scholarly journals Comparative Genomic Analyses Reveal Potential Factors Responsible for the ST6 Oxacillin-Resistant Staphylococcus lugdunensis Endemic in a Hospital

2021 ◽  
Vol 12 ◽  
Author(s):  
Shih-Cheng Chang ◽  
Lee-Chung Lin ◽  
Jang-Jih Lu
Keyword(s):  
Multidrug Resistant ◽  
Comparative Genomic ◽  
Staphylococcus Lugdunensis ◽  
Healthcare Settings ◽  
Resistant Genes ◽  
Similar Drug ◽  
Genomic Analyses ◽  
Life Threatening ◽  
Potential Factors ◽  
Successful Colonization

Oxacillin-resistant Staphylococcus lugdunensis (ORSL) is considered a life-threatening isolate in healthcare settings. Among ORSL clones, ST6-SCCmec II strains are associated with an endemic spread in hospitals. We analyzed the complete genome of ORSL CGMH-SL118, a representative strain. Results revealed that this strain contained three MGEs (two prophages and one plasmid) other than the SCCmec II element, which showed remarkable differences in genome organization compared to the reference strains from NCBI. Eight multidrug-resistant genes were identified. All but blaZ were carried by MGEs, such as the SCCmec II element [mecA, ant (9)-Ia, and ermA] and the prophage φSPbeta [aac (6')-aph (2'), aph (3')-III, and ant (6)-Ia], indicating that MGEs carrying multidrug-resistant genes may be important for ST6 strains. The prophage φSPbeta contains sasX gene, which was responsible for the pathogenesis of Staphylococcus aureus. A phage-mediated resistant island containing fusB (SlRIfusB-118) was found near φSPbeta, which was highly homologous to type III SeRIfusB-5907 of Staphylococcus epidermidis. In contrast to previous studies, over 20% of ST6 isolates showed a fusidic acid-resistant phenotype, suggesting that phage-mediated intraspecies transmission of resistant islands may become an important issue for ST6 strains. Sixty-eight clinical isolates of ST6 Staphylococcus lugdunensis (50 OSSL, oxacillin-sensitive S. lugdunensis, and 18 ORSL, including CGMH-SL118) collected from various types of specimens in the hospital were studied. Among these isolates in this study, ORSL showed similar drug-resistant genes and phenotypes as CGMH-SL118. The comparative genomic analyses highlight the contribution of MGEs in the development and dissemination of antimicrobial resistance in ST6 strains, suggesting that resistance determinants and virulence factors encoded by MGEs provide a survival advantage for successful colonization and spread in healthcare settings.

scholarly journals Distinct evolutionary dynamics of horizontal gene transfer in drug resistant and virulent clones ofKlebsiella pneumoniae

2018 ◽  
Author(s):  
Kelly L Wyres ◽  
Ryan R Wick ◽  
Louise M Judd ◽  
Roni Froumine ◽  
Alex Tokolyi ◽  
...  
Keyword(s):  
Evolutionary Dynamics ◽  
Virulence Gene ◽  
Pyogenic Liver Abscess ◽  
Multidrug Resistant ◽  
Comparative Genomic ◽  
Gene Acquisition ◽  
High Prevalence ◽  
Genomic Analyses ◽  
Invasive Infections ◽  
Healthcare Associated

AbstractKlebsiella pneumoniae(Kp) has emerged as an important cause of two distinct public health threats: multidrug resistant (MDR) healthcare-associated infections1and community-acquired invasive infections, particularly pyogenic liver abscess2. The majority of MDR hospital outbreaks are caused by a subset ofKpclones with a high prevalence of acquired antimicrobial resistance (AMR) genes, while the majority of community-acquired invasive infections are caused by ‘hypervirulent’ clones that rarely harbour acquired AMR genes but have high prevalence of key virulence loci3–5. Worryingly, the last few years have seen increasing reports of convergence of MDR and the key virulence genes within individualKpstrains6, but it is not yet clear whether these represent a transient phenomenon or a significant ongoing threat. Here we perform comparative genomic analyses for 28 distinctKpclones, including 6 hypervirulent and 8 MDR, to better understand their evolutionary histories and the risks of convergence. We show that MDR clones are highly diverse with frequent chromosomal recombination and gene content variability that far exceeds that of the hypervirulent clones. Consequently, we predict a much greater risk of virulence gene acquisition by MDRKpclones than of resistance gene acquisition by hypervirulent clones.

scholarly journals Functional and comparative genome analysis reveals clade-specific genome innovations in the killer fungus Candida auris

