The researchers reconstructed the evolutionary and geographic history of CRF01_AE using viral sequences and Bayesian phylogeographic methods. Their analysis indicates that, after entering Thailand in the early 1980s, CRF01_AE spread across Southeast Asia and into China. Repeated movement across national borders was central to this continental expansion.

The reconstructed history also shows that many lineages circulated for years before detection, revealing substantial cryptic transmission before surveillance recognized them. Once established, transmission clusters persisted for decades and sustained local epidemics long after their initial introduction. These findings demonstrate that the regional spread of CRF01_AE unfolded over many years rather than through a single detectable event.

By showing that viral lineages remained undetected for years and that transmission clusters continued for decades, the study provides a historical context for the emergence of CRF01_AE across Asia. The authors identify early molecular surveillance and coordinated regional strategies as important for detecting emerging lineages and interrupting cross-border transmission.

Subject of Research: Evolutionary and geographic spread of HIV-1 CRF01_AE from Central Africa across Asia

Article Title: Global spread and evolutionary trajectories of HIV-1 CRF01_AE: Insights from phylogenetic analysis

Article References: Li, X., Jorgensen, D., Liu, H., Nie, Q., Bates, C., & Gu, Q. (2026). Global spread and evolutionary trajectories of HIV-1 CRF01_AE: Insights from phylogenetic analysis. PLOS One, 21(10), e0360404. https://doi.org/10.1371/journal.pone.0360404

Image Credits: AI Generated

DOI: 10.1371/journal.pone.0360404

Keywords: HIV-1, CRF01_AE, phylogenetics, Bayesian reconstruction, viral evolution, genome sequencing, molecular surveillance, cross-border transmission, Southeast Asia, China, Thailand, Central Africa

Researchers collected skin, hair and nail specimens from patients attending private mycology clinics and governmental university hospitals in Ardabil, Fars, Golestan, Isfahan, Khuzestan, Mazandaran, Razavi Khorasan, Tehran and West Azerbaijan. Every included patient had fungal elements visible by direct KOH microscopy in at least one sample, and culture recovered dermatophytes from 1,568 of the 2,211 suspected cases, a yield of 70.9%.

The researchers combined a lineage-specific PCR with ITS rDNA sequencing, restriction analysis and haplotype comparisons. The specific PCR identified 1,191 isolates as T. mentagrophytes var. indotineae. Sequencing of 78 randomly selected PCR-positive isolates confirmed their placement within the lineage: 57 represented two sub-genotypes of ITS genotype VIII, while 20 belonged to a previously unrecognised genotype XXIX within the T. mentagrophytes var. indotineae lineage. The study used the variety designation in line with taxonomic databases and recent population-genetic studies.

Clinical forms involving the groin and trunk predominated. Tinea cruris accounted for 656 cultured infections, or 41.8% of the total, followed by tinea corporis with 376 cases, or 23.9%; mixed tinea cruris and tinea corporis accounted for 144 cases, or 9.2%, and generalised infection accounted for 128, or 8.2%. T. mentagrophytes var. indotineae was identified in 544 of 656 tinea cruris cases, 279 of 376 tinea corporis cases, 110 of 144 mixed cruris and corporis cases, and 112 of 128 generalised infections. It was also found in 17 of 29 nail infections and 17 of 45 cases of tinea capitis.

Patients with T. mentagrophytes var. indotineae infection had a mean age of 34.5 ± 13.6 years, a median of 35 and a range of 1–85. The group included 588 males and 603 females, with no statistically significant difference in sex distribution (p = 0.664). Species distribution was associated with age group, province, clinical form and involved body site, with all reported p-values below 0.001. The largest numbers of confirmed infections came from Khuzestan, with 607 cases, followed by Mazandaran with 130 and Ardabil and Fars with 115 each.

Among 73 confirmed cases with reliable patient histories, none had documented travel abroad. This absence of recorded international travel does not establish where infection was acquired, but it means travel alone cannot explain the lineage’s presence in the surveyed population. Retrospective analysis placed several Iranian isolates collected in 2011 and 2015 within genotype VIII, indicating that the lineage was already present before the earliest reports from the Indian subcontinent. The study also identified genotype XXIX, adding to previously reported local genetic diversity. Related lineages have been recovered from sheep in rural Iran, but a local animal reservoir remains an unconfirmed hypothesis, and the data do not resolve the lineage’s geographic origin or centre of diversity.

Partial sequencing of the squalene epoxidase gene, SQLE, in 410 T. mentagrophytes var. indotineae isolates detected mutations in 184 isolates, or 44.8%. The mutations comprised the F397L amino-acid substitution in 132 mutant isolates, representing 71.7%, and L393S in 52, representing 28.3%. Mutation proportions were highest in Khuzestan at 52.4% and Fars at 46%, and lowest in Golestan at 8.5%. Both substitutions have previously been associated with terbinafine resistance in isolates from Asia and Europe. The reported 44.8% frequency was higher than mutation rates of 17.8% in an Iranian survey from 2020 and 14.35% in one from 2024, although the present study sequenced only part of the SQLE gene and targeted mutations at positions 393 and 397, so other mutations may not have been detected.

No antifungal susceptibility testing was performed, and the study did not collect clinical outcome data demonstrating treatment failure. The findings therefore identify a substantial proportion of isolates carrying mutations associated with likely terbinafine resistance, but they do not directly establish phenotypic resistance or explain individual treatment outcomes. The hospital-based design and reliance on patients referred to specialised clinics also limit how directly the observed proportions can be applied to Iran’s general population.

Overall, the survey documents a major shift in the epidemiology of referred dermatophytosis in Iran: T. mentagrophytes var. indotineae was the leading identified cause across the sampled settings and was detected in skin, scalp and nail infections. The authors said the findings highlight the need for routine molecular identification, SQLE genotyping and stronger national surveillance, while broader genomic studies and integration of clinical outcome data are needed to clarify transmission, origin and therapeutic implications.

Subject of Research: Epidemiology and terbinafine-resistance-associated SQLE mutations in Iranian dermatophyte isolates

Article Title: Dermatophytosis in Iran: a sharp increase in cases caused by Trichophyton mentagrophytes var. indotineae

Article References: Takesh, A., Wennrich, A., Kolařík, M., Zarei-Mahmoudabadi, A., Kiasat, N., Pazyar, N., Rafiei, A., Abastabar, M., Haghani, I., Kharazi, M., Basiri, S., Jahanshiri, Z., Khodadadi, H., Mohammadi, R., Zarrinfar, H., Seifi, Z., Diba, K., Kamali Sarvestani, H., & Rezaei-Matehkolaei, A. (2026). Dermatophytosis in Iran: a sharp increase in cases caused by Trichophyton mentagrophytes var. indotineae. IMA Fungus, 17, Article e180817. https://doi.org/10.3897/imafungus.17.180817

Image Credits: AI Generated

DOI: 10.3897/imafungus.17.180817

Keywords: dermatophytosis, Trichophyton mentagrophytes, T. mentagrophytes var. indotineae, Iran, terbinafine resistance, SQLE mutations, tinea cruris, tinea corporis, molecular surveillance, fungal infection, sharp, increase

Sixteen additional monitoring plots were established in 2021 near former vineyard sites, while additional traps and a longer sampling period beginning in mid-July were used in 2022 to increase the chances of capturing leafhoppers during their population peak. Investigators analyzed 16 O. ishidae specimens captured in 2021 and 267 captured in 2022. The infected insect was one of three O. ishidae caught in 2021 at an additional plot near Cugnasco on the southern slope of the Swiss Alps.

It had been captured between 1 and 14 October 2021. Four grapevines sampled at the Cugnasco plot in 2021 had no external symptoms associated with Grapevine Yellows and their molecular analyses did not detect phytoplasmas. Each insect was homogenized separately, and nucleic acids were extracted with a CTAB-based protocol.

