Whole genome sequencing of bacteria in cystic fibrosis as a model for bacterial genome adaptation and evolution

2014 ◽  
Vol 12 (3) ◽  
pp. 343-355 ◽  
Author(s):  
Poonam Sharma ◽  
Sushim Kumar Gupta ◽  
Jean-Marc Rolain
Keyword(s):  
Cystic Fibrosis ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Bacterial Genome ◽  
Whole Genome

scholarly journals High-Level Antibiotic Tolerance of a Clinically Isolated Enterococcus faecalis Strain

2020 ◽  
Vol 87 (1) ◽  
Author(s):  
Huan Gu ◽  
Sweta Roy ◽  
Xiaohui Zheng ◽  
Tian Gao ◽  
Huilin Ma ◽  
...  
Keyword(s):  
Cystic Fibrosis ◽  
Whole Genome Sequencing ◽  
Cystic Fibrosis Patient ◽  
Enterococcus Faecalis ◽  
Antibiotic Treatment ◽  
Genome Sequencing ◽  
Efflux Pump ◽  
Whole Genome ◽  
Content Type ◽  
High Level

ABSTRACT Bacteria can survive antibiotic treatment both by acquiring antibiotic resistance genes and through mechanisms of tolerance that are based on phenotypic changes and the formation of metabolically inactive cells. Here, we report an Enterococcus faecalis strain (E. faecalis UM001B) that was isolated from a cystic fibrosis patient and had no increase in resistance but extremely high-level tolerance to ampicillin, vancomycin, and tetracycline. Specifically, the percentages of cells that survived 3.5-h antibiotic treatment (at 100 μg · ml−1) were 25.4% ± 4.3% and 51.9% ± 4.0% for ampicillin and tetracycline, respectively; vancomycin did not exhibit any significant killing. Consistent with the changes in antibiotic susceptibility, UM001B was found to have reduced penetration of ampicillin and vancomycin and accumulation of tetracycline compared to the reference strain ATCC 29212. Based on whole-genome sequencing, four amino acid substitutions were identified in one of the tetracycline efflux pump repressors (TetRs), compared to ATCC 29212. Results of molecular simulations and experimental assays revealed that these mutations could lead to higher levels of tetracycline efflux activity. Consistently, replicating these mutations in Escherichia coli MG1655 increased its tolerance to tetracycline. Overall, these findings provide new insights into the development of multidrug tolerance in E. faecalis, which can facilitate future studies to better control enterococcal infections. IMPORTANCE Enterococcus faecalis represents a major group of pathogens causing nosocomial infections that are resistant to multiple classes of antibiotics. An important challenge associated with E. faecalis infection is the emergence of multidrug-tolerant strains, which have normal MICs but do not respond to antibiotic treatment. Here, we report a strain of E. faecalis that was isolated from a cystic fibrosis patient and demonstrated high-level tolerance to ampicillin, vancomycin, and tetracycline. Whole-genome sequencing revealed critical substitutions in one of the tetracycline efflux pump repressors that are consistent with the increased tolerance of E. faecalis UM001B to tetracycline. These findings provide new information about bacterial antibiotic tolerance and may help develop more effective therapeutics.

Evolutionary insight from whole-genome sequencing ofPseudomonas aeruginosafrom cystic fibrosis patients

2015 ◽  
Vol 10 (4) ◽  
pp. 599-611 ◽  
Author(s):  
Rasmus Lykke Marvig ◽  
Lea M Sommer ◽  
Lars Jelsbak ◽  
Søren Molin ◽  
Helle Krogh Johansen
Keyword(s):  
Cystic Fibrosis ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Whole Genome

scholarly journals Carriage of a Single Strain of NontoxigenicCorynebacterium diphtheriaebv. Belfanti (Corynebacterium belfantii) in Four Patients with Cystic Fibrosis

