Surveillance Strategies Research Articles

Sequence Types and Antimicrobial Resistance Profiles of Salmonella Typhimurium in the Food Chain in Singapore.

Salmonella remains a significant foodborne pathogen globally with S. Typhimurium presenting as a frequently occurring serovar. This study aimed to characterize 67 S. Typhimurium isolates from humans, food, farms, and slaughterhouses collected in Singapore from 2016 to 2017. Using whole-genome sequencing analysis, the isolates were found to belong to either ST19 (n = 33) or ST36 (n = 34). ST36 predominated in human intestinal and chicken isolates, while human extra-intestinal and non-chicken food isolates belonged to ST19. Plasmids were predicted in 88.1% (n = 59) of the isolates with the most common incompatibility group profiles being IncFIB(S), IncFII(S) and IncQ1. IncFIB(S) (adjusted p-value < 0.05) and IncFII(S) (adjusted p-value < 0.05) were significantly more prevalent in ST19 isolates, while Col156 (adjusted p-value < 0.05) was more significantly found in ST36 isolates. ST36 isolates exhibited higher resistance to multiple antibiotic classes such as penicillins, phenicols, folate pathway inhibitors, aminoglycosides, β-lactam/β-lactamase inhibitor combinations, tetracyclines, and fluoroquinolones. Phylogenetics analysis suggested potential shared routes of transmission among human, chicken, farm and slaughterhouse environments. Taken together, this study offers a cross-sectional epidemiological insight into the genomic epidemiology and antimicrobial landscape of S. Typhimurium isolates in Singapore, informing strategies for future public health and food safety surveillance.

Notes from the Field: Support for Wastewater Monitoring and Influence on Protective Behavioral Intentions Among Adults - United States, July 2024.

In 2020, during the COVID-19 pandemic, CDC established the National Wastewater Surveillance System and later expanded it to include mpox and influenza A data dashboards.† Wastewater utility partners have cited community health benefits as a motivating factor for participating in wastewater surveillance; a lack of public support for wastewater surveillance activities might lead utility partners to cease participation (1,2). However, little is known about public support for wastewater monitoring and its influence on protective health behaviors. As innovative surveillance strategies such as wastewater surveillance evolve, ethical considerations, including understanding public perceptions regarding support for these activities and potential risks to communities, are essential (3).

Diversity, vertical stratification and detection of Leishmania DNA in sand flies (Diptera: Psychodidae) collected in the Mapinguari National Park, Brazilian Amazon

This study aimed to assess the diversity patterns of sand fly fauna across different strata and detect Leishmania DNA in these insects in the Mapinguari National Park in Rondônia and Amazonas states, Northern Brazil. Sand flies were collected with “HP” light traps in the canopy (15 m) and at ground level (1 m) on two trails, during August and November 2021 and March and August 2022. Polymerase chain reaction and DNA sequencing were used to identify Leishmania species. A total of 8,040 individuals (2,303♂ – 28.64 %, 5,737♀ – 71.36 %) were collected and 53 species and 13 genera were identified. The most abundant species were Psychodopygus chagasi (21.00 %), Trichophoromyia ubiquitalis (13.61 %) Psychodopygus davisi (11.69 %), Nyssomyia fraihai (10.58 %), Nyssomyia antunesi (6.68 %) and Nyssomyia richardwardi (5.55 %). Species diversity was greater in the canopy (Shannon index H' = 10.8 common species) when compared to ground level (H' = 10.5 common species). We observed a minimum infection rate of 0.45 % (22/4,868 females), in which Leishmania braziliensis DNA was found in Ps. chagasi and Le. lainsoni DNA in Ps. chagasi, Ny. richardwardi, Ps. ayrozai and Th. ubiquitalis. The minimum infection rate of Leishmania in the canopy was 0.47 % (19/4,031) and in the ground was 0.52 % (3/567). In the present study, we observed Le. lainsoni DNA in females of Ny. richardwardi for the first time. The data presented in this study contribute to understanding sand fly diversity and its distribution between the states of Rondônia and Amazonas. They may be useful for implementing targeted control measures to reduce the spread of leishmaniasis and implement entomological surveillance strategies.

