Epidemiology of transmissible diseases: Array hybridization and next generation sequencing as universal nucleic acid-mediated typing tools

Dunne, W. Michael; Pouseele, Hannes; Monecke, Stefan; Ehricht, Ralf; Belkum, Alex van

doi:10.1016/j.meegid.2017.09.019

Cited by 20 publications

(11 citation statements)

References 166 publications

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“…In recent years, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) has been applied as a wide-range technique for bacterial identification [ 36 ]. Microarray systems are well-established tools for rapid genotypic characterization of bacteria and identification of resistance and virulence-associated determinants [ 37 ]. The data can be obtained in a single experiment with the benefit of saving time and money [ 38 – 40 ].…”

Section: Introductionmentioning

confidence: 99%

Antimicrobial resistance in Enterobacteriaceae from healthy broilers in Egypt: emergence of colistin-resistant and extended-spectrum β-lactamase-producing Escherichia coli

et al. 2018

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BackgroundPoultry remains one of the most important reservoir for zoonotic multidrug resistant pathogens. The global rise of antimicrobial resistance in Gram-negative bacteria is of reasonable concern and demands intensified surveillance.MethodsIn 2016, 576 cloacal swabs were collected from 48 broiler farms located in five governorates in northern Egypt. Isolates of Enterobacteriaceae could be cultivated on different media and were identified by MALDI-TOF MS and PCR. Escherichia coli isolates were genotyped by DNA-microarray-based assays. The antimicrobial susceptibility to 14 antibiotics was determined and resistance-associated genes were detected. The VITEK-2 system was applied for phenotypical confirmation of extended-spectrum β-lactamase-producing isolates. The determination of colistin resistance was carried out phenotypically using E-test and genotypically using PCR for detection of the mcr-1 gene.ResultsOut of 576 samples, 72 representatives of Enterobacteriaceae were isolated and identified as 63 E. coli (87.5%), 5 Enterobacter cloacae (6.9%), 2 Klebsiella pneumoniae (2.8%) and 2 Citrobacter spp. (2.8%). Seven out of 56 cultivated E. coli (12.5%) were confirmed as ESBL-producing E. coli and one isolate (1.8%) as ESBL/carbapenemase-producing E. coli. Five out of 63 E. coli isolates (7.9%) recovered from different poultry flocks were phenotypically resistant to colistin and harboured mcr-1 gene.ConclusionsThis is the first study reporting colistin resistance and emergence of multidrug resistance in Enterobacteriaceae isolated from healthy broilers in the Nile Delta region, Egypt. Colistin-resistant E. coli in poultry is of public health significance. The global rise of ESBL- and carbapenemase-producing Gram-negative bacteria demands intensified surveillance. ESBL-producing E. coli in poultry farms in Egypt are of major concern that emphasizes the possibility of spread of such strains to humans. The results also reinforce the need to develop strategies and to implement specific control procedures to reduce the use of antibiotics.

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Section: Introductionmentioning

confidence: 99%

Antimicrobial resistance in Enterobacteriaceae from healthy broilers in Egypt: emergence of colistin-resistant and extended-spectrum β-lactamase-producing Escherichia coli

et al. 2018

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“…With two large core genomic replacements being present in one single isolate, we assume that such-large scale horizontal gene transfers might be more common in S. aureus than previously perceived, and that the resolution of MLST with seven markers is not high enough to identify all chimeric strains. However, the combination and interaction of microarray-based assays as screening tool and NGS allows reliable identification and detailed analysis of such strains [45].…”

Section: Discussionmentioning

confidence: 99%

Molecular investigations on a chimeric strain of Staphylococcus aureus sequence type 80

et al. 2020

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A PVL-positive, methicillin-susceptible Staphylococcus aureus was cultured from pus from cervical lymphadenitis of a patient of East-African origin. Microarray hybridisation assigned the isolate to clonal complex (CC) 80 but revealed unusual features, including the presence of the ORF-CM14 enterotoxin homologue and of an ACME-III element as well as the absence of etD and edinB. The isolate was subjected to both, Illumina and Nanopore sequencing allowing characterisation of deviating regions within the strain´s genome. Atypical features of this strain were attributable to the presence of two genomic regions that originated from other S. aureus lineages and that comprised, respectively, 3% and 1.4% of the genome. One deviating region extended from walJ to sirB. It comprised ORF-CM14 and the ACME-III element. A homologous but larger fragment was also found in an atypical S. aureus CC1/ST567 strain whose lineage might have served as donor of this genomic region. This region itself is a chimera comprising fragments from CC1 as well as fragments of unknown origin. The other deviating region comprised the region from htsB to ecfA2, i.e., another 3% of the genome. It was very similar to CC1 sequences. Either this suggests an incorporation of CC1 DNA into the study strain, or alternatively a recombination event affecting "canonical" CC80. Thus, the study strain bears witness of several recombination events affecting supposedly core genomic genes. Although the exact mechanism is not yet clear, such chimerism seems to be an additional pathway in the evolution of S. aureus. This could facilitate also a transmission of virulence and resistance factors and therefore offer an additional evolutionary advantage.

