Laboratory Capacity Research Articles

Clinical Performance of the Reverse Transcription-Loop-Mediated Isothermal Amplification Assay for the Diagnosis of COVID-19 in a Thai Community Hospital at the Thailand-Myanmar Border.

Coronavirus disease 2019 (COVID-19) continues to be a global health threat and is a public health issue in Thailand and other countries. The extensive cross-border between Thailand and Myanmar is considered to be at a potentially high risk for COVID-19 distribution in this region. In this instance, simple and cost-effective tests for rapid and early detection of COVID-19 would be useful for effective patient management and control of the disease. This study was conducted at Mae Sot Hospital on the border of Thailand-Myanmar to evaluate the diagnostic performance of a simple colorimetric reverse transcription-loop-mediated isothermal amplification (RT-LAMP) assay developed recently for the rapid detection of SARS-CoV-2. Nasopharyngeal specimens were routinely collected and processed through automated nucleic acid extraction followed by real-time reverse transcription-polymerase chain reaction (rRT-PCR) using the Molaccu® COVID-19 Detection Kit. The RT-LAMP assay was further performed on remnant RNA samples, and the visual results were compared to those of rRT-PCR as a reference. Of the 727 samples tested, the RT-LAMP assay could detect 322 out of 374 samples positive for SARS-CoV-2 by rRT-PCR with 100% (n = 353/353) negative agreement. The comparative analysis demonstrated the overall accuracy, sensitivity, specificity, positive predictive value, and negative predictive valueof the RT-LAMP at 92.85% (n = 675/727, 95% CI: 90.73-94.61), 86.10% (n = 322/374, 95% CI: 82.17-89.44), 100% (n = 353/353, 95% CI: 98.96-100), 100% (n = 322/322, 95% CI: 98.86-100), and 87.16% (n = 353/405, 95% CI: 84.06-89.73), respectively. This RT-LAMP assay showed good diagnostic performance in the hospital setting. It can increase laboratory capacity for rapid SARS-CoV-2 testing and has the potential for use as an alternative or a backup assay at the point of need, especially where alternatives are unavailable for any reason, such as a decline in COVID-19 cases.

Conducting nationwide cohort COVID-19 serology surveys on a nation with limited resources and decentralized governance: Evidence from Indonesia

Knowing the level of SARS-CoV-2 transmission is crucial for decision-making on Coronavirus disease (COVID-19) handling. Guidelines for measuring SARS-CoV-2 antibodies to estimate seroprevalence are conceptually straightforward and internationally available. However, challenges exist for developing countries with limited laboratory capacity, diverse geographical topography, fragmented health information systems and limited resources such as Indonesia. One year after the first case was confirmed in Indonesia, approximately ten infections were undiagnosed or underreported for every reported case. Under those circumstances, we described the method and lessons learned in conducting nationwide cohort COVID-19 serology surveys in a nation with limited resources, such as Indonesia. •Strong cross-sectoral collaboration between ministries and levels of governance (central and subnational) enables strategic use of civil registration database for efficient sampling.•All agglomeration districts (highly dense population and urban area) were selected as study sites, and additional non-agglomeration districts were selected using probability-proportional-to-size (PPS).•Involving the experienced phlebotomist in community health service provider and district laboratory cut down preparation time.

A phased strengthening of laboratory capacity in the Eastern Mediterranean Region during the COVID-19 pandemic.

The Eastern Mediterranean Region (EMR) faces ongoing challenges in its public health system due to limited resources, logistical issues, and political disruptions. The COVID-19 pandemic accelerated the need for stronger laboratory capacities to handle the increased demand for testing. In a phased response, EMR countries utilized the National Influenza Centers to rapidly establish and scale molecular testing for SARS-CoV-2, the causative agent of COVID-19. The expansion of capacity included strong collaborations between public health bodies and private and academic sectors to decentralize and expand testing to the subnational level. To ensure that the quality of testing was not impacted by rapid expansion, national and subnational laboratories were enrolled in external quality assurance programs for the duration of the response. Implementation of genomic surveillance was prioritized for variant tracking, leading to the establishment of regional sequencing reference laboratories and the distribution of MinION sequencing platforms to complex emergency countries who previously had limited experience with pathogen sequencing. Challenges included a lack of technical expertise, including in implementing novel diagnostic assays and sequencing, a lack of bioinformatics expertise in the region, and significant logistical and procurement challenges. The collaborative approach, coordinated through the WHO Eastern Mediterranean Regional Office, enabled all 22 countries to achieve SARS-CoV-2 diagnostic capabilities, highlighting the pivotal role of laboratories in global health security.

