Molecular Epidemiological Studies Research Articles

Exposure to food additive mixtures and type 2 diabetes risk in the NutriNet-Santé cohort

Abstract Background So far, the safety evaluation of food additives has been performed substance by substance, while in real life, millions of individuals are exposed to mixtures of food additives daily. According to preliminary experimental data, some of these chemicals, alone and/or in synergy are suspected to impact metabolic health. The objective of this study was to investigate for the first time the associations between exposure to mixtures of food additives and type 2 diabetes (T2D) risk in a large prospective cohort of French adults. Methods Participants (n = 108,783, 79.2% women, mean age=42.4 years, SD = 14.6) from the NutriNet-Santé cohort (2009-2024) completed repeated 24h-dietary records, detailing industrial product brands. Additive exposure was assessed using composition databases and laboratory assays. Five mixtures of additives were identified through non-negative matrix factorisation (NMF). Associations between these mixtures and the risk of T2D were characterised using multivariable proportional hazards Cox models adjusted for known risk factors. Findings 1115 participants were identified with T2D during follow-up. Two additive mixtures were associated with increased T2D risk. The first mixture included higher exposure to modified starches E14xx, pectins E440, guar gum E412, carrageenan E407, and polyphosphates E452 (HRper 1SD increment=1.11 [1.05-1.18]), p < 0.0001). The second mixture comprised citric acid E330, sodium citrates E331, phosphoric acid E338, sulphite ammonia caramel E150d, acesulfame-K E950, aspartame E951, sucralose E955 and arabic gum E414 (HR1SD=1.13 [1.08-1.18]), p < 0.0001). Interpretation This large prospective cohort study revealed direct associations between T2D risk and exposure to two food additive mixtures. Molecular epidemiology and experimental studies will be necessary to depict underlying mechanisms and potential cocktail effects. Key messages • Consumed together, widely used food additives may contribute to T2D aetiology, shedding light on the detrimental impact of highly processed foods on metabolic health. • This study highlights positives associations between T2D risk and exposure to two food additive mixtures.

Whole genome sequencing of M. tuberculosis for disease control in high-burden settings: study protocol for a cluster randomized controlled trial evaluating different community-wide intervention strategies in rural Madagascar

BackgroundRetrospective and descriptive molecular epidemiology studies have shown that Mycobacterium tuberculosis whole genome sequencing can identify outbreaks and disease transmission events with higher resolution than conventional epidemiological investigations. Those studies have strengthened our understanding of genomic polymorphisms correlating with person-to-person transmission and helped resolve putative transmission clusters. To date, systematic genomic surveillance programs implemented for M. tuberculosis were only implemented in low-incidence settings. The purpose of this study is to determine whether there is an impact of routine M. tuberculosis whole genome sequencing on tuberculosis case detection in a high-incidence setting.MethodsA cluster randomized controlled trial will be performed. Forty-eight rural village groups (or Fokontany) in the Vohibato district of Madagascar will be randomized to one of three interventions arms. Arm 1 (standard of care) involves healthcare facility-based passive case detection with smear microscopy testing. Arm 2 (best practice) consists of active case finding and Xpert MTB/RIF Ultra PCR testing followed by household contact investigations. Arm 3 (novel intervention) includes the same interventions as arm 2, with addition of sputum culture and M. tuberculosis whole genome sequencing for all newly diagnosed cases. In arm 3, molecular suggested putative outbreaks are investigated, and additional TB suspects are appropriately tested. The intervention observational period will be 2 years. The primary outcome will be the number of detected cases/100,000/year in each arm after 1 year of intervention.DiscussionThis study is designed to determine whether there is an impact of prospective whole genome sequencing-based molecular typing on tuberculosis case detection in high-incidence settings. Investigating potential outbreaks and focusing active case finding in spatiotemporal settings where disease transmission is suggested by genomic typing is hypothesized to improve case detection in rural communities.Trial registrationClinicalTrials.gov NCT05406453. Retrospectively registered on June 6, 2022.

Surveillance of Food and Waterborne Pathogens in North-East India: Protocol for a Laboratory-Based Sentinel Surveillance Study.