The investigators used quantitative PCR targeting 16SrV-group phytoplasmas, followed by nested PCR amplification of the map and imp gene loci. Amplicons were checked by agarose-gel electrophoresis, purified, and sequenced in forward and reverse directions by Sanger sequencing. Maximum-likelihood phylogenetic analyses used the General Time Reversible model and 500 bootstrap replicates, and the resulting trees were visualized in iTOL.

The Swiss imp amplicon differed by one nucleotide, a single-nucleotide polymorphism, from German isolate MT668492, corresponding to 99.78% identity. ‘Candidatus Phytoplasma ulmi’ belongs to ribosomal subgroup 16SrV-A and is associated with dieback, shoot proliferation, and yellows on several Ulmus species. It has previously been recorded in European countries including Italy, Germany, and France.

A recent report from northwestern Italy also identified infected Carpinus betulus, Prunus domestica, and Prunus ulmifolius, showing that the phytoplasma can occur in hosts beyond elm. Previously identified competent vectors include Scaphoideus luteolus in the United States, Macropsis glandacea in Italy, and Amplicephalus curtulus in Chile. The study established only that the phytoplasma was present in one captured insect.

The detection rate among the analyzed O. ishidae was 1 in 283, and the positive result came from monitoring designed primarily to investigate Flavescence dorée vectors rather than from a dedicated survey of Ca. O. ishidae is native to Asia and was first recorded in Europe in 1998. It has since spread across most of the continent and occurs in pre-Alpine and Alpine regions.

Reported host plants include Corylus avellana, Acer species, Alnus glutinosa, Salix species, and Carpinus betulus, many of which are common near vineyards. Previous studies documented its ability to acquire Flavescence dorée phytoplasmas and other phytoplasmas from additional ribosomal groups. The insect can also lay eggs on grapevines and gone-wild grapevines, potentially giving newly hatched nymphs direct access to plant material.

The single positive insect also does not establish a transmission pathway or quantify population-level prevalence. The authors describe O. ishidae as a potential “wild-card” in several phytoplasma pathosystems and call for research on its ecology, agricultural relevance, and possible effects on spontaneous woody plants across the Alpine region.

Subject of Research: First Swiss detection of a phytoplasma in Orientus ishidae through molecular surveillance

Article Title: First detection of ‘ Candidatus Phytoplasma ulmi’ in Switzerland and in Orientus ishidae Matsumura, 1902

Article References: Oggier, A., Debonneville, C., Conedera, M., Schumpp, O., & Rizzoli, A. (2024). First detection of ‘Candidatus Phytoplasma ulmi’ in Switzerland and in Orientus ishidae Matsumura, 1902. Alpine Entomology, 8, 29-34. https://doi.org/10.3897/alpento.8.115588

Image Credits: AI Generated

DOI: 10.3897/alpento.8.115588

Keywords: Candidatus Phytoplasma ulmi, Orientus ishidae, Canton Ticino, molecular surveillance, leafhoppers, phytoplasma, Flavescence dorée, plant pathology, Switzerland, 16SrV-A, First, detection

The investigation was conducted in January 2025 in the Altay Mountain area of Wenquan County, Xinjiang Uygur Autonomous Region, at an elevation of 2,200 metres and at coordinates 44°47′30″ N, 80°53′30″ E. Investigators collected 89 fleas from the body surfaces of 23 free-ranging sheep, taking two to six fleas from each animal. Six representative specimens—three males and three females—were selected for morphological identification. The remaining 83 fleas, all female, were processed individually for DNA extraction and pathogen screening. Three female samples were also used to confirm the flea species by sequencing the mitochondrial cytochrome c oxidase subunit II, or COII, gene.

Morphological examination supported the identification of V. alakurt. The specimens had dark-brown heads and thoraxes, developed eyes and round antennal clubs with seven segments. Their labial palpi contained 10 to 15 segments and extended beyond the forecoxae, while their hind tibiae each had six notches. Male body length ranged from 3.7 to 4.9 millimetres, and female body length ranged from 5.6 to 7.5 millimetres. Fatty tissue occupied the posterior three-quarters of the female abdomen. The COII sequences shared 99.41 percent identity across 674 of 678 base pairs with the V. alakurt reference sequence OP433454.1, providing molecular support for the morphological assignment.

Researchers used separate genetic markers to screen for the four pathogen genera: the 16S ribosomal RNA gene for Anaplasma, the Com1 gene for Coxiella, and the 18S ribosomal RNA gene for Babesia and Theileria. Each PCR run included distilled water as a negative control and positive controls from the investigators’ laboratories. Amplified products were purified, sequenced and compared with reference sequences in GenBank. The authors reported that the molecular identifications were confirmed after three repetitions. Anaplasma ovis was detected in 6 of 83 fleas, a proportion of 7.23 percent; Coxiella burnetii in 37, or 44.58 percent; Babesia in 8, or 9.64 percent; and Theileria annulata in 4, or 4.82 percent. The Babesia category comprised seven detections designated as Babesia sp. and one assigned to Babesia ovis.

Phylogenetic analyses placed the detected sequences in clades associated with their respective pathogen groups. The local Anaplasma ovis sequences clustered with a sheep-derived Xinjiang reference strain, PX682654, and showed genetic divergence from sequences attributed to Iran, Spain and Kenya. The authors interpreted this pattern as evidence for locally differentiated A. ovis lineages in alpine pastoral areas along the China–Kazakhstan border. Their analysis did not directly measure how widely any particular genotype circulated among livestock or fleas, however, and the phylogenetic result alone does not describe population prevalence. The study sequences were deposited in GenBank under accession numbers PZ263706 and PZ263708 for the Anaplasma 16S rRNA target.

Coxiella burnetii sequences clustered with strains obtained from ticks, fleas, humans and animals in Xinjiang and Kazakhstan. The closest reported homology was to a Hyalomma sp. strain, PV976747, from Shihezi in Xinjiang, while the flea-derived sequences differed from reference strains from Europe, the United States, Japan, South Korea and India. The authors proposed that the close relationship between the flea sequences and local tick isolates was consistent with long-term co-circulation involving ticks, fleas and livestock in the border mountain pastures. The two Com1 sequences generated in the study were deposited as PZ444052 and PZ390894. Even so, genetic similarity between organisms found in different arthropod groups does not by itself establish a transmission route or show that the flea maintained the organism during development.

The Babesia and Theileria comparisons also matched the study sequences with reference organisms from domestic and foreign sources. Theileria annulata sequences were associated with records from Xinjiang and Kazakhstan, including references MG645811 and PQ056497, while Babesia ovis clustered with sheep-derived reference material. The broader Babesia sp. sequences corresponded with an organism reported from Ornithodoros lahorensis and from ticks, including reference sequences OM438140.1 and KY464046.1. In the analysis, clear genetic boundaries separated the target organisms from Theileria equi and Babesia caballi. The relevant 18S rRNA sequences were deposited in GenBank as PZ429426, PZ263724, PZ263721, PZ429427 and PZ263716. These comparisons support the molecular assignments, but sequence matching cannot establish that fleas acquired the organisms by feeding, replicated them in their tissues or passed them to vertebrate hosts.

Several fleas carried more than one detected pathogen. Coxiella burnetii occurred together with Anaplasma ovis in fleas numbered 25, 27 and 37. A second group—fleas numbered 3, 45 and 75—contained C. burnetii together with Babesia and Theileria species. The authors noted that concurrent infections have been documented in other blood-feeding arthropods, including simultaneous detections of Borrelia burgdorferi and Anaplasma phagocytophilum in human fleas and co-detections of C. burnetii, Borrelia species and Babesia microti in ticks collected from camels. The co-detections in the present study show that several targeted organisms were present together in individual V. alakurt, adding to the documented diversity of pathogen profiles encountered in fleas and ticks.

