Modeling transmission of pathogens in healthcare settings.

PURPOSE OF REVIEW: Mathematical, statistical, and computational models provide insight into the transmission mechanisms and optimal control of healthcare-associated infections. To contextualize recent findings, we offer a summative review of recent literature focused on modeling transmission of pathogens in healthcare settings. RECENT FINDINGS: The COVID-19 pandemic has led to a dramatic shift in the modeling landscape as the healthcare community has raced to characterize the transmission dynamics of SARS-CoV-2 and develop effective interventions. Inequities in COVID-19 outcomes have inspired new efforts to quantify how structural bias impacts both health outcomes and model parameterization. Meanwhile, developments in the modeling of methicillin-resistant Staphylococcus aureus, Clostridioides difficile, and other nosocomial infections continue to advance. Machine learning continues to be applied in novel ways, and genomic data is being increasingly incorporated into modeling efforts. SUMMARY: As the type and amount of data continues to grow, mathematical, statistical, and computational modeling will play an increasing role in healthcare epidemiology. Gaps remain in producing models that are generalizable to a variety of time periods, geographic locations, and populations. However, with effective communication of findings and interdisciplinary collaboration, opportunities for implementing models for clinical decision-making and public health decision-making are bound to increase.

Respiratory surveillance wards as a strategy to reduce nosocomial transmission of COVID-19 through early detection: The experience of a tertiary-care hospital in Singapore.

OBJECTIVES: Patients with COVID-19 may present with respiratory syndromes indistinguishable from those caused by common viruses. Early isolation and containment is challenging. Although screening all patients with respiratory symptoms for COVID-19 has been recommended, the practicality of such an effort has yet to be assessed. METHODS: Over a 6-week period during a SARS-CoV-2 outbreak, our institution introduced a "respiratory surveillance ward" (RSW) to segregate all patients with respiratory symptoms in designated areas, where appropriate personal protective equipment (PPE) could be utilized until SARS-CoV-2 testing was done. Patients could be transferred when SARS-CoV-2 tests were negative on 2 consecutive occasions, 24 hours apart. RESULTS: Over the study period, 1,178 patients were admitted to the RSWs. The mean length-of-stay (LOS) was 1.89 days (SD, 1.23). Among confirmed cases of pneumonia admitted to the RSW, 5 of 310 patients (1.61%) tested positive for SARS-CoV-2. This finding was comparable to the pickup rate from our isolation ward. In total, 126 HCWs were potentially exposed to these cases; however, only 3 (2.38%) required quarantine because most used appropriate PPE. In addition, 13 inpatients overlapped with the index cases during their stay in the RSW; of these 13 exposed inpatients, 1 patient subsequently developed COVID-19 after exposure. No patient-HCW transmission was detected despite intensive surveillance. CONCLUSIONS: Our institution successfully utilized the strategy of an RSW over a 6-week period to contain a cluster of COVID-19 cases and to prevent patient-HCW transmission. However, this method was resource-intensive in terms of testing and bed capacity.

Role of hospital environmental surfaces in the transmission of the severe acute respiratory syndrome - Coronavirus-2.

INTRODUCTION: Severe acute respiratory syndrome - Coronavirus-2 (SARS-CoV-2) is mainly transmitted via respiratory secretions through coughing, sneezing, or contact with contaminated surfaces. This virus can be present in feces and many body fluids. The study aimed to screen the hospital environment as a potential source for SARS-CoV-2 transmission and identify the hospital zones with the highest contamination levels. METHODOLOGY: Swabs were collected from different sites in the hospital before and after routine cleaning/disinfection, transported in vials containing 1-3 mL of viral transport medium, and stored at -80 ℃ as soon as possible until the time of testing. The real-time reverse-transcription PCR (rRT-PCR) system targeting RNA-dependent RNA polymerase and E genes was used to detect the SARS-CoV-2 RNA. RESULTS: Moderate environmental contamination by SARS-CoV-2 RNA was detected by rRT-PCR before routine cleaning/disinfection (52% of the swabs were positive). The hospital surfaces with the highest contamination levels were elevators' buttons, sinks and faucets' handles at the waiting rooms, patient's room and bathroom, call buttons and telephones in the patient's room, toilet bowl surface, the doorknob and light switches at the X-ray room, and the computer keyboard at the staffroom. All the swabs collected after routine cleaning/disinfection were negative for SARS-CoV-2 RNA by rRT-PCR. CONCLUSIONS: The hospital environment is a high-risk area that can be contaminated by SARS-CoV-2 through contact, respiratory, and maybe fecal shedding of the virus. To limit this fatal virus transmission, strict adherence to proper hand hygiene with frequent optimal decontamination of hospital environmental surfaces is essential.

