Microbial Genomics最新文献

{"title":"Comparative genomic and resistance characterization of ST2 and ST164 carbapenem-resistant <i>Acinetobacter baumannii</i> from hospital environments and clinical specimens.","authors":"Xiao Wang, Tongsheng Xu, Yue Zhang, Ye Qiu, Yanru Liang, Jun Feng, Yuanping Wang, Bing Zhao, Lili Ren","doi":"10.1099/mgen.0.001679","DOIUrl":"https://doi.org/10.1099/mgen.0.001679","url":null,"abstract":"&lt;p&gt;&lt;p&gt;Carbapenem-resistant &lt;i&gt;Acinetobacter baumannii&lt;/i&gt; (CRAB) represents a formidable nosocomial pathogen, with healthcare environments acting as critical reservoirs for its dissemination. In this study, we investigated the prevalence, antimicrobial resistance profiles and genomic characteristics of CRAB isolates collected from hospitals in Shanghai, China, between June and December 2024, identifying ST2&lt;sup&gt;Pas&lt;/sup&gt; (84.13%) and ST164&lt;sup&gt;Pas&lt;/sup&gt; (15.08%) as the predominant lineages among the 126 CRAB isolates recovered from clinical (&lt;i&gt;n&lt;/i&gt;=94), environmental (&lt;i&gt;n&lt;/i&gt;=29) and healthcare worker (&lt;i&gt;n&lt;/i&gt;=3) sources. Environmental CRAB accounted for the highest proportions on patient-contact surfaces (34.48%), medical devices (31.03%) and shared items (24.14%). Within the dominant ST2&lt;sup&gt;Pas&lt;/sup&gt; lineage, clinical isolates exhibited higher resistance rates to ampicillin/sulbactam, cefoperazone/sulbactam and levofloxacin, with significantly higher carriage rates of &lt;i&gt;bla&lt;/i&gt; &lt;sub&gt;TEM-1D&lt;/sub&gt; compared to environmental isolates. Compared to ST164&lt;sup&gt;Pas&lt;/sup&gt;, ST2&lt;sup&gt;Pas&lt;/sup&gt; CRAB isolates exhibited greater resistance to amikacin, gentamicin, trimethoprim/sulfamethoxazole and minocycline and a higher prevalence of &lt;i&gt;aph&lt;/i&gt;(3')-Ia, &lt;i&gt;aph&lt;/i&gt;(3″)-Ib, &lt;i&gt;aph(3'&lt;/i&gt;)-VI, &lt;i&gt;aph&lt;/i&gt;(6)-Id, &lt;i&gt;arm&lt;/i&gt;A, &lt;i&gt;bla&lt;/i&gt; &lt;sub&gt;OXA-66&lt;/sub&gt; &lt;i&gt;, bla&lt;/i&gt; &lt;sub&gt;TEM-1D&lt;/sub&gt;, &lt;i&gt;mph&lt;/i&gt;(E) and &lt;i&gt;tet&lt;/i&gt;(B), but lower rates of &lt;i&gt;bla&lt;/i&gt; &lt;sub&gt;CARB-16&lt;/sub&gt;, &lt;i&gt;bla&lt;/i&gt; &lt;sub&gt;NDM-1&lt;/sub&gt; and &lt;i&gt;bla&lt;/i&gt; &lt;sub&gt;OXA-91&lt;/sub&gt; (&lt;i&gt;P&lt;&lt;/i&gt;0.05). Notably, comparative genomic analysis suggested putative adaptive differences between the two lineages. ST2&lt;sup&gt;Pas&lt;/sup&gt; retained the T6SS and biofilm-associated genes (&lt;i&gt;bap&lt;/i&gt;), descriptive genomic features that suggest a potential capacity for active colonization. Conversely, the ST164&lt;sup&gt;Pas&lt;/sup&gt; clone lacked the T6SS gene cluster but was enriched with the surface adhesin &lt;i&gt;ata&lt;/i&gt; and immune evasion-related genes. Concordantly, ST164&lt;sup&gt;Pas&lt;/sup&gt; CRAB isolates exhibited significantly stronger biofilm-forming capacities than ST2&lt;sup&gt;Pas&lt;/sup&gt; &lt;i&gt;in vitro&lt;/i&gt;. We hypothesize that these genomic alterations and phenotypic traits may represent a fitness trade-off, potentially conferring a survival advantage under antibiotic pressure. Furthermore, &lt;i&gt;bla&lt;/i&gt; &lt;sub&gt;OXA-23&lt;/sub&gt; in ST2&lt;sup&gt;Pas&lt;/sup&gt; was predominantly carried on conjugative plasmids restricted to &lt;i&gt;Acinetobacter&lt;/i&gt; species, whereas &lt;i&gt;bla&lt;/i&gt; &lt;sub&gt;NDM-1&lt;/sub&gt; in ST164&lt;sup&gt;Pas&lt;/sup&gt; was localized on a broad-host-range non-mobile plasmid, potentially facilitating cross-genus transmission. Although our ST164&lt;sup&gt;Pas&lt;/sup&gt; isolates shared high homology with clinical strains from Zhejiang, China, the genomic localization of &lt;i&gt;bla&lt;/i&gt; &lt;sub&gt;NDM-1&lt;/sub&gt; differed between the plasmid and chromosome, respectively. These descriptive genomic findings highlight the putative adaptive trajectories of the predominant ST2&lt;sup&gt;Pas&lt;/sup&gt; and emerging ST164&lt;sup&gt;Pas&lt;/su","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"12 4","pages":""},"PeriodicalIF":4.0,"publicationDate":"2026-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147633929","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The novel pseudo-compound transposon Tn<i>7086</i> carries aminoglycoside resistance genes in <i>Enterococcus faecalis</i>.","authors":"Lorenzo Colombini, Mariana Tirziu, Stefano De Giorgi, Anna Maria Cuppone, Giuseppe Sangiorgio, Carmelo Bonomo, Dafne Bongiorno, Stefania Stefani, Susanna