scholarly journals Enterococcus faecium genome dynamics during long-term asymptomatic patient gut colonization

2019 ◽  
Vol 5 (7) ◽  
Author(s):  
Jumamurat R. Bayjanov ◽  
Jery Baan ◽  
Malbert R. C. Rogers ◽  
Annet Troelstra ◽  
Rob J. L. Willems ◽  
...  
Keyword(s):  
Enterococcus Faecium ◽  
Type Species ◽  
Multidrug Resistant ◽  
Gene Gain ◽  
Nucleotide Polymorphisms ◽  
Nosocomial Pathogen ◽  
Content Type ◽  
Link Type ◽  
Gut Colonization ◽  
Genome Dynamics

Enterococcus faecium is a gut commensal of humans and animals. In addition, it has recently emerged as an important nosocomial pathogen through the acquisition of genetic elements that confer resistance to antibiotics and virulence. We performed a whole-genome sequencing-based study on 96 multidrug-resistant E. faecium strains that asymptomatically colonized five patients with the aim of describing the genome dynamics of this species. The patients were hospitalized on multiple occasions and isolates were collected over periods ranging from 15 months to 6.5 years. Ninety-five of the sequenced isolates belonged to E. faecium clade A1, which was previously determined to be responsible for the vast majority of clinical infections. The clade A1 strains clustered into six clonal groups of highly similar isolates, three of which consisted entirely of isolates from a single patient. We also found evidence of concurrent colonization of patients by multiple distinct lineages and transfer of strains between patients during hospitalization. We estimated the evolutionary rate of two clonal groups that each colonized single patients at 12.6 and 25.2 single-nucleotide polymorphisms (SNPs)/genome/year. A detailed analysis of the accessory genome of one of the clonal groups revealed considerable variation due to gene gain and loss events, including the chromosomal acquisition of a 37 kbp prophage and the loss of an element containing carbohydrate metabolism-related genes. We determined the presence and location of 12 different insertion sequence (IS) elements, with ISEfa5 showing a unique pattern of location in 24 of the 25 isolates, suggesting widespread ISEfa5 excision and insertion into the genome during gut colonization. Our findings show that the E. faecium genome is highly dynamic during asymptomatic colonization of the human gut. We observed considerable genomic flexibility due to frequent horizontal gene transfer and recombination, which can contribute to the generation of genetic diversity within the species and, ultimately, can contribute to its success as a nosocomial pathogen.

Comparative study of multidrug-resistant Enterococcus faecium obtained from different hosts

2021 ◽  
Author(s):  
Aleksandra Trościańczyk ◽  
Aneta Nowakiewicz ◽  
Sebastian Gnat ◽  
Dominik Łagowski ◽  
Marcelina Osińska ◽  
...  
Keyword(s):  
Antimicrobial Resistance ◽  
Resistance Genes ◽  
Host Species ◽  
Enterococcus Faecium ◽  
Type Species ◽  
Animal Species ◽  
Multidrug Resistant ◽  
Content Type ◽  
Link Type ◽  
High Level

Introduction. The possible transfer of antimicrobial resistance genes between Enterococcus faecium isolates from humans and different animal species, including those not covered by monitoring programs (e.g. pet and wildlife), poses a serious threat to public health. Hypothesis/Gap Statement. Little is known about occurrence and mechanisms of phenomenon of multidrug resistance of E. faecium isolated from various host species in Poland. Aim. The aim of the study was to characterize multidrug-resistant E. faecium isolated from humans and animals (livestock, pets and wildlife) in terms of the occurrence of genetic markers determining resistance. Methodology. Bacterial isolates were tested for phenotypic resistance and the presence of genes encoding resistance to macrolides, tetracycline, aminoglycosides, aminocyclitols and phenicols as well as efflux pump (emeA), resolvase (tndX) and integrase (Int-Tn) genes. The quinolone resistance-determining regions of gyrA and parC were sequenced. Results. Human isolates of E. faecium were characterized by high-level resistance to: ciprofloxacin, enrofloxacin, erythromycin (100 %), as well, as aminoglycosides resistance (kanamycin – 100%, streptomycin – 78 %, gentamicin – 78%). Regardless of the animal species, high level of resistance of E. faecium to tetracycline (from 88–100 %), erythromycin (from 82–94 %) and kanamycin (from 36–100 %) was observed. All E. faecium isolates from wildlife were resistant to fluoroquinolones. However, full susceptibility to vancomycin was observed in all isolates tested. Phenotypic antimicrobial resistance of E. faecium was identified in the presence of the following resistance genes: erm(B) (70%), msr(A) (50 %), tet(L) (35 %), tet(K) (34 %), tet(M) (76 %), aac(6’)-Ie-aph(2″)-Ia (25%), ant(6)-Ia (31%), aph(3)-IIIa (68 %), (tndX) (23 %), and integrase gene (Int-Tn) (34 %). A correlation between an amino acid substitution at positions 83 and 87 of gyrA and position 80 of parC and the high-level fluoroquinolone resistance in E. faecium has been observed as well. Conclusion. The level and range of antimicrobial resistance and the panel of resistance determinants is comparable between E. faecium isolates, despite host species.

