The results establish a regional genomic baseline for a selected high-risk clinical subset, rather than a population-wide estimate of resistance prevalence. The State Public Health Laboratory of Aguascalientes processed 3,454 E. coli and Klebsiella isolates from regional hospitals during the study period, including 683 E. coli, 679 K. pneumoniae and 92 organisms initially identified by MALDI-TOF mass spectrometry and phenotypic testing as K. oxytoca. Whole-genome sequencing reclassified two of the latter isolates as K. michiganensis.

Of the processed isolates, 246 met the study definitions for multidrug resistance or extensive drug resistance, and 65 were selected for sequencing after confirmation of species identity, availability of pure clinically relevant cultures and satisfaction of DNA-quality requirements. Almost all the sequenced isolates—94%—were recovered from patients in critical-care units, and clinical records classified 97.1% of Klebsiella cases and 93.3% of E. coli cases as severe illness. This referral pattern is central to interpreting the findings: the dataset represents severe, treatment-refractory or otherwise difficult-to-manage infections and is enriched for highly resistant organisms rather than representing community circulation.

p>Phenotypic susceptibility testing showed broad resistance across major antibiotic classes, including several drugs commonly used for urinary, respiratory and inpatient infections. Every sequenced isolate carried extended-spectrum beta-lactamase genes, consistent with cephalosporin resistance reaching 97.1% among the 35 Klebsiella isolates and 100% among the 30 E. coli isolates. Resistance to ciprofloxacin and levofloxacin exceeded 90% in both groups, while trimethoprim-sulfamethoxazole resistance was 82.8% in Klebsiella and 90% in E. coli.

Carbapenem resistance occurred in 31.4% of Klebsiella isolates and 13.3% of E. coli isolates. Amikacin retained activity against more isolates than most tested agents, although resistance was present in 11.4% of the Klebsiella group. Among Klebsiella respiratory isolates, tigecycline resistance increased from 0% in 2022 to 40% in 2023.

The study also found that E. coli XDR phenotypes were confined to the 2023 collection, while later Klebsiella isolates showed more dynamic carbapenem and tigecycline resistance patterns. p>Integrating phenotypic susceptibility results with genomic predictions produced 78.9% overall concordance across 689 antibiotic-class comparisons. Agreement exceeded 90% for fluoroquinolones, sulfonamides and macrolides, whose resistance determinants are comparatively well characterized, and reached 100% for E. coli against cephalosporins and for both macrolide results in Klebsiella. Concordance was substantially lower for aminoglycosides and carbapenems.

Some Klebsiella isolates were phenotypically resistant to carbapenems without carrying canonical blaKPC, blaNDM or blaOXA-48 genes; combinations of OXA-type beta-lactamases, porin disruption and efflux systems were instead associated with the phenotype. These findings identify possible non-classical contributors but do not directly prove their causal effects. Genomic predictions can also be affected by gene expression, regulatory mutations, epistasis, promoter efficiency and laboratory conditions, so the authors emphasize that gene detection alone cannot replace phenotypic susceptibility testing. p>Phylogenomic analysis placed the Aguascalientes genomes within a broader but unevenly sampled Mexican genomic landscape.

The comparative dataset included 268 public genomes: 139 E. coli, 85 K. pneumoniae and 44 K. michiganensis, the last comprising three Mexican isolates and 41 international reference genomes. Mexico City and Puebla were relatively well represented, whereas more than half of Mexico’s states were under-represented or absent. The 30 E. coli isolates from Aguascalientes fell into 15 sequence types and were distributed across the phylogeny rather than forming one local cluster.

They were interspersed with genomes from other states, indicating that the lineages detected locally overlapped with broader national patterns. Because sampling was neither population-based nor geographically uniform, the national comparison cannot establish population prevalence or a continuous national transmission route. The E. coli collection included established high-risk lineages such as ST131 and ST69, which also occurred most frequently among the public Mexican E. coli genomes.

Six isolates could not be assigned to a recognized sequence type; these untyped genomes carried the largest resistance-gene burdens, averaging more than 100 antimicrobial-resistance genes per genome. The blaCTX-M-15 gene was present in 90% of the Aguascalientes isolates, compared with 18% of public Mexican E. coli genomes. Polymyxin-associated regulators, including arnA, eptA, mgrB and members of the pmrB, pmrC and pmrF family, also occurred at higher frequencies in the referral collection.

Detection of these genes establishes their genomic presence, not phenotypic colistin resistance or the transfer of a particular plasmid. Across 169 E. coli genomes, the researchers identified 345 mobile genetic elements in the LESPA isolates, including 26 plasmid-associated elements and 319 of uncertain chromosomal origin. MITEEc1 had the largest number of reported associations, including links with ompT and virulence-associated loci.

p>Resistance genes were frequently located in mobile contexts, a pattern consistent with possible horizontal gene-transfer dynamics in clinical environments. The analysis catalogued 211 mobile genetic elements among the sequenced K. pneumoniae isolates and identified associations involving plasmids, transposons and insertion sequences. K. pneumoniae served as a principal sharing hub in the cross-species network, linking genes including the CTX-M-15, sul1, sul2, tetA, mphA and dfrA families with both E. coli and Klebsiella.

The two K. michiganensis isolates carried NDM-7, VIM-1 and MCR-9.1, which were absent from the sequenced E. coli and K. pneumoniae mobilomes. These observations identify mobile contexts and candidate routes of dissemination, but the study did not perform long-read sequencing or reconstruct complete plasmids. Genomic proximity alone therefore does not demonstrate patient-to-patient transmission or prove that a particular element transferred between species. p>The K. michiganensis isolates expanded the limited genomic record for an undercharacterized member of the K. oxytoca complex in Mexico.

One belonged to ST180 and clustered with genomes from China and the United States, while the other had an unknown sequence type and grouped with Mexican and North American isolates. Their phylogenetic positions were consistent with separate introductions into the regional collection, but the sample of two was too small to establish the species’ broader epidemiology. They were also the first multidrug-resistant K. michiganensis genomes reported from Aguascalientes and occupied separate resistance-gene clusters.

Pangenome analysis showed open, accessory-rich genomes for all three species. Cloud genes, defined as genes present in fewer than 15% of genomes, accounted for 81.7% of the E. coli pangenome, 76.1% of K. pneumoniae and 63.8% of the K. oxytoca complex dataset, illustrating substantial genomic diversity without directly demonstrating its origin or rate of evolution. p>Clinical complexity accompanied the molecular findings. Coinfections were recorded in 60% of Klebsiella cases and 36.7% of E. coli cases, with Acinetobacter baumannii, Enterococcus faecalis and Pseudomonas aeruginosa among the most frequent co-occurring organisms.

Among E. coli, virulence analysis identified seven units found only in the LESPA collection, including a shu hemin-uptake operon, afaC-VIII and galU; no K. pneumoniae virulence units exclusive to the new isolates were found. Temporal comparisons showed richer resistomes, more XDR phenotypes and more frequent coinfections among post-2020 isolates than in the older public collection, including a rise in carbapenem resistance among Klebsiella respiratory isolates from 0% in 2022 to 83% in 2023. These observations cannot be attributed to the COVID-19 pandemic or antibiotic use from this referral-heavy dataset, and they do not demonstrate population-wide temporal change.

The study instead supports routine whole-genome sequencing, standardized metadata and continued phenotypic testing as components of more representative antimicrobial-resistance surveillance across Mexico.

Subject of Research: Genomic surveillance of multidrug-resistant E. coli and Klebsiella in Aguascalientes, Mexico

Article Title: Genomic surveillance uncovers high-risk resistance profiles in Escherichia coli and Klebsiella spp. from Central Mexico

Article References: Lozano Gamboa, M. S., Muñoz Gomez, B., Maldonado Gonzaga, A. Y., Alejo Hernández, M. A., Cazares, A., Diaz, D., Marmolejo, A. P., & Ceapă, C. D. (2026). Genomic surveillance uncovers high-risk resistance profiles in Escherichia coli and Klebsiella spp. from Central Mexico. Frontiers in Cellular and Infection Microbiology, 16, 1939440. https://doi.org/10.3389/fcimb.2026.1939440

Image Credits: AI Generated

DOI: 10.3389/fcimb.2026.1939440

Keywords: antimicrobial resistance, genomic surveillance, Escherichia coli, Klebsiella pneumoniae, Klebsiella michiganensis, whole-genome sequencing, resistome, mobile genetic elements, Mexico, clinical microbiology, Genomic, surveillance

The analysis included studies from lower-middle-income countries in which children under five with acute diarrhea were tested using stool specimens. For studies examining rotavirus, the researchers required that data collection begin in or after the year of national rotavirus vaccine introduction. Norovirus studies were not restricted by publication year. Eligible designs included cross-sectional studies, case-control studies and large-scale surveillance studies, with a minimum sample size of 50 participants.

Researchers searched PubMed, Scopus, ScienceDirect, Embase and Web of Science from February 20 to February 28, 2026. They removed duplicates, screened titles and abstracts, reviewed full texts and extracted data with two investigators working independently. The review protocol was registered in PROSPERO as CRD420261349950. The investigators used the Joanna Briggs Institute checklist for studies reporting prevalence; all 45 included reports were rated moderate or high quality, with scores ranging from 55.5% to 100%.

Most of the evidence base consisted of cross-sectional studies, while 11 reports were large-scale surveillance studies. Detection methods also varied: 23 studies used RT-PCR, 19 used both RT-PCR and ELISA, and three used ELISA and multiplex RT-PCR. Individual study sample sizes ranged from 55 to 5,408. India contributed 20 studies, followed by Bangladesh and Ethiopia with four each, and Nigeria with three. Limited representation from several regions and the large number of Indian studies limited geographic representativeness, the authors said.

