SEARCH · Search PubMed

Results for “local transmission”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

SourceResearch connectionFrom yearThrough year

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 19 recordsLinked to original sources

PubMed2026

Genomic Epidemiology and Clinical Characteristics of Mpox Lineage C.1 Outbreak in Thailand, 2023-2024.

Since 2022, human monkeypox virus (hMPXV) has emerged in non-endemic regions, including Thailand. However, the genomic dynamics and clinical correlates of local transmission remain incompletely defined. Whole-genome sequencing was performed on hMPXV from 16 patients in Thailand (2023-2024) using targeted amplicon NGS. Phylogenetic analyses integrated global reference sequences. Mutational profiles, specifically non-synonymous substitutions and APOBEC3-associated signatures, were analyzed in relation to clinical data. Phylogenetic reconstruction identified three temporal phases. Early 2022 cases (clade IIb lineages A and B) were interspersed with global sequences, consistent with multiple introductions. In contrast, 2023-2024 cases were dominated by lineage C.1. All 16 genomes belonged to C.1 (one C.1.1), and formed a distinct mid-2023 cluster, designated C.1/Thai/Cluster, supporting sustained local transmission. APOBEC3-associated mutations were pervasive across the C.1 lineage overall, including within C.1/Thai/Cluster, without evidence of significant enrichment specific to this cluster. The cohort comprised exclusively male patients (81% HIV-positive, MSM), with predominantly genital painful lesions and a median recovery time of 23 days. No significant associations were detected between viral genetic variation and clinical outcomes. Mpox transmission in Thailand evolved from multiple introductions to sustained C.1-dominated local spread, underscoring the importance of continued genomic surveillance.

Humans↗

PubMed1978

Graded synaptic transmission between local interneurones and motor neurones in the metathoracic ganglion of the locust.

1. In the metathoracic ganglion of the locust some neurones can effect changes in the membrane potential of identified post-synaptic motor neurones without themselves spiking. 2. These 'non-spiking' neurones have processes only within the metathoracic ganglion, and therefore are local intraganglionic interneurones. 3. The absence of spikes in the interneurones reflects their normal physiological state and is not due to the experimental conditions. 4. When the interneurones are depolarized by the injection of current pulses lasting several hundred milliseconds, post-synaptic motor neurones are either depolarized, or hyperpolarized, for the duration of the pulse. 5. The magnitude of the change in post-synaptic voltage is graded according to the amount of presynaptic current. 6. A number of physiological tests indicate that the graded effects upon motor neurones are mediated by chemical synaptic transmission. For example, an evoked hyperpolarization of a motor neurone can be reversed in polarity by simultaneously hyperpolarizing the motor neurone with injected current. 7. At their resting potential some interneurones tonically release sufficient transmitter to have a measurable post-synaptic effect. The injection of depolarizing and hyperpolarizing currents into these interneurones effects opposite changes in post-synaptic potential. 8. Other interneurones must be depolarized from resting potential before a post-synaptic effect is observed, and hyperpolarizing currents have no post-synaptic effect. In these interneurones it is estimated that a depolarization of only 2 mV is sufficient to effect the release of transmitter. 9. The membrane potentials of non-spiking interneurones can fluctuate by as much as 15 mV during active movements of the hind legs and individual p.s.p.s as large as 5 mV can be recorded. Therefore, summed p.s.p.s or even single ones are expected to be the electrophysiological signals effecting transmitter release from these interneurones.

Action Potentials↗

PubMed1976

Facilitation of adrenergic transmission by locally generated angiotensin II in rat mesenteric arteries.

When studied on isolated rat mesenteric arteries perfused with Tyrode's solution, angiotensin I and angiotensin II (1 ng/ml), a synthetic tetradecapeptide renin substrate, and a purified hog renin substance (50-100 ng/ml) potentiated vasoconstrictor responses to sympathetic nerve stimulation and to injected norepinephrine without altering basal pressure. These agents produced a greater augmentation of the vasoconstrictor responses to nerve stimulation than to injected norepinephrine. The potentiation of vasoconstrictor responses to sympathetic nerve stimulation and injected norepinephrine which was elicited by renin substrate and angiotensin I was abolished by an inhibitor of angiotensin I-converting enzyme, SQ 20,881, and by an angiotensin II receptor antagonist, [Sar1-Ile8]angiotensin II. In contrast, the potentiating effect of angiotensin II was blocked only by the latter compound. We conclude that utilization of renin substrate within the vascular wall by renin or renin-like enzymes results in the formation of angiotensin I, which is converted to angiotensin II. Angiotensin in turn potentiates the vasoconstrictor responses to adrenergic stimuli presumably by augmenting release of the adrenergic transmitter and inhibiting its neuronal reuptake as well as by increasing vascular reactivity to norepinephrine.