scholarly journals Enterococcus faeciumgenome dynamics during long-term asymptomatic patient gut colonization

2019 ◽  
Author(s):  
Jumamurat R. Bayjanov ◽  
Jery Baan ◽  
Malbert R.C. Rogers ◽  
Annet Troelstra ◽  
Rob J.L. Willems ◽  
...  
Keyword(s):  
Insertion Sequence ◽  
Evolutionary Rate ◽  
Multidrug Resistant ◽  
Gene Gain ◽  
Nucleotide Polymorphisms ◽  
Single Patient ◽  
Nosocomial Pathogen ◽  
Single Nucleotide ◽  
Gut Colonization

AbstractBackgroundE. faeciumis a gut commensal of humans and animals. In addition, it has recently emerged as an important nosocomial pathogen through the acquisition of genetic elements that confer resistance to antibiotics and virulence. We performed a whole-genome sequencing based study on 96 multidrug-resistantE. faeciumstrains that asymptomatically colonized five patients with the aim to describe the genome dynamics of this species.ResultsThe patients were hospitalized on multiple occasions and isolates were collected over periods ranging from 15 months to 6.5 years. Ninety-five of the sequenced isolates belonged toE. faeciumclade A1, which was previously determined to be responsible for the vast majority of clinical infections. The clade A1 strains clustered into six clonal groups of highly similar isolates, three of which entirely consisted of isolates from a single patient. We also found evidence of concurrent colonization of patients by multiple distinct lineages and transfer of strains between patients during hospitalisation. We estimated the evolutionary rate of two clonal groups that colonized a single patient at 12.6 and 25.2 single nucleotide polymorphisms (SNPs)/genome/year. A detailed analysis of the accessory genome of one of the clonal groups revealed considerable variation due to gene gain and loss events, including the chromosomal acquisition of a 37 kbp prophage and the loss of an element containing carbohydrate metabolism-related genes. We determined the presence and location of twelve different Insertion Sequence (IS) elements, with ISEfa5showing a unique pattern of location in 24 of the 25 isolates, suggesting widespread ISEfa5excision and insertion into the genome during gut colonization.ConclusionsOur findings show that theE. faeciumgenome is highly dynamic during asymptomatic colonization of the patient gut. We observe considerable genomic flexibility due to frequent horizontal gene transfer and recombination, which can contribute to the generation of genetic diversity within the species and, ultimately, can contribute to its success as a nosocomial pathogen.

scholarly journals Genomic rearrangements uncovered by genome-wide co-evolution analysis of a major nosocomial pathogen, Enterococcus faecium

2020 ◽  
Vol 6 (12) ◽  
Author(s):  
Janetta Top ◽  
Sergio Arredondo-Alonso ◽  
Anita C. Schürch ◽  
Santeri Puranen ◽  
Maiju Pesonen ◽  
...  
Keyword(s):  
Enterococcus Faecium ◽  
Type Species ◽  
Hospitalized Patients ◽  
Genomic Islands ◽  
Hospital Environment ◽  
Genomic Rearrangements ◽  
Nosocomial Pathogen ◽  
Content Type ◽  
Link Type ◽  
Genome Wide