Using a restricted maximum likelihood random-effects model, the review estimated combined pooled prevalence for norovirus and rotavirus at 18% (95% confidence interval, 15%–21%). The virus-specific estimates were 24% (95% CI, 19.6%–28.3%) for rotavirus and 13% (95% CI, 11%–15%) for norovirus. Norovirus prevalence ranged from 3.12% to 30.50% across studies, while rotavirus prevalence ranged from 17.90% to 46.50%.

Results varied substantially across the included studies. The combined analysis showed very high heterogeneity, with I² reported at approximately 98.7%–98.9% and Cochran’s Q significant at p<0.001. Regional pooled estimates ranged from 11% (95% CI, 9%–14%) in the Middle East to 26% (95% CI, 8%–45%) in Southern Africa. Pooled prevalence was 17% (95% CI, 14%–20%) in cross-sectional studies and 21% (95% CI, 16%–27%) in surveillance studies. By detection method, estimates were 25% for ELISA combined with RT-PCR, 18% for ELISA combined with multiplex PCR and 13% for RT-PCR alone.

Genotype information was available from 43 studies. Among 9,889 samples sequenced, the review identified 1,840 genotypes. For norovirus, genogroup GII predominated, with a pooled prevalence of 76% (95% CI, 61%–91%), followed by GI at 23% (95% CI, 9%–37%). GII.4 was the most frequent norovirus subgenotype, accounting for a pooled 53% of cases (95% CI, 39%–68%). GII.3 was also reported, with 145 detections across included studies.

For rotavirus, the most frequently observed genotype combinations were G3P[8] and G1P[8], with pooled prevalences of 39% (95% CI, 28%–51%) and 17% (95% CI, 10%–25%), respectively. G3P[8] accounted for 1,437 detections, primarily from India but also from Ethiopia and Kenya. G1P[8] accounted for 501 detections from Morocco, Ethiopia and India, while G2P[4] accounted for 489 detections from India, Ethiopia, Honduras and Zambia. The review also recorded 384 mixed-type rotavirus detections, five partially typable detections and 16 non-typable detections.

Several limitations constrain interpretation of the pooled estimates. Most included studies were cross-sectional and therefore could not establish temporal associations. The English-language restriction may have introduced language bias, heterogeneity was substantial, and statistical tests indicated possible small-study effects and publication bias. Although a trim-and-fill analysis left the overall pooled estimate unchanged, a leave-one-out analysis found that removing individual studies did not materially alter it. The authors cautioned that the findings should not be considered conclusive because of these limitations, geographic gaps and the disproportionate contribution of studies from India.

Subject of Research: Prevalence and genotype distribution of norovirus and rotavirus among children under five with diarrhea in lower-middle-income countries

Article Title: Prevalence and genotype distribution of norovirus and rotavirus among children under five with diarrheal infection in lower-middle-income countries after Rotavirus vaccine introduction: A systematic review and meta-analysis

Article References: Ayele, F., Assebe, T., Mandefro, M., Admassu Ayana, D., & Assefa, N. (2026). Prevalence and genotype distribution of norovirus and rotavirus among children under five with diarrheal infection in lower-middle-income countries after Rotavirus vaccine introduction: A systematic review and meta-analysis. PLOS One, 21(10), e0359886. https://doi.org/10.1371/journal.pone.0359886

Image Credits: AI Generated

DOI: 10.1371/journal.pone.0359886

Keywords: norovirus, rotavirus, childhood diarrhea, systematic review, meta-analysis, viral prevalence, genotype distribution, lower-middle-income countries, vaccine introduction, genomic surveillance, Prevalence, genotype

The findings were assembled by researchers from the United Nations University Institute for Water, Environment and Health, the University of Oxford, Imperial College London, the London School of Hygiene and Tropical Medicine, King’s College London, Nagasaki University, the Japan Institute for Health Security, the Public Health Foundation of India and the Middle East Liver Disease Center. Published in October 2026 as “Best Practices in Global Vaccination Roll-Out to Reduce Health Inequity,” the policy brief reviews modelling studies and peer-reviewed evidence on the unequal timing and scale of COVID-19 vaccination. It accompanies a September 2026 publication in the journal Expert Review of Vaccines. The analysis concerns pandemic preparedness rather than a new clinical trial, and its central mortality figures are counterfactual model estimates rather than deaths directly observed after a policy intervention.

COVID-19 vaccines were introduced across countries more quickly and, by some measures, more equitably than earlier vaccines, yet access remained sharply unequal. By the end of 2021, high- and upper-middle-income countries had administered at least one dose per person on average. In contrast, lower-middle-income countries had administered one dose for every three people, while low-income countries had administered one for every 25 people. The disparity is historically unusual: earlier vaccines against Haemophilus influenzae type b and human papillomavirus often reached low-income countries 10 to 30 years after reaching high-income countries. Thus, the speed of COVID-19 vaccine development represented a scientific achievement, but the distribution system did not ensure that protection arrived with comparable speed or scale.

Several studies reviewed in the publication estimate the potential effect of narrowing the roll-out gap. If lower-middle- and low-income countries had matched the vaccination rates of high-income countries, as many as half of their COVID-19 deaths might have been averted by 1 October 2021. A separate estimate suggests that more equitable sharing of existing vaccine supply could have prevented 1.3 million deaths worldwide by the end of 2021. These are modelled counterfactual scenarios, not evaluations of a vaccination programme in which the proposed changes were fully implemented. They indicate the scale of the inequity documented by the research. The publication also reports that vaccination averted far fewer deaths per capita in low-income countries, particularly in the Eastern Mediterranean and African regions, than in high-income countries.

Delayed protection in lower-resource settings also had consequences beyond mortality. Prolonged opportunities for transmission increased the risk that new variants could emerge, while slower control of the epidemic weakened economic recovery and reduced health and economic security across national borders. The modelling reviewed by the brief estimated the lives saved by an earlier roll-out at more than 8 million, with those life-years valued at US$14 trillion. Parallel investment in manufacturing capacity and health systems was associated with an additional modelled 3 million lives saved and a corresponding monetary value of US$5 trillion. These valuation figures are model outputs that translate mortality effects into economic terms; they are not direct measurements of realised savings.

The authors propose an “equity-by-design” framework in which vaccine development is linked systematically to financing, procurement, manufacturing, allocation, delivery, uptake, safety monitoring and accountability. The approach is intended to translate broad commitments to pandemic solidarity into mechanisms that can operate before the next emergency. It draws on the World Health Organization Pandemic Agreement, adopted in May 2025, and amended International Health Regulations, in force for most States Parties since September 2025. The brief argues that allocation principles should be established in advance so that limited supplies can be distributed according to epidemiological evidence, including disease burden, risk of severe outcomes and transmission speed, rather than negotiated after a crisis has begun.

Six practical recommendations structure the proposed framework. Governments and international organisations should prepare pooled procurement, research funding, surveillance, scalable manufacturing, supply chains and regional stockpiles before an emergency. Vaccine allocation should build on COVAX’s pooled-demand and needs-based approach while adding earlier and predictable finance, enforceable access commitments, predefined dose-sharing triggers and public tracking of roll-out timelines. Advance purchase agreements should require transparent prices, flexible delivery and automatic sharing when agreed triggers are met, while diversified vaccine portfolios could reduce supply risks. The recommendations also call for transparent reporting of cases, hospital admissions, deaths, adverse events and vaccination by age, sex, geography and risk group in standard, machine-readable formats, supported by community engagement and monitoring of misinformation.

International institutions and national authorities are further advised to insulate vaccine policy from political distortion by strengthening regulatory standards and independent advisory committees, and to support rather than penalise countries that report outbreaks and dangerous variants early. The research team argues that punitive responses, including travel restrictions, may have discouraged timely reporting during COVID-19. Timely sharing of high-quality, geographically representative genomic data should instead be encouraged through recognition of contributors and equitable access to benefits, including vaccines and other countermeasures. Sustained investment in pathogen surveillance, sequencing, analysis and workforce training is also needed to detect emerging threats and inform vaccine responses. The proposal is intended to make surveillance and data sharing part of preparedness, rather than treating them as separate from the vaccine system.

Delivery capacity and regional production form the final foundation of the framework. The authors caution that regional manufacturing is not a stand-alone solution: it requires long-term demand, predictable finance, regulatory convergence and a skilled workforce. Health facilities, trained personnel, cold chains and real-time monitoring of vaccine stocks and temperatures must also be strengthened, particularly in low-resource and conflict-affected settings. Within countries, vaccination should be targeted toward vulnerable and high-risk groups using models that account for health and socioeconomic vulnerability, with independent national oversight. The study therefore treats equity as an operational property of the entire vaccine system, linking surveillance and innovation to manufacturing, procurement, allocation and last-mile delivery rather than treating equitable access as a distribution step added after production.

The policy brief does not report a retrospective vaccination programme that prevented all of the modelled deaths; instead, it quantifies losses associated with a historically unequal roll-out and identifies mechanisms intended to prevent repetition. Its central technical conclusion is that pandemic technologies cannot deliver their full public-health value unless financing, supply allocation, manufacturing and health-system delivery are designed in advance around equity. A start 100 days after viral sequencing might have saved more than 8 million lives, but the additional 3 million-life estimate from parallel capacity investments shows why the broader response also matters. The proposed solution is a pre-agreed global operating system for vaccine access, one that can turn scientific speed into timely protection across countries by ensuring that surveillance, finance, production and delivery are addressed together before the next health emergency.

Subject of Research: Modelled effects of global COVID-19 vaccine equity and pandemic preparedness

Article Title: Scientific triumph, equity failure: Faster, fairer COVID-19 vaccine roll-out could have saved millions of lives, UN University publication reveals

Article References: Scientific triumph, equity failure: Faster, fairer COVID-19 vaccine roll-out could have saved millions of lives, UN University publication reveals. Original publication (Bibliographic details unavailable.)

