Publications 2021

2021  Peer-review Publications

1.      Al Kassaa I, El Omari S, Abbas N, Papon N, Drider D, Kassem II, Osman M. High association of COVID-19 severity with poor gut health score in Lebanese patients. PLoS One. 2021 Oct 21;16(10):e0258913. doi: 10.1371/journal.pone.0258913. PMID: 34673813; PMCID: PMC8530309

2.      Den Bakker HC, Katz L. 2021. Sepia, a taxonomy oriented read classifier in Rust. Journal of Open Source Software, 6(68), 3839.

3.      Brewer SS, Lowe CA, Beuchat LR, Ortega YR. 2021. Survival of Salmonella and Shiga toxin-producing Escherichia coli and changes in indigenous microbiota during fermentation of kombucha made from home-brewing kits. J Food Prot. 84:1366-1373 doi: 10.4315/JFP-20-483.

4.      Chung MY, Kim H, Beuchat LR, Ryu JH. Antimicrobial activities of plant essential oil vapours against Acidovorax citrulli and Xanthomonas campestris on Cucurbitaceae, Brassicaceae and Solanaceae seeds. J Appl Microbiol. 2021 Nov 1. doi: 10.1111/jam.15352.

5.      Chiarelli PG, Pegg RB, Dev Kumar G, Solval KM. 2021. Exploring the feasibility of developing novel gelatin powders from salted, dried cannonball jellyfish (Stomolophus meleagris). Food Biosci. 44:101397.

6.      Dagher LA, Hassan J, Kharroubi S, Jaafar H, Kassem II. 2021.Nationwide assessment of water quality in rivers across Lebanon by quantifying fecal indicators densities and profiling antibiotic resistance of Escherichia coli. Antibiotics. 10:883.

7.      Den Bakker M, den Bakker HC, Diez-Gonzalez F. 2021. Heat inactivation of Listeria monocytogenes on pecans, macadamia nuts, and sunflower seeds. Microbiol. Spect. 9: e01134-21.

8.      Deng X, Cao S, Horn AL. 2021. Emerging applications of machine learning in food safety. Annu Rev Food Sci Technol. doi: 10.1146/annurev-food-071720-024112.

9.      Gregory TV, Ellis K, Valeriani R, Khan F, Wu X, Murin L, Alibayov B, Vidal AGJ, Zhao T, Vidal JE. 2021. MoWa: a disinfectant for hospital surfaces contaminated with methicillin-resistant Staphylococcus aureus (MRSA) and other nosocomial pathogens. Front Cell Infect Microbiol.11:676638. doi: 10.3389/fcimb.2021.676638.

10.  Halimeh, F.B., Rafei, R., Osman, M, Kassem II, Diene S M, Dabboussi F, Rolain J-M. Hamze M. 2021. Historical, current, and emerging tools for identification and serotyping of Shigella. Braz J Microbiol.

11.  Hassan J, Mann D, Li S, Deng X, Kassem II. First report of the mobile colistin resistance gene, mcr-9.1, in Morganella morganii isolated from sewage in Georgia, USA. J Glob Antimicrob Resist. 9:S2213-7165(21)00267-8. doi: 10.1016/j.jgar.2021.11.013.

12.  Hassan J, Mann D, Li S, Deng X, Kassem II. 2021. Emergence of the mobile colistin resistance gene, mcr-1, in multidrug-resistant E. coli isolated from the fecal matter of toddlers in a community. Antimmicrob Agents Chem AAC.00243-21; DOI: 10.1128/AAC.00243-21.

13.  Hayman K, Oguadinma IC, Mishra A., Dev Kumar G. 2021. Evaluation of the use of ampicillin‐and streptomycin‐resistant Shiga toxin‐producing Escherichia coli to reduce the burden of background microbiota during food safety studies. Journal of Food Safety, e12950.