ANÁLISE TEMPORAL DA INCIDÊNCIA DE CASOS NOTIFICADOS DA DOENÇA DE CHAGAS NO BRASIL, NO PERÍODO DE 2010-2019

Chagas disease is caused by Trypanosoma cruzi and remains an important public health concern in Brazil, despite control measures adopted over the last few decades. The objective of this study is to carry out a temporal analysis of the incidence of reported cases of Chagas Disease in Brazil from 2010 to 2019, identifying trends and possible associated factors. Secondary data from the Notifiable Diseases Information System (SINAN) were used to calculate incidence rates by region and year. The statistical analysis included linear regression models to evaluate the temporal variation of notifications. The results indicate an overall reduction in notifications in the country during the period analyzed, with significant regional variations. The North region showed an increase in notifications, suggesting the need for greater surveillance and control strategies. In contrast, the Southeast and South regions maintained a stable downward trend, as a result of continued vector control measures. It is concluded that, although cases of Chagas disease are declining in much of Brazil, the disease still represents a public health challenge in some regions, especially in areas where oral transmission and vector synanthropy are on the rise.

The first detection of SARS-CoV-2 RNA in the wastewater of Bucharest, Romania

Wastewater-based epidemiology (WBE) has been previously used as a tool for pathogen identification within communities. After the SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) outbreak, in 2020, Daughton proposed the implementation of a wastewater surveillance strategy that could determine the incidence of COVID-19 (coronavirus disease 2019) nationally. Individuals in various stages of SARS-CoV-2 infection, including presymptomatic, asymptomatic and symptomatic patients, can be identified as carriers of the virus in their urine, saliva, stool and other bodily secretions. Studies using this method were conducted to monitor the prevalence of the virus in high-density populations, such as cities but also in smaller communities, such as schools and college campuses. The aim of this pilot study was to assess the feasibility and effectiveness of wastewater surveillance in Bucharest, Romania, and wastewater samples were collected weekly from seven locations between July and September 2023. RNA (ribonucleic acid) extraction, followed by dPCR (digital polymerase chain reaction) analysis, was performed to detect viral genetic material. Additionally, NGS (next generation sequencing) technology was used to identify the circulating variants within the wastewater of Bucharest, Romania. Preliminary results indicate the successful detection of SARS-CoV-2 RNA in wastewater, providing valuable insights into the circulation of the virus within the community.

Long-Term Outcome of Patients with Low-Risk Differentiated Thyroid Cancer Treated with Total Thyroidectomy Alone.

Differentiated thyroid carcinoma (DTC), mainly papillary (PTC), at low risk of recurrence is currently managed with active surveillance strategies or less aggressive surgeries. However, total thyroidectomy with 131I treatment is still performed both if these tumors are diagnosed before or occasionally after surgery. This real-life study aimed to evaluate the rate of biochemical, structural, and functional events in a large series of consecutive DTCs at low risk of recurrence treated by total thyroidectomy, but not with 131I, in a medium-long-term follow-up. We evaluated clinical-pathologic data of 383 consecutive patients (2006-2012) with unifocal DTC [T1a/b(s)] at low risk of recurrence, treated with total thyroidectomy but without lymph node dissection and 131I treatment after surgery. We evaluated if structural, biochemical, and functional events were detected during the follow-up. Females accounted for 75.7% of our study group, and the median age was 50 years. The median tumor dimension was 0.4 cm (range 0.1-1.2). Most of the patients had a unifocal T1a tumor (98.9%), and 73.6% had a classic variant of PTC. We divided the patients according to the absence (group A-n = 276) or presence (group B-n = 107) of interfering TgAb at first control after surgery. After a median follow-up of 10 years, no structural events were detected. Sixteen out of three hundred and eighty-three (4.2%) patients developed biochemical events: 12/276 (4.3%) in group A and 4/107 (3.7%) in group B. The median time elapsed from surgery to detecting a biochemical event was 14.5 and 77.5 months in groups A and B, respectively. No patients performed additional treatments and were followed up with an active surveillance strategy. This study confirmed that patients with DTC at low risk of recurrence showed an excellent outcome in a medium long-term follow-up since no structural events were diagnosed. Significant variations in Tg/TgAb were detected in a few cases, all managed with an active surveillance strategy without the need for other treatments. Therefore, a relaxed follow-up with neck ultrasound and Tg/TgAb measurement is enough to early identify those very unusual cases of recurrence.

