OBJECTIVES:Emerging genomic evidence has identified ancestral strains of Yersinia pestis in ancient human populations, which has sparked debates about its pathogenic role in later Neolithic societies. Here, we review published evidence linking anthropological and biological data reflecting the past natural history of Y. pestis infection. MATERIALS AND METHODS:Review of reported ancient Y. pestis genomes, paleomicrobiological, archaeological, and ecological data related to ancient plague. RESULTS AND DISCUSSION:While some researchers attributed the Scandinavian Neolithic population decline to plague epidemics, we argue that early Y. pestis strains were more likely associated with outbreaks of food-borne enteritis rather than flea-borne plague. This hypothesis is supported by genetic, archaeological, and ecological analyses, which indicate that Y. pestis evolved key flea-borne transmission mechanisms only later in its history.

The characterization of Staphylococcus aureus (S. aureus) isolates superinfecting cutaneous lesions of Buruli ulcer (BU), a neglected tropical disease caused by non-tuberculous Mycobacterium ulcerans, remains limited. In Burkina Faso, we investigated eight S. aureus isolates from BUs and three from non-BUs using phenotypic analysis, including antibiotic susceptibility testing and genomic analysis (whole genome sequencing, average nucleotide identity, resistome, virulome, multilocus sequence typing, pangenome, and multiple correspondence analysis). All isolates were firmly identified at the species level as S. aureus subsp. aureus but did not cluster according to the group to which they belonged. These 11 isolates were in vitro susceptible to most antibiotics, except for penicillin G, erythromycin, and ciprofloxacin, to which some were resistant (11/11, 3/11, and 3/11, respectively). S. aureus isolates were assigned to different spacer-types (STs) including ST5 (2/11), ST1472 (1/11), ST1 (2/11), ST2434 (1/11), ST152 (3/11), and a previously unreported ST7358 (2/11). The spa types included t8921, t318, t127, t084, t355, t559, and t311. Several phages, antibiotic resistance genes, and virulence factors, including immunomodulators, adhesins, exoenzymes, and toxins such as Panton-Valentine leucocidin, were identified in all groups. No mec genes were detected in any of the S. aureus strains studied. OrthoANI, pangenome, and multiple correspondence analysis did not specify any S. aureus genotype associated with BU. In conclusion, we found no specificity of S. aureus strains to BU, which leads us to speculate that this microorganism behaves only as an opportunistic pathogen of the lesion.

Tuberculosis remains a pressing public health issue in Lebanon. The aim of this study was whole-genome-based determination of species and sub-species and antibiotic susceptibility profiles of Mycobacterium tuberculosis complex (MTBC) isolates recovered from a major tertiary care center in Lebanon. A total of 48 clinical MTBC isolates were identified and characterized through whole genome sequence using Illumina MiSeq. Genomic analysis revealed that 39/48 (81.25

OBJECTIVES:Granehäll et al. (2021) identified TS-2 as an unknown Methanobrevibacter lineage abundant in ancient dental calculus, less prevalent in modern samples, and not linked to any cultivated representative. We aimed (i) to determine whether TS-2 corresponds to the cultivated oral archaeon Methanobrevibacter massiliense using genome-based species delineation, and (ii) to assess the antiquity of the association between M. massiliense and Pyramidobacter piscolens in ancient and modern dental calculus. DESIGN:This fully in silico study combined comparative genomics with re-analysis of 97 ancient and modern dental calculus metagenomic datasets. Species-level relationships were assessed using average nucleotide identity, digital DNA-DNA hybridization, and 16S rRNA phylogeny. Metagenomic associations were examined using Kraken2-based taxonomic profiling, with Methanobrevibacter sp. YE315 as a proxy because M. massiliense was absent from the classifier database, and direct competitive read mapping to M. massiliense. Associations with P. piscolens were evaluated using Spearman correlation and negative binomial regression. RESULTS:Comparative genomics supported TS-2 and M. massiliense as the same species-level taxon, with > 95% average nucleotide identity and > 90% digital DNA-DNA hybridization. In metagenomic analyses, the YE315 proxy was positively associated with P. piscolens in Kraken2 Spearman analysis (ρ = 0.3506, q = 0.0026), and mapped M. massiliense reproduced this pattern (ρ = 0.2939, q = 0.0153). Negative binomial models showed concordant but weaker support, whereas the signal for M. oralis was less consistent. CONCLUSION:These results identify M. massiliense as the cultivated representative of TS-2 and support an ancient, recurrent association between M. massiliense and P. piscolens in dental calculus.

