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1.
Genome Med ; 13(1): 182, 2021 11 17.
Article in English | MEDLINE | ID: covidwho-1523323

ABSTRACT

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.


Subject(s)
COVID-19/pathology , Cross Infection/transmission , Metagenomics , Anti-Bacterial Agents/therapeutic use , COVID-19/virology , Coinfection/drug therapy , Coinfection/microbiology , Corynebacterium/genetics , Corynebacterium/isolation & purification , Cross Infection/microbiology , DNA, Bacterial/chemistry , DNA, Bacterial/metabolism , Drug Resistance, Multiple, Bacterial/genetics , Female , Humans , Intensive Care Units , Klebsiella pneumoniae/genetics , Klebsiella pneumoniae/isolation & purification , Male , Middle Aged , Polymorphism, Single Nucleotide , SARS-CoV-2/isolation & purification , Sequence Analysis, DNA , beta-Lactamases/genetics
2.
Infect Dis Clin North Am ; 35(4): 1055-1075, 2021 12.
Article in English | MEDLINE | ID: covidwho-1487740

ABSTRACT

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.


Subject(s)
Cross Infection/prevention & control , Cross Infection/virology , Respiratory Tract Infections/prevention & control , Respiratory Tract Infections/virology , COVID-19/epidemiology , COVID-19/prevention & control , COVID-19/transmission , Cross Infection/epidemiology , Cross Infection/transmission , Guideline Adherence , Health Personnel/standards , Humans , Infection Control/standards , Respiratory Tract Infections/epidemiology , Respiratory Tract Infections/transmission , SARS-CoV-2/pathogenicity , Vaccination , Viruses/classification , Viruses/pathogenicity
3.
Epidemiol Infect ; 149: e210, 2021 09 16.
Article in English | MEDLINE | ID: covidwho-1411625

ABSTRACT

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.


Subject(s)
COVID-19/epidemiology , COVID-19/transmission , General Surgery/statistics & numerical data , Adult , COVID-19/diagnosis , Critical Care/statistics & numerical data , Cross Infection/diagnosis , Cross Infection/epidemiology , Cross Infection/transmission , Female , Health Personnel/statistics & numerical data , Hospital Mortality , Hospitalization , Humans , Male , Middle Aged , Retrospective Studies , SARS-CoV-2/genetics , SARS-CoV-2/isolation & purification , Turkey/epidemiology
4.
Ann Emerg Med ; 77(1): 19-31, 2021 01.
Article in English | MEDLINE | ID: covidwho-1382201

ABSTRACT

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.


Subject(s)
Cross Infection/transmission , Infectious Disease Transmission, Patient-to-Professional , Oxygen Inhalation Therapy , Severe Acute Respiratory Syndrome/transmission , Cross Infection/therapy , Humans , Oxygen Inhalation Therapy/adverse effects , Risk Factors , Severe Acute Respiratory Syndrome/therapy
5.
Infect Control Hosp Epidemiol ; 41(10): 1209-1211, 2020 Oct.
Article in English | MEDLINE | ID: covidwho-1387076

ABSTRACT

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.


Subject(s)
Coronavirus Infections/diagnosis , Infectious Disease Transmission, Professional-to-Patient , Physicians , Pneumonia, Viral/diagnosis , Betacoronavirus/isolation & purification , COVID-19 , Contact Tracing , Coronavirus Infections/transmission , Cross Infection/transmission , Cross Infection/virology , Female , Germany , Hospitals , Humans , Masks , Pandemics , Pneumonia, Viral/transmission , SARS-CoV-2
8.
Br J Surg ; 107(13): 1708-1712, 2020 12.
Article in English | MEDLINE | ID: covidwho-1384126

ABSTRACT

This study used a national administrative database to estimate perioperative SARS-CoV-2 infection risk, and associated mortality, relative to nosocomial transmission rates. The impact of nosocomial transmission was greatest after major emergency surgery, whereas laparoscopic surgery may be protective owing to reduced duration of hospital stay. Procedure-specific risk estimates are provided to facilitate surgical decision-making and informed consent. Estimated risks.


