ABSTRACT
Intro: It is hypothesized that metagenomics could contribute to the effective sentinel surveillance of emerging infections to identify plausible cause of respiratory symptoms in the population. Method(s): This study forms part of a longitudinal household cohort study involving the collection of respiratory symptoms and vaccination history in Hong Kong. As a pilot, selected households were provided with swab collection kit for collecting nasopharyngeal and throat samples when there was an influenza-like illness (ILI) during a 4-month presumptive period of the year's winter influenza season. Sequence-Independent Single Primer Amplification (SISPA) and nanopore metagenomic sequencing were performed. After basecalling, demultiplexing, and quality filtering, taxonomic classification was done. Unclassified and host reads were removed and only taxon with over 0.1% abundance were included in the analysis. Finding(s): Between December 2021 and April 2022, of 101 collection kits delivered, 36 (36%) participants returned the samples. Two (6%) had previous COVID-19 diagnosis and almost all (97%) received at least one dose of COVID-19 vaccination. Metagenomics sequencing was performed on 13 samples collected from participants when ILI was present. Of the 1,592,219 reads obtained, 5308 taxa were identified and 136 had over 0.1% abundance, including 128 bacteria, 6 fungi, and 1 virus, which was a bacteriophage. The five most abundant genera of bacteria included Neisseria (19%), Streptococcus (10%), Haemophilus (9%), Veillonella (3%), and Rothia (3%). Haemophilus parainfluenzae was the most abundant species with 97,542 (6%) reads, followed by Neisseria meningitides (5%). Other bacteria identified included Rothia mucilaginosa, Acinetobacter baumannii, Lautropia mirabilis, Veillonella atypica, Streptococcus salivarius, and Streptococcus pneumonia. Inter-participant abundance profile was significantly different (p<0.001). Conclusion(s): The absence of viral infections identified echoed the extremely low proportion (3/21986, or 0.01%) of respiratory specimens testing positive for influenza virus by the government laboratory during the same period. The metagenomic profile could be useful for identifying the likely ILI-causing pathogen.Copyright © 2023
ABSTRACT
BACKGROUND: Antibiotics are commonly prescribed for respiratory tract infections (RTIs) among older adults in long-term care facilities (LTCFs), and this contributes to the emergence of antimicrobial resistance. The objective of this study was to determine the antibiotic prescribing rate for RTIs among LTCF residents, and to analyse the antibiotic consumption patterns with the AwaRe monitoring tool, developed by the World Health Organization. METHODS: MEDLINE, EMBASE and CINAHL were searched from inception to March 2022. Original articles reporting antibiotic use for RTIs in LTCFs were included in this review. Study quality was assessed using the Joanna Briggs Institute's Critical Appraisal Checklist for Prevalence Data. A random-effects meta-analysis was employed to calculate the pooled estimates. Subgroup analysis was conducted by type of RTI, country, and study start year. RESULTS: In total, 47 articles consisting of 50 studies were included. The antibiotic prescribing rate ranged from 21.5% to 100% (pooled estimate 69.8%, 95% confidence interval 55.2-82.6%). The antibiotic prescribing rate for lower respiratory tract infections (LRTIs) was higher than the rates for viral and general RTIs. Compared with Italy, France and the USA, the Netherlands had lower antibiotic use for LRTIs. A proportion of viral RTIs were treated with antibiotics, and all the antibiotics were from the Watch group. Use of antibiotics in the Access group was higher in the Netherlands, Norway, Switzerland and Slovenia compared with the USA and Australia. CONCLUSION: The antibiotic prescribing rate for RTIs in LTCFs was high, and AWaRe antibiotic use patterns varied by type of RTI and country. Improving antibiotic use may require coordination efforts.
