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2.
Clin Infect Dis ; 78(5): 1204-1213, 2024 May 15.
Article in English | MEDLINE | ID: mdl-38227643

ABSTRACT

BACKGROUND: Infection prevention (IP) measures are designed to mitigate the transmission of pathogens in healthcare. Using large-scale viral genomic and social network analyses, we determined if IP measures used during the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic were adequate in protecting healthcare workers (HCWs) and patients from acquiring SARS-CoV-2. METHODS: We performed retrospective cross-sectional analyses of viral genomics from all available SARS-CoV-2 viral samples collected at UC San Diego Health and social network analysis using the electronic medical record to derive temporospatial overlap of infections among related viromes and supplemented with contact tracing data. The outcome measure was any instance of healthcare transmission, defined as cases with closely related viral genomes and epidemiological connection within the healthcare setting during the infection window. Between November 2020 through January 2022, 12 933 viral genomes were obtained from 35 666 patients and HCWs. RESULTS: Among 5112 SARS-CoV-2 viral samples sequenced from the second and third waves of SARS-CoV-2 (pre-Omicron), 291 pairs were derived from persons with a plausible healthcare overlap. Of these, 34 pairs (12%) were phylogenetically linked: 19 attributable to household and 14 to healthcare transmission. During the Omicron wave, 2106 contact pairs among 7821 sequences resulted in 120 (6%) related pairs among 32 clusters, of which 10 were consistent with healthcare transmission. Transmission was more likely to occur in shared spaces in the older hospital compared with the newer hospital (2.54 vs 0.63 transmission events per 1000 admissions, P < .001). CONCLUSIONS: IP strategies were effective at identifying and preventing healthcare SARS-CoV-2 transmission.


Subject(s)
COVID-19 , Genome, Viral , Health Personnel , SARS-CoV-2 , Humans , COVID-19/transmission , COVID-19/epidemiology , COVID-19/virology , SARS-CoV-2/genetics , Retrospective Studies , Cross-Sectional Studies , Male , Female , Adult , Middle Aged , Aged , Social Network Analysis , Contact Tracing , Genomics , Young Adult , Adolescent , Child , Aged, 80 and over , Cross Infection/transmission , Cross Infection/virology , Cross Infection/epidemiology , Child, Preschool
3.
J Clin Virol ; 164: 105497, 2023 07.
Article in English | MEDLINE | ID: mdl-37253299

ABSTRACT

BACKGROUND: Rotavirus group A (RVA) is a causative agent of acute gastroenteritis among young children worldwide, despite the global expansion of rotavirus vaccination. In Korea, although the prevalence of RVA has been reduced among young children owing to vaccination, nosocomial infections still occur among neonates. OBJECTIVES: The aim of this study was to investigate the molecular epidemiology of RVA strains associated with several neonatal outbreaks in Seoul from 2017 to 2020. STUDY DESIGN: Clinical and environmental samples were collected and screened for the presence of RVA using ELISA and PCR targeting VP6, respectively. RVA-positive strains were genotyped via RT-PCR and subsequent sequencing of VP4 and VP7 and were phylogenetically compared with RVA strains from other countries. RESULTS: During 2017-2020, a total of 15 RVA outbreaks occurred at neonatal facilities (six in hospital neonatal wards and nine in postpartum care centers) in Seoul, and only two RVA genotypes were detected: G4P[6] and G8P[6]. G8P[6] emerged in Seoul November 2018 and immediately became the predominant genotype among neonates, at least up to 2020. Phylogenetic analysis revealed that the G8P[6] genotype in this study was closely related to G8P[6] strains first identified in Korea in 2017, but differed from G8P[6] strains detected in Africa. CONCLUSIONS: A novel G8P[6] genotype of RVA strains has emerged and caused outbreaks among neonates in Seoul. Continued surveillance for circulating RVA genotypes is imperative to monitor genotype changes and their potential risks to public health.


