Experience on the first national anti-TB drug resistance survey (DRS) in Timor-Leste.

Background: A national drug resistance survey (DRS) was implemented for the first time in Timor-Leste (TL) in 2019. The primary objective of the survey was to assess the prevalence of drug resistance among new and previously treated pulmonary TB patients in the country.

Methods: This nation-wide cross-sectional survey was conducted in 2019 targeting all new and previously treated sputum smear-positive pulmonary TB patients.

25 years of surveillance of drug-resistant tuberculosis: achievements, challenges, and way forward.

Tuberculosis is second only to COVID-19 as a cause of death from a single infectious agent. In 2020, almost 10 million people were estimated to have developed tuberculosis and it caused 1·5 million deaths. Around a quarter of deaths caused by antimicrobial resistance are due to rifampicin-resistant tuberculosis.

Population-level faecal metagenomic profiling as a tool to predict antimicrobial resistance in isolates causing invasive infections: An exploratory study across Cambodia, Kenya, and the UK.

Background: Antimicrobial resistance (AMR) in is a global health threat. Capacity for individual-level surveillance remains limited in many countries, whilst population-level surveillance approaches could inform empiric antibiotic treatment guidelines.

Methods: In this exploratory study, a novel approach to population-level prediction of AMR in clinical isolates using metagenomic (Illumina) profiling of pooled DNA extracts from human faecal samples was developed and tested.

Infection prevention and control during the COVID-19 pandemic: challenges and opportunities for Kenyan public hospitals.

Infection prevention and control, and water sanitation and hygiene have an essential role in ensuring the quality of care and patient outcomes in hospitals. Using a modification of the World Health Organization's water sanitation and hygiene facility improvement tool, we undertook assessments in 14 public hospitals in Kenya in 2018. The hospitals received written feedback on areas where they could make improvements.

Antibiotic use in Kenyan public hospitals: Prevalence, appropriateness and link to guideline availability.

Objective: To examine prescription patterns and explore to what extent guidelines are available and how they might influence treatment appropriateness among hospitalised patients in Kenyan hospitals.

Methods: Data on antimicrobial usage were collected from hospitalised patients across 14 Kenyan public hospitals. For each prescription, appropriateness of treatment was defined using available local and international treatment guidelines and through consensus with local medical specialists.

Evaluating hospital performance in antibiotic stewardship to guide action at national and local levels in a lower-middle income setting.

Background: Inappropriate use of antibiotics can lead to the development of resistant pathogens. Ensuring proper use of these important drugs in all healthcare facilities is essential. Unfortunately, however, very little is known about how antibiotics are used in LMIC clinical settings, nor to what degree antibiotic stewardship programmes are in place and effective.

Extending the use of the World Health Organisations' water sanitation and hygiene assessment tool for surveys in hospitals - from WASH-FIT to WASH-FAST.

Background: Poor water sanitation and hygiene (WASH) in health care facilities increases hospital-associated infections, and the resulting greater use of second-line antibiotics drives antimicrobial resistance. Recognising the existing gaps, the World Health Organisations' Water and Sanitation for Health Facility Improvement Tool (WASH-FIT) was designed for self-assessment. The tool was designed for small primary care facilities mainly providing outpatient and limited inpatient care and was not designed to compare hospital performance.

Evaluating the foundations that help avert antimicrobial resistance: Performance of essential water sanitation and hygiene functions in hospitals and requirements for action in Kenya.

Background: Water Sanitation and Hygiene (WASH) in healthcare facilities is critical in the provision of safe and quality care. Poor WASH increases hospital-associated infections and contributes to the rise of antimicrobial resistance (AMR). It is therefore essential for governments and hospital managers to know the state of WASH in these facilities to set priorities and allocate resources.

Using a common data platform to facilitate audit and feedback on the quality of hospital care provided to sick newborns in Kenya.

Essential interventions to reduce neonatal deaths that can be effectively delivered in hospitals have been identified. Improving information systems may support routine monitoring of the delivery of these interventions and outcomes at scale. We used cycles of audit and feedback (A&F) coupled with the use of a standardised newborn admission record (NAR) form to explore the potential for creating a common inpatient neonatal data platform and illustrate its potential for monitoring prescribing accuracy.

Frequent Undetected Ward-Based Methicillin-Resistant Staphylococcus aureus Transmission Linked to Patient Sharing Between Hospitals.

Background: Recent evidence suggests that hospital transmission of methicillin-resistant Staphylococcus aureus (MRSA) is uncommon in UK centers that have implemented sustained infection control programs. We investigated whether a healthcare-network analysis could shed light on transmission paths currently sustaining MRSA levels in UK hospitals.