Enterococcus faecium is a gut commensal of the gastro-digestive tract, but also known as nosocomial pathogen among hospitalized patients. Population genetics based on whole-genome sequencing has revealed that E. faecium strains from hospitalized patients form a distinct clade, designated clade A1, and that plasmids are major contributors to the emergence of nosocomial E. faecium . Here we further explored the adaptive evolution of E. faecium using a genome-wide co-evolution study (GWES) to identify co-evolving single-nucleotide polymorphisms (SNPs). We identified three genomic regions harbouring large numbers of SNPs in tight linkage that are not proximal to each other based on the completely assembled chromosome of the clade A1 reference hospital isolate AUS0004. Close examination of these regions revealed that they are located at the borders of four different types of large-scale genomic rearrangements, insertion sites of two different genomic islands and an IS30-like transposon. In non-clade A1 isolates, these regions are adjacent to each other and they lack the insertions of the genomic islands and IS30-like transposon. Additionally, among the clade A1 isolates there is one group of pet isolates lacking the genomic rearrangement and insertion of the genomic islands, suggesting a distinct evolutionary trajectory. In silico analysis of the biological functions of the genes encoded in three regions revealed a common link to a stress response. This suggests that these rearrangements may reflect adaptation to the stringent conditions in the hospital environment, such as antibiotics and detergents, to which bacteria are exposed. In conclusion, to our knowledge, this is the first study using GWES to identify genomic rearrangements, suggesting that there is considerable untapped potential to unravel hidden evolutionary signals from population genomic data.

VicRK and CovR polymorphisms in Streptococcus mutans strains associated with cardiovascular infections

2021 ◽  
Vol 70 (12) ◽  
Author(s):  
Letícia T. Oliveira ◽  
Lívia A. Alves ◽  
Erika N. Harth-Chu ◽  
Ryota Nomura ◽  
Kazuhiko Nakano ◽  
...  
Keyword(s):  
Streptococcus Mutans ◽  
Type Species ◽  
Virulence Gene ◽  
Common Species ◽  
Oral Microbiome ◽  
Nucleotide Polymorphisms ◽  
Content Type ◽  
Virulence Gene Expression ◽  
Coding Regions ◽  
Link Type

Introduction. Streptococcus mutans , a common species of the oral microbiome, expresses virulence genes promoting cariogenic dental biofilms, persistence in the bloodstream and cardiovascular infections. Gap statement. Virulence gene expression is variable among S. mutans strains and controlled by the transcription regulatory systems VicRK and CovR. Aim. This study investigates polymorphisms in the vicRK and covR loci in S. mutans strains isolated from the oral cavity or from the bloodstream, which were shown to differ in expression of covR, vicRK and downstream genes. Methodology. The transcriptional activities of covR, vicR and vicK were compared by RT-qPCR between blood and oral strains after exposure to human serum. PCR-amplified promoter and/or coding regions of covR and vicRK of 18 strains (11 oral and 7 blood) were sequenced and compared to the reference strain UA159. Results. Serum exposure significantly reduced covR and vicR/K transcript levels in most strains (P<0.05), but reductions were higher in oral than in blood strains. Single-nucleotide polymorphisms (SNPs) were detected in covR regulatory and coding regions, but SNPs affecting the CovR effector domain were only present in two blood strains. Although vicR was highly conserved, vicK showed several SNPs, and SNPs affecting VicK regions important for autokinase activity were found in three blood strains. Conclusions. This study reveals transcriptional and structural diversity in covR and vicR/K, and identifies polymorphisms of functional relevance in blood strains, indicating that covR and vicRK might be important loci for S. mutans adaptation to host selective pressures associated with virulence diversity.

scholarly journals Genomic evolution and local epidemiology of Klebsiella pneumoniae from a major hospital in Beijing, China, over a 15 year period: dissemination of known and novel high-risk clones

2021 ◽  
Author(s):  
Mattia Palmieri ◽  
Kelly L. Wyres ◽  
Caroline Mirande ◽  
Zhao Qiang ◽  
Ye Liyan ◽  
...  
Keyword(s):  
High Risk ◽  
Klebsiella Pneumoniae ◽  
Type Species ◽  
Treatment Options ◽  
Multidrug Resistant ◽  
Virulence Plasmid ◽  
Content Type ◽  
Origin And Evolution ◽  
Link Type ◽  
Beijing China