V. alakurt belongs to the endemic flea family Vermipsyllidae, whose recognized species are distributed mainly across alpine regions of China and neighboring countries. The species was first recorded in Xinjiang in 1965, and adults are mainly active from December through March in alpine pastures. It primarily infests sheep, with goats, cattle, yaks, horses and red deer listed as secondary hosts. Heavy infestations can produce pruritus, emaciation, progressive anaemia and abortion in pregnant females and can cause mortality in severe cases, resulting in economic losses for local animal husbandry. The complete life cycle includes egg, three larval instars, pupa and adult; larvae and pupae live freely in soil, marmot burrows and environmental debris, whereas adults parasitize animals and take blood meals mainly in winter.

The results do not establish that V. alakurt is an effective vector for any of the detected pathogens. The researchers examined only adult fleas, leaving eggs, larvae and pupae untested, and they did not screen the source sheep for infection. Consequently, pathogen DNA in a flea could have arrived in ingested host blood. The study could not distinguish replication within flea tissues from transient persistence in the digestive tract, determine the developmental stage at which acquisition occurred, or show that the organisms passed onward to sheep or humans. The interactions among ticks, fleas and livestock also remained unresolved. The observed genetic closeness between the flea C. burnetii sequences and local tick-derived isolates, together with the co-detection of several pathogens, is an epidemiological signal that warrants further study, but it is not direct evidence of pathogen transmission through the flea.

Taken together, the study expands the known pathogen spectrum associated with V. alakurt and documents Anaplasma, Coxiella, Babesia and Theileria in fleas collected from sheep in the China–Kazakhstan border area. Its strongest finding concerns carriage and co-detection: the sampled female fleas contained DNA from four pathogen genera, with C. burnetii detected most frequently and several fleas harbouring multiple targets. Determining whether the findings represent a distinct epidemiological role for V. alakurt will require screening its immature stages, surveying the livestock from which fleas are collected, and experimentally establishing whether the organisms survive, replicate or move through the flea–host interface. Until those steps are completed, the results should be understood as the first molecular evidence of these four pathogen genera in this flea species rather than proof that it transmits them.

Subject of Research: Molecular detection of tick-associated pathogen DNA in the alpine livestock flea Vermipsylla alakurt

Article Title: Anaplasma spp., Coxiella, Babesia and Theileria Infections in Vermipsylla Alakurt Fleas

Article References: Jiushikun, J., Yizigeleke, T., Fan, Y., Li, W., Zhang, Y., Zhao, G., Tang, L., & Wang, Y. (2026). Anaplasma spp., Coxiella, Babesia and Theileria Infections in Vermipsylla Alakurt Fleas. Acta Parasitologica, 71(6), Article 240. https://doi.org/10.1007/s11686-026-01428-5

Image Credits: AI Generated

DOI: 10.1007/s11686-026-01428-5

Keywords: Vermipsylla alakurt, alpine fleas, vector-borne pathogens, Coxiella burnetii, Anaplasma ovis, Babesia, Theileria annulata, livestock health, Xinjiang, molecular surveillance, Anaplasma, Coxiella

The research team, led by Rameen Parvez and Mohsin Khurshid of the Institute of Microbiology at Government College University Faisalabad, with collaborators including James Jacob Sasanya of the International Atomic Energy Agency in Vienna, sampled three distinct tiers of the poultry economy between September 2024 and April 2025. By including commercial broiler operations, small-scale backyard flocks and retail markets, the design captured the full trajectory of poultry production from intensive rearing to point of sale. This matters because each tier represents a different interface between bacteria and humans, from farm workers exposed directly to birds and litter, to consumers handling raw meat in their kitchens.

Identification of the isolates was rigorous. The team combined conventional biochemical testing with API 20E strips, matrix-assisted laser desorption ionization time-of-flight mass spectrometry, a proteomic technique that fingerprints bacterial species by their protein profiles, and amplification of the rpoB gene, a molecular marker widely used to confirm species identity. This layered approach guards against the misidentification that has plagued some earlier surveys, since K. pneumoniae and its close relative K. oxytoca can be difficult to distinguish phenotypically. Of the 900 samples, 303, or 33.7 percent, yielded K. pneumoniae, a prevalence figure that underscores how thoroughly this organism has colonized the poultry environment.

The resistance picture that emerged was grim. Among the 303 isolates, 199, or 65.7 percent, qualified as multidrug-resistant under internationally accepted definitions, meaning they were nonsusceptible to at least one agent in three or more antibiotic classes. A further 48 isolates, 15.8 percent, were extensively drug-resistant, a category reserved for bacteria that have lost susceptibility to agents in all but one or two classes. Perhaps most tellingly, isolates from commercial broiler farms carried a heavier resistance burden than those recovered from backyard flocks or retail markets, a gradient consistent with the intensive antimicrobial use documented on industrial poultry operations in the region.

At the molecular level, polymerase chain reaction screening revealed a familiar but troubling cast of resistance genes. The dominant extended-spectrum beta-lactamase determinants were blaCTX-M-15 and blaTEM, enzymes that hydrolyze third-generation cephalosporins, workhorse antibiotics in both human and veterinary medicine. CTX-M-15 in particular is a global success story for the bacterium, having spread explosively through human clinical populations over the past two decades. Its prominence in poultry-associated isolates suggests that the farm environment is not merely a passive reservoir but an active participant in the circulation of the very genes that compromise treatment of urinary tract infections, bloodstream infections and hospital-acquired pneumonia.

More alarming still was the detection of carbapenemase genes among carbapenem-resistant isolates. The team identified blaNDM, blaKPC and blaOXA-48, three of the most clinically consequential carbapenemase families known. Carbapenems are often described as last-line antibiotics for infections caused by gram-negative bacteria, and the World Health Organization lists carbapenem-resistant K. pneumoniae as a critical-priority pathogen. The presence of NDM-type enzymes, which originated on the Indian subcontinent and have since spread worldwide, in bacteria recovered from poultry points to a plausible environmental bridge by which these determinants could move between animal, food and human compartments.

Colistin, a polymyxin antibiotic revived as a treatment of last resort when carbapenems fail, fared no better. Resistance to colistin was detected in 5.9 percent of the isolates, and the plasmid-mediated mcr-1 gene was identified among the resistant strains. The mcr-1 gene is of particular concern because, unlike chromosomal mutations that confer colistin resistance, it sits on mobile genetic elements that can hop between bacterial species and genera with relative ease. First described in Chinese pigs and pork in 2015, mcr-1 has since been reported on every inhabited continent, and its presence in poultry systems in Pakistan adds another node to its global distribution network.

One of the study’s most striking findings is the sheer combinatorial diversity of the resistance determinants. The researchers identified twenty-one distinct resistance gene combinations, including combinations that unite ESBL genes, carbapenemase genes and colistin resistance determinants within the same isolates. Co-occurrence of this kind is the molecular nightmare scenario for antimicrobial resistance control, because a single plasmid carrying multiple determinants can simultaneously confer resistance to front-line, last-line and reserve antibiotics. Such plasmids can be transferred laterally to other Enterobacteriaceae, including Escherichia coli and Salmonella, multiplying the number of pathogenic species that can acquire the resistance package in a single horizontal gene transfer event.

The authors frame their findings within a One Health perspective, the recognition that human, animal and environmental health are inextricably linked. Poultry production is a recognized amplifier of resistance: antimicrobials are used for growth promotion, prophylaxis and treatment in many low- and middle-income settings, selective pressure favors resistant clones, and resistant bacteria and their genes disperse through litter, wastewater, workers, carcasses and meat. Prior studies have documented intermingled K. pneumoniae populations between retail meats and human urinary tract infections, and the persistence of multidrug-resistant strains long after colistin withdrawal in poultry production, suggesting that contamination events can leave durable legacies in the food chain.

