Antimicrobial resistance in commensal opportunistic pathogens isolated from non-sterile sites can be an effective proxy for surveillance in bloodstream infections

Antimicrobial resistance (AMR) surveillance in bloodstream infections (BSIs) is challenging in low/middle-income countries (LMICs) given limited laboratory capacity. Other specimens are easier to collect and process and are more likely to be culture-positive. In 8102 E. coli BSIs, 322,087 E. coli urinary tract infections, 6952 S. aureus BSIs and 112,074 S. aureus non-sterile site cultures from Oxfordshire (1998–2018), and other (55,296 isolates) rarer commensal opportunistic pathogens, antibiotic resistance trends over time in blood were strongly associated with those in other specimens (maximum cross-correlation per drug 0.51–0.99). Resistance prevalence was congruent across drug-years for each species (276/312 (88%) species-drug-years with prevalence within ± 10% between blood/other isolates). Results were similar across multiple countries in high/middle/low income-settings in the independent ATLAS dataset (103,559 isolates, 2004–2017) and three further LMIC hospitals/programmes (6154 isolates, 2008–2019). AMR in commensal opportunistic pathogens cultured from BSIs is strongly associated with AMR in commensal opportunistic pathogens cultured from non-sterile sites over calendar time, suggesting the latter could be used as an effective proxy for AMR surveillance in BSIs.

Antimicrobial resistance detection in Southeast Asian hospitals is critically important from both patient and societal perspectives, but what is its cost?

Antimicrobial resistance (AMR) is a major threat to global health. Improving laboratory capacity for AMR detection is critically important for patient health outcomes and population level surveillance. We aimed to estimate the financial cost of setting up and running a microbiology laboratory for organism identification and antimicrobial susceptibility testing as part of an AMR surveillance programme. Financial costs for setting up and running a microbiology laboratory were estimated using a top-down approach based on resource and cost data obtained from three clinical laboratories in the Mahidol Oxford Tropical Medicine Research Unit network. Costs were calculated for twelve scenarios, considering three levels of automation, with equipment sourced from either of the two leading manufacturers, and at low and high specimen throughput. To inform the costs of detection of AMR in existing labs, the unit cost per specimen and per isolate were also calculated using a micro-costing approach. Establishing a laboratory with the capacity to process 10,000 specimens per year ranged from $254,000 to $660,000 while the cost for a laboratory processing 100,000 specimens ranged from $394,000 to $887,000. Excluding capital costs to set up the laboratory, the cost per specimen ranged from $22–31 (10,000 specimens) and $11–12 (100,000 specimens). The cost per isolate ranged from $215–304 (10,000 specimens) and $105–122 (100,000 specimens). This study provides a conservative estimate of the costs for setting up and running a microbiology laboratory for AMR surveillance from a healthcare provider perspective. In the absence of donor support, these costs may be prohibitive in many low- and middle- income country (LMIC) settings. With the increased focus on AMR detection and surveillance, the high laboratory costs highlight the need for more focus on developing cheaper and cost-effective equipment and reagents so that laboratories in LMICs have the potential to improve laboratory capacity and participate in AMR surveillance.

227 Multiple Outbreak Of SARS-COVID-19 In Surgical Wards at The Tertiary Hospital

Background Since the second surge of SARS-COVID-19 on 18th of September, additional several measures were introduced, and pathways created in order to execute safe surgical practices and protect both patients and staff from SARS-COVID-19. Despite these measures, there have been reported cases of outbreaks in various parts of UK amongst patients and clinical staff. Method Three outbreaks in the past 6 weeks (10, September 2020 to 21, October 2020) were reported in our surgical wards and we compiled the timing, initial source, number of affected individuals and immediate management steps taken. Results Following the first outbreak on wards, 28-day surveillance helped us understand responsible variants. Several staff members were found walking out of hospital, in groups once they had removed their PPEs. Communal lunching with inadequate social distancing, attending work with symptoms (albeit atypical for COVID), sharing cars to/from work or not wearing PPE correctly were highlighted in the subsequent investigations. The reduction in number of affected individuals during the last two incidents reflected a degree of efficacy of the implemented preventative measures, which were reviewed again following the subsequent incidents. Conclusions In the present climate, a robust and prompt response to outbreaks is required. Continual iteration with regards to the need for PPE, adequate social distancing and avoiding over-crowding in communal areas is paramount to reduce the probability of ward outbreaks and inter-professional transmission. Asymptomatic staff testing, particularly in high-risk areas could also be considered but would require adequate laboratory capacity and rapid turnaround of test results.

