{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,23]],"date-time":"2026-10-23T00:08:37Z","timestamp":1792714117802,"version":"4.5.0"},"reference-count":81,"publisher":"American Society for Microbiology","issue":"7","license":[{"start":{"date-parts":[[2025,7,1]],"date-time":"2025-07-01T00:00:00Z","timestamp":1751328000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2025,7,1]],"date-time":"2025-07-01T00:00:00Z","timestamp":1751328000000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/journals.asm.org\/non-commercial-tdm-license"}],"funder":[{"DOI":"10.13039\/501100001804","name":"Canada Research Chairs","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100001804","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000046","name":"National Research Council Canada","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100000046","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["journals.asm.org"],"crossmark-restriction":true},"short-container-title":["Microbiol Spectr"],"published-print":{"date-parts":[[2025,7]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n                  <jats:sec>\n                    <jats:title\/>\n                    <jats:p>\n                      <jats:italic toggle=\"yes\">Acinetobacter baumannii<\/jats:italic>\n                      is a significant nosocomial bacterial pathogen that poses a substantial infection risk due to its high resistance to antibiotics and ability to survive in hospital environments. In this study, we performed comprehensive\n                      <jats:italic toggle=\"yes\">in silico<\/jats:italic>\n                      and\n                      <jats:italic toggle=\"yes\">in vitro<\/jats:italic>\n                      analyses on\n                      <jats:italic toggle=\"yes\">79 A. baumannii<\/jats:italic>\n                      clinical isolates from different geographical locations to uncover their genomic and epidemiological characteristics as well as their antibiotic and phage susceptibilities. Our findings revealed considerable genomic diversity among the isolates, as shown by average nucleotide identity (ANI) heat maps, multilocus sequence typing (MLST), and core genome MLST (cgMLST). We identified several international clones known for their high antibiotic resistance and global prevalence. Surprisingly, we also observed that the number of antimicrobial resistance genes (ARGs) was higher in isolates containing CRISPR-Cas systems. Plaque assays with 13 phages indicated that\n                      <jats:italic toggle=\"yes\">Acinetobacter<\/jats:italic>\n                      phages have a narrow host range, with capsule loci (KL) serving as a good indicator of phage-bacteria interactions. The presence of CRISPR-Cas systems and other antiviral defense mechanisms in\n                      <jats:italic toggle=\"yes\">A. baumannii<\/jats:italic>\n                      genomes also appears to play a key role in providing phage resistance, regardless of the phage receptors. We also found that spacers associated with subtypes I-F1 and I-F2 CRISPR-Cas systems predominantly target prophages, suggesting a role in maintaining genomic stability and contributing to phage-bacteria co-evolution. Overall, this study provides a set of highly characterized\n                      <jats:italic toggle=\"yes\">A. baumannii<\/jats:italic>\n                      clinical isolates for future studies on antibiotic-phage-bacteria interactions.\n                    <\/jats:p>\n                    <jats:sec>\n                      <jats:title>IMPORTANCE<\/jats:title>\n                      <jats:p>\n                        <jats:italic toggle=\"yes\">Acinetobacter baumannii<\/jats:italic>\n                        poses a significant challenge to the healthcare system due to its antibiotic resistance and strong survival mechanisms. This study examines a diverse collection of 79 clinical isolates to deepen our understanding of\n                        <jats:italic toggle=\"yes\">A. baumannii<\/jats:italic>\n                        \u2019s genetic characteristics and its defense mechanisms against both antibiotics and phages. Genomic analysis revealed globally prevalent, highly resistant clones and uncovered a complex role for CRISPR-Cas systems. Although CRISPR-Cas systems were not widespread among these isolates, they primarily targeted prophages. Additionally, the study emphasizes the importance of capsule types as indicators of phage susceptibility. Together, these findings provide insights into the pathogen\u2019s resilience and evolutionary adaptations, potentially guiding future research on infection control strategies and new therapeutic approaches to combat\n                        <jats:italic toggle=\"yes\">A. baumannii<\/jats:italic>\n                        infections.