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At least 19 recordsLinked to original sources
PubMed2026

Whole genome analysis of a multidrug-resistant blaNDM-5-carrying Escherichia coli Sequence Type (ST) 167 strain isolated from seafood in Mumbai, India.

BACKGROUND: E. coli ST167 is an emerging extraintestinal pathogenic Escherichia coli (ExPEC) clone. This study reports the whole genome sequence analysis of a multidrug-resistant, blaNDM-5 harboring E. coli ST167 (EC121) isolated from seafood. The antibiotic susceptibility pattern was determined using the standard disc diffusion method. Genomic DNA was extracted, purified, and sequenced using the Illumina platform. The whole genome sequence was analyzed to determine the genome characteristics, including sequence type, serotype, phylogroup, antibiotic resistance genes, virulence attributes, and phylogenetic analysis. RESULTS: Phenotypically, this isolate was resistant to 26 of the 33 antibiotics tested, which correlated well with in-silico prediction. Multilocus sequence typing (MLST) analysis revealed that this strain belonged to sequence type 167, serotype O101:H9, and phylogroup A and harbored different virulence genes, suggesting it was a potential human pathogen. Many acquired antibiotic resistance genes were detected, including blaNDM-5, blaCMY-42, blaOXA-1, blaTEM-116, catA1, sul2, and tet(B). Point mutations in gyrA and parC responsible for quinolone resistance were also detected. CONCLUSION: The combinations of virulence and antibiotic resistance genes in this strain highlight the significant risk associated with emerging E. coli clonal types contaminating the seafood supply chain. Fecal contamination of seafood can contribute to the community dissemination of multidrug-resistant E. coli, necessitating effective monitoring measures.

Seafood↗
PubMed2026

Core genome and whole genome multi-locus sequence typing of Cronobacter isolates.

UNLABELLED: Cronobacter species, especially C. sakazakii and C. malonaticus, are opportunistic pathogens that are linked to severe infections in infants with high case fatality rates. In this study, we investigated whole genome sequencing (WGS) analysis approaches, specifically 7-gene multi-locus sequence typing (7-gene MLST), core genome MLST (cgMLST), and whole genome MLST (wgMLST) to subtype Cronobacter isolates. We analyzed a comprehensive set of 743 Cronobacter isolates derived from clinical, food, and environmental sources. We also evaluated high-quality single nucleotide polymorphism (hqSNP), cgMLST, and wgMLST to cluster epidemiologically related and differentiate sporadic C. sakazakii isolates. Our results indicate that both cgMLST and wgMLST accurately identify closely related isolates and are consistent with epidemiological findings. The allele-based analyses were also comparable with hqSNP analyses, the current gold standard. Our workflow also outputs 7-gene MLST allele calls, Cronobacter sequence types, and clonal complexes, which may be useful for historic comparisons during outbreak investigations. Following the recent classification of Cronobacter infections as nationally notifiable in the United States, our findings demonstrate the efficacy of WGS-based approaches within the PulseNet framework to improve outbreak detection and response strategies for Cronobacter. IMPORTANCE: Cronobacter species, specifically C. sakazakii and C. malonaticus, are opportunistic pathogens linked to severe infections in infants with high case fatality rates. This study highlights the critical importance of advanced molecular techniques in public health surveillance, using whole genome sequencing (WGS) methodologies such as multi-locus sequence typing (7-gene MLST), core genome MLST (cgMLST), and whole genome MLST (wgMLST). The validation of these WGS-based approaches within the PulseNet framework is timely, especially following the recent classification of Cronobacter infections as nationally notifiable in the United States. WGS methods not only enhance outbreak detection but can also inform public health guidance aimed at preventing infections and reducing mortality in vulnerable populations, especially infants. Our research supports implementation of cgMLST as a standardized approach for routine PulseNet surveillance of Cronobacter, with wgMLST and hqSNP analyses providing additional discriminatory power for outbreak investigations and high resolution phylogenetic analysis.

Multilocus Sequence Typing↗
PubMed2005

Population structure and properties of Candida albicans, as determined by multilocus sequence typing.