2021 ◽  
Author(s):  
Aswathy Narayanan ◽  
Rakesh Netha Vadnala ◽  
Promit Ganguly ◽  
Pavitra Selvakumar ◽  
Shivaprakash M Rudramurthy ◽  
...  
Keyword(s):  
Genome Analysis ◽  
Multidrug Resistant ◽  
Comparative Genomic ◽  
Candida Auris ◽  
Evolutionary Trajectory ◽  
Molecular Events ◽  
Genomic Analyses ◽  
Centromere Inactivation ◽  
Chromosomal Changes ◽  
Systemic Infections

AbstractThe thermotolerant multidrug-resistant ascomycete Candida auris rapidly emerged since 2009 and simultaneously evolved in different geographical zones worldwide, causing superficial as well as systemic infections. The molecular events that orchestrated this sudden emergence of the killer fungus remain mostly elusive. Here, we identify centromeres in C. auris and related species, using a combined approach of chromatin immunoprecipitation and comparative genomic analyses. We find that C. auris and multiple other species in the Clavispora/Candida clade shared a conserved small regional centromere landscape lacking pericentromeres. Further, a centromere inactivation event led to karyotypic alterations in this species complex. Inter-species genome analysis identified several structural chromosomal changes around centromeres. In addition, centromeres are found to be rapidly evolving loci among the different geographical clades of the same species of C. auris. Finally, we reveal an evolutionary trajectory of the unique karyotype associated with clade 2 that consists of the drug susceptible isolates of C. auris.

Comparative genomic analyses of two novel qnrVC6 carrying multidrug-resistant Pseudomonas. spp strains

2018 ◽  
Vol 123 ◽  
pp. 269-274 ◽  
Author(s):  
Junyan Liu ◽  
Ling Yang ◽  
Lin Li ◽  
Bing Li ◽  
Dingqiang Chen ◽  
...  
Keyword(s):  
Multidrug Resistant ◽  
Comparative Genomic ◽  
Pseudomonas Spp ◽  
Genomic Analyses

scholarly journals A novel chemical biology and computational approach to expedite the discovery of new-generation polymyxins against life-threatening Acinetobacter baumannii

2021 ◽  
Author(s):  
Xukai Jiang ◽  
Nitin A. Patil ◽  
Mohammad A. K. Azad ◽  
Hasini Wickremasinghe ◽  
Heidi Yu ◽  
...  
Keyword(s):  
Public Health ◽  
Chemical Biology ◽  
Multidrug Resistant ◽  
Computational Approach ◽  
Gram Negative Bacteria ◽  
Global Public Health ◽  
Gram Negative ◽  
Life Threatening ◽  
New Generation ◽  
Novel Antibiotics

Multidrug-resistant Gram-negative bacteria have been an urgent threat to global public health. Novel antibiotics are desperately needed to combat these 'superbugs'.

scholarly journals The domestication of Cucurbita argyrosperma as revealed by the genome of its wild relative

2021 ◽  
Vol 8 (1) ◽  
Author(s):  
Josué Barrera-Redondo ◽  
Guillermo Sánchez-de la Vega ◽  
Jonás A. Aguirre-Liguori ◽  
Gabriela Castellanos-Morales ◽  
Yocelyn T. Gutiérrez-Guerrero ◽  
...  
Keyword(s):  
Defense Mechanisms ◽  
Population Level ◽  
Growth Hormones ◽  
Comparative Genomic ◽  
Structural Variants ◽  
Closely Related Species ◽  
Level Data ◽  
Genomic Analyses ◽  
Genotype By Sequencing ◽  
Regulation Of Growth

AbstractDespite their economic importance and well-characterized domestication syndrome, the genomic impact of domestication and the identification of variants underlying the domestication traits in Cucurbita species (pumpkins and squashes) is currently lacking. Cucurbita argyrosperma, also known as cushaw pumpkin or silver-seed gourd, is a Mexican crop consumed primarily for its seeds rather than fruit flesh. This makes it a good model to study Cucurbita domestication, as seeds were an essential component of early Mesoamerican diet and likely the first targets of human-guided selection in pumpkins and squashes. We obtained population-level data using tunable Genotype by Sequencing libraries for 192 individuals of the wild and domesticated subspecies of C. argyrosperma across Mexico. We also assembled the first high-quality wild Cucurbita genome. Comparative genomic analyses revealed several structural variants and presence/absence of genes related to domestication. Our results indicate a monophyletic origin of this domesticated crop in the lowlands of Jalisco. We found evidence of gene flow between the domesticated and wild subspecies, which likely alleviated the effects of the domestication bottleneck. We uncovered candidate domestication genes that are involved in the regulation of growth hormones, plant defense mechanisms, seed development, and germination. The presence of shared selected alleles with the closely related species Cucurbita moschata suggests domestication-related introgression between both taxa.

