- Volume 11, Issue 7, 2025

Serovar detector is a new bioinformatic tool for determining the serovar of Actinobacillus pleuropneumoniae using whole genome sequencing. The composition of cps genes of isolates is compared to those of the serovar reference strains, and the outcome is determined both by the number of common genes and the similarities between the homologous genes. The validation of the bioinformatic tool utilized a broad collection of 732 isolates, including representatives from all described serovars. The isolates included had been characterized by conventional serotyping, PCR tests or different bioinformatic tools. The collection also includes isolates that have been difficult to allocate to a serovar using serology to test the performance of the Serovar detector when potential new varieties or combinations of cps genes are present. Out of the 732 isolates included in the investigation, only 36 isolates (4.9%) could not be allocated to the 19 recognized serovars. The validation showed that the Serovar detector is a robust method for determining the serovar of an isolate and a valuable tool for further characterization of the genetic heterogeneity both within serovars and within the A. pleuropneumoniae species.

When pathogens are repeatedly introduced into new environments, host jumps may occur into naïve taxa. Given the magnitude of the global plant trade, this process can lead to frequent disease emergence as interactions between previously isolated pathogens and new plant hosts become possible. Xylella fastidiosa is a recurring nuisance. This bacterial pathogen has recently emerged in novel geographic locations infecting a breadth of host plants. An introduction of X. fastidiosa subsp. fastidiosa from Central America to the USA several hundred years ago has since been the source of outbreaks across the globe. In the USA, particularly in California, the introduced bacterium is frequently found in European grapevine (Vitis vinifera). In this study, we demonstrated that the introduced strains do not persistently infect Coffea arabica. Furthermore, we did not observe an overall increase in the virulence of the introduced strains towards coffee, indicating a lack of hypervirulence. Then, using X. fastidiosa subsp. fastidiosa whole-genome sequences, 15 from the source region of Costa Rica and 289 from the introduced clade, we tested for traces of adaptation to grapevines. We found both genes and SNPs that are associated with the host shift to grapevines. These results support the hypothesis that a host jump with genetic adaptation occurred following the introduction of the pathogen into the USA.

Extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli are resistant to the critically important third- and fourth-generation cephalosporin antibiotics and present a risk to animal and human health. In Zimbabwe, there is an evidence gap concerning the prevalence and diversity of ESBL-producing E. coli in poultry. In this study, we screened for ESBL-E. coli at farms (n=50) and markets (n=10) using MacConkey agar supplemented with 4 µg ml−1 ceftriaxone. ESBL-E. coli were detected at every market and at 21 farms, giving a farm-level prevalence of 42%. Seventy isolates were obtained and tested for antimicrobial susceptibility, whilst 69 of these were further analysed by whole-genome sequencing. A total of eight distinct bla CTX-M variants were identified, and 69 out of 70 isolates were multidrug-resistant. Genomic analysis revealed evidence for clonal expansion of an ESBL-producing clone and horizontal gene transfer via plasmids being responsible for the dissemination of ESBL-E. coli. Geographic Information System mapping was used to visualize the distribution of the ESBL-producing clones. For example, ST1141 isolates were clonal, having a highly conserved core genome, and harboured bla CTX-M-15 and 11 additional antimicrobial resistance genes on a ~338 kbp IncHI2 plasmid which was not present in other isolates. This clone was present at nine farms. In contrast, a conserved ~93 kbp IncFII plasmid harbouring bla CTX-M-55 was present in isolates from three different multilocus sequence types obtained from six farms. This study provides insight into the burden and distribution of ESBL-E. coli at poultry farms in Zimbabwe and provides molecular genetic evidence for clonal expansion and plasmid transfer as being important mechanisms for the dissemination of ESBL-E. coli in this setting. This study underscores the importance of adopting measures, such as prudent antimicrobial use and farm biosecurity, that can limit the development and dissemination of ESBL-producing E. coli.