Food safety is a global concern, which is often underestimated owing to challenges in investigating foodborne diseases. These challenges arise from the increased globalization of the food trade, advancements in agricultural practices, and shifts in environmental factors. In North-East India, common diarrheal outbreaks from fermented foods pose significant health risks. Despite these challenges, systematic data on foodborne pathogens is lacking in India, highlighting a crucial gap in understanding food safety issues. The aim of this research protocol is to establish an integrated surveillance system to identify enteric pathogens circulating within humans, food animals, and the environment through a health approach in North-East India, and to conduct outbreak investigations. The Indian Council of Medical Research (ICMR) initiated a surveillance study across all 8 North-East states in India, employing a centralized digital database for data collation. The project aims to enhance theinfrastructure for microbial culture, antibiotic sensitivity testing, and molecular epidemiological studies. The study involves laboratory-based surveillance of foodborne pathogens in market foods, hospitalized diarrheal patients, poultry and animal farms, slaughterhouses, butcher shops, and diarrheal outbreaks. A standardized case report form ensures consistent data collection of age, sex, signs, symptoms, and admission dates for diarrheal cases. Stool and rectal swabs will undergo testing for pathogen identification and antimicrobial resistance. Similarly, samples of market foods, food animals, and the environment will be collected. Outbreaks confirmed by the Integrated Disease Surveillance Project (IDSP) will be thoroughly investigated following standardized guidelines. In phase I, 5 surveillance centers were established across 4 states (ie, Assam [Dibrugarh and Guwahati], Tripura, Sikkim, and Arunachal Pradesh) in 2020. Following an interim phase I data assessment and the successful establishment of a streamlined system for data procurement, investigation, recording, and analysis, along with the implementation of regular training and monitoring programs, phase II expansion was initiated in 2023-24. This includes the addition of 7 more centers (including 3 veterinary centers) in the remaining 4 states (ie, Manipur, Meghalaya, Mizoram, and Nagaland), eventually covering the entire North-Eastern Region of India. Food and waterborne diseases are a constant public health problem in many countries. Key challenges to the enhancement of food safety policy include the paucity of systematic data and awareness. With this background, ICMR's initiative is the first systematic surveillance study in the country to adopt a single health approach. Data obtained from this project will help to understand the risk of acquiring food and waterborne pathogens, their transmission pathways, and antimicrobial resistance patterns. The scientific evidence generated through this project will be helpful in formulating and strengthening food safety policy and in initiating government programs to protect the health of the nation. DERR1-10.2196/56469.

Interpreting the Epidemiological Characteristics of HIV-1 in Heterosexually Transmitted Population Based on Molecular Transmission Network in Kunming, Yunnan: A Retrospective Cohort Study.

Heterosexuals have become the most prevalent group of HIV-1 in Kunming, Yunnan Province. Utilizing the principle of genetic similarity between their gene sequences, we built a molecular transmission network by gathering data from earlier molecular epidemiological studies. This allowed us to analyze the epidemiological features of this group and offer fresh concepts and approaches for the prevention and management of HIV-1 epidemics. Cytoscope was used to visualize and characterize the network following the processing of the sample gene sequences by BioEdit and HyPhy. The number of possible links and the size of the clusters were investigated as influencing factors using a zero-inflated Poisson model and a logistic regression model, respectively. A scikit-learn-based prediction model was developed to account for the dynamic changes in the HIV-1 molecular network. Six noteworthy modular clusters with network scores ranging from 4 to 9 were found from 150 clusters using Molecular Complex Detection analysis at a standard genetic distance threshold of 0.01. The size of the number of possible links and the network's clustering rate were significantly impacted by sampling time, marital status, and CD4+ T lymphocytes (all p < 0.05). The gradient boosting machine (GBM) model had the highest area under the curve value, 0.884 ± 0.051, according to scikit-learn. Though not all cluster subtypes grew equally, the network clusters were relatively specific and aggregated. The largest local transmission-risk group for HIV-1CRF08_BC is now the heterosexual transmission population. The most suitable model for constructing the HIV-1 molecular network dynamics prediction model was found to be the GBM model.

Molecular and cell phenotype programs in oral epithelial cells directed by co-exposure to arsenic and smokeless tobacco.

