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1. Household Transmission of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Alpha Variant-United States, 2021.

Author

Donnelly, Marisa, Chuey, Meagan, Soto, Raymond, Schwartz, Noah, Chu, Victoria, Konkle, Stacey, Sleweon, Sadia, Ruffin, Jasmine, Haberling, Dana, Guagliardo, Sarah, Stoddard, Robyn, Anderson, Raydel, Morgan, Clint, Rossetti, Rebecca, McCormick, David, Magleby, Reed, Sheldon, Sarah, Dietrich, Elizabeth, Uehara, Anna, Retchless, Adam, Tong, Suxiang, Folster, Jennifer, Drobeniuc, Jan, Petway, Marla, Austin, Brett, Stous, Sarah, McDonald, Eric, Jain, Seema, Hudziec, Meghan, Stringer, Ginger, Albanese, Bernadette, Totten, Sarah, Staples, J, Killerby, Marie, Hughes, Laura, Matanock, Almea, Beatty, Mark, Tate, Jacqueline, Kirking, Hannah, and Hsu, Christopher

Subjects
Alpha, COVID-19, SARS-CoV-2, household, transmission, COVID-19, Family Characteristics, Humans, SARS-CoV-2, United States
Abstract

BACKGROUND: In Spring 2021, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) B.1.1.7 (Alpha) became the predominant variant in the United States. Research suggests that Alpha has increased transmissibility compared with non-Alpha lineages. We estimated household secondary infection risk (SIR), assessed characteristics associated with transmission, and compared symptoms of persons with Alpha and non-Alpha infections. METHODS: We followed households with SARS-CoV-2 infection for 2 weeks in San Diego County and metropolitan Denver, January to April 2021. We collected epidemiologic information and biospecimens for serology, reverse transcription-polymerase chain reaction (RT-PCR), and whole-genome sequencing. We stratified SIR and symptoms by lineage and identified characteristics associated with transmission using generalized estimating equations. RESULTS: We investigated 127 households with 322 household contacts; 72 households (56.7%) had member(s) with secondary infections. SIRs were not significantly higher for Alpha (61.0% [95% confidence interval, 52.4-69.0%]) than non-Alpha (55.6% [44.7-65.9%], P = .49). In households with Alpha, persons who identified as Asian or Hispanic/Latino had significantly higher SIRs than those who identified as White (P = .01 and .03, respectively). Close contact (eg, kissing, hugging) with primary cases was associated with increased transmission for all lineages. Persons with Alpha infection were more likely to report constitutional symptoms than persons with non-Alpha (86.9% vs 76.8%, P = .05). CONCLUSIONS: Household SIRs were similar for Alpha and non-Alpha. Comparable SIRs may be due to saturation of transmission risk in households due to extensive close contact, or true lack of difference in transmission rates. Avoiding close contact within households may reduce SARS-CoV-2 transmission for all lineages among household members.

Published
2022

2. Household Transmission and Symptomology of Severe Acute Respiratory Syndrome Coronavirus 2 Alpha Variant among Children-California and Colorado, 2021.

Author

Waltenburg, Michelle, Whaley, Melissa, Chancey, Rebecca, Donnelly, Marisa, Chuey, Meagan, Soto, Raymond, Schwartz, Noah, Chu, Victoria, Sleweon, Sadia, McCormick, David, Uehara, Anna, Retchless, Adam, Tong, Suxiang, Folster, Jennifer, Petway, Marla, Thornburg, Natalie, Drobeniuc, Jan, Austin, Brett, Hudziec, Meghan, Stringer, Ginger, Albanese, Bernadette, Totten, Sarah, Matzinger, Shannon, Staples, J, Killerby, Marie, Hughes, Laura, Matanock, Almea, Beatty, Mark, Tate, Jacqueline, Kirking, Hannah, and Hsu, Christopher

Subjects
COVID-19, alpha variant, children, household transmission, Adult, COVID-19, California, Child, Colorado, Humans, SARS-CoV-2
Abstract

OBJECTIVE: To assess the household secondary infection risk (SIR) of B.1.1.7 (Alpha) and non-Alpha lineages of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) among children. STUDY DESIGN: During January to April 2021, we prospectively followed households with a SARS-CoV-2 infection. We collected questionnaires, serial nasopharyngeal swabs for reverse transcription polymerase chain reaction testing and whole genome sequencing, and serial blood samples for serology testing. We calculated SIRs by primary case age (pediatric vs adult), household contact age, and viral lineage. We evaluated risk factors associated with transmission and described symptom profiles among children. RESULTS: Among 36 households with pediatric primary cases, 21 (58%) had secondary infections. Among 91 households with adult primary cases, 51 (56%) had secondary infections. SIRs among pediatric and adult primary cases were 45% and 54%, respectively (OR, 0.79; 95% CI, 0.41-1.54). SIRs among pediatric primary cases with Alpha and non-Alpha lineage were 55% and 46%, respectively (OR, 1.52; 95% CI, 0.51-4.53). SIRs among pediatric and adult household contacts were 55% and 49%, respectively (OR, 1.01; 95% CI, 0.68-1.50). Among pediatric contacts, no significant differences in the odds of acquiring infection by demographic or household characteristics were observed. CONCLUSIONS: Household transmission of SARS-CoV-2 from children and adult primary cases to household members was frequent. The risk of secondary infection was similar among child and adult household contacts. Among children, household transmission of SARS-CoV-2 and the risk of secondary infection was not influenced by lineage. Continued mitigation strategies (eg, masking, physical distancing, vaccination) are needed to protect at-risk groups regardless of virus lineage circulating in communities.

