Primary Series and Booster Coronavirus Disease 2019 Vaccine Effectiveness in a Cohort of Healthcare Workers in Albania During a BA.1 and BA.2 Variant Period, January-May 2022

Background

Healthcare workers (HCWs) have experienced high rates of coronavirus disease 2019 (COVID-19) morbidity and mortality. We estimated COVID-19 2-dose primary series and monovalent booster vaccine effectiveness (VE) against symptomatic severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron (BA.1 and BA.2) infection among HCWs in 3 Albanian hospitals during January-May 2022.

Methods

Study participants completed weekly symptom questionnaires, underwent polymerase chain reaction (PCR) testing when symptomatic, and provided quarterly blood samples for serology. We estimated VE using Cox regression models (1 - hazard ratio), with vaccination status as the time-varying exposure and unvaccinated HCWs as the reference group, adjusting for potential confounders: age, sex, prior SARS-CoV-2 infection (detected by PCR, rapid antigen test, or serology), and household size.

Results

At the start of the analysis period, 76% of 1462 HCWs had received a primary series, 10% had received a booster dose, and 9% were unvaccinated; 1307 (89%) HCWs had evidence of prior infection. Overall, 86% of primary series and 98% of booster doses received were BNT162b2. The median time interval from the second dose and the booster dose to the start of the analysis period was 289 (interquartile range [IQR], 210-292) days and 30 (IQR, 22-46) days, respectively. VE against symptomatic PCR-confirmed infection was 34% (95% confidence interval [CI], -36% to 68%) for the primary series and 88% (95% CI, 39%-98%) for the booster.

Conclusions

Among Albanian HCWs, most of whom had been previously infected, COVID-19 booster dose offered improved VE during a period of Omicron BA.1 and BA.2 circulation. Our findings support promoting booster dose uptake among Albanian HCWs, which, as of January 2023, was only 20%. Clinical Trials Registration. NCT04811391.

Investigating resistance in clinical Mycobacterium tuberculosis complex isolates with genomic and phenotypic antimicrobial susceptibility testing: a multicentre observational study

BACKGROUND

Whole-genome sequencing (WGS) of Mycobacterium tuberculosis complex has become an important tool in diagnosis and management of drug-resistant tuberculosis. However, data correlating resistance genotype with quantitative phenotypic antimicrobial susceptibility testing (AST) are scarce.

METHODS

In a prospective multicentre observational study, 900 clinical M tuberculosis complex isolates were collected from adults with drug-resistant tuberculosis in five high-endemic tuberculosis settings around the world (Georgia, Moldova, Peru, South Africa, and Viet Nam) between Dec 5, 2014, and Dec 12, 2017. Minimum inhibitory concentrations (MICs) and resulting binary phenotypic AST results for up to nine antituberculosis drugs were determined and correlated with resistance-conferring mutations identified by WGS.

FINDINGS

Considering WHO-endorsed critical concentrations as reference, WGS had high accuracy for prediction of resistance to isoniazid (sensitivity 98·8% [95% CI 98·5-99·0]; specificity 96·6% [95% CI 95·2-97·9]), levofloxacin (sensitivity 94·8% [93·3-97·6]; specificity 97·1% [96·7-97·6]), kanamycin (sensitivity 96·1% [95·4-96·8]; specificity 95·0% [94·4-95·7]), amikacin (sensitivity 97·2% [96·4-98·1]; specificity 98·6% [98·3-98·9]), and capreomycin (sensitivity 93·1% [90·0-96·3]; specificity 98·3% [98·0-98·7]). For rifampicin, pyrazinamide, and ethambutol, the specificity of resistance prediction was suboptimal (64·0% [61·0-67·1], 83·8% [81·0-86·5], and 40·1% [37·4-42·9], respectively). Specificity for rifampicin increased to 83·9% when borderline mutations with MICs overlapping with the critical concentration were excluded. Consequently, we highlighted mutations in M tuberculosis complex isolates that are often falsely identified as susceptible by phenotypic AST, and we identified potential novel resistance-conferring mutations.

