korea
| | - Jieun Kim
- Department of Internal Medicine, Hanyang University College of Medicine, Seoul, Korea.,Korean Society of Infectious Diseases, Seoul, Korea
| | - Sang Taek Heo
- Korean Society of Infectious Diseases, Seoul, Korea.,Division of Infectious Diseases, Department of Internal Medicine, Jeju National University College of Medicine, Jeju, Korea
| | - Mi Suk Lee
- Korean Society of Infectious Diseases, Seoul, Korea.,Department of Internal Medicine, Kyung Hee University College of Medicine, Seoul, Korea
| | - Shinwon Lee
- Korean Society of Infectious Diseases, Seoul, Korea.,Department of Internal Medicine, Pusan National University School of Medicine and Medical Research Institute, Pusan National University Hospital, Busan, Korea
| | - Ki-Tae Kwon
- Korean Society for Antimicrobial Therapy, Seoul, Korea.,Division of Infectious Diseases, Department of Internal Medicine, Kyungpook National University Chilgok Hospital, School of Medicine, Kyungpook National University, Daegu, Korea
| | - Shin-Woo Kim
- Korean Society for Antimicrobial Therapy, Seoul, Korea.,Department of Internal Medicine, School of Medicine, Kyungpook National University, Daegu, Korea
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4
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Ratnasekera IU, Johnson A, Powell EE, Henderson A, Irvine KM, Valery PC. Epidemiology of ascites fluid infections in patients with cirrhosis in Queensland, Australia from 2008 to 2017: A population-based study. Medicine (Baltimore) 2022; 101:e29217. [PMID: 35608422 PMCID: PMC9276389 DOI: 10.1097/md.0000000000029217] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Accepted: 03/14/2022] [Indexed: 01/04/2023] Open
Abstract
Spontaneous bacterial peritonitis (SBP), a common infection in patients with cirrhosis and ascites, is associated with high morbidity and mortality. The aim of this study was to investigate changes in the epidemiology of ascites fluid infections over time in an Australian population, including patient demographics, trends in mortality, length of hospital stay and the nature and antibiotic resistance profile of causative organisms.An observational descriptive population-based epidemiological study of patients with cirrhosis admitted to public hospitals in Queensland during 2008-2017 was performed, linking demographic/clinical and microbiology data.Among 103,165 hospital admissions of patients with cirrhosis, ascites was present in 16,550 and in 60% (9977) a sample of ascitic fluid was tested. SBP was diagnosed in 770 admissions (neutrophil count >250/ml) and bacterascites in 552 (neutrophil count <250/ml with positive culture). The number of admissions with an ascites fluid infection increased by 76% from 2008 to 2017, paralleling an 84% increase in cirrhosis admissions over the same timeframe. Patients with SBP had a longer hospital stay (median 15.7 vs 8.3 days for patients without SBP, P < .001) and higher in-hospital mortality, although this decreased from 39.5% in 2008 to 2010 to 24.8% in 2015 to 2017 (P < .001). Common Gram-positive isolates included coagulase negative staphylococci (37.9%), viridans group streptococci (12.1%), and Staphylococcus aureus (7.2%). Common Gram-negative isolates included Escherichia coli (13.0%), Klebsiella pneumoniae (3.1%) and Enterobacter cloacae (2.6%). The prevalence of resistance to any tested antibiotic was <10%.SBP remains associated with high in-hospital mortality and long hospital stay. Typical skin and bowel pathogens were common, therefore, empirical antibiotic therapy should target these pathogens. This study provides valuable evidence informing infection management strategies in this vulnerable patient population.