Transient dynamics of infection transmission in a simulated intensive care unit.

Healthcare-associated infections (HAIs) remain a serious public health problem. In previous work, two models of an intensive care unit (ICU) showed that differing population structures had markedly different rates of Staphylococcus aureus (MRSA) transmission. One explanation for this difference is the models having differing long-term equilbrium dynamics, resulting from different basic reproductive numbers, R0. We find in this system however that this is not the case, and that both models had the same value for R0. Instead, short-term, transient dynamics, characterizing a series of small, self-limiting outbreaks caused by pathogen reintroduction were responsible for the differences. These results show the importance of these short-term factors for disease systems where reintroduction events are frequent, even if they are below the epidemic threshold. Further, we examine how subtle changes in how a hospital is organized-or how a model assumes a hospital is organized-in terms of the admission of new patients may impact transmission rates. This has implications for both novel pathogens introduced into ICUs, such as Ebola, MERS or COVID-19, as well as existing healthcare-associated infections such as carbapenem-resistant Enterobacteriaceae.

Characterising within-hospitalSARS-CoV-2 transmission events using epidemiological and viral genomic data across two pandemic waves.

Hospital outbreaks of COVID19 result in considerable mortality and disruption to healthcare services and yet little is known about transmission within this setting. We characterise within hospital transmission by combining viral genomic and epidemiological data using Bayesian modelling amongst 2181 patients and healthcare workers from a large UK NHS Trust. Transmission events were compared between Wave 1 (1st March to 25th J'uly 2020) and Wave 2 (30th November 2020 to 24th January 2021). We show that staff-to-staff transmissions reduced from 31.6% to 12.9% of all infections. Patient-to-patient transmissions increased from 27.1% to 52.1%. 40%-50% of hospital-onset patient cases resulted in onward transmission compared to 4% of community-acquired cases. Control measures introduced during the pandemic likely reduced transmissions between healthcare workers but were insufficient to prevent increasing numbers of patient-to-patient transmissions. As hospital-acquired cases drive most onward transmission, earlier identification of nosocomial cases will be required to break hospital transmission chains.

First reported nosocomial SARS-CoV-2 outbreak in a hospital-based laundry facility.

Nosocomial severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) outbreaks among health care workers have been scarcely reported so far. This report presents the results of an epidemiologic and molecular investigation of a SARS-CoV-2 outbreak among laundromat facility workers in a large tertiary centre in Israel. Following the first three reported cases of SARS-CoV-2 among laundromat workers, all 49 laundromat personnel were screened by qRT-PCR tests using naso- and oropharingeal swabs. Epidemiologic investigations included questionnaires, interviews and observations of the laundromat facility. Eleven viral RNA samples were then sequenced, and a phylogenetic analysis was performed using MEGAX.The integrated investigation defined three genetic clusters and helped identify the index cases and the assumed routes of transmission. It was then deduced that shared commute and public showers played a role in SARS-CoV-2 transmission in this outbreak, in addition to improper PPE use and social gatherings (such as social eating and drinking). In this study, we present an integrated epidemiologic and molecular investigation may help detect the routes of SARS-CoV-2 transmission, emphasising such routes that are less frequently discussed. Our work reinforces the notion that person-to-person transmission is more likely to cause infections than environmental contamination (e.g. from handling dirty laundry).