\n                      <\/jats:p>\n                    <\/jats:sec>\n                  <\/jats:sec>","DOI":"10.1128\/spectrum.02849-24","type":"journal-article","created":{"date-parts":[[2025,5,16]],"date-time":"2025-05-16T09:00:51Z","timestamp":1747386051000},"update-policy":"https:\/\/doi.org\/10.1128\/asmj-crossmark-policy-page","source":"Crossref","is-referenced-by-count":7,"title":["<i>In silico<\/i>\n                    and\n                    <i>in vitro<\/i>\n                    comparative analysis of 79\n                    <i>Acinetobacter baumannii<\/i>\n                    clinical isolates"],"prefix":"10.1128","volume":"13","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-4300-2818","authenticated-orcid":false,"given":"Martina","family":"Scarrone","sequence":"first","affiliation":[{"id":[{"id":"https:\/\/ror.org\/04sjchr03","id-type":"ROR","asserted-by":"publisher"}],"name":"D\u00e9partement de biochimie, de microbiologie et de bio-Informatique, Facult\u00e9 des sciences et de g\u00e9nie, Universit\u00e9 Laval","place":["Quebec City, Canada"]},{"id":[{"id":"https:\/\/ror.org\/04sjchr03","id-type":"ROR","asserted-by":"publisher"}],"name":"Institut de biologie int\u00e9grative et des syst\u00e8mes (IBIS), Universit\u00e9 Laval","place":["Quebec City, Canada"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dann","family":"Turner","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/02nwg5t34","id-type":"ROR","asserted-by":"publisher"}],"name":"School of Applied Sciences, College of Health, Science and Society, University of the West of England","place":["Bristol, United Kingdom"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mo\u00efra","family":"Dion","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/04sjchr03","id-type":"ROR","asserted-by":"publisher"}],"name":"D\u00e9partement de biochimie, de microbiologie et de bio-Informatique, Facult\u00e9 des sciences et de g\u00e9nie, Universit\u00e9 Laval","place":["Quebec City, Canada"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0008-7544-1739","authenticated-orcid":false,"given":"Denise","family":"Tremblay","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/04sjchr03","id-type":"ROR","asserted-by":"publisher"}],"name":"D\u00e9partement de biochimie, de microbiologie et de bio-Informatique, Facult\u00e9 des sciences et de g\u00e9nie, Universit\u00e9 Laval","place":["Quebec City, Canada"]},{"id":[{"id":"https:\/\/ror.org\/04sjchr03","id-type":"ROR","asserted-by":"publisher"}],"name":"Institut de biologie int\u00e9grative et des syst\u00e8mes (IBIS), Universit\u00e9 Laval","place":["Quebec City, Canada"]},{"id":[{"id":"https:\/\/ror.org\/04sjchr03","id-type":"ROR","asserted-by":"publisher"}],"name":"F\u00e9lix d\u2019H\u00e9relle Reference Center for Bacterial Viruses, Universit\u00e9 Laval","place":["Quebec City, Canada"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2832-5101","authenticated-orcid":true,"given":"Sylvain","family":"Moineau","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/04sjchr03","id-type":"ROR","asserted-by":"publisher"}],"name":"D\u00e9partement de biochimie, de microbiologie et de bio-Informatique, Facult\u00e9 des sciences et de g\u00e9nie, Universit\u00e9 Laval","place":["Quebec City, Canada"]},{"id":[{"id":"https:\/\/ror.org\/04sjchr03","id-type":"ROR","asserted-by":"publisher"}],"name":"Institut de biologie int\u00e9grative et des syst\u00e8mes (IBIS), Universit\u00e9 Laval","place":["Quebec City, Canada"]},{"id":[{"id":"https:\/\/ror.org\/04sjchr03","id-type":"ROR","asserted-by":"publisher"}],"name":"F\u00e9lix d\u2019H\u00e9relle Reference Center for Bacterial Viruses, Universit\u00e9 Laval","place":["Quebec