Angiotensin II↗

PubMed1976

Cariogenic flora: establishment, localization, and transmission.

The foregoing is a review of current information on various aspects of the development of the cariogenic flora and it illustrates some of the complexities involved. The multifactorial nature of dental caries makes it necessary to look at this disease in a special way. Etiologic forces represented by a complex bacterial flora and a variable dietary influence are in competition with resistance factors of the host, which include the immune system. This creates a situation where it is difficult to segregate individual aspects of the disease for study. One approach is to design study models that emphasize the factor under investigation in relation to other contributing factors. For example the currently used animal caries test models are deliberately exaggerated in terms of the cariogenic challenge applied. Very young animals are continuously exposed to a high sucrose diet and are infected with a high dosage of cariogenic organisms. The clinical counterpart of this model should use subjects with high caries activity, because it is reasonable to assume that etiologic factors are exaggerated in human populations where the disease is rampant. However, if the purpose is to study resistance factors such as immunity, it may be more profitable to investigate their influence in either animal or human models where the cariogenic challenge is reduced. This, in effect, proportionally increases the influence of a comparatively subtle factor such as immunity. Davies has made a similar point in relation to the influence of hereditary factors in dental caries. He states the belief that regions of low caries prevalence would be the most promising for epidemiological investigation of resistance factors. Investigations into the role of immunity in dental caries have not been too productive in the past. However, it now is possible to focus on selected target organisms and to apply recently acquired information about the immune system operating in the oral cavity. Detailed knowledge of the origins and development of the cariogenic flora and the mechanisms by which it is maintained in individuals and in populations should permit a rational attack on the problem.

Age Factors↗

PubMed2026

Genomic surveillance of enterovirus D68 circulating in 2025 reveals the emergence of a novel A2/B3 recombinant lineage.

Enterovirus D68 (EV-D68) has re-emerged over the past decade as a significant respiratory pathogen associated with severe respiratory disease and acute flaccid myelitis. Its circulation has typically followed a biennial pattern, with predominance in late summer and early fall, a pattern that was temporarily disrupted during the COVID-19 pandemic. Surveillance in 2025 revealed off-season circulation of EV-D68. This study describes the genomic characteristics of the 2025 EV-D68 viruses and the clinical features of affected patients. Between May and December 2025, remnant respiratory specimens positive for rhinovirus/enterovirus were screened for EV-D68 and subjected to whole-genome sequencing. Phylogenetic analyses were performed using maximum-likelihood methods. Recombination was assessed using subgenomic phylogenies, SimPlot similarity and BootScan analyses, and read-level inspection. Among 1,321 patients tested, 147 (11.1%) were EV-D68-positive, and 119 (81.0%) yielded complete genomes. EV-D68 positivity increased in July 2025, peaked in August (~21%), and remained elevated through September and October, exceeding levels observed in 2024. Patients had a median age of 36 years, with infections disproportionately affecting older adults. Phylogenetic analysis demonstrated exclusive circulation of subclade A2. Five genomes formed a distinct recombinant lineage (A2-Re). Subgenomic phylogenies showed clustering with A2 viruses in the P1 region and with B3 viruses in the P2-P3 regions. SimPlot and BootScan analyses identified a recombination breakpoint near the 2A/2B junction (~nt 3,700). The recombinant lineage was associated with temporally clustered cases in September-October. These findings demonstrate recombination between distinct EV-D68 subclades and underscore the importance of whole-genome surveillance for accurate viral characterization. Continued genomic monitoring is essential for detecting emerging variants with potential implications for transmissibility, pathogenicity, and public health preparedness.IMPORTANCEThis study highlights an increased off-season circulation of Enterovirus D68 (EV-D68) and a higher burden of disease in adults in 2025. The identification of a novel A2-B3 recombinant lineage provides evidence of ongoing viral evolution through recombination, a mechanism that may alter transmissibility, virulence, or immune responses. Detection of this lineage in temporally clustered cases suggests local transmission and underscores the potential for rapid spread of newly emerged variants. These findings emphasize the limitations of partial genomic approaches and the critical role of whole-genome sequencing in accurately characterizing circulating strains and identifying recombination events. Enhanced genomic surveillance is essential to detect emerging variants in real time, inform diagnostic assay performance, and support public health responses. Continued monitoring of EV-D68 evolution will be important for anticipating changes in disease burden, guiding clinical awareness, and strengthening preparedness for future outbreaks.

