Probabilistic transmission models incorporating sequencing data for healthcare-associated Clostridioides difficile outperform heuristic rules and identify strain-specific differences in transmission

Fitting stochastic transmission models to electronic patient data can offer detailed insights into the transmission of healthcare-associated infections and improve infection control. Pathogen whole-genome sequencing may improve the precision of model inferences, but computational constraints have limited modelling applications predominantly to small datasets and specific outbreaks, whereas large-scale sequencing studies have mostly relied on simple rules for identifying/excluding plausible transmission. We present a novel approach for integrating detailed epidemiological data on patient contact networks in hospitals with large-scale pathogen sequencing data. We apply our approach to study Clostridioides difficile transmission using a dataset of 1223 infections in Oxfordshire, UK, 2007–2011. 262 (21% [95% credibility interval 20–22%]) infections were estimated to have been acquired from another known case. There was heterogeneity by sequence type (ST) in the proportion of cases acquired from another case with the highest rates in ST1 (ribotype-027), ST42 (ribotype-106) and ST3 (ribotype-001). These same STs also had higher rates of transmission mediated via environmental contamination/spores persisting after patient discharge/recovery; for ST1 these persisted longer than for most other STs except ST3 and ST42. We also identified variation in transmission between hospitals, medical specialties and over time; by 2011 nearly all transmission from known cases had ceased in our hospitals. Our findings support previous work suggesting only a minority of C. difficile infections are acquired from known cases but highlight a greater role for environmental contamination than previously thought. Our approach is applicable to other healthcare-associated infections. Our findings have important implications for effective control of C. difficile.

Download Full-text

Infection preventionist staffing levels and rates of 10 types of healthcare-associated infections: A 9-year ambidirectional observation

Infection Control and Hospital Epidemiology ◽

10.1017/ice.2021.507 ◽

2022 ◽

pp. 1-6

Author(s):

Robert J. Clifford ◽

Donna Newhart ◽

Maryrose R. Laguio-Vila ◽

Jennifer L. Gutowski ◽

Melissa Z. Bronstein ◽

...

Keyword(s):

Control Charts ◽

Bloodstream Infections ◽

Central Line ◽

Healthcare Associated Infections ◽

Full Time ◽

Staffing Levels ◽

Clostridioides Difficile ◽

Carbapenem Resistant ◽

Healthcare Associated ◽

Carbapenem Resistant Enterobacteriaceae

Abstract Objective: To quantitatively evaluate relationships between infection preventionists (IPs) staffing levels, nursing hours, and rates of 10 types of healthcare-associated infections (HAIs). Design and setting: An ambidirectional observation in a 528-bed teaching hospital. Patients: All inpatients from July 1, 2012, to February 1, 2021. Methods: Standardized US National Health Safety Network (NHSN) definitions were used for HAIs. Staffing levels were measured in full-time equivalents (FTE) for IPs and total monthly hours worked for nurses. A time-trend analysis using control charts, t tests, Poisson tests, and regression analysis was performed using Minitab and R computing programs on rates and standardized infection ratios (SIRs) of 10 types of HAIs. An additional analysis was performed on 3 stratifications: critically low (2–3 FTE), below recommended IP levels (4–6 FTE), and at recommended IP levels (7–8 FTE). Results: The observation covered 1.6 million patient days of surveillance. IP staffing levels fluctuated from ≤2 IP FTE (critically low) to 7–8 IP FTE (recommended levels). Periods of highest catheter-associated urinary tract infection SIRs, hospital-onset Clostridioides difficile and carbapenem-resistant Enterobacteriaceae infection rates, along with 4 of 5 types of surgical site SIRs coincided with the periods of lowest IP staffing levels and the absence of certified IPs and a healthcare epidemiologist. Central-line–associated bloodstream infections increased amid lower nursing levels despite the increased presence of an IP and a hospital epidemiologist. Conclusions: Of 10 HAIs, 8 had highest incidences during periods of lowest IP staffing and experience. Some HAI rates varied inversely with levels of IP staffing and experience and others appeared to be more influenced by nursing levels or other confounders.