INTERPRETATION

The combined analysis of mutations and quantitative phenotypes shows the potential of WGS to produce a refined interpretation of resistance, which is needed for individualised therapy, and eventually could allow differential drug dosing. However, variability of MIC data for some M tuberculosis complex isolates carrying identical mutations also reveals limitations of our understanding of the genotype and phenotype relationships (eg, including epistasis and strain genetic background).

FUNDING

Bill & Melinda Gates Foundation, German Centre for Infection Research, German Research Foundation, Excellence Cluster Precision Medicine of Inflammation (EXC 2167), and Leibniz ScienceCampus EvoLUNG.

Investigation of and Strategies to Control the Final Cluster of the 2018-2020 Ebola Virus Disease Outbreak in the Eastern Democratic Republic of Congo

Background

On April 10, 2020, while the independent committee of the International Health Regulation was meeting to decide whether the 10th Ebola outbreak in the Demogratic Republic of Congo still constituted a Public Health Emergency of International Concern, a new confirmed case was reported in the city of Beni, the last epicenter of the epidemic. This study aimed to understand the source of this cluster and learn from the implemented control strategies for improved response in the future.

Methods

We conducted a combined epidemiological and genomic investigation to understand the origins and dynamics of transmission within this cluster and describe the strategy that successfully controlled the outbreak.

Results

Eight cases were identified as belonging to this final cluster. A total of 1028 contacts were identified. Whole-genome sequencing revealed that all cases belonged to the same cluster, the closest sequence to which was identified as a case from the Beni area with symptom onset in July 2019 and a difference of just 31 nucleotides. Outbreak control measures included community confinement of high-risk contacts.

Conclusions

This study illustrates the high risk of additional flare-ups in the period leading to the end-of-outbreak declaration and the importance of maintaining enhanced surveillance and confinement activities to rapidly control Ebola outbreaks.

Risk factors associated with an outbreak of COVID-19 in a meat processing plant in southern Germany, April to June 2020

Meat processing plants have been prominent hotspots for coronavirus disease (COVID-19) outbreaks around the world. We describe infection prevention measures and risk factors for infection spread at a meat processing plant in Germany with a COVID-19 outbreak from April to June 2020. We analysed a cohort of all employees and defined cases as employees with either a PCR or ELISA positive result. Of 1,270 employees, 453 (36%) had evidence of SARS-CoV-2 infection. The highest attack rates were observed in meat processing and slaughtering areas. Multivariable analysis revealed that being a subcontracted employee (adjusted risk ratio (aRR)): 1.43, 95% CI: 1.06–1.96), working in the meat cutting area (aRR: 2.44, 95% CI: 1.45–4.48), working in the slaughtering area (aRR: 2.35, 95% CI: 1.32–4.45) and being a veterinary inspector (aRR: 4.77, 95% CI: 1.16–23.68) increased infection risk. Sharing accommodation or transportation were not identified as risk factors for infection. Our results suggest that workplace was the main risk factor for infection spread. These results highlight the importance of implementing preventive measures targeting meat processing plants. Face masks, distancing, staggering breaks, increased hygiene and regular testing for SARS-CoV2 helped limit this outbreak, as the plant remained open throughout the outbreak.

Updating the approaches to define susceptibility and resistance to anti-tuberculosis agents: implications for diagnosis and treatment

Approximately 85 000 deaths globally in 2019 were due to drug-resistant tuberculosis (TB), which corresponds to 7% of global deaths attributable to bacterial antimicrobial resistance [1]. Yet concerns have been mounting that drug-resistant TB was being underestimated because the approaches to define susceptibility and resistance to anti-TB agents had not kept up with those used for other major bacterial pathogens [2–9]. Here, we outline the recent, evidence-based initiatives spearheaded by the World Health Organization (WHO) and others to update breakpoints (traditionally referred to as critical concentrations (CCs)) that are used for phenotypic antimicrobial susceptibility testing (AST), also called drug susceptibility testing in the TB literature.