We submitted a panel of 416 isolates of Candida albicans from separate sources to multilocus sequence typing (MLST). The data generated determined a population structure in which four major clades of closely related isolates were delineated, together with eight minor clades comprising five or more isolates. By Fisher's exact test, a statistically significant association was found between particular clades and the anatomical source, geographical source, ABC genotype, decade of isolation, and homozygosity versus heterozygosity at the mating type-like locus (MTL) of the isolates in the clade. However, these associations may have been influenced by confounding variables, since in a univariate analysis of variance, only the clade associations with ABC type and anatomical source emerged as statistically significant, providing the first indication of possible differences between C. albicans strain type clades and their propensity to infect or colonize different anatomical locations. There were no significant differences between clades with respect to distributions of isolates resistant to fluconazole, itraconazole, or flucytosine. However, the majority of flucytosine-resistant isolates belonged to clade 1, and these isolates, but not flucytosine-resistant isolates in other clades, bore a unique mutation in the FUR1 gene that probably accounts for their resistance. A significantly higher proportion of isolates resistant to fluconazole, itraconazole, and flucytosine were homozygous at the MTL, suggesting that antifungal pressure may trigger a common mechanism that leads both to resistance and to MTL homozygosity. The utility of MLST for determining clade assignments of clinical isolates will form the basis for strain selection for future research into C. albicans virulence.

Analysis of Variance↗
PubMed1992

Identification of sequence types among the M-nontypeable group A streptococci.

Streptococcal diseases, namely, acute glomerulonephritis and acute rheumatic fever, are common features in the aboriginal population of the Northern Territory of Australia. We examined the group A streptococcal M types identified during various surveys conducted since 1987. Streptococci were predominantly isolated from skin infections. A high proportion of the isolates could not be serotyped by conventional means and were designated M nontypeable (MNT). M-specific DNA sequences from the MNT isolates were examined, and sequence types were proposed for the classification of MNTs. This allowed a more precise estimate of the M types present in a population study.

Amino Acid Sequence↗
PubMed2025

Global emergence and transmission dynamics of carbapenemase-producing Citrobacter freundii sequence type 22 high-risk international clone: a retrospective, genomic, epidemiological study.

BACKGROUND: Carbapenemase-producing Citrobacter (CPC) species have recently been recognised as emerging pathogens associated with nosocomial infections in humans. The increased rate of Citrobacter freundii infections is a public health concern and there is a paucity of genomic data regarding its global transmission dynamics. We aimed to characterise the genetic features of CPC species, and their associated carbapenemase-encoding plasmids, obtained from hospitalised patients in China and from publicly available global data, with a particular focus on high-risk clones. METHODS: This was a retrospective, genomic epidemiological study of CPC species obtained from a tertiary hospital in Zhejiang Province, China, from March 5, 2013, to March 5, 2023. We used antimicrobial susceptibility testing, short-read and long-read whole-genome sequencing, phylogenomic analysis, and plasmid structure analysis. A global dataset of complete plasmid sequences encoding blaKPC, blaNDM, and blaIMP was constructed from the National Center for Biotechnology Information (NCBI) RefSeq database to provide insights into their diversity and distribution. All carbapenemase-producing Citrobacter freundii genomes from the NCBI GenBank database were incorporated in the comparative genomic analyses. Bayesian phylogeographical analysis and growth rate assays were carried out to characterise the high-risk C freundii sequence type (ST) 22 clone. FINDINGS: 1724 Citrobacter species isolates were collected from diverse clinical specimens, with 48 identified as CPC species. Citrobacter koseri (22 [46%] of 48) and C freundii (20 [42%]) were the predominant CPC species. Comparative analysis found C freundii carried significantly higher median numbers of plasmid replicons (5&#xb7;0 [IQR 3&#xb7;3-6&#xb7;0] vs 2&#xb7;0 [2&#xb7;0-3&#xb7;0]; p<0&#xb7;0001) and acquired antimicrobial resistance genes (12&#xb7;0 [7&#xb7;3-15&#xb7;8] vs 3&#xb7;0 [3&#xb7;0-5&#xb7;3]; p<0&#xb7;0001) than did C koseri. Molecular characterisation identified Inc-type plasmids, In823::Kl.pn.I3/In1589-like/In837-like integrons, Tn6296/Tn125/Tn5060 transposons, and insertion sequences (eg, IS26, IS3000, IS5, ISAba125, ISCR1), collectively facilitating the dissemination of carbapenemase genes. Global analysis of 3126 carbapenemase-encoding plasmids found epidemic plasmids with broad host ranges and global diversity. Phylogenetic investigation of predominant carbapenemase-encoding plasmids showed their persistence across geographical regions, temporal spans, and Enterobacterales species, exhibiting high genetic similarity to our clinical plasmids. A phylogenetic tree of 726 global carbapenemase-producing C freundii genomes showed that ST22 (227 [31&#xb7;3%]) represents the predominant multidrug-resistant clone across community, health-care, and environmental niches. Transmission across continents contributes to the global predominance of the ST22 clone, which carries a high load of resistance genes (median 15&#xb7;0 [IQR 11&#xb7;0-17&#xb7;0] vs 12&#xb7;0 [3&#xb7;0-16&#xb7;0]; p<0&#xb7;0001) and enhanced plasmid maintenance capacity (median replicons 5&#xb7;0 [IQR 4&#xb7;0-7&#xb7;0] vs 4&#xb7;0 [3&#xb7;0-6&#xb7;0]; p<0&#xb7;0001) relative to non-ST22 clones. INTERPRETATION: Our study provides evidence to suggest that Citrobacter species are emerging carriers of carbapenem-resistance genes. These findings provide insight into the population structure of CPC species and highlight C freundii ST22 as a prominent high-risk international clone. FUNDING: National Natural Science Foundation of China, National Health Commission Scientific Research Fund-Zhejiang Provincial Major Health Science and Technology Plan Project, Zhejiang Province Natural Science Foundation Project, Outstanding Youth Foundation of Jiangsu Province of China, the Priority Academic Program Development of Jiangsu Higher Education Institutions, and Postgraduate Research and Practice Innovation Program of Jiangsu Province.

