- Volume 11, Issue 11, 2025

Infections caused by carbapenem-resistant Acinetobacter baumannii (CRAB) are of great concern, as mortality is high, and treatment options are very limited. Despite having among the highest rates reported worldwide, scarce genomic data are available on CRAB strains from the Middle East. Here, we report the global emergence of a novel International Clone (IC), designated IC12, based on the epidemiological, phenotypic and genome sequencing data (short reads and long reads) of a set of 60 A. baumannii isolates belonging to multilocus sequence type 158 (Pasteur scheme). IC12, prevailing in the Middle East since 2007, has also been found in Europe, Asia and South America. Alleles OXA-65 and ADC-117, coded by the bla OXA-51-like and bla ADC A. baumannii-intrinsic genes, respectively, were hallmarks shared by all the isolates. Plasmid pIC12-2 (80,000 bp), which carries a repAci6 replication initiator (RP-T1) and a type IV conjugative transfer system, played a major role in the antimicrobial resistance profile of 54/60 of the IC12 isolates. This resistance was mediated by three mobile genetic elements, namely Tn2008, MITEAb-IC12 and TnaphA6. All four Peruvian IC12 isolates lacked pIC12-2 and carried a different set of plasmids. Two of the Peruvian isolates carried a chromosomal resistance island of 79,396 bp long (designated IC12-RI) marked by the occurrence of tet(X3). The global spread of IC12 is worrying and calls for further studies on the virulence features and clinical impact of this clone.

Enterococcus faecium is a pathogen that frequently causes infections and outbreaks in hospitals. Despite the increasing need for genomic surveillance of E. faecium, a standardized genomic analysis framework for this pathogen is lacking. We aim to conduct a comprehensive global epidemiological overview and propose a genomic analysis framework. We analysed 21,058 public E. faecium genomes from 80 countries to create a comprehensive snapshot of E. faecium resistome and virulence in association with geography and population structure. We compared strain clustering based on SNP-based and sequence typing-based approaches with ST80 genomes as examples, to establish the methodological comparability for outbreak investigations using different approaches. Focusing on the resistance genotypes against vancomycin and linezolid, we observed within-sequence type (ST) dynamics, such as a vanA-to-vanB transition within ST80 isolates in Denmark driven by the clonal expansion and dissemination of mobile linezolid resistance among ST22 and ST32. We established that the popularly used 25 allele distance threshold based on core genome multi-locus sequence typing corresponds to 86 core genome SNPs or 380 whole-genome SNPs. Finally, we introduce GenoFaecium, a user-friendly analytical tool to streamline the genomic surveillance of E. faecium, which enables consistent interpretation of antimicrobial resistance and virulence profiles from E. faecium genome sequences. By providing this tool and empirically bridging the outbreak investigation thresholds of different phylogenetic methods, our study facilitates and improves the genomic surveillance of E. faecium.

Eimeria spp. are common coccidian parasites of a wide range of vertebrates, causing diarrhoea, poor weight gain and significant mortality in domestic animals and birds. However, there is a paucity of genomic data on these important pathogens. Of the 11 common Eimeria species in rabbits, only Eimeria stiedae invades biliary epithelial cells rather than the intestine, and the determinants of coccidian tissue tropism remain unclear. In this study, we sequenced the genomes of five common rabbit Eimeria species, including E. stiedae, Eimeria flavescens, Eimeria intestinalis, Eimeria magna and Eimeria media. Comparative genomic analysis reveals that the genome of E. stiedae appears more compact than the genomes of intestinal Eimeria species. It shows reductions in the numbers of rhoptry proteins, dense granule proteins, microneme adhesive repeats and TA4 surface antigens, suggesting that surface and invasion-associated proteins may be involved in the tissue tropism of Eimeria spp. In addition, E. stiedae-specific motifs are identified in a cluster of hypothetical surface antigens. These data provide not only new insights into the biological characteristics of coccidia but also valuable resources for functional research and drug and vaccine development.

