Tracking Staphylococcus aureus in the intensive care unit using whole-genome sequencing

Longitudinal two-year comparative genomic analysis of respiratory Staphylococcus aureus isolates from intensive care unit mechanically ventilated patients

BACKGROUND

Ventilator-associated pneumonia (VAP) is the main healthcare-associated infection in intensive care units with Staphylococcus aureus as the first pathogen in early VAP.

AIM

To compare, using whole-genome sequencing (WGS), consecutive S. aureus isolates from lower respiratory samples of mechanically ventilated patients for identification of potential cross-transmissions; and to determine a potential link between S. aureus WGS data and patients with S. aureus early VAP.

METHODS

All mechanically ventilated patients with a documentation of respiratory S. aureus isolates were included over a two-year period. WGS allowed typing, comparative genomic and phylogenic analyses, as well as analyses of antibiotic resistance genes and virulence genes. Virulence genes were compared between patients who developed respiratory infectious event and those who did not.

FINDINGS

A total of 172 S. aureus isolates from 167 patients were sequenced. WGS revealed that the S. aureus population was polyclonal with only two potential healthcare cross-transmissions, each involving two isolates (2.3%). A very low resistance rate was observed with a strong genotypic/phenotypic association, and with a virulence profile highly dependent on the sequence type. No significant correlation was observed between VAP and virulence profile.

CONCLUSION

This study on consecutive respiratory S. aureus isolates of mechanically ventilated patients revealed a very low level of cross-transmission. No association was observed between S. aureus WGS data and VAP occurrence.

Trends in viable microbial bioburden on surfaces within a paediatric bone marrow transplant unit

BACKGROUND

Despite their role being historically overlooked, environmental surfaces have been shown to play a key role in the transmission of pathogens causative of healthcare-associated infection. To guide infection prevention and control (IPC) interventions and inform clinical risk assessments, more needs to be known about microbial surface bioburdens.

AIM

To identify the trends in culturable bacterial contamination across communal touch sites over time in a hospital setting.

METHODS

Swab samples were collected over nine weeks from 22 communal touch sites in a paediatric bone marrow transplant unit. Samples were cultured on Columbia blood agar and aerobic colony counts (ACC) per 100 cm2 were established for each site. Individual colony morphologies were grouped and identified by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry or 16s rDNA sequencing.

FINDINGS

Highest mean counts were observed for sites associated with ward management activity and computer devices (3.29 and 2.97 ACC/100 cm2 respectively). A nurses' station keyboard had high mean ACC/100 cm2 counts (10.67) and diversity, while laundry controls had high mean ACC/100 cm2 counts (4.70) and low diversity. Micrococcus luteus was identified in all sampling groups. Clinical staff usage sites were contaminated with similar proportions of skin and environmental flora (52.19-46.59% respectively), but sites associated with parental activities were predominantly contaminated by environmental microflora (86.53%).

CONCLUSION

The trends observed suggest patterns in microbial loading based on site activities, surface types and user groups. Improved understanding of environmental surface contamination could help support results interpretation and IPC interventions, improving patient safety.

Hospital cleaning: past, present, and future

INTRODUCTION

The importance of hospital cleaning for controlling healthcare-associated infection (HAI) has taken years to acknowledge. This is mainly because the removal of dirt is inextricably entwined with gender and social status, along with lack of evidence and confusion over HAI definitions. Reducing so-called endogenous infection due to human carriage entails patient screening, decolonisation and/or prophylaxis, whereas adequate ventilation, plumbing and cleaning are needed to reduce exogenous infection. These infection types remain difficult to separate and quantitate. Patients themselves demonstrate wide-ranging vulnerability to infection, which further complicates attempted ranking of control interventions, including cleaning. There has been disproportionate attention towards endogenous infection with less interest in managing environmental reservoirs.

QUANTIFYING CLEANING AND CLEANLINESS

Finding evidence for cleaning is compromised by the fact that modelling HAI rates against arbitrary measurements of cleaning/cleanliness requires universal standards and these are not yet established. Furthermore, the distinction between cleaning (soil removal) and cleanliness (soil remaining) is usually overlooked. Tangible bench marking for both cleaning methods and all surface types within different units, with modification according to patient status, would be invaluable for domestic planning, monitoring and specification.