Chronic arsenic exposure can lead to various health issues, including cancer. Concerns have been mounting about the enhancement of arsenic toxicity through co-exposure to various prevalent lifestyle habits. Smokeless tobacco products are commonly consumed in South Asian countries, where their use frequently co-occurs with exposure to arsenic from contaminated groundwater. To decipher the in vitro molecular and cellular responses to arsenic and/or smokeless tobacco, we performed temporal multi-omics analysis of the transcriptome and DNA methylome remodelling in exposed hTERT-immortalized human normal oral keratinocytes (NOK), as well as arsenic and/or smokeless tobacco genotoxicity and mutagenicity investigations in NOK cells and in human p53 knock-in murine embryonic fibroblasts (Hupki MEF). RNAseq results from acute exposures to arsenic alone and in combination with smokeless tobacco extract revealed upregulation of genes with roles in cell cycle changes, apoptosis and inflammation responses. This was in keeping with global DNA hypomethylation affecting genes involved in the same processes in response to chronic treatment in NOK cells. At the phenotypic level, we observed a dose-dependent decrease in NOK cell viability, induction of DNA damage, cell cycle changes and increased apoptosis, with the most pronounced effects observed under arsenic and SLT co-exposure conditions. Live-cell imaging experiments indicated that the DNA damage likely resulted from induction of apoptosis, an observation validated by a lack of exome-wide mutagenesis in response to chronic exposure to arsenic and/or smokeless tobacco. In sum, our integrative omics study provides novel insights into the acute and chronic responses to arsenic and smokeless tobacco (co-)exposure, with both types of responses converging on several key mechanisms associated with cancer hallmark processes. The generated rich catalogue of molecular programs in oral cells regulated by arsenic and smokeless tobacco (co-)exposure may provide bases for future development of biomarkers for use in molecular epidemiology studies of exposed populations at risk of developing oral cancer.

Emergence of lineage ST150 and linezolid resistance in Enterococcus faecalis: a molecular epidemiology study of UTIs in Tehran, Iran.

Urinary tract infections (UTIs) represent one of the most prevalent bacterial infections, with Enterococcus species now recognized as the second leading cause of these infections. This study focused on symptomatic UTI cases to investigate the risk factors associated with Enterococcus faecalis clinical isolates in patients from Tehran, Iran. Urine samples were collected from patients presenting with symptomatic UTIs. The identification of E. faecalis isolates was performed using standard microbiological techniques, with confirmation via polymerase chain reaction (PCR). Antibiotic susceptibility testing was conducted using the Kirby-Bauer disc diffusion method. The presence of virulence genes was determined through PCR, and biofilm formation was assessed using the microtiter plate method. Additionally, multi-locus sequence typing (MLST) was utilized to genotype linezolid-resistant isolates. Out of 300 UTI cases, E. faecalis was identified as the causative agent in 160 instances. Notably, a high proportion of these isolates exhibited resistance to tetracycline (83.8%) and minocycline (82.5%). Linezolid resistance was observed in 1.3% (n = 2) of the isolates. Conversely, the highest susceptibility rates were observed for vancomycin, penicillin G, ampicillin, and nitrofurantoin, each demonstrating a 98.8% susceptibility rate. Biofilm formation was detected in 25% of the E. faecalis isolates. A significant majority (93.8%) of the isolates harbored the efbA and ace genes, with varying frequencies of esp (72.5%), asa1 (61.2%), cylA (52.5%), and gelE (88.8%) genes. MLST analysis demonstrated that both linezolid-resistant isolates, characterized by strong biofilm formation and the presence of virulence genes, were assigned to the ST150 lineage, which has not been previously documented in clinical settings. The emergence of the ST150 clonal lineage, underscores its clinical significance, particularly in relation to linezolid resistance in E. faecalis. This study adds to the growing body of evidence linking specific clonal lineages with antibiotic resistance, highlighting the critical need for ongoing surveillance and molecular characterization of resistant pathogens.

Spatio-temporal distribution and international context of bovine viral diarrhoea virus genetic diversity in France

Bovine viral diarrhoea (BVD) is one of the most economically damaging livestock enzootic diseases in the world. BVD aetiological agents are three pestiviruses (BVDV-1, -2 and HoBi-like pestivirus), which exhibit high genetic diversity and complex transmission cycles. This considerably hampers the management of the disease, which is why eradication plans have been implemented in several countries. In France, a national plan has been in place since 2019. Our understanding of its impact on the distribution of BVDV genotypes is limited by the availability of French genetic data. Here, we conducted a molecular epidemiology study to refine our knowledge of BVDV genetic diversity in France, characterise its international relationships, and analyse national spatio-temporal genotypic distribution. We collated 1037 BVDV-positive samples throughout France between 2011 and 2023, with a greater sampling effort in two major cattle production areas. We developed a high-throughput sequencing protocol which we used to complete the 5’UTR genotyping of this collection. We show that two main BVDV-1 genotypes, 1e and 1b, account for 88% of genotyped sequences. We also identified seven other BVDV-1 genotypes occurring at low frequencies and three BVDV-2 samples (genotype 2c). Phylogenetic analyses indicate different worldwide distribution patterns between the two main BVDV-1 genotypes. Their relative frequencies present no major changes in France since the 1990s and few variations at the national scale. We also found some degree of local spatial structuring in western France. Overall, our results demonstrate the potential of large-scale sequence-based surveillance to monitor changes in the epidemiological situation of enzootic diseases.