The study’s conclusions point toward concrete interventions: strengthened antimicrobial stewardship to curb unnecessary drug use, improved farm-level biosecurity to reduce the infection pressure that drives treatment, and integrated molecular surveillance that tracks resistance genes across the production chain rather than in isolated snapshots. The work was funded under an International Atomic Energy Agency Coordinated Research Project, and the authors report no competing interests. As resistance genes continue to accumulate in the animals that feed billions of people, the Faisalabad survey serves as a quantitative warning that the poultry sector, if left unmonitored, can function as both a reservoir and a launchpad for some of medicine’s most feared resistance determinants.

Subject of Research: Molecular characterization of antimicrobial resistance genes in Klebsiella pneumoniae from poultry production systems in Pakistan

Article Title: Molecular characterization and co-occurrence of ESBL, carbapenemase and mcr-1 genes in Klebsiella pneumoniae from poultry production systems in Pakistan

Article References: Parvez, R., Khurshid, M., Rasool, M. H., Aslam, B., & Sasanya, J. J. (2026). Molecular characterization and co-occurrence of ESBL, carbapenemase and mcr-1 genes in Klebsiella pneumoniae from poultry production systems in Pakistan. Molecular Biology Reports, 53(1), Article 1538. https://doi.org/10.1007/s11033-026-12718-6

Image Credits: AI Generated

DOI: 10.1007/s11033-026-12718-6

Keywords: Klebsiella pneumoniae, antimicrobial resistance, ESBL, carbapenemase, mcr-1, colistin resistance, poultry, One Health, Pakistan, multidrug resistance, food chain, molecular surveillance

Diagnosing M. bovis, however, has remained a stubborn bottleneck. Traditional microbiological culture is definitive but labor-intensive and may require days to weeks because of the fastidious growth requirements of the organism, a turnaround time fundamentally incompatible with outbreak decision-making. Serologic assays deliver faster results but often cannot reliably distinguish active infection from past exposure or maternal antibody. Nucleic acid amplification tests such as quantitative polymerase chain reaction have therefore become the gold standard thanks to their high analytical sensitivity and specificity, yet PCR-based methods are tethered to centralized laboratories, requiring sophisticated thermal cycling infrastructure and trained personnel. For the bison industry, where repeated animal handling for resampling is stressful and can pose substantial safety risks, the need for a rapid chute-side diagnostic that delivers actionable results during a single handling event has been especially acute.

To close this gap, researchers have now engineered and validated a diagnostic assay that synergistically couples recombinase polymerase amplification with CRISPR-Cas12a detection, achieving the low-copy analytical sensitivity of gold-standard qPCR while operating entirely under isothermal conditions. The work, published in MicrobiologyOpen, targets the uvrC gene, a conserved housekeeping marker widely used for molecular identification of M. bovis. Although uvrC is broadly conserved among Mycoplasma species, species-specific sequence polymorphisms within the selected target region permit differentiation of M. bovis from closely related species, and the gene is highly conserved among M. bovis isolates, making it a preferred species-specific qPCR target for routine diagnostic detection in cattle.

The technical logic of the platform rests on two complementary molecular engines. Recombinase polymerase amplification, unlike PCR, operates at a constant low temperature of 37 to 42 degrees Celsius and can tolerate inhibitors commonly present in clinical matrices such as nasal swabs and lung tissue extracts. Standalone isothermal assays, however, often suffer from non-specific amplification, producing false positives when coupled with non-specific detection methods like intercalating dyes. The Type V effector Cas12a resolves this by adding an additional layer of sequence specificity. Upon binding a target DNA sequence complementary to its guide RNA, Cas12a is activated and non-specifically cleaves nearby single-stranded DNA reporters, generating a fluorescence signal only when the intended amplicon is present in the appropriate PAM-dependent context.

Optimization began with the amplification step. A 558-base-pair region of the uvrC gene was PCR-amplified from M. bovis genomic DNA extracted from lung tissue of a PCR-confirmed infected bison with gross pulmonary lesions, then cloned into a plasmid vector to serve as the standard DNA control. Eight primer-pair combinations targeting fragments of roughly 100 to 400 base pairs were evaluated in RPA reactions incubated at 39 degrees Celsius for 20 minutes. Most primer pairs yielded distinct bands at the expected sizes, and primer pair PP7 was selected for all subsequent optimization and validation because it demonstrated robust and specific amplification and provided suitable target sites for the design of three distinct guide RNAs within the amplified region.

The CRISPR effector step was then tuned with equal care. Three guide RNAs were designed to target distinct sites within the amplified uvrC region, each adjacent to a 5′-TTTG-3′ protospacer-adjacent motif and selected for low sequence homology to other Mycoplasma species. All three guides enabled Cas12a-mediated detection of the plasmid standard, producing a green fluorescence signal within 30 to 60 minutes, with gRNA3 producing the fastest and most intense response. The single-stranded DNA fluorophore-quencher reporter concentration was optimized to balance time-to-threshold, signal intensity, and background fluorescence; while maximal fluorescence was reached at 5 micromolar, higher reporter concentrations also increased background in negative controls, and 0.75 micromolar provided the best visual readout with minimal background. Cas12a protein titration indicated best fluorescence intensity at 50 nanomolar.

A central finding of the work is the requirement for RPA pre-amplification to achieve clinically relevant detection limits. When M. bovis genomic DNA from three PCR-confirmed positive samples was tested directly in the CRISPR-Cas12a reaction, no fluorescence signal was detected with any of the guide RNAs, whereas the plasmid standard produced bright fluorescence. After the same genomic DNA samples were first subjected to RPA amplification, positive fluorescence signals were obtained, peaking at approximately 20 to 25 minutes before plateauing. Benchmarking against qPCR on serial dilutions of the plasmid standard made the sensitivity gap stark: qPCR reliably detected as few as roughly 8 copies, direct Cas12a detection without pre-amplification produced no measurable fluorescence at any copy number, and RPA-coupled detection recovered robust fluorescence across the dilution series, including at the 8-copy level. In mass units, direct Cas12a interrogation generated visible fluorescence only between 700 and 7 nanograms of the standard, with no signal below 7 nanograms even after 60 minutes.

Clinical validation across 110 samples demonstrated complete diagnostic performance. All 50 M. bovis PCR-positive clinical samples from bison and cattle, spanning lung tissue, milk, nasal swabs, and nasopharyngeal swabs, were positive by the RPA-CRISPR-Cas12a assay. All 13 M. canis-positive samples from dogs and all 10 M. felis-positive samples from cats were negative, confirming the absence of cross-reactivity with closely related species. Among 37 samples positive by PCR for Mycoplasma species that had not initially been speciated, three were positive by the M. bovis assay and were subsequently confirmed as M. bovis by species-specific qPCR. Overall, the assay showed 100 percent sensitivity, 100 percent specificity, and 100 percent concordance with reference PCR-qPCR, with exact 95 percent confidence intervals of 93.3 to 100 percent for sensitivity and 93.7 to 100 percent for specificity. M. bovis-positive samples carried PCR Ct values ranging from approximately 15 to 38, and all were detected following RPA pre-amplification, with fluorescence intensity showing an inverse association with Ct values, Spearman’s rho of negative 0.575, hinting at semi-quantitative potential for bacterial load estimation.