Rapid antigen testing as a reactive response to surges in nosocomial SARS-CoV-2 outbreak risk.

Healthcare facilities are vulnerable to SARS-CoV-2 introductions and subsequent nosocomial outbreaks. Antigen rapid diagnostic testing (Ag-RDT) is widely used for population screening, but its health and economic benefits as a reactive response to local surges in outbreak risk are unclear. We simulate SARS-CoV-2 transmission in a long-term care hospital with varying COVID-19 containment measures in place (social distancing, face masks, vaccination). Across scenarios, nosocomial incidence is reduced by up to 40-47% (range of means) with routine symptomatic RT-PCR testing, 59-63% with the addition of a timely round of Ag-RDT screening, and 69-75% with well-timed two-round screening. For the latter, a delay of 4-5 days between the two screening rounds is optimal for transmission prevention. Screening efficacy varies depending on test sensitivity, test type, subpopulations targeted, and community incidence. Efficiency, however, varies primarily depending on underlying outbreak risk, with health-economic benefits scaling by orders of magnitude depending on the COVID-19 containment measures in place.

Nosocomial Transmission of SARS-CoV-2 Involving Vaccinated Health Care Workers.

COVID-19 vaccination has proven to be effective at preventing symptomatic disease but there are scarce data to fully understand whether vaccinated individuals can still behave as SARS-CoV-2 transmission vectors. Based on viral genome sequencing and detailed epidemiological interviews, we report a nosocomial transmission event involving two vaccinated health care-workers (HCWs) and four patients, one of them with fatal outcome. Strict transmission control measures, as during the prevaccination period, must be kept between HCWs and HCWs-patients in nosocomial settings. IMPORTANCE COVID-19 vaccination has proven to be effective at preventing symptomatic disease. Although some transmission events involving vaccinated cases have also been reported, scarce information is still available to fully understand whether vaccinated individuals may still behave as vectors in SARS-CoV-2 transmission events. Here, we report a SARS-CoV-2 nosocomial transmission event, supported on whole genome sequencing, in early March 2021 involving two vaccinated HCWs and four patients in our institution. Strict transmission control measures between HCWs and HCWs - patients in nosocomial settings must not be relaxed, and should be kept as strictly as during the prevaccination period.

Hidden hazards of SARS-CoV-2 transmission in hospitals: A systematic review.

Despite their considerable prevalence, dynamics of hospital-associated COVID-19 are still not well understood. We assessed the nature and extent of air- and surface-borne SARS-CoV-2 contamination in hospitals to identify hazards of viral dispersal and enable more precise targeting of infection prevention and control. PubMed, ScienceDirect, Web of Science, Medrxiv, and Biorxiv were searched for relevant articles until June 1, 2021. In total, 51 observational cross-sectional studies comprising 6258 samples were included. SARS-CoV-2 RNA was detected in one in six air and surface samples throughout the hospital and up to 7.62 m away from the nearest patients. The highest detection rates and viral concentrations were reported from patient areas. The most frequently and heavily contaminated types of surfaces comprised air outlets and hospital floors. Viable virus was recovered from the air and fomites. Among size-fractionated air samples, only fine aerosols contained viable virus. Aerosol-generating procedures significantly increased (ORair  = 2.56 (1.46-4.51); ORsurface  = 1.95 (1.27-2.99)), whereas patient masking significantly decreased air- and surface-borne SARS-CoV-2 contamination (ORair  = 0.41 (0.25-0.70); ORsurface  = 0.45 (0.34-0.61)). The nature and extent of hospital contamination indicate that SARS-CoV-2 is likely dispersed conjointly through several transmission routes, including short- and long-range aerosol, droplet, and fomite transmission.

Evaluating the potential for respiratory metagenomics to improve treatment of secondary infection and detection of nosocomial transmission on expanded COVID-19 intensive care units.