Subject(s)
Cross Infection , Disease Outbreaks , Molecular Epidemiology , Phylogeny , Rotavirus Infections , Rotavirus , Female , Humans , Infant, Newborn , Feces/virology , Genotype , Rotavirus/genetics , Rotavirus Infections/epidemiology , Rotavirus Infections/virology , Seoul/epidemiology , Cross Infection/epidemiology , Cross Infection/virology , Capsid Proteins/genetics , Environmental Microbiology , Male
4.
J Infect Dev Ctries ; 16(9): 1432-1438, 2022 09 30.
Article in English | MEDLINE | ID: mdl-36223618

ABSTRACT

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.


Subject(s)
COVID-19 , Cross Infection , Equipment Contamination , Hospitals , COVID-19/transmission , Cross Infection/transmission , Cross Infection/virology , Humans , RNA, Viral/genetics , SARS-CoV-2/genetics
5.
N Engl J Med ; 386(24): 2283-2294, 2022 06 16.
Article in English | MEDLINE | ID: mdl-35704480

ABSTRACT

BACKGROUND: In June 2019, the Bolivian Ministry of Health reported a cluster of cases of hemorrhagic fever that started in the municipality of Caranavi and expanded to La Paz. The cause of these cases was unknown. METHODS: We obtained samples for next-generation sequencing and virus isolation. Human and rodent specimens were tested by means of virus-specific real-time quantitative reverse-transcriptase-polymerase-chain-reaction assays, next-generation sequencing, and virus isolation. RESULTS: Nine cases of hemorrhagic fever were identified; four of the patients with this illness died. The etiologic agent was identified as Mammarenavirus Chapare mammarenavirus, or Chapare virus (CHAPV), which causes Chapare hemorrhagic fever (CHHF). Probable nosocomial transmission among health care workers was identified. Some patients with CHHF had neurologic manifestations, and those who survived had a prolonged recovery period. CHAPV RNA was detected in a variety of human body fluids (including blood; urine; nasopharyngeal, oropharyngeal, and bronchoalveolar-lavage fluid; conjunctiva; and semen) and in specimens obtained from captured small-eared pygmy rice rats (Oligoryzomys microtis). In survivors of CHHF, viral RNA was detected up to 170 days after symptom onset; CHAPV was isolated from a semen sample obtained 86 days after symptom onset. CONCLUSIONS: M. Chapare mammarenavirus was identified as the etiologic agent of CHHF. Both spillover from a zoonotic reservoir and possible person-to-person transmission were identified. This virus was detected in a rodent species, O. microtis. (Funded by the Bolivian Ministry of Health and others.).


Subject(s)
Arenaviruses, New World , Hemorrhagic Fever, American , RNA, Viral , Rodentia , Animals , Arenaviruses, New World/genetics , Arenaviruses, New World/isolation & purification , Bolivia/epidemiology , Cross Infection/transmission , Cross Infection/virology , Disease Transmission, Infectious , Hemorrhagic Fever, American/complications , Hemorrhagic Fever, American/genetics , Hemorrhagic Fever, American/transmission , Hemorrhagic Fever, American/virology , Hemorrhagic Fevers, Viral/genetics , Hemorrhagic Fevers, Viral/transmission , Hemorrhagic Fevers, Viral/virology , High-Throughput Nucleotide Sequencing , Humans , Polymerase Chain Reaction , RNA, Viral/genetics , RNA, Viral/isolation & purification , Rats/virology , Rodentia/virology , Viral Zoonoses/transmission , Viral Zoonoses/virology
6.
J Hosp Infect ; 126: 1-9, 2022 Aug.
Article in English | MEDLINE | ID: mdl-35562074

