Whole-genome sequence analysis reveals evolution of antimicrobial resistance in a Ugandan colistin resistant Acinetobacter baumannii

AbstractIn recent times, pan-drug resistant Acinetobacter baumannii have emerged and continue to spread among critically ill patients, this poses an urgent risk to global and local human health. This study sought to provide the first genomic analysis of a pan-drug resistant Acinetobacter baumannii from Uganda and Africa, and to tell a story of mobile genetic element-mediated antibiotic resistance evolution in the isolate. It was an in-silico study in which intrinsic and acquired antibiotic resistance genes, and/or chromosomal resistance mutations were identified using PATRIC, CARD, NDARO and ResFinder. Screening for insertion sequences was done using ISfinder. Also, plasmid screening, phylogenetic analysis and sequence typing were performed using PlasmidFinder, PATRIC and Gubbin, and MLST respectively.The isolate belonged to the Sequence type 136, belonging to Clonal complex 208 and Global complex 2. This isolate shared close homology with strains from Tanzania. Resistance in the isolate was chromosomally and mobile genetic element-mediated by Acinetobacter-derived cephalosporinases and carbapenem hydrolyzing class D β-lactamses, blaOXA-2, 51, 5 88, 317, blaADC-2, 25. Colistin resistance was associated with previously documented mutants, lpxA and lpxC. Other key resistance genes identified were: aph(3”)-lb, aph(6)-ld, aph(3’)-la, aac(3)-lld, aac(3)-lla, aph(3’)-l, aph(3”)-l, aph(6)-lc, aph(6)-ld, aac(3)-II, III, IV, VI, VIII, IX, X, macA, macB, tetA, tetB, tetR, dfrA, and those of the floR family. RSF1010 like IncQ broad-host-range plasmids and features of pACICU1, pACICU2, and p3ABAYE Acinetobacter baumannii plasmids namely partitioning proteins ParA and B were present. Insertion sequences present included IS3, IS5, IS66 and those of the ISLre2 families.The study described for the first time a pan-drug resistant Acinetobacter baumannii from Uganda, and told a story of mobile genetic element-mediated antibiotic resistance evolution in the isolate despite being limited by pan-drug resistance phenotypic data. It provides a basis to track trends in antibiotic resistance and identification of emerging resistance patterns in Acinetobacter baumannii in Uganda.

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Acquisition of a genomic resistance island (AbGRI5) from global clone 2 through homologous recombination in a clinical Acinetobacter baumannii isolate

Journal of Antimicrobial Chemotherapy ◽

10.1093/jac/dkaa389 ◽

2020 ◽

Vol 76 (1) ◽

pp. 65-69

Author(s):

Xiaoting Hua ◽

Robert A Moran ◽

Qingye Xu ◽

Jintao He ◽

Youhong Fang ◽

...

Keyword(s):

Antibiotic Resistance ◽

Acinetobacter Baumannii ◽

Resistance Genes ◽

Antibiotic Resistance Genes ◽

Whole Genome Sequence ◽

Oxford Nanopore ◽

History Of ◽

Agar Dilution ◽

Resistance Island ◽

New Location

Abstract Objectives To reconstruct the evolutionary history of the clinical Acinetobacter baumannii XH1056, which lacks the Oxford scheme allele gdhB. Methods Susceptibility testing was performed using broth microdilution and agar dilution. The whole-genome sequence of XH1056 was determined using the Illumina and Oxford Nanopore platforms. MLST was performed using the Pasteur scheme and the Oxford scheme. Antibiotic resistance genes were identified using ABRicate. Results XH1056 was resistant to all antibiotics tested, apart from colistin, tigecycline and eravacycline. MLST using the Pasteur scheme assigned XH1056 to ST256. However, XH1056 could not be typed with the Oxford MLST scheme as gdhB is not present. Comparative analyses revealed that XH1056 contains a 52 933 bp region acquired from a global clone 2 (GC2) isolate, but is otherwise closely related to the ST23 A. baumannii XH858. The acquired region in XH1056 also contains a 34 932 bp resistance island that resembles AbGRI3 and contains the armA, msrE-mphE, sul1, blaPER-1, aadA1, cmlA1, aadA2, blaCARB-2 and ere(B) resistance genes. Comparison of the XH1056 chromosome to that of GC2 isolate XH859 revealed that the island in XH1056 is in the same chromosomal region as that in XH859. As this island is not in the standard AbGRI3 position, it was named AbGRI5. Conclusions XH1056 is a hybrid isolate generated by the acquisition of a chromosomal segment from a GC2 isolate that contains a resistance island in a new location—AbGRI5. As well as generating ST256, it appears likely that a single recombination event is also responsible for the acquisition of AbGRI5 and its associated antibiotic resistance genes.