BACKGROUND: Clinical metagenomics (CMg) has the potential to be translated from a research tool into routine service to improve antimicrobial treatment and infection control decisions. The SARS-CoV-2 pandemic provides added impetus to realise these benefits, given the increased risk of secondary infection and nosocomial transmission of multi-drug-resistant (MDR) pathogens linked with the expansion of critical care capacity. METHODS: CMg using nanopore sequencing was evaluated in a proof-of-concept study on 43 respiratory samples from 34 intubated patients across seven intensive care units (ICUs) over a 9-week period during the first COVID-19 pandemic wave. RESULTS: An 8-h CMg workflow was 92% sensitive (95% CI, 75-99%) and 82% specific (95% CI, 57-96%) for bacterial identification based on culture-positive and culture-negative samples, respectively. CMg sequencing reported the presence or absence of ß-lactam-resistant genes carried by Enterobacterales that would modify the initial guideline-recommended antibiotics in every case. CMg was also 100% concordant with quantitative PCR for detecting Aspergillus fumigatus from 4 positive and 39 negative samples. Molecular typing using 24-h sequencing data identified an MDR-K. pneumoniae ST307 outbreak involving 4 patients and an MDR-C. striatum outbreak involving 14 patients across three ICUs. CONCLUSION: CMg testing provides accurate pathogen detection and antibiotic resistance prediction in a same-day laboratory workflow, with assembled genomes available the next day for genomic surveillance. The provision of this technology in a service setting could fundamentally change the multi-disciplinary team approach to managing ICU infections. The potential to improve the initial targeted treatment and rapidly detect unsuspected outbreaks of MDR-pathogens justifies further expedited clinical assessment of CMg.

Health Care-Acquired Viral Respiratory Diseases.

Health care-acquired viral respiratory infections are common and cause increased patient morbidity and mortality. Although the threat of viral respiratory infection has been underscored by the coronavirus disease 2019 (COVID-19) pandemic, respiratory viruses have a significant impact in health care settings even under normal circumstances. Studies report decreased nosocomial transmission when aggressive infection control measures are implemented, with more success noted when using a multicomponent approach. Influenza vaccination of health care personnel furthers decrease rates of transmission; thus, mandatory vaccination is becoming more common. This article discusses the epidemiology, transmission, and control of health care-associated respiratory viral infections.

Managing Emergent Surgery for Ruptured Abdominal Aortic Aneurysm during the COVID-19 Pandemic.

BACKGROUND: Coronavirus disease 2019 (COVID-19) has become a global pandemic which may compromise the management of vascular emergencies. An uncompromised treatment for ruptured abdominal aortic aneurysm (rAAA) during such a health crisis represents a challenge. This study aimed to demonstrate the treatment outcomes of rAAA and the perioperative prevention of cross-infection under the COVID-19 pandemic. METHODS: In cases of rAAA during the pandemic, a perioperative workflow was applied to expedite coronavirus testing and avoid pre-operative delay, combined with a strategy for preventing cross-infection. Data of rAAA treated in 11 vascular centers between January-March 2020 collected retrospectively were compared to the corresponding period in 2018 and 2019. RESULTS: Eight, 12, and 14 rAAA patients were treated in 11 centers in January-March 2018, 2019, and 2020, respectively. An increased portion were treated at local hospitals with a comparable outcome compared with large centers in Guangzhou. With EVAR-first strategy, 85.7% patients with rAAA in 2020 underwent endovascular repair, similar to that in 2018 and 2019. The surgical outcomes during the pandemic were not inferior to that in 2018 and 2019. The average length of ICU stay was 1.8 ± 3.4 days in 2020, tending to be shorter than that in 2018 and 2019, whereas the length of hospital stay was similar among 3 years. The in-hospital mortality of 2018, 2019, and 2020 was 37.5%, 25.0%, and 14.3%, respectively. Three patients undergoing emergent surgeries were suspected of COVID-19, though turned out to be negative after surgery. CONCLUSIONS: Our experience for emergency management of rAAA and infection prevention for healthcare providers is effective in optimizing emergent surgical outcomes during the COVID-19 pandemic.