Published
2022

3. List of contributors

Author

Aizawa, Shin-Ichi, primary, Alberdi, Pilar, additional, Alexander, David C., additional, Alía, Alberto, additional, Allison, D.G., additional, Amyes, Sebastian G.B., additional, An, Haoran, additional, Andrade, María J., additional, Antelmann, Haike, additional, Arias, Cesar A., additional, Asensio, Miguel A., additional, Axell-House, Dierdre B., additional, Bae, Hee-Won, additional, Baena, Laura Muñoz, additional, Baig, Abdul Mannan, additional, Bailey, Spenser O., additional, Baize, Sylvain, additional, Baldi, Pablo C., additional, Barbosa, Angela Silva, additional, Barbuddhe, Sukhadeo B., additional, Bard, Emilie, additional, Barry, Eileen M., additional, Basarab, Gregory S., additional, Beloborodova, N.V, additional, Bermúdez, Elena, additional, Bidmos, Fadil A., additional, Bisgaard, Magne, additional, Blakely, Garry W., additional, Bloch, Evan, additional, Boesen, Thias Oberg, additional, Bose, Dipayan, additional, Botero, Javier Enrique, additional, Bouabe, Hicham, additional, Bouchard, Michael J., additional, Bozue, Joel A., additional, Bradbury, Richard S., additional, Brett Moreau, G., additional, Cabezas-Cruz, Alejandro, additional, Cai, Rong-Jun, additional, Calderón, Enrique J., additional, Cao, Boyang, additional, Carmena, David, additional, Carvalho, Eneas, additional, Caulfield, Amanda D., additional, Cen, Shan, additional, Chai, Jong-Yil, additional, Chamberland, Robin R., additional, Champredon, David, additional, Chan, Edward D., additional, Charbon, Godefroid, additional, Chato, Connor, additional, Chelomina, G.N., additional, Chen, Jingyu, additional, Chen, Min, additional, Chen, Shuyu, additional, Chen, Suilin, additional, Chen, Yanfei, additional, Chen, Zhaoyuan, additional, Cheng, Aimin, additional, Cheng, Keding, additional, Chiu, Charles Y., additional, Cho, You-Hee, additional, Christensen, Henrik, additional, Chrtdernevskaya, E.A., additional, Contreras, Adolfo, additional, Contreras, Marinela, additional, Córdoba, Juan J., additional, Córdoba, María G., additional, Costa, Rita, additional, Cote, Christopher K., additional, Cui, Xiangling, additional, Cui, Yujun, additional, Dacal, Elena, additional, Dammann, Allison N., additional, Das, Shubhagata, additional, Dashti, Alejandro, additional, de la Fuente, José, additional, de la Garza, Mireya, additional, Delgado, Josué, additional, Delgado-Cuesta, Juan, additional, Deng, Haiteng, additional, Deng, Li, additional, Dey, Debajit, additional, Dhama, Kuldeep, additional, Diego, Juan García-Bernalt, additional, Ding, Hao, additional, Doern, Christopher D., additional, Dorman, Charles J., additional, Du, Zongmin, additional, Dunbar, Sherry A., additional, Duthie, Malcolm, additional, Dybvig, Kevin F., additional, Eakin, Ann E., additional, Eallonardo, Samuel J., additional, Eberly, Allison R., additional, Echeverry, Adriana Jaramillo, additional, Egland, Paul G., additional, El Zowalaty, Mohamed E., additional, Endsley, Janice Jones, additional, Eom, Keeseon S., additional, Evans, Benjamin A., additional, Falkinham, Joseph O., additional, Feng, Siwei, additional, Feng, Yaoyu, additional, Feng, Zongdi, additional, Fernández-Soto, Pedro, additional, Ferreira, Roux-Cil, additional, Flores-Huerta, Nadia, additional, Foster, Timothy J., additional, Fox-Moon, Sandra M., additional, Fraga, Tatiana Rodrigues, additional, Fredricks, David N., additional, Freitag, Nancy E., additional, Frimodt-Møller, Jakob, additional, Fuller, Risa, additional, Ganesh, Balasubramanian, additional, Gao, Ning, additional, García-Carnero, Laura C., additional, Garzetti, Debora, additional, Geoghegan, Joan A., additional, Ghenim, Raed, additional, Giambartolomei, Guillermo H., additional, Gilbert, Nicole M., additional, Gillis, Thomas Phillip, additional, Gladstone, Camilla A., additional, Gómez-Gaviria, Manuela, additional, Gómez-Marín, Jorge E., additional, Gong, Tengfang, additional, González, Ramón A., additional, Gray-Owen, Scott D., additional, Gu, Bing, additional, Guzmán-Téllez, Paula, additional, Hajal, Caroline, additional, Han, Yanping, additional, Hao, Yi, additional, Harrington, Amanda T., additional, Harris, Jason B., additional, Harvill, Eric T., additional, Hasan, S. Saif, additional, He, Guang-Jun, additional, He, Yongqun, additional, Heffron, Jared D., additional, Hidalgo, Paloma, additional, Hindiyeh, Musa Y., additional, Hreha, Teri N., additional, Hu, Xiaoyu, additional, Huang, Guanghua, additional, Huang, Jiangqing, additional, Huang, Liang, additional, Huang, Shifeng, additional, Huang, Xingxu, additional, Huang, Xueting, additional, Huang, Yilun, additional, Huffman, Anthony, additional, Humphreys, Tricia L., additional, Hunstad, David A., additional, Inglis, Timothy J.J., additional, Isaac, Lourdes, additional, Jacobs, Samantha E., additional, Janowicz, Diane M., additional, Jeon, Hyeong-Kyu, additional, Ji, Quanjiang, additional, Jia, Qi, additional, Jia, Wei, additional, Jin, Shouguang, additional, Jneidi, Lama, additional, Jose, Shinsmon, additional, Jung, Bong-Kwang, additional, Kattan, Randa, additional, Kaushik, Rahul, additional, Khare, Reeti, additional, Kim, Eun Sook, additional, Kirn, Thomas J., additional, Koo, Hyun, additional, Köster, Pamela C., additional, Krause, Peter J., additional, Kumar, Sanjai, additional, Kupz, Andreas, additional, Lambert, P.A., additional, Lamont, Richard J., additional, Langford, Paul R., additional, Lebeaux, David, additional, Legname, Giuseppe, additional, Li, Bin, additional, Li, Chunhao, additional, Li, Fen, additional, Li, Jun, additional, Li, Lanjuan, additional, Li, Ruofan, additional, Li, Ruoyu, additional, Li, Ting, additional, Li, Yang-Yang, additional, Li, Yanhua, additional, Li, Zhuorong, additional, Liang, Xiaomeng, additional, Liao, Guojian, additional, Lin, Ping, additional, Ling, Yun, additional, Liu, Bo, additional, Liu, Dongyou, additional, Liu, Guohua, additional, Liu, Huidi, additional, Liu, Jiafeng, additional, Liu, Jintao, additional, Liu, Qi, additional, Liu, Shu-Lin, additional, Liu, Taiping, additional, Liu, Tongbao, additional, Liu, Wei, additional, Liu, Yan, additional, Liu, Yanni, additional, Liu, Yisong, additional, Liu, Yuan, additional, Løbner-Olesen, Anders, additional, Loeffelholz, Michael, additional, Lu, Hongzhou, additional, Luna, Brian, additional, Ma, Bingting, additional, Ma, Chengying, additional, Ma, Shuang, additional, Ma, TianLi, additional, Madan, Rajat, additional, Mahle, Rachael