scholarly journals Infection with Clostridioides difficile ribotype 046 in a paediatric liver transplant patient

2021 ◽  
Vol 3 (10) ◽  
Author(s):  
Hildenia B. R. Nogueira ◽  
Cecília L. Costa ◽  
Conceição S. Martins ◽  
Maria Luana G. S. Morais ◽  
Carlos Quesada-Gómez ◽  
...  
Keyword(s):  
Molecular Characterization ◽  
Type Species ◽  
Transplant Patient ◽  
Antibiotic Use ◽  
Female Child ◽  
Content Type ◽  
Link Type ◽  
Clostridioides Difficile ◽  
History Of

Clostridioides difficile causes nosocomial diarrhoea associated with antibiotic use and immunodeficiency. Although the number of paediatric C. difficile infections (CDIs) has increased worldwide, there are few studies on the molecular characterization of strains causing CDIs among children. We report the clinical features and strain molecular characterization of a CDI in a female child with a history of liver transplantation at 7 months of age. This is the first report of the 046 ribotype causing paediatric diarrhoea.

Eikenella glucosivorans sp. nov., isolated from a human throat swab, and emendation of the genus Eikenella to include saccharolytic species

2021 ◽  
Vol 71 (9) ◽  
Author(s):  
Silvio Hering ◽  
Moritz K. Jansson ◽  
Michael E. J. Buhl
Keyword(s):  
Type Species ◽  
Throat Swab ◽  
Novel Species ◽  
Phylogenetic Analyses ◽  
Routine Care ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
Bacterium Strain

A novel species within the genus Eikenella is described, based on the phenotypical, biochemical and genetic characterization of a strain of a facultatively anaerobic, Gram-negative rod-shaped bacterium. Strain S3360T was isolated from the throat swab of a patient sampled during routine care at a hospital. Phylogenetic analyses (full-length 16S rRNA gene and whole-genome sequences) placed the strain in the genus Eikenella , separate from all recognized species but with the closest relationship to Eikenella longinqua (NML 02-A-017T). Eikenella is one of the genera in the HACEK group known to be responsible for rare cases of endocarditis in humans. Until the recent descriptions of Eikenella exigua , Eikenella halliae and Eikenella longinqua , Eikenella corrodens had been the only validly published species in this genus since its description as Bacteroides corrodens in 1958. Unlike these species, strain S3360T is able to metabolize carbohydrates (glucose). The average nucleotide identities of strain S3360T with E. longinqua (NML 02-A-017T) and E. corrodens (NCTC 10596T), the type species of the genus, were 90.5 and 84.7 %, respectively, and the corresponding genome-to-genome distance values were 41.3 and 29.0 %, respectively. The DNA G+C content of strain S3360T was 58.4 mol%. Based on the phenotypical, biochemical and genetic findings, strain S3360T is considered to represent a novel species within the genus Eikenella , for which the name Eikenella glucosivorans sp. nov. is proposed. The type strain is S3360T (DSM 110714T=CCOS 1935T=CCUG 74293T). In addition, an emendation of the genus Eikenella is proposed to include species which are saccharolytic.

Biochemical and functional characterization of Mycobacterium tuberculosis ketol-acid reductoisomerase

Microbiology ◽  
2021 ◽  
Vol 167 (9) ◽  
Author(s):  
Nirbhay Singh ◽  
Anu Chauhan ◽  
Ram Kumar ◽  
Sudheer Kumar Singh
Keyword(s):  
Amino Acids ◽  
Mycobacterium Tuberculosis ◽  
Type Species ◽  
Low Ph ◽  
Stress Conditions ◽  
Starvation Stress ◽  
Content Type ◽  
E Coli ◽  
Link Type

Branched-chain amino acids (BCAAs) are essential amino acids, but their biosynthetic pathway is absent in mammals. Ketol-acid reductoisomerase (IlvC) is a BCAA biosynthetic enzyme that is coded by Rv3001c in Mycobacterium tuberculosis H37Rv (Mtb-Rv) and MRA_3031 in M. tuberculosis H37Ra (Mtb-Ra). IlvCs are essential in Mtb-Rv as well as in Escherichia coli . Compared to wild-type and IlvC-complemented Mtb-Ra strains, IlvC knockdown strain showed reduced survival at low pH and under low pH+starvation stress conditions. Further, increased expression of IlvC was observed under low pH and starvation stress conditions. Confirmation of a role for IlvC in pH and starvation stress was achieved by developing E. coli BL21(DE3) IlvC knockout, which was defective for growth in M9 minimal medium, but growth could be rescued by isoleucine and valine supplementation. Growth was also restored by complementing with over-expressing constructs of Mtb-Ra and E. coli IlvCs. The E. coli knockout also had a survival deficit at pH=5.5 and 4.5 and was more susceptible to killing at pH=3.0. The biochemical characterization of Mtb-Ra and E. coli IlvCs confirmed that both have NADPH-dependent activity. In conclusion, this study demonstrates the functional complementation of E. coli IlvC by Mtb-Ra IlvC and also suggests that IlvC has a role in tolerance to low pH and starvation stress.