Prevalence and identification of cyathocotylid trematodes infecting African catfish in Egypt.

The trematode family Cyathocotylidae infects various hosts worldwide, including birds, mammals, reptiles, and fish. However, the lack of molecular data from adult worms hinders phylogenetic, epidemiological, and host association studies. This study aims to identify the common cyathocotylid trematodes infecting African catfish in Egypt using morphological and molecular evidence. Out of 142Clarias gariepinus, 123 fish (86.6%) harbored cyathocotylid metacercariae, with a mean metacercarial intensity of 201 ± 38.5/g. Cyathocotylid metacercariae prevalence gradually rose as host size increased. Although there was no significant difference between groups, larger fish had a higher mean metacercarial intensity. The prevalence and intensity were unrelated to the fish gender. Histopathological examination of metacercariae-infected catfish revealed varying degrees of degenerative changes, including intermuscular edema leading to muscle fiber dispersion and atrophy, involving 11% to over 81% of muscle sections. We identified three cyathocotylid metacercariae and eight cyathocotylid adult species from experimental infection using morphometric and molecular data, including internal transcribed spacer (ITS) and/or mitochondrial cytochrome c oxidase subunit 1 (cox1) sequences. We determined the phylogenetic position of these cyathocotylid samples.The ITS sequence analysis linked the isolated Cyathocotylidae sp. 1 and 2 metacercariae to Prohemistomum vivax adults. Mesostephanus appendiculatoides and Paracoenogonimus ovatus were reported for the first time in Egypt. These findings may provide valuable genetic data for future molecular epidemiological and phylogenetic studies of cyathocotylid trematodes.

Insights into the molecular network characteristics of major HIV-1 subtypes in developed Eastern China: a study based on comprehensive molecular surveillance data.

This study aimed to conduct a comprehensive molecular epidemiology study of major HIV-1 subtypes in developed Eastern China (Zhejiang Province). Plasma samples and epidemiological information were collected from 4180 newly diagnosed HIV-1 positive patients in Zhejiang Province in 2021. Pol sequences were obtained to determine the subtypes via multiple analytical tools. HIV-1 molecular networks were constructed on the basis of genetic distances to analyze transmission patterns among major subtypes. Furthermore, the birth-death skyline (BDSKY) model was utilized to estimate the transmission risks associated with large clusters (LCs). In 4180 patients, 3699 (88.49%) pol sequences were successfully obtained and classified into four subtype groups. In the networks under an optimal genetic distance of 0.01 substitutions/site, the majority of links (74.52%, 1383/1856) involved individuals within the same city, highlighting the predominant role of local transmission in driving the HIV-1 epidemic. In the CRF07_BC, CRF01_AE, and others/URFs networks, men who have sex with men (MSM) were the primary sexual transmission population, with the younger MSM group (< 30 years old) exhibiting higher linkage frequencies. Within the CRF08_BC network, 93.98% of individuals were infected primarily through heterosexual contact and had a significantly greater risk of localized clustering than other subtypes did. Moreover, fifteen identified LCs were predominantly transmitted through commercial heterosexual contact (CHC), exhibiting localized clustering and high potential for sustained diffusion. Overall, our findings reveal a diverse and heterogeneous distribution of HIV-1 subtypes in Zhejiang Province, with noticeable variations in hotspots across different geographic areas and populations.

Molecular cluster, transmission characteristics, origin and dynamics analysis of HIV-1 CRF59_01B in China: A molecular epidemiology study

PurposeThis study investigated for the HIV-1 CRF59_01B epidemic's spatiotemporal dynamics and its transmission networks in China. MethodsBetween 2007 and 2020, a total of 250 partial pol gene sequences of HIV-1 CRF59_01B were collected from four regions (10 Chinese provinces). Phylogenetic tree construction and cluster identification were then performed. The Bayesian skyline and birth–death susceptible–infected–removed models were employed for the phylodynamic analyses of subtypes and large clusters, respectively. Phylogenetic analyses and trait diffusion of these sequences were performed using Bayesian phylogenetic methods (beast-classic package). Distance-based molecular network analyses were performed to identify putative relationships. ResultsUsing a genetic distance threshold of 1.3 %, We identified 45 clusters that included 62.40 % (156/250) of the sequences. Three clusters (6.67 %, 3/45) had 10 or more sequences, and were considered "large clusters". Six clusters (13.33 %) included sequences from different regions (Southeast, Northeast, Southeast, and Central China). Thirteen clusters (28.89 %) included sequences of men who had sex with men only, three clusters (6.67 %) included sequences of heterosexuals only, and 12 clusters (26.67 %) included sequences of both groups. The substitution rate of CRF59_01B was 1.91 × 10–3 substitutions per site per year [95 % highest posterior density (HPD) interval: 1.39 × 10−3–2.49 × 10−3)], the time to the most recent common ancestor of CRF59_01B was to be 1992.83 (95 % HPD: 1977.97–2002.81). A Bayesian skyline plot revealed that the effective population size of CRF59_01B increased from 2000 to 2015 and remained stable after 2015. The large clusters showed continuous growth from 2013 to 2020. Phylogeographic analysis showed that CRF59_01B B most likely originated in Southeast China, with a posterior probability of 97.44 %, and then spread to other regions. ConclusionsOur study revealed the temporal and geographical origins of HIV-1 CRF59_01B as well as the process of transmission among various regions and risk groups in China, which can help develop targeted HIV prevention strategies.