Optimal Surveillance of Metachronous Gastric Lesion after Endoscopic Resection of Early Gastric Cancer.

Endoscopic resection (ER)-a minimal invasive procedure, compared to surgical gastrectomy, with the advantage of preserving the entire stomach and maintaining the patient's quality of life-is a widely used curative treatment for early gastric cancers (EGCs). Despite its advantages, such as the preservation of the whole stomach, a large area of the gastric mucosa with histologic changes such as atrophy and intestinal metaplasia remains after ER, and so does the risk of metachronous gastric cancers (MGCs). Therefore, regular surveillance endoscopy after curative ER of EGCs is important so that MGCs are detected early and so minimally invasive ER remains a treatment option. To date, the optimal interval for surveillance endoscopy after curative ER of EGCs has not been established. Therefore, this review summarizes the results of the published studies on this topic with the aim of establishing the optimal surveillance interval for early identification of MGCs. Based on my review, the median timing of MGC occurrence is within 3 years, and reports suggest biannual endoscopy during the first 3 years; however, the evidence suggests that individual patient characteristics may influence the risk of MGCs. Therefore, stratified endoscopic strategies for surveillance based on patient characteristics, such as age, family history of gastric cancer, synchronous gastric lesions, and corpus intestinal metaplasia, should be applied.

Cascade testing in mitochondrial diseases: a cross-sectional retrospective study

BackgroundCascade testing can offer improved surveillance and timely introduction of clinical management for the at-risk biological relatives. Data on cascade testing and costs in mitochondrial diseases are lacking. To address this gap, we performed a cross-sectional retrospective study to provide a framework for cascade testing in mitochondrial diseases, to estimate the eligibility versus real-time uptake of cascade testing and to evaluate the cost of the genetic diagnosis of index cases and the cost of predictive cascade testing.MethodsData was collected through retrospective chart review. The variant inheritance pattern guided the identification of eligible first-degree relatives: (i) Males with mitochondrial DNA (mtDNA) single nucleotide variants (SNVs) – siblings and mothers. (ii) Females with mtDNA SNVs – siblings, mothers and offspring. (iii) Autosomal Dominant (AD) nuclear DNA (nDNA) variants – siblings, offspring and both parents. (iv) Autosomal Recessive (AR) nDNA variants – siblings.ResultsWe recruited 99 participants from the Adult Mitochondrial Disease Clinic in Sydney. The uptake of cascade testing was 55.2% in the mtDNA group, 55.8% in the AD nDNA group and 0% in AR nDNA group. Of the relatives in mtDNA group who underwent cascade testing, 65.4% were symptomatic, 20.5% were oligosymptomatic and 14.1% were asymptomatic. The mean cost of cascade testing for eligible first-degree relatives (mtDNA group: $694.7; AD nDNA group: $899.1) was lower than the corresponding index case (mtDNA group: $4578.4; AD nDNA group: $5715.1) (p < 0.001).ConclusionThe demand for cascade testing in mitochondrial diseases varies according to the genotype and inheritance pattern. The real-time uptake of cascade testing can be influenced by multiple factors. Early diagnosis of at-risk biological relatives of index cases through cascade testing, confirms the diagnosis in those who are symptomatic and facilitates implementation of surveillance strategies and clinical care at an early stage of the disease.

The Mpox outbreak is a public health emergency of international concern: Implications for mental health and global preparedness.

The Mpox, a zoonotic viral disease that has historically affected Central and West Africa, has been declared a Public Health Emergency of International Concern by the World Health Organization. Rapid transmission and recent dissemination in Africa may imply significant challenges to global health, including mental health. We reviewed the mental health implications of the Mpox outbreak according to the published literature. We also discussed the psychological effects of the global spreading of this infection and public health preparedness strategies. Key areas of intervention may include the epidemiological surveillance, vaccine development, and mental health strategies. The Mpox outbreak calls for a robust global preparedness to address potential health emergencies. Strengthening epidemiological surveillance, ensuring equitable vaccine distribution, and building resilient public health infrastructure are crucial. Additionally, addressing mental health consequences may require immediate, intermediate, and long-term strategies, including telepsychiatry, stress management training, and the integration of mental health into primary care.