Klebsiella pneumoniae is a frequent cause of nosocomial and severe community-acquired infections. Multidrug-resistant (MDR) and hypervirulent (hv) strains represent major threats, and tracking their emergence, evolution and the emerging convergence of MDR and hv traits is of major importance. We employed whole-genome sequencing (WGS) to study the evolution and epidemiology of a large longitudinal collection of clinical K. pneumoniae isolates from the H301 hospital in Beijing, China. Overall, the population was highly diverse, although some clones were predominant. Strains belonging to clonal group (CG) 258 were dominant, and represented the majority of carbapenemase-producers. While CG258 strains showed high diversity, one clone, ST11-KL47, represented the majority of isolates, and was highly associated with the KPC-2 carbapenemase and several virulence factors, including a virulence plasmid. The second dominant clone was CG23, which is the major hv clone globally. While it is usually susceptible to multiple antibiotics, we found some isolates harbouring MDR plasmids encoding for ESBLs and carbapenemases. We also reported the local emergence of a recently described high-risk clone, ST383. Conversely to strains belonging to CG258, which are usually associated to KPC-2, ST383 strains seem to readily acquire carbapenemases of different types. Moreover, we found several ST383 strains carrying the hypervirulence plasmid. Overall, we detected about 5 % of simultaneous carriage of AMR genes (ESBLs or carbapenemases) and hypervirulence genes. Tracking the emergence and evolution of such strains, causing severe infections with limited treatment options, is fundamental in order to understand their origin and evolution and to limit their spread. This article contains data hosted by Microreact.

Functional characterization of a gene cluster responsible for inositol catabolism associated with hospital-adapted isolates of Enterococcus faecium

Microbiology ◽  
2021 ◽  
Vol 167 (9) ◽  
Author(s):  
Janetta Top ◽  
Jery Baan ◽  
Adinda Bisschop ◽  
Sergio Arredondo-Alonso ◽  
Willem van Schaik ◽  
...  
Keyword(s):  
Mouse Model ◽  
Gene Cluster ◽  
Enterococcus Faecium ◽  
Type Species ◽  
Integration Site ◽  
Functional Characterization ◽  
Donor Strain ◽  
Integrase Gene ◽  
Content Type ◽  
Link Type

Enterococcus faecium is a nosocomial, multidrug-resistant pathogen. Whole genome sequence studies revealed that hospital-associated E. faecium isolates are clustered in a separate clade A1. Here, we investigated the distribution, integration site and function of a putative iol gene cluster that encodes for myo-inositol (MI) catabolism. This iol gene cluster was found as part of an ~20 kbp genetic element (iol element), integrated in ICEEfm1 close to its integrase gene in E. faecium isolate E1679. Among 1644 E. faecium isolates, ICEEfm1 was found in 789/1227 (64.3 %) clade A1 and 3/417 (0.7 %) non-clade A1 isolates. The iol element was present at a similar integration site in 180/792 (22.7 %) ICEEfm1-containing isolates. Examination of the phylogenetic tree revealed genetically closely related isolates that differed in presence/absence of ICEEfm1 and/or iol element, suggesting either independent acquisition or loss of both elements. E. faecium iol gene cluster containing isolates E1679 and E1504 were able to grow in minimal medium with only myo-inositol as carbon source, while the iolD-deficient mutant in E1504 (E1504∆iolD) lost this ability and an iol gene cluster negative recipient strain gained this ability after acquisition of ICEEfm1 by conjugation from donor strain E1679. Gene expression profiling revealed that the iol gene cluster is only expressed in the absence of other carbon sources. In an intestinal colonization mouse model the colonization ability of E1504∆iolD mutant was not affected relative to the wild-type E1504 strain. In conclusion, we describe and functionally characterise a gene cluster involved in MI catabolism that is associated with the ICEEfm1 island in hospital-associated E. faecium isolates. We were unable to show that this gene cluster provides a competitive advantage during gut colonisation in a mouse model. Therefore, to what extent this gene cluster contributes to the spread and ecological specialisation of ICEEfm1-carrying hospital-associated isolates remains to be investigated.

scholarly journals Genomic epidemiology of tuberculosis in eastern Malaysia: insights for strengthening public health responses

2021 ◽  
Vol 7 (5) ◽  
Author(s):  
Arnold Bainomugisa ◽  
Ella M. Meumann ◽  
Giri Shan Rajahram ◽  
Rick Twee-Hee Ong ◽  
Lachlan Coin ◽  
...  
Keyword(s):  
Public Health ◽  
Type Species ◽  
Multidrug Resistant ◽  
Resistant Isolate ◽  
Recent Common Ancestor ◽  
Resistance Mutations ◽  
Content Type ◽  
Genomic Epidemiology ◽  
Link Type ◽  
Lineage 2

