Respiratory References

CE Express Course References

The Revenge of the Microbes: The Conjugate Congress of Antibiotic Resistance

Acharyya, S., Sarkar, P., Saha, D. R., Patra, A., Ramamurthy, T., & Bag, P. K. (2015). Intracellular and membrane-damaging activities of methyl gallate isolated from Terminalia chebula against multidrug- resistant Shigella spp. Journal of Medical Microbiology, 64(8), 901-909.

Allen, H. K., Cloud-Hansen, K. A., Wolinski, J. M., Guan, C., Greene, S., Lu, S., … Handelsman, J. (2009). Resident microbiota of the gypsy moth midgut harbors antibiotic resistance determinants. DNA and Cell Biology, 28(3), 109-117.

Allen, H. K., Donato, J., Wang, H. H., Cloud-Hansen, K. A., Davies, J., & Handelsman, J. (2010). Call of the wild: Antibiotic resistance genes in natural environments. Nature Reviews Microbiology, 8(4), 251-259.

Allen, H. K., Moe, L. A., Rodbumrer, J., Gaarder, A., & Handelsman, J. (2009). Functional metagenomics reveals diverse β-lactamases in a remote Alaskan soil. ISME Journal, 3(2), 243-251.

Aminov, R. I. (2009). The role of antibiotics and antibiotic resistance in nature. Environmental Microbiology, 11(12), 2970-2988.

Anandan, S., Damodaran, S., Gopi, R., Bakthavatchalam, Y. D., & Veeraraghavan, B. (2015). Rapid screening for carbapenem resistant organisms: Current results and future approaches. Journal of Clinical and Diagnostic Research, 9(9), DM01-DM03.

Bager, F., Madsen, M., Christensen, J., & Aarestrup, F. M. (1997). Avoparcin used as a growth promoter is associated with the occurrence of vancomycin-resistant Enterococcus faecium on Danish poultry and pig farms. Preventive Veterinary Medicine, 31(1-2), 95-112.

Bantubani, N., Kabera, G., Connolly, C., Rustomjee, R., Reddy, T., Cohen, T., & Pym, A. S. (2014). High rates of potentially infectious tuberculosis and multidrug-resistant tuberculosis (MDR-TB) among hospital inpatients in KwaZulu Natal, South Africa indicate risk of nosocomial transmission. PLOS ONE, 9(3), e90868.

Baquero, F., Martínez, J. L., & Cantón, R. (2008). Antibiotics and antibiotic resistance in water environments. Current Opinion in Biotechnology, 19(3), 260-265.

Berger, C. N., Sodha, S. V., Shaw, R. K., Griffin, P. M., Pink, D., Hand, P., & Frankel, G. (2010). Fresh fruit and vegetables as vehicles for the transmission of human pathogens. Environmental Microbiology, 12(9), 2385-2397.

Brito, G., Sullivan, G., Ciesla, W., Jr., Carper, H., Mandell, G., & Guerrant, R. (2002). Clostridium difficile toxin A alters in vitro-adherent neutrophil morphology and function. The Journal of Infectious Diseases, 185(9), 1297-1306.

Camp, C., & Tatum, O. A. (2010). Review of Acinetobacter baumannii as a highly successful pathogen in times of war. Laboratory Medicine, 41(11), 649-657.

Cantón, R. (2009). Antibiotic resistance genes from the environment: A perspective through newly identified antibiotic resistance mechanisms in the clinical setting. Clinical Microbiology and Infection, 15(Suppl. 1), S20-S25.

Choffnes, E. R., Relman, D. A., & Mack, A. (2010). Antibiotic resistance: Implications for global health and novel intervention strategies. Workshop summary. Forum on microbial threats, Institute of Medicine, Washington, DC.

Clatworthy, A. E., Pierson, E., & Hung, D. T. (2007). Targeting virulence: A new paradigm for antimicrobial therapy. Nature Chemical Biology, 3(9), 541-548.

Crump, J. A., Sjölund-Karlsson, M., Gordon, M. A., & Parry, C. M. (2015). Epidemiology, clinical presentation, laboratory diagnosis, antimicrobial resistance, and antimicrobial management of invasive Salmonella infections. Clinical Microbiology Reviews, 28(4), 901-937.

Dantas, G., Sommer, M. O. A., Oluwasegun, R. D., & Church, G. M. (2008). Bacteria subsisting on antibiotics. Science, 320(5872), 100-103.