ABSTRACT

AIM: To provide a detailed genomic-epidemiological description of a complex multi-ward SARS-CoV-2 outbreak, which originated in the crowded emergency department (ED) in our hospital during the third wave of the COVID-19 pandemic, and was elucidated promptly by local whole-genome sequencing (WGS). METHODS: SARS-CoV-2 was detected by reverse transcriptase real-time polymerase chain reaction on viral RNA extracted from nasopharyngeal swabs. WGS was performed using an Oxford MinION Mk1C instrument following the ARTIC v3 sequencing protocol. High-quality consensus genomes were assembled with the artic-ncov2019 bioinformatics pipeline and viral phylogenetic trees were built, inferred by maximum-likelihood. Clusters were defined using a threshold of 0-1 single nucleotide polymorphisms (SNPs) between epidemiologically linked sequences. RESULTS: In April 2021, outbreaks of COVID-19 were declared on two wards at University Hospital Limerick after 4 healthcare-associated SARS-CoV-2 infections were detected by post-admission surveillance testing. Contact tracing identified 12 further connected cases; all with direct or indirect links to the ED 'COVID Zone'. All sequences were assigned to the Pangolin B.1.1.7 lineage by WGS, and SNP-level analysis revealed two distinct but simultaneous clusters of infections. Repeated transmission in the ED was demonstrated, involving patients accommodated on trolleys in crowded areas, resulting in multiple generations of infections across three inpatient hospital wards and subsequently to the local community. These findings informed mitigation efforts to prevent cross-transmission in the ED. CONCLUSION: Cross-transmission of SARS-CoV-2 occurred repeatedly in an overcrowded emergency department. Viral WGS elucidated complex viral transmission networks in our hospital and informed infection, prevention and control practice.


Subject(s)
COVID-19 , Cross Infection , Emergency Service, Hospital , COVID-19/epidemiology , COVID-19/transmission , Cross Infection/epidemiology , Cross Infection/virology , Genome, Viral , Humans , Ireland/epidemiology , Pandemics/prevention & control , Phylogeny , SARS-CoV-2/genetics , Whole Genome Sequencing
7.
BMC Infect Dis ; 22(1): 139, 2022 Feb 10.
Article in English | MEDLINE | ID: mdl-35139811

ABSTRACT

BACKGROUND: Individuals with intellectual and developmental disabilities (IDD) living in congregated settings have increased risk of COVID-19 infection and mortality. Little is known about variant B.1.1.519 with spike mutation T478K, dominant in Mexico. We describe a linked SARS-CoV-2 B.1.1.519 outbreak in three IDD facilities in the Netherlands. METHODS: Following notification of the index, subsequent cases were identified through serial PCR group testing. Positive specimens were submitted for whole-genome-sequencing. Clinical information was gathered through interviews with staff members of the three facilities. RESULTS: Attack rate (AR) in clients of the index facility was 92% (23/25), total AR in clients 45% (33/73) and in staff members 24% (8/34). 55% (18/33) of client cases were asymptomatic, versus 25% (2/8) of staff members. Five client cases (15%) were hospitalized, two died (6%). Sequencing yielded the same specific B.1.1.519 genotype in all three facilities. No significant difference in median viral load was established comparing the B.1.1.519 variant with other circulating variants. The index of the linked outbreak reported no travel history or link to suspected or confirmed cases suggesting regional surveillance. Observed peak regional prevalence of B.1.1.519 during the outbreak supports this. CONCLUSION: AR, morbidity and mortality prior to control measures taking effect were high, probably related to the specific characteristics of the IDD setting and its clients. We assessed no evidence for intrinsic contributing properties of variant B.1.1.519. Our study argues for enhanced infection prevention protocols in the IDD setting, and prioritization of this group for vaccination against COVID-19.


Subject(s)
Assisted Living Facilities , COVID-19 , Cross Infection , COVID-19/epidemiology , COVID-19/virology , Cross Infection/epidemiology , Cross Infection/virology , Developmental Disabilities , Disease Outbreaks , Humans , Mutation , Netherlands/epidemiology , SARS-CoV-2 , Spike Glycoprotein, Coronavirus/genetics
8.
Viruses ; 14(2)2022 02 21.
Article in English | MEDLINE | ID: mdl-35216039