Ramadan and Eid al-Fitr: Population movement, mass gathering and escalating of COVID-19 – A perspective from Indonesia

In Indonesia, the most populous Moslem-majority country, despite the possibility of underreported coronavirus disease (COVID-19) cases, 6,248 confirmed cases and 535 deaths have been recorded. With upcoming Ramadan and Eid al-Fitr, between 18-23 million of Indonesians may move from urban locations (with high counts of COVDI-19) to rural areas with fewer cases currently but less laboratory capacity to diagnose cases. This review summaries the current situation of CO.VID-19 in Indonesia and discusses the possible impacts of mass population movement, Ramadan-related activities, and Eid al-Fitr celebration days on COVID-19 transmission in the country.

Lessons Learned From the Implementation of a Participant-Collected, Mail-Based SARS-CoV-2 Serological Survey in Massachusetts, USA

The rapid spread of SARS-CoV-2 is largely driven by pre-symptomatic or mildly symptomatic individuals who transmit the virus. Serological tests to identify antibodies against SARS-CoV-2 are an important tool to characterize subclinical infection exposure, which is critical in determining transmission trajectories and consequent population immunity. During the summer of 2020, a mail-based serological survey with self-collected dried blood spot (DBS) samples was implemented among university affiliates and their household members in Massachusetts, USA. Described here are some of the challenges faced and novel procedures used during the implementation of this study to assess the prevalence of SARS-CoV-2 antibodies amid the global pandemic. Important challenges included remote and contact-minimized participant recruitment, limited availability of commodities and laboratory capacity, a potentially biased sample population, and policy changes impacting the distribution of clinical results to study participants. Methods used to surmount these challenges and lessons learned are presented to inform similar studies. Key lessons relate to the acceptability and feasibility of DBS sampling, supply requirements, the logistics of packing and shipping packages, data linkages to enrolled household members, and the utility of having an on-call nurse available for participant concerns during sample collection.Future studies might consider additional recruitment techniques such as conducting studies during academic semesters when recruiting in a university setting, partnerships with supply and shipping specialists, and using a stratified sampling approach to minimize potential biases in recruitment. This study design highlights the feasibility and acceptability of self-collected bio-samples and has broad applicability for other serological surveys for a range of pathogens.

Predicting the environmental suitability for onchocerciasis in Africa as an aid to elimination planning

Recent evidence suggests that, in some foci, elimination of onchocerciasis from Africa may be feasible with mass drug administration (MDA) of ivermectin. To achieve continental elimination of transmission, mapping surveys will need to be conducted across all implementation units (IUs) for which endemicity status is currently unknown. Using boosted regression tree models with optimised hyperparameter selection, we estimated environmental suitability for onchocerciasis at the 5 × 5-km resolution across Africa. In order to classify IUs that include locations that are environmentally suitable, we used receiver operating characteristic (ROC) analysis to identify an optimal threshold for suitability concordant with locations where onchocerciasis has been previously detected. This threshold value was then used to classify IUs (more suitable or less suitable) based on the location within the IU with the largest mean prediction. Mean estimates of environmental suitability suggest large areas across West and Central Africa, as well as focal areas of East Africa, are suitable for onchocerciasis transmission, consistent with the presence of current control and elimination of transmission efforts. The ROC analysis identified a mean environmental suitability index of 0·71 as a threshold to classify based on the location with the largest mean prediction within the IU. Of the IUs considered for mapping surveys, 50·2% exceed this threshold for suitability in at least one 5 × 5-km location. The formidable scale of data collection required to map onchocerciasis endemicity across the African continent presents an opportunity to use spatial data to identify areas likely to be suitable for onchocerciasis transmission. National onchocerciasis elimination programmes may wish to consider prioritising these IUs for mapping surveys as human resources, laboratory capacity, and programmatic schedules may constrain survey implementation, and possibly delaying MDA initiation in areas that would ultimately qualify.