Davies, J., & Davies, D. (2010). Origins and evolution of antibiotic resistance. Microbiology and Molecular Biology Reviews, 74(3), 417-433.

D’Costa, V. M., Griffiths, E., & Wright, G. D. (2007). Expanding the soil antibiotic resistome: Exploring environmental diversity. Current Opinions in Microbiology, 10, 481-489.

Demanèche, S., Sanguin, H., Poté, J., Navarro, E., Bernillon, D., Mavingui, P., … Simonet, P. (2008). Antibiotic-resistant soil bacteria in transgenic plant fields. Proceedings of the National Academies of Science, 105, 3957-3962.

Deschamps, C., Clermont, O., Hipeaux, M. C., Arlet, G., Denamur, E., & Branger, C. (2009). Multiple acquisitions of CTX-M plasmids in the rare D2 genotype of Escherichia coli provide evidence for convergent evolution. Microbiology, 155, 1656-1668.

Dethlefsen, L., & Relman, D. A. (2011). Incomplete recovery and individualized responses of the human distal gut microbiota to repeated antibiotic perturbation. Proceedings of the National Academies of Science, 108(Suppl. 1), S4554-S4561.

Donato, J. J., Moe, L. A., Converse, B. J., Smart, K. D., Berklein, F. C., McManus, P. S., & Handelsman, J. (2010). Metagenomic analysis of apple orchard soil reveals antibiotic resistance genes encoding predicted bifunctional proteins. Applied and Environmental Microbiology, 76, 4396-4401.

Durso, L. M., Harhay, G. P., Bono, J. L., & Smith, T. P. L. (2011). Virulence-associated and antibiotic resistance genes of microbial populations in cattle feces analyzed using a metagenomic approach. Journal of Microbiological Methods, 84, 278-282.

Edelblute, C. M., Pakhomova, O. N., Li, F., Hargrave, B. Y., & Heller, L. C. (2015). Donor platelet plasma components inactivate sensitive and multidrug resistant Acinetobacter baumannii isolates. Pathogens and Disease, 73(9). doi:10.1093/femspd/ftv095

Edwards, B., Andini, R., Esposito, S., Grossi, P., Lew, D., Mazzei, T., & Gould, I. M. (2014). Treatment options for methicillin-resistant Staphylococcus aureus (MRSA) infection: Where are we now? Journal of Global Antimicrobial Resistance, 2(3), 133-140.

Elmi, O. S., Hasan, H., Abdullah, S., Mat Jeab, M. Z., Bin Alwi, Z., & Naing, N. N. (2015). Multidrugresistant tuberculosis and risk factors associated with its development: A retrospective study. Journal of Infection in Developing Countries, 9(10), 1076-1085.

Fajardo, A., & Martínez, J. L. (2008). Antibiotics as signals that trigger specific bacterial responses. Current Opinion in Microbiology, 11, 161-167.

Freeman, J., Bauer, M., Baines, S., Corver, J., Fawley, W., Goorhuis, B., & Wilcox, M. (2010). The changing epidemiology of Clostridium difficile infections. Clinical Microbiology Reviews, 23(3), 529-549.

Gupta, N., Limbago, B. M., Patel, J. B., & Kallen, A. J. (2011). Carbapenem-resistant Enterobacteriaceae: Epidemiology and prevention. Clinical Infectious Diseases, 53(1), 60-67.

Hegstad, K., Mikalsen, T., Coque, T. M., Werner, G., & Sundsfjord, A. (2010). Mobile genetic elements and their contribution to the emergence of antimicrobial resistant Enterococcus faecalis and Enterococcus faecium. Clinical Microbiology and Infection, 16(6), 541-554.

Jakobsson, H. E., Jernberg, C., Andersson, A. F., Sjölund-Karlsson, M., Jansson, J. K., & Engstrand, L. (2010). Short-term antibiotic treatment has differing long-term impacts on the human throat and gut microbiome. PLOS ONE, 5, e9836.

Jernberg, C., Löfmark, S., Edlund, C., & Jansson, J. K. (2010). Long-term impacts of antibiotic exposure on the human intestinal microbiota. Microbiology, 156, 3216-3223.

Jeters, R. T., Wang, G. R., Moon, K., Shoemaker, N. B., & Salyers, A. A. (2009). Tetracyclineassociated transcriptional regulation of transfer genes of the Bacteroides conjugative transposon CTnDOT. Journal of Bacteriology, 191, 6374-6382.