Klebsiella pneumoniae is a primary bacterial pathogen responsible for various human infections with the emergence of carbapenem-resistant K. pneumoniae (CRKP) as a significant clinical challenge. Although previous studies have classified K. pneumoniae based on homology of conserved genes, the biological implications of these classifications remain unclear. In this study, we extracted 47,222 centroid coding sequences (CDSs), representative sequences selected from clusters of highly similar CDSs, from 3,592 complete genomes and analysed the genomic characteristics of 4,458 CRKP strains using these centroid CDSs. This approach revealed substantial genomic diversity among CRKP strains, with classification results largely aligning with the multilocus sequence typing (MLST) method. Associations between centroid CDSs and MLST sequence types (STs) were identified, and the biological functions enriched in each ST including those linked to resistance and virulence mechanisms were highlighted. Moreover, the coexistence of CDSs annotated as antibiotic resistance and virulence genes was observed, particularly between a group of carbapenem resistance genes and those encoding proteins for type I and III fimbriae, efflux pumps, type II secretion system and siderophore-mediated iron acquisition. These findings provide an alternative approach for classifying CRKP strains, offering insights into their genomic characteristics.

NOD-like receptors (NLRs) are intracellular immune receptors that detect pathogen-associated cues and trigger defence mechanisms, including regulated cell death. In filamentous fungi, some NLRs mediate heterokaryon incompatibility, a self-/non-self-recognition process that prevents the vegetative fusion of genetically distinct individuals, reducing the risk of parasitism. The het-d and het-e NLRs in Podospora anserina are highly polymorphic incompatibility genes (het genes) whose products recognize different allelic variants of the HET-C protein via a sensor domain composed of WD40 repeats. These repeats display unusually high sequence identity maintained by concerted evolution. However, some sites within individual repeats are hypervariable and under diversifying selection. Despite extensive genetic studies, inconsistencies in the reported WD40 domain sequence have hindered functional and evolutionary analyses. Here, we confirm that the WD40 domain can be accurately reconstructed from long-read sequencing (Oxford Nanopore and PacBio) data, but not from Illumina-based assemblies. Functional alleles are usually formed by 11 highly conserved repeats, with different repeat combinations underlying the same phenotypic het-d and het-e incompatibility reactions. AlphaFold 3 structure models suggest that their WD40 domain folds into two 7-blade β-propellers composed of the highly conserved repeats, as well as three cryptic divergent repeats at the C-terminus. We additionally show that one particular het-e allele does not have an incompatibility reaction with common het-c alleles, despite being 11-repeats long. Finally, we present evidence that the recognition phenotypes of het-e and het-d arose through convergent evolution. Our findings provide a robust foundation for future research into the molecular mechanisms and evolutionary dynamics of het NLRs, while also highlighting both the fragility and the flexibility of β-propellers as immune sensor domains.

Acne vulgaris is a common skin condition marked by the formation of comedones, papules, pustules and nodules, with its underlying causes still not fully understood. This study explores the impact of microbial dysbiosis and virulence factors on acne development. Through high-throughput 16S rRNA sequencing, we identified significant disruptions in the skin microbiome, particularly in comedones. Key virulence factors of Cutibacterium acnes, known as Christie–Atkins–Munch-Peterson (CAMP) factors, were assessed using both in vitro and in vivo models. Among these, CAMP2 and CAMP5 demonstrated the highest inflammatory and haemolytic activities in keratinocytes. Topical anti-IL-8 treatment in a murine model effectively reduced inflammation and suppressed CAMP expression. Structural analysis of CAMP3 uncovered distinct pathogenic features that, alongside CAMP5, were found to aggravate acne-like inflammation and sebaceous gland atrophy. These findings advance our understanding of the interplay between microbial dysbiosis and CAMP factors in acne pathogenesis, offering potential avenues for therapeutic intervention.