Mapping Transmission Dynamics and Drug Resistance Surveillance in the Cyprus HIV-1 Epidemic (2017-2021).

The human immunodeficiency virus type 1 (HIV-1) epidemic has been a major public health threat on a global scale since the early 1980s. Despite the introduction of combination antiretroviral therapy (cART), the incidence of new HIV-1 infections continues to rise in some regions around the world. Thus, with the continuous transmission of HIV-1 and the lack of a cure, it is imperative for molecular epidemiological studies to be performed, to monitor the infection and ultimately be able to control the spread of this virus. This work provides a comprehensive molecular epidemiological analysis of the HIV-1 infection in Cyprus, through examining 305 HIV-1 sequences collected between 9 March 2017 and 14 October 2021. Employing advanced statistical and bioinformatic techniques, the research delved deeply into understanding the transmission dynamics of the HIV-1 epidemic in Cyprus, as well as the monitoring of HIV-1's genetic diversity and the surveillance of transmitted drug resistance. The characterization of Cyprus's HIV-1 epidemic revealed a diverse landscape, comprising 21 HIV-1 group M pure subtypes and circulating recombinant forms (CRFs), alongside numerous uncharacterized recombinant strains. Subtypes A1 and B emerged as the most prevalent strains, followed by CRF02_AG. The findings of this study also revealed high levels of transmitted drug resistance (TDR) patterns, raising concerns for the efficacy of cART. The demographic profiles of individuals involved in HIV-1 transmission underscored the disproportionate burden borne by young to middle-aged Cypriot males, particularly those in the MSM community, who reported contracting the virus in Cyprus. An assessment of the spatiotemporal evolutionary dynamics illustrated the global interconnectedness of HIV-1 transmission networks, implicating five continents in the dissemination of strains within Cyprus: Europe, Africa, Asia, North America, and Oceania. Overall, this study advances the comprehension of the HIV-1 epidemic in Cyprus and highlights the importance of understanding HIV-1's transmission dynamics through continuous surveillance efforts. Furthermore, this work emphasizes the critical role of state-of-the-art bioinformatics analyses in addressing the challenges posed by HIV-1 transmission globally, laying the groundwork for public health interventions aimed at curbing its spread and improving patient outcomes.

Development of a PCR assay for detection and identification of Eimeria spp. in cattle

Eimeria spp. are important coccidian parasites causing diarrhea and significant mortality in cattle worldwide. To date, at least 13 Eimeria species with varying pathogenicity have been identified in cattle. Efficient detection and identification of Eimeria spp. is therefore essential for the prevention and control of bovine coccidiosis. However, the commonly used microscopic examination for Eimeria spp. is time-consuming and requires considerable expertise. In this study, we aligned the nucleotide sequences of the small subunit (SSU) rRNA gene of common Eimeria species and developed a nested PCR assay targeting the polymorphic SSU rRNA region of Eimeria spp. from cattle. Initially, the SSU rRNA gene PCR assay was compared with microscopic examination for sensitivity and detection range of Eimeria species using fecal samples from dairy cattle. Of the 193 fecal samples, 131 (67.9 %) and 78 (40.4 %) were positive for Eimeria by PCR and microscopy, respectively. Sequence analysis of the PCR products identified six Eimeria species, including E. cylindrica (n = 76), E. bovis (n = 54), E. auburnensis (n = 30), E. zuernii (n = 25), E. wyomingensis (n = 10), E. canadensis (n = 1), and co-infections of 2–4 species (n = 55). In contrast, only the first four species and co-infections of 2–3 species were identified by microscopy. The PCR assay was able to detect as few as 50 Eimeria oocysts per gram of feces. Thus, the developed SSU rRNA gene PCR assay has a high sensitivity and allowed easy identification of at least six common Eimeria species and their co-infections in cattle. It should be useful in molecular epidemiological studies of bovine coccidiosis.