Image Credits: AI Generated

DOI: Not provided

Keywords: COVID-19 vaccines, vaccine equity, pandemic preparedness, global health, health inequity, vaccine allocation, regional manufacturing, genomic surveillance, United Nations University, health systems, Scientific, triumph

Poxviruses are large double-stranded DNA viruses, and recombination has long been recognized as a fundamental engine of their evolution. Laboratory studies dating back to the late 1980s demonstrated high levels of genetic exchange among poxvirus DNAs in infected cells, and comparative genomics of variola, the smallpox virus, revealed signatures of past recombination events in its evolutionary history. Recombination requires co-infection of a single cell by two genetically distinct viruses, after which the cellular and viral machinery can copy alternating templates, stitching together segments from each parent. In principle, mpox viruses from different clades could recombine wherever their transmission chains overlap — in a co-infected individual or, more plausibly given the epidemiology, in an animal reservoir host where viruses from distinct phylogeographic lineages might meet.

The Indian case came to light through the country’s mpox diagnostic network, which the Indian Council of Medical Research has been strengthening since the global outbreak of clade IIb virus began in 2022. The patient, who acquired the infection through travel, was managed clinically while specimens were forwarded for molecular testing and whole-genome sequencing. Initial real-time PCR screening could not have distinguished this virus from any other mpox infection, since standard assays target conserved genes shared across clades. Only when the researchers assembled the complete genome did the mosaic structure become apparent: stretches of sequence unambiguously derived from clade Ib, the lineage that emerged in Central Africa and spread internationally in 2024, alternating with stretches characteristic of clade IIb, the West African lineage behind the 2022 worldwide epidemic.

Detailed comparative analysis showed that the recombinant genome carries clade-defining mutations from both parental lineages. Clade-defining mutations are the fixed single-nucleotide changes that distinguish the major mpox clades Ia, Ib, IIa and IIb from one another; their simultaneous presence in a single genome, arranged in a block-like pattern along the chromosome, is the molecular fingerprint of recombination rather than convergent mutation. The team mapped 34 recombinant tracts — continuous segments of the genome inherited from one or the other parental clade — and identified 21 mutations that define the recombinant lineage itself. This pattern mirrors that of the UK recombinant virus, which likewise displayed 34 recombinant tracts and 21 recombinant lineage-associated mutations, a coincidence of architecture that points to a shared ancestry.

Phylogenetic analysis reinforced that conclusion. When individual recombinant tracts were extracted and placed on separate phylogenetic trees, each tract clustered with reference genomes from its parental clade, alternating between Ib and IIb positions depending on the segment examined. When whole recombinant genomes were compared with representative sequences from all four clades, the Indian and UK viruses formed a distinct group positioned intermediate between clades Ib and IIb. A phylogenetic network constructed with SplitsTree placed the recombinants in a characteristic box-like structure, a visual signature of reticulate evolution that arises when sequence relationships cannot be explained by a single branching tree. Statistical testing supported the inference of recombination among these viruses.

Beyond the phylogenetics, the team went a step further than most surveillance studies by isolating live virus. Clinical material was propagated in Vero CCL-81 cells, and cytopathic effects were observed by the third day after infection at the second passage, with the experiment repeated three times with consistent results. Virus isolation matters because it confirms that the recombinant genome was not an artefact of mixed sequencing reads from a co-infected patient but a viable, replicating virus. It also provides reagents for phenotypic characterization — growth kinetics, drug susceptibility, antigenicity — that sequence data alone cannot deliver. Both the clinical sample sequence and the isolate sequence were deposited publicly in the Pathoplexus database and the International Nucleotide Sequence Database Collaboration, under accession numbers that allow any laboratory to verify or extend the analysis.

The practical consequences for diagnostics are among the most important implications of the work. Several multiplex real-time PCR assays have been developed to differentiate mpox clades, exploiting clade-specific mutations to classify infections rapidly, and targeted assays exist specifically to detect the novel clade Ib lineage. A recombinant virus that combines genetic material from two clades can scramble such classifications: depending on which primer and probe sets are used, a single specimen might be typed as Ib, as IIb, or yield discordant results across targets. In the worst case, a diagnostic algorithm keyed to a clade Ib-specific mutation that falls inside a clade IIb-derived tract of the recombinant genome could produce a false negative for clade Ib classification. The authors outline a diagnostic workflow for the preliminary identification of suspected recombinant MPXV isolates, emphasizing that clade-typing assays should be interpreted alongside whole-genome sequencing whenever results are discordant or epidemiologically unexpected.

The broader epidemiological question raised by the finding is where and how these recombination events occurred. The Indian virus was imported through travel, and the UK virus was likewise detected in a traveller returning from Asia, yet both genomes cluster together, implying a common recombinant ancestor rather than two independent recombination events. That places the origin of this lineage in a location where clade Ib and clade IIb viruses circulate in proximity — a region where the 2024 clade Ib outbreak overlapped geographically with lingering clade IIb transmission. If such co-circulation is sustained, further recombinants can be expected. The properties of any recombinant cannot be assumed in advance: recombination can combine, dilute, or disrupt adaptive mutations affecting transmissibility, immune evasion, or antiviral susceptibility, and only phenotypic study of isolated viruses will resolve those questions.

For surveillance programmes, the lesson is that clade-labelled snapshots are no longer sufficient. The 2022 global mpox epidemic demonstrated how quickly a localized zoonotic spillover can become an international epidemic once a virus adapts to sustained human transmission, and the emergence of clade Ib in 2024 with higher reported severity underscored the cost of delayed recognition. Recombination adds a third dimension of unpredictability on top of mutation and geographic spread. Wastewater surveillance, which has successfully detected mpox in environmental samples, offers one complementary channel for tracking viral diversity at the population level, but it too depends on downstream sequencing to reveal recombinant structure. What the Indian and UK detections prove is that the global sequencing network, when properly resourced and connected to rapid data-sharing platforms such as Pathoplexus, can catch these events and alert the international community within the timeframe that matters for public health response.

The Indian study also illustrates the value of linking clinical care, laboratory diagnostics and research sequencing under a single coordinated response. State health authorities in Kerala coordinated disease control activities, clinical teams managed the patient, and the virology team at ICMR–NIV Pune performed molecular testing, genome sequencing, phylogenetic analysis and virus isolation as an integrated pipeline, supported by intramural funding and by the Department of Health Research’s programme to expand the national mpox laboratory network. The result is a complete characterization of a rare viral entity within weeks of detection — from bedside to genome to viable isolate to publicly shared sequence data. As mpox continues to circulate in humans and presumably in animal reservoirs, recombinant lineages such as this Ib/IIb mosaic will serve as markers of where distinct viral populations meet, and continued genomic surveillance, backed by standardized diagnostics capable of recognizing their mosaic genomes, will determine whether the world spots the next such virus before it spreads.

Subject of Research: Recombinant Clade Ib and IIb monkeypox virus identified in an imported mpox case in India

Article Title: Genomic surveillance of an imported recombinant Clade Ib and IIb monkeypox virus case in India

Article References: Sahay, R. R., Khurana, J., Moorkoth, A. P., PP, B., Shete, A. M., Yadav, S., Majumdar, T., Rani, S., Vijay, N., Mali, D., Kamble, S., Gavari, S., Gawande, P., Marathe, H., Acharya, A. K., Gupta, N., & Yadav, P. D. (2026). Genomic surveillance of an imported recombinant Clade Ib and IIb monkeypox virus case in India. Nature Microbiology. https://doi.org/10.1038/s41564-026-02508-y

Image Credits: AI Generated

DOI: 10.1038/s41564-026-02508-y

Keywords: mpox, monkeypox virus, recombination, Clade Ib, Clade IIb, genomic surveillance, whole-genome sequencing, phylogenetics, virus isolation, diagnostics, India, public health

The biological logic behind the connection between a foodborne diarrhoeal pathogen and a paralysing neurological disease is molecular mimicry. Certain C. jejuni strains express sialylated lipooligosaccharide (LOS) structures on their outer membrane that structurally resemble human peripheral nerve gangliosides such as GM1, GD1a, and GT1a. IgG autoantibodies raised against these bacterial LOS molecules cross-react with gangliosides on human nerve cells, damaging them and triggering the syndrome. The fine specificity of this mimicry is determined in part by a single amino acid polymorphism at position 51 of the sialyltransferase Cst-II: an asparagine residue (Asn51) renders the enzyme bifunctional, producing disialylated GT1a and GD3 mimics associated with Miller Fisher syndrome, whereas a threonine residue (Thr51) yields a monofunctional enzyme that generates GM1 and GD1a mimics linked to the acute motor axonal neuropathy variant of Guillain-Barré syndrome.

The second major surface antigen of C. jejuni is the capsular polysaccharide (CPS), the primary serodeterminant of the bacterium. CPS biosynthetic genes sit within a large, highly variable chromosomal segment flanked by conserved ABC-transporter genes, and variation in these genes gives rise to at least 47 heat-stable (HS) serotypes identified by the classical Penner agglutination system. These 47 serotypes represent approximately 35 distinct capsule types, many of which share more than 97 percent DNA similarity and are therefore clustered into complexes. Beyond its protective role, the capsule mediates serum resistance to complement-mediated killing, facilitates host colonization, and is required for full invasiveness. Epidemiological studies have repeatedly linked certain Penner types, including HS19, HS41, HS23/36, HS4, HS2, and HS1/44, to Guillain-Barré syndrome, with HS19 infection raising the risk of the syndrome at least six-fold compared with other capsular types.