Citrobacter freundii↗
PubMed1990

Induced reversion of a spontaneous point mutation within the Chinese hamster HPRT gene to the wild-type sequence.

The Chinese hamster hypoxanthine-guanine phosphoribosyltransferase (HPRT)-deficient cell line TG15 produces apparently normal HPRT mRNA by northern analysis and was therefore presumed to contain a point mutation within the coding region. Sequencing cDNA from the TG15 cell line revealed an A to G transition which results in the substitution of the amino acid glycine for aspartic acid at position 135. TG15 cells revert to wild-type HPRT activity upon exposure to monofunctional alkylating agents. A rapid test to assay the site of the TG15 point mutation has been developed, utilizing the polymerase chain reaction and allele-specific oligonucleotide screening. In all revertants studied, the original point mutation has been corrected to the wild-type sequence. The TG15 point mutation lies within a proposed catalytic domain of the HPRT protein in common with other phosphoribosyltransferases.

Animals↗
PubMed2024

Virulence-associated variants in Cryptococcus neoformans sequence type 93 are less likely to be associated with population structure compared to independent rare mutations.

Cryptococcus neoformans is a pathogenic yeast that is the causative agent of cryptococcal meningitis. While it is well known that the genotype of C. neoformans impacts patient outcomes, the reason for this association has not been well elucidated. In this study, we examined the relationship between two subpopulations in the sequence type 93 clade of C. neoformans: ST93A and ST93B. We found extensive linkage disequilibrium (LD) among the single nucleotide polymorphisms (SNPs) that differentiate ST93A from ST93B. We also found differences in the extent of linkage among SNPs within each subpopulation; LD was more extensive within ST93B than ST93A. SNPs associated with virulence were in long-range linkage disequilibrium with less frequency than recurrent SNPs not associated with virulence. We investigated the karyotype of ST93A and ST93B using contour-clamped gel electrophoresis and long-read sequencing and found that the extensive long-range linkage was not due to chromosomal rearrangements. Overall, we found that the two subpopulations in ST93 are driven by SNPs in LD. We additionally found that recurrent SNPs associated with virulence were less frequently evolutionarily linked and were two times more likely to be independent, congruent mutations rather than tied to phylogeny.IMPORTANCECryptococcus neoformans is an important pathogen that is widely distributed and ubiquitous in the environment. The majority of the human population has a latent, controlled infection suggesting that C. neoformans is uniquely adapted to cause infection. In spite of this, the reason C. neoformans is a pathogen remains unknown; interestingly, most environmental isolates are avirulent but are genetically very similar to disease-causing virulent isolates. Recent evidence from genome-wide association studies shows that small mutations in key virulence-associated genes are associated with the virulence of specific isolates. The data presented here provide an evolutionary framework for those small mutations. The mutations that impact disease are not being collected over long-term evolution. The mutations may instead occur independently during infection. Identifying these genes that are more likely to be mutated during infection will be fundamental for understanding C. neoformans virulence.