The global rise of antimicrobial resistance has intensified efforts in bioprospecting, with researchers increasingly exploring unique marine environments for novel antimicrobials. In line with this trend, our study focused on bacteria isolated from the unique microbiome of crustose coralline algae (CCA), which has yet to be investigated for antimicrobial discovery. In the present work, bacteria were isolated from a CCA collected from Varadero Reef located in Cartagena Bay, Colombia. After performing antimicrobial assays against antibiotic-resistant human and marine pathogens, three isolates were selected for genome sequencing using the Oxford Nanopore technology. Genome mining of the high-quality assemblies revealed 115 putative biosynthetic gene clusters (BGCs) and identified genes in relevant biosynthetic pathways across the three genomes. Nonetheless, we hypothesize that the biosynthesis of antimicrobial compounds results from the expression of undescribed BGCs. Further analysis revealed the absence of genes pertaining to the synthesis of coral larvae settling molecule tetrabromopyrrole, commonly produced by CCA-associated bacteria. We also discuss how differential representation of gene functions between the three isolates may be attributed to the distinct ecological niches they occupy within the CCA. This study provides valuable resources for future research aimed at the discovery of novel antimicrobials, particularly in the face of the antibiotic-resistance global crisis, and highlights the potential of specialized marine environments like CCA.

Preterm infants experience abnormal microbial colonization, which coupled with their vulnerable physiology can increase the risk of disease. Understanding the factors influencing the complex relationship between the temporal development of the gut microbiome and functional metabolites derived from microbe–microbe and microbe–host interaction is therefore critical. In this study, 266 longitudinal stool samples from 66 very preterm infants underwent 16S rRNA gene sequencing to analyse gut microbial structure. To further explore the functional status of these gut members, a subset of these samples underwent stool metabolomics (n=101). Statistically significant associations were found with age for both the gut microbiota (P<0.001) and metabolite profiles (P<0.001). Relationships between the gut microbiome and metabolome showed concordance, with 691 significant correlations after adjustment between the top 10 most abundant bacterial taxa and all 977 identified metabolites. Lactobacillus had the highest number of significant correlations (31%), amongst which was a strong positive correlation with equol sulphate, an oestrogen produced by intestinal bacteria. This study reveals consistent relationships between the diet, gut microbiota composition and metabolic function. The findings provide valuable insights into the microbial and metabolic dynamics of the preterm gut and the relationships underlying gut microbiome structure and function in vulnerable preterm infants. Further research is needed to confirm these findings and explore their implications for infant health and development.

Proteins of the multinuclear non-haem iron-dependent oxidative (MNIO) enzyme superfamily catalyse various modification reactions on the precursors of ribosomally synthesized post-translationally modified peptides (RiPPs). We recently identified two large families of MNIO-modified RiPPs called bufferins, which enhance bacterial growth under copper stress by chelating the excess metal ions. Here, we explored the diversity of potential MNIO substrates by performing extensive in silico studies. Analyses of MNIO-coding biosynthetic gene clusters (BGCs) identified various groups of putative precursors, most of which are characterized by specific Cys-containing motifs, throughout the eubacterial phylogenetic tree. The precursors of most MNIO-modified RiPPs harbour N-terminal Sec-dependent signal peptides, a rare feature among bacterial RiPPs. Some precursors are very long relative to those of typical RiPPs, indicating that MNIO enzymes could modify both peptide and protein substrates. We also identified a distinct family of integral membrane proteins with large predicted extra-cytoplasmic domains mostly found in Actinomycetota, frequently but not systematically associated with MNIOs. Most MNIO BGCs harbour genes coding for DUF2063 domain-containing proteins or structurally related proteins, serving as partners of the enzymes for precursor modification. We uncovered a correlation between the presence or the absence of Sec signal peptides in the precursors and the types of partner proteins of the MNIO enzymes. This study depicts the global landscape of potential MNIO-dependent natural products by unveiling groups of peptides and proteins genetically associated with MNIOs. It reveals a treasure trove of potential new RiPP precursors which likely represent a widespread bacterial strategy to deal with copper stress, and most likely other stresses, in natural environments.

Background. Diarrhoea remains a major threat to children in developing nations, with diarrhoeagenic Escherichia coli (DEC) being the primary causative agent. Characterizing prevalent DEC strains is crucial, yet comprehensive genomic analyses of major DEC strains, including enteropathogenic E. coli (EPEC), enteroaggregative E. coli (EAEC) and enterotoxigenic E. coli (ETEC), are lacking in India.

