Land-use change is predicted to act as a driver of zoonotic disease emergence through human exposure to novel microbial diversity, but evidence for the effects of environmental change on microbial ...communities in vertebrates is lacking. We sample wild birds at 99 wildlife-livestock-human interfaces across Nairobi, Kenya, and use whole genome sequencing to characterise bacterial genes known to be carried on mobile genetic elements (MGEs) within avian-borne Escherichia coli (n = 241). By modelling the diversity of bacterial genes encoding virulence and antimicrobial resistance (AMR) against ecological and anthropogenic forms of urban environmental change, we demonstrate that communities of avian-borne bacterial genes are shaped by the assemblage of co-existing avian, livestock and human communities, and the habitat within which they exist. In showing that non-random processes structure bacterial genetic communities in urban wildlife, these findings suggest that it should be possible to forecast the effects of urban land-use change on microbial diversity.
Severe Acute Respiratory Syndrome coronavirus-2 (SARS-CoV-2) has challenged public health agencies globally. In order to effectively target government responses, it is critical to identify the ...individuals most at risk of coronavirus disease-19 (COVID-19), developing severe clinical signs, and mortality. We undertook a systematic review of the literature to present the current status of scientific knowledge in these areas and describe the need for unified global approaches, moving forwards, as well as lessons learnt for future pandemics.
Medline, Embase and Global Health were searched to the end of April 2020, as well as the Web of Science. Search terms were specific to the SARS-CoV-2 virus and COVID-19. Comparative studies of risk factors from any setting, population group and in any language were included. Titles, abstracts and full texts were screened by two reviewers and extracted in duplicate into a standardised form. Data were extracted on risk factors for COVID-19 disease, severe disease, or death and were narratively and descriptively synthesised.
One thousand two hundred and thirty-eight papers were identified post-deduplication. Thirty-three met our inclusion criteria, of which 26 were from China. Six assessed the risk of contracting the disease, 20 the risk of having severe disease and ten the risk of dying. Age, gender and co-morbidities were commonly assessed as risk factors. The weight of evidence showed increasing age to be associated with severe disease and mortality, and general comorbidities with mortality. Only seven studies presented multivariable analyses and power was generally limited. A wide range of definitions were used for disease severity.
The volume of literature generated in the short time since the appearance of SARS-CoV-2 has been considerable. Many studies have sought to document the risk factors for COVID-19 disease, disease severity and mortality; age was the only risk factor based on robust studies and with a consistent body of evidence. Mechanistic studies are required to understand why age is such an important risk factor. At the start of pandemics, large, standardised, studies that use multivariable analyses are urgently needed so that the populations most at risk can be rapidly protected.
This review was registered on PROSPERO as CRD42020177714 .
Carbapenemase-producing organisms (CPO) have been largely responsible for the extensive spread of carbapenem resistance, and their prevalence is increasing in many parts of the world.
To evaluate ...clinical and molecular epidemiology and mortality associated with CPO among patients.
All CPO from clinical and long-term healthcare surveillance cultures across Scotland in 2003–2017 were reviewed retrospectively. Polymerase chain reaction was used to detect genes coding for carbapenemases. A generalized linear mixed model was used to identify risk factors for mortality.
In total, 290 individuals with CPO were identified. The overall incidence increased over time (P<0.001) from 0.02 to 1.38 per 100,000 population between 2003 and 2017. A total of 243 distinct CPO isolates were obtained from 269 isolations in 214 individuals with available metadata. The majority of the isolates were Enterobacterales (206/243, 84.8%), and Klebsiella pneumoniae (65/206, 31.6%) and Enterobacter cloacae (52/206, 25.2%) were the most common species. VIM (75/243, 30.9%) and NDM (56/243, 23.0%) were the most common carbapenemases. The crude 30-day mortality rate was 11.8% (25/211), while the case fatality rate was 5.7% (12/211). Age >60 years adjusted odds ratio (aOR) 3.36, 95% confidence interval (CI) 1.06–10.63; P=0.033, presence of non-fermenters (aOR 4.88, 95% CI 1.64–14.47; P=0.005), and systemic infection or organ failure (aOR 4.21, 95% CI 1.38–12.81; P=0.032) were independently associated with 30-day mortality.
The incidence of CPO in Scotland is low but increasing. Awareness is required that inpatients aged >60 years, patients with systemic infection or organ failure, and patients presenting with non-fermenters are at higher risk of death from CPO.
Staphylococcus aureus clonal complex 398 (CC398) is associated with disease in humans and livestock, and its origins and transmission have generated considerable interest. We performed a time-scaled ...phylogenetic analysis of CC398, including sequenced isolates from the United Kingdom (Scotland), along with publicly available genomes. Using state-of-the-art methods for mapping traits onto phylogenies, we quantified transitions between host species to identify sink and source populations for CC398 and employed a novel approach to investigate the gain and loss of antibiotic resistance in CC398 over time. We identified distinct human- and livestock-associated CC398 clades and observed multiple transmissions of CC398 from livestock to humans and between countries, lending quantitative support to previous reports. Of note, we identified a subclade within the livestock-associated clade comprised of isolates from hospital environments and newborn babies, suggesting that livestock-associated CC398 is capable of onward transmission in hospitals. In addition, our analysis revealed significant differences in the dynamics of resistance to methicillin and tetracycline related to contrasting historical patterns of antibiotic usage between the livestock industry and human medicine. We also identified significant differences in patterns of gain and loss of different tetracycline resistance determinants, which we ascribe to epistatic interactions between the resistance genes and/or differences in the modes of inheritance of the resistance determinants.
