Temporal and Gene Reassortment Analysis of Influenza C Virus Outbreaks in Hong Kong, SAR, China.

From 2014 to week 07/2020 the Centre for Health Protection in Hong Kong conducted screening for influenza C virus (ICV). A retrospective analysis of ICV detections to week 26/2019 revealed persistent low-level circulation with outbreaks occurring biennially in the winters of 2015 to 2016 and 2017 to 2018 (R. S. Daniels et al., J Virol 94:e01051-20, 2020, https://doi.org/10.1128/JVI.01051-20). Here, we report on an outbreak occurring in 2019 to 2020, reinforcing the observation of biennial seasonality in Hong Kong. All three outbreaks occurred in similar time frames, were subsequently dwarfed by seasonal epidemics of influenza types A and B, and were caused by similar proportions of C/Kanagawa/1/76 (K)-lineage and C/São Paulo/378/82 S1- and S2-sublineage viruses. Ongoing genetic drift was observed in all genes, with some evidence of amino acid substitution in the hemagglutinin-esterase-fusion (HEF) glycoprotein possibly associated with antigenic drift. A total of 61 ICV genomes covering the three outbreaks were analyzed for reassortment, and 9 different reassortant constellations were identified, 1 K-lineage, 4 S1-sublineage, and 4 S2-sublineage, with 6 of these being identified first in the 2019-1920 outbreak (2 S2-lineage and 4 S1-lineage). The roles that virus interference/enhancement, ICV persistent infection, genome evolution, and reassortment might play in the observed seasonality of ICV in Hong Kong are discussed. IMPORTANCE Influenza C virus (ICV) infection of humans is common, with the great majority of people being infected during childhood, though reinfection can occur throughout life. While infection normally results in "cold-like" symptoms, severe disease cases have been reported in recent years. However, knowledge of ICV is limited due to poor systematic surveillance and an inability to propagate the virus in large amounts in the laboratory. Following recent systematic surveillance in Hong Kong SAR, China, and direct ICV gene sequencing from clinical specimens, a 2-year cycle of disease outbreaks (epidemics) has been identified, with gene mixing playing a significant role in ICV evolution. Studies like those reported here are key to developing an understanding of the impact of influenza C virus infection in humans, notably where comorbidities exist and severe respiratory disease can develop.

Molecular Characterization of Influenza C Viruses from Outbreaks in Hong Kong SAR, China.

In 2014, the Centre for Health Protection in Hong Kong introduced screening for influenza C virus (ICV) as part of its routine surveillance for infectious agents in specimens collected from patients presenting with symptoms of respiratory viral infection, including influenza-like illness (ILI). A retrospective analysis of ICV detections up to week 26 of 2019 revealed persistent low-level circulation, with two outbreaks having occurred in the winters of 2015 to 2016 and 2017 to 2018. These outbreaks occurred at the same time as, and were dwarfed by, seasonal epidemics of influenza types A and B. Gene sequencing studies on stored ICV-positive clinical specimens from the two outbreaks have shown that the hemagglutinin-esterase (HE) genes of the viruses fall into two of the six recognized genetic lineages (represented by C/Kanagawa/1/76 and C/São Paulo/378/82), with there being significant genetic drift compared to earlier circulating viruses within both lineages. The location of a number of encoded amino acid substitutions in hemagglutinin-esterase fusion (HEF) glycoproteins suggests that antigenic drift may also have occurred. Observations of ICV outbreaks in other countries, with some of the infections being associated with severe disease, indicates that ICV infection has the potential to have significant clinical and health care impacts in humans.IMPORTANCE Influenza C virus infection of humans is common, and reinfection can occur throughout life. While symptoms are generally mild, severe disease cases have been reported, but knowledge of the virus is limited, as little systematic surveillance for influenza C virus is conducted and the virus cannot be studied by classical virologic methods because it cannot be readily isolated in laboratories. A combination of systematic surveillance in Hong Kong SAR, China, and new gene sequencing methods has been used in this study to assess influenza C virus evolution and provides evidence for a 2-year cycle of disease outbreaks. The results of studies like that reported here are key to developing an understanding of the impact of influenza C virus infection in humans and how virus evolution might be associated with epidemics.

