The Slizovskiy Laboratory of Infectious
Diseases and Antimicrobial Resistance
Research (LIDAAR)
Journal articles
[J22] Bravo J., Slizovskiy, I.B., Bonin, N., Oliva, M., Noyes, N., Boucher, C. The TELCoMB protocol for high-sensitivity detection of ARG-MGE colocalizations in complex microbial communities. Current Protocols. 2024.4:e70031; https://doi.org/10.1002/cpz1.70031
[J21] Slizovskiy, I.B., Bonin, N., Bravo, J.E., Ferm, P.M., Singer, J., Boucher, C., Noyes, N.R. Factors impacting target-enriched long-read sequencing of resistomes and mobilomes. Genome Research. 2024.34:1-13; https://doi.org/10.1101/gr.279226.124
[J20] Gaire, T.N., Odland, C.A., Bingzhou, Z., Slizovskiy, I.B., Jorgenson, B., Wehri, T., Meneguzzi, M., Wass, B., Schuld, J., Hanson, D., Doster, E., Singer, J., Cannon, J., Asmus, A., Ray, T., Dee, S., Nerem, J., Davies, P., Noyes, N.R. Slaughtering process impact microbial communities and antimicrobial resistance genes of pig carcasses. Science of the Total Environment. 2024.946:10;
https://doi.org/10.1016/j.scitotenv.2024.174394
[J19] Makau,
D.N.*, Slizovskiy,
I.B.*, Obanda, V., Noyes, N.R., Johnson, J.R., Oakes, M., Travis,
D., VanderWaal, K., Omondi, G.P. Factors influencing usage of antimicrobial
drugs among pastoralists of Kenya. Tropical animal health and production.
2022.54:332; https://doi.org/10.1007/s11250-022-03326-0
[J18] Slizovskiy,
I.B.*, Oliva, M.*, Settle, J.K., Zyskina, L.V.,
Boucher, C., Noyes, N.R. Targeted-enrichment and long-read sequencing (TELSeq)
contextualizes antibiotic resistance genes in metagenomes. Microbiome.
2022;10:185; https://doi.org/10.1186/s40168-022-01368-y
[J17] Alanko J.N., Slizovskiy, I.B.,
Lokshtanov D., Gagie T., Noyes, N.R., Boucher, C. SYOTTI: Scalable bait
design for DNA enrichment. Bioinformatics. 2022.38:i177-i184; https://doi.org/10.1093/bioinformatics/btac226.
[J16] Nayar G., Terrizzano, I., Seabolt, E.,
Agarwal, A., Boucher C., Ruiz J., Slizovskiy, I.B., Kaufman, J.H.,
Noyes, N.R. ggMOB: Elucidation of genomic conjugative features
and associated cargo genes across bacterial genera using genus-genus
mobilization networks. Front. Genet. 2022; (13);1024577; https://doi.org/10.3389/fgene.2022.1024577
[J15] Marini, S., Oliva, M., Slizovskiy, I.B., Das,
R.A., Noyes, N.R., Kahveci, T., Boucher, C., Prosperi, M. AMR-meta: A
k-mer and metafeature approach to classify antimicrobial resistance from
high-throughput short-read metagenomics data. GigaScience. 2022;11(giac029):1-11.;
https://doi.org/10.1093/gigascience/giac029
[J14] Noyes, N.R., Slizovskiy, I.B.,
Singer, R.S. Beyond antimicrobial use: A framework for prioritizing
antimicrobial resistance interventions. Annu. Rev. Anim. Biosci.
2021;9:313332.
[J13] Marini S., Slizovskiy, I.B.,
Noyes, N., Boucher C., Prosperi M. Learning antimicrobial resistance
through secondary structure of protein variants. Front. Genet. 2021;
(12); https://doi.org/10.3389/fgene.2021.564186
[J12] Dean, C., Slizovskiy, I.B.,
Crone, K.K., Pfennig, A.X., Heinz, B.J., Caixeta, L.S., Noyes, N.R.