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Affiliation(s)
| | - Amy Johnson
- Department of Gastroenterology and Hepatology, Princess Alexandra Hospital, Brisbane, QLD, Australia
- Centre for Liver Disease Research, Faculty of Medicine, the University of Queensland, Brisbane, QLD, Australia
| | - Elizabeth E. Powell
- Department of Gastroenterology and Hepatology, Princess Alexandra Hospital, Brisbane, QLD, Australia
- Centre for Liver Disease Research, Faculty of Medicine, the University of Queensland, Brisbane, QLD, Australia
| | - Andrew Henderson
- Infection Management Services, Princess Alexandra Hospital, Brisbane, Australia
- University of Queensland Centre for Clinical Research, Herston, Brisbane, Australia
| | - Katharine M. Irvine
- Mater Research Institute, the University of Queensland, Brisbane, QLD, Australia
- Centre for Liver Disease Research, Faculty of Medicine, the University of Queensland, Brisbane, QLD, Australia
| | - Patricia C. Valery
- Centre for Liver Disease Research, Faculty of Medicine, the University of Queensland, Brisbane, QLD, Australia
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
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5
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Schöneweck F, Schmitz RPH, Rißner F, Scherag A, Löffler B, Pletz MW, Weis S, Brunkhorst FM, Hagel S. The epidemiology of bloodstream infections and antimicrobial susceptibility patterns in Thuringia, Germany: a five-year prospective, state-wide surveillance study (AlertsNet). Antimicrob Resist Infect Control 2021; 10:132. [PMID: 34493334 PMCID: PMC8424790 DOI: 10.1186/s13756-021-00997-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 08/21/2021] [Indexed: 11/24/2022] Open
Abstract
Background Monitoring pathogens of bloodstream infections (BSI) and their antibiotic susceptibility is important to guide empiric antibiotic treatment strategies and prevention programs. This study assessed the epidemiology of BSI and antibiotic resistance patterns at the German Federal State of Thuringia longitudinally. Methods A surveillance network consisting of 26 hospitals was established to monitor BSIs from 01/2015 to 12/2019. All blood culture results, without restriction of age of patients, of the participating hospitals were reported by the respective microbiological laboratory. A single detection of obligate pathogens and a repeated detection of coagulase-negative staphylococci, Bacillus spp., Corynebacterium spp., Micrococcus spp. and Propionibacterium spp., within 96 h were regarded as a relevant positive blood culture. If one of the aforementioned non-obligate pathogens has been detected only once within 96 h, contamination has been assumed. Logistic regression models were applied to analyse the relationship between resistance, year of BSI and hospital size. Generalized estimating equations were used to address potential clustering. Results A total of 343,284 blood cultures (BC) of 82,527 patients were recorded. Overall, 2.8% (n = 9571) of all BCs were classified as contaminated. At least one relevant pathogen was identified in 13.2% (n = 45,346) of BCs. Escherichia coli (25.4%) was the most commonly detected pathogen, followed by Staphylococcus aureus (15.2%), Staphylococcus epidermidis (8.1%) and Klebsiella pneumoniae (4.6%). In S. aureus, we observed a decline of methicillin resistance (MRSA) from 10.4% in 2015 to 2.5% in 2019 (p < 0.001). The rate of vancomycin resistance in Enterococcus faecium (VRE) has increased from 16.7% in 2015 to 26.9% in 2019 (p < 0.001), with a peak in 2018 (42.5%). In addition, we observed an increase of Cefotaxime (3GC) resistance in E. coli from 10.7% in 2015 to 14.5% in 2019 (p = 0.007) whereas 3GC resistance in K. pneumoniae was stable (2015: 9.9%; 2019: 7.4%, p = 0.35). Carbapenem resistance was less than 1% for both pathogens. These patterns were robustly observed across sensitivity analyses. Conclusions We observed evidence for a decline in MRSA, an increase in VRE and a very low rate of carbapenem resistance in gram-negative bacteria. 3GC resistance in E. coli increased constantly over time. Supplementary Information The online version contains supplementary material available at 10.1186/s13756-021-00997-6.