AIMS AND OBJECTIVES

This narrative review will focus on recent history and current status of cleaning in hospitals. While its importance is now generally accepted, cleaning practices still need attention in order to determine how, when and where to clean. Renewed interest in removal and monitoring of surface bioburden would help to embed risk-based practice in hospitals across the world.

Environmental cleaning to prevent hospital-acquired infections on non-intensive care units: a pragmatic, single-centre, cluster randomized controlled, crossover trial comparing soap-based, disinfection and probiotic cleaning

Background

The impact of environmental hygiene on the occurrence of hospital-acquired infections (HAIs) remains a subject of debate. We determined the effect of three different surface-cleaning strategies on the incidence of HAIs.

Methods

Between June 2017 and August 2018 we conducted a pragmatic, cluster-randomized controlled crossover trial at 18 non-ICU wards in the university hospital of Berlin, Germany. Surfaces in patient rooms on the study wards were routinely cleaned using one of three agents: Soap-based (reference), disinfectant and probiotic. Each strategy was used on each ward for four consecutive months (4m-4m-4m). There was a one-month wash-in period at the beginning of the study and after each change in strategy. The order of strategies used was randomized for each ward. Primary outcome was the incidence of HAIs. The trial was registered with the German Clinical Trials Register, DRKS00012675.

Findings

13,896 admitted patients met the inclusion criteria, including 4708 in the soap-based (reference) arm, 4535 in the disinfectant arm and 4653 in the probiotic arm. In the reference group, the incidence density of HAIs was 2.31 per 1000 exposure days. The incidence density was similar in the disinfectant arm 2.21 cases per 1000 exposure days (IRR 0.95; 95% CI 0.69-1.31; p = 0.953) and the probiotic arm 2.21 cases per 1000 exposure days (IRR 0.96; 95% CI 0.69-1.32; p = 0.955).

Interpretation

In non-ICU wards, routine surface disinfection proved not superior to soap-based or probiotic cleaning in terms of HAI prevention. Thus, probiotic cleaning could be an interesting alternative, especially in terms of environmental protection.

Funding

Federal Ministry of Education and Research of Germany (03Z0818C). Bill and Melinda Gates Foundation (INV-004308).

Effectiveness of a Self-Decontaminating Coating Containing Usnic Acid in Reducing Environmental Microbial Load in Tertiary-Care Hospitals

Surfaces have been implicated in the transmission of pathogens in hospitals. This study aimed to assess the effectiveness of an usnic-acid-containing self-decontaminating coating in reducing microbial surface contamination in tertiary-care hospitals. Samples were collected from surfaces 9 days before coating application, and 3, 10, and 21 days after its application (phases 1, 2, 3, and 4, respectively). Samples were tested for bacteria, fungi, and SARS-CoV2. In phase 1, 53/69 (76.8%) samples tested positive for bacteria, 9/69 (13.0%) for fungi, and 10/139 (7.2%) for SARS-CoV-2. In phase 2, 4/69 (5.8%) samples tested positive for bacteria, while 69 and 139 samples were negative for fungi and SARS-CoV-2, respectively. In phase 3, 3/69 (4.3%) samples were positive for bacteria, 1/139 (0.7%) samples tested positive for SARS-CoV-2, while 69 samples were negative for fungi. In phase 4, 1/69 (1.4%) tested positive for bacteria, while no fungus or SARS-CoV-2 were detected. After the coating was applied, the bacterial load was reduced by 87% in phase 2 (RR = 0.132; 95% CI: 0.108-0.162); 99% in phase 3 (RR = 0.006; 95% CI: 0.003-0.015); and 100% in phase 4 (RR = 0.001; 95% CI: 0.000-0.009). These data indicate that the usnic-acid-containing coating was effective in eliminating bacterial, fungal, and SARS-CoV-2 contamination on surfaces in hospitals.Our findings support the benefit ofan usnic-acid-containing coating in reducing the microbial load on healthcare surfaces.