Traditional typing of these two loci has long been cumbersome. Penner serotyping is laborious, the antisera are expensive, and a proportion of outbreak and sporadic strains fail to type due to phase variation or limited antiserum availability. Early molecular alternatives such as restriction fragment length polymorphism analysis, pulsed-field gel electrophoresis, and ribotyping offered improved discrimination but were too costly and complex for routine use. Multiplex PCR assays eventually replaced many serotypic tests, expanding from 17 capsule types to all 47 Penner serotypes, yet PCR-based methods remain culture-dependent, require separate assays for LOS class identification, and do not integrate virulence or antimicrobial-resistance profiling. Moreover, novel capsule loci continue to be discovered in strains from South and Southeast Asia, underscoring the advantage of flexible BLAST-based genomic approaches over PCR schemes with fixed primer sets.

CjejuniTyper addresses this gap as a modular pipeline implemented as a Bash shell script with embedded Python 3 modules. It accepts whole-genome assemblies in FASTA format and executes seven sequential stages: assembly quality control, Mash species confirmation, multilocus sequence typing (MLST), Penner HS capsule typing, LOS class typing, virulence-factor detection, and antimicrobial-resistance profiling. Species confirmation uses Mash v2.3 screening against a reference sketch containing C. jejuni and C. coli genomes, with a shared-hash ratio above 0.5 defining a supported call; C. coli or species-uncertain assemblies remain visible in the output but skip downstream C. jejuni-specific typing. Assembly quality control flags genomes with lengths outside the normal C. jejuni range of 1.3 to 2.0 megabases, GC content outside 27.5 to 33.5 percent, or more than 500 contigs.

Penner prediction in the pipeline replaces antibody-based serology with genomic detection of serotype-associated sequence markers and entire CPS loci. BLASTN searches against a curated marker-gene database evaluate hits across three hierarchical decision tiers, with the most stringent tier requiring at least 99.5 percent nucleotide identity and 80 percent coverage. Full CPS locus alignment provides fallback and supporting evidence, and selected complexes are further resolved using poly-G/C tract analysis for HS23_36c, amino-acid BLASTX analysis for HS8_17c, and in silico PCR confirmation for types including HS29, HS55, and HS58. The pipeline reports 31 conservative HS categories and complexes representing the 47 recognized Penner serotypes, because several serotypes share highly similar CPS loci that cannot be reliably separated from genome assemblies alone. Where sufficient genomic information exists, bracketed subtype predictions such as HS23_36c(HS36) are reported, with an asterisk indicating a predicted genomic subtype rather than a proven serological type.

LOS class assignment relies on a best-hit BLAST scoring system based on the product of percentage identity and fractional coverage, organized into seven decision tiers of decreasing stringency, from STRICT (at least 99.5 percent identity and 96 percent coverage) down to LOOSE (at least 90 percent identity and 60 percent coverage). Close-call rules distinguish the highly similar Classes A and B, and an orf11 BLAST step separates Class A from the mosaic Class R. The pipeline examines codon 51 of Cst-II directly from the query assembly, detecting accessory transferase genes cgtA, cgtB, and wlaN to infer putative ganglioside-mimic biosynthetic potential. A rule-based interpretation engine then combines LOS sialylation status, Penner GBS-associated serotypes, Cst-II allele status, and mimic genotype into a three-tier GBS-associated genomic classification, alongside virulence-factor detection covering cytolethal distending toxin and Type IV secretion system genes and antimicrobial-resistance profiling via AMRFinderPlus, all reported in a single tab-delimited output.

Validation was extensive. LOS typing was evaluated against 617 C. jejuni genome assemblies spanning all 19 implemented LOS classes, including 125 complete genomes and 492 draft assemblies. CjejuniTyper correctly assigned 595 of 617 assemblies, an accuracy of 96.4 percent with Cohen’s kappa of 0.958 and a Matthews correlation coefficient of 0.958, and typing coverage was 100 percent. Penner typing was evaluated against 96 assemblies with verified reference labels covering 14 of the 31 implemented CPS reference categories, collectively representing 27 individual Penner serotypes. The pipeline correctly classified 93 of 96 assemblies, an accuracy of 96.9 percent with kappa of 0.961 and MCC of 0.962, achieving perfect recall for HS41 and HS2. Most errors involved closely related or structurally overlapping loci in fragmented draft assemblies, particularly between the clinically important but computationally difficult LOS Classes A and B.

For the Guillain-Barré syndrome evaluation, the team used 113 retained genomes comprising 89 isolates previously reported from GBS patients and 24 enteritis controls from Bangladesh and international public datasets. Among 84 GBS-associated genomes with published LOS-class assignments, CjejuniTyper produced 83 concordant calls, corresponding to 98.8 percent concordance. In the Bangladesh case-control cohort, HIGH or MODERATE genomic profiles were identified in 34 of 38 GBS-associated isolates and 10 of 24 enteritis controls, corresponding to 89.5 percent sensitivity, 58.3 percent specificity, and 73.9 percent balanced accuracy, with an odds ratio of 11.90 for the association between a positive genomic profile and the GBS clinical group. Across all 89 retained GBS-associated genomes, 81, or 91.0 percent, received HIGH or MODERATE profiles. Targeted analysis showed that four of the ten positive controls contained full-length, high-identity mimicry-pathway proteins, indicating genuine genomic potential rather than analytical error.

The authors are careful to frame the tool’s scope. Because HIGH or MODERATE profiles were also present in some enteritis controls, the integrated classification indicates genomic mimicry-associated potential rather than patient-level clinical prediction; the presence of sialylated LOS and mimicry-associated genes in controls reveals genuine biological overlap between GBS-associated and enteritis isolates. The pipeline also currently supports only the implemented reference LOS classes and CPS types, so isolates carrying previously undescribed or highly divergent loci may be assigned to the closest reference or remain untypeable, and future updates will incorporate newly described reference sequences and expanded validation datasets. Nevertheless, CjejuniTyper represents, to the authors’ knowledge, the first publicly available pipeline that simultaneously performs capsule typing, LOS class assignment, Cst-II allele calling, virulence-gene profiling, and interpretation of GBS-associated genomic markers from genome assemblies. The workflow is freely available on GitHub and archived on Zenodo under an MIT License, designed to run on Linux with a bundled Conda environment, and suited to high-throughput genomic surveillance where numerous assemblies must be typed rapidly without culture-based serology, supporting the ongoing transition from phenotypic to genomic characterization of C. jejuni in clinical and public health microbiology.

Subject of Research: An automated bioinformatic pipeline for in silico typing of Campylobacter jejuni capsule and lipooligosaccharide loci with Guillain-Barré syndrome-associated genomic profiling

Article Title: CjejuniTyper: integrated in silico typing of Campylobacter jejuni capsule and lipooligosaccharide loci with GBS-associated genomic profiling

Article References: Jurić, D., Ferenčak, I., Grginić, A. G., Žmak, L., & Tabain, I. (2026). CjejuniTyper: integrated in silico typing of Campylobacter jejuni capsule and lipooligosaccharide loci with GBS-associated genomic profiling. Frontiers in Microbiology, 17, Article 1943123. https://doi.org/10.3389/fmicb.2026.1943123

Image Credits: AI Generated

DOI: 10.3389/fmicb.2026.1943123

Keywords: Campylobacter jejuni, CjejuniTyper, Guillain-Barré syndrome, lipooligosaccharide, capsular polysaccharide, Penner serotyping, ganglioside mimicry, bioinformatics, genomic surveillance, molecular mimicry, whole-genome sequencing, infectious disease

The finding matters because the diagnostic backbone of tuberculosis control in high-burden countries is built around rifampicin. Rapid molecular tests such as Xpert MTB/RIF detect mutations in the rpoB gene that confer rifampicin resistance, and a rifampicin-susceptible result is generally treated as a green light for standard first-line therapy. When isoniazid resistance flies under that radar, patients may receive regimens that are partially ineffective, promoting treatment failure, relapse, and the further accumulation of resistance mutations. The study’s authors argue that the predominance of Hr-TB in western Kenya means rifampicin-based diagnostics risk systematically under-detecting a substantial share of drug-resistant disease.

To look beneath the surface of routine testing, the team selected an enriched subset of 316 isolates for whole-genome sequencing, of which 290 yielded high-quality genomes. The sequencing workflow was technically thorough: genomic DNA was extracted with a modified cetyltrimethylammonium bromide method optimized for the tough mycobacterial cell wall, libraries were prepared with the NEBNext Ultra II FS kit, and paired-end 2 by 150 base pair reads were generated on the Element AVITI platform. Bioinformatic processing used the DuffyNGS pipeline, aligning reads to the H37Rv reference genome with Bowtie2 and calling variants with Samtools and BCFtools, while TBProfiler annotated resistance determinants against the World Health Organization mutation catalogue, version 2.

The genomic data confirmed the classical resistance mechanisms. Rifampicin resistance was driven mainly by the rpoB S450L substitution, the canonical mutation in the RNA polymerase gene that most molecular assays are designed to catch. Isoniazid resistance was dominated by katG S315T, which disables the catalase-peroxidase that activates the drug, together with mutations in the inhA promoter, including the -15 C>T and -8 T>A variants, which alter expression of the enzyme targeted by both isoniazid and ethionamide. Pyrazinamide resistance mapped largely to pncA mutations such as L172P, ethambutol resistance to embB M306V, streptomycin resistance to rpsL K43R, and fluoroquinolone resistance to gyrA mutations. Notably, no resistance-conferring mutations were found for newer or repurposed agents such as bedaquiline and clofazimine, and all isolates were genotypically susceptible to the injectables amikacin and kanamycin.

Among the 290 sequenced isolates, whole-genome sequencing identified resistance-associated mutations in 43 cases, or 14.8 percent. Within this enriched subset, Hr-TB was again the most frequent resistance class at 16 isolates, followed by rifampicin-resistant tuberculosis at 11 and multidrug-resistant tuberculosis at 9, with three isolates classified as pre-extensively drug-resistant based on fluoroquinolone resistance mutations layered onto multidrug resistance. The sequenced population skewed male, at 72 percent, with a median age of 34 years, and 36 percent of patients were living with HIV, reflecting the heavy HIV-TB co-infection burden of the region.