Polyomaviruses and papillomaviruses are icosahedral viruses with small circular dsDNA genomes. Limited information on their diversity and evolution in avian hosts is available, with even less known regarding Antarctic penguins. Prior to this study, only one polyomavirus and two papillomaviruses had been identified in Adélie penguins (Pygoscelis adeliae). To expand our knowledge of these viruses in Antarctic penguins, we collected faecal and cloacal swab samples from 246 Adélie penguins over 3 breeding seasons (2021–2024) and 10 emperor penguins (Aptenodytes forsteri) during the 2023–2024 season on Ross Island (Ross Sea). Additionally, we sampled 66 Adélie, 40 chinstrap (Pygoscelis antarcticus) and 71 gentoo (Pygoscelis papua) penguins during the 2022–2023 season across various sites on the Antarctic Peninsula. All samples were screened for papillomaviruses and polyomaviruses. We identified 31 polyomaviruses in Adélie, gentoo and chinstrap penguins and 4 papillomaviruses in Adélie penguins sampled in both eastern and western Antarctica. The 31 penguin polyomaviruses belong to a single species but form four distinct variants that are host species specific with strong geographic clustering. The four papillomaviruses represent three different types, of which two are new types from Adélie penguins sampled on Yalour Island in the West Antarctic Peninsula. Co-occurrence of two polyomavirus variants was identified in two individual gentoo penguins. Both of these variants appear to be circulating in gentoo penguins at Cierva Cove, Hope Bay in Trinity Peninsula along the Antarctic Peninsula, and at Hannah Point on Livingstone Island and Stranger Point on King George Island in the South Shetland Islands. Here, we expand the known diversity, host and geographical ranges of penguin polyomaviruses and, together with a previously identified polyomavirus on Ross Island from 2012 to 2013, show that they form five distinct lineages. The four papillomaviruses identified in this study, together with two previously identified from Ross Island in 2012 and 2013 breeding seasons, show substantial diversity reflecting four papillomavirus types across three viral species and two distinct genera. Continued surveillance and viral genomic analysis across a larger geographical framework will help understand the evolution, transmission and incidence rates of these viruses.

Salmonella enterica serovar Kentucky (S. Kentucky) sequence type (ST) 198 has emerged as a globally disseminated multidrug-resistant (MDR) lineage posing significant public health challenges. The aim of this study was to characterise 125 S. Kentucky ST198 isolates collected from various sources in Algeria, including humans, animals, food and the environment, or obtained from humans in France (travellers returning from Algeria), between 2015 and 2022. Whole-genome sequencing was performed on 125 isolates to assess their genetic diversity and antimicrobial resistance (AMR) profiles. Phylogenetic analysis revealed that the Algerian S. Kentucky ST198 isolates were closely related to each other and belonged to the MDR lineage that emerged in Egypt before disseminating into Africa, the Middle East, Asia and Europe. These isolates also clustered closely with European and North African isolates carrying the gyrA_D87N mutation. We found that 90% of the isolates had MDR phenotypes, with resistance to critically important antibiotics, including ciprofloxacin, third-generation cephalosporins, azithromycin and chloramphenicol. Genomic analysis revealed that all the isolates had the three known non-synonymous resistance mutations in the quinolone-resistance-determining regions of DNA gyrase (gyrA) and DNA topoisomerase IV (parC). Multiple AMR genes were also identified, including bla CTX-M-15, bla CMY-2, bla CMY-4, qnrB19, mph(A), cmlA1 and floR. The Algerian isolates also contained the main variant of SGI1, SGI1-K, with multiple rearrangements. Plasmid replicon analysis revealed that the most frequent plasmid types were IncI1 (13.6%), Col156 (8.8%) and Col(pVC) (8%). This study provides the first comprehensive genomic insight into S. Kentucky ST198 in Algeria, highlighting the urgent need for a reinforcement of AMR surveillance and control measures in the region. These findings enhance our overall understanding of the epidemiology and evolution of MDR Salmonella and highlight the importance of a One Health approach for combating the spread of resistant pathogens.

