High-throughput whole-genome sequencing to dissect the epidemiology of Acinetobacter baumannii isolates from a hospital outbreak

Lewis, Thomas P.; Loman, Nicholas J.; Bingle, Lewis; Jumaa, P.; Weinstock, George M.; Mortiboy, D.; Pallen, Mark J.

doi:10.1016/j.jhin.2010.01.012

Cited by 138 publications

(104 citation statements)

References 24 publications

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“…And their recent origins allow easier reconstructions of their history than is possible with most other microbes. The recent recognition that some lineages have high mutation rates, almost as high as those of some RNA viruses, means that real time evolution can be used for epidemiological [77] and forensic [78] tracking. I anticipate a veritable flood of publications using comparative genomics for such purposes in the near future because the technological challenges are now relatively minor.…”

Section: Discussionmentioning

confidence: 99%

Insights from genomic comparisons of genetically monomorphic bacterial pathogens

Achtman

2012

Phil. Trans. R. Soc. B

116

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Some of the most deadly bacterial diseases, including leprosy, anthrax and plague, are caused by bacterial lineages with extremely low levels of genetic diversity, the so-called 'genetically monomorphic bacteria'. It has only become possible to analyse the population genetics of such bacteria since the recent advent of high-throughput comparative genomics. The genomes of genetically monomorphic lineages contain very few polymorphic sites, which often reflect unambiguous clonal genealogies. Some genetically monomorphic lineages have evolved in the last decades, e.g. antibiotic-resistant Staphylococcus aureus, whereas others have evolved over several millennia, e.g. the cause of plague, Yersinia pestis. Based on recent results, it is now possible to reconstruct the sources and the history of pandemic waves of plague by a combined analysis of phylogeographic signals in Y. pestis plus polymorphisms found in ancient DNA. Different from historical accounts based exclusively on human disease, Y. pestis evolved in China, or the vicinity, and has spread globally on multiple occasions. These routes of transmission can be reconstructed from the genealogy, most precisely for the most recent pandemic that was spread from Hong Kong in multiple independent waves in 1894.

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Section: Discussionmentioning

confidence: 99%

Insights from genomic comparisons of genetically monomorphic bacterial pathogens

Achtman

2012

Phil. Trans. R. Soc. B

116

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“…Many hospitals worldwide already appreciate the power of WGS analysis, having integrated it into several published investigations [5][6][7] . The advantages of WGS are most accessible through the use of short-read sequencing as exemplified by the Illumina platform.…”

Section: Short-read Sequencing In Nosocomial Settingsmentioning

confidence: 99%

From isolate to answer: how whole genome sequencing is helping us rapidly characterise nosocomial bacterial outbreaks

Roberts¹

2017

Microbiol. Aust.

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The occurrence of highly resistant bacterial pathogens has risen in recent years, causing immense strain on the healthcare industry. Hospital-acquired infections are arguably of most concern, as bacterial outbreaks in clinical settings provide an ideal environment for proliferation among vulnerable populations. Understanding these outbreaks beyond what can be determined with traditional clinical diagnostics and implementing these new techniques routinely in the hospital environment has now become a major focus. This brief review will discuss the three main whole genome sequence techniques available today, and how they are being used to further discriminate bacterial outbreaks in nosocomial settings.In recent decades, society has witnessed a rapid and alarming increase in highly resistant pathogens causing human disease, to the extent that the World Health Organization (WHO) has labelled antimicrobial resistance (AMR) as, 'a serious threat to global public health' 1 . The challenge of AMR is arguably greatest in health-care facilities, which present a unique environment for pathogens to proliferate and infect those most vulnerable. Once within the hospital, these pathogens can be readily spread due to the close proximity of patients and the mass of shared vectors in the envi- Short-read sequencing in nosocomial settingsMany hospitals worldwide already appreciate the power of WGS analysis, having integrated it into several published investigations [5][6][7] . The advantages of WGS are most accessible through the use of short-read sequencing as exemplified by the Illumina platform. In addition to being both high-throughput and cost-effective, analysis tools specific for short-read sequencing are well established, making it a useful and reliable research tool.One of the main advantages of WGS is the ability to detect single nucleotide variants (SNV). Detection of SNV can allow prediction of phenotypic changes, such as enhanced resistant to antibiotics (for example, via the loss of a functional outer membrane porin cause by indels or point mutations [8][9][10] ). When coupled with metadata, SNV data can also be used to predict transmission pathways by inferring transmission directionality via the accumulation of SNV over time. Short-read data are also routinely used to determine presence or absence of genes using read mapping or short-read assembly techniques.Carbapenem-resistant Enterobacteriaceae (CRE) are among the most prevalent clinically relevant organisms, designated as an urgent threat by the Centers for Disease Control and Prevention 11 .Snitkin et al. 12 were amongst the first to apply WGS to identify transmission pathways in a CRE outbreak that could not be resolved using traditional epidemiological investigations alone. Recently, we have used WGS to investigate a suspected CRE outbreak in a Brisbane hospital 13 . Using Illumina short-read sequencing, we were able to determine transmission of a carbapenemaseproducing Enterobacter cloacae sequence type (ST) 90 strain within the intensive care unit (ICU) be...