ABSTRACT

Coinfection rates with other pathogens in coronavirus disease 2019 (COVID-19) varied during the pandemic. We assessed the latest prevalence of coinfection with viruses, bacteria, and fungi in COVID-19 patients for more than one year and its impact on mortality. A total of 436 samples were collected between August 2020 and October 2021. Multiplex real-time PCR, culture, and antimicrobial susceptibility testing were performed to detect pathogens. The coinfection rate of respiratory viruses in COVID-19 patients was 1.4%. Meanwhile, the rates of bacteria and fungi were 52.6% and 10.5% in hospitalized COVID-19 patients, respectively. Respiratory syncytial virus, rhinovirus, Acinetobacter baumannii, Escherichia coli, Pseudomonas aeruginosa, and Candida albicans were the most commonly detected pathogens. Ninety percent of isolated A. baumannii was non-susceptible to carbapenem. Based on a multivariate analysis, coinfection (odds ratio [OR] = 6.095), older age (OR = 1.089), and elevated lactate dehydrogenase (OR = 1.006) were risk factors for mortality as a critical outcome. In particular, coinfection with bacteria (OR = 11.250), resistant pathogens (OR = 11.667), and infection with multiple pathogens (OR = 10.667) were significantly related to death. Screening and monitoring of coinfection in COVID-19 patients, especially for hospitalized patients during the pandemic, are beneficial for better management and survival.


Subject(s)
Bacterial Infections/epidemiology , COVID-19/epidemiology , Coinfection/microbiology , Coinfection/virology , Mycoses/epidemiology , Virus Diseases/epidemiology , Adolescent , Adult , Bacteria/classification , Bacteria/pathogenicity , COVID-19/microbiology , COVID-19/virology , Coinfection/epidemiology , Coinfection/mortality , Cross Infection/epidemiology , Cross Infection/microbiology , Cross Infection/virology , Female , Fungi/classification , Fungi/pathogenicity , Humans , Male , Middle Aged , Prevalence , Republic of Korea/epidemiology , Viruses/classification , Viruses/pathogenicity , Young Adult
9.
Microbiol Spectr ; 10(1): e0153221, 2022 02 23.
Article in English | MEDLINE | ID: mdl-34985301

ABSTRACT

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.


Subject(s)
COVID-19 Vaccines/administration & dosage , COVID-19/prevention & control , Cross Infection/transmission , SARS-CoV-2/immunology , COVID-19/transmission , COVID-19/virology , Cross Infection/epidemiology , Cross Infection/prevention & control , Cross Infection/virology , Health Personnel/statistics & numerical data , Humans , Phylogeny , SARS-CoV-2/classification , SARS-CoV-2/genetics , SARS-CoV-2/isolation & purification , Vaccination , Whole Genome Sequencing
10.
Ann Vasc Surg ; 79: 114-121, 2022 Feb.
Article in English | MEDLINE | ID: mdl-34644628

ABSTRACT

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.


Subject(s)
Aortic Aneurysm, Abdominal/surgery , Aortic Rupture/surgery , COVID-19/prevention & control , Cross Infection/prevention & control , Infection Control , Vascular Surgical Procedures , Aged , Aged, 80 and over , Aortic Aneurysm, Abdominal/diagnosis , Aortic Rupture/diagnosis , COVID-19/diagnosis , COVID-19/transmission , COVID-19/virology , COVID-19 Testing , China , Cross Infection/diagnosis , Cross Infection/transmission , Cross Infection/virology , Emergencies , Female , Humans , Male , Middle Aged , Patient Safety , Retrospective Studies , Risk Assessment , Risk Factors , Time Factors , Treatment Outcome , Vascular Surgical Procedures/adverse effects , Workflow
12.
PLoS One ; 16(12): e0260714, 2021.
Article in English | MEDLINE | ID: mdl-34855869

ABSTRACT

The first confirmed case of COVID-19 in Quebec, Canada, occurred at Verdun Hospital on February 25, 2020. A month later, a localized outbreak was observed at this hospital. We performed tiled amplicon whole genome nanopore sequencing on nasopharyngeal swabs from all SARS-CoV-2 positive samples from 31 March to 17 April 2020 in 2 local hospitals to assess viral diversity (unknown at the time in Quebec) and potential associations with clinical outcomes. We report 264 viral genomes from 242 individuals-both staff and patients-with associated clinical features and outcomes, as well as longitudinal samples and technical replicates. Viral lineage assessment identified multiple subclades in both hospitals, with a predominant subclade in the Verdun outbreak, indicative of hospital-acquired transmission. Dimensionality reduction identified two subclades with mutations of clinical interest, namely in the Spike protein, that evaded supervised lineage assignment methods-including Pangolin and NextClade supervised lineage assignment tools. We also report that certain symptoms (headache, myalgia and sore throat) are significantly associated with favorable patient outcomes. Our findings demonstrate the strength of unsupervised, data-driven analyses whilst suggesting that caution should be used when employing supervised genomic workflows, particularly during the early stages of a pandemic.