Humans↗

PubMed2024

Expansion of Oropouche virus in non-endemic Brazilian regions: analysis of genomic characterisation and ecological drivers.

BACKGROUND: Oropouche virus (OROV) is an arbovirus endemic in the Amazon region that closely resembles other arboviruses in terms of human disease, leading to potential misdiagnoses. The virus ecology has mostly restricted its occurrence to the Amazon biome; however, after a large 2023-24 OROV epidemic in the Brazilian Amazon region, outbreaks are being reported across Brazil and in other countries in Latin America. Here, we investigate the OROV spread outside Amazonia. METHODS: In this genomic and epidemiological study, OROV cases from January, 2023, to July, 2024, provided by the General Coordination of Public Health Laboratories of Brazil on Aug 1, 2024, were compared by geographical location (Amazon vs non-Amazon) and municipal population size, and a linear mixed model was employed to assess the relationship between agricultural area size and cases. OROV-positive samples from central laboratories of five non-Amazonian Brazilian states were sequenced using an amplicon-based approach. Bayesian phylogeographical analysis was performed with near full-length viral genomes, incorporating individual travel histories when relevant. The estimated dates of viral introductions in each sampled location were then contextualised with public epidemiological data. FINDINGS: Epidemic data show that outside the Amazon region, OROV cases frequency was 3·9-times higher in small municipalities than in large municipalities. The planted areas of some agricultural products, such as banana plantations, were positively correlated (r=0·39, p<0·0001) with OROV cases. The linear mixed model revealed that, besides banana, cassava also has larger (p<0·05) planted areas in municipalities with OROV cases when compared with those with no cases. The phylogenetic analysis of 32 new OROV genomes reconstructed multiple exportation events of the newly identified reassortant lineage from the Amazon to other Brazilian regions between January and March, 2024. At least three of the previously described OROV phylogenetic clades circulating in the Amazon were the source of viral introductions. Molecular clock analysis estimated that viral introductions happened from 50 days to 100 days before detecting the outbreaks in each state. INTERPRETATION: Our results confirm that the novel OROV reassortant lineage spread from the Amazon to other regions in early 2024, successfully establishing local transmission. The fact that outbreaks were observed in small municipalities, instead of large urban centres, suggests that local ecological conditions that are ideal for OROV vector occurrence, such as the banana plantation environment, might be important factors driving its spread in Brazil. FUNDING: DECIT, CNPq, FAPEAM, and Inova-Fiocruz. TRANSLATION: For the Portuguese translation of the abstract see Supplementary Materials section.

Brazil↗

PubMed2026

Detection and genomic characterization of a travel-associated ECSA lineage chikungunya virus infection in Mexico.

BACKGROUND: In 2013, chikungunya virus (CHIKV), a re-emerging Aedes-borne virus, was introduced into the Americas. This led to synchronous epidemics across the region associated mainly with the Asian lineage, which eventually subsided. Resurgent outbreaks have been recorded since, principally in South America, largely driven by the East-Central-South-African (ECSA) lineage. In 2025, more than 300,000 CHIKV suspected cases were reported in Brazil and Cuba. CASE SUMMARY: In November 2025, a healthy adult male traveling from Cuba arrived in Merida, Mexico, and shortly after presented febrile symptoms consistent with an arboviral infection. CHIKV infection was diagnosed by RT-qPCR. Though the infection was mild, the patient developed a rash on the abdomen and neck that persisted for up to a month, with further inflammation of the joints of the left leg. Phylogenetic analysis of the viral genome indicated placement within the ECSA lineage, clustering with other contemporaneous virus genomes sampled from Brazil that belong to a recently described clade II within the country, in which viral genomes from Cuba also cluster. CONCLUSION: We identify a travel-associated ECSA lineage CHIKV case in Mexico. This viral lineage has not previously been detected in the country. This finding highlights the risk for subsequent local transmission and is consistent with reports of the presence of this lineage in Cuba. Ten years since the last CHIKV epidemic in Mexico, strengthened surveillance is required to anticipate potential local outbreaks within the region.