The dual-guide strategy emerged as a particularly interesting kinetic trade-off. While some reports suggest that multiplexing guides leads to additive signal intensity, the researchers observed lower peak fluorescence but faster time-to-threshold with the dual-guide complex. This likely reflects competing dynamics: multiple guides increase the probability of rapid initial target capture, reducing the lag phase, but they compete for the available Cas12a pool, slightly dampening the maximum trans-cleavage velocity per target molecule. For diagnostic purposes, the accelerated onset of the signal is more valuable than absolute peak height, as it potentially allows shorter incubation times, and requiring recognition by two guides imposes higher stringency, reducing the likelihood of off-target activation by closely related Mycoplasma species. The gRNA2 plus gRNA3 combination was therefore adopted as the optimal balance of signal strength and assay complexity.

Before the platform can become a true pen-side tool, several adaptations remain. The current workflow relies on a two-step transfer of RPA product into the Cas12a mix, which introduces a risk of amplicon contamination in high-throughput environments, and developing a one-pot formulation remains challenging due to the competing buffer and temperature requirements of the enzymes. The assay still requires DNA extraction and cold-chain storage for protein-based reagents, and the guide RNAs were not challenged against non-mycoplasmal agents associated with bovine respiratory disease complex such as Mannheimia haemolytica, Pasteurella multocida, and Histophilus somni. Matrix tolerance to inhibitors in minimally processed antemortem samples was not directly evaluated, since all testing used purified DNA extracts identical to those used for reference PCR. Future iterations should focus on non-invasive sampling methods such as deep nasopharyngeal swabs or transtracheal washes, lyophilized reagents, and a transition from fluorescence to a visual lateral flow readout, in which a biotin-FAM labeled reporter is cleaved upon Cas12a activation and the released FAM molecule binds anti-FAM antibodies at a test line, producing a visible band. With these developments, the study lays a foundational framework for rapid, instrument-free, on-site diagnostics that could facilitate early intervention and improved herd health management in resource-limited agricultural settings.

Subject of Research: Development and clinical validation of an RPA-CRISPR-Cas12a isothermal assay for sensitive detection of Mycoplasma bovis

Article Title: Synergistic Integration of Recombinase Polymerase Amplification and CRISPR–Cas12a Enables High‐Sensitivity Detection of Mycoplasma bovis

Article References: Yaghoubi, D., & V. Pillai, V. (2026). Synergistic Integration of Recombinase Polymerase Amplification and CRISPR–Cas12a Enables High‐Sensitivity Detection of Mycoplasma bovis. MicrobiologyOpen, 15(5), Article e70435. https://doi.org/10.1002/mbo3.70435

Image Credits: AI Generated

DOI: 10.1002/mbo3.70435

Keywords: Mycoplasma bovis, CRISPR-Cas12a, recombinase polymerase amplification, isothermal amplification, bovine respiratory disease, point-of-care diagnostics, uvrC gene, qPCR, cattle, bison, lateral flow assay, molecular surveillance

The warning rests on hard evidence. Partial resistance to artemisinin, encoded by mutations in the Plasmodium falciparum kelch13 gene, has emerged independently and repeatedly inside Africa rather than arriving through a single importable front. The kelch13 R561H mutation was confirmed in Rwanda in 2020; clinical and molecular evidence of resistant parasites followed in Uganda; and in Eritrea, resistant parasites were found already carrying the diagnosis-evading trait of HRP2 deletion. Validated and candidate kelch13 polymorphisms, among them P441L, C469Y, R561H, R622I, and A675V, are now distributed across the Great Rift Valley, and the World Health Organization records confirmed or suspected partial resistance in at least eight African countries.

The stakes could hardly be higher. The WHO estimates 282 million malaria cases and 610,000 deaths in 2024, with the African Region carrying roughly 94 percent of cases and 95 percent of deaths, about three-quarters of them in children under five. The WHO’s 2025 report names antimalarial drug resistance, alongside deletions of the histidine-rich protein 2 and 3 genes that blind many rapid diagnostic tests, as a direct and growing threat to case management. Africa has been here before: chloroquine and sulfadoxine-pyrimethamine were both lost across the continent within years of resistance taking hold, and in each case policy reacted only once failure was undeniable, too late to save the drug.

Southeast Asia has already run the experiment to its conclusion. In Pursat, Cambodia, the efficacy of dihydroartemisinin-piperaquine fell from 98 percent in 2005 to 63 percent by 2013 as the prevalence of kelch13 mutants rose from 40 to 77 percent. Between 2015 and 2018, multi-country efficacy of the same regimen had sunk to 50 percent, with treatment failure exceeding 85 percent at the worst sites. The reactive response became a treadmill: as one combination therapy failed, programs switched to another, only to watch resistance follow, until the region’s strategic answer was an outright push to eliminate falciparum malaria before it became untreatable.

Critically, that collapse began with the partner drug rather than the artemisinin. Partial resistance on its own rarely causes a combination therapy to fail: kelch13 mutations slow the clearance of young ring-stage parasites, leaving more of them for the partner drug to remove, but a fully effective partner can still cure the infection. Failure arrives when resistance to the partner joins in. Once artemisinin can no longer reliably suppress the parasite burden, survivors meet the partner drug almost as a monotherapy, which accelerates selection for partner-drug resistance. The molecular basis is well characterized: amplification of the plasmepsin-2 and plasmepsin-3 genes and mutations in the chloroquine resistance transporter underlie piperaquine failure, while changes in mdr1 and related loci shift susceptibility to lumefantrine and amodiaquine. In northern Uganda, parasites with reduced susceptibility to both dihydroartemisinin and lumefantrine have already been documented, and validated kelch13 mutations have climbed to substantial frequencies at several Ugandan sites.

Africa is not a milder version of the Greater Mekong; in several respects it is a harder place to fight resistance. Transmission across much of sub-Saharan Africa is far more intense, meaning more infections, more drug exposure, and faster spread of any resistant lineage that gains a foothold. Partial immunity acquired through repeated infection helps many African patients clear parasites even when a drug is failing, which masks treatment failure and delays its detection precisely where the trigger threshold matters most. A larger, more diverse parasite population offers more genetic raw material for resistance to arise and recombine. And Africa is not one epidemiological place: transmission ranges from holoendemic to near-elimination, so resistance can establish in one zone while a national average stays below the alarm level, which means any preemptive strategy must be stratified sub-nationally.

The conventional trigger for changing first-line therapy is a treatment failure rate above 10 percent. As a brake on premature, costly policy churn, the threshold is sensible. But as a strategy for a continent at the start of a resistance trajectory, the author argues, it carries a structural defect: by the time failure is common enough to be measured reliably, resistance is already widespread, and changing a national regimen takes years to plan, finance, procure, and deliver. The deeper problem is an asymmetry of errors. Switching too early wastes money; switching too late costs lives during the lag and can cost the drug itself. Drug efficacy is best understood as a shared, exhaustible resource, and when the two kinds of error carry such unequal consequences, waiting for certainty is not caution but risk. The author frames the calculus as ethical as well as epidemiological: the cost of a lost first-line drug falls hardest on young children in high-transmission, low-income settings, and deferring action until failure is statistically unambiguous means discovering the loss through their deaths.

The financing environment sharpens the point. The abrupt contraction of United States assistance in 2025, including the dismantling of the President’s Malaria Initiative and its implementing agency, has disrupted commodity supply, surveillance, and the technical partnerships on which resistance monitoring depends; one modeling study attributes roughly half of the malaria mortality reduction of the past two decades to US development assistance and warns of large avoidable mortality if the cuts stand. With total malaria investment flat near US$4 billion against a WHO target of more than US$9 billion, the surveillance and procurement capacity that reactive policy depends on is precisely what is most exposed. The preemptive agenda itself, however, is built largely from tools that already exist. Deploying several different first-line combination therapies across a population at once spreads drug pressure and slows selection against any one partner drug; a Rwanda-specific modeling study that evaluated 26 policy options found this single change could lower projected treatment failures by approximately half, with the largest gains when adopted before resistance became common. The WHO already recommends six artemisinin-based combinations for uncomplicated malaria.