Implementation and evaluation of the human papillomavirus (HPV) vaccination pilot for men who have sex with men (MSM), England, April 2016 to March 2017.

BACKGROUND: Opportunistic human papillomavirus (HPV) vaccination for men who have sex with men (MSM) was piloted in sexual health clinics (SHC) in England between 2016 and 2018. AIM: to evaluate the pilot's first year (April 2016-March 2017) in terms of feasibility, acceptability, uptake, impact and equity and interpret the outcome in the context of wide HPV vaccination policy. METHODS: Attendance and uptake data from routine SHC surveillance datasets and a cross-sectional survey administered to individuals receiving the vaccine were analysed. RESULTS: Among 18,875 eligible MSM, 8,580 (45.5%) were recorded as having received one HPV vaccine dose, decreasing slightly with increasing age, and uptake was higher in rural than urban areas. Survey results suggested that of those receiving the first dose of HPV vaccine, 8% were new attendees and that among those, less than 11% attended just to receive the vaccine. Of those having their first HPV vaccination, 95% indicated they would like to receive the next vaccine doses at the same clinic and 85% of patients reported accessing other services when visiting SHC for the first dose of vaccine. CONCLUSION: An opportunistic HPV vaccination programme for MSM can be delivered in an acceptable and, as far as can be evaluated, equitable manner, without major disruption to SHC and HIV clinics.

Influenza A(H5N1) Virus Infection in a Child With Encephalitis Complicated by Obstructive Hydrocephalus.

A 2-year-old boy with highly pathogenic avian influenza A(H5N1) virus infection with minimal respiratory symptoms developed encephalitis complicated by obstructive hydrocephalus. Viral RNA was detectable in cerebrospinal fluid. The virus belonged to H5N1 clade 2.3.2.1b and had acquired the mammalian adaptation mutation PB2 Q591K.

Japanese Encephalitis Virus Transmitted Via Blood Transfusion, Hong Kong, China.

Japanese encephalitis virus (JEV) is a mosquitoborne virus endemic to China and Southeast Asia that causes severe encephalitis in <1% of infected persons. Transmission of JEV via blood transfusion has not been reported. We report transmission of JEV via blood donation products from an asymptomatic viremic donor to 2 immunocompromised recipients. One recipient on high-dose immunosuppressive drugs received JEV-positive packed red blood cells after a double lung transplant; severe encephalitis and a poor clinical outcome resulted. JEV RNA was detected in serum, cerebrospinal fluid, and bronchoalveolar lavage fluid specimens. The second recipient had leukemia and received platelets after undergoing chemotherapy. This patient was asymptomatic; JEV infection was confirmed in this person by IgM seroconversion. This study illustrates that, consistent with other pathogenic flaviviruses, JEV can be transmitted via blood products. Targeted donor screening and pathogen reduction technologies could be used to prevent transfusion-transmitted JEV infection in highly JEV-endemic areas.

Population-Based Pediatric Hospitalization Burden of Lineage-Specific Influenza B in Hong Kong, 2004-2014.