To compare the repertoire of anti-beta-Coronavirus antibodies detected in dental pulp samples (systemic immunity) collected from individuals from the early 19th century previously investigated for dental calculus (local immunity) serological response, We investigated 10 dental pulp samples collected from 10 individuals excavated from a 1810-1813 military site in Charleville-Mézières, France. The samples had previously been investigated for dental calculus serology. Dental pulp serology performed under a mini-blot format, incorporated one positive and one negative control, and conjugated antibodies against the five classes of immunoglobulins. Dental pulp IgE serological response reliability was assessed by in silico analyses. Controls yielded expected results. Anti-Coronavirus antibodies were detected in three individuals, comprising anti-beta Coronavirus IgE in three individuals, IgG in two individuals, and IgA in one individual. IgA and IgG anti-alpha Coronavirus were each detected in one individual. These results agreed with those previously obtained from the same 10 individuals with anti-beta-Coronavirus pooled IgG/IgA/IgM dental calculus paleoserology. Dental pulp paleoserology confirmed Coronavirus exposure in three individuals from the start of the 19th century in France. Translating these data into the modern medical literature, we propose that two centuries ago, some individuals suffered a yet unidentified beta-Coronavirus infection.

Evolving genomic diversity of Mycobacterium tuberculosis complex pathogens is poorly known in French Polynesia, a remote archipelago in the southern Pacific Ocean. A total of 321 mycobacteria sampled from 321 patients presenting pulmonary tuberculosis between 1998 and 2010 at the microbiology laboratory of the French Polynesia Hospital Centre in Tahiti were whole genome sequenced (WGS), disclosing three major M. tuberculosis sensu stricto sublineages: L4.4.1.1 S-type, L4.1.1.3 X-Type, and L4.1.2.1 Haarlem. Furthermore, 20 isolates were identified as nontuberculous mycobacteria, including Mycobacterium fortuitum, which accounted for 65% of the identified nontuberculous mycobacteria, as well as Mycobacterium paragordonae and Mycobacterium gordonae identified with M. tuberculosis in two samples. Two further isolates were potentially representative of novel species in the Mycobacterium and Actinomadura genera. In total, 43 isolates exhibited in silico predicted antibiotic resistance to first- and second-line antibiotics. Combined with previously published data, the data reported here indicate a 12-year trend of decreasing diversity among the M. tuberculosis population circulating in Tahiti and the seemingly unsuccessful implantation of a recently imported of East African-Indian sublineage (L1.2.1.2.1). These findings contrast with the long-term persistence and predominance of the X-type family with L4.1.1.3; the S-type family with L4.4.1.1 and L4.4.2; the Haarlem family with L4.1.2 and L4.1.2.1, and the LAM family with L4.3.3, L4.3.2, and L4.3.4.2. These observations suggest that in remote territories such as the French Polynesia archipelago M. tuberculosis may rapidly adapt to local ecosystems.