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Affiliation(s)
- Franziska Schöneweck
- Center for Sepsis Control and Care (CSCC), Jena University Hospital - Friedrich Schiller University Jena, Jena, Germany.,Research Group Clinical Epidemiology, CSCC, Jena University Hospital - Friedrich Schiller University Jena, Jena, Germany
| | - Roland P H Schmitz
- Center for Sepsis Control and Care (CSCC), Jena University Hospital - Friedrich Schiller University Jena, Jena, Germany.,Center for Clinical Studies Jena (ZKS), Jena University Hospital - Friedrich Schiller University Jena, Jena, Germany
| | - Florian Rißner
- Center for Clinical Studies Jena (ZKS), Jena University Hospital - Friedrich Schiller University Jena, Jena, Germany
| | - André Scherag
- Center for Sepsis Control and Care (CSCC), Jena University Hospital - Friedrich Schiller University Jena, Jena, Germany.,Research Group Clinical Epidemiology, CSCC, Jena University Hospital - Friedrich Schiller University Jena, Jena, Germany.,Institute of Medical Statistics, Computer and Data Sciences, Jena University Hospital - Friedrich Schiller University Jena, Jena, Germany
| | - Bettina Löffler
- Center for Sepsis Control and Care (CSCC), Jena University Hospital - Friedrich Schiller University Jena, Jena, Germany.,Institute of Medical Microbiology, Jena University Hospital - Friedrich Schiller University Jena, Jena, Germany
| | - Mathias W Pletz
- Institute for Infectious Diseases and Infection Control, Jena University Hospital - Friedrich Schiller University Jena, Am Klinikum 1, 07747, Jena, Germany
| | - Sebastian Weis
- Center for Sepsis Control and Care (CSCC), Jena University Hospital - Friedrich Schiller University Jena, Jena, Germany.,Institute for Infectious Diseases and Infection Control, Jena University Hospital - Friedrich Schiller University Jena, Am Klinikum 1, 07747, Jena, Germany.,Department of Anesthesiology and Intensive Care Therapy, Jena University Hospital - Friedrich Schiller University Jena, Jena, Germany
| | - Frank M Brunkhorst
- Center for Clinical Studies Jena (ZKS), Jena University Hospital - Friedrich Schiller University Jena, Jena, Germany
| | - Stefan Hagel
- Institute for Infectious Diseases and Infection Control, Jena University Hospital - Friedrich Schiller University Jena, Am Klinikum 1, 07747, Jena, Germany.
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6
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Pimentel R, Leitão J, Gregório C, Santos L, Carvalho A, Figueiredo P. Spontaneous Bacterial Peritonitis in Cirrhotic Patients: A Shift in the Microbial Pattern? A Retrospective Analysis. GE-PORTUGUESE JOURNAL OF GASTROENTEROLOGY 2021; 29:256-266. [PMID: 35979243 PMCID: PMC9274822 DOI: 10.1159/000518585] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 07/08/2021] [Indexed: 11/19/2022]
Abstract
<b><i>Introduction:</i></b> Over the last decade, a shift in the spontaneous bacterial peritonitis (SBP) microbial pattern toward an increasing incidence of gram-positive and multidrug-resistant (MDR) bacteria has been reported. Systematic surveillance of the local microbiological scenario and antibiotic resistance is crucial to SBP treatment success. The main objective of this study was to evaluate the microbiological profile and bacterial resistance of SBP pathogens in a Portuguese cohort to allow selection of the most appropriate empirical antibiotics. <b><i>Methods:</i></b> This is a single-center retrospective study including 63 adult cirrhotic patients with culture-positive SBP. Patients were identified using a hospital general diagnostic database and searching for all SBP events (neutrophil count in ascitic fluid ≥250/mm<sup>3</sup>) from January 1, 2012, to December 31, 2017. Patients were excluded if they had culture-negative SBP, secondary peritonitis, peritoneal dialysis, a liver transplant, or immunodeficiency. The site of SBP acquisition was classified as nosocomial if it was diagnosed 48 h or longer after hospitalization or as nonnosocomial if it was diagnosed within the first 48 h. MDR bacteria were those with an acquired resistance to at least 1 agent in 3 or more antimicrobial categories. All statistical analyses were carried out using IBM SPSS Statistics software version 22 (IBM, New York, USA). <b><i>Results:</i></b> The study cohort comprised 53 (84.1%) men. The mean age of the patients was 60.6 ± 