An integrated strategy for pathogen surveillance unveiled Xylella fastidiosa ST1 outbreak in hidden agricultural compartments in the Apulia region (Southern Italy)

AbstractAnnual surveillance programs for the plant pathogenic bacterium Xylella fastidiosa are implemented in Europe as part of the preventive phytosanitary strategies enforced to face the emergence of the detrimental infections reported in olives in southern Italy. The programs include inspections and sampling of host plants by prioritizing those showing suspicious symptoms or those known to be highly susceptible to different strains and subspecies of the bacterium. In the framework of these programs numerous outbreaks have been unraveled, with several strains and subspecies found to infect a relatively large host range in France, Spain, Portugal and Italy. Here we report the results of an integrated surveillance approach implemented in the Apulia Region (southern Italy), where a conventional survey program on host plants is complemented by monitoring and testing for X. fastidiosa the insect vectors. In the framework of this program, bacterium-positive spittlebugs were intercepted in the Xylella-free area of the region, close to one of the most relevant Italian table grape production district. Such findings prompted further investigation to identify the bacterial reservoir in the host plants. Almond and grapevine were found to be the most frequently infected hosts, with infections caused by isolates of X. fastidiosa subspecies fastidiosa ST1. Investigations are ongoing to assess the extent and history of the outbreak, to assess and estimate the potential impacts, and define the best options for its containment.

Resilience in the Face of Uncertainty: Navigating Supply Chain Challenges Through Proactive Risk Surveillance and Mitigation Strategies among SMEs in ASEAN countries

Background Supply chain risk management is crucial for the consumer products industry due to its vulnerability to uncertainties and risks. This study investigates the relationship between supply chain risks and performance among SMEs in the ASEAN countries. Supply chain performance, defined as meeting end-customer demands, involves ensuring commodity availability, on-time deliveries, and maintaining sufficient inventory and capacity across organizational boundaries from raw materials to the final consumer. Methods The study utilized a sample of 385 entrepreneurs from the consumer products industry in ASEAN countries. The research was analyzed using Partial Least Squares Structural Equation Modeling (PLS-SEM) to establish the correlation between supply chain performance and risks. Factors related to the ASEAN Economic Community (AEC) for economic integration and regional trade agreements were incorporated to understand the diverse economic development, infrastructure, and regulatory environments across nations. Results The analysis revealed a strong correlation between supply chain risks and performance. Entrepreneurs in the consumer products industry should collaborate closely with governmental organizations to address the unique challenges posed by regulatory landscapes, cross-border logistics, and geopolitical risks within the ASEAN region. Adapting to cultural nuances and market variations, along with optimizing logistics and infrastructure, are crucial for successful supply chain risk management. Conclusions Effective supply chain risk management significantly enhances the performance of the consumer products industry’s supply chain. Entrepreneurs in this sector should align their strategies with regional and national governments to proactively address issues and mitigate risks. Continuous monitoring and adaptive measures are necessary to handle emerging risks in the dynamic market landscape. The study provides valuable insights for policymakers, suggesting that supportive frameworks and policies are necessary to bolster SME capabilities in risk management. By fostering a collaborative environment between the public and private sectors, ASEAN countries can enhance overall supply chain resilience. Future research could explore sector-specific risk management practices and their impact on supply chain robustness, underscoring the imperative for SMEs to adopt proactive and integrated risk management approaches to thrive in a complex and evolving economic environment.

Molecular xenomonitoring as an indicator of microfilaraemia prevalence for lymphatic filariasis in Samoa in 2019