Direct Molecular Characterization of Acid-Fast Bacilli Smear of Nontuberculosis Mycobacterium Species Causing Pulmonary Tuberculosis in Guna Yala Region, Panama

Mycobacterium tuberculosis (MTB) stands out as the main causative agent of pulmonary tuberculosis (TB). However, nontuberculous mycobacteria (NTM) species also have the potential to infect and cause TB in susceptible individuals. The objective of this study was to identify NTM species that cause public health problems in remote areas. The study was carried out using 105 sputum smears obtained from patients from the Guna Yala Region of Panama with clinical signs suggestive of TB. DNA was extracted from sputum smears. Nontuberculous mycobacteria and MTB were characterized using polymerase chain reaction restriction analysis (hsp65, rpob) and an evaluation of 24-mycobacterial interspersed repetitive units–variable number of tandem repeats loci. Twenty-six Mycobacterium species were characterized; 19 (18%) were identified as MTB, and 7 (6.7%) were identified as NTM (four M. avium complex, two M. haemophilum, one M. tusciae). These results suggest that at least one in five cases of pulmonary TB among this population is caused by an NTM. Thus, identifying the bacteria causing pulmonary disease is key even in remote regions of the world where standard diagnosis and culture are not available. Strengthening the laboratory capacity within the Guna Yala Region is needed to identify NTM infections promptly.

SARS-CoV-2 screening: effectiveness and risk of increasing transmission

Testing asymptomatic people for SARS-CoV-2 aims to reduce COVID-19 transmission. Screening programmes’ effectiveness depends upon testing strategy, sample handling logistics, test sensitivity and individual behaviour, in addition to dynamics of viral transmission. The interaction between these factors is not fully characterized. We investigated the interaction between these factors to determine how to optimize reduction of transmission. We estimate that under idealistic assumptions 70% of transmission may be averted, but under realistic assumptions only 7% may be averted. We show that programmes that overwhelm laboratory capacity or reduce isolation of those with minor symptoms have increased transmission compared with those that do not: programmes need to be designed to avoid these issues, or they will be ineffective or even counter-productive. Our model allows optimal selection of whom to test, quantifies the balance between accuracy and timeliness, and quantifies potential impacts of behavioural interventions. We anticipate our model can be used to understand optimal screening strategies for other infectious diseases with substantially different dynamics.

Studi Komparatif Penanganan Pandemi di Taiwan: SARS, H1N1, dan COVID-19

Taiwan is considered as one of the countries that has successfully controlled the spread of COVID-19. Taiwan stated that their success in controlling the spread of COVID-19 was inseparable from their experience in dealing with SARS in 2003. This paper aims to compare Taiwan's response to SARS 2003, H1N1 in 2009, and COVID-19. By comparing Taiwan's response, this article detailing the transformation of Taiwan's policy in every pandemic and analyze the lesson learn for developing countries, including Indonesia, in dealing with a pandemic of communicable diseases in the future. In 2003 Taiwan had made some negligence as developing countries did when the outbreak of COVID-19. By looking at the transformation of Taiwan's policy, we can draw conclusions about the steps that developing countries can take in the future in controlling the spread of infectious diseases. This paper uses the tradition of empiricism with an indirect observation mechanism through the study of literature to describe the transformation of Taiwan's policies and analyze the lessons that can be taken by developing countries. The learning relates to communicable disease monitoring, border quarantine, communicable disease reporting, response planning, contact tracing, laboratory capacity building, public health education, open and transparent information.