Comparison of pulsed-field gel electrophoresis and whole-genome-sequencing-based typing confirms the accuracy of pulsed-field gel electrophoresis for the investigation of local Pseudomonas aeruginosa outbreaks

Martak, Daniel; Meunier, Alexandre; Sauget, Marlène; Cholley, Pascal; Thouverez, Michelle; Bertrand, Xavier; Valot, Benoı̂t; Hocquet, Didier

doi:10.1016/j.jhin.2020.06.013

Cited by 14 publications

(16 citation statements)

References 24 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“… 30 However, some studies have confirmed that PFGE is still appropriate for the investigation of local outbreaks and is more economic than WGS. 31 …”

Section: Discussionmentioning

confidence: 99%

Outbreak of Multidrug-Resistant OXA-232-Producing ST15 Klebsiella pneumoniae in a Teaching Hospital in Wenzhou, China

Jia¹,

Zhang²,

Ye³

et al. 2021

IDR

View full text Add to dashboard Cite

Background OXA-232-producing carbapenem-resistant Klebsiella pneumoniae (CRKP) has the potential to become the “third epidemic” of carbapenem-resistant Klebsiella strain after KPC-2 and NDM in China. We investigated the first outbreak of CRKP in the First Affiliated Hospital of Wenzhou Medical University. Methods We collected 610 clinical isolates of CRKP from the First Affiliated Hospital of Wenzhou Medical University between January 2019 and September 2020 and screened them by Polymerase Chain Reaction (PCR). The multilocus sequence typing and pulsed-field gel electrophoresis were used to determine the genetic relatedness of the strains. The antimicrobial susceptibility test was performed to determine the drug resistance of the clinical isolates. The molecular mechanism underlying carbapenem resistance was elucidated by performing PCR and conjugation experiments. The virulence potential of the strains was determined by the string test, detection of virulence-associated genes and capsular serotypes, and Galleria mellonella larval infection model. Results Between September 2019 and May 2020, 26 OXA-232-producing CRKP were obtained from 12 patients in our hospital. Ten patients were hospitalized in the intensive care units (ICU) and the overall mortality of the inpatients involved in the outbreak was 50% (6/12). Epidemiological investigations reported that all the OXA-232-producing CRKP strains belonged to the sequence type ST15 and can be clonally transmitted among the inpatients in the ICU. All the strains had low virulence and were resistant to commonly used clinical antibiotics except for ceftazidime/avibactam, colistin, and tigecycline. The OXA-232-producing CRKP was sensitive to triclosan and chlorhexidine, and its eradication from our hospital can be achieved by the use of disinfectants in the ICU. Conclusion In our study, OXA-232-producing CRKP isolates appeared to be clonally transmitted and the sequence type ST15 was responsible for the outbreak. Therefore, effective measurements for the infection control of CRKP are urgently needed to prevent its epidemic in the nearby region in the future.

show abstract

“… 30 However, some studies have confirmed that PFGE is still appropriate for the investigation of local outbreaks and is more economic than WGS. 31 …”

Section: Discussionmentioning

confidence: 99%

Outbreak of Multidrug-Resistant OXA-232-Producing ST15 Klebsiella pneumoniae in a Teaching Hospital in Wenzhou, China

Jia¹,

Zhang²,

Ye³

et al. 2021

IDR

View full text Add to dashboard Cite

show abstract

“…Using the Pulse Gel Electrophoresis (PFGE) methodology, the spread of identical bacterial strains among COVID-19 patients in the Department of Anesthesiology, Resuscitation and Intensive Care was revealed. PFGE was considered to be a gold standard for bacterial typing for a long time and even now, in cases when it is redundant to use whole-genome sequencing (e.g., evaluation of potential clonal spread within local outbreak as in our case), this method is still suitable and useful [ 41 ]. Studies, which were performed in this department in the previous years (2011–2021) using PFGE, did not reveal significant clonal spread of bacterial pathogens [ 42 , 43 , 44 ].…”

Section: Discussionmentioning

confidence: 99%

Bacterial Resistance to Antibiotics and Clonal Spread in COVID-19-Positive Patients on a Tertiary Hospital Intensive Care Unit, Czech Republic