Detection and partial characterization of extracellular inducers of persistence in Staphylococcus epidermidis and Staphylococcus aureus

2021 ◽  
Vol 70 (6) ◽  
Author(s):  
Elyse C. Curry ◽  
Ryan G. Hart ◽  
Danni Y. Habtu ◽  
Neal R. Chamberlain
Keyword(s):  
Molecular Weight ◽  
Staphylococcus Aureus ◽  
Staphylococcus Epidermidis ◽  
Type Species ◽  
Proteinase K ◽  
Partial Characterization ◽  
Content Type ◽  
Link Type ◽  
Inducing Factors

Introduction. This study describes the identification and partial characterization of persistence-inducing factors (PIFs) from staphylococci. Hypothesis/Gap Statement. Increases in persisters during mid-log phase growth indicate that quorum-sensing factors might be produced by staphylococci. Aim. To identify and partially characterize PIFs from Staphylococcus epidermidis RP62A and Staphylococcus aureus SH1000. Methodology. Others have demonstrated a significant increase in persister numbers during mid-log phase. Inducers of this mid-log increase have yet to be identified in staphylococci. Optical density at 600 nm (OD600) was used instead of time to determine when persister numbers increased during logarithmic growth. Concentrated culture filtrates (CCFs) from S. epidermidis and S. aureus were obtained at various OD600s and following incubation at 16 h. The CCFs were used to develop a PIF assay. The PIF assay was used to partially characterize PIF from S. epidermidis and S. aureus for sizing of PIF activity, temperature and protease sensitivity and inter-species communications. Results. The optimal OD600s for S. epidermidis and S. aureus PIF assays were 2.0 and 0.5, respectively. The highest PIF activity for both species was from CCF following incubation overnight (16 h). S. epidermidis ’ PIF activity was decreased by storage at 4 oC but not at 20 oC (16 h), 37 oC (1 h) or 100 oC (15 min). S. aureus ’ PIF activity was decreased following storage at 4 oC (2 weeks) and after boiling at 100 oC for 5 min but not after incubation at 37 oC (1 h). PIF activity from both species went through a 3000 molecular weight cutoff ultrafilter. Proteinase K treatment of S. aureus PIF decreased activity but did not decrease the PIF activity of S. epidermidis . PIF from S. epidermidis did not increase persisters when used to treat S. aureus cells and nor did PIF from S. aureus increase persisters when used to treat S. epidermidis cells. Conclusions. Attempts to discover PIFs for staphylococci were unsuccessful due to the time-based means used to identify mid-log. Both staphylococcal species produce extracellular, low-molecular-weight inducers of persistence when assayed using an OD600 -based PIF assay.

Molecular characterization of Vibrio cholerae O1 isolates obtained from outbreaks in the Philippines, 2015–2016

2021 ◽  
Vol 70 (11) ◽  
Author(s):  
Mark Philip Bugayong ◽  
Hidemasa Izumiya ◽  
Josie M. Bilar ◽  
Masatomo Morita ◽  
Eiji Arakawa ◽  
...  
Keyword(s):  
Vibrio Cholerae ◽  
Type Species ◽  
Variable Number Tandem Repeat ◽  
The Philippines ◽  
Large Chromosome ◽  
Content Type ◽  
Link Type ◽  
Mlva Type ◽  
El Tor

