Whole genome sequencing (WGS) can help identify transmission of pathogens causing healthcare-associated infections (HAIs). However, the current gold standard of short-read, Illumina-based WGS is labor and time intensive. Given recent improvements in long-read Oxford Nanopore Technologies (ONT) sequencing, we sought to establish a low resource approach providing accurate WGS-pathogen comparison within a time frame allowing for infection prevention and control (IPC) interventions.

WGS was prospectively performed on pathogens at increased risk of potential healthcare transmission using the ONT MinION sequencer with R10.4.1 flow cells and Dorado basecaller. Potential transmission was assessed via Ridom SeqSphere+ for core genome multilocus sequence typing and MINTyper for reference-based core genome single nucleotide polymorphisms using previously published cutoff values. The accuracy of our ONT pipeline was determined relative to Illumina.

Over a six-month period, 242 bacterial isolates from 216 patients were sequenced by a single operator. Compared to the Illumina gold standard, our ONT pipeline achieved a mean identity score of Q60 for assembled genomes, even with a coverage rate as low as 40×. The mean time from initiating DNA extraction to complete analysis was 2 days (IQR 2–3.25 days). We identified five potential transmission clusters comprising 21 isolates (8.7% of sequenced strains). Integrating ONT with epidemiological data, >70% (15/21) of putative transmission cluster isolates originated from patients with potential healthcare transmission links.

Via a stand-alone ONT pipeline, we detected potentially transmitted HAI pathogens rapidly and accurately, aligning closely with epidemiological data. Our low-resource method has the potential to assist in IPC efforts.

Cases of novel coronavirus disease 2019 (COVID-19) were first reported in Wuhan, China, in December 2019. In this report, we describe 3 clusters of COVID-19 infections among healthcare workers (HCWs), not associated with patient exposure, and the interventions undertaken to halt ongoing exposure and transmission at our cancer center.

A cluster of cases was defined as 2 or more cases of severe acute respiratory coronavirus virus 2 (SARS-CoV-2)–positive COVID-19 among HCWs who work in the same unit area at the same time. Cases were identified by real-time reverse transcription polymerase chain reaction testing. Contact tracing, facility observations, and infection prevention assessments were performed to investigate the 3 clusters between March 1 and April 30, 2020, with subsequent implementation of containment strategies.

The initial cluster involved HCWs from an ancillary services unit, with contacts traced back to a gathering in a break room in which 1 employee was symptomatic, although not yet diagnosed with COVID-19, with subsequent transmission to 7 employees. The second cluster involved 4 employees and was community related. The third cluster involved only 2 employees with possible transmission while working in the same office at the same time. A step-up approach was implemented to control the spread of infection among employees, including universal masking, enhanced cleaning, increase awareness, and surveillance testing. No nosocomial transmission to patients transpired.

To our knowledge, this is the first report of a hospital-based cluster of COVID-19 infections among HCWs in a cancer hospital describing our steps to mitigate further transmission.

Prolonged survival of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) on environmental surfaces and personal protective equipment may lead to these surfaces transmitting this pathogen to others. We sought to determine the effectiveness of a pulsed-xenon ultraviolet (PX-UV) disinfection system in reducing the load of SARS-CoV-2 on hard surfaces and N95 respirators.

Chamber slides and N95 respirator material were directly inoculated with SARS-CoV-2 and were exposed to different durations of PX-UV.

For hard surfaces, disinfection for 1, 2, and 5 minutes resulted in 3.53 log10, >4.54 log10, and >4.12 log10 reductions in viral load, respectively. For N95 respirators, disinfection for 5 minutes resulted in >4.79 log10 reduction in viral load. PX-UV significantly reduced SARS-CoV-2 on hard surfaces and N95 respirators.

With the potential to rapidly disinfectant environmental surfaces and N95 respirators, PX-UV devices are a promising technology to reduce environmental and personal protective equipment bioburden and to enhance both healthcare worker and patient safety by reducing the risk of exposure to SARS-CoV-2.

To examine the impact of cleaning and directional airflow on environmental contamination with Aspergillus species in hospital rooms filtered with high-efficiency particulate air (HEPA) filters that house patients with hematologic malignancy.

Detailed environmental assessment.

A 475-bed tertiary cancer center in the southern United States.

From April to October 2004, 1,258 surface samples and 627 bioaerosol samples were obtained from 74 HEPA-filtered rooms (in addition, 88 outdoor bioaerosol samples were obtained). Samples were collected from rooms cleaned within 1 hour after patient discharge and from rooms before cleaning. Positive and negative airflows were evaluated using air-current tubes at entrances to patient rooms.

Of 1,258 surface samples, 3.3% were positive for Aspergillus species. Univariate analysis showed no relationship between cleaning status and occurrence of Aspergillus species. Of 627 bioaerosol samples, 7.3% were positive for Aspergillus species. Multiple logistic analysis revealed independently significant associations with detection of Aspergillus species. Cleaned rooms positive for Aspergillus species had a higher geometric mean density of colonies than that of rooms sampled before cleaning (18.9 vs 5.5 colony-forming units [cfu] per cubic meter; P = .0047). Rooms with positive airflow had a detection rate for bioaerosol samples equivalent to that of rooms with negative airflow (7.3% vs 7.8%; P = .8). There was no significant difference in the density of Aspergillus species between rooms with negative airflow and rooms with positive airflow (12.5 vs 8.4 cfu/m3; P = .33).

Concentration of bioaerosol contamination with Aspergillus species was increased in rooms sampled 1 hour after cleaning compared with rooms sampled before cleaning, suggesting a possible correlation between reentrained bioaerosols (ie, those suspended by activity in the room) after cleaning and the risk of nosocomial invasive aspergillosis.