11.2 years. Alcohol was the most common etiology (88.9%) and most patients had advanced liver cirrhosis (87.1%, Child C). Gram-negative bacteria were slightly more frequent than gram-positive bacteria (56.9 vs. 43.1%). <i>Escherichia coli</i> was the most common pathogen (33.8%). Nineteen (31.7%) bacteria were classified as MDR. Resistance to third-generation cephalosporins, quinolones, piperacillin-tazobactam, and carbapenems was found in 31.7, 35, 26.7, and 18.3% of the cases, respectively. The rates of gram-positive bacteria were similar between nosocomial and nonnosocomial episodes (45 vs. 42.2%; <i>p</i> = 0.835). MDR bacteria were more common in the nosocomial group (50 vs. 23.8%; <i>p</i> = 0.046). Resistance to third-generation cephalosporins (50 vs. 23.8%; <i>p</i> = 0.046), piperacillin-tazobactam (44.4 vs. 19.1%; <i>p</i> = 0.041), and carbapenems (33.3 vs. 11.9%; <i>p</i> = 0.049) occurred more frequently in nosocomial episodes. Resistance to first-line antibiotic occurred in 29.3% of the patients, being more common in the nosocomial group (44.4 vs. 22.5%; <i>p</i> = 0.089). <b><i>Conclusion:</i></b> Although gram-negative bacteria remain the most common causative microorganisms, our results emphasize the shift in SBP microbiological etiology, as almost half of the isolated microorganisms were gram positive. The emergence of bacteria resistant to traditionally recommended empirical antibiotics underlines the importance of basing this choice on local flora and antibiotic susceptibility data, allowing a more rational and successful use of antibiotics.
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Affiliation(s)
- Raquel Pimentel
- Department of Gastroenterology, Centro Hospitalar e Universitário de Coimbra, Coimbra, Portugal
- *Raquel Pimentel,
| | - Jorge Leitão
- Department of Internal Medicine, Centro Hospitalar e Universitário de Coimbra, Coimbra, Portugal
- Faculty of Medicine, University of Coimbra, Coimbra, Portugal
| | - Carlos Gregório
- Department of Gastroenterology, Centro Hospitalar e Universitário de Coimbra, Coimbra, Portugal
| | - Lélita Santos
- Department of Internal Medicine, Centro Hospitalar e Universitário de Coimbra, Coimbra, Portugal
- Faculty of Medicine, University of Coimbra, Coimbra, Portugal
| | - Armando Carvalho
- Department of Internal Medicine, Centro Hospitalar e Universitário de Coimbra, Coimbra, Portugal
- Faculty of Medicine, University of Coimbra, Coimbra, Portugal
| | - Pedro Figueiredo
- Department of Gastroenterology, Centro Hospitalar e Universitário de Coimbra, Coimbra, Portugal
- Faculty of Medicine, University of Coimbra, Coimbra, Portugal
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7
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Shamsaddini A, Gillevet PM, Acharya C, Fagan A, Gavis E, Sikaroodi M, McGeorge S, Khoruts A, Albhaisi S, Fuchs M, Sterling RK, Bajaj JS. Impact of Antibiotic Resistance Genes in Gut Microbiome of Patients With Cirrhosis. Gastroenterology 2021; 161:508-521.e7. [PMID: 33857456 PMCID: PMC9069394 DOI: 10.1053/j.gastro.2021.04.013] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 04/02/2021] [Accepted: 04/05/2021] [Indexed: 02/07/2023]
Abstract
BACKGROUND AND AIMS Cirrhosis is associated with changes in intestinal microbiota that can lead to hepatic encephalopathy (HE) and infections, especially with antibiotic-resistant organisms. However, the impact of gut microbial antibiotic resistance gene (ARG) burden on clinical outcomes is unclear. The aims of the study were to determine the impact of ARGs in cirrhosis-related gut metagenome on outcomes and disease progression, study the effect of rifaximin on ARG burden, and compare ARGs in cirrhosis with chronic kidney disease (CKD) and diabetes. METHODS In outpatients with cirrhosis who underwent metagenomics, we evaluated change in ARG abundances with progression and their multivariable impact on 90-day hospitalizations and deaths over 1 year. We also studied ARGs pre- and 8 weeks post-rifaximin in patients with compensated cirrhosis in an open-label trial. Finally, ARGs from CKD and diabetes studies were compared with cirrhosis on machine learning. RESULTS A total of 163 patients with cirrhosis (43 compensated, 20 ascites-only, 30 HE-only, 70 both) and 40 controls were included. ARG abundances were higher in cirrhosis versus controls and worsened with advancing