ABSTRACT
INTRODUCTION: This study evaluated the preparedness of family doctors during the early phase of the coronavirus disease 2019 (COVID-19) outbreak in Hong Kong. METHODS: All members of the Hong Kong College of Family Physicians were invited to participate in a cross-sectional online survey using a 20-item questionnaire to collect information on practice preparedness for the COVID-19 outbreak through an email followed by a reminder SMS message between 31 January 2020 and 3 February 2020. RESULTS: Of 1589 family doctors invited, 491 (31%) participated in the survey, including 242 (49%) from private sector. In all, 98% surveyed doctors continued to provide clinical services during the survey period, but reduced clinic service demands were observed in 45% private practices and 24% public clinics. Almost all wore masks during consultation and washed hands between or before patient contact. Significantly more private than public doctors (80% vs 26%, P<0.001) experienced difficulties in stocking personal protective equipment (PPE); more public doctors used guidelines to manage suspected patients. The main concern of the respondents was PPE shortage. Respondents appealed for effective public health interventions including border control, quarantine measures, designated clinic setup, and public education. CONCLUSION: Family doctors from public and private sectors demonstrated preparedness to serve the community from the early phase of the COVID-19 outbreak with heightened infection control measures and use of guidelines. However, there is a need for support from local health authorities to secure PPE supply and institute public health interventions.
Subject(s)
Coronavirus Infections/epidemiology , Coronavirus Infections/prevention & control , Disease Outbreaks/prevention & control , Family Practice/organization & administration , Health Care Surveys/methods , Pandemics/prevention & control , Pneumonia, Viral/epidemiology , Pneumonia, Viral/prevention & control , Surveys and Questionnaires , COVID-19 , COVID-19 Testing , Clinical Laboratory Techniques/methods , Clinical Laboratory Techniques/statistics & numerical data , Communicable Disease Control/methods , Coronavirus Infections/diagnosis , Disease Outbreaks/statistics & numerical data , Female , Hong Kong/epidemiology , Humans , Male , Outcome Assessment, Health Care , Physicians, Family/statistics & numerical dataSubject(s)
Coronavirus Infections , Lung/diagnostic imaging , Pandemics , Pneumonia, Viral , Respiratory Tract Infections/diagnosis , Tomography, X-Ray Computed/methods , Betacoronavirus/isolation & purification , COVID-19 , Coronavirus Infections/diagnosis , Coronavirus Infections/epidemiology , Diagnosis, Differential , Humans , Pneumonia, Viral/diagnosis , Pneumonia, Viral/diagnostic imaging , Pneumonia, Viral/epidemiology , Pneumonia, Viral/etiology , SARS-CoV-2Subject(s)
COVID-19 , Communicable Disease Control , Delivery of Health Care/organization & administration , Physicians, Primary Care , Primary Health Care , COVID-19/epidemiology , COVID-19/prevention & control , COVID-19/therapy , Communicable Disease Control/organization & administration , Communicable Disease Control/standards , Hong Kong , Humans , Physicians, Primary Care/standards , Physicians, Primary Care/supply & distribution , Primary Health Care/methods , Primary Health Care/trends , Professional Role , SARS-CoV-2Subject(s)
COVID-19 , Education, Nonprofessional , Foreign Bodies , Rectum , Urethra , Urologic Surgical Procedures, Male/methods , Adolescent , COVID-19/epidemiology , COVID-19/prevention & control , Child , Communicable Disease Control/methods , Constipation/therapy , Education, Distance , Foreign Bodies/diagnostic imaging , Foreign Bodies/etiology , Foreign Bodies/psychology , Foreign Bodies/surgery , Humans , Male , Psychological Tests , SARS-CoV-2 , Self Care/adverse effects , Self Care/psychology , Treatment OutcomeSubject(s)
Coronavirus Infections/prevention & control , Internationality , Pandemics/prevention & control , Pneumonia, Viral/prevention & control , Practice Guidelines as Topic , Preventive Health Services/statistics & numerical data , Preventive Health Services/standards , Quarantine/statistics & numerical data , Quarantine/standards , Betacoronavirus , COVID-19 , Humans , SARS-CoV-2ABSTRACT
Super-spreading events in an outbreak can change the nature of an epidemic. Therefore, it is useful for public health teams to determine whether an ongoing outbreak has any contribution from such events, which may be amenable to interventions. We estimated the basic reproductive number (R0) and the dispersion factor (k) from empirical data on clusters of epidemiologically linked coronavirus disease 2019 (COVID-19) cases in Hong Kong, Japan and Singapore. This allowed us to infer the presence or absence of super-spreading events during the early phase of these outbreaks. The relatively large values of k implied that large cluster sizes, compatible with super-spreading, were unlikely.