Complete chloroplast genomes of Leptodermis scabrida complex: comparative genomic analyses and phylogenetic relationships

Gene ◽  
2021 ◽  
pp. 145715
Author(s):  
Ying Zhang ◽  
Zhengfeng Wang ◽  
Yanan Guo ◽  
Sheng Chen ◽  
Xianyi Xu ◽  
...  
Keyword(s):  
Phylogenetic Relationships ◽  
Comparative Genomic ◽  
Chloroplast Genomes ◽  
Genomic Analyses

scholarly journals Pseudomonas aeruginosa PAO 1 In Vitro Time–Kill Kinetics Using Single Phages and Phage Formulations—Modulating Death, Adaptation, and Resistance

Antibiotics ◽  
2021 ◽  
Vol 10 (7) ◽  
pp. 877
Author(s):  
Ana Mafalda Pinto ◽  
Alberta Faustino ◽  
Lorenzo M. Pastrana ◽  
Manuel Bañobre-López ◽  
Sanna Sillankorva
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Phage Therapy ◽  
Multidrug Resistant ◽  
Resistant Bacteria ◽  
Chronic Infections ◽  
Swarming Motility ◽  
Resistance Development ◽  
Healthcare Settings ◽  
Time Kill

Pseudomonas aeruginosa is responsible for nosocomial and chronic infections in healthcare settings. The major challenge in treating P. aeruginosa-related diseases is its remarkable capacity for antibiotic resistance development. Bacteriophage (phage) therapy is regarded as a possible alternative that has, for years, attracted attention for fighting multidrug-resistant infections. In this work, we characterized five phages showing different lytic spectrums towards clinical isolates. Two of these phages were isolated from the Russian Microgen Sextaphage formulation and belong to the Phikmvviruses, while three Pbunaviruses were isolated from sewage. Different phage formulations for the treatment of P. aeruginosa PAO1 resulted in diversified time–kill outcomes. The best result was obtained with a formulation with all phages, prompting a lower frequency of resistant variants and considerable alterations in cell motility, resulting in a loss of 73.7% in swimming motility and a 79% change in swarming motility. These alterations diminished the virulence of the phage-resisting phenotypes but promoted their growth since most became insensitive to a single or even all phages. However, not all combinations drove to enhanced cell killings due to the competition and loss of receptors. This study highlights that more caution is needed when developing cocktail formulations to maximize phage therapy efficacy. Selecting phages for formulations should consider the emergence of phage-resistant bacteria and whether the formulations are intended for short-term or extended antibacterial application.

scholarly journals Radiation-Inactivated Acinetobacter baumannii Vaccine Candidates

Vaccines ◽  
2021 ◽  
Vol 9 (2) ◽  
pp. 96
Author(s):  
Stephen J. Dollery ◽  
Daniel V. Zurawski ◽  
Elena K. Gaidamakova ◽  
Vera Y. Matrosova ◽  
John K. Tobin ◽  
...  
Keyword(s):  
Acinetobacter Baumannii ◽  
Treatment Options ◽  
Bacterial Pathogen ◽  
Multidrug Resistant ◽  
Bacterial Cells ◽  
Wound Infections ◽  
Protein Profiles ◽  
Vaccine Candidates ◽  
Rich Media ◽  
Life Threatening

Acinetobacter baumannii is a bacterial pathogen that is often multidrug-resistant (MDR) and causes a range of life-threatening illnesses, including pneumonia, septicemia, and wound infections. Some antibiotic treatments can reduce mortality if dosed early enough before an infection progresses, but there are few other treatment options when it comes to MDR-infection. Although several prophylactic strategies have been assessed, no vaccine candidates have advanced to clinical trials or have been approved. Herein, we rapidly produced protective whole-cell immunogens from planktonic and biofilm-like cultures of A. baumannii, strain AB5075 grown using a variety of methods. After selecting a panel of five cultures based on distinct protein profiles, replicative activity was extinguished by exposure to 10 kGy gamma radiation in the presence of a Deinococcus antioxidant complex composed of manganous (Mn2+) ions, a decapeptide, and orthophosphate. Mn2+ antioxidants prevent hydroxylation and carbonylation of irradiated proteins, but do not protect nucleic acids, yielding replication-deficient immunogenic A. baumannii vaccine candidates. Mice were immunized and boosted twice with 1.0 × 107 irradiated bacterial cells and then challenged intranasally with AB5075 using two mouse models. Planktonic cultures grown for 16 h in rich media and biofilm cultures grown in static cultures underneath minimal (M9) media stimulated immunity that led to 80–100% protection.

