An overview of various typing methods for clinical epidemiology of the emerging pathogen Stenotrophomonas maltophilia

Gherardi, Giovanni; Creti, Roberta; Pompilio, Arianna; Bonaventura, Giovanni Di

doi:10.1016/j.diagmicrobio.2014.11.005

Cited by 41 publications

(35 citation statements)

References 110 publications

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“…However, MLST enabled identification of the clonal groups associated with the strain STs, which facilitates their monitoring worldwide. In addition, MLST provides information about the population structure as well as the long-term global and evolution history (Gherardi et al, 2015). For instance in our study, the S. maltophilia strains isolated from blood samples were associated with five pulsotypes and three STs.…”

Section: Discussionmentioning

confidence: 66%

“…P3 (Env3 and Env4) and P7 (Env1, Env2, Env6, Env7, and Env8) were associated with ST304, whereas P2 (Env5 and Env9) was associated with ST24. These results indicate that PFGE remains the gold standard for DNA fingerprinting and exhibits substantial power for genetic and epidemiological discrimination in the evaluation of hospital outbreaks (Gherardi et al, 2015). However, MLST enabled identification of the clonal groups associated with the strain STs, which facilitates their monitoring worldwide.…”

Section: Discussionmentioning

confidence: 97%

“…S. maltophilia has high genetic diversity, as demonstrated with various typing methods (Gherardi et al, 2015;Pompilio et al, 2016;Alcaraz et al, 2018;Guvenir et al, 2018). However, in Mexico, 75-100% similarity has been obtained among strains collected from the same hospital source over a period of 7 years (Flores-Trevino et al, 2014).…”

Section: Discussionmentioning

confidence: 99%

“…Outbreaks of S. maltophilia strains have been associated with a high clonal diversity by pulsed-field gel electrophoresis (PFGE), and these analyses included investigations of the population structure of bacteria from cystic fibrosis patients (Nicoletti et al, 2011;Vidigal et al, 2014). PFGE has been used to analyze the profiles of the environmental reservoirs of epidemic clones, mainly in damp areas (taps, water reservoirs of humidifiers, assisted ventilation equipment, aspirators, and ventilators), and their modes of transmission (Valdezate et al, 2004;Gherardi et al, 2015). Outbreaks of S. maltophilia clinical strains have been associated with intensive care units (ICUs), emergency departments, respiratory units, oncology units, and surgery wards (Brooke, 2012).…”

Section: Introductionmentioning

confidence: 99%

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Molecular Epidemiology, Antibiotic Resistance, and Virulence Traits of Stenotrophomonas maltophilia Strains Associated With an Outbreak in a Mexican Tertiary Care Hospital

Cruz‐Córdova

Mancilla-Rojano

Luna-Pineda

et al. 2020

Front. Cell. Infect. Microbiol.

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Stenotrophomonas maltophilia, an emerging opportunistic pathogen, is widely distributed in the environment the resistance mechanisms, and virulence factors of this bacterium facilitate its dissemination in hospitals. This study aimed to characterize the molecular epidemiology of S. maltophilia strains associated with an outbreak in the Children's Hospital of México Federico Gómez (HIMFG). Twenty-one clinical S. maltophilia strains were recovered from cultures of blood and urine samples from 10 pediatric patients at the emergency department, and nine environmental S. maltophilia strains recovered from faucets in the same area were also included. Two of the 10 patients were related with health care-associated infections (HCAIs), and the other eight patients (8/10) were infected with environmental S. maltophilia strains. The outbreak was controlled by monthly disinfection of the faucets in the emergency department. Typing using pulsedfield gel electrophoresis (PFGE) showed a 52% genetic diversity with seven pulsotypes denoted P1-P7 among all S. maltophilia strains. Three pulsotypes (P2, P3, and P7) were identified among both the clinical and environmental S. maltophilia strains and associated with two type sequences (STs), namely, ST304 and ST24. Moreover, 80% (24/30) of the strains exhibited resistance mainly to tetracycline, 76.66% (23/30) to trimethoprimsulfamethoxazole, and 23.33% (7/30) to the extended-spectrum β-lactamase (ESBL) phenotype. The main resistance genes identified by multiplex PCR were sul1 in 100% (30/30), qnr in 86.66% (26/30), and intl1 in 80% (24/30) of the samples, respectively. Furthermore, the pilU, hlylII, and rmlA genes were identified in 96.6% (29/30), 90% (27/30), and 83.33% (25/30) of the samples, respectively. Additionally, 76.66% (23/30) of the S. maltophilia strains exhibited high swimming motility, 46.66% (14/30) showed moderate biofilm formation capacity, 43.33% (13/30) displayed moderate Cruz-Córdova et al. Outbreak Associated With Stenotrophomonas maltophilia twitching motility, and 20% (6/30) exhibited high adherence. The clinical S. maltophilia strains isolated from blood most strongly adhered to HTB-9 cells. In conclusion, the molecular epidemiology and some of the features such as resistance, and virulence genes associated with colonization patterns are pathogenic attributes that can promote S. maltophilia dissemination, persistence, and facilitate the outbreak that occurred in the HIMFG. This study supports the need for faucet disinfection as a control strategy for clinical outbreaks.