Methods: A cross-sectional observational study was performed in 2 National Health Service hospital groups and a general district hospital in Southeast London.

Universal hospital admission screening for carbapenemase-producing organisms in a low-prevalence setting.

Background: Carbapenemase-producing Enterobacteriaceae (CPE) are an emerging threat for healthcare providers worldwide.

Objectives: To determine CPE carriage rates and risk factors in an unselected hospital cohort at the time of admission.

Methods: We approached 4567 patients within 72 h of admission to provide a rectal swab and answer a questionnaire on risk factors for carriage.

Evidence for Community Transmission of Community-Associated but Not Health-Care-Associated Methicillin-Resistant Staphylococcus Aureus Strains Linked to Social and Material Deprivation: Spatial Analysis of Cross-sectional Data.

Background: Identifying and tackling the social determinants of infectious diseases has become a public health priority following the recognition that individuals with lower socioeconomic status are disproportionately affected by infectious diseases. In many parts of the world, epidemiologically and genotypically defined community-associated (CA) methicillin-resistant Staphylococcus aureus (MRSA) strains have emerged to become frequent causes of hospital infection. The aim of this study was to use spatial models with adjustment for area-level hospital attendance to determine the transmission niche of genotypically defined CA- and health-care-associated (HA)-MRSA strains across a diverse region of South East London and to explore a potential link between MRSA carriage and markers of social and material deprivation.

Co-infections determine patterns of mortality in a population exposed to parasite infection.

Many individual hosts are infected with multiple parasite species, and this may increase or decrease the pathogenicity of the infections. This phenomenon is termed heterologous reactivity and is potentially an important determinant of both patterns of morbidity and mortality and of the impact of disease control measures at the population level. Using infections with Theileria parva (a tick-borne protozoan, related to Plasmodium) in indigenous African cattle [where it causes East Coast fever (ECF)] as a model system, we obtain the first quantitative estimate of the effects of heterologous reactivity for any parasitic disease.

Impact of mupirocin resistance on the transmission and control of healthcare-associated MRSA.

Objectives: The objectives of this study were to estimate the relative transmissibility of mupirocin-resistant (MupR) and mupirocin-susceptible (MupS) MRSA strains and evaluate the long-term impact of MupR on MRSA control policies.

Methods: Parameters describing MupR and MupS strains were estimated using Markov chain Monte Carlo methods applied to data from two London teaching hospitals. These estimates parameterized a model used to evaluate the long-term impact of MupR on three mupirocin usage policies: 'clinical cases', 'screen and treat' and 'universal'.

Clonal variation in high- and low-level phenotypic and genotypic mupirocin resistance of MRSA isolates in south-east London.

Objectives: Both low-level mupirocin resistance (LMR) and high-level mupirocin resistance (HMR) have been identified. The aim of this study was to determine the epidemiology of LMR and HMR in MRSA isolates at five hospitals that have used mupirocin for targeted decolonization as part of successful institutional control programmes.

Methods: All MRSA identified in three microbiology laboratories serving five central and south-east London hospitals and surrounding communities between November 2011 and February 2012 were included.

Implications of targeted versus universal admission screening for meticillin-resistant Staphylococcus aureus carriage in a London hospital.

Universal admission screening for meticillin-resistant Staphylococcus aureus (MRSA) has been performed in England since 2010. We evaluated the predictive performance of a regression model derived from the first year of universal screening for detecting MRSA at hospital admission. If we had used our previous targeted screening policy, 75% fewer patients (21,699 per year) would have been screened.

Design and descriptive epidemiology of the Infectious Diseases of East African Livestock (IDEAL) project, a longitudinal calf cohort study in western Kenya.

Background: There is a widely recognised lack of baseline epidemiological data on the dynamics and impacts of infectious cattle diseases in east Africa. The Infectious Diseases of East African Livestock (IDEAL) project is an epidemiological study of cattle health in western Kenya with the aim of providing baseline epidemiological data, investigating the impact of different infections on key responses such as growth, mortality and morbidity, the additive and/or multiplicative effects of co-infections, and the influence of management and genetic factors.A longitudinal cohort study of newborn calves was conducted in western Kenya between 2007-2009.

Clustering of antimicrobial resistance outbreaks across bacterial species in the intensive care unit.

Background: There are frequent reports of intensive care unit (ICU) outbreaks due to transmission of particular antibiotic-resistant bacteria. Less is known about the burden of outbreaks of resistance due to horizontal transfer of mobile genetic elements between species. Moreover, the potential of existing statistical software as a preliminary means for detecting such events has never been assessed.