Not in their hands only: hospital hygiene, evidence and collective moral responsibility

Hospital acquired infections (HAIs) are a major threat to patient safety. This paper addresses the following question: given what is known about the causes of and possible interventions on HAIs, to whom or what should the moral responsibility for preventing these infections be attributed? First, we show how generating robust evidence on the effectiveness of preventive hygiene measures is a complex endeavour and review the existing evidence on the causes of HAIs. Second, we demonstrate that the existing literature on the ethical aspects of infection control has focused on responsibility at the individual-level. Thirdly, we argue that these accounts do not accommodate systemic factors relevant for HAI prevention. We show that the notion of collective responsibility is useful for making understandable how systemic factors, such as employment conditions in hospitals, are both causally and ethically relevant in infection control.

Molecular epidemiology of methicillin-sensitive Staphylococcus aureus in the neonatal intensive care unit

BACKGROUND

Staphylococcus aureus-both meticillin-resistant S. aureus (MRSA) and meticillin-sensitive S. aureus (MSSA)-is a major cause of neonatal infections. Infection control measures have not lowered the incidence of MSSA infections to the same degree as that of MRSA infections.

AIM

To investigate the transmission pathway of MSSA in neonatal intensive care unit (NICU) using genetic analysis.

METHODS

We swab-tested neonatal patients, their parents, and healthcare workers (HCW) in the NICU at our hospital at the time of hospitalisation and then every month thereafter from 1^st October 2018 to 31^st March 2019. We performed whole-genome sequencing (WGS) to test for MSSA strains. Multilocus sequence typing (MLST) and single nucleotide polymorphism (SNP) analysis were used to identify strains and understand their relatedness.

FINDINGS

There were 16 MSSA-positive patients. Four MSSA-positive patients shared strains from the same phylogenetic groups as those of HCW. One presented the same strain as the parent. MSSA-positive twin neonates shared the same strain. Ten had sporadic strains; 32 of the ninety-seven tested healthcare workers were MSSA positive.

CONCLUSION

The findings of this study suggest that the route of transmission of MSSA in NICU may be through MSSA in the hospital environment in addition to horizontal transmission via healthcare workers. Along with hand hygiene with alcohol, thorough environmental maintenance and parental education are important for infection control in NICUs targeting MSSA.

MRSA Transmission in Intensive Care Units: Genomic Analysis of Patients, Their Environments, and Healthcare Workers

BACKGROUND

Methicillin-resistant Staphylococcus aureus (MRSA)-and now USA300 MRSA-is a significant intensive care unit (ICU) pathogen; healthcare worker (HCW) contamination may lead to patient cross-transmission.

METHODS

From September 2015 to February 2016, to study the spread of MRSA, we enrolled HCWs in 4 adult ICUs caring for patients on MRSA contact precautions. Samples were collected from patient body sites and high-touch surfaces in patient rooms. HCW hands, gloves, and personal protective equipment were sampled pre/post-patient encounter. Whole genome sequencing (WGS) was used to compare isolates from patients, HCWs, and environment.

RESULTS

There were 413 MRSA isolates sequenced (38% USA300, 52% USA100) from 66 patient encounters. Six of 66 HCWs were contaminated with MRSA prior to room entry. Isolates from a single patient encounter were typically either USA100 or USA300; in 8 (12%) encounters both USA300 and USA100 were isolated. WGS demonstrated that isolates from patients, HCWs, and environment often were genetically similar, although there was substantial between-encounter diversity. Strikingly, there were 5 USA100 and 1 USA300 clusters that contained similar strains (<22 single-nucleotide variants [SNVs], with most <10 SNVs) within the cluster despite coming from different encounters, suggesting intra- and inter-ICU spread of strains, that is, 4 of these genomic clusters were from encounters in the same ICU; 5 of 6 clusters occurred within 1 week.

CONCLUSIONS

We demonstrated frequent spread of MRSA USA300 and USA100 strains among patients, environment, and HCWs. WGS identified possible spread within and even between ICUs. Future analysis with detailed contact tracing in conjunction with genomic data may further elucidate pathways of MRSA spread and points for intervention.