Subject(s)
Coronavirus Infections/epidemiology , Cross Infection/transmission , Elective Surgical Procedures/adverse effects , Infection Control/methods , Length of Stay/statistics & numerical data , Pneumonia, Viral/epidemiology , Surgical Wound Infection/mortality , COVID-19 , Cause of Death , Coronavirus Infections/prevention & control , Cross Infection/prevention & control , Databases, Factual , Elective Surgical Procedures/methods , Emergencies , Female , Humans , Incidence , Male , Pandemics/prevention & control , Pandemics/statistics & numerical data , Pneumonia, Viral/prevention & control , Prognosis , Risk Assessment , Surgical Wound Infection/prevention & control , Survival Analysis
9.
mSphere ; 6(4): e0038921, 2021 08 25.
Article in English | MEDLINE | ID: covidwho-1341306

ABSTRACT

SARS-CoV-2 nosocomial outbreaks in the first COVID-19 wave were likely associated with a shortage of personal protective equipment and scarce indications on control measures. Having covered these limitations, updates on current SARS-CoV-2 nosocomial outbreaks are required. We carried out an in-depth analysis of a 27-day nosocomial outbreak in a gastroenterology ward in our hospital, potentially involving 15 patients and 3 health care workers. Patients had stayed in one of three neighboring rooms in the ward. The severity of the infections in six of the cases and a high fatality rate made the clinicians suspect the possible involvement of a single virulent strain persisting in those rooms. Whole-genome sequencing (WGS) of the strains from 12 patients and 1 health care worker revealed an unexpected complexity. Five different SARS-CoV-2 strains were identified, two infecting a single patient each, ruling out their relationship with the outbreak; the remaining three strains were involved in three independent, overlapping, limited transmission clusters with three, three, and five cases. Whole-genome sequencing was key to understand the complexity of this outbreak. IMPORTANCE We report a complex epidemiological scenario of a nosocomial COVID-19 outbreak in the second wave, based on WGS analysis. Initially, standard epidemiological findings led to the assumption of a homogeneous outbreak caused by a single SARS-CoV-2 strain. The discriminatory power of WGS offered a strikingly different perspective consisting of five introductions of different strains, with only half of them causing secondary cases in three independent overlapping clusters. Our study exemplifies how complex the SARS-CoV-2 transmission in the nosocomial setting during the second COVID-19 wave occurred and leads to extending the analysis of outbreaks beyond the initial epidemiological assumptions.


Subject(s)
COVID-19/epidemiology , COVID-19/transmission , Cross Infection/epidemiology , Cross Infection/transmission , SARS-CoV-2/pathogenicity , Adolescent , Adult , Aged , COVID-19/virology , Cross Infection/virology , Disease Outbreaks/prevention & control , Female , Genome, Viral/genetics , Health Personnel , Hospitals , Humans , Male , Middle Aged , Phylogeny , SARS-CoV-2/genetics , Whole Genome Sequencing/methods , Young Adult
10.
Curr Opin Infect Dis ; 34(4): 365-371, 2021 08 01.
Article in English | MEDLINE | ID: covidwho-1341151

ABSTRACT

PURPOSE OF REVIEW: The coronavirus disease (COVID-19) pandemic has resulted in necessary modifications of infection control policies and practices in acute healthcare facilities globally. This is often accompanied by infrastructure modifications, ward redesignations, as well as healthcare staff redeployments and changes to infection prevention and control (IPC) practices. We review the potential for both negative and positive impacts these major changes can have on nosocomial transmission of multidrug-resistant organisms (MDROs). RECENT FINDINGS: Healthcare facilities around the world have reported outbreaks of MDROs during the COVID-19 pandemic. In contrast some centres have reported a decrease in baseline rates due to a number of possible factors. SUMMARY: While implementing crucial preventive measures for COVID-19, is it important to consider any collateral effects of changes in IPC and antimicrobial stewardship program (ASP) practices. The disruption caused to IPC and ASP practices during the pandemic are likely to see a counter intuitive increase in transmission of MDROs.


Subject(s)
COVID-19/epidemiology , Cross Infection/epidemiology , Cross Infection/etiology , Cross Infection/transmission , Drug Resistance, Microbial , Drug Resistance, Multiple , SARS-CoV-2 , Acute Disease , Anti-Infective Agents/pharmacology , Anti-Infective Agents/therapeutic use , Cross Infection/drug therapy , Disease Outbreaks , Hospitals , Humans , Infection Control/methods , Pandemics , Public Health Surveillance
14.
J Breath Res ; 15(4)2021 07 30.
Article in English | MEDLINE | ID: covidwho-1320288

ABSTRACT

The coronavirus disease 2019 (COVID-19) pandemic has imposed a considerable burden on hospitals and healthcare workers (HCWs) worldwide, increasing the risk of outbreaks and nosocomial transmission to 'non-COVID-19' patients, who represent the highest-risk population in terms of mortality, and HCWs. Since HCWs are at the interface between hospitals on the one hand and the community on the other, they are potential reservoirs, carriers, or victims of severe acute respiratory syndrome coronavirus 2 cross-transmission. In addition, there has been a paradigm shift in the management of viral respiratory outbreaks, such as the widespread testing of patients and HCWs, including asymptomatic individuals. In hospitals, there is a risk of aerosol transmission in poorly ventilated spaces, and when performing aerosol-producing procedures, it is imperative to take measures against aerosol transmission. In particular, spatial separation of the inpatient ward for non-COVID-19 patients from that designated for patients with suspected or confirmed COVID-19 as well as negative-pressure isolation on the floor of the ward, using an airborne infection isolation device could help prevent nosocomial infection.


