Establishing molecular microbiology facilities in developing countries

Polydopamine functionalized dendritic fibrous silica nanoparticles as a generic platform for nucleic acid-based biosensing

Accurate and rapid detection of nucleic acid sequences is of utmost importance in various fields, including disease monitoring, clinical treatment, gene analysis and drug discovery. In this study, we developed a "turn-on" fluorescence biosensor that enables simple and highly efficient detection of nucleic acid biomarkers. Our approach involves the utilization of 6-carboxyfluorescein modified single-stranded DNA (FAM-ssDNA) as molecular recognition element, along with polydopamine-functionalized dendritic fibrous nanosilica (DFNS). FAM-ssDNA serves as both specific molecular recognition element for the target analyte and reporter capable of transducing a detectable signal through Watson-Crick base pairing. The polydopamine-functionalized DFNS (DFNS@DA) exhibits strong binding to FAM-ssDNA via polyvalent metal mediated coordination leading to effective quenching by fluorescence resonance energy transfer. In the presence of a complementary target sequence, FAM-ssDNA forms hybridized structure and detaches from DFNS@DA, which causes an increased fluorescence emission. The analytical system based on FAM-ssDNA and DFNS@DA demonstrates exceptional sensitivity, selectivity, and rapid response for the detection of nucleic acid sequences, leveraging the high adsorption and quenching properties of DFNS@DA. For the first proof of concept, we demonstrated the successful detection of microRNA (miR-21) in cancer cells using the FAM-ssDNA/DFNS@DA system. Our results highlight the promising capabilities of DFNS@DA and nucleic acid-based biosensors, offering a generic and cost-effective solution for the detection of nucleic acid-related biomarkers.

Global Landscape of Encephalitis: Key Priorities to Reduce Future Disease Burden

Encephalitis affects people across the lifespan, has high rates of mortality and morbidity, and results in significant neurological sequelae with long-term consequences to quality of life and wider society. The true incidence is currently unknown due to inaccurate reporting systems. The disease burden of encephalitis is unequally distributed across the globe being highest in low- and middle-income countries where resources are limited. Here countries often lack diagnostic testing, with poor access to essential treatments and neurological services, and limited surveillance and vaccination programs. Many types of encephalitis are vaccine preventable, whereas others are treatable with early diagnosis and appropriate management. In this viewpoint, we provide a narrative review of key aspects of diagnosis, surveillance, treatment, and prevention of encephalitis and highlight priorities for public health, clinical management, and research, to reduce the disease burden.

BioBlocksLab: A portable DIY Bio Lab using BioBlocks language

Standard molecular biology laboratories are usually made with complex, sophisticated, and expensive equipment. Unfortunately, most of these labs are not affordable for everyone. In this paper, we show how we built a portable bio lab BioBlocksLab, made of four modules: a centrifuge, a thermocycler, electrophoresis, and an incubator. We also propose a new version of a blockly programming language to describe experimental lab protocols, called BioBlocks 2.0, which is based on the Microsoft MakeCode platform from the open-source project Microsoft Programming Experience Toolkit (PXT). We run BioBlocks programs of real lab protocols to control different hardware modules with biological reagents and get positive results. We offer an easy, affordable, and open-source way for everyone to do experiments with Do-It-Yourself (DIY) portable bio-labs.

A Review of Bartonella Infections in California-Implications for Public and Veterinary Health

Bartonella are vector-transmitted, intracellular bacteria that infect a wide variety of blood-feeding arthropods and their vertebrate hosts. In California, more than 13 species of Bartonella have been described from companion animals, livestock, and wildlife, of which four have been associated with human disease. Infections in humans cause a range of symptoms from relatively mild to severe, especially in immunocompromised individuals. Exposure to infected domestic animals and wildlife, and their ectoparasites, may increase the risk of cross-species transmission. The objective of this review was to compile and summarize published materials on human and animal Bartonella infections in California. Medical and veterinary case reports of bartonellosis were highlighted in an effort to increase the awareness of this poorly understood and potentially under-recognized disease among healthcare professionals and veterinarians.