Protective effect of SARS-CoV-2 preventive measures against ESKAPE and Escherichia coli infections.

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.

Are surgical and non-operating room intervention safe in the COVID-19 pandemic? A retrospective study.

Little is known about the impact of COVID-19 on the outcomes of patients undergoing surgery and intervention. This study was conducted between 20 March and 20 May 2020 in six hospitals in Istanbul, and aimed to investigate the effects of surgery and intervention on COVID-19 disease progression, intensive care (ICU) need, mortality and virus transmission to patients and healthcare workers. Patients were examined in three groups: group I underwent emergency surgery, group II had an emergency non-operating room intervention, and group III received inpatient COVID-19 treatment but did not have surgery or undergo intervention. Mortality rates, mechanical ventilation needs and rates of admission to the ICU were compared between the three groups. During this period, patient and healthcare worker transmissions were recorded. In total, 1273 surgical, 476 non-operating room intervention patients and 1884 COVID-19 inpatients were examined. The rate of ICU requirement among patients who had surgery was nearly twice that for inpatients and intervention patients, but there was no difference in mortality between the groups. The overall mortality rates were 2.3% in surgical patients, 3.3% in intervention patients and 3% in inpatients. COVID-19 polymerase chain reaction positivity among hospital workers was 2.4%. Only 3.3% of infected frontline healthcare workers were anaesthesiologists. No deaths occurred among infected healthcare workers. We conclude that emergency surgery and non-operating room interventions during the pandemic period do not increase postoperative mortality and can be performed with low transmission rates.

Oxygen Therapy and Risk of Infection for Health Care Workers Caring for Patients With Viral Severe Acute Respiratory Infection: A Systematic Review and Meta-analysis.

STUDY OBJECTIVE: To synthesize the evidence regarding the infection risk associated with different modalities of oxygen therapy used in treating patients with severe acute respiratory infection. Health care workers face significant risk of infection when treating patients with a viral severe acute respiratory infection. To ensure health care worker safety and limit nosocomial transmission of such infection, it is crucial to synthesize the evidence regarding the infection risk associated with different modalities of oxygen therapy used in treating patients with severe acute respiratory infection. METHODS: MEDLINE, EMBASE, and the Cochrane Central Register of Controlled Trials were searched from January 1, 2000, to April 1, 2020, for studies describing the risk of infection associated with the modalities of oxygen therapy used for patients with severe acute respiratory infection. The study selection, data extraction, and quality assessment were performed by independent reviewers. The primary outcome measure was the infection of health care workers with a severe acute respiratory infection. Random-effect models were used to synthesize the extracted data. RESULTS: Of 22,123 citations, 50 studies were eligible for qualitative synthesis and 16 for meta-analysis. Globally, the quality of the included studies provided a very low certainty of evidence. Being exposed or performing an intubation (odds ratio 6.48; 95% confidence interval 2.90 to 14.44), bag-valve-mask ventilation (odds ratio 2.70; 95% confidence interval 1.31 to 5.36), and noninvasive ventilation (odds ratio 3.96; 95% confidence interval 2.12 to 7.40) were associated with an increased risk of infection. All modalities of oxygen therapy generate air dispersion. CONCLUSION: Most modalities of oxygen therapy are associated with an increased risk of infection and none have been demonstrated as safe. The lowest flow of oxygen should be used to maintain an adequate oxygen saturation for patients with severe acute respiratory infection, and manipulation of oxygen delivery equipment should be minimized.

Comprehensive investigation of an in-hospital transmission cluster of a symptomatic SARS-CoV-2-positive physician among patients and healthcare workers in Germany.

We investigated potential transmissions of a symptomatic SARS-CoV-2-positive physician in a tertiary-care hospital who worked for 15 cumulative hours without wearing a face mask. No in-hospital transmissions occurred, despite 254 contacts among patients and healthcare workers. In conclusion, exposed hospital staff continued work, accompanied by close clinical and virologic monitoring.