E., additional, Mahlen, Steven D., additional, Malik, Satya Veer Singh, additional, Malik, Yashpal Singh, additional, Malvy, Denis, additional, Mann, Barbara J., additional, Marasini, Daya, additional, Maris, Alexander S., additional, Marjomäki, Varpu, additional, Marjuki, Henju, additional, Martín, Alberto, additional, Martín, Irene, additional, Martínez-Castillo, Moisés, additional, Martínez-Pabón, María Cecilia, additional, Mathison, Blaine A., additional, Ma’ayeh, Showgy, additional, McDowell, Andrew, additional, McLaughlin, Stephanie E., additional, McSheffrey, Gordon G., additional, Medrano, Francisco J., additional, Meehan, Conor J., additional, Mehta, Dhwani, additional, Mejía-Oquendo, Manuela, additional, Melo-Cristino, José, additional, Mendoza-Barberá, Elena, additional, Meng, Xinan, additional, Merino, Susana, additional, Merritt, Adam J., additional, Miller, Steve, additional, Miller, William R., additional, Minamino, Tohru, additional, Mirzaei, Mohammadali Khan, additional, Mora-Montes, Héctor M., additional, Mortensen, Joel, additional, Mostafa, Heba H., additional, Muhsen, Khitam, additional, Mujahed, Ahlam, additional, Muro, Antonio, additional, Murphy, Olwen C., additional, Newton, Hayley J., additional, Nguyen, April H., additional, Nichols, Wright W., additional, Niu, Siqiang, additional, Núñez, Félix, additional, Obregon, Dasiel, additional, Okamoto, Akira, additional, Okutani, Akiko, additional, Olabode, Abayomi, additional, Omar, Muna, additional, Ong, Edison, additional, Ouyang, Zhiming, additional, Pacak, Christina A., additional, Pacheco-Yépez, Judith, additional, Palmer, John, additional, Pang, Xiaoli, additional, Paredes-Sabja, Daniel, additional, Peng, Zhong, additional, Peng, Zonggen, additional, Pérez-Nevado, Francisco, additional, Poon, Art, additional, Pospíšilová, Petra, additional, Potts, Caelin C., additional, Pu, Qinqin, additional, Pujic, Petar, additional, Qi, Rui, additional, Qian, Chenyun, additional, Qian, Liu, additional, Qin, Aiping, additional, Qu, Fen, additional, Rakin, Alexander, additional, Ramesh, Ashwin, additional, Ramirez, Mario, additional, Rao, Yu, additional, Ratner, Adam J., additional, Rawool, Deepak B., additional, Rehman, Asma, additional, Ren, Jie, additional, Ren, Ping, additional, Retchless, Adam C., additional, Robertson, Erle S., additional, Rodríguez, Alicia, additional, Rodriguez, Azucena, additional, Rodríguez-Medina, Carolina, additional, Rodriguez-Nava, Veronica, additional, Rohde, Manfred, additional, Romero-Rodríguez, Alba, additional, Rosales-Morgan, Gabriela, additional, Rosenkranz, Andrea L., additional, Ruiz-Moyano, Santiago, additional, Ruokolainen, Visa, additional, Sabateen, Ali, additional, Sahu, Radhakrishna, additional, Sails, Andrew, additional, Sang, Yu, additional, Santana, Clarissa H., additional, Santos, Jesus A., additional, Santos, Renato L., additional, Schmitz, Jonathan E., additional, Serrano-Luna, Jesús, additional, Shen, Jianzhong, additional, Shen, Zhangqi, additional, Shibayama, Mineko, additional, Shirtliff, Mark E., additional, Silva-Costa, Catarina, additional, Silva-Olivares, Angélica, additional, Singh, Niraj Kumar, additional, Šmajs, David, additional, Smith, Robert P., additional, Smith, Sophie, additional, Snyder, Lori A.S., additional, Song, Yinggai, additional, Soro, Aurea Simon, additional, Spearman, Paul, additional, Spellberg, Brad, additional, Sprague, Lisa D., additional, Stratton, Charles W., additional, Strenk, Susan M., additional, Strugnell, Richard A., additional, Sun, Keer, additional, Suo, Xun, additional, Suzuki-Hatano, Silveli, additional, Svärd, Staffan, additional, Talbot, Elizabeth A., additional, Tamez-Castrellón, Alma K., additional, Tan, Nie, additional, Tang, Cynthia Y., additional, Tang, Yi-Wei, additional, Tao, Jia, additional, Tao, Lili, additional, Terrero-Salcedo, David, additional, Tharmalingam, Jayaraman, additional, Thwe, Phyu M., additional, Tiamani, Kawtar, additional, Tomás, Juan M., additional, Topaz, Nadav, additional, Tsai, Ang-Chen, additional, Tsalik, Ephraim L., additional, Tuomanen, Elaine I., additional, Turenne, Christine Y., additional, Tyagi, Anuj, additional, Uprety, Priyanka, additional, Valour, Florent, additional, van Hensbergen, Vincent P., additional, Venkatesan, Arun, additional, Vergis, Jess, additional, Villar, Margarita, additional, Vollmer, Waldemar, additional, Waites, Ken B., additional, Wan, Xiu-Feng, additional, Wang, Guiqing, additional, Wang, Lijun, additional, Wang, Lin, additional, Wang, Linqi, additional, Wang, Xiangru, additional, Wang, Xin, additional, Wang, Xinjie, additional, Wang, Ya-Ting, additional, Wang, Yang, additional, Wang, Yating, additional, Weil, Ana A., additional, Welkos, Susan L., additional, Wengenack, Nancy L., additional, Westblade, Lars F., additional, Whitfield, Chris, additional, Wu, Hui, additional, Wu, Lijuan, additional, Wu, Min, additional, Wu, Yarong, additional, Wu, Zhaowei, additional, Xiang, Ye, additional, Xiao, Di, additional, Xiao, Li, additional, Xiao, Lihua, additional, Xu, Tao, additional, Xu, Wenyue, additional, Xu, Xinping, additional, Xue, Jinling, additional, Yadav, Jay Prakash, additional, Yan, Junxiang, additional, Yan, Yixin, additional, Yang, Changmei, additional, Yang, Ruifu, additional, Yang, Ying, additional, Yao, Kaihu, additional, Yao, Yu-Feng, additional, Yeakle, Kyle C., additional, Yu, Demin, additional, Yu, Hao, additional, Yu, Xue-Jie, additional, Yuan, Zhenghong, additional, Zai, Wenjing, additional, Zhang, Jianzhong, additional, Zhang, Jing-Ren, additional, Zhang, Lanyue, additional, Zhang, Lijie, additional, Zhang, Qiwei, additional, Zhang, Wenbao, additional, Zhang, Wenhong, additional, Zhang, Xinxin, additional, Zhao, Youbao, additional, Zhou, Chuanmin, additional, Zhu, Feng, additional, Zhu, Jingting, additional, and Zhu, Yongqun, additional