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An Analysis of the Antibiotic Resistance Genes of Multi-Drug Resistant (MDR)Acinetobacter baumannii

Korean Journal of Clinical Laboratory Science ◽

10.15324/kjcls.2016.48.3.217 ◽

2016 ◽

Vol 48 (3) ◽

pp. 217-224 ◽

Cited By ~ 2

Author(s):

Jina Lim ◽

Gyusang Lee ◽

Yeonim Choi ◽

Jongbae Kim

Keyword(s):

Antibiotic Resistance ◽

Acinetobacter Baumannii ◽

Resistance Genes ◽

Antibiotic Resistance Genes ◽

Drug Resistant

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Genomic Analysis of the Multidrug-Resistant Acinetobacter baumannii Strain MDR-ZJ06 Widely Spread in China

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.01134-10 ◽

2011 ◽

Vol 55 (10) ◽

pp. 4506-4512 ◽

Cited By ~ 77

Author(s):

Hua Zhou ◽

Tongwu Zhang ◽

Dongliang Yu ◽

Borui Pi ◽

Qing Yang ◽

...

Keyword(s):

Antibiotic Resistance ◽

Acinetobacter Baumannii ◽

Resistance Genes ◽

Antibiotic Resistance Genes ◽

Genomic Analysis ◽

Multidrug Resistant ◽

Whole Genome Sequence ◽

Whole Genome ◽

Content Type ◽

Resistance Island

ABSTRACTWe previously reported that the multidrug-resistant (MDR)Acinetobacter baumanniistrain MDR-ZJ06, belonging to European clone II, was widely spread in China. In this study, we report the whole-genome sequence of this clinically important strain. A 38.6-kb AbaR-type genomic resistance island (AbaR22) was identified in MDR-ZJ06. AbaR22 has a structure similar to those of the resistance islands found inA. baumanniistrains AYE and AB0057, but it contained only a few antibiotic resistance genes. The region of resistant gene accumulation as previously described was not found in AbaR22. In the chromosome of the strain MDR-ZJ06, we identified the geneblaoxa-23in a composite transposon (Tn2009). Tn2009shared the backbone with otherA. baumanniitransponsons that harborblaoxa-23, but it was bracketed by two ISAba1elements which were transcribed in the same orientation. MDR-ZJ06 also expressed thearmAgene on its plasmid pZJ06, and this gene has the same genetic environment as thearmAgene of theEnterobacteriaceae. These results suggest variability of resistance acquisition even in closely relatedA. baumanniistrains.

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Genomewide Analysis of Divergence of Antibiotic Resistance Determinants in Closely Related Isolates of Acinetobacter baumannii

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.00057-10 ◽

2010 ◽

Vol 54 (9) ◽

pp. 3569-3577 ◽

Cited By ~ 69

Author(s):

Mark D. Adams ◽

E. Ricky Chan ◽

Neil D. Molyneaux ◽

Robert A. Bonomo

Keyword(s):

Antibiotic Resistance ◽

Acinetobacter Baumannii ◽

Resistance Gene ◽

Resistance Genes ◽

Rapid Evolution ◽

Antibiotic Resistance Genes ◽

Whole Genome Sequence ◽

Dynamic Resistance ◽

Gene Repertoire ◽

Ample Evidence

ABSTRACT Multidrug resistance has emerged as a significant concern with infections caused by Acinetobacter baumannii. Ample evidence supports the involvement of mobile genetic elements in the transfer of antibiotic resistance genes, but the extent of variability and the rate of genetic change associated with the acquisition of antibiotic resistance have not been studied in detail. Whole-genome sequence analysis of six closely related clinical isolates of A. baumannii, including four from the same hospital, revealed extensive divergence of the resistance genotype that correlated with observed differences in antimicrobial susceptibility. Resistance genes associated with insertion sequences, plasmids, and a chromosomal resistance gene island all showed variability. The highly dynamic resistance gene repertoire suggests rapid evolution of drug resistance.

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Whole-genome sequence analyses of Glaesserella parasuis isolates reveals extensive genomic variation and diverse antibiotic resistance determinants

PeerJ ◽

10.7717/peerj.9293 ◽

2020 ◽

Vol 8 ◽

pp. e9293

Author(s):

Xiulin Wan ◽

Xinhui Li ◽

Todd Osmundson ◽

Chunling Li ◽

He Yan

Keyword(s):