ECSA↗

PubMed2025

VANTAGE: van-based real-time HIV sequencing for transmission mapping and drug resistance profiling in war-affected Ukraine.

We deployed the VANTAGE (VAN for Transmissible Agent Genomic Epidemiology) mobile system in Lviv, Ukraine, demonstrating end-to-end sequencing of dried blood spot samples within a clinic van usually serving de-occupied and frontline regions. HIV-1 pol sequences were obtained from 50% of samples, all subtype A6. Median time to 100× coverage was 38 min. Phylogenetic analysis revealed a local transmission cluster including a displaced person and the non-nucleoside reverse transcriptase inhibitor (NNRTI) resistance mutation E138A, supporting real-time HIV genomic surveillance in humanitarian crises.

Humans↗

PubMed2026

Genomic insights into low-level rifampicin resistance mediated by borderline rpoB mutations in Mycobacterium tuberculosis: prevalence and phylogeny in Northeast China.

The emergence of low-level rifampicin (RIF) resistance in Mycobacterium tuberculosis poses a challenge to tuberculosis (TB) control, as it often leads to discordance between genotypic resistance detected by molecular assays (e.g., Xpert MTB/RIF) and phenotypic susceptibility in conventional drug susceptibility testing (DST). In this study, we performed whole-genome sequencing (WGS) on 17 clinical isolates from Changchun, Northeast China, which exhibited such discordance. All isolates harbored functional borderline mutations in the rpoB RRDR region, predominantly Leu452Pro and Leu430Pro (29% each), followed by His445Asn (18%). RIF minimum inhibitory concentration (MIC) values ranged from ≤0.25 to 1.0 mg/L, confirming low-level resistance. Notably, 53% (9/17) of the isolates were co-resistant to fluoroquinolones and 24% (4/17) to isoniazid (INH). According to WHO classification, 59% (10/17) were pre-extensively drug-resistant TB (Pre-XDR-TB) or multidrug-resistant TB (MDR-TB). Phylogenetic analysis revealed that 94% (16/17) belonged to the East Asian Beijing lineage (Lineage 2.2.1), with no evidence of recent local transmission. These findings underscore the complexity of low-level RIF resistance and its frequent association with broader drug resistance in a dominant lineage, highlighting the need for integrating MIC and WGS into diagnostic algorithms to guide appropriate treatment and surveillance.IMPORTANCEThe accurate detection of RIF resistance is critical for the management of TB, yet standard phenotypic methods often fail to identify strains with low-level resistance conferred by borderline rpoB mutations. This study provides the first genomic characterization of such discordant isolates in Northeast China, revealing a high prevalence of co-resistance to other key drugs and a strong association with the locally dominant Beijing lineage. The findings emphasize that reliance on phenotypic DST alone may lead to underestimation of drug resistance and inappropriate treatment, potentially contributing to the emergence and spread of Pre-XDR-TB and MDR-TB. Incorporating MIC determination and WGS into routine diagnostics could enhance detection, inform tailored therapy, and improve surveillance of these clinically significant strains.

Mycobacterium tuberculosis↗

PubMed2026

A new highly discriminatory typing scheme for Treponema pallidum reveals similar levels of genetic variability across lineages.