Geographically, the study revealed striking heterogeneity. Resistant isolates clustered heavily in the Lake Victoria basin, with the highest counts in Kisii, Homa Bay, Migori, and Siaya counties, while Bomet and Bungoma contributed none. Kisii alone accounted for 12 of the 43 WGS-detected resistant isolates, or 27.9 percent. The authors suggest this concentration points to localized transmission or shared epidemiologic drivers within the basin, and they emphasize that such county-level variation argues for granular, local genomic surveillance rather than reliance on national averages that can mask hotspots.

The genetic population structure of the isolates was diverse. Susceptible isolates were spread across Lineage 4, the globally distributed Euro-American lineage, at about 40 percent, Lineage 3, common in East Africa and South Asia, at about 38 percent, and Lineage 2 at about 21 percent, with a single Mycobacterium bovis isolate also identified, a reminder of potential zoonotic transmission through cattle or unpasteurized dairy. Among resistant isolates, Lineage 4 and Lineage 3 predominated, though no statistically significant association between lineage and resistance emerged, suggesting that drug resistance is arising across multiple co-circulating strain populations rather than within one dominant clone. Resistance appeared particularly prominent within sub-lineages 4.3.3 and 4.6.1.2, although the authors caution that small sample sizes make some sub-lineage estimates unstable.

The most consequential result, however, was the discordance between routine testing and sequencing. Routine methods, either line probe assays or phenotypic drug susceptibility testing in liquid culture, flagged 56 isolates as resistant, while WGS called only 43 resistant. Concordant resistance was seen in 35 isolates, but 21 isolates were resistant by routine testing yet genomically susceptible, and 8 were resistant by WGS yet susceptible or untested by routine methods. A McNemar’s test with continuity correction confirmed the difference was statistically significant, with p equal to 0.026. Critically, re-evaluation against the WHO catalogue showed that 18 of the 21 routine-positive, WGS-negative cases carried mutations classified as being of uncertain significance, meaning the global reference database simply cannot yet interpret them confidently.

This discordance cuts both ways and exposes the limits of each method. For drugs such as pyrazinamide and ethambutol, resistance mechanisms are incompletely defined, and phenotypic testing itself suffers from technical variability in critical concentrations and pH sensitivity. Biological factors such as heteroresistance, transient efflux pump activity, and altered cell wall permeability can produce phenotypic resistance without any detectable resistance mutation, and culture-based sequencing may itself select subpopulations that do not represent the full within-host diversity. Conversely, the eight WGS-positive, routine-negative isolates included genuine discordant cases involving rifampicin, isoniazid, fluoroquinolones, and capreomycin, plus two streptomycin resistance mutations that routine testing had never evaluated, showing that sequencing can also catch resistance that conventional workflows miss.

The authors conclude that whole-genome sequencing and phenotypic testing should operate as complementary tools rather than competitors, with sequencing providing genome-wide, high-resolution mutation detection while phenotypic assays confirm resistance where genomic interpretation remains uncertain. Their recommendations are concrete: integrate WGS into Kenya’s national tuberculosis surveillance, beginning at central reference laboratories, and prioritize better detection of isoniazid resistance given the prominence of Hr-TB. They also stress that continued generation of local genomic and phenotypic data from high-burden settings is essential for refining the global mutation catalogues on which genomic resistance prediction depends. The study’s limitations, including its retrospective design, referral-laboratory sampling that enriches for resistant cases, and the absence of SNP-based transmission clustering, mean the proportions reported describe the study population rather than true regional prevalence. Even so, the message is clear: in western Kenya, a hidden epidemic of isoniazid resistance is circulating beneath a rifampicin-focused diagnostic screen, and closing that gap will require both wider sequencing capacity and a more complete global map of what tuberculosis resistance mutations actually mean.

Subject of Research: Genomic surveillance of drug-resistant Mycobacterium tuberculosis in western Kenya

Article Title: Genomic characterization of drug-resistant Mycobacterium tuberculosis complex in western Kenya reveals predominance of isoniazid resistance and discordance with routine susceptibility testing

Article References: Musau, S., Odera, S., Musyoki, V. M., Lamont, E. I., Onyango, N., Morrison, B., Murithi, W., Wandiga, S., Nduba, V., Sherman, D., & Mureithi, M. W. (2026). Genomic characterization of drug-resistant Mycobacterium tuberculosis complex in western Kenya reveals predominance of isoniazid resistance and discordance with routine susceptibility testing. Frontiers in Tuberculosis, 4, Article 1855780. https://doi.org/10.3389/ftubr.2026.1855780

Image Credits: AI Generated

DOI: 10.3389/ftubr.2026.1855780

Keywords: tuberculosis, whole-genome sequencing, drug resistance, isoniazid, rifampicin, Mycobacterium tuberculosis, Kenya, Hr-TB, diagnostics, WHO mutation catalogue, genomic surveillance, line probe assay

Carbapenems have long been considered the most reliable last line of defense against severe Gram-negative bacterial infections. Yet the growing prevalence of carbapenemase-producing organisms, particularly among Enterobacteriaceae and non-fermenting Gram-negative bacilli, has severely restricted treatment options and is associated with alarming mortality rates exceeding 50% in some regions. Carbapenem resistance is primarily mediated by carbapenemase enzymes encoded by genes such as blaKPC, blaNDM, blaIMP, blaVIM, and blaOXA-48. These resistance determinants are frequently located on mobile genetic elements like plasmids, transposons, and integrons, facilitating horizontal gene transfer among diverse bacterial species. While the co-occurrence of multiple carbapenemase genes within individual bacterial isolates represents an escalating global concern, the simultaneous detection of multiple carbapenemase genes within a single clinical specimen remains rare.

To characterize the pathogens and resistance genes present in the lavage fluid, the team employed metagenomic next-generation sequencing (mNGS), a culture-independent approach that enables identification of pathogens and resistance genes directly from clinical samples. The BALF sample was processed within 24 hours of collection, with DNA extracted using a magnetic bead-based kit and libraries sequenced on the MGI200 platform using DNA Nanoball technology, generating over 10 million single-end 50-bp raw reads. After quality filtering and removal of human sequences, the remaining reads were aligned to reference databases containing genomes of viruses, bacteria, fungi, and parasites. Microbial identification required at least three non-overlapping reads per organism that were either undetected in negative controls or present at counts at least 10 times higher than in controls.

The metagenomic analysis detected Pseudomonas stutzeri, Klebsiella pneumoniae, Shewanella algae, and Elizabethkingia anophelis in the sample. Beyond the four carbapenemase genes, the specimen contained a diverse array of antimicrobial resistance genes spanning multiple categories, including beta-lactamase genes such as blaCTX-M-65, blaSHV-66, blaOXA-55, and blaOXA-246; aminoglycoside-modifying enzymes; sulfamethoxazole resistance genes sul1 and sul2; trimethoprim resistance determinants dfrA27, dfrA6, and dfrB3; tetracycline, chloramphenicol, rifampicin, fluoroquinolone, and macrolide resistance genes. Various virulence-associated genes were also detected, including those involved in iron acquisition, fimbriae formation, and outer membrane protein synthesis, suggesting a virulence-associated genetic profile within the polymicrobial community.

Using selective culturing techniques with LB agar plates containing 0.5 µg/mL of imipenem, three carbapenemase-producing strains were isolated from the same specimen. Klebsiella pneumoniae strain CQPMC-KpYD carried blaKPC-2, Shewanella algae strain CQPMC-SheW1 harbored blaNDM-1, and Pseudomonas stutzeri strain CQPMC-PStu co-harbored both blaIMP-1 and blaAFM-1. Targeted reanalysis of the BALF sequencing data yielded 148, 477, 232, and 325 reads compatible with blaKPC-2, blaNDM-1, blaAFM-1, and blaIMP-1, respectively, with corresponding coverage breadths exceeding 99% and mean depths ranging from 8.39× to 29.34×. All three isolates showed minimum inhibitory concentrations of ≥16 µg/mL for imipenem, meropenem, and ertapenem, confirming high-level carbapenem resistance across distinct bacterial species.

Whole-genome sequencing using Oxford Nanopore Technologies on the MinION platform revealed the genetic architecture underlying these resistance determinants. The K. pneumoniae isolate was identified as an ST11 strain, a predominant clone associated with carbapenem resistance and linked to hospital outbreaks and high mortality rates across multiple continents. The blaKPC-2 gene was located on a 132,742 bp plasmid designated pCQPMC-KpYD1, which harbors 172 predicted open reading frames and contains IncFII(pHN7A8) and IncR replicons. BLAST database comparisons showed that this plasmid shares 100% coverage and 99.99% identity with the K. pneumoniae plasmid pCRKP-35_KPC, isolated from a patient’s blood sample in China in 2019. Further searches identified 45 plasmids with over 99% identity and coverage, all from K. pneumoniae isolates across various regions in China—43 from hospital patients and 2 from animals—suggesting that related plasmid backbones may contribute to blaKPC-2 dissemination.

The K. pneumoniae isolate also harbored virulence genes including iucABCD, iutA, rmpA, rmpD, and rmpC, located on a 200,970 bp IncHI1B-IncFIB hybrid plasmid lacking additional antibiotic resistance genes. Genetic analysis revealed that the core structure of the blaKPC-2 gene region, termed variable region 1, comprises IS26-ΔTn3-ISKpn27-blaKPC-2-ISKpn6-korC-orf-klcA-ΔrepB. Two additional resistance gene clusters adjacent to blaKPC-2 were identified: a mercury resistance gene cluster flanked by IS5057 and TnpA, and a cluster containing blaSHV-12 enclosed by TnAs1 and IS26. These genetic contexts suggest potential roles for transposition and recombination in the genetic diversity and mobility of blaKPC-2-carrying plasmids.