Antibiotic Resistance ◽

Genetic Variation ◽

Genome Sequence ◽

Resistance Genes ◽

Genomic Variation ◽

Whole Genome Sequence ◽

Comparative Genomic ◽

Broad Host Range ◽

Whole Genome ◽

Resistance Determinants

Background Glaesserella parasuis (G. parasuis) is a respiratory pathogen of swine and the etiological agent of Glässer’s disease. The structural organization of genetic information, antibiotic resistance genes, potential pathogenicity, and evolutionary relationships among global G. parasuis strains remain unclear. The aim of this study was to better understand patterns of genetic variation, antibiotic resistance factors, and virulence mechanisms of this pathogen. Methods The whole-genome sequence of a ST328 isolate from diseased swine in China was determined using Pacbio RS II and Illumina MiSeq platforms and compared with 54 isolates from China sequenced in this study and 39 strains from China and eigtht other countries sequenced by previously. Patterns of genetic variation, antibiotic resistance, and virulence mechanisms were investigated in relation to the phylogeny of the isolates. Electrotransformation experiments were performed to confirm the ability of pYL1—a plasmid observed in ST328—to confer antibiotic resistance. Results The ST328 genome contained a novel Tn6678 transposon harbouring a unique resistance determinant. It also contained a small broad-host-range plasmid pYL1 carrying aac(6’)-Ie-aph(2”)-Ia and blaROB-1; when transferred to Staphylococcus aureus RN4220 by electroporation, this plasmid was highly stable under kanamycin selection. Most (85.13–91.74%) of the genetic variation between G. parasuis isolates was observed in the accessory genomes. Phylogenetic analysis revealed two major subgroups distinguished by country of origin, serotype, and multilocus sequence type (MLST). Novel virulence factors (gigP, malQ, and gmhA) and drug resistance genes (norA, bacA, ksgA, and bcr) in G. parasuis were identified. Resistance determinants (sul2, aph(3”)-Ib, norA, bacA, ksgA, and bcr) were widespread across isolates, regardless of serovar, isolation source, or geographical location. Conclusions Our comparative genomic analysis of worldwide G. parasuis isolates provides valuable insight into the emergence and transmission of G. parasuis in the swine industry. The result suggests the importance of transposon-related and/or plasmid-related gene variations in the evolution of G. parasuis.

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Molecular epidemiological study and detection of multi-drug resistant Acinetobacter baumannii -related resistance genes

African Journal of Microbiology Research ◽

10.5897/ajmr2013.6109 ◽

2013 ◽

Vol 7 (48) ◽

pp. 5496-5502 ◽

Cited By ~ 4

Author(s):

J Jiang M ◽

P Zhao Sh ◽

M Li J ◽

S Zhang F

Keyword(s):

Acinetobacter Baumannii ◽

Epidemiological Study ◽

Resistance Genes ◽

Drug Resistant ◽

Molecular Epidemiological Study

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Insertion sequences associated with antibiotic resistance genes in Enterococcus isolates from an inpatient with prolonged bacteremia.

10.1101/2021.07.22.453447 ◽

2021 ◽

Author(s):

Zulema Udaondo ◽

Kaleb Z Abram ◽

Atul Kothari ◽

Se-Ran Jun

Keyword(s):

Antibiotic Resistance ◽

Transposable Elements ◽

Resistance Genes ◽

Antibiotic Resistance Genes ◽

Insertion Sequences ◽

Rapid Adaptation ◽

Resistance Mutations ◽

New Paradigm ◽

Novel Association ◽

Extended Analysis

Insertion sequences (ISs) and other transposable elements are associated with the mobilization of antibiotic resistance determinants and the modulation of pathogenic characteristics. In this work, we aimed to investigate the association between ISs and antibiotic resistance genes, and their role in dissemination and modification of antibiotic resistance phenotype. To that end, we leveraged fully resolved Enterococcus faecium and Enterococcus faecalis genomes of isolates collected over four days from an inpatient with prolonged bacteremia. Isolates from both species harbored similar IS family content but showed significant species-dependent differences in copy number and arrangements of ISs throughout their replicons. Here, we describe two inter-specific IS-mediated recombination events, and IS-medicated excision events in plasmids of E. faecium isolates. We also characterize a novel arrangement of the IS in a Tn1546-like transposon in E. faecalis isolates likely implicated in a vancomycin genotype-phenotype discrepancy. Furthermore, an extended analysis revealed a novel association between daptomycin resistance mutations in liaSR genes and a putative composite transposon in E. faecium offering a new paradigm for the study of daptomycin-resistance and novel insights into the route of daptomycin resistance dissemination. In conclusion, our study highlights the role ISs and other transposable elements play in rapid adaptation and response to clinically relevant stresses such as aggressive antibiotic treatment in enterococci.

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Genome Assessment of Antibiotic Resistance Genes in Probiotic Bacteria and a Literature Review

10.21203/rs.3.rs-254514/v1 ◽

2021 ◽

Author(s):

Mehdi Fatahi-Bafghi ◽

Sara Naseri ◽

Ali Alizehi

Keyword(s):

Antibiotic Resistance ◽

Genome Sequence ◽

Resistance Genes ◽

Pathogenic Bacteria ◽

Antibiotic Resistance Genes ◽

Probiotic Bacteria ◽

Whole Genome Sequence ◽

Probiotic Properties ◽

Antibiotic Resistant ◽

To Come

Abstract Having various clinical applications, probiotic bacteria are currently used in the diet. There are reports of antibiotic resistance genes (ARGs) in these bacteria that can be transferred to other microflora and pathogenic bacteria. The aim of the study is to examine whole-genome sequence analysis in bacteria with probiotic properties. Moreover, this study follows existing issues about the importance and presence of ARGs in these bacteria the dangers of which may affect human health in the years to come. In the present study, 126 complete probiotic bacterial genomes were collected and analysed for ARGs. The results of the study shows there are various antibiotic resistant genes of in these bacteria some of which can be transmitted to other bacteria. We propose microorganisms be applied as a probiotic element in various types of products, antibiogram be conducted for a large number of antibiotics and analysis of complete genome sequence for ARGs prediction.

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