Download Full-text

The Role of Environmental Contamination in the Transmission of Nosocomial Pathogens and Healthcare-Associated Infections

Current Infectious Disease Reports ◽

10.1007/s11908-018-0620-2 ◽

2018 ◽

Vol 20 (6) ◽

Cited By ~ 25

Author(s):

Geehan Suleyman ◽

George Alangaden ◽

Ana Cecilia Bardossy

Keyword(s):

Environmental Contamination ◽

Healthcare Associated Infections ◽

Nosocomial Pathogens ◽

Healthcare Associated

Download Full-text

Combating hepatitis B and C by 2030: achievements, gaps, and options for actions in China

BMJ Global Health ◽

10.1136/bmjgh-2020-002306 ◽

2020 ◽

Vol 5 (6) ◽

pp. e002306

Author(s):

Shu Chen ◽

Wenhui Mao ◽

Lei Guo ◽

Jiahui Zhang ◽

Shenglan Tang

Keyword(s):

Information Systems ◽

Hepatitis B ◽

Viral Hepatitis ◽

Large Scale ◽

Epidemiological Data ◽

Risk Groups ◽

Chronic Viral Hepatitis ◽

Nucleic Acid Amplification ◽

Effective Control ◽

Governance System

China has the highest number of hepatitis B and C cases globally. Despite remarkable achievements, China faces daunting challenges in achieving international targets for hepatitis elimination. As part of a large-scale project assessing China’s progress in achieving health-related Sustainable Development Goals using quantitative, qualitative data and mathematical modelling, this paper summarises the achievements, gaps and challenges, and proposes options for actions for hepatitis B and C control. China has made substantial progress in controlling chronic viral hepatitis. The four most successful strategies have been: (1) hepatitis B virus childhood immunisation; (2) prevention of mother-to-child transmission; (3) full coverage of nucleic acid amplification testing in blood stations and (4) effective financing strategies to support treatment. However, the total number of deaths due to hepatitis B and C is estimated to increase from 434 724 in 2017 to 527 829 in 2030 if there is no implementation of tailored interventions. Many health system barriers, including a fragmented governance system, insufficient funding, inadequate service coverage, unstandardised treatment and flawed information systems, have compromised the effective control of hepatitis B and C in China. We suggest five strategic priority actions to help eliminate hepatitis B and C in China: (1) restructure the viral hepatitis control governance system; (2) optimise health resource allocation and improve funding efficiency; (3) improve access to and the quality of the health benefits package, especially for high-risk groups; (4) strengthen information systems to obtain high-quality hepatitis epidemiological data; (5) increase investment in viral hepatitis research and development.

Download Full-text

Rapid feedback on hospital onset SARS-CoV-2 infections combining epidemiological and sequencing data

10.1101/2020.11.12.20230326 ◽

2020 ◽

Author(s):

Oliver T Stirrup ◽

Joseph Hughes ◽

Matthew Parker ◽

David G Partridge ◽

James G Shepherd ◽

...

Keyword(s):

Mutation Rate ◽

Sequence Data ◽

Rapid Assessment ◽

Epidemiological Data ◽

Rapid Identification ◽

Infection Prevention And Control ◽

Sequencing Data ◽

Additional Information ◽

Close Sequence ◽

Healthcare Associated

AbstractBackgroundRapid identification and investigation of healthcare-associated infections (HCAIs) is important for suppression of SARS-CoV-2, but the infection source for hospital onset COVID-19 infections (HOCIs) cannot always be readily identified based only on epidemiological data. Viral sequencing data provides additional information regarding potential transmission clusters, but the low mutation rate of SARS-CoV-2 can make interpretation using standard phylogenetic methods difficult.MethodsWe developed a novel statistical method and sequence reporting tool (SRT) that combines epidemiological and sequence data in order to provide a rapid assessment of the probability of HCAI among HOCI cases (defined as first positive test >48 hours following admission) and to identify infections that could plausibly constitute outbreak events. The method is designed for prospective use, but was validated using retrospective datasets from hospitals in Glasgow and Sheffield collected February-May 2020.ResultsWe analysed data from 326 HOCIs. Among HOCIs with time-from-admission ≥8 days the SRT algorithm identified close sequence matches from the same ward for 160/244 (65.6%) and in the remainder 68/84 (81.0%) had at least one similar sequence elsewhere in the hospital, resulting in high estimated probabilities of within-ward and within-hospital transmission. For HOCIs with time-from-admission 3-7 days, the SRT probability of healthcare acquisition was >0.5 in 33/82 (40.2%).ConclusionsThe methodology developed can provide rapid feedback on HOCIs that could be useful for infection prevention and control teams, and warrants further prospective evaluation. The integration of epidemiological and sequence data is important given the low mutation rate of SARS-CoV-2 and its variable incubation period.