cirrhosis severity; 44 patients were hospitalized and 14 died. ARG abundances were associated with hospitalizations and mortality while controlling for cirrhosis complications, medications, and demographics. Rifaximin trial: ARG abundance patterns were minimally affected in 19 patients post-rifaximin. CKD/diabetes comparison: ARG abundance patterns in cirrhosis are distinguishable on machine learning and include more gram-positive ARGs. CONCLUSIONS Cirrhosis is associated with high gut microbial ARG gene burden compared with controls, which worsens with disease progression and may be different from CKD and diabetes. ARGs are not affected by rifaximin and are associated with hospitalizations and death.
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Affiliation(s)
| | | | - Chathur Acharya
- Division of Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University and Central Virginia Veterans Healthcare System, Richmond, Virginia
| | - Andrew Fagan
- Division of Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University and Central Virginia Veterans Healthcare System, Richmond, Virginia
| | - Edith Gavis
- Division of Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University and Central Virginia Veterans Healthcare System, Richmond, Virginia
| | | | - Sara McGeorge
- Division of Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University and Central Virginia Veterans Healthcare System, Richmond, Virginia
| | - Alexander Khoruts
- Department of Internal Medicine, Virginia Commonwealth University, Richmond, Virginia
| | - Somaya Albhaisi
- Division of Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University and Central Virginia Veterans Healthcare System, Richmond, Virginia
| | - Michael Fuchs
- Division of Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University and Central Virginia Veterans Healthcare System, Richmond, Virginia
| | - Richard K. Sterling
- Division of Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University and Central Virginia Veterans Healthcare System, Richmond, Virginia
| | - Jasmohan S. Bajaj
- Division of Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University and Central Virginia Veterans Healthcare System, Richmond, Virginia
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8
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Wilson GM, Suda KJ, Fitzpatrick MA, Bartle B, Pfeiffer CD, Jones M, Rubin MA, Perencevich E, Evans M, Evans CT. Risk Factors Associated with Carbapenemase Producing Carbapenem-Resistant Enterobacteriaceae (CP-CRE) Positive Cultures in a Cohort of U.S. Veterans. Clin Infect Dis 2021; 73:1370-1378. [PMID: 33973631 DOI: 10.1093/cid/ciab415] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Indexed: 12/30/2022] Open
Abstract
INTRODUCTION Carbapenem-resistant Enterobacterales (CRE) cause approximately 13,100 infections with 8% mortality in the United States annually. The subset of carbapenemase-producing CRE (CP-CRE) infections have much higher mortality rates (40% -50%). There has been little research on characteristics unique to CP-CRE. The goal of this study was to assess differences between those with nonCP-CRE and CP-CRE cultures in U.S. Veterans. METHODS A retrospective cohort of Veterans with CRE cultures from 2013-2018 and their demographic, medical, and facility level covariates were collected. Clustered multiple logistic regression models were used to assess independent factors associated with CP-CRE. RESULTS 3,096 unique patients with cultures positive for either nonCP-CRE or CP-CRE were included. Being African American (Odds Ratio (OR)=1.44 (95% Confidence Interval (CI) 1.15,1.80), diagnosis in 2017 (OR=3.11 (95% CI 2.13,4.54)) or 2018 (OR=3.93 (95%CI 2.64,5.84)), congestive heart failure (OR=1.35 (95%CI 1.11,1.64)), and gastroesophageal reflux disease (OR=1.39 (95%CI 1.03,1.87)) were associated with CP-CRE cultures. 752 (24.3%) patients had no known antibiotic exposure in the year before culture; these individuals had a comparatively increased frequency of prolonged PPI use (17.3% vs 5.6%). DISCUSSION Among a cohort of patients with CRE, African Americans, individuals with congestive heart failure, and patients with gastroesophageal reflux disease had greater odds of having a CP-CRE culture. Roughly one in four patients with CP-CRE had no known antibiotic exposure in the year before their positive culture.