Doubravská

Sedláková²,

Fišerová³

et al. 2022

Antibiotics

View full text Add to dashboard Cite

This observational retrospective study aimed to analyze whether/how the spectrum of bacterial pathogens and their resistance to antibiotics changed during the worst part of the COVID-19 pandemic (1 November 2020 to 30 April 2021) among intensive care patients in University Hospital Olomouc, Czech Republic, as compared with the pre-pandemic period (1 November 2018 to 30 April 2019). A total of 789 clinically important bacterial isolates from 189 patients were cultured during the pre-COVID-19 period. The most frequent etiologic agents causing nosocomial infections were strains of Klebsiella pneumoniae (17%), Pseudomonas aeruginosa (11%), Escherichia coli (10%), coagulase-negative staphylococci (9%), Burkholderia multivorans (8%), Enterococcus faecium (6%), Enterococcus faecalis (5%), Proteus mirabilis (5%) and Staphylococcus aureus (5%). Over the comparable COVID-19 period, a total of 1500 bacterial isolates from 372 SARS-CoV-2-positive patients were assessed. While the percentage of etiological agents causing nosocomial infections increased in Enterococcus faecium (from 6% to 19%, p < 0.0001), Klebsiella variicola (from 1% to 6%, p = 0.0004) and Serratia marcescens (from 1% to 8%, p < 0.0001), there were significant decreases in Escherichia coli (from 10% to 3%, p < 0.0001), Proteus mirabilis (from 5% to 2%, p = 0.004) and Staphylococcus aureus (from 5% to 2%, p = 0.004). The study demonstrated that the changes in bacterial resistance to antibiotics are ambiguous. An increase in the frequency of ESBL-positive strains of some species (Serratia marcescens and Enterobacter cloacae) was confirmed; on the other hand, resistance decreased (Escherichia coli, Acinetobacter baumannii) or the proportion of resistant strains remained unchanged over both periods (Klebsiella pneumoniae, Enterococcus faecium). Changes in pathogen distribution and resistance were caused partly due to antibiotic selection pressure (cefotaxime consumption increased significantly in the COVID-19 period), but mainly due to clonal spread of identical bacterial isolates from patient to patient, which was confirmed by the pulse field gel electrophoresis methodology. In addition to the above shown results, the importance of infection prevention and control in healthcare facilities is discussed, not only for dealing with SARS-CoV-2 but also for limiting the spread of bacteria.

show abstract

“…For example, within 1 month in 2020 cgMLST schemes have been published for Campylobacter jejuni (Hsu et al ., 2020), Leptospira spp. (Grillová and Picardeau, 2020), Pseudomonas aeruginosa (De Sales et al ., 2020; Martak et al ., 2020; Stanton et al ., 2020), Streptococcus mutans (Liu et al ., 2020) and Vibrio cholera (Liang et al ., 2020). cgMLST schemes consist of a fixed set of conserved genome‐wide genes.…”

Section: Bacterial Strain Typing: Sequence‐based Typing Methodsmentioning

confidence: 99%

“…cgMLST schemes consist of a fixed set of conserved genome‐wide genes. The three cgMLST schemes for P. aeruginosa consist of 3831 (Martak et al ., 2020); 2653 (De Sales et al ., 2020) or 4400 core genes (Stanton et al ., 2020) which probably will give rise to confusion in the next years when P. aeruginosa genotypes will be published that are based on different typing schemes. A cgMLST scheme is fixed and agreed upon number of genes for each species or group of closely related species.…”

Section: Bacterial Strain Typing: Sequence‐based Typing Methodsmentioning

confidence: 99%

“…Since the recognition sites of most restriction endonucleases are randomly distributed in the chromosome, fragment patterns represent unbiased genomic fingerprints and can thus be exploited to assign clonal relationships between strains (Grothues and Tümmler, 1991). A single enzyme restriction pattern is less discriminatory than genome sequencing (Martak et al, 2020), but PFGE analysis can be refined by the addition of more single and double digests with further rare-cutting restriction endonucleases. Agarose-embedded high-molecular weight DNA is stable when stored in Tris-EDTA buffer at 4 C. In our hands, 20 year old agarose plugs still produced identical fragment fingerprints.…”

Section: Bacterial Strain Typing: Anonymous Fingerprinting Techniquesmentioning

confidence: 99%

See 1 more Smart Citation

Molecular epidemiology in current times

Tümmler

2020

Environmental Microbiology

View full text Add to dashboard Cite

Motivated to find options for prevention or intervention, molecular epidemiology aims to identify the host and microbial factors that determine the transmission, manifestation and progression of infectious disease. The genotyping of cultivatable bacterial strains is performed by either anonymous fingerprinting techniques or sequence-based exploration of variable genomic sites. Multilocus sequence typing of housekeeping genes and allele profiling of the core genome have become standard techniques of bacterial strain typing that may be supplemented by whole genome sequencing to explore all single nucleotide variants and/or the composition of the accessory genome. Next, novel protocols to investigate host and microbiome based upon smart third generation sequencing technologies are being developed for an effective surveillance, rapid diagnosis and real-time tracking of infectious diseases.

show abstract

Comparison of pulsed-field gel electrophoresis and whole-genome-sequencing-based typing confirms the accuracy of pulsed-field gel electrophoresis for the investigation of local Pseudomonas aeruginosa outbreaks

Cited by 14 publications

References 24 publications

Outbreak of Multidrug-Resistant OXA-232-Producing ST15 Klebsiella pneumoniae in a Teaching Hospital in Wenzhou, China

Outbreak of Multidrug-Resistant OXA-232-Producing ST15 Klebsiella pneumoniae in a Teaching Hospital in Wenzhou, China

Bacterial Resistance to Antibiotics and Clonal Spread in COVID-19-Positive Patients on a Tertiary Hospital Intensive Care Unit, Czech Republic

Molecular epidemiology in current times

Contact Info

Product

Resources

About