City, Canada"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"235","reference":[{"key":"e_1_3_4_2_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.jinf.2019.09.012"},{"key":"e_1_3_4_3_2","doi-asserted-by":"publisher","DOI":"10.1128\/CMR.00058-07"},{"key":"e_1_3_4_4_2","doi-asserted-by":"publisher","DOI":"10.1016\/S1473-3099(17)30753-3"},{"key":"e_1_3_4_5_2","doi-asserted-by":"publisher","DOI":"10.1186\/s12866-019-1687-0"},{"key":"e_1_3_4_6_2","doi-asserted-by":"publisher","DOI":"10.1093\/ofid\/ofaa378"},{"key":"e_1_3_4_7_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.ijid.2013.03.021"},{"key":"e_1_3_4_8_2","doi-asserted-by":"publisher","DOI":"10.1007\/s11356-015-5586-0"},{"key":"e_1_3_4_9_2","doi-asserted-by":"publisher","DOI":"10.1111\/jcpt.13787"},{"key":"e_1_3_4_10_2","doi-asserted-by":"publisher","DOI":"10.3389\/fcimb.2023.1053968"},{"key":"e_1_3_4_11_2","doi-asserted-by":"publisher","DOI":"10.1128\/CMR.00058-16"},{"key":"e_1_3_4_12_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.ppat.1009291"},{"key":"e_1_3_4_13_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0062160"},{"key":"e_1_3_4_14_2","doi-asserted-by":"publisher","DOI":"10.1099\/mgen.0.000878"},{"key":"e_1_3_4_15_2","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2018.03301"},{"key":"e_1_3_4_16_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.95.6.3140"},{"key":"e_1_3_4_17_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-017-04707-4"},{"key":"e_1_3_4_18_2","doi-asserted-by":"publisher","DOI":"10.3201\/eid2501.180374"},{"key":"e_1_3_4_19_2","doi-asserted-by":"publisher","DOI":"10.1186\/s42522-020-0010-1"},{"key":"e_1_3_4_20_2","doi-asserted-by":"publisher","DOI":"10.1099\/mgen.0.000339"},{"key":"e_1_3_4_21_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.ijantimicag.2021.106470"},{"key":"e_1_3_4_22_2","doi-asserted-by":"publisher","DOI":"10.1080\/22221751.2020.1822757"},{"key":"e_1_3_4_23_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2024.09.009"},{"key":"e_1_3_4_24_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41396-020-00860-3"},{"key":"e_1_3_4_25_2","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2022.909886"},{"key":"e_1_3_4_26_2","doi-asserted-by":"publisher","DOI":"10.21769\/BioProtoc.97"},{"key":"e_1_3_4_27_2","doi-asserted-by":"publisher","DOI":"10.1002\/cpbi.102"},{"key":"e_1_3_4_28_2","doi-asserted-by":"publisher","DOI":"10.1089\/cmb.2009.0238"},{"key":"e_1_3_4_29_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41592-023-01940-w"},{"key":"e_1_3_4_30_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0179228"},{"key":"e_1_3_4_31_2","doi-asserted-by":"publisher","DOI":"10.1099\/mgen.0.000166"},{"key":"e_1_3_4_32_2","doi-asserted-by":"publisher","DOI":"10.1186\/s13073-023-01196-1"},{"key":"e_1_3_4_33_2","doi-asserted-by":"publisher","DOI":"10.1101\/gr.232397.117"},{"key":"e_1_3_4_34_2","doi-asserted-by":"publisher","DOI":"10.1093\/molbev\/msaa015"},{"key":"e_1_3_4_35_2","doi-asserted-by":"publisher","DOI":"10.1038\/nmeth.4285"},{"key":"e_1_3_4_36_2","doi-asserted-by":"publisher","DOI":"10.5281\/zenodo.854445"},{"key":"e_1_3_4_37_2","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkae268"},{"key":"e_1_3_4_38_2","doi-asserted-by":"publisher","DOI":"10.12688\/wellcomeopenres.14826.1"},{"key":"e_1_3_4_39_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0010034"},{"key":"e_1_3_4_40_2","volume-title":"Performance Standards for Antimicrobial Susceptibility Testing","year":"2021","unstructured":"2021. Performance Standards for Antimicrobial Susceptibility Testing. 31st ed. Clinical and Laboratory Standards Institute.","edition":"31"},{"key":"e_1_3_4_41_2","doi-asserted-by":"publisher","DOI":"10.1093\/jac\/dkaa345"},{"key":"e_1_3_4_42_2","doi-asserted-by":"publisher","DOI":"10.1128\/AEM.00582-07"},{"key":"e_1_3_4_43_2","first-page":"141","volume-title":"Bacteriophages: methods and protocols, volume 1: isolation, characterization, and interactions","author":"Kutter E","year":"2009","unstructured":"Kutter E. 2009. Phage host range and efficiency of plating BT, p 141\u2013149. In Bacteriophages: methods and protocols, volume 1: isolation, characterization, and interactions. Humana Press, Totowa, NJ."