Before the coronavirus 2019 (COVID-19) pandemic began, antimicrobial resistance (AMR) was among the top priorities for global public health. Already a complex challenge, AMR now needs to be addressed in a changing healthcare landscape. Here, we analyse how changes due to COVID-19 in terms of antimicrobial usage, infection prevention, and health systems affect the emergence, transmission, and burden of AMR. Increased hand hygiene, decreased international travel, and decreased elective hospital procedures may reduce AMR pathogen selection and spread in the short term. However, the opposite effects may be seen if antibiotics are more widely used as standard healthcare pathways break down. Over 6 months into the COVID-19 pandemic, the dynamics of AMR remain uncertain. We call for the AMR community to keep a global perspective while designing finely tuned surveillance and research to continue to improve our preparedness and response to these intersecting public health challenges.

BackgroundDynamic transmission models are increasingly being used to improve our understanding of the epidemiology of healthcare-associated infections (HCAI). However, there has been no recent comprehensive review of this emerging field. This paper summarises how mathematical models have informed the field of HCAI and how methods have developed over time.MethodsMEDLINE, EMBASE, Scopus, CINAHL plus and Global Health databases were systematically searched for dynamic mathematical models of HCAI transmission and/or the dynamics of antimicrobial resistance in healthcare settings.ResultsIn total, 96 papers met the eligibility criteria. The main research themes considered were evaluation of infection control effectiveness (64%), variability in transmission routes (7%), the impact of movement patterns between healthcare institutes (5%), the development of antimicrobial resistance (3%), and strain competitiveness or co-colonisation with different strains (3%). Methicillin-resistant Staphylococcus aureus was the most commonly modelled HCAI (34%), followed by vancomycin resistant enterococci (16%). Other common HCAIs, e.g. Clostridum difficile, were rarely investigated (3%). Very few models have been published on HCAI from low or middle-income countries.The first HCAI model has looked at antimicrobial resistance in hospital settings using compartmental deterministic approaches. Stochastic models (which include the role of chance in the transmission process) are becoming increasingly common. Model calibration (inference of unknown parameters by fitting models to data) and sensitivity analysis are comparatively uncommon, occurring in 35% and 36% of studies respectively, but their application is increasing. Only 5% of models compared their predictions to external data.ConclusionsTransmission models have been used to understand complex systems and to predict the impact of control policies. Methods have generally improved, with an increased use of stochastic models, and more advanced methods for formal model fitting and sensitivity analyses. Insights gained from these models could be broadened to a wider range of pathogens and settings. Improvements in the availability of data and statistical methods could enhance the predictive ability of models.

IntroductionHealth service use among the public can decline during outbreaks and had been predicted among low and middle-income countries during the COVID-19 pandemic. In March 2020, the government of the Democratic Republic of the Congo (DRC) started implementing public health measures across Kinshasa, including strict lockdown measures in the Gombe health zone.MethodsUsing monthly time series data from the DRC Health Management Information System (January 2018 to December 2020) and interrupted time series with mixed effects segmented Poisson regression models, we evaluated the impact of the pandemic on the use of essential health services (outpatient visits, maternal health, vaccinations, visits for common infectious diseases and non-communicable diseases) during the first wave of the pandemic in Kinshasa. Analyses were stratified by age, sex, health facility and lockdown policy (ie, Gombe vs other health zones).ResultsHealth service use dropped rapidly following the start of the pandemic and ranged from 16% for visits for hypertension to 39% for visits for diabetes. However, reductions were highly concentrated in Gombe (81% decline in outpatient visits) relative to other health zones. When the lockdown was lifted, total visits and visits for infectious diseases and non-communicable diseases increased approximately twofold. Hospitals were more affected than health centres. Overall, the use of maternal health services and vaccinations was not significantly affected.ConclusionThe COVID-19 pandemic resulted in important reductions in health service utilisation in Kinshasa, particularly Gombe. Lifting of lockdown led to a rebound in the level of health service use but it remained lower than prepandemic levels.

HA-CDI contributes to patients' expected LOS and risk of mortality. However, when quantifying the health and economic burden of hospital-onset of HA-CDI, the heterogeneity in the impact of HA-CDI should be accounted for.