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“…Some STs corresponds to a single RT, other STs corresponds to multiple RTs, and RT not always may predict the ST ( Griffiths et al, 2010 ). While MLST and PCR ribotyping were similar in discriminatory abilities, both methods are useful for large-scale analysis, and combined strain nomenclature is often based on more than one typing, none of these can discriminate between genetically monomorphic lineages, such as those from the epidemic C. difficile 027 RT/ST1 clade ( Kumar et al, 2016 ; Michael Dunne et al, 2018 ).…”

Section: Introductionmentioning

confidence: 99%

“…However, WGS-based typing of C. difficile , based on single nucleotide variants (SNVs) and on allelic profiling of core genome genes, named core genome MLST (cgMLST), is still hampered by the lack of standardized nomenclature ( Bletz et al, 2018 ). Despite this, using WGS of C. difficile seems to be of practical importance in clinical settings as exemplified by several reports ( Griffiths et al, 2010 ; Bletz et al, 2018 ; Kociolek et al, 2018 ; Mancini et al, 2018 ; Michael Dunne et al, 2018 ; Pightling et al, 2018 ; Aoki et al, 2019 ; Berger et al, 2019 ; Janezic and Rupnik, 2019 ; Kong et al, 2019 ; Cho et al, 2020 ). As recently reported, WGS better differentiates C. difficile relapse from reinfection than do definitions based on timing of recurrence ( Cho et al, 2020 ).…”

Section: Introductionmentioning

confidence: 99%

High Prevalence of Genetically Related Clostridium Difficile Strains at a Single Hemato-Oncology Ward Over 10 Years

et al. 2020

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Aims: Clostridium difficile ( C. difficile ) infection (CDI) is the main cause of healthcare-associated infectious diarrhea. We used whole-genome sequencing (WGS) to measure the prevalence and genetic variability of C. difficile at a single hemato-oncology ward over a 10 year period. Methods: Between 2008 and 2018, 2077 stool samples were obtained from diarrheal patients hospitalized at the Department of Lymphoma; of these, 618 were positive for toxin A/B. 140 isolates were then subjected to WGS on Ion Torrent PGM sequencer. Results: 36 and 104 isolates were recovered from 36 to 46 patients with single and multiple CDIs, respectively. Of these, 131 strains were toxigenic. Toxin gene profiles tcdA(+);tcdB(+);cdtA/cdtB(+) and tcdA(+);tcdB(+);cdtA/cdtB(-) were identified in 122 and nine strains, respectively. No isolates showed reduced susceptibility to metronidazole and vancomycin. All tested strains were resistant to ciprofloxacin, and 72.9, 42.9, and 72.9% of strains were resistant to erythromycin, clindamycin, or moxifloxacin, respectively. Multi-locus sequence typing (MLST) identified 23 distinct sequence types (STs) and two unidentified strains. Strains ST1 and ST42 represented 31 and 30.1% of all strains tested, respectively. However, while ST1 was detected across nearly all years studied, ST42 was detected only from 2009 to 2011. Conclusion: The high proportion of infected patients in 2008–2011 may be explained by the predominance of more transmissible and virulent C. difficile strains. Although this retrospective study was not designed to define outbreaks of C. difficile , the finding that most isolates exhibited high levels of genetic relatedness suggests nosocomial acquisition.

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Epidemiology of transmissible diseases: Array hybridization and next generation sequencing as universal nucleic acid-mediated typing tools

Cited by 20 publications

References 166 publications

Antimicrobial resistance in Enterobacteriaceae from healthy broilers in Egypt: emergence of colistin-resistant and extended-spectrum β-lactamase-producing Escherichia coli

Antimicrobial resistance in Enterobacteriaceae from healthy broilers in Egypt: emergence of colistin-resistant and extended-spectrum β-lactamase-producing Escherichia coli

Molecular investigations on a chimeric strain of Staphylococcus aureus sequence type 80

High Prevalence of Genetically Related Clostridium Difficile Strains at a Single Hemato-Oncology Ward Over 10 Years

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