Comparative evaluation of indirect-ELISA and DOT blot assay for serodetection of Mycoplasma gallisepticum and Mycoplasma synoviae antibodies in poultry

Avian mycoplasmosis, mainly caused by Mycoplasma gallisepticum (MG) and Mycoplasma synoviae (MS) is an economically important disease of the poultry industry. The present study was aimed to develop whole cell based indirect-ELISA (i-ELISA) and DOT blot assay (DOT-ELISA) as rapid, sensitive, specific and economical sero-detection tests for MG and MS. A total of 306 blood samples were collected from birds slaughtered at local meat shops of different districts of Haryana, India to detect MG and MS antibodies. Sonicated antigens prepared from freshly grown culture of MG and MS were used to develop i-ELISA and DOT blot assay. In i-ELISA, 50.32% and 61.76% serum samples were found to be positive for MG and MS antibodies, respectively. However in DOT blot assay, 41.83% and 53.92% serum samples were found positive for MG and MS antibodies, respectively. The relative diagnostic sensitivity and specificity of DOT-ELISA were measured considering i-ELISA as a reference test. The relative diagnostic sensitivity of the DOT blot assay was found to be 69.48% and 82.01%; whereas relative diagnostic specificity was 86.18% and 91.45% for the detection of MG and MS antibodies, respectively. The developed serological assays may be used as rapid and economical diagnostic tools for large scale screening of poultry sera for MG and MS antibodies.

A cost of illness comparison for toxigenic Clostridioides difficile diagnosis algorithms in developing countries

BACKGROUND

Availability of several commercial tests with different Clostridioides difficile targets contributes to uncertainty and controversies around the optimal diagnostic algorithm. While numerous studies have estimated the financial impact of C. difficile infection, models to guide testing strategies decisions in developing countries, where economic value significantly impacts clinical practice, are currently not available.

AIM

To determine the cost of illness of different C. difficile infection (CDI) diagnostic strategies in developing countries.

METHODS

Cost-comparison analysis was performed to compare eleven different algorithms of CDI diagnosis. The basis of calculation was a hypothetical cohort of 1000 adult inpatients suspected of CDI. We analyzed turnaround time of test results (i.e., time from taking sample to results emission), test performance (i.e., sensitivity and specificity) and testing costs. Patients were divided in true positive, false positive, true negative and false negative in order to integrate test performance and economics effects. Additional medical costs were calculated: costs of hygiene, medication, length of stay and intensive care unit costs, based on a Brazilian University Hospital costs. CDI prevalence was considered 22.64%.

FINDINGS

From laboratory-assisted tests, simultaneous glutamate dehydrogenase (GDH) and toxin A/B rapid immunoassay arbitrated by nucleic acid amplification test (NAAT) presented the lowest cost of illness (450,038.70 USD), whereas standalone NAAT had the highest (523,709.55 USD). Empirical diagnosis only presented the highest overall cost (809,605.44 USD).

CONCLUSION

The two-step algorithm with simultaneous GDH and toxin A/B rapid immunoassay arbitrated by NAAT seems to be the best strategy for CDI diagnosis in developing countries.

Considerations for Group Testing: A Practical Approach for the Clinical Laboratory

Group testing, also known as pooled sample testing, was first proposed by Robert Dorfman in 1943. While sample pooling has been widely practiced in blood-banking, it is traditionally seen as anathema for clinical laboratories. However, the ongoing COVID-19 pandemic has re-ignited interest for group testing among clinical laboratories to mitigate supply shortages. We propose five criteria to assess the suitability of an analyte for pooled sample testing in general and outline a practical approach that a clinical laboratory may use to implement pooled testing for SARS-CoV-2 PCR testing. The five criteria we propose are: (1) the analyte concentrations in the diseased persons should be at least one order of magnitude (10 times) higher than in healthy persons; (2) sample dilution should not overly reduce clinical sensitivity; (3) the current prevalence must be sufficiently low for the number of samples pooled for the specific protocol; (4) there is no requirement for a fast turnaround time; and (5) there is an imperative need for resource rationing to maximise public health outcomes. The five key steps we suggest for a successful implementation are: (1) determination of when pooling takes place (pre-pre analytical, pre-analytical, analytical); (2) validation of the pooling protocol; (3) ensuring an adequate infrastructure and archival system; (4) configuration of the laboratory information system; and (5) staff training. While pool testing is not a panacea to overcome reagent shortage, it may allow broader access to testing but at the cost of reduction in sensitivity and increased turnaround time.