Parechovirus A Circulation and Testing Capacities in Europe, 2015-2021.

Parechovirus infections usually affect neonates and young children; manifestations vary from asymptomatic to life-threatening. We describe laboratory capacity in Europe for assessing parechovirus circulation, seasonality, and epidemiology. We used retrospective anonymized data collected from parechovirus infection case-patients identified in Europe during January 2015-December 2021. Of 21 laboratories from 18 countries that participated in the study, 16 (76%) laboratories with parechovirus detection capacity reported 1,845 positive samples; 12/16 (75%) with typing capability successfully identified 517 samples. Parechovirus A3 was the most common type (n = 278), followed by A1 (153), A6 (50), A4 (13), A5 (22), and A14 (1). Clinical data from 1,269 participants highlighted correlation of types A3, A4, and A5 with severe disease in neonates. We observed a wide capacity in Europe to detect, type, and analyze parechovirus data. To enhance surveillance and response for PeV outbreaks, sharing typing protocols and data on parechovirus-positive cases should be encouraged.

Global-PPS targets for antimicrobial stewardship in paediatric patients at hospitals in Sanandaj, Western Iran, compared with Southeast Asian and European hospitals

Point prevalence surveys (PPS) provide valuable data on patterns of hospital antimicrobial administration. To identify quality improvement indicators, we evaluated antimicrobial prescribing patterns in children and neonates admitted to three referral centres in Sanandaj, Western Iran, and compared these with Southeast Asian and European paediatric benchmark data. The standardised Global-PPS was performed to assess antimicrobial use in Southeast Asia, including Sanandaj and European hospitals, in 2019. Of the 4118, 2915, and 443 paediatric patients enrolled in Southeast Asian, European and Sanandaj hospitals, 2342 (56.9%), 833 (28.6%) and 332 (74.9%), respectively, received at least one antimicrobial in 2019. The most administered antibiotics in neonates were ampicillin in Southeast Asia (30.3%) and Sanandaj (41.5%, often in combination with cefotaxime (29.0%)), compared with amoxicillin in Europe (20.0%). In children, ceftriaxone was most prescribed in Sanandaj (62.4%) and Southeast Asia (20.5%) as opposed to amoxicillin (11.8%) in Europe. Twice as many Watch antibiotics (83.0%) were prescribed on paediatric wards in Sanandaj compared with European paediatric wards (41.1%). All antimicrobials in Sanandaj hospitals were prescribed empirically, and prolonged surgical prophylaxis was common (75.5%). The high prevalence of antibiotic prescribing, high empirical therapies, and poor outcomes for antibiotic quality indicators strongly suggest the urgent need for an antibiotic stewardship program in Sanandaj hospitals, where improved diagnostic laboratory capacity and reconsideration of training may be good targets for intervention in their hospitals.

Invisible and undervalued: A qualitative study of laboratory workers' experiences and perceptions of laboratory strengthening in Sierra Leone.

