Browsing by Subject "Acinetobacter baumannii"

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  • Badawy, Shimaa; Pajunen, Maria I.; Haiko, Johanna; Baka, Zakaria A. M.; Abou-Dobara, Mohamed; El-Sayed, Ahmed K. A.; Skurnik, Mikael (2020)
    Acinetobacter baumanniiis an opportunistic pathogen that presents a serious clinical challenge due to its increasing resistance to all available antibiotics. Phage therapy has been introduced recently to treat antibiotic-incurableA. baumanniiinfections. In search for newA. baumanniispecific bacteriophages, 20 clinicalA. baumanniistrains were used in two pools in an attempt to enrich phages from sewage. The enrichment resulted in induction of resident prophage(s) and three temperate bacteriophages, named vB_AbaS_fEg-Aba01, vB_AbaS_fLi-Aba02 and vB_AbaS_fLi-Aba03, all able to infect only one strain (#6597) of the 20 clinical strains, were isolated. Morphological characteristics obtained by transmission electron microscopy together with the genomic information revealed that the phages belong to the familySiphoviridae. The ca. 35 kb genomic sequences of the phages were >99% identical to each other. The linear ds DNA genomes of the phages contained 10 nt cohesive end termini, 52-54 predicted genes, anattPsite and one tRNA gene each. A database search revealed an >99% identical prophage in the genome ofA. baumanniistrain AbPK1 (acc. no. CP024576.1). Over 99% identical prophages were also identified from two of the original 20 clinical strains (#5707 and #5920) and both were shown to be spontaneously inducible, thus very likely being the origins of the isolated phages. The phage vB_AbaS_fEg-Aba01 was also able to lysogenize the susceptible strain #6597 demonstrating that it was fully functional. The phages showed a very narrow host range infecting only twoA. baumanniistrains. In conclusion, we have isolated and characterized three novel temperateSiphoviridaephages that infectA.baumannii.
  • Tyni, Olga (Helsingin yliopisto, 2021)
    Mikrobilääkeresistenssi on globaali kansanterveydellinen uhka. Mikrobilääkeresistenssin leviämisen ehkäisemisessä tärkeää on resistenssiseuranta, joka tuottaa tietoa resistenttien mikrobien ja resistenssigeenien esiintymisestä. Seurannalla saatavan datan perusteella voidaan kohdentaa resistenssin leviämistä hillitseviä toimenpiteitä. Jätevedet ovat kiinnostava kohde resistenssiseurannalle, sillä jätevesiin päätyy mikrobeja suuresta, pääosin terveestä väestöstä. Tämä alkuperäistutkimuksen sisältävä lisensiaatintyö on osa Helsingin yliopiston, Tampereen yliopiston ja Terveyden ja hyvinvoinnin laitoksen kolmivuotista (2020–2023) WastPan-hanketta, jota rahoittaa Suomen Akatemia. Hanke kehittää jätevesiseurantaa pandemioiden varautumistyökaluna. Työn tavoitteena on alustavasti selvittää, löytyykö jätevesistä ihmisten infektioille tyypillisiä moniresistenttejä mikrobeja. Lisäksi selvitetään käytettyjen menetelmien toimivuutta jätevedestä eristettyjen mikrobien tutkimisessa. Työssä tutkittiin kymmenen suomalaisen kaupungin jätevedenpuhdistamoilta helmi-, huhti- ja toukokuussa 2021 kerättyjen jätevesinäytteiden sisältämiä karbapenemaasi- ja ESBL-entsyymejä tuottavia bakteereja, metislliiniresistenttejä Staphylococcus aureus -bakteereja sekä Candida auris -hiivasieniä. Näytteet viljeltiin mikrobilääkeresistenttejä kantoja seuloville maljoille, joilta eristettiin Citrobacter freundii- (n=24), Klebsiella pneumoniae- (n=15), Escherichia coli- (n=11), Enterobacter cloacae- (n=3), A. baumannii- (n=3) ja S. aureus (n=2) -bakteereja. ESBL-entsyymejä tuottavia kantoja seulovalta maljalta eristettiin E. coli -bakteereja (n=77), joista kuitenkin vain 10 % (2/20) osoittautui kiekkoherkkyysmäärityksessä ESBL-tuottajiksi. Tutkimuksessa selektiivisiltä maljoilta eristettiin myös herkkiä A. baumannii ja C. freundii -isolaatteja. C. auris -hiivasienen (n=2) lajintunnistukseen ei työssä saatu varmuutta. Isolaattien mikrobilääkeresistenssiä tutkittiin kiekkoherkkyys- ja liemilaimennosmenetelmillä. Resistenssigeenejä tutkittiin polymeraasiketjureaktiolla (PCR). Kokogenomisekvensoinnilla (WGS) tutkittiin karbapenemaaseja koodaavia geenejä sekä sekvenssityyppejä. Tutkimuksessa eristettiin tunnetusti kliinisiä infektioita aiheuttavia moniresistenttejä