Kaur, J., & Jain, S. (2012). Role of antigens and virulence factors of Salmonella enterica serovar Typhi in its pathogenesis. Microbiological Research, 167(4), 199-210.

Khanam, F., Sayeed, M. A., Choudhury, F. K., Sheikh, A., Ahmed, D., Goswami, D., … Qadri, F. (2015). Typhoid fever in young children in Bangladesh: Clinical findings, antibiotic susceptibility pattern and immune responses. PLOS Neglected Tropical Diseases, 9(4), e0003619.

Koenig, J. E., Spor, A., Scalfone, N., Fricker, A. D., Stombaugh, J., Knight, R., … Ley, R. E. (2011). Succession of microbial consortia in the developing infant gut microbiome. Proceedings of the National Academy of Sciences, 108(Suppl. 1), S4578-S4585.

Kotsanas, D., Wijesooriya, W. R., Korman, T. M., Gillespie, E. E., Wright, L., Snook, K., … Stuart, R. L. (2013). “Down the drain”: Carbapenem-resistant bacteria in intensive care unit patients and handwashing sinks. Medical Journal of Australia, 198(5), 267-269.

Kristiansson, E., Fick, J., Janzon, A., Grabic, R., Rutgersson, C., Weijdegård, B., … Larsson, D. G. (2011). Pyrosequencing of antibiotic-contaminated river sediments reveals high levels of resistance and gene transfer elements. PLOS ONE, 6, e17038.

Kupsch, E., Knepper, B., Kuroki, T., Heuer, I., & Meyer, T. (1993). Variable opacity (Opa) outer membrane proteins account for the cell tropisms displayed by Neisseria gonorrhoeae for human leukocytes and epithelial cells. The EMBO Journal, 12(2), 641-650.

Lang, K. S., Anderson, J. M., Schwarz, S., Williamson, L., Handelsman, J., & Singer, R. S. (2010). Novel florfenicol and chloramphenicol resistance gene discovered in Alaskan soil by using functional metagenomics. Applied and Environmental Microbiology, 76, 5321-5326.

Leinonen, R., Sugawara, H., & Shumway, M. (2011). The sequence read archive. Nucleic Acids Research, 39, D19-D21.

Ley, R. E., Peterson, D. A., & Gordon, J. I. (2006). Ecological and evolutionary forces shaping microbial diversity in the human intestine. Cell, 124, 837-848.

Linares, J. F., Gustafsson, I., Baquero, F., & Martinez, J. L. (2006). Antibiotics as intermicrobial signaling agents instead of weapons. Proceedings of the National Academy of Sciences, 103, 19484-19489.

Lu, K., Asano, R., & Davies, J. (2004). Antimicrobial resistance gene delivery in animal feeds. Emerging Infectious Diseases, 10, 679-683.

Martinez, J. L. (2009). Environmental pollution by antibiotics and by antibiotic resistance determinants. Environmental Pollution, 157, 2893-2902.

Martinez, J. L., Sánchez, M. B., Martínez-Solano, L., Hernandez, A., Garmendia, L., Fajardo, A., & Alvarez-Ortega, C. (2009). Functional role of bacterial multidrug efflux pumps in microbial natural ecosystems. FEMS Microbiology Review, 33, 430-449.

Mirzaagha, P., Louie, M., Sharma, R., Yanke, L. J., Topp, E., & McAllister, T. A. (2011). Distribution and characterization of ampicillin- and tetracycline-resistant Escherichia coli from feedlot cattle fed subtherapeutic antimicrobials. BMC Microbiology, 11, 78.

Monier, J. M., Demanèche, S., Delmont, T. O., Mathieu, A., Vogel, T. M., & Simonet, P. (2011). Metagenomic exploration of antibiotic resistance in soil. Current Opinion in Microbiology, 14, 229-235.

Moran, M. A. (2009). Metatranscriptomics: Eavesdropping on complex microbial communities. Microbe, 4, 329-335.

Morar, M., & Wright, G. D. (2010). The genomic enzymology of antibiotic resistance. Annual Review of Genetics, 44, 25-51.

Mori, T., Mizuta, S., Suenaga, H., & Miyazaki, K. (2008). Metagenomic screening for bleomycin resistance genes. Applied and Environmental Microbiology, 74, 6803-6805.