Further elements of the agenda include preparing triple artemisinin-based combination therapies as a deployable contingency, since adding a second partner drug forces a parasite to overcome both compounds at once; artemether-lumefantrine-amodiaquine and artesunate-mefloquine-piperaquine have proved efficacious and well tolerated even in multidrug-resistant settings, and modeling indicates early adoption delays resistance emergence rather than merely reacting to it. On the pipeline front, the non-artemisinin combination ganaplacide-lumefantrine met its primary endpoint in the Phase 3 KALUMA trial in 2025, the first such advance in more than two decades and one that held up against partial-resistance mutants, though approval and deployment lie years ahead. Prevention is part of the same strategy: two WHO-recommended vaccines, R21/Matrix-M with roughly 75 percent efficacy against clinical malaria in seasonal use and RTS,S linked to a 13 percent decrease in all-cause child mortality, have reached children in more than 17 African countries, and every infection prevented is one less course of drugs and one less chance for resistance to spread. Underpinning it all, the author insists, molecular surveillance tracking kelch13, partner-drug markers, and pfhrp2 and pfhrp3 deletions must be funded as routine national infrastructure rather than grant-dependent research, because it is the sensor without which preemptive policy is blind and reactive policy is merely slow. The biology in Africa has not yet reached the Southeast Asian endpoint of routine treatment failure. That, the Perspective concludes, is the entire point and the entire opportunity: the window to act ahead of failure is open, narrow, and closing.

Subject of Research: Preemptive treatment policy to counter emerging artemisinin partial resistance in African falciparum malaria

Article Title: Holding the line against artemisinin partial resistance in Africa: the case for preemptive treatment policy

Article References: Sriram, S. (2026). Holding the line against artemisinin partial resistance in Africa: the case for preemptive treatment policy. Frontiers in Malaria, 4, Article 1916099. https://doi.org/10.3389/fmala.2026.1916099

Image Credits: AI Generated

DOI: 10.3389/fmala.2026.1916099

Keywords: artemisinin partial resistance, Plasmodium falciparum, kelch13, artemisinin-based combination therapy, malaria drug resistance, multiple first-line therapies, triple artemisinin-based combination therapy, molecular surveillance, pfhrp2 deletions, malaria vaccines, Africa, treatment policy

The research, led by scientists at the Kenya Medical Research Institute in collaboration with the Walter Reed Army Institute of Research–Africa and the University of Nairobi, examined 350 archived whole-blood samples collected from multiple malaria-endemic regions of Kenya. Ninety-five samples dated from 2003 to 2005, before the nationwide rollout of rapid diagnostic tests in 2012, while 255 came from 2013 to 2017, the years immediately following widespread adoption. The hospitals contributing samples spanned Kisumu, Kombewa, Kericho, Malindi, and Alupe, capturing high-transmission lake-endemic zones, epidemic-prone highland areas, and coastal malaria regions.

The diagnostic target in question is Plasmodium falciparum histidine-rich protein 2, or PfHRP2, an antigen that is abundant and stable in peripheral blood and therefore an excellent marker for infection. More than 90 percent of rapid diagnostic tests used in sub-Saharan Africa are built around this protein. A related paralog, PfHRP3, shares epitopes with PfHRP2 and can sometimes be cross-detected, but its expression is generally too low to be reliably picked up at low parasite densities. Parasites that lose the pfhrp2 gene, and sometimes the pfhrp3 gene alongside it, can therefore slip past the most common point-of-care test entirely, resulting in false-negative results that allow untreated infections to sustain transmission and worsen clinical outcomes.

Kenya sits in a region of particular concern. Neighboring countries in the Horn of Africa have reported alarmingly high deletion prevalences: Eritrea documented 80 percent of samples producing false-negative results, while Djibouti reported double pfhrp2 and pfhrp3 deletions in 86.5 percent of tested parasites. These findings have prompted Ethiopia, Eritrea, and Djibouti to shift national diagnostic policy away from PfHRP2-based tests. Kenya, by contrast, has previously recorded deletion rates below the World Health Organization’s 5 percent action threshold, though global modeling work has classified it as a country at high risk for the potential expansion of deletion-bearing parasites.

To establish whether selection pressure from routine diagnostic use has begun reshaping the Kenyan parasite population, the team first screened all samples by quantitative real-time PCR targeting the 18S ribosomal RNA gene. Of the 350 samples, 327, or 93.4 percent, were confirmed as P. falciparum positive. Ten samples fell below the 30 parasites per microliter threshold corresponding to the approximate detection limit of rapid diagnostic tests and were excluded, leaving 317 samples for genotyping. Nested PCR assays were then used to determine the presence or absence of pfhrp2, pfhrp3, and the flanking genes on either side of each locus, with laboratory strains 3D7, Dd2, and HB3 serving as positive and negative controls.

The results were strikingly reassuring. Overall, single pfhrp2 deletions were found in just 0.3 percent of samples, one of 317, while single pfhrp3 deletions appeared in 1.3 percent, four of 317. Every single pre-rollout sample, collected between 2003 and 2005, carried intact copies of both genes. Among the 224 post-rollout samples, deletions remained rare: 0.4 percent for pfhrp2 alone and 1.8 percent for pfhrp3 alone. Critically, no sample exhibited a triple deletion of pfhrp2 and both of its flanking genes, or of pfhrp3 and both of its flanking genes, the pattern that would suggest a coordinated chromosomal loss of the kind seen in parts of South America.

That said, the flanking regions told a more nuanced story. For pfhrp2, 41 samples, 12.9 percent, had lost the 5′ flanking gene while retaining the diagnostic gene itself, and four samples lacked the 3′ flanking gene. At the pfhrp3 locus, 10 samples showed upstream flanking deletions and 16 showed downstream flanking deletions, all with the gene intact. The authors interpret these independent flanking-gene losses as distinct genetic events rather than the coordinated multi-gene deletion mechanisms reported in Honduras, Colombia, and Peru, where deletion of the antigen gene typically occurs together with loss of one or both neighboring regions. This pattern suggests that in Kenya the parasite population has not yet undergone the concerted genomic rearrangements that would signal strong selection for immune evasion of diagnostics.

The study also examined why rapid diagnostic tests sometimes fail despite intact genes. Among 195 PCR-confirmed samples with adequate parasite densities that were positive on the pan-Plasmodium lactate dehydrogenase band, 21, or 10.8 percent, were negative on the PfHRP2-based test, giving an overall test sensitivity of 89.2 percent. Notably, 20 of these 21 false-negative samples, 95.2 percent, carried intact pfhrp2 and pfhrp3 genes, and none lacked pfhrp2 at all. Firth-corrected logistic regression found no significant association between false-negative results and deletion of either gene. Low parasitemia, which reduces antigen concentration below the test’s detection threshold, is the most likely explanation, along with possible sample degradation over long-term storage.

False-negative rates varied considerably by site and year, with Malindi recording the highest cumulative prevalence at 31.6 percent, followed by Kericho at 13.7 percent and Kombewa at 4.9 percent, but no consistent temporal or spatial trend emerged across the study period. Interestingly, the lone pfhrp2-deleted sample was actually RDT-positive, most likely because an intact pfhrp3 gene produced enough cross-reactive antigen to generate a signal, or because a mixed infection contained parasites still expressing PfHRP2. Such observations underscore the complexity of interpreting single-locus results in polyclonal infections, where dominant strains may mask minor deletion-bearing clones that nested PCR cannot reliably detect.

