Trends in invasive bacterial diseases during the first 2 years of the COVID-19 pandemic: analyses of prospective surveillance data from 30 countries and territories in the IRIS Consortium.

BACKGROUND: The Invasive Respiratory Infection Surveillance (IRIS) Consortium was established to assess the impact of the COVID-19 pandemic on invasive diseases caused by Streptococcus pneumoniae, Haemophilus influenzae, Neisseria meningitidis, and Streptococcus agalactiae. We aimed to analyse the incidence and distribution of these diseases during the first 2 years of the COVID-19 pandemic compared to the 2 years preceding the pandemic. METHODS: For this prospective analysis, laboratories in 30 countries and territories representing five continents submitted surveillance data from Jan 1, 2018, to Jan 2, 2022, to private projects within databases in PubMLST. The impact of COVID-19 containment measures on the overall number of cases was analysed, and changes in disease distributions by patient age and serotype or group were examined. Interrupted time-series analyses were done to quantify the impact of pandemic response measures and their relaxation on disease rates, and autoregressive integrated moving average models were used to estimate effect sizes and forecast counterfactual trends by hemisphere. FINDINGS: Overall, 116 841 cases were analysed: 76 481 in 2018-19, before the pandemic, and 40 360 in 2020-21, during the pandemic. During the pandemic there was a significant reduction in the risk of disease caused by S pneumoniae (risk ratio 0·47; 95% CI 0·40-0·55), H influenzae (0·51; 0·40-0·66) and N meningitidis (0·26; 0·21-0·31), while no significant changes were observed for S agalactiae (1·02; 0·75-1·40), which is not transmitted via the respiratory route. No major changes in the distribution of cases were observed when stratified by patient age or serotype or group. An estimated 36 289 (95% prediction interval 17 145-55 434) cases of invasive bacterial disease were averted during the first 2 years of the pandemic among IRIS-participating countries and territories. INTERPRETATION: COVID-19 containment measures were associated with a sustained decrease in the incidence of invasive disease caused by S pneumoniae, H influenzae, and N meningitidis during the first 2 years of the pandemic, but cases began to increase in some countries towards the end of 2021 as pandemic restrictions were lifted. These IRIS data provide a better understanding of microbial transmission, will inform vaccine development and implementation, and can contribute to health-care service planning and provision of policies. FUNDING: Wellcome Trust, NIHR Oxford Biomedical Research Centre, Spanish Ministry of Science and Innovation, Korea Disease Control and Prevention Agency, Torsten Söderberg Foundation, Stockholm County Council, Swedish Research Council, German Federal Ministry of Health, Robert Koch Institute, Pfizer, Merck, and the Greek National Public Health Organization.

Changes in the incidence of invasive disease due to Streptococcus pneumoniae, Haemophilus influenzae, and Neisseria meningitidis during the COVID-19 pandemic in 26 countries and territories in the Invasive Respiratory Infection Surveillance Initiative: a prospective analysis of surveillance data.

BACKGROUND: Streptococcus pneumoniae, Haemophilus influenzae, and Neisseria meningitidis, which are typically transmitted via respiratory droplets, are leading causes of invasive diseases, including bacteraemic pneumonia and meningitis, and of secondary infections subsequent to post-viral respiratory disease. The aim of this study was to investigate the incidence of invasive disease due to these pathogens during the early months of the COVID-19 pandemic. METHODS: In this prospective analysis of surveillance data, laboratories in 26 countries and territories across six continents submitted data on cases of invasive disease due to S pneumoniae, H influenzae, and N meningitidis from Jan 1, 2018, to May, 31, 2020, as part of the Invasive Respiratory Infection Surveillance (IRIS) Initiative. Numbers of weekly cases in 2020 were compared with corresponding data for 2018 and 2019. Data for invasive disease due to Streptococcus agalactiae, a non-respiratory pathogen, were collected from nine laboratories for comparison. The stringency of COVID-19 containment measures was quantified using the Oxford COVID-19 Government Response Tracker. Changes in population movements were assessed using Google COVID-19 Community Mobility Reports. Interrupted time-series modelling quantified changes in the incidence of invasive disease due to S pneumoniae, H influenzae, and N meningitidis in 2020 relative to when containment measures were imposed. FINDINGS: 27 laboratories from 26 countries and territories submitted data to the IRIS Initiative for S pneumoniae (62 837 total cases), 24 laboratories from 24 countries submitted data for H influenzae (7796 total cases), and 21 laboratories from 21 countries submitted data for N meningitidis (5877 total cases). All countries and territories had experienced a significant and sustained reduction in invasive diseases due to S pneumoniae, H influenzae, and N meningitidis in early 2020 (Jan 1 to May 31, 2020), coinciding with the introduction of COVID-19 containment measures in each country. By contrast, no significant changes in the incidence of invasive S agalactiae infections were observed. Similar trends were observed across most countries and territories despite differing stringency in COVID-19 control policies. The incidence of reported S pneumoniae infections decreased by 68% at 4 weeks (incidence rate ratio 0·32 [95% CI 0·27-0·37]) and 82% at 8 weeks (0·18 [0·14-0·23]) following the week in which significant changes in population movements were recorded. INTERPRETATION: The introduction of COVID-19 containment policies and public information campaigns likely reduced transmission of S pneumoniae, H influenzae, and N meningitidis, leading to a significant reduction in life-threatening invasive diseases in many countries worldwide. FUNDING: Wellcome Trust (UK), Robert Koch Institute (Germany), Federal Ministry of Health (Germany), Pfizer, Merck, Health Protection Surveillance Centre (Ireland), SpID-Net project (Ireland), European Centre for Disease Prevention and Control (European Union), Horizon 2020 (European Commission), Ministry of Health (Poland), National Programme of Antibiotic Protection (Poland), Ministry of Science and Higher Education (Poland), Agencia de Salut Pública de Catalunya (Spain), Sant Joan de Deu Foundation (Spain), Knut and Alice Wallenberg Foundation (Sweden), Swedish Research Council (Sweden), Region Stockholm (Sweden), Federal Office of Public Health of Switzerland (Switzerland), and French Public Health Agency (France).

