Microbial Genomics最新文献

Investigation of clonal development of dominant persistent clones of avian pathogenic Escherichia coli (APEC) is important to understand their evolution and to gain knowledge to improve their control in poultry production. Whole-genomic sequencing, including hybrid assembled genomes of short and long reads, was used to analyse clonal persistence and evolution of APEC. Two vertically transferred E. coli clones, represented by ten isolates from sequence type (ST) 95-PFGE type 65 and eight isolates from ST131-PFGE type 47, were selected to identify genomic variations. The isolates had been sampled in broiler production during a period of 9 months in a previous study. The main differences among strains within each clone were related to plasmids, transposases, incomplete phage elements and amino acid substitutions which by far exceeded the genetic variation related to core-genome SNPs (cgSNPs). Fourier-transform infrared spectroscopy was, for the most part, only able to trace clones within the same ST. The genome-wide mutation rate was equivalent to 1.48 mutations per genome per year for ST95-PFGE65 and 2.86 for ST131-PFGE47, respectively. The most recent common ancestors were estimated back to 2009 for ST95-PFGE65 and to 2011 for ST131-PFGE47, with further divergence occurring in years until sampling in 2014-2015. The methodology introduced is able to trace the temporal origin of APEC clones. The conventional threshold of ten or fewer cgSNPs to include strains in the same clone did not consider any gain or loss of plasmids for the strains compared. On average, one plasmid transfer event was predicted every second year. For strains expected to be vertically transferred during the long production periods of great-grandparents over grandparents and parents to broilers, one to two plasmid transfers are therefore predicted, and several cgSNPs may be introduced, whereas up to one cgSNP is expected to be manifested during a broiler production cycle and rarely involving plasmid transfer.

Routine use of pneumococcal conjugate vaccines (PCV) in South Africa caused a decline in vaccine-associated invasive pneumococcal disease (IPD), followed by the emergence of non-PCV serotypes, driven mainly by pre-existing lineages. We determined the molecular epidemiology of isolates causing IPD among adults in South Africa from 2020 to 2025 before and following the implementation of PCV in 2009. We performed whole-genome sequencing on randomly selected isolates causing IPD among adults aged ≥18 years (N=1 581) during the four vaccine periods [pre-PCV (2005-2008), PCV7 (2009-2010), early-PCV13 (2011-2014) and late-PCV13 (2015-2020)]. We assigned in silico serotype, multi-locus sequence type, clonal complex (CC) and global pneumococcal sequence cluster (GPSC) and determined antimicrobial non-susceptibility profiles in silico. Poisson regression was used to calculate incidence rate ratios of imputed individual GPSC lineages using IPD incidence rate estimated per year for the three vaccine periods (PCV7, early-PCV13 and late-PCV13), compared to the pre-PCV period. Overall, our dataset represented 3.7% (n=270), 3.4% (n=128), 4.9% (n=287) and 13.5% (n=896) of adult pneumococcal isolates received during the four periods, respectively. We identified 135 GPSCs with the majority of isolates [68.7%(1 086/1 581)] clustering into 1 of 23 dominant GPSCs defined as GPSCs that comprised ≥20 genomes in the dataset. Compared to the pre-PCV7 period, a decrease in incidence of vaccine type lineages normally associated with vaccine serotypes was observed during the late-PCV13 period. GPSC2 (serotype 1) declined from 1.4 to 0.039/100,000 population (P<0.001). Some non-PCV lineages increased. GPSC26 (serotype 12F) increased from 0.07 to 0.3 (P<0.001). Of the 23 dominant GPSCs, 11 expressed ≥2 serotypes. While the majority of GPSC5/CC172 isolates expressed serotype 23F during the pre-PCV period (61.5%, 7/12), serotype 35B was the most common serotype (57.1%, 12/21) expressed by GPSC5/CC172 isolates during the late-PCV13 period. All GPSC9/CC63 isolates sequenced from the pre-PCV period (n=3) expressed serotype 14; however, during the late-PCV13 period, nearly all (88.2%, 15/17) were serotype 15A. The emergence among non-PCV13 serotypes, of lineages usually associated with PCV13 serotypes (such as GPSC5/CC172 and GPSC9/CC63), warrants continued genomic surveillance in South Africa, more so as PCV10 (Pneumosil) replaced PCV13 in South Africa in 2024.