Introduction. The Philippines, comprising three island groups, namely, Luzon, Visayas and Mindanao, experienced an increase in cholera outbreaks in 2016. Previous studies have shown that Vibrio cholerae isolates obtained from the Philippines are novel hybrid El Tor strains that have evolved in the country and are clearly distinct from those found in Mozambique and Cameroon. Gap statement. The characterization of the strains isolated from outbreaks has been limited to phenotypic characteristics, such as biochemical and serological characteristics, in most previous studies. Aim. We performed multilocus variable-number tandem repeat (VNTR) analysis (MLVA) for V. cholerae isolates obtained from 2015 to 2016 to further characterize and understand the emergence and dissemination of the strains in the Philippines. Methodology. A total of 139 V . cholerae O1 Ogawa biotype El Tor isolates were obtained from the Philippines during diarrhoeal outbreaks in 18 provinces between 2015 and 2016. VNTR data were analysed to classify the MLVA profiles where the large-chromosome types (LCTs) were applied for grouping. Results. We identified 50 MLVA types among 139 isolates originating from 18 provinces, and 14 LCTs. The distribution of the LCTs was variable, and a few were located in specific areas or even in specific provinces. Based on eBURST analysis, 99 isolates with 7 LCTs and 32 MLVA types belonged to 1 group, suggesting that they were related to each other. LCT A was predominant (n=67) and was isolated from Luzon and Visayas. LCT A had 14 MLVA types; however, it mostly emerged during a single quarter of a year. Eight clusters were identified, each of which involved specific MLVA type(s). The largest cluster involved 23 isolates showing 3 MLVA types, 21 of which were MLVA type A-14 isolated from Negros Occidental during quarter 4 of 2016. Comparative analysis showed that almost all isolates from the Philippines were distinct from those in other countries. Conclusions. The genotypic relationship of the V. cholerae isolates obtained during outbreaks in the Philippines was studied, and their emergence and dissemination were elucidated. MLVA revealed the short-term dynamics of V. cholerae genotypes in the Philippines.

scholarly journals Isolation and Characterization of Akhmeta Virus from Wild-Caught Rodents (Apodemus spp.) in Georgia

2019 ◽  
Vol 93 (24) ◽  
Author(s):  
Jeffrey B. Doty ◽  
Giorgi Maghlakelidze ◽  
Irakli Sikharulidze ◽  
Shin-Lin Tu ◽  
Clint N. Morgan ◽  
...  
Keyword(s):  
Natural History ◽  
Molecular Characterization ◽  
Small Mammals ◽  
Skin Lesions ◽  
Human Populations ◽  
Content Type ◽  
Subsequent Investigation ◽  
Isolation And Characterization ◽  
History Of

ABSTRACT In 2013, a novel orthopoxvirus was detected in skin lesions of two cattle herders from the Kakheti region of Georgia (country); this virus was named Akhmeta virus. Subsequent investigation of these cases revealed that small mammals in the area had serological evidence of orthopoxvirus infections, suggesting their involvement in the maintenance of these viruses in nature. In October 2015, we began a longitudinal study assessing the natural history of orthopoxviruses in Georgia. As part of this effort, we trapped small mammals near Akhmeta (n = 176) and Gudauri (n = 110). Here, we describe the isolation and molecular characterization of Akhmeta virus from lesion material and pooled heart and lung samples collected from five wood mice (Apodemus uralensis and Apodemus flavicollis) in these two locations. The genomes of Akhmeta virus obtained from rodents group into 2 clades: one clade represented by viruses isolated from A. uralensis samples, and one clade represented by viruses isolated from A. flavicollis samples. These genomes also display several presumptive recombination events for which gene truncation and identity have been examined. IMPORTANCE Akhmeta virus is a unique Orthopoxvirus that was described in 2013 from the country of Georgia. This paper presents the first isolation of this virus from small mammal (Rodentia; Apodemus spp.) samples and the molecular characterization of those isolates. The identification of the virus in small mammals is an essential component to understanding the natural history of this virus and its transmission to human populations and could guide public health interventions in Georgia. Akhmeta virus genomes harbor evidence suggestive of recombination with a variety of other orthopoxviruses; this has implications for the evolution of orthopoxviruses, their ability to infect mammalian hosts, and their ability to adapt to novel host species.

scholarly journals Mycobacterium celeriflavum sp. nov., a rapidly growing scotochromogenic bacterium isolated from clinical specimens

2015 ◽  
Vol 65 (Pt_2) ◽  
pp. 510-515 ◽  
Author(s):  
Abdolrazagh Hashemi Shahraki ◽  
Cengiz Çavuşoğlu ◽  
Emanuele Borroni ◽  
Parvin Heidarieh ◽  
Orhan Kaya Koksalan ◽  
...  
Keyword(s):  
Type Strain ◽  
Type Species ◽  
Sequence Similarity ◽  
Housekeeping Genes ◽  
Mycolic Acid ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
Polyphasic Characterization