Ricci, Gianni Pozzi, Francesco Santoro, Francesco Iannelli","doi":"10.1099/mgen.0.001680","DOIUrl":"10.1099/mgen.0.001680","url":null,"abstract":"<p><p><i>Enterococcus faecalis</i> is a member of the human gut microbiota and a pathogen responsible for mild and severe infections. Here, genome analysis of <i>E. faecalis</i> strains isolated from different body sites revealed the presence of a novel family of IS<i>1216E</i>-flanked pseudo-compound transposons carrying aminoglycoside resistance genes and other resistance determinants. The representative element, named Tn<i>7086</i>, is 25,380 bp long, contains 27 ORFs and shows a mosaic structure containing (i) the macrolide-lincosamide-streptogramin resistance gene <i>erm</i>(B), (ii) the aminoglycoside-streptothricin resistance gene cluster <i>ant(6')-Ia-sat4-aph(3')-IIIa</i>, (iii) the gentamicin resistance determinant <i>acc(6')-aph(2</i>″) and (iv) a toxin-antitoxin cassette. Tn<i>7086</i> family members contain deletions and/or insertions including three DNA segments, two of which carry antimicrobial resistance genes. All elements integrate downstream of a conserved 8-bp target site within the chromosomal <i>panE</i> gene, located between <i>lysR</i> and <i>rbgA</i> and encoding a 2-dehydropantoate 2-reductase. Genome-wide analysis of 646 complete <i>E. faecalis</i> genomes showed <i>panE</i> disruption in 12.7% of isolates due to the presence of Tn<i>7086</i> family members (10.7%) or <i>IS1216E</i> (2%), while an intact <i>panE</i> gene was found in the other genomes. Element integration produced either target-site duplication or DNA deletions, with or without the target site. PCR and sequencing analysis showed that Tn<i>7086</i> and Tn<i>7086</i>-like elements excise from the chromosome and produce circular translocatable units at frequencies of 1.24±0.03 to 22.4±17.7 copies per 10⁶ chromosomes. In conclusion, we describe the novel Tn<i>7086</i> family of IS<i>1216E</i>-flanked pseudo-compound transposons in <i>E. faecalis</i>, which carry multiple antimicrobial resistance genes, integrate at a specific chromosomal site within <i>panE</i> and are capable of excision to form circular translocatable units.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"12 4","pages":""},"PeriodicalIF":4.0,"publicationDate":"2026-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13055272/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147628017","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genomic and statistical models to characterize <i>Streptococcus pneumoniae</i> transmission patterns in Malawi.","authors":"Rory Cave, James Chirombo, Uri Obolski, Sophie Belman, Akuzike Kalizang'oma, Thandie S Mwalukomo, Arox Kamng'ona, Comfort Brown, Jacquline Msefula, Farouck Bonomali, Roseline Nyirenda, Todd D Swarthout, Brenda Kwambana-Adams, Neil French, Robert S Heyderman","doi":"10.1099/mgen.0.001667","DOIUrl":"https://doi.org/10.1099/mgen.0.001667","url":null,"abstract":"<p><p>Controlling the carriage and transmission of <i>Streptococcus pneumoniae</i> in children from high-burden settings is critical for disease prevention. To investigate the rate and drivers of transmission following pneumococcal conjugate vaccine (PCV) introduction, we estimated evolutionary divergence times using whole-genome sequences of <i>S. pneumoniae</i> from 1,617 children in Blantyre, Malawi (2015-2019). The cohort included PCV13-vaccinated children aged 2-7 years and unvaccinated children aged 5-10 years who were vaccine ineligible at the time of rollout into routine use. Using generalized additive mixed models and relative risk frameworks that incorporated household geospatial distances, we found that pneumococcal lineages spread widely across Blantyre within ~4 years, with transmission most likely between neighbouring households. Logistic regression and random forest models identified higher transmission risk among preschool-aged children in densely populated, higher socioeconomic areas. Recent transmission events were primarily associated with expanding, non-vaccine serotype lineages that were non-susceptible to penicillin. These findings highlight the potential for extended valency PCVs to reduce the spread of disease-causing and antimicrobial-resistant pneumococcal lineages among preschool-aged children, particularly in high-density areas - thereby strengthening herd protection for vulnerable groups such as young infants and individuals living with HIV.