The 2013-2016 West Africa Ebola outbreak highlighted the importance of laboratory capacity to outbreak response while also revealing its long-standing neglect. The outbreak prompted massive international investment into strengthening laboratory services across multiple healthcare settings. In this article, we explore hospital-based clinical laboratory workers' experiences and perceptions of their everyday working environment in Sierra Leone, and how recent investments in laboratory strengthening have shaped these. This qualitative study draws on in-depth interviews with eight laboratory workers and participant observation of laboratory practices at a tertiary referral hospital in Freetown between April 2019 and December 2019. Interview and observational data were coded and analysed using a reflexive thematic approach. The Ebola outbreak prompted international investments in automated devices, biosafety training, and a new dedicated infectious diseases laboratory. However, little investment was made in the infrastructure and supply systems needed to sustain routine laboratory work or keep machines functioning. Laboratory workers perceived their work to be under-recognised and undervalued by the government, hospital managers and clinical staff, a perception compounded by under-use of the hospital's laboratory services by clinicians. Understanding laboratory technicians' views, experiences, and priorities is essential to any sustainable laboratory-strengthening effort. Investments in personnel should match investments in technologies and infrastructure for outbreak response. This study contributes to an understanding of how clinical laboratory personnel in Sierra Leone view and experience their work, and introduces the concept of social invisibility to explain these experiences.

Epidemics In The 21st Century: A Multifaceted Challenge

In the intricate tapestry of human history, the 21st century stands as a chapter marked by the recurring emergence of epidemics, each weaving its unique thread into the fabric of global health. From the haunting reappearances of familiar adversaries like influenza to the unexpected onslaught of novel viruses such as SARS-CoV-2, this era has borne witness to a diverse array of health crises that have tested the resilience of societies worldwide. The canvas of epidemics in the 21st century encompasses a spectrum of formidable adversaries. Changes in host population ecology, genetic mutations in pathogen reservoirs, the lack of disease control, the growing population, overcrowded urban areas, climate change, and globalization have resulted in the development of several epidemics and pandemics. The intermittent waves of influenza, with their ability to swiftly mutate, present an enduring challenge to containment and mitigation efforts. The advent of novel viruses like SARS-CoV, MERS-CoV, and most notably, the unprecedented COVID-19 pandemic, underscores the unpredictability and rapid global spread inherent in emerging infectious diseases. Monkeypox, yet another disfiguring and deadly infection, is reported in 20 countries and carries the potential to become another pandemic. Dengue is yet another significant challenge for the healthcare system of many under-developed countries, especially Pakistan, affecting many people each year. Pakistan is experiencing major public health threats in the face of the current massive flood that facilitates the transmission of this deadly disease. Almost one-third of Pakistan’s population is suffering from life-threatening infections, including cholera, malaria, typhoid, etc., due to flood consequences. The silent yet pervasive threat posed by antimicrobial resistance looms large, rendering conventional treatments ineffective and elevating the urgency for novel therapeutic strategies. The surge in non-communicable diseases, including obesity, diabetes, and cardiovascular ailments, amplifies the burden on healthcare systems and demands multifaceted preventive measures. Amidst the convoluted landscape of epidemics, medical professionals confront an amalgamation of challenges. The imperative for robust preparedness, encompassing early detection, rapid response mechanisms, and efficient resource allocation, forms the cornerstone of epidemic management. Strengthening public health infrastructure remains pivotal, advocating for improved surveillance systems, enhanced laboratory capacities, and a resilient healthcare workforce. Addressing health disparities and ensuring equitable access to healthcare resources, especially in underserved communities, emerges as a fundamental tenet in epidemic management. The interconnectedness of our world mandates cohesive international collaborations, fostering information-sharing, research partnerships, and coordinated responses to combat epidemics transcending geographical boundaries. The crucible of epidemics in the 21st century compels us to acknowledge the imperativeness of collective resilience and concerted efforts. As we navigate the uncharted territories of emerging infectious threats and persisting health challenges, the amalgamation of scientific innovation, proactive policy interventions, and unwavering global solidarity becomes indispensable. In the pursuit of a healthier, more resilient future, the role of medical professionals stands as a beacon of hope, steering us through the turbulent seas of epidemics with unwavering dedication and expertise. Let us, as a global community, harness our collective strength and fortitude to confront these challenges, transcending boundaries, and fostering a world where health equity and preparedness prevail.

Bridging the Gap from Molecular Surveillance to Programmatic Decisions for Malaria Control and Elimination.