Methods. We sequenced 24 EAEC and 23 EPEC strains from Indian patients with diarrhoea and conducted an extensive database search for DEC human isolates from India. Detailed phylogenetic analyses, virulence gene subtyping and examinations of accessory virulence and antimicrobial resistance (AMR) genes were performed.

Results. The analysed DEC strains included 32 EAEC, 25 EPEC, 32 ETEC and 1 each of the EPEC/ETEC-hybrid and ETEC/EAEC-hybrid pathotypes. These strains were predominantly classified into phylogroups A (35.2%) and B1 (41.8%) and dispersed within these phylogroups without pathotype-specific clustering. One ETEC strain was classified into cryptic clade 1. Subtypes of hallmark virulence genes varied substantially amongst strains in each pathotype, and 31 accessory virulence genes were detected either specifically within certain pathotypes or across multiple pathotypes at varying frequencies, indicating diversification of the virulence gene repertoire within each pathotype. Acquired AMR genes were found in 73.6% of the strains, with frequent identification of AMR genes for aminoglycosides (40.0%), β-lactams (64.8%), sulphonamides (49.5%) and trimethoprim (42.9%). Known quinolone-resistant mutations were found in 74.7% of the strains, whereas AMR genes for macrolide (30.8%), phenicol (11.0%) and tetracycline (27.4%) were less frequent.

Conclusions. The diverse virulence potential and trends in AMR gene prevalence amongst major DEC strains in India are highlighted in this study. Continuous monitoring of DEC strain characteristics is essential for the effective control and treatment of DEC infections in India.

Streptococcus pneumoniae, a clinically significant pathogen, causes invasive diseases in children and older adults. Pneumococcal conjugate vaccines (PCVs) have substantially reduced the incidence of vaccine serotype (VT) pneumococcal diseases. However, serotype replacement, characterized by the emergence of non-vaccine serotypes (NVTs), presents a persistent challenge to disease prevention. To address this, we analysed 236 pneumococcal isolates collected in South Korea between 1997 and 2023, spanning both pre- and post-PCV13 periods. Whole-genome sequencing was performed to assess serotypes, antimicrobial resistance, virulence factors and global pneumococcal sequence clusters (GPSCs). Capsular switching events and the relationships among pneumococcal lineages, serotypes and disease invasiveness were also evaluated. Among the 37 identified serotypes, NVTs such as 23A, 15B/15C and 10A were dominant post-PCV13. Serotype 10A, associated with invasive pneumococcal diseases (IPDs), belonged to GPSC634-ST11189 and showed elevated minimum inhibitory concentrations for β-lactams. Capsular switching events were observed between VTs and NVTs, highlighting the adaptability of pneumococcal populations. Antimicrobial non-susceptibility was highest for azithromycin (82.7%), followed by tetracycline (76.5%) and co-trimoxazole (70.4%), with higher rates observed in the post-PCV13 period. Notably, amoxicillin (P=0.049) and meropenem (P=0.002) showed significant non-susceptibility in the post-PCV13 period. Virulence factors pspA and pfbA were associated with IPDs, while pilus islet PI-1-related genes were more frequent in non-invasive cases. These findings underscore the importance of genomic surveillance to monitor pneumococcal population dynamics and inform public health strategies. The inclusion of serotype 10A in the recently approved PCV20 offers promise for further reducing the global burden of IPDs, including in South Korea.

In the UK, the COVID-19 Genomics UK Consortium (COG-UK) established a real-time national genomic surveillance system during the COVID-19 pandemic, producing centralized data for monitoring severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). As a COG-UK partner, Quadram Institute Bioscience in Norfolk sequenced over 87,000 SARS-CoV-2 genomes as part of the national effort, contributing to the region becoming densely sequenced. Retrospective analysis of SARS-CoV-2 lineage dynamics in this region may contribute to preparedness for future pandemics. In total, 29,406 SARS-CoV-2 whole genome sequences and corresponding metadata from Norfolk were extracted from the COG-UK dataset, sampled between March 2020 and December 2022, representing 9.9% of regional COVID-19 cases. Sequences were lineage typed using Pangolin, with subsequent lineage analysis carried out in R using RStudio and related packages, including graphical analysis using ggplot2. In total, 401 global lineages were identified, with 69.8% appearing more than once and 31.2% over ten times. Temporal clustering identified six lineage communities based on first lineage emergence. Alpha, Delta and Omicron variants of concern (VOCs) accounted for 8.6, 34.9 and 48.5% of sequences, respectively. These formed four regional epidemic waves alongside the remaining lineages which were observed in the early pandemic prior to VOC designation and were termed ‘pre-VOC’ lineages. Regional comparison highlighted variability in VOC epidemic wave dates dependent on location. This study is the first to assess SARS-CoV-2 diversity in Norfolk across a large timescale within the COVID-19 pandemic. SARS-CoV-2 was both highly diverse and dynamic throughout the Norfolk region between March 2020 and December 2022, with a strong VOC presence within the latter two-thirds of the study period. The study also displays the utility of incorporating genomic epidemiological methods into pandemic response.