Murray, J. L., Kwon, T., Marcotte, E. M., & Whiteley, M. (2015). Intrinsic antimicrobial resistance determinants in the superbug Pseudomonas aeruginosa. MBio, 6(6), e01603- e01615.

Nasrollahi, Z., Yadegari, M. H., Roudbar Mohammadi, S., Roudbary, M., Hosseini Poor, M., Nikoomanesh, F., & Rajabi Bazl, M. (2015). Fluconazole resistance Candida albicans in females with recurrent vaginitis and pir1 overexpression. Jundishapur Journal of Microbiology, 8(9), e21468.

North, E. J., Jackson, M., & Lee, R. E. (2014). New approaches to target the mycolic acid biosynthesis pathway for the development of tuberculosis therapeutics. Current Pharmaceutical Design, 20(27), 4357-4378.

Pallecchi, L., Bartoloni, A., Paradisi, F., & Rossolini, G. M. (2008). Antibiotic resistance in the absence of antimicrobial use: Mechanisms and implications. Expert Review of Anti-infective Therapy, 6, 725-732.

Palmer, K. L., Kos, V. N., & Gilmore, M. S. (2010). Horizontal gene transfer and the genomics of enterococcal antibiotic resistance. Current Opinion in Microbiology, 13, 632-639.

Pappas, G. (2011). An animal farm called extended-spectrum β-lactamase: Antimicrobial resistance as a zoonosis. Clinical Microbiology and Infection, 17(6), 797-798.

Paredes-Sabja, D., Shen, A., & Sorg, J. (2014). Clostridium difficile spore biology: Sporulation, germination, and spore structural proteins. Trends in Microbiology, 22(7), 406-416.

Parsley, L. C., Consuegra, E. J., Kakirde, K. S., Land, A. M., Harper, W. F., Jr., & Liles, M. R. (2010). Identification of diverse antimicrobial resistance determinants carried on bacterial, plasmid, or viral metagenomes from an activated sludge microbial assemblage. Applied and Environmental Microbiology, 76, 3753-3757.

Peterson, J., Garges, S., Giovanni, M., McInnes, P., Wang, L., Schloss, J. A., … Guyer, M. (2009). The NIH human microbiome project. Genome Research, 19(12), 2317-2323.

Qin, J., Li, R., Raes, J., Arumugam, M., Burgdorf, K. S., Manichanh, C., … Wang J. (2010). A human gut microbial gene catalogue established by metagenomic sequencing. Nature, 464, 59-65.

Rieg, S., Küpper, M. F., de With, K., Serr, A., Bohnert, J. A., & Kern, W. V. (2015). Intestinal decolonization of Enterobacteriaceae producing extended-spectrum β-lactamases (ESBL): A retrospective observational study in patients at risk for infection and a brief review of the literature. BMC Infectious Diseases, 15, 475.

Roumie, C. L., Halasa, N. B., Grijalva, C. G., Edwards, K. M., Zhu, Y., Dittus, R. S., & Griffin, M. R. (2005). Trends in antibiotic prescribing for adults in the United States – 1995 to 2002. Journal of General Internal Medicine, 20, 697-702.

Schadt, E. E., Linderman, M. D., Sorenson, J., Lee, L., & Nolan, G. P. (2010). Computational solutions to large-scale data management and analysis. Nature Reviews Genetics, 11, 647-657.

Schlüter, A., Krause, L., Szczepanowski, R., Goesmann, A., & Pühler, A. (2008). Genetic diversity and composition of a plasmid metagenome from a wastewater treatment plant. Journal of Biotechnology, 136, 65-76.

Seville, L. A., Patterson, A. J., Scott, K. P., Mullany, P., Quail, M. A., Parkhill, J., … Roberts, A. P. (2009). Distribution of tetracycline and erythromycin resistance genes among human oral and fecal metagenomic DNA. Microbial Drug Resistance, 15, 159-166.

Shaheen, B. W., Wang, C., Johnson, C. M., Kaltenboeck, B., & Boothe, D. M. (2009). Detection of fluoroquinolone resistance level in clinical canine and feline Escherichia coli pathogens using rapid real-time PCR assay. Veterinary Microbiology, 139, 379-385.

Singh, A., Kumar, D., Ali, M., & Chander, Y. (2014). Antimicrobial susceptibility profile of extended spectrum β-lactamase (ESBL) producing Escherichia coli from various clinical samples. Infectious Diseases, 7, 1-8.