Subject(s)
COVID-19/virology , Cross Infection/virology , Disease Outbreaks , Genome, Viral/genetics , SARS-CoV-2/genetics , Adolescent , Adult , Aged , Aged, 80 and over , COVID-19/epidemiology , COVID-19/mortality , Child , Child, Preschool , Cross Infection/epidemiology , Disease Outbreaks/statistics & numerical data , Female , Haplotypes/genetics , Humans , Male , Middle Aged , Phylogeny , Quebec/epidemiology , SARS-CoV-2/pathogenicity , Sequence Analysis, RNA , Treatment Outcome , Young Adult
13.
Infect Dis Clin North Am ; 35(4): 1055-1075, 2021 12.
Article in English | MEDLINE | ID: mdl-34752220

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
14.
Ann Intern Med ; 174(12): 1710-1718, 2021 12.
Article in English | MEDLINE | ID: mdl-34748374

ABSTRACT

Policies to prevent respiratory virus transmission in health care settings have traditionally divided organisms into Droplet versus Airborne categories. Droplet organisms (for example, influenza) are said to be transmitted via large respiratory secretions that rapidly fall to the ground within 1 to 2 meters and are adequately blocked by surgical masks. Airborne pathogens (for example, measles), by contrast, are transmitted by aerosols that are small enough and light enough to carry beyond 2 meters and to penetrate the gaps between masks and faces; health care workers are advised to wear N95 respirators and to place these patients in negative-pressure rooms. Respirators and negative-pressure rooms are also recommended when caring for patients with influenza or SARS-CoV-2 who are undergoing "aerosol-generating procedures," such as intubation. An increasing body of evidence, however, questions this framework. People routinely emit respiratory particles in a range of sizes, but most are aerosols, and most procedures do not generate meaningfully more aerosols than ordinary breathing, and far fewer than coughing, exercise, or labored breathing. Most transmission nonetheless occurs at close range because virus-laden aerosols are most concentrated at the source; they then diffuse and dilute with distance, making long-distance transmission rare in well-ventilated spaces. The primary risk factors for nosocomial transmission are community incidence rates, viral load, symptoms, proximity, duration of exposure, and poor ventilation. Failure to appreciate these factors may lead to underappreciation of some risks (for example, overestimation of the protection provided by medical masks, insufficient attention to ventilation) or misallocation of limited resources (for example, reserving N95 respirators and negative-pressure rooms only for aerosol-generating procedures or requiring negative-pressure rooms for all patients with SARS-CoV-2 infection regardless of stage of illness). Enhanced understanding of the factors governing respiratory pathogen transmission may inform the development of more effective policies to prevent nosocomial transmission of respiratory pathogens.


Subject(s)
Infection Control/methods , Respiratory Tract Infections/transmission , Respiratory Tract Infections/virology , Aerosols , COVID-19/prevention & control , COVID-19/transmission , COVID-19/virology , Cross Infection/prevention & control , Cross Infection/virology , Health Policy , Humans , Infectious Disease Transmission, Patient-to-Professional/prevention & control , Influenza, Human/prevention & control , Influenza, Human/transmission , Influenza, Human/virology , Masks , Personnel, Hospital , SARS-CoV-2 , United States/epidemiology , Ventilation
15.
PLoS One ; 16(10): e0257513, 2021.
Article in English | MEDLINE | ID: mdl-34634076