Sampling considerations for conducting large-scale microbial ecology
studies of cow udder epithelium. J. Dairy Sci. 2021;104:644-661.
[J11] Kaufman, J.H., Terrizzano, I., Nayar, G.,
Seabolt, E., Agarwal, A., Slizovskiy, I.B., Noyes, N.R.
Integrative and Conjugative Elements (ICE) and associated cargo genes
within and across hundreds of bacterial genera. bioRxiv 2020.04.07.030320; https://doi.org/10.1101/2020.04.07.030320
[J10] Slizovskiy, I.B., Mukherjee, K.,
Dean, C.J., Boucher, C., Noyes, N. R. Mobilization of antibiotic
resistance: Are current approaches for colocalizing resistomes and
mobilomes useful? Front. Microbiol. 2020; (11) https://doi.org/10.3389/fmicb.2020.01376
[J9] Slizovskiy,
I.B., Conti, L.A., Trufan S.J., Reif, J.S., Lamers, V.T., Stowe, M.H.,
Dziura, J., Rabinowitz P.M. Reported health conditions in animals residing near
natural gas wells in southwestern Pennsylvania. J. Environ. Sci. Health,
Part A, 2015;50(5): 473-481, Special Issue.
[J8] Shen, H., Heuzey, E., Mori, D., Colangelo,
C., Chung, L., Bruce, C., Slizovskiy, I.B., Booth, C.J.,
Kreisel, D., Goldstein, D.R. Haptoglobin enhances cardiac transplant
rejection. Circulation research. 2015; 116: 1670-1679.
[J7] Rabinowitz, P.M., Slizovskiy, I.B.,
Lamers, V., Trufan, S.J., Holford, T.R., Dziura, J.D., Peduzzi, P.N., Kane
M.J., Reif, J.S., Weiss, T.R., Stowe, M.H. Proximity to natural gas wells
and reported health status: Results of a household survey in Washington
County, Pennsylvania. Environmental Health Perspectives. 2015;123(1):
21-26.
[J6] Slizovskiy, I.B. Health survey
of households near shale gas extraction sites. Thesis. Yale University. ProQuest
Dissertation Publishing. 2013. Publication no. 1569241.
[J5] Slizovskiy, I.B., Hatzinger,
P.B., Kelsey, J.W. Surfactant-facilitated remediation of metalcontaminated
soils: Efficacy and toxicological consequences to earthworms. J.
Environmental Toxicology and Chemistry. 2011; 30:112–125.
[J4] Kelsey, J.W., Slizovskiy, I.B.,
Petriello, M., Butler, K. Influence of plant-earthworm interactions on SOM
chemistry and p,p’DDE bioaccumulation. Chemosphere.
2011; 83:897–902.
[J3] Slizovskiy,
I.B. White,
J.C.; Kelsey, J.W. Technical Note: Evaluation of extraction methodologies
for the determination of pesticide residues in vegetation. Int. J.
Phytorem. 2010; 12:820–832.
[J2] Kelsey, J.W. Slizovskiy, I.B.,
Peters, R., Melnick, A. Gamma irradiation and autoclaving affects chemical
and physical properties of soil organic matter and the bioaccumulation of
spiked p,p'-DDE and anthracene to the earthworms Eisenia fetida and Lumbricus
terrestris. J. Environmental Pollution. 2010; 158: 2251–2257.
[J1] Slizovskiy, I.B., Kelsey, J.W.
Soil sterilization techniques affect aging-related sequestration and
bioavailability of p,p’DDE and anthracene to
earthworms. J. Environmental Pollution. 2010; 158: 3285–3289.
