55 Is whole genome sequencing necessary to exclude cross infection with Mycobacterium abscessus ST26 in paediatric cystic fibrosis patients?

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.

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

Future Microbiology ◽

10.2217/fmb.15.3 ◽

2015 ◽

Vol 10 (4) ◽

pp. 599-611 ◽

Cited By ~ 25

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

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148 Use of whole-genome sequencing to identify transmission of Pseudomonas aeruginosa between cystic fibrosis patients

Journal of Cystic Fibrosis ◽

10.1016/s1569-1993(14)60284-8 ◽

2014 ◽

Vol 13 ◽

pp. S84 ◽

Cited By ~ 1

Author(s):

N. Loman ◽

S. Manzoor ◽

J. Quick ◽

J.L. Fothergill ◽

S. Gossain ◽

...

Keyword(s):

Cystic Fibrosis ◽

Pseudomonas Aeruginosa ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Whole Genome

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Whole Genome Sequencing of Nontuberculous Mycobacterium (NTM) Isolates from Sputum and Environmental Specimens in Co-Habiting Patients with NTM Pulmonary Disease

10.21203/rs.2.17722/v1 ◽

2019 ◽

Author(s):

Jung-Ki Yoon ◽

Taek Soo Kim ◽

Jong-Il Kim ◽

Jae-Joon Yim

Keyword(s):

Whole Genome Sequencing ◽

Pulmonary Disease ◽

Genome Sequencing ◽

Genetic Distances ◽

Mycobacterium Abscessus ◽

Nontuberculous Mycobacterium ◽

Whole Genome ◽

Nucleotide Polymorphisms ◽

Single Nucleotide ◽

Next Generation Sequencing Ngs

Abstract Background : Nontuberculous mycobacterium (NTM) species are ubiquitous microorganisms. NTM pulmonary disease (NTM-PD) is caused not by human-to-human transmission but by independent environmental acquisition. However, recent studies using next-generation sequencing (NGS) have reported trans-continental spread of Mycobacterium abscessus among patients with cystic fibrosis. Results : We investigated NTM genomes through NGS to examine transmission patterns in three pairs of co-habiting NTM-PD patients who were suspected of patient-to-patient transmission. Three pairs of patients with NTM-PD co-habiting for at least 15 years were enrolled: a mother and a daughter with M. avium PD, a couple with M. intracellulare PD, and a second couple, one of whom was infected with M. intracellulare PD and the other of whom was infected with M. abscessus subsp. massiliense PD. Whole genome sequencing was performed using NTM colonies isolated from patients and environmental specimens. Genetic distances were estimated based on single nucleotide polymorphisms (SNPs) in the NTM genomes. Comparing SNPs in the consensus regions, the minimum pairwise SNP distances of NTM isolates derived from the two pairs of patients infected with the same NTM species were over 10,000. In phylogenetic analysis, the NTM isolates from patients with M. avium PD clustered with isolates from different environmental sources. Conclusions : In conclusion, considering the genetic distances between NTM strains, the likelihood of patient-to-patient transmission in pairs of co-habiting NTM-PD patients without overt immune deficiency is minimal.

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

Journal of Clinical Microbiology ◽

10.1128/jcm.00042-19 ◽

2019 ◽

Vol 57 (5) ◽

Cited By ~ 3

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.

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

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.00720-18 ◽

2018 ◽

Vol 62 (12) ◽

Cited By ~ 7

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.

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