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"12 4","pages":""},"PeriodicalIF":4.0,"publicationDate":"2026-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147639292","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Reducing mapping reference and lineage bias in <i>Mycobacterium tuberculosis</i>.","authors":"Arturo Torres Ortiz, Xavier Didelot, Louis Grandjean","doi":"10.1099/mgen.0.001690","DOIUrl":"10.1099/mgen.0.001690","url":null,"abstract":"<p><p>Whole-genome sequencing provides a vast amount of genetic information, but its use in clinical and epidemiological studies often depends on the accurate inference of genomic variants. Comparative genomic studies in <i>Mycobacterium tuberculosis</i> typically involve mapping short reads from a diverse population to the same reference genome. This approach can lead to the incorrect characterization of many genomic regions that are susceptible to mapping bias when the reference is too distantly related to the sample. We analysed the consequences of mapping reads from different lineages of <i>M. tuberculosis</i> to the commonly used reference H37Rv and showed that the mapping bias varied depending on both the lineage and the gene mapped. To resolve these issues, we propose a new hybrid workflow which involves three steps: first, building a <i>de novo</i> assembly from short reads; second, aligning this assembly to a reference genome; and finally, mapping the reads to this aligned assembly. We show that many of the lineage and gene biases were corrected using this approach, which leads to a better characterization of lineages and hypervariable regions in comparative analysis. Our proposed approach will enable researchers to elucidate more genetic variations in <i>M. tuberculosis</i> and other bacterial pathogens.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"12 4","pages":""},"PeriodicalIF":4.0,"publicationDate":"2026-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13068375/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147645855","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Lifestyle-associated variation in type IV secretion systems between phytopathogenic and environmental <i>Ralstonia</i>.","authors":"Tabitha C Cowell, Matthew L Cope-Arguello, Gi Yoon Shin, Adam J Bogdanove, Sara C D Carpenter, Kamrun Nahar, Apurba Saha, Tiffany M Lowe-Power","doi":"10.1099/mgen.0.001676","DOIUrl":"10.1099/mgen.0.001676","url":null,"abstract":"<p><p>Type IV secretion systems (T4SSs) are versatile machines with variable functions including DNA uptake and release, protein translocation, and DNA conjugation. However, the diversity, distribution, and functional roles of the T4SS in the <i>Ralstonia</i> genus remain poorly understood. The <i>Ralstonia solanacearum</i> species complex (RSSC) comprises three species of plant-pathogenic bacteria that cause bacterial wilt disease. The <i>Ralstonia</i> genus also includes non-RSSC species that are primarily environmental bacteria and rare opportunistic human pathogens. This study compared the diversity and phylogenetic distribution of T4SSs in the RSSC phytopathogens vs. non-RSSC environmentals. Phylogenetic analysis of VirB4 sequences and synteny analysis revealed 16 distinct T4SS clusters in <i>Ralstonia</i>, with 10 clusters found in RSSC phytopathogen genomes, 12 in non-RSSC environmental genomes, and 6 clusters in both groups. Collectively, these gene clusters were more prevalent in non-RSSC environmental genomes. The presence of type IV coupling protein and relaxase genes suggests that at least 14 of these T4SS gene clusters are putative DNA-conjugation systems. The clusters were encoded on accessory plasmids of various sizes or as integrative and conjugative elements on the chromosome or megaplasmid. The putative regions of transfer for T4SS gene clusters in the RSSC phytopathogen genomes often contained type III effectors, type VI secretion toxin/antitoxin clusters, and haemagglutinin gene clusters. In contrast, the non-RSSC environmentals were enriched in heavy metal metabolism and resistance genes. One of the 16 T4SS clusters, cluster i, exhibited evidence of specialization for the RSSC phytopathogens. These findings shed light on the eco-evolutionary differences within the genus <i>Ralstonia</i>.