Evolution of Acinetobacter baumannii in Clinical Bacteremia Patients

References

• AntunesLC, ViscaP, TownerKJ. Acinetobacter baumannii: evolution of a global pathogen. Pathog Dis. 2014;71(3):292–301. doi:10.1111/2049-632X.1212524376225
   PubMed Web of Science ®Google Scholar
• JinL, ZhaoC, LiH, WangR, WangQ, WangH. Clinical profile, prognostic factors, and outcome prediction in hospitalized patients with bloodstream infection: results from a 10-Year Prospective Multicenter Study. Front Med (Lausanne). 2021;8:629671. doi:10.3389/fmed.2021.62967134095163
   PubMed Web of Science ®Google Scholar
• BallouzT, AridiJ, AfifC, et al. Risk factors, clinical presentation, and outcome of Acinetobacter baumannii bacteremia. Front Cell Infect Microbiol. 2017;7:156. doi:10.3389/fcimb.2017.0015628523249
   PubMed Web of Science ®Google Scholar
• WangX, ZhangL, SunA, et al. Acinetobacter baumannii bacteraemia in patients with haematological malignancy: a multicentre retrospective study from the infection working party of Jiangsu society of hematology. Eur J Clin Microbiol Infect Dis. 2017;36(7):1073–1081. doi:10.1007/s10096-016-2895-228101785
   PubMed Web of Science ®Google Scholar
• Di FrancoS, AlfieriA, PaceMC, et al. Blood stream infections from MDR bacteria. Life (Basel). 2021;11(6):575. doi:10.3390/life1106057534207043
   PubMed Web of Science ®Google Scholar
• HuF, ZhuD, WangF, WangM. Current status and trends of antibacterial resistance in China. Clin Infect Dis. 2018;67(suppl_2):S128–S134. doi:10.1093/cid/ciy65730423045
   PubMed Web of Science ®Google Scholar
• LemosEV, de la HozFP, EinarsonTR, et al. Carbapenem resistance and mortality in patients with Acinetobacter baumannii infection: systematic review and meta-analysis. Clin Microbiol Infect. 2014;20(5):416–423. doi:10.1111/1469-0691.1236324131374
   PubMed Web of Science ®Google Scholar
• MarchaimD, Navon-VeneziaS, SchwartzD, et al. Surveillance cultures and duration of carriage of multidrug-resistant Acinetobacter baumannii. J Clin Microbiol. 2007;45(5):1551–1555. doi:10.1128/JCM.02424-0617314222
   PubMed Web of Science ®Google Scholar
• ChenYP, LiangCC, ChangR, et al. Detection and colonization of multidrug resistant organisms in a regional teaching hospital of Taiwan. Int J Environ Res Public Health. 2019;16(7):1104. doi:10.3390/ijerph16071104
   Web of Science ®Google Scholar
• NgD, MarimuthuK, LeeJJ, et al. Environmental colonization and onward clonal transmission of carbapenem-resistant Acinetobacter baumannii (CRAB) in a medical intensive care unit: the case for environmental hygiene. Antimicrob Resist Infect Control. 2018;7(1):51. doi:10.1186/s13756-018-0343-z29644052
   PubMed Web of Science ®Google Scholar
• DidelotX, WalkerAS, PetoTE, CrookDW, WilsonDJ. Within-host evolution of bacterial pathogens. Nat Rev Microbiol. 2016;14(3):150–162. doi:10.1038/nrmicro.2015.1326806595
   PubMed Web of Science ®Google Scholar
• LeeJY, KangCI, KoJH, et al. Clinical features and risk factors for development of breakthrough gram-negative bacteremia during carbapenem therapy. Antimicrob Agents Chemother. 2016;60(11):6673–6678. doi:10.1128/AAC.00984-1627572416
   PubMed Web of Science ®Google Scholar
• KimSY, ChoSI, BangJH. Risk factors associated with bloodstream infection among patients colonized by multidrug-resistant Acinetobacter baumannii: a 7-Year Observational Study in a general hospital. Am J Infect Control. 2020;48(5):581–583. doi:10.1016/j.ajic.2019.07.02531540833
   PubMedGoogle Scholar
• WenH, WangK, LiuY, et al. Population dynamics of an Acinetobacter baumannii clonal complex during colonization of patients. J Clin Microbiol. 2014;52(9):3200–3208. doi:10.1128/JCM.00921-1424951812
   PubMed Web of Science ®Google Scholar
• KimSJ, KimYJ, KoKS. Genomic analysis of consecutive Acinetobacter baumannii strains from a single patient. Front Microbiol. 2018;9:2840. doi:10.3389/fmicb.2018.0284030542330
   PubMed Web of Science ®Google Scholar
• WrightMS, IovlevaA, JacobsMR, BonomoRA, AdamsMD. Genome dynamics of multidrug-resistant Acinetobacter baumannii during infection and treatment. Genome Med. 2016;8(1):26. doi:10.1186/s13073-016-0279-y26939581
   PubMed Web of Science ®Google Scholar
• HuaX, ZhouZ, YangQ, et al. Evolution of Acinetobacter baumannii in vivo: international clone II, more resistance to ceftazidime, mutation in ptk. Front Microbiol. 2017;8:1256. doi:10.3389/fmicb.2017.0125628740486
   PubMed Web of Science ®Google Scholar
• GersonS, BettsJW, LucassenK, et al. Investigation of novel pmrB and eptA mutations in isogenic Acinetobacter baumannii isolates associated with colistin resistance and increased virulence in vivo. Antimicrob Agents Chemother. 2019;63(3):e01586–18. doi:10.1128/AAC.01586-1830617096
   PubMed Web of Science ®Google Scholar
• MaranoV, MarascioN, PaviaG, et al. Identification of pmrB mutations as putative mechanism for colistin resistance in A. baumannii strains isolated after in vivo colistin exposure. Microb Pathog. 2020;142:104058. doi:10.1016/j.micpath.2020.10405832058026
   PubMed Web of Science ®Google Scholar
• Clinicaland Laboratory Standards Institute. Performance Standards for Antimicrobial Susceptibility Testing: Twenty-Ninth Informational Supplement. M100S-S29. Wayne, PA: Clinical and Laboratory Standards Institute; 2019.