Conference proceedings and abstracts
[C22] Jimenez-Lopez, O., Ray, T., Dean, C., Slizovskiy,
I., Deere, J., Wolf, T., Primus, A., Hoy-Petersen, J., Finstad, S., Mo, J.,
Sorum, H., Noyes, N. Paired metagenomic and metatranscriptomic sequencing
reveals the gastrointestinal resistome and microbiome of yellow perch (Perca
flavescencs) in Minnesota lakes. The 15th European Wildlife
Disease Conference. European Wildlife Disease Association (EWDA).
Stralsund, Germany, 2024.
[C21] Diaz Ortiz, G.R., Slizovskiy, I.B., Torremorell,
M., Noyes, N.R. A metagenomic investigation of the work-related microbiome in U.S.
swine workers. Cold Spring Harbor
Laboratory Conference: Genome informatics. Cold Spring Harbor, NY, 2023.
[C20] Slizovskiy, I.B., Gaire,
T.N., Ferm, P., Odland, C., Dee, S., Nerem, J., Boucher, C., Noyes, N.R.
Profiling the agricultural labor-OME: Showering disrupts work-related shifts in
swine worker skin microbiomes, resistome, and mobilomes. SafePork 2023; The
14th International Symposium on the Epidemiology and Control of
Biological, Chemical and Physical Hazards in Pigs and Pork, New
Orleans, LA, 2023.
[C19] Diaz, G.R., Gaire, T.N., Danesh, M., Ferm, P., Slizovskiy,
I.B., Goldsmith, T., Caixeta, L., Armstrong, J., Noyes, N.R. Rapid
rumen microbiome change driven by weaning strategy of beef calves. Conference
of Research Workers in Animal Diseases (CRWAD), Chicago, IL, 2023.
[C18] Gaire, T.N., Wehri, T., Brown, D., Snow, C.,
Hsu, J., Slizovskiy, I.B., Jimenez-Lopez, O., Ortiz, G.R.D.,
Meneguzzi, M., Young, J., De Abreu C., Canturi, A., Pena-Mosca, F., Medrano, M., Miller, L.,
Lie, S., Ruch, M., Schwartz, M., Singer, R., Pieters, M., Noyes, N.R. Effect of
commingling and dietary fiber interventions on select performance metrics of
suckling and weaned pigs. Conference of Research Workers in Animal Diseases
(CRWAD),Chicago, IL, 2023.
[C17] Slizovskiy,
I.B., Gaire, T.N., Ferm, P., Odland, C., Dee, S., Nerem, J.,
Boucher, C., Noyes, N.R. Showering as a biosecurity intervention to disrupt
work-related shifts in swine worker skin microbiomes. Conference of Research
Workers in Animal Diseases (CRWAD), Chicago, IL, 2023.
[C16] Slizovskiy,
I.B., Oliva, M., Settle, J.K., Zyskina, L.V., Prosperi, M.C.F.,
Boucher, C., Noyes, N.R. Target-enriched long-read sequencing (TELSeq)
contextualizes antimicrobial resistance risk in metagenomes. International
Society for Computational Biology (ISCB), Madison, WI: 549.
2022.
[C15] Slizovskiy,
I.B, Boucher, C.A., Noyes, N.R. Metagenomic profiling of foodborne
pathogens, antimicrobial resistance, virulence, and mobilization potential in
public health surveillance. International Association of Food Protection
(IAFP): National Conference. Pheonix, AZ. 2021.
[C14] Slizovskiy,
I.B, Alanko, J. Lokshtanov, D., Gagie, T., Boucher, C.A., Noyes,
N.R. Molecular enrichment of whole bacterial genomes for metagenomic profiling
of foodborne pathogens. Conference of Research Workers in Animal Diseases
(CRWAD): Section of food safety. Chicago, IL, 2021.
[C13] Gaire,
T. Slizovskiy, I., Crooker, B., Noyes, N. Holstein cow genotype affects mammary skin
microbiome during experimentally induced E. coli mastitis.
Conference of Research Workers in Animal Diseases (CRWAD): Section of food
safety. Chicago, IL, 2021.