Cryptococcus neoformans↗
PubMed2026

Whole Genome Characterization of Klebsiella Strains in European Hedgehogs and Human Nosocomial Settings Identified Shared Sequence Types, Antimicrobial Resistance Genes and Plasmids.

INTRODUCTION: Klebsiella pneumoniae is a pathogen associated with healthcare-acquired infections and antimicrobial resistance (AMR) to beta-lactams and carbapenems. Although wild animals are not typically exposed to antibiotics, they can harbour resistant strains. The European hedgehog (Erinaceus europaeus) is increasingly found in urban areas, where it interacts with humans and livestock. Studies have identified concerning levels of AMR in hedgehogs, including Extended-Spectrum &#x3b2;-Lactam (ESBL) and carbapenems-resistant Klebsiella pneumoniae strains. METHODS: This study focuses on Klebsiella spp. isolated in hedgehogs from urban areas, using whole-genome sequencing (WGS). We compared these isolates with openly available strains isolated from humans in the same region with the objective to have a thorough understanding of ST, AMR gene, and plasmid overlap between human and environmental compartments. RESULTS: High AMR gene levels, including the carbapenemase blaOXA-48, were found in the hedgehog population. Notably, human nosocomial clones, including ST307 and ST392, globally distributed sequence types also found in wildlife, were identified in both hedgehogs and humans. The presence of conjugative plasmids, including IncFIB(K) and IncL1 types, was identified in both hedgehogs and humans, highlighting plasmid dissemination as a significant factor in AMR spread. CONCLUSIONS: Although no direct transmission from wildlife to hospital settings has been conclusively demonstrated, our findings suggest that hedgehogs may play a role in bridging environmental and healthcare environments. The study underscores the need for further investigation into multidrug-resistant Klebsiella spp. and other resistant bacteria in wildlife to better understand their potential role in the dissemination of resistance genes across ecosystems.

Animals↗
PubMed1985

Structure of a murine alpha interferon pseudogene with a repetitive R-type sequence in the 3' flanking region.

A murine alpha interferon pseudogene was identified in a mouse genomic library. The nucleotide sequence revealed several in-phase termination codons within the gene and repetitive oligonucleotides in the flanking regions. The nucleotide sequences and the amino acids of the peptide signal sequences were compared with known human alpha interferon genes and the pseudogene.

Amino Acid Sequence↗
PubMed1989

Chloroplast ribosomal protein gene rps12 of Chlamydomonas reinhardtii. Wild-type sequence, mutation to streptomycin resistance and dependence, and function in Escherichia coli.

The chloroplast rps12 gene encoding ribosomal protein S12 from wild-type as well as from streptomycin-resistant and -dependent mutants of Chlamydomonas reinhardtii was cloned and sequenced. At least six mRNA transcripts ranging in size from 800 to 4800 nucleotides were found to contain the rps12 coding sequence. As in Escherichia coli and Euglena, the C. reinhardtii rps12 gene is continuous, in contrast to its trans-spliced structure in higher plants. However, rps12 of C. reinhardtii is no longer immediately adjacent to the rps7 gene encoding ribosomal protein S7 as it is in other organisms. The deduced amino acid sequence of C. reinhardtii S12 protein shows strong homologies (48-79% identity) to S12 protein sequences of other organisms, but it has extra amino acid residues at its C terminus. Single base pair changes at different sites result in streptomycin-resistant or -dependent mutants with amino acid changes identical to comparable mutations in the E. coli S12 protein. The chloroplast rps12 gene is also expressed under the control of its own promoter in E. coli cells, and the C. reinhardtii S12 protein produced assembles into the E. coli ribosomes where it appears to function efficiently.

