Revisiting the taxonomy of the genus Elizabethkingia using whole-genome sequencing, optical mapping, and MALDI-TOF, along with proposal of three novel Elizabethkingia species: Elizabethkingia bruuniana sp. nov., Elizabethkingia ursingii sp. nov., and Elizabethkingia occulta sp. nov.

Abstract Background A number of episodes of nosocomial Agrobacterium spp. bacteremia (two cases per year) were observed at Bern University Hospital, Switzerland, from 2015 to 2017. This triggered an outbreak investigation. Methods Cases of Agrobacterium spp. bacteremias that occurred between August 2011 and February 2017 were investigated employing line lists, environmental sampling, rapid protein- (MALDI-TOF MS), and genome-based typing (pulsed field gel electrophoresis and whole genome sequencing) of the clinical isolates. Results We describe a total of eight bacteremia episodes due to A. radiobacter (n = 2), Agrobacterium genomovar G3 (n = 5) and A. pusense (n = 1). Two tight clusters were observed by WGS typing, representing the two A. radiobacter isolates (cluster I, isolated in 2015) and four of the Agrobacterium genomovar G3 isolates (cluster II, isolated in 2016 and 2017), suggesting two different point sources. The epidemiological investigations revealed two computer tomography (CT) rooms as common patient locations, which correlated with the two outbreak clusters. MALDI-TOF MS permitted faster evaluation of strain relatedness than DNA-based methods. High resolution WGS-based typing confirmed the MALDI-TOF MS clustering. Conclusions We report clinical and epidemiological characteristics of two outbreak clusters with Agrobacterium. spp. bacteremia likely acquired during CT contrast medium injection and highlight the use of MALDI-TOF MS as a rapid tool to assess relatedness of rare gram-negative pathogens in an outbreak investigation.

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Ornithobacterium rhinotracheale: MALDI-TOF MS and Whole Genome Sequencing Confirm That Serotypes K, L and M Deviate from Well-Known Reference Strains and Numerous Field Isolates

Microorganisms ◽

10.3390/microorganisms9051006 ◽

2021 ◽

Vol 9 (5) ◽

pp. 1006

Author(s):

Merima Alispahic ◽

Lukas Endler ◽

Michael Hess ◽

Claudia Hess

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

Whole Genome ◽

Maldi Tof Ms ◽

Maldi Tof ◽

Identification And Characterization ◽

Reference Strains ◽

Ornithobacterium Rhinotracheale ◽

Tof Ms

Ornithobacterium rhinotracheale is one of the most important bacterial agents of respiratory diseases in poultry. For correct identification and characterization of this fastidious bacterium, reliable diagnostic tools are essential. Still, phenotypic tests are used to identify O. rhinotracheale and serotyping is the most common method for characterization, despite known drawbacks and disadvantages such as divergent results, cross-reactivity between strains, or the non-typeability of strains. The intention of the present study was to evaluate MALDI-TOF MS and whole genome sequencing for the identification and characterization of O. rhinotracheale. For this purpose, a selection of 59 well-defined reference strains and 47 field strains derived from outbreaks on Austrian turkey farms were investigated by MALDI-TOF MS. The field strains originated from different geographical areas in Austria with some of the isolates derived from multiple outbreaks on farms within a year, or recurrent outbreaks over several years. MALDI-TOF MS proved a suitable method for identification of O. rhinotracheale to genus or species level except for 3 strains representing serotypes M, K and F. Phylogenetic analysis showed that most strains grouped within one cluster even though they were comprised of different serotypes, while serotypes F, K, and M clearly formed a different cluster. All field isolates from turkey farms clustered together, independent of the origin of the isolates, e.g., geographical area, multiple outbreaks within a year or recurrent outbreaks over several years. Whole genome sequencing of serotype M, K and F strains confirmed the extraordinary status and deviation from known fully-sequenced strains due to a lack of sequence similarity. This was further confirmed by alignments of single genes (16S-RNA and rpoB) and multilocus sequence typing although the demarcation was less obvious. Altogether, the results indicate that these three serotypes belong to a different species than O. rhinotracheale, and might even be members of multiple new species.

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Lactobacillus fermentum 90 TC-4 taxonomic status confirmation using whole genome sequencing and MALDI TOF mass spectrum

Russian Journal of Genetics ◽

10.1134/s1022795416090039 ◽

2016 ◽

Vol 52 (9) ◽

pp. 907-913 ◽

Cited By ~ 2

Author(s):

I. V. Belova ◽

A. G. Tochilina ◽

I. V. Solovyeva ◽

E. I. Efimov ◽

I. S. Gorlova ◽

...

Keyword(s):

Mass Spectrum ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Taxonomic Status ◽

Lactobacillus Fermentum ◽

Whole Genome ◽

Maldi Tof

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Methicillin-Resistant and Methicillin-Susceptible Staphylococcus from Vervet Monkeys (Chlorocebus sabaeus) in Saint Kitts

Antibiotics ◽

10.3390/antibiotics10030290 ◽

2021 ◽

Vol 10 (3) ◽

pp. 290

Author(s):

Andreas Hoefer ◽

Filip Boyen ◽

Amy Beierschmitt ◽

Arshnee Moodley ◽

Marilyn C. Roberts ◽

...