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Affiliation(s)
- Geneva M Wilson
- Center of Innovation for Complex Chronic Healthcare (CINCCH), Hines Jr. Veterans Affairs Hospital, Hines, IL,USA
| | - Katie J Suda
- Center for Health Equity Research and Promotion, VA Pittsburgh Heath Care System, Pittsburgh, PA, USA.,University of Pittsburgh School of Medicine, Department of Medicine, Pittsburgh, PA, USA
| | - Margaret A Fitzpatrick
- Center of Innovation for Complex Chronic Healthcare (CINCCH), Hines Jr. Veterans Affairs Hospital, Hines, IL,USA.,Department of Medicine, Division of Infectious Diseases, Loyola University Chicago Stritch School of Medicine, Maywood, IL, USA
| | - Brian Bartle
- Center of Innovation for Complex Chronic Healthcare (CINCCH), Hines Jr. Veterans Affairs Hospital, Hines, IL,USA
| | - Christopher D Pfeiffer
- Department of Veterans Affairs, Portland VA Healthcare System, Portland, OR, USA.,Department of Medicine, Division of Infectious Diseases, Oregon Health Science University, Portland, OR, USA
| | - Makoto Jones
- Department of Veterans Affairs, VA Salt Lake City Healthcare System, Salt Lake City, UT, USA.,Department of Medicine, Division of Epidemiology, University of Utah, Salt Lake City, UT, USA
| | - Michael A Rubin
- Department of Veterans Affairs, Center for Access & Delivery Research and Evaluation, Iowa City VA Health Care System, Iowa City, IA, USA.,Department of Internal Medicine, University of Iowa Carver College of Medicine, Iowa City, IA, USA
| | - Eli Perencevich
- Department of Veterans Affairs, Center for Access & Delivery Research and Evaluation, Iowa City VA Health Care System, Iowa City, IA, USA.,Department of Internal Medicine, University of Iowa Carver College of Medicine, Iowa City, IA, USA
| | - Martin Evans
- Department of Veterans Affairs, Lexington VA Medical Center, Lexington, KY, USA
| | - Charlesnika T Evans
- Center of Innovation for Complex Chronic Healthcare (CINCCH), Hines Jr. Veterans Affairs Hospital, Hines, IL,USA.,Department of Preventive Medicine, Center for Health Services and Outcomes Research, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
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Bajaj JS, Shamsaddini A, Fagan A, Sterling RK, Gavis E, Khoruts A, Fuchs M, Lee H, Sikaroodi M, Gillevet PM. Fecal Microbiota Transplant in Cirrhosis Reduces Gut Microbial Antibiotic Resistance Genes: Analysis of Two Trials. Hepatol Commun 2021; 5:258-271. [PMID: 33553973 PMCID: PMC7850310 DOI: 10.1002/hep4.1639] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 10/21/2020] [Accepted: 10/22/2020] [Indexed: 02/06/2023] Open
Abstract
Antibiotic resistance leads to poor outcomes in cirrhosis. Fecal microbiota transplant (FMT) is associated with reduction in antibiotic resistance gene (ARG) burden in patients without cirrhosis; however, the impact in cirrhosis is unclear. We aimed to study the effect of capsule and enema FMT on ARG abundance in fecal samples, which were collected during two published FMT trials in patients with cirrhosis on rifaximin, lactulose, and proton pump inhibitors. ARGs were identified using metagenomics and mapped against the Comprehensive Antibiotic Resistance Database. Changes in ARG abundance were studied within/between groups. The capsule FMT trial involved a one-time FMT or placebo capsule administration with stool collection at baseline and week 4 postintervention. Antibiotics+enema FMT included preprocedure antibiotics followed by FMT enema versus standard-of-care (SOC). Stool was collected at baseline, postantibiotics, and day 7/15 postintervention. Both trials included 20 patients each. There was no safety/infection signal linked to FMT. In the capsule trial, beta-lactamase (OXY/LEN) expression decreased post-FMT versus baseline. Compared to placebo, patients who were post-FMT had lower abundance of vancomycin (VanH), beta-lactamase (ACT), and rifamycin ARGs; the latter was associated with cognitive improvement. No changes were seen within patients treated with placebo. In