Whole genome sequencing for predicting clarithromycin resistance in Mycobacterium abscessus

Lipworth, Samuel; Hough, Natasha; Leach, Laura; Morgan, Marcus; Jeffrey, Katie; Andersson, Monique; Robinson, Esther; Smith, Grace; Crook, Derrick W.; Peto, Tim; Walker, Timothy M

doi:10.1101/251918

Cited by 6 publications

(8 citation statements)

References 46 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…These difficulties are similar to those seen in Legionella pneumophila outbreaks where the majority of cases can belong to only a few sequence types [26]. L. pneumophila can also display different scales of genetic diversity within different sequence or genotypes and so it is also recognised that a single SNV threshold cut-off will not provide sufficient discriminatory power [27]. When using WGS to infer relatedness in M. abscessus there has previously been an attempt to find an absolute threshold which can rule in or rule out strains into a transmission event.…”

Section: Discussionmentioning

confidence: 93%

“…This study has shown that whole genome sequencing of M. abscessus isolates can determine sub-species, identify previously reported AMR associated mutations and provide common typing definitions in a single workflow. This single method can replace the multiple existing molecular assays used in clinical microbiology laboratories to provide the same information and could be used to predict novel resistance variants [27]. We used the WGS data to investigate the likelihood of cross-transmission and found 43 (69%) patients had unique isolates that did not cluster with other patients.…”

Section: Discussionmentioning

confidence: 99%

See 1 more Smart Citation

Cross-transmission is not the source of newMycobacterium abscessusinfections in a multi-centre cohort of cystic fibrosis patients

Doyle

Rubio

Dixon

et al. 2019

Preprint

View full text Add to dashboard Cite

BackgroundMycobacterium abscessusis an extensively drug resistant pathogen that causes pulmonary disease particularly in cystic fibrosis (CF) patients. Identifying direct patient-to-patient transmission ofM. abscessusis critically important in directing infection control policy for the management of risk in CF patients. A variety of clinical labs have used molecular epidemiology to investigate transmission. However there is still conflicting evidence as to howM. abscessusis acquired and whether cross-transmission occurs. Recently labs have applied whole-genome sequencing (WGS) to investigate this further and in this study we investigate whether WGS can reliably identify cross-transmission inM. abscessus.MethodsWe retrospectively sequenced the whole genomes of 145M. abscessusisolates from 62 patients seen at four hospitals in two countries over 16 years.ResultsWe have shown that a comparison of a fixed number of core single nucleotide variants (SNVs) alone cannot be used to infer cross-transmission inM. abscessusbut does provide enough information to replace multiple existing molecular assays. We detected one episode of possible direct patient-to-patient transmission in a sibling pair. We found that patients acquired uniqueM. abscessusstrains even after spending considerable time on the same wards with otherM. abscessuspositive patients.ConclusionsThis novel analysis has demonstrated that the majority of patients in this study have not acquiredM. abscessusthrough direct patient-patient transmission or a common reservoir. Tracking transmission using WGS will only realise its full potential with proper environmental screening as well as patient sampling.Key pointsWhole genome sequencing should replace current molecular typing used routinely in clinical microbiology laboratories.Patient-to-patient spread ofM. abscessusis not common.Environmental screening may provide a better understanding acquisition ofM. abscessusinfections.

show abstract

Section: Discussionmentioning

confidence: 93%

Section: Discussionmentioning

confidence: 99%

Cross-transmission is not the source of newMycobacterium abscessusinfections in a multi-centre cohort of cystic fibrosis patients

Doyle

Rubio

Dixon

et al. 2019

Preprint

View full text Add to dashboard Cite

show abstract

“…Several investigations have recently built models for predicting AMR phenotypes from WGS data. To date, the most common approach has relied on using a curated reference set of genes and polymorphisms that are implicated in AMR (25)(26)(27)(28)(29)(30)(31)(32)(33). This reference-guided approach best predicts susceptibility and resistance when organisms are well studied and the AMR mechanisms are known.…”

mentioning

confidence: 99%

Using Machine Learning To Predict Antimicrobial MICs and Associated Genomic Features for Nontyphoidal Salmonella