Draft Genome Sequences of 19 Clinical Isolates of Candida auris from Hong Kong.

Candida auris is an emerging human pathogen associated with multidrug resistance and nosocomial outbreaks. We report the draft genome sequences of 19 C. auris isolates that were associated with a cluster of cases in a hospital in Hong Kong.

Epidemiological analysis of Streptococcus pyogenes infections in Hong Kong.

AIMS: The aim of this study was to characterise clinical and microbiological features of isolates obtained from both invasive and non-invasive Streptococcus pyogenes infections in Hong Kong, between October 2005 and April 2008. METHOD: Clinical data of invasive isolates were collected retrospectively. Altogether 281 isolates were emm sequence typed and tested for antimicrobial susceptibility using disk diffusion method. Detection of the presence of the streptococcal pyrogenic exotoxin genes was also carried out. RESULTS: emm1, emm4 and emm12 were the most prevalent in both the invasive and non-invasive groups with an increase in incidence of emm22 compared with a previous study. emm22 was associated with invasive cellulitis and wound infection. The overall rate of erythromycin resistance was 25.6% and was significantly higher in emm22 strains (85.7%). The phage-encoded superantigen gene speA was exclusively associated with emm1 in both invasive and non-invasive isolates. CONCLUSION: This study revealed a changing epidemiology of S. pyogenes infection in Hong Kong, with a unique pattern compared with other Asian countries. Invasiveness is not related to the presence of speA, speC or ssa genes and the antimicrobial resistance rate was high for macrolides. The findings have an implication on the use and efficacy of the polyvalent S. pyogenes vaccine under development.

Quinolone resistance and correlation to other antimicrobial resistances in faecal isolates of Escherichia coli in Hong Kong.

In an attempt to assess the level of quinolone resistance and its association with other antimicrobial resistance in faecal Escherichia coli isolated from routine outpatient specimens in Hong Kong, ciprofloxacin-supplemented MacConkey agar was used to screen for resistant isolates. Antimicrobial susceptibility testing of the isolates was done by VITEK 2 and previous amplification-based methods were employed to characterize the genetic determinants behind some of the resistance phenotypes. One hundred and seventy-six (43%) of 409 specimens had quinolone-resistant E. coli isolated (199 isolates). Quinolone resistance was found to be associated with resistances to penicillins (>80%) and co-trimoxazole (69%). Nonsusceptibility to combinations of penicillins and clavulanic acid was above 20% and up to 50% for the aminoglycosides gentamicin and tobramycin. CTX-M-type extended-spectrum beta-lactamases were found responsible for most cephalosporin resistances but the transferable quinolone resistance determinant qnrA was not detected. Our data suggested that a high percentage of E. coli isolates as part of the alleged normal intestinal microflora in humans appeared to be resistant to quinolones. Co-resistance to various other frequently used antimicrobials was also observed. Transferable genetic determinants were found to be involved in some cases.

Rapid pulsed-field gel electrophoresis protocol for subtyping of Streptococcus suis serotype 2.

A rapid pulsed-field gel electrophoresis (PFGE) protocol for subtyping of Streptococcus suis serotype 2 was developed and evaluated using 27 clinical isolates from 22 epidemiologically unrelated patients. Results were matched against antibiogram, virulence genotyping and multi locus sequence typing (MLST). PFGE appeared to be the most discriminatory with numerical index of discrimination (D) equal to 0.87.

Plasmid-mediated resistance to ciprofloxacin and cefotaxime in clinical isolates of Salmonella enterica serotype Enteritidis in Hong Kong.

OBJECTIVES: To characterize the genetic determinants involved in the reduced susceptibility to ciprofloxacin and cefotaxime in Salmonella enterica serotype Enteritidis clinical isolates obtained from four patients in summer 2003 in Hong Kong. METHODS: Three Salmonella Enteritidis isolates from blood culture and one from stool were collected due to their increased resistance to ciprofloxacin and cefotaxime. PFGE analysis was used to investigate their genetic relatedness. Conjugation experiments were employed to show if the genetic determinants involved were plasmid-mediated. MICs of various antimicrobials were determined by VITEK 2 and Etest. Based on the susceptibility and conjugation experiment results, previously described PCR methods were employed to detect sequences homologous to qnr and bla(CTX-M) suspected to be involved in the reduced susceptibility to ciprofloxacin and cefotaxime, respectively. RESULTS: PFGE analysis showed that the four Salmonella isolates were clonally unrelated. The presence of a qnr-like gene and the CTX-M allele bla(CTX-M-14) on four different transferable plasmids harboured by the four isolates was confirmed. CONCLUSIONS: This is the first report of transferable fluoroquinolone resistance due to a new qnr allele, which appeared to be linked to bla(CTX-M-14), in isolates of Salmonella Enteritidis in Hong Kong.