Amino Acid Sequence↗
PubMed1976

Serum glycoprotein-type sequence of monosaccharides in membrane glycoproteins of Semliki Forest virus.

Semliki Forest virus was grown in BHK-21 cells and labelled in vivo with radioactive monosaccharides. The virus was disrupted with sodium dodecyl sulphate and the polypeptides were hydrolyzed with pronase. A mixture of type A glycopeptides (for nomenclature, see Johnson and Clamp (1971) Biochem. J. 123, 739-745) of the membrane glycoproteins E1 and E3 was isolated by gel filtration and subjected to sequential degradation with exo-glycosidases. The reduction in the apparent molecular weight and the cleavage of radioactive monosaccharides were monitored with gel filtration. The results suggest that the type A oligosaccharides have similar average structures and contain at the non-reducing terminus 3.4 mol of alpha-D-sialic acid and 0.7 mol of alpha-L-focose, folloled by 3.1 mol of beta-D-galactose, 4.2 mol of N-acetyl-beta-D-glucosamine, 0.7-1.5 mol of alpha-D-mannose, 0.5 mol of beta-D-mannose and 0.6-2.2 mol of N-acetyl-beta-D-glucosamine attached to 1.0 mol of N-acetylglucosamine resistant to N-acetyl-beta-D-glucosaminidase. This innermost monosaccharide unit, therefore, appears to be attached to the peptide. The peptides attached to this N-acetyl-glucosamine had an apparent molecular weight of 720+/-100. We propose the following average structure, compatible with most of our data, for the type A glycopeptides of Semliki Forest virus:.

Animals↗
PubMed1989

Identification of an enhancer-type sequence that is responsive to Z and R trans-activators of Epstein-Barr virus.

We studied the regulatory region of the open reading frame BHRF1 of Epstein-Barr virus (EBV) DNA that was responsive to two trans-activators (Z and R) encoded by the BZLF1 and BRLF1, respectively. The 200-bp sequence, nucleotide numbers 53,617 to 53,817 on the EBV map, was sufficient for conferring responsiveness to Z and R. This 200-bp sequence also enhanced expression of the chloramphenicol acetyltransferase (CAT) gene from the simian virus 40 promoter in response to both Z and R, even when inserted downstream of the cat gene. The results indicate that the Z and R response sequence upstream of the BHRF1 has the properties of an enhancer.

Base Sequence↗
PubMed2025

Universal versus targeted chlorhexidine and mupirocin decolonisation and clinical and molecular epidemiology of Staphylococcus epidermidis bloodstream infections in patients in intensive care in Scotland, UK: a controlled time-series and longitudinal genotypic study.