Molecular epidemiology of brucellosis in Asia: insights from genotyping analyses.

Brucellosis infects humans and animals worldwide but is particularly prevalent in Asia. In many Asian countries, molecular diagnostic tools for accurate molecular diagnostics and molecular epidemiology are lacking. Nonetheless, some countries have conducted in-depth molecular epidemiological studies. The objective of this study was to reveal the genetic relationships, geographic origins, and distributions of Brucella strains across Asia for two primary species, B. abortus and B. melitensis. For this, we systematically searched genotyping data from published studies on the molecular epidemiology of Brucella species for both humans and livestock in Asia. We used data from multilocus sequence typing (MLST), multiple-locus variable-number tandem repeat analysis (MLVA), and whole genome sequencing analysis of Brucella strains. We also analyzed the MLVA genotypes of 129 B. abortus isolates and 242 B. melitensis isolates with known origins in Asia from an online MLVA database using MLVA-11 data in minimum spanning trees and MLVA-16 data in neighbor-joining trees. We found that the B. melitensis East Mediterranean lineage is predominant across the continent, with only a small number of samples from the Africa and Americas lineages, and none from the West Mediterranean lineage. The "abortus C" genotype was the most common group of B. abortus in Asia, with limited genetic variation for this species. Several studies also reported that Near Eastern countries frequently encounter human brucellosis cases of B. abortus from genotypes 42 and 43. Our study highlights the inconsistent collection of genetic data for Brucella species across Asia and a need for more extensive sampling in most countries. Finally, a consistent nomenclature is necessary to define various groupings of strains within a lineage (i.e., clade) so uniform terminology should denote particular genetic groups that are understood by all researchers.

Torque Teno Sus Virus 1: A Potential Surrogate Pathogen to Study Pig-Transmitted Transboundary Animal Diseases.

Understanding the epidemiology and transmission dynamics of transboundary animal diseases (TADs) among wild pigs (Sus scrofa) will aid in preventing the introduction or containment of TADs among wild populations. Given the challenges associated with studying TADs in free-ranging populations, a surrogate pathogen system may predict how pathogens may circulate and be maintained within wild free-ranging swine populations, how they may spill over into domestic populations, and how management actions may impact transmission. We assessed the suitability of Torque teno sus virus 1 (TTSuV1) to serve as a surrogate pathogen for molecular epidemiological studies in wild pigs by investigating the prevalence, persistence, correlation with host health status and genetic variability at two study areas: Archbold's Buck Island Ranch in Florida and Savannah River Site in South Carolina. We then conducted a molecular epidemiological case study within Archbold's Buck Island Ranch site to determine how analysis of this pathogen could inform transmission dynamics of a directly transmitted virus. Prevalence was high in both study areas (40%, n = 190), and phylogenetic analyses revealed high levels of genetic variability within and between study areas. Our case study showed that pairwise host relatedness and geographic distance were highly correlated to pairwise viral genetic similarity. Molecular epidemiological analyses revealed a distinct pattern of direct transmission from pig to pig occurring within and between family groups. Our results suggest that TTSuV1 is highly suitable for molecular epidemiological analyses and will be useful for future studies of transmission dynamics in wild free-ranging pigs.

Nationwide upsurge in invasive disease in the context of longitudinal surveillance of carriage and invasive Streptococcus pyogenes 2009-2023, the Netherlands: a molecular epidemiological study.