the antibiotics+enema trial for postantibiotics at day 7 versus baseline, there was an increase in vancomycin and beta-lactamase ARGs, which decreased at day 15. However, quinolone resistance increased at day 15 versus baseline. Between SOC and FMT, day 7 had largely lower ARG (CfxA beta-lactamase, VanW, and VanX) that continued at day 15 (cepA beta-lactamase, VanW). No changes were seen within the SOC group. Conclusion: Despite differences in routes of administration and preintervention antibiotics, we found that ARG abundance is largely reduced after FMT compared to pre-FMT baseline and non-FMT groups in decompensated cirrhosis.
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Affiliation(s)
- Jasmohan S Bajaj
- Gastroenterology, Hepatology, and NutritionVirginia Commonwealth University and Central Virginia Veterans Healthcare SystemRichmondVAUSA
| | | | - Andrew Fagan
- Gastroenterology, Hepatology, and NutritionVirginia Commonwealth University and Central Virginia Veterans Healthcare SystemRichmondVAUSA
| | - Richard K Sterling
- Gastroenterology, Hepatology, and NutritionVirginia Commonwealth University and Central Virginia Veterans Healthcare SystemRichmondVAUSA
| | - Edith Gavis
- Gastroenterology, Hepatology, and NutritionVirginia Commonwealth University and Central Virginia Veterans Healthcare SystemRichmondVAUSA
| | - Alexander Khoruts
- Gastroenterology, Hepatology, and NutritionBiotechnology Institute University of MinnesotaMinneapolisMNUSA
| | - Michael Fuchs
- Gastroenterology, Hepatology, and NutritionVirginia Commonwealth University and Central Virginia Veterans Healthcare SystemRichmondVAUSA
| | - Hannah Lee
- Gastroenterology, Hepatology, and NutritionVirginia Commonwealth University and Central Virginia Veterans Healthcare SystemRichmondVAUSA
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Vancomycin-Resistant Enterococci (VRE) in Nigeria: The First Systematic Review and Meta-Analysis. Antibiotics (Basel) 2020; 9:antibiotics9090565. [PMID: 32882963 PMCID: PMC7558171 DOI: 10.3390/antibiotics9090565] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 08/23/2020] [Accepted: 08/26/2020] [Indexed: 12/15/2022] Open
Abstract
Vancomycin-Resistant Enterococci (VRE) are on the rise worldwide. Here, we report the first prevalence of VRE in Nigeria using systematic review and meta-analysis. International databases MedLib, PubMed, International Scientific Indexing (ISI), Web of Science, Scopus, Google Scholar, and African journals online (AJOL) were searched. Information was extracted by two independent reviewers, and results were reviewed by the third. Two reviewers independently assessed the study quality using the Preferred Reporting Items for Systematic Reviews and Meta-Analysis (PRISMA) checklist. OpenMeta analyst was used. The random effect was used, and publication bias was assessed using a funnel plot. Between-study heterogeneity was assessed, and the sources were analysed using the leave-one-out meta-analysis, subgroup analysis, and meta-regression. Nineteen studies met the eligibility criteria and were added to the final meta-analysis, and the study period was from 2009–2018. Of the 2552 isolates tested, 349 were VRE, and E. faecalis was reported the most. The pooled prevalence of VRE in Nigeria was estimated at 25.3% (95% CI; 19.8–30.8%; I2 = 96.26%; p < 0.001). Between-study variability was high (t2 = 0.011; heterogeneity I2 = 96.26% with heterogeneity chi-square (Q) = 480.667, degrees of freedom (df) = 18, and p = 0.001). The funnel plot showed no publication bias, and the leave-one-out forest plot did not affect the pooled prevalence. The South-East region had a moderate heterogeneity though not significant (I2 = 51.15%, p = 0.129). Meta-regression showed that all the variables listed contributed to the heterogeneity except for the animal isolate source (p = 0.188) and studies that were done in 2013 (p = 0.219). Adherence to proper and accurate antimicrobial usage, comprehensive testing, and continuous surveillance of VRE are required.