Published
2024
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4. Haemophilus influenzae

Author

Retchless, Adam C., primary, Topaz, Nadav, additional, Marjuki, Henju, additional, Marasini, Daya, additional, Potts, Caelin C., additional, and Wang, Xin, additional

Published
2024
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6. Draft Whole-Genome Sequences of Xylella fastidiosa subsp. fastidiosa Strains TPD3 and TPD4, Isolated from Grapevines in Hou-li, Taiwan.

Author

Castillo, Andreina I, Tuan, Shu-Jen, Retchless, Adam C, Hu, Fei-Ting, Chang, Hsun-Yin, and Almeida, Rodrigo PP

Abstract

We report the draft assemblies of TPD3 and TPD4, two Xylella fastidiosa subsp. fastidiosa isolates infecting grapevines in Hou-li, Taiwan. TPD3 and TPD4 showed similar characteristics regarding genome size (2,483,503 bp and 2,491,539 bp, respectively), GC content (51.49% and 51.47%, respectively), and number of protein-coding sequences (2,394 and 2,413, respectively).

Published
2019

7. Genomic Diversity and Recombination among Xylella fastidiosa Subspecies.

Author

Vanhove, Mathieu, Retchless, Adam C, Sicard, Anne, Rieux, Adrien, Coletta-Filho, Helvecio D, De La Fuente, Leonardo, Stenger, Drake C, and Almeida, Rodrigo PP

Subjects
Biological Sciences, Genetics, Biotechnology, Human Genome, Genetic Variation, Genome, Bacterial, Homologous Recombination, Phylogeny, Xylella, Xylella fastidiosa, emerging disease, genomic diversity, recombination, Xylella fastidiosa, Microbiology, Medical microbiology
Abstract

Xylella fastidiosa is an economically important bacterial plant pathogen. With insights gained from 72 genomes, this study investigated differences among the three main subspecies, which have allopatric origins: X. fastidiosa subsp. fastidiosa, multiplex, and pauca The origin of recombinogenic X. fastidiosa subsp. morus and sandyi was also assessed. The evolutionary rate of the 622 genes of the species core genome was estimated at the scale of an X. fastidiosa subsp. pauca subclade (7.62 × 10-7 substitutions per site per year), which was subsequently used to estimate divergence time for the subspecies and introduction events. The study characterized genes present in the accessory genome of each of the three subspecies and investigated the core genome to detect genes potentially under positive selection. Recombination is recognized to be the major driver of diversity in X. fastidiosa, potentially facilitating shifts to novel plant hosts. The relative effect of recombination in comparison to point mutation was calculated (r/m = 2.259). Evidence of recombination was uncovered in the core genome alignment; X. fastidiosa subsp. fastidiosa in the United States was less prone to recombination, with an average of 3.22 of the 622 core genes identified as recombining regions, whereas a specific clade of X. fastidiosa subsp. multiplex was found to have on average 9.60 recombining genes, 93.2% of which originated from X. fastidiosa subsp. fastidiosa Interestingly, for X. fastidiosa subsp. morus, which was initially thought to be the outcome of genome-wide recombination between X. fastidiosa subsp. fastidiosa and X. fastidiosa subsp. multiplex, intersubspecies homologous recombination levels reached 15.30% in the core genome. Finally, there is evidence of X. fastidiosa subsp. pauca strains from citrus containing genetic elements acquired from strains infecting coffee plants as well as genetic elements from both X. fastidiosa subsp. fastidiosa and X. fastidiosa subsp. multiplex In summary, our data provide new insights into the evolution and epidemiology of this plant pathogen.IMPORTANCEXylella fastidiosa is an important vector-borne plant pathogen. We used a set of 72 genomes that constitutes the largest assembled data set for this bacterial species so far to investigate genetic relationships and the impact of recombination on phylogenetic clades and to compare genome content at the subspecies level, and we used a molecular dating approach to infer the evolutionary rate of X. fastidiosa The results demonstrate that recombination is important in shaping the genomes of X. fastidiosa and that each of the main subspecies is under different selective pressures. We hope insights from this study will improve our understanding of X. fastidiosa evolution and biology.

Published
2019

8. Household Transmission and Symptomology of Severe Acute Respiratory Syndrome Coronavirus 2 Alpha Variant among Children—California and Colorado, 2021

Author

Alford, Alexis, Baird, Samuel, Bankers, Laura, Bello, Jazmin, Bolcen, Shanna, Browning, Peter, Cook, Peter W., David, Ebenezer, Harcourt, Jennifer L., Hareland, Geir, Jr., Hetherington-Rauth, Molly C., Ir, Diana, Jain, Shilpi, Jia, Tao Lily, Johnson, Ralen, Kelleher, Anna, Kim, Gimin, Li, Yan, Lynch, Brian, Mallal, Daniel, Maniatis, Panagiotis, Marine, Rachel, Medrzycki, Magdalena, Metz, John M., Montmayeur, Anna Maria, Moss, Kimberly M., Justin Ng, Han Jia, Nyugen, Van, Ortiz, Kristina, Paden, Clinton R., Park, So Hee, Queen, Krista, Rossheim, Alexandria E.B., Semenova, Vera, Shepard, Samuel S., Tamin, Azaibi, Tao, Ying, Tejada-Strop, Alexandra, Wong, Phili, Zellner, Briana, Zhang, Jing, Waltenburg, Michelle A., Whaley, Melissa J., Chancey, Rebecca J., Donnelly, Marisa A.P., Chuey, Meagan R., Soto, Raymond, Schwartz, Noah G., Chu, Victoria T., Sleweon, Sadia, McCormick, David W., Uehara, Anna, Retchless, Adam C., Tong, Suxiang, Folster, Jennifer M., Petway, Marla, Thornburg, Natalie J., Drobeniuc, Jan, Austin, Brett, Hudziec, Meghan M., Stringer, Ginger, Albanese, Bernadette A., Totten, Sarah E., Matzinger, Shannon R., Staples, J. Erin, Killerby, Marie E., Hughes, Laura J., Matanock, Almea, Beatty, Mark, Tate, Jacqueline E., Kirking, Hannah L., and Hsu, Christopher H.