Sommer, M. O. A., Church, G. M., & Dantas, G. (2010). The human microbiome harbors a diverse reservoir of antibiotic resistance genes. Virulence, 1(4), 299-303.

Sommer, M. O. A., Dantas, G., & Church, G. M. (2009). Functional characterization of the antibiotic resistance reservoir in the human microflora. Science, 325, 1128-1131.

Spížek, J., Novotná, J., Rezanka, T., & Demain, A. L. (2010). Do we need new antibiotics? The search for new targets and new compounds. Journal of Industrial Microbiology and Biotechnology, 37, 1241-1248.

Sterling, S. A., Miller, W. R., Pryor, J., Puskarich, M. A., & Jones, A. E. (2015). The impact of timing of antibiotics on outcomes in severe sepsis and septic shock: A systematic review and meta-analysis. Critical Care Medicine, 43(9), 1907-1915.

Su, X. H., Wang, B. X., Le, W. J., Liu, Y. R., Wan, C., Li, S., … Rice, P. A. (2015). Multidrug resistant Neisseria gonorrhoeae from Nanjing are sensitive to killing by a novel DNA gyrase inhibitor, ETX0914 (AZD0914). Antimicrobial Agents and Chemotherapy, 60(1), 621-623. doi:10.1128/AAC.01211-15

Sun, S., Chen, J., Li, W., Altintas, I., Lin, A., Peltier, S., … Wooley, J. (2011). Community cyberinfrastructure for advanced microbial ecology research and analysis: The CAMERA resource. Nucleic Acids Research, 39, D546-D551.

Szczepanowski, R., Linke, B., Krahn, I., Gartemann, K. H., Gützkow, T., Eichler, W., … Schlüter, A. (2009). Detection of 140 clinically relevant antibiotic-resistance genes in the plasmid metagenome of wastewater treatment plant bacteria showing reduced susceptibility to selected antibiotics. Microbiology, 155, 2306-2319.

Tong, S. Y., Davis, J. S., Eichenberger, E., Holland, T. L., & Fowler, V. G. (2015). Staphylococcus aureus infections: Epidemiology, pathophysiology, clinical manifestations, and management. Clinical Microbiology Reviews, 28(3), 603-661.

Torres-Cortés, G., Millán, V., Ramírez-Saad, H. C., Nisa-Martínez, R., Toro, N., & Martínez-Abarca, F. (2011). Characterization of novel antibiotic resistance genes identified by functional metagenomics on soil samples. Environmental Microbiology, 13, 1101-1114. Trevors, J. T. (2010). One gram of soil: A microbial biochemical gene library. Antonie van Leeuwenhoek, 97(2), 99-106.

Tringe, S. G., & Rubin, E. M. (2005). Metagenomics: DNA sequencing of environmental samples. Nature Reviews Genetics, 6, 805-814.

Uchiyama, T., & Miyazaki, K. (2009). Functional metagenomics for enzyme discovery: Challenges to efficient screening. Current Opinion in Biotechnology, 20, 616-622.

Wegley, L., Edwards, R., Rodriguez-Brito, B., Liu, H., & Rohwer, F. (2007). Metagenomic analysis of the microbial community associated with the coral Porites astreoides. Environmental Microbiology, 9, 2707-2719.

Williams, M. M., Armbruster, C. R., & Arduino, M. J. (2013). Plumbing of hospital premises is a reservoir for opportunistically pathogenic microorganisms: A review. Biofouling, 29(2), 147-162.

Wright, G. D. (2010). Antibiotic resistance in the environment: A link to the clinic? Current Opinion in Microbiology, 13, 589-594.

Xi, C., Zhang, Y., Marrs, C. F., Ye, W., Simon, C., Foxman, B., & Nriagu, J. (2009). Prevalence of antibiotic resistance in drinking water treatment and distribution systems. Applied and Environmental Microbiology, 75, 5714-5718.

Yim, G., Wang, H. H., & Davies, J. (2007). Antibiotics as signaling molecules. Philosophical Transactions of the Royal Society B Biological Sciences, 362, 1195-1200.

Zarrilli, R., Triassi, M., & Khan, A. U. (2012). Multidrug-resistant Acinetobacter baumannii: An emerging threat in health care facilities. In A. U. Khan & R. Zarrilli (Eds.), Multi drug resistance: A global concern (pp. 142-150). Oak Park, IL: Bentham Science.