We report the presence of the emerging plant pathogen ‘Xanthomonas cannabis’ in Australia through a comprehensive analysis of five historical isolates and all publicly available genomes of the species. Using comparative genomics, we characterized four isolates collected from Zinnia spp. and one from Cucurbita pepo. Our findings show that the Zinnia isolates form a distinct phylogroup with the pathotype strain of ‘X. cannabis’ pv. zinniae. This group possesses genes for the type 3 secretion system (T3SS) and effectors, a variety of genes unique within the species, and nine genomic islands associated with virulence and drug resistance. In contrast, the C. pepo isolate is genetically distinct and lacks the T3SS but contains its own genes unique within the species. Hypersensitivity response assays confirmed the pathogenic potential of all five isolates in black bean, eggplant, green bean, tomato, sunflower, zinnia and zucchini plants. These results highlight the genetic diversity and evolving threat of this pathogen in Australia, underscoring the critical need for ongoing biosecurity surveillance.

Members of the family Rhizobiaceae typically have multipartite genomes that are split between two or more replicons, including the chromosome and a variable number of extrachromosomal replicons (chromids and plasmids). Nearly all Rhizobiaceae replicons sequenced and described to date have a circular topology, except the linear chromid found in the genomes of most Agrobacterium spp. In this study, genomes of five non-pathogenic Agrobacterium strains and one plant tumourigenic Allorhizobium strain were fully sequenced. Surprisingly, genome analysis revealed that these six strains each carry an 80-kbp linear plasmid. Linear plasmids have so far not been identified in this bacterial family or other bacteria within the class Alphaproteobacteria. The ends of all six plasmids identified in this study have a hairpin structure with covalently closed ends. The plasmid sequences showed a high degree of homology, clearly indicating their common ancestry. Database searches led to the identification of additional linear plasmids in previously published Rhizobiaceae genome assemblies that were not previously recognized to have linear plasmids, suggesting that these replicons may be more widespread. Most likely, linear plasmids may be even more widely distributed than anticipated. Although the biological functions of the linear plasmids identified in this study remain unknown, they are associated with both non-pathogenic and plant tumourigenic Rhizobiaceae strains.

Pathogens adapting to the human host and to vaccination-induced immunity may follow parallel evolutionary paths. Bordetella parapertussis (Bpp) contributes significantly to the burden of whooping cough (pertussis) and shares vaccine antigens with Bordetella pertussis (Bp); both pathogens are phylogenetically related and ecological competitors. Bp vaccine antigen-coding genes have accumulated variation, including pertactin (PRN) disruptions, after the introduction of acellular vaccines in the 1990s. We aimed to evaluate evolutionary parallelisms in Bpp, even though pertussis vaccines were designed against Bp. We sequenced 242 Bpp isolates collected in France, the USA and Spain between 1937 and 2019, spanning pre-vaccine and two vaccines eras. We investigated the temporal evolution of Bpp sublineages using a Bayesian approach based on whole-genome SNPs and performed comparative genomic analyses focusing on antigen and virulence gene loci. The most recent common ancestor of all sequenced Bpp isolates was estimated around the year 1877, making it one of the youngest human pathogens, and the Bpp evolutionary rate we estimated (2.12×10−7 substitutions per site per year) was remarkably similar to the one previously reported for Bp (2.24×10−7). PRN antigen deficiency in Bpp was driven by 18 disruptive mutations, including deletion prn:ΔG-1895 estimated to have occurred around 1998 and observed in 73.8 % (149/202) of post-2007 Bpp isolates. In addition, we detected two early (year ~1900) mutations in the bvgA-fhaB intergenic region, which controls multiple virulence factors including the filamentous haemagglutinin antigen. Gene clusters for pertussis toxin and fimbriae showed a surprising lack of gene decay. Our findings suggest early adaptation of Bpp to humans through modulation of the bvgAS regulon, and a rapid adaptation through the loss of PRN expression, representing a late evolutionary parallelism concomitant with acellular vaccination against whooping cough.

Here, we describe a putatively hypervirulent, carbapenem-resistant Klebsiella pneumoniae (hv-CRKP) outbreak. Nanopore sequencing guided the infection prevention and control (IPC) responses during the outbreak. Twelve patients were identified as either being colonized and/or having clinical infections with the putative hv-CRKP, with an all-cause mortality within 6 months of 36%. Multiple IPC responses were put in place, with enhanced cleaning of the environment being the key intervention to halt the outbreak. All isolates were ST395 and contained at least one bla NDM carbapenemase gene, along with a variable array of other antimicrobial resistance and virulence genes, due to a rapidly evolving set of plasmids.