An increasing number of molecular and genomic assays are available to study malaria parasite populations. However, so far they have played a marginal role in informing policy and programmatic decision-making. Currently, molecular data are mainly used for monitoring drug efficacy against Plasmodium falciparum; assessing molecular markers of drug and insecticide resistance; and assessing P. falciparum histidine-rich protein 2 and 3 genes (Pfhrp2/3) deletion. We argue that additional use cases for molecular routine surveillance could be implemented in the near future, especially in transmission settings approaching elimination. These would include using quantitative polymerase chain reaction to monitor the prevalence of sub-patent infections in asymptomatic carriers, monitoring parasite genetic diversity as transmission intensity is changing, using genomic data to determine the origin of imported infections and characterize transmission chains in settings with very low malaria transmission, and using serology to monitor recent and past exposures in low-transmission settings. Molecular surveillance could inform control programs on adapting novel strategies, such as reactive case detection or focal mass drug administration, and help evaluate the impact of interventions currently in place. To better integrate molecular and genomic data into control program decision-making, engagement of national malaria control experts is crucial. Local laboratory capacity needs to be strengthened, shortening the time from sample collection to data availability. Here, we discuss opportunities and challenges of the use of molecular and genomic data for supporting malaria control and elimination efforts, as well as the avenues to link molecular and genomic data with gold standard epidemiological measurements through mathematical modeling.

Methodological Approach to Identify and Expand the Volume of Antimicrobial Resistance (AMR) Data in the Human Health Sector in Low- and Middle-Income Countries in Asia: Implications for Local and Regional AMR Surveillance Systems Strengthening.

Antimicrobial resistance (AMR) is a multifaceted global health problem disproportionately affecting low- and middle-income countries (LMICs). The Capturing data on Antimicrobial resistance Patterns and Trends in Use in Regions of Asia (CAPTURA) project was tasked to expand the volume of AMR and antimicrobial use data in Asia. The CAPTURA project used 2 data-collection streams: facility data and project metadata. Project metadata constituted information collected to map out data sources and assess data quality, while facility data referred to the retrospective data collected from healthcare facilities. A down-selection process, labelled "the funnel approach" by the project, was adopted to use the project metadata in prioritizing and selecting laboratories for retrospective AMR data collection. Moreover, the metadata served as a guide for understanding the AMR data once they were collected. The findings from CAPTURA's metadata add to the current discourse on the limitation of AMR data in LMICs. There is generally a low volume of AMR data generated as there is a lack of microbiology laboratories with sufficient antimicrobial susceptibility testing capacity. Many laboratories in Asia are still capturing data on paper, resulting in scattered or unused data not readily accessible or shareable for analyses. There is also a lack of clinical and epidemiological data captured, impeding interpretation and in-depth understanding of the AMR data. CAPTURA's experience in Asia suggests that there is a wide spectrum of capacity and capability of microbiology laboratories within a country and region. As local AMR surveillance is a crucial instrument to inform context-specific measures to combat AMR, it is important to understand and assess current capacity-building needs while implementing activities to enhance surveillance systems.

An ecotoxicologically relevant approach to water quality monitoring for contaminants of emerging concern

Contaminants of Emerging Concern (CECs) have been documented across the seven continents, including Antarctica, and are likely an impediment to the sustainable management of natural resources. Most studies to date have relied on sweeping chemistry surveys, reliant upon sophisticated instrumentation. This approach is expensive, relies on limited laboratory capacity, and generates results that are spatially and temporally constrained. Here we review existing approaches that can overcome these limitations by focusing on effects-based monitoring. Passive samplers can generate long-term records regarding the occurrence of CECs. As samples are concentrated, their analysis can be achieved using equipment that will be more common and less expensive. A second approach involves rapid test methods for single compounds, including test strips, ELISA assays, and mobile phone-based analytic tools. These can provide inexpensive CEC presence data for many field sites and can be used to stratify sampling and thereby reduce cost. Identifying the presence of a single compound can often shed light on the likely presence of entire groups of chemicals. Pairing these chemistry-derived approaches with geospatial modeling to predict CEC presence and concentrations across watersheds has already been applied in several large watersheds. Utilizing available ecotoxicological knowledge bases provides an opportunity to link modeled CEC occurrence and concentrations with likely adverse biological responses. Finally, confirmatory on-site exposure experiments can corroborate the presence or absence of biological effects hypothesized from the above chain of evidence to provide natural resource managers with information to make conservation decisions.