BackgroundLymphatic filariasis (LF) is a globally significant, vector-borne, neglected tropical disease that can result in severe morbidity and disability. As the World Health Organization (WHO) Global Programme to Eliminate Lymphatic Filariasis makes progress towards LF elimination, there is greater need to develop sensitive strategies for post-intervention surveillance. Molecular xenomonitoring (MX), the detection of pathogen DNA in vectors, may provide a sensitive complement to traditional human-based surveillance techniques, including detection of circulating filarial antigen and microfilaraemia (Mf). This study aims to explore the relationship between human Mf prevalence and the prevalence of polymerase chain reaction (PCR)-positive mosquitoes using MX.MethodsThis study compared Mf and MX results from a 2019 community-based survey conducted in 35 primary sampling units (PSUs) in Samoa. This study also investigated concordance between presence and absence of PCR-positive mosquitoes and Mf-positive participants at the PSU level, and calculated sensitivity and negative predictive values for each indicator using presence of any Mf-positive infection in humans or PCR-positive mosquitoes as a reference. Correlation between prevalence of filarial DNA in mosquitoes and Mf in humans was estimated at the PSU and household/trap level using mixed-effect Bayesian multilevel regression analysis.ResultsMf-positive individuals were identified in less than half of PSUs in which PCR-positive mosquito pools were present (13 of 28 PSUs). Prevalence of PCR-positive mosquitoes (each species separately) was positively correlated with Mf prevalence in humans at the PSU level. Analysed at the species level, only Aedes polynesiensis demonstrated strong evidence of positive correlation (r) with human Mf prevalence at both PSU (r: 0.5, 95% CrI 0.1–0.8) and trap/household levels (r: 0.6, 95% CrI 0.2–0.9).ConclusionsFindings from this study demonstrate that MX can be a sensitive surveillance method for identifying residual infection in low Mf prevalence settings. MX identified more locations with signals of transmission than Mf-testing. Strong correlation between estimated PCR-positive mosquitoes in the primary vector species and Mf in humans at small spatial scales demonstrates the utility of MX as an indicator for LF prevalence in Samoa and similar settings. Further investigation is needed to develop MX guidelines to strengthen the ability of MX to inform operational decisions.Graphical abstract

Multidisciplinary Collaboration in Combatting Antimicrobial Resistance: Insights and Outcomes From the National Alliance of Medical Professionals on Antimicrobial Resistance (NAMP-AMR) Initiative.

Antimicrobial resistance (AMR) poses a critical global health challenge, requiring a coordinated and vigorous response. Despite numerous global and national efforts, a unified multidisciplinary approach has been missing. The National Alliance of Medical Professionals on Antimicrobial Resistance (NAMP-AMR), led by the Indian Medical Association in collaboration with key stakeholders such as NITI Aayog and the Ministry of Health, seeks to address this gap. This alliance unites 52 medical specialty organizations and associations to enhance efforts across various sectors, developing comprehensive strategies for awareness, surveillance, infection control, and optimization of antimicrobial use. The foundational meeting of NAMP-AMR on July 7, 2024, established a collaborative roadmap, promising to bolster India's efforts against AMR and support the forthcoming National Action Plan on AMR 2.0. The meeting concentrated on six key areas: improving AMR awareness and advocacy; strengthening laboratory capacities and surveillance; enhancing infection prevention and control (IPC); optimizing antimicrobial use through stricter regulations and stewardship programs; advancing AMR research and innovation; and fostering strong national and international collaborations. This initiative marks a significant advancement in combating AMR and positions India as a leader in global health efforts against this critical issue.

The first characterization of Escherichia coli isolates recovered from three wastewater treatment plants in Romania

ABSTRACT The global growth of antimicrobial resistance (AMR) raises significant challenges to public health, necessitating comprehensive surveillance and intervention strategies. This study investigates the prevalence and resistance profiles of Escherichia coli isolated from three different wastewater treatment plants (WWTPs) in Romania during the warm season of 2023. Through systematic sampling and subsequent microbiological and molecular analyses, we identified a 50% prevalence of E. coli in wastewater samples, with a concerning 83.34% of isolates displaying resistance to multiple antibiotics. The resistance was notably high against ampicillin, ticarcillin/clavulanic acid, and cefalotin, with observed multidrug resistance suggesting a robust presence of antibiotic-resistant bacteria (ARB) within treated effluents. Molecular characterization confirmed the presence of multiple antibiotic resistance genes (ARGs), including β-lactamase producers and markers for tetracycline and sulphonamide resistance. These findings underscore the critical role of WWTPs as both reservoirs and potential dissemination points for ARB and ARGs, highlighting the need for integrated surveillance systems and enhanced wastewater treatment protocols to mitigate the spread of AMR. This study emphasizes the necessity of bridging clinical and environmental monitoring to develop effective public health strategies against the threat of antibiotic resistance.