UNLABELLED: The global resurgence of treponematoses, particularly syphilis, poses a growing public health challenge. Despite advances in sequencing technologies, obtaining complete Treponema pallidum genome sequences for epidemiological studies remains challenging due to clinical sampling and methodological constraints. There is, therefore, a need for rapid, cost-effective, and accessible typing methods. Based on the analysis of 121 T. pallidum genomes spanning all three subspecies (TPA, TPE, and TEN) from diverse regions, we selected seven highly variable genes (tp0136, tp0326, tp0548, tp0705, tp0858, tp0865, and tp1031) to form a new typing system, combined with analysis of macrolide resistance mutations in the 23S rRNA gene. The scheme was validated on 542 global T. pallidum samples, using either Sanger reads or whole genome sequence data, obtaining 82 sequence types (STs) among the 415 fully typed samples. Macrolide resistance mutations were frequently detected, highlighting the need for ongoing epidemiological surveillance. Phylogenetic analyses based on concatenated multilocus typing (MLST) loci recovered the expected subspecies and lineage structure. Consistently, almost all sequence types formed monophyletic groups, indicating strong concordance between MLST-based classification and whole-genome phylogenies. In addition, population genetic analyses revealed comparable levels of within-lineage diversity across subspecies and lineages, despite pronounced differences in geographic distribution, and identified distinct regional genetic clusters consistent with localized transmission dynamics. Importantly, the scheme employs a single-step PCR for all seven targets, facilitating implementation in standard laboratories and is publicly accessible through PubMLST. Overall, our novel MLST scheme offers a rapid, cost-effective tool to advance molecular epidemiology of T. pallidum, facilitate transmission and resistance tracking, and support global surveillance to strengthen public health interventions for syphilis and endemic treponematoses control. IMPORTANCE: We have developed a new multilocus typing (MLST) scheme useful for all Treponema pallidum lineages after the analysis of 121 complete genome sequences of this species. The new scheme can be used directly with uncultured clinical samples, thus providing an excellent contribution to the molecular surveillance of syphilis and other treponematoses. The application of this MLST scheme to over 500 samples from all lineages and main geographical regions has revealed similar levels of genetic variation within them. Furthermore, the analyses show a complex pattern of spread, with global and local contributions to the observed distribution of genetic variation in the syphilis-producing sublineages. The new scheme represents a significant improvement over previous proposals and also reveals unsuspected levels of variability in T. pallidum lineages.

Treponema pallidum↗

PubMed2026

Uncovering the genomic landscape of Mycobacterium bovis in Wales.

Bovine tuberculosis (bTB), caused by the bacterium Mycobacterium bovis, is one of the most pressing animal health issues in Wales today. It negatively impacts cattle health, affects profitability and trade, and can decimate years of genetic improvement towards desirable production traits. It also imposes substantial financial, social, and psychological burdens on farming communities. Eradication of bTB requires an understanding of local transmission pathways to target effective disease-control interventions. In this study, we characterised the genomic diversity of M. bovis across Wales by analysing the genome sequence of 379 M. bovis isolates obtained from culture-positive animals in Wales in 2021. Analyses uncovered three prevalent clusters that are geographically distinct. A further three clusters containing fewer isolates were also geographically separated, two of which had particularly large SNP distances from most other Welsh isolates, suggesting independent introductions of M. bovis strains that are not endemic to Wales. Fine-scale and epidemiologically relevant genetic structuring was identified within the six main clusters, indicating region-specific evolution, which can drive local disease dynamics. Finally, SNPs were identified in coding genes that have the potential for important advantageous physiological consequences that may impact host-pathogen interactions and necessitate further investigation.

Animals↗

PubMed2025

Genetic analysis of Schistosoma mansoni in a low-transmission area in Brazil suggests population sharing between wild-hosts and humans and geographical isolation.

BACKGROUND: The fluke Schistosoma mansoni is the causative agent of intestinal schistosomiasis, a neglected tropical disease, and remains prevalent in certain regions of Brazil. In the municipality of Sumidouro, state of Rio de Janeiro, Brazil, a low-endemic area for S. mansoni, water rats (Nectomys squamipes) are naturally infected by this trematode. The S. mansoni populations infecting humans and water-rats in Sumidouro exhibit distinct patterns of cercarial emergence (chronotypes) and phenotypic differences between hosts. Previous studies have shown that the adaptation of S. mansoni populations to human hosts (diurnal chronotype) and water rats (nocturnal chronotype) could result in prezygotic isolation. To test this hypothesis, we employed the mitochondrial cytochrome c oxidase subunit 1 gene (MT-CO1) and microsatellite loci as genetic markers. PRINCIPAL FINDINGS: We assessed the population structure between the definitive host species and geographically distant isolates collected from two endemic localities (Pamparrão-PAM and Encanto-Soledade-ENC-SOL) in Sumidouro. Additionally, we evaluated the phylogenetic relationships between S. mansoni from Sumidouro and those from other countries. Five haplotypes of the MT-CO1 gene were identified, with haplotypes 3 and 4 exclusive to ENC-SOL, and haplotypes 1, 2, and 3 were shared between humans and water rats. Haplotype 1 was also shared with other Brazilian localities, South American countries and a single locality in West Africa. The remaining haplotypes were exclusive to Sumidouro, indicating local genetic diversity. Population structure analysis revealed no genetic differentiation associated with host species but rather geographical structuring, probably due to the sedentary habits of rodents and the limited movement of humans between localities. This finding indicates that S. mansoni populations with different chronotypes are not genetically isolated and that significant gene flow occurs between them. CONCLUSIONS: In conclusion, our findings confirm that wild rodents contribute to the maintenance of the S. mansoni life cycle in Sumidouro and can serve as indicators of local transmission hotspots.