},{"key":"e_1_3_4_44_2","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkab883"},{"key":"e_1_3_4_45_2","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gky425"},{"key":"e_1_3_4_46_2","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkm360"},{"key":"e_1_3_4_47_2","doi-asserted-by":"publisher","DOI":"10.1186\/s12864-016-2627-0"},{"key":"e_1_3_4_48_2","doi-asserted-by":"publisher","DOI":"10.3390\/v10110602"},{"key":"e_1_3_4_49_2","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2105-10-421"},{"key":"e_1_3_4_50_2","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkab1111"},{"key":"e_1_3_4_51_2","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gky1050"},{"key":"e_1_3_4_52_2","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.01021-06"},{"key":"e_1_3_4_53_2","doi-asserted-by":"publisher","DOI":"10.1128\/mbio.02696-23"},{"key":"e_1_3_4_54_2","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2019.00930"},{"key":"e_1_3_4_55_2","doi-asserted-by":"publisher","DOI":"10.3390\/microorganisms11082115"},{"key":"e_1_3_4_56_2","doi-asserted-by":"publisher","DOI":"10.3390\/antibiotics10050596"},{"key":"e_1_3_4_57_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.diagmicrobio.2014.03.006"},{"key":"e_1_3_4_58_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.ijantimicag.2020.106195"},{"key":"e_1_3_4_59_2","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2023.1264030"},{"key":"e_1_3_4_60_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.ijantimicag.2015.04.002"},{"key":"e_1_3_4_61_2","doi-asserted-by":"publisher","DOI":"10.1007\/s40121-017-0153-2"},{"key":"e_1_3_4_62_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.jinf.2018.10.001"},{"key":"e_1_3_4_63_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-022-31455-5"},{"key":"e_1_3_4_64_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41564-020-00830-7"},{"key":"e_1_3_4_65_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.ppat.1010928"},{"key":"e_1_3_4_66_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41579-019-0278-2"},{"key":"e_1_3_4_67_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41564-022-01219-4"},{"key":"e_1_3_4_68_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41564-020-0777-y"},{"key":"e_1_3_4_69_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41579-019-0299-x"},{"key":"e_1_3_4_70_2","doi-asserted-by":"publisher","DOI":"10.3390\/pathogens10020205"},{"key":"e_1_3_4_71_2","doi-asserted-by":"publisher","DOI":"10.1038\/nrmicro.2015.14"},{"key":"e_1_3_4_72_2","doi-asserted-by":"publisher","DOI":"10.1098\/rstb.2020.0464"},{"key":"e_1_3_4_73_2","doi-asserted-by":"publisher","DOI":"10.1093\/lambio\/ovae003"},{"key":"e_1_3_4_74_2","doi-asserted-by":"publisher","DOI":"10.1128\/mBio.00227-10"},{"key":"e_1_3_4_75_2","doi-asserted-by":"publisher","DOI":"10.1099\/mgen.0.000309"},{"key":"e_1_3_4_76_2","doi-asserted-by":"publisher","DOI":"10.1126\/science.1179555"},{"key":"e_1_3_4_77_2","doi-asserted-by":"publisher","DOI":"10.1111\/nyas.14918"},{"key":"e_1_3_4_78_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.scitotenv.2022.159497"},{"key":"e_1_3_4_79_2","doi-asserted-by":"publisher","DOI":"10.1098\/rstb.2018.0384"},{"key":"e_1_3_4_80_2","doi-asserted-by":"publisher","DOI":"10.1128\/spectrum.00829-22"},{"key":"e_1_3_4_81_2","doi-asserted-by":"publisher","DOI":"10.1093\/ismejo\/wrae005"},{"key":"e_1_3_4_82_2","doi-asserted-by":"publisher","DOI":"10.3390\/ijms232416195"}],"container-title":["Microbiology Spectrum"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/journals.asm.org\/doi\/pdf\/10.1128\/spectrum.02849-24","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/journals.asm.org\/doi\/pdf\/10.1128\/spectrum.02849-24","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,7,1]],"date-time":"2025-07-01T09:04:26Z","timestamp":1751360666000},"score":1,"resource":{"primary":{"URL":"https:\/\/journals.asm.org\/doi\/10.1128\/spectrum.02849-24"}},"subtitle":[],"editor":[{"given":"Victor","family":"Gonzalez","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2025,7]]},"references-count":81,"journal-issue":{"issue":"7","published-print":{"date-parts":[[2025,7]]}},"alternative-id":["10.1128\/spectrum.02849-24"],"URL":"https:\/\/doi.org\/10.1128\/spectrum.02849-24","relation":{},"ISSN":["2165-0497"],"issn-type":[{"value":"2165-0497","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,7]]},"assertion":[{"value":"2024-11-12","order":0,"name":"received","label":"Received","group":{"name":"publication_history","label":"Publication History"}},{"value":"2025-04-08","order":2,"name":"accepted","label":"Accepted","group":{"name":"publication_history","label":"Publication History"}},{"value":"2025-05-16","order":3,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}],"article-number":"e02849-24"}}