Published
2022
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9. Genomic Surveillance for SARS-CoV-2 Variants Circulating in the United States, December 2020–May 2021

Author

Paul, Prabasaj, France, Anne Marie, Aoki, Yutaka, Batra, Dhwani, Biggerstaff, Matthew, Dugan, Vivien, Galloway, Summer, Hall, Aron J., Johansson, Michael A., Kondor, Rebecca J., Halpin, Alison Laufer, Lee, Brian, Lee, Justin S., Limbago, Brandi, MacNeil, Adam, MacCannell, Duncan, Paden, Clinton R., Queen, Krista, Reese, Heather E., Retchless, Adam C., Slayton, Rachel B., Steele, Molly, Tong, Suxiang, Walters, Maroya S., Wentworth, David E., and Silk, Benjamin J.

Published
2021

14. Epidemiologic and Genomic Evidence for Zoonotic Transmission of SARS-CoV-2 among People and Animals on a Michigan Mink Farm, United States, 2020

Author

Ghai, Ria R., primary, Straily, Anne, additional, Wineland, Nora, additional, Calogero, Jennifer, additional, Stobierski, Mary Grace, additional, Signs, Kimberly, additional, Blievernicht, Melissa, additional, Torres-Mendoza, Yaritbel, additional, Waltenburg, Michelle A., additional, Condrey, Jillian A., additional, Blankenship, Heather M., additional, Riner, Diana, additional, Barr, Nancy, additional, Schalow, Michele, additional, Goodrich, Jarold, additional, Collins, Cheryl, additional, Ahmad, Ausaf, additional, Metz, John Michael, additional, Herzegh, Owen, additional, Straka, Kelly, additional, Arsnoe, Dustin M., additional, Duffiney, Anthony G., additional, Shriner, Susan A., additional, Kainulainen, Markus H., additional, Carpenter, Ann, additional, Whitehill, Florence, additional, Wendling, Natalie M., additional, Stoddard, Robyn A., additional, Retchless, Adam C., additional, Uehara, Anna, additional, Tao, Ying, additional, Li, Yan, additional, Zhang, Jing, additional, Tong, Suxiang, additional, and Barton Behravesh, Casey, additional

Published
2023
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16. Outbreak of Neisseria meningitidis serogroup C outside the meningitis belt—Liberia, 2017: an epidemiological and laboratory investigation

Author

Konway, Youhn, Wiah, Samson Q, Doedeh, Vivian, Bao, Umaru, Senneh, George, Gorwor, Lawrence, Gonotee, Philemon, Paasewe, Thomas, Tamatai, George, Yarkeh, James, Smith, Samuel, Brima-Davis, Annette, Dauda, George, Monger, Thomas, Gornor-Pewu, Leleh W, Lombeh, Siafa, Wilson, Himiede W, Korvayan, Mark, Dovillie, Nathaniel, Jetoh, Ralph, Taweh, Fahn, Vera Walker, Yatta, Hardy, Patrick, Freeman, Maxwell, George, Geraldine, Kerwillain, Garrison, Toe, Sylvester, Ghartey, Emmanuel, Larway, Lawrence, Gweh, Dedesco, Allen, Denise, Friesen, Suzanne, Gwesa, Gulu, Kinkade, Carl, Reed, Mulbah, Chang, Arthur, George, Josiah, Schier, Joshua, Thomas, Jerry, Diaz, Maureen H, Jenkins, Laurel T, Mahon, Barbara E, Schmink, Susanna E, Joseph, Sandeep J, Waller, Jessica L, Whaley, Melissa J, Winchell, Jonas M, Arthur, Ray R, Fuller, Serena, Christian, Kira, Redd, John T, Yealue, Kwuakuan D M, II, Naiene, Jeremias, Asamoah Frimpong, Joseph, Amo-Addae, Maame, Stephen, Olayinka, Von Gottberg, Anne, Taha, Muhamed, Bozio, Catherine H, Vuong, Jeni, Dokubo, E Kainne, Fallah, Mosoka P, McNamara, Lucy A, Potts, Caelin C, Doedeh, John, Gbanya, Miatta, Retchless, Adam C, Patel, Jaymin C, Clark, Thomas A, Kohar, Henry, Nagbe, Thomas, Clement, Peter, Katawera, Victoria, Mahmoud, Nuha, Djingarey, Harouna M, Perrocheau, Anne, Naidoo, Dhamari, Stone, Mardia, George, Roseline N, Williams, Desmond, Gasasira, Alex, Nyenswah, Tolbert, Wang, Xin, and Fox, LeAnne M

Published
2018
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18. Large Cluster of Neisseria meningitidis Urethritis in Columbus, Ohio, 2015

Author

Bazan, Jose A., Turner, Abigail Norris, Kirkcaldy, Robert D., Retchless, Adam C., Kretz, Cecilia B., Briere, Elizabeth, Tzeng, Yih-Ling, Stephens, David S., Maierhofer, Courtney, Del Rio, Carlos, Abrams, A. Jeanine, Trees, David L., Ervin, Melissa, Licon, Denisse B., Fields, Karen S., Roberts, Mysheika Williams, Dennison, Amanda, and Wang, Xin

Published
2017

25. One Health Investigation of SARS-CoV-2 in People and Animals on Multiple Mink Farms in Utah

Author

Cossaboom, Caitlin M., primary, Wendling, Natalie M., additional, Lewis, Nathaniel M., additional, Rettler, Hannah, additional, Harvey, Robert R., additional, Amman, Brian R., additional, Towner, Jonathan S., additional, Spengler, Jessica R., additional, Erickson, Robert, additional, Burnett, Cindy, additional, Young, Erin L., additional, Oakeson, Kelly, additional, Carpenter, Ann, additional, Kainulainen, Markus H., additional, Chatterjee, Payel, additional, Flint, Mike, additional, Uehara, Anna, additional, Li, Yan, additional, Zhang, Jing, additional, Kelleher, Anna, additional, Lynch, Brian, additional, Retchless, Adam C., additional, Tong, Suxiang, additional, Ahmad, Ausaf, additional, Bunkley, Paige, additional, Godino, Claire, additional, Herzegh, Owen, additional, Drobeniuc, Jan, additional, Rooney, Jane, additional, Taylor, Dean, additional, and Barton Behravesh, Casey, additional