Subject(s)
COVID-19/prevention & control , Cross Infection/prevention & control , Health Personnel/statistics & numerical data , Hospitals , Infection Control , Physical Distancing , Ventilation , Aerosols , COVID-19/diagnosis , COVID-19/epidemiology , COVID-19/transmission , COVID-19 Testing , Cross Infection/diagnosis , Cross Infection/epidemiology , Cross Infection/transmission , Humans , Infection Control/methods , Infection Control/statistics & numerical data , SARS-CoV-2 , Ventilation/methods , Ventilation/statistics & numerical data
17.
Ann Surg ; 274(2): 234-239, 2021 08 01.
Article in English | MEDLINE | ID: covidwho-1304022

ABSTRACT

OBJECTIVE: The aim of this study was to assess the outcomes of tracheostomy in patients with COVID-19 respiratory failure. SUMMARY BACKGROUND DATA: Tracheostomy has an essential role in managing COVID-19 patients with respiratory failure who require prolonged mechanical ventilation. However, limited data are available on how tracheostomy affects COVID-19 outcomes, and uncertainty surrounding risk of infectious transmission has led to divergent recommendations and practices. METHODS: It is a multicenter, retrospective study; data were collected on all tracheostomies performed in COVID-19 patients at 7 hospitals in 5 tertiary academic medical systems from February 1, 2020 to September 4, 2020. RESULT: Tracheotomy was performed in 118 patients with median time from intubation to tracheostomy of 22 days (Q1-Q3: 18-25). All tracheostomies were performed employing measures to minimize aerosol generation, 78.0% by percutaneous technique, and 95.8% at bedside in negative pressure rooms. Seventy-eight (66.1%) patients were weaned from the ventilator and 18 (15.3%) patients died from causes unrelated to tracheostomy. No major procedural complications occurred. Early tracheostomy (≤14 days) was associated with decreased ventilator days; median ventilator days (Q1-Q3) among patients weaned from the ventilator in the early, middle and late groups were 21 (21-31), 34 (26.5-42), and 37 (32-41) days, respectively with P = 0.030. Compared to surgical tracheostomy, percutaneous technique was associated with faster weaning for patients weaned off the ventilator [median (Q1-Q3): 34 (29-39) vs 39 (34-51) days, P = 0.038]; decreased ventilator-associated pneumonia (58.7% vs 80.8%, P = 0.039); and among patients who were discharged, shorter intensive care unit duration [median (Q1-Q3): 33 (27-42) vs 47 (33-64) days, P = 0.009]; and shorter hospital length of stay [median (Q1-Q3): 46 (33-59) vs 59.5 (48-80) days, P = 0.001]. CONCLUSION: Early, percutaneous tracheostomy was associated with improved outcomes compared to surgical tracheostomy in a multi-institutional series of ventilated patients with COVID-19.


Subject(s)
COVID-19/therapy , Pneumonia, Viral/therapy , Respiration, Artificial , Respiratory Insufficiency/therapy , Respiratory Insufficiency/virology , Tracheostomy/methods , Adult , Aged , Cross Infection/transmission , Female , Humans , Male , Middle Aged , Pneumonia, Viral/virology , Retrospective Studies , SARS-CoV-2 , Tracheotomy/methods , United States
18.
Med Sci (Basel) ; 9(3)2021 06 30.
Article in English | MEDLINE | ID: covidwho-1288951