BACKGROUND: There are concerns that biocide skin and mucous membrane decolonisation, which is widely used to prevent health-care-associated infections in intensive care units (ICUs), might select for multidrug-resistant pathogens. We aimed to evaluate the effects of de-escalating from universal to targeted skin and nasal decolonisation on Staphylococcus epidermidis bloodstream infections (SE-BSI). METHODS: We did a retrospective, before-after-control-impact time-series analysis and longitudinal genotypic study in two ICUs with divergent decolonisation practice in tertiary care hospitals of adjacent health boards in Scotland, UK. Participants were aged at least 16 years and admitted between July 1, 2009, and Feb 28, 2022. There were no exclusion criteria for the study. In ICU one (intervention site) universal decolonisation in all admissions was de-escalated to targeted decolonisation of meticillin-resistant Staphylococcus aureus (MRSA) carriers on Feb 1, 2019, while in ICU two (control site) targeted decolonisation was applied throughout. We collected bloodstream infection data from all causes, including clinically significant SE-BSI. Antimicrobial susceptibility testing was used to define meticillin-resistant S epidermidis (MRSE) and chlorhexidine susceptibility. We used multilocus sequence typing to identify sequence types from archived SE-BSI isolates. Whole-genome sequencing was applied to a sample from ICU one. The primary outcomes were incidence densities of all bloodstream infections, SE-BSI, and meticillin-resistant S epidermidis bloodstream infections (MRSE-BSI), and the percentage probability that SE-BSI were MRSE-BSI. The effects of de-escalation on primary outcomes were estimated by differences between the intervention and control sites, before and after de-escalation, using a before-after-control-impact time-series design. Secondary outcomes included the proportion of multidrug resistant sequence types, carriage of mobile genetic elements and genes for multidrug resistance and biofilm production. FINDINGS: Between July 1, 2009, and Feb 28, 2022, S epidermidis was identified in 334 (45%) of 735 bloodstream infections in ICU one, of which 197 occurred before the de-escalation intervention in Feb 1, 2019, and S epidermidis was identified in 167 (60%) of 278 bloodstream infections in ICU two. There was no increase in all bloodstream infection incidence coinciding with de-escalation in ICU one, whereas MRSE-BSI incidence declined significantly from 10&#xb7;4 cases per 1000 occupied bed days (OBDs; 95% credible interval [CrI] 7&#xb7;2-15&#xb7;4) to 4&#xb7;3 cases per 1000 OBDs (2&#xb7;5-6&#xb7;7), as did the percentage probability of MRSE (from 89&#xb7;2%, 95% CrI 77&#xb7;8-96&#xb7;5 to 56&#xb7;7%, 34&#xb7;3-77&#xb7;5%). No significant changes in the primary outcomes were seen in ICU two. MRSE-BSI incidence density was positively associated with chlorhexidine use, but not mupirocin use. De-escalation was associated with a reduced proportion of SE-BSI due to multidrug-resistant sequence types and reduced carriage of mobile genetic elements and genes for multidrug resistance and biofilm production, as observed by multi-locus sequence typing and whole genome sequencing. INTERPRETATION: In ICU settings with low MRSA incidence, the benefits of universal decolonisation should be balanced against the risks of selecting MRSE sequence types adapted for invasive and device-associated infection. FUNDING: National Health Service Grampian Charity.

Humans↗
PubMed2025

New Delhi metallo-&#x3b2;-lactamase-producing Acinetobacter baumannii in the USA from October, 2013, to March, 2022: a retrospective molecular epidemiological analysis.

BACKGROUND: Most US carbapenem-resistant Acinetobacter baumannii (CRAB) isolates harbour carbapenem-hydrolysing class D &#x3b2;-lactamases. Other carbapenemases, such as New Delhi metallo-&#x3b2;-lactamase (NDM), are uncommon but emerging. We describe the epidemiology of NDM-producing CRAB reported to the US Centers for Disease Control and Prevention (CDC). METHODS: We defined cases as A baumannii with blaNDM confirmed by molecular testing and isolated from any specimen source from a patient in the USA between Oct 1, 2013, and March 31, 2022, and passively reported to the CDC from regional, state, local public health, and CDC laboratories. Epidemiologically linked cases had epidemiological linkage (eg, overlapping health-care facility stay) with one or more other cases. We assessed case relatedness through analysis of whole-genome sequence data using traditional multilocus sequence typing (MLST; Oxford scheme [sequence typeOX]) and core genome MLST. To understand the potential origins of NDM-CRAB in the USA, we compared sequences of cases to US CRAB without NDM and to NDM-CRAB from non-US locations. FINDINGS: We identified 327 NDM-CRAB cases from 264 patients in 21 US states. Among patients with available epidemiological information, 192 (90%) of 214 had epidemiological linkage to at least one additional case and 13 (7%) of 193 were hospitalised outside the USA 12 months or less before index specimen collection. Five regionally distinct sequence type clusters were identified among the 264 case patients; three (sequence type OX218, sequence type OX281, and sequence type OX1697) were closely related to international NDM-CRAB isolates. INTERPRETATION: We identified regionally distinct NDM-CRAB strains, suggesting localised transmission in the USA. Some NDM-CRAB strains in the USA are closely related to strains identified outside the USA, suggesting that spread followed importation. FUNDING: None.

Acinetobacter baumannii↗