Download Full-text

Disinfectant Wipes Transfer Clostridioides difficile Spores from Contaminated Surfaces to Uncontaminated Surfaces during the Disinfection Process

10.21203/rs.3.rs-16122/v2 ◽

2020 ◽

Author(s):

Carine A. Nkemngong ◽

Gurpreet K. Chaggar ◽

Xiaobao Li ◽

Peter J. Teska ◽

Haley F Oliver

Keyword(s):

Hydrogen Peroxide ◽

Quaternary Ammonium ◽

Healthcare Associated Infections ◽

Cross Contamination ◽

Healthcare Facilities ◽

Contamination Risk ◽

Clostridioides Difficile ◽

Disinfection Process ◽

The Us ◽

Healthcare Associated

Abstract Background: Pre-wetted disinfectant wipes are increasingly being used in healthcare facilities to help address the risk of healthcare associated infections (HAI). However, HAIs are still a major problem in the US with Clostridioides difficile being the most common cause, leading to approximately 12,800 deaths annually in the US. An underexplored risk when using disinfectant wipes is that they may cross-contaminate uncontaminated surfaces during the wiping process. The objective of this study was to determine the cross-contamination risk that pre-wetted disinfectant towelettes may pose when challenged with C. difficile spores. We hypothesized that although the tested disinfectant wipes had no sporicidal claims, they will reduce spore loads. We also hypothesized that hydrogen peroxide disinfectant towelettes would present a lower cross-contamination risk than quaternary ammonium products. Methods: We evaluated the risk of cross-contamination when disinfectant wipes are challenged with C. difficile ATCC 43598 spores on Formica surfaces. A disinfectant wipe was used to wipe a Formica sheet inoculated with C. difficile. After the wiping process, we determined log10 CFU on previously uncontaminated pre-determined distances from the inoculation point and on the used wipes. Results: We found that the disinfectant wipes transferred C. difficile spores from inoculated surfaces to previously uncontaminated surfaces. We also found that wipes physically removed C. difficile spores and that hydrogen peroxide disinfectants were more sporicidal than the quaternary ammonium disinfectants. Conclusion: Regardless of the product type, all disinfectant wipes had some sporicidal effect but transferred C. difficile spores from contaminated to otherwise previously uncontaminated surfaces. Disinfectant wipes retain C. difficile spores during and after the wiping process.

Download Full-text

Electronically assisted surveillance systems of healthcare-associated infections: a systematic review

Eurosurveillance ◽

10.2807/1560-7917.es.2020.25.2.1900321 ◽

2020 ◽

Vol 25 (2) ◽

Cited By ~ 2

Author(s):

H Roel A Streefkerk ◽

Roel PAJ Verkooijen ◽

Wichor M Bramer ◽

Henri A Verbrugh

Keyword(s):

Systematic Review ◽

Control Programme ◽

Mature Stage ◽

Surveillance Systems ◽

Healthcare Associated Infections ◽

Medical Specialties ◽

Specificity And Sensitivity ◽

Healthcare Associated ◽

Traditional Surveillance

Background Surveillance of healthcare-associated infections (HAI) is the basis of each infection control programme and, in case of acute care hospitals, should ideally include all hospital wards, medical specialties as well as all types of HAI. Traditional surveillance is labour intensive and electronically assisted surveillance systems (EASS) hold the promise to increase efficiency. Objectives To give insight in the performance characteristics of different approaches to EASS and the quality of the studies designed to evaluate them. Methods In this systematic review, online databases were searched and studies that compared an EASS with a traditional surveillance method were included. Two different indicators were extracted from each study, one regarding the quality of design (including reporting efficiency) and one based on the performance (e.g. specificity and sensitivity) of the EASS presented. Results A total of 78 studies were included. The majority of EASS (n = 72) consisted of an algorithm-based selection step followed by confirmatory assessment. The algorithms used different sets of variables. Only a minority (n = 7) of EASS were hospital-wide and designed to detect all types of HAI. Sensitivity of EASS was generally high (> 0.8), but specificity varied (0.37–1). Less than 20% (n = 14) of the studies presented data on the efficiency gains achieved. Conclusions Electronically assisted surveillance of HAI has yet to reach a mature stage and to be used routinely in healthcare settings. We recommend that future studies on the development and implementation of EASS of HAI focus on thorough validation, reproducibility, standardised datasets and detailed information on efficiency.