The Shewanella algae strain CQPMC-SheW1 presented an equally striking genomic picture. Its 4,891,834 bp chromosome assembly contained two blaNDM-1 copies in the same orientation, with start positions separated by 6,399 bp in repeated ISCR1-associated contexts. The related context was ISCR1-partial trpF-bleMBL-blaNDM-1-ΔISAba125-catB3-arr-3-qacEΔ1-sul1. Remarkably, a similar ISCR1-NDM-1 structure is observed in E. coli strain Y5, which shares 100% homology with the chromosomal ISCR1-NDM-1 element in CQPMC-SheW1. Downstream of blaNDM-1, an IntI1 integron with a cassette of six resistance genes was identified. Comparative analysis indicates that the blaNDM-1 gene and its surrounding resistance cluster share up to 99% homology with plasmid p6061604-KPC from E. coli strain 2016061604, highlighting potential cross-species transmission. While that plasmid contains only one complete ISCR1-NDM-1 element, CQPMC-SheW1 exhibits a more complex composition with two same-orientation blaNDM-1 copies, possibly resulting from recombination or transposition events.

The Pseudomonas stutzeri strain CQPMC-PStu, with a 5,242,803 bp genome and 62.2% GC content, co-harbored blaAFM-1 and blaIMP-1, genes encoding metallo-β-lactamases that confer high-level resistance to carbapenems. The blaAFM-1 gene is located within an approximately 12 kb multidrug-resistant region primarily composed of an ISCR29 element and two class 1 integrons. Comparative genomic analysis revealed that this region is highly similar to the chromosome of clinically isolated Pseudomonas qingdaonensis strain L1712hy, exhibiting 99.9% nucleotide identity. The blaIMP-1 gene is located within a truncated class 1 integron arranged as IntI1-blaIMP-1-aac(6′)-IIa-aph(3′)-VIa, a structure closely resembling integron In86. Notably, this multidrug-resistant region exhibits high homology with the chromosome of P. putida strain AHSWHJXPP1, demonstrating 100% coverage and 99% identity, and that strain also carries both blaAFM-1 and blaIMP-1. Similar genomic compositions have been discovered in plasmids of three P. aeruginosa strains, revealing related resistance-associated regions across several bacterial species and suggesting potential mobility of the associated determinants.

The coexistence of four carbapenemase genes within one clinical sample highlights the complexity of polymicrobial carbapenem resistance and underscores the importance of genomic surveillance. The authors note important limitations: the absence of direct transfer experiments and longitudinal evidence limits inference of horizontal gene transfer within the patient, the contribution of each organism and its resistance determinants to the fatal outcome could not be established, and BALF short reads do not establish isolate origin or copy-specific coverage, with independent long-read validation across the SheW1 repeat junctions not established. Nevertheless, the mobile-element-associated genetic contexts of these co-occurring genes suggest their potential mobility, and the findings emphasize the value of comprehensive genomic surveillance networks to detect and monitor the spread of highly resistant organisms, informing international infection control measures and guiding effective therapeutic strategies against the growing global threat of antibiotic resistance.

Subject of Research: Co-occurrence and genetic contexts of four carbapenemase genes in a single clinical specimen from a critically ill patient

Article Title: Co-occurrence and genetic contexts of NDM-1, KPC-2, IMP-1, and AFM-1 carbapenemase genes in a critically ill patient

Article References: Zhang, Y., Zhang, Z., Ying, S., Wang, S., & Xiang, R. (2026). Co-occurrence and genetic contexts of NDM-1, KPC-2, IMP-1, and AFM-1 carbapenemase genes in a critically ill patient. Frontiers in Cellular and Infection Microbiology, 16, Article 1973471. https://doi.org/10.3389/fcimb.2026.1973471

Image Credits: AI Generated

DOI: 10.3389/fcimb.2026.1973471

Keywords: carbapenemase, antimicrobial resistance, NDM-1, KPC-2, IMP-1, AFM-1, metagenomic sequencing, whole-genome sequencing, Klebsiella pneumoniae, Pseudomonas stutzeri, Shewanella algae, genomic surveillance

The urgency is grounded in recent experience. Uganda has faced repeated Sudan virus disease outbreaks, including the large 2022 event and a shorter 2025 outbreak that the World Health Organization declared on 30 January 2025 and ended on 26 April 2025 after 14 total cases, including 12 confirmed cases, two probable cases and four deaths. Small does not mean simple: that outbreak still spanned multiple districts, exposed health workers and required the tracing, monitoring and support of numerous contacts. Meanwhile, vaccine readiness remains uneven across Ebola viruses. The rVSV-ZEBOV vaccine, whose ring vaccination in Guinea showed substantial protection against Zaire ebolavirus, represents one of the great achievements of outbreak vaccinology. But Sudan and Bundibugyo ebolaviruses, both central to regional risk, still lack licensed vaccines, and their development pipelines have been thinner, slower and more dependent on emergency improvisation.

The authors, Ugwu Okechukwu Paul-Chima and Martin Nduwimana of Kampala International University, contend that East Africa needs a platform mindset rather than a product mindset. A product mindset waits for a specific vaccine; a platform mindset prepares the system that can update, test, produce and deliver candidates as threats change. Ebola risk is species-specific, geographically uneven and socially fast-moving. A district can move from one suspicious death to hundreds of monitored contacts within days, and if the scientific system starts only after laboratory confirmation, it is already late. The 2025 Uganda response illustrated both the danger and the opportunity: WHO and partners worked with Ugandan investigators, regulators and international filovirus experts so that candidate vaccines and treatments could be accessed once Sudan virus disease was detected, and a clinical efficacy trial for a Sudan virus vaccine was launched during the emergency, a landmark moment for Sudan virus disease vaccine evaluation. That speed deserves celebration, the authors argue, but it should also make the region restless. If so much had to be assembled under pressure, the next task is to make readiness less heroic and more ordinary, aligning with the 100 Days Mission framework and the Coalition for Epidemic Preparedness Innovations’ platform technology approach, which emphasize moving from viral detection to vaccine deployment within shorter timeframes.

The scientific case for mRNA Ebola vaccines rests on the platform’s distinctive technical features. mRNA vaccines deliver genetic instructions that allow host cells to produce a target antigen, typically through lipid nanoparticle delivery. The platform enables rapid design after sequence availability, manufacturing processes that can be standardized across targets, and the option of testing updated constructs without rebuilding the entire production chain. For Ebola disease, the glycoprotein remains the obvious starting point because it mediates viral entry and has been the central antigen for several vaccine approaches. The evidence base is early but no longer empty. Meyer and colleagues reported that lipid nanoparticle-formulated modified mRNA vaccines based on Ebola virus glycoprotein induced Ebola-specific IgG and neutralizing antibody responses and protected guinea pigs after challenge. O’Donnell and colleagues extended the RNA platform logic to Sudan virus, showing single-dose replicon RNA protection in female guinea pigs. Stromberg and colleagues reported that an mRNA vaccine expressing Ebola virus glycoprotein induced high neutralizing antibody titers and protected mice against lethal challenge. These are not field efficacy data, and the authors are careful not to oversell them, but they justify serious platform development, especially for viral species where licensed vaccines remain unavailable.

Other vaccine platforms reinforce the same point from a different angle. Vesicular stomatitis virus-based Sudan virus vaccines have protected macaques in challenge studies, and a bivalent ChAdOx1 Ebola and Sudan virus vaccination has shown early clinical safety and immunogenicity in adults. The field is clearly moving beyond Zaire-only preparedness. mRNA candidates should therefore be judged alongside these approaches on durability, T cell responses, reactogenicity, tropical stability, dosing schedule, performance in previously exposed populations and feasibility during ring vaccination. Excitement, the authors warn, is useful only if it survives field reality.

A serious argument for mRNA Ebola preparedness cannot stop at biotechnology; the region needs an ecosystem. Genomic surveillance should identify the viral species and sequence relevant targets quickly. Regional laboratories should handle sequencing data, immunological assays and quality control. Regulators should maintain pre-reviewed emergency pathways that preserve rigour without wasting time. Trial sites need trained staff, community networks, adverse event monitoring and data systems before an outbreak begins. Parts of this architecture already exist. Uganda has strong research institutions and considerable outbreak experience. The WHO mRNA technology transfer hub in South Africa was established to strengthen mRNA vaccine production capacity on the continent and support African manufacturing self-determination beyond COVID-19, offering East Africa the prospect of developing capacity in antigen design, batch release and quality assurance through partnership rather than importing finished products. Africa CDC’s Partnerships for African Vaccine Manufacturing places vaccine production within a wider continental health security agenda, while the African Medicines Agency is positioned to accelerate preparedness by developing convergent regulatory standards and pre-approved trial protocols for investigational mRNA vaccines, reducing the time and cost of bringing candidates into outbreak response trials across fragmented national jurisdictions.

Community trust is part of the platform, not a soft add-on. Ebola vaccination is a social act carried out during fear: communities may be grieving, angry or suspicious, health workers exhausted, and rumors may move faster than contact tracing teams. The term mRNA may also bring back memories of COVID-19 disputes, political messaging and online misinformation. If mRNA Ebola preparedness is built only in laboratories, it may fail at the clinic gate, the village meeting or the burial negotiation. Survivors, religious leaders, local journalists, market leaders, ambulance teams, nurses, burial teams and community health workers should be part of the conversation from the start, understanding why a Sudan virus outbreak may require a different vaccine from a Zaire virus outbreak and why trial participation can be ethical during an emergency. Religious institutions deserve particular attention: during the 2014–2016 West Africa Ebola epidemic, faith leaders were pivotal in shaping community responses to safe burial practices, quarantine compliance and rumor messaging, and their networks can amplify misinformation with the same efficiency with which they transmit reassurance. Engaging faith leaders early, before outbreaks rather than during them, is therefore a structural requirement.

