The research team, led by Abdulwasid Abubakari and Charity Ahiabor of Accra Technical University in Ghana, together with George Osei-Adjei and corresponding author Hizbullah Khan of Guangdong Medical University in China, assembled and analyzed 467 high-quality P. aeruginosa genome assemblies. Every genome included in the analysis met a strict quality threshold of greater than 95 percent completeness, and the collection spanned 17 African countries over a remarkable 26-year window, from 1998 to 2024. All of the data were drawn from publicly available assemblies in the NCBI database, meaning the study required no new sampling or ethics approvals, but its systematic reanalysis with standardized tools allowed comparisons that had previously been impossible across such a geographically and temporally scattered dataset.

The methodological backbone of the study was a pangenome analysis, an approach that partitions the collective gene repertoire of a bacterial species into the core genome shared by all isolates and the accessory genome carried by only some. The researchers used iterative pangenome clustering across seven amino acid identity thresholds ranging from 50 to 98 percent, a strategy that captures gene families at different levels of evolutionary relatedness. They complemented this with exploratory core-genome single nucleotide polymorphism phylogenetics to reconstruct the evolutionary relationships among isolates, and with pangenome-wide association studies, or Pan-GWAS, to detect accessory genes whose presence correlates with specific geographic regions.

The results revealed an exceptionally “open” pangenome architecture, quantified by a scaling exponent of gamma equal to 0.23. In pangenome mathematics, a low gamma value signals that each newly sequenced genome is likely to bring a substantial number of previously unseen genes into the catalogue, indicating enormous genetic diversity and extensive gene acquisition. Across the African population, the analysis catalogued 25,501 distinct gene families, a figure that underscores how genetically versatile this pathogen is on the continent. An open pangenome also has practical implications for surveillance: it suggests that local African isolates may carry functional repertoires that global reference-based analyses routinely miss, and that continued sampling will keep yielding new genetic material rather than approaching a saturation point.

Phylogenomic reconstruction resolved 466 unique core genome SNP profiles, and the resulting tree was characterized by strong regional clustering. In other words, isolates from the same part of the continent tended to be more closely related to each other than to isolates from distant regions, a pattern consistent with largely local transmission and evolution rather than a single continental epidemic lineage sweeping across borders. This regional structure matters for public health planning, because it implies that resistance control strategies may need to be tailored to regional population dynamics rather than applied as one uniform continental blueprint.

Perhaps the most striking finding is what the authors describe as an “African Clonal Inversion.” Globally, the sequence type known as ST235 is regarded as the archetypal P. aeruginosa super-clone, a multidrug-resistant lineage that has spread through hospitals worldwide and dominates high-risk clone surveys on other continents. In the African dataset, however, the picture is reversed. Among the 71 isolates identified as belonging to high-risk clones, ST111 accounted for 46.5 percent, or 33 of 71 isolates, outnumbering ST235, which represented 14.1 percent or 10 of 71, by more than three-fold. This inversion suggests that the forces shaping P. aeruginosa success in African healthcare settings differ from those driving the global spread of ST235, and it raises the possibility that ST111 possesses ecological or resistance advantages that are particularly effective in African hospital environments.

The study also mapped the resistome, the complete set of antimicrobial resistance genes carried by the isolates, and found it to be geographically stratified in a way that has direct clinical consequences. The gene blaNDM-1, which encodes the New Delhi metallo-beta-lactamase and confers resistance to some of the most powerful last-line carbapenem antibiotics, dominated in Northern and Eastern African country subsets. Meanwhile, blaVIM-2, another metallo-beta-lactamase gene but from a distinct enzymatic family, was concentrated in Southern Africa. Because both genes threaten the carbapenem class that clinicians rely on when treating severe P. aeruginosa infections, their uneven continental distribution means that empirical treatment guidelines and diagnostic panels may need to account for which resistance determinants are actually circulating in a given region rather than assuming a homogeneous African resistance landscape.

Beyond resistance genes, the Pan-GWAS analysis uncovered regional associations in the accessory genome that hint at how local P. aeruginosa populations differ in their broader functional biology. The researchers found enrichment of a Type VI Secretion System component, the tla3 gene, in North African isolates. The Type VI Secretion System is a molecular spear-like apparatus that bacteria use to inject effector proteins into competing microbes and host cells, playing a major role in interbacterial competition and virulence. In West Africa, the analysis identified enrichment of phenazine biosynthesis clusters, including the phzA2 gene. Phenazines are redox-active secondary metabolites that contribute to P. aeruginosa’s survival, biofilm formation and pathogenicity. These regional functional signatures suggest that different African populations may have evolved distinct ecological strategies, potentially shaped by local hospital conditions, antibiotic prescribing practices, microbial competition and environmental reservoirs.