We aimed to assess the reliability of a screening questionnaire for Active Pulmonary Tuberculosis (APTB) in a population of sheltered homeless persons (HP). Participants from two homeless shelters completed a questionnaire specially designed to identify patients at high-risk of APTB (available at www.tb-screen.ch), underwent a Chest X-ray (CXR), and provided sputum samples. Computed Tomography (CT) scanning was subsequently performed on those which had images consistent with APTB. Microscopical examination, real-time polymerase chain reaction (qPCR) and culture testing were applied for Mycobacterium tuberculosis complex detection. Additionally, we retrospectively selected 16 HP hospitalised in our hospital between 2017 and 2019 with biologically confirmed tuberculosis and typical CXR images, and retrospectively documented a screening questionnaire by reviewing their medical files. Overall, the population (n = 383 HP) was predominantly migrants (87%). Forty-seven individuals (11.7%) had positive screening questionnaire scores and four (2.4%) displayed abnormal CXR features consistent with APTB. Three of them three underwent CT scanning that ruled out APTB and one was lost to follow-up. None tested positive through microbiological investigation. Fifteen (of 16, 93.8%) hospitalised patients with biologically confirmed APTB had a positive screening questionnaire score. The sensitivity and specificity of questionnaire for confirmed APTB were 93.8% and 87.7%, respectively. Screening questionnaires can be used as a first assessment tool in people arriving at homeless shelters and to refer those screening positive for a CXR.

The capacity of the 49 sub-Saharan African countries, which account for 85% of tuberculosis cases in Africa (WHO, 2025), to monitor the genomic dynamics of Mycobacterium tuberculosis complex strains responsible for the disease was examined for the period 2000-2025. A total of 8141 GenBank entries, supplemented by 163 as yet unreported whole genome sequences prepared at the Institut Hospitalier-Universitaire, Marseille, France and the Institut de Recherche en Santé, de Surveillance Épidémiologique et de Formation, Dakar, Sénégal were analysed using TB-Profiler. M. tuberculosis sub-lineage L2.2.1 dominated the sub-continent, while other lineages and sub-lineages featured a discrete pattern of geographical distribution, here illustrated by interactive maps. Although three-quarters of the genomes showed a predicted antibiotic-susceptibility, the predicted resistant recovered in 80% countries largely comprised multidrug-resistant (MDR) genomes (12.19% of genomes), followed by Rifampicin-susceptible, isoniazid-resistant (HR-TB) genomes (4.47%), Rifampicin-resistant TB (RR-TB) genomes (3.31%), extensively drug-resistant (XDR) genomes (1.78%), and pre-XDR genomes (0.64%). Resistance to second-line antibiotics was observed with prevalence lower than that of first-line drugs. This review gives an updated, accurate, and interactive overview of tuberculosis in sub-Saharan Africa and provides a strong basis for following the current evolution of tuberculosis in African regions.

Background: Closely related bacterial pathogens, Yersinia pseudotuberculosis, Yersinia pestis (the plague agent), and Yersinia enterocolitica, reside in environmental ecosystems that may be the source of infection for animals and humans. Reliable field-deployable detection methods are essential for monitoring these pathogens in natural ecosystems. Methods: A colorimetric loop-mediated isothermal amplification (LAMP) assay targeting the mglB gene (shared by Y. pseudotuberculosis and Y. pestis) and the chbG gene (specific to Y. enterocolitica) was developed. Specificity was evaluated using six Yersinia isolates, and sensitivity was determined from serial dilutions of Y. enterocolitica and Y. pseudotuberculosis cultures. The optimized LAMP assays were then applied to 28 environmental samples collected from two plague-endemic regions and one plague-free region in Algeria, and results were compared with those obtained using conventional PCR. Results: No Yersinia species were detected in any environmental samples by either LAMP or PCR. However, both assays successfully detected 1.5 × 108 CFU/mL of Y. pseudotuberculosis or Y. enterocolitica when samples were artificially spiked, confirming that no environmental inhibitors interfered with detection. Conclusion: The reported LAMP assays show characteristics that make them well suited for field deployment in the environmental monitoring of Yersinia species of medical and veterinary importance.