Animals↗

PubMed2025

Characterizing the genetic diversity and population structure of Plasmodium knowlesi in Aceh Province, Indonesia.

As in other parts of Southeast Asia, efforts to achieve or sustain malaria elimination in Indonesia have been threatened by the emergence of human infection with the primate species P. knowlesi. To understand the transmission dynamics of this species, investigation of P. knowlesi genetic diversity and population structure is needed. A molecular surveillance study was conducted in two phases between June 2014 and September 2018 at five primary health facilities in Aceh Province, Indonesia, an area nearing malaria elimination. Dried blood spot samples were collected from patients presenting with suspected malaria and testing positive for malaria by microscopy. PCR was performed for molecular confirmation and species identification. Forty-six samples were confirmed to be P. knowlesi, of which 41 were amplified with genotyping targeting ten known P. knowlesi microsatellite markers. For samples within a site, nearly all (9 of 10 loci) or all loci were polymorphic. Across sites, multiple identical haplotypes were observed, though linkage distribution in the population was low (index of association (IAS) = 0.008). The parasite population was indicative of low diversity (expected heterozygosity [HE] =  0.63) and low complexity demonstrated by 92.7% monoclonal infections, a mean multiplicity of infection of 1.06, and a mean within-host infection fixation index (FST) of 0.05. Principal coordinate and neighbour-joining tree analyses indicated that P. knowlesi strains from Aceh were distinct from those reported in Malaysia. In a near-elimination setting in Indonesia, we demonstrate the first evidence that P. knowlesi strains were minimally diverse and were genetically distinct from Malaysian strains, suggesting highly localized transmission and limited connectivity to Malaysia. Ongoing genetic surveillance of P. knowlesi in Indonesia can inform tracking and planning of malaria control and elimination efforts.

Plasmodium knowlesi↗

PubMed2026

Molecular Epidemiology of Human Metapneumovirus in Kilifi, Coastal Kenya, 2016-2017 and 2021-2024.

BACKGROUND: Human metapneumovirus (hMPV) is a major contributor of acute respiratory infections (ARI) in childhood and vulnerable adults. It comprises two antigenically distinct lineages (A and B), with multiple sub-lineages. Genomic analyses of hMPV strains enable monitoring of viral evolution and transmission to inform future interventions but remain underutilized in Africa. METHODS: We generated 52 near-complete hMPV genomes from respiratory samples collected in Kilifi, Coastal Kenya, using a tiled-amplicon approach and Oxford Nanopore Technologies sequencing. These samples had been identified as hMPV positive by quantitative PCR during (a) a multi-facility outpatient ARI surveillance in nine health facilities in Kilifi between 2016 and 2017, and 2021 to 2023 and (b) a community-based respiratory infection cohort surveillance study between 2023-2024 that sampled enrolled participants irrespective of symptom status. RESULTS: Of the 192 positive samples analyzed from the two studies, children under 5 years accounted for most hMPV cases (134/186, 72%). 52 samples were sequenced (>70% genome coverage), and hMPV-A (27/52, 53.8%) and hMPV-B (25/52, 46.2%) lineages were identified. The recovered sequences mapped into sub-lineages A2c (27/52, 53.8%), B1 (12/52, 21.2%), and B2b (13/52, 25%). A shift in the predominant sub-lineage was observed from B2b (2016) to B1 (2021), and finally to A2c-wild type (2023). In February 2021, for the first time, we detected a single A2c strain with a 111-nucleotide duplication in the G gene among Kenyan samples. CONCLUSION: Our study expands the global nucleotide sequence database for hMPV by adding new whole-genome sequences from Kenya collected over the last decade. It highlights the ongoing replacement of locally predominant hMPV lineages and the importation and local transmission of globally circulating strains. These findings underscore the importance of sustained hMPV genomic surveillance to detect emerging variants and monitor lineage circulation patterns that may impact viral transmission, molecular detection, and future control measures.