Evidence regarding the seasonality of urinary tract infection (UTI) consultations in primary care is conflicting and methodologically poor. To our knowledge, this is the first study to determine whether this seasonality exists in the UK, identify the peak months and describe seasonality by age. The monthly number of UTI consultations (N = 992 803) and nitrofurantoin and trimethoprim prescriptions (N = 1 719 416) during 2008-2015 was extracted from The Health Improvement Network (THIN), a large nationally representative UK dataset of electronic patient records. Negative binomial regression models were fitted to these data to investigate seasonal fluctuations by age group (14-17, 18-24, 25-45, 46-69, 70-84, 85+) and by sex, accounting for a change in the rate of UTI over the study period. A September to November peak in UTI consultation incidence was observed for ages 14-69. This seasonality progressively faded in older age groups and no seasonality was found in individuals aged 85+, in whom UTIs were most common. UTIs were rare in males but followed a similar seasonal pattern than in females. We show strong evidence of an autumnal seasonality for UTIs in individuals under 70 years of age and a lack of seasonality in the very old. These findings should provide helpful information when interpreting surveillance reports and the results of interventions against UTI.

Antibiotic-induced perturbation of the human gut flora is expected to play an important role in mediating the relationship between antibiotic use and the population prevalence of antibiotic resistance in bacteria, but little is known about how antibiotics affect within-host resistance dynamics. Here we develop a data-driven model of the within-host dynamics of extended-spectrum beta-lactamase (ESBL) producing Enterobacteriaceae. We use blaCTX-M (the most widespread ESBL gene family) and 16S rRNA (a proxy for bacterial load) abundance data from 833 rectal swabs from 133 ESBL-positive patients followed up in a prospective cohort study in three European hospitals. We find that cefuroxime and ceftriaxone are associated with increased blaCTX-M abundance during treatment (21% and 10% daily increase, respectively), while treatment with meropenem, piperacillin-tazobactam, and oral ciprofloxacin is associated with decreased blaCTX-M (8% daily decrease for all). The model predicts that typical antibiotic exposures can have substantial long-term effects on blaCTX-M carriage duration.

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Background Approximately 2.5 billion people are at risk from dengue infection. Dengue is endemic to urban populations in tropical areas; large epidemics have occurred less frequently in subtropical regions, and rarely in cities in temperate regions. The virus is transmitted by the freshwater mosquito, Aedes aegypti. During the past century, surface temperatures have increased by a global average of 0.75°C. Temperature increases of this magnitude may be associated with substantial increases in dengue epidemic potential.Objective We aimed to describe the geographic distribution of dengue transmission (current and historical) and to estimate possible impacts on transmission from climate change. MethodsWe conducted two systematic reviews. We searched PubMed, digital books and archives for literature describing geographically defined outbreaks of dengue. We also searched PubMed and Scopus for studies modelling the potential effects of climate change on dengue transmission. Data from studies meeting the inclusion criteria were considered by all of our team and we collaborated to draw our conclusions. No meta-analysis was attempted.Results One hundred and one articles met the eligibility criteria for the first review; there were some contradictions and ambiguities in the data. Current global distribution of dengue is generally less extensive than historical limits of dengue-like illness. In recent years, several countries have reported local transmission of dengue for the first time, but it is unclear whether this represents true geographic spread, rather than increased awareness and reporting. Areas of geographic contraction of dengue include the southern states of North America, much of Australia, parts of southern Europe, Japan, China and South Africa. Piped water supplies, removal of water storage tanks, changes in housing conditions and vector control measures have plausibly contributed to this contraction.Six papers met the inclusion criteria for the second review. The findings of theoretical and statistical models of dengue and climate are broadly consistent: the transmission of dengue is highly sensitive to climate. Relatively small increases in temperature (around 1°C) can lead to substantial increases in transmission potential. Studies modelling the potential effects of climate change on dengue project that there will be increases in climatic suitability for transmission and an expansion of the geographic regions at risk of dengue during this century.Conclusions Geographic distribution of dengue has generally contracted, despite increases in global average temperature in the past century. Theoretically, however, temperature trends have increased the risk of dengue in some areas. The independent effect of climate change on historical patterns of dengue transmission cannot be quantified based on current evidence, as existing models of disease transmission provide limited, incomplete, projections of disease risk. The geographic limits of dengue result from a complex interaction between physical, ecological and so...