Cholera is an acute diarrhoeal disease caused by Vibrio cholerae. It remains a major public health challenge worldwide, and particularly in the endemic region around the Bay of Bengal. Over decadal time scales, one lineage typically dominates and spreads in global pandemic waves. However, it remains unclear to what extent diverse lineages co-circulate during a single outbreak. Defining the pool of diversity over finer time-scales is important because the selective pressures that impact V. cholerae, namely antibiotics and phages, are dynamic on these scales. To study the nationwide diversity of V. cholerae, we long-read sequenced 273 V. cholerae genomes from seven hospitals over 1 year (2018) in Bangladesh. Four major V. cholerae lineages were identified: three known lineages, BD-1, BD-2a and BD-2b, and a novel lineage that we call BD-3. In 2022, BD-1 caused a large cholera outbreak in Dhaka, at which point it had replaced BD-2 as the most common lineage in Bangladesh. We show that, in 2018, BD-1 was already predominant in the five northern regions, including Dhaka, consistent with an origin from northern India. By contrast, we observed a higher diversity of lineages in the two southern regions near the coast. The four lineages differed in pangenome content, including integrative and conjugative elements (ICEs) and genes involved in resistance to bacteriophages and antibiotics. Notably, BD-2a lacked an ICE and is predicted to be more sensitive to phages and antibiotics, yet persisted throughout the sampling period. Genes previously associated with antibiotic resistance in V. cholerae isolated from Bangladesh in the prior decade were entirely absent from all lineages in 2018–2019, suggesting shifting costs and benefits of encoding these genes. Our results highlight the diverse nature of the V. cholerae pangenome and geographic structure within a single outbreak season. This diversity provides the raw material for adaptation to antibiotics, phages and other selective pressures.

Streptococcus uberis is a leading cause of bovine mastitis, resulting in large economic losses and welfare issues for affected cows. However, relatively little is known about the global distribution and emergence of bovine mastitis-causing lineages and dissemination of antimicrobial resistance or virulence genes in the species. Here, we present a global framework for S. uberis based on whole-genome sequencing data from isolates across four continents (n=1,070). Internationally, S. uberis isolates show extensive genetic heterogeneity driven by homologous recombination and high levels of accessory genome content. Within the population, 35% (n=374/1,070) of isolates had at least one acquired antimicrobial resistance gene, while 59% (n=631/1,070) of isolates harboured a mutation in the penicillin-binding proteins (pbp2b or pbp2x) associated with decreased penicillin susceptibility, the front-line antimicrobial for mastitis infections. All described S. uberis virulence factors and currently proposed vaccine candidates were investigated for carriage and sequence heterogeneity to guide potential vaccine development, with two vaccine candidates (GapC and Sua) and seven putative virulence proteins (Fba, FbpS, Vru, GlnA, SUB0888, SUB0241 and haemolysin-like protein) having low naturally occurring sequence variation and high (>99%) coverage. This study will facilitate improved genomic surveillance for the emergence of antimicrobial resistance and virulence in this important mastitis pathogen.