A2c-111nt-dup↗

PubMed2026

Early use of genomics to guide acquisition investigation of Salmonella Typhi.

BACKGROUND: As most Salmonella Typhi (S. Typhi) cases notified to public health units in Australia are acquired overseas, a case without recent travel raises concerns of local transmission. We describe a case of S. Typhi in a hospital inpatient without recent travel, where early use of genomic sequencing suggested remote acquisition from Chile in the 1980s, with chronic asymptomatic carriage. This facilitated the stand-down of a complex acquisition investigation. CASE: A notification of S. Typhi on stool culture was received for a female aged over 90 years living in Melbourne, Australia in October 2023. She had been hospitalised for three weeks (unrelated illness) and transferred into a residential aged care facility (RACF) six days prior to the result being known. She was asymptomatic and the sample was collected due to a recent ward gastroenteritis outbreak. INVESTIGATION: Epidemiological investigation identified the case had emigrated to Australia in 1981 from Chile. Recent typhoid-like illness, overseas travel or contact with travellers from endemic areas were excluded. Subsequent genomic sequencing identified the isolate was multilocus sequence type 2 and did not cluster with any strains isolated in Victorian or international databases, most closely clustering with historical South American strains, with potential in-host changes over time. MANAGEMENT: The case was presumed infectious throughout their hospital stay, with chronic carriage. There were 18 contacts, of whom 14 provided screening samples and were negative. Antibiotic case clearance was not recommended by the treating clinician due to patient comorbidity, treatment toxicity risks and unlikely treatment success without gallbladder removal. Enhanced infection control measures were instituted in the RACF (e.g. private bathroom, contact precautions for personal care, no food preparation). No additional cases were reported after two incubation periods (60 days). CONCLUSION: Early genomic sequencing enhanced the efficiency of the public health investigation by rapidly confirming overseas acquisition and chronic carriage, obviating the need for extensive local upstream investigation.

Humans↗

PubMed2025

Oropouche Virus Importation in Southern Brazil and Emerging Concern Calling for Enhanced Public Health Surveillance.

Oropouche virus (OROV), an arthropod-borne virus transmitted by Culicoides paraensis, is an endemic arbovirus that historically circulates mostly in the Amazon basin. Between 2022 and 2024, it reemerged as a more widespread public health concern in South America. We conducted a pooled-sample molecular surveillance study to understand the prevalence of Oropouche fever in Brazil's southernmost state. Over 18 months, we analyzed 4060 samples to monitor the virus emergence in the Rio Grande do Sul state. We detected the first human case of OROV in the state, and our phylogenetic reconstruction indicated a travel-related introduction from the Amazon region into Rio Grande do Sul. Despite the absence of local transmission, the invasion of Culicoides paraensis and enzootic circulation of the OROV in Rio Grande do Sul highlight the risk of Oropouche fever outbreaks in the region. We demonstrated that pooled-sample surveillance effectively monitors virus introduction during periods of low endemic circulation, serving as an essential active surveillance tool for the timely detection of virus emergence and enhancing public health preparedness. The multiple introductions of distinct OROV lineages into southern Brazil underscore the importance of genomic surveillance and public health strategies to monitor and mitigate arbovirus spread in the region.

Brazil↗

PubMed2026

Temporal shifts in K-locus composition and expansion of dual-carbapenemase-producing ST11-KL62 Klebsiella pneumoniae: a retrospective genomic surveillance study.