Since 2022, many countries have reported an upsurge in invasive group A streptococcal (iGAS) infections. We explored whether changes in Streptococcus pyogenes carriage rates or emergence of strains with potentially altered virulence, such as emm1 variants M1UK and M1DK, contributed to the 2022/2023 surge in the Netherlands. We determined emm (sub)type distribution for 2,698 invasive and 351 S. pyogenes carriage isolates collected between January 2009 and March 2023. Genetic evolution of emm1 was analyzed by whole-genome sequencing of 497 emm1 isolates. The nationwide iGAS upsurge coincided with a sharp increase of emm1.0 from 18% (18/100) of invasive isolates in Q1 2022 to 58% (388/670) in Q1 2023 (Fisher's exact test, P < 0.0001). M1UK became dominant among invasive emm1 isolates in 2016 and further expanded from 72% in Q1 2022 to 96% in Q1 2023. Phylogenetic comparison revealed evolution and clonal expansion of four new M1UK clades in 2022/2023. DNase Spd1 and superantigen SpeC were acquired in 9% (46/497) of emm1 isolates. S. pyogenes carriage rates and emm1 proportions in carriage isolates remained stable during this surge, and the expansion of M1UK in iGAS was not reflected in carriage isolates. During the 2022/2023 iGAS surge in the Netherlands, expansion of four new M1UK clades was observed among invasive isolates, but not carriage isolates, suggesting increased virulence and fitness of M1UK compared to contemporary M1 strains. The emergence of more virulent clades has important implications for public health strategies such as antibiotic prophylaxis for close contacts of iGAS patients.IMPORTANCEThis study describes the molecular epidemiology of invasive group A streptococcal (iGAS) infections in the Netherlands based on >3,000 Streptococcus pyogenes isolates from both asymptomatic carriers and iGAS patients collected before, during, and after the COVID-19 pandemic period (2009-2023) and is the first to assess whether changes in carriage rates or carried emm types contributed to the alarming post-COVID-19 upsurge in iGAS infections. We show that the 2022/2023 iGAS surge coincided with a sharp increase of emm1, particularly the toxicogenic M1UK variant, in invasive isolates, but not in carriage isolates. These findings suggest that increased virulence and fitness of M1UK likely contributes to an increased dissemination between hosts. The emergence of a more virulent and fit lineage has important implications for iGAS control interventions such as antibiotic prophylaxis for close contacts of iGAS patients and calls for a reappraisal of iGAS control interventions and guidelines.

Clinical and genomic diversity of Treponema pallidum subspecies pallidum to inform vaccine research: an international, molecular epidemiology study

The increase in syphilis rates worldwide necessitates development of a vaccine with global efficacy. Weaimed to explore Treponema pallidum subspecies pallidum (TPA) molecular epidemiology essential for vaccine research by analysing clinical data and specimens from early syphilis patients using whole-genome sequencing (WGS) and publicly available WGS data. In this multicentre, cross-sectional, molecular epidemiology study, we enrolled patients with primary, secondary, or early latent syphilis from clinics in China, Colombia, Malawi, and the USA between Nov 28, 2019, and May 27, 2022. Participants aged 18years or older with laboratory confirmation of syphilis by direct detection methods or serological testing, or both, were included. Patients were excluded from enrolment if they were unwilling or unable to give informed consent, did not understand the study purpose or nature of their participation, or received antibiotics active against syphilis in the past 30days. TPA detection and WGS were conducted on lesion swabs, skin biopsies, skin scrapings, whole blood, or rabbit-passaged isolates. We compared our WGS data to publicly available genomes and analysed TPA populations to identify mutations associated with lineage and geography. We screened 2802patients and enrolled 233participants, of whom 77 (33%) had primary syphilis, 154 (66%) had secondary syphilis, and two (1%) had early latent syphilis. The median age of participants was 28years (IQR22-35); 154 (66%) participants were cisgender men, 77 (33%) were cisgender women, and two (1%) were transgender women. Of the cisgender men, 66 (43%) identified as gay, bisexual, or other sexuality. Among all participants, 56(24%) had HIV co-infection. WGS data from 113participants showed a predominance of SS14-lineage strains with geographical clustering. Phylogenomic analyses confirmed that Nichols-lineage strains were more genetically diverse than SS14-lineage strains and clustered into more distinct subclades. Differences in single nucleotide variants (SNVs) were evident by TPA lineage and geography. Mapping of highly differentiated SNVs to three-dimensional protein models showed population-specific substitutions, some in outer membrane proteins (OMPs) of interest. Our study substantiates the global diversity of TPA strains. Additional analyses to explore TPA OMP variability within strains is vital for vaccine development and understanding syphilis pathogenesis on a population level. US National Institutes of Health National Institute for Allergy and Infectious Disease, the Bill & Melinda Gates Foundation, Connecticut Children's, and the Czech Republic National Institute of Virology and Bacteriology.

Identification of a Novel HIV-1 Circulating Recombinant Form (CRF150_Cpx) Among Men Who Have Sex with Men in China.

Recent studies have reported increasing complexity in human immunodeficiency virus 1 (HIV-1) genotypes among men who have sex with men (MSM) in China. In an HIV-1 molecular epidemiological study conducted among MSM in Yunnan Province, China, we discovered that four samples could potentially represent a circulating recombinant form (CRF). In this study, we conducted further analysis on their nearly full-length genome (NFLG) sequences. The NFLG sequences formed a distinct monophyletic clade in the phylogenetic tree. Recombination analysis indicated that the four sequences were constructed upon the backbone of CRF149_01B, with the insertion of three CRF07_BC fragments. Consequently, they were designated as CRF150_cpx. Evolutionary analyses suggested that CRF150_cpx emerged between approximately 2014 and 2015. The identification of new CRFs not only deepens our understanding of HIV recombination but also aids in comprehending the prevalence and transmission history of HIV among specific populations.

