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Weekly Digest: Infection-fatality risk of SARS-CoV-2 in New York City; The problem of microbial dark matter in neonatal sepsis; Successful end-of-treatment outcomes of drug-resistant TB patients; Growing concern on the spread of circulating vaccine derived polioviruses.


Infection-fatality risk of SARS-CoV-2 in New York City during the spring 2020 pandemic wave. Researchers in the US used a meta-population network model to estimate the SARS-CoV-2 infection rate in New York City during the spring pandemic wave (March – June 2020). The overall infection-fatality risk was 1.39% (95% CI 1.04 to 1.77), with variation across age groups and neighborhoods; the risk spanned from 0.116% (0.0729 to 0.148) for those aged 25–44 years to 19.1% (14.7 to 21.9) for those aged 75 years and older, and was estimated to be highest in the Bronx and lowest in Manhattan. The findings, based on more complete ascertainment of COVID-19-associated deaths, represent higher infection-fatality rates than reported elsewhere, probably reflecting a more accurate, higher burden of death from COVID-19. [The Lancet Infectious Disease]

Living risk prediction algorithm (QCOVID) for risk of hospital admission and mortality from coronavirus 19 in adults. Researchers in the UK conducted a population-based cohort study and used data linked to COVID-19 test results to develop a risk algorithm with very high levels of discrimination for deaths and hospital admissions due to COVID-19.  The algorithm demonstrated a sensitivity of 75.7% in identifying deaths within 97 days for the top 5% of patients with the highest predicted risks of death, while those in the top 20% of predicted risks of death accounted for 94% of all deaths from COVID-19. The authors noted that while the algorithm requires updating as absolute risk will change over time, it has the potential to discriminate those at risk of severe outcomes and to support public health policy by enabling shared decision making between clinicians and patients, targeted recruitment for clinical trials, and prioritization for vaccination. [BMJ]

 The effect of prior ACEI/ARB treatment on COVID-19 susceptibility and outcome. A systematic review and meta-analysis on the effect of renin-angiotensin inhibitor drugs (ACEI/ARB) on COVID-19 susceptibility, revealed no association between prior treatment and risk of infection with COVID-19 (adjusted OR 1.00, 95% CI 0.94 to 1.05). Similarly, no association was observed with risk of mortality (adjusted OR 0.87, 95% CI 0.66 to 1.04) and severe outcomes (adjusted OR 0.95, 95%CI 0.73 to 1.24), supporting current medical guidelines and position statements that treatment for cardiovascular and metabolic comorbidities should not be discontinued. However,  no evidence was found to support initiating a short-term ACEI/ARB regimen as prevention or treatment for COVID-19.  [Clinical Infectious Diseases]

Study provides estimates of the effect of introducing and lifting physical distancing measures on COVID-19 reproduction (R) number. A large modelling study with data from 131 countries estimated reductions in COVID-19 reproduction (R) number by 28% and 52% following mitigation strategies ranging from the least comprehensive measures to those similar to a lockdown. Changes in the R number occurred 1 to 3 weeks following imposing or lifting of measures and those most strongly associated with an increase in R numbers were lifting bans on gatherings of more than ten people and re-opening of schools (25% and 24% after 28 days). While the authors acknowledged that the estimations came with some limitations, because differences in measure implementations could not be controlled across countries, the findings suggested that combinations of measures rather and single ones were more effective in reducing the R number for COVID-19. [The Lancet Infectious Diseases]

 Leveraging molecular test capacity of tuberculosis laboratories for rapid COVID-19 case-finding. In a letter to Emerging Infectious Diseases, researchers explored the potential of leveraging existing tuberculosis diagnostic infrastructure for the detection of SARS-CoV-2. While using TB testing infrastructure could present a way to increase SARS-CoV-2 detection in the context of limited-resource settings, aspects such as biosafety, technical expertise, capacity planning, and funding needed to be considered in order to prevent any disruptions in TB services during the COVID-19 response. [Emerging Infectious Diseases]