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Melese A, Genet C, Andualem T. Prevalence of Vancomycin resistant enterococci (VRE) in Ethiopia: a systematic review and meta-analysis. BMC Infect Dis 2020; 20:124. [PMID: 32046668 PMCID: PMC7014939 DOI: 10.1186/s12879-020-4833-2] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Accepted: 01/28/2020] [Indexed: 12/18/2022] Open
Abstract
Background The emergence of Vancomycin resistant enterococci (VRE) poses a major public health problem since it was first reported. Although the rising rates of VRE infections are being reported elsewhere in the worldwide; there is limited national pooled data in Ethiopia. Therefore, this study was aimed to estimate the pooled prevalence of VRE and antimicrobial resistance profiles of enterococci in Ethiopia. Methods Literature search was done at PubMed, EMBASE, Google scholar, African Journals online (AJOL) and Addis Ababa University repository following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guideline. Both published and unpublished studies reporting the prevalence of VRE until June 30, 2019 were included. Data were extracted using Microsoft Excel and copied to Comprehensive Meta-analysis (CMA 2.0) for analysis. Pooled estimate of VRE was computed using the random effects model and the 95% CIs. The level of heterogeneity was assessed using Cochran’s Q and I2 tests. Publication bias was checked by visual inspection of funnel plots and Begg’s and/or Egger’s test. Results Twenty studies fulfilled the eligibility criteria and found with relevant data. A total of 831 enterococci and 71 VRE isolates were included in the analysis. The pooled prevalence of VRE was 14.8% (95% CI; 8.7–24.3; I2 = 74.05%; P < 0.001). Compared to vancomycin resistance, enterococci had higher rate of resistance to Penicillin (60.7%), Amoxicillin (56.5%), Doxycycline (55.1%) and Tetracycline (53.7%). Relatively low rate of resistance was found for Daptomycin and Linezolid with a pooled estimate of 3.2% (95% CI, 0.5–19.7%) and 9.9% (95% CI, 2.8–29.0%); respectively. The overall pooled multidrug resistance (MDR) rate of enterococci was 60.0% (95% CI, 42.9–75.0%). Conclusion The prevalence of VRE and drug resistant enterococci are on the rise in Ethiopia. Enterococcal isolates showed resistance to one or more of the commonly prescribed drugs in different or the same drug lines. Multidrug resistant (MDR) enterococci were also found. Although the rates were low, the emergence of resistance to Daptomycin and Linezolid is an alarm for searching new ways for the treatment and control of VRE infections. Adherence to antimicrobial stewardship, comprehensive testing and ongoing monitoring of VRE infections in the health care settings are required.
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Affiliation(s)
- Addisu Melese
- Department of Medical Laboratory Science, College of Medicine and Health Sciences, Bahir Dar University, Bahir Dar, Ethiopia.
| | - Chalachew Genet
- Department of Medical Laboratory Science, College of Medicine and Health Sciences, Bahir Dar University, Bahir Dar, Ethiopia
| | - Tesfaye Andualem
- Department of Medical Laboratory Science, College of Health Sciences, Debre Tabor University, Debre Tabor, Ethiopia
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