Published
2022
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29. Whole-genome characterization of epidemic Neisseria meningitides serogroup C and resurgence of serogroup W, Niger, 2015

Author

Kretz, Cecilia B., Retchless, Adam C., Sidikou, Fati, Issaka, Bassira, Ousmane, Sani, Schwartz, Stephanie, Tate, Ashley H., Pana, Assimawe, Njanpop-Lafourcade, Berthe-Marie, Nzeyimana, Innocent, Nse, Ricardo Obama, Deghmane, Ala-Eddine, Hong, Eva, Brynildsrud, Ola Bronstad, Novak, Ryan T., Meyer, Sarah A., Oukem-Boyer, Odile Ouwe Missi, Ronveaux, Olivier, Caugant, Dominique A., Taha, Muhamed-Kheir, and Wang, Xin

Subjects
United States. Centers for Disease Control and Prevention -- Analysis, Meningitis -- Genetic aspects -- Analysis, Epidemics -- Genetic aspects -- Sub-Saharan Africa -- Burkina Faso -- Nigeria -- Analysis, Genomics -- Analysis, Genomes -- Analysis, Phylogeny -- Analysis, Antibiotics -- Analysis, Health, World Health Organization, Trumenba (Vaccine)
Abstract

Teisseria meningitidis commonly causes meningitis in the African meningitis belt, where periodic meningococcal epidemics have contributed to the highest reported incidence of meningococcal meningitis in the world (1). Most meningococcal [...]

Published
2016
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31. Benchmark datasets for SARS-CoV-2 surveillance bioinformatics

Author

Xiaoli, Lingzi, primary, Hagey, Jill V., additional, Park, Daniel J., additional, Gulvik, Christopher A., additional, Young, Erin L., additional, Alikhan, Nabil-Fareed, additional, Lawsin, Adrian, additional, Hassell, Norman, additional, Knipe, Kristen, additional, Oakeson, Kelly F., additional, Retchless, Adam C., additional, Shakya, Migun, additional, Lo, Chien-Chi, additional, Chain, Patrick, additional, Page, Andrew J., additional, Metcalf, Benjamin J., additional, Su, Michelle, additional, Rowell, Jessica, additional, Vidyaprakash, Eshaw, additional, Paden, Clinton R., additional, Huang, Andrew D., additional, Roellig, Dawn, additional, Patel, Ketan, additional, Winglee, Kathryn, additional, Weigand, Michael R., additional, and Katz, Lee S., additional

Published
2022
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32. Household Transmission and Symptomology of Severe Acute Respiratory Syndrome Coronavirus 2 Alpha Variant among Children—California and Colorado, 2021

Author

Waltenburg, Michelle A., primary, Whaley, Melissa J., additional, Chancey, Rebecca J., additional, Donnelly, Marisa A.P., additional, Chuey, Meagan R., additional, Soto, Raymond, additional, Schwartz, Noah G., additional, Chu, Victoria T., additional, Sleweon, Sadia, additional, McCormick, David W., additional, Uehara, Anna, additional, Retchless, Adam C., additional, Tong, Suxiang, additional, Folster, Jennifer M., additional, Petway, Marla, additional, Thornburg, Natalie J., additional, Drobeniuc, Jan, additional, Austin, Brett, additional, Hudziec, Meghan M., additional, Stringer, Ginger, additional, Albanese, Bernadette A., additional, Totten, Sarah E., additional, Matzinger, Shannon R., additional, Staples, J. Erin, additional, Killerby, Marie E., additional, Hughes, Laura J., additional, Matanock, Almea, additional, Beatty, Mark, additional, Tate, Jacqueline E., additional, Kirking, Hannah L., additional, Hsu, Christopher H., additional, Alford, Alexis, additional, Baird, Samuel, additional, Bankers, Laura, additional, Bello, Jazmin, additional, Bolcen, Shanna, additional, Browning, Peter, additional, Cook, Peter W., additional, David, Ebenezer, additional, Harcourt, Jennifer L., additional, Hareland, Geir, additional, Hetherington-Rauth, Molly C., additional, Ir, Diana, additional, Jain, Shilpi, additional, Jia, Tao Lily, additional, Johnson, Ralen, additional, Kelleher, Anna, additional, Kim, Gimin, additional, Li, Yan, additional, Lynch, Brian, additional, Mallal, Daniel, additional, Maniatis, Panagiotis, additional, Marine, Rachel, additional, Medrzycki, Magdalena, additional, Metz, John M., additional, Montmayeur, Anna Maria, additional, Moss, Kimberly M., additional, Justin Ng, Han Jia, additional, Nyugen, Van, additional, Ortiz, Kristina, additional, Paden, Clinton R., additional, Park, So Hee, additional, Queen, Krista, additional, Rossheim, Alexandria E.B., additional, Semenova, Vera, additional, Shepard, Samuel S., additional, Tamin, Azaibi, additional, Tao, Ying, additional, Tejada-Strop, Alexandra, additional, Wong, Phili, additional, Zellner, Briana, additional, and Zhang, Jing, additional

Published
2022
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34. Invasive Meningococcal Disease Among People Experiencing Homelessness—United States, 2016–2019

Author

Rudmann, Keegan C, primary, Brown, Nicole E, additional, Rubis, Amy B, additional, Burns, Meagan, additional, Ramsey, April, additional, De Las Nueces, Denise, additional, Martin, Tasha, additional, Barnes, Meghan, additional, Davizon, Emily Spence, additional, Retchless, Adam C, additional, Potts, Caelin, additional, Wang, Xin, additional, Hariri, Susan, additional, and McNamara, Lucy A, additional

Published
2022
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35. Detection of Ciprofloxacin-Resistant, β-Lactamase–Producing Neisseria meningitidis Serogroup Y Isolates — United States, 2019–2020

Author

McNamara, Lucy A., Potts, Caelin, Blain, Amy E., Retchless, Adam C., Reese, Natashia, Swint, Stephanie, Lonsway, David, Karlsson, Maria, Lunquest, Kristy, Sweitzer, John J., Wang, Xin, Hariri, Susan, Fox, LeAnne M., Dhungana, Nirmala, Gabrio-Brannon, Ryan, Kyle, Jennifer, Martin, Brittany, Barnes, Meghan, Moore, Ashley, Hannagan, Susan, Keating, Page, Li, Sandy, Albertson, Justin, Fleming, Wayne, Lurie, Perrianne, Russell, Christina, Reid, Kara, Sanders, Kelsey, DeBolt, Chas, Graff, Nicholas, Lam, Esther, Hanisch, Benjamin, and Taormina, Gillian