14.  He Y, Chen R, Qi Y, Salazar JK, Zhang S, Tortorello ML, Deng X, Zhang W. 2021. Survival and transcriptomic response of Salmonella enterica on fresh-cut fruits. Int J Food Microbiol. 348:109201. doi: 10.1016/j.ijfoodmicro.2021.109201

15.  Helmy YA, Kassem II, Rajashekara G. 2021. Immuno-modulatory effect of probiotic E. coli Nissle 1917 in polarized human colonic cells against Campylobacter jejuni infection. Gut Microbes. 13:1-16. doi: 10.1080/19490976.2020.1857514. 

16.  Hudson LK, Orellana LAG, Bryan DW, Moore A, Munafo JP, den Bakker HC, Denes TG. 2022. Phylogeny of the Bacillus altitudinis complex and characterization of a newly isolated strain with antilisterial activity. J Food Prot. 84(8):1321-1332. doi: 10.4315/JFP-20-498.

17.  Hudson LK, Peters TL, Bryan DW, Song Y, den Bakker HC, Denes TG. 2021. Complete Genome sequences of three Listeria monocytogenes bacteriophage propagation strains. Microbiol Resour Announc. 10(1):e01159-20. doi: 10.1128/MRA.01159-20.

18.  Hyeon J-Y, Li S, Mann DA, Zhang S, Kim K-J, Lee D-H, Deng X, Song C-S. 2021 Whole-genome sequencing analysis of Salmonella Enterica serotype enteritidis isolated from poultry sources in South Korea, 2010–2017. Pathogens. 10(1):45.

19.  Jeffer SB, Kassem II, Kharroubi SA, Abebe GK. 2021. Analysis of food safety management systems in the beef meat processing and distribution chain in Uganda. Foods. 10:2244.

20.  Juneja VK, Osoria M, Altuntas EG, Salazar JK, Kumar GD, Sehgal S, and Baker D. 2021. Inactivation of Listeria monocytogenes, Escherichia coli O157:H7, and Salmonella spp. on dates by antimicrobial washes. J Food Process Preserv. Manuscript e15282.

21.  Juneja, V. K., Osoria, M., Purohit, A. S., Golden, C. E., Mishra, A., Taneja, N. K., Salazar JK, Thippareddi H, Dev Kumar G. 2021. Predictive model for growth of Clostridium perfringens during cooling of cooked pork supplemented with sodium chloride and sodium pyrophosphate. Meat Sci, 180, 108557.

22.  Juneja VK, Purohit AS, Golden M, Osoria M, Glass KA, Mishra A, Thippareddi H, Dev Kumar G, Mohr TB, Minocha U and Silverman M. 2021. A predictive growth model for Clostridium botulinum during cooling of cooked uncured ground beef. Food Microbiol. 93: p.103618.

23.  Juneja VK, Xu X, Osoria M, Glass KA, Schill KM, Golden MC, Schaffner DW, Dev Kumar G, Dunn L, Jadeja R, Shrestha S, Mishra, A. 2021. Predictive model for growth of Clostridium botulinum from spores during cooling of cooked ground chicken. Food Res. Intl, 149: 110695.

24.  Kassem II, Mann D, Li S, Deng X. 2021. Draft genome sequences and resistome analysis of multidrug-resistant mcr-1-harbouring Escherichia coli isolated from pre-harvest poultry in Lebanon. J Glob Antimicrob Resist. 25:114-116. doi: 10.1016/j.jgar.2021.03.001.

25.  Lamm KW, Randall NL, Diez-Gonzalez F. 2021. Critical food safety issues facing the food industry: A Delphi Analysis. J Food Prot. 84:680-687. doi: 10.4315/JFP-20-372.

26.  Levent G, Schlochtermeier A, Ives SE, Norman KN, Lawhon SD, Loneragan GH, Anderson RC, Vinasco J, Den Bakker HC, Scott HM. 2021. High-resolution genomic comparisons within Salmonella enterica serotypes derived from beef feedlot cattle: parsing the roles of cattle source, pen, animal, sample type and production period. Appl Environ Microbiol. Apr 16:AEM.00485-21. doi: 10.1128/AEM.00485-21.

27.  Li S, He Y, Mann DA, Deng X. 2021. Global spread of Salmonella Enteritidis via centralized sourcing and international trade of poultry breeding stocks. Nat Commun. 12:5109. doi: 10.1038/s41467-021-25319-7.