Head-to-head comparison of two loop-mediated isothermal amplification (LAMP) kits for diagnosis of malaria in a non-endemic setting

BackgroundLight microscopy and rapid diagnostic tests (RDT) have long been the recommended diagnostic methods for malaria. However, in recent years, loop-mediated isothermal amplification (LAMP) techniques have been shown to offer superior performance, in particular concerning low-grade parasitaemia, by delivering higher sensitivity and specificity with low laboratory capacity requirements in little more than an hour. In this study, the diagnostic performance of two LAMP kits were assessed head-to-head, compared to highly sensitive quantitative real time PCR (qPCR), in a non-endemic setting.MethodsIn this retrospective validation study two LAMP kits; Alethia® Illumigene Malaria kit and HumaTurb Loopamp™ Malaria Pan Detection (PDT) kit, were evaluated head-to-head for detection of Plasmodium-DNA in 133 biobanked blood samples from suspected malaria cases at the Clinical Microbiology Laboratory of Region Skåne, Sweden to determine their diagnostic performance compared to qPCR.ResultsOf the 133 samples tested, qPCR detected Plasmodium DNA in 41 samples (defined as true positives), and the two LAMP methods detected 41 and 37 of those, respectively. The results from the HumaTurb Loopamp™ Malaria PDT kit were in complete congruence with the qPCR, with a sensitivity of 100% (95% CI 91.40–100%) and specificity of 100% (95% CI 96.07–100%). The Alethia® Illumigene Malaria kit had a sensitivity of 90.24% (95% CI 76.87–97.28) and a specificity of 95.65% (95% CI 89.24–98.80) as compared to qPCR.ConclusionsThis head-to-head comparison showed higher performance indicators of the HumaTurb Loopamp™ Malaria PDT kit compared to the Alethia® illumigene Malaria kit for detection of malaria.

The Burden of Neglected Tropical Diseases in Sub-Saharan Africa

Health is a fundamental human right. However, a large population of the world is dogged with ill health which adversely affects the economy and development of nations. Although neglected tropical diseases (NTDs) cause enormous suffering, rob individuals of social and economic opportunities, and set-back countries’ development efforts, they receive only 0.6% health fund of official development assistance. Globally, more than one billion people suffer from one or more NTDs, and unfortunately, 500,000 die yearly. Despite remarkable progress in the effort against NTDs globally, they still persist in SSA. The objective of this study was to determine the burden of NTDs and suggest ways of reducing the burden. A scoping review of literature was conducted through Google Scholar according to Arksey and O’Malley (2005) methodology using the search terms “Burden” and “Neglected Tropical Diseases” or “NTDs” and “Sub-Saharan Africa” or “SSA”. Eligible studies were those addressing NTDs in SSA, published in English, for which the full text were available, and published between 2021 and 2023 in peer-reviewed scientific journals. Out of 20,800 identified studies, only 36 fully met the inclusion criteria. The study concluded that: SSA has a high burden of NTDs; communities in the region, including healthcare workers, have inadequate knowledge on NTDs; lack of community participation and engagement, and offering of fragmented care to people affected by NTDs; and lack of a robust clinical, public health, laboratory, pharmaceutical, and research capacity. The study recommends educating communities, as well as healthcare workers, on NTDs; ensuring community participation and engagement, and provision of holistic care to people affected by NTDs; and ensuring a robust clinical, public health, laboratory, pharmaceutical, and research capacity in SSA.

Application of diagnostic network optimization in Kenya and Nepal to design integrated, sustainable and efficient bacteriology and antimicrobial resistance surveillance networks.