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“…It is important to stress that these mutations have never been reported to induce polymyxins resistance in accordance to the phenotypic susceptibility tests (MIC ≤ 1 mg/ml). [18,19] Sulfonamide resistance in gram-negative bacteria is dependent on genes encoding dihydropteroate-synthase sul1 and sul2. [32] In our analysis we found that both ST195 isolates are characterized by the sul2 sulphonamide resistance determinant, while the ST281 strain presented the sul1 gene.…”

Section: Resistomamentioning

confidence: 99%

“…[16] To trace HAI it is necessary to use the best high resolution typing approach that unequivocally identifies Acinetobacter species and their clonality, in order to search for the index case and to define the strains relatedness to avoid nosocomial cross transmission. [17][18][19] This study described the use of whole genome sequencing (WGS) by Ion Torrent Personal Genome Machine to analyze Acinetobacter-calcoaceticusbaumannii complex strains isolated in a possible outbreak occurring in a Intensive Care Unit of a pediatric hospital. De novo assembled sequences from 13 strains were analyzed to define strains clonality and Resistoma.…”

Section: Introductionmentioning

confidence: 99%

The whole genome sequencing of Acinetobacter-calcoaceticus-baumannii complex strains involved in suspected outbreak in an Intensive Care Unit of a pediatric hospital

Ugolotti

Marco

Bandettini

et al. 2016

JHA

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Background: To analyze the genetic characteristics of Acinetobacter-calcoaceticus-baumannii complex strains isolated in suspected outbreak in a Intensive Care Unit of a pediatric hospital in order to promptly stop the dissemination of this dangerous strain. Methods: This study described the use of whole genome obtained by Next Generation Sequencing to define the clonality of 13 Acinetobacter-calcoaceticus-baumannii complex strains and to study their Resistoma. This was required because Acinetobacter baumannii is known to be resistant to desiccation and to disinfectants and is difficult to treat and eradicate. Thus, this microorganism is a major problem that demands a rigorous outbreak monitoring program to prevent and control the spread of the dangerous strain. Results: The first result of our analysis has been to describe precisely the characteristics of isolates involved in the nosocomial infection, reduce the dimension of the more problematic isolates sustaining the outbreak and promptly facilitate the control of the strains diffusion. Indeed, our study indicated that among the 13 Acinetobacter baumannii-calcoacteticus complex strains, identified by biochemical and mass-spectrometry assays, 7 were Acinetobacter baumannii, 5 were Acinetobacter calcoaceticus, and one was Acinetobacter haemolyticus. The analysis of clonality of Acinetobacter baumannii indicated that three strains of ST744 were identical for > 99.8% among them and thus have sustained an outbreak in Intensive Care Unit. All personnel and possible environment samples were also monitored and all the procedures aimed to the prevention and control of Hospital Acquired Infections (HAI), have been strictly enforced by the Hospital Infection Control Committee. This gave the possibility to trace a strain from an environmental contamination characterized by high degree of clonality with the one isolated from a patient. On the contrary Acinetobacter calcoaceticus strains were different from each other and thus they were not responsible for any outbreak. The Resistoma analysis indicated a correspondence between phenotypic and genotypic characteristics of analyzed strains. Conclusions: Next Generation Sequencing is an appropriate technique to trace the circulation of dangerous strains sustaining nosocomial infections. The combination of the high resolution genotyping together with the definition of the antibiotic genetic determinants and the precise species identification make this technique a useful tool employed as standard practice to control HAI.

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High-throughput whole-genome sequencing to dissect the epidemiology of Acinetobacter baumannii isolates from a hospital outbreak

Cited by 138 publications

References 24 publications

Insights from genomic comparisons of genetically monomorphic bacterial pathogens

Insights from genomic comparisons of genetically monomorphic bacterial pathogens

From isolate to answer: how whole genome sequencing is helping us rapidly characterise nosocomial bacterial outbreaks

The whole genome sequencing of Acinetobacter-calcoaceticus-baumannii complex strains involved in suspected outbreak in an Intensive Care Unit of a pediatric hospital

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