OBJECTIVES: To characterize longitudinal changes in carbapenem-resistant Klebsiella pneumoniae (CRKP) and investigate the recent increase in dual-carbapenemase-producing ST11-KL62 isolates. METHODS: We retrospectively analysed 1,239 non-duplicate CRKP isolates recovered at a tertiary hospital in China during 2018-2025. Antimicrobial susceptibility testing, whole-genome sequencing, K-locus and resistance/virulence gene profiling, core-genome single-nucleotide polymorphism analysis, reference-guided plasmid comparison, conjugation and stability assays, and a murine lethality model were used. RESULTS: ST11 accounted for 936/1,239 isolates (75.5%). KL47 declined from 39/151 (25.8%) in 2018-2019 to 45/755 (6.0%) in 2024-2025, whereas KL62 increased from 3/151 (2.0%) to 147/755 (19.5%). Among 148 ST11-KL62 isolates, 13/148 (8.8%) co-harboured blaKPC-2 and blaNDM-1, of which 12/13 (92.3%) met the study's molecular definition of hypervirulent CRKP. Pairwise single-nucleotide polymorphism distances among local ST11-KL62 isolates ranged from 0 to 43 (median, 14), suggesting that clonal expansion may have contributed to their increase. Complete genome analysis of ZD872 located blaKPC-2, blaNDM-1, and major virulence-associated genes on distinct plasmids; related plasmid backbones were predicted in other isolates using short-read comparisons. ZD872 exhibited a hypervirulent phenotype in the murine model. CONCLUSIONS: The ST11 CRKP population underwent temporal shifts in K-locus composition, including expansion of a closely related ST11-KL62 subset carrying dual carbapenemases and hypervirulence-associated markers. These findings support integrating longitudinal genomic surveillance with local transmission analysis.

Carbapenem-resistant Klebsiella pneumoniae↗

PubMed2026

Epidemiological and phylogenetic analysis of anthrax in Kazakhstan in 2024.

BACKGROUND: Anthrax remains an important zoonotic disease in Kazakhstan due to the persistence of environmental reservoirs and long-standing endemic foci. Despite ongoing surveillance, the epidemiological characteristics and genetic diversity of circulating Bacillus anthracis strains in the country remain incompletely understood. METHODS: A retrospective epidemiological and phylogenetic investigation of anthrax outbreaks reported in Kazakhstan during 2024 was conducted. Epidemiological data were collected for all laboratory-confirmed human cases and associated outbreak foci. Confirmation of infection was performed by PCR, and B. anthracis isolates were obtained from clinical, environmental and animal-associated samples. Whole-genome sequencing and core-genome single nucleotide polymorphism (cgSNP) analysis were used to characterize the genetic relationships among isolates and to determine their phylogenetic placement. RESULTS: Nine anthrax outbreaks were identified across four regions of Kazakhstan (Almaty, Zhambyl, Atyrau, and West Kazakhstan), resulting in 20 confirmed human cases. All patients were male, with the highest proportion occurring among individuals aged 36-55 years (45%). The mean patient age was 43.9 years (range: 16-64 years). Most infections were associated with slaughtering infected livestock (65%), followed by handling contaminated meat (15%). PCR confirmed infection in all 20 human cases. Culture yielded 17 human-derived B. anthracis isolates from 14 patients and 17 environmental/animal-derived isolates, resulting in 34 isolates in total. Of these, 22 representative isolates underwent whole-genome sequencing. Phylogenetic analysis revealed the circulation of two major lineages. Isolates from Atyrau and West Kazakhstan clustered within the Trans-Eurasian (TEA/STI) lineage. Atyrau isolates formed a tight cluster differing by only 21-32 cgSNPs, consistent with a shared epidemiolocal source, whereas the West Kazakhstan isolate was highly divergent. Zhambyl and Almaty region belonged to the A.Br.Ames lineage but diverged into two distinct sublineages. Zhambyl region isolates demonstrated minimal divergence from the global reference genome Ames Ancestor, differing by only 16-31 SNPs. Almaty region isolates formed an endemic subclone, separated from the reference group by approximately 114 SNPs. Comparison with the Ames Ancestor and Sterne reference strains demonstrated substantial genetic divergence. CONCLUSION: Anthrax outbreaks in Kazakhstan during 2024 were primarily associated with livestock exposure and occurred within established endemic regions. Whole-genome sequencing revealed the coexistence of distinct TEA and Ames lineages, including evidence of persistent local transmission and long-term evolutionary stability of endemic B. anthracis populations. These findings enhance understanding of anthrax epidemiology in Central Asia and support the integration of genomic surveillance into national outbreak investigation programs.

Anthrax↗