Clostridium tetani (C. tetani) bacteraemia is a rare situation, with only four case reports in the literature. Fourteen teeth from the 1590 plague site in Fédons, France, were surface decontaminated before the pulp was cultured under strict anaerobiosis with negative controls. Colonies were identified by mass spectrometry and whole genome sequencing, and C. tetani-specific PCR was performed using DNA extracted from dental pulps, calculus and sediments. C. tetani cultured in two dental pulp specimens from two individuals was firmly identified by MALDI-TOF mass spectrometry, and whole genome sequencing confirmed toxigenic C. tetani. In the remaining twelve individuals, no such C. tetani was recovered and further detection by PCR and palaeoculturomics of dental calculus and sediments surrounding the teeth in these two individuals remained negative. Toxigenic C. tetani which did not result from mere environmental contamination, caused bacteraemia in two individuals from a modern time plague site in France.

Six camels exhumed from a 17th-century Silk Route site in Romania, along with negative controls, were blindly investigated via dental pulp paleometagenomics and paleoproteomics for traces of Yersinia pseudotuberculosis complex including the plague agent Yersinia pestis. Specific reads were detected in sample R04 (one read) and R05 (two reads) which also yielded a 16S rRNA guanine transferase specific for Y. pestis and one other Y. pseudotuberculosis complex peptide. Taken together, these validated data diagnosed plague in these ancient camels which likely participated in plague dissemination along ancient Silk Routes during the large Medieval and Modern Times pandemic in Europe.

Diagnosis of ancient infectious diseases has seen remarkable advances, contributing significantly to understanding historical health challenges and shaping medical research. This review explores the evolution of diagnostic methods and features emerging diagnostic techniques. The early detection of ancient infectious diseases primarily relied on observational evidence, skeletal remains, and historical records. Notable outbreaks such as the Black Death in the 14th century and smallpox epidemics, have left historical imprints. Pioneering diagnostic methods included the paleopathological analysis of the remains of bones and tissue lesions. Later, microbiology methods were adapted to ancient materials, including molecular and serological techniques such as PCR, serology and immunodetection, which were employed to detect DNA or antibodies from ancient pathogens under the name of the paleomicrobiology approach. This emerged as a distinct field, making it possible to isolate and identify ancient pathogens from preserved samples. Advances in next generation sequencing are now revolutionising the diagnosis of ancient diseases, enabling the retrieval of ancient pathogen genomes from well-preserved samples such as dental pulp, tartar, bone and mummified tissues, helping understand disease evolution and transmission patterns. Ongoing improvements in DNA sequencing and metagenomics will enhance the accuracy and scope of the diagnosis of ancient diseases. Collaboration between archaeologists, historians, paleomicrobiologists, geneticists and epidemiologists will drive further breakthroughs. Advances in paleocytology, metagenomic analysis, including non-invasive techniques, such as mass spectrometry, may offer new avenues for identifying ancient pathogens. Current technologies and interdisciplinary collaboration hold promise for uncovering even more insights from the past and potentially informing future disease prevention strategies.

The Journal of Clinical Medicine Editorial Office retracts the article, “Rapid Isothermal Amplification for the Buccal Detection SARS-CoV-2 in the Context of Out-Patient COVID-19 Screening” [...]

Methanobrevibacter smithii (M. smithii), the predominant methanogen in the human digestive tract, plays a key role in methane production. Despite its importance, the genomic diversity of M. smithii is poorly characterised, especially in extra-digestive sites such as the urinary and respiratory tracts, and the blood. Understanding this diversity would help unravel its potential role in human health and diseases. We report the genome of M. smithii strain U29, isolated from urine, expanding the known diversity of the species. The M. smithii U29 genome (scaffold level; 1̵822‒124-bp, 1745 protein-coding sequences) lacks Candidatus Nanopusillus sequences, unlike digestive tract strains. Comparative analysis has revealed a high similarity (99.86