ABSTRACT

Aim: To determine the frequency, mode of transmission, and outcome of Coronavirus Disease 2019 (COVID-19) among healthcare workers (HCWs) in a tertiary care cardiac center in the Kingdom of Saudi Arabia (KSA). Methods: This is a retrospective study of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infected HCWs and was conducted from 2 March to 31 December 2020. Data related to the presence of COVID-19 symptoms, mode of transmission, hospitalization, and mortality were collected from the patients' medical records. Results: Of the 4462 patients tested for COVID-19 by real-time reverse transcriptase polymerase chain reaction (RT-PCR), 203 (4.5%) HCWs were positive; of these, 125 (61.6%) were males, and the most common age group was <40 years. The most commonly encountered health professionals were nurses (74, 36.4%), followed by therapists/technicians (48, 23.6%), housekeepers (25, 12.3%), and physicians (21, 10.4%). The majority (184, 90.6%) of the HCWs contracted COVID-19 in the community, and only 19 (9.4%) were healthcare-associated infections. Of the infected HCWs, 169 (83.3%) had mild symptoms and were managed in home isolation. The most common symptoms were fever (128, 63.1%), body ache (124, 61.8%), headache (113, 55.7%), dry cough (123, 60.6%), sore throat (97, 47.8%), body weakness (97, 47.8%), and fatigue (94, 46.3%). Comparing males and females, there was a significantly higher number of female nurses; in contrast, there was a higher number of male physicians, housekeepers, therapists/technicians, and other specialty HCWs. A significantly lower number of nurses, therapists/technicians were infected in the ≥40 years age group compared to <40 years. Furthermore, a significantly higher difference was observed among non-Saudi nurses compared to Saudi nurses. No mortality was documented among the included HCWs. Conclusions: In the largest tertiary cardiac center in KSA, most HCWs who contracted COVID-19 developed mild symptoms; nurses and those aged <40 years were most commonly infected, and most infections were acquired in the community. HCWs' adherence to mitigation measures outside of the workplace is vital to curb the current pandemic and decrease nosocomial transmission risk.


Subject(s)
COVID-19/transmission , Cross Infection/epidemiology , Health Personnel/statistics & numerical data , Tertiary Care Centers , Adult , COVID-19/epidemiology , Cardiology , Cross Infection/transmission , Female , Hospitalization/statistics & numerical data , Humans , Male , Middle Aged , Retrospective Studies , Saudi Arabia , Young Adult
19.
Respir Med ; 186: 106516, 2021 09.
Article in English | MEDLINE | ID: covidwho-1275693

ABSTRACT

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is transmitted through respiratory droplets, aerosols and close contact. Cross infections occur because viruses spread rapidly among humans. Nineteen percent (19%) of the infected patients developed severe pneumonia and acute respiratory distress syndrome (ARDS). Hypoxemia usually occurs and patients may require oxygen therapy or mechanical ventilation (MV) support. In this article, recently published clinical experience and observational studies were reviewed. Corresponding respiratory therapy regarding different stages of infection is proposed. Infection control principles and respiratory strategies including oxygen therapy, non-invasive respiratory support (NIRS), intubation evaluation, equipment preparation, ventilator settings, special maneuvers comprise of the prone position (PP), recruitment maneuver (RM), extracorporeal membrane oxygenation (ECMO), weaning and extubation are summarized. Respiratory equipment and device disinfection recommendations are worked up. We expect this review article could be used as a reference by healthcare workers in patient care while minimizing the risk of environmental contamination.


Subject(s)
COVID-19/prevention & control , COVID-19/therapy , Critical Care/methods , Critical Illness , Extracorporeal Membrane Oxygenation/methods , Infection Control/methods , Oxygen Inhalation Therapy/methods , Respiration, Artificial/methods , SARS-CoV-2/pathogenicity , COVID-19/complications , COVID-19/transmission , Cannula , Cross Infection/prevention & control , Cross Infection/transmission , Cross Infection/virology , Humans , Hypoxia/etiology , Hypoxia/therapy , Pneumonia, Viral/etiology , Pneumonia, Viral/therapy , Respiratory Distress Syndrome/etiology , Respiratory Distress Syndrome/therapy
20.
Infect Control Hosp Epidemiol ; 42(6): 746-750, 2021 06.
Article in English | MEDLINE | ID: covidwho-1263424

ABSTRACT

A questionnaire was distributed to hospitals in Tokyo (N = 38) regarding their preparedness against and in-facility transmission of coronavirus disease 2019 (COVID-19). As of May 31, 2020, 284 HCP had contracted COVID-19, and in-facility COVID-19 transmission occurred at 13 hospitals, negatively impacting hospital functions and patient care.


Subject(s)
COVID-19/epidemiology , Cross Infection/epidemiology , Personnel, Hospital/psychology , Adult , Aged , Aged, 80 and over , COVID-19/prevention & control , COVID-19/therapy , COVID-19/transmission , Cross Infection/prevention & control , Cross Infection/therapy , Cross Infection/transmission , Female , Humans , Infectious Disease Transmission, Patient-to-Professional/prevention & control , Infectious Disease Transmission, Patient-to-Professional/statistics & numerical data , Male , Middle Aged , Personnel, Hospital/statistics & numerical data , Surveys and Questionnaires , Tokyo/epidemiology , Young Adult
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