Antimicrobial resistance (AMR) is a major global public health concern, particularly in low- and middle-income countries, which experience the highest burden of AMR. Critical to combatting AMR is ensuring there are effective, accessible diagnostic networks in place to diagnose, monitor and prevent AMR, but many low- and middle-income countries lack such networks. Consequently, there is substantial need for approaches that can inform the design of efficient AMR laboratory networks and sample referral systems in lower-resource countries. Diagnostic network optimization (DNO) is a geospatial network analytics approach to plan diagnostic networks and ensure greatest access to and coverage of services, while maximizing the overall efficiency of the system. In this intervention, DNO was applied to strengthen bacteriology and AMR surveillance network design in Kenya and Nepal for human and animal health, by informing linkages between health facilities and bacteriology testing services and sample referral routes between farms, health facilities and laboratories. Data collected from the target settings in each country were entered into the open-access DNO tool OptiDx, to generate baseline scenarios, which depicted the current state of AMR laboratory networks and sample referral systems in the countries. Subsequently, baselines were adjusted to evaluate changing factors such as samples flows, transport frequency, transport costs, and service distances. Country stakeholders then compared resulting future scenarios to identify the most feasible solution for their context. The DNO analyses enabled a wealth of insights that will facilitate strengthening of AMR laboratory and surveillance networks in both countries. Overall, the project highlights the benefits of using a data-driven approach for designing efficient diagnostic networks, to ensure better health resource allocation while maximizing the impact and equity of health interventions. Given the critical need to strengthen AMR laboratory and surveillance capacity, DNO should be considered an integral part of diagnostic strategic planning in the future.

Role of Laboratory in Emerging Infectious Disease Control in Iran, Pasteur Institute of Iran, and national laboratory network.

Strengthening surveillance systems is a key aspect of outbreak response and was particularly important during the COVID-19 pandemic. Respiratory pathogens spread rapidly, and laboratory capacity is key to monitoring the spread. Prior to the pandemic, Iran had established a rapid response team and laboratory network to provide identification, monitoring, and detection of emerging infectious diseases, but did not have the laboratory capacity to respond to COVID-19. Following the announcement of the COVID-19 pandemic, the rapid response team diverted all attention to supporting COVID-19 surveillance. Iran built on the existing national laboratory infrastructure to incorporate SARS-CoV-2 surveillance into the response network. Based on existing international protocols, in-house molecular diagnosis capacity was operationalized, and commercial controls and assays were acquired and validated to national standards. The first COVID-19 laboratory was operational by January 25, less than 4 weeks before the initial detection of SARS-CoV-2 was announced. Assays and support were expanded and rolled out to form the COVID-19 National Laboratory Network, which consists of 560 multi-sectoral laboratories covering all provinces of Iran. The national laboratory network supports a wide range of operational capacities, including assay validation and protocol development, quality assurance, respiratory pathogen diagnosis and surveillance, and variant identification and assessment using multiple sequencing platforms. This network has supported the testing of over 55 million samples over the past 36 months using RT-qPCR and has sequenced approximately 2200 samples across the country, contributing the data to international databases, including GISAID.

Improving the Treatment of Neonatal Sepsis in Resource-Limited Settings: Gaps and Recommendations.

Neonatal sepsis causes significant global morbidity and mortality, with the highest burden in resource-limited settings where 99% of neonatal deaths occur. There are multiple challenges to achieving successful treatment of neonates in this setting. Firstly, reliable and low-cost strategies for risk identification are urgently needed to facilitate treatment as early as possible. Improved laboratory capacity to allow identification of causative organisms would support antimicrobial stewardship. Antibiotic treatment is still hampered by availability, but also increasingly by antimicrobial resistance - making surveillance of organisms and judicious antibiotic use a priority. Finally, supportive care is key in the management of the neonate with sepsis and has been underrecognized as a priority in resource-limited settings. This includes fluid balance and nutritional support in the acute phase, and follow-up care in order to mitigate complications and optimise long-term outcomes. There is much more work to be done in identifying the holistic needs of neonates and their families to provide effective family-integrated interventions and complete the package of neonatal sepsis management in resource-limited settings.

Prevention, protocols, and lab capacity: lessons from a norovirus outbreak in the Algarve.