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"12 4","pages":""},"PeriodicalIF":4.0,"publicationDate":"2026-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13046425/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147609245","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Evolution of genomic architecture of the plant-pathogenic fungus <i>Alternaria</i> revealed by comparative analyses of 12 chromosome-level assemblies.","authors":"Jeremy R Dettman, Natalie E Kim, Kasia Dadej","doi":"10.1099/mgen.0.001686","DOIUrl":"10.1099/mgen.0.001686","url":null,"abstract":"<p><p>Gapless, chromosome-level assemblies provide unparalleled resolution for studying the architecture and evolution of genomes. We produced new telomere-to-telomere genome assemblies for five strains representing four species from the plant-pathogenic fungal genus <i>Alternaria</i>, focusing on section <i>Alternaria</i>. These new genomic resources were combined with seven previously published assemblies, allowing for detailed comparative analyses of genome architecture, chromosome structure and associated evolutionary dynamics. All strains possessed a stable complement of ten core chromosomes with highly conserved macrosynteny; only a few large-scale structural rearrangements were observed. Consensus genomic features, such as chromosome length, centromeres, subtelomeres, GC composition, gene density and repetitive content, were characterized in depth and were highly similar in most genomes. A metric for quantifying inter-genomic orthogroup retention revealed a consistent gradient of elevated homologue gain/loss toward chromosome ends. The increased rate of gene turnover is an inherent property of these dynamic regions and is not driven by the enrichment of certain functional classes of embedded genes. Despite the plasticity of chromosome ends, multiple complementary analyses found no evidence for physical or functional bipartite (or 'two-speed') compartmentalization as a whole. For example, candidate effector genes did not display biased localization to gene-sparse regions. Collectively, our results demonstrate that <i>Alternaria</i> section <i>Alternaria</i> has a conserved, stable genomic architecture yet retains evolutionarily dynamic regions localized to chromosomal termini. These gapless genomes provide a framework to support further studies on chromosomal evolution and pathogenicity-related diversification in this economically important fungal group.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"12 4","pages":""},"PeriodicalIF":4.0,"publicationDate":"2026-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13068351/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147645802","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Factors contributing to the frequent interspecies transmission of G4P[6] <i>Rotavirus alphagastroenteritidis</i> strains from pigs to humans in Vietnam: molecular epidemiological insights.","authors":"Miho Kaneko, Thi Nguyen Hoa-Tran, Toyoko Nakagomi, Hung Manh Vu, Taichiro Takemura, Futoshi Hasebe, Anh Thi Hai Dao, Pham Hong Quynh Anh, Anh The Nguyen, Varja Grabovac, Anh Duc Dang, Noriyuki Nishida, Osamu Nakagomi","doi":"10.1099/mgen.0.001685","DOIUrl":"https://doi.org/10.1099/mgen.0.001685","url":null,"abstract":"<p><p>In parts of Asia, including Vietnam, <i>Rotavirus alphagastroenteritidis</i> (formerly known as <i>Rotavirus A</i>; RVA) strains of porcine origin, particularly G4P[6] strains, have been detected in humans at relatively high frequencies. This study investigated the origins of G4P[6] strains identified in Vietnamese children and examined possible factors underlying their frequent detection, based on molecular epidemiological analyses. Among the 1,252 RVA-positive faecal specimens collected over a 2-year period, 28 (2.2%) contained only the G4P[6] strain. Of these, 23 (1.8%) G4P[6] strains were successfully sequenced for their whole genomes, all of which were confirmed to be entirely of porcine RVA origin, with no evidence of genomic reassortment with human RVA strains. Two distinct clusters of G4P[6] strains (comprising two and three strains, respectively) shared identical genome sequences, suggesting the possibility of limited human-to-human transmission. In contrast, the remaining 18 G4P[6] strains were genetically distinct from one another, indicating multiple, independent interspecies transmission events from pigs to humans. Phylogenetic analysis revealed that the P[6] genome segments of porcine RVA or porcine-like human RVA strains, including those identified in this study, were genetically distinct from those of typical human RVA strains and showed notable geographic variation in detection frequency. Comparative analysis of the variable regions of P[6] amino acid sequences identified characteristic residues that distinguish porcine RVA-like P[6] from human RVA-like P[6], some of which correspond to known glycan-binding sites. This study revealed a high frequency of pig-to-human spillover transmission of porcine-derived G4P[6] rotavirus strains in Vietnamese children. The findings suggest that these cases were not the result of newly emerging strains capable of sustained human-to-human transmission. Furthermore, distinct amino acid characteristics in the porcine RVA P[6] protein were identified that may play a role in facilitating the cross-species transmission of rotavirus from pigs to humans.