Tuberculosis is a leading public health priority in eastern Malaysia. Knowledge of the genomic epidemiology of tuberculosis can help tailor public health interventions. Our aims were to determine tuberculosis genomic epidemiology and characterize resistance mutations in the ethnically diverse city of Kota Kinabalu, Sabah, located at the nexus of Malaysia, Indonesia, Philippines and Brunei. We used an archive of prospectively collected Mycobacterium tuberculosis samples paired with epidemiological data. We collected sputum and demographic data from consecutive consenting outpatients with pulmonary tuberculosis at the largest tuberculosis clinic from 2012 to 2014, and selected samples from tuberculosis inpatients from the tertiary referral centre during 2012–2014 and 2016–2017. Two hundred and eight M . tuberculosis sequences were available for analysis, representing 8 % of cases notified during the study periods. Whole-genome phylogenetic analysis demonstrated that most strains were lineage 1 (195/208, 93.8 %), with the remainder being lineages 2 (8/208, 3.8 %) or 4 (5/208, 2.4 %). Lineages or sub-lineages were not associated with patient ethnicity. The lineage 1 strains were diverse, with sub-lineage 1.2.1 being dominant (192, 98 %). Lineage 1.2.1.3 isolates were geographically most widely distributed. The greatest diversity occurred in a border town sub-district. The time to the most recent common ancestor for the three major lineage 1.2.1 clades was estimated to be the year 1966 (95 % HPD 1948–1976). An association was found between failure of culture conversion by week 8 of treatment and infection with lineage 2 (4/6, 67 %) compared with lineage 1 strains (4/83, 5 %) (P<0.001), supporting evidence of greater virulence of lineage 2 strains. Eleven potential transmission clusters (SNP difference ≤12) were identified; at least five included people living in different sub-districts. Some linked cases spanned the whole 4-year study period. One cluster involved a multidrug-resistant tuberculosis strain matching a drug-susceptible strain from 3 years earlier. Drug resistance mutations were uncommon, but revealed one phenotype–genotype mismatch in a genotypically multidrug-resistant isolate, and rare nonsense mutations within the katG gene in two isolates. Consistent with the regionally mobile population, M. tuberculosis strains in Kota Kinabalu were diverse, although several lineage 1 strains dominated and were locally well established. Transmission clusters – uncommonly identified, likely attributable to incomplete sampling – showed clustering occurring across the community, not confined to households or sub-districts. The findings indicate that public health priorities should include active case finding and early institution of tuberculosis management in mobile populations, while there is a need to upscale effective contact investigation beyond households to include other contacts within social networks.

scholarly journals Antimicrobial resistance profiles and genetic basis of resistance among non-fastidious Gram-negative bacteria recovered from ready-to-eat foods in Kibera informal housing in Nairobi, Kenya

2021 ◽  
Vol 3 (6) ◽  
Author(s):  
John Maina ◽  
Perpetual Ndung’u ◽  
Anne Muigai ◽  
John Kiiru
Keyword(s):  
Antimicrobial Resistance ◽  
Type Species ◽  
Multidrug Resistant ◽  
Essential Elements ◽  
Enterobacter Agglomerans ◽  
Cross Sectional ◽  
Content Type ◽  
Link Type ◽  
Antimicrobial Resistance Genes ◽  
Contamination Levels

Objective. This cross-sectional study conducted in Kibera, Kenya, sought to gain insights on relative microbial contamination levels of popular unprocessed food types, determine antimicrobial resistance (AMR) burden and the carriage of integrons that are essential elements for spreading antimicrobial resistance genes (ARG). Foods analysed consisted of cooked vegetables (kale, cabbage, and nightshades), boiled cereal foods (beans, rice, and Githeri, which is a mixture of beans and maize), meat, Omena fish (fried silver cyprinids), and Ugali (a product of simmered maize flour in boiled water). Results. The analysis detected contamination levels exceeding 2×104 c.f.u. ml−1 in 106 (38 %) of the 281 ready-to-eat foods analysed. The majority of food types had microbial contaminations of between 4.0×104 and 2.3×106 c.f.u. ml−1. Kale was the most contaminated with a mean of 2.3×106 c.f.u. ml−1, while Omena was the least contaminated with 4.0×104 c.f.u. ml−1. Foods sold close to open sewage and refuse sites were more contaminated than those sold in relatively ‘cleaner’ settings (P <0.0001, O.R 0.1162, C.I 0.1162–0.120). A total of 405 bacterial isolates were recovered and included; Klebsiella spp 116 (29 %), Escherichia coli 104 (26 %), Enterobacter agglomerans 88 (22 %), Proteus mirabilis 30 (7 %), Salmonella spp 28 (7 %), Citrobacter freundii 27 (7 %) and Serratia marcescens 12 (3 %). Imipenem (IPM, 100 %) was the most effective antimicrobial agent, followed by cefepime (98 %). Ampicillin (AMP, 33 %), trimethoprim (TMP, 27 %), and sulfamethoxazole (SMX, 23 %) on the other hand, were the least effective antimicrobials. The analysis also found ten isolates (2 %) that had co-resistance to third-generation cephalosporins, fluoroquinolone (CIP), quinolones (NAL) and aminoglycosides (GEN); hereby we refer to this phenotype as the βFQA. The prevalence of multidrug-resistant (MDR) strains was 23 % (93), while that of extended-spectrum β-lactamases (ESBL) producing strains was 4 % (17). The bla TEM was the most prevalent (55 %) β-lactamase (bla) gene among the screened 93 MDR-strains. Carriage of class one integrons (intI1) was more common (23 %) than intl2 (3 %) among these MDR-strains. Bacterial diversity analysis using the GTG5-PCR found no significant clusters for analysed E. coli and K. pneumoniae, suggesting recovered isolates were genetically diverse and not due to non-clonal expansion. The findings of this study are an indication that contaminated foods can be a reservoir for enteric pathogens and a source of AMR strains.