ABSTRACT

BACKGROUND: Coronavirus disease (COVID-19) is associated with a high mortality rate in older adults; therefore, it is important for medical institutions to take measures to prevent severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission. This study aimed to assess the risk of SARS-CoV-2 infection among healthcare workers (HCWs) and the effectiveness of infection control measures. METHODS: This study had a cross-sectional component and a prospective cohort component. The cross-sectional component comprised an anti-SARS-CoV-2 antibody survey among HCWs at a medical center in Saitama City, Japan. In the prospective cohort component, HCWs at the same medical center were tested for anti-SARS-CoV-2 antibodies monthly over a 3-month period (May to July 2020) to assess the effectiveness of infection prevention measures, including personal protective equipment use. All participants in the cohort study also participated in the antibody survey. The primary outcome was anti-SARS-CoV-2 antibody (measured using Elecsys® Anti-SARS-CoV-2) positivity based on whether participants were engaged in COVID-19-related medical care. Other risk factors considered included occupational category, age, and sex. RESULTS: In total, 607 HCWs participated in the antibody survey and 116 doctors and nurses participated in the cohort study. Only one of the 607 participants in the survey tested positive for anti-SARS-CoV-2 antibodies. All participants in the cohort study were anti-SARS-CoV-2 antibody negative at baseline and remained antibody negative. Engaging in the care of COVID-19 patients did not increase the risk of antibody positivity. During the study period, a total of 30 COVID-19 in-patients were treated in the hospital. CONCLUSIONS: The infection control measures in the hospital protected HCWs from nosocomially acquired SARS-CoV-2 infection; thus, HCWs should engage in COVID-19-related medical care with confidence provided that they adhere to infectious disease precautions.


Subject(s)
COVID-19/prevention & control , COVID-19/transmission , Cross Infection/prevention & control , Health Personnel , Infection Control/methods , SARS-CoV-2/immunology , Adult , Antibodies, Viral/blood , Antibodies, Viral/immunology , COVID-19/epidemiology , COVID-19/virology , Cross Infection/blood , Cross Infection/virology , Cross-Sectional Studies , Female , Hospitals , Humans , Immunoglobulin G/blood , Immunoglobulin G/immunology , Incidence , Japan/epidemiology , Male , Prospective Studies , Risk Factors , Seroepidemiologic Studies
16.
Antimicrob Resist Infect Control ; 10(1): 137, 2021 09 26.
Article in English | MEDLINE | ID: mdl-34565476

ABSTRACT

We describe the lessons learned during a SARS-CoV-2 variant-of-concern Alpha outbreak investigation at a normal care unit in a university hospital in Amsterdam in December 2020. The outbreak consisted of nine nurses and two roomed-in patient family members. (attack rate 18%). One nurse tested positive with a phylogenetically distinct variant, after a documented infection 83 days prior. Three key points were taken from this investigation. First, it was controlled by adherence to existing guidelines, despite increased transmissibility of the variant. Second, viral sequencing can inform transmission cluster inference, but the epidemiological context is essential to draw appropriate conclusions. Third, reinfections with Alpha variants can occur rapidly after primary infection.


Subject(s)
COVID-19/epidemiology , Reinfection/virology , COVID-19/virology , Cross Infection/epidemiology , Cross Infection/virology , Disease Outbreaks , Guideline Adherence , Humans , Infection Control , Inpatients , Netherlands , Nurses , Phylogeny , Reinfection/epidemiology , SARS-CoV-2/genetics
17.
Epidemiol Infect ; 150: e18, 2021 09 15.
Article in English | MEDLINE | ID: mdl-34521489

ABSTRACT

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).


Subject(s)
COVID-19/epidemiology , Disease Outbreaks , Laundry Service, Hospital , SARS-CoV-2 , Adult , COVID-19/transmission , Cohort Studies , Contact Tracing , Cross Infection/epidemiology , Cross Infection/transmission , Cross Infection/virology , Disease Outbreaks/statistics & numerical data , Female , Humans , Israel/epidemiology , Male , Middle Aged , Phylogeny , RNA, Viral/chemistry , RNA, Viral/isolation & purification , SARS-CoV-2/classification , SARS-CoV-2/genetics
18.
J Infect Dev Ctries ; 15(8): 1074-1079, 2021 08 31.
Article in English | MEDLINE | ID: mdl-34516413