Genomic characterization and cluster analysis of Carbapenem-resistant Klebsiella pneumoniae

To investigate the genomic features and perform cluster analysis of Carbapenem-resistant Klebsiella pneumoniae (CRKP) to provide an experimental basis for guiding the prevention and treatment of CRKP infections.A retrospective case-cohort study was conducted on 19 non-redundant CRKP strains isolated from the Tenth Affiliated Hospital of Southern Medical University between January and June 2023. Whole genome sequencing (WGS) and multilocus sequence typing (MLST) were performed to compare genomic features and analyze the resistance genes and homology of the strains.The results showed that the 19 CRKP strains were isolated from 8 different clinical departments, mainly from respiratory specimens. The whole genome sequencing revealed that the genomic lengths of CRKP ranged from 4.90 to 5.85 Mbp, with contigs N50 values>20 kb for each genome. The median overall GC content was 57.0% (50.4%-57.1%). Comparative genomic analysis identified three regions with high genomic variability. WGS detected 32 resistance genes across 11 categories. All 19 strains carried carbapenem resistance genes (blaKPC-2 and blaOXA-48), blaTEM-1B extended-spectrum β-lactamase resistance genes, qnrS1 quinolone resistance gene, and fosA fosfomycin resistance gene, with each strain carrying only one carbapenemase gene. The detection rate of blaKPC-2 was 94.7% (18/19). MLST identified three sequence types: ST11, ST437 and ST147, with ST11 being predominant (89.5%, 17/19). Clustering analysis based on acquired resistance genes revealed three clonal transmission patterns among strains 72 and 90, and strains 88, 84, 66 and 79.In conclusion, CRKP strains carry multiple resistance genes, and clustering analysis indicating that nosocomial clonal transmission is closely related to acquired resistance genes. The ST11-blaKPC-2 type strain is the predominant clone. Strengthened surveillance and effective control strategies are necessary to reduce nosocomial transmission of CRKP.

Metagenomic Profiling of Internationally Sourced Sewage Influents and Effluents Yields Insight into Selecting Targets for Antibiotic Resistance Monitoring.

It has been debated whether wastewater treatment plants (WWTPs) primarily act to attenuate or amplify antibiotic resistance genes (ARGs). However, ARGs are highly diverse with respect to their resistance mechanisms, mobilities, and taxonomic hosts and therefore their behavior in WWTPs should not be expected to be universally conserved. We applied metagenomic sequencing to wastewater influent and effluent samples from 12 international WWTPs to classify the behavior of specific ARGs entering and exiting WWTPs. In total, 1079 different ARGs originating from a variety of bacteria were detected. This included ARGs that could be mapped to assembled scaffolds corresponding to nine human pathogens. While the relative abundance (per 16S rRNA gene) of ARGs decreased during treatment at 11 of the 12 WWTPs sampled and absolute abundance (per mL) decreased at all 12 WWTPs, increases in relative abundance were observed for 40% of the ARGs detected at the 12th WWTP. Also, the relative abundance of mobile genetic elements (MGE) increased during treatment, but the fraction of ARGs known to be transmissible between species decreased, thus demonstrating that increased MGE prevalence may not be generally indicative of an increase in ARGs. A distinct conserved resistome was documented in both influent and effluent across samples, suggesting that well-functioning WWTPs generally attenuate influent antibiotic resistance loads. This work helps inform strategies for wastewater surveillance of antibiotic resistance, highlighting the utility of tracking ARGs as indicators of treatment performance and relative risk reduction.

Prevalence and dynamics of antimalarial drug resistance mutations among the Plasmodium falciparum isolates in TAK Province, Thailand, during the period of 1998-2001.

Despite the overall decline in malaria cases in Thailand, continuous surveillance in endemic areas remains crucial. This retrospective analysis examined Plasmodium falciparum samples from Tak province, Thailand, collected in 1998, 1999, and 2001, to investigate the prevalence and evolution of antimalarial genotypic drug resistance. The study revealed a high prevalence of drug-resistant P. falciparum, particularly to mefloquine and sulfadoxine/pyrimethamine, with significant mutations in genes associated with resistance. Notably, mutations indicative of artemisinin resistance, such as those in the kelch13 gene, were detected at low frequencies, suggesting an evolving resistance pattern. The underlying cause of these resistance mutations appears to be the historical and widespread use of these antimalarial drugs, which exerted selective pressure on the parasite population. These findings underscore the necessity of ongoing surveillance and adaptive control strategies to manage drug resistance, guide treatment policies, and prevent potential outbreaks, even as malaria cases decrease. Continuous monitoring and research are imperative to sustain malaria elimination efforts and address the dynamic challenges posed by evolving drug-resistant strains.