BACKGROUND: Influenza B virus has been perceived to cause less disease burden and milder disease compared with influenza A, but recent studies suggest that influenza B does have a significant impact. We aimed to estimate the burden of influenza B virus infections on hospitalizations in Hong Kong, in the context of virus lineage changes over time. METHODS: The pediatric age-specific rates of influenza B hospitalization in Hong Kong for 2004-2014 were estimated based on admissions to 2 hospitals that together catered for 72.5% of all pediatric admissions on Hong Kong Island. Influenza B virus was detected by immunofluorescence and culture on nasopharyngeal aspirates. Lineage typing was performed by real-time reverse-transcription polymerase chain reaction. RESULTS: A total of 5085 children were recruited on 1 designated day each week, year-round during the 11 years, and 221 (4.3%) tested positive for influenza B. Hospitalization rates were highest in children aged 2 to <5 years with year-to-year variation. Victoria-lineage viruses appeared to be associated with a greater fraction of influenza B hospitalizations in children than of influenza B infections in the general community. Influenza B did not cause significant hospitalization in infants <1 year of age. CONCLUSIONS: We report one of the first population-based, age- and lineage-specific studies of pediatric hospitalization for influenza B. We found that changes in lineage were associated with higher hospitalization rates and documented that Victoria lineage viruses were associated with greater pediatric hospitalization burden compared with Yamagata lineage viruses.

Cyclosporiasis in travellers returning to the United Kingdom from Mexico in 2017: lessons from the recent past to inform the future.

During the summers of 2015 and 2016, the United Kingdom experienced large outbreaks of cyclosporiasis in travellers returning from Mexico. As the source of the outbreaks was not identified, there is the potential for a similar outbreak to occur in 2017; indeed 78 cases had already been reported as at 27 July 2017. Early communication and international collaboration is essential to provide a better understanding of the source and extent of this recurring situation.

A Systematic Review on Harmful Alcohol Use Among Civilian Populations Affected by Armed Conflict in Low- and Middle-Income Countries.

BACKGROUND: There are currently over 55 million refugees and internally displaced persons due to armed conflict. In addition, there are around 150 million more conflict-affected residents who remain in their home communities. Armed conflict poses a number of potential risks for harmful alcohol use. OBJECTIVE: The objective of the study was to systematically examine evidence on harmful alcohol use among conflict-affected populations in low- and middle-income countries. METHODS: A systematic review methodology was used following PRISMA guidelines. Quantitative studies were selected with outcomes relating to harmful alcohol use among conflict-affected populations in low- and middle-income countries. Seven bibliographic databases and a range of gray literature sources were searched. Descriptive analysis was applied and a quality assessment conducted using the Newcastle-Ottawa Quality Assessment Scale. RESULTS: The search yielded 10,037 references of which 22 studies met inclusion criteria. Twenty-one of the studies used a cross-sectional design, and 1 used a case series design. Evidence on risk factors for harmful alcohol use was weak overall. Factors associated with harmful alcohol use were male gender, older age, cumulative trauma event exposure, and depression. There were no studies on the effectiveness of interventions for harmful alcohol use. The strength of evidence was also limited by the generally moderate quality of the studies. CONCLUSIONS: Substantially more evidence is required to understand the scale of conflict-associated harmful alcohol use, key risk factors, association of alcohol use with physical and mental disorders, and effectiveness of interventions to address harmful alcohol use in conflict-affected populations.

First Report of a Fatal Case Associated with EV-D68 Infection in Hong Kong and Emergence of an Interclade Recombinant in China Revealed by Genome Analysis.

A fatal case associated with enterovirus D68 (EV-D68) infection affecting a 10-year-old boy was reported in Hong Kong in 2014. To examine if a new strain has emerged in Hong Kong, we sequenced the partial genome of the EV-D68 strain identified from the fatal case and the complete VP1, and partial 5'UTR and 2C sequences of nine additional EV-D68 strains isolated from patients in Hong Kong. Sequence analysis indicated that a cluster of strains including the previously recognized A2 strains should belong to a separate clade, clade D, which is further divided into subclades D1 and D2. Among the 10 EV-D68 strains, 7 (including the fatal case) belonged to the previously described, newly emerged subclade B3, 2 belonged to subclade B1, and 1 belonged to subclade D1. Three EV-D68 strains, each from subclades B1, B3, and D1, were selected for complete genome sequencing and recombination analysis. While no evidence of recombination was noted among local strains, interclade recombination was identified in subclade D2 strains detected in mainland China in 2008 with VP2 acquired from clade A. This study supports the reclassification of subclade A2 into clade D1, and demonstrates interclade recombination between clades A and D2 in EV-D68 strains from China.