sekvenssityyppejä, kuten K. pneumoniae ST512 ja ST307, jotka ovat aiheuttaneet tartuntaryppäitä Suomessa. Jätevesistä eristettiin myös kansainvälisiä, usein patogeenisia sekvenssityyppejä, kuten ST410-E. coli ja ST252-E. cloacae. Tutkimuksessa 46 % (n=18) bakteereista, joilla oli karbapenemaasigeeni, kantoivat KPC-3-karbapenemaasia koodaavaa geeniä. Toisiksi yleisin oli blaKPC-2 (18 %, n=7). PCR- ja WGS-menetelmillä saatiin toisistaan poikkeavia tuloksia karbapenemaasigeeneistä. WGS:llä ei tunnistettu yhtäkään blaIMP- tai blaVIM-geeniä, joita PCR:llä löydettiin 35 %:lta (n=14) ja 8 %:lta (n=3) karbapenemaasia tuottavista bakteereista. Toisaalta WGS:llä pystyttiin tunnistamaan karbapenemaasigeenejä, kuten blaGES-5, joita ei ollut mukana PCR-protokollassa. Tutkimuksen tulokset ovat alustava näyttö siitä, että jätevesiseurannalla voidaan tunnistaa jätevedestä kliinisiä infektioita aiheuttavia resistenttejä mikrobeja. Jätevesistä löydettiin myös mikrobeja, jotka voivat mahdollisesti aiheuttaa infektioita Suomessa tulevaisuudessa. Pitkäaikaista jätevesiseurantaa tarvitaan, jotta saadaan kattavaa tietoa resistenttien mikrobien ja resistenssigeenien esiintymisestä ja leviämisestä jätevesissä, sekä niiden yhteydestä ihmisten kliinisiin infektioihin. Toimivalla jätevesiseurannalla voidaan mahdollisesti tunnistaa tulevia epidemioita.
  • Vaara, Martti (2019)
    Polymyxins (polymyxin B (PMB) and polymyxin E (colistin)) are cyclic lipodecapeptide antibiotics, highly basic due to five free amino groups, and rapidly bactericidal against Gram-negative bacteria, such as the majority of Enterobacteriaceae as well as Acinetobacter baumannii and Pseudomonas aeruginosa. Their clinical use was abandoned in the 1960s because of nephrotoxicity and because better-tolerated drugs belonging to other antibiotic classes were introduced. Now, due to the global dissemination of extremely-drug resistant Gram-negative bacterial strains, polymyxins have resurged as the last-line drugs against those strains. Novel derivatives that are less toxic and/or more effective at tolerable doses are currently under preclinical development and their properties have recently been described in several extensive reviews. Other derivatives lack any direct bactericidal activity but damage the outermost permeability barrier, the outer membrane, of the target bacteria and make it more permeable to many other antibiotics. This review describes the properties of three thus far best-characterized permeabilizer derivatives, i.e., the classic permeabilizer polymyxin B nonapeptide (PMBN), NAB7061, and SPR741/NAB741, a compound that recently successfully passed the clinical phase 1. Also, a few other permeabilizer compounds are brought up.
  • Gilbert-Girard, Shella; Savijoki, Kirsi; Yli-Kauhaluoma, Jari; Fallarero, Adyary (2020)
    In an effort to find new repurposed antibacterial compounds, we performed the screening of an FDA-approved compounds library against Staphylococcus aureus American Type Culture Collection (ATCC) 25923. Compounds were evaluated for their capacity to prevent both planktonic growth and biofilm formation as well as to disrupt pre-formed biofilms. One of the identified initial hits was fingolimod (FTY720), an immunomodulator approved for the treatment of multiple sclerosis, which was then selected for follow-up studies. Fingolimod displayed a potent activity against S. aureus and S. epidermidis with a minimum inhibitory concentration (MIC) within the range of 12-15 mu M at which concentration killing of all the bacteria was confirmed. A time-kill kinetic study revealed that fingolimod started to drastically reduce the viable bacterial count within two hours and we showed that no resistance developed against this compound for up to 20 days. Fingolimod also displayed a high activity against Acinetobacter baumannii (MIC 25 mu M) as well as a modest activity against Escherichia coli and Pseudomonas aeruginosa. In addition, fingolimod inhibited quorum sensing in Chromobacterium violaceum and might therefore target this signaling pathway in certain Gram-negative bacteria. In conclusion, we present the identification of fingolimod from a compound library and its evaluation as a potential repurposed antibacterial compound.