Manufacturing, cold chain and delivery pose equally blunt questions. mRNA readiness will mean little if the vaccine cannot leave the capital. Ebola outbreaks may occur in rural districts, conflict-affected zones, mining corridors, crowded urban settlements or border communities where electricity, roads and internet coverage are unreliable, and some mRNA products have demanding cold chain requirements, although formulation and stability work continues to improve. Delivery models should match outbreak epidemiology: ring vaccination remains attractive because it targets contacts and contacts of contacts around confirmed cases, while health worker vaccination may be needed early because nurses, laboratory staff, ambulance teams and cleaners can become both victims and amplifiers if infection prevention fails. Supply chain fragility presents a structural obstacle: African laboratories and health facilities have long depended on imported reagents, cold chain equipment and consumables, and disruptions caused by procurement bottlenecks, shipping delays, foreign exchange shortfalls or export restrictions can halt testing and undermine biosafety. The COVID-19 pandemic exposed this dependence acutely, with diagnostic reagents becoming scarce precisely when demand was highest. Manufacturing is also political: East Africa does not need every country to build a full mRNA plant, but it does need meaningful participation in antigen selection, batch release, quality systems, pharmacovigilance, trial leadership, fill-and-finish capacity where feasible and data ownership, otherwise mRNA preparedness risks becoming another form of dependence with better branding.

Perhaps the most formidable obstacle is the way science is funded on the African continent. Readiness is a continuous state of institutional memory, trained personnel, functional infrastructure and regularly rehearsed protocols, and that continuity is extremely difficult to sustain through the dominant model of competitive international grants won institution by institution and often year by year. When a grant cycle ends, trained laboratory scientists may leave for better-paid positions, data systems may go unmaintained and community engagement networks may go dormant. The recent and severe contraction of international research funding, including cuts to United States foreign assistance and the rollback of major global health funding streams, has affected African research institutions, clinical trial networks, surveillance systems and community health programs simultaneously. The epidemiological case for a different model is clear: every gap in surveillance and every hiatus in laboratory maintenance is a gap in which an outbreak can move from a single case to a regional emergency before detection. The cost of reactive response in 2014 was estimated in the tens of billions of dollars, while the cost of sustained preparedness is a fraction of that. The authors propose treating Ebola preparedness as a recurrent line item in national health budgets, pooling contributions through East African Community and African Union frameworks, and establishing a credible business case for mRNA manufacturing by diversifying platform applications toward improved malaria vaccines, tuberculosis boosters or maternal immunization strategies, providing continuous production and stabilized revenue streams that justify capital investment.

The deeper argument is readiness. East Africa has shown that emergency vaccine trials can be activated quickly when prior planning exists, and the region should now ask what it would take to make such speed normal. That requires investment in people as much as platforms: trial nurses, laboratory scientists, data managers, regulators, logisticians, community engagement teams and manufacturing specialists, along with political seriousness, because preparedness budgets are easy to cut when there is no outbreak on the evening news. There are risks: mRNA Ebola vaccines are not yet proven field tools, preclinical protection in guinea pigs or mice does not guarantee effectiveness in humans exposed during an outbreak, and reactogenicity, dosing schedules, durability and cold chain demands could limit use. There is also a fairness risk if the technology is developed mainly through external ownership, with African sites used only when outbreaks occur. Still, the opportunity is real. Ebola preparedness has often been framed as a race against time, and mRNA platforms can help with time, but only if the region prepares the track before the race begins. The next Ebola outbreak should not find East Africa beginning again; it should find a prepared ecosystem already capable of moving from viral sequence to local readiness with speed, fairness and scientific confidence, and the financial architecture to sustain that capability between outbreaks.

Subject of Research: Virology and infectious disease

Article Title: From outbreak response to regional readiness: reimagining mRNA vaccine platforms for Ebola preparedness in East Africa

Article References: Paul-Chima, U. O., & Nduwimana, M. (2026). From outbreak response to regional readiness: reimagining mRNA vaccine platforms for Ebola preparedness in East Africa. Frontiers in Tropical Diseases, 7, Article 1887687. https://doi.org/10.3389/fitd.2026.1887687

Image Credits: AI Generated

DOI: 10.3389/fitd.2026.1887687

Keywords: mRNA vaccines, Ebola, East Africa, Sudan virus, Bundibugyo virus, outbreak preparedness, genomic surveillance, vaccine manufacturing, Africa CDC, health policy, outbreak, response

The first line of defense operates at the parasite membrane. By mutating, deleting, or amplifying transporters, parasites can keep intracellular drug concentrations below toxic thresholds even when patients receive correctly dosed regimens. In Plasmodium falciparum, the digestive-vacuole transporter PfCRT exports protonated chloroquine away from its site of action, undermining the drug’s interference with heme detoxification, while PfMDR1 modulates the partitioning of chloroquine, mefloquine, and artemisinin-combination partner drugs between cytosol and vacuole. Field data from Benin show that more than a decade after artemisinin-based combination therapy deployment, wild-type Pfcrt K76 alleles have re-emerged as predominant, consistent with restored chloroquine sensitivity, while Pfmdr1 N86 and Y184F variants linked to reduced lumefantrine susceptibility remain frequent in artemether-lumefantrine-treated populations. Additional ATP-binding cassette transporters such as PfMRP1, which exports glutathione conjugates and several antimalarials, add functional redundancy that makes transporter-based resistance robust.

Kinetoplastid parasites deploy an equally sophisticated transport strategy. Pentavalent antimonials must be reduced to the active trivalent form, which enters Leishmania mainly through the aquaglyceroporin AQP1; resistant isolates commonly show reduced AQP1 expression, inactivating mutations, or gene deletions. Simultaneously, the ABC transporter MRPA, amplified on episomes or through chromosome 23 polysomy, sequesters antimony-trypanothione conjugates into intracellular vesicles, a mechanism strongly associated with high-grade antimonial resistance on the Indian subcontinent. Miltefosine resistance follows a parallel route centered on the LdMT/LdRos3 flippase complex, where point mutations, truncations, and subtelomeric deletions can reduce drug uptake by more than 95 percent, with accompanying shifts in fatty-acid composition and ergosterol content further limiting drug partitioning into membranes. In Trypanosoma brucei, loss of the aquaglyceroporin AQP2, which imports melarsoprol and pentamidine, is the definitive driver of clinical resistance to these drugs.

The second major mechanism involves changing the molecules drugs bind to. In P. falciparum, antifolate resistance is the textbook case: stepwise accumulation of dhfr mutations N51I, C59R, and S108N together with dhps mutations such as A437G and K540E progressively reduces binding of sulfadoxine-pyrimethamine while preserving folate metabolism. Deep-sequencing surveillance in Benin has documented high frequencies of the dhfr triple mutant and the dhps A437G mutation, though the absence of K540E suggests the highest-level resistance genotypes remain rare, allowing some continued utility for intermittent preventive treatment. Artemisinin resistance adds complexity through mutations in the kelch13 propeller domain, validated by gene editing as causal drivers of reduced susceptibility, alongside pfk13-independent routes involving pfcoronin, chromosome 14 copy-number variants, and the endocytosis regulators pfap2mu and pfubp1.

Where Plasmodium relies on discrete point mutations, Leishmania exploits extreme genomic plasticity. Amphotericin B-resistant isolates remodel sterol biosynthesis, decreasing ergosterol and accumulating alternative intermediates such as cholesta-5,7,24-trien-3β-ol through mutations and copy-number changes in sterol C24-methyltransferase and C5-desaturase, thereby reducing the drug’s preferred membrane binding sites. Whole-genome sequencing of Leishmania donovani demonstrates that aneuploidy is adaptive and environment-dependent: chromosomes bearing resistance or virulence genes can become polysomic under in vitro drug selection and then revert toward disomy in the mammalian host. This reversible gene-dosage modulation provides a rapid mechanism for adjusting effective target abundance, and ribosome profiling of antimony-resistant Leishmania tropica reveals a further post-transcriptional layer, with thousands of transcripts, including those encoding trypanothione metabolism and redox enzymes, differentially loaded onto ribosomes even in the absence of drug pressure.

Metabolic reprogramming forms a third protective tier. Antimony-resistant Leishmania strains consistently elevate intracellular thiols such as trypanothione, glutathione, and cysteine, which facilitate sequestration of antimony-thiol conjugates via MRPA and enhance detoxification of reactive oxygen species. Overexpression of trypanothione pathway enzymes and tryparedoxin peroxidase strengthens antioxidant defenses. For nitroheterocyclic drugs used against trypanosomes, resistance often arises through loss or reduction of the nitroreductase enzymes required to activate the prodrugs, blurring the boundary between metabolic adaptation and target modification. In P. falciparum, resistance to compounds such as fosmidomycin and halofuginone has been linked to adaptive metabolic responses including altered proline metabolism, suggesting that metabolic rewiring acts as a background layer that lowers effective drug potency and facilitates the selection of high-level resistance alleles.

Perhaps the most clinically troubling mechanism is persistence. Subpopulations of Plasmodium, Trypanosoma, and Leishmania can enter dormant, persister-like states characterized by slowed proliferation, reduced metabolic activity, condensed chromatin, and extensive transcriptomic and translational reorganization, evading both immune clearance and chemotherapy. Brief exposure of P. falciparum to dihydroartemisinin enriches for dormant ring-stage parasites that resume proliferation days after treatment ends, a phenotype pronounced in kelch13-mutant parasites. Plasmodium vivax hypnozoites exemplify long-term dormancy, with expression signatures dominated by RNA-binding proteins and translational repressors. Emerging mechanisms extend this theme: kelch13 and pfap2mu mutations reduce hemoglobin endocytosis, lowering the free heme pool needed to activate artemisinin, while mutations in the PfCARL locus and vesicle-associated proteins threaten next-generation antimalarials such as ganaplacide by disrupting intracellular drug trafficking.