2019 ◽  
Vol 57 (5) ◽  
Author(s):  
Diane Pivot ◽  
Annlyse Fanton ◽  
Edgar Badell-Ocando ◽  
Marion Benouachkou ◽  
Karine Astruc ◽  
...  
Keyword(s):  
Cystic Fibrosis ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Antimicrobial Agents ◽  
Care Center ◽  
Whole Genome ◽  
Single Strain ◽  
Content Type ◽  
Microbiological Methods ◽  
Cross Transmission

ABSTRACTCystic fibrosis (CF) patients are commonly colonized by bacterial pathogens, which can induce persistent lung inflammation and may contribute to clinical deterioration. Colonization of CF patients and cross-transmission byCorynebacterium diphtheriaehave not been reported so far. The aim of this article was to investigate the possibility of a cross-transmission ofC. diphtheriaebiovar Belfanti between four patients of a CF center.C. diphtheriaebiovar Belfanti (now formally calledC. belfantii) isolates were collected from four patients in a single CF care center over a period of 6 years and analyzed by microbiological methods and whole-genome sequencing. Epidemiological links among patients were investigated. Ten isolates were collected from 4 patients. Whole-genome sequencing of one isolate from each patient showed that a single strain was shared among them. In addition, one patient was found to have the same strain in two consecutive samplings performed 9 months apart. The strain was nontoxigenic and was susceptible to most antimicrobial agents. Ciprofloxacin resistance was observed in one patient. The idea of transmission of the strain among patients was supported by the occurrence of same-day visits to the CF center. This study demonstrated colonization of CF patients byC. diphtheriaebiovar Belfanti (C. belfantii), and the data suggest persistence and transmission of a unique strain during at least 6 years in a single CF patient care center.

scholarly journals Emergence and Within-Host Genetic Evolution of Methicillin-ResistantStaphylococcus aureusResistant to Linezolid in a Cystic Fibrosis Patient

2018 ◽  
Vol 62 (12) ◽  
Author(s):  
Caroline Rouard ◽  
Fabien Garnier ◽  
Jeremy Leraut ◽  
Margaux Lepainteur ◽  
Lalaina Rahajamananav ◽  
...  
Keyword(s):  
Cystic Fibrosis ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Generation Time ◽  
Strong Increase ◽  
Whole Genome ◽  
Content Type ◽  
Mrsa Infection ◽  
Host Genetic ◽  
Mrsa Strains

ABSTRACTMethicillin-resistantStaphylococcus aureus(MRSA) infection has increased in recent years among cystic fibrosis (CF) patients. Linezolid (LZD) is one of the antistaphylococcal antibiotics widely used in this context. Although LZD resistance is rare, it has been described as often associated with long-term treatments. Thirteen MRSA strains isolated over 5 years from one CF patient were studied for LZD resistance emergence and subjected to whole-genome sequencing (WGS). Resistance emerged after three 15-day LZD therapeutic regimens over 4 months. It was associated with the mutation of G to T at position 2576 (G2576T) in all 5rrlcopies, along with a very high MIC (>256 mg/liter) and a strong increase in the generation time. Resistant strains isolated during the ensuing LZD therapeutic regimens and until 13 months after LZD stopped harbored only 3 or 4 mutatedrrlcopies, associated with lower MICs (8 to 32 mg/liter) and low to moderate generation time increases. Despite these differences, whole-genome sequencing allowed us to determine that all isolates, including the susceptible one isolated before LZD treatment, belonged to the same lineage. In conclusion, LZD resistance can emerge rapidly in CF patients and persist without linezolid selective pressure in colonizing MRSA strains belonging to the same lineage.

scholarly journals Whole-genome sequencing to identify transmission of Mycobacterium abscessus between patients with cystic fibrosis: a retrospective cohort study