Whole-genome sequencing as part of national and international surveillance programmes for antimicrobial resistance: a roadmap

The global spread of antimicrobial resistance (AMR) and lack of novel alternative treatments have been declared a global public health emergency by WHO. The greatest impact of AMR is experienced in resource-poor settings, because of lack of access to alternative antibiotics and because the prevalence of multidrug-resistant bacterial strains may be higher in low-income and middle-income countries (LMICs). Intelligent surveillance of AMR infections is key to informed policy decisions and public health interventions to counter AMR. Molecular surveillance using whole-genome sequencing (WGS) can be a valuable addition to phenotypic surveillance of AMR. WGS provides insights into the genetic basis of resistance mechanisms, as well as pathogen evolution and population dynamics at different spatial and temporal scales. Due to its high cost and complexity, WGS is currently mainly carried out in high-income countries. However, given its potential to inform national and international action plans against AMR, establishing WGS as a surveillance tool in LMICs will be important in order to produce a truly global picture. Here, we describe a roadmap for incorporating WGS into existing AMR surveillance frameworks, including WHO Global Antimicrobial Resistance Surveillance System, informed by our ongoing, practical experiences developing WGS surveillance systems in national reference laboratories in Colombia, India, Nigeria and the Philippines. Challenges and barriers to WGS in LMICs will be discussed together with a roadmap to possible solutions.

Comparing conventional, biochemical and genotypic methods for accurate identification of Klebsiella pneumoniae in Sudan

Klebsiella pneumoniae is recognized as one of the most important healthcare-associated pathogens worldwide due to its tendency to develop antibiotic resistance and cause fatal outcomes. Bacterial identification methods such as culture and biochemical tests are routinely used with limited accuracy in many low- and middle-income countries, including Sudan. The aim of this study was to test the accuracy of identification of K. pneumoniae in Khartoum, Sudan. Two hundred and fifty K. pneumoniae isolates were collected and identified using conventional phenotypic methods, biochemically using API 20E and genotypically by amplification of 16S−23S rDNA and sequencing of rpoB, gapA and pgi. Only 139 (55.6 %) of the isolates were confirmed as K. pneumoniae genotypically by PCR and 44.4 % were identified as non-K. pneumoniae. The results demonstrate that the identification panels used by the hospitals were inaccurately identifying K. pneumonia and led to overestimation of the prevalence of this organism. The current identification methods used in Khartoum hospitals are highly inaccurate, and therefore we recommend the use of a comprehensive biochemical panel or molecular methods, when possible, for accurate identification of K. pneumoniae.

Guidelines for various laboratory sections in view of COVID-19: Recommendations from the Indian Association of Pathologists and Microbiologists

Declared as a pandemic by WHO on March 11, 2020, COVID-19 has brought about a dramatic change in the working of different laboratories across the country. Diagnostic laboratories testing different types of samples play a vital role in the treatment management. Irrespective of their size, each laboratory has to follow strict biosafety guidelines. Different sections of the laboratory receive samples that are variably infectious. Each sample needs to undergo a proper and well-designed processing system so that the personnel involved are not infected and also their close contacts. It takes a huge effort so as to limit the risk of exposure of the working staff during the collection, processing, reporting or dispatching of biohazard samples. Guidelines help in preventing the laboratory staff and healthcare workers from contracting the disease which has a known human to human route of transmission and high rate of mortality. A well-knit approach is the need of the hour to combat this fast spreading disease. We anticipate that the guidelines described in this article will be useful for continuing safe work practices by all the laboratories in the country.