Detecting these layered defenses depends on advanced genomics. Next-generation sequencing has replaced phenotypic assays as the gold standard for surveillance, providing the depth needed to detect low-frequency resistant subclones within mixed infections before they become clinically dominant. The computational challenges are substantial: the P. falciparum genome exceeds 80 percent AT content, reaching roughly 90 percent in non-coding regions, causing PCR amplification bias and uneven coverage that demand specialized mapping algorithms. For kinetoplastids, pipelines must resolve aneuploidy, copy-number variation, and environment-dependent polysomy, and integrate ribosome-profiling data to map translational reprogramming. The authors emphasize that resistance must be embedded into the earliest stages of drug discovery rather than treated as a clinical afterthought, incorporating pharmacokinetic and pharmacodynamic modeling with transmission dynamics to predict population-level outcomes.

Looking forward, the review highlights parasite-specific targets that lack human homologues, such as calcium-dependent protein kinases in apicomplexans and parasite-derived secreted kinases in kinetoplastids, as routes to potent efficacy with minimal host toxicity. CRISPR/Cas9 gene editing, now workable even in previously intractable trypanosomatids, enables rigorous validation of candidate targets and resistance loci, while 3D bioengineered tissues, organoids, and humanized mice offer ethically sound, human-relevant alternatives to conventional rodent models. The central message is that durable antiprotozoal therapy will require compounds designed from the outset to withstand transporter redundancy, genomic flexibility, and persistence-related tolerance, combined with genomic surveillance, molecular diagnostics, and mathematical modeling to anticipate rather than merely react to the next wave of resistance.

Subject of Research: Molecular mechanisms of drug resistance in protozoan parasites including Plasmodium, Leishmania, and Trypanosoma

Article Title: Molecular mechanisms underlying drug resistance in protozoan parasites: emerging mechanisms and therapeutic perspectives

Article References: Uduwela, K., & Ranasinghe, K. (2026). Molecular mechanisms underlying drug resistance in protozoan parasites: emerging mechanisms and therapeutic perspectives. Frontiers in Parasitology, 5, Article 1934996. https://doi.org/10.3389/fpara.2026.1934996

Image Credits: AI Generated

DOI: 10.3389/fpara.2026.1934996

Keywords: drug resistance, protozoan parasites, Plasmodium falciparum, Leishmania, Trypanosoma brucei, malaria, artemisinin resistance, PfCRT, genomic plasticity, aneuploidy, parasite persistence, genomic surveillance

The scale of the problem is considerable. Globally, an estimated 13 percent of deaths attributed to antimicrobial resistance are due to drug-resistant tuberculosis, much of which remains undetected. In 2024, roughly 390,000 people were estimated to have developed rifampicin-resistant or multidrug-resistant TB, defined as resistance to both rifampicin and isoniazid, the two most critical first-line anti-TB drugs. Missed or erroneous detection of resistance creates gaps in surveillance and can lead to mismanagement of treatment, perpetuating transmission and driving the epidemic.

For decades, culture-based phenotypic drug susceptibility testing has been considered the gold standard for detecting resistance, but the method has known limitations, including inaccuracy in detecting particular cases of resistance to rifampicin. Genotypic tests, such as the Xpert MTB/RIF assay and line probe assays, have accelerated the turnaround time for confirming drug-resistant TB, but they interrogate only narrow regions within a limited number of resistance-associated genes. Sequencing-based detection offers a more comprehensive approach and is included in global guidance for programmatic implementation, yet practical barriers related to cost, laboratory infrastructure, and technical expertise have hindered adoption in many high-burden countries.

Nigeria, a high HIV/TB and multidrug-resistant TB burden country, prioritized addressing DR-TB in its National Strategic Plan for 2021 to 2025. Under the leadership of the National Tuberculosis and Leprosy Control Programme, and with support from the U.S. Centers for Disease Control and Prevention, the country established its first sequencing model for DR-TB surveillance in 2022. The approach deliberately leveraged sequencing laboratories previously established for HIV drug-resistance monitoring, integrating services for these pathogens for the first time and demonstrating how limited resources can be stretched through a multi-disease platform.

The technical workflow began at zonal and national TB reference laboratories, where clinical sputum specimens from health facilities across the country are routinely subjected to genotypic tests. Drug-resistant isolates are then referred for phenotypic testing using the automated BACTEC MGIT 960 system. For the sequencing pilot, 49 Mycobacterium tuberculosis isolates previously identified as resistant to rifampicin and/or isoniazid were selected proportionately across all six geopolitical zones. Mycobacterial cultures were inactivated using heat at 95 degrees Celsius for 20 minutes and ultrasonication for 15 minutes, and genomic DNA was extracted on site before being shipped through a courier-based referral pathway to sequencing laboratories, where quality and quantity were assessed using spectrophotometry and fluorometry.

Rather than sequencing whole genomes, the team designed a targeted Sanger sequencing algorithm covering eight genomic regions associated with resistance to six anti-TB drugs, a strategy intended to maximize programmatic value while keeping costs manageable. The rpoB gene, linked to rifampicin resistance, was sequenced for all isolates to confirm results or identify resistance missed by other tests. Rv0678 and atpE, associated with resistance to the newer drugs bedaquiline and clofazimine, were also sequenced for all isolates. Genes including gyrA, gyrB, katG, the inhA promoter, and rrs were sequenced conditionally, only for isolates determined to be susceptible to the corresponding drug classes, in order to detect mutations not targeted by line probe assays. Identified mutations were cross-referenced with the World Health Organization’s global catalogue of resistance-associated mutations.

Implementation proceeded in four phases over two years: planning, validation of the new method, rollout, and data analysis for programmatic use. Laboratory staff received training, standard operating procedures were developed, and sequencing-specific quality control measures and performance indicators were established. Validation was successful at all participating laboratories, which exceeded established acceptance criteria. Of the 49 isolates selected, genomic DNA suitable for sequencing was extracted from 96 percent, adherence to the sequencing algorithm reached 100 percent, and high-quality results were obtained for 623 of 642 sequencing reactions, or 97 percent.

The results demonstrated the added value of sequencing in striking terms. While sequencing largely confirmed resistance reported by routine tests, it identified additional rifampicin resistance in 5 of 47 isolates, or 11 percent, and additional isoniazid resistance in 1 isolate, or 2 percent, that had been missed by phenotypic or genotypic testing. Discordance between the two routine methods was also notable, observed for rifampicin in 9 percent of isolates, isoniazid in 15 percent, fluoroquinolones in 9 percent, and second-line injectables in 6 percent. In several cases, sequencing settled these disagreements, confirming rpoB mutations that one method had detected and the other had not.

Particularly significant were nine borderline mutations in rpoB associated with low-level rifampicin resistance, identified in isolates from all geopolitical zones. Phenotypic testing can fail to detect these clinically relevant variants, which may fuel transmission of resistance if left undiagnosed. The study found that phenotypic testing missed rifampicin resistance in two isolates with confirmed borderline mutations, L452P and L430P, findings consistent with comparative studies from other high-burden settings. The analysis also revealed the limits of automated bioinformatics software: one potential instance of rifampicin heteroresistance, indicated by a double chromatogram peak, and a unique insertion mutation in rpoB were missed by automated tools, which are often restricted to a database of defined mutations.

Not every result favored sequencing. No additional resistance was detected in genes associated with fluoroquinolone or second-line injectable resistance among isolates deemed susceptible by routine tests, and no mutations were found in Rv0678 or atpE even among the small number of isolates phenotypically resistant to bedaquiline or clofazimine, underscoring that phenotypic testing remains essential for newer drugs whose resistance mechanisms are not yet fully understood. The authors also acknowledge limitations, including the small sample size and algorithm constraints that restrict generalizability, and the inability to repeat phenotypic testing due to resource restrictions.

Following the analysis, the National Tuberculosis and Leprosy Control Programme convened a stakeholder meeting to review lessons learned and chart the path forward. Leveraging existing laboratory infrastructure and workforce expertise, along with the targeted algorithm design, supported cost-effective implementation. Building on the pilot’s success, the program is now transitioning from Sanger sequencing at HIV laboratories to targeted next-generation sequencing at the Nigeria Centre for Disease Control and Prevention’s multi-disease testing laboratory. Next-generation sequencing offers higher throughput and improved sensitivity for detecting heteroresistance at lower frequencies, and commercially available end-to-end solutions with automated bioinformatic pipelines may expand uptake. The work demonstrates feasibility and provides a practical model for operationalizing DR-TB sequencing in a national program setting, offering an example for other high-burden countries seeking to strengthen genomic surveillance, improve drug selection and treatment for TB patients, and guide testing policies as new treatment regimens are scaled up.

Subject of Research: Implementation of DNA sequencing-based surveillance for drug-resistant tuberculosis in Nigeria

Article Title: Implementation of sequencing-based surveillance for drug-resistant tuberculosis in Nigeria

Article References: McLaughlin, H. P., Audu, I., Tola, M., Onwuamah, C. K., Ogwu, J., Atoe, K., Kunle-Ope, C. N., Ahmadu, I., Gowon, J., Meshak, D. B., Iwakun, M., Ude, C. E., Abiona, M., Momoh, A. E., Ore, T., Ogbu, C. A., Abiodun, T. A., Dawson, J., Hall-Eidson, P., … Chukwuma, A. (2026). Implementation of sequencing-based surveillance for drug-resistant tuberculosis in Nigeria. Frontiers in Tuberculosis, 4, Article 1855903. https://doi.org/10.3389/ftubr.2026.1855903

Image Credits: AI Generated

DOI: 10.3389/ftubr.2026.1855903

Keywords: tuberculosis, drug resistance, genomic surveillance, Sanger sequencing, Nigeria, Mycobacterium tuberculosis, rifampicin, isoniazid, drug susceptibility testing, next-generation sequencing, public health, antimicrobial resistance