The findings carry clear implications. PfHRP2-based rapid diagnostic tests remain reliable for malaria diagnosis in the regions surveyed, and the near-absence of deletions both before and up to five years after the 2012 rollout suggests that diagnostic-driven selection has not yet taken hold in Kenya, likely owing to high transmission intensity that sustains parasite genetic diversity, frequent polyclonal infections that limit the spread of mutants, and comparatively modest selection pressure. The authors caution, however, that the situation in the Horn of Africa demonstrates how quickly this can change under sustained exclusive reliance on a single antigen target. Continuous molecular surveillance, they argue, is essential to identify emerging deletion hotspots early and to safeguard the long-term effectiveness of the diagnostics on which Kenya’s malaria control program depends.

Subject of Research: Prevalence of Plasmodium falciparum pfhrp2 and pfhrp3 gene deletions affecting malaria rapid diagnostic tests in Kenya

Article Title: Low prevalence of Plasmodium falciparum pfhrp2 and pfhrp3 gene deletions in archived samples collected before and after nationwide malaria-RDT rollout in Kenya

Article References: Kivecu, M. N., Mobegi, V., Mgawe, C., Kania, B. M., Chemwor, G. C., Okoth, R. O., Mwakio, E. W., Obiero, G., Mutisya, J. M., Juma, J. A., Cheruiyot, A. C., Opot, B. H., Roth, A. L., Ogutu, B. R., Juma, D. W., Ochola-Oyier, L. I., Andagalu, B., & Akala, H. M. (2026). Low prevalence of Plasmodium falciparum pfhrp2 and pfhrp3 gene deletions in archived samples collected before and after nationwide malaria-RDT rollout in Kenya. Frontiers in Epidemiology, 6, Article 1817539. https://doi.org/10.3389/fepid.2026.1817539

Image Credits: AI Generated

DOI: 10.3389/fepid.2026.1817539

Keywords: malaria, Plasmodium falciparum, pfhrp2, pfhrp3, gene deletions, rapid diagnostic tests, Kenya, molecular surveillance, diagnostics, public health, KEMRI, parasite genomics

The central promise of malaria molecular surveillance is deceptively simple: read the parasite’s genome and you can read the epidemic. Genetic data can reveal whether infections are imported or locally acquired, how transmission clusters shift across space and time, and whether drug-resistant lineages are quietly expanding. High-throughput sequencing, increasingly complemented by targeted and portable platforms, now makes it feasible to genotype parasites at the scale programs require, while a maturing analytical toolkit converts raw sequence data into epidemiologically meaningful signals. Yet the editors are candid about persistent obstacles: methods must be accessible, appropriately matched to the question at hand, and able to deliver actionable information to the program officers who need it.

A recurring barrier has been the cost, infrastructure, and specialist expertise that next-generation sequencing demands, which are often unavailable precisely where surveillance is most needed. Several contributions tackle this head-on by validating targeted approaches that recover information comparable to whole genome sequencing at a fraction of the cost. Niaré and colleagues present a highly multiplexed molecular inversion probe panel for Plasmodium falciparum that targets common single-nucleotide polymorphisms and approximates whole-genome-based assessments of selection and relatedness, effectively bringing genome-scale inference within reach of programmatic budgets. In a complementary evaluation, Cabrera-Sosa and colleagues benchmark newly developed SNP barcode panels for both P. falciparum and P. vivax against established microsatellite markers in the Peruvian Amazon, offering evidence-based recommendations for panel selection in endemic settings.

Accessibility extends beyond cost savings to physical location. Adegbola and colleagues applied portable Oxford Nanopore sequencing to characterize drug-resistance loci within an antenatal-care population in Nigeria, demonstrating how decentralized platforms can lower the barrier to in-country genotyping and embed genomic analysis in routine clinical touchpoints. The technical significance is considerable: nanopore sequencers are compact, relatively inexpensive, and can operate outside well-resourced reference laboratories, meaning that resistance profiling no longer depends on shipping samples across continents. On the vector side, Boddé and colleagues demonstrate improved species assignment across the entire Anopheles genus using a targeted-sequencing assay for mosquito genotyping paired with updated reference databases, a critical advance given that accurate vector identification underpins every entomological intervention from bed nets to larval source management.

The second theme of the collection is translation: turning genomic data into programmatically actionable outputs that resolve transmission dynamics and parasite connectivity. Pereus and colleagues evaluated P. falciparum diversity across mainland Tanzania using genetic metrics of complexity of infection, parasite connectivity, and transmission intensity, revealing heterogeneity that conventional indicators such as case counts and prevalence surveys can miss. In malaria-endemic regions, transmission is often intensely focal, with hotspots and residual pockets persisting even as overall burden falls, and genomic signatures can pinpoint these pockets with a resolution that routine surveillance cannot match.

That sensitivity to changing dynamics is equally valuable for Plasmodium vivax, the stubborn relapsing parasite that poses unique elimination challenges. Fola and colleagues used population genetic metrics to track P. vivax transmission indicators through a period of transmission decline and subsequent rebound in two endemic areas of Papua New Guinea, showing that genomic signals can capture changing transmission dynamics precisely where they are hardest to measure by conventional means. As countries push toward elimination and case numbers dwindle, traditional metrics lose statistical power; genetic relatedness among the few remaining infections becomes one of the few reliable signals of whether transmission is truly interrupted or quietly continuing.

Perhaps the most consequential use case is antimalarial drug resistance, which remains one of the greatest threats to malaria control globally. Kattenberg and colleagues used genetic surveillance to document the spread of artemisinin-combination-therapy resistance during a period of malaria decline in Vietnam between 2018 and 2020, producing outputs with immediate implications for treatment guidelines and containment efforts. The finding illustrates the operational value of molecular surveillance: when resistance genotypes are mapped in near real time, national programs can adjust first-line therapies, target containment measures to affected regions, and anticipate further spread before it overwhelms treatment policy. The Oxford Nanopore-based profiling of crt, dhfr, and dhps resistance markers in pregnant women reported by Adegbola and colleagues points toward new approaches for embedding resistance genotyping into existing clinical infrastructure such as antenatal care, where pregnant women already receive routine screening and treatment.

Yet real gaps remain between capability and routine use. Safarpour and colleagues synthesized the challenge for one critical elimination use case: distinguishing imported from locally acquired infections. They found that current methods are still limited by cost, by an inability to reliably discriminate between imported and local parasites, by difficulties tracking parasite movement across borders and at within-country or smaller spatial scales, and by reliance on cross-sectional summary statistics that capture only snapshots of transmission rather than its continuous evolution. Their review also highlights a persistent neglect of P. vivax and other non-falciparum species. While P. falciparum accounts for the major burden of global malaria cases, eradication will require concerted efforts to address the unique biology of the relapsing, dormant-liver-stage parasites that characterize vivax malaria.

Encouragingly, several contributions reflect expanding sequencing and bioinformatics capacity, along with growing scientific leadership, within malaria-endemic regions themselves. Investments in regional sequencing hubs, local expertise, and collaborative research networks are enabling countries to generate and interpret genomic data relevant to their own public health priorities rather than exporting samples and analysis abroad. The editors stress that this momentum must be sustained if molecular surveillance is to become routine public health practice rather than remain constrained to research. The next phase, they argue, should focus on generating fit-for-purpose data at the scale and timeliness necessary for translation into decision-making, which will require sustained investment in local infrastructure, harmonized and tailored analytical frameworks, and closer engagement between genomic scientists and national programs.

The editors also emphasize that the future of malaria genomics lies in integration: combining parasite and vector data, and layering molecular, epidemiological, clinical, and environmental information into a coherent picture of transmission. As national programs confront evolving biological and operational challenges, from drug resistance to climate-driven shifts in vector ranges, genetic data will play an increasingly central role in guiding interventions, informing policy, and sustaining progress toward elimination. The collection stands as both a technical benchmark and a roadmap, showing that the tools for genome-informed malaria elimination largely exist, and that the decisive work ahead is making them routine, equitable, and fast enough for the programs that depend on them.