28.  Nasser NA, Alhaj Sulaiman A, Mann D, Li S, Deng X, Kassem II. 2021. Draft genome sequences of multidrug-resistant and mcr-1.1- harboring Escherichia coli isolated from drinking and well waters used in Syrian refugee camps. Microbiol Resour Announc 10:e01252-20.

29.  Nasser NA, Mann D, Li S, Deng X, Kassem II. 2021 Draft genome sequences of colistin-resistant and mcr-1.1-carrying Escherichia coli strains isolated from irrigation water. Microbiol Resour Announc. 10:e00120-21.

30.  Olszewska MA, Diez-Gonzalez F. 2021. Characterization of binary biofilms of Listeria monocytogenes and Lactobacillus and their response to chlorine treatment. Front. Microbiol.

31.  Osman M, Kasir D, Kassem II, Hamze M. 2021. Shortage in appropriate diagnostics of antimicrobial resistance in Lebanese clinical settings: a crisis amplified by COVID-19 and economic collapse. J Glob Antimicrob Resist. S2213-7165(21)00200-9. doi: 10.1016/j.jgar.2021.08.008.

32.  Osman M, Kasir D, Rafei R, Kassem II, Ismail MB, El Omari K, Dabboussi F, Cazer C, Papon N, Bouchara JP, Hamze M. Trends in the epidemiology of dermatophytosis in the Middle East and North Africa region. Int J Dermatol. 2021 Nov 12. doi: 10.1111/ijd.15967.

33.  Peters TL, Hudson LK, Bryan DW, Song Y, den Bakker HC, Kucerova Z, Denes TG. 2021. Complete genome sequence of a serotype 7 Listeria monocytogenes strain, FSL R9-0915. Microbiol Resour Announc. 2021 Jan 7;10(1):e01158-20. doi: 10.1128/MRA.01158-20.

34.  Smith CJ, Olszewska MA, Diez-Gonzalez F. 2021. Selection and application of natural antimicrobials to control Clostridium perfringens in sous-vide chicken breasts. Int J Food Microbiol. 347:109193. doi: 10.1016/j.ijfoodmicro.2021.109193.

35.  White E, Dev Kumar G, da Silva ALBR, Kerr WL, Cimowsky S, Widmer JA, Dunn LL. 2021. Postharvest reduction of Salmonella enterica on tomatoes using a pelargonic acid emulsion. Foods. 10(1):178.

36.  Wu X, Luo H, Xu F, Ge C, Li S, Deng X, Wiedmann M, Baker RC, Stevenson A, Zhang G, Tang S. 2021. Evaluation of Salmonella serotype prediction with multiplex nanopore sequencing. Front Microbiol. 12:637771. doi: 10.3389/fmicb.2021.637771. eCollection 2021.

37.  Xu F, Ge C, Li S, Tang S, Wu X, Luo H, Deng X, Zhang G, Stevenson A, Baker RC. 2021. Evaluation of nanopore sequencing technology to identify Salmonella enterica Choleraesuis var. Kunzendorf and Orion var. 15+, 34. Int J Food Microbiol. 346:109167. doi: 10.1016/j.ijfoodmicro.2021.109167.

38.  Xu X, Rothrock MJ Jr, Mohan A, Dev Kumar G, Mishra A. 2021. Using farm management practices to predict Campylobacter prevalence in pastured poultry farms. Poult Sci. 100:101122. doi: 10.1016/j.psj.2021.101122.

39.  Yeom W, Kim H, Beuchat LR, Ryu JH. 2021. Inactivation of Escherichia coli O157:H7 on radish and cabbage seeds by combined treatments with gaseous chlorine dioxide and heat at high relative humidity. Food Microbiol. 99:103805. doi: 10.1016/

40.  ZeinEddine R, Nasser N, Kassem II, Saoud IP. Effect of the human probiotic bacterium Escherichia coli Nissle (1917) on performance and immune response of Nile tilapia Oreochromis niloticus. J Appl Aquacult. 15:1-5.