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"12 4","pages":""},"PeriodicalIF":4.0,"publicationDate":"2026-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13108923/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147775903","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Temporal genomic dynamics of sequence type 39 <i>Klebsiella pneumoniae</i> in a neonatal unit in Blantyre, Malawi.","authors":"Allan M Zuza, Oliver Pearse, Daryl B Domman, Zoe A Dyson, Kondwani Kawaza, Patrick Musicha, Nicholas A Feasey, Eva Heinz","doi":"10.1099/mgen.0.001673","DOIUrl":"10.1099/mgen.0.001673","url":null,"abstract":"<p><p><b>Background</b> <i>. Klebsiella pneumoniae</i> (<i>Kpn</i>) is an important cause of healthcare-associated infections (HAIs). In low- and middle-income countries, HAI due to <i>Kpn</i> disproportionately affects neonates. In this study, we investigated the genomic changes that occurred during long-term circulation of a <i>Kpn</i> sequence type (ST) 39 clone, causing a disproportionate number of infections on the neonatal ward at a tertiary healthcare facility in Malawi in 2017.<b>Methods.</b> We analysed whole-genome sequences of <i>Kpn</i> ST39 collected from Queen Elizabeth Central Hospital over a 20-year period, including the generation of several high-quality hybrid genomes. We compared virulence markers, antibiotic resistance determinants and mobile genetic elements, focusing on variable regions between strains from the outbreak clone in 2017 and genomes from other co-occurring ST39 lineages.<b>Results.</b> We identified eight variable genomic regions that demonstrate the plasticity of <i>Kpn</i> within ST, including the role of bacteriophages in shaping the genome of ST39.<b>Conclusions.</b> The analysed <i>Kpn</i> ST39 lineages have a highly variable genome capable of incorporating large genomic regions during prolonged hospital circulation, which may offer a selective advantage in hospital environments and provide resistance to antimicrobial agents.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"12 4","pages":""},"PeriodicalIF":4.0,"publicationDate":"2026-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13043184/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147593243","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Are the genomes of motile <i>Aeromonas</i> species from the aquatic environment shaped by local geography and host species?","authors":"Christopher J Payne, Vo Hong Phuong, Heri Kurniawan, Francis S Legario, Le Hong Phuoc, Margaret Crumlish","doi":"10.1099/mgen.0.001618","DOIUrl":"https://doi.org/10.1099/mgen.0.001618","url":null,"abstract":"<p><p><i>Aeromonas dhakensis</i> and <i>Aeromonas hydrophila</i> cause significant economic losses within the global aquaculture sector, affecting numerous farmed fish species and posing a zoonotic threat to human health. In this study, we sequenced, assembled and analysed the genomes of seven and five <i>A. dhakensis</i> and <i>A. hydrophila</i> isolates, respectively, recovered from disease outbreaks in various fish hosts across Southeast Asia using a hybrid sequencing approach with Illumina and Oxford Nanopore technologies. To assess the relatedness of our isolates with those from the global aquatic environment, with particular reference to aquaculture-relevant systems, and compare their resistome and virulome profiles, we also conducted comparative genomic analysis with an additional 57 publicly available genomes of <i>A. dhakensis</i> and <i>A. hydrophila</i>, recovered from different aquatic sources. Findings from this study revealed large genomic variability across global <i>Aeromonas</i> populations, with a clear distinction in the pan-genome between <i>Aeromonas</i> species. <i>In silico</i> multi-locus sequence type analysis revealed a wide distribution of sequence types (STs) 656 and 251 in Asia in <i>A. dhakensis</i> and <i>A. hydrophila</i>, respectively, although the