To make these findings actionable rather than merely archival, the team integrated the entire dataset into a live interactive dashboard hosted on Microreact, a widely used platform for visualizing genomic epidemiology. This means that researchers, public health officials and clinicians across Africa and beyond can explore the phylogenetic trees, geographic distributions and resistance gene patterns themselves, updating the picture as new genomes are deposited. Such open infrastructure is particularly valuable on a continent where surveillance capacity varies widely between countries, because it lowers the technical barrier for local laboratories to place their own isolates in continental and global context.

The study’s authors are careful to frame their work as a foundation rather than a finished map. The dataset, while the largest of its kind for the continent, still reflects the uneven distribution of sequencing capacity and data deposition across Africa, and the researchers themselves categorized some countries with limited sampling as yielding only exploratory Pan-GWAS results. Nevertheless, by demonstrating that African P. aeruginosa populations have their own clonal hierarchy, their own resistance geography and their own accessory gene signatures, the analysis makes a compelling case that the continent can no longer be treated as a footnote in global pathogen genomics. As antimicrobial resistance continues to escalate worldwide, understanding how Priority 1 pathogens evolve in undermapped regions is not just an African concern but a global one, and this study provides both the evidence and the tools to begin that work in earnest.

Subject of Research: Pan-African genomic population structure and antimicrobial resistance distribution of Pseudomonas aeruginosa

Article Title: Pan-African genomics of Pseudomonas aeruginosa highlights regional population structure and AMR stratification

Article References: Abubakari, A., Ahiabor, C., Osei-Adjei, G., & Khan, H. (2026). Pan-African genomics of Pseudomonas aeruginosa highlights regional population structure and AMR stratification. BMC Genomics. https://doi.org/10.1186/s12864-026-13365-8

Image Credits: AI Generated

DOI: 10.1186/s12864-026-13365-8

Keywords: Pseudomonas aeruginosa, pangenomics, antimicrobial resistance, Africa, genomic epidemiology, high-risk clones, resistome, ST111, ST235, Pan-GWAS, MLST, BMC Genomics

Sand flies are small, hairy flies of the subfamily Phlebotominae whose blood-feeding females transmit a range of pathogens, most notably Leishmania parasites, as well as phleboviruses such as those causing sand fly fever. More than one billion people live in areas where they are exposed to sand fly-borne infections, and with no effective human vaccines available for most of these diseases, vector control remains the principal line of defense. Traditional measures such as insecticide spraying face growing challenges from resistance and environmental concerns, prompting researchers to explore alternative strategies. Among the most promising of these is the use of Wolbachia, an intracellular bacterium that infects an enormous range of arthropods and can be deployed to suppress mosquito populations or reduce their ability to transmit pathogens such as dengue and Zika viruses.

Despite the success of Wolbachia-based approaches in mosquitoes, surprisingly little is known about the bacterium’s natural presence in sand flies. This gap in knowledge motivated a team of researchers at the Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia-Romagna in Brescia, led by Maya Carrera and colleagues, to undertake a systematic survey of Wolbachia infections in wild-caught sand flies across Northern Italy. The study, conducted between 2023 and 2025, set out to determine not only how common the bacterium is in these populations but also which genetic types of Wolbachia are circulating, information that is essential for judging whether the endosymbiont is already interacting with local vector populations in ways that could be exploited.

The fieldwork covered 24 collection sites distributed across Northern Italy, a region where sand fly activity is seasonal and where Phlebotomus perniciosus dominates the vector community. The researchers deployed two complementary trapping methods: CO2-baited traps, which mimic the breath of vertebrate hosts and attract host-seeking females, and CDC light traps, a standard tool for sampling nocturnal flying insects. Captured specimens were pooled according to sex, collection site, and date, a pooling strategy that balances the practical constraints of molecular screening with the need to estimate infection prevalence across a large sample. Male sand flies, which can be identified by examining morphological features of their genitalia and other structures, were identified to species under the microscope, while females, which are harder to distinguish morphologically, were screened directly for Wolbachia DNA using polymerase chain reaction, or PCR.

The scale of the sampling effort was considerable. In total, 1,158 male sand flies were morphologically identified, revealing seven species in the region. Phlebotomus perniciosus was by far the most abundant, accounting for 751 specimens, followed by P. perfiliewi, P. neglectus, P. ariasi, Sergentomyia minuta, P. mascittii, and P. papatasi. For the molecular screening, 1,937 sand flies were divided into 124 pools, including 10 male pools that could not be assigned to a species morphologically. When these pools were tested for Wolbachia, the results were striking: the overall prevalence of infection was 38.7 percent, a remarkably high figure for a vector group in which Wolbachia had been considered rare or poorly documented.