Methicillin-resistant Staphylococcus aureus (MRSA) surveillance in regions with mass gatherings presents unique challenges for public health systems. Saudi Arabia, hosting millions of pilgrims annually, provides a distinctive setting for studying how human mobility shapes bacterial populations, yet comprehensive genomic surveillance data from this region remain limited. Here, we present an integrated analysis of S. aureus isolates collected across seven Saudi Arabian regions, combining whole-genome sequencing with extensive antimicrobial susceptibility testing and standardized metadata following findability, accessibility, interoperability and reusability data principles. Our analysis revealed striking differences between pilgrimage and non-pilgrimage cities. Pilgrimage cities showed significantly higher genetic diversity and antimicrobial resistance rates, harbouring numerous international strains, including recognized clones from diverse geographic origins. Reported lineage dynamics are changing, expanding toward community clones. While genomic prediction of antimicrobial resistance showed high accuracy for some antibiotics, particularly beta-lactams, with varying performance for others, it highlights the necessity for phenotypic testing in clinical settings. Our findings demonstrate how mass gatherings drive bacterial population structures and emphasize the importance of integrated surveillance approaches in regions with significant global connectivity and travel.

With a limited number of traditional virulence factors, the success of the nosocomial pathogen Acinetobacter baumannii is largely attributed to its ability to persist and resist. The niches encountered during infection vary significantly from the more commonly studied laboratory setting, and consequently, the genes responsible for in vivo pathogenesis have yet to be fully elucidated. This study utilized the A. baumannii AB5075-UW transposon mutant library with unbiased genome-wide transposon sequencing to identify the genetic basis for survival and fitness during pneumonia and septicaemia infections. We identified 128 genes essential for in-host survival, including 22 required for survival in all tissues. Additionally, 302 genes with significantly altered fitness in vivo were also identified. Tissue specificity was observed, highlighting the importance of genes associated with aa biosynthesis in the lungs, cell shape and structure in the kidneys and metal acquisition during septicaemia. The majority (89%) of the genes with aberrant fitness were constituents of the core A. baumannii genome. The findings were validated using a subset of targeted mutants, including those required for infection (phoB, cysI and hom) or specifically septicaemia (corA, lepA and purN) or pneumonia (argC, hisC and leuD), confirming that these observations were a result of specific in vivo fitness defects rather than aberrant in vitro growth. Taken together, these data provide the first global profile of genes required for in vivo fitness of A. baumannii during different disease states and growth in different tissues.

Roseobacters are prevalent in marine environments and play a crucial role in global carbon and sulphur cycles. Although many roseophages that infect roseobacters have been characterized, those infecting members of the ecologically dominant pelagic Roseobacter cluster (PRC) remain largely unexplored due to the challenges of culturing these organisms. In this study, we isolated 7 phylogenetically related roseophages from 3 PRC lineages and retrieved 279 uncultured viral genomes (UViGs) related to these roseophages from marine environmental viral databases. Comparative genomic and phylogenetic analyses revealed that these roseophages and their related UViGs form a novel family-level phage group (designated the CRP-822-type group) comprising at least five subgroups. These subgroups display distinct genomic features in terms of G+C content, amino acid usage and codon usage, suggesting host-range specialization. Host prediction suggests that subgroup V with low G+C content may infect the SAR86 clade, while the high G+C subgroup IV likely infects the high G+C KI89A clade. Finally, viromic read-mapping analyses revealed that CRP-822-type phages are widely distributed across the global ocean and are adapted to diverse marine environments. All members of subgroup IV were more abundant in trade, westerlies and coastal regions with high temperatures. The other four subgroups exhibited more divergent biogeographic patterns, with some members more abundant in trade and westerlies ocean regions, whereas others dominated in polar or estuarine regions. Collectively, this study elucidates the genetic diversity and ecology of a previously unrecognized marine phage group that infects PRC roseobacters and other important marine bacteria.

Whole-genome sequencing (WGS) holds promise for accurate and comprehensive diagnosis of drug resistance in Mycobacterium tuberculosis and identification of transmission events. 'Early positive cultures' (EPC) are increasingly used when WGS is implemented to guide clinical care to reduce the turnaround time. We performed a systematic literature review to compare methods used for EPC-based WGS and performed an individual sample data meta-analysis to identify variables associated with bioinformatic quality measures. Of 423 studies identified, 15 met eligibility criteria. We analysed 1,065 FASTQ files from 11 studies using Illumina sequencing; 96.1% passed all quality control thresholds. Median genome coverage was 65× (IQR, 63-82), with a pooled mapping percentage of 91.2%. The meta-analysis showed that the number of sequencing cycles was significantly associated with improved sequencing quality, while other laboratory variables had no consistent effect. Based on these findings, we suggest replacing the term EPC with 'clinical primary culture' and propose a standardized workflow and reporting checklist for WGS on primary Mycobacteria Growth Indicator Tube (MGIT) cultures.