Subject of Research: Malaria molecular surveillance and genomics

Article Title: Editorial: Advanced genetic and genomic methods and applications for malaria surveillance

Article References: Ruybal-Pesántez, S., Kattenberg, J. H., Ghansah, A., & Auburn, S. (2026). Editorial: Advanced genetic and genomic methods and applications for malaria surveillance. Frontiers in Genetics, 17, Article 2000967. https://doi.org/10.3389/fgene.2026.2000967

Image Credits: AI Generated

DOI: 10.3389/fgene.2026.2000967

Keywords: malaria, genomics, molecular surveillance, drug resistance, Plasmodium falciparum, Plasmodium vivax, Anopheles, public health, Editorial, Advanced, genetic, genomic

The research team, led by Tongjit Thanchomnang of Mahasarakham University together with colleagues at Burapha University and the University of Lincoln, screened 960 schoolchildren attending five public schools in urban and rural areas of Chonburi Province between May and July 2024. The overall prevalence of pediculosis, the medical term for head louse infestation, came out at 20.42 percent, with a 95 percent confidence interval of 17.91 to 23.11 percent. That figure masks a striking geographic pattern: infestation was markedly more common in rural schools than in urban ones. The study was approved by the Institutional Review Board of Burapha University, and written informed consent was obtained from parents or legal guardians before any child took part, with age-appropriate assent from the children themselves.

Beyond the headline prevalence number, the team used logistic regression to identify which characteristics of the children were statistically associated with carrying lice. Four factors stood out: sex, school level, hair length, and a reported history of pediculicide use, meaning the use of chemical lice treatments. The association with reported pediculicide use is perhaps the most intriguing of the four, because it hints at a self-reinforcing cycle in which children who have been treated remain infested, either because the treatment failed or because reinfection occurred quickly, prompting yet more rounds of chemical exposure. The authors are careful to frame these as epidemiological associations rather than proof of causation, but the pattern is consistent with what happens in populations where the parasites are no longer reliably killed by the standard drugs.

To understand what was happening at the molecular level, the researchers collected lice from infested children and first confirmed their identity. Every sample examined was morphologically identified as Pediculus humanus capitis, the head louse, and analysis of the mitochondrial cytochrome c oxidase subunit 1 gene, known as cox1, placed the insects in mitochondrial clades A or C. These clades describe the deep maternal lineages of head lice and are used by researchers worldwide to track louse populations. Clade A is the most widespread lineage globally, while clade C has a more patchy distribution, and finding both in the same school settings gives a snapshot of the genetic diversity circulating among Thai schoolchildren.

The heart of the study, however, lies in its exploratory search for knockdown resistance mutations, commonly abbreviated as kdr. These mutations occur in the gene encoding the voltage-sensitive sodium channel, or VSSC, a protein in the nerve cell membranes of insects that is the primary molecular target of pyrethroid insecticides. Pyrethroids, the synthetic compounds modeled on natural chrysanthemum-derived toxins, work by binding to this channel and holding it open, paralyzing and killing the insect. Permethrin, the pyrethroid most commonly formulated against head lice, depends entirely on this mechanism. When specific amino acid substitutions appear in the sodium channel protein, the insecticide binds less effectively, the insect survives exposure, and the mutation spreads through the population under the relentless selection pressure of repeated treatments.

Two such mutations are the classic markers of pyrethroid resistance in head lice: T917I, in which the amino acid threonine at position 917 of the channel protein is replaced by isoleucine, and L920F, in which leucine at position 920 is replaced by phenylalanine. Using polymerase chain reaction and sequencing on a stratified subsample of the collected lice, the researchers detected these resistance-associated mutations in the Thai lice populations. More significantly, they identified homozygous resistant genotypes, in which an individual louse carries two copies of the resistance-associated allele, one inherited from each parent. These homozygous resistant individuals, the genotype most strongly linked to survival after pyrethroid exposure, were found in lice collected from four of the sampled schools, indicating that the resistance-associated variants are not isolated curiosities but established features of the local louse populations.

Perhaps the most sobering detail is that resistance-associated genotypes were detected among lice collected from children both with and without reported histories of permethrin treatment. This suggests that the resistant insects are circulating through the school community regardless of whether an individual child has been directly exposed to the drug, carried from head to head by the close contact that defines childhood social life. A louse carrying resistance mutations does not need its host to have used permethrin; it simply needs to have descended from a lineage that survived such exposure somewhere in the local population. In this way, individual treatment decisions ripple outward, shaping the genetic composition of parasites that infest the entire community.

The authors are appropriately measured in their interpretation. Molecular detection of kdr mutations, they emphasize, cannot by itself confirm clinical resistance, because genotype is a proxy rather than a direct measurement of treatment failure. Confirming that permethrin genuinely fails in the clinic would require phenotypic validation studies, in which live lice are exposed to controlled doses of the insecticide and their survival is measured. Nevertheless, the molecular findings carry weight in context. Previous studies in the region have reported incomplete treatment outcomes following permethrin use, and the new genetic data provide a plausible mechanism for those observations. The convergence of epidemiological signals, molecular markers, and prior clinical reports paints a coherent picture of a treatment under strain.

What makes this study particularly valuable is its integrated design. Rather than measuring prevalence, risk factors, and molecular resistance in separate investigations, the team combined all three within the same school settings, allowing a direct link to be drawn between the children experiencing infestations and the genetic character of the lice infesting them. This kind of joined-up surveillance is exactly what public health authorities need when deciding how to respond. If resistance mutations are present, simply recommending more frequent permethrin applications may be futile or even counterproductive, intensifying the selection pressure that drives resistance further. Alternative non-pyrethroid therapies exist, and the study’s ethical protocol already reflected this reality: when treatment failure was suspected, alternative non-pyrethroid treatments were recommended in consultation with local healthcare professionals.

The broader implications extend well beyond Chonburi Province. Pyrethroid resistance in head lice has now been documented across multiple continents, and each new geographic confirmation reinforces the case for coordinated management approaches rather than ad hoc, drug-by-drug responses. The researchers call for continued molecular surveillance, phenotypic validation studies, and future evaluation of coordinated management strategies in endemic settings. For the millions of families worldwide who reach for a permethrin shampoo at the first sign of lice, the message is that the era of assuming the first bottle will work is drawing to a close. Head lice remain a common and treatable condition, but treating them effectively in the twenty-first century increasingly requires knowing what the local lice look like, genetically speaking, before choosing the weapon. Studies like this one provide exactly that knowledge, and they suggest that in eastern Thailand, the lice have already adapted to the old playbook.

Subject of Research: Head louse infestation prevalence and knockdown resistance mutations in schoolchildren in eastern Thailand

Article Title: High prevalence of pediculosis, associated factors, and exploratory detection of the knockdown resistance mutations in head lice from school settings in Chonburi Province, eastern Thailand

Article References: Thanchomnang, T., Gordon, C. N., Krittanan, P., Yangthaworn, K., Thetkathuek, A., Clegg, S. R., Mano, C., & Yingklang, M. (2026). High prevalence of pediculosis, associated factors, and exploratory detection of the knockdown resistance mutations in head lice from school settings in Chonburi Province, eastern Thailand. Parasites & Vectors, 19(1), Article 391. https://doi.org/10.1186/s13071-026-07672-y

Image Credits: AI Generated

DOI: 10.1186/s13071-026-07672-y

Keywords: head lice, pediculosis, kdr mutations, pyrethroid resistance, permethrin, schoolchildren, Thailand, molecular surveillance, voltage-sensitive sodium channel, cox1, public health, Parasites & Vectors