   Google Scholar
• ZerbinoDR, BirneyE. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res. 2008;18(5):821–829. doi:10.1101/gr.074492.10718349386
   PubMed Web of Science ®Google Scholar
• SeemannT. Prokka: rapid prokaryotic genome annotation. Bioinformatics. 2014;30(14):2068–2069. doi:10.1093/bioinformatics/btu15324642063
   PubMed Web of Science ®Google Scholar
• PageAJ, CumminsCA, HuntM, et al. Roary: rapid large-scale prokaryote pan genome analysis. Bioinformatics. 2015;31(22):3691–3693. doi:10.1093/bioinformatics/btv42126198102
   PubMed Web of Science ®Google Scholar
• StamatakisA. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics. 2014;30(9):1312–1313. doi:10.1093/bioinformatics/btu03324451623
   PubMed Web of Science ®Google Scholar
• LarsenMV, CosentinoS, RasmussenS, et al. Multilocus sequence typing of total-genome-sequenced bacteria. J Clin Microbiol. 2012;50(4):1355–1361. doi:10.1128/JCM.06094-1122238442
   PubMed Web of Science ®Google Scholar
• DarlingAE, MauB, PernaNT, StajichJE. progressiveMauve: multiple genome alignment with gene gain, loss and rearrangement. PLoS One. 2010;5(6):e11147. doi:10.1371/journal.pone.001114720593022
   PubMed Web of Science ®Google Scholar
• CroucherNJ, PageAJ, ConnorTR, et al. Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using gubbins. Nucleic Acids Res. 2015;43(3):e15. doi:10.1093/nar/gku119625414349
   PubMed Web of Science ®Google Scholar
• Huerta-CepasJ, SzklarczykD, HellerD, et al. eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses. Nucleic Acids Res. 2019;47(D1):D309–D314. doi:10.1093/nar/gky108530418610
   PubMed Web of Science ®Google Scholar
• CingolaniP, PlattsA, WangLL, et al. A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: sNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3. Fly (Austin). 2012;6(2):80–92. doi:10.4161/fly.1969522728672
   PubMed Web of Science ®Google Scholar
• LetunicI, BorkP. Interactive Tree of Life (iTOL) v4: recent updates and new developments. Nucleic Acids Res. 2019;47(W1):W256–W259. doi:10.1093/nar/gkz23930931475
   PubMed Web of Science ®Google Scholar
• HolmesCL, AndersonMT, MobleyH, BachmanMA. Pathogenesis of gram-negative bacteremia. Clin Microbiol Rev. 2021;34(2):e00234–20. doi:10.1128/CMR.00234-2033692149
   PubMed Web of Science ®Google Scholar
• LiuCP, ShihSC, WangNY, et al. Risk factors of mortality in patients with carbapenem-resistant Acinetobacter baumannii bacteremia. J Microbiol Immunol Infect. 2016;49(6):934–940. doi:10.1016/j.jmii.2014.10.00625553994
   PubMedGoogle Scholar
• LiuY, WangQ, ZhaoC, et al. Prospective multi-center evaluation on risk factors, clinical characteristics and outcomes due to carbapenem resistance in Acinetobacter baumannii complex bacteraemia: experience from the Chinese Antimicrobial Resistance Surveillance of Nosocomial Infections (CARES) network. J Med Microbiol. 2020;69(7):949–959. doi:10.1099/jmm.0.00122232584215
   PubMed Web of Science ®Google Scholar
• von EiffC, BeckerK, MachkaK, StammerH, PetersG. Nasal carriage as a source of Staphylococcus aureus bacteremia. Study Group. N Engl J Med. 2001;344(1):11–16. doi:10.1056/NEJM20010104344010211136954
   PubMed Web of Science ®Google Scholar
• YoungBC, GolubchikT, BattyEM, et al. Evolutionary dynamics of Staphylococcus aureus during progression from carriage to disease. Proc Natl Acad Sci U S A. 2012;109(12):4550–4555. doi:10.1073/pnas.111321910922393007
   PubMed Web of Science ®Google Scholar