  • Vaara, Martti; Vaara, Timo; Tyrrell, Jonathan M. (2017)
    Recent years have brought in an increased interest to develop improved polymyxins. The currently used polymyxins, i.e. polymyxin B and colistin (polymyxin E) are pentacationic lipopeptides that possess a cyclic heptapeptide part with three positive charges, a linear "panhandle" part with two positive charges, and a fatty acyl tail. Unfortunately, their clinical use is shadowed by their notable nephrotoxicity. We have previously developed a polymyxin derivative NAB739 which lacks the positive charges in the linear part. This derivative is better tolerated than polymyxin B in cynomolgus monkeys and is, in contrast to polymyxin B, excreted into urine in monkeys and rats. Here we have conducted further structure-activity relationship (SAR) studies on 17 derivatives with three positive charges only. We discovered a remarkably antibacterial class, as exemplified by NAB815, that carries two positive charges only in the cyclic part. (C) 2017 Elsevier Inc. All rights reserved.
  • Kolsi, Anna (Helsingin yliopisto, 2020)
    The objective of this thesis was to isolate and characterized phages from Beninese wastewater samples against clinical Acinetobacter baumannii strains for phage therapy use. A. baumannii is one of the most threatening nosocomial bacteria because most of the strains are resistant towards all commonly used antibiotics. One promising alternative treatment method could be phage therapy that utilizes lytic phages to dispose of specific bacteria. In this thesis, seven phages infecting clinical A. baumannii strains were isolated and two of them were characterized more in detail. Phages vB_AbaA_fBenAci001 (fBen-Aci001) and vB_Aba_fBenAci002 (fBen-Aci002) were members of the Friunavirus genus of the Autographiviridae family. In addition, they were the only phages characterised from their respective species to date. The genome analysis revealed 82.2% identity between the phages. No genes indicating lysogenic lifecycle, or genes encoding bacterial toxins or antibiotic resistance were identified from either of them. Phage fBen-Aci001 were infecting 4% and fBen-Aci002 were infecting 9% of tested 23 clinical A. baumannii isolates. Phylogenetic tree which was constructed based on whole genome sequences was compared to the trees that were made using tailspike proteins and capsid proteins. No correlation between genome-wide tree and trees built based on single genes were seen. In conclusion, the Beninese hospital wastewater appeared to be a good source for A. baumannii phages, as several phages were isolated and they were infecting clinical multidrug resistant strains isolated from Finnish patients. Phages fBen-Aci001 and fBen-Aci002 were concluded to be potential candidates to be used in the phage therapy though the narrow host range might negatively affect their usability.
  • Tyrrell, Jonathan M.; Aboklaish, Ali F.; Walsh, Timothy R.; Vaara, Timo; Vaara, Martti (2019)
    The antibiotic crisis has reinstated polymyxins, once abandoned because of their toxicity. Now, preclinical studies have revealed better tolerated and more effective derivatives of polymyxins such as NAB739. Simultaneously, polymyxin-resistant (PMR) strains such as the mcr-1 strains have received lots of justified publicity, even though they are still very rare. Here we show that NAB739 sensitizes the PMR strains to rifampin, a classic "anti-Gram-positive" antibiotic excluded by the intact outer membrane (OM) permeability barrier, as well as to retapamulin, the surrogate of lefamulin, an antibiotic under development against Gram-positive bacteria. Polymyxin B was used as a comparator. The combination of NAB739 and rifampin was synergistic against ten out of eleven PMR strains of Escherichia coll. (Fractional Synergy Indices, FICs, 0.14-0.19) and that of NAB739 and retapamulin against all the tested eleven strains (FICs 0.19-0.25). Against PMR Klebsiella pneumoniae (n = 7), the FICs were 0.13-0.27 for NAB739 + rifampin and 0.14-0.28 for NAB739 + retapamulin. Against Acinetobacter baumannii (n = 2), the combination of NAB739 and rifampin had the FIC of 0.09-0.19. Furthermore, NAB739 and meropenem were synergistic (FICs 0.25-0.50) against four out of five PMR strains that were simultaneously resistant to meropenem.