Identification of microorganisms grown on chromogenic media by MALDI-TOF MS

Lüthje, Petra; Pranada, Arthur B.; Carruthers-Lay, Duncan; Desjardins, Marc; Gaillot, Olivier; Wareham, David W.; Ciesielczuk, Holly; Özenci, Volkan

doi:10.1016/j.mimet.2017.03.001

Cited by 10 publications

(5 citation statements)

References 11 publications

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“…Analysis was carried out with the Biotyper 3.1 software (Bruker Daltonik GmbH). The following interpretation of results was performed according to the manufacturer's recommendation: A score of ≥ 2.3 represented reliable species-level identification; a score of 2.0-2.29 represented probable species level identification; a score of 1.7-1.9 represented probable genuslevel identification; and a score ≤ 1.7 was considered an unreliable identification [31]. Pure cultures were stored appropriately in cryo-tubes at -80 °C (Mast Diagnostica GmbH, Reinfeld, Germany).…”

Section: Maldi-tof Msmentioning

confidence: 99%

Whole genome sequencing of Salmonella enterica serovars isolated from humans, animals, and the environment in Lagos, Nigeria

et al. 2023

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Background Salmonella infections remain an important public health issue worldwide. Some serovars of non-typhoidal Salmonella (NTS) have been associated with bloodstream infections and gastroenteritis, especially in children in Sub-Saharan Africa with circulating S. enterica serovars with drug resistance and virulence genes. This study identified and verified the clonal relationship of Nigerian NTS strains isolated from humans, animals, and the environment. Methods In total, 2,522 samples were collected from patients, animals (cattle and poultry), and environmental sources between December 2017 and May 2019. The samples were subjected to a standard microbiological investigation. All the isolates were identified using Microbact 24E, and MALDI-TOF MS. The isolates were serotyped using the Kauffmann-White scheme. Antibiotic susceptibility testing was conducted using the disc diffusion method and the Vitek 2 compact system. Virulence and antimicrobial resistance genes, sequence type, and cluster analysis were investigated using WGS data. Results Forty-eight (48) NTS isolates (1.9%) were obtained. The prevalence of NTS from clinical sources was 0.9%, while 4% was recorded for animal sources. The serovars identified were S. Cotham (n = 17), S. Give (n = 16), S. Mokola (n = 6), S. Abony (n = 4), S. Typhimurium (n = 4), and S. Senftenberg (n = 1). All 48 Salmonella isolates carried intrinsic and acquired resistant genes such as aac.6…Iaa, mdf(A), qnrB, qnrB19 genes and golT, golS, pcoA, and silP, mediated by plasmid Col440I_1, incFIB.B and incFII. Between 100 and 118 virulence gene markers distributed across several Salmonella pathogenicity islands (SPIs), clusters, prophages, and plasmid operons were found in each isolate. WGS revealed that strains of each Salmonella serovar could be assigned to a single 7-gene MLST cluster, and strains within the clusters were identical strains and closely related as defined by the 0 and 10 cgSNPs and likely shared a common ancestor. The dominant sequence types were S. Give ST516 and S. Cotham ST617. Conclusion We found identical Salmonella sequence types in human, animal, and environmental samples in the same locality, which demonstrates the great potential of the applied tools to trace back outbreak strains. Strategies to control and prevent the spread of NTS in the context of one’s health are essential to prevent possible outbreaks.

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Section: Maldi-tof Msmentioning

confidence: 99%

Whole genome sequencing of Salmonella enterica serovars isolated from humans, animals, and the environment in Lagos, Nigeria

et al. 2023

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“…Analysis was carried out with the Biotyper 3.1 software (Bruker Daltonik GmbH). Interpretation of results was performed according to the manufacturer's recommendation: score of ≥ 2.3 represented reliable species level identification; score 2.0-2.29, probable species level identification; score 1.7-1.9, probable genus level identification, and score ≤ 1.7 was considered an unreliable identification (Lüthje et al, 2017).…”

Section: Identification By Maldi-tof Msmentioning

confidence: 99%

Antimicrobial Resistance Genes Associated with Enterococci from Poultry in Egypt, First Reporting of mecA in Enterococcus from Poultry Source

Ahmed¹,

Hotzel²,

Neubauer³

et al. 2020

Adv. Anim. Vet. Sci.