scholarly journals The roles of antimicrobial resistance, phage diversity, isolation source and selection in shaping the genomic architecture of Bacillus anthracis

2021 ◽  
Vol 7 (8) ◽  
Author(s):  
Spencer A. Bruce ◽  
Yen-Hua Huang ◽  
Pauline L. Kamath ◽  
Henriette van Heerden ◽  
Wendy C. Turner
Keyword(s):  
Antimicrobial Resistance ◽  
Bacillus Anthracis ◽  
Type Species ◽  
Large Scale ◽  
Genomic Structure ◽  
Nucleotide Polymorphisms ◽  
Content Type ◽  
Link Type ◽  
Population Genomic ◽  
Antimicrobial Resistance Genes

Bacillus anthracis, the causative agent of anthrax disease, is a worldwide threat to livestock, wildlife and public health. While analyses of genetic data from across the globe have increased our understanding of this bacterium’s population genomic structure, the influence of selective pressures on this successful pathogen is not well understood. In this study, we investigate the effects of antimicrobial resistance, phage diversity, geography and isolation source in shaping population genomic structure. We also identify a suite of candidate genes potentially under selection, driving patterns of diversity across 356 globally extant B. anthracis genomes. We report ten antimicrobial resistance genes and 11 different prophage sequences, resulting in the first large-scale documentation of these genetic anomalies for this pathogen. Results of random forest classification suggest genomic structure may be driven by a combination of antimicrobial resistance, geography and isolation source, specific to the population cluster examined. We found strong evidence that a recombination event linked to a gene involved in protein synthesis may be responsible for phenotypic differences between comparatively disparate populations. We also offer a list of genes for further examination of B. anthracis evolution, based on high-impact single nucleotide polymorphisms (SNPs) and clustered mutations. The information presented here sheds new light on the factors driving genomic structure in this notorious pathogen and may act as a road map for future studies aimed at understanding functional differences in terms of B. anthracis biogeography, virulence and evolution.

scholarly journals Genomic epidemiology of nontoxigenic Corynebacterium diphtheriae from King County, Washington State, USA between July 2018 and May 2019

2020 ◽  
Vol 6 (12) ◽  
Author(s):  
Lingzi Xiaoli ◽  
Eileen Benoliel ◽  
Yanhui Peng ◽  
Janessa Aneke ◽  
Pamela K. Cassiday ◽  
...  
Keyword(s):  
Type Species ◽  
Respiratory Infections ◽  
Corynebacterium Diphtheriae ◽  
King County ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Content Type ◽  
Genomic Epidemiology ◽  
Link Type ◽  
Content Variation

Between July 2018 and May 2019, Corynebacterium diphtheriae was isolated from eight patients with non-respiratory infections, seven of whom experienced homelessness and had stayed at shelters in King County, WA, USA. All isolates were microbiologically identified as nontoxigenic C. diphtheriae biovar mitis. Whole-genome sequencing confirmed that all case isolates were genetically related, associated with sequence type 445 and differing by fewer than 24 single-nucleotide polymorphisms (SNPs). Compared to publicly available C. diphtheriae genomic data, these WA isolates formed a discrete cluster with SNP variation consistent with previously reported outbreaks. Virulence-related gene content variation within the highly related WA cluster isolates was also observed. These results indicated that genome characterization can readily support epidemiology of nontoxigenic C. diphtheriae .

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