The influence of social and spatial processes on the epidemiology of environmentally transmitted pathogens in wildlife: implications for management.

Social and spatial structures of host populations play important roles in pathogen transmission. For environmentally transmitted pathogens, the host space use interacts with both the host social structure and the pathogen's environmental persistence (which determines the time-lag across which two hosts can transmit). Together, these factors shape the epidemiological dynamics of environmentally transmitted pathogens. While the importance of both social and spatial structures and environmental pathogen persistence has long been recognized in epidemiology, they are often considered separately. A better understanding of how these factors interact to determine disease dynamics is required for developing robust surveillance and management strategies. Here, we use a simple agent-based model where we vary host mobility (spatial), host gregariousness (social) and pathogen decay (environmental persistence), each from low to high levels to uncover how they affect epidemiological dynamics. By comparing epidemic peak, time to epidemic peak and final epidemic size, we show that longer infectious periods, higher group mobility, larger group size and longer pathogen persistence lead to larger, faster growing outbreaks, and explore how these processes interact to determine epidemiological outcomes such as the epidemic peak and the final epidemic size. We identify general principles that can be used for planning surveillance and control for wildlife host-pathogen systems with environmental transmission across a range of spatial behaviour, social structure and pathogen decay rates. This article is part of the theme issue 'The spatial-social interface: a theoretical and empirical integration'.

The rise of pathogen genomics in Africa.

The routine genomic surveillance of pathogens in diverse geographical settings and equitable data sharing are critical to inform effective infection control and therapeutic development. The coronavirus disease 2019 (COVID-19) pandemic highlighted the importance of routine genomic surveillance of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) to detect emerging variants of concern. However, the majority of high-income countries sequenced >0.5% of their COVID-19 cases, unlike low- and middle-income countries. By the end of 2022, many countries around the world had managed to establish capacity for pathogen genomic surveillance. Notably, Beta and Omicron; 2 of the 5 current SARS-CoV-2 variants of concern were first discovered in Africa through an aggressive sequencing campaign led by African scientists. To sustain such infrastructure and expertise beyond this pandemic, other endemic pathogens should leverage this investment. Therefore, countries are establishing multi-pathogen genomic surveillance strategies. Here we provide a catalog of the current landscape of sequenced and publicly shared pathogens in different countries in Africa. Drawing upon our collective knowledge and expertise, we review the ever-evolving challenges and propose innovative recommendations.

Changing Epidemiology of Chronic Hepatitis C: A University Hospital Experience

Background: Hepatitis C virus (HCV) infection remains a significant public health problem worldwide, with varying epidemiological trends over time necessitating continual surveillance and intervention strategies. Objectives: This retrospective study aimed to examine trends in demographics, transmission routes, and disease characteristics among 635 patients diagnosed with HCV infection between 2003 and 2023. Methods: Data on demographics, HCV RNA levels, liver enzymes, genotype distribution, and transmission routes were retrospectively analyzed. The study period was divided into four segments for detailed analysis. Results: There was a gradual increase in the diagnosed cases over the study period, particularly noticeable after 2012. The mean age at diagnosis remained stable from 2003 - 2007 to 2008 - 2012 but decreased significantly in the following years (P = 0.001). Male predominance was observed throughout the study, with a notable increase in the male/female ratio over time (P &lt; 0.001). Intravenous drug use (IVDU) emerged as the predominant transmission route, reaching 68.3% in 2018 - 2022 (P &lt; 0.001). The prevalence of incarceration history among patients increased significantly, reaching 24.6% in 2018 - 2022 (P &lt; 0.001). Disease characteristics varied between periods; median HCV RNA levels were highest in 2018 - 2022, and median alanine aminotransferase (ALT) levels differed significantly between periods (P = 0.001). The genotype distribution showed a shift over time, with genotype 1 predominating initially and genotypes 3, 4, and 5 becoming more prevalent in later years (P &lt; 0.001). Conclusions: This study highlights the dynamic changes in hepatitis C epidemiology over two decades in southern Turkey, highlighting the increasing burden in younger populations, the increasing prevalence of IVDU as a transmission route, and the changing genotype distribution.