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P oultry has been reported to carry increasingly antibiotic-resistant bacteria in its digestive tract. In the past, enterococci of the gut of humans and animals were considered to be common and harmless with little or no clinical relevance (Fisher and Phillips, 2009; Marshall and Levy, 2011). Meanwhile, they are the second and third most important etiologic agents of urinary tract infections and nosocomial bacteremia in humans, respectively. In intensive care units enterococci may be found in 14.3% of patients (Papadimitriou-Olivgeris et al., 2014). The most common species isolated from clinical samples of humans are Enterococcus (E.) faecalis and E. faecium (Panesso et al., 2008). One of the main reasons that enterococci can survive in the hospital environment is their intrinsic resistance to some research Article Abstract | Little information available for the Egyptian setting. 117 cloacal swabs were collected from diseased poultry located in 6 districts in Egypt. Isolates were identified using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). The antibiotic susceptibility testing of Enterococcus faecium and Enterococcus gallinarum isolates against 22 antibiotics was performed with the MICRONAUT system for Gram-positive bacteria. The presence of 12 resistance-associated genes (tetK, tetL, tetM, tetS, tetO, erm(B), msrC, aac6-aph2, vanA, vanB, vanC1 and mecA) was investigated by PCR. Thirty one Enterococcus isolates have been detected, Enterococcus faecium (n=22) and Enterococcus gallinarum (n=9) strains were isolated. All Enterococcus faecium and Enterococcus gallinarum isolates were multidrug-resistant. More than 15% of Enterococcus faecium isolates were resistant to vancomycin. Resistance rates to other antibiotics ranged between 31.8% for teicoplanin to 86.4% for penicillin G, respectively. Enterococcus gallinarum isolates showed a resistance rate of 100% to cefoxitin, ceftaroline, clindamycin, daptomycin, erythromycin, gentamicin and oxacillin. The resistance genes most often found were msrC, erm(B), aac6-aph2 and mecA. The vanB gene was identified in two Enterococcus faecium isolates from which one was resistant to vancomycin whereas vanC1 was detected in 6 Enterococcus faecium and Enterococcus gallinarum isolates. Tetracycline resistance-associated genes (tetK, tetL, tetM, tetO and tetS) were found in 25 isolates whereas mecA was detected in nine isolates. The study is the first report for mecA gene in Enterococcus. The development of resistance to antibiotics in poultry production needs special attention and investigation. The usage of antimicrobials in Egypt should follow WHO and OIE recommendations.

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“…Further taxonomic classification and identification of S. aureus can be done via agglutination assays or (commercially available) biochemical reactivity (e.g., API strips). Using combinations of simple phenotypic tests has been shown to allow for the adequate distinction of MSSA and MRSA ( Verroken et al, 2016 ; Lüthje et al, 2017 ; Rees and Barr, 2017 ; Ábrók et al, 2018 ). Recent immunochromatographic methods such as the BinaxNOW (Alere, Scarborough, ME, United States) and the Clearview Exact PBP2a assay (Alere, Scarborough, ME, United States) have acquired a good position in the clinical laboratory given their modest price, rapidity, and good sensitivity and specificity (e.g., Kong et al, 2014 ).…”

Section: Culture-based Detection Of Mssa and Mrsamentioning

confidence: 99%

Laboratory-Based and Point-of-Care Testing for MSSA/MRSA Detection in the Age of Whole Genome Sequencing

Belkum

Rochas

2018

Front. Microbiol.

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Staphylococcus aureus is an opportunistic pathogen of animals and humans that is capable of both colonizing and infecting its eukaryotic host. It is frequently detected in the clinical microbiology routine laboratory. S. aureus is capable of acquiring antibiotic resistance traits with ease and, given its rapid global dissemination, resistance to meticillin in S. aureus has received extensive coverage in the popular and medical press. The detection of meticillin-resistant versus meticillin-susceptible S. aureus (MRSA and MSSA) is of significant clinical importance. Detection of meticillin resistance is relatively straightforward since it is defined by a single determinant, penicillin-binding protein 2a’, which exists in a limited number of genetic variants carried on various Staphylococcal Cassette Chromosomes mec. Diagnosis of MRSA and MSSA has evolved significantly over the past decades and there has been a strong shift from culture-based, phenotypic methods toward molecular detection, especially given the close correlation between the presence of the mec genes and phenotypic resistance. This brief review summarizes the current state of affairs concerning the mostly polymerase chain reaction-mediated detection of MRSA and MSSA in either the classical laboratory setting or at the point of care. The potential diagnostic impact of the currently emerging whole genome sequencing (WGS) technology will be discussed against a background of diagnostic, surveillance, and infection control parameters. Adequate detection of MSSA and MRSA is at the basis of any subsequent, more generic antibiotic susceptibility testing, epidemiological characterization, and detection of virulence factors, whether performed with classical technology or WGS analyses.

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Identification of microorganisms grown on chromogenic media by MALDI-TOF MS

Cited by 10 publications

References 11 publications

Whole genome sequencing of Salmonella enterica serovars isolated from humans, animals, and the environment in Lagos, Nigeria

Whole genome sequencing of Salmonella enterica serovars isolated from humans, animals, and the environment in Lagos, Nigeria

Antimicrobial Resistance Genes Associated with Enterococci from Poultry in Egypt, First Reporting of mecA in Enterococcus from Poultry Source

Laboratory-Based and Point-of-Care Testing for MSSA/MRSA Detection in the Age of Whole Genome Sequencing

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