Neisseria meningitidis is a colonizer of the human nasopharynx which occasionally causes invasive meningococcal disease. Despite numerous reports of penicillin-resistant isolates, antimicrobial-resistant meningococcal clones have historically not persisted over long time periods or become globally distributed, presumably due to the imposed fitness cost associated with antimicrobial resistance. One exception is a penicillin-resistant clade of serogroup W clonal complex 11 (MenW:cc11) isolates identified in Western Australia in 2013, which has since caused disease globally. Here, we investigated the genomic changes associated with penicillin resistance in MenW:cc11 isolated during the 2013-2020 Western Australian meningococcal outbreak. Seventy-six MenW:cc11 disease-causing isolates underwent short-read whole genome sequencing. Reference genomes were generated for three isolates. In accordance with previous analysis, two phylogenetically distinct clusters were identified: cluster A (12 penicillin-susceptible isolates) and cluster B (63 penicillin-resistant isolates). Genomic comparison of the cluster A and cluster B isolates revealed 128 allelic differences present at the branching point between the two lineages. The differences included polymorphisms in genes associated with cell wall regulation, pilus biogenesis and the MtrR transcriptional regulator. A further 60 allelic changes were identified in the Western Australian isolates which were not identified in globally distributed cluster B isolates. In a search of the PubMLST Neisseria database, all allelic variants associated with the emergence of cluster B were found exclusively in other hypervirulent lineages. Taken together, the data suggest the global success of the penicillin-resistant N. meningitidis is due to compensatory mutations acquired through horizontal exchange from other hypervirulent lineages.

Over 60 years ago, researchers started the genetic analysis of bacterial cell division by isolating conditional, temperature-sensitive mutants of essential Escherichia coli cell division genes. These early mutants were obtained by mutagenesis with chemical agents that introduced dozens to hundreds of mutations in the bacterial genomes. In this work, we present the complete genome sequences of six of these original mutants on ftsA, ftsZ and ftsQ genes, along with two of the strains used to generate them. The genomes of mutants obtained by exposure to nitrosoguanidine had 100 to 400 mutations. Transducing target alleles into a new strain effectively reduced the number of mutations, but those near the target gene were co-transduced with it. In contrast, a mutant generated by site-directed mutagenesis maintained the genomic background intact. The genomic analysis improves our understanding of these foundational strains, offering insights into the effects of historical mutagenesis techniques. These findings underscore the importance of genomic characterization in ensuring accurate interpretations of experimental results in microbiological research.

Salmonella enterica serovar Paratyphi A is a significant but under-characterised cause of enteric fever in South Asia. In Pakistan, where the typhoid conjugate vaccine has been introduced to combat S. Typhi, S. Paratyphi A remains a prominent cause of bacteraemia, raising concerns about shifts in disease burden and antimicrobial resistance (AMR). Here, we provide a comprehensive genomic and phylogenetic analysis of 354 S. Paratyphi A isolates collected from three provinces in Pakistan between 2017 and early 2022. Whole-genome sequencing revealed the dominance of genotypes 2.3.3 and 2.4.5, indicating a largely stable population structure over time, and the presence of widespread fluoroquinolone-associated gyrA mutations. Although multidrug resistance was not detected, we identified one isolate harbouring an acrB-R717Q mutation associated with azithromycin resistance. Plasmid and replicon analysis revealed low prevalence of extrachromosomal elements, including cryptic plasmids with unknown function. Phylogenetic placement of these isolates in a global context demonstrated close relatedness to contemporary South Asian organisms. Our findings establish a genomic baseline for S. Paratyphi A in Pakistan, essential for future surveillance, AMR monitoring, and evaluating the potential impact of forthcoming paratyphoid vaccines.

Papillomaviruses are non-enveloped, double-stranded DNA viruses capable of infecting a wide range of vertebrates, from chondrichthyans to mammals. In this study, we report for the first time the identification and complete genome of a papillomavirus in the thornback skate (Raja clavata), named Raja clavata papillomavirus 1 (RclaPV1). The genomic sequence was determined using a metagenomic approach and subsequently confirmed by PCR. The RclaPV1 genome is 5,539 bp in length and displays the typical organization of papillomaviruses, encoding 4 core proteins on a single DNA strand: two early genes (E1 and E2) and two late genes (L1 and L2). Maximum likelihood phylogenetic analyses of the L1 and E1 genes indicate that RclaPV1 belongs to the Secondpapillomavirinae subfamily, clustering with fish and amphibian papillomaviruses and showing closer evolutionary relationships to amphibians than to fish.