et al. 2019

View full text Add to dashboard Cite

NontyphoidalSalmonellaspecies are the leading bacterial cause of foodborne disease in the United States. Whole-genome sequences and paired antimicrobial susceptibility data are available forSalmonellastrains because of surveillance efforts from public health agencies. In this study, a collection of 5,278 nontyphoidalSalmonellagenomes, collected over 15 years in the United States, was used to generate extreme gradient boosting (XGBoost)-based machine learning models for predicting MICs for 15 antibiotics. The MIC prediction models had an overall average accuracy of 95% within ±1 2-fold dilution step (confidence interval, 95% to 95%), an average very major error rate of 2.7% (confidence interval, 2.4% to 3.0%), and an average major error rate of 0.1% (confidence interval, 0.1% to 0.2%). The model predicted MICs with noa prioriinformation about the underlying gene content or resistance phenotypes of the strains. By selecting diverse genomes for the training sets, we show that highly accurate MIC prediction models can be generated with less than 500 genomes. We also show that our approach for predicting MICs is stable over time, despite annual fluctuations in antimicrobial resistance gene content in the sampled genomes. Finally, using feature selection, we explore the important genomic regions identified by the models for predicting MICs. To date, this is one of the largest MIC modeling studies to be published. Our strategy for developing whole-genome sequence-based models for surveillance and clinical diagnostics can be readily applied to other important human pathogens.

show abstract

“…This is perhaps due to unknown mechanism that renders the isolate susceptible to clarithromycin. Extending the search to look for additional mutations did not show erm(41) C19T and hence evidence of susceptibility is lacking [23]. The fth discordant result was resistant on day 3 of susceptibility testing indicating an acquired resistance to clarithromycin, but had no mutations found on positions 2058 of rrl with sequencing.…”

Section: Discussionmentioning

confidence: 99%

A Real-Time PCR Assay for Rapid Identification of Inducible and Acquired Clarithromycin Resistance in Mycobacterium abscessus

Sharma

Janella

et al. 2020

Preprint

View full text Add to dashboard Cite

Background: Mycobacterium abscessus is a rapidly growing mycobacteria involved in severe infections of the lung, skin, or soft tissue. Macrolides such as clarithromycin are the recommended first line drugs for treatment of M. abscessus infections. However, M. abscessus has dual mechanisms of resistance to macrolides, making treatment by macrolides difficult. A functional erm(41) gene confers for inducible resistance while acquired mutations on the 23S rRNA rrl gene confer for constitutive resistance. Methods: We have developed a real-time PCR assay to detect both inducible and acquired resistance to clarithromycin, and compared the results to traditional erm(41) and rrl sequencing and phenotypic susceptibility testing using Sensititre™ plates. Results: Of the total 126 M. abscessus isolates tested, truncated erm(41) was found in 23/126 (18.3%) of the samples, 27/126 (21.4%) had a T28C mutation in erm(41), and 2/126 (1.6%) had an acquired A2058C mutation in rrl. The phenotypic results correlated with the expected sequencing results in 121/126 samples (96%). Phenotypic testing compared to real-time PCR resolved 2 of these discrepancies by showing the existence of both erm(41) alleles in the isolates that sequencing missed. One culture was found to be mixed with two M. abscessus subsp. as per hsp65 sequencing and 2 isolates had discordance between molecular and phenotypic results. It was presumed that 3 isolates showed discrepancy between sequencing and real-time PCR, but one culture was mixed and other 2 detected both alleles by real-time PCR leading to 100% concordance when compared to sequencing. Conclusion: In conclusion, real-time PCR is more accurate for detection of both acquired and induced clarithromycin resistance, specifically when mixed genic profiles are present in a sample.

show abstract

Whole genome sequencing for predicting clarithromycin resistance in Mycobacterium abscessus

Cited by 6 publications

References 46 publications

Cross-transmission is not the source of newMycobacterium abscessusinfections in a multi-centre cohort of cystic fibrosis patients

Cross-transmission is not the source of newMycobacterium abscessusinfections in a multi-centre cohort of cystic fibrosis patients

Using Machine Learning To Predict Antimicrobial MICs and Associated Genomic Features for Nontyphoidal Salmonella

A Real-Time PCR Assay for Rapid Identification of Inducible and Acquired Clarithromycin Resistance in Mycobacterium abscessus

Contact Info

Product

Resources

About