Prevalence was not static across the study period. In 2023, 44.9 percent of the screened pools tested positive for the bacterium. The following year, the figure dropped to 21.3 percent, less than half the initial rate, before rebounding sharply to 57.1 percent in 2025. This year-to-year variation suggests that Wolbachia infection dynamics in sand fly populations are influenced by fluctuating ecological conditions, whether climatic, related to host population structure, or driven by other factors that the study was not designed to disentangle. Understanding what drives these swings will be important for any future attempt to model or manipulate the bacterium’s spread through wild populations.

To characterize the Wolbachia strains genetically, the team amplified five housekeeping genes used in the standard multi-locus sequence typing scheme for the bacterium: coxA, fbpA, ftsZ, gatB, and hcpA. Because Wolbachia is classified into supergroups based on such sequence data, this approach allows precise assignment of strains to evolutionary lineages. In addition, the researchers amplified the cytochrome oxidase I gene, or COI, a widely used DNA barcoding marker, to confirm the identity of the host sand flies, and for four samples they also sequenced a partial fragment of the wsp gene, which encodes a Wolbachia surface protein. Samples for which all target genes were successfully amplified were then subjected to nanopore sequencing, a long-read technology that enables rapid and relatively inexpensive generation of sequence data.

The genetic results were unambiguous and, in one respect, quite unexpected. Complete MLST profiles were obtained for 11 samples, and every one of them belonged to Wolbachia Supergroup B, one of the major divisions of the bacterium. COI barcoding confirmed that all 11 infected hosts were Phlebotomus perniciosus. More remarkable still, all 11 sequenced Wolbachia shared an identical sequence type, despite having been collected across different years and from different habitats within the study region. This genetic uniformity points to a single, well-established strain circulating in P. perniciosus populations across Northern Italy, rather than a diverse community of unrelated infections. When the researchers compared this profile against public sequence databases, they found no exact match; the closest known profile came from the confused flour beetle, Tribolium confusum, hinting at possible evolutionary links between the sand fly strain and Wolbachia found in other insect hosts.

The significance of these findings extends beyond basic microbiology. Wolbachia’s appeal as a control agent rests on two well-documented phenomena. The first is cytoplasmic incompatibility, a reproductive manipulation in which males carrying certain Wolbachia strains can only successfully breed with females carrying the same or a compatible strain, a mechanism that can be exploited to suppress populations or to drive desirable traits through a population. The second is the ability of some strains to reduce vector competence, meaning the infected insect becomes less able to support and transmit pathogens. Both mechanisms have been deployed successfully against Aedes mosquitoes in programs targeting dengue. Whether the Supergroup B strain found in P. perniciosus exhibits similar properties is not yet known, but the new study provides the essential baseline: researchers now know which strain is present, how common it is, and that it persists stably across years and habitats.

The authors emphasize that this work is a foundation rather than a conclusion. Future studies will need to examine the effects of the identified Wolbachia strain on sand fly reproduction, survival, and, crucially, vector competence for Leishmania parasites and phleboviruses. The demonstration that a single, genetically uniform strain infects a large fraction of the most important sand fly vector in Northern Italy raises the possibility that natural Wolbachia infections could already be influencing transmission dynamics in the region, or that they could be augmented through release strategies similar to those used against mosquitoes. As climate change and land-use shifts continue to expand the range of sand flies and the diseases they carry, tools that can complement or replace chemical insecticides will only grow in importance. This survey of Italian sand flies offers a detailed genetic portrait of a candidate ally hiding within the insects themselves, and it opens a concrete path toward testing whether that ally can be turned against the pathogens the flies transmit.

Subject of Research: Wolbachia endosymbiont infections in wild sand fly populations in Northern Italy

Article Title: Phylogenetic insights into Wolbachia natural infections in sand flies of Northern Italy

Article References: Carrera, M., Bertasio, C., Carta, V., Marelli, A., Muratore, R., Tolini, C., Lelli, D., Sozzi, E., Moreno, A., & Defilippo, F. (2026). Phylogenetic insights into Wolbachia natural infections in sand flies of Northern Italy. Parasites & Vectors. https://doi.org/10.1186/s13071-026-07578-9

Image Credits: AI Generated

DOI: 10.1186/s13071-026-07578-9

Keywords: Wolbachia, sand flies, Phlebotomus perniciosus, leishmaniasis, vector control, MLST, nanopore sequencing, Italy, endosymbiont, biological control, Parasites & Vectors, entomology