Molecular detection using hybridization capture and next-generation sequencing reveals cross-species transmission of feline coronavirus type-1 between a domestic cat and a captive wild felid.

Feline coronavirus (FCoV) is highly prevalent in domestic cats worldwide and has also been reported in wild felids, including endangered species, in which it has caused substantial population declines. Characterizing the genetic diversity of FCoV is crucial due to recent reports of novel pathogenic recombinant variants causing high mortality in feral cats in Cyprus. In this retrospective molecular epidemiology study, we used archived samples collected in a zoological institution in the U.S. in which a domestic and a wild felid succumbed to FCoV. Using hybridization capture (HC) and next-generation sequencing, we show for the first time that FCoV can be naturally transmitted between domestic and wild felids. We demonstrate the efficacy of HC for detecting and sequencing the whole genome of FCoV, which is essential to characterize its different genotypes.

Feline vector-borne haemopathogens in Türkiye: the first molecular detection of Mycoplasma wenyonii and ongoing Babesia ovis DNA presence in unspecific hosts

BackgroundCats are hosts and reservoirs for many haemopathogens such as piroplasms, Rickettsia, hemotropic Mycoplasma, Bartonella, Ehrlichia, and Anaplasma, which are transmitted by various vector arthropods and some of which have a zoonotic concern. Although it is noteworthy that the rate of ownership of companion animals has increased in Türkiye in recent years and that cats account for a large proportion of these animals, there is limited research on the vector-borne infectious agents carried by them. The present study aimed to provide a comprehensive molecular epidemiological data and molecular characterization of feline vector-borne haemopathogens (FVBHs), including piroplasms, anaplasmataceae, rickettsias, haemoplasmas, and Bartonella species in Türkiye. In total, 250 feline blood samples were collected from client-owned cats (n = 203) and shelter cats (n = 47) brought to the Small Animal Hospital of Selcuk University, Veterinary Faculty.ResultsOverall, 40 (16%) cats were found to be infected with at least one of the investigated haemopathogens and piroplasm, Mycoplasma spp. and Bartonella spp. prevalence was 1.6%, 11.2%, and 4.8%, respectively. No Anaplasma/Ehrlichia spp. and Rickettsia spp. DNA was detected in the investigated feline samples. Sequence analysis revealed that all four piroplasms belonged to Babesia ovis with a 97.93–99.82% nucleotide sequence identity to 18S rRNA gene sequences from Spain and Türkiye, while some sequenced hemoplasmas were Mycoplasma haemofelis (Mhf), Candidatus Mycoplasma haemominutum (CMhm) and Mycoplasma wenyonii, and Bartonella spp. were Bartonella henselae and Bartonella koehlerae species. Co-infections with Mycoplasma spp. and Bartonella spp. were also detected in 4 cats (1.6%) in this study, where single infections were predominant.ConclusionThis study provides valuable information on zoonotically important feline vector-borne hemopathogens in Türkiye, some of which have received attention under the One Health perspective, and is the first molecular epidemiological study to demonstrate the presence of Babesia ovis, the causative agent of ovine babesiosis, and Mycoplasma wenyonii DNA, the causative agent of bovine haemotropic mycoplasmosis, in cats. Further studies on the roles of such pathogens detected in unspecific hosts and the host specificity of the vectors that transmit them will contribute to the elucidation of this situation.

The Impact of the Mycobacterium tuberculosis RDRio Subfamily on Multidrug-Resistant Tuberculosis in Latin America: A Comprehensive Review.

Latin American region is a high-burden setting for tuberculosis where multidrug-resistant tuberculosis (MDR-TB) is among the main challenge to move forward the End TB Strategy goals. It has been shown that MDR-TB is associated to certain Mycobacterium tuberculosis (MTB) lineages like L2-Beijing sublineage or L4-LAM. Although L2-Beijing is present in South America, the L4 lineage is the most prevalent with values ranging from 75% to 99% depending on the country. Within L4, Latin American-Mediterranean (LAM) family is the most prevalent. Moreover, within LAM, RDRio subfamily is present in high prevalence in several countries in South America like Venezuela or Brazil. RDRio has been associated to MDR-TB in several studies in Brazil but more epidemiological information is needed for South America. Here we discuss the problem of MDR-TB in Latin America and the potential threat that RDRio could represent. At this time, more molecular epidemiology studies are necessary to improve TB surveillance programs in Latin America by tracking MTB strains potentially responsible for MDR-TB spread.