novel STs detected in Indonesia and the Philippines suggest local adaptation of populations circulating in these countries. Analysis of mobile genetic elements revealed plasmids, insertion sequences and genomic islands to be country- or host-specific. Exploration of resistome data revealed a high prevalence of multidrug resistance across Southeast Asia, with genomes frequently carrying resistance genes against antibiotic classes commonly used across the aquaculture sector, including potentiated sulphonamides and tetracyclines. However, several antimicrobial resistance genes were found to be country- or host-specific, suggesting local adaptation to anthropogenic or environmental conditions within specific regions. A diverse repertoire of virulence genes was also detected in this study, with <i>A. hydrophila</i> demonstrating greater diversity in virulence genes compared with <i>A. dhakensis</i>. Country-specific virulence pathways were also noted for several toxins and secretion systems, including <i>aerA/act</i>, <i>rtx</i> and type III and IV secretion systems. This work provides new insights into the genomic features and relatedness of <i>Aeromonas</i> spp. circulating within aquaculture systems in Southeast Asia. Further, findings from comparative genomic analysis highlight the influence of geographical or host pressures on the molecular drivers of antimicrobial resistance and pathogenicity, directly impacting animal health and aquaculture production.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"12 4","pages":""},"PeriodicalIF":4.0,"publicationDate":"2026-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13108608/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147775864","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genomic characterization of mobile genetic elements associated with antimicrobial resistance in <i>Streptococcus pneumoniae</i> from Australia.","authors":"Gabriel Temitope Sunmonu, Rosa C Coldbeck-Shackley, Rikki M A Graham, Lex Ex Leong, Abiodun David Ogunniyi, Anna E Sheppard","doi":"10.1099/mgen.0.001662","DOIUrl":"10.1099/mgen.0.001662","url":null,"abstract":"<p><p>The emergence and spread of antimicrobial resistance (AMR) in <i>Streptococcus pneumoniae</i> threatens current antibiotic treatment strategies. While <i>β</i>-lactams remain the first-line therapy for pneumococcal infections in Australia, resistance to macrolides, tetracyclines and other antibiotics, driven by resistance genes carried on mobile genetic elements (MGEs), is increasingly reported. In this study, we conducted a comprehensive analysis of 573 <i>S</i>. <i>pneumoniae</i> genomes from South Australia, Queensland and Victoria to investigate the distribution of MGEs and their association with acquired AMR genes. Resistance genes and MGEs were identified using AMRFinderPlus and MobileElementFinder. Serotypes, sequence types and global pneumococcal sequence clusters (GPSCs) were assigned using SeroBA, MLST and the GPS pipeline. Out of the 573 genomes, 547 passed quality checks. Tn<i>916</i>-like (Tn<i>916</i>, Tn<i>6002</i>, Tn<i>2010</i>, Tn<i>6003</i> and ICE<i>Spn</i>Tw19F14) and Tn<i>5253</i>-like (Tn<i>5253</i>, ICE<i>Spn</i>529IQ) integrative conjugative elements carried various combinations of <i>erm</i>B, <i>mef</i>A, <i>msr</i>D, <i>tet</i>M, <i>cat</i>A and <i>cat</i>A16 genes, supporting horizontal gene transfer as a key mechanism of resistance spread. Macrolide and tetracycline resistance genes co-occurred in 192/239 (80.7%) MGE-positive genomes. The most common MGE-positive serotypes were 33F/ST717/GPSC3 (15.6%, <i>n</i>=30), serotype 4/ST2759/GPSC162 (15.1%, <i>n</i>=29), serotype 15A/ST63/GPSC9 (7.3%, <i>n</i>=14), serotype 23A/ST338/GPSC5 (5.7%, <i>n</i>=11), serotype 15A/ST8625/GPSC9 (3.6%, <i>n</i>=7) and serotype 19A/ST3111/GPSC932 (3.6%, <i>n</i>=7). Our results reflect global trends of MGE-associated resistance in expanding non-vaccine serotypes (such as 15A and 23A) and multidrug-resistant clones. These findings underscore the evolutionary role of MGEs associated with AMR in shaping the pneumococcal resistome and highlight the continuous need for genomic surveillance to inform antibiotic stewardship and vaccine strategies in Australia.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"12 4","pages":""},"PeriodicalIF":4.0,"publicationDate":"2026-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13085319/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147633967","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}