A systematic review on tobacco use among civilian populations affected by armed conflict.

OBJECTIVE: To systematically examine evidence on tobacco use among conflict-affected civilian populations. DATA SOURCES: Primary quantitative and qualitative studies published in English up to April 2014. Bibliographic databases searched were EMBASE, Global Health, MEDLINE, PsycEXTRA, PsycINFO, Web of Science, Cochrane; with the main terms of: (Smoke*, tobacco*, cigarette*, nicotine, beedi, bidi, papirosi, dip, chew, snuff, snus, smokeless tobacco) AND (armed-conflict, conflict-affected, conflict, war, refugee, internally displaced, forcibly displaced, asylum, humanitarian). Grey literature was searched using humanitarian databases, websites and search engines. STUDY SELECTION: Studies were independently selected by two reviewers, with a study outcome of tobacco use and a population of conflict-affected civilian populations such as internally displaced persons, refugees, residents in conflict-affected areas, residents and returning forcibly displaced populations returning in stabilised and postconflict periods. 2863 studies were initially identified. DATA EXTRACTION: Data were independently extracted. The Quality Assessment Tool for Quantitative Studies and the Critical Appraisal Skills Programme for qualitative studies were used to assess study quality. DATA SYNTHESIS: 39 studies met inclusion criteria and descriptive analysis was used. Findings were equivocal on the effect of conflict on tobacco use. Evidence was clearer on associations between post-traumatic stress and other mental disorders with nicotine dependence. However, there were too few studies for definitive conclusions. No study examined the effectiveness of tobacco-related interventions. The quantitative studies were moderate (N=13) or weak (N=22) quality, and qualitative studies were moderate (N=3) or strong (N=2). CONCLUSIONS: Some evidence indicates links between conflict and tobacco use but substantially more research is required.

Recombinant coxsackievirus A2 and deaths of children, Hong Kong, 2012.

A natural recombinant of coxsackievirus A2 was found in 4 children with respiratory symptoms in Hong Kong, China, during the summer of 2012. Two of these children died. Vigilant monitoring of this emerging recombinant enterovirus is needed to prevent its transmission to other regions.

Genetic characterization of EV71 isolates from 2004 to 2010 reveals predominance and persistent circulation of the newly proposed genotype D and recent emergence of a distinct lineage of subgenotype C2 in Hong Kong.

BACKGROUND: Enterovirus 71 (EV71) is a common etiological agent of hand, foot and mouth disease (HFMD) in children. EV71 epidemics have been reported in Hong Kong in recent years, and yet the genetic information of EV71 strains circulating in our locality is limited. The objective of this study was to investigate the genetic evolution of these EV71 isolates in Hong Kong over a 7-year period. METHODS: Twenty-two EV71 isolates from Hong Kong during 2004-2010 were included for phylogenetic analysis using partial VP2-VP3, 2C and 3D regions. Eight EV71 strains were selected for complete genome sequencing and recombination analysis. RESULTS: Among the 22 EV71 isolates, 20 belonged to subgenotype C4 and 2 belonged to subgenotype C2 based on the phylogenetic analysis of partial VP2-VP3, 2C and 3D gene regions. Phylogenetic, similarity plot and bootscan analyses using complete genome sequences of seven EV71 isolates of subgenotype C4 supported that the "double-recombinant" strains of subgenotype C4 persistently circulating in Hong Kong should belong to a newly proposed genotype D. Further analysis revealed two clusters, subgenotypes C4b and C4a (proposed genotypes D1a and D1b respectively), with "genotype D1b" strains being predominant in recent years in Hong Kong. A distinct lineage of EV71 subgenotype C2 has emerged in Hong Kong in 2008. The evolutionary rate of EV71 was 3.1 × 10-3 nucleotide substitutions per site per year similar to that of other enterovirus, such as EV68, but was relatively lower than those of echovirus 30 and poliovirus. Molecular clock analysis using VP1 gene dated the time to the most recent common ancestor of all EV71 genotypes to 1900s, while the EV71 "double-recombinant" strains of "genotype D" were detected as early as 1998. CONCLUSIONS: This study provides the molecular basis for proposing a new "genotype D" of EV71 and assigning a discrete lineage of subgenotype C2. EV71 strains of "genotype D" have been circulating in Hong Kong for over 7 years, with "genotype D1b" being predominant.