Download Full-text

Epidemiology of community-acquired and recurrent Clostridioides difficile infection

Therapeutic Advances in Gastroenterology ◽

10.1177/17562848211016248 ◽

2021 ◽

Vol 14 ◽

pp. 175628482110162

Author(s):

Yichun Fu ◽

Yuying Luo ◽

Ari M Grinspan

Keyword(s):

Large Scale ◽

Infection Prevention ◽

The United States ◽

Future Research ◽

Clostridioides Difficile ◽

Epidemiologic Surveillance ◽

Scale Population ◽

Clostridioides Difficile Infection ◽

Healthcare Associated ◽

Hospital Acquired

Clostridioides difficile infection is a leading cause of healthcare-associated infections with significant morbidity and mortality. For the past decade, the bulk of infection prevention and epidemiologic surveillance efforts have been directed toward mitigating hospital-acquired C. difficile. However, the incidence of community-associated infection is on the rise. Patients with community-associated C. difficile tend to be younger and have lower mortality rate. Rates of recurrent C. difficile infection overall have decreased in the United States, but future research and public health endeavors are needed to standardize and improve disease detection, stratify risk factors in large-scale population studies, and to identify regional and local variations in strain types, reservoirs and transmission routes to help characterize and combat the changing epidemiology of C. difficile.

Download Full-text

Disinfectant Wipes with Nonsporicidal Claims Transfer Clostridioides difficile Spores from Contaminated Surfaces to Uncontaminated Surfaces during the Disinfection Process

10.21203/rs.3.rs-16122/v1 ◽

2020 ◽

Author(s):

Carine A. Nkemngong ◽

Gurpreet K. Chaggar ◽

Xiaobao Li ◽

Peter J. Teska ◽

Haley F Oliver

Keyword(s):

Hydrogen Peroxide ◽

Quaternary Ammonium ◽

Healthcare Associated Infections ◽

Cross Contamination ◽

Healthcare Facilities ◽

Contamination Risk ◽

Clostridioides Difficile ◽

Disinfection Process ◽

The Us ◽

Healthcare Associated

Download Full-text

Contribution of microbiology to an effective control of healthcare-associated infections

Orvosi Hetilap ◽

10.1556/oh.2011.29062 ◽

2011 ◽

Vol 152 (11) ◽

pp. 437-442

Author(s):

István Barcs ◽

Aranka Kovács ◽

Katalin Antmann ◽

Anita Becker ◽

Gyula Domján

Keyword(s):

Dna Sequences ◽

Antibiotic Sensitivity ◽

Nasal Carriage ◽

Effective Control ◽

Clinical Samples ◽

Specific Method ◽

Healthcare Associated Infections ◽

Healthcare Associated Infection ◽

And Cluster Analysis ◽

Healthcare Associated

An effective control of healthcare-associated infections is not realized without an intensive participation of microbiologic activities. Authors present the model of a centre for healthcare-associated infection control established in 2008 at Semmelweis University. The new model of the surveillance system is based on diagnostic and experimental microbiologic data. Clinical and epidemiological microbiologic examinations are performed in the same laboratory using identical methods, and the results are continually compared. Reports consist of two functional parts; namely list of pathogens isolated and antibiotic sensitivity patterns for clinicians and messages especially for epidemiologists including abbreviated information on bacteria of nosocomial importance. Rapid detection of the most important pathogens both from clinical samples and from those obtained for detecting nasal carriage is carried out by a sensitive and specific method of an automated real time PCR. Biotyping of isolates by detailed biochemical substrate spectrum, genotyping by ready-to-use kits depending on polymorphism of repetitive DNA sequences, and cluster analysis of data are used for up-to-date survey of nosocomial situation. Statistical analysis of reports is performed by the multifactorial software OSIRIS Epidemiology. Orv. Hetil., 2011, 152, 437–442.

Download Full-text