This brief report presents the findings of an epidemiological investigation into a large-scale outbreak of norovirus gastroenteritis that occurred in a hotel in Algarve, Portugal, in August 2022. A total of 244 cases were reported, primarily affecting Portuguese families, with the parents aged 40-50 years and the children aged 0-19 years. Reported symptoms included vomiting, nausea, abdominal pain, and diarrhoea. Norovirus genotype GI.3 [P3] was detected in stool samples from eight probable cases, while food samples tested negative for norovirus and common pathogenic bacteria. The investigation data collected suggest that the source of the outbreak was likely in the hotel's common areas, with subsequent person-to-person transmission in other areas. The final report emphasizes the importance of improving outbreak prevention and control measures, including the development of a foodborne outbreak investigation protocol, the establishment of an outbreak response team, and the enhancement of regional laboratory capacity.

Trichophyton indotineae and other terbinafine-resistant dermatophytes in North America.

Dermatophyte infections (a.k.a. ringworm, tinea) affect an estimated 20%-25% of the world's population. In North America, most dermatophytoses are caused by Trichophyton rubrum or Trichophyton mentagrophytes species complexes. Severe and antifungal-resistant dermatophytoses are a growing global public health problem. A new species of the T. mentagrophytes species complex, Trichophyton indotineae, has recently emerged and is notable for the severe infections it causes, its propensity for antifungal resistance, and its global spread. In this issue of the Journal of Clinical Microbiology, C. F. Cañete-Gibas, J. Mele, H. P. Patterson, et al. (J Clin Microbiol 61:e00562-23, 2023, https://doi.org/10.1128/JCM.00562-23) summarize the results of speciation and AFST performed on North American dermatophyte isolates received at a fungal diagnostic reference laboratory. Within their collection, 18.6% of isolates were resistant to terbinafine (a first-line oral antifungal for dermatophytoses), and similar proportions of T. rubrum and T. indotineae demonstrated terbinafine resistance. The authors also found that T. indotineae has been present in North America since at least 2017. These findings highlight the importance of increased surveillance efforts to monitor trends in severe and antifungal-resistant dermatophytoses and the need for antifungal stewardship efforts, the success of which is contingent upon improving laboratory capacity for dermatophyte speciation and AFST.

Central nervous system infection in a pediatric population in West Java.

Central nervous system (CNS) viral infections are critical causes of morbidity and mortality in children; however, comprehensive data on etiology is lacking in developing countries such as Indonesia. To study the etiology of CNS infections in a pediatric population, 50 children admitted to two hospitals in Bandung, West Java, during 2017-2018 were enrolled in a CNS infection study. Cerebrospinal fluid and serum specimens were tested using molecular, serological, and virus isolation platforms for a number of viral and bacteriological agents. Causal pathogens were identified in 10 out of 50 (20%) and included cytomegalovirus (n = 4), Streptococcus pneumoniae (n = 2), tuberculosis (n = 2), Salmonella serotype Typhi (n = 1) and dengue virus (n = 1). Our study highlights the importance of using a wide range of molecular and serological detection methods to identify CNS pathogens, as well as the challenges of establishing the etiology of CNS infections in pediatric populations of countries with limited laboratory capacity.