Infection of healthcare workers despite a high vaccination rate during the fifth wave of COVID-19 due to Omicron variant in Hong Kong.

Background: No nosocomial infection was recorded in our healthcare workers (HCWs) during the early phase of the coronavirus disease 2019 (COVID-19) pandemic. With the emergence of the Omicron variant of increased transmissibility, infection in HCWs occurred as expected. We aimed to study the epidemiology of infection in HCWs and to describe the infection control measures during the outbreak of the Omicron variant. Methods: With daily rapid antigen testing and molecular confirmation test for COVID-19, infected HCWs were interviewed by infection control nurses (ICNs) to investigate the potential source of infection. The epidemiology of COVID-19 in Hong Kong served as reference. Results: During the fifth wave of COVID-19 (31 December 2021 to 31 May 2022), 1,200,068 cases were reported (incidence 95 times higher than in preceding waves in Hong Kong; 162,103 vs 1,707 per million population respectively, P<0.001). The proportion of infected HCWs was significantly higher than that of the general population (24.9%, 1,607/6,452 vs 16.2%, 1,200,068/7,403,100 respectively; P<0.01). The proportion of infected non-clinical staff was significantly higher than that of clinical staff (31.8%, 536/1,687 vs 22.5%, 1,071/4,765 respectively; P<0.001). Of 82.8% (1,330/1,607) infected HCWs interviewed by ICNs, 99.5% (1,324/1,330) had been fully vaccinated; 49.5% (659/1,330) had no identifiable source; 40.7% (541/1,330) were probably infected from household members; 9.8% (130/1,330) had possible exposure to confirmed patients or HCWs, but no lapse in infection control measures or inappropriate use of personal protective equipment was recalled. Conclusion: Omicron variant is highly transmissible such that breakthrough infection occurred despite high level of vaccination.

Air dispersal of severe acute respiratory coronavirus virus 2 (SARS-CoV-2): Implications for hospital infection control during the fifth wave of coronavirus disease 2019 (COVID-19) due to the SARS-CoV-2 omicron variant in Hong Kong.

We obtained 24 air samples in 8 general wards temporarily converted into negative-pressure wards admitting coronavirus disease 2019 (COVID-19) patients infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) omicron variant BA.2.2 in Hong Kong. SARS-CoV-2 RNA was detected in 19 (79.2%) of 24 samples despite enhanced indoor air dilution. It is difficult to prevent airborne transmission of SARS-CoV-2 in hospitals.

Scarlet fever epidemic, Hong Kong, 2011.

More than 900 cases of scarlet fever were recorded in Hong Kong during January-July, 2011. Six cases were complicated by toxic shock syndrome, of which 2 were fatal. Pulsed-field gel electrophoresis patterns suggested a multiclonal epidemic; emm12 was the predominant circulating type. We recommend genetic testing of and antimicrobial resistance monitoring for this reportable disease.

Surveillance of gonococcal antimicrobial susceptibility resulting in early detection of emerging resistance.