Subjects
Adult, Male, Health (social science), Cefotaxime, Adolescent, Epidemiology, medicine.drug_class, Health, Toxicology and Mutagenesis, Antibiotics, Neisseria meningitidis, Meningococcal disease, medicine.disease_cause, Serogroup, 01 natural sciences, beta-Lactamases, Microbiology, 03 medical and health sciences, Young Adult, 0302 clinical medicine, Antibiotic resistance, Health Information Management, Ciprofloxacin, Ampicillin, Medicine, Humans, 030212 general & internal medicine, Full Report, 0101 mathematics, Antibiotic prophylaxis, Child, Aged, business.industry, 010102 general mathematics, Infant, Drug Resistance, Microbial, General Medicine, Middle Aged, medicine.disease, United States, Penicillin, Child, Preschool, Female, business, medicine.drug
Abstract

Meningococcal disease is a sudden-onset, life-threatening illness caused by the bacterium Neisseria meningitidis. Prompt empiric antibiotic treatment can reduce morbidity and mortality among patients, and antibiotic prophylaxis can prevent secondary disease in close contacts. Historically, N. meningitidis isolates in the United States have largely been susceptible to the antibiotics recommended for treatment and prophylaxis, including penicillin and ciprofloxacin. This report describes detection of penicillin-resistant and ciprofloxacin-resistant N. meningitidis serogroup Y (NmY) isolates in the United States. NmY isolates containing a blaROB-1 β-lactamase enzyme gene conferring resistance to penicillins (1) were recovered from 33 cases reported during 2013-2020. Isolates from 11 of these cases, reported during 2019-2020, harbored a ciprofloxacin resistance-associated mutation in a chromosomal gene (gyrA). Cases were reported from 12 geographically disparate states; a majority of cases (22 of 33, 67%) occurred in Hispanic persons. These cases represent a substantial increase in penicillin-resistant and ciprofloxacin-resistant meningococci in the United States since 2013. Ceftriaxone and cefotaxime, the recommended first-line agents for empiric bacterial meningitis treatment, can continue to be used for treatment, but health care providers should ascertain susceptibility of meningococcal isolates to penicillin before switching to penicillin or ampicillin. Ongoing monitoring for antimicrobial resistance among meningococcal isolates and prophylaxis failures will be important to inform treatment and prophylaxis recommendations.

Published
2020

38. Transmission of SARS‐CoV‐2 Delta variant (B.1.617.2) from a fully vaccinated human to a canine in Georgia, July 2021

Author

Wendling, Natalie M., primary, Carpenter, Ann, additional, Liew, Amanda, additional, Ghai, Ria R., additional, Gallardo‐Romero, Nadia, additional, Stoddard, Robyn A., additional, Tao, Ying, additional, Zhang, Jing, additional, Retchless, Adam C., additional, Ahmad, Ausaf, additional, Bunkley, Paige, additional, Godino, Claire, additional, Mauldin, Matthew R., additional, Varela, Kate, additional, Ritter, Jana M., additional, Hennebelle, Janemarie, additional, Feldpausch, Amanda, additional, Gabel, Julie, additional, Kainulainen, Markus H., additional, Herzegh, Owen, additional, Tong, Suxiang, additional, Spengler, Jessica R., additional, and Barton Behravesh, Casey, additional

Published
2022
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40. Investigation of SARS-CoV-2 Transmission Associated With a Large Indoor Convention — New York City, November–December 2021

Author

Sami, Samira, primary, Horter, Libby, additional, Valencia, Diana, additional, Thomas, Isabel, additional, Pomeroy, Mary, additional, Walker, Brianna, additional, Smith-Jeffcoat, Sarah E., additional, Tate, Jacqueline E., additional, Kirking, Hannah L., additional, Kyaw, Nang Thu Thu, additional, Burns, Rebecca, additional, Blaney, Kathleen, additional, Dorabawila, Vajeera, additional, Hoen, Rebecca, additional, Zirnhelt, Zachary, additional, Schardin, Cody, additional, Uehara, Anna, additional, Retchless, Adam C., additional, Brown, Vance R., additional, Gebru, Yonathan, additional, Powell, Charles, additional, Bart, Stephen M., additional, Vostok, Johanna, additional, Lund, Hannah, additional, Kaess, Jessica, additional, Gumke, Megan, additional, Propper, Randy, additional, Thomas, Deepam, additional, Ojo, Mojisola, additional, Green, Alison, additional, Wieck, Morgan, additional, Wilson, Erica, additional, Hollingshead, Ryan J., additional, Nunez, Sheila V., additional, Saady, Dawn M., additional, Porse, Charsey Cole, additional, Gardner, Kyle, additional, Drociuk, Daniel, additional, Scott, Julia, additional, Perez, Taidy, additional, Collins, Jim, additional, Shaffner, Julie, additional, Pray, Ian, additional, Rust, Laura T., additional, Brady, Shane, additional, Kerins, Janna L., additional, Teran, Richard A., additional, Hughes, Victoria, additional, Sepcic, Victoria, additional, Low, Eleanor W., additional, Kemble, Sarah K., additional, Berkley, Alexandra, additional, Cleavinger, Kate, additional, Safi, Haytham, additional, Webb, Lindsey Martin, additional, Hutton, Scott, additional, Dewart, Courtney, additional, Dickerson, Kristen, additional, Hawkins, Eric, additional, Zafar, Javeria, additional, Krueger, Anna, additional, Bushman, Dena, additional, Ethridge, Bailee, additional, Hansen, Katrina, additional, Tant, Jake, additional, Reed, Christy, additional, Boutwell, Carla, additional, Hanson, Jennifer, additional, Gillespie, Meagan, additional, Donahue, Matthew, additional, Lane, Pilar, additional, Serrano, Ruby, additional, Hernandez, Lorena, additional, Dethloff, Michelle A., additional, Lynfield, Ruth, additional, Como-Sabetti, Kathryn, additional, Lutterloh, Emily, additional, Ackelsberg, Joel, additional, and Ricaldi, Jessica N., additional

Published
2022
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41. Genomic Insights on Variation Underlying Capsule Expression in Meningococcal Carriage Isolates From University Students, United States, 2015–2016