617. Laboratory capacities to diagnose and treat Invasive Fungal Infections in Europe: results from an ECMM survey

Abstract Background Invasive fungal infections (IFI) are a major threat for patients under immunosuppression or with viral respiratory infections, like influenza or coronavirus disease 2019 (COVID-19). Access to appropriate tools is vital for early diagnosis and clinical management. The European Confederation of Medical Mycology (ECMM) survey on laboratory capacities in Europe aims to decipher the current diagnostic capacity and availability of treatments for IFIs in order to guide health professionals, patients, and policymakers. Methods The ECMM IFI diagnostic capacity survey is online accessible at www.clinicalsurveys.net/uc/IFI_management_capacity/. A campaign seeking for mycologist feedback was launched. The survey was disseminated to all European mycologists affiliated with the ECMM and via social media (i.e., LinkedIn or Twitter) and email. Collected variables were a) institution profile, b) perceptions on invasive fungal disease in the respective institution, c) microscopy, d) culture and fungal identification, e) serology, f) antigen detection, g) molecular tests and h) therapeutic drug monitoring. Results 258 centers from 41 countries have participated in the survey (Figure 1). Germany (n=30), France (n=28), Italy, Spain (n=23, each) and Turkey (n=21) were the origin country of almost half of the respondents. Incidence of IFI was considered as very low or low in 46.9% of the institutions, and moderate in 38.0%. Candida spp. (95.0%) and Aspergillus spp. (89.9%) were considered the most relevant pathogens. All the institutions had access (on site or outsourced) to cultures (68.2% of which could also perform susceptibility tests in molds and yeasts, 26.4% only in yeasts, 4.7% in none and 0.8% only in molds). Regarding availability of other diagnostic tests, 84.5% could also utilize microscopy, 83.7% antigen detection tests (89.8% of which at least Aspergillus galactomannan test), 73.3% molecular tests (mainly PCR), and 62.4% to serology. At least one triazole was available for prescribing in 93.0% of the institutions, whereas at least one echinocandin in 90.3% and liposomal amphotericin B in 80.2%. Conclusion Europe is generally well prepared to diagnose and treat invasive fungal infections. However, some institutions miss access to certain diagnostic tools and antifungal drugs. Disclosures Martin Hoenigl, n/a, Astellas: Grant/Research Support|Euroimmun: Grant/Research Support|F2G: Grant/Research Support|Gilead: Grant/Research Support|Immy: Grant/Research Support|MSD: Grant/Research Support|Mundipharma: Grant/Research Support|Pfizer: Grant/Research Support|Pulmocide: Grant/Research Support|Scynexis: Grant/Research Support Oliver A. Cornely, MD PhD, DZIF: Advisor/Consultant|DZIF: Board Member|DZIF: Grant/Research Support|DZIF: Honoraria|DZIF: Stocks/Bonds

Performance of CHROMagar ESBL media for the surveillance of extended-spectrum cephalosporin-resistant Enterobacterales (ESCrE) from rectal swabs in Botswana.

Introduction. Lack of laboratory capacity hampers consistent national antimicrobial resistance (AMR) surveillance. Chromogenic media may provide a practical screening tool for detection of individuals colonized by extended-spectrum beta-lactamase (ESBL)-producing organisms.Hypothesis. CHROMagar ESBL media represent an adequate screening method for the detection of extended-spectrum cephalosporin-resistant Enterobacterales (ESCrE), isolated from rectal swabs.Aim. To evaluate the performance of CHROMagar ESBL media to accurately identify ESCrE isolates from rectal swab samples attained from hospitalized and community participants.Methodology. All participants provided informed consent prior to enrolment. Rectal swabs from 2469 hospital and community participants were inoculated onto CHROMagar ESBL. The performance of CHROMagar ESBL to differentiate Escherichia coli and Klebsiella spp., Enterobacter spp. and Citrobacter spp. (KEC spp.) as well as select for extended-spectrum cephalosporin resistance were compared to matrix-assisted laser desorption/ionization-time-of-flight MS (MALDI-TOF-MS) and VITEK-2 automated susceptibility testing.Results. CHROMagar ESBL had a positive and negative agreement of 91.2 % (95 % CI, 88.4-93.3) and 86.8 % (95 % CI, 82.0-90.7) for E. coli and 88.1 % (95 % CI 83.2-92.1) and 87.6 % (95 % CI 84.7-90.2) for KEC spp. differentiation, respectively, when compared to species ID by MALDI-TOF-MS. When evaluated for phenotypic susceptibilities (VITEK-2), 88.1 % (714/810) of the isolates recovered on the selective agar exhibited resistance to third-generation cephalosporins.Conclusion. The performance characteristics of CHROMagar ESBL media suggest that they may be a viable screening tool for the identification of ESCrE from hospitalized and community participants and could be used to inform infection prevention and control practices in Botswana and potentially other low-and middle-income countries (LMICs). Further studies are required to analyse the costs and the impact on time-to-result of the media in comparison with available laboratory methods for ESCrE surveillance in the country.