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Section: Discussionmentioning

confidence: 66%

Section: Discussionmentioning

confidence: 97%

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Molecular Epidemiology, Antibiotic Resistance, and Virulence Traits of Stenotrophomonas maltophilia Strains Associated With an Outbreak in a Mexican Tertiary Care Hospital

Cruz‐Córdova

Mancilla-Rojano

Luna-Pineda

et al. 2020

Front. Cell. Infect. Microbiol.

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“…There have also been studies demonstrating the importance of considering environmental samples in defining nosocomial transmission for some species. Environmental sampling, which can be quite labor-intensive and may be most appropriate in selected circumstances (26)(27)(28), was not included in the study by Mellmann et al…”

mentioning

confidence: 99%

Commentary: Next-Generation Epidemiology: Using Real-Time Core Genome Multilocus Sequence Typing To Support Infection Control Policy

Dekker

Frank

2016

J Clin Microbiol

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M ultilocus sequencing typing (MLST), introduced by Maiden and colleagues in 1998, has come to represent one of the most widely used and successful molecular methods for strainlevel classification of bacterial isolates (1). MLST schemes work by indexing sequence variation in a small set of housekeeping genes to a numerical classification system. Each novel sequence occurring at any of the selected loci is named as a unique numbered allele, and the profile of a given isolate is specified by the numbers representing the allelic composition. Each combination of alleles is assigned a unique sequence type (ST), and STs, in turn, can be grouped into higher levels of classification (2, 3). The ability of MLST to resolve closely related strains is limited in principle by the absolute sequence diversity present in the loci covered by the scheme and by the manner in which this sequence diversity distributes across the population to be classified. As MLST schemes require conserved PCR primer binding sites, the targets must also be sufficiently conserved so that the method works robustly, and this puts limits on the resolution of classical MLST (3). MLST schemes have now been developed for Ͼ100 genera and species, and continuously updated databases are maintained by the University of Oxford, United Kingdom (pubmlst.org), Imperial College London, London, United Kingdom (http://www.mlst.net/), and others.Classical MLST analysis, developed to be compatible with Sanger sequencing methods, is based on 400-to-500-nucleotide segments of (usually) seven genes, encompassing Ͻ0.2% of the bacterial genome in many cases (3). Advances in whole-genome sequencing (WGS) and the availability of a large number of assembled bacterial genomes have made possible new approaches to strain-and clone-level epidemiologic tracking of isolates, including the ability to apply MLST schemes on a genome-wide scale. Inference of clonal relationships from the comparison of wholegenome sequences for the purpose of epidemiologic investigations can involve a bit more subtlety than classical MLST analysis, however, and there are abundant opportunities for drawing incorrect conclusions. Perhaps the simplest of the many available approaches is that of direct-alignment-based (single nucleotide polymorphism [SNP]-based) phylogenetic analysis, often built on the underlying statistical assumptions of independent individual substitution events. Direct-alignment-based phylogenetic analyses have been used to study the population structures of bacterial outbreaks and to construct transmission maps in a variety of epidemiologic investigations (4-6). However, single recombination events, mobile genetic element insertions, or other horizontal genetic transfer events can result in multiple SNPs or more-complex rearrangements over a contiguously exchanged or interrupted region. Consequently, genome-wide direct-alignment methods, in addition to being computationally expensive, may result in the generation of incorrect tree topologies due to such rearrangements (7). Alternative...

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New Generation DNA Sequencing (NGS): Mining for Genes and the Potential of Extremophiles

Rekadwad

Gonzalez

2017

Microbial Applications Vol.1

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An overview of various typing methods for clinical epidemiology of the emerging pathogen Stenotrophomonas maltophilia

Cited by 41 publications

References 110 publications

Molecular Epidemiology, Antibiotic Resistance, and Virulence Traits of Stenotrophomonas maltophilia Strains Associated With an Outbreak in a Mexican Tertiary Care Hospital

Molecular Epidemiology, Antibiotic Resistance, and Virulence Traits of Stenotrophomonas maltophilia Strains Associated With an Outbreak in a Mexican Tertiary Care Hospital

Commentary: Next-Generation Epidemiology: Using Real-Time Core Genome Multilocus Sequence Typing To Support Infection Control Policy

New Generation DNA Sequencing (NGS): Mining for Genes and the Potential of Extremophiles

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