The Lancet ◽  
2013 ◽  
Vol 381 (9877) ◽  
pp. 1551-1560 ◽  
Author(s):  
Josephine M Bryant ◽  
Dorothy M Grogono ◽  
Daniel Greaves ◽  
Juliet Foweraker ◽  
Iain Roddick ◽  
...  
Keyword(s):  
Cystic Fibrosis ◽  
Cohort Study ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Retrospective Cohort Study ◽  
Retrospective Cohort ◽  
Mycobacterium Abscessus ◽  
Whole Genome

scholarly journals Whole-Genome Sequencing of Three Clonal Clinical Isolates of B. cenocepacia from a Patient with Cystic Fibrosis

PLoS ONE ◽  
2015 ◽  
Vol 10 (11) ◽  
pp. e0143472 ◽  
Author(s):  
Ruth R. Miller ◽  
Trevor J. Hird ◽  
Patrick Tang ◽  
James E. A. Zlosnik
Keyword(s):  
Cystic Fibrosis ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Clinical Isolates ◽  
Whole Genome

scholarly journals 1256. New Acquisitions of ET-12 Burkholderia cenocepacia in Adults With Cystic Fibrosis: Role of Whole Genome Sequencing in Outbreak Investigation

2018 ◽  
Vol 5 (suppl_1) ◽  
pp. S383-S383 ◽  
Author(s):  
Ana C Blanchard ◽  
Manal Tadros ◽  
Lin Tang ◽  
Matthew Muller ◽  
Theodore Spilker ◽  
...  
Keyword(s):  
Cystic Fibrosis ◽  
Hospital Admission ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Hospital Admissions ◽  
Burkholderia Cenocepacia ◽  
Infection Prevention And Control ◽  
Snp Analysis ◽  
Whole Genome ◽  
Nucleotide Polymorphisms

Abstract Background Transmission of Burkholderia cenocepacia ET-12 strain (ET-12Bc) can cause epidemics in the cystic fibrosis (CF) population. The Toronto Adult CF center currently follows 500 patients; 20% have infection with B. cepacia complex (BCC), including 48 patients infected with ET-12Bc. The center adheres to the 2013 infection prevention and control guidelines and patients are also segregated by clinics. Despite this, there have been 11 new acquisitions of ET-12Bc since 2008. The objective of this study was to describe the investigation of an ET-12Bc outbreak in CF patients, using whole-genome sequencing (WGS). Methods Investigations included multilocus sequence typing (MLST) and WGS of 34 isolates (11 new ET-12Bc acquisitions, 18 isolates of known ET-12Bc patients (including all patients with hospital admissions that overlapped with new acquisitions), four isolates from CF patients in the USA and the J2315 reference strain). Each of the seven MLST alleles from ET12Bc strain J2315 was downloaded from PubMLST and used to “Blast” each of the 16 WGS databases. WGS was done using 150 bp paired-end runs on an Illumina HiSeq4000. Single nucleotide polymorphisms (SNPs) between the newly sequenced strains and J2315 were profiled. Results Ten patients had a hospital admission within the 2 months preceding their first ET-12Bc positive sputum culture, except for one in whom ET-12Bc was detected 12 months following hospital admission. In all isolates, the seven alleles (atpD, gltB, gyrB, recA, lepA, phaC and trpB) matched 100% to sequence type 28 and clonal complex 31, and were identical to J2315. WGS SNP analysis confirmed that transmission occurred from known cases on the unit in 10/11 (90.9%) patients. To date, 8/11 patients with new acquisitions have died (median survival of 95 days). Conclusion Our investigations found epidemiological evidence suggestive of ET-12Bc transmission on the CF unit, which was confirmed by MLST and WGS SNP analysis. Compared with MLST, WGS SNP analysis had better discriminatory power and was well correlated with the identified epidemiological links between patients. Recognition of ET-12Bc transmission with associated high mortality rates has led to a change in our hospital policy. ET-12Bc positive patients will no longer be cared for on the same unit as ET-12Bc negative patients with CF. Disclosures All authors: No reported disclosures.

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