• GiulieriSG, BainesSL, GuerillotR, et al. Genomic exploration of sequential clinical isolates reveals a distinctive molecular signature of persistent Staphylococcus aureus bacteraemia. Genome Med. 2018;10(1):65. doi:10.1186/s13073-018-0574-x30103826
   PubMed Web of Science ®Google Scholar
• ChilambiGS, NordstromHR, EvansDR, et al. Evolution of vancomycin-resistant Enterococcus faecium during colonization and infection in immunocompromised pediatric patients. Proc Natl Acad Sci U S A. 2020;117(21):11703–11714. doi:10.1073/pnas.191713011732393645
   PubMed Web of Science ®Google Scholar
• MoradigaravandD, GouliourisT, BlaneB, et al. Within-host evolution of Enterococcus faecium during longitudinal carriage and transition to bloodstream infection in immunocompromised patients. Genome Med. 2017;9(1):119. doi:10.1186/s13073-017-0507-029282103
   PubMed Web of Science ®Google Scholar
• WeberBS, KinsellaRL, HardingCM, FeldmanMF. The secrets of Acinetobacter secretion. Trends Microbiol. 2017;25(7):532–545. doi:10.1016/j.tim.2017.01.00528216293
   PubMed Web of Science ®Google Scholar
• HardingCM, HennonSW, FeldmanMF. Uncovering the mechanisms of Acinetobacter baumannii virulence. Nat Rev Microbiol. 2018;16(2):91–102. doi:10.1038/nrmicro.2017.14829249812
   PubMed Web of Science ®Google Scholar
• YouJ, SunL, YangX, et al. Regulatory protein SrpA controls phage infection and core cellular processes in Pseudomonas aeruginosa. Nat Commun. 2018;9(1):1846. doi:10.1038/s41467-018-04232-629748556
   PubMed Web of Science ®Google Scholar
• SomvanshiVS, ViswanathanP, JacobsJL, MulksMH, SundinGW, CicheTA. The type 2 secretion Pseudopilin, gspJ, is required for multihost pathogenicity of Burkholderia cenocepacia AU1054. Infect Immun. 2010;78(10):4110–4121. doi:10.1128/IAI.00558-1020660607
   PubMed Web of Science ®Google Scholar
• KinsellaRL, LopezJ, PalmerLD, et al. Defining the interaction of the protease CpaA with its type II secretion chaperone CpaB and its contribution to virulence in Acinetobacter species. J Biol Chem. 2017;292(48):19628–19638. doi:10.1074/jbc.M117.80839428982978
   PubMed Web of Science ®Google Scholar
• ElhosseinyNM, El-TayebOM, YassinAS, LoryS, AttiaAS. The secretome of Acinetobacter baumannii ATCC 17978 type II secretion system reveals a novel plasmid encoded phospholipase that could be implicated in lung colonization. Int J Med Microbiol. 2016;306(8):633–641. doi:10.1016/j.ijmm.2016.09.00627713027
   PubMed Web of Science ®Google Scholar
• MichelG, AguzziA, BallG, SosciaC, BlevesS, VoulhouxR. Role of fimV in type II secretion system-dependent protein secretion of Pseudomonas aeruginosa on solid medium. Microbiology (Reading). 2011;157(Pt 7):1945–1954. doi:10.1099/mic.0.045849-021527471
   PubMed Web of Science ®Google Scholar
• WaackU, WarnockM, YeeA, et al. CpaA is a glycan-specific adamalysin-like protease secreted by Acinetobacter baumannii that inactivates coagulation factor XII. Mbio. 2018;9(6):e01606–18. doi:10.1128/mBio.01606-1830563903
   PubMed Web of Science ®Google Scholar
• FischerW, TegtmeyerN, StinglK, BackertS. Four chromosomal type IV secretion systems in Helicobacter pylori: composition, structure and function. Front Microbiol. 2020;11:1592. doi:10.3389/fmicb.2020.0159232754140
   PubMed Web of Science ®Google Scholar
• AllenJL, TomlinsonBR, CasellaLG, ShawLN. Regulatory networks important for survival of Acinetobacter baumannii within the host. Curr Opin Microbiol. 2020;55:74–80. doi:10.1016/j.mib.2020.03.00132388085
   PubMed Web of Science ®Google Scholar