Vaccination has proved a powerful defence against a range of infectious diseases of humans and animals. However, its potential to control major epidemics of foot-and-mouth disease (FMD) in livestock ...is contentious. Using an individual farm-based model, we consider either national prophylactic vaccination campaigns in advance of an outbreak, or combinations of reactive vaccination and culling strategies during an epidemic. Consistent with standard epidemiological theory, mass prophylactic vaccination could reduce greatly the potential for a major epidemic, while the targeting of high-risk farms increases efficiency. Given sufficient resources and preparation, a combination of reactive vaccination and culling might control ongoing epidemics. We also explore a reactive strategy, 'predictive' vaccination, which targets key spatial transmission loci and can reduce markedly the long tail that characterizes many FMD epidemics. These analyses have broader implications for the control of human and livestock infectious diseases in heterogeneous spatial landscapes.
The conventional objective of vaccination programmes is to eliminate infection by reducing the reproduction number of an infectious agent to less than one, which generally requires vaccination of the ...majority of individuals. In populations of endangered wildlife, the intervention required to deliver such coverage can be undesirable and impractical; however, endangered populations are increasingly threatened by outbreaks of infectious disease for which effective vaccines exist. As an alternative, wildlife epidemiologists could adopt a vaccination strategy that protects a population from the consequences of only the largest outbreaks of disease. Here we provide a successful example of this strategy in the Ethiopian wolf, the world's rarest canid, which persists in small subpopulations threatened by repeated outbreaks of rabies introduced by domestic dogs. On the basis of data from past outbreaks, we propose an approach that controls the spread of disease through habitat corridors between subpopulations and that requires only low vaccination coverage. This approach reduces the extent of rabies outbreaks and should significantly enhance the long-term persistence of the population. Our study shows that vaccination used to enhance metapopulation persistence through elimination of the largest outbreaks of disease requires lower coverage than the conventional objective of reducing the reproduction number of an infectious agent to less than one.
The prevalence of Escherichia coli O157 displays striking variability across the Scottish cattle population. On 78% of farms, in a cross-sectional survey of 952, no shedding of E. coli O157 was ...detected, but on a small proportion, ∼2%, very high prevalences of infection were found (with 90–100% of pats sampled being positive). We ask whether this variation arises from the inherent stochasticity in transmission dynamics or whether it is a signature of underlying heterogeneities in the cattle population. A novel approach is taken whereby the cross-sectional data are viewed as providing independent snapshots of a dynamic process. Using maximum-likelihood methods to fit time-dependent epidemiological models to the data we obtain estimates for the rates of immigration and transmission of E. coli O157 infection – parameters which have not been previously quantified in the literature. A comparison of alternative model fits reveals that the variation in the prevalence data is best explained when a proportion of the cattle are assumed to transmit infection at much higher levels than the rest – the so-called super-shedders. Analysis of a second dataset, comprising samples taken from 32 farms at monthly intervals over a period of 1 year, additionally yields an estimate for the rate of recovery from infection. The pattern of prevalence displayed in the second dataset also strongly supports the super-shedder hypothesis.
Summary
To formally quantify the level of under‐detection of Trypanosoma brucei rhodesiense sleeping sickness (SS) during an epidemic in Uganda, a decision tree (under‐detection) model was developed; ...concurrently, to quantify the subset of undetected cases that sought health care but were not diagnosed, a deterministic (subset) model was developed. The values of the under‐detection model parameters were estimated from previously published records of the duration of symptoms prior to presentation and the ratio of early to late stage cases in 760 SS patients presenting at LIRI hospital, Tororo, Uganda during the 1988–1990 epidemic of SS. For the observed early to late stage ratio of 0.47, we estimate that the proportion of under‐detection in the catchment area of LIRI hospital was 0.39 (95% CI 0.37–0.41) i.e. 39% of cases are not reported. Based on this value, it is calculated that for every one reported death of SS, 12.0 (95% CI 11.0–13.0) deaths went undetected in the LIRI hospital catchment area – i.e. 92% of deaths are not reported. The deterministic (subset) model structured on the possible routes of a SS infection to either diagnosis or death through the health system or out of it, showed that of a total of 73 undetected deaths, 62 (CI 60–64) (85%) entered the healthcare system but were not diagnosed, and 11 (CI 11–12) died without seeking health care from a recognized health unit. The measure of early to late stage presentation provides a tractable measure to determine the level of rhodesiense SS under‐detection and to gauge the effects of interventions aimed at increasing treatment coverage.
PDF