Streptococcus pyogenes is a leading cause of infection-related mortality in humans globally. The characteristic cell wall-anchored group A carbohydrate (GAC) is expressed by all S. pyogenes strains and consists of a polyrhamnose backbone with alternating N-acetylglucosamine (GlcNAc) side chains, of which 25% are decorated with glycerol phosphate (GroP). The genes in the gacA-L cluster are critical for GAC biosynthesis, with gacH-L being responsible for the characteristic GlcNAc–GroP decoration, which confers the agglutination in rapid test diagnostic assays and contributes to S. pyogenes pathogenicity. Historical research papers described S. pyogenes isolates, so-called A-variant strains, that lost the characteristic GlcNAc side chain following serial animal passage. Genomic analysis of a single viable historic parent/A-variant strain pair revealed a premature inactivating stop codon in gacI, explaining the described loss of the GlcNAc side chain. Subsequently, we analysed the genetic variation of the 12 gacA-L genes in a collection of 2021 S. pyogenes genome sequences. Although all gac genes (gacA-L) displayed genetic variation, we only identified 26 isolates (1.3%) with a premature stop codon in one of the gac genes. Twelve out of 26 (46%) isolates contained a premature stop codon in gacH, which encodes the enzyme responsible for the GroP modification. To study the functional consequences of the different premature stop codons for GacH function, we plasmid-expressed three gacH variants in a S. pyogenes gacH-deficient strain. Cell wall analysis confirmed GacH loss of function for the studied gacH variants through the significant reduction of GAC GroP, complete resistance to killing by the human bactericidal enzyme group IIA-secreted phospholipase and susceptibility to zinc toxicity. Overall, our data provide a comprehensive overview of the genetic variation of the gacA-L cluster in a global population of S. pyogenes strains and the functional consequences of rare inactivating mutations in gacH for host interaction.

Streptococcus pneumoniae is a leading pathogen in terms of deaths attributable to or associated with antimicrobial resistance globally. Thus, monitoring antibiotic resistance determinants constitutes a key aspect of surveillance efforts for this microbe. Leveraging publicly available whole-genome sequencing (WGS) data, we aimed to investigate the presence and distribution patterns of antibiotic resistance determinants in S. pneumoniae with a focus on multidrug resistance (MDR) and serotype distribution. Metadata and genomes were obtained from the National Center for Biotechnology Information Pathogen Detection database. Curation and harmonization were performed in R and SPSS. Data on resistance patterns were defined according to AMRFinderPlus, and a combination of prediction tools was employed for in silico serotyping. Analyses involved 75,161 genomes totalling 122,673 gene/allele counts from 14 antibiotic classes. MDR was observed in 16.7% of isolates, with the highest increasing rates in Asia and South America. Within antibiotic classes, an increase in macrolide resistance genes was highlighted, particularly in the proportion of genomes presenting mef(A)/msr(D). Over a third of isolates with serotypes 19F, 23F, 15A, 6B and 19A showed MDR. We further observed the highest significant increases in the presence of resistance in 33F, 22F, 10A and 23A. Serotype 13, not included in any vaccine formulation, presented high MDR rates with a strong increasing trend. The findings of this study highlight variations in resistance determinants globally and across serotypes over time. Collectively, these data underscore the added value of utilizing public WGS data to investigate the effectiveness and repercussions of treatment and vaccination strategies on managing antibiotic resistance.

Introduction. Campylobacter fetus causes reproductive diseases in livestock and can lead to zoonotic infections such as bacteraemia, particularly in immunocompromised individuals. Despite its significance, its genomic characteristics remain poorly understood. This study analysed 114 publicly available C. fetus genomes to provide global insights into genetic diversity, antimicrobial resistance (AMR) and zoonotic risk.