OBJECTIVES: To undertake laboratory and clinical surveillance of gonococcal antimicrobial susceptibility to various therapeutic agents in Hong Kong, so as to monitor for emerging resistance and to inform on appropriate choice of empirical therapy. METHODS: Trends in susceptibility of gonococci to ceftriaxone, spectinomycin, ceftibuten and azithromycin were monitored over time. Isolates with reduced susceptibility to oral extended-spectrum cephalosporins were further characterized by detection of the mosaic penA gene and typing by Neisseria gonorrhoeae multi-antigen sequence typing (NG-MAST). Correlation with clinical and epidemiological findings was undertaken on isolates positive for the mosaic penA gene. RESULTS: Trends in susceptibility of gonococci to ceftriaxone, spectinomycin and ceftibuten remained stable between 2005 and 2010. In 2010, 30.3% of tested strains were not susceptible to azithromycin. The percentage of gonococcal strains harbouring the mosaic penA gene increased from 1.0% during April to December 2010 to 8.2% during January to September 2011 (P < 0.0001). Review of available clinical records showed that, out of 35 patients infected by strains positive for the mosaic penA gene, 30 had laboratory-documented treatment failure. CONCLUSIONS: This study showed that ceftriaxone and spectinomycin remained effective against gonorrhoea in Hong Kong. There was an alarming increase in strains with reduced susceptibility to oral extended-spectrum cephalosporins associated with clinical treatment failure. One-third of gonococcal isolates were non-susceptible to azithromycin. The need to switch to agents other than oral extended-spectrum cephalosporins for empirical treatment is imminent. Continued surveillance with strain characterization is essential to monitor the effectiveness of currently recommended therapy.

Hong Kong experiences the 'Ultimate superbug': NDM-1 Enterobacteriaceae.

We report the second imported case of New Delhi metallo-beta-lactamase (NDM-1) Enterobacteriaceae encountered in Hong Kong soon after the patient's arrival in the territory for medical care. As NDM-1 is spreading throughout the world via international travel, being an international city, Hong Kong was always expected to encounter the same public health threat. This case also illustrates the importance of active surveillance of at-risk patients in preventing the spread of this 'superbug'.

Evolution and Control of COVID-19 Epidemic in Hong Kong.

Hong Kong SAR has adopted universal masking, social distancing, testing of all symptomatic and high-risk groups for isolation of confirmed cases in healthcare facilities, and quarantine of contacts as epidemiological control measures without city lockdown or border closure. These measures successfully suppressed the community transmission of pre-Omicron SARS-CoV-2 variants or lineages during the first to the fourth wave. No nosocomial SARS-CoV-2 infection was documented among healthcare workers in the first 300 days. The strategy of COVID-19 containment was adopted to provide additional time to achieve population immunity by vaccination. The near-zero COVID-19 situation for about 8 months in 2021 did not enable adequate immunization of the eligible population. A combination of factors was identified, especially population complacency associated with the low local COVID-19 activity, together with vaccine hesitancy. The importation of the highly transmissible Omicron variant kickstarted the fifth wave of COVID-19, which could no longer be controlled by our initial measures. The explosive fifth wave, which was partially contributed by vertical airborne transmission in high-rise residential buildings, resulted in over one million cases of infection. In this review, we summarize the epidemiology of COVID-19 and the infection control and public health measures against the importation and dissemination of SARS-CoV-2 until day 1000.

Gastrointestinal Colonization of Carbapenem-Resistant Acinetobacter baumannii: What Is the Implication for Infection Control?