[C12] Kaufman,
J.H., Agarwal A., Beck, K.L., Mukherjee V., Nayar G., Seabolt, E., Terrizzano, I., Slizovskiy, I.B., Noyes,
N.R. Evidence for mobile proteins associated with AMR, virulence, and CRISPR in
genomes with integrative conjugative elements. American Society of
Microbiology: MICROBE Conference. Chicago, IL, 2020.
[C11] Marini
S., Slizovskiy, I., Noyes, N., Boucher C., Prosperi M.
Learning antimicrobial resistance through secondary structure of protein
variants. International Society for Computational Biology: Intelligent
Systems for Molecular Biology. Virtual conference (https://www.iscb.org/ismb2020). 2016.
[C10] Makau
D.N., Slizovskiy, I.B, VanderWaal, K., Obanda, V., Noyes, N.R., Johnson,
J.R., Oakes, M., Travis, D., Omondi, G. Drivers of antimicrobial use in
pastoral communities in Kenya. Conference
of Research Workers in Animal Diseases (CRWAD): Section in antimicrobial
stewardship in cattle. Virtual Conference. 2020.
[C9] Slizovskiy,
I.B, Settle, J.K., Boucher C., Noyes, N.R. Targeted-enrichment and
long read sequencing (TELS) uncovers mobility potential of antibiotic
resistance in microbiomes. American Society for Microbiology: Conference on
Rapid Applied Microbial Next-Generation Sequencing and Bioinformatic Pipelines.
Virtual Conference. 2020.
[C8] Iglesias,
I. Slizovskiy, I.B., Perez A., Martinez, M., DE LA Torre, A.,
HPAI Risk mapping based on environmental factors in Ramsar wetlands of Europe. Spatial
Statistics, Sitges, Spain. 2019.
[C7] Slizovskiy
I.B., Kaufman J.H., Terrizzano I.G., Nayar G., Seabolt E.E., Agarwal
A., Roth M.A., Noyes N.R. Big data survey of Integrative Conjugative Elements
and associated cargo genes across hundreds of thousands of bacterial genera. 100th
Annual Conference of Research Workers in Animal Diseases (CRWAD). Chicago,
IL, 2019.
[C6] Dean,
C., Slizovskiy, I.B., Crone, K., Heinz, B., Caixeta, L.,
Noyes, N. Sampling considerations for conducting large-scale microbial ecology
studies of cow udder epithelium. Proceedings of the 99th Annual Conference
of Research Workers in Animals Disease, Chicago, IL, 2015.
[C5] Slizovskiy,
I.B., Dean, C.J., Belk, K.E., Morley, P.S., Noyes, N. R.
Characterizing Risks of Mobilizing Antibiotic Resistance in Beef Production: A
Metagenomics-Network Approach. Proceedings of the 99th Annual
Conference of Research Workers in Animal Disease, Chicago, IL, 2018.
[C4] Surfactant-facilitated
Remediation of Metal-contaminated Soils: Efficacy and Toxicological Consequences.
Presented at the 27th Annual International Conference on Soils, Sediments,
Water, and Energy, University of Massachusetts, Amherst, MA, USA. (2010).
[C3] Sterilization
Affects Soil Organic Matter Chemistry and Bioaccumulation of Spiked p,p’DDE and
Anthracene by Earthworms. Presented at the Student Research
Symposium, Muhlenberg College, Allentown, Pennsylvania, USA. (2008).
[C2] Sterilization
Affects Soil Organic Matter Chemistry and Bioaccumulation of Spiked p,p’-DDE
and Anthracene by Earthworms. Presented at the Pennsylvania
Undergraduate Research at the Capitol Program, Pennsylvania State Capitol,
Harrisburg, Pennsylvania, USA. (2008).
[C1] Effect
of Heavy Metal co-contamination on the Phytoremediation of p,p’DDE by
Cucurbita pepo spp. pepo Zucchini Squash Plants. Presented at the
Student Research Symposium, Muhlenberg College, Allentown, Pennsylvania, USA.
(2006).