Results. A total of 32 distinct sequence types (STs) were identified across 111 of the 114 C. fetus genomes, spanning 6 continents and diverse hosts (cattle, humans, sheep and reptiles). The majority of strains from cattle (75.6%, n/N=34/45) were assigned to ST-4, which was the most prevalent overall (n=45), while human-associated genomes exhibited the highest diversity with 16 STs. C. fetus subsp. venerealis (Cfv) and its biovar intermedius (Cfvi) genomes clustered closely, forming distinct branches at the biovar level; however, six Cfv genomes were located within Cfvi clades, suggesting a shared ancestry. C. fetus subsp. testudinum (Cft), primarily isolated from humans (60.0%, n/N=18/30), exhibited a more diverse genetic profile, with 20 STs. Cfv from North America and Cfvi from South America formed distinct geographic clusters, while C. fetus subsp. fetus genomes showed no clear geographic patterns, indicating global spread. Pangenomic analysis revealed substantial variation in gene presence/absence in Cft. Five AMR genes were detected, with tet(O) (n=3) being the most common. A total of 220 plasmid contigs were identified across 47 genomes, predominantly in Cfvi (66.8%, n/N=147/220) and Cfv (29.1%, n/N=64/220). Horizontal gene transfer analysis identified 140 genomic islands across 41 genomes, and virulence factor analysis revealed cheY as the sole conserved virulence gene across 35 genomes.

Conclusion. These findings provide critical insights into the genomic diversity, zoonotic potential and global distribution of C. fetus, emphasizing the need for integrated genomic and epidemiological strategies to assess its impact on human and animal health.

Purpose. Invasive pneumococcal disease (IPD) remains a major global public health concern due to its high morbidity and mortality rates, particularly among children and the elderly. This study aimed to apply whole-genome sequencing (WGS) to characterize Streptococcus pneumoniae strains responsible for IPD in south Tunisia, including serotype distribution, clonal relationship and antimicrobial resistance (AMR) profiles.

Methods. A total of 148 IPD S. pneumoniae isolates were collected from the microbiology laboratory at Habib Bourguiba University Hospital in Sfax, Tunisia, between 2012 and 2022. These isolates underwent WGS using Illumina technology. Bioinformatic analyses were performed to determine serotype distribution, sequence types (STs), Global Pneumococcal Sequence Clusters (GPSCs), phylogenetic relationships and AMR determinants.

Results. Twenty-six different serotypes were identified, with the most prevalent being 14 (18%), 3 (13%), 19A (12%) and 19F (11%). The isolates showed high genomic diversity, as they belonged to 32 GPSCs and 59 STs. The most common GPSCs were GPSC-6, GPSC-10 and GPSC-44, associated with serotypes 14, 19A and 19F, respectively. The most frequent STs were ST2918, ST179 and ST3772. The most common resistance genes were ermB (53%) and tetM (55%), which were linked to resistance against erythromycin and tetracycline, respectively. There was a considerable concordance between WGS-based and phenotypic resistance profiles for most tested antibiotics, with few major and very major errors for most antibiotics. Temporal analysis showed a decline in serotypes 19F and 9V throughout the study period, which was associated with slight decreases in GPSC-6 and GPSC-44, while serotype 19A and GPSC-10 sharply increased.

Conclusion. This study highlights the substantial genomic diversity, serotype distribution and high prevalence of AMR among IPD S. pneumoniae isolates in south Tunisia, underscoring the need for continued surveillance and effective vaccination strategies to combat this persistent public health threat.

We studied the genomic evolution and transmission dynamics of multidrug-resistant ST15 (Institut Pasteur scheme) Acinetobacter baumannii, examining resistance gene acquisition, clonal diversification, geographic distribution and origin of this high-risk clone. One hundred and fifty-two (n=152) ST15 genomes from 18 countries (1997–2024), including 42 isolates from U.S. Military Treatment Facilities and 110 publicly available genomes in GenBank, were analysed. Whole-genome sequencing, assembly and annotation were performed using established bioinformatics pipelines. Phylogenetic analysis based on core-genome SNPs – filtered for recombination with Gubbins – was combined with mobile element and resistance gene identification. ST15 isolates separated into two main clades with distinct subclades and variable resistance profiles. Homologous recombination drove the diversification of resistance determinants, including multiple ampC alleles. Key resistance genes, such as bla OXA-23, were disseminated via known transposons (Tn2006 or Tn2008), while plasmid exchange, including dif module acquisitions, also played a role in the spread of bla CARB. Patristic analysis identified Argentina as the likely origin for the emergence of ST15, aligning with early 1997 isolates. Recombination, transposon-mediated gene transfer and plasmid exchange have been central in driving the evolution and global dissemination of ST15.