Six strains of a rapidly growing scotochromogenic mycobacterium were isolated from pulmonary specimens of independent patients. Biochemical and cultural tests were not suitable for their identification. The mycolic acid pattern analysed by HPLC was different from that of any other mycobacterium. Genotypic characterization, targeting seven housekeeping genes, revealed the presence of microheterogeneity in all of them. Different species were more closely related to the test strains in various regions: the type strain of Mycobacterium moriokaense showed 99.0 % 16S rRNA gene sequence similarity, and 91.5–96.5 % similarity for the remaining six regions. The whole genome sequences of the proposed type strain and that of M. moriokaense presented an average nucleotide identity (ANI) of 82.9 %. Phylogenetic analysis produced poorly robust trees in most genes with the exception of rpoB and sodA where Mycobacterium flavescens and Mycobacterium novocastrense were the closest species. This phylogenetic relatedness was confirmed by the tree inferred from five concatenated genes, which was very robust. The polyphasic characterization of the test strains, supported by the ANI value, demonstrates that they belong to a previously unreported species, for which the name Mycobacterium celeriflavum sp. nov. is proposed. The type strain is AFPC-000207T ( = DSM 46765T = JCM 18439T).

scholarly journals Molecular Characterization of a Voriconazole-Resistant, Posaconazole-Susceptible Aspergillus fumigatus Isolate in a Lung Transplant Recipient in the United States

2015 ◽  
Vol 60 (2) ◽  
pp. 1129-1133 ◽  
Author(s):  
Jose A. Vazquez ◽  
Elias K. Manavathu
Keyword(s):  
United States ◽  
Aspergillus Fumigatus ◽  
Molecular Characterization ◽  
Lung Transplant ◽  
Transplant Patient ◽  
The United States ◽  
Azole Resistance ◽  
Content Type ◽  
High Level

ABSTRACTMolecular characterization ofcyp51Afrom the azole-resistantAspergillus fumigatusisolate 50593 from a lung transplant patient showed Y121F/T289A changes coupled with a 46-bp tandem repeat (TR46) on the promoter, whereascyp51Afrom the pretherapy isolate,A. fumigatus47381, showed no changes. This is the first reported case ofA. fumigatusazole resistance due to Y121F/T289A/TR46 in the United States, suggesting that multiple mutational alterations ofcyp51Aresulting in high-level azole resistance could occur during prolonged antifungal therapy.

scholarly journals Molecular characterization of a novel bla CTX-M-3-carrying Tn6741 transposon in Morganella morganii isolated from swine

2020 ◽  
Vol 69 (8) ◽  
pp. 1089-1094
Author(s):  
Xingwei Luo ◽  
Yajun Zhai ◽  
Dandan He ◽  
Xiaodie Cui ◽  
Yingying Yang ◽  
...  
Keyword(s):  
Type Species ◽  
Susceptibility Testing ◽  
Morganella Morganii ◽  
Ionization Time ◽  
Content Type ◽  
Genetic Environment ◽  
Link Type ◽  
Flight Mass Spectrometry ◽  
First Time

Introduction. The bla CTX-M-3 gene has rarely been reported in Morganella morganii strains and its genetic environment has not yet been investigated. Aim. To identify the bla CTX-M-3 gene in M. morganii isolated from swine and characterize its genetic environment. Methodology. A M. morganii isolate (named MM1L5) from a deceased swine was identified using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) and subjected to antimicrobial susceptibility testing. The bla genes were detected and then the genetic location and environment of bla CTX-M-3 were investigated by Southern blot and PCR mapping, respectively. The M. morganii bla CTX-M-3 gene was cloned and expressed in Escherichia coli . Results. Isolate MM1L5 harboured the bla CTX-M-3 and bla TEM-1 genes. The bla CTX-M-3 gene, located on the chromosome, was co-carried with an IS26 and bla TEM-1 gene by a novel 6361 bp IS26-flanked composite transposon, designated Tn6741. This transposon consisted of a novel bla CTX-M-3-containing module, IS26-ΔISEcp1-bla CTX-M-3-Δorf477-IS26 (named Tn6710), and a bla TEM-1-containing module, IS26-Δorf477-bla TEM-1-tnpR-IS26, differing from previous reports. Phylogenetic analysis showed a significant variation based on the sequence of Tn6741, as compared to those of other related transposons. Interestingly, although the cloned bla CTX-M-3 gene could confer resistance to ceftiofur, cefquinome, ceftriaxone and cefotaxime, one amino acid substitution (Ile-142-Thr) resulted in a significant reduction of resistance to these antimicrobials. Conclusion. This is the first time that bla CTX-M-3 has been identified on a chromosome from a M. morganii isolate. Furthermore, the bla CTX-M-3 gene was located with an IS26 element and bla TEM-1 gene on a novel IS26-flanked composite transposon, Tn6741, suggesting that Tn6741 might act as a reservoir for the bla CTX-M-3 and bla TEM-1 genes and may become an important vehicle for their dissemination among M. morganii .