The genus Borrelia has been divided into Borreliella spp., which can cause Lyme Disease (LD), and Borrelia spp., which can cause Relapsing Fever (RF). The distribution of genus Borrelia has broadened due to factors such as climate change, alterations in land use, and enhanced human and animal mobility. Consequently, there is an increasing necessity for a One Health strategy to identify the key components in the Borrelia transmission cycle by monitoring the human-animal-environment interactions. The aim of this study is to summarize all accessible data to increase our understanding and provide a comprehensive overview of Borrelia distribution in the Mediterranean region. Databases including PubMed, Google Scholar, and Google were searched to determine the presence of Borreliella and Borrelia spp. in vectors, animals, and humans in countries around the Mediterranean Sea. A total of 3026 were identified and screened and after exclusion of papers that did not fulfill the including criteria, 429 were used. After examination of the available literature, it was revealed that various species associated with LD and RF are prevalent in vectors, animals, and humans in Mediterranean countries and should be monitored in order to effectively manage and prevent potential infections.

Background Tuberculosis is a pressing public health issue in Lebanon, a country of approximately five million people, including around 1.5 million refugees from Palestine and Syria. Prior research has revealed uncontrolled animal sources of Mycobacterium bovis , emphasizing the necessity for a comprehensive approach to combat tuberculosis in the region. Methods 48 clinical Mycobacterium tuberculosis complex isolates were identified through whole genome sequence. Also, 43 animal fecal samples were collected from various farms across Lebanon to investigate the presence of the M. tuberculosis complex using CRISPR-csm4 PCR. Results Genomic analysis revealed that 39/48 (81.25%) of isolates were M. tuberculosis and 9/48 (18.75%) were M. bovis. M. tuberculosis was distributed over four lineages, Indo-Oceanic L1 (n = 3/39)(7.6%), East-Asian L2 (n = 1/39)(2.5%), East-African Indian L3 (n = 5/39)(12.8%) and Euro-American L4 (n = 30/39)(76.9%). Sub-lineage L4.8 (Euro-American (mainly T), comprising 8/39 of the isolates (20.5%) was predominant, followed by sub-lineages L3 (East-African Indian, n = 5/39 isolates)(12.8%), L4.2.2.2 (Euro-American (Ural), n= 4/39 isolates)(10.2%) and L4.6.5 (Euro American, n=4/39 isolates)(10.2%). Nine M. bovis were classified into two clades, designated as unknown2 (n=2/9; 22.2%) and unknown3 (n=7/9; 77.8%). Interestingly, none of the clades or others were detected in the 48 faecal samples using CRISPR standard PCR and qPCR. Conclusions This study offers insights into human and bovine tuberculosis in Lebanon, emphasizing M. tuberculosis lineages prevalence and M. bovis distribution into two clades, aiding the fight against tuberculosis, especially bovine tuberculosis, and renewing our understanding of tuberculosis dynamics in Lebanon. ### Competing Interest Statement The authors have declared no competing interest.

To further assess the spectrum of nanoarchaea in human microbiota, we prospectively searched for nanoarchaea in 110 leftover stool specimens, using the complementary approaches of PCR-sequencing screening, fluorescent in situ hybridization, scanning electron microscopy and metagenomics. These investigations yielded a nanoarchaea, Candidatus Nanopusillus phoceensis sp. nov., detected in stool samples by specific PCR-based assays. Microscopic observations indicated its close contact with the archaea Methanobrevibacter smithii. Genomic sequencing revealed 607,775-bp contig with 24.5% G + C content encoding 30 tRNAs, 3 rRNA genes, and 1,403 coding DNA sequences, of which 719 were assigned to clusters of orthologous groups. Ca. Nanopusillus phoceensis is only the second nanoarchaea to be detected in humans, expanding our knowledge of the repertoire of nanoarchaea associated with the human microbiota and encouraging further research to explore the repertoire of this emerging group of nanomicrobes in clinical samples.