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

Mobile Genetic Elements ◽

Pcr Analysis ◽

Whole Genome ◽

Vervet Monkeys ◽

Methicillin Resistant ◽

Genetic Elements ◽

Maldi Tof ◽

Staphylococcus Spp

Antimicrobial resistance has been described in all ecosystems, including wildlife. Here we investigated the presence of methicillin-resistant and susceptible staphylococci in both colony-born and wild vervet monkeys (Chlorocebus sabaeus). Through selective isolation, PCR, MALDI-TOF, and whole-genome sequencing, methicillin-resistant and susceptible Staphylococcus spp. isolated from vervet monkeys were characterized. We obtained putatively methicillin-resistant staphylococci from 29 of the 34 nasal samples collected. Strains were identified by MALDI-TOF analysis. Staphylococcus cohnii (n = 15) was the most commonly isolated species, while nine other species were isolated one or two times. PCR analysis indicated that eight [28%] strains were mecA positive. The whole-genome sequencing [WGS] included eight methicillin-resistant strains (S. epidermidis (n = 2), S. cohnii (n = 3), S. arlettae (n = 2) and S. hominis (n = 1)), nine additional S. cohnii strains and two strains that could not be identified by MALDI-TOF, but genetically characterized as one S. cohnii and one S. warneri. Different resistance genes carried by different mobile genetic elements, mainly blaZ (n = 10) and tet(K) (n = 5) were found, while msr(A), cat, fosB, dfrG, erm(C), mph(C) and str were identified in one to three strains. Phylogenetic analysis of the S. cohnii strains based on SNPs indicated four clusters associated with colony born or wild. In addition, one singleton S. cohnii isolated did not form a separate group and clustered within other S. cohnii strains submitted to the NCBI. In this study, we demonstrated the presence of AMR and mobile genetic elements to both colony-born and wild vervet monkeys. We also identified a previously undescribed prevalence of S. cohnii in the nasal flora of these monkeys, which merits further investigation.

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Evaluating transmission dynamics of Shiga toxin-producing E. coli (STEC) in New Zealand cattle from farm to slaughter using PCR/MALDI-TOF and genome sequencing

Applied and Environmental Microbiology ◽

10.1128/aem.02907-20 ◽

2021 ◽

Author(s):

A. Springer Browne ◽

Anne C. Midwinter ◽

Helen Withers ◽

Adrian L. Cookson ◽

Patrick J. Biggs ◽

...

Keyword(s):

New Zealand ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Shiga Toxin ◽

Whole Genome ◽

Meat Processing ◽

Serious Illness ◽

E Coli ◽

Maldi Tof ◽

Processing Plants

Cattle are asymptomatic carriers of Shiga toxin-producing E. coli (STEC) that can cause serious illness or death in humans. In New Zealand, contact with cattle feces and living near cattle populations are known risk factors for human STEC infection. Contamination of fresh meat with STECs also has the potential for rejection of consignments by importing countries. We used a combination of PCR/MALDI-TOF and whole genome sequencing to evaluate the presence and transmission of STEC on farms and in processing plants to better understand the potential pathways for human exposure and thus mitigate risk. Animal and environmental samples (n=2,580) were collected from six farms and three meat processing plants in New Zealand during multiple sampling sessions in spring of 2015 and 2016. PCR/MALDI-TOF analysis revealed 6.2% were positive for ‘Top 7’ STEC. ‘Top 7’ STEC were identified in all sample sources (n=17) tested. A marked increase in ‘Top 7’ STEC prevalence was observed between calf hides on-farm (6.3% prevalence), and calf hides at processing plants (25.1% prevalence). Whole genome sequencing was performed on ‘Top 7’ STEC bacterial isolates (n=40). Analysis of STEC O26 (n=25 isolates) revealed relatively low genetic diversity on individual farms, consistent with the presence of a resident strain disseminated within the farm environment. Public health efforts should focus on minimizing human contact with fecal material on farms and during handling, transport and slaughter of calves. Meat processing plants should focus on minimizing cross-contamination between the hides of calves in a cohort during transport, lairage and slaughter. Importance Cattle are asymptomatic carriers of Shiga toxin-producing E. coli (STEC), which can cause serious illness or death in humans. Contact with cattle feces and living near cattle are known risk factors for human STEC infection. This study evaluated STEC carriage in young calves and the farm environment with an in-depth evaluation of six farms and three meat processing plants over two years. An advanced molecular detection method and whole genome sequencing were used to provide a detailed evaluation of the transmission of STEC both within and between farms. The study revealed widespread STEC contamination within the farm environment, but no evidence of recent spread between farms. Contamination of young dairy calf hides increased following transport and holding at meat processing plants. The elimination of STEC in farm environments may be very difficult given the multiple transmission routes; interventions should be targeted at decreasing fecal contamination of calf hides during transport, lairage, and processing.

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