scholarly journals A global to local genomics analysis of Clostridioides difficile ST1/RT027 identifies cryptic transmission events in a northern Arizona healthcare network

2019 ◽  
Vol 5 (7) ◽  
Author(s):  
Charles H. D. Williamson ◽  
Nathan E. Stone ◽  
Amalee E. Nunnally ◽  
Heidie M. Hornstra ◽  
David M. Wagner ◽  
...  
Keyword(s):  
Type Species ◽  
Sequence Type ◽  
Infection Prevention And Control ◽  
Polymorphism Analysis ◽  
Whole Genome ◽  
Content Type ◽  
Northern Arizona ◽  
Healthcare Network ◽  
Link Type ◽  
Clostridioides Difficile

Clostridioides difficile is a ubiquitous, diarrhoeagenic pathogen often associated with healthcare-acquired infections that can cause a range of symptoms from mild, self-limiting disease to toxic megacolon and death. Since the early 2000s, a large proportion of C. difficile cases have been attributed to the ribotype 027 (RT027) lineage, which is associated with sequence type 1 (ST1) in the C. difficile multilocus sequence typing scheme. The spread of ST1 has been attributed, in part, to resistance to fluoroquinolones used to treat unrelated infections, which creates conditions ideal for C. difficile colonization and proliferation. In this study, we analysed 27 isolates from a healthcare network in northern Arizona, USA, and 1352 publicly available ST1 genomes to place locally sampled isolates into a global context. Whole genome, single nucleotide polymorphism analysis demonstrated that at least six separate introductions of ST1 were observed in healthcare facilities in northern Arizona over an 18-month sampling period. A reconstruction of transmission networks identified potential nosocomial transmission of isolates, which were only identified via whole genome sequence analysis. Antibiotic resistance heterogeneity was observed among ST1 genomes, including variability in resistance profiles among locally sampled ST1 isolates. To investigate why ST1 genomes are so common globally and in northern Arizona, we compared all high-quality C. difficile genomes and identified that ST1 genomes have gained and lost a number of genomic regions compared to all other C. difficile genomes; analyses of other toxigenic C. difficile sequence types demonstrate that this loss may be anomalous and could be related to niche specialization. These results suggest that a combination of antimicrobial resistance and gain and loss of specific genes may explain the prominent association of this sequence type with C. difficile infection cases worldwide. The degree of genetic variability in ST1 suggests that classifying all ST1 genomes into a quinolone-resistant hypervirulent clone category may not be appropriate. Whole genome sequencing of clinical C. difficile isolates provides a high-resolution surveillance strategy for monitoring persistence and transmission of C. difficile and for assessing the performance of infection prevention and control strategies.

scholarly journals Genetic diversity and epidemiology of accessory gene regulator loci in Clostridioides difficile

2020 ◽  
Vol 2 (7) ◽  
Author(s):  
Yuta Okada ◽  
Shu Okugawa ◽  
Mahoko Ikeda ◽  
Tatsuya Kobayashi ◽  
Ryoichi Saito ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
In Silico ◽  
Type Species ◽  
Clinical Samples ◽  
Pcr Analysis ◽  
Accessory Gene ◽  
Content Type ◽  
Link Type ◽  
Accessory Gene Regulator ◽  
Clostridioides Difficile

Quorum sensing is known to regulate bacterial virulence, and the accessory gene regulator (agr) loci is one of the genetic loci responsible for its regulation. Recent reports examining Clostridioides difficile show that two agr loci, agr1 and agr2, regulate toxin production, but the diversity of agr loci and their epidemiology is unknown. In our study, in silico analysis was performed to research genetic diversity of agr, and C. difficile isolates from clinical samples underwent multilocus sequence typing (MLST) and PCR analysis of agr loci. To reveal the distribution of agr among different strains, phylogenetic analysis was also performed. In our in silico analysis, two different subtypes, named agr2R and agr2M, were found in agr2, which were previously reported. PCR analysis of 133 C . difficile isolates showed that 131 strains had agr1, 61 strains had agr2R, and 26 strains had agr2M; agr2R was mainly found in clade 1 or clade 2 organisms, whereas agr2M was only found in clade 4. With rare exception, agr1-negative sequence types (STs) belonged to clade C-Ⅰ and C-Ⅲ, and one clade 4 strain had agr2R. Our study revealed subtypes of agr2 not previously recognized, and the distribution of several agr loci in C. difficile . These findings provide a foundation for further functional and clinical research of the agr loci.

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