ABSTRACT

INTRODUCTION: Public life in China is gradually returning to normal with strong measures in coronavirus 2019 (COVID-19) control. Because of the long-term effects of COVID-19, medical institutions had to make timely adjustments to control policies and priorities to balance between COVID-19 prevention and daily medical services. METHODOLOGY: The framework for infection prevention and control in the inpatient department was effectively organized at both hospital and department levels. A series of prevention and control strategies was implemented under this leadership: application of rigorous risk assessment and triage before admission through a query list; classifying patients into three risk levels and providing corresponding medical treatment and emergency handling; establishing new ward visiting criteria for visitors; designing procedures for PPE and stockpile management; executing specialized disinfection and medical waste policies. RESULTS: Till June 2020, the bed occupancy had recovered from 20.0% to 88.1%. In total, 13045 patients were received in our hospital, of which 54 and 127 patients were identified as high-risk and medium-risk, respectively, and 2 patients in the high-risk group were eventually laboratory-confirmed with COVID-19. No hospital-acquired infection of COVID-19 has been observed since the emergency appeared. CONCLUSIONS: The strategies ensured early detection and targeted prevention of COVID-19 following the COVID-19 pandemic, which improved the recovery of medical services after the pandemic.


Subject(s)
COVID-19/prevention & control , Cross Infection/prevention & control , Hospitals/statistics & numerical data , Infection Control/methods , COVID-19/epidemiology , China/epidemiology , Cross Infection/epidemiology , Cross Infection/virology , Hospitalization/statistics & numerical data , Hospitals/standards , Humans , Infection Control/instrumentation , Inpatients/statistics & numerical data , Patient Isolation/methods , Personal Protective Equipment , Risk Assessment , Triage
19.
Antimicrob Resist Infect Control ; 10(1): 133, 2021 09 10.
Article in English | MEDLINE | ID: mdl-34507617

ABSTRACT

OBJECTIVES/PURPOSE: High-touch surfaces are a critical reservoir in the spread of nosocomial infections. Although disinfection and infection control protocols are well developed, they lack the ability to passively reduce the pathogenic load of high-touch surfaces. Copper and its alloys have been suggested as a surface that exhibit continuous biocidal effects. Antimicrobial studies on these surfaces are prevalent, while virucidal studies are not as well explored. The goal of this study was to first determine the virucidal activity of a copper-nickel-zinc alloy and to then examine the effect of soiling and virus preparation on virucidal activity. METHODS: A baculovirus vector was used as an easily quantifiable model of an infectious enveloped animal cell virus. Droplets containing virus were deposited on surfaces and allowed to stay wet using humidity control or were dried onto the surface. Virus was then recovered from the surface and assayed for infectivity. To examine how the composition of the droplet affected the survival of the virus, 3 different soiling conditions were tested. The first two were recommended by the United States Environmental Protection Agency and the third consisted of cell debris resulting from virus amplification. RESULTS: A copper-nickel-zinc alloy was shown to have strong virucidal effects for an enveloped virus. Copper, nickel, and zinc ions were all shown to leach from the alloy surface and are the likely cause of virucidal activity by this surface. Virucidal activity was achieved under moderate soiling but lost under high soiling generated by routine virus amplification procedures. The surface was able to repeatably inactivate dried virus droplets under moderate soiling conditions, but unable to do so for virus droplets kept wet using high humidity. CONCLUSION: Ion leaching was associated with virucidal activity in both wet and dried virus conditions. Soiling protected the virus by quenching metal ions, and not by inhibiting leaching. The composition of the solution containing virus plays a critical role in evaluating the virucidal activity of surfaces and surface coatings.


Subject(s)
Antiviral Agents/administration & dosage , Cross Infection/prevention & control , Cross Infection/virology , Disinfection/methods , Virus Diseases/prevention & control , Alloys/pharmacology , Alloys/therapeutic use , Antiviral Agents/pharmacology , Copper/pharmacology , Copper/therapeutic use , Culture Media, Conditioned , Disinfection/standards , Humans , Indicator Dilution Techniques , Nickel/pharmacology , Nickel/therapeutic use , Virus Diseases/virology , Zinc/pharmacology , Zinc/therapeutic use
20.
mSphere ; 6(4): e0038921, 2021 08 25.
Article in English | MEDLINE | ID: mdl-34346709

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
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