A Distinct Microbiome Signature in Posttreatment Lyme Disease Patients

Most patients with acute Lyme disease are cured with antibiotic intervention, but 10 to 20% endure debilitating symptoms such as fatigue, neurological complications, and myalgias after treatment, a condition known as posttreatment Lyme disease syndrome (PTLDS). The etiology of PTLDS is not understood, and objective diagnostic tools are lacking. PTLDS symptoms overlap several diseases in which patients exhibit alterations in their microbiome. We found that patients with PTLDS have a distinct microbiome signature, allowing for an accurate classification of over 80% of analyzed cases. The signature is characterized by an increase in Blautia, a decrease in Bacteroides, and other changes. Importantly, this signature supports the validity of PTLDS and is the first potential biological diagnostic tool for the disease.

Lyme disease is the most common vector-borne disease in the United States, with an estimated incidence of 300,000 infections annually. Antibiotic intervention cures Lyme disease in the majority of cases; however, 10 to 20% of patients develop posttreatment Lyme disease syndrome (PTLDS), a debilitating condition characterized by chronic fatigue, pain, and cognitive difficulties. The underlying mechanism responsible for PTLDS symptoms, as well as a reliable diagnostic tool, has remained elusive. We reasoned that the gut microbiome may play an important role in PTLDS given that the symptoms overlap considerably with conditions in which a dysbiotic microbiome has been observed, including mood, cognition, and autoimmune disorders. Analysis of sequencing data from a rigorously curated cohort of patients with PTLDS revealed a gut microbiome signature distinct from that of healthy control subjects, as well as from that of intensive care unit (ICU) patients. Notably, microbiome sequencing data alone were indicative of PTLDS, which presents a potential, novel diagnostic tool for PTLDS.

Dynamic Transmission of Staphylococcus Aureus in the Intensive Care Unit

Staphylococcus aureus is an important bacterial pathogen. This study utilized known staphylococcal epidemiology to track S. aureus between patients, surfaces, staff hands and air in a ten-bed intensive care unit (ICU).

METHODS

Patients, air and surfaces were screened for total colony counts and S. aureus using dipslides, settle plates and an MAS-100 slit-sampler once a month for 10 months. Data were modelled against proposed standards for air and surfaces, and ICU-acquired staphylococcal infection. Whole-cell genomic typing (WGS) demonstrated possible transmission pathways between reservoirs.

RESULTS

Frequently touched sites were more likely to be contaminated (>12 cfu/cm2; p = 0.08). Overall, 235 of 500 (47%) sites failed the surface standard (≤2.5 cfu/cm2); 20 of 40 (50%) passive air samples failed the "Index of Microbial Air" standard (2 cfu/9 cm plate/h), and 15/40 (37.5%) air samples failed the air standard (<10 cfu/m3). Settle plate data were closer to surface counts than automated air data; the surface count most likely to reflect pass/fail rates for air was 5 cfu/cm2. Surface counts/bed were associated with staphylococcal infection rates (p = 0.012). Of 34 pairs of indistinguishable S. aureus, 20 (59%) showed autogenous transmission, with another four (12%) occurring between patients. Four (12%) pairs linked patients with hand-touch sites and six (18%) linked airborne S. aureus, staff hands and hand-touch sites.

CONCLUSION

Most ICU-acquired S. aureus infection is autogenous, while staff hands and air were rarely implicated in onward transmission. Settle plates could potentially be used for routine environmental screening. ICU staphylococcal infection is best served by admission screening, systematic cleaning and hand hygiene.

'Off the rails': hospital bed rail design, contamination, and the evaluation of their microbial ecology

Microbial contamination of the near-patient environment is an acknowledged reservoir for nosocomial pathogens. The hospital bed and specifically bed rails have been shown to be frequently and heavily contaminated in observational and interventional studies. Whereas the complexity of bed rail design has evolved over the years, the microbial contamination of these surfaces has been incompletely evaluated. In many published studies, key design variables are not described, compromising the extrapolation of results to other settings. This report reviews the evolving structure of hospital beds and bed rails, the possible impact of different design elements on microbial contamination and their role in pathogen transmission. Our findings support the need for clearly defined standardized assessment protocols to accurately assess bed rail and similar patient zone surface levels of contamination, as part of environmental hygiene investigations.