Drug Resistance and Global Health

The problem of microbial dark matter in neonatal sepsis. Researchers from the University of Pennsylvania outlined challenges related to the detection of pathogens responsible for neonatal sepsis (NS), affecting approximately 3 million neonates per year and responsible for 750,000 deaths worldwide. The ability to identify responsible pathogens in blood cultures was hindered by low levels of bacteremia, contamination, and polymicrobial infections among others and sensitive methods involving  DNA and RNA sequencing came with a high cost and were too specialized to be implemented in routine diagnostics. The authors proposed a predictive, personalized public health approach, where the population-wide discovery of pathogens could be performed on samples collected across different treatment sites and then analyzed in specialized sequencing centers. Mapping of the most likely pathogens responsible for NS in different locations could then inform clinicians faced with limited choices, on which antimicrobials to use.  [Emerging Infectious Diseases]

Inpatient antibiotic utilization in the Veterans Administration during the COVID-19 pandemic. A team of investigators in the US assessing antibiotic use in years 2015 to 2020 (between the months of January to May), across 84 inpatient VA facilities, observed a shift in trends of antibiotic use with the emergence of the COVID-19 pandemic. While antibiotic use decreased from 638 to 602 DOT/1000 DP between 2015 and 2019, an increase to 628 DOT/1000 DP was detected between January and May 2020, with broad-spectrum agents used for the community- and hospital-onset infections having some of the largest increases. The increase in antibiotic use was not restricted to areas with the highest case burden of COVID-19, implying that issues not directly related to COVID-19 management, such as a reluctance to obtain diagnostic specimens and diversion of stewardship activities, may have also contributed to the increase. [Infection Control & Hospital Epidemiology]

Successful end-of-treatment outcomes of drug-resistant TB patients who received concomitant bedaquiline and delamanid in Mumbai, India. Researchers in India conducted a retrospective cohort study based on data from 70 patients with drug-resistant tuberculosis (DR-TB), to assess treatment outcome and serious-adverse-events  (SAEs) resulting from a regimen of concomitant Bedaquiline (BDQ) and Delamanid (DLM). About 43% of the patients reported SAEs and 69% of the patients had culture conversion before 24 weeks of treatment. For 87% of the patients, treatment was extended beyond 24 weeks and successful outcomes were reported for 70%, indicating that the BDQ and DLM combination regimen may represent a life-saving treatment option for DR-TB.  [Clinical Infectious Diseases]

Growing concern on the spread of circulating vaccine-derived polioviruses (cVDPV). In a statement to the WHO, International Health Regulations (IHR) polio Emergency Committee expressed concerns on the spread of circulating vaccine-derived polioviruses (cVDPV) in Pakistan, Afghanistan, and several countries across Africa. Lack of access to vaccination has made some populations highly susceptible to ongoing transmission, however, disruptions in routine immunizations and vaccine shortages due to the COVID-19 pandemic have exacerbated this issue, leading to new transmissions across a large geographic spread.  The number of cVDPV type 2 cases in 2020 was 409 as of Oct 5, compared with 378 cases reported for all of 2019. With the risk of international spread of wild poliovirus type 1 and cVDPV2 rising, the committee proposed a set of recommendations that included increasing coverage of routine immunization and establishing a set of criteria to regulate travel into and out of the affected countries. [WHO]

Multidrug-resistant hypervirulent Group B Streptococcus in neonatal invasive infections, France, 2007–2019. A large study analyzing 1,262 neonatal invasive infections between 2007-2019 in France, representing 30% of the total estimated national cases, revealed that the hypervirulent clonal complex (CC) 17 group B Streptococcus (GBS) was responsible for 66% (827/1,262) of the cases. All isolates were susceptible to penicillin, amoxicillin, and vancomycin, however,  high – level resistance to amikacin and erythromycin increased over the years. Similar to what was observed from surveillance data in France, the study revealed an increase in late-onset disease over the 13-year study period with a growing prevalence of the hypervirulent CC17 GBS and its MDR sublineage. The findings warranted continued surveillance of GBS diseases and further investigations on whether the observed trends resulted from a higher tropism of the MDR sublineage or from antibiotic selection pressure. [Emerging Infectious Diseases]


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