Inappropriately high breakpoints have resulted in systematic false-susceptible AST results to anti-TB drugs. MIC, PK/PD and clinical outcome data should be combined when setting breakpoints to minimise the emergence and spread of antimicrobial resistance. https://bit.ly/3i43wb6

Evaluation of Early Warning, Alert and Response System for Ebola Virus Disease, Democratic Republic of the Congo, 2018-2020

The 10th and largest Ebola virus disease epidemic in the Democratic Republic of the Congo (DRC) was declared in North Kivu Province in August 2018 and ended in June 2020. We describe and evaluate an Early Warning, Alert and Response System (EWARS) implemented in the Beni health zone of DRC during August 5, 2018–June 30, 2020. During this period, 194,768 alerts were received, of which 30,728 (15.8%) were validated as suspected cases. From these, 801 confirmed and 3 probable cases were detected. EWARS showed an overall good performance: sensitivity and specificity >80%, nearly all (97%) of alerts investigated within 2 hours of notification, and good demographic representativeness. The average cost of the system was US $438/case detected and US $1.8/alert received. The system was stable, despite occasional disruptions caused by political insecurity. Our results demonstrate that EWARS was a cost-effective component of the Ebola surveillance strategy in this setting.

Outcomes of patients on second- and third-line ART enrolled in ART adherence clubs in Maputo, Mozambique

Objectives

Adherence clubs (AC) offer patient‐centred access to antiretroviral therapy (ART) while reducing the burden on health facilities. AC were implemented in a health centre in Mozambique specialising in patients with a history of HIV treatment failure. We explored the impact of AC on retention in care and VL suppression of these patients.

Methods

We performed a retrospective analysis of patients enrolled in AC receiving second‐ or third‐line ART. The Kaplan–Meier estimates were used to analyse retention in care in health facility, retention in AC and viral load (VL) suppression (VL < 1000 copies/mL). Predictors of attrition and VL rebound (VL ≥ 1000 copies/mL) were assessed using multivariable proportional hazards regression.

Results

The analysed cohort contained 699 patients, median age 40 years [IQR: 35–47], 428 (61%) female and 97% second‐line ART. Overall, 9 (1.3%) patients died, and 10 (1.4%) were lost to follow‐up. Retention in care at months 12 and 24 was 98.9% (95% CI: 98.2–99.7) and 96.4% (95% CI: 94.6–98.2), respectively. Concurrently, 85.8% (95% CI: 83.1–88.2) and 80.9% (95% CI: 77.8–84.1) of patients maintained VL suppression. No association between predictors and all‐cause attrition or VL rebound was detected. Among 90 patients attending AC and simultaneously having VL rebound, 64 (71.1%) achieved VL resuppression, 10 (11.1%) did not resuppress, and 14 (15.6%) had no subsequent VL result.

Conclusion

Implementation of AC in Mozambique was successful and demonstrated that patients with a history of HIV treatment failure can be successfully retained in care and have high VL suppression rate when enrolled in AC. Expansion of the AC model in Mozambique could improve overall retention in care and VL suppression while reducing workload in health facilities.

Transmission of SARS-CoV-2 in children aged 0 to 19 years in childcare facilities and schools after their reopening in May 2020, Baden-Württemberg, Germany

We investigated data from severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infected 0–19 year olds, who attended schools/childcare facilities, to assess their role in SARS-CoV-2 transmission after these establishments’ reopening in May 2020 in Baden-Württemberg, Germany. Child-to-child transmission in schools/childcare facilities appeared very uncommon. We anticipate that, with face mask use and frequent ventilation of rooms, transmission rates in schools/childcare facilities would remain low in the next term, even if classes’ group sizes were increased.