The epidemiology of patients with gastrointestinal colonization of carbapenem-resistant Acinetobacter baumannii (CRAB) has not been systematically analyzed. We aimed to analyze the incidence, risk factors, and clinical outcomes of patients with newly identified gastrointestinal colonization of CRAB in a healthcare region in Hong Kong, where a multi-pronged screening strategy for gastrointestinal colonization of CRAB, together with other multidrug-resistant organisms (MDROs), was conducted by collecting fecal specimens (rectal swab or stool) upon admission and during hospitalization. From 1 October 2015 to 31 December 2019, a total of 161,339 fecal specimens from 63,588 patients, 61,856 (97.3%) of whom were hospitalized patients, and 54,525 (88.1%) were screened upon admission, with 1309 positive for CRAB (2.4% prevalence). Among patients positive for CRAB in fecal specimens, 698 (53.3%) had newly detected gastrointestinal colonization of CRAB, giving an incidence of 10.03 per 10,000 patient admissions and constituting 2646 CRAB colonization days in the general wards. Excluding the 164 patients with co-colonization of other MDROs, 534 patients had gastrointestinal colonization with only CRAB, and 12.5% (67/534) developed symptomatic CRAB infections at a median of 61 days (range: 2 to 671 days), during prospective follow-up for 2 years. Compared with age- and sex-matched controls, patients being referred from residential care homes for the elderly, the presence of indwelling devices, use of beta-lactam/beta-lactamase inhibitors, carbapenems, and proton pump inhibitors in the preceding 6 months, and history of hospitalization in the past 6 months were significantly associated with gastrointestinal colonization with CRAB, as shown by multivariable analysis. Log-rank test showed that cases had significantly shorter survival duration than controls (p < 0.001). The adjusted hazard ratio of gastrointestinal colonization of CRAB was 1.8 (95% CI: 1.5−2.2; p < 0.001), as shown by Cox regression analysis. Whole-genome sequencing of eight patients with CRAB isolates in their blood cultures and rectal swabs during the same episode of hospitalization revealed ST-195 as the predominant type, as shown by multilocus sequencing type. Gastrointestinal colonization of CRAB poses a considerable challenge for infection prevention and control.

Decreased Antibiotic Consumption Coincided with Reduction in Bacteremia Caused by Bacterial Species with Respiratory Transmission Potential during the COVID-19 Pandemic.

Nonpharmaceutical interventions implemented during the COVID-19 pandemic (2020−2021) have provided a unique opportunity to understand their impact on the wholesale supply of antibiotics and incidences of infections represented by bacteremia due to common bacterial species in Hong Kong. The wholesale antibiotic supply data (surrogate indicator of antibiotic consumption) and notifications of scarlet fever, chickenpox, and tuberculosis collected by the Centre for Health Protection, and the data of blood cultures of patients admitted to public hospitals in Hong Kong collected by the Hospital Authority for the last 10 years, were tabulated and analyzed. A reduction in the wholesale supply of antibiotics was observed. This decrease coincided with a significant reduction in the incidence of community-onset bacteremia due to Streptococcus pyogenes, Streptococcus pneumoniae, Haemophilus influenzae, and Neisseria meningitidis, which are encapsulated bacteria with respiratory transmission potential. This reduction was sustained during two pandemic years (period 2: 2020−2021), compared with eight pre-pandemic years (period 1: 2012−2019). Although the mean number of patient admissions per year (1,704,079 vs. 1,702,484, p = 0.985) and blood culture requests per 1000 patient admissions (149.0 vs. 158.3, p = 0.132) were not significantly different between periods 1 and 2, a significant reduction in community-onset bacteremia due to encapsulated bacteria was observed in terms of the mean number of episodes per year (257 vs. 58, p < 0.001), episodes per 100,000 admissions (15.1 vs. 3.4, p < 0.001), and per 10,000 blood culture requests (10.1 vs. 2.1, p < 0.001), out of 17,037,598 episodes of patient admissions with 2,570,164 blood culture requests. Consistent with the findings of bacteremia, a reduction in case notification of scarlet fever and airborne infections, including tuberculosis and chickenpox, was also observed; however, there was no reduction in the incidence of hospital-onset bacteremia due to Staphylococcus aureus or Escherichia coli. Sustained implementation of non-pharmaceutical interventions against respiratory microbes may reduce the overall consumption of antibiotics, which may have a consequential impact on antimicrobial resistance. Rebound of conventional respiratory microbial infections is likely with the relaxation of these interventions.