Investing in Food Safety for Developing Countries: Opportunities and Challenges in Applying Whole-Genome Sequencing for Food Safety Management

Whole-genome sequencing (WGS) has become a significant tool in investigating foodborne disease outbreaks and some countries have incorporated WGS into national food control systems. However, WGS poses technical challenges that deter developing countries from incorporating it into their food safety management system. A rapid scoping review was conducted, followed by a focus group session, to understand the current situation regarding the use of WGS for foodborne disease surveillance and food monitoring at the global level and identify key limiting factors for developing countries in adopting WGS for their food control systems. The results showed that some developed nations routinely use WGS in their food surveillance systems resulting in more precise understanding of the causes of outbreaks. In developing nations, knowledge of WGS exists in the academic/research sectors; however, there is limited understanding at the government level regarding the usefulness of WGS for food safety regulatory activities. Thus, incorporation of WGS is extremely limited in most developing nations. While some countries lack the capacity to collect and analyze the data generated from WGS, the most significant technical gap in most developing countries is in data interpretation using bioinformatics. The gaps in knowledge and capacities between developed and developing nations regarding use of WGS likely introduce an inequality in international food trade, and thus, relevant international organizations, as well as the countries that are already proficient in the use of WGS, have significant roles in assisting developing nations to be able to fully benefit from the technology and its applications in food safety management.

Monitoring and Treatment of Patients Undergoing Immunotherapy With Anti-CD20 Who are Exposed to HBV

Reactivation of hepatitis B virus (HBV) is a potentially fatal complication of immunosuppressive therapy, and can occur in individuals who are hepatitis B surface antigen (HBsAg) negative but positive for hepatitis B core antibody (anti-HBc). While anti-HBc positivity indicates prior HBV exposure, it may also reflect clearance of HBsAg, but with viral persistence at low intrahepatic replicative and transcriptional levels.¹ HBV reactivation can still occur during intense immunosuppression, including B cell-depleting therapy with anti-CD20 antibodies² and hematopoietic stem cell transplantation.³ While prevention via antiviral prophylaxis is recommended, it remains uncertain, from a global perspective, if this is an ideal and cost-effective strategy. An alternative is regular HBV DNA monitoring.⁴ However, this approach is problematic in resource-constrained regions, where the logistics of sample collection, transportation, and molecular analysis in dedicated facilities poses challenges.⁵ We aimed to evaluate the effectiveness of simple monitoring strategies using routine liver biochemistry and serum HBsAg in preventing HBV-related complications during anti-CD20 therapy.

Emerging infectious disease prevention: Where should we invest our resources and efforts?

Strategies focused on the prevention of emerging infectious disease outbreaks are currently in the spotlight of discussions among researchers committed to infectious disease control. In this mini-review, we provided a brief update on this discussion and characterized the three main targets for investments in emerging infectious disease prevention: animals, human sentinels for spillover events, and the general human population. Furthermore, the pros and cons of each target are highlighted. Despite the particularities of the proposed targets, each of them can fill different gaps in the surveillance of infectious diseases. When all three targets are focused on together, they create a powerful strategy of emerging infectious disease prevention.

Elements Associated With Early Mortality in Children With B Cell Acute Lymphoblastic Leukemia in Chiapas, Mexico: A Case-control Study

Childhood Lymphoblastic leukemia's (ALL) early mortality (EM) is an undesirable treatment outcome for a disease for which >90% long term success is achievable. In the Western world EM constitutes no >3%; yet, in Chiapas, Mexico, remains around 15%. With the objective of improving on EM, we determined associated elements in 28 ALL who died within 60 days of arriving at Hospital de Especialidades Pediátricas in Chiapas (HEP), by comparing them to those in 84 controls who lived beyond the first 90 days. χ, t test, and binary logistic regression (BLR) were used to determine significant individual and multiple variables associated to outcome. On arrival, fever, liver and spleen enlargement, active bleeding, lower albumin, less platelets, higher creatinine, and uric acid, more diploid and less hyperdiploid cases were associated with EM cases. Time to diagnosis, nutritional status, risk group and leukocyte count were not related. Antileukemic treatment approach was similar in both groups. The BLR model including fever, active bleeding, liver enlargement, <10,000 platelets/µL, and >2X upper normal lactic dehydrogenase, determined outcome in 66.7% EM and 90.2% controls. To improve on EM in ALL, patients with characteristics defined here ought to be treated differently at HEP.