scholarly journals Candida auris and Carbapenemase-Producing Organism Prevalence in an Extended Stay Pediatric Hospital, Chicago, Illinois, 2019

2020 ◽  
Vol 41 (S1) ◽  
pp. s145-s146
Author(s):  
Kelly Walblay ◽  
Tristan McPherson ◽  
Elissa Roop ◽  
David Soglin ◽  
Ann Valley ◽  
...  
Keyword(s):  
The United States ◽  
Multidrug Resistant ◽  
Pediatric Hospital ◽  
Mechanical Ventilators ◽  
Candida Auris ◽  
Term Care ◽  
Healthcare Settings ◽  
High Acuity ◽  
Gastrostomy Tubes

Background:Candida auris and carbapenemase-producing organisms (CPO) are multidrug-resistant organisms that can colonize people for prolonged periods and can cause invasive infections and spread in healthcare settings, particularly in high-acuity long-term care facilities. Point-prevalence surveys (PPSs) conducted in long-term acute-care hospitals in the Chicago region identified median prevalence of colonization to be 31% for C. auris and 24% for CPO. Prevalence of C. auris colonization has not been described in pediatric populations in the United States, and limited data exist on CPO colonization in children outside intensive care units. The Chicago Department of Public Health (CDPH) conducted a PPS to assess C. auris and CPO colonization in a pediatric hospital serving high-acuity patients with extended lengths of stay (LOS). Methods: CDPH conducted a PPS in August 2019 in a pediatric hospital with extended LOS to screen for C. auris and CPO colonization. Medical devices (ie, gastrostomy tubes, tracheostomies, mechanical ventilators, and central venous catheters [CVC]) and LOS were documented. Screening specimens consisted of composite bilateral axillae and groin swabs for C. auris and rectal swabs for CPO testing. The Wisconsin State Laboratory of Hygiene tested all specimens. Real-time polymerase chain reaction (PCR) assays were used to detect C. auris DNA and carbapenemase genes: blaKPC, blaNDM, blaVIM, blaOXA-48, and blaIMP (Xpert Carba-R Assay, Cepheid, Sunnyvale, CA). All axillae and groin swabs were processed by PCR and culture to identify C. auris. For CPO, culture was only performed on PCR-positive specimens. Results: Of the 29 patients hospitalized, 26 (90%) had gastrostomy tubes, 24 (83%) had tracheostomies, 20 (69%) required mechanical ventilation, and 3 (10%) had CVCs. Also, 25 (86%) were screened for C. auris and CPO; 4 (14%) lacked parental consent and were not swabbed. Two rectal specimens were unsatisfactory, producing invalid CPO test results. Median LOS was 35 days (range, 1–300 days). No patients were positive for C. auris. From CPO screening, blaOXA-48 was detected in 1 patient sample, yielding a CPO prevalence of 3.4% (1 of 29). No organism was recovered from the blaOXA-48 positive specimen. Conclusions: This is the first documented screening of C. auris colonization in a pediatric hospital with extended LOS. Despite a high prevalence of C. auris and CPOs in adult healthcare settings of similar acuity in the region, C. auris was not identified and CPOs were rare at this pediatric facility. Additional evaluations in pediatric hospitals should be conducted to further understand C. auris and CPO prevalence in this population.Funding: NoneDisclosures: None

Evidence from comparative genomic analyses indicating that Lactobacillus-mediated irritable bowel syndrome alleviation is mediated by the conjugated linoleic acid synthesis

2021 ◽  
Author(s):  
Yang Liu ◽  
Wei Xiao ◽  
Leilei Yu ◽  
Fengwei Tian ◽  
Gang Wang ◽  
...  
Keyword(s):  
Irritable Bowel Syndrome ◽  
Linoleic Acid ◽  
Gut Microbiota ◽  
Acid Synthesis ◽  
Comparative Genomic ◽  
Low Grade ◽  
Genomic Analyses ◽  
Irritable Bowel ◽  
Low Grade Inflammation ◽  
Gut Microbiota Dysbiosis

Irritable bowel syndrome (IBS) is a chronic intestinal disorder accompanied by low-grade inflammation, visceral hypersensitivity, and gut microbiota dysbiosis. Several studies have indicated that Lactobacillus supplementation can help to alleviate...

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