Author

Whaley, Melissa J., primary, Vuong, Jeni T., additional, Topaz, Nadav, additional, Chang, How-Yi, additional, Thomas, Jennifer Dolan, additional, Jenkins, Laurel T., additional, Hu, Fang, additional, Schmink, Susanna, additional, Steward-Clark, Evelene, additional, Mathis, Marsenia, additional, Rodriguez-Rivera, Lorraine D., additional, Retchless, Adam C., additional, Joseph, Sandeep J., additional, Chen, Alexander, additional, Acosta, Anna M., additional, McNamara, Lucy, additional, Soeters, Heidi M., additional, Mbaeyi, Sarah, additional, Marjuki, Henju, additional, and Wang, Xin, additional

Published
2022
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43. Detection of Ciprofloxacin-Resistant, [beta]-Lactamase-Producing Neisseria meningitidis Serogroup Y Isolates--United States, 2019-2020

Author

McNamara, Lucy A., Potts, Caelin, Blain, Amy E., Retchless, Adam C., Reese, Natashia, Swint, Stephanie, Lonsway, David, Karlsson, Maria, Lunquest, Kristy, Sweitzer, John J., Wang, Xin, Hariri, Susan, and Fox, LeAnne M.

Subjects
Penicillins -- Health aspects, Meningitis -- Prevention -- Care and treatment, Beta lactamases -- Health aspects, Ciprofloxacin -- Health aspects, Health
Abstract

Meningococcal disease is a sudden-onset, life-threatening illness caused by the bacterium Neisseria meningitidis. Prompt empiric antibiotic treatment can reduce morbidity and mortality among patients, and antibiotic prophylaxis can prevent secondary [...]

Published
2020

47. Genetic Diversity of Meningococcal Serogroup B Vaccine Antigens among Carriage Isolates Collected from Students at Three Universities in the United States, 2015–2016

Author

Marjuki, Henju, primary, Chang, How-Yi, additional, Topaz, Nadav, additional, Whaley, Melissa J., additional, Vuong, Jeni, additional, Chen, Alexander, additional, Jenkins, Laurel T., additional, Hu, Fang, additional, Schmink, Susanna, additional, Retchless, Adam C., additional, Thomas, Jennifer D., additional, Acosta, Anna M., additional, McNamara, Lucy A., additional, Soeters, Heidi M., additional, Mbaeyi, Sarah, additional, and Wang, Xin, additional

Published
2021
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49. Benchmark datasets for SARS-CoV-2 surveillance bioinformatics.

Author

Lingzi Xiaoli, Hagey, Jill V., Park, Daniel J., Gulvik, Christopher A., Young, Erin L., Alikhan, Nabil-Fareed, Lawsin, Adrian, Hassell, Norman, Knipe, Kristen, Oakeson, Kelly F., Retchless, Adam C., Shakya, Migun, Chien-Chi Lo, Chain, Patrick, Page, Andrew J., Metcalf, Benjamin J., Su, Michelle, Rowell, Jessica, Vidyaprakash, Eshaw, and Paden, Clinton R.

Subjects
SARS-CoV-2, COVID-19, BIOINFORMATICS software, NUCLEOTIDE sequencing, WHOLE genome sequencing
Abstract

Background. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the cause of coronavirus disease 2019 (COVID-19), has spread globally and is being surveilled with an international genome sequencing effort. Surveillance consists of sample acquisition, library preparation, and whole genome sequencing. This has necessitated a classification scheme detailing Variants of Concern (VOC) and Variants of Interest (VOI), and the rapid expansion of bioinformatics tools for sequence analysis. These bioinformatic tools are means for major actionable results: maintaining quality assurance and checks, defining population structure, performing genomic epidemiology, and inferring lineage to allow reliable and actionable identification and classification. Additionally, the pandemic has required public health laboratories to reach high throughput proficiency in sequencing library preparation and downstream data analysis rapidly. However, both processes can be limited by a lack of a standardized sequence dataset. Methods. We identified six SARS-CoV-2 sequence datasets from recent publications, public databases and internal resources. In addition, we created a method to mine public databases to identify representative genomes for these datasets. Using this novel method, we identified several genomes as either VOI/VOC representatives or non-VOI/VOC representatives. To describe each dataset, we utilized a previously published datasets format, which describes accession information and whole dataset information. Additionally, a script from the same publication has been enhanced to download and verify all data from this study. Results. The benchmark datasets focus on the two most widely used sequencing platforms: long read sequencing data from the Oxford Nanopore Technologies platform and short read sequencing data from the Illumina platform. There are six datasets: three were derived from recent publications; two were derived from data mining public databases to answer common questions not covered by published datasets; one unique dataset representing common sequence failures was obtained by rigorously scrutinizing data that did not pass quality checks. The dataset summary table, data mining script and quality control (QC) values for all sequence data are publicly available on GitHub: https://github.com/CDCgov/datasets-sars-cov-2. Discussion. The datasets presented here were generated to help public health laboratories build sequencing and bioinformatics capacity, benchmark different workflows and pipelines, and calibrate QC thresholds to ensure sequencing quality. Together, improvements in these areas support accurate and timely outbreak investigation and surveillance, providing actionable data for pandemic management. Furthermore, these publicly available and standardized benchmark data will facilitate the development and adjudication of new pipelines. [ABSTRACT FROM AUTHOR]

Published
2022
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50. Genomic Insights into Xylella fastidiosa Interactions with Plant and Insect Hosts

Author

Retchless, Adam C, Labroussaa, Fabien, Shapiro, Lori, Stenger, Drake C, Lindow, Steven E, and Almeida, Rodrigo PP

Subjects
Genetics, Human Genome, Biotechnology
Abstract

The genome of Xylella fastidiosa encodes the properties that enable it to alternately colonize its plant and insect hosts. In this chapter, we take a holistic approach and explore X. fastidiosa evolution, biology, and management based on information and insights that would not have been possible, or would have been technically challenging, during the pre-genomics period of plant pathology. Analysis of genome sequences illustrates the major physiological differences between X. fastidiosa and plant pathogens in the sibling genus Xanthomonas, which possess substantially larger genomes and a variety of genes that are essential for pathogenicity, yet absent from the X. fastidiosa genome. Genome sequence data have enabled reverse-genetic approaches to transfer knowledge from more genetically tractable organisms, along with examination of gene regulatory effects that are involved in colonization of the various hosts. The availability of reference genome sequences has also facilitated the examination of genetic diversity among X. fastidiosa found in different geographic regions and different host plants. Existing data demonstrates the importance of mobile genetic elements in producing genetic diversity among X. fastidiosa isolates. Genome-